From fisidoro at ethz.ch  Sun Oct  2 04:50:24 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Sun, 2 Oct 2016 08:50:24 +0000
Subject: [ITK] [ITK-users] itk Python Wrapping: supported metrics and
	optimizers
Message-ID: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>

Hallo,

I am using itk v 9.0 with Python wrapping.

Which metrics and optimizers are supported in the wrapped version? I see that the metrics of itkv3 are not.

Thank you,
Fabio.

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From michkapopoff at gmail.com  Sun Oct  2 16:32:58 2016
From: michkapopoff at gmail.com (Michka Popoff)
Date: Sun, 2 Oct 2016 22:32:58 +0200
Subject: [ITK] [ITK-users] itk Python Wrapping: supported metrics
	and	optimizers
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>
Message-ID: <73989CE5-3400-4AE3-A943-F0DD7D1E87E2@gmail.com>

Hi

I think you are talking about itk V4 ?
If you want to use wrappings, it is really recommended to used one of the latests versions
of ITK. There were many improvements lately, and support for newer compilers was added.

The following metrics and optimizers are available:
https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Metricsv4/wrapping <https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Metricsv4/wrapping>
https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Numerics/Optimizersv4/wrapping <https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Numerics/Optimizersv4/wrapping>

If you need a specific metric or optimizer which is missing, feel free to ask,
we will try to add it.

Michka

> On 2 Oct 2016, at 10:50, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
> 
> Hallo,
>  
> I am using itk v 9.0 with Python wrapping.
>  
> Which metrics and optimizers are supported in the wrapped version? I see that the metrics of itkv3 are not.
>  
> Thank you,
> Fabio.
>  
> _____________________________________
> Powered by www.kitware.com <http://www.kitware.com/>
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php <http://www.kitware.com/products/protraining.php>
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users <http://public.kitware.com/mailman/listinfo/insight-users>
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From matt.mccormick at kitware.com  Sun Oct  2 21:14:29 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 2 Oct 2016 21:14:29 -0400
Subject: [ITK] [ITK-users] itk Python Wrapping: supported metrics
	and	optimizers
In-Reply-To: <73989CE5-3400-4AE3-A943-F0DD7D1E87E2@gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409435BC7EB2@MBX212.d.ethz.ch>
 <73989CE5-3400-4AE3-A943-F0DD7D1E87E2@gmail.com>
Message-ID: <CALzTN-QKi4_ROSe9DvVikgFihF9q3KmLQK9TXtuJES6MznZh_g@mail.gmail.com>

In addition, the ITKv3 wrapped metrics can be found here:

  https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Common/wrapping

As Michka mentioned, if there is a missing class, it can be added.

Thanks,
Matt

On Sun, Oct 2, 2016 at 4:32 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Hi
>
> I think you are talking about itk V4 ?
> If you want to use wrappings, it is really recommended to used one of the
> latests versions
> of ITK. There were many improvements lately, and support for newer compilers
> was added.
>
> The following metrics and optimizers are available:
> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Registration/Metricsv4/wrapping
> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Numerics/Optimizersv4/wrapping
>
> If you need a specific metric or optimizer which is missing, feel free to
> ask,
> we will try to add it.
>
> Michka
>
> On 2 Oct 2016, at 10:50, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
> Hallo,
>
> I am using itk v 9.0 with Python wrapping.
>
> Which metrics and optimizers are supported in the wrapped version? I see
> that the metrics of itkv3 are not.
>
> Thank you,
> Fabio.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
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From adariush at ast.cam.ac.uk  Mon Oct  3 10:01:49 2016
From: adariush at ast.cam.ac.uk (adariush)
Date: Mon, 03 Oct 2016 15:01:49 +0100
Subject: [ITK] [ITK-users] read/write images in ITK
Message-ID: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>

Hello,

I am using ITK 10.0 on a MacBook Pro running on OS X El Capitan.

I have problem with reading/writing images. For example to read/write 
PNG image formats, I expect to do something like this:

=========================================================
#include "itkImage.h"
#include "itkImageFileReader.h"

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName('image name');
reader->Update();
=========================================================
However, the above code returns an error since it seems that 
"itkImage.h" does nothing at all!

Instead every time I want to read/write a PNG image, I should modify the 
above code as follow:


=========================================================
#include "itkImageFileReader.h"
#include "itkPNGImageIOFactory.h"                        // new line

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
itk::PNGImageIOFactory::RegisterOneFactory();             // new line
reader->SetFileName('image name');
reader->Update();
=========================================================


In short, I expect by including "itkImage.h", ITK automatically identify 
input/output image format. However, I have to do it manually. The 
problem is when I want to read for example a '.mha' file format.

Does anyone know what might be the problem and how could I 'SOLVE' it?

Thanks, Ali
_____________________________________
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From tevain at telecom-paristech.fr  Mon Oct  3 10:47:44 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 3 Oct 2016 16:47:44 +0200 (CEST)
Subject: [ITK] [ITK-users]   read/write images in ITK
In-Reply-To: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
References: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
Message-ID: <529249601.78344932.1475506064097.JavaMail.zimbra@enst.fr>

Hi,

Including the itkImage header as nothing to do with the ImageReader correctly calling the needed ImageIO.
Could you provide the error that arise when you try to read your image ?

Tim

----- Mail original -----
De: "adariush" <adariush at ast.cam.ac.uk>
?: insight-users at itk.org
Envoy?: Lundi 3 Octobre 2016 16:01:49
Objet: [ITK] [ITK-users] read/write images in ITK

Hello,

I am using ITK 10.0 on a MacBook Pro running on OS X El Capitan.

I have problem with reading/writing images. For example to read/write 
PNG image formats, I expect to do something like this:

=========================================================
#include "itkImage.h"
#include "itkImageFileReader.h"

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName('image name');
reader->Update();
=========================================================
However, the above code returns an error since it seems that 
"itkImage.h" does nothing at all!

Instead every time I want to read/write a PNG image, I should modify the 
above code as follow:


=========================================================
#include "itkImageFileReader.h"
#include "itkPNGImageIOFactory.h"                        // new line

typedef unsigned char  InputPixelType;
typedef itk::Image< InputPixelType , 2 > InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
itk::PNGImageIOFactory::RegisterOneFactory();             // new line
reader->SetFileName('image name');
reader->Update();
=========================================================


In short, I expect by including "itkImage.h", ITK automatically identify 
input/output image format. However, I have to do it manually. The 
problem is when I want to read for example a '.mha' file format.

Does anyone know what might be the problem and how could I 'SOLVE' it?

Thanks, Ali
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community
_____________________________________
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From francois.budin at kitware.com  Mon Oct  3 10:49:32 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 3 Oct 2016 10:49:32 -0400
Subject: [ITK] [ITK-users] read/write images in ITK
In-Reply-To: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
References: <a966606a6cc0759eeb622a0003a8be40@ast.cam.ac.uk>
Message-ID: <CAHwLD2VdU_JvkFH7a4M2m9O7kr3QnYMjei9+9KFQ=PkkKaMx7A@mail.gmail.com>

Hello,

If you use the ITK IO factory, your first piece of code should work. The
automatic detection of the image format does not rely on the inclusion of
"itkImage.h", but relies on itkImageFileReader.h.
Do you use CMake to configure your project? If so, if you have the
following lines in your CMakeLists files, everything should be done
automatically:
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

After configuring your project, your build directory should contain a
folder named ITKIOFactoryRegistration.
If you do not use CMake to configure your project, I strongly suggest you
to do so. It will simplify a lot of things.
You can also manually register the ITK IOs that you want to support before
use reading your file. You can find some information in the last part of
the documentation provided on this page:
https://itk.org/Wiki/ITK/FAQ

Hope this helps,

Francois


On Mon, Oct 3, 2016 at 10:01 AM, adariush <adariush at ast.cam.ac.uk> wrote:

> Hello,
>
> I am using ITK 10.0 on a MacBook Pro running on OS X El Capitan.
>
> I have problem with reading/writing images. For example to read/write PNG
> image formats, I expect to do something like this:
>
> =========================================================
> #include "itkImage.h"
> #include "itkImageFileReader.h"
>
> typedef unsigned char  InputPixelType;
> typedef itk::Image< InputPixelType , 2 > InputImageType;
> typedef itk::ImageFileReader<InputImageType> ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName('image name');
> reader->Update();
> =========================================================
> However, the above code returns an error since it seems that "itkImage.h"
> does nothing at all!
>
> Instead every time I want to read/write a PNG image, I should modify the
> above code as follow:
>
>
> =========================================================
> #include "itkImageFileReader.h"
> #include "itkPNGImageIOFactory.h"                        // new line
>
> typedef unsigned char  InputPixelType;
> typedef itk::Image< InputPixelType , 2 > InputImageType;
> typedef itk::ImageFileReader<InputImageType> ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> itk::PNGImageIOFactory::RegisterOneFactory();             // new line
> reader->SetFileName('image name');
> reader->Update();
> =========================================================
>
>
> In short, I expect by including "itkImage.h", ITK automatically identify
> input/output image format. However, I have to do it manually. The problem
> is when I want to read for example a '.mha' file format.
>
> Does anyone know what might be the problem and how could I 'SOLVE' it?
>
> Thanks, Ali
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From swetha.bsharma at gmail.com  Tue Oct  4 06:37:51 2016
From: swetha.bsharma at gmail.com (swetha)
Date: Tue, 4 Oct 2016 03:37:51 -0700 (MST)
Subject: [ITK] [ITK-users] C# wrapper ITk -unresolved external symbol issues
Message-ID: <1475577471463-7589328.post@n2.nabble.com>

Hi, 

  I have developed an application using itk and I am trying to integrate it
with c#.I have written a wrapper ,in the wrapper application I have included
all ITK .libs in the linker input tab.I am still getting unresolved external
errors. These are the errors which I am getting: 


Error	4	error LNK2019: unresolved external symbol __imp__UuidCreate at 4
referenced in function "protected: static bool __cdecl
gdcm::UIDGenerator::GenerateUUID(unsigned char *)"
(?GenerateUUID at UIDGenerator@gdcm@@KA_NPAE at Z)
\ObliquePlaneWrapper\itkgdcmMSFF-4.9.lib(gdcmUIDGenerator.obj)
ObliquePlaneWrapper 


Error	2	error LNK2019: unresolved external symbol _gethostname at 8 referenced
in function "public: static bool __cdecl gdcm::System::GetHostName(char *
const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
\ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
ObliquePlaneWrapper 

Error	1	error LNK2019: unresolved external symbol _WSACleanup at 0 referenced
in function "public: static bool __cdecl gdcm::System::GetHostName(char *
const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
\ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
ObliquePlaneWrapper 

Error	3	error LNK2019: unresolved external symbol _WSAStartup at 8 referenced
in function "public: static bool __cdecl gdcm::System::GetHostName(char *
const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
\ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
ObliquePlaneWrapper 


How do i fix these errors? 
-swetha 



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/C-wrapper-ITk-unresolved-external-symbol-issues-tp7589328.html
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_____________________________________
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From dzenanz at gmail.com  Tue Oct  4 10:15:27 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 4 Oct 2016 10:15:27 -0400
Subject: [ITK] [ITK-users] C# wrapper ITk -unresolved external symbol
	issues
In-Reply-To: <1475577471463-7589328.post@n2.nabble.com>
References: <1475577471463-7589328.post@n2.nabble.com>
Message-ID: <CAPf2UMTvv6DAhyWTemt=AnsWe1NhPCjR+BR4OGe4BDLiaRAk5Q@mail.gmail.com>

Hi Swetha,

are you using CMake to configure you wrapper "application", or are you
manually listing all the libraries? Manual enumeration is very error-prone
(some parts of GDCM seem to be missing). If so, try configuring one example
application using CMake to see which libraries get linked to it. Here is a
part of list on my computer which contains "gdcm", copy pasted from Visual
Studio project properties->linker->input->additional dependencies:
C:\Dev\ITK-2015\lib\Debug\itkgdcmDICT-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmMSFF-4.11.lib
C:\Dev\ITK-2015\lib\Debug\ITKIOGDCM-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmIOD-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmDSED-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmCommon-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmjpeg8-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmjpeg12-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmjpeg16-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmopenjpeg-4.11.lib
C:\Dev\ITK-2015\lib\Debug\itkgdcmcharls-4.11.lib

Are you trying to link a C# library into a C++ application or the other way
around?

Regards,
D?enan

On Tue, Oct 4, 2016 at 6:37 AM, swetha <swetha.bsharma at gmail.com> wrote:

> Hi,
>
>   I have developed an application using itk and I am trying to integrate it
> with c#.I have written a wrapper ,in the wrapper application I have
> included
> all ITK .libs in the linker input tab.I am still getting unresolved
> external
> errors. These are the errors which I am getting:
>
>
> Error   4       error LNK2019: unresolved external symbol
> __imp__UuidCreate at 4
> referenced in function "protected: static bool __cdecl
> gdcm::UIDGenerator::GenerateUUID(unsigned char *)"
> (?GenerateUUID at UIDGenerator@gdcm@@KA_NPAE at Z)
> \ObliquePlaneWrapper\itkgdcmMSFF-4.9.lib(gdcmUIDGenerator.obj)
> ObliquePlaneWrapper
>
>
> Error   2       error LNK2019: unresolved external symbol _gethostname at 8
> referenced
> in function "public: static bool __cdecl gdcm::System::GetHostName(char *
> const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
> \ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
> ObliquePlaneWrapper
>
> Error   1       error LNK2019: unresolved external symbol _WSACleanup at 0
> referenced
> in function "public: static bool __cdecl gdcm::System::GetHostName(char *
> const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
> \ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
> ObliquePlaneWrapper
>
> Error   3       error LNK2019: unresolved external symbol _WSAStartup at 8
> referenced
> in function "public: static bool __cdecl gdcm::System::GetHostName(char *
> const)" (?GetHostName at System@gdcm@@SA_NQAD at Z)
> \ObliquePlaneWrapper\itkgdcmCommon-4.9.lib(gdcmSystem.obj)
> ObliquePlaneWrapper
>
>
> How do i fix these errors?
> -swetha
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/C-wrapper-ITk-unresolved-external-symbol-issues-
> tp7589328.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From matt.mccormick at kitware.com  Tue Oct  4 11:52:47 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 4 Oct 2016 11:52:47 -0400
Subject: [ITK] [ITK-dev] ITK Confab Hangout Links
Message-ID: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>

Hi,

Chatting with Jc about the Slicer community's use of Hangout's, Google
has now dropped support for G+ / Hangouts.

As suggested by Francois and Jc, I suggest we use a Google Calendar
entry with a Hangout link, then make the entry publicly visible. We
can publish a public hyperlink that people can use to join. This
worked well for the Slicer community.

Thanks,
Matt
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From francois.budin at kitware.com  Tue Oct  4 11:55:55 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 4 Oct 2016 11:55:55 -0400
Subject: [ITK] [ITK-dev] ITK Confab Hangout Links
In-Reply-To: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
References: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
Message-ID: <CAHwLD2UvmY03vd1pH20j=Df-HaiVfZzMJJkpBUMNJxxYVnk9iw@mail.gmail.com>

Great idea. Thanks for looking more into that!

On Tue, Oct 4, 2016 at 11:52 AM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi,
>
> Chatting with Jc about the Slicer community's use of Hangout's, Google
> has now dropped support for G+ / Hangouts.
>
> As suggested by Francois and Jc, I suggest we use a Google Calendar
> entry with a Hangout link, then make the entry publicly visible. We
> can publish a public hyperlink that people can use to join. This
> worked well for the Slicer community.
>
> Thanks,
> Matt
>
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From matt.mccormick at kitware.com  Tue Oct  4 11:56:31 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 4 Oct 2016 11:56:31 -0400
Subject: [ITK] [ITK-dev] V4 Registration having trouble converging while
 V3 works fine
In-Reply-To: <CAM7sfn22Yvi8Eo==QnwE4KsYoYs3y+urOw3MdCmr_s9W39Ha8w@mail.gmail.com>
References: <CAM7sfn22Yvi8Eo==QnwE4KsYoYs3y+urOw3MdCmr_s9W39Ha8w@mail.gmail.com>
Message-ID: <CALzTN-Tc7+WaoW_ssrUJsKt3R0p32ayd0fFfkw8bpisz+sm3Fg@mail.gmail.com>

Hi Sepide,

The parameters are not quite equivalent in the ITKv3 and ITKv4
frameworks. In particular, you may need to relax the convergence
criteria for ITKv4 to get the same behavior as ITKv3.

HTH,
Matt

On Fri, Sep 30, 2016 at 3:24 PM, sepideh movaghati
<sepideh.movaghati at gmail.com> wrote:
>
> Hi,
>
>
>
> I was comparing v3 and v4 registration performance on a set of 3D images. In
> few cases, I noticed that v4 registration is diverging while v3 converges to
> a reasonable result without any problem.
> I wonder if you have ever noticed a problem with v4 optimizer that could
> cause similar issues.
>
>
> I copied my code for v3 and v4 registration below. I tried to keep the
> registration configuration very similar in both versions. In v3 I set the
> NumberOfSpatialSamples to 380000 which is about 10% of voxels. I also tried
> with full sampling but the behavior stays the same.
>
>
> In the attached csv file you can see the metric value at each iteration of
> the optimizer for both v3 and v4 version. It is clear that v3 converges
> smoothly, but v4 makes the initial metric value worse after too many
> iterations.
>
>
>
> Thanks a lot in advance.
> Regards,
> Sepide
>
>
> auto interpolator = itk::LinearInterpolateImageFunction<ImageType,
> double>::New();
>
> auto transform = itk::AffineTransform<double>::New();
>
> transform->SetIdentity();
>
> itk::Array<double> scales;
>
> scales.SetSize(12);
>
> scales.Fill(1.0);
>
> scales[9] =  0.001; //translation parameters scales
>
> scales[10] =  0.001;
>
> scales[11] =  0.001;
>
>
>
> // Registration V3 ----------------------- :
>
>     auto metric = itk::MattesMutualInformationImageToImageMetric<ImageType,
> ImageType>::New();
>
>     auto optimizer = itk::RegularStepGradientDescentOptimizer::New();
>
>     auto registration = itk::ImageRegistrationMethod<ImageType,
> ImageType>::New();
>
>
>
>     int NumberOfSpatialSamples = 380000;
>
>
>
>     metric->SetNumberOfSpatialSamples(NumberOfSpatialSamples);
>
>     optimizer->SetScales(scales);
>
>     registration->SetMetric(metric);
>
>     registration->SetOptimizer(optimizer);
>
>     registration->SetInterpolator(interpolator);
>
>     registration->SetTransform(transform);
>
>     registration->SetFixedImage(fixedImage);
>
>     registration->SetMovingImage(movingImage);
>
>     registration->SetFixedImageRegion(fixedImage->GetBufferedRegion());
>
>     registration->SetInitialTransformParameters(transform->GetParameters());
>
>     registration->Update();
>
>
>
>
>
> // Registration V4 ----------------------- :
>
>     auto metric =
> itk::MattesMutualInformationImageToImageMetricv4<ImageType,
> ImageType>::New();
>
>     auto optimizer = itk::RegularStepGradientDescentOptimizerv4::New();
>
>     auto registration = itk::ImageRegistrationMethodv4<ImageType,
> ImageType>::New();
>
>
>
>     optimizer->SetScales(scales);
>
>     optimizer->SetDoEstimateScales(false);
>
>     optimizer->SetDoEstimateLearningRateAtEachIteration(false);
>
>     optimizer->SetDoEstimateLearningRateOnce(false);
>
>     optimizer->SetMetric(metric);
>
>
>
>     registration->SetNumberOfLevels(1);
>
>     registration->SetSmoothingSigmasPerLevel(0);
>
>     registration->SetShrinkFactorsPerLevel(1);
>
>     registration->SetMetricSamplingPercentagePerLevel(0.1);
>
>
>
>     registration->SetMetric(metric);
>
>     registration->SetOptimizer(optimizer);
>
>     registration->SetFixedImage(fixedImage);
>
>     registration->SetMovingImage(movingImage);
>
>     registration->SetMetricSamplingStrategy(RegistrationType::REGULAR);
>
>     registration->SetInitialTransform(transform);
>
>
>
>     registration->Update();
>
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
_______________________________________________
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From matt.mccormick at kitware.com  Tue Oct  4 12:01:52 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 4 Oct 2016 12:01:52 -0400
Subject: [ITK] [ITK-dev] ITK Confab Hangout Links
In-Reply-To: <1957E440-0637-4DE1-85DC-789BBDB15186@mail.nih.gov>
References: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
 <1957E440-0637-4DE1-85DC-789BBDB15186@mail.nih.gov>
Message-ID: <CALzTN-QAOvEwDjwT-fPy0RxVg7t07KB7645aZkg6Ar=D8w9y-A@mail.gmail.com>

On Tue, Oct 4, 2016 at 11:58 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Subscribing to a calendar would work well for me too.

Great!


> So G+ with Hangout is being dropped, but support for Google Hangout is still good?

Right.


> What about keeping ITK release dates on there too? Maybe other import ITK events/dates there too?

Maybe we should have an ITK calendar?


M
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From blowekamp at mail.nih.gov  Tue Oct  4 11:58:58 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 4 Oct 2016 15:58:58 +0000
Subject: [ITK] [ITK-dev] ITK Confab Hangout Links
In-Reply-To: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
References: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
Message-ID: <1957E440-0637-4DE1-85DC-789BBDB15186@mail.nih.gov>

Subscribing to a calendar would work well for me too.

So G+ with Hangout is being dropped, but support for Google Hangout is still good?

What about keeping ITK release dates on there too? Maybe other import ITK events/dates there too?

Brad


> On Oct 4, 2016, at 11:52 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
> Hi,
> 
> Chatting with Jc about the Slicer community's use of Hangout's, Google
> has now dropped support for G+ / Hangouts.
> 
> As suggested by Francois and Jc, I suggest we use a Google Calendar
> entry with a Hangout link, then make the entry publicly visible. We
> can publish a public hyperlink that people can use to join. This
> worked well for the Slicer community.
> 
> Thanks,
> Matt

_______________________________________________
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From matt.mccormick at kitware.com  Tue Oct  4 12:34:16 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 4 Oct 2016 12:34:16 -0400
Subject: [ITK] [ITK-dev] ITK Confab Hangout Links
In-Reply-To: <CALzTN-QAOvEwDjwT-fPy0RxVg7t07KB7645aZkg6Ar=D8w9y-A@mail.gmail.com>
References: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
 <1957E440-0637-4DE1-85DC-789BBDB15186@mail.nih.gov>
 <CALzTN-QAOvEwDjwT-fPy0RxVg7t07KB7645aZkg6Ar=D8w9y-A@mail.gmail.com>
Message-ID: <CALzTN-TMVz6q=Opz_JUzxk_2WkfBTU_j6q1DEsLzEftqbGeVPw@mail.gmail.com>

On Tue, Oct 4, 2016 at 12:01 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> On Tue, Oct 4, 2016 at 11:58 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
> <blowekamp at mail.nih.gov> wrote:
>> Subscribing to a calendar would work well for me too.
>
> Great!
>
>
>> So G+ with Hangout is being dropped, but support for Google Hangout is still good?
>
> Right.
>
>
>> What about keeping ITK release dates on there too? Maybe other import ITK events/dates there too?
>
> Maybe we should have an ITK calendar?

Here it is:

  https://calendar.google.com/calendar/embed?src=jhm9h5t9un1gbm21jktej2qvh0%40group.calendar.google.com&ctz=America/New_York


I'll be out on vacation this week, and I will not be able to join on Friday.

Thanks,
Matt
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From blowekamp at mail.nih.gov  Tue Oct  4 13:15:31 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 4 Oct 2016 17:15:31 +0000
Subject: [ITK] [ITK-dev] ITK Confab Hangout Links
In-Reply-To: <CALzTN-QAOvEwDjwT-fPy0RxVg7t07KB7645aZkg6Ar=D8w9y-A@mail.gmail.com>
References: <CALzTN-S6W+YtQ+PFg6OiJu-_et5Mg9Z-n+Re1Xet+6xCFH_qvw@mail.gmail.com>
 <1957E440-0637-4DE1-85DC-789BBDB15186@mail.nih.gov>
 <CALzTN-QAOvEwDjwT-fPy0RxVg7t07KB7645aZkg6Ar=D8w9y-A@mail.gmail.com>
Message-ID: <527B62C0-B562-45B9-B414-C8E2F895D223@mail.nih.gov>


> On Oct 4, 2016, at 12:01 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
> On Tue, Oct 4, 2016 at 11:58 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
> <blowekamp at mail.nih.gov> wrote:
>> Subscribing to a calendar would work well for me too.
> 
> Great!
> 
> 
>> So G+ with Hangout is being dropped, but support for Google Hangout is still good?
> 
> Right.
> 
> 
>> What about keeping ITK release dates on there too? Maybe other import ITK events/dates there too?
> 
> Maybe we should have an ITK calendar?
> 
> 

Yes, what do you looks good. I thought that is what your initial proposal was :)

> M

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From swetha.bsharma at gmail.com  Wed Oct  5 01:57:39 2016
From: swetha.bsharma at gmail.com (swetha)
Date: Tue, 4 Oct 2016 22:57:39 -0700 (MST)
Subject: [ITK] [ITK-users] C# wrapper ITk -unresolved external symbol
	issues
In-Reply-To: <CAPf2UMTvv6DAhyWTemt=AnsWe1NhPCjR+BR4OGe4BDLiaRAk5Q@mail.gmail.com>
References: <1475577471463-7589328.post@n2.nabble.com>
 <CAPf2UMTvv6DAhyWTemt=AnsWe1NhPCjR+BR4OGe4BDLiaRAk5Q@mail.gmail.com>
Message-ID: <1475647059485-7589330.post@n2.nabble.com>

Hi Dzenan,

  I used CMAKe and it worked,I had manually added all the .lib files.
Thankyou so much Dzenan.
-swetha



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/C-wrapper-ITk-unresolved-external-symbol-issues-tp7589328p7589330.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
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From ivan.granata.na at gmail.com  Wed Oct  5 01:50:13 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 4 Oct 2016 22:50:13 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
Message-ID: <1475646613139-37633.post@n7.nabble.com>

i tried this example and after 161 iteration


itk::simple::Transform
 TranslationTransform (0000000019D26F10)
   RTTI typeinfo:   class itk::TranslationTransform<double,3>
   Reference Count: 3
   Modified Time: 3008
   Debug: Off
   Object Name: 
   Observers: 
     none
   Offset: [-6.65479, -19.5028, -85.532]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Step too
small after 162 iterations. Current step (0.0078125) is less than minimum
step (0.01).
 Iteration: 163
 Metric value: 3451114,037376


run this error:    



Exception thrown in SimpleITK Transform_writeTransform:
c:\d\vs9-pkg\simpleitk-build\itk-prefix\include\itk-4.7\itkTransformFileWriter.hxx:202:
itk::ERROR: TransformFileWriterTemplate(0000000019D2DBA0): Can't Create IO
object for file
C:\Users\Ivan\workspace\ImageRegistrationMethod1\registrata.nii



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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37633.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From blowekamp at mail.nih.gov  Wed Oct  5 08:53:51 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 5 Oct 2016 12:53:51 +0000
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <1475646613139-37633.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
Message-ID: <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>

What is the command line you used?

Does the output path C:\Users\Ivan\workspace\ImageRegistrationMethod1? already exists?

Brad

> On Oct 5, 2016, at 1:50 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> i tried this example and after 161 iteration
> 
> 
> itk::simple::Transform
> TranslationTransform (0000000019D26F10)
>   RTTI typeinfo:   class itk::TranslationTransform<double,3>
>   Reference Count: 3
>   Modified Time: 3008
>   Debug: Off
>   Object Name: 
>   Observers: 
>     none
>   Offset: [-6.65479, -19.5028, -85.532]
> 
> Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Step too
> small after 162 iterations. Current step (0.0078125) is less than minimum
> step (0.01).
> Iteration: 163
> Metric value: 3451114,037376
> 
> 
> run this error:    
> 
> 
> 
> Exception thrown in SimpleITK Transform_writeTransform:
> c:\d\vs9-pkg\simpleitk-build\itk-prefix\include\itk-4.7\itkTransformFileWriter.hxx:202:
> itk::ERROR: TransformFileWriterTemplate(0000000019D2DBA0): Can't Create IO
> object for file
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\registrata.nii
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37633.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

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From ivan.granata.na at gmail.com  Wed Oct  5 07:51:30 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 04:51:30 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
Message-ID: <1475668290769-37635.post@n7.nabble.com>

i must coreg these 
CT with T1

the path already exist, yes


i use eclipse ide with these arguments
C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\Headt1mpragesagp2iso08s007a1001.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\registrata.nii


i tried this
http://review.source.kitware.com/#/c/21596/1/Examples/Java/ImageRegistrationMethod1.java
, but several errors appear
if i change parameters...change error

for example
i take a  minStep > 0.01; and error is on numberOfIterazions
i take a numberOfIterations > 20 or <200 and the error return on minStep
  same things on relaxationFactor = 0.5; or =0.8

i tried also this script but it is the same


import org.itk.simple.*;


class IterationUpdate  extends Command {

	  private ImageRegistrationMethod m_Method;

	  public IterationUpdate(ImageRegistrationMethod m) {
	    super();
	    m_Method=m;
	  }

	  public void execute() {
	    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
	    System.out.format("%3d = %10.5f : [%f, %f]\n",
	                      m_Method.getOptimizerIteration(),
	                      m_Method.getMetricValue(),
	                      pos.get(0), pos.get(1));
	  }
	}

class ImageRegistrationMethod1 {

  public static void main(String argv[]) {

  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethod1");
      System.exit(-1);
    }

  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );

  reader.setFileName(argv[0]);
  Image fixed = reader.execute();

  reader.setFileName(argv[1]);
  Image moving = reader.execute();

  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
  
  
  

  
 
   int numberOfBins = 64;
  
  R.setMetricAsMattesMutualInformation(numberOfBins);
  
  double LearningRate = 8.0;
  long numberOfIterations = 100;
  double convergenceMinimumValue = 1e-6;
  long convergenceWindowSize = 10;
  double lineSearchLowerLimit = 0;
  
  R.setOptimizerAsGradientDescentLineSearch( LearningRate,
          numberOfIterations,
          convergenceMinimumValue,
          convergenceWindowSize,
          lineSearchLowerLimit
          );
  
  

  R.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkLinear );

  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);

  org.itk.simple.Transform outTx = R.execute( fixed, moving );

  System.out.println("-------");
  System.out.println(outTx.toString());
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());

  outTx.writeTransform(argv[2]);

  }

}






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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37635.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From blowekamp at mail.nih.gov  Wed Oct  5 09:24:17 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 5 Oct 2016 13:24:17 +0000
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <1475668290769-37635.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
Message-ID: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>

I would look at the test parameter used for this example:

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Java/CMakeLists.txt#L24

The third parameter is a transform and not an image format. Supported extensions include ?txt?, ?hdf5? and I believe ?mat?.

Please try to reproduce the test before moving on.

Brad

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From ivan.granata.na at gmail.com  Wed Oct  5 08:12:56 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:12:56 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475669576013-37637.post@n7.nabble.com>

and the output?
i would read System.out.format( "Usage: %s <fixedImageFilter>
<movingImageFile> <outputTransformFile>\n", "ImageRegistrationMethod1");



C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\Headt1mpragesagp2iso08s007a1001.nii 

..........  third arguments?



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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37637.html
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_____________________________________
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From ivan.granata.na at gmail.com  Wed Oct  5 08:22:42 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:22:42 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475670162009-37638.post@n7.nabble.com>

ok i use these

C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\Headt1mpragesagp2iso08s007a1001.nii
C:\Users\Ivan\workspace\ImageRegistrationMethod1\reg.txt

but if i open txt file i've 

#Insight Transform File V1.0
#Transform 0
Transform: TranslationTransform_double_3_3
Parameters: 2.4513961563310462 -15.82828376173809 -69.1961914372912
FixedParameters: 



what about this? i would an image coreg



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From ivan.granata.na at gmail.com  Wed Oct  5 08:23:57 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:23:57 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475670237866-37639.post@n7.nabble.com>

i receive this

  0 = 665122,88518 : [0,134024, -1,321073]
  1 = 669400,27636 : [0,251056, -2,660742]
  2 = 674931,78583 : [0,349982, -4,100354]
  3 = 681844,66614 : [0,474374, -5,702413]
  4 = 689465,45986 : [0,626028, -7,323900]
  5 = 698185,32936 : [0,843615, -9,192783]
  6 = 707489,19565 : [1,050153, -10,999621]
  7 = 717268,70721 : [1,204555, -12,460959]
  8 = 743987,25838 : [1,327348, -13,160174]
  9 = 757137,55193 : [1,453234, -13,474015]
 10 = 771437,65405 : [1,623318, -13,741873]
 11 = 786922,16242 : [1,816794, -14,097160]
 12 = 803545,10774 : [2,077654, -14,547859]
 13 = 840861,28970 : [2,338309, -14,986500]
 14 = 858852,80038 : [2,454045, -15,316711]
 15 = 877420,96469 : [2,459722, -15,519754]
 16 = 893981,36101 : [2,456281, -15,687996]
 17 = 902994,83757 : [2,451396, -15,828284]
-------
itk::simple::Transform
 TranslationTransform (0000000019B04710)
   RTTI typeinfo:   class itk::TranslationTransform<double,3>
   Reference Count: 3
   Modified Time: 2576
   Debug: Off
   Object Name: 
   Observers: 
     none
   Offset: [2.4514, -15.8283, -69.1962]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Gradient
magnitude tolerance met after 18 iterations. Gradient magnitude (0) is less
than gradient magnitude tolerance (0.0001).
 Iteration: 19
 Metric value:
179769313486231570000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000,000000




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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37639.html
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_____________________________________
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From ivan.granata.na at gmail.com  Wed Oct  5 08:34:29 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 05:34:29 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
Message-ID: <1475670869976-37640.post@n7.nabble.com>

with my example where i use


  R.setMetricAsMattesMutualInformation(numberOfBins);
  
  double LearningRate = 8.0;
  double minStep = 0.001;
  long numberOfIterations = 100;
  double relaxationFactor = 0.5;
  double gradientMagnitudeTolerance = 1e-006;
  
  R.setOptimizerAsRegularStepGradientDescent



 i receive a txt file and this video output

  0 =   -0,15630 : [0,746321, -7,955376]
  1 =   -0,17854 : [1,437118, -15,910358]
  2 =   -0,19452 : [1,031387, -23,317717]
  3 =   -0,20341 : [3,410042, -21,038059]
  4 =   -0,19856 : [1,526970, -21,439759]
  5 =   -0,20108 : [0,143113, -22,783732]
  6 =   -0,20340 : [1,089391, -22,619125]
  7 =   -0,20366 : [1,647981, -21,912288]
  8 =   -0,20073 : [1,184824, -22,085392]
  9 =   -0,20140 : [0,993548, -22,508374]
 10 =   -0,20281 : [1,192105, -22,356475]
 11 =   -0,20253 : [1,117475, -22,167086]
 12 =   -0,20169 : [1,075827, -22,241268]
 13 =   -0,20225 : [1,126952, -22,206076]
 14 =   -0,20222 : [1,122912, -22,147089]
 15 =   -0,20209 : [1,108291, -22,166964]
 16 =   -0,20222 : [1,118988, -22,159212]
 17 =   -0,20224 : [1,125776, -22,145295]
 18 =   -0,20224 : [1,118157, -22,146866]
 19 =   -0,20226 : [1,119790, -22,149387]
-------
itk::simple::Transform
 TranslationTransform (0000000019CD54D0)
   RTTI typeinfo:   class itk::TranslationTransform<double,3>
   Reference Count: 3
   Modified Time: 2659
   Debug: Off
   Object Name: 
   Observers: 
     none
   Offset: [1.11979, -22.1494, 4.96231]

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Gradient
magnitude tolerance met after 20 iterations. Gradient magnitude (9.89e-007)
is less than gradient magnitude tolerance (1e-006).
 Iteration: 21
 Metric value: -0,202264




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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37640.html
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_____________________________________
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From francois.budin at kitware.com  Wed Oct  5 15:24:43 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 5 Oct 2016 15:24:43 -0400
Subject: [ITK] [ITK-users]  Linker errors on example
In-Reply-To: <1475689968144-37641.post@n7.nabble.com>
References: <CAPEEyN5p03uQ7TeEAkZi1dihT-=U5KsMufwXZ7s-kdS8JiHS4A@mail.gmail.com>
 <CADZJ4hOYhZT5TwUaVy+r=DYEk1+QAEg_QTPwHyiZLdnrHJrYWw@mail.gmail.com>
 <CAPEEyN4KGmayTk0arRegTakUrAJ0QCFuu+QAMXgY66=n+CJ4DA@mail.gmail.com>
 <CALzTN-TVB=bdBzbXogtXypwkbmBouxxYGZ1ZQLEketfOztJ72w@mail.gmail.com>
 <1475689968144-37641.post@n7.nabble.com>
Message-ID: <CAHwLD2V+FxvuRjvJW_mr+-sn6nc54vVndjrf3-Y=kP0DEZ9ybA@mail.gmail.com>

Hello Ibraheem,

ITK does not provide visualization as part of the toolkit. If you want to
look at the output of this example, I would advise you to either use an
existing tool, such as ITKSnap [1] or 3DSlicer[ 2], or if you want to
create your own visualization tool, you can use VTK [3] with ITK.
Hope this helps,

Francois
[1] http://www.itksnap.org/pmwiki/pmwiki.php
[2] https://www.slicer.org/
[3] https://itk.org/Wiki/ITK/Examples/IO/ImageToVTKImageFilter

On Wed, Oct 5, 2016 at 1:52 PM, Ibraheem via Insight-users <
insight-users at itk.org> wrote:

> I just downloaded the example. It works but I think the visualization part
> is
> missing. I think it is already implemented because of the figures. Is it
> possible to add the QuickView part or itkImageFileWriter to visualize the
> result? I tried to do so but it didn't works.
> Best regards!
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-ITK-Linker-errors-on-example-tp33858p37641.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From ivan.granata.na at gmail.com  Thu Oct  6 02:27:14 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Wed, 5 Oct 2016 23:27:14 -0700 (MST)
Subject: [ITK] [ITK-users] SITK Java Multicomponent
 PatchBasedDenoisingImageFilter not run for 4D images or multicomponent.. a
 similar filter for 4D images?
Message-ID: <1475735234617-37644.post@n7.nabble.com>

i tried PatchBasedDenoisingImageFilter simple itk  Java version for 4d images
but it work just with 3d images

can anyone know some similar filter for 4d images?

something for multicomponent filter?

thx



--
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From ivan.granata.na at gmail.com  Thu Oct  6 08:32:21 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 05:32:21 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK JAVA ImageSeriesReader and
 PatchBasedDenoisingImageFilter and 4d images
Message-ID: <1475757141426-37645.post@n7.nabble.com>

hi 

can anyone help me how to write ImageSeriesReader in Java with simple itk

i wolud read a dicom series in a path and after apply a
PatchBasedDenoisingImageFilter

if possible i would work also with 4d image (multicomponent filter)


thx


this is my code

import org.itk.simple.*;

import java.util.Vector; 
class PatchBasedDenoisingImageFilter {
public static void main(String argv[]) {
		
	if ( argv.length < 5 ) {
System.out.println("Immetti prima:  <input_img> <patch_radius> <smoothness>
<patch_number> <noise_sigma> <output_img>");
return;
}

org.itk.simple.ImageSeriesReader reader = new
org.itk.simple.ImageSeriesReader();

VectorString inputdicom = new VectorString();
inputdicom.toString(argv[0]);
reader.setFileNames(inputdicom);


//reader.setVectorString (argv[0]);
//reader.setFileNames(inputdicom);


Image img = reader.execute();

System.out.println(img.getDimension());

org.itk.simple.PatchBasedDenoisingImageFilter filter = new
org.itk.simple.PatchBasedDenoisingImageFilter();

filter.getAlwaysTreatComponentsAsEuclidean ();
boolean setKBE = false;
filter.setKernelBandwidthEstimation ( setKBE );
//filter.getKernelBandwidthUpdateFrequency ();
//filter.getKernelBandwidthFractionPixelsForEstimation ();
//filter.getKernelBandwidthMultiplicationFactor ();
//filter.getKernelBandwidthSigma ();
filter.setNoiseModel(org.itk.simple.PatchBasedDenoisingImageFilter.NoiseModelType.GAUSSIAN);
filter.getNumberOfIterations (); //cablato
filter.getSampleVariance ();
filter.setPatchRadius ( Long.valueOf ( argv[1] ).longValue() );
filter.setNoiseModelFidelityWeight ( Double.valueOf ( argv[2]
).doubleValue() );

if ( argv.length < 5 ) filter.getNumberOfSamplePatches ();
else filter.setNumberOfSamplePatches ( Long.valueOf ( argv[3] ).longValue()
);

if ( argv.length < 6 ) 
	filter.getNoiseSigma ();
else filter.setNoiseSigma (Double.valueOf ( argv[4] ).doubleValue() );

Image blurredImg  = filter.execute(img);

CastImageFilter caster = new CastImageFilter();
caster.setOutputPixelType( img.getPixelIDValue() );
Image castImg = caster.execute( blurredImg );
ImageFileWriter writer = new ImageFileWriter();

writer.setFileName(argv[5]);
writer.execute( castImg ); 
}


}
}












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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-JAVA-ImageSeriesReader-and-PatchBasedDenoisingImageFilter-and-4d-images-tp37645.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From blowekamp at mail.nih.gov  Thu Oct  6 10:01:24 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 6 Oct 2016 14:01:24 +0000
Subject: [ITK] [ITK-users] SimpleITK JAVA ImageSeriesReader and
 PatchBasedDenoisingImageFilter and 4d images
In-Reply-To: <1475757141426-37645.post@n7.nabble.com>
References: <1475757141426-37645.post@n7.nabble.com>
Message-ID: <6858503C-9EEE-44DF-8DEC-636AF4ACA3FA@mail.nih.gov>

I would look at the python examples and usage for reference:

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/DicomSeriesReader.py
https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/DicomSeriesReader2.py

https://github.com/SimpleITK/SimpleITK/blob/master/Examples/Python/CMakeLists.txt#L73-L89

HTH,
Brad

> On Oct 6, 2016, at 8:32 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> hi 
> 
> can anyone help me how to write ImageSeriesReader in Java with simple itk
> 
> i wolud read a dicom series in a path and after apply a
> PatchBasedDenoisingImageFilter
> 
> if possible i would work also with 4d image (multicomponent filter)
> 
> 
> thx
> 
> 
> this is my code
> 
> import org.itk.simple.*;
> 
> import java.util.Vector; 
> class PatchBasedDenoisingImageFilter {
> public static void main(String argv[]) {
> 		
> 	if ( argv.length < 5 ) {
> System.out.println("Immetti prima:  <input_img> <patch_radius> <smoothness>
> <patch_number> <noise_sigma> <output_img>");
> return;
> }
> 
> org.itk.simple.ImageSeriesReader reader = new
> org.itk.simple.ImageSeriesReader();
> 
> VectorString inputdicom = new VectorString();
> inputdicom.toString(argv[0]);
> reader.setFileNames(inputdicom);
> 
> 
> //reader.setVectorString (argv[0]);
> //reader.setFileNames(inputdicom);
> 
> 
> Image img = reader.execute();
> 
> System.out.println(img.getDimension());
> 
> org.itk.simple.PatchBasedDenoisingImageFilter filter = new
> org.itk.simple.PatchBasedDenoisingImageFilter();
> 
> filter.getAlwaysTreatComponentsAsEuclidean ();
> boolean setKBE = false;
> filter.setKernelBandwidthEstimation ( setKBE );
> //filter.getKernelBandwidthUpdateFrequency ();
> //filter.getKernelBandwidthFractionPixelsForEstimation ();
> //filter.getKernelBandwidthMultiplicationFactor ();
> //filter.getKernelBandwidthSigma ();
> filter.setNoiseModel(org.itk.simple.PatchBasedDenoisingImageFilter.NoiseModelType.GAUSSIAN);
> filter.getNumberOfIterations (); //cablato
> filter.getSampleVariance ();
> filter.setPatchRadius ( Long.valueOf ( argv[1] ).longValue() );
> filter.setNoiseModelFidelityWeight ( Double.valueOf ( argv[2]
> ).doubleValue() );
> 
> if ( argv.length < 5 ) filter.getNumberOfSamplePatches ();
> else filter.setNumberOfSamplePatches ( Long.valueOf ( argv[3] ).longValue()
> );
> 
> if ( argv.length < 6 ) 
> 	filter.getNoiseSigma ();
> else filter.setNoiseSigma (Double.valueOf ( argv[4] ).doubleValue() );
> 
> Image blurredImg  = filter.execute(img);
> 
> CastImageFilter caster = new CastImageFilter();
> caster.setOutputPixelType( img.getPixelIDValue() );
> Image castImg = caster.execute( blurredImg );
> ImageFileWriter writer = new ImageFileWriter();
> 
> writer.setFileName(argv[5]);
> writer.execute( castImg ); 
> }
> 
> 
> }
> }
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-JAVA-ImageSeriesReader-and-PatchBasedDenoisingImageFilter-and-4d-images-tp37645.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From dzenanz at gmail.com  Thu Oct  6 10:25:58 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 10:25:58 -0400
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <1475670162009-37638.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670162009-37638.post@n7.nabble.com>
Message-ID: <CAPf2UMSF+oT9u=k7KZ+-Jp2Vqb1GHucg132Y5qYLEYANkGhe9Q@mail.gmail.com>

Hi Ivan,

the reg.txt file is a saved transform, and you should be able to use it to
resample <https://itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html>
your input image to the space of your target image.

Regards,
D?enan

On Wed, Oct 5, 2016 at 8:22 AM, ivan <ivan.granata.na at gmail.com> wrote:

> ok i use these
>
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\CT.nii
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\
> Headt1mpragesagp2iso08s007a1001.nii
> C:\Users\Ivan\workspace\ImageRegistrationMethod1\reg.txt
>
> but if i open txt file i've
>
> #Insight Transform File V1.0
> #Transform 0
> Transform: TranslationTransform_double_3_3
> Parameters: 2.4513961563310462 -15.82828376173809 -69.1961914372912
> FixedParameters:
>
>
>
> what about this? i would an image coreg
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37638.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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Kitware offers ITK Training Courses, for more information visit:
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From dzenanz at gmail.com  Thu Oct  6 10:28:22 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 10:28:22 -0400
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <1475670869976-37640.post@n7.nabble.com>
References: <1475138722111-37600.post@n7.nabble.com>
 <CAPf2UMSX_zuStXVcucYH_Tu4ys200i9fSXPMpvPFwN9VDS7S+g@mail.gmail.com>
 <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
Message-ID: <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>

Hi Ivan,

the optimizers in ITK minimize the metric, and since mutual information
needs to be "bigger" it is prefixed by a minus so that optimizers try to
increase its absolute value.

Regards,
D?enan

On Wed, Oct 5, 2016 at 8:34 AM, ivan <ivan.granata.na at gmail.com> wrote:

> with my example where i use
>
>
>   R.setMetricAsMattesMutualInformation(numberOfBins);
>
>   double LearningRate = 8.0;
>   double minStep = 0.001;
>   long numberOfIterations = 100;
>   double relaxationFactor = 0.5;
>   double gradientMagnitudeTolerance = 1e-006;
>
>   R.setOptimizerAsRegularStepGradientDescent
>
>
>
>  i receive a txt file and this video output
>
>   0 =   -0,15630 : [0,746321, -7,955376]
>   1 =   -0,17854 : [1,437118, -15,910358]
>   2 =   -0,19452 : [1,031387, -23,317717]
>   3 =   -0,20341 : [3,410042, -21,038059]
>   4 =   -0,19856 : [1,526970, -21,439759]
>   5 =   -0,20108 : [0,143113, -22,783732]
>   6 =   -0,20340 : [1,089391, -22,619125]
>   7 =   -0,20366 : [1,647981, -21,912288]
>   8 =   -0,20073 : [1,184824, -22,085392]
>   9 =   -0,20140 : [0,993548, -22,508374]
>  10 =   -0,20281 : [1,192105, -22,356475]
>  11 =   -0,20253 : [1,117475, -22,167086]
>  12 =   -0,20169 : [1,075827, -22,241268]
>  13 =   -0,20225 : [1,126952, -22,206076]
>  14 =   -0,20222 : [1,122912, -22,147089]
>  15 =   -0,20209 : [1,108291, -22,166964]
>  16 =   -0,20222 : [1,118988, -22,159212]
>  17 =   -0,20224 : [1,125776, -22,145295]
>  18 =   -0,20224 : [1,118157, -22,146866]
>  19 =   -0,20226 : [1,119790, -22,149387]
> -------
> itk::simple::Transform
>  TranslationTransform (0000000019CD54D0)
>    RTTI typeinfo:   class itk::TranslationTransform<double,3>
>    Reference Count: 3
>    Modified Time: 2659
>    Debug: Off
>    Object Name:
>    Observers:
>      none
>    Offset: [1.11979, -22.1494, 4.96231]
>
> Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Gradient
> magnitude tolerance met after 20 iterations. Gradient magnitude (9.89e-007)
> is less than gradient magnitude tolerance (1e-006).
>  Iteration: 21
>  Metric value: -0,202264
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37640.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From ivan.granata.na at gmail.com  Thu Oct  6 09:32:51 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 06:32:51 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
References: <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
Message-ID: <1475760771636-37649.post@n7.nabble.com>

and so < TInputImage, TOutputImage, TInterpolatorPrecisionType,
TTransformPrecisionType >


what about TInterpolatorPrecisionType, TTransformPrecisionType ???



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37649.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Thu Oct  6 11:53:29 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 11:53:29 -0400
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <1475760771636-37649.post@n7.nabble.com>
References: <1475150752914-37606.post@n7.nabble.com>
 <18387BD2-EF1B-44D0-9259-E197567C7711@mail.nih.gov>
 <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
Message-ID: <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>

Hi Ivan,

the defaults for those two are double. What is unclear about that?

Regards,
D?enan

On Thu, Oct 6, 2016 at 9:32 AM, ivan <ivan.granata.na at gmail.com> wrote:

> and so < TInputImage, TOutputImage, TInterpolatorPrecisionType,
> TTransformPrecisionType >
>
>
> what about TInterpolatorPrecisionType, TTransformPrecisionType ???
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37649.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From ivan.granata.na at gmail.com  Thu Oct  6 12:41:01 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 09:41:01 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
References: <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
Message-ID: <1475772061671-37651.post@n7.nabble.com>

if i use my original image here < TInputImage, TOutputImage

where i can use my reg.txt (ImageRegistration function output)

so ok TInterpolatorPrecisionType, TTransformPrecisionType these are other
parameters....and reg.txt file output?



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37651.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Thu Oct  6 14:16:54 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 14:16:54 -0400
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <1475772061671-37651.post@n7.nabble.com>
References: <1475155818302-37612.post@n7.nabble.com>
 <5E715AAE-04D7-474B-8626-669280DD8F9F@mail.nih.gov>
 <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
Message-ID: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>

Have you read section "2.9.4 Resample Image Filter" from
itk.org/ItkSoftwareGuide? The reg.txt file contains the transformation
which you want to apply to an image.

Regards

On Thu, Oct 6, 2016 at 12:41 PM, ivan <ivan.granata.na at gmail.com> wrote:

> if i use my original image here < TInputImage, TOutputImage
>
> where i can use my reg.txt (ImageRegistration function output)
>
> so ok TInterpolatorPrecisionType, TTransformPrecisionType these are other
> parameters....and reg.txt file output?
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-
> registration-tp37600p37651.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From ivan.granata.na at gmail.com  Thu Oct  6 13:36:06 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 6 Oct 2016 10:36:06 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
References: <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
 <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
Message-ID: <1475775366240-37653.post@n7.nabble.com>

yes  i read but in Java i ve some problems 



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37653.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Thu Oct  6 15:14:43 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 6 Oct 2016 15:14:43 -0400
Subject: [ITK] Resample image in Java
Message-ID: <CAPf2UMSNpU746m0MYDoF2UN1fYGx9DREGWBYZ0e0+erWec842Q@mail.gmail.com>

Hi people,

Ivan is trying to register CT with T1wMRI using SimpleITK in Java. So far
he got a registering transform saved into a file. He now wonders how to
resample his first image into the same space of the second image using the
given transform. Can anyone provide guidance?

Regards
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From francois.budin at kitware.com  Thu Oct  6 17:43:55 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 6 Oct 2016 17:43:55 -0400
Subject: [ITK] [ANN] ITK 4.10.0 has been released!
Message-ID: <CAHwLD2X5XbGycZmtnfoZYibxPeiuZgHxF+X1W2UGN=KApn35hQ@mail.gmail.com>

On behalf of the Insight Toolkit Community, we are happy to announce the
release of ITK 4.10.1!

Release files can be downloaded from:

 http://itk.org/ITK/resources/software.html

This is a patch release that fixes critical issues, regressions,
documentation, and compiler support. Of the numerous issues addressed in
this release, most notable is a fix to the ITK Python wrapping lazy
loading. This improves load times for many Python scripts by an order of
magnitude! Other important fixes include Python builds with GCC 6.2, which
defaults to C++14, TBB 4.4/VTK 7 compatibility, and CUDA / C++11
compatibility.

The next feature release, 4.11.0, is scheduled for mid-December.

Enjoy ITK!


Changes from v4.10.0 to v4.10.1:

Bradley Lowekamp (9):

     COMP: Address VS9 ambiguous std::abs call in Haung calculator

     COMP: Fix undefined NumericTraits::Zero and One errors with mingw64

     BUG: Address itkHDF5ImageIO test failures for mingw64

     ENH: Enable CMP0063 New behavior

     COMP: Enable hidden visibility property with vxl static libraries

    COMP: Enable hidden visibility property with HDF5 static libraries

     BUG: Match Add2 function to AddImageFilter documentation

     COMP: Bypass XCode 7.3,8 internal compilation error

     ENH: Separate TransformFactory class into separate module

D?enan Zuki? (2):

     COMP: enables TBB 4.4 back-end for VTK7's SMP

     BUG: fixing buffer growing endlessly, as reported by Timothee Evain

Francois Budin (3):

     BUG: lazyAttributes dictionary keys could be over-ridden

     BUG: Missing associated test data

     ENH: Bump CMakeLists.txt version to 4.10.1.

Gert Wollny (1):

     BUG: Relax vnl_complex floating point comparisons for i386

Hans Johnson (1):

     COMP: Add long long usage for HDF5

Hastings Greer (4):

     BUG: ITK-3448 Wrap itkQuadEdgeCellTraitsInfo more specifically

     BUG: remove lsqr because of license issues ITK 1160

     BUG: make itkTriangleHelper instantiable to ease wrapping

     BUG: initialize X to zero in lsmr Solve

Matthew McCormick (13):

     BUG: Fix H5File memory leak in HDF5ImageIO.

     BUG: Limit WRAP_ITK_MODULES when building externally

     COMP: Fix wrapping with a space in the Python include path

     BUG: ResampleImageFilter honor isInside output of the transform method

     COMP: Avoid recursive include of itkMath.h

     COMP: Use add_python_test PythonLazyLoadingImage

     BUG: Index,Size,Offset constructors present in Python with C++11

     COMP: Address missing override it itkFactoryTestLib.cxx

     BUG: Address memory leak, remove NumPy build dep in BridgeNumPy

     COMP: Do not set ITK_LIBRARY_BUILD_TYPE in ITKTransformFactory

     BUG: Check when ITK_WRAP_VECTOR_COMPONENTS doesn't include
ITK_WRAP_IMAGE_DIMS

     BUG: RichardsonLucyDeconvolutionImageFilter with non-null input Image
Origin

     BUG: Fix inconsistent Twister start with Initialize(seed) and
SetSeed(seed)

Pierre Barbier de Reuille (1):

     COMP: Fix function naming error when using FFTWD

Simon Rit (1):

     COMP: remove C++11 compiler warning for CUDA compilations

Vladimir S. FONOV (1):

     COMP: Build against GCC 5.3.1

Ziv Yaniv (1):
     BUG: Metric sampling percentage accepted values outside (0.0, 1.0].
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From c.spanakis83 at gmail.com  Fri Oct  7 18:48:22 2016
From: c.spanakis83 at gmail.com (Constantinus Spanakis)
Date: Sat, 8 Oct 2016 01:48:22 +0300
Subject: [ITK] Problem with normalized mutual information
Message-ID: <CAOZihbcA8dG8mNtSmmmXYiGftQj8mEze+WXadg+5vNZpYT_xVw@mail.gmail.com>

Hello I tried to modify the MutualInformationImageToImageFilter example and
tried to make it read images and calculate their normalized mutual
informaion. Here is the code:

#include "itkMutualInformationImageToImageMetric.h"
#include "itkRandomImageSource.h"
#include "itkTranslationTransform.h"
#include"itkCenteredRigid2DTransform.h"
#include "itkLinearInterpolateImageFunction.h"
#include"itkImageFileReader.h"
#include"itkNormalizedMutualInformationHistogramImageToImageMetric.h"


typedef itk::Image< unsigned char, 2>  ImageType;
//typedef itk::Image< float, 2> ImageType;

int main( int argc, char *argv[] )
{

const    unsigned int    ImageDimension = 2;
typedef  signed short    PixelType;
typedef itk::Image<PixelType, ImageDimension> FixedImage;
typedef itk::Image<PixelType, ImageDimension> MovingImage;

typedef itk::ImageFileReader<FixedImage> FixedImageTypeReader;
typedef itk::ImageFileReader<MovingImage> MovingImageTypeReader;

FixedImageTypeReader::Pointer fixedreader = FixedImageTypeReader::New();
MovingImageTypeReader::Pointer movingreader = MovingImageTypeReader::New();

fixedreader->SetFileName(argv[1]);
movingreader->SetFileName(argv[2]);

fixedreader->Update();
movingreader->Update();
FixedImage::Pointer fixedImage = fixedreader->GetOutput();
MovingImage::Pointer movingImage = movingreader->GetOutput();


  typedef itk::TranslationTransform<double, 2> TranslationTransformType; //
This cannot be float for some reason?
  TranslationTransformType::Pointer transform =
TranslationTransformType::New();

  /*typedef itk::MutualInformationImageToImageMetric<FixedImage,
MovingImage >    MetricType;*/

  typedef
itk::NormalizedMutualInformationHistogramImageToImageMetric<FixedImage,
MovingImage> MetricType;


  MetricType::Pointer metric = MetricType::New();

  metric->SetTransform(transform);


  metric->SetFixedImageRegion(fixedImage->GetLargestPossibleRegion());

  MetricType::HistogramType::SizeType histogramSize;
  histogramSize.SetSize(2);
  histogramSize[0] = 64;
  histogramSize[1] = 64;

  metric->SetHistogramSize(histogramSize);

  const unsigned int numberOfParameters =
transform->GetNumberOfParameters();
  typedef MetricType::ScalesType ScalesType;
  ScalesType scales(numberOfParameters);

  scales.Fill(1.0);

  metric->SetDerivativeStepLengthScales(scales);

  metric->SetFixedImage(fixedImage);
  metric->SetMovingImage(movingImage);

  metric->SetFixedImageRegion(fixedImage->GetLargestPossibleRegion());

  itk::LinearInterpolateImageFunction<MovingImage, double>::Pointer
interpolator = itk::LinearInterpolateImageFunction<MovingImage,
double>::New();
  interpolator->SetInputImage(fixedImage);
  metric->SetInterpolator(interpolator);

  TranslationTransformType::ParametersType parameters;
  parameters.SetSize(2);
  parameters.Fill(0);
  std::cout << "parameters: " << parameters << std::endl;
  printf("before problem\n");
  MetricType::MeasureType value = metric->GetValue(parameters);
  printf("after problem\n");
  std::cout << "Value: " << value << std::endl;

  return EXIT_SUCCESS;
}

The problem is that every time I call metric->GetValue(parameters); the
programme crashes. What could be the problem???
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From sunle2009 at gmail.com  Sat Oct  8 04:36:27 2016
From: sunle2009 at gmail.com (Le Sun)
Date: Sat, 8 Oct 2016 19:36:27 +1100
Subject: [ITK] itk::InvalidRequestedRegionError: Requested region is (at
 least partially) outside the largest possible region
Message-ID: <CAAXyqguVncngS=UYRi77O3vVnmkirWCfPxcCDA5i8BU+dEWPQA@mail.gmail.com>

Hi,

I am running the code of 'Segmentation code for the 3D ray features
described in our <http://people.inf.ethz.ch/alucchi/code/rays3d.zip>' on
page http://people.inf.ethz.ch/alucchi/code.php.

When run the first example in the readme.txt in the code package:test3dRays
/home/le/Documents/rays3d/data/sphere 1 2 8 16

I got the following error:
*******************************************************
Error while running this filter.
itk::InvalidRequestedRegionError (0x2e7ebc0)
Location: "void itk::NeighborhoodOperatorImageFilter<TInputImage,
TOutputImage, TOperatorValueType>::GenerateInputRequestedRegion() [with
TInputImage = itk::Image<float, 3u>; TOutputImage = itk::Image<float, 3u>;
TOperatorValueType = double]"
File: /usr/local/include/ITK-4.10/itkNeighborhoodOperatorImageFilter.hxx
Line: 72
Description: Requested region is (at least partially) outside the largest
possible region.
*******************************************************

I added ' -> UpdateLargestPossibleRegion()' for each Filter in the .cpp and
.cxx files. However, couldn't solve this problem.

Thank you for your help.

Best Regards
Le
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From dzenanz at gmail.com  Sat Oct  8 15:48:26 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 8 Oct 2016 15:48:26 -0400
Subject: [ITK] itk::InvalidRequestedRegionError: Requested region is (at
 least partially) outside the largest possible region
In-Reply-To: <CAAXyqguVncngS=UYRi77O3vVnmkirWCfPxcCDA5i8BU+dEWPQA@mail.gmail.com>
References: <CAAXyqguVncngS=UYRi77O3vVnmkirWCfPxcCDA5i8BU+dEWPQA@mail.gmail.com>
Message-ID: <CAPf2UMRKCeWmSgJm0=s5cAC=hOSN-gHRTaTz+sgim3XVHZKUAQ@mail.gmail.com>

Hi Le,

the first paragraph of the readme says:
*This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY. If you find any bug, please contact Aurelien Lucchi
<aurelien.lucchi at gmail.com <aurelien.lucchi at gmail.com>> or Kevin Smith
<kevin.smith at epfl.ch <kevin.smith at epfl.ch>>.*
Have you done so?

I tried building the mentioned library, after commenting out the hard-coded
paths in CMakeLists, I could still not build it. Errors are unrelated to
ITK, e.g.:
2>c:\misc\rays3d\Display.h(23): fatal error C1083: Cannot open include
file: 'GL/glut.h': No such file or directory
2>C:\Misc\rays3d\rays3d_utils.cpp(20): fatal error C1083: Cannot open
include file: 'dirent.h': No such file or directory
(I have given a path to GLUT and OpenCV).

Can you create a minimum working example <http://sscce.org/>? Attached are
my modifications to the CMakeListst.txt.

Regards,
D?enan

On Sat, Oct 8, 2016 at 4:36 AM, Le Sun <sunle2009 at gmail.com> wrote:

> Hi,
>
> I am running the code of 'Segmentation code for the 3D ray features
> described in our <http://people.inf.ethz.ch/alucchi/code/rays3d.zip>' on
> page http://people.inf.ethz.ch/alucchi/code.php.
>
> When run the first example in the readme.txt in the code
> package:test3dRays /home/le/Documents/rays3d/data/sphere 1 2 8 16
>
> I got the following error:
> *******************************************************
> Error while running this filter.
> itk::InvalidRequestedRegionError (0x2e7ebc0)
> Location: "void itk::NeighborhoodOperatorImageFilter<TInputImage,
> TOutputImage, TOperatorValueType>::GenerateInputRequestedRegion() [with
> TInputImage = itk::Image<float, 3u>; TOutputImage = itk::Image<float, 3u>;
> TOperatorValueType = double]"
> File: /usr/local/include/ITK-4.10/itkNeighborhoodOperatorImageFilter.hxx
> Line: 72
> Description: Requested region is (at least partially) outside the largest
> possible region.
> *******************************************************
>
> I added ' -> UpdateLargestPossibleRegion()' for each Filter in the .cpp
> and .cxx files. However, couldn't solve this problem.
>
> Thank you for your help.
>
> Best Regards
> Le
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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#######################################################################
# This program is free software; you can redistribute it and/or       #
# modify it under the terms of the GNU General Public License         #
# version 2 as published by the Free Software Foundation.             #
#                                                                     #
# This program is distributed in the hope that it will be useful, but #
# WITHOUT ANY WARRANTY; without even the implied warranty of          #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU   #
# General Public License for more details.                            #
#                                                                     #
# Written and (C) by Aurelien Lucchi and Kevin Smith                  #
# Contact aurelien.lucchi (at) gmail.com or kevin.smith (at) epfl.ch  # 
# for comments & bug reports                                          #
#######################################################################

cmake_minimum_required(VERSION 2.4)

PROJECT(rays3d)
INCLUDE_REGULAR_EXPRESSION("^.*$")

# set(CMAKE_C_COMPILER "g++")
# set(CMAKE_CXX_COMPILER "g++")

# SET(CMAKE_BUILD_TYPE Release)
#SET(CMAKE_BUILD_TYPE Debug)

set(CMAKE_MODULE_PATH "modules")

option(USE_OPENGL "use OPENGL library" off)
mark_as_advanced(USE_OPENGL)

# set(CMAKE_CXX_FLAGS_DEBUG   "${CMAKE_CXX_FLAGS} -g -pg")
# set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O3")

# set(CMAKE_C_FLAGS         ${CMAKE_CXX_FLAGS})
# set(CMAKE_C_FLAGS_DEBUG   ${CMAKE_CXX_FLAGS_DEBUG})
# set(CMAKE_C_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})

###################################################################### PACKAGES


#SET(OpenCV_FIND_COMPONENTS   CV CXCORE CVAUX HIGHGUI ML)
SET(OpenCV_FIND_REQUIRED_COMPONENTS   CV CXCORE CVAUX HIGHGUI ML)
# set(OpenCV_DIR ~/src/ThirdParty/OpenCV-2.4.2/)
FIND_PACKAGE(OpenCV REQUIRED)
# add include directories
include_directories(${OPENCV_INCLUDE_DIR})
include_directories(${OpenCV_DIR}/include/)
include_directories(${OpenCV_DIR}/include/opencv/)

#find_library(ML_LIBRARY NAMES opencv_ml PATHS ${OpenCV_DIR}/lib/)
#find_library(ML_LIBRARY NAMES ml PATHS ${OpenCV_DIR}/lib/)
#SET(OpenCV_LIBS ${OpenCV_LIBS} ${ML_LIBRARY})
message("OpenCV")
message(STATUS ${OpenCV_LIBS})
message(STATUS ${OpenCV_LIBRARIES})
SET(OpenCV_LIBS ${OpenCV_LIBRARIES})

# include_directories(~/src/ThirdParty/OpenCV-2.0.0/include/opencv/)
# set(OpenCV_ROOT_DIR  ~/src/ThirdParty/OpenCV-2.0.0/lib/)
# find_library(OpenCV_CV_LIBRARY   
#   NAMES cv opencv
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_CVAUX_LIBRARY
#   NAMES cvaux
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_CXCORE_LIBRARY  
#   NAMES cxcore
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_HIGHGUI_LIBRARY  
#   NAMES highgui
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_ML_LIBRARY  
#   NAMES ml
#   PATHS ${OpenCV_ROOT_DIR})
# SET(OPENCV_LIBRARIES ${OpenCV_CV_LIBRARY} ${OpenCV_CVAUX_LIBRARY} ${OpenCV_CXCORE_LIBRARY} ${OpenCV_HIGHGUI_LIBRARY} ${OpenCV_ML_LIBRARY})

if(USE_OPENGL)

#CHECK OPENGL  DEPENDENCY
FIND_PACKAGE(OpenGL REQUIRED)
IF (OPENGL_FOUND) 
   MESSAGE(STATUS  "OpenGL Found")
ELSE (OPENGL_FOUND) 
   MESSAGE(FATAL_ERROR "OpenGL Not Found (required to compile modules)")
   SET(BUILD_MODULE FALSE)
ENDIF (OPENGL_FOUND) 

#CHECK GLUT  DEPENDENCY
FIND_PACKAGE(GLUT REQUIRED)
IF (GLUT_FOUND) 
   MESSAGE(STATUS  "GLUT Found")
ELSE (GLUT_FOUND) 
   MESSAGE(FATAL_ERROR  "GLUT Not Found (required to compile modules)")
   SET(BUILD_MODULE FALSE)
ENDIF (GLUT_FOUND) 

#include_directories(${GLEW_INCLUDE_DIR}/lib/misc/include)
find_package(GLEW REQUIRED)
IF (GLEW_FOUND)
   include_directories(${GLEW_INCLUDE_DIR})
ELSE (GLEW_FOUND) 
   MESSAGE(FATAL_ERROR  "GLEW Not Found (required to compile modules)")
   SET(BUILD_MODULE FALSE)
   #include_directories(${GLEW_INCLUDE_DIR}/lib/misc/include)
ENDIF (GLEW_FOUND)

endif(USE_OPENGL)


# set(ITK_DIR "/home/lucchi/src/ThirdParty/InsightToolkit-3.20.1/build")
message(${ITK_DIR})

find_package(ITK REQUIRED)
IF(ITK_FOUND)
  INCLUDE(${ITK_USE_FILE})
ENDIF(ITK_FOUND)

###################################################################### EXECUTABLE

ADD_EXECUTABLE(test3dRays
combnk.cpp
pca.cpp
rays3d.cpp
test_rays3d.cpp
rays3d_utils.cpp
rays3dVolume.cpp
Display.cpp
)

TARGET_LINK_LIBRARIES(test3dRays ${ITK_LIBRARIES} ${OPENCV_LIBRARIES})
if(USE_OPENGL) # additional libraries
TARGET_LINK_LIBRARIES(test3dRays ${OPENGL_LIBRARIES} ${GLUT_LIBRARIES} ${GLEW_LIBRARY})
endif(USE_OPENGL)

# SET_TARGET_PROPERTIES(test3dRays PROPERTIES COMPILE_FLAGS -fPIC)

#set(CMAKE_CXX_FLAGS_SAVED  ${CMAKE_CXX_FLAGS})
set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -D RAYS_MULTITHREADING")
#SET_SOURCE_FILES_PROPERTIES(rays3d.cpp COMPILE_FLAGS ${CMAKE_CXX_FLAGS})
#SET_SOURCE_FILES_PROPERTIES(rays3d.cpp COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -D EXPORTSWC -D RAYS_TESTING")
#SET_SOURCE_FILES_PROPERTIES(rays3d.cpp COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -D RAYS_TESTING")

#TARGET_LINK_LIBRARIES(test3dRays ${SLICEME_THIRD_PARTY_LIBRARIES}))

ADD_LIBRARY(rays3d
combnk.cpp
pca.cpp
rays3d.cpp
rays3d_utils.cpp
)

#set(CMAKE_CXX_FLAGS  ${CMAKE_CXX_FLAGS_SAVED})
#SET_SOURCE_FILES_PROPERTIES(COMPILE_FLAGS ${CMAKE_CXX_FLAGS})

TARGET_LINK_LIBRARIES(rays3d ${ITK_LIBRARIES} ${OPENCV_LIBRARIES})
# SET_TARGET_PROPERTIES(rays3d PROPERTIES COMPILE_FLAGS -fPIC)

From dzenanz at gmail.com  Sat Oct  8 15:59:32 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 8 Oct 2016 15:59:32 -0400
Subject: [ITK] Problem with normalized mutual information
In-Reply-To: <CAOZihbcA8dG8mNtSmmmXYiGftQj8mEze+WXadg+5vNZpYT_xVw@mail.gmail.com>
References: <CAOZihbcA8dG8mNtSmmmXYiGftQj8mEze+WXadg+5vNZpYT_xVw@mail.gmail.com>
Message-ID: <CAPf2UMQ2OJVETdP+JQdcVMxbyjzHoJrK1FGdN+3oYqfer6Q3=g@mail.gmail.com>

Hi Constantinus,

you did not set lower and upper bounds to the metric's histogram. The
following addition alleviates crashing:
metric->SetLowerBound(histogramSize);
metric->SetUpperBound(histogramSize);

Regards,
D?enan

On Fri, Oct 7, 2016 at 6:48 PM, Constantinus Spanakis <
c.spanakis83 at gmail.com> wrote:

> Hello I tried to modify the MutualInformationImageToImageFilter example
> and tried to make it read images and calculate their normalized mutual
> informaion. Here is the code:
>
> #include "itkMutualInformationImageToImageMetric.h"
> #include "itkRandomImageSource.h"
> #include "itkTranslationTransform.h"
> #include"itkCenteredRigid2DTransform.h"
> #include "itkLinearInterpolateImageFunction.h"
> #include"itkImageFileReader.h"
> #include"itkNormalizedMutualInformationHistogramImageToImageMetric.h"
>
>
> typedef itk::Image< unsigned char, 2>  ImageType;
> //typedef itk::Image< float, 2> ImageType;
>
> int main( int argc, char *argv[] )
> {
>
> const    unsigned int    ImageDimension = 2;
> typedef  signed short    PixelType;
> typedef itk::Image<PixelType, ImageDimension> FixedImage;
> typedef itk::Image<PixelType, ImageDimension> MovingImage;
>
> typedef itk::ImageFileReader<FixedImage> FixedImageTypeReader;
> typedef itk::ImageFileReader<MovingImage> MovingImageTypeReader;
>
> FixedImageTypeReader::Pointer fixedreader = FixedImageTypeReader::New();
> MovingImageTypeReader::Pointer movingreader = MovingImageTypeReader::New();
>
> fixedreader->SetFileName(argv[1]);
> movingreader->SetFileName(argv[2]);
>
> fixedreader->Update();
> movingreader->Update();
> FixedImage::Pointer fixedImage = fixedreader->GetOutput();
> MovingImage::Pointer movingImage = movingreader->GetOutput();
>
>
>   typedef itk::TranslationTransform<double, 2> TranslationTransformType;
> // This cannot be float for some reason?
>   TranslationTransformType::Pointer transform =
> TranslationTransformType::New();
>
>   /*typedef itk::MutualInformationImageToImageMetric<FixedImage,
> MovingImage >    MetricType;*/
>
>   typedef itk::NormalizedMutualInformationHistogramImageToImageMetric<FixedImage,
> MovingImage> MetricType;
>
>
>   MetricType::Pointer metric = MetricType::New();
>
>   metric->SetTransform(transform);
>
>
>   metric->SetFixedImageRegion(fixedImage->GetLargestPossibleRegion());
>
>   MetricType::HistogramType::SizeType histogramSize;
>   histogramSize.SetSize(2);
>   histogramSize[0] = 64;
>   histogramSize[1] = 64;
>
>   metric->SetHistogramSize(histogramSize);
>
>   const unsigned int numberOfParameters = transform->
> GetNumberOfParameters();
>   typedef MetricType::ScalesType ScalesType;
>   ScalesType scales(numberOfParameters);
>
>   scales.Fill(1.0);
>
>   metric->SetDerivativeStepLengthScales(scales);
>
>   metric->SetFixedImage(fixedImage);
>   metric->SetMovingImage(movingImage);
>
>   metric->SetFixedImageRegion(fixedImage->GetLargestPossibleRegion());
>
>   itk::LinearInterpolateImageFunction<MovingImage, double>::Pointer
> interpolator = itk::LinearInterpolateImageFunction<MovingImage,
> double>::New();
>   interpolator->SetInputImage(fixedImage);
>   metric->SetInterpolator(interpolator);
>
>   TranslationTransformType::ParametersType parameters;
>   parameters.SetSize(2);
>   parameters.Fill(0);
>   std::cout << "parameters: " << parameters << std::endl;
>   printf("before problem\n");
>   MetricType::MeasureType value = metric->GetValue(parameters);
>   printf("after problem\n");
>   std::cout << "Value: " << value << std::endl;
>
>   return EXIT_SUCCESS;
> }
>
> The problem is that every time I call metric->GetValue(parameters); the
> programme crashes. What could be the problem???
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From sunle2009 at gmail.com  Sat Oct  8 22:10:58 2016
From: sunle2009 at gmail.com (Le Sun)
Date: Sun, 9 Oct 2016 13:10:58 +1100
Subject: [ITK] itk::InvalidRequestedRegionError: Requested region is (at
 least partially) outside the largest possible region
In-Reply-To: <CAPf2UMRKCeWmSgJm0=s5cAC=hOSN-gHRTaTz+sgim3XVHZKUAQ@mail.gmail.com>
References: <CAAXyqguVncngS=UYRi77O3vVnmkirWCfPxcCDA5i8BU+dEWPQA@mail.gmail.com>
 <CAPf2UMRKCeWmSgJm0=s5cAC=hOSN-gHRTaTz+sgim3XVHZKUAQ@mail.gmail.com>
Message-ID: <CAAXyqgu_2Q_aSm5-fpw5VaE5WMYfJtqy0gRGmtzJjXEjYBH1pA@mail.gmail.com>

Hi?D?enan?

Thanks very much for your reply. I also spent a lot of time to build it.
Attached is my CMakeLists.txt.
I contacted with

*Aurelien Lucchi last week, but haven't get any answer yet.*

*Best Regards*

*Le*

On 9 October 2016 at 06:48, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Le,
>
> the first paragraph of the readme says:
> *This program is distributed in the hope that it will be useful, but
> WITHOUT ANY WARRANTY. If you find any bug, please contact Aurelien Lucchi
> <aurelien.lucchi at gmail.com <aurelien.lucchi at gmail.com>> or Kevin Smith
> <kevin.smith at epfl.ch <kevin.smith at epfl.ch>>.*
> Have you done so?
>
> I tried building the mentioned library, after commenting out the
> hard-coded paths in CMakeLists, I could still not build it. Errors are
> unrelated to ITK, e.g.:
> 2>c:\misc\rays3d\Display.h(23): fatal error C1083: Cannot open include
> file: 'GL/glut.h': No such file or directory
> 2>C:\Misc\rays3d\rays3d_utils.cpp(20): fatal error C1083: Cannot open
> include file: 'dirent.h': No such file or directory
> (I have given a path to GLUT and OpenCV).
>
> Can you create a minimum working example <http://sscce.org/>? Attached
> are my modifications to the CMakeListst.txt.
>
> Regards,
> D?enan
>
> On Sat, Oct 8, 2016 at 4:36 AM, Le Sun <sunle2009 at gmail.com> wrote:
>
>> Hi,
>>
>> I am running the code of 'Segmentation code for the 3D ray features
>> described in our <http://people.inf.ethz.ch/alucchi/code/rays3d.zip>' on
>> page http://people.inf.ethz.ch/alucchi/code.php.
>>
>> When run the first example in the readme.txt in the code
>> package:test3dRays /home/le/Documents/rays3d/data/sphere 1 2 8 16
>>
>> I got the following error:
>> *******************************************************
>> Error while running this filter.
>> itk::InvalidRequestedRegionError (0x2e7ebc0)
>> Location: "void itk::NeighborhoodOperatorImageFilter<TInputImage,
>> TOutputImage, TOperatorValueType>::GenerateInputRequestedRegion() [with
>> TInputImage = itk::Image<float, 3u>; TOutputImage = itk::Image<float, 3u>;
>> TOperatorValueType = double]"
>> File: /usr/local/include/ITK-4.10/itkNeighborhoodOperatorImageFilter.hxx
>> Line: 72
>> Description: Requested region is (at least partially) outside the largest
>> possible region.
>> *******************************************************
>>
>> I added ' -> UpdateLargestPossibleRegion()' for each Filter in the .cpp
>> and .cxx files. However, couldn't solve this problem.
>>
>> Thank you for your help.
>>
>> Best Regards
>> Le
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>
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#######################################################################
# This program is free software; you can redistribute it and/or       #
# modify it under the terms of the GNU General Public License         #
# version 2 as published by the Free Software Foundation.             #
#                                                                     #
# This program is distributed in the hope that it will be useful, but #
# WITHOUT ANY WARRANTY; without even the implied warranty of          #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU   #
# General Public License for more details.                            #
#                                                                     #
# Written and (C) by Aurelien Lucchi and Kevin Smith                  #
# Contact aurelien.lucchi (at) gmail.com or kevin.smith (at) epfl.ch  # 
# for comments & bug reports                                          #
#######################################################################

cmake_minimum_required(VERSION 2.4)

PROJECT(rays3d)
INCLUDE_REGULAR_EXPRESSION("^.*$")

set(CMAKE_C_COMPILER "g++")
set(CMAKE_CXX_COMPILER "g++")

SET(CMAKE_BUILD_TYPE Release)
#SET(CMAKE_BUILD_TYPE Debug)

set(CMAKE_MODULE_PATH "modules")

option(USE_OPENGL "use OPENGL library" off)
mark_as_advanced(USE_OPENGL)

set(CMAKE_CXX_FLAGS_DEBUG   "${CMAKE_CXX_FLAGS} -g -pg")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O3")

set(CMAKE_C_FLAGS         ${CMAKE_CXX_FLAGS})
set(CMAKE_C_FLAGS_DEBUG   ${CMAKE_CXX_FLAGS_DEBUG})
set(CMAKE_C_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})

###################################################################### PACKAGES

#SET(OpenCV_FIND_COMPONENTS   CV CXCORE CVAUX HIGHGUI ML)
#SET(OpenCV_FIND_REQUIRED_COMPONENTS   CV CXCORE CVAUX HIGHGUI ML)
set(OpenCV_DIR /usr/)
#include_directories(${OpenCV_DIR}/include/)
#include_directories(${OpenCV_DIR}/include/opencv/)
FIND_PACKAGE(OpenCV REQUIRED)
# add include directories
include_directories(${OPENCV_INCLUDE_DIR})
#find_library(ML_LIBRARY NAMES opencv_ml PATHS ${OpenCV_DIR}/lib/)
#find_library(ML_LIBRARY NAMES ml PATHS ${OpenCV_DIR}/lib/)
#SET(OpenCV_LIBS ${OpenCV_LIBS} ${ML_LIBRARY})
message("OpenCV")
message(STATUS ${OpenCV_LIBS})
message(STATUS ${OpenCV_LIBRARIES})
SET(OpenCV_LIBS ${OpenCV_LIBRARIES})

INCLUDE_DIRECTORIES(/usr/include/tclap)

# include_directories(~/src/ThirdParty/OpenCV-2.0.0/include/opencv/)
# set(OpenCV_ROOT_DIR  ~/src/ThirdParty/OpenCV-2.0.0/lib/)
# find_library(OpenCV_CV_LIBRARY   
#   NAMES cv opencv
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_CVAUX_LIBRARY
#   NAMES cvaux
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_CXCORE_LIBRARY  
#   NAMES cxcore
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_HIGHGUI_LIBRARY  
#   NAMES highgui
#   PATHS ${OpenCV_ROOT_DIR})
# find_library(OpenCV_ML_LIBRARY  
#   NAMES ml
#   PATHS ${OpenCV_ROOT_DIR})
# SET(OPENCV_LIBRARIES ${OpenCV_CV_LIBRARY} ${OpenCV_CVAUX_LIBRARY} ${OpenCV_CXCORE_LIBRARY} ${OpenCV_HIGHGUI_LIBRARY} ${OpenCV_ML_LIBRARY})

#if(USE_OPENGL)
#CHECK OPENGL  DEPENDENCY
#FIND_PACKAGE(OpenGL REQUIRED)
#IF (OPENGL_FOUND) 
 #  MESSAGE(STATUS  "OpenGL Found")
#ELSE (OPENGL_FOUND) 
 #  MESSAGE(FATAL_ERROR "OpenGL Not Found (required to compile modules)")
  # SET(BUILD_MODULE FALSE)
#ENDIF (OPENGL_FOUND) 

set(OpenGL_DIR /usr/)
FIND_PACKAGE(OpenGL REQUIRED)
# add include directories
include_directories(${OPENGL_INCLUDE_DIR})
message("OpenGL")
message(STATUS ${OpenGL_LIBS})
message(STATUS ${OpenGL_LIBRARIES})
SET(OpenGL_LIBS ${OpenGL_LIBRARIES})

#CHECK GLUT  DEPENDENCY
#FIND_PACKAGE(GLUT REQUIRED)
#IF (GLUT_FOUND) 
#   MESSAGE(STATUS  "GLUT Found")
#ELSE (GLUT_FOUND) 
#   MESSAGE(FATAL_ERROR  "GLUT Not Found (required to compile modules)")
#   SET(BUILD_MODULE FALSE)
#ENDIF (GLUT_FOUND) 

set(GLUT_DIR /usr/)
FIND_PACKAGE(GLUT REQUIRED)
# add include directories
include_directories(${GLUT_INCLUDE_DIR})
message("GLUT")
message(STATUS ${GLUT_LIBS})
message(STATUS ${GLUT_LIBRARIES})
SET(GLUT_LIBS ${GLUT_LIBRARIES})

#include_directories(${GLEW_INCLUDE_DIR}/lib/misc/include)
#find_package(GLEW REQUIRED)
#IF (GLEW_FOUND)
#   include_directories(${GLEW_INCLUDE_DIR})
#ELSE (GLEW_FOUND) 
#   MESSAGE(FATAL_ERROR  "GLEW Not Found (required to compile modules)")
#   SET(BUILD_MODULE FALSE)
#   #include_directories(${GLEW_INCLUDE_DIR}/lib/misc/include)
#ENDIF (GLEW_FOUND)

set(GLEW_DIR /usr/)
FIND_PACKAGE(GLEW REQUIRED)
# add include directories
include_directories(${GLEW_INCLUDE_DIR})
message("GLEW")
message(STATUS ${GLEW_LIBS})
message(STATUS ${GLEW_LIBRARIES})
SET(GLEW_LIBS ${GLEW_LIBRARIES})

#endif(USE_OPENGL)

set(ITK_DIR "/usr/local/src/InsightToolkit-4.10.0")
message(${ITK_DIR})

find_package(ITK REQUIRED)
IF(ITK_FOUND)
  INCLUDE(${ITK_USE_FILE})
ENDIF(ITK_FOUND)

###################################################################### EXECUTABLE

ADD_EXECUTABLE(test3dRays
combnk.cpp
pca.cpp
rays3d.cpp
test_rays3d.cpp
rays3d_utils.cpp
rays3dVolume.cpp
Display.cpp
)

#if(USE_OPENGL)
#TARGET_LINK_LIBRARIES(test3dRays ITKIO ITKStatistics ${OPENCV_LIBRARIES} ${OPENGL_LIBRARIES} ${GLUT_LIBRARIES} ${GLEW_LIBRARY})
TARGET_LINK_LIBRARIES(test3dRays ${ITK_LIBRARIES} ITKStatistics ${OpenCV_LIBS} ${OPENCV_LIBRARIES} ${OPENGL_LIBRARIES} ${GLUT_LIBRARIES} ${GLEW_LIBRARY})
#else(USE_OPENGL)
#TARGET_LINK_LIBRARIES(test3dRays ITKIO ITKStatistics ${OPENCV_LIBRARIES})
#TARGET_LINK_LIBRARIES(test3dRays ${ITK_LIBRARIES} ITKStatistics ${OpenCV_LIBS} ${OPENCV_LIBRARIES})
#endif(USE_OPENGL)

SET_TARGET_PROPERTIES(test3dRays PROPERTIES COMPILE_FLAGS -fPIC)

#set(CMAKE_CXX_FLAGS_SAVED  ${CMAKE_CXX_FLAGS})
set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -D RAYS_MULTITHREADING")
#SET_SOURCE_FILES_PROPERTIES(rays3d.cpp COMPILE_FLAGS ${CMAKE_CXX_FLAGS})
#SET_SOURCE_FILES_PROPERTIES(rays3d.cpp COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -D EXPORTSWC -D RAYS_TESTING")
#SET_SOURCE_FILES_PROPERTIES(rays3d.cpp COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -D RAYS_TESTING")

#TARGET_LINK_LIBRARIES(test3dRays ${SLICEME_THIRD_PARTY_LIBRARIES}))

if(COMMAND cmake_policy)
   cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)

ADD_LIBRARY(rays3d
combnk.cpp
pca.cpp
rays3d.cpp
rays3d_utils.cpp
)

#set(CMAKE_CXX_FLAGS  ${CMAKE_CXX_FLAGS_SAVED})
#SET_SOURCE_FILES_PROPERTIES(COMPILE_FLAGS ${CMAKE_CXX_FLAGS})

#TARGET_LINK_LIBRARIES(rays3d ITKIO ITKStatistics ${OPENCV_LIBRARIES})
TARGET_LINK_LIBRARIES(rays3d ${ITK_LIBRARIES} ITKStatistics ${OpenCV_LIBS} ${OPENCV_LIBRARIES} ${OPENGL_LIBRARIES} ${GLUT_LIBRARIES} ${GLEW_LIBRARY})
SET_TARGET_PROPERTIES(rays3d PROPERTIES COMPILE_FLAGS -fPIC)

From ivan.granata.na at gmail.com  Sun Oct  9 02:43:30 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Sat, 8 Oct 2016 23:43:30 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK JAVA ImageRegistrationMethod --> after
 ResampleImageFilter, how?
Message-ID: <1475995410853-37655.post@n7.nabble.com>

i tried to write a registration with simple ITK java code with
ImageRegistrationMethod

in input i've fixedimage movingimage 
in output i've a trasform.txt file


transform.txt contains these informations:



but as final output i want an image coreg not just a parameters in txt

so i read ResampleImageFilter for this goal  (i think is good) but in java i
don't understand how i can integrate in my code

Plese someone can help me?




this is my code



import org.itk.simple.*;


class IterationUpdate  extends Command {

  private ImageRegistrationMethod m_Method;

  public IterationUpdate(ImageRegistrationMethod m) {
    super();
    m_Method=m;
  }

  public void execute() {
    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
    System.out.format("%3d = %10.5f : [%f, %f]\n",
                      m_Method.getOptimizerIteration(),
                      m_Method.getMetricValue(),
                      pos.get(0), pos.get(1));
  }
}

class ImageRegistrationMethodNaplab {

  public static void main(String argv[]) {

  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }

  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );

  reader.setFileName(argv[0]);
  Image fixed = reader.execute();

  reader.setFileName(argv[1]);
  Image moving = reader.execute();

  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
  R.setMetricAsMattesMutualInformation();
  double maxStep = 4.0;
  double minStep = 0.001;
  int numberOfIterations = 200;
  double relaxationFactor = 0.5;
  R.setOptimizerAsRegularStepGradientDescent( maxStep,
                                              minStep,
                                              numberOfIterations,
                                              relaxationFactor );
  R.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkLinear );

  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);

  org.itk.simple.Transform outTx = R.execute( fixed, moving );

  System.out.println("-------");
  System.out.println(outTx.toString());
  //System.out.format(" Fixed Initial Transform: %d\n",
R.getFixedInitialTransform());
  //System.out.format(" Moving Initial Transform: %d\n",
R.getMovingInitialTransform());
  //System.out.format(" Initial Transform: %d\n", R.getInitialTransform());
  System.out.format(" Optimizer Position: %d\n", R.getOptimizerPosition());
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());
  System.out.format(" Interpolator: %f\n", R.getInterpolator());
  //System.out.format(" Translation X", R.getTranslationAlongX());
 // System.out.format(" Translation Y", R.getTranslationAlongY());
  outTx.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
 
  //org.itk.simple.Transform.writeTransform(argv[4]);
  //org.itk.simple.ResampleImageFilter image = new
org.itk.simple.ResampleImageFilter();
  //image.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
 // image.getOutputPixelType(); 
 // image.getSize ();

  //ImageFileWriter writer = new ImageFileWriter();

 // writer.setFileName(argv[5]);
  



  }  

  
 
  
  
  
  
}
  



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-JAVA-ImageRegistrationMethod-after-ResampleImageFilter-how-tp37655.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From dzenanz at gmail.com  Mon Oct 10 08:33:59 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 10 Oct 2016 08:33:59 -0400
Subject: [ITK] itk::InvalidRequestedRegionError: Requested region is (at
 least partially) outside the largest possible region
In-Reply-To: <CAAXyqgu_2Q_aSm5-fpw5VaE5WMYfJtqy0gRGmtzJjXEjYBH1pA@mail.gmail.com>
References: <CAAXyqguVncngS=UYRi77O3vVnmkirWCfPxcCDA5i8BU+dEWPQA@mail.gmail.com>
 <CAPf2UMRKCeWmSgJm0=s5cAC=hOSN-gHRTaTz+sgim3XVHZKUAQ@mail.gmail.com>
 <CAAXyqgu_2Q_aSm5-fpw5VaE5WMYfJtqy0gRGmtzJjXEjYBH1pA@mail.gmail.com>
Message-ID: <CAPf2UMTEhDPCLPrhRsWW_sCERFesRw+shkysnoz18-gA1vt1mg@mail.gmail.com>

Hi Le,

this CMakeLists.txt isn't any better than the one I came up with (I also
have to comment out the hardcoded paths, as I am on Windows). I still get
the same compile errors.

If you isolate the ITK-related code into a separate example, I will
probably be able to help you find the problem.

Regards,
D?enan

On Sat, Oct 8, 2016 at 10:10 PM, Le Sun <sunle2009 at gmail.com> wrote:

> Hi?D?enan?
>
> Thanks very much for your reply. I also spent a lot of time to build it.
> Attached is my CMakeLists.txt.
> I contacted with
>
> *Aurelien Lucchi last week, but haven't get any answer yet.*
>
> *Best Regards*
>
> *Le*
>
> On 9 October 2016 at 06:48, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Le,
>>
>> the first paragraph of the readme says:
>> *This program is distributed in the hope that it will be useful, but
>> WITHOUT ANY WARRANTY. If you find any bug, please contact Aurelien Lucchi
>> <aurelien.lucchi at gmail.com <aurelien.lucchi at gmail.com>> or Kevin Smith
>> <kevin.smith at epfl.ch <kevin.smith at epfl.ch>>.*
>> Have you done so?
>>
>> I tried building the mentioned library, after commenting out the
>> hard-coded paths in CMakeLists, I could still not build it. Errors are
>> unrelated to ITK, e.g.:
>> 2>c:\misc\rays3d\Display.h(23): fatal error C1083: Cannot open include
>> file: 'GL/glut.h': No such file or directory
>> 2>C:\Misc\rays3d\rays3d_utils.cpp(20): fatal error C1083: Cannot open
>> include file: 'dirent.h': No such file or directory
>> (I have given a path to GLUT and OpenCV).
>>
>> Can you create a minimum working example <http://sscce.org/>? Attached
>> are my modifications to the CMakeListst.txt.
>>
>> Regards,
>> D?enan
>>
>> On Sat, Oct 8, 2016 at 4:36 AM, Le Sun <sunle2009 at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I am running the code of 'Segmentation code for the 3D ray features
>>> described in our <http://people.inf.ethz.ch/alucchi/code/rays3d.zip>'
>>> on page http://people.inf.ethz.ch/alucchi/code.php.
>>>
>>> When run the first example in the readme.txt in the code
>>> package:test3dRays /home/le/Documents/rays3d/data/sphere 1 2 8 16
>>>
>>> I got the following error:
>>> *******************************************************
>>> Error while running this filter.
>>> itk::InvalidRequestedRegionError (0x2e7ebc0)
>>> Location: "void itk::NeighborhoodOperatorImageFilter<TInputImage,
>>> TOutputImage, TOperatorValueType>::GenerateInputRequestedRegion() [with
>>> TInputImage = itk::Image<float, 3u>; TOutputImage = itk::Image<float, 3u>;
>>> TOperatorValueType = double]"
>>> File: /usr/local/include/ITK-4.10/itkNeighborhoodOperatorImageFilter.hxx
>>> Line: 72
>>> Description: Requested region is (at least partially) outside the
>>> largest possible region.
>>> *******************************************************
>>>
>>> I added ' -> UpdateLargestPossibleRegion()' for each Filter in the .cpp
>>> and .cxx files. However, couldn't solve this problem.
>>>
>>> Thank you for your help.
>>>
>>> Best Regards
>>> Le
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>
>
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From kenji.tsumura at neosoftmedical.com  Mon Oct 10 10:20:46 2016
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 10 Oct 2016 14:20:46 +0000
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
Message-ID: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>

Hi,

When I tried to configure ITK, I had the following warning.
I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
Apparently, due to this warning, I can't use classes in the LevelSetV4Visualization module,
when I tried to build an example downloaded from the ITK website.
(https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)

I can modify the cmake file directly, but "Generate" action erases the changes I made.
So I am not sure what to do.


CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMake/ITKModuleAPI.cmake:26 (itk_module_load)
  CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
  D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68 (itk_module_config)
  Examples/CMakeLists.txt:5 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.


My environment is ...
OS: Windows 7
CMake 3.1.1
ITK 4.10.1
VTK 7.0.0

I would appreciate any advice.
Thank you in advance!

Kenji
Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.
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From francois.budin at kitware.com  Mon Oct 10 11:38:16 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 10 Oct 2016 11:38:16 -0400
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
Message-ID: <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>

Hello Kenji,

I do not seem to be able to reproduce your error on Ubuntu 16.04:
cmake 3.1.1
ITK 4.10.1
VTK 7.0.0

Did you change any of the default values in CMake beside BUILD_EXAMPLES and
Module_ITKLevelSetsv4Visualization?

Francois

On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura <
kenji.tsumura at neosoftmedical.com> wrote:

> Hi,
>
>
>
> When I tried to configure ITK, I had the following warning.
>
> I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in
> CMake.
>
> Apparently, due to this warning, I can't use classes in the
> LevelSetV4Visualization module,
>
> when I tried to build an example downloaded from the ITK website.
>
> (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/
> VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>
>
>
> I can modify the cmake file directly, but "Generate" action erases the
> changes I made.
>
> So I am not sure what to do.
>
>
>
>
>
> CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>
>   Syntax Warning in cmake code at
>
>
>
>     D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/
> Modules/ITKLevelSetsv4Visualization.cmake:41:91
>
>
>
>   Argument not separated from preceding token by whitespace.
>
> Call Stack (most recent call first):
>
>   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>
>   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>
>   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> (itk_module_config)
>
>   Examples/CMakeLists.txt:5 (find_package)
>
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
>
> My environment is ...
>
> OS: Windows 7
>
> CMake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
>
>
> I would appreciate any advice.
>
> Thank you in advance!
>
>
>
> Kenji
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From kenji.tsumura at neosoftmedical.com  Mon Oct 10 11:55:55 2016
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 10 Oct 2016 15:55:55 +0000
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
Message-ID: <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>

Hi Francois,

I tried again and saw the same problem.
I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.

I forgot to mention that I use Visual Studio 2013.

Thank you,

Kenji

From: Francois Budin [mailto:francois.budin at kitware.com]
Sent: Monday, October 10, 2016 10:38 AM
To: Kenji Tsumura
Cc: community at itk.org
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hello Kenji,
I do not seem to be able to reproduce your error on Ubuntu 16.04:
cmake 3.1.1
ITK 4.10.1
VTK 7.0.0
Did you change any of the default values in CMake beside BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
Francois

On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
Hi,

When I tried to configure ITK, I had the following warning.
I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
Apparently, due to this warning, I can't use classes in the LevelSetV4Visualization module,
when I tried to build an example downloaded from the ITK website.
(https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)

I can modify the cmake file directly, but "Generate" action erases the changes I made.
So I am not sure what to do.


CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMake/ITKModuleAPI.cmake:26 (itk_module_load)
  CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
  D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68 (itk_module_config)
  Examples/CMakeLists.txt:5 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.


My environment is ...
OS: Windows 7
CMake 3.1.1
ITK 4.10.1
VTK 7.0.0

I would appreciate any advice.
Thank you in advance!

Kenji
Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
http://public.kitware.com/mailman/listinfo/community

Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.
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From matt.mccormick at kitware.com  Mon Oct 10 12:53:05 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 10 Oct 2016 12:53:05 -0400
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
Message-ID: <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>

Hi Kenji,

Could you please share the content of

  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

?

Thanks,
Matt

On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura
<kenji.tsumura at neosoftmedical.com> wrote:
> Hi Francois,
>
>
>
> I tried again and saw the same problem.
>
> I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
>
>
>
> I forgot to mention that I use Visual Studio 2013.
>
>
>
> Thank you,
>
>
>
> Kenji
>
>
>
> From: Francois Budin [mailto:francois.budin at kitware.com]
> Sent: Monday, October 10, 2016 10:38 AM
> To: Kenji Tsumura
> Cc: community at itk.org
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
>
>
> Hello Kenji,
>
> I do not seem to be able to reproduce your error on Ubuntu 16.04:
>
> cmake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
> Did you change any of the default values in CMake beside BUILD_EXAMPLES and
> Module_ITKLevelSetsv4Visualization?
>
> Francois
>
>
>
> On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> <kenji.tsumura at neosoftmedical.com> wrote:
>
> Hi,
>
>
>
> When I tried to configure ITK, I had the following warning.
>
> I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
>
> Apparently, due to this warning, I can't use classes in the
> LevelSetV4Visualization module,
>
> when I tried to build an example downloaded from the ITK website.
>
> (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>
>
>
> I can modify the cmake file directly, but "Generate" action erases the
> changes I made.
>
> So I am not sure what to do.
>
>
>
>
>
> CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>
>   Syntax Warning in cmake code at
>
>
>
>
> D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91
>
>
>
>   Argument not separated from preceding token by whitespace.
>
> Call Stack (most recent call first):
>
>   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>
>   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>
>   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> (itk_module_config)
>
>   Examples/CMakeLists.txt:5 (find_package)
>
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
>
> My environment is ...
>
> OS: Windows 7
>
> CMake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
>
>
> I would appreciate any advice.
>
> Thank you in advance!
>
>
>
> Kenji
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From kenji.tsumura at neosoftmedical.com  Mon Oct 10 13:35:59 2016
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 10 Oct 2016 17:35:59 +0000
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
Message-ID: <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>

Hi Matt,

                                                                                                                                                                        |
                                                                                                                                                                        V
    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-4.10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h"")

I think adding spaces after starting double quotation and before ending double quotation solves the warning.
But the problem is that this file ITKLvelSetsv4Visualization.cmake is auto-generated...

Thank you,

Kenji

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com]
Sent: Monday, October 10, 2016 11:53 AM
To: Kenji Tsumura
Cc: Francois Budin; community at itk.org
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hi Kenji,

Could you please share the content of

  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

?

Thanks,
Matt

On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com> wrote:
> Hi Francois,
>
>
>
> I tried again and saw the same problem.
>
> I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
>
>
>
> I forgot to mention that I use Visual Studio 2013.
>
>
>
> Thank you,
>
>
>
> Kenji
>
>
>
> From: Francois Budin [mailto:francois.budin at kitware.com]
> Sent: Monday, October 10, 2016 10:38 AM
> To: Kenji Tsumura
> Cc: community at itk.org
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
>
>
> Hello Kenji,
>
> I do not seem to be able to reproduce your error on Ubuntu 16.04:
>
> cmake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
> Did you change any of the default values in CMake beside
> BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
>
> Francois
>
>
>
> On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> <kenji.tsumura at neosoftmedical.com> wrote:
>
> Hi,
>
>
>
> When I tried to configure ITK, I had the following warning.
>
> I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
>
> Apparently, due to this warning, I can't use classes in the
> LevelSetV4Visualization module,
>
> when I tried to build an example downloaded from the ITK website.
>
> (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
> /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>
>
>
> I can modify the cmake file directly, but "Generate" action erases the
> changes I made.
>
> So I am not sure what to do.
>
>
>
>
>
> CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>
>   Syntax Warning in cmake code at
>
>
>
>
> D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
> ules/ITKLevelSetsv4Visualization.cmake:41:91
>
>
>
>   Argument not separated from preceding token by whitespace.
>
> Call Stack (most recent call first):
>
>   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>
>   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>
>   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> (itk_module_config)
>
>   Examples/CMakeLists.txt:5 (find_package)
>
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
>
> My environment is ...
>
> OS: Windows 7
>
> CMake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
>
>
> I would appreciate any advice.
>
> Thank you in advance!
>
>
>
> Kenji
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

From francois.budin at kitware.com  Mon Oct 10 13:45:54 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 10 Oct 2016 13:45:54 -0400
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
Message-ID: <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>

Hello Kenji,

Could you add these extra space in
ITK/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt line 98
and line 130 and see if that solves your issue?

Thanks,
Francois

On Mon, Oct 10, 2016 at 1:35 PM, Kenji Tsumura <
kenji.tsumura at neosoftmedical.com> wrote:

> Hi Matt,
>
>
>
>                   |
>
>
>                   V
>     set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS
> "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-
> 4.10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_
> vtkRenderingFreeType_vtkRenderingOpenGL2.h"")
>
> I think adding spaces after starting double quotation and before ending
> double quotation solves the warning.
> But the problem is that this file ITKLvelSetsv4Visualization.cmake is
> auto-generated...
>
> Thank you,
>
> Kenji
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Monday, October 10, 2016 11:53 AM
> To: Kenji Tsumura
> Cc: Francois Budin; community at itk.org
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
> Hi Kenji,
>
> Could you please share the content of
>
>   Syntax Warning in cmake code at
>
>     D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/
> Modules/ITKLevelSetsv4Visualization.cmake:41:91
>
> ?
>
> Thanks,
> Matt
>
> On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <
> kenji.tsumura at neosoftmedical.com> wrote:
> > Hi Francois,
> >
> >
> >
> > I tried again and saw the same problem.
> >
> > I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
> >
> >
> >
> > I forgot to mention that I use Visual Studio 2013.
> >
> >
> >
> > Thank you,
> >
> >
> >
> > Kenji
> >
> >
> >
> > From: Francois Budin [mailto:francois.budin at kitware.com]
> > Sent: Monday, October 10, 2016 10:38 AM
> > To: Kenji Tsumura
> > Cc: community at itk.org
> > Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
> >
> >
> >
> > Hello Kenji,
> >
> > I do not seem to be able to reproduce your error on Ubuntu 16.04:
> >
> > cmake 3.1.1
> >
> > ITK 4.10.1
> >
> > VTK 7.0.0
> >
> > Did you change any of the default values in CMake beside
> > BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
> >
> > Francois
> >
> >
> >
> > On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> > <kenji.tsumura at neosoftmedical.com> wrote:
> >
> > Hi,
> >
> >
> >
> > When I tried to configure ITK, I had the following warning.
> >
> > I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in
> CMake.
> >
> > Apparently, due to this warning, I can't use classes in the
> > LevelSetV4Visualization module,
> >
> > when I tried to build an example downloaded from the ITK website.
> >
> > (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
> > /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
> >
> >
> >
> > I can modify the cmake file directly, but "Generate" action erases the
> > changes I made.
> >
> > So I am not sure what to do.
> >
> >
> >
> >
> >
> > CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
> >
> >   Syntax Warning in cmake code at
> >
> >
> >
> >
> > D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
> > ules/ITKLevelSetsv4Visualization.cmake:41:91
> >
> >
> >
> >   Argument not separated from preceding token by whitespace.
> >
> > Call Stack (most recent call first):
> >
> >   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
> >
> >   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
> >
> >   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> > (itk_module_config)
> >
> >   Examples/CMakeLists.txt:5 (find_package)
> >
> > This warning is for project developers.  Use -Wno-dev to suppress it.
> >
> >
> >
> >
> >
> > My environment is ...
> >
> > OS: Windows 7
> >
> > CMake 3.1.1
> >
> > ITK 4.10.1
> >
> > VTK 7.0.0
> >
> >
> >
> > I would appreciate any advice.
> >
> > Thank you in advance!
> >
> >
> >
> > Kenji
> >
> > Disclaimer: The information contained in this communication may be
> > confidential, is intended only for the use of the recipient(s) named
> > above, and may be legally privileged. If the reader of this message is
> > not the intended recipient, you are hereby notified that any
> > dissemination, distribution, or copying of this communication, or any
> > of its contents, is strictly prohibited. If you have received this
> > communication in error, please return it to the sender immediately and
> > delete the original message and any copy of it from your computer
> > system. If you have any questions concerning this message, please
> contact the sender.
> >
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
> >
> >
> > Disclaimer: The information contained in this communication may be
> > confidential, is intended only for the use of the recipient(s) named
> > above, and may be legally privileged. If the reader of this message is
> > not the intended recipient, you are hereby notified that any
> > dissemination, distribution, or copying of this communication, or any
> > of its contents, is strictly prohibited. If you have received this
> > communication in error, please return it to the sender immediately and
> > delete the original message and any copy of it from your computer
> > system. If you have any questions concerning this message, please
> contact the sender.
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
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From kenji.tsumura at neosoftmedical.com  Mon Oct 10 14:06:22 2016
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 10 Oct 2016 18:06:22 +0000
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
 <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>
Message-ID: <10285631702C4D4CB5C4921DC143379554982F93@neocoilexch01>

Hi Francois,

The problem still persists.
I changed the CMakeList.txt like this: spaces before and after ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}.

Line 98:
  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \" ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
Line 130:
  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \" ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")

In the generated file, there are spaces after the first double quotation and before the last double quotation.
I think spaces are required for the double quotations of the path.

  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS " vtkRenderingCore_INCLUDE="D:/workspace_itk_org/InsightToolkit-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h" ")

Thank you,

Kenji
From: Francois Budin [mailto:francois.budin at kitware.com]
Sent: Monday, October 10, 2016 12:46 PM
To: Kenji Tsumura
Cc: Matt McCormick; community at itk.org
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hello Kenji,
Could you add these extra space in ITK/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt line 98 and line 130 and see if that solves your issue?
Thanks,
Francois

On Mon, Oct 10, 2016 at 1:35 PM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
Hi Matt,

                                                                                                                                                                        |
                                                                                                                                                                        V
    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-4.10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h"")

I think adding spaces after starting double quotation and before ending double quotation solves the warning.
But the problem is that this file ITKLvelSetsv4Visualization.cmake is auto-generated...

Thank you,

Kenji

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>]
Sent: Monday, October 10, 2016 11:53 AM
To: Kenji Tsumura
Cc: Francois Budin; community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hi Kenji,

Could you please share the content of

  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

?

Thanks,
Matt

On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
> Hi Francois,
>
>
>
> I tried again and saw the same problem.
>
> I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
>
>
>
> I forgot to mention that I use Visual Studio 2013.
>
>
>
> Thank you,
>
>
>
> Kenji
>
>
>
> From: Francois Budin [mailto:francois.budin at kitware.com<mailto:francois.budin at kitware.com>]
> Sent: Monday, October 10, 2016 10:38 AM
> To: Kenji Tsumura
> Cc: community at itk.org<mailto:community at itk.org>
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
>
>
> Hello Kenji,
>
> I do not seem to be able to reproduce your error on Ubuntu 16.04:
>
> cmake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
> Did you change any of the default values in CMake beside
> BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
>
> Francois
>
>
>
> On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
>
> Hi,
>
>
>
> When I tried to configure ITK, I had the following warning.
>
> I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
>
> Apparently, due to this warning, I can't use classes in the
> LevelSetV4Visualization module,
>
> when I tried to build an example downloaded from the ITK website.
>
> (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
> /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>
>
>
> I can modify the cmake file directly, but "Generate" action erases the
> changes I made.
>
> So I am not sure what to do.
>
>
>
>
>
> CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>
>   Syntax Warning in cmake code at
>
>
>
>
> D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
> ules/ITKLevelSetsv4Visualization.cmake:41:91
>
>
>
>   Argument not separated from preceding token by whitespace.
>
> Call Stack (most recent call first):
>
>   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>
>   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>
>   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> (itk_module_config)
>
>   Examples/CMakeLists.txt:5 (find_package)
>
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
>
> My environment is ...
>
> OS: Windows 7
>
> CMake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
>
>
> I would appreciate any advice.
>
> Thank you in advance!
>
>
>
> Kenji
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community
>
Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.
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From francois.budin at kitware.com  Mon Oct 10 14:39:18 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 10 Oct 2016 14:39:18 -0400
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <10285631702C4D4CB5C4921DC143379554982F93@neocoilexch01>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
 <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F93@neocoilexch01>
Message-ID: <CAHwLD2WvKAPAQBxB8-ZTwh8YsKJ4jYQSO1+CkZmRestSy=4ZdQ@mail.gmail.com>

Hello Kenji,

Can you try to add this line before Line 98?
string(REGEX REPLACE "\""
         "\\\\\"" ITKLevelSetsv4Visualization_VTK_DEFINITIONS
         "${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}")

The idea is to escape the quote characters that are added in the variable
ITKLevelSetsv4Visualization_VTK_DEFINITIONS.
The result should be:
set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "
vtkRenderingCore_INCLUDE=*\"*D:/workspace_itk_org/InsightToolkit-4.10.1-bin/
CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_
vtkRenderingFreeType_vtkRenderingOpenGL2.h*\"* ")

On Mon, Oct 10, 2016 at 2:06 PM, Kenji Tsumura <
kenji.tsumura at neosoftmedical.com> wrote:

> Hi Francois,
>
>
>
> The problem still persists.
>
> I changed the CMakeList.txt like this: spaces before and after
> ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}.
>
>
>
> Line 98:
>
>   set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \"
> ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
>
> Line 130:
>
>   set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \"
> ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
>
>
>
> In the generated file, there are spaces after the first double quotation
> and before the last double quotation.
>
> I think spaces are required for the double quotations of the path.
>
>
>
>   set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "
> vtkRenderingCore_INCLUDE="D:/workspace_itk_org/InsightToolkit-4.10.1-bin/
> CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_
> vtkRenderingFreeType_vtkRenderingOpenGL2.h" ")
>
>
>
> Thank you,
>
>
>
> Kenji
>
> *From:* Francois Budin [mailto:francois.budin at kitware.com]
> *Sent:* Monday, October 10, 2016 12:46 PM
> *To:* Kenji Tsumura
> *Cc:* Matt McCormick; community at itk.org
>
> *Subject:* Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
>
>
> Hello Kenji,
>
> Could you add these extra space in ITK/Modules/Segmentation/
> LevelSetsv4Visualization/CMakeLists.txt line 98 and line 130 and see if
> that solves your issue?
>
> Thanks,
>
> Francois
>
>
>
> On Mon, Oct 10, 2016 at 1:35 PM, Kenji Tsumura <
> kenji.tsumura at neosoftmedical.com> wrote:
>
> Hi Matt,
>
>
>
>                   |
>
>
>                   V
>     set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS
> "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-
> 4.10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_
> vtkRenderingFreeType_vtkRenderingOpenGL2.h"")
>
> I think adding spaces after starting double quotation and before ending
> double quotation solves the warning.
> But the problem is that this file ITKLvelSetsv4Visualization.cmake is
> auto-generated...
>
> Thank you,
>
> Kenji
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Monday, October 10, 2016 11:53 AM
> To: Kenji Tsumura
>
> Cc: Francois Budin; community at itk.org
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
> Hi Kenji,
>
> Could you please share the content of
>
>   Syntax Warning in cmake code at
>
>     D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/
> Modules/ITKLevelSetsv4Visualization.cmake:41:91
>
> ?
>
> Thanks,
> Matt
>
> On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <
> kenji.tsumura at neosoftmedical.com> wrote:
> > Hi Francois,
> >
> >
> >
> > I tried again and saw the same problem.
> >
> > I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
> >
> >
> >
> > I forgot to mention that I use Visual Studio 2013.
> >
> >
> >
> > Thank you,
> >
> >
> >
> > Kenji
> >
> >
> >
> > From: Francois Budin [mailto:francois.budin at kitware.com]
> > Sent: Monday, October 10, 2016 10:38 AM
> > To: Kenji Tsumura
> > Cc: community at itk.org
> > Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
> >
> >
> >
> > Hello Kenji,
> >
> > I do not seem to be able to reproduce your error on Ubuntu 16.04:
> >
> > cmake 3.1.1
> >
> > ITK 4.10.1
> >
> > VTK 7.0.0
> >
> > Did you change any of the default values in CMake beside
> > BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
> >
> > Francois
> >
> >
> >
> > On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> > <kenji.tsumura at neosoftmedical.com> wrote:
> >
> > Hi,
> >
> >
> >
> > When I tried to configure ITK, I had the following warning.
> >
> > I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in
> CMake.
> >
> > Apparently, due to this warning, I can't use classes in the
> > LevelSetV4Visualization module,
> >
> > when I tried to build an example downloaded from the ITK website.
> >
> > (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
> > /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
> >
> >
> >
> > I can modify the cmake file directly, but "Generate" action erases the
> > changes I made.
> >
> > So I am not sure what to do.
> >
> >
> >
> >
> >
> > CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
> >
> >   Syntax Warning in cmake code at
> >
> >
> >
> >
> > D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
> > ules/ITKLevelSetsv4Visualization.cmake:41:91
> >
> >
> >
> >   Argument not separated from preceding token by whitespace.
> >
> > Call Stack (most recent call first):
> >
> >   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
> >
> >   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
> >
> >   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> > (itk_module_config)
> >
> >   Examples/CMakeLists.txt:5 (find_package)
> >
> > This warning is for project developers.  Use -Wno-dev to suppress it.
> >
> >
> >
> >
> >
> > My environment is ...
> >
> > OS: Windows 7
> >
> > CMake 3.1.1
> >
> > ITK 4.10.1
> >
> > VTK 7.0.0
> >
> >
> >
> > I would appreciate any advice.
> >
> > Thank you in advance!
> >
> >
> >
> > Kenji
> >
> > Disclaimer: The information contained in this communication may be
> > confidential, is intended only for the use of the recipient(s) named
> > above, and may be legally privileged. If the reader of this message is
> > not the intended recipient, you are hereby notified that any
> > dissemination, distribution, or copying of this communication, or any
> > of its contents, is strictly prohibited. If you have received this
> > communication in error, please return it to the sender immediately and
> > delete the original message and any copy of it from your computer
> > system. If you have any questions concerning this message, please
> contact the sender.
> >
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
> >
> >
> > Disclaimer: The information contained in this communication may be
> > confidential, is intended only for the use of the recipient(s) named
> > above, and may be legally privileged. If the reader of this message is
> > not the intended recipient, you are hereby notified that any
> > dissemination, distribution, or copying of this communication, or any
> > of its contents, is strictly prohibited. If you have received this
> > communication in error, please return it to the sender immediately and
> > delete the original message and any copy of it from your computer
> > system. If you have any questions concerning this message, please
> contact the sender.
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
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From francois.budin at kitware.com  Mon Oct 10 17:56:04 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 10 Oct 2016 17:56:04 -0400
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <CAHwLD2WvKAPAQBxB8-ZTwh8YsKJ4jYQSO1+CkZmRestSy=4ZdQ@mail.gmail.com>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
 <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F93@neocoilexch01>
 <CAHwLD2WvKAPAQBxB8-ZTwh8YsKJ4jYQSO1+CkZmRestSy=4ZdQ@mail.gmail.com>
Message-ID: <CAHwLD2UO5C+HXFuAHwi5QPhqmz8wxa4+V7MGjVQ3XDMD=-VQOQ@mail.gmail.com>

Hello Kenji,

Thanks for your report. I found the bug that was causing you problems. I
have submitted a correction that is under review now:
http://review.source.kitware.com/#/c/21611/

Feel free to look at it, and test it on your machine.

Best,
Francois

On Mon, Oct 10, 2016 at 2:39 PM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Kenji,
>
> Can you try to add this line before Line 98?
> string(REGEX REPLACE "\""
>          "\\\\\"" ITKLevelSetsv4Visualization_VTK_DEFINITIONS
>          "${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}")
>
> The idea is to escape the quote characters that are added in the variable
> ITKLevelSetsv4Visualization_VTK_DEFINITIONS.
> The result should be:
> set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "
> vtkRenderingCore_INCLUDE=*\"*D:/workspace_itk_org/InsightToolk
> it-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_
> vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h*\"* ")
>
> On Mon, Oct 10, 2016 at 2:06 PM, Kenji Tsumura <
> kenji.tsumura at neosoftmedical.com> wrote:
>
>> Hi Francois,
>>
>>
>>
>> The problem still persists.
>>
>> I changed the CMakeList.txt like this: spaces before and after
>> ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}.
>>
>>
>>
>> Line 98:
>>
>>   set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \"
>> ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
>>
>> Line 130:
>>
>>   set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \"
>> ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
>>
>>
>>
>> In the generated file, there are spaces after the first double quotation
>> and before the last double quotation.
>>
>> I think spaces are required for the double quotations of the path.
>>
>>
>>
>>   set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "
>> vtkRenderingCore_INCLUDE="D:/workspace_itk_org/InsightToolki
>> t-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_
>> vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h" ")
>>
>>
>>
>> Thank you,
>>
>>
>>
>> Kenji
>>
>> *From:* Francois Budin [mailto:francois.budin at kitware.com]
>> *Sent:* Monday, October 10, 2016 12:46 PM
>> *To:* Kenji Tsumura
>> *Cc:* Matt McCormick; community at itk.org
>>
>> *Subject:* Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>>
>>
>>
>> Hello Kenji,
>>
>> Could you add these extra space in ITK/Modules/Segmentation/Level
>> Setsv4Visualization/CMakeLists.txt line 98 and line 130 and see if that
>> solves your issue?
>>
>> Thanks,
>>
>> Francois
>>
>>
>>
>> On Mon, Oct 10, 2016 at 1:35 PM, Kenji Tsumura <
>> kenji.tsumura at neosoftmedical.com> wrote:
>>
>> Hi Matt,
>>
>>
>>
>>                   |
>>
>>
>>                   V
>>     set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS
>> "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-4
>> .10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteract
>> ionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h"")
>>
>> I think adding spaces after starting double quotation and before ending
>> double quotation solves the warning.
>> But the problem is that this file ITKLvelSetsv4Visualization.cmake is
>> auto-generated...
>>
>> Thank you,
>>
>> Kenji
>>
>> -----Original Message-----
>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Sent: Monday, October 10, 2016 11:53 AM
>> To: Kenji Tsumura
>>
>> Cc: Francois Budin; community at itk.org
>> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>>
>> Hi Kenji,
>>
>> Could you please share the content of
>>
>>   Syntax Warning in cmake code at
>>
>>     D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/
>> ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91
>>
>> ?
>>
>> Thanks,
>> Matt
>>
>> On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <
>> kenji.tsumura at neosoftmedical.com> wrote:
>> > Hi Francois,
>> >
>> >
>> >
>> > I tried again and saw the same problem.
>> >
>> > I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
>> >
>> >
>> >
>> > I forgot to mention that I use Visual Studio 2013.
>> >
>> >
>> >
>> > Thank you,
>> >
>> >
>> >
>> > Kenji
>> >
>> >
>> >
>> > From: Francois Budin [mailto:francois.budin at kitware.com]
>> > Sent: Monday, October 10, 2016 10:38 AM
>> > To: Kenji Tsumura
>> > Cc: community at itk.org
>> > Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>> >
>> >
>> >
>> > Hello Kenji,
>> >
>> > I do not seem to be able to reproduce your error on Ubuntu 16.04:
>> >
>> > cmake 3.1.1
>> >
>> > ITK 4.10.1
>> >
>> > VTK 7.0.0
>> >
>> > Did you change any of the default values in CMake beside
>> > BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
>> >
>> > Francois
>> >
>> >
>> >
>> > On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
>> > <kenji.tsumura at neosoftmedical.com> wrote:
>> >
>> > Hi,
>> >
>> >
>> >
>> > When I tried to configure ITK, I had the following warning.
>> >
>> > I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in
>> CMake.
>> >
>> > Apparently, due to this warning, I can't use classes in the
>> > LevelSetV4Visualization module,
>> >
>> > when I tried to build an example downloaded from the ITK website.
>> >
>> > (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
>> > /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>> >
>> >
>> >
>> > I can modify the cmake file directly, but "Generate" action erases the
>> > changes I made.
>> >
>> > So I am not sure what to do.
>> >
>> >
>> >
>> >
>> >
>> > CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>> >
>> >   Syntax Warning in cmake code at
>> >
>> >
>> >
>> >
>> > D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
>> > ules/ITKLevelSetsv4Visualization.cmake:41:91
>> >
>> >
>> >
>> >   Argument not separated from preceding token by whitespace.
>> >
>> > Call Stack (most recent call first):
>> >
>> >   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>> >
>> >   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>> >
>> >   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
>> > (itk_module_config)
>> >
>> >   Examples/CMakeLists.txt:5 (find_package)
>> >
>> > This warning is for project developers.  Use -Wno-dev to suppress it.
>> >
>> >
>> >
>> >
>> >
>> > My environment is ...
>> >
>> > OS: Windows 7
>> >
>> > CMake 3.1.1
>> >
>> > ITK 4.10.1
>> >
>> > VTK 7.0.0
>> >
>> >
>> >
>> > I would appreciate any advice.
>> >
>> > Thank you in advance!
>> >
>> >
>> >
>> > Kenji
>> >
>> > Disclaimer: The information contained in this communication may be
>> > confidential, is intended only for the use of the recipient(s) named
>> > above, and may be legally privileged. If the reader of this message is
>> > not the intended recipient, you are hereby notified that any
>> > dissemination, distribution, or copying of this communication, or any
>> > of its contents, is strictly prohibited. If you have received this
>> > communication in error, please return it to the sender immediately and
>> > delete the original message and any copy of it from your computer
>> > system. If you have any questions concerning this message, please
>> contact the sender.
>> >
>> >
>> > _______________________________________________
>> > Community mailing list
>> > Community at itk.org
>> > http://public.kitware.com/mailman/listinfo/community
>> >
>> >
>> >
>> > Disclaimer: The information contained in this communication may be
>> > confidential, is intended only for the use of the recipient(s) named
>> > above, and may be legally privileged. If the reader of this message is
>> > not the intended recipient, you are hereby notified that any
>> > dissemination, distribution, or copying of this communication, or any
>> > of its contents, is strictly prohibited. If you have received this
>> > communication in error, please return it to the sender immediately and
>> > delete the original message and any copy of it from your computer
>> > system. If you have any questions concerning this message, please
>> contact the sender.
>> >
>> > _______________________________________________
>> > Community mailing list
>> > Community at itk.org
>> > http://public.kitware.com/mailman/listinfo/community
>> >
>> Disclaimer: The information contained in this communication may be
>> confidential, is intended only for the use of the recipient(s) named above,
>> and may be legally privileged. If the reader of this message is not the
>> intended recipient, you are hereby notified that any dissemination,
>> distribution, or copying of this communication, or any of its contents, is
>> strictly prohibited. If you have received this communication in error,
>> please return it to the sender immediately and delete the original message
>> and any copy of it from your computer system. If you have any questions
>> concerning this message, please contact the sender.
>>
>>
>> Disclaimer: The information contained in this communication may be
>> confidential, is intended only for the use of the recipient(s) named above,
>> and may be legally privileged. If the reader of this message is not the
>> intended recipient, you are hereby notified that any dissemination,
>> distribution, or copying of this communication, or any of its contents, is
>> strictly prohibited. If you have received this communication in error,
>> please return it to the sender immediately and delete the original message
>> and any copy of it from your computer system. If you have any questions
>> concerning this message, please contact the sender.
>>
>
>
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From kenji.tsumura at neosoftmedical.com  Mon Oct 10 18:06:15 2016
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 10 Oct 2016 22:06:15 +0000
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <CAHwLD2WvKAPAQBxB8-ZTwh8YsKJ4jYQSO1+CkZmRestSy=4ZdQ@mail.gmail.com>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
 <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F93@neocoilexch01>
 <CAHwLD2WvKAPAQBxB8-ZTwh8YsKJ4jYQSO1+CkZmRestSy=4ZdQ@mail.gmail.com>
Message-ID: <10285631702C4D4CB5C4921DC143379554982FFF@neocoilexch01>

Hi Francois,

I tried but didn?t work. I got the following error.

CMake Warning (dev) in Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:98:23

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:98:25

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:99:11

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:99:17

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:100:11

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt:100:57

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMake/ITKModuleAPI.cmake:26 (itk_module_load)
  CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
  D:/workspace_itk_org/InsightToolkit-4.10.1-bin/ITKConfig.cmake:68 (itk_module_config)
  Examples/CMakeLists.txt:5 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.


So I added spaces like this.

string(REGEX REPLACE " \" "
         " \\\\\" " ITKLevelSetsv4Visualization_VTK_DEFINITIONS
         " ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} ")


But the original warning persists.

CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
  Syntax Warning in cmake code at

    D:/workspace_itk_org/InsightToolkit-4.10.1-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMake/ITKModuleAPI.cmake:26 (itk_module_load)
  CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
  D:/workspace_itk_org/InsightToolkit-4.10.1-bin/ITKConfig.cmake:68 (itk_module_config)
  Examples/CMakeLists.txt:5 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.


Thank you,

Kenji
From: Francois Budin [mailto:francois.budin at kitware.com]
Sent: Monday, October 10, 2016 1:39 PM
To: Kenji Tsumura
Cc: Matt McCormick; community at itk.org
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hello Kenji,
Can you try to add this line before Line 98?
string(REGEX REPLACE "\""
         "\\\\\"" ITKLevelSetsv4Visualization_VTK_DEFINITIONS
         "${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}")
The idea is to escape the quote characters that are added in the variable ITKLevelSetsv4Visualization_VTK_DEFINITIONS.
The result should be:
set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS " vtkRenderingCore_INCLUDE=\"D:/workspace_itk_org/InsightToolkit-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h\" ")

On Mon, Oct 10, 2016 at 2:06 PM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
Hi Francois,

The problem still persists.
I changed the CMakeList.txt like this: spaces before and after ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}.

Line 98:
  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \" ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
Line 130:
  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \" ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")

In the generated file, there are spaces after the first double quotation and before the last double quotation.
I think spaces are required for the double quotations of the path.

  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS " vtkRenderingCore_INCLUDE="D:/workspace_itk_org/InsightToolkit-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h" ")

Thank you,

Kenji
From: Francois Budin [mailto:francois.budin at kitware.com<mailto:francois.budin at kitware.com>]
Sent: Monday, October 10, 2016 12:46 PM
To: Kenji Tsumura
Cc: Matt McCormick; community at itk.org<mailto:community at itk.org>

Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hello Kenji,
Could you add these extra space in ITK/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt line 98 and line 130 and see if that solves your issue?
Thanks,
Francois

On Mon, Oct 10, 2016 at 1:35 PM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
Hi Matt,

                                                                                                                                                                        |
                                                                                                                                                                        V
    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-4.10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h"")

I think adding spaces after starting double quotation and before ending double quotation solves the warning.
But the problem is that this file ITKLvelSetsv4Visualization.cmake is auto-generated...

Thank you,

Kenji

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>]
Sent: Monday, October 10, 2016 11:53 AM
To: Kenji Tsumura
Cc: Francois Budin; community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hi Kenji,

Could you please share the content of

  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

?

Thanks,
Matt

On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
> Hi Francois,
>
>
>
> I tried again and saw the same problem.
>
> I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
>
>
>
> I forgot to mention that I use Visual Studio 2013.
>
>
>
> Thank you,
>
>
>
> Kenji
>
>
>
> From: Francois Budin [mailto:francois.budin at kitware.com<mailto:francois.budin at kitware.com>]
> Sent: Monday, October 10, 2016 10:38 AM
> To: Kenji Tsumura
> Cc: community at itk.org<mailto:community at itk.org>
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
>
>
> Hello Kenji,
>
> I do not seem to be able to reproduce your error on Ubuntu 16.04:
>
> cmake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
> Did you change any of the default values in CMake beside
> BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
>
> Francois
>
>
>
> On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
>
> Hi,
>
>
>
> When I tried to configure ITK, I had the following warning.
>
> I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
>
> Apparently, due to this warning, I can't use classes in the
> LevelSetV4Visualization module,
>
> when I tried to build an example downloaded from the ITK website.
>
> (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
> /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>
>
>
> I can modify the cmake file directly, but "Generate" action erases the
> changes I made.
>
> So I am not sure what to do.
>
>
>
>
>
> CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>
>   Syntax Warning in cmake code at
>
>
>
>
> D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
> ules/ITKLevelSetsv4Visualization.cmake:41:91
>
>
>
>   Argument not separated from preceding token by whitespace.
>
> Call Stack (most recent call first):
>
>   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>
>   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>
>   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> (itk_module_config)
>
>   Examples/CMakeLists.txt:5 (find_package)
>
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
>
> My environment is ...
>
> OS: Windows 7
>
> CMake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
>
>
> I would appreciate any advice.
>
> Thank you in advance!
>
>
>
> Kenji
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community
>
Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.
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From kenji.tsumura at neosoftmedical.com  Mon Oct 10 18:11:05 2016
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 10 Oct 2016 22:11:05 +0000
Subject: [ITK] Module_ITKLevelSetsv4Visualization warning
In-Reply-To: <CAHwLD2UO5C+HXFuAHwi5QPhqmz8wxa4+V7MGjVQ3XDMD=-VQOQ@mail.gmail.com>
References: <10285631702C4D4CB5C4921DC143379554982EF8@neocoilexch01>
 <CAHwLD2UuxCMS-s9rFTu2rZ46EfWSMk6EWDMRQ_DQei7yCnJemA@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F43@neocoilexch01>
 <CALzTN-RfW=Bqvtp2433j0OLDuOjPvEsqRkhCwtMJ5UEg4xKg=A@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F74@neocoilexch01>
 <CAHwLD2UfStbhHrrwuGOzEE7Azi3dpc_kwZi_rnWoJUpGH=MAnQ@mail.gmail.com>
 <10285631702C4D4CB5C4921DC143379554982F93@neocoilexch01>
 <CAHwLD2WvKAPAQBxB8-ZTwh8YsKJ4jYQSO1+CkZmRestSy=4ZdQ@mail.gmail.com>
 <CAHwLD2UO5C+HXFuAHwi5QPhqmz8wxa4+V7MGjVQ3XDMD=-VQOQ@mail.gmail.com>
Message-ID: <10285631702C4D4CB5C4921DC143379554983015@neocoilexch01>

Hi Francois,

The patch works.
Thank you!

Kenji

From: Francois Budin [mailto:francois.budin at kitware.com]
Sent: Monday, October 10, 2016 4:56 PM
To: Kenji Tsumura
Cc: Matt McCormick; community at itk.org
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hello Kenji,
Thanks for your report. I found the bug that was causing you problems. I have submitted a correction that is under review now: http://review.source.kitware.com/#/c/21611/
Feel free to look at it, and test it on your machine.

Best,
Francois

On Mon, Oct 10, 2016 at 2:39 PM, Francois Budin <francois.budin at kitware.com<mailto:francois.budin at kitware.com>> wrote:
Hello Kenji,
Can you try to add this line before Line 98?
string(REGEX REPLACE "\""
         "\\\\\"" ITKLevelSetsv4Visualization_VTK_DEFINITIONS
         "${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}")
The idea is to escape the quote characters that are added in the variable ITKLevelSetsv4Visualization_VTK_DEFINITIONS.
The result should be:
set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS " vtkRenderingCore_INCLUDE=\"D:/workspace_itk_org/InsightToolkit-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h\" ")

On Mon, Oct 10, 2016 at 2:06 PM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
Hi Francois,

The problem still persists.
I changed the CMakeList.txt like this: spaces before and after ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS}.

Line 98:
  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \" ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")
Line 130:
  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS \" ${ITKLevelSetsv4Visualization_VTK_DEFINITIONS} \")

In the generated file, there are spaces after the first double quotation and before the last double quotation.
I think spaces are required for the double quotations of the path.

  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS " vtkRenderingCore_INCLUDE="D:/workspace_itk_org/InsightToolkit-4.10.1-bin/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h" ")

Thank you,

Kenji
From: Francois Budin [mailto:francois.budin at kitware.com<mailto:francois.budin at kitware.com>]
Sent: Monday, October 10, 2016 12:46 PM
To: Kenji Tsumura
Cc: Matt McCormick; community at itk.org<mailto:community at itk.org>

Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hello Kenji,
Could you add these extra space in ITK/Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt line 98 and line 130 and see if that solves your issue?
Thanks,
Francois

On Mon, Oct 10, 2016 at 1:35 PM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
Hi Matt,

                                                                                                                                                                        |
                                                                                                                                                                        V
    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "vtkRenderingCore_INCLUDE="D:/workspace_itk/InsightToolkit-4.10.1-bin-2/CMakeFiles/vtkRenderingCore_AUTOINIT_vtkInteractionStyle_vtkRenderingFreeType_vtkRenderingOpenGL2.h"")

I think adding spaces after starting double quotation and before ending double quotation solves the warning.
But the problem is that this file ITKLvelSetsv4Visualization.cmake is auto-generated...

Thank you,

Kenji

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>]
Sent: Monday, October 10, 2016 11:53 AM
To: Kenji Tsumura
Cc: Francois Budin; community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning

Hi Kenji,

Could you please share the content of

  Syntax Warning in cmake code at

    D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Modules/ITKLevelSetsv4Visualization.cmake:41:91

?

Thanks,
Matt

On Mon, Oct 10, 2016 at 11:55 AM, Kenji Tsumura <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
> Hi Francois,
>
>
>
> I tried again and saw the same problem.
>
> I turned on only BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization.
>
>
>
> I forgot to mention that I use Visual Studio 2013.
>
>
>
> Thank you,
>
>
>
> Kenji
>
>
>
> From: Francois Budin [mailto:francois.budin at kitware.com<mailto:francois.budin at kitware.com>]
> Sent: Monday, October 10, 2016 10:38 AM
> To: Kenji Tsumura
> Cc: community at itk.org<mailto:community at itk.org>
> Subject: Re: [ITK] Module_ITKLevelSetsv4Visualization warning
>
>
>
> Hello Kenji,
>
> I do not seem to be able to reproduce your error on Ubuntu 16.04:
>
> cmake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
> Did you change any of the default values in CMake beside
> BUILD_EXAMPLES and Module_ITKLevelSetsv4Visualization?
>
> Francois
>
>
>
> On Mon, Oct 10, 2016 at 10:20 AM, Kenji Tsumura
> <kenji.tsumura at neosoftmedical.com<mailto:kenji.tsumura at neosoftmedical.com>> wrote:
>
> Hi,
>
>
>
> When I tried to configure ITK, I had the following warning.
>
> I turned on Module_ITKLevelSetsv4Visualization and BUILD_EXAMPLES in CMake.
>
> Apparently, due to this warning, I can't use classes in the
> LevelSetV4Visualization module,
>
> when I tried to build an example downloaded from the ITK website.
>
> (https://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization
> /VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html)
>
>
>
> I can modify the cmake file directly, but "Generate" action erases the
> changes I made.
>
> So I am not sure what to do.
>
>
>
>
>
> CMake Warning (dev) at CMake/ITKModuleAPI.cmake:54 (include):
>
>   Syntax Warning in cmake code at
>
>
>
>
> D:/workspace_itk/InsightToolkit-4.10.1-java-bin/lib/cmake/ITK-4.10/Mod
> ules/ITKLevelSetsv4Visualization.cmake:41:91
>
>
>
>   Argument not separated from preceding token by whitespace.
>
> Call Stack (most recent call first):
>
>   CMake/ITKModuleAPI.cmake:26 (itk_module_load)
>
>   CMake/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
>
>   D:/workspace_itk/InsightToolkit-4.10.1-java-bin/ITKConfig.cmake:68
> (itk_module_config)
>
>   Examples/CMakeLists.txt:5 (find_package)
>
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
>
>
> My environment is ...
>
> OS: Windows 7
>
> CMake 3.1.1
>
> ITK 4.10.1
>
> VTK 7.0.0
>
>
>
> I would appreciate any advice.
>
> Thank you in advance!
>
>
>
> Kenji
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
> _______________________________________________
> Community mailing list
> Community at itk.org<mailto:Community at itk.org>
> http://public.kitware.com/mailman/listinfo/community
>
Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.


Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.
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From tevain at telecom-paristech.fr  Tue Oct 11 12:51:39 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Tue, 11 Oct 2016 18:51:39 +0200 (CEST)
Subject: [ITK] Efficient Shortest Paths algorithm
In-Reply-To: <968485681.6422787.1476204261338.JavaMail.zimbra@enst.fr>
Message-ID: <1391129720.6425804.1476204699716.JavaMail.zimbra@enst.fr>

Hello people,

Does anyone know an efficient c++ implementation of shortest paths algorithms for large graphs (like the ones obtained by considering images as graph, which result in numerous vertices and edges)?
I'm interested in the Floyd Warshall algorithm as well as the Dijkstra's one. 

Tim  

From blowekamp at mail.nih.gov  Tue Oct 11 13:06:21 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 11 Oct 2016 17:06:21 +0000
Subject: [ITK] Efficient Shortest Paths algorithm
In-Reply-To: <1391129720.6425804.1476204699716.JavaMail.zimbra@enst.fr>
References: <1391129720.6425804.1476204699716.JavaMail.zimbra@enst.fr>
Message-ID: <821DB1DA-0868-4BF6-B3DD-08E70E1704A0@mail.nih.gov>

Hello,

The CollidingFrontsImageFilter[1] may have been used for a similar purposes for vessel segmentation. I believe Luca Antiga has been involved with this algorithms and his VMTK toolkit, is you need additional starting place to search for more information on how to use the method.

HTH,
Brad



[1] http://public.kitware.com/Insight/Doxygen/html/classitk_1_1CollidingFrontsImageFilter.html

> On Oct 11, 2016, at 12:51 PM, Timothee Evain <tevain at telecom-paristech.fr> wrote:
> 
> Hello people,
> 
> Does anyone know an efficient c++ implementation of shortest paths algorithms for large graphs (like the ones obtained by considering images as graph, which result in numerous vertices and edges)?
> I'm interested in the Floyd Warshall algorithm as well as the Dijkstra's one. 
> 
> Tim  
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From dan.muel at gmail.com  Wed Oct 12 01:00:51 2016
From: dan.muel at gmail.com (Dan Mueller)
Date: Wed, 12 Oct 2016 15:30:51 +1030
Subject: [ITK] Efficient Shortest Paths algorithm
In-Reply-To: <1391129720.6425804.1476204699716.JavaMail.zimbra@enst.fr>
References: <968485681.6422787.1476204261338.JavaMail.zimbra@enst.fr>
 <1391129720.6425804.1476204699716.JavaMail.zimbra@enst.fr>
Message-ID: <CAPNvZ5YLxK3d=tJjogZrDv2+FKx5OiaD5Opj6=mE32EZt-zXRA@mail.gmail.com>

Hi Tim,

For a continuous minimal path algorithm see here:
https://itk.org/Doxygen/html/group__MinimalPathExtraction.html
https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction

I believe there was also a discrete Dijkstra implementation published in
the Insight Journal.

Hope this helps, Dan

On 12 Oct 2016 3:21 am, "Timothee Evain" <tevain at telecom-paristech.fr>
wrote:

> Hello people,
>
> Does anyone know an efficient c++ implementation of shortest paths
> algorithms for large graphs (like the ones obtained by considering images
> as graph, which result in numerous vertices and edges)?
> I'm interested in the Floyd Warshall algorithm as well as the Dijkstra's
> one.
>
> Tim
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From ivan.granata.na at gmail.com  Wed Oct 12 02:02:35 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 11 Oct 2016 23:02:35 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
References: <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
 <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
Message-ID: <1476252155238-37656.post@n7.nabble.com>


I have solved. I have applied the txt to "moving" image



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View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37656.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From ivan.granata.na at gmail.com  Wed Oct 12 02:41:39 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 11 Oct 2016 23:41:39 -0700 (MST)
Subject: [ITK] [ITK-users]  Image Fusion SimpleITK for Java with wavelet?
Message-ID: <1476254499226-37657.post@n7.nabble.com>

Can anyone help me to find something for apply fusion image in SimpleITK JAVA
version? in particular fusion with wavelet image fusion

something in "org.itk.simple" for image fusion and wavelet image fusion?


Best Regards


Ivan



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From tevain at telecom-paristech.fr  Wed Oct 12 05:32:38 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Wed, 12 Oct 2016 11:32:38 +0200 (CEST)
Subject: [ITK] Efficient Shortest Paths algorithm
In-Reply-To: <CAPNvZ5YLxK3d=tJjogZrDv2+FKx5OiaD5Opj6=mE32EZt-zXRA@mail.gmail.com>
References: <968485681.6422787.1476204261338.JavaMail.zimbra@enst.fr>
 <1391129720.6425804.1476204699716.JavaMail.zimbra@enst.fr>
 <CAPNvZ5YLxK3d=tJjogZrDv2+FKx5OiaD5Opj6=mE32EZt-zXRA@mail.gmail.com>
Message-ID: <1394777717.6948585.1476264758759.JavaMail.zimbra@enst.fr>

Dan, Brad,

Your suggestions have been very helpful, I've tried the MinimalPathExtraction and it seems to fulfill all my needs for now.
Many thanks!

Tim

----- Mail original -----
De: "Dan Mueller" <dan.muel at gmail.com>
?: "Timothee Evain" <tevain at telecom-paristech.fr>
Cc: community at itk.org
Envoy?: Mercredi 12 Octobre 2016 07:00:51
Objet: Re: [ITK] Efficient Shortest Paths algorithm

Hi Tim,

For a continuous minimal path algorithm see here:
https://itk.org/Doxygen/html/group__MinimalPathExtraction.html
https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction

I believe there was also a discrete Dijkstra implementation published in
the Insight Journal.

Hope this helps, Dan

On 12 Oct 2016 3:21 am, "Timothee Evain" <tevain at telecom-paristech.fr>
wrote:

> Hello people,
>
> Does anyone know an efficient c++ implementation of shortest paths
> algorithms for large graphs (like the ones obtained by considering images
> as graph, which result in numerous vertices and edges)?
> I'm interested in the Floyd Warshall algorithm as well as the Dijkstra's
> one.
>
> Tim
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From matt.mccormick at kitware.com  Wed Oct 12 09:58:06 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 12 Oct 2016 09:58:06 -0400
Subject: [ITK] [ITK-dev] CDash submissions for 2016-10-12
Message-ID: <CALzTN-QgbCWToJKJ623Jxv7AkSO6xrXtnOL2+Q8+SxtyzTrFXQ@mail.gmail.com>

Hi folks,

FYI - open.cdash.org had a hiccup last night, which explains why all
submissions are not on the dashboard today. They are all expected to
return tomorrow.

Matt
_______________________________________________
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From cr at neuro.ma.uni-heidelberg.de  Wed Oct 12 11:57:05 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Wed, 12 Oct 2016 17:57:05 +0200
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
Message-ID: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>

Hi,

I think it would be helpful if the documentation of the filter would 
mention that there are two outputs, one with the surviving labels and 
the second with the removed labels (the input image is the union of 
these images). What is the workflow to achieve this?

Christina

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From matt.mccormick at kitware.com  Wed Oct 12 12:03:41 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 12 Oct 2016 12:03:41 -0400
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
Message-ID: <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>

Hello Christina,

Good idea.

To update the documentation, the class Doxygen documentation can be editted:

  https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46

and after a patch is submitted:

  https://itk.org/Wiki/ITK/Git/Develop

it will show up on the Doxygen web pages.

Please let us know if you have any questions.

Thanks,
Matt

On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
<cr at neuro.ma.uni-heidelberg.de> wrote:
> Hi,
>
> I think it would be helpful if the documentation of the filter would mention
> that there are two outputs, one with the surviving labels and the second
> with the removed labels (the input image is the union of these images). What
> is the workflow to achieve this?
>
> Christina
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
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From avlachomitrou at dxo.com  Thu Oct 13 03:24:52 2016
From: avlachomitrou at dxo.com (Anna Vlachomitrou)
Date: Thu, 13 Oct 2016 07:24:52 +0000
Subject: [ITK] LINK PROBLEM
Message-ID: <DM5PR05MB31317796785711468EFFC745A0DC0@DM5PR05MB3131.namprd05.prod.outlook.com>

Dear ITK community,
 I am currently trying to build ITK so as to use some prebuilded libs  in Python.
-I downloaded the 4.10 version
- I used cmake to get the itk.sln for vs2010 32b (and also tried vs2015 32b)
- I launch the ALLBUILD
-I get some errors: all errors are related to _hypot. Here is an example:
450>     Creating library D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPython.lib and object D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPython.exp
450>itkImageMomentsCalculatorPython.obj : error LNK2019: unresolved external symbol "double __cdecl vnl_math::_hypot(double,double)" (?_hypot at vnl_math@@YANNN at Z) referenced in function "double __cdecl itk::Math::_hypot<double>(double,double)" (??$_hypot at N@Math at itk@@YANNN at Z)
450>D:\DATA\InsightToolkit-4.10.1\build\lib\Release\_ITKImageStatisticsPython.pyd : fatal error LNK1120: 1 unresolved externals
450>

Do you have any idea of how i can fix these build errors ?
 Thanks in advance,
Anna


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From CAOwens at mdanderson.org  Thu Oct 13 10:48:32 2016
From: CAOwens at mdanderson.org (Owens,Constance A)
Date: Thu, 13 Oct 2016 14:48:32 +0000
Subject: [ITK] [ITK-users] Lesion Sizing Toolkit Build not successful
Message-ID: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>

I was hoping to speak with someone who may be able to help me with installing and building Lesion Sizing Toolkit. Originally I tried to build LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I'm using Visual Studio 9 2008 64x), 6 projects fail with the following errors:

Error      1              fatal error C1083: Cannot open include file: 'itkLesionSegmentationImageFilter8.h': No such file or directory                c:\itk2\src\modules\remote\lesionsizingtoolkit\examples\itkLesionSegmentationCommandLineProgressReporter.h                22
Error      2              fatal error C1083: Cannot open include file: 'itkImageFileReader.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx   1
Error      3              fatal error C1083: Cannot open include file: 'itkVector.h': No such file or directory                c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\vtkContourVisualizationModule.h                22
Error      4              fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\LesionSurfaceExtraction.cxx     21
Error      5              fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx                21
Error      6              fatal error C1083: Cannot open include file: 'itkVector.h': No such file or directory                c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\vtkContourVisualizationModule.h                22
Error      7              fatal error C1083: Cannot open include file: 'itkCommand.h': No such file or directory                c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\ViewImageAndSegmentationSurface.cxx                18
Error      8              error C2039: 'MetaEvent' : is not a member of '`global namespace''                c:\itk2\src\modules\core\spatialobjects\include\itkMetaEvent.h             35
Error      9              error C2499: 'itk::MetaEvent' : a class cannot be its own base class                c:\itk2\src\modules\core\spatialobjects\include\itkMetaEvent.h             35
Error      10           error C2146: syntax error : missing ';' before identifier 'MetaObjectType'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          55
Error      11           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          55
Error      12           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          55
Error      13           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          64
Error      14           error C2143: syntax error : missing ',' before '*'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          64
Error      15           error C2143: syntax error : missing ';' before '*'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType' : 'virtual' not permitted on data declarations             c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      17           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      18           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          67
Error      20           error C2143: syntax error : missing ';' before '*'                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType' : 'virtual' not permitted on data declarations             c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      22           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      23           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h          77
Error      25           error C2143: syntax error : missing ';' before '*'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   100
Error      26           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   100
Error      27           error C4430: missing type specifier - int assumed. Note: C++ does not support default-int                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   102
Error      29           error C2061: syntax error : identifier 'MetaScene'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   104
Error      30           error C2065: 'MetaObject' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   112
Error      31           error C2059: syntax error : '>'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   112
Error      32           error C2143: syntax error : missing ';' before '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   116
Error      33           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   117
Error      34           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   117
Error      35           error C2143: syntax error : missing ';' before '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   121
Error      36           error C2143: syntax error : missing ';' before '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   124
Error      37           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   125
Error      38           error C2653: 'TConverter' : is not a class or namespace name                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   125
Error      39           error C2143: syntax error : missing ';' before '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   127
Error      40           error C2065: 'transform' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   128
Error      41           error C2143: syntax error : missing ',' before ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   128
Error      42           error C2065: 'MetaObject' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   130
Error      43           error C2065: 'obj' : undeclared identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   130
Error      44           error C2143: syntax error : missing ',' before ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   130
Error      45           error C2143: syntax error : missing ';' before '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   141
Error      46           fatal error C1004: unexpected end-of-file found                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h   141

Additionally, I am using CMake v3.6.1.

I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the ITK Bar Camp document provided by this link:
http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/LungNoduleSegmentationWithLSTK.html

However, cmake showed an error requesting a version of VTK 6.0.0 or newer. I will try this version in the meantime, but was hoping to get some help on building LSTK.


Thanks,
Constance Owens
Graduate Research Assistant

The University of Texas Graduate School of Biomedical Sciences at Houston
Medical Physics
CAOwens at mdanderson.org<https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
tel 713-745-3679 | cel 281-770-5210

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
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From dzenanz at gmail.com  Thu Oct 13 11:20:07 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Oct 2016 11:20:07 -0400
Subject: [ITK] [ITK-users] Lesion Sizing Toolkit Build not successful
In-Reply-To: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
Message-ID: <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>

Hi Constance,

the lesion sizing toolkit builds with master version of ITK with examples
and tests turned off. I will now try building with those on to see if some
problems appear. I used VS2013 x64.

Regards,
D?enan

On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <CAOwens at mdanderson.org>
wrote:

> I was hoping to speak with someone who may be able to help me with
> installing and building Lesion Sizing Toolkit. Originally I tried to build
> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>
>
>
> Error      1              fatal error C1083: Cannot open include file: '
> itkLesionSegmentationImageFilter8.h': No such file or
> directory                c:\itk2\src\modules\remote\
> lesionsizingtoolkit\examples\itkLesionSegmentationCommandLi
> neProgressReporter.h                22
>
> Error      2              fatal error C1083: Cannot open include file:
> 'itkImageFileReader.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
> 1
>
> Error      3              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      4              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> LesionSurfaceExtraction.cxx     21
>
> Error      5              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> IsoSurfaceVolumeEstimation.cxx                21
>
> Error      6              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      7              fatal error C1083: Cannot open include file:
> 'itkCommand.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> ViewImageAndSegmentationSurface.cxx                18
>
> Error      8              error C2039: 'MetaEvent' : is not a member of
> '`global namespace''                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
> be its own base class                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      10           error C2146: syntax error : missing ';' before
> identifier 'MetaObjectType'                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaConverterBase.h          55
>
> Error      11           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      12           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      13           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      14           error C2143: syntax error : missing ',' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      15           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      17           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      18           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      20           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      22           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      23           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      25           error C2143: syntax error : missing ';' before
> '*'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      26           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      27           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 102
>
> Error      29           error C2061: syntax error : identifier
> 'MetaScene'                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   104
>
> Error      30           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      31           error C2059: syntax error : '>'
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      32           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 116
>
> Error      33           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      34           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      35           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 121
>
> Error      36           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 124
>
> Error      37           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      38           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      39           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 127
>
> Error      40           error C2065: 'transform' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      41           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      42           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      43           error C2065: 'obj' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      44           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      45           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
> Error      46           fatal error C1004: unexpected end-of-file
> found                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
>
>
> Additionally, I am using CMake v3.6.1.
>
>
>
> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
> ITK Bar Camp document provided by this link:
>
> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/
> LungNoduleSegmentationWithLSTK.html
>
>
>
> However, cmake showed an error requesting a version of VTK 6.0.0 or newer.
> I will try this version in the meantime, but was hoping to get some help on
> building LSTK.
>
>
>
>
>
> Thanks,
>
> Constance Owens
>
> Graduate Research Assistant
>
> *The University of Texas Graduate School of Biomedical Sciences at Houston*
> Medical Physics
>
> CAOwens at mdanderson.org
> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
> tel 713-745-3679 | cel 281-770-5210
>
>
>
> The information contained in this e-mail message may be privileged,
> confidential, and/or protected from disclosure. This e-mail message may
> contain protected health information (PHI); dissemination of PHI should
> comply with applicable federal and state laws. If you are not the intended
> recipient, or an authorized representative of the intended recipient, any
> further review, disclosure, use, dissemination, distribution, or copying of
> this message or any attachment (or the information contained therein) is
> strictly prohibited. If you think that you have received this e-mail
> message in error, please notify the sender by return e-mail and delete all
> references to it and its contents from your systems.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Thu Oct 13 11:29:27 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Oct 2016 11:29:27 -0400
Subject: [ITK] [ITK-users] Lesion Sizing Toolkit Build not successful
In-Reply-To: <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>
Message-ID: <CAPf2UMTDVVLJLYuqfyuuvOXe5m6gDF_8_K5ZHiE21bCV9UaCLA@mail.gmail.com>

Hi Constance,

building it outside of ITK I also get similar errors, e.g.:
5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx(21):
fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such
file or directory

I will investigate later, and in the meantime you can try building it as
part of ITK (turn Module_LesionSizingToolkit ON).

Regards,
D?enan

On Thu, Oct 13, 2016 at 11:20 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Constance,
>
> the lesion sizing toolkit builds with master version of ITK with examples
> and tests turned off. I will now try building with those on to see if some
> problems appear. I used VS2013 x64.
>
> Regards,
> D?enan
>
> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
>> I was hoping to speak with someone who may be able to help me with
>> installing and building Lesion Sizing Toolkit. Originally I tried to build
>> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
>> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>>
>>
>>
>> Error      1              fatal error C1083: Cannot open include file:
>> 'itkLesionSegmentationImageFilter8.h': No such file or
>> directory                c:\itk2\src\modules\remote\les
>> ionsizingtoolkit\examples\itkLesionSegmentationCommandLinePr
>> ogressReporter.h                22
>>
>> Error      2              fatal error C1083: Cannot open include file:
>> 'itkImageFileReader.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
>> 1
>>
>> Error      3              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      4              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\LesionSurfaceExtraction.cxx     21
>>
>> Error      5              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\IsoSurfaceVolumeEstimation.cxx                21
>>
>> Error      6              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      7              fatal error C1083: Cannot open include file:
>> 'itkCommand.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\ViewImageAndSegmentationSurface.cxx                18
>>
>> Error      8              error C2039: 'MetaEvent' : is not a member of
>> '`global namespace''                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
>> be its own base class                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      10           error C2146: syntax error : missing ';' before
>> identifier 'MetaObjectType'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          55
>>
>> Error      11           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      12           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      13           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 64
>>
>> Error      14           error C2143: syntax error : missing ',' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          64
>>
>> Error      15           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          67
>>
>> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      17           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      18           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      20           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          77
>>
>> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      22           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      23           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      25           error C2143: syntax error : missing ';' before
>> '*'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   100
>>
>> Error      26           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 100
>>
>> Error      27           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 102
>>
>> Error      29           error C2061: syntax error : identifier
>> 'MetaScene'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   104
>>
>> Error      30           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   112
>>
>> Error      31           error C2059: syntax error : '>'
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 112
>>
>> Error      32           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   116
>>
>> Error      33           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      34           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      35           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   121
>>
>> Error      36           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   124
>>
>> Error      37           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      38           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      39           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   127
>>
>> Error      40           error C2065: 'transform' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      41           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      42           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      43           error C2065: 'obj' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      44           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      45           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>> Error      46           fatal error C1004: unexpected end-of-file
>> found                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>>
>>
>> Additionally, I am using CMake v3.6.1.
>>
>>
>>
>> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
>> ITK Bar Camp document provided by this link:
>>
>> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/
>> ITK/LungNoduleSegmentationWithLSTK.html
>>
>>
>>
>> However, cmake showed an error requesting a version of VTK 6.0.0 or
>> newer. I will try this version in the meantime, but was hoping to get some
>> help on building LSTK.
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance Owens
>>
>> Graduate Research Assistant
>>
>> *The University of Texas Graduate School of Biomedical Sciences at
>> Houston*
>> Medical Physics
>>
>> CAOwens at mdanderson.org
>> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
>> tel 713-745-3679 | cel 281-770-5210
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From matt.mccormick at kitware.com  Thu Oct 13 12:06:49 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 13 Oct 2016 12:06:49 -0400
Subject: [ITK] LINK PROBLEM
In-Reply-To: <DM5PR05MB31317796785711468EFFC745A0DC0@DM5PR05MB3131.namprd05.prod.outlook.com>
References: <DM5PR05MB31317796785711468EFFC745A0DC0@DM5PR05MB3131.namprd05.prod.outlook.com>
Message-ID: <CALzTN-Q8cGSUEspVQF-7RnSvSkmtk8Ohkrbo0ay8ddp_MZ-TjQ@mail.gmail.com>

Hi Anna,

Are there any other errors reported in your build?

Thanks,
Matt

On Thu, Oct 13, 2016 at 3:24 AM, Anna Vlachomitrou
<avlachomitrou at dxo.com> wrote:
> Dear ITK community,
>
>  I am currently trying to build ITK so as to use some prebuilded libs  in
> Python.
>
> -I downloaded the 4.10 version
>
> - I used cmake to get the itk.sln for vs2010 32b (and also tried vs2015 32b)
>
> - I launch the ALLBUILD
>
> -I get some errors: all errors are related to _hypot. Here is an example:
>
> 450>     Creating library
> D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPython.lib
> and object
> D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPython.exp
>
> 450>itkImageMomentsCalculatorPython.obj : error LNK2019: unresolved external
> symbol "double __cdecl vnl_math::_hypot(double,double)"
> (?_hypot at vnl_math@@YANNN at Z) referenced in function "double __cdecl
> itk::Math::_hypot<double>(double,double)" (??$_hypot at N@Math at itk@@YANNN at Z)
>
> 450>D:\DATA\InsightToolkit-4.10.1\build\lib\Release\_ITKImageStatisticsPython.pyd
> : fatal error LNK1120: 1 unresolved externals
>
> 450>
>
>
>
> Do you have any idea of how i can fix these build errors ?
>
>  Thanks in advance,
>
> Anna
>
>
>
>
> ------------------------------------------------------------------------------
> This message and any attachments (the "message") are confidential and
> intended solely for the addressee(s). Any unauthorized use or dissemination
> is prohibited. E-mails are susceptible to alteration. Neither DxO Labs nor
> any of its subsidiaries or affiliates shall be liable for the message if
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> Ce message et toutes les pi?ces jointes (ci-apr?s le "message") sont
> confidentiels et ?tablis ? l'intention exclusive de ses destinataires. Toute
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From dzenanz at gmail.com  Thu Oct 13 18:31:18 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Oct 2016 18:31:18 -0400
Subject: [ITK] [ITK-users] FW: Lesion Sizing Toolkit Build not successful
In-Reply-To: <603A32F9BAA25B4FBF30F3ADF057B0872C75D09F@DCPWPEXMBX01.mdanderson.edu>
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Message-ID: <CAPf2UMTTrteznwnx5VZ5fFL1tMcL3JDnE7oGZaHej-OffmpN_w@mail.gmail.com>

Hi Constance,

I am using a recent VTK master.

I am right now looking into lesion sizing toolkit. I have push a commit to
my fork:
https://github.com/dzenanz/LesionSizingToolkit

This solves compile errors for me. I still have link errors (when building
outside of ITK build tree, your first approach).

It is end of workday in US Eastern so I will probably have to postpone this
for tomorrow. But maybe someone else on the list will suggest a fix
meanwhile :)

Regards,
D?enan

On Thu, Oct 13, 2016 at 6:20 PM, Owens,Constance A <CAOwens at mdanderson.org>
wrote:

> Hi D?enan,
>
> My advisor wanted me to ask you what VTK version did you use exactly? He
> tried with VS2015 and still gets the same error. Below was his response to
> me:
>
>
>
> Using the VS2015 doesn?t help. Same errors.
>
>
>
> I believe it?s the problem of combination of ITK and VTK. Try to check
> with Dzenan what the VTK version he used and the cmake options for VTK. It
> seems that when VTK was included, all ITK header files could not be
> located. No ITK directories were included (as shown).
>
>
>
>
>
>
>
> Thanks,
>
> Constance
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 1:45 PM
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Subject:* Re: FW: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> I am using 3.6.2.
>
>
>
> On Thu, Oct 13, 2016 at 2:22 PM, Owens,Constance A <CAOwens at mdanderson.org>
> wrote:
>
> Hi D?enan,
>
> What version of Cmake are you using? So I can rule it out as being a
> possible cause for the issues.
>
>
>
> Thanks,
>
> Constance
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 1:17 PM
>
>
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Hi Constance,
>
>
>
> those are the steps. What could be going on is that LesionSizingToolkit
> does not support such an old VisualStudio. You could try a newer VS, such
> as 2013 or 2015.
>
>
>
> Also, I will try to figure out the problem in standalone build later.
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 1:10 PM, Owens,Constance A <CAOwens at mdanderson.org>
> wrote:
>
> Hi D?enan,
>
> These are the steps that I followed:
>
>
>
> ?  Download ITK
>
> -        Use Git Clone and place in folder C:\ITK-v4.11\src
>
> o   https://itk.org/Wiki/ITK/Git/Download
>
> -        Open Cmake
>
> o   Set source to folder C:\ITK-v4.11\src\ITK
>
> o   Set build to folder C:\ITK-v4.11\bin-x64
>
> o   Click ?configure?
>
> ?         Set settings to ?Visual Studio 9 2008 Win64?
>
> -        Once configuration is complete:
>
> o   These configuration parameters were suggested by ITK
>
> o   Enable
>
> ?         Module_LesionSizingToolkit
>
> ?         LSTK_USE_VTK (Maybe I should not have done this?)
>
> o   Disable
>
> ?         Build_Shared_Libs
>
> ?         Build_Examples
>
> ?         Build_Testing
>
> o   Click ?Configure?, again
>
> -        Generate
>
> -        Double click on file ?ITK.sln?
>
> o   This can be found in folder: C:\ITK-v4.11\bin-x64
>
> -        Right click on ?ALL_BUILD?
>
> o   Select ?Build?
>
> And I still got all the errors that I mentioned in the first e-mail. My
> apologies if I am not understanding the steps you suggested. I am very new
> to Cmake and Visual Studio, having experience only with MATLAB prior to
> this.
>
>
>
> I would like to be able to see the segmentation results when using LSTK.
> The goal would be to run LSTK with their data first, and then to use it on
> our data.
>
>
>
> Thanks,
> Constance
>
>
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 11:57 AM
>
>
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Hi Constance,
>
>
>
> the "master version" is master branch in the official git repository:
>
> git://itk.org/ITK.git
>
> To see how to get it you can take a look here:
>
> itk.org/Wiki/ITK/Git/Develop
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 12:48 PM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
> Hi D?enan,
>
> What exactly is meant by ?master version? of ITK? Am I correct to assume
> that it is the most current release available at the link provided below?
>
> https://itk.org/ITK/resources/software.html
>
>
>
> Thanks,
> Constance
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 10:44 AM
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>
>
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Yes, that's what was successful for me. You can also try turning
> Build_Examples and Build_Testing on later. I mainly keep them off to reduce
> build time - as you might guess, I rebuild ITK a lot :)
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 11:38 AM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
> Hi D?enan,
>
>
>
> Just to confirm, when I configure in Cmake, I should turn OFF
> Build_Examples and Build_Testing, but turn ON Module_LesionSizingToolkit?
>
>
>
> Thanks,
>
> Constance
>
>
>
>
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, October 13, 2016 10:29 AM
> *To:* Owens,Constance A <CAOwens at mdanderson.org>
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>
>
>
> Hi Constance,
>
>
>
> building it outside of ITK I also get similar errors, e.g.:
>
> 5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\
> IsoSurfaceVolumeEstimation.cxx(21): fatal error C1083: Cannot open
> include file: 'vtkPolyDataWriter.h': No such file or directory
>
>
>
> I will investigate later, and in the meantime you can try building it as
> part of ITK (turn Module_LesionSizingToolkit ON).
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 11:20 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
> Hi Constance,
>
>
>
> the lesion sizing toolkit builds with master version of ITK with examples
> and tests turned off. I will now try building with those on to see if some
> problems appear. I used VS2013 x64.
>
>
>
> Regards,
>
> D?enan
>
>
>
> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
> CAOwens at mdanderson.org> wrote:
>
> I was hoping to speak with someone who may be able to help me with
> installing and building Lesion Sizing Toolkit. Originally I tried to build
> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>
>
>
> Error      1              fatal error C1083: Cannot open include file: '
> itkLesionSegmentationImageFilter8.h': No such file or
> directory                c:\itk2\src\modules\remote\
> lesionsizingtoolkit\examples\itkLesionSegmentationCommandLi
> neProgressReporter.h                22
>
> Error      2              fatal error C1083: Cannot open include file:
> 'itkImageFileReader.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
> 1
>
> Error      3              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      4              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> LesionSurfaceExtraction.cxx     21
>
> Error      5              fatal error C1083: Cannot open include file:
> 'vtkPolyDataWriter.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> IsoSurfaceVolumeEstimation.cxx                21
>
> Error      6              fatal error C1083: Cannot open include file:
> 'itkVector.h': No such file or directory
> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\visualization\
> vtkContourVisualizationModule.h                22
>
> Error      7              fatal error C1083: Cannot open include file:
> 'itkCommand.h': No such file or directory
> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Visualization\
> ViewImageAndSegmentationSurface.cxx                18
>
> Error      8              error C2039: 'MetaEvent' : is not a member of
> '`global namespace''                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
> be its own base class                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      10           error C2146: syntax error : missing ';' before
> identifier 'MetaObjectType'                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaConverterBase.h          55
>
> Error      11           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      12           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          55
>
> Error      13           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      14           error C2143: syntax error : missing ',' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      15           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      17           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      18           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          67
>
> Error      20           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
> : 'virtual' not permitted on data declarations
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      22           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      23           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> c:\itk2\src\modules\core\spatialobjects\include\
> itkMetaConverterBase.h          77
>
> Error      25           error C2143: syntax error : missing ';' before
> '*'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      26           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 100
>
> Error      27           error C4430: missing type specifier - int assumed.
> Note: C++ does not support default-int
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 102
>
> Error      29           error C2061: syntax error : identifier
> 'MetaScene'                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   104
>
> Error      30           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      31           error C2059: syntax error : '>'
> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 112
>
> Error      32           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 116
>
> Error      33           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      34           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      35           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 121
>
> Error      36           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 124
>
> Error      37           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      38           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      39           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 127
>
> Error      40           error C2065: 'transform' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      41           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      42           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      43           error C2065: 'obj' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      44           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      45           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
> Error      46           fatal error C1004: unexpected end-of-file
> found                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
>
>
> Additionally, I am using CMake v3.6.1.
>
>
>
> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
> ITK Bar Camp document provided by this link:
>
> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/
> LungNoduleSegmentationWithLSTK.html
>
>
>
> However, cmake showed an error requesting a version of VTK 6.0.0 or newer.
> I will try this version in the meantime, but was hoping to get some help on
> building LSTK.
>
>
>
>
>
> Thanks,
>
> Constance Owens
>
> Graduate Research Assistant
>
> *The University of Texas Graduate School of Biomedical Sciences at Houston*
> Medical Physics
>
> CAOwens at mdanderson.org
> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
> tel 713-745-3679 | cel 281-770-5210
>
>
>
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From bakkari.abdelkhalek at hotmail.fr  Thu Oct 13 19:05:50 2016
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Thu, 13 Oct 2016 23:05:50 +0000
Subject: [ITK] [ITK-users] Region Growing after seed points
Message-ID: <AM2PR09MB0562AD6C4A1B930FB8CF8D5583DC0@AM2PR09MB0562.eurprd09.prod.outlook.com>

Dear insight-users,


After applying the vtkSeedWidget in order to get Seed Points, I am trying to use the Seed Points to apply the region growing algorithm.

My question is : How to get the index of the seed points as seed[0], seed[1] and seed[2] ?





 void PlaceSeed(double x, double y, double z, vtkRenderWindowInteractor * interactor, vtkRenderer * renderer);
   vtkHandleWidget * GetSeed(int index);
   void RemoveSeeds();


   // Set seed
  ImageType::IndexType seed;
  seed[0] = x ;
  seed[1] = y ;
  seed[2] = z ;


Thank you in advance.

Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From avlachomitrou at dxo.com  Fri Oct 14 03:44:55 2016
From: avlachomitrou at dxo.com (Anna Vlachomitrou)
Date: Fri, 14 Oct 2016 07:44:55 +0000
Subject: [ITK] LINK PROBLEM
In-Reply-To: <CALzTN-Q8cGSUEspVQF-7RnSvSkmtk8Ohkrbo0ay8ddp_MZ-TjQ@mail.gmail.com>
References: <DM5PR05MB31317796785711468EFFC745A0DC0@DM5PR05MB3131.namprd05.prod.outlook.com>
 <CALzTN-Q8cGSUEspVQF-7RnSvSkmtk8Ohkrbo0ay8ddp_MZ-TjQ@mail.gmail.com>
Message-ID: <DM5PR05MB3131AC1AA9EBE14C3658CF55A0DF0@DM5PR05MB3131.namprd05.prod.outlook.com>

Hi Matt,
Thanks for replying.
All the errors are related to external> symbol "double __cdecl vnl_math::_hypot(double,double)"
I have several projects that don't build. All of them have the same error. You want a full log?

Best,
Anna
-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com]
Sent: jeudi 13 octobre 2016 18:07
To: Anna Vlachomitrou <avlachomitrou at dxo.com>
Cc: community at itk.org
Subject: Re: [ITK] LINK PROBLEM

Hi Anna,

Are there any other errors reported in your build?

Thanks,
Matt

On Thu, Oct 13, 2016 at 3:24 AM, Anna Vlachomitrou <avlachomitrou at dxo.com> wrote:
> Dear ITK community,
>
>  I am currently trying to build ITK so as to use some prebuilded libs
> in Python.
>
> -I downloaded the 4.10 version
>
> - I used cmake to get the itk.sln for vs2010 32b (and also tried
> vs2015 32b)
>
> - I launch the ALLBUILD
>
> -I get some errors: all errors are related to _hypot. Here is an example:
>
> 450>     Creating library
> D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPyth
> on.lib
> and object
> D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPyth
> on.exp
>
> 450>itkImageMomentsCalculatorPython.obj : error LNK2019: unresolved
> 450>external
> symbol "double __cdecl vnl_math::_hypot(double,double)"
> (?_hypot at vnl_math@@YANNN at Z) referenced in function "double __cdecl
> itk::Math::_hypot<double>(double,double)"
> (??$_hypot at N@Math at itk@@YANNN at Z)
>
> 450>D:\DATA\InsightToolkit-4.10.1\build\lib\Release\_ITKImageStatistic
> 450>sPython.pyd
> : fatal error LNK1120: 1 unresolved externals
>
> 450>
>
>
>
> Do you have any idea of how i can fix these build errors ?
>
>  Thanks in advance,
>
> Anna
>
>
>
>
> ----------------------------------------------------------------------
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> unauthorized use or dissemination is prohibited. E-mails are
> susceptible to alteration. Neither DxO Labs nor any of its
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> Ce message et toutes les pi?ces jointes (ci-apr?s le "message") sont
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>
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Ce message et toutes les pi?ces jointes (ci-apr?s le "message") sont confidentiels et ?tablis ? l'intention exclusive de ses destinataires. Toute utilisation ou diffusion non autoris?e est interdite. Tout message ?lectronique est susceptible d'alt?ration. DxO Labs et ses filiales d?clinent toute responsabilit? au titre de ce message s'il a ?t? alt?r?, modifi? ou falsifi?.

From francois.budin at kitware.com  Fri Oct 14 07:09:15 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Fri, 14 Oct 2016 07:09:15 -0400
Subject: [ITK] [ITK-users] Region Growing after seed points
In-Reply-To: <AM2PR09MB0562AD6C4A1B930FB8CF8D5583DC0@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB0562AD6C4A1B930FB8CF8D5583DC0@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <CAHwLD2VzHt5o4tTiRW5ea8fna7_MCkqjb_syhnu+j_B7E9rUgg@mail.gmail.com>

Dear Abdelkhalek,

You may want to contact the VTK user mailing list for your question as it
concerns VTK. You can register on this webpage:
http://www.vtk.org/mailing-lists/ .You will get better answers there.

Best,
Francois

On Thu, Oct 13, 2016 at 7:05 PM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Dear insight-users,
>
>
> After applying the vtkSeedWidget in order to get Seed Points, I am trying
> to use the Seed Points to apply the region growing algorithm.
>
> My question is : How to get the index of the seed points as seed[0],
> seed[1] and seed[2] ?
>
>
>
>
>
>  void PlaceSeed(double x, double y, double z, vtkRenderWindowInteractor *
> interactor, vtkRenderer * renderer);
>    vtkHandleWidget * GetSeed(int index);
>    void RemoveSeeds();
>
>
>    // Set seed
>   ImageType::IndexType seed;
>   seed[0] = x ;
>   seed[1] = y ;
>   seed[2] = z ;
>
> Thank you in advance.
>
> Best regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From cr at neuro.ma.uni-heidelberg.de  Fri Oct 14 08:52:35 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 14 Oct 2016 14:52:35 +0200
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
Message-ID: <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>

Hi Matt,

I've forked on github, extended the documentation and created a pull 
request. Or is gerrit the only way to get a patch merged?

Christina


On 12.10.2016 18:03, Matt McCormick wrote:
> Hello Christina,
>
> Good idea.
>
> To update the documentation, the class Doxygen documentation can be editted:
>
>    https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>
> and after a patch is submitted:
>
>    https://itk.org/Wiki/ITK/Git/Develop
>
> it will show up on the Doxygen web pages.
>
> Please let us know if you have any questions.
>
> Thanks,
> Matt
>
> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>> Hi,
>>
>> I think it would be helpful if the documentation of the filter would mention
>> that there are two outputs, one with the surviving labels and the second
>> with the removed labels (the input image is the union of these images). What
>> is the workflow to achieve this?
>>
>> Christina
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users


_____________________________________
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Please keep messages on-topic and check the ITK FAQ at:
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Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Fri Oct 14 09:00:48 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Oct 2016 09:00:48 -0400
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
Message-ID: <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>

Hi Christina,

gerrit is the only way to merge patches. Can you submit it as a patch to
gerrit?

Thanks,
D?enan

On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> Hi Matt,
>
> I've forked on github, extended the documentation and created a pull
> request. Or is gerrit the only way to get a patch merged?
>
> Christina
>
>
>
> On 12.10.2016 18:03, Matt McCormick wrote:
>
>> Hello Christina,
>>
>> Good idea.
>>
>> To update the documentation, the class Doxygen documentation can be
>> editted:
>>
>>    https://github.com/InsightSoftwareConsortium/ITK/blob/
>> master/Modules/Filtering/LabelMap/include/itkAttributeSelect
>> ionLabelMapFilter.h#L27-L46
>>
>> and after a patch is submitted:
>>
>>    https://itk.org/Wiki/ITK/Git/Develop
>>
>> it will show up on the Doxygen web pages.
>>
>> Please let us know if you have any questions.
>>
>> Thanks,
>> Matt
>>
>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>>> Hi,
>>>
>>> I think it would be helpful if the documentation of the filter would
>>> mention
>>> that there are two outputs, one with the surviving labels and the second
>>> with the removed labels (the input image is the union of these images).
>>> What
>>> is the workflow to achieve this?
>>>
>>> Christina
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From dzenanz at gmail.com  Fri Oct 14 09:21:18 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Oct 2016 09:21:18 -0400
Subject: [ITK] [ITK-users] FW: Lesion Sizing Toolkit Build not successful
In-Reply-To: <CAPf2UMTTrteznwnx5VZ5fFL1tMcL3JDnE7oGZaHej-OffmpN_w@mail.gmail.com>
References: <603A32F9BAA25B4FBF30F3ADF057B0872C75CF77@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRSz72-gn6UNys4OijstnRiWr98+RoMqOyrRrHhMWBvcw@mail.gmail.com>
 <CAPf2UMTDVVLJLYuqfyuuvOXe5m6gDF_8_K5ZHiE21bCV9UaCLA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75CFD3@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMSfX7ne3047BmWNNR+bjyU92Ye17XuYqfu2kxQT12h7Lw@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75CFEB@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMTnfo=e0kHDZCiQOHOEDPamqgtHaHQvm_hMEdtMOy-+NQ@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D003@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMSx=swhrf4+PLLLkZAJA=hBT0rJ29+nrxF75V9y7f-MKA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D045@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMRVhVOi9D1awQHZpbRNmjip0HfuW_M1UcsRJYB=B0UzwA@mail.gmail.com>
 <603A32F9BAA25B4FBF30F3ADF057B0872C75D09F@DCPWPEXMBX01.mdanderson.edu>
 <CAPf2UMTTrteznwnx5VZ5fFL1tMcL3JDnE7oGZaHej-OffmpN_w@mail.gmail.com>
Message-ID: <CAPf2UMQKXv2xa_8-B2FvMjq=xzO3mCxemCDZP2RJhebcjKbJ4A@mail.gmail.com>

Hi Christina,

I pushed a new commit to my fork
<https://github.com/dzenanz/LesionSizingToolkit> which resolves all build
and link errors on my VS2013 setup. Can you give it a try?

Regards,
D?enan

On Thu, Oct 13, 2016 at 6:31 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Constance,
>
> I am using a recent VTK master.
>
> I am right now looking into lesion sizing toolkit. I have push a commit to
> my fork:
> https://github.com/dzenanz/LesionSizingToolkit
>
> This solves compile errors for me. I still have link errors (when building
> outside of ITK build tree, your first approach).
>
> It is end of workday in US Eastern so I will probably have to postpone
> this for tomorrow. But maybe someone else on the list will suggest a fix
> meanwhile :)
>
> Regards,
> D?enan
>
> On Thu, Oct 13, 2016 at 6:20 PM, Owens,Constance A <CAOwens at mdanderson.org
> > wrote:
>
>> Hi D?enan,
>>
>> My advisor wanted me to ask you what VTK version did you use exactly? He
>> tried with VS2015 and still gets the same error. Below was his response to
>> me:
>>
>>
>>
>> Using the VS2015 doesn?t help. Same errors.
>>
>>
>>
>> I believe it?s the problem of combination of ITK and VTK. Try to check
>> with Dzenan what the VTK version he used and the cmake options for VTK. It
>> seems that when VTK was included, all ITK header files could not be
>> located. No ITK directories were included (as shown).
>>
>>
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 1:45 PM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: FW: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> I am using 3.6.2.
>>
>>
>>
>> On Thu, Oct 13, 2016 at 2:22 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>> What version of Cmake are you using? So I can rule it out as being a
>> possible cause for the issues.
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 1:17 PM
>>
>>
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> those are the steps. What could be going on is that LesionSizingToolkit
>> does not support such an old VisualStudio. You could try a newer VS, such
>> as 2013 or 2015.
>>
>>
>>
>> Also, I will try to figure out the problem in standalone build later.
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 1:10 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>> These are the steps that I followed:
>>
>>
>>
>> ?  Download ITK
>>
>> -        Use Git Clone and place in folder C:\ITK-v4.11\src
>>
>> o   https://itk.org/Wiki/ITK/Git/Download
>>
>> -        Open Cmake
>>
>> o   Set source to folder C:\ITK-v4.11\src\ITK
>>
>> o   Set build to folder C:\ITK-v4.11\bin-x64
>>
>> o   Click ?configure?
>>
>> ?         Set settings to ?Visual Studio 9 2008 Win64?
>>
>> -        Once configuration is complete:
>>
>> o   These configuration parameters were suggested by ITK
>>
>> o   Enable
>>
>> ?         Module_LesionSizingToolkit
>>
>> ?         LSTK_USE_VTK (Maybe I should not have done this?)
>>
>> o   Disable
>>
>> ?         Build_Shared_Libs
>>
>> ?         Build_Examples
>>
>> ?         Build_Testing
>>
>> o   Click ?Configure?, again
>>
>> -        Generate
>>
>> -        Double click on file ?ITK.sln?
>>
>> o   This can be found in folder: C:\ITK-v4.11\bin-x64
>>
>> -        Right click on ?ALL_BUILD?
>>
>> o   Select ?Build?
>>
>> And I still got all the errors that I mentioned in the first e-mail. My
>> apologies if I am not understanding the steps you suggested. I am very new
>> to Cmake and Visual Studio, having experience only with MATLAB prior to
>> this.
>>
>>
>>
>> I would like to be able to see the segmentation results when using LSTK.
>> The goal would be to run LSTK with their data first, and then to use it on
>> our data.
>>
>>
>>
>> Thanks,
>> Constance
>>
>>
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 11:57 AM
>>
>>
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> the "master version" is master branch in the official git repository:
>>
>> git://itk.org/ITK.git
>>
>> To see how to get it you can take a look here:
>>
>> itk.org/Wiki/ITK/Git/Develop
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 12:48 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>> What exactly is meant by ?master version? of ITK? Am I correct to assume
>> that it is the most current release available at the link provided below?
>>
>> https://itk.org/ITK/resources/software.html
>>
>>
>>
>> Thanks,
>> Constance
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 10:44 AM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>>
>>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Yes, that's what was successful for me. You can also try turning
>> Build_Examples and Build_Testing on later. I mainly keep them off to reduce
>> build time - as you might guess, I rebuild ITK a lot :)
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 11:38 AM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi D?enan,
>>
>>
>>
>> Just to confirm, when I configure in Cmake, I should turn OFF
>> Build_Examples and Build_Testing, but turn ON Module_LesionSizingToolkit?
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>>
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 10:29 AM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Cc:* insight-users at itk.org
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> building it outside of ITK I also get similar errors, e.g.:
>>
>> 5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx(21):
>> fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such
>> file or directory
>>
>>
>>
>> I will investigate later, and in the meantime you can try building it as
>> part of ITK (turn Module_LesionSizingToolkit ON).
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 11:20 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>> Hi Constance,
>>
>>
>>
>> the lesion sizing toolkit builds with master version of ITK with examples
>> and tests turned off. I will now try building with those on to see if some
>> problems appear. I used VS2013 x64.
>>
>>
>>
>> Regards,
>>
>> D?enan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> I was hoping to speak with someone who may be able to help me with
>> installing and building Lesion Sizing Toolkit. Originally I tried to build
>> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I?m using
>> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>>
>>
>>
>> Error      1              fatal error C1083: Cannot open include file:
>> 'itkLesionSegmentationImageFilter8.h': No such file or
>> directory                c:\itk2\src\modules\remote\les
>> ionsizingtoolkit\examples\itkLesionSegmentationCommandLinePr
>> ogressReporter.h                22
>>
>> Error      2              fatal error C1083: Cannot open include file:
>> 'itkImageFileReader.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
>> 1
>>
>> Error      3              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      4              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\LesionSurfaceExtraction.cxx     21
>>
>> Error      5              fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\IsoSurfaceVolumeEstimation.cxx                21
>>
>> Error      6              fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h                22
>>
>> Error      7              fatal error C1083: Cannot open include file:
>> 'itkCommand.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\ViewImageAndSegmentationSurface.cxx                18
>>
>> Error      8              error C2039: 'MetaEvent' : is not a member of
>> '`global namespace''                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
>> be its own base class                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h             35
>>
>> Error      10           error C2146: syntax error : missing ';' before
>> identifier 'MetaObjectType'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          55
>>
>> Error      11           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      12           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error      13           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 64
>>
>> Error      14           error C2143: syntax error : missing ',' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          64
>>
>> Error      15           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          67
>>
>> Error      16           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      17           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      18           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error      20           error C2143: syntax error : missing ';' before
>> '*'                c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h          77
>>
>> Error      21           error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      22           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      23           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error      25           error C2143: syntax error : missing ';' before
>> '*'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   100
>>
>> Error      26           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 100
>>
>> Error      27           error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 102
>>
>> Error      29           error C2061: syntax error : identifier
>> 'MetaScene'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   104
>>
>> Error      30           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   112
>>
>> Error      31           error C2059: syntax error : '>'
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 112
>>
>> Error      32           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   116
>>
>> Error      33           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      34           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   117
>>
>> Error      35           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   121
>>
>> Error      36           error C2143: syntax error : missing ';' before
>> '{'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   124
>>
>> Error      37           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      38           error C2653: 'TConverter' : is not a class or
>> namespace name                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   125
>>
>> Error      39           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   127
>>
>> Error      40           error C2065: 'transform' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      41           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   128
>>
>> Error      42           error C2065: 'MetaObject' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      43           error C2065: 'obj' : undeclared
>> identifier                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      44           error C2143: syntax error : missing ',' before
>> ')'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   130
>>
>> Error      45           error C2143: syntax error : missing ';' before
>> '}'                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>> Error      46           fatal error C1004: unexpected end-of-file
>> found                C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h   141
>>
>>
>>
>> Additionally, I am using CMake v3.6.1.
>>
>>
>>
>> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
>> ITK Bar Camp document provided by this link:
>>
>> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/
>> ITK/LungNoduleSegmentationWithLSTK.html
>>
>>
>>
>> However, cmake showed an error requesting a version of VTK 6.0.0 or
>> newer. I will try this version in the meantime, but was hoping to get some
>> help on building LSTK.
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance Owens
>>
>> Graduate Research Assistant
>>
>> *The University of Texas Graduate School of Biomedical Sciences at
>> Houston*
>> Medical Physics
>>
>> CAOwens at mdanderson.org
>> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
>> tel 713-745-3679 | cel 281-770-5210
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
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>> strictly prohibited. If you think that you have received this e-mail
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>>
>>
>>
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>>
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>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
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>> strictly prohibited. If you think that you have received this e-mail
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>> references to it and its contents from your systems.
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>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
>> strictly prohibited. If you think that you have received this e-mail
>> message in error, please notify the sender by return e-mail and delete all
>> references to it and its contents from your systems.
>>
>>
>>
>> The information contained in this e-mail message may be privileged,
>> confidential, and/or protected from disclosure. This e-mail message may
>> contain protected health information (PHI); dissemination of PHI should
>> comply with applicable federal and state laws. If you are not the intended
>> recipient, or an authorized representative of the intended recipient, any
>> further review, disclosure, use, dissemination, distribution, or copying of
>> this message or any attachment (or the information contained therein) is
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From cr at neuro.ma.uni-heidelberg.de  Fri Oct 14 09:21:33 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 14 Oct 2016 15:21:33 +0200
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
 <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
Message-ID: <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>

When visiting review.source.kitware.com -> sign in -> provide github 
credentials  I find myself on a page telling me "forbidden". But without 
a gerrit user I'm stuck...Any hints? I've double checked the credentials 
by signing in into github.

Christina

On 14.10.2016 15:00, D?enan Zuki? wrote:
> Hi Christina,
>
> gerrit is the only way to merge patches. Can you submit it as a patch 
> to gerrit?
>
> Thanks,
> D?enan
>
> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith 
> <cr at neuro.ma.uni-heidelberg.de <mailto:cr at neuro.ma.uni-heidelberg.de>> 
> wrote:
>
>     Hi Matt,
>
>     I've forked on github, extended the documentation and created a
>     pull request. Or is gerrit the only way to get a patch merged?
>
>     Christina
>
>
>
>     On 12.10.2016 18:03, Matt McCormick wrote:
>
>         Hello Christina,
>
>         Good idea.
>
>         To update the documentation, the class Doxygen documentation
>         can be editted:
>
>         https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>         <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46>
>
>         and after a patch is submitted:
>
>         https://itk.org/Wiki/ITK/Git/Develop
>         <https://itk.org/Wiki/ITK/Git/Develop>
>
>         it will show up on the Doxygen web pages.
>
>         Please let us know if you have any questions.
>
>         Thanks,
>         Matt
>
>         On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>         <cr at neuro.ma.uni-heidelberg.de
>         <mailto:cr at neuro.ma.uni-heidelberg.de>> wrote:
>
>             Hi,
>
>             I think it would be helpful if the documentation of the
>             filter would mention
>             that there are two outputs, one with the surviving labels
>             and the second
>             with the removed labels (the input image is the union of
>             these images). What
>             is the workflow to achieve this?
>
>             Christina
>
>             _____________________________________
>             Powered by www.kitware.com <http://www.kitware.com>
>
>             Visit other Kitware open-source projects at
>             http://www.kitware.com/opensource/opensource.html
>             <http://www.kitware.com/opensource/opensource.html>
>
>             Kitware offers ITK Training Courses, for more information
>             visit:
>             http://www.kitware.com/products/protraining.php
>             <http://www.kitware.com/products/protraining.php>
>
>             Please keep messages on-topic and check the ITK FAQ at:
>             http://www.itk.org/Wiki/ITK_FAQ
>             <http://www.itk.org/Wiki/ITK_FAQ>
>
>             Follow this link to subscribe/unsubscribe:
>             http://public.kitware.com/mailman/listinfo/insight-users
>             <http://public.kitware.com/mailman/listinfo/insight-users>
>
>
>
>     _____________________________________
>     Powered by www.kitware.com <http://www.kitware.com>
>
>     Visit other Kitware open-source projects at
>     http://www.kitware.com/opensource/opensource.html
>     <http://www.kitware.com/opensource/opensource.html>
>
>     Kitware offers ITK Training Courses, for more information visit:
>     http://www.kitware.com/products/protraining.php
>     <http://www.kitware.com/products/protraining.php>
>
>     Please keep messages on-topic and check the ITK FAQ at:
>     http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
>     Follow this link to subscribe/unsubscribe:
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>     <http://public.kitware.com/mailman/listinfo/insight-users>
>
>

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Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
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From dzenanz at gmail.com  Fri Oct 14 09:23:38 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Oct 2016 09:23:38 -0400
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
 <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
 <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>
Message-ID: <CAPf2UMST7UHoxc8s1U6irZwt2A2dFrDa7i4S=XPBP1GBdKjeog@mail.gmail.com>

Matt, what was the problem with this?

On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> When visiting review.source.kitware.com -> sign in -> provide github
> credentials  I find myself on a page telling me "forbidden". But without a
> gerrit user I'm stuck...Any hints? I've double checked the credentials by
> signing in into github.
>
> Christina
>
>
> On 14.10.2016 15:00, D?enan Zuki? wrote:
>
> Hi Christina,
>
> gerrit is the only way to merge patches. Can you submit it as a patch to
> gerrit?
>
> Thanks,
> D?enan
>
> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith <
> cr at neuro.ma.uni-heidelberg.de> wrote:
>
>> Hi Matt,
>>
>> I've forked on github, extended the documentation and created a pull
>> request. Or is gerrit the only way to get a patch merged?
>>
>> Christina
>>
>>
>>
>> On 12.10.2016 18:03, Matt McCormick wrote:
>>
>>> Hello Christina,
>>>
>>> Good idea.
>>>
>>> To update the documentation, the class Doxygen documentation can be
>>> editted:
>>>
>>>    https://github.com/InsightSoftwareConsortium/ITK/blob/maste
>>> r/Modules/Filtering/LabelMap/include/itkAttributeSelectionL
>>> abelMapFilter.h#L27-L46
>>>
>>> and after a patch is submitted:
>>>
>>>    https://itk.org/Wiki/ITK/Git/Develop
>>>
>>> it will show up on the Doxygen web pages.
>>>
>>> Please let us know if you have any questions.
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I think it would be helpful if the documentation of the filter would
>>>> mention
>>>> that there are two outputs, one with the surviving labels and the second
>>>> with the removed labels (the input image is the union of these images).
>>>> What
>>>> is the workflow to achieve this?
>>>>
>>>> Christina
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
>
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From matt.mccormick at kitware.com  Fri Oct 14 10:46:00 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 14 Oct 2016 10:46:00 -0400
Subject: [ITK] [ITK-users] Documentation:
	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <CAPf2UMST7UHoxc8s1U6irZwt2A2dFrDa7i4S=XPBP1GBdKjeog@mail.gmail.com>
References: <e766aaea-36d7-2355-4254-14f8c95d7789@neuro.ma.uni-heidelberg.de>
 <CALzTN-Q+XvHgNXKWjDXkrhxpC4nh_waEtNkd1JYtKhuPctu6cg@mail.gmail.com>
 <fc7b9849-69c9-bd97-0e3c-7a374380e166@neuro.ma.uni-heidelberg.de>
 <CAPf2UMRYBC=WbSZhJW9rpbnC1FfHXHrFrjr-ew4jyf4ZZARTLg@mail.gmail.com>
 <a492fe8d-adfb-d482-290b-cc56f9b18832@neuro.ma.uni-heidelberg.de>
 <CAPf2UMST7UHoxc8s1U6irZwt2A2dFrDa7i4S=XPBP1GBdKjeog@mail.gmail.com>
Message-ID: <CALzTN-QP+kQ3fHm0dUZEhQDAG-NtdQa1L+8zj=3RJZ+bsi+TTQ@mail.gmail.com>

Hi,

This is a problem with old accounts that were not used for a few years
after the GitHub authentication transition. I will contact the
sys-admins to get it resolved.

Thanks,
Matt

On Fri, Oct 14, 2016 at 9:23 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Matt, what was the problem with this?
>
> On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>> When visiting review.source.kitware.com -> sign in -> provide github
>> credentials  I find myself on a page telling me "forbidden". But without a
>> gerrit user I'm stuck...Any hints? I've double checked the credentials by
>> signing in into github.
>>
>> Christina
>>
>>
>> On 14.10.2016 15:00, D?enan Zuki? wrote:
>>
>> Hi Christina,
>>
>> gerrit is the only way to merge patches. Can you submit it as a patch to
>> gerrit?
>>
>> Thanks,
>> D?enan
>>
>> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> Hi Matt,
>>>
>>> I've forked on github, extended the documentation and created a pull
>>> request. Or is gerrit the only way to get a patch merged?
>>>
>>> Christina
>>>
>>>
>>>
>>> On 12.10.2016 18:03, Matt McCormick wrote:
>>>>
>>>> Hello Christina,
>>>>
>>>> Good idea.
>>>>
>>>> To update the documentation, the class Doxygen documentation can be
>>>> editted:
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>>>>
>>>> and after a patch is submitted:
>>>>
>>>>    https://itk.org/Wiki/ITK/Git/Develop
>>>>
>>>> it will show up on the Doxygen web pages.
>>>>
>>>> Please let us know if you have any questions.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I think it would be helpful if the documentation of the filter would
>>>>> mention
>>>>> that there are two outputs, one with the surviving labels and the
>>>>> second
>>>>> with the removed labels (the input image is the union of these images).
>>>>> What
>>>>> is the workflow to achieve this?
>>>>>
>>>>> Christina
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>
_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From francois.budin at kitware.com  Sun Oct 16 21:49:51 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Sun, 16 Oct 2016 21:49:51 -0400
Subject: [ITK] [ITK-dev] BUILD_SHARED_LIBS vs ITK_BUILD_SHARED
Message-ID: <CAHwLD2V3FRXt_-v1eOob+Pd4BevDJ24k=46_XbpgOoMEdArneA@mail.gmail.com>

Hello fellow ITK developers,

I was having linking errors on Windows when compiling a project that was
using the CMake variable BUILD_SHARED_LIBS and setting it to ON when I had
compiled ITK with BUILD_SHARED_LIBS to OFF.
I realized that when ITK gets included and used and when the project using
ITK using the IO factory mechanism, UseITK.cmake uses the variable
BUILD_SHARED_LIBS to set some parameters. I was wondering if instead of
using BUILD_SHARED_LIBS which could have a different value in ITK and the
project I am trying to compile, UseITK.cmake should not use
ITK_BUILD_SHARED instead (which is set when ITK is configured). If I modify
UseITK.cmake to use ITK_BUILD_SHARED instead of BUILD_SHARED_LIBS, the
linking error I was having disappears. Is this a bug or is there a reason
behind that design?

Thanks,
Francois

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/UseITK.cmake#L201
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From tamanupadhaya at gmail.com  Mon Oct 17 08:35:23 2016
From: tamanupadhaya at gmail.com (Tmn)
Date: Mon, 17 Oct 2016 05:35:23 -0700 (MST)
Subject: [ITK] [ITK-users] ITK GLCM Matrix
Message-ID: <1476707723670-7589370.post@n2.nabble.com>

I am using itk library to extract Haralick texture feature using
itk::Statistics::ScalarImageToTextureFeaturesFilter<>; But I am unable to
find the function to print GLCM matrix.

Can someone please provide me a small example on how to print the GLCM
matrix?

Thank you for your time!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-GLCM-Matrix-tp7589370.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From tevain at telecom-paristech.fr  Mon Oct 17 08:50:36 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 17 Oct 2016 14:50:36 +0200 (CEST)
Subject: [ITK] [ITK-users]   ITK GLCM Matrix
In-Reply-To: <1476707723670-7589370.post@n2.nabble.com>
References: <1476707723670-7589370.post@n2.nabble.com>
Message-ID: <1774750007.10144382.1476708636069.JavaMail.zimbra@enst.fr>

Hi,

If you want to access directly to the matrix, I would suggest to use the Statistics::ScalarImageToCooccurrenceMatrixFilter, which output what you want as a histogram.

HTH,

Tim

----- Mail original -----
De: "Tmn" <tamanupadhaya at gmail.com>
?: insight-users at itk.org
Envoy?: Lundi 17 Octobre 2016 14:35:23
Objet: [ITK] [ITK-users] ITK GLCM Matrix

I am using itk library to extract Haralick texture feature using
itk::Statistics::ScalarImageToTextureFeaturesFilter<>; But I am unable to
find the function to print GLCM matrix.

Can someone please provide me a small example on how to print the GLCM
matrix?

Thank you for your time!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-GLCM-Matrix-tp7589370.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users
_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community
_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

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From blowekamp at mail.nih.gov  Mon Oct 17 08:56:35 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 17 Oct 2016 12:56:35 +0000
Subject: [ITK] [ITK-dev] BUILD_SHARED_LIBS vs ITK_BUILD_SHARED
In-Reply-To: <CAHwLD2V3FRXt_-v1eOob+Pd4BevDJ24k=46_XbpgOoMEdArneA@mail.gmail.com>
References: <CAHwLD2V3FRXt_-v1eOob+Pd4BevDJ24k=46_XbpgOoMEdArneA@mail.gmail.com>
Message-ID: <87193762-E7B5-4B00-9F88-240D2EB0FBB0@mail.nih.gov>

Looks like a bug to me. This is relatively new code too [1].

You proposal sounds good to me too.

Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/commit/1000370eec20511850c543cb3c02aa5118563ccc



On Oct 16, 2016, at 9:49 PM, Francois Budin <francois.budin at kitware.com<mailto:francois.budin at kitware.com>> wrote:

Hello fellow ITK developers,

I was having linking errors on Windows when compiling a project that was using the CMake variable BUILD_SHARED_LIBS and setting it to ON when I had compiled ITK with BUILD_SHARED_LIBS to OFF.
I realized that when ITK gets included and used and when the project using ITK using the IO factory mechanism, UseITK.cmake uses the variable BUILD_SHARED_LIBS to set some parameters. I was wondering if instead of using BUILD_SHARED_LIBS which could have a different value in ITK and the project I am trying to compile, UseITK.cmake should not use ITK_BUILD_SHARED instead (which is set when ITK is configured). If I modify UseITK.cmake to use ITK_BUILD_SHARED instead of BUILD_SHARED_LIBS, the linking error I was having disappears. Is this a bug or is there a reason behind that design?

Thanks,
Francois

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/UseITK.cmake#L201
_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

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From tevain at telecom-paristech.fr  Mon Oct 17 09:25:16 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 17 Oct 2016 15:25:16 +0200 (CEST)
Subject: [ITK] [ITK-users] ITK GLCM Matrix
In-Reply-To: <CAAb67p3pToKmEW4+e18d2e3oCRD_-gCBBuog9eyUZ-Do5mbenw@mail.gmail.com>
References: <1476707723670-7589370.post@n2.nabble.com>
 <1774750007.10144382.1476708636069.JavaMail.zimbra@enst.fr>
 <CAAb67p3pToKmEW4+e18d2e3oCRD_-gCBBuog9eyUZ-Do5mbenw@mail.gmail.com>
Message-ID: <16183274.10178518.1476710716629.JavaMail.zimbra@enst.fr>

You can refer to the description of the filter which is quite complete [1] and to the wiki example for the global structure [2] (even if the example mimic the full process to feature image as in the ScalarImageToTextureFeaturesFilter case, look to the lines concerning the "glcmGenerator").
After setting-up and updating the filter, the ->GetOutput() method will return the GLCM matrix, in the form of an itk Histogram [3].
Basically you could acces to each element through the ->GetFrequency (const IndexType &index) method where the "index" is an itk Index containing the line/row indexes to acces.

HTH,

Tim 


[1]https://itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToCooccurrenceMatrixFilter.html
[2]https://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
[3]https://itk.org/Doxygen/html/classitk_1_1Statistics_1_1Histogram.html

----- Mail original -----
De: "Taman Upadhaya" <tamanupadhaya at gmail.com>
?: "Timothee Evain" <tevain at telecom-paristech.fr>
Envoy?: Lundi 17 Octobre 2016 14:52:10
Objet: Re: [ITK] [ITK-users] ITK GLCM Matrix

Hi Tim,

First of all thank you for your reply.
Can you direct me to the piece of code to do that.
I am still new to ITK.

Thanks

On Mon, Oct 17, 2016 at 2:50 PM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> Hi,
>
> If you want to access directly to the matrix, I would suggest to use the
> Statistics::ScalarImageToCooccurrenceMatrixFilter, which output what you
> want as a histogram.
>
> HTH,
>
> Tim
>
> ----- Mail original -----
> De: "Tmn" <tamanupadhaya at gmail.com>
> ?: insight-users at itk.org
> Envoy?: Lundi 17 Octobre 2016 14:35:23
> Objet: [ITK] [ITK-users] ITK GLCM Matrix
>
> I am using itk library to extract Haralick texture feature using
> itk::Statistics::ScalarImageToTextureFeaturesFilter<>; But I am unable to
> find the function to print GLCM matrix.
>
> Can someone please provide me a small example on how to print the GLCM
> matrix?
>
> Thank you for your time!
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/ITK-GLCM-Matrix-tp7589370.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From tamanupadhaya at gmail.com  Mon Oct 17 09:32:24 2016
From: tamanupadhaya at gmail.com (Taman Upadhaya)
Date: Mon, 17 Oct 2016 15:32:24 +0200
Subject: [ITK] [ITK-users] ITK GLCM Matrix
In-Reply-To: <16183274.10178518.1476710716629.JavaMail.zimbra@enst.fr>
References: <1476707723670-7589370.post@n2.nabble.com>
 <1774750007.10144382.1476708636069.JavaMail.zimbra@enst.fr>
 <CAAb67p3pToKmEW4+e18d2e3oCRD_-gCBBuog9eyUZ-Do5mbenw@mail.gmail.com>
 <16183274.10178518.1476710716629.JavaMail.zimbra@enst.fr>
Message-ID: <CAAb67p2Auz71ynZPafB-Nha71fag0s5eW01nVvjM69X81g-cfw@mail.gmail.com>

Hi Tim,

Thank you for your help.
I will do as you suggested.


On Mon, Oct 17, 2016 at 3:25 PM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> You can refer to the description of the filter which is quite complete [1]
> and to the wiki example for the global structure [2] (even if the example
> mimic the full process to feature image as in the
> ScalarImageToTextureFeaturesFilter case, look to the lines concerning the
> "glcmGenerator").
> After setting-up and updating the filter, the ->GetOutput() method will
> return the GLCM matrix, in the form of an itk Histogram [3].
> Basically you could acces to each element through the ->GetFrequency
> (const IndexType &index) method where the "index" is an itk Index
> containing the line/row indexes to acces.
>
> HTH,
>
> Tim
>
>
> [1]https://itk.org/Doxygen/html/classitk_1_1Statistics_1_
> 1ScalarImageToCooccurrenceMatrixFilter.html
> [2]https://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
> [3]https://itk.org/Doxygen/html/classitk_1_1Statistics_1_1Histogram.html
>
> ----- Mail original -----
> De: "Taman Upadhaya" <tamanupadhaya at gmail.com>
> ?: "Timothee Evain" <tevain at telecom-paristech.fr>
> Envoy?: Lundi 17 Octobre 2016 14:52:10
> Objet: Re: [ITK] [ITK-users] ITK GLCM Matrix
>
> Hi Tim,
>
> First of all thank you for your reply.
> Can you direct me to the piece of code to do that.
> I am still new to ITK.
>
> Thanks
>
> On Mon, Oct 17, 2016 at 2:50 PM, Timothee Evain <
> tevain at telecom-paristech.fr
> > wrote:
>
> > Hi,
> >
> > If you want to access directly to the matrix, I would suggest to use the
> > Statistics::ScalarImageToCooccurrenceMatrixFilter, which output what you
> > want as a histogram.
> >
> > HTH,
> >
> > Tim
> >
> > ----- Mail original -----
> > De: "Tmn" <tamanupadhaya at gmail.com>
> > ?: insight-users at itk.org
> > Envoy?: Lundi 17 Octobre 2016 14:35:23
> > Objet: [ITK] [ITK-users] ITK GLCM Matrix
> >
> > I am using itk library to extract Haralick texture feature using
> > itk::Statistics::ScalarImageToTextureFeaturesFilter<>; But I am unable
> to
> > find the function to print GLCM matrix.
> >
> > Can someone please provide me a small example on how to print the GLCM
> > matrix?
> >
> > Thank you for your time!
> >
> >
> >
> > --
> > View this message in context: http://itk-insight-users.
> > 2283740.n2.nabble.com/ITK-GLCM-Matrix-tp7589370.html
> > Sent from the ITK Insight Users mailing list archive at Nabble.com.
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
>
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From matt.mccormick at kitware.com  Mon Oct 17 09:57:58 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 17 Oct 2016 09:57:58 -0400
Subject: [ITK] [ITK-dev] BUILD_SHARED_LIBS vs ITK_BUILD_SHARED
In-Reply-To: <87193762-E7B5-4B00-9F88-240D2EB0FBB0@mail.nih.gov>
References: <CAHwLD2V3FRXt_-v1eOob+Pd4BevDJ24k=46_XbpgOoMEdArneA@mail.gmail.com>
 <87193762-E7B5-4B00-9F88-240D2EB0FBB0@mail.nih.gov>
Message-ID: <CALzTN-Tstpa-7fJXi+TLZQ_DN8-G5rg5+9Vu=LkFVG4iQ3EbMg@mail.gmail.com>

Hi Francois,

Good observation. Yes, UseITK.cmake should be using ITK_BUILD_SHARED
from ITKConfig.cmake for ITK library build settings here [1].

Thanks,
Matt

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/UseITK.cmake#L201




On Mon, Oct 17, 2016 at 8:56 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Looks like a bug to me. This is relatively new code too [1].
>
> You proposal sounds good to me too.
>
> Brad
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/commit/1000370eec20511850c543cb3c02aa5118563ccc
>
>
>
>
> On Oct 16, 2016, at 9:49 PM, Francois Budin <francois.budin at kitware.com>
> wrote:
>
> Hello fellow ITK developers,
>
> I was having linking errors on Windows when compiling a project that was
> using the CMake variable BUILD_SHARED_LIBS and setting it to ON when I had
> compiled ITK with BUILD_SHARED_LIBS to OFF.
> I realized that when ITK gets included and used and when the project using
> ITK using the IO factory mechanism, UseITK.cmake uses the variable
> BUILD_SHARED_LIBS to set some parameters. I was wondering if instead of
> using BUILD_SHARED_LIBS which could have a different value in ITK and the
> project I am trying to compile, UseITK.cmake should not use ITK_BUILD_SHARED
> instead (which is set when ITK is configured). If I modify UseITK.cmake to
> use ITK_BUILD_SHARED instead of BUILD_SHARED_LIBS, the linking error I was
> having disappears. Is this a bug or is there a reason behind that design?
>
> Thanks,
> Francois
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/UseITK.cmake#L201
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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_______________________________________________
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From swetha.bsharma at gmail.com  Wed Oct 19 05:49:55 2016
From: swetha.bsharma at gmail.com (swetha)
Date: Wed, 19 Oct 2016 02:49:55 -0700 (MST)
Subject: [ITK] [ITK-users] Cmake clrsupport c# wrapper for itk
Message-ID: <1476870595135-7589372.post@n2.nabble.com>

Hi,

   I am trying to create a wrapper in c# for c++ code in itk. Because I am
using ITK i am forced to use cmake to add the relevant header files which i
would need.

This is the script which i have added

SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "/clr") 
 STRING(REPLACE "/EHsc" "/EHa" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
 STRING(REPLACE "/RTC1" "" CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /clr") 

The problem I've found, is that while CMake sets the "Common Language
RunTime Support" option in the C/C++ section of the configuration properties
if "/clr" is in the CXX_FLAGS, it does not set the "Common Language RunTime
Support" in the general configuration properties, and that causes problems
with linking/.NET references.

How do i solve this?
-swetha



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Cmake-clrsupport-c-wrapper-for-itk-tp7589372.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
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From zeinsalah at gmail.com  Wed Oct 19 06:55:10 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Wed, 19 Oct 2016 12:55:10 +0200
Subject: [ITK] Loading multiframe dicom with itk
Message-ID: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>

Hi,

to organizational reasons, I must use an old release of itk (3.14).

I am trying to load multiframe dicom images with itk reader. I noticed
 a strange behavior in the itk::ImageFileReader.
when I load a multiframe dicom image with the reader, the output of the reader
has a correct z-spacing. But the x- and y- spacings are always 1.0. I
also could reproduce this using itk 3.20.1.

I also noticed that at lease the orientation is wrong.

a short search led me to this:

http://www.na-mic.org/Bug/view.php?id=725

is this aknow issue in itk? has it been fiyed in later versions?

Thanks,
Zein

From dzenanz at gmail.com  Wed Oct 19 09:29:59 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 19 Oct 2016 09:29:59 -0400
Subject: [ITK] [ITK-users]   Cmake clrsupport c# wrapper for itk
In-Reply-To: <1476870595135-7589372.post@n2.nabble.com>
References: <1476870595135-7589372.post@n2.nabble.com>
Message-ID: <CAPf2UMRP7wfZywKnYGSY5Gk9txz3TafwXuEmvn86FdbHWAAFUg@mail.gmail.com>

Hi Swetha,

this sounds more like a question for CMake mailing list. Can you try
searching if it was already answered or posting it there?

Regards,
D?enan

On Wed, Oct 19, 2016 at 5:49 AM, swetha <swetha.bsharma at gmail.com> wrote:

> Hi,
>
>    I am trying to create a wrapper in c# for c++ code in itk. Because I am
> using ITK i am forced to use cmake to add the relevant header files which i
> would need.
>
> This is the script which i have added
>
> SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "/clr")
>  STRING(REPLACE "/EHsc" "/EHa" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
>  STRING(REPLACE "/RTC1" "" CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
>  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /clr")
>
> The problem I've found, is that while CMake sets the "Common Language
> RunTime Support" option in the C/C++ section of the configuration
> properties
> if "/clr" is in the CXX_FLAGS, it does not set the "Common Language RunTime
> Support" in the general configuration properties, and that causes problems
> with linking/.NET references.
>
> How do i solve this?
> -swetha
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/Cmake-clrsupport-c-wrapper-for-itk-tp7589372.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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_____________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
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From matt.mccormick at kitware.com  Wed Oct 19 09:40:32 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Oct 2016 09:40:32 -0400
Subject: [ITK] Loading multiframe dicom with itk
In-Reply-To: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>
References: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>
Message-ID: <CALzTN-SsLtOdZV6Yz+=i-jDU0_3wxaE8BK0Q7RT6XxycAGLaDQ@mail.gmail.com>

Hi Zein,

There has been fixes for this issue in later versions of ITK via both
ITK's handling of the spacing and the DICOM library used to parse the
files. It is worthwhile to try with a recent version of ITK to see if
the issue has been addressed.

HTH,
Matt

On Wed, Oct 19, 2016 at 6:55 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hi,
>
> to organizational reasons, I must use an old release of itk (3.14).
>
> I am trying to load multiframe dicom images with itk reader. I noticed
>  a strange behavior in the itk::ImageFileReader.
> when I load a multiframe dicom image with the reader, the output of the reader
> has a correct z-spacing. But the x- and y- spacings are always 1.0. I
> also could reproduce this using itk 3.20.1.
>
> I also noticed that at lease the orientation is wrong.
>
> a short search led me to this:
>
> http://www.na-mic.org/Bug/view.php?id=725
>
> is this aknow issue in itk? has it been fiyed in later versions?
>
> Thanks,
> Zein
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From matt.mccormick at kitware.com  Wed Oct 19 09:45:33 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Oct 2016 09:45:33 -0400
Subject: [ITK] [ITK-users]  Cmake clrsupport c# wrapper for itk
In-Reply-To: <CAPf2UMRP7wfZywKnYGSY5Gk9txz3TafwXuEmvn86FdbHWAAFUg@mail.gmail.com>
References: <1476870595135-7589372.post@n2.nabble.com>
 <CAPf2UMRP7wfZywKnYGSY5Gk9txz3TafwXuEmvn86FdbHWAAFUg@mail.gmail.com>
Message-ID: <CALzTN-SG4c8FsSk4TAmj4vd6zGXsOjWDEk55e8Gmx9a37q+Utg@mail.gmail.com>

Hi Swetha,

There is improved C# support in the "csharp" branch of this repository:

  https://github.com/micst/CMake

they are working on upstreaming the improvements. You may want to try
it out and prove feedback on the CMake mailing lists.

HTH,
Matt

On Wed, Oct 19, 2016 at 9:29 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Swetha,
>
> this sounds more like a question for CMake mailing list. Can you try
> searching if it was already answered or posting it there?
>
> Regards,
> D?enan
>
> On Wed, Oct 19, 2016 at 5:49 AM, swetha <swetha.bsharma at gmail.com> wrote:
>>
>> Hi,
>>
>>    I am trying to create a wrapper in c# for c++ code in itk. Because I am
>> using ITK i am forced to use cmake to add the relevant header files which
>> i
>> would need.
>>
>> This is the script which i have added
>>
>> SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "/clr")
>>  STRING(REPLACE "/EHsc" "/EHa" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
>>  STRING(REPLACE "/RTC1" "" CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
>>  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /clr")
>>
>> The problem I've found, is that while CMake sets the "Common Language
>> RunTime Support" option in the C/C++ section of the configuration
>> properties
>> if "/clr" is in the CXX_FLAGS, it does not set the "Common Language
>> RunTime
>> Support" in the general configuration properties, and that causes problems
>> with linking/.NET references.
>>
>> How do i solve this?
>> -swetha
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/Cmake-clrsupport-c-wrapper-for-itk-tp7589372.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From cr at neuro.ma.uni-heidelberg.de  Wed Oct 19 10:35:11 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Wed, 19 Oct 2016 16:35:11 +0200
Subject: [ITK] [ITK-users] Fwd: Re: Documentation:
 itk::AttributeSelectionLabelMapFilter
In-Reply-To: <224c14a0-de28-6c4c-fc8f-6f160b4c7d4d@neuro.ma.uni-heidelberg.de>
References: <224c14a0-de28-6c4c-fc8f-6f160b4c7d4d@neuro.ma.uni-heidelberg.de>
Message-ID: <5817e91f-8551-66fd-45d9-f160a9e70ff9@neuro.ma.uni-heidelberg.de>

And now the copy for the ML

Christina



-------- Forwarded Message --------
Subject: 	Re: [ITK-users] Documentation: 
itk::AttributeSelectionLabelMapFilter
Date: 	Wed, 19 Oct 2016 16:33:44 +0200
From: 	Chr. Rossmanith <cr at neuro.ma.uni-heidelberg.de>
To: 	Matt McCormick <matt.mccormick at kitware.com>



Hi Matt,

login is working now for reviews.source.kitware.com, but authentication
on the command line fails, maybe because I'm behind a firewall. Now I'm
sending the patch to the mailing list as recommended on
https://itk.org/Wiki/ITK/Git/Account#Gerrit

Christina

On 14.10.2016 18:55, Matt McCormick wrote:
> Hi Christina,
>
> Could you please try logging into to review.source.kitware.com again?
>
> Thanks,
> Matt
>
> On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>> When visiting review.source.kitware.com -> sign in -> provide github
>> credentials  I find myself on a page telling me "forbidden". But without a
>> gerrit user I'm stuck...Any hints? I've double checked the credentials by
>> signing in into github.
>>
>> Christina
>>
>>
>> On 14.10.2016 15:00, D?enan Zuki? wrote:
>>
>> Hi Christina,
>>
>> gerrit is the only way to merge patches. Can you submit it as a patch to
>> gerrit?
>>
>> Thanks,
>> D?enan
>>
>> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>> Hi Matt,
>>>
>>> I've forked on github, extended the documentation and created a pull
>>> request. Or is gerrit the only way to get a patch merged?
>>>
>>> Christina
>>>
>>>
>>>
>>> On 12.10.2016 18:03, Matt McCormick wrote:
>>>> Hello Christina,
>>>>
>>>> Good idea.
>>>>
>>>> To update the documentation, the class Doxygen documentation can be
>>>> editted:
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
>>>>
>>>> and after a patch is submitted:
>>>>
>>>>     https://itk.org/Wiki/ITK/Git/Develop
>>>>
>>>> it will show up on the Doxygen web pages.
>>>>
>>>> Please let us know if you have any questions.
>>>>
>>>> Thanks,
>>>> Matt
>>>>
>>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
>>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>> Hi,
>>>>>
>>>>> I think it would be helpful if the documentation of the filter would
>>>>> mention
>>>>> that there are two outputs, one with the surviving labels and the second
>>>>> with the removed labels (the input image is the union of these images).
>>>>> What
>>>>> is the workflow to achieve this?
>>>>>
>>>>> Christina
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>


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From matt.mccormick at kitware.com  Wed Oct 19 10:47:17 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 19 Oct 2016 10:47:17 -0400
Subject: [ITK] [ITK-users] Fwd: Re:
	Documentation:	itk::AttributeSelectionLabelMapFilter
In-Reply-To: <5817e91f-8551-66fd-45d9-f160a9e70ff9@neuro.ma.uni-heidelberg.de>
References: <224c14a0-de28-6c4c-fc8f-6f160b4c7d4d@neuro.ma.uni-heidelberg.de>
 <5817e91f-8551-66fd-45d9-f160a9e70ff9@neuro.ma.uni-heidelberg.de>
Message-ID: <CALzTN-S1DoeAkGo6pgMzu_jthh2jyMZTgqRFOoaWrUg87XGsKw@mail.gmail.com>

Thanks for your persistence and the contribution, Christina!

The patch has been uploaded here:

  http://review.source.kitware.com/#/c/21646/

On Wed, Oct 19, 2016 at 10:35 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> And now the copy for the ML
>
> Christina
>
>
> -------- Forwarded Message --------
> Subject: Re: [ITK-users] Documentation: itk::
> AttributeSelectionLabelMapFilter
> Date: Wed, 19 Oct 2016 16:33:44 +0200
> From: Chr. Rossmanith <cr at neuro.ma.uni-heidelberg.de>
> <cr at neuro.ma.uni-heidelberg.de>
> To: Matt McCormick <matt.mccormick at kitware.com>
> <matt.mccormick at kitware.com>
>
>
> Hi Matt,
>
> login is working now for reviews.source.kitware.com, but authentication
> on the command line fails, maybe because I'm behind a firewall. Now I'm
> sending the patch to the mailing list as recommended on https://itk.org/Wiki/ITK/Git/Account#Gerrit
>
> Christina
>
> On 14.10.2016 18:55, Matt McCormick wrote:
> > Hi Christina,
> >
> > Could you please try logging into to review.source.kitware.com again?
> >
> > Thanks,
> > Matt
> >
> > On Fri, Oct 14, 2016 at 9:21 AM, Chr. Rossmanith
> > <cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >> When visiting review.source.kitware.com -> sign in -> provide github
> >> credentials  I find myself on a page telling me "forbidden". But without a
> >> gerrit user I'm stuck...Any hints? I've double checked the credentials by
> >> signing in into github.
> >>
> >> Christina
> >>
> >>
> >> On 14.10.2016 15:00, D?enan Zuki? wrote:
> >>
> >> Hi Christina,
> >>
> >> gerrit is the only way to merge patches. Can you submit it as a patch to
> >> gerrit?
> >>
> >> Thanks,
> >> D?enan
> >>
> >> On Fri, Oct 14, 2016 at 8:52 AM, Chr. Rossmanith
> >> <cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>> Hi Matt,
> >>>
> >>> I've forked on github, extended the documentation and created a pull
> >>> request. Or is gerrit the only way to get a patch merged?
> >>>
> >>> Christina
> >>>
> >>>
> >>>
> >>> On 12.10.2016 18:03, Matt McCormick wrote:
> >>>> Hello Christina,
> >>>>
> >>>> Good idea.
> >>>>
> >>>> To update the documentation, the class Doxygen documentation can be
> >>>> editted:
> >>>>
> >>>>
> >>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkAttributeSelectionLabelMapFilter.h#L27-L46
> >>>>
> >>>> and after a patch is submitted:
> >>>>
> >>>>     https://itk.org/Wiki/ITK/Git/Develop
> >>>>
> >>>> it will show up on the Doxygen web pages.
> >>>>
> >>>> Please let us know if you have any questions.
> >>>>
> >>>> Thanks,
> >>>> Matt
> >>>>
> >>>> On Wed, Oct 12, 2016 at 11:57 AM, Chr. Rossmanith
> >>>> <cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> I think it would be helpful if the documentation of the filter would
> >>>>> mention
> >>>>> that there are two outputs, one with the surviving labels and the second
> >>>>> with the removed labels (the input image is the union of these images).
> >>>>> What
> >>>>> is the workflow to achieve this?
> >>>>>
> >>>>> Christina
> >>>>>
> >>>>> _____________________________________
> >>>>> Powered by www.kitware.com
> >>>>>
> >>>>> Visit other Kitware open-source projects at
> >>>>> http://www.kitware.com/opensource/opensource.html
> >>>>>
> >>>>> Kitware offers ITK Training Courses, for more information visit:
> >>>>> http://www.kitware.com/products/protraining.php
> >>>>>
> >>>>> Please keep messages on-topic and check the ITK FAQ at:
> >>>>> http://www.itk.org/Wiki/ITK_FAQ
> >>>>>
> >>>>> Follow this link to subscribe/unsubscribe:
> >>>>> http://public.kitware.com/mailman/listinfo/insight-users
> >>>
> >>>
> >>> _____________________________________
> >>> Powered by www.kitware.com
> >>>
> >>> Visit other Kitware open-source projects at
> >>> http://www.kitware.com/opensource/opensource.html
> >>>
> >>> Kitware offers ITK Training Courses, for more information visit:
> >>> http://www.kitware.com/products/protraining.php
> >>>
> >>> Please keep messages on-topic and check the ITK FAQ at:
> >>> http://www.itk.org/Wiki/ITK_FAQ
> >>>
> >>> Follow this link to subscribe/unsubscribe:
> >>> http://public.kitware.com/mailman/listinfo/insight-users
> >>
> >>
> >>
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
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>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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From CAOwens at mdanderson.org  Wed Oct 19 11:07:40 2016
From: CAOwens at mdanderson.org (Owens,Constance A)
Date: Wed, 19 Oct 2016 15:07:40 +0000
Subject: [ITK] [ITK-users] Lesion Sizing Toolkit (Visualization errors)
Message-ID: <603A32F9BAA25B4FBF30F3ADF057B0872C75E5B9@DCPWPEXMBX01.mdanderson.edu>

Hi,

I am using ITKv4.11.0, VTKv7.0.0 with CMAKE 3.6.1.

I am trying to use LSTK (Lesion Sizing Toolkit).

I am using Windows. After typing in Command Prompt (as per this link's instructions https://public.kitware.com/LesionSizingKit/index.php/Users/Run_LesionSegmentation )


LesionSegmentation.exe -InputDICOMDir ./54478 -OutputImage ./outputTumorImage.mha -Seeds 3 23.35 115.93 -73.8 -MaximumRadius 20 -OutputROI ./outputROI.mhd -OutputMesh ./output.stl -Visualize 1 -Screenshot ./screenShotTumor


LesionSegmentation.exe is inside the directory: C:\ITKv4.11.0\bin-x64\bin\Debug
I placed the series of DICOM images inside the directory: C:\ITKv4.11.0\bin-x64\bin\Debug\54478


Inside the vtkOutputWindow I get several errors saying 'no override found for 'vtkRenderer'... etc (I put a printscreen below)

[cid:image002.png at 01D229F0.9BCB7DA0]

And another screen pops up to tell me that there is an APPCRASH:

Problem signature:
  Problem Event Name:                        APPCRASH
  Application Name:                             LesionSegmentation.exe
  Application Version:                           0.0.0.0
  Application Timestamp:                     58068b71
  Fault Module Name:                          LesionSegmentation.exe
  Fault Module Version:                        0.0.0.0
  Fault Module Timestamp:                  58068b71
  Exception Code:                                  c0000005
  Exception Offset:                                00000000008f2118
  OS Version:                                          6.1.7601.2.1.0.256.4
  Locale ID:                                             1033
  Additional Information 1:                  45a3
  Additional Information 2:                  45a37769920ca79c15f1c3d86dd9b3c1
  Additional Information 3:                  aa5b
  Additional Information 4:                  aa5b3031c12edfd5a504d3d326ceefa3



I was hoping someone could point me in the right direction in order to resolve this issue. Additionally, I noticed that there is a Visualization.sln file inside (C:\ITKv4.11.0\bin-x64\Modules\Remote\LesionSizingToolkit\Utilities\Visualization) and was wondering if this could be part of the issue, as I have not built it yet.

On the website, there was no mention to build this for the lesion segmentation to work. I followed directions given by video here: https://www.youtube.com/watch?v=dFtipGL6SEs


Thanks,
Constance Owens
Graduate Research Assistant

The University of Texas Graduate School of Biomedical Sciences at Houston
Medical Physics
CAOwens at mdanderson.org<https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
tel 713-745-3679 | cel 281-770-5210

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
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From ivan.granata.na at gmail.com  Thu Oct 20 04:20:08 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 20 Oct 2016 01:20:08 -0700 (MST)
Subject: [ITK] [ITK-users] SimpleITK for Java Image Fusion and
	Co-registration?
In-Reply-To: <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
References: <1475646613139-37633.post@n7.nabble.com>
 <B7E0F6D3-8059-4867-834B-0929E2270D5F@mail.nih.gov>
 <1475668290769-37635.post@n7.nabble.com>
 <806D954D-F7B4-4B85-AD83-0F5DFC93BDBD@mail.nih.gov>
 <1475670869976-37640.post@n7.nabble.com>
 <CAPf2UMSddTYKvTD-5ebG=YRLoGT4VF=uAHE=+Ux2=w24EvYdBw@mail.gmail.com>
 <1475760771636-37649.post@n7.nabble.com>
 <CAPf2UMT1KECqcs6PTSeUvpFN2kJm1A8t2khV3JGkFtMWYozang@mail.gmail.com>
 <1475772061671-37651.post@n7.nabble.com>
 <CAPf2UMQ+h5SPdZbEv85j1SasNakDLeQgx4C7oBpqK1F01JXQgg@mail.gmail.com>
Message-ID: <1476951608524-37682.post@n7.nabble.com>

i solved for TranslationTransofrm in Java

but now i would to try a deformable transform (Java)


with simple itk i've found these class but i don't now how to convert in
java

BSplineTransform	2D or 3D, deformable transformation represented by a sparse
regular grid of control points.
DisplacementFieldTransform	2D or 3D, deformable transformation represented
as a dense regular grid of vectors.

anyone can help me?

thx



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-for-Java-Image-Fusion-and-Co-registration-tp37600p37682.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From ivan.granata.na at gmail.com  Thu Oct 20 04:23:12 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 20 Oct 2016 01:23:12 -0700 (MST)
Subject: [ITK] [ITK-users] Deformable Transformation for Coregistration
 Simple ITK JAVA code
Message-ID: <1476951792366-37683.post@n7.nabble.com>

i solved for TranslationTransofrm in Java with this
http://review.source.kitware.com/#/c/21596/1/Examples/Java/ImageRegistrationMethod1.java
and some change in source code to obtain final image

but now i would to try a deformable transform (Java)


with simple itk i've found these class but i don't now how to convert in
java

BSplineTransform	2D or 3D, deformable transformation represented by a sparse
regular grid of control points.
DisplacementFieldTransform	2D or 3D, deformable transformation represented
as a dense regular grid of vectors.

anyone can help me?

thx



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Deformable-Transformation-for-Coregistration-Simple-ITK-JAVA-code-tp37683.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From blowekamp at mail.nih.gov  Thu Oct 20 08:56:12 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 20 Oct 2016 12:56:12 +0000
Subject: [ITK] [ITK-users] Deformable Transformation for Coregistration
 Simple ITK JAVA code
In-Reply-To: <1476951792366-37683.post@n7.nabble.com>
References: <1476951792366-37683.post@n7.nabble.com>
Message-ID: <8DC4E43E-8021-4807-8463-5AE5C2BCDB2F@mail.nih.gov>

Ivan,

Have you found the python examples:

https://github.com/SimpleITK/SimpleITK/blob/522e60bb293a2581b8a56912658aff824b7e6c1c/Examples/Python/ImageRegistrationMethodBSpline1.py

https://github.com/SimpleITK/SimpleITK/blob/522e60bb293a2581b8a56912658aff824b7e6c1c/Examples/Python/ImageRegistrationMethodDisplacement1.py

Hopefully you have figured out the SimpleITK Java interface a little more so that you can translate this python code into the Java.

Also keep in mind that these deformable registration is are generally for finer grain registration after gross transform initialization and affine registration has been done. The latter displacement example show how this is done with a composite transform. You will need to consult the ITK Software Guide [1] for more information about ITK registration framework. As well as being familiar with the theory [2].

HTH,
Brad


[1] https://itk.org/ITK/help/documentation.html 
[2] http://journal.frontiersin.org/article/10.3389/fninf.2014.00044/full



> On Oct 20, 2016, at 4:23 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> i solved for TranslationTransofrm in Java with this
> http://review.source.kitware.com/#/c/21596/1/Examples/Java/ImageRegistrationMethod1.java
> and some change in source code to obtain final image
> 
> but now i would to try a deformable transform (Java)
> 
> 
> with simple itk i've found these class but i don't now how to convert in
> java
> 
> BSplineTransform	2D or 3D, deformable transformation represented by a sparse
> regular grid of control points.
> DisplacementFieldTransform	2D or 3D, deformable transformation represented
> as a dense regular grid of vectors.
> 
> anyone can help me?
> 
> thx
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Deformable-Transformation-for-Coregistration-Simple-ITK-JAVA-code-tp37683.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
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From ivan.granata.na at gmail.com  Thu Oct 20 07:51:55 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Thu, 20 Oct 2016 04:51:55 -0700 (MST)
Subject: [ITK] [ITK-users] Deformable Transformation for Coregistration
 Simple ITK JAVA code
In-Reply-To: <8DC4E43E-8021-4807-8463-5AE5C2BCDB2F@mail.nih.gov>
References: <1476951792366-37683.post@n7.nabble.com>
 <8DC4E43E-8021-4807-8463-5AE5C2BCDB2F@mail.nih.gov>
Message-ID: <1476964315973-37685.post@n7.nabble.com>

i try with this code

Affine and After BSpline

but after 190 iterations return error code

-------
itk::simple::Transform
 AffineTransform (000000001966EA60)
   RTTI typeinfo:   class itk::AffineTransform<double,3>
   Reference Count: 3
   Modified Time: 3451
   Debug: Off
   Object Name: 
   Observers: 
     none
   Matrix: 
     -0.0283494 0.437495 -0.558782 
     -0.215329 2.14011 2.01216 
     0.661568 -8.35499 1.81576 
   Offset: [0.0377555, -0.0313043, -0.251059]
   Center: [0, 0, 0]
   Translation: [0.0377555, -0.0313043, -0.251059]
   Inverse: 
     -435.991 -81.6103 -43.7342 
     -36.2773 -6.70277 -3.73619 
     -8.07294 -1.10745 -0.706396 
   Singular: 0

Optimizer stop condition: RegularStepGradientDescentOptimizerv4: Maximum
number of iterations (200) exceeded.
 Iteration: 200
 Metric value: -0,176593
Exception in thread "main" java.lang.RuntimeException: Exception thrown in
SimpleITK new_BSplineTransform:
..\..\..\..\..\SimpleITK\Code\Common\src\sitkBSplineTransform.cxx:188:
sitk::ERROR: Transform is not of type BSplineTransform!
	at org.itk.simple.SimpleITKJNI.new_BSplineTransform__SWIG_3(Native Method)
	at org.itk.simple.BSplineTransform.<init>(BSplineTransform.java:75)
	at ImageRegistrationMethodNaplab.main(IterationUpdate.java:68)


this is my code



import org.itk.simple.*;
class IterationUpdate  extends Command {
  private ImageRegistrationMethod m_Method;
  public IterationUpdate(ImageRegistrationMethod m) {
    super();
    m_Method=m;
  }
  
  public void execute() {
    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
    System.out.format("%3d = %10.5f : [%f, %f]\n",
                      m_Method.getOptimizerIteration(),
                      m_Method.getMetricValue(),
                      pos.get(0), pos.get(1));
  }
}

class ImageRegistrationMethodNaplab {
  public static void main(String argv[]) {
  if ( argv.length < 3 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }
  
  

  int   ImageDimension = 3;
  char   PixelType;

  
  
  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
  reader.setFileName(argv[0]);
  Image fixed  = reader.execute();
  reader.setFileName(argv[1]);
  Image moving = reader.execute();
  
  
  
  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
  R.setMetricAsMattesMutualInformation();
  double maxStep = 4.0;
  double minStep = 0.01;
  int numberOfIterations = 200;
  double relaxationFactor = 0.5;
  R.setOptimizerAsRegularStepGradientDescent( maxStep,
                                              minStep,
                                              numberOfIterations,
                                              relaxationFactor );
  R.setInitialTransform( new org.itk.simple.AffineTransform(
fixed.getDimension() ) );
  R.setInterpolator( InterpolatorEnum.sitkBSpline );
  IterationUpdate cmd = new IterationUpdate(R);
  R.addCommand( EventEnum.sitkIterationEvent, cmd);
  
  
  org.itk.simple.Transform outTx = R.execute( fixed, moving );
  System.out.println("-------");
  System.out.println(outTx.toString());
  
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());

  outTx.writeTransform(argv[2]);
  
  org.itk.simple.BSplineTransform R2 = new 
org.itk.simple.BSplineTransform(outTx);
    
  
  
  
  fixed.getSpacing();
  fixed.getOrigin();
  //fixed.getLargestPossibleRegion();
  fixed.getDirection();
   

 int SplineOrder = 3;
  long SpaceDimension = ImageDimension;
 double CoordinateRepType;
  
  
 
 //org.itk.simple.Transform R = new 
org.itk.simple.BSplineTransform(SpaceDimension,SplineOrder);
 
 

 
  
  //org.itk.simple.BSplineTransformInitializerFilter R = new 
org.itk.simple.BSplineTransformInitializerFilter();
  //R.getTransformDomainMeshSize();
  //R.getOrder();
  
 
  //org.itk.simple.Transform outTx = R.execute(moving);
  
  //org.itk.simple.BSplineTransform R2 = new 
org.itk.simple.BSplineTransform(outTx);
  //R2.getDomainOrigin();
  
 
  
  
  
 // IterationUpdate cmd = new IterationUpdate(R);
 // R.addCommand( EventEnum.sitkIterationEvent, cmd);
  

  
  
  

  //getDimension Return the dimension of the Transform ( 2D or 3D )
 // R.setInitialTransform( new
org.itk.simple.BSplineTransform(SplineOrder,SpaceDimension ) );
 //R.getDomainDirection();
 
  //fixed.getDimension()
  
    
  
  System.out.println("-------");
  System.out.println(outTx.toString());
  //System.out.format(" Fixed Initial Transform: %d\n",
R.getFixedInitialTransform());
  //System.out.format(" Moving Initial Transform: %d\n",
R.getMovingInitialTransform());
  //System.out.format(" Initial Transform: %d\n", R.getInitialTransform());
  //System.out.format(" Optimizer Position: %d\n",
R.getOptimizerPosition());
               //System.out.format("Optimizer stop condition: %s\n",
R2.getOptimizerStopConditionDescription());
              //System.out.format(" Iteration: %d\n",
R2.getOptimizerIteration());
                        //System.out.format(" Metric value: %f\n",
R2.getMetricValue());
  //System.out.format(" Interpolator: %f\n", R.getInterpolator());
  //System.out.format(" Translation X", R.getTranslationAlongX());
 // System.out.format(" Translation Y", R.getTranslationAlongY());
  R2.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
   //org.itk.simple.Transform.writeTransform(argv[4]);
  //org.itk.simple.ResampleImageFilter image = new
org.itk.simple.ResampleImageFilter();
  //image.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
 // image.getOutputPixelType(); 
 // image.getSize ();
  //ImageFileWriter writer = new ImageFileWriter();
 // writer.setFileName(argv[5]);
    org.itk.simple.Transform transform = new org.itk.simple.Transform();
  reader.setFileName(argv[2]);
  // Write result image
  ImageFileWriter writer2 = new org.itk.simple.ImageFileWriter();
  writer2.setFileName(argv[3]);
  
  
  
  org.itk.simple.ResampleImageFilter transf = new 
org.itk.simple.ResampleImageFilter();
    transf.setReferenceImage(fixed);
  transf.setTransform(outTx);
  transf.setOutputPixelType(PixelIDValueEnum.sitkUInt32);
  //InterpolatorEnum interp = 
		  transf.getInterpolator();
  //transf.setInterpolator(interp);
//  VectorDouble orig = 
		  transf.getOutputOrigin();
  //VectorDouble spac = 
		  transf.getOutputSpacing();
 // VectorDouble dir = 
		  transf.getOutputDirection();
  //Double pix = 
		  transf.getDefaultPixelValue();
  //transf.setInterpolator(dir);
  //VectorUInt32 pts = new VectorUInt32();
  transf.getSize();
  transf.execute(moving);
   Image blurredImg = transf.execute(moving);
    //Image castImg = caster.execute(blurredImg);
    ImageFileWriter writer3 = new ImageFileWriter();
    writer3.setFileName(argv[3]);
     writer3.execute(blurredImg);
     //writer.execute(transform.getResultImage()); 
     // transform.setParameters(reader.execute());
      //Image transform = reader.execute();
  //Transform.setParameters();
    // Perform warp
//  transform.logToConsoleOn();
 // transform.execute();
    }  
}




--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Deformable-Transformation-for-Coregistration-Simple-ITK-JAVA-code-tp37683p37685.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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From matt.mccormick at kitware.com  Thu Oct 20 10:23:19 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 20 Oct 2016 10:23:19 -0400
Subject: [ITK] [ITK-users] [vtkusers] Testing ITK/VTK/PV contributions
	with	(kitware) Gitlab-CI
In-Reply-To: <CAPf2UMQOckvhyn0fd_XmYPgfh=kU+uj60JONT5gFH-0qnxx6eg@mail.gmail.com>
References: <b559f993-9283-7f14-b7ad-66eb85c5d52a@mh-hannover.de>
 <20160908131417.GB13993@megas.kitware.com>
 <CAPf2UMRfLtz1Cd_kYy0uX3V3nA96F2BqGuNGn=zY6_wg_5mkEw@mail.gmail.com>
 <ddc193b4-0cc5-7cb5-4cd6-47c2409435ba@mh-hannover.de>
 <CAPf2UMQOckvhyn0fd_XmYPgfh=kU+uj60JONT5gFH-0qnxx6eg@mail.gmail.com>
Message-ID: <CALzTN-RbcRnPc0k9ppbLxza2dj7EgPFwQ2oGC0SdPo_dafVKNQ@mail.gmail.com>

Hi,

Yes, the Insight and Midas journals testing infrastructure is no
longer functional.

Matt

On Mon, Sep 12, 2016 at 9:10 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Roman,
>
> I don't think that Insight and Midas journals' testing infrastructure is
> functional any more. Perhaps Matt can provide more info?
>
> Regards,
> D?enan
>
> On Mon, Sep 12, 2016 at 5:49 AM, Grothausmann, Roman Dr.
> <grothausmann.roman at mh-hannover.de> wrote:
>>
>> Many thanks Ben and D?enan for Your replies and pointing me to CircleCI. I
>> see that testing contributions employing PV,VTK and ITK all together is
>> rather challenging.
>>
>> I wonder though why my pure VTK (PV) based contribution did not get tested
>> when submitted to the VTK-Journal, e.g.
>> http://www.midasjournal.org/browse/publication/949
>>
>> Is the testing the VTK/Midas Journals used to do not available any more?
>>
>> Regards,
>> Roman
>>
>> On 08/09/16 16:26, D?enan Zuki? wrote:
>>>
>>> Hi Roman,
>>>
>>> some of ITK's remote modules are using CircleCI for testing. Two recent
>>> examples
>>> are RLEImage <https://github.com/KitwareMedical/ITKRLEImage> and
>>> MorphologicalContourInterpolation
>>> <https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation>.
>>> Of
>>> course, you should be familiar, or familiarize yourself with CircleCI
>>> <https://circleci.com/docs/configuration/>.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Thu, Sep 8, 2016 at 9:14 AM, Ben Boeckel <ben.boeckel at kitware.com
>>> <mailto:ben.boeckel at kitware.com>> wrote:
>>>
>>>     On Thu, Sep 08, 2016 at 12:36:40 +0200, Grothausmann, Roman Dr.
>>> wrote:
>>>     > Just getting to know Gitlab-CI, I am wondering whether it is
>>> possible to test
>>>     > contributions to ITK/VTK/PV with Gitlab-CI from gitlab.com
>>> <http://gitlab.com> or
>>>     > gitlab.kitware.com <http://gitlab.kitware.com>. As far as I
>>> understand, this
>>>     basically needs runners, in
>>>     > this case specific to ITK/VTK/PV. Since kitware has done CI even
>>> before the use
>>>     > of gitlab, I wonder if the former testing environments are
>>> available for use
>>>     > with Gitlab-CI and if so how to use them.
>>>
>>>     We're (VTK and ParaView) using buildbot to manage our testing. The
>>>     number of settings we test across machines is hard to specify in YAML
>>>     files (machines also have different settings based on what you're
>>>     testing, e.g., load up a different compiler or Qt4 or Qt5 and the
>>> paths
>>>     they live in, etc.). We're working on improving the hardware
>>> situation
>>>     buildbot is currently in; things should be getting better over the
>>> next
>>>     few months on that front.
>>>
>>>     > For example, none of my contributions to the ITK/VTK/Midas Journals
>>> got into the
>>>     > testing phase even though marked for testing during submission. So
>>> a possibility
>>>     > to use Gitlab-CI to test the compilation and to run the project
>>> test would be
>>>     > really great, especially for continued development and testing on
>>> other OSs.
>>>     > Specifically, for e.g. testing my FacetAnalyser contribution
>>>     > (http://www.midasjournal.org/browse/publication/951
>>>     <http://www.midasjournal.org/browse/publication/951>
>>>     > https://gitlab.com/romangrothausmann/FacetAnalyser
>>>     <https://gitlab.com/romangrothausmann/FacetAnalyser>) I would need a
>>> runner
>>>     > environment with PV, VTK and ITK ideally for Linux, MacOS and
>>> Windows.
>>>
>>>     ITK is using Gerrit and Jenkins, not Gitlab.
>>>
>>>     --Ben
>>>     _______________________________________________
>>>     Powered by www.kitware.com <http://www.kitware.com>
>>>
>>>     Visit other Kitware open-source projects at
>>>     http://www.kitware.com/opensource/opensource.html
>>>     <http://www.kitware.com/opensource/opensource.html>
>>>
>>>     Please keep messages on-topic and check the VTK FAQ at:
>>>     http://www.vtk.org/Wiki/VTK_FAQ <http://www.vtk.org/Wiki/VTK_FAQ>
>>>
>>>     Search the list archives at: http://markmail.org/search/?q=vtkusers
>>>     <http://markmail.org/search/?q=vtkusers>
>>>
>>>     Follow this link to subscribe/unsubscribe:
>>>     http://public.kitware.com/mailman/listinfo/vtkusers
>>>     <http://public.kitware.com/mailman/listinfo/vtkusers>
>>>
>>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-2900
>
>
_____________________________________
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From zeinsalah at gmail.com  Fri Oct 21 08:30:04 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Fri, 21 Oct 2016 14:30:04 +0200
Subject: [ITK] Loading multiframe dicom with itk
In-Reply-To: <CALzTN-SsLtOdZV6Yz+=i-jDU0_3wxaE8BK0Q7RT6XxycAGLaDQ@mail.gmail.com>
References: <CADiSopMytGwNQ1nf0oU+PREE0ojfL+jHEdyQRzsLjB-x_arxJg@mail.gmail.com>
 <CALzTN-SsLtOdZV6Yz+=i-jDU0_3wxaE8BK0Q7RT6XxycAGLaDQ@mail.gmail.com>
Message-ID: <CADiSopPqqVe1kpF3FqUZdWgjfwQJKfg1U_MN_qN1edUNFuUb-g@mail.gmail.com>

Hi Matt,

thanks for the response!

I tested with itk 4.10 and have the following remarks/questions:

1. First, the behavior is different from itk 3.14 and 3.20, but I
think the reader still has bugs.

2. for some data sets, I got a negative z spacing, what does this mean?

3. I have a multiframe-dicom in which the image patient positions
(0020,0032) are stored
individually for each frame under the PerFrame Functional Group
Sequence. Are these positions
taken into account when reconstructing the 3D volume from the block of
data is read?
I am asking because the positions of the slices are going in the
negative z-direction,
which means that the slices are stored in the oopsite order, i.e., the
farthest slice in z
is stored first. Does the reader respect this?

thanks,
Zein



2016-10-19 15:40 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
> Hi Zein,
>
> There has been fixes for this issue in later versions of ITK via both
> ITK's handling of the spacing and the DICOM library used to parse the
> files. It is worthwhile to try with a recent version of ITK to see if
> the issue has been addressed.
>
> HTH,
> Matt
>
> On Wed, Oct 19, 2016 at 6:55 AM, Zein Salah <zeinsalah at gmail.com> wrote:
>> Hi,
>>
>> to organizational reasons, I must use an old release of itk (3.14).
>>
>> I am trying to load multiframe dicom images with itk reader. I noticed
>>  a strange behavior in the itk::ImageFileReader.
>> when I load a multiframe dicom image with the reader, the output of the reader
>> has a correct z-spacing. But the x- and y- spacings are always 1.0. I
>> also could reproduce this using itk 3.20.1.
>>
>> I also noticed that at lease the orientation is wrong.
>>
>> a short search led me to this:
>>
>> http://www.na-mic.org/Bug/view.php?id=725
>>
>> is this aknow issue in itk? has it been fiyed in later versions?
>>
>> Thanks,
>> Zein
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community

From seun at rogue-research.com  Fri Oct 21 08:50:11 2016
From: seun at rogue-research.com (Seun Odutola)
Date: Fri, 21 Oct 2016 08:50:11 -0400
Subject: [ITK] [ITK-dev] H5pubconf.h missing during installation (ITK master)
Message-ID: <A215321D-686B-495A-ACC1-161A9C6DC9CA@rogue-research.com>

Hello everyone,

   I recently tried to update my ITK to the latest on master and stumbled upon an error during installation - ?H5pubconf.h file not found?. The file H5pubconf.h is being included in H5public.h found in "include/ITK-4.11/itkhdf5/", although H5pubconf.h is present in the "/Modules/ThirdParty/HDF5/src/itkhdf5/? it's somehow missing during installation so I decided to copy H5pubconf.h over to the directory ?itkhdf5? where H5public.h was situated and on building my project it worked. I just thought I mention this and hopefully it gets fixed as it seems to be an installation bug.

Regards,
   Seun
_______________________________________________
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From seun at rogue-research.com  Fri Oct 21 09:24:54 2016
From: seun at rogue-research.com (Seun Odutola)
Date: Fri, 21 Oct 2016 09:24:54 -0400
Subject: [ITK] [ITK-dev] Naming inconsistency in ITK HDF5 lib in Debug and
	Release
Message-ID: <788B9F09-C262-4128-B711-6F6483C5A3BE@rogue-research.com>

Hello,

   I'm currently trying out the latest on ITK master and on successfully building/ installing and compiling my project (see my other post on "H5pubconf.h missing during installation (ITK master)?) all seems to work but only after a slight tweak. The tweak was necessary because I realised that the generated lib for hdf5 in both debug and release mode were named differently compared to the other libs. In Debug, all libs are named accordingly libITK... or libitk? ending with .a except that of libitkhdf5_cpp_debug.a & libitkhdf5_debug.a, whereas in Release it?s not the case as they are named libitkhdf5_cpp.a & libitkhdf5.a. It?s worth mentioning that the latter was how the libs were named prior to me updating my ITK to 4.11 (on master) which made linking against these libs easier in my case as I had only to provide the names in my configuration file without having to distinguish between debug or release. In a nutshell, why is this the case with HDF5, is this another one of ITK installation bugs or is this deliberate for some reason if so can someone explain why, thanks.

Regards,
  Seun
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From matt.mccormick at kitware.com  Fri Oct 21 10:57:35 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 21 Oct 2016 10:57:35 -0400
Subject: [ITK] LINK PROBLEM
In-Reply-To: <DM5PR05MB3131AC1AA9EBE14C3658CF55A0DF0@DM5PR05MB3131.namprd05.prod.outlook.com>
References: <DM5PR05MB31317796785711468EFFC745A0DC0@DM5PR05MB3131.namprd05.prod.outlook.com>
 <CALzTN-Q8cGSUEspVQF-7RnSvSkmtk8Ohkrbo0ay8ddp_MZ-TjQ@mail.gmail.com>
 <DM5PR05MB3131AC1AA9EBE14C3658CF55A0DF0@DM5PR05MB3131.namprd05.prod.outlook.com>
Message-ID: <CALzTN-S1-HQxKaDgxwE6gECu7Lyn6r5wQmC6O2uHryGTJCgh7g@mail.gmail.com>

Hi Anna,

I tried to reproduce your build error with

- VS2015, a 32bit Release build
- ITK 4.10.1
- The source and build path that you used.
- 32-bit CPython 3.5

but the build succeeded without any errors. Maybe your source code
download is corrupted? Or, there is some other factor we are missing.

HTH,
Matt

On Fri, Oct 14, 2016 at 3:44 AM, Anna Vlachomitrou
<avlachomitrou at dxo.com> wrote:
> Hi Matt,
> Thanks for replying.
> All the errors are related to external> symbol "double __cdecl vnl_math::_hypot(double,double)"
> I have several projects that don't build. All of them have the same error. You want a full log?
>
> Best,
> Anna
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: jeudi 13 octobre 2016 18:07
> To: Anna Vlachomitrou <avlachomitrou at dxo.com>
> Cc: community at itk.org
> Subject: Re: [ITK] LINK PROBLEM
>
> Hi Anna,
>
> Are there any other errors reported in your build?
>
> Thanks,
> Matt
>
> On Thu, Oct 13, 2016 at 3:24 AM, Anna Vlachomitrou <avlachomitrou at dxo.com> wrote:
>> Dear ITK community,
>>
>>  I am currently trying to build ITK so as to use some prebuilded libs
>> in Python.
>>
>> -I downloaded the 4.10 version
>>
>> - I used cmake to get the itk.sln for vs2010 32b (and also tried
>> vs2015 32b)
>>
>> - I launch the ALLBUILD
>>
>> -I get some errors: all errors are related to _hypot. Here is an example:
>>
>> 450>     Creating library
>> D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPyth
>> on.lib
>> and object
>> D:/DATA/InsightToolkit-4.10.1/build/lib/Release/ITKImageStatisticsPyth
>> on.exp
>>
>> 450>itkImageMomentsCalculatorPython.obj : error LNK2019: unresolved
>> 450>external
>> symbol "double __cdecl vnl_math::_hypot(double,double)"
>> (?_hypot at vnl_math@@YANNN at Z) referenced in function "double __cdecl
>> itk::Math::_hypot<double>(double,double)"
>> (??$_hypot at N@Math at itk@@YANNN at Z)
>>
>> 450>D:\DATA\InsightToolkit-4.10.1\build\lib\Release\_ITKImageStatistic
>> 450>sPython.pyd
>> : fatal error LNK1120: 1 unresolved externals
>>
>> 450>
>>
>>
>>
>> Do you have any idea of how i can fix these build errors ?
>>
>>  Thanks in advance,
>>
>> Anna
>>
>>
>>
>>
>> ----------------------------------------------------------------------
>> -------- This message and any attachments (the "message") are
>> confidential and intended solely for the addressee(s). Any
>> unauthorized use or dissemination is prohibited. E-mails are
>> susceptible to alteration. Neither DxO Labs nor any of its
>> subsidiaries or affiliates shall be liable for the message if altered,
>> changed or falsified.
>> Ce message et toutes les pi?ces jointes (ci-apr?s le "message") sont
>> confidentiels et ?tablis ? l'intention exclusive de ses destinataires.
>> Toute utilisation ou diffusion non autoris?e est interdite. Tout
>> message ?lectronique est susceptible d'alt?ration. DxO Labs et ses
>> filiales d?clinent toute responsabilit? au titre de ce message s'il a
>> ?t? alt?r?, modifi? ou falsifi?.
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>
> ------------------------------------------------------------------------------
> This message and any attachments (the "message") are confidential and intended solely for the addressee(s). Any unauthorized use or dissemination is prohibited. E-mails are susceptible to alteration. Neither DxO Labs nor any of its subsidiaries or affiliates shall be liable for the message if altered, changed or falsified.
> Ce message et toutes les pi?ces jointes (ci-apr?s le "message") sont confidentiels et ?tablis ? l'intention exclusive de ses destinataires. Toute utilisation ou diffusion non autoris?e est interdite. Tout message ?lectronique est susceptible d'alt?ration. DxO Labs et ses filiales d?clinent toute responsabilit? au titre de ce message s'il a ?t? alt?r?, modifi? ou falsifi?.

From matt.mccormick at kitware.com  Fri Oct 21 16:25:33 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 21 Oct 2016 16:25:33 -0400
Subject: [ITK] [ITK-dev] H5pubconf.h missing during installation (ITK
	master)
In-Reply-To: <A215321D-686B-495A-ACC1-161A9C6DC9CA@rogue-research.com>
References: <A215321D-686B-495A-ACC1-161A9C6DC9CA@rogue-research.com>
Message-ID: <CALzTN-TxiNZ8JfmWm7-69Xp8cD1J-RnbZr2exy9NaXxWLKY+fQ@mail.gmail.com>

Hi Sean,

Thanks for reporting the issue.  Please review this patch:

  http://review.source.kitware.com/#/c/21651/

Thanks,
Matt

On Fri, Oct 21, 2016 at 8:50 AM, Seun Odutola <seun at rogue-research.com> wrote:
> Hello everyone,
>
>    I recently tried to update my ITK to the latest on master and stumbled upon an error during installation - ?H5pubconf.h file not found?. The file H5pubconf.h is being included in H5public.h found in "include/ITK-4.11/itkhdf5/", although H5pubconf.h is present in the "/Modules/ThirdParty/HDF5/src/itkhdf5/? it's somehow missing during installation so I decided to copy H5pubconf.h over to the directory ?itkhdf5? where H5public.h was situated and on building my project it worked. I just thought I mention this and hopefully it gets fixed as it seems to be an installation bug.
>
> Regards,
>    Seun
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
_______________________________________________
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Please keep messages on-topic and check the ITK FAQ at:
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From matt.mccormick at kitware.com  Fri Oct 21 16:27:31 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 21 Oct 2016 16:27:31 -0400
Subject: [ITK] [ITK-dev] Naming inconsistency in ITK HDF5 lib in Debug
	and	Release
In-Reply-To: <788B9F09-C262-4128-B711-6F6483C5A3BE@rogue-research.com>
References: <788B9F09-C262-4128-B711-6F6483C5A3BE@rogue-research.com>
Message-ID: <CALzTN-Top7WKnWf_rEX9jgKwXdHTp=YCfkFZwz4eDczbd-5QRA@mail.gmail.com>

Hi Seun,

In ITK 4.11 (master), we upgraded the internal version of HDF5 to
1.8.17, and the library name change was something that was done in
upstream HDF5.

HTH,
Matt

On Fri, Oct 21, 2016 at 9:24 AM, Seun Odutola <seun at rogue-research.com> wrote:
> Hello,
>
>    I'm currently trying out the latest on ITK master and on successfully
> building/ installing and compiling my project (see my other post on
> "H5pubconf.h missing during installation (ITK master)?) all seems to work
> but only after a slight tweak. The tweak was necessary because I realised
> that the generated lib for hdf5 in both debug and release mode were named
> differently compared to the other libs. In Debug, all libs are named
> accordingly libITK... or libitk? ending with .a except that of
> libitkhdf5_cpp_debug.a & libitkhdf5_debug.a, whereas in Release it?s not the
> case as they are named libitkhdf5_cpp.a & libitkhdf5.a. It?s worth
> mentioning that the latter was how the libs were named prior to me updating
> my ITK to 4.11 (on master) which made linking against these libs easier in
> my case as I had only to provide the names in my configuration file without
> having to distinguish between debug or release. In a nutshell, why is this
> the case with HDF5, is this another one of ITK installation bugs or is this
> deliberate for some reason if so can someone explain why, thanks.
>
> Regards,
>   Seun
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
_______________________________________________
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From bnagaev at gmail.com  Sun Oct 23 17:09:29 2016
From: bnagaev at gmail.com (Nagaev Boris)
Date: Mon, 24 Oct 2016 00:09:29 +0300
Subject: [ITK] [ITK-users] mingw,
	gcc5: "too many sections" and "undefined reference to vtable" errors
Message-ID: <CAFC_Vt6KrHP4uOjRZUpb05dgz3mzKdb0iDFGc5DTZ0yGUp6KoA@mail.gmail.com>

Hello,

I need help building ITK 4.8.0. I cross-compile on gcc 5.3.0 from
Linux to Windows using MinGW-w64. Everything was Ok on gcc 4.9.4.

I get the same errors as in this tread:
https://cmake.org/pipermail/insight-users/2015-September/052511.html
My log: https://git.io/vPNmf

I added -Wa,-mbig-obj flags and the same error:
https://cmake.org/pipermail/insight-users/2015-September/052512.html
My log: https://git.io/vPNqh
I added the flags by adding the following to cmake command:
-DCMAKE_C_FLAGS='-Wa,-mbig-obj'
-DCMAKE_CXX_FLAGS='-Wa,-mbig-obj'

If I add these flags and compile with gcc 4.9.0, it works.

-- 
Best regards,
Boris Nagaev
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From bnagaev at gmail.com  Sun Oct 23 18:57:34 2016
From: bnagaev at gmail.com (Nagaev Boris)
Date: Mon, 24 Oct 2016 01:57:34 +0300
Subject: [ITK] [ITK-users] mingw,
 gcc5: "too many sections" and "undefined reference to vtable" errors
In-Reply-To: <CAFC_Vt6KrHP4uOjRZUpb05dgz3mzKdb0iDFGc5DTZ0yGUp6KoA@mail.gmail.com>
References: <CAFC_Vt6KrHP4uOjRZUpb05dgz3mzKdb0iDFGc5DTZ0yGUp6KoA@mail.gmail.com>
Message-ID: <CAFC_Vt6xxjBU26KLomL+p11c4RHr7LQeiUfSMk5fPS4K71kr4A@mail.gmail.com>

On Mon, Oct 24, 2016 at 12:09 AM, Nagaev Boris <bnagaev at gmail.com> wrote:
> Hello,
>
> I need help building ITK 4.8.0. I cross-compile on gcc 5.3.0 from
> Linux to Windows using MinGW-w64. Everything was Ok on gcc 4.9.4.
>
> I get the same errors as in this tread:
> https://cmake.org/pipermail/insight-users/2015-September/052511.html
> My log: https://git.io/vPNmf
>
> I added -Wa,-mbig-obj flags and the same error:
> https://cmake.org/pipermail/insight-users/2015-September/052512.html
> My log: https://git.io/vPNqh
> I added the flags by adding the following to cmake command:
> -DCMAKE_C_FLAGS='-Wa,-mbig-obj'
> -DCMAKE_CXX_FLAGS='-Wa,-mbig-obj'
>
> If I add these flags and compile with gcc 4.9.0, it works.

Latest ITK (4.10.1) builds successfully with gcc 6 after disabling
try-run (https://gist.github.com/starius/b7b1ee84faa76de1f52efe3f1959dc1d).


-- 
Best regards,
Boris Nagaev
_____________________________________
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From mustafa at inode.at  Mon Oct 24 06:02:00 2016
From: mustafa at inode.at (Mustafa Arikan)
Date: Mon, 24 Oct 2016 12:02:00 +0200
Subject: [ITK] [ITK-users] Reading a DICOM file in SimpleITK and ITK
	(spacing	error)
Message-ID: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>

Dear all,

reading a DICOM file (.dcm) in SimpleITK leads to following problem:

> RuntimeError: Exception thrown in SimpleITK ReadImage: 
> c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageBase.hxx:192:
> itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not allowed: 
> Spacing is [0, 0, 1]

The code looks like this:

> import SimpleITK
>
> inputFileName = 
> "D:\\workspace\\exports\\51871876-25-ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZVWGHRLQ+TNXWEN\\bscan.dcm"
> reader = SimpleITK.ImageSeriesReader()
> image= SimpleITK.ReadImage(inputFileName)
> reader.SetFileName ( inputFileName )
> imageIn = reader.Execute()

And I am getting the same error within ITK.

But opening the .dcm file with some DICOM-Viewer works.


thanks in advance,
Mustafa

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From zeinsalah at gmail.com  Mon Oct 24 08:50:39 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 24 Oct 2016 14:50:39 +0200
Subject: [ITK] meaning of negative spacing
Message-ID: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>

Hi,

I have a question regarding reading dicom files with itk,
particularly, multiframe dicom file (all slices in one single file).

I have read an image with itk 4.10 and write it into an mhd-raw image.
I noticed that the z-spacin is negative.
What does negative spacing mean?

thanks,
Zein

From ivan.granata.na at gmail.com  Mon Oct 24 08:53:53 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Mon, 24 Oct 2016 05:53:53 -0700 (MST)
Subject: [ITK] [ITK-users] Coregistration Transform Phyton to Java please
	help me
Message-ID: <1477313633399-37692.post@n7.nabble.com>

i've this

https://itk.org/SimpleITKDoxygen/html/Python_2ImageRegistrationMethodDisplacement1_8py-example.html


and in java i try to translate in this:
 but i've some errors
can anyone help me please?






import org.itk.simple.*;
class IterationUpdate  extends Command {
  private ImageRegistrationMethod m_Method;
  public IterationUpdate(ImageRegistrationMethod m) {
    super();
    m_Method=m;
  }
  
  public void execute() {
    org.itk.simple.VectorDouble pos = m_Method.getOptimizerPosition();
    System.out.format("%3d = %10.5f : [%f, %f]\n",
                      m_Method.getOptimizerIteration(),
                      m_Method.getMetricValue(),
                      pos.get(0), pos.get(1));
  }
}

class ImageRegistrationMethodNaplab {
  public static void main(String argv[]) {
  if ( argv.length < 4 )
    {
      System.out.format( "Usage: %s <fixedImageFilter> <movingImageFile>
<outputTransformFile>\n", "ImageRegistrationMethodNaplab");
      System.exit(-1);
    }
  
  

  int   ImageDimension = 3;
  char   PixelType;

  
  
  org.itk.simple.ImageFileReader reader = new
org.itk.simple.ImageFileReader();
  reader.setOutputPixelType( PixelIDValueEnum.sitkFloat32 );
  reader.setFileName(argv[0]);
  Image fixed  = reader.execute();
  reader.setFileName(argv[1]);
  Image moving = reader.execute();
  

  
  
  
  org.itk.simple.Transform initialTx = new org.itk.simple.Transform();
  
  //initialTx.CenteredTransformInitializerFilter( new
org.itk.simple.AffineTransform( fixed.getDimension() ) );
  
    
 initialTx.execute( fixed, moving, AffineTransform( fixed.getDimension() ));
  
  
  
  //org.itk.simple.Transform transf1 = new org.itk.simple.Transform();
  //org.itk.simple.AffineTransform afftransf = new
org.itk.simple.AffineTransform();
  //CenteredTransformInitializerFilter initialTx =
transf1.execute(fixed,moving, Transform.Affine(fixed.getDimension()));
  //org.itk.simple.AffineTransform Aff = new 
org.itk.simple.AffineTransform();
  
 // org.itk.simple.ImageRegistrationMethod initialTx = new 
org.itk.simple.ImageRegistrationMethod();
  
 // CenteredTransformInitializerFilter transform1 = new
CenteredTransformInitializerFilter();
 // initialTx.execute(fixed, moving, transform1( fixed.getDimension()));
  
  
  //initialTx.CenteredTransformInitializerFilter( new
org.itk.simple.AffineTransform( fixed.getDimension() ) );

 // Transform initialTx = new Transform();
  //ord.add(initialTx);
  
  //org.itk.simple.Transform transform =  new Transform();
  
 // initialTx.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );

  
 // initialTx.setInitialTransform( new org.itk.simple.TranslationTransform(
fixed.getDimension() ) );
  
  
  
  
  // initialTx.setTransform( new org.itk.simple.AffineTransform(
fixed.getDimension() ) );
  
//
 
  //org.itk.simple.Transform initialTx =
CenteredTransformInitializerFilter.execute(fixed, moving, Aff);
 
  //fixed, moving, Transform(fixed.getDimension(),TransformEnum.sitkAffine)
  
  
  org.itk.simple.ImageRegistrationMethod R = new 
org.itk.simple.ImageRegistrationMethod();
 
//VectorUInt32 b = [(3,2,1)];
  //VectorUInt32 b = new VectorUInt32 {(3,2,1)};
  long a1= 321;
  VectorUInt32 x1 = new VectorUInt32(a1);
  R.setShrinkFactorsPerLevel(x1);
  //Vector<Double> (3,2,1);
  
  
  long b1 = 211;
  VectorDouble y1 = new VectorDouble(b1);
 
  R.setSmoothingSigmasPerLevel(y1);
  
  //SET Metric
  R.setMetricAsMattesMutualInformation(20);
  //R.setMetricAsJointHistogramMutualInformation(20);
  R.setMetricUseFixedImageGradientFilter(false);
  
  double learningRate = 1.0 ;
  double minStep = 0.01;
  int numberOfIterations = 100;
  
  R.setOptimizerAsRegularStepGradientDescent( learningRate,
                                              minStep,
                                              numberOfIterations);
  //R.setOptimizerAsGradientDescent(learningRate=1.0,  // 
numberOfIterations=100, //  estimateLearningRate = R.EachIteration)
  
  
  
//SET Optimizer
  R.setOptimizerScalesFromPhysicalShift();
  
  
  R.setInitialTransform(initialTx,true);
  
//SET Interpolator
  R.setInterpolator(InterpolatorEnum.sitkLinear);
  
  
  org.itk.simple.Transform outTx = R.execute( fixed, moving );
  System.out.println("-------");
  System.out.println(outTx.toString());
  
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());
  
  
  
 org.itk.simple.Image displacementField = new 
org.itk.simple.Image(fixed.getSize(), PixelIDValueEnum.sitkVectorFloat64);
  
  //displacementField.Image();
  
  org.itk.simple.DisplacementFieldTransform displacementTx =  new
org.itk.simple.DisplacementFieldTransform(displacementField);
  
  double varianceForUpdateField = 0.0 ;
  double varianceForTotalField = 1.5;
  
  displacementTx.setSmoothingGaussianOnUpdate(varianceForUpdateField,
varianceForTotalField);
  
  
  R.setMovingInitialTransform(outTx);
  R.setInitialTransform(displacementTx,true);
  
 
    
  R.setMetricAsANTSNeighborhoodCorrelation(4);
  R.setMetricUseFixedImageGradientFilter(false);
  R.setMetricUseFixedImageGradientFilter(false);
  
  
  //VectorUInt32 b = [(3,2,1)];
  //VectorUInt32 b = new VectorUInt32 {(3,2,1)};
  long a2= 321;
  VectorUInt32 x2 = new VectorUInt32(a2);
  R.setShrinkFactorsPerLevel(x2);
  //Vector<Double> (3,2,1);
  
  
  long b2 = 211;
  VectorDouble y2 = new VectorDouble(b2);
 
  R.setSmoothingSigmasPerLevel(y2);

  
  R.setOptimizerScalesFromPhysicalShift();
  
  double learningRate2 = 1.0 ;
  double minStep2 = 0.01;
  int numberOfIterations2 = 300;
  
  R.setOptimizerAsRegularStepGradientDescent( learningRate2,
                                              minStep2,
                                              numberOfIterations2);
  
  
  
  
  
  //outTx.AddTransform( R.Execute(fixed, moving) )
  
  outTx.addTransform ( R.execute( fixed, moving ));
  System.out.println("-------");
  System.out.println(outTx.toString());
  
  System.out.format("Optimizer stop condition: %s\n",
R.getOptimizerStopConditionDescription());
  System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
  System.out.format(" Metric value: %f\n", R.getMetricValue());
  
  
  
  outTx.writeTransform(argv[2]);
  System.out.println("Parametri Trasformazione Generati e Salvati");
  
  
  
  org.itk.simple.Transform transform = new org.itk.simple.Transform();
  reader.setFileName(argv[2]);
  // Write result image
  ImageFileWriter writer2 = new org.itk.simple.ImageFileWriter();
  writer2.setFileName(argv[3]);
  
  
  
  org.itk.simple.ResampleImageFilter transf = new 
org.itk.simple.ResampleImageFilter();
    transf.setReferenceImage(fixed);
  transf.setTransform(outTx);
  transf.setOutputPixelType(PixelIDValueEnum.sitkUInt32);
  //InterpolatorEnum interp = 
		  transf.getInterpolator();
  //transf.setInterpolator(interp);
//  VectorDouble orig = 
		  transf.getOutputOrigin();
  //VectorDouble spac = 
		  transf.getOutputSpacing();
 // VectorDouble dir = 
		  transf.getOutputDirection();
  //Double pix = 
		  transf.getDefaultPixelValue();
  //transf.setInterpolator(dir);
  //VectorUInt32 pts = new VectorUInt32();
  transf.getSize();
  transf.execute(moving);
   Image blurredImg = transf.execute(moving);
    //Image castImg = caster.execute(blurredImg);
    ImageFileWriter writer3 = new ImageFileWriter();
    writer3.setFileName(argv[3]);
     writer3.execute(blurredImg);
     //writer.execute(transform.getResultImage()); 
     // transform.setParameters(reader.execute());
      //Image transform = reader.execute();
  //Transform.setParameters();
    // Perform warp
//  transform.logToConsoleOn();
 // transform.execute();
  }

private static Transform AffineTransform(long dimension) {
	// TODO Auto-generated method stub
	return null;
}
  }




--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Coregistration-Transform-Phyton-to-Java-please-help-me-tp37692.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From tofijoy at gmail.com  Mon Oct 24 10:50:20 2016
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Mon, 24 Oct 2016 10:50:20 -0400
Subject: [ITK] Decode a medical image from memory buffer in ITK
Message-ID: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>

Hi all,

I'm wondering if ITK can decode a medical image from a buffer.

For example, if I have a DICOM file read into a buffer buf using fread(),
is there an API in ITK that I can use to get an itk::Image pointer from buf?

Thank you,
Fijoy
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From dzenanz at gmail.com  Mon Oct 24 10:55:14 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 10:55:14 -0400
Subject: [ITK] meaning of negative spacing
In-Reply-To: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
References: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
Message-ID: <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>

Hi Zein,

I suppose you could invert the 3rd row (Z component) of the TransformMatrix
and have the spacing positive. It should have the same effect and is more
logical.

Regards,
D?enan

On Mon, Oct 24, 2016 at 8:50 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi,
>
> I have a question regarding reading dicom files with itk,
> particularly, multiframe dicom file (all slices in one single file).
>
> I have read an image with itk 4.10 and write it into an mhd-raw image.
> I noticed that the z-spacin is negative.
> What does negative spacing mean?
>
> thanks,
> Zein
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From dzenanz at gmail.com  Mon Oct 24 10:57:29 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 10:57:29 -0400
Subject: [ITK] Decode a medical image from memory buffer in ITK
In-Reply-To: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>
References: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>
Message-ID: <CAPf2UMT7Kb=MzXRqr5M-_jDb+3Kt_PjwsZgBtB1ZPTRsH8k5_Q@mail.gmail.com>

Hi Fijoy,

that is the job of Import
<https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html> filter.

Regards,
D?enan

On Mon, Oct 24, 2016 at 10:50 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
wrote:

> Hi all,
>
> I'm wondering if ITK can decode a medical image from a buffer.
>
> For example, if I have a DICOM file read into a buffer buf using fread(),
> is there an API in ITK that I can use to get an itk::Image pointer from buf?
>
> Thank you,
> Fijoy
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From dzenanz at gmail.com  Mon Oct 24 11:01:02 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 11:01:02 -0400
Subject: [ITK] [ITK-users] Reading a DICOM file in SimpleITK and ITK
	(spacing	error)
In-Reply-To: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
References: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
Message-ID: <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>

Hi Mustafa,

since the offending .dcm is in folder "exports", I assume some tool's DICOM
export is broken. Spacing should never be 0. If spacing is not known, it
should be set to 1. ITK has a right to complain about this. Can you
re-export this file, and perhaps fiddle with export settings a bit?

Regards,
D?enan

On Mon, Oct 24, 2016 at 6:02 AM, Mustafa Arikan <mustafa at inode.at> wrote:

> Dear all,
>
> reading a DICOM file (.dcm) in SimpleITK leads to following problem:
>
> RuntimeError: Exception thrown in SimpleITK ReadImage:
> c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\
> include\itkImageBase.hxx:192:
> itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not allowed:
> Spacing is [0, 0, 1]
>
> The code looks like this:
>
> import SimpleITK
>
> inputFileName = "D:\\workspace\\exports\\51871876-25-
> ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZ
> VWGHRLQ+TNXWEN\\bscan.dcm"
> reader = SimpleITK.ImageSeriesReader()
> image= SimpleITK.ReadImage(inputFileName)
> reader.SetFileName ( inputFileName )
> imageIn = reader.Execute()
>
> And I am getting the same error within ITK.
>
> But opening the .dcm file with some DICOM-Viewer works.
>
>
> thanks in advance,
> Mustafa
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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_____________________________________
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From zeinsalah at gmail.com  Mon Oct 24 11:12:49 2016
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 24 Oct 2016 17:12:49 +0200
Subject: [ITK] meaning of negative spacing
In-Reply-To: <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>
References: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
 <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>
Message-ID: <CADiSopOgno7=XAm-ZDqgjfaMV5YDk=RWH6WJzfC2rD7eZq7-Lw@mail.gmail.com>

Hi D?enan,

thanks for the response.

but I still wonder what does this mean. The reason for the question is:

The input image is a multiframe dicom, in which the image position
patient (0020, 0032)
is stored in the header for every frame. and these values are having
decreasing values
in the z-coordinate. So I am asking myself

1. if the itkimagereader considers this when it reconstructs the 3D volume?

2. if this is the reason for negative z-spacing? if this is the case,
I can this to
interpret the meaning of the z-spacing.




2016-10-24 16:55 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
> Hi Zein,
>
> I suppose you could invert the 3rd row (Z component) of the TransformMatrix
> and have the spacing positive. It should have the same effect and is more
> logical.
>
> Regards,
> D?enan
>
> On Mon, Oct 24, 2016 at 8:50 AM, Zein Salah <zeinsalah at gmail.com> wrote:
>>
>> Hi,
>>
>> I have a question regarding reading dicom files with itk,
>> particularly, multiframe dicom file (all slices in one single file).
>>
>> I have read an image with itk 4.10 and write it into an mhd-raw image.
>> I noticed that the z-spacin is negative.
>> What does negative spacing mean?
>>
>> thanks,
>> Zein
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>
>

From tofijoy at gmail.com  Mon Oct 24 11:13:44 2016
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Mon, 24 Oct 2016 11:13:44 -0400
Subject: [ITK] Decode a medical image from memory buffer in ITK
In-Reply-To: <CAPf2UMT7Kb=MzXRqr5M-_jDb+3Kt_PjwsZgBtB1ZPTRsH8k5_Q@mail.gmail.com>
References: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>
 <CAPf2UMT7Kb=MzXRqr5M-_jDb+3Kt_PjwsZgBtB1ZPTRsH8k5_Q@mail.gmail.com>
Message-ID: <CAHE0P1XjwQS6JxMmpdCvDu+aNpmW-Uoz1z7nft=KVSea4Dkwzw@mail.gmail.com>

Hi D?enan,

Correct me if I'm wrong, but the Import filter assumes that I have the
medical image metadata (size, resolution, etc.), and the decompressed data
(the C-array). However, I do not have these.

All I have is a buffer *buf* containing the encoded image, i.e., *buf* is
filled like so:

unsigned char buf[MAX_FILE_SIZE];
f = fopen("myImage.dcm", "rb");
n = fread(buf, MAX_FILE_SIZE, 1, f);

In other words, I'm looking for a class that can read an image from a
buffer, just like ImageFileReader reads from a file. Does such a class
exist?

Thanks,
Fijoy

On Mon, Oct 24, 2016 at 10:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Fijoy,
>
> that is the job of Import
> <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html> filter.
>
> Regards,
> D?enan
>
> On Mon, Oct 24, 2016 at 10:50 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
> wrote:
>
>> Hi all,
>>
>> I'm wondering if ITK can decode a medical image from a buffer.
>>
>> For example, if I have a DICOM file read into a buffer buf using fread(),
>> is there an API in ITK that I can use to get an itk::Image pointer from buf?
>>
>> Thank you,
>> Fijoy
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>
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From dzenanz at gmail.com  Mon Oct 24 11:16:35 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 11:16:35 -0400
Subject: [ITK] meaning of negative spacing
In-Reply-To: <CADiSopOgno7=XAm-ZDqgjfaMV5YDk=RWH6WJzfC2rD7eZq7-Lw@mail.gmail.com>
References: <CADiSopPEWDn0tsriS=g913DRqUsr5quzVHE3Tst2B7D67Ckb+A@mail.gmail.com>
 <CAPf2UMTih9YdBDoUh0z4JXUsi3ErWBXPjv+yqCG9tWvXW+guyw@mail.gmail.com>
 <CADiSopOgno7=XAm-ZDqgjfaMV5YDk=RWH6WJzfC2rD7eZq7-Lw@mail.gmail.com>
Message-ID: <CAPf2UMTtxYznJ9zuyEH0wyPmQiQzNg7HgU69KsO1hgKT+nXfFQ@mail.gmail.com>

Hi Zein,

image position patient is the authoritative tag to reconstruct slice
spacing and the vector of Z position/orientation. But I am surprised that
result is negative spacing instead of negative direction cosine
(orientation vector). Can you provide the offending DICOM file?

Regards,
D?enan

On Mon, Oct 24, 2016 at 11:12 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi D?enan,
>
> thanks for the response.
>
> but I still wonder what does this mean. The reason for the question is:
>
> The input image is a multiframe dicom, in which the image position
> patient (0020, 0032)
> is stored in the header for every frame. and these values are having
> decreasing values
> in the z-coordinate. So I am asking myself
>
> 1. if the itkimagereader considers this when it reconstructs the 3D volume?
>
> 2. if this is the reason for negative z-spacing? if this is the case,
> I can this to
> interpret the meaning of the z-spacing.
>
>
>
>
> 2016-10-24 16:55 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
> > Hi Zein,
> >
> > I suppose you could invert the 3rd row (Z component) of the
> TransformMatrix
> > and have the spacing positive. It should have the same effect and is more
> > logical.
> >
> > Regards,
> > D?enan
> >
> > On Mon, Oct 24, 2016 at 8:50 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> I have a question regarding reading dicom files with itk,
> >> particularly, multiframe dicom file (all slices in one single file).
> >>
> >> I have read an image with itk 4.10 and write it into an mhd-raw image.
> >> I noticed that the z-spacin is negative.
> >> What does negative spacing mean?
> >>
> >> thanks,
> >> Zein
> >> _______________________________________________
> >> Community mailing list
> >> Community at itk.org
> >> http://public.kitware.com/mailman/listinfo/community
> >
> >
>
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From dzenanz at gmail.com  Mon Oct 24 11:23:10 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 24 Oct 2016 11:23:10 -0400
Subject: [ITK] Decode a medical image from memory buffer in ITK
In-Reply-To: <CAHE0P1XjwQS6JxMmpdCvDu+aNpmW-Uoz1z7nft=KVSea4Dkwzw@mail.gmail.com>
References: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>
 <CAPf2UMT7Kb=MzXRqr5M-_jDb+3Kt_PjwsZgBtB1ZPTRsH8k5_Q@mail.gmail.com>
 <CAHE0P1XjwQS6JxMmpdCvDu+aNpmW-Uoz1z7nft=KVSea4Dkwzw@mail.gmail.com>
Message-ID: <CAPf2UMR6FiES4Bab49j5K_=d1fWJJXour0+cVnf5BCePuXNZ3w@mail.gmail.com>

Hi Fijoy,

as far as I am aware, there is no class to read an image from buffer
instead of file. But the possible workaround is to write that buffer into a
file in temp folder and read that file.

HTH,
D?enan

On Mon, Oct 24, 2016 at 11:13 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
wrote:

> Hi D?enan,
>
> Correct me if I'm wrong, but the Import filter assumes that I have the
> medical image metadata (size, resolution, etc.), and the decompressed data
> (the C-array). However, I do not have these.
>
> All I have is a buffer *buf* containing the encoded image, i.e., *buf* is
> filled like so:
>
> unsigned char buf[MAX_FILE_SIZE];
> f = fopen("myImage.dcm", "rb");
> n = fread(buf, MAX_FILE_SIZE, 1, f);
>
> In other words, I'm looking for a class that can read an image from a
> buffer, just like ImageFileReader reads from a file. Does such a class
> exist?
>
> Thanks,
> Fijoy
>
> On Mon, Oct 24, 2016 at 10:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Fijoy,
>>
>> that is the job of Import
>> <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html> filter.
>>
>> Regards,
>> D?enan
>>
>> On Mon, Oct 24, 2016 at 10:50 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I'm wondering if ITK can decode a medical image from a buffer.
>>>
>>> For example, if I have a DICOM file read into a buffer buf using
>>> fread(), is there an API in ITK that I can use to get an itk::Image pointer
>>> from buf?
>>>
>>> Thank you,
>>> Fijoy
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>
>
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From sg.ele.eng at gmail.com  Mon Oct 24 12:49:06 2016
From: sg.ele.eng at gmail.com (Sara Gh)
Date: Mon, 24 Oct 2016 12:49:06 -0400
Subject: [ITK] [ITK-users] SimpleITK - Subpixel shift detection in MRI
Message-ID: <CACjcMuaszDddNws2X01qcK9WxMKH2sncsAcLWSvxyzo35KJMAA@mail.gmail.com>

Hello,

I have three orthogonal intrasubject MRI volumes. Is there any way in
SimpleITK to check if the volumes have subpixel (subvoxel) shifts or not?

Thanks,
Sara Gh
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_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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From francois.budin at kitware.com  Mon Oct 24 13:18:03 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 24 Oct 2016 13:18:03 -0400
Subject: [ITK] Decode a medical image from memory buffer in ITK
In-Reply-To: <CAPf2UMR6FiES4Bab49j5K_=d1fWJJXour0+cVnf5BCePuXNZ3w@mail.gmail.com>
References: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>
 <CAPf2UMT7Kb=MzXRqr5M-_jDb+3Kt_PjwsZgBtB1ZPTRsH8k5_Q@mail.gmail.com>
 <CAHE0P1XjwQS6JxMmpdCvDu+aNpmW-Uoz1z7nft=KVSea4Dkwzw@mail.gmail.com>
 <CAPf2UMR6FiES4Bab49j5K_=d1fWJJXour0+cVnf5BCePuXNZ3w@mail.gmail.com>
Message-ID: <CAHwLD2XyFkLx+zku+DZ5P+j+jkF96jXbaoG=Cb6fEP3mW+VhqQ@mail.gmail.com>

Hi Fijoy,

ITK will need the image information such as the size and the dimension to
know what your buffer corresponds to. If you do have these informations
then you can use the import filter D?enan mentioned. If you do not have
these informations, then
there is no way for ITK to know if your image has dimension (x*y*z)*(1)*(1)
or (x*y)*(z)*(1) or any possible combination that would lead to the same
buffer size.
Hope this helps,

Francois

On Mon, Oct 24, 2016 at 11:23 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Fijoy,
>
> as far as I am aware, there is no class to read an image from buffer
> instead of file. But the possible workaround is to write that buffer into a
> file in temp folder and read that file.
>
> HTH,
> D?enan
>
> On Mon, Oct 24, 2016 at 11:13 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
> wrote:
>
>> Hi D?enan,
>>
>> Correct me if I'm wrong, but the Import filter assumes that I have the
>> medical image metadata (size, resolution, etc.), and the decompressed data
>> (the C-array). However, I do not have these.
>>
>> All I have is a buffer *buf* containing the encoded image, i.e., *buf* is
>> filled like so:
>>
>> unsigned char buf[MAX_FILE_SIZE];
>> f = fopen("myImage.dcm", "rb");
>> n = fread(buf, MAX_FILE_SIZE, 1, f);
>>
>> In other words, I'm looking for a class that can read an image from a
>> buffer, just like ImageFileReader reads from a file. Does such a class
>> exist?
>>
>> Thanks,
>> Fijoy
>>
>> On Mon, Oct 24, 2016 at 10:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>>> Hi Fijoy,
>>>
>>> that is the job of Import
>>> <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html>
>>> filter.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Mon, Oct 24, 2016 at 10:50 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com
>>> > wrote:
>>>
>>>> Hi all,
>>>>
>>>> I'm wondering if ITK can decode a medical image from a buffer.
>>>>
>>>> For example, if I have a DICOM file read into a buffer buf using
>>>> fread(), is there an API in ITK that I can use to get an itk::Image pointer
>>>> from buf?
>>>>
>>>> Thank you,
>>>> Fijoy
>>>>
>>>> _______________________________________________
>>>> Community mailing list
>>>> Community at itk.org
>>>> http://public.kitware.com/mailman/listinfo/community
>>>>
>>>>
>>>
>>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From zivrafael.yaniv at nih.gov  Mon Oct 24 16:29:12 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Mon, 24 Oct 2016 20:29:12 +0000
Subject: [ITK] [ITK-users] SimpleITK - Subpixel shift detection in MRI
In-Reply-To: <CACjcMuaszDddNws2X01qcK9WxMKH2sncsAcLWSvxyzo35KJMAA@mail.gmail.com>
References: <CACjcMuaszDddNws2X01qcK9WxMKH2sncsAcLWSvxyzo35KJMAA@mail.gmail.com>
Message-ID: <D433E71A.D26C%yanivz@mail.nih.gov>

Hello Sara,

As you did not give the specifics of the problem you want to address the  suggested approaches are rather generic. Assuming here that the anatomical structure of interest in the scans did not deform (not MRs of the heart in different phases of the cardiac cycle):

1. Prospective approach -

If you can accurately identify three or more corresponding points in each of the datasets you can use the LandmarkBasedTransformInitializer (https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1LandmarkBasedTransformInitializerFilter.html) to estimate the transformation. Ideally these points can be localized with sub-voxel accuracy - possibly derived from markers which occupy a large number of voxels so that undersegmentation/oversegmentation has minimal impact on the point localization.

2. Retrospective approach -

Run a rigid registration between the images and see if the results have a visibly better alignment. After registration you can use a linked cursor to see if corresponding points appear closer to their expected locations.

An example of using a linked cursor with SimpleITK Python notebooks can be found here:
https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/master/67_Registration_Semiautomatic_Homework.ipynb

Another option is to resample the moving image and view the images using ITK-SNAP's linked cursor.

    Ziv


From: Sara Gh <sg.ele.eng at gmail.com<mailto:sg.ele.eng at gmail.com>>
Date: Monday, October 24, 2016 at 12:49 PM
To: "insight-users at itk.org<mailto:insight-users at itk.org>" <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: [ITK-users] SimpleITK - Subpixel shift detection in MRI

Hello,

I have three orthogonal intrasubject MRI volumes. Is there any way in SimpleITK to check if the volumes have subpixel (subvoxel) shifts or not?

Thanks,
Sara Gh

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_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From ndel314 at gmail.com  Mon Oct 24 17:43:26 2016
From: ndel314 at gmail.com (Nico Del Piano)
Date: Mon, 24 Oct 2016 18:43:26 -0300
Subject: [ITK] [ITK-users] Unknown issue (realloc() invalid pointer)
Message-ID: <CAAq9_B4aF=nLCt_k6McGQ1bzQVQwaEXQ-u7mPLBj5uZQnpMadQ@mail.gmail.com>

Hello,

I have a project which uses ITK + VTK + Qt: it worked well till I
messed up something with some of the libraries/frameworks already
mentioned. I remember installing a new version of either ITK or VTK,
and then the program, after being compiled, returns the following
error when executed:

$ ./app
*** Error in `./app': realloc(): invalid pointer: 0x00007f5065aa3840 ***
Aborted (core dumped)

As I said, it worked well and stopped working after compiling a new
version of ITK or VTK. I don't know what to do, since I haven't
changed the program's code.

Sorry about this *horrible* description of my problem, but if someone
have run into this and could help me, or have an idea of how to fix
it, I'd really appreciate that :).

Thanks,

Nico.
_____________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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From ivan.granata.na at gmail.com  Tue Oct 25 03:42:24 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 25 Oct 2016 00:42:24 -0700 (MST)
Subject: [ITK] [ITK-users]  VectorUInt32 and VectorDouble in Java...How?
Message-ID: <1477381344050-37700.post@n7.nabble.com>

hi 

how can i specify  VectorUInt32 and VectorDouble in Java...

i ve this in python
R.SetShrinkFactorsPerLevel([3,2,1])
R.SetSmoothingSigmasPerLevel([2,1,1])

SetShrinkFactorsPerLevel would  VectorUInt32 
and
SetSmoothingSigmasPerLevel would  VectorDouble 


thanks





--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-VectorUInt32-and-VectorDouble-in-Java-How-tp37700.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From johannes.keustermans at gmail.com  Tue Oct 25 08:39:50 2016
From: johannes.keustermans at gmail.com (Johannes Keustermans)
Date: Tue, 25 Oct 2016 14:39:50 +0200
Subject: [ITK] [ITK-dev] description AdaptiveHistogramEqualizationImageFilter
Message-ID: <011901d22ebc$e0dd8930$a2989b90$@gmail.com>

Dear all,

 

 

The description of the AdaptiveHistogramEqualizationImageFilter is not
entirely correct in my (humble) opinion. From the description it seems that
the filter, depending on the parameter alpha, ranges from standard histogram
equalization (alpha = 0) to unsharp masking (alpha = 1). However, from the
paper and the implementation, the parameter alpha is used to steer between
standard histogram equalization and local mean subtraction. The rationale
for this connection is due to the fact that local mean subtraction is an
approximation for histogram equalization with a strongly gaussian smoothed
histogram. The parameter beta controls the level of local mean addition.

 

 

Kind regards,

Johannes Keustermans

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_______________________________________________
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From blowekamp at mail.nih.gov  Tue Oct 25 08:57:26 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 25 Oct 2016 12:57:26 +0000
Subject: [ITK] [ITK-users] VectorUInt32 and VectorDouble in Java...How?
In-Reply-To: <1477381344050-37700.post@n7.nabble.com>
References: <1477381344050-37700.post@n7.nabble.com>
Message-ID: <CD7E50E4-6BCF-4C04-8B01-4C5E193C471B@mail.nih.gov>

Hello,

That is a very good question I can help with!

These vector classes are wrappers for the C++ std::vector<T> template classes. SWIG generates these data structures, and provides a JAVA like interface for the object. Unlike Python, JAVA is a strongly type language and requires explicit types and constructors. Here is the snippet that I think you need:

VectorUInt32 shrinkFactors = new VectorUIn32(3)
shrinkFactors.set(3)
shrinkFactors.set(2)
shrinkFactors.set(1)

VectorDouble smoothingSigmas = new VectorDouble(3)
smoothingSigmas.set(2)
smoothingSigmas.set(1)
smoothingSigmas.set(1)

HTH,
Brad



> On Oct 25, 2016, at 3:42 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> hi 
> 
> how can i specify  VectorUInt32 and VectorDouble in Java...
> 
> i ve this in python
> R.SetShrinkFactorsPerLevel([3,2,1])
> R.SetSmoothingSigmasPerLevel([2,1,1])
> 
> SetShrinkFactorsPerLevel would  VectorUInt32 
> and
> SetSmoothingSigmasPerLevel would  VectorDouble 
> 
> 
> thanks
> 
> 
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-VectorUInt32-and-VectorDouble-in-Java-How-tp37700.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From dzenanz at gmail.com  Tue Oct 25 09:52:12 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 25 Oct 2016 09:52:12 -0400
Subject: [ITK] [ITK-users] Unknown issue (realloc() invalid pointer)
In-Reply-To: <CAAq9_B4aF=nLCt_k6McGQ1bzQVQwaEXQ-u7mPLBj5uZQnpMadQ@mail.gmail.com>
References: <CAAq9_B4aF=nLCt_k6McGQ1bzQVQwaEXQ-u7mPLBj5uZQnpMadQ@mail.gmail.com>
Message-ID: <CAPf2UMRBWL-8j4rkFw7WFK-0-BK5Vcd3FYt0VH2AVRyq6SuOkw@mail.gmail.com>

Hi Nico,

try doing a clean build of all the libraries and your program. If that does
not solve the problem, compile it in debug mode and you should get more
useful information about where does the crash occur.

Regards,
D?enan

On Mon, Oct 24, 2016 at 5:43 PM, Nico Del Piano <ndel314 at gmail.com> wrote:

> Hello,
>
> I have a project which uses ITK + VTK + Qt: it worked well till I
> messed up something with some of the libraries/frameworks already
> mentioned. I remember installing a new version of either ITK or VTK,
> and then the program, after being compiled, returns the following
> error when executed:
>
> $ ./app
> *** Error in `./app': realloc(): invalid pointer: 0x00007f5065aa3840 ***
> Aborted (core dumped)
>
> As I said, it worked well and stopped working after compiling a new
> version of ITK or VTK. I don't know what to do, since I haven't
> changed the program's code.
>
> Sorry about this *horrible* description of my problem, but if someone
> have run into this and could help me, or have an idea of how to fix
> it, I'd really appreciate that :).
>
> Thanks,
>
> Nico.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From dzenanz at gmail.com  Tue Oct 25 09:57:47 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 25 Oct 2016 09:57:47 -0400
Subject: [ITK] [ITK-dev]
	description	AdaptiveHistogramEqualizationImageFilter
In-Reply-To: <011901d22ebc$e0dd8930$a2989b90$@gmail.com>
References: <011901d22ebc$e0dd8930$a2989b90$@gmail.com>
Message-ID: <CAPf2UMSnTXv_x6amuxEJdHHeEaSOJHx+91aL1oK0j3bLaBd59Q@mail.gmail.com>

Dear Johannes,

this is an excellent opportunity to contribute to ITK by improving the
documentation! Following these instructions
<https://itk.org/Wiki/ITK/Git/Develop>, modify the comments
<https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageStatistics/include/itkAdaptiveHistogramEqualizationImageFilter.h#L27-L69>
before the filter declaration and submit a patch to Gerrit code review
system. Add a few active participants of the list as reviewers.

Regards,
D?enan

On Tue, Oct 25, 2016 at 8:39 AM, Johannes Keustermans <
johannes.keustermans at gmail.com> wrote:

> Dear all,
>
>
>
>
>
> The description of the AdaptiveHistogramEqualizationImageFilter is not
> entirely correct in my (humble) opinion. From the description it seems that
> the filter, depending on the parameter alpha, ranges from standard
> histogram equalization (alpha = 0) to unsharp masking (alpha = 1). However,
> from the paper and the implementation, the parameter alpha is used to steer
> between standard histogram equalization and local mean subtraction. The
> rationale for this connection is due to the fact that local mean
> subtraction is an approximation for histogram equalization with a strongly
> gaussian smoothed histogram. The parameter beta controls the level of local
> mean addition.
>
>
>
>
>
> Kind regards,
>
> Johannes Keustermans
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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_______________________________________________
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From ivan.granata.na at gmail.com  Tue Oct 25 12:18:06 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Tue, 25 Oct 2016 09:18:06 -0700 (MST)
Subject: [ITK] [ITK-users] VectorUInt32 and VectorDouble in Java...How?
In-Reply-To: <CD7E50E4-6BCF-4C04-8B01-4C5E193C471B@mail.nih.gov>
References: <1477381344050-37700.post@n7.nabble.com>
 <CD7E50E4-6BCF-4C04-8B01-4C5E193C471B@mail.nih.gov>
Message-ID: <1477412286443-37703.post@n7.nabble.com>

i tried whit this

what do u think about? is it the same?

  VectorUInt32 pts1 = new VectorUInt32(3);
 // org.itk.simple.VectorUInt32 pts1;
  pts1.clear();
  pts1.push_back(3);
  pts1.push_back(2);
  pts1.push_back(1);
  
  
  System.out.println(pts1);
  R.setShrinkFactorsPerLevel(pts1);



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-SimpleITK-VectorUInt32-and-VectorDouble-in-Java-How-tp37700p37703.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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http://www.kitware.com/opensource/opensource.html

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From Brian.Chapman at utah.edu  Tue Oct 25 17:15:48 2016
From: Brian.Chapman at utah.edu (Brian E Chapman)
Date: Tue, 25 Oct 2016 21:15:48 +0000
Subject: [ITK] [ITK-users] Using Python SimpleITK to Read/Write to BytesIO
 instance rather than file
Message-ID: <7812F318-6175-47DA-986B-54969007D094@umail.utah.edu>

Hi,

We are looking at using SimpleITK in conjunction with Girder to read images from girder manipulate the images with a Python script and then write the contents back up to Girder. We would prefer to do this using Byte streams rather than saving to a local file, reading/writing to the local file and then uploading the file to Girder, but we have not been able to find a way within SimpleITK (within Python) to read and write from/to streams rather than files.

Any guidance would be appreciated.

Brian

_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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From zivrafael.yaniv at nih.gov  Wed Oct 26 10:22:43 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 26 Oct 2016 14:22:43 +0000
Subject: [ITK] [ITK-users] Using Python SimpleITK to Read/Write to
 BytesIO instance rather than file
Message-ID: <D43633E7.D293%yanivz@mail.nih.gov>

Hi Brian,

Currently ITK/SimpleITK do not have components for reading an image
directly from a stream. We usually download, save to disk, and read from
disk using the appropriate IO. We used this approach with our Jupyter
notebooks where the read function either finds the data in a cache or
fetches it from MIDAS into the cache and then reads it
(https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/mast
er/downloaddata.py).

The challenge with streaming is that we currently don't have a protocol
for interpreting the streamed data (meta-data-dictionary + intensity/color
values). A possible solution is to use a client-server architecture with
the OpenIGTLink protocol (http://openigtlink.org). You can transfer
meta-data (patient name etc.) and complete images. See the specification
on their website.

Out of curiosity, what is the motivation for the streaming only approach
(girder -> SimpleITK -> girder)?

   hope this helps
     Ziv





On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:

>Hi,
>
>We are looking at using SimpleITK in conjunction with Girder to read
>images from girder manipulate the images with a Python script and then
>write the contents back up to Girder. We would prefer to do this using
>Byte streams rather than saving to a local file, reading/writing to the
>local file and then uploading the file to Girder, but we have not been
>able to find a way within SimpleITK (within Python) to read and write
>from/to streams rather than files.
>
>Any guidance would be appreciated.
>
>Brian
>
>_____________________________________
>Powered by www.kitware.com
>
>Visit other Kitware open-source projects at
>http://www.kitware.com/opensource/opensource.html
>
>Kitware offers ITK Training Courses, for more information visit:
>http://www.kitware.com/products/protraining.php
>
>Please keep messages on-topic and check the ITK FAQ at:
>http://www.itk.org/Wiki/ITK_FAQ
>
>Follow this link to subscribe/unsubscribe:
>http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From Brian.Chapman at utah.edu  Wed Oct 26 11:26:48 2016
From: Brian.Chapman at utah.edu (Brian E Chapman)
Date: Wed, 26 Oct 2016 15:26:48 +0000
Subject: [ITK] [ITK-users] Using Python SimpleITK to Read/Write to
 BytesIO instance rather than file
In-Reply-To: <D43633E7.D293%yanivz@mail.nih.gov>
References: <D43633E7.D293%yanivz@mail.nih.gov>
Message-ID: <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>

Ziv,

Thanks for your reply and the pointer to opneigtlink. Our main motivation is speed: just trying to save the write-to-disk/read-from-disk costs. Using PyDICOM we can read directly from Girder via streams and I believe we also can with nibabel. But ultimately our processing will be done with ITK and I was hoping to have SimpleITK so I was hoping to avoid all the challenges of reading in one format, passing to simpleitk and trying to keep track of all the meta data appropriately in the process.

Brian

------
Brian E. Chapman, Ph.D.
Associate Professor
Department of Radiology and Imaging Sciences
University of Utah

> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> 
> Hi Brian,
> 
> Currently ITK/SimpleITK do not have components for reading an image
> directly from a stream. We usually download, save to disk, and read from
> disk using the appropriate IO. We used this approach with our Jupyter
> notebooks where the read function either finds the data in a cache or
> fetches it from MIDAS into the cache and then reads it
> (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/mast
> er/downloaddata.py).
> 
> The challenge with streaming is that we currently don't have a protocol
> for interpreting the streamed data (meta-data-dictionary + intensity/color
> values). A possible solution is to use a client-server architecture with
> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
> meta-data (patient name etc.) and complete images. See the specification
> on their website.
> 
> Out of curiosity, what is the motivation for the streaming only approach
> (girder -> SimpleITK -> girder)?
> 
>   hope this helps
>     Ziv
> 
> 
> 
> 
> 
> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
> 
>> Hi,
>> 
>> We are looking at using SimpleITK in conjunction with Girder to read
>> images from girder manipulate the images with a Python script and then
>> write the contents back up to Girder. We would prefer to do this using
>> Byte streams rather than saving to a local file, reading/writing to the
>> local file and then uploading the file to Girder, but we have not been
>> able to find a way within SimpleITK (within Python) to read and write
>> from/to streams rather than files.
>> 
>> Any guidance would be appreciated.
>> 
>> Brian
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From tofijoy at gmail.com  Wed Oct 26 11:36:57 2016
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Wed, 26 Oct 2016 11:36:57 -0400
Subject: [ITK] Data buffer length
Message-ID: <CAHE0P1X9JF19OvDAdqB15J8+FOkfUW5vag=C51XPTQpFKm8a2Q@mail.gmail.com>

Hi all,

What's the easiest way to get the length of the data buffer of an
itk::Image in bytes?

I see that GetBufferPointer() gives me a pointer to the buffer, but I also
need the length of the buffer in bytes. I can calculate this as a product
of image size components and pixel size in bytes, but I'm wondering if that
is the easiest way.

Thanks,
Fijoy
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From blowekamp at mail.nih.gov  Wed Oct 26 11:37:26 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 26 Oct 2016 15:37:26 +0000
Subject: [ITK] [ITK-users] Using Python SimpleITK to Read/Write to
 BytesIO instance rather than file
In-Reply-To: <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>
References: <D43633E7.D293%yanivz@mail.nih.gov>
 <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>
Message-ID: <3E57C5F3-1776-4601-9CB5-FBBD0B12335C@mail.nih.gov>

Hi,

Have you done a performance comparison? These other libraries may just download and cache the files, before doing file IO.

I recall there was a URL/HTTP based ITK ImageIO, but that just downloaded the files and then use the actual file ImageIO. It was wrapped in a nice package to enable seamless passing of ?http? URLS as filename strings to ITK.

HTH,
Brad

> On Oct 26, 2016, at 11:26 AM, Brian E Chapman <Brian.Chapman at utah.edu> wrote:
> 
> Ziv,
> 
> Thanks for your reply and the pointer to opneigtlink. Our main motivation is speed: just trying to save the write-to-disk/read-from-disk costs. Using PyDICOM we can read directly from Girder via streams and I believe we also can with nibabel. But ultimately our processing will be done with ITK and I was hoping to have SimpleITK so I was hoping to avoid all the challenges of reading in one format, passing to simpleitk and trying to keep track of all the meta data appropriately in the process.
> 
> Brian
> 
> ------
> Brian E. Chapman, Ph.D.
> Associate Professor
> Department of Radiology and Imaging Sciences
> University of Utah
> 
>> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
>> 
>> Hi Brian,
>> 
>> Currently ITK/SimpleITK do not have components for reading an image
>> directly from a stream. We usually download, save to disk, and read from
>> disk using the appropriate IO. We used this approach with our Jupyter
>> notebooks where the read function either finds the data in a cache or
>> fetches it from MIDAS into the cache and then reads it
>> (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/mast
>> er/downloaddata.py).
>> 
>> The challenge with streaming is that we currently don't have a protocol
>> for interpreting the streamed data (meta-data-dictionary + intensity/color
>> values). A possible solution is to use a client-server architecture with
>> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
>> meta-data (patient name etc.) and complete images. See the specification
>> on their website.
>> 
>> Out of curiosity, what is the motivation for the streaming only approach
>> (girder -> SimpleITK -> girder)?
>> 
>>  hope this helps
>>    Ziv
>> 
>> 
>> 
>> 
>> 
>> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
>> 
>>> Hi,
>>> 
>>> We are looking at using SimpleITK in conjunction with Girder to read
>>> images from girder manipulate the images with a Python script and then
>>> write the contents back up to Girder. We would prefer to do this using
>>> Byte streams rather than saving to a local file, reading/writing to the
>>> local file and then uploading the file to Girder, but we have not been
>>> able to find a way within SimpleITK (within Python) to read and write
>>> from/to streams rather than files.
>>> 
>>> Any guidance would be appreciated.
>>> 
>>> Brian
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> 
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

_____________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From francois.budin at kitware.com  Wed Oct 26 12:00:32 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 26 Oct 2016 12:00:32 -0400
Subject: [ITK] Data buffer length
In-Reply-To: <CAHE0P1X9JF19OvDAdqB15J8+FOkfUW5vag=C51XPTQpFKm8a2Q@mail.gmail.com>
References: <CAHE0P1X9JF19OvDAdqB15J8+FOkfUW5vag=C51XPTQpFKm8a2Q@mail.gmail.com>
Message-ID: <CAHwLD2UQP=sQ6Z64pp2R4_qLn7W4tg=DE_tn0gQwcGWs-zwKJw@mail.gmail.com>

Hello Fijoy,

I don't think there is a way to do that without computing the product of
the image size by the pixel size. Here is an example where it is done:
https://itk.org/pipermail/insight-users/2007-May/022351.html

Francois

On Wed, Oct 26, 2016 at 11:36 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
wrote:

> Hi all,
>
> What's the easiest way to get the length of the data buffer of an
> itk::Image in bytes?
>
> I see that GetBufferPointer() gives me a pointer to the buffer, but I also
> need the length of the buffer in bytes. I can calculate this as a product
> of image size components and pixel size in bytes, but I'm wondering if that
> is the easiest way.
>
> Thanks,
> Fijoy
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From dzenanz at gmail.com  Wed Oct 26 12:31:42 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 26 Oct 2016 12:31:42 -0400
Subject: [ITK] Data buffer length
In-Reply-To: <CAHwLD2UQP=sQ6Z64pp2R4_qLn7W4tg=DE_tn0gQwcGWs-zwKJw@mail.gmail.com>
References: <CAHE0P1X9JF19OvDAdqB15J8+FOkfUW5vag=C51XPTQpFKm8a2Q@mail.gmail.com>
 <CAHwLD2UQP=sQ6Z64pp2R4_qLn7W4tg=DE_tn0gQwcGWs-zwKJw@mail.gmail.com>
Message-ID: <CAPf2UMR89nEV8OHa1j3m_XgLFx+E-Z-BTo47oQu09_-z0sf3hA@mail.gmail.com>

Hi Fijoy,

you can calculate it like this:
SizeValueType
numBytes=sizeof(TPixel)*image->GetBufferedRegion().GetNumberOfPixels();

Regards,
D?enan

On Wed, Oct 26, 2016 at 12:00 PM, Francois Budin <francois.budin at kitware.com
> wrote:

> Hello Fijoy,
>
> I don't think there is a way to do that without computing the product of
> the image size by the pixel size. Here is an example where it is done:
> https://itk.org/pipermail/insight-users/2007-May/022351.html
>
> Francois
>
> On Wed, Oct 26, 2016 at 11:36 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
> wrote:
>
>> Hi all,
>>
>> What's the easiest way to get the length of the data buffer of an
>> itk::Image in bytes?
>>
>> I see that GetBufferPointer() gives me a pointer to the buffer, but I
>> also need the length of the buffer in bytes. I can calculate this as a
>> product of image size components and pixel size in bytes, but I'm wondering
>> if that is the easiest way.
>>
>> Thanks,
>> Fijoy
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From matt.mccormick at kitware.com  Wed Oct 26 13:46:38 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 26 Oct 2016 13:46:38 -0400
Subject: [ITK] Decode a medical image from memory buffer in ITK
In-Reply-To: <CAHwLD2XyFkLx+zku+DZ5P+j+jkF96jXbaoG=Cb6fEP3mW+VhqQ@mail.gmail.com>
References: <CAHE0P1WoEVFYMd++8+CqXj7BjsEUwVWZBvekRNoqxzLOcZadyg@mail.gmail.com>
 <CAPf2UMT7Kb=MzXRqr5M-_jDb+3Kt_PjwsZgBtB1ZPTRsH8k5_Q@mail.gmail.com>
 <CAHE0P1XjwQS6JxMmpdCvDu+aNpmW-Uoz1z7nft=KVSea4Dkwzw@mail.gmail.com>
 <CAPf2UMR6FiES4Bab49j5K_=d1fWJJXour0+cVnf5BCePuXNZ3w@mail.gmail.com>
 <CAHwLD2XyFkLx+zku+DZ5P+j+jkF96jXbaoG=Cb6fEP3mW+VhqQ@mail.gmail.com>
Message-ID: <CALzTN-QzjeUnnTWQbt-+MRO=9R5PQjo_ruwR2_VChTa+wUNNXg@mail.gmail.com>

Hi Fijoy,

While this approach does not apply as-is when the buffer is in a
format like DICOM, reading an image from an in memory by passing the
address and possibly also the metadata through the FileName is
demonstrated here:

  https://github.com/InsightSoftwareConsortium/ITK/blob/33e56685e6bc2323cdff9457fb48b7967c60a6e5/Modules/IO/ImageBase/test/itkFileFreeImageIO.h

  https://github.com/Slicer/Slicer/blob/d4b177c3c78d6ebc6ddcee7d7e0ba917652e0026/Libs/MRML/IDImageIO/itkMRMLIDImageIO.h

HTH,
Matt

On Mon, Oct 24, 2016 at 1:18 PM, Francois Budin
<francois.budin at kitware.com> wrote:
> Hi Fijoy,
>
> ITK will need the image information such as the size and the dimension to
> know what your buffer corresponds to. If you do have these informations then
> you can use the import filter D?enan mentioned. If you do not have these
> informations, then
> there is no way for ITK to know if your image has dimension (x*y*z)*(1)*(1)
> or (x*y)*(z)*(1) or any possible combination that would lead to the same
> buffer size.
> Hope this helps,
>
> Francois
>
> On Mon, Oct 24, 2016 at 11:23 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>> Hi Fijoy,
>>
>> as far as I am aware, there is no class to read an image from buffer
>> instead of file. But the possible workaround is to write that buffer into a
>> file in temp folder and read that file.
>>
>> HTH,
>> D?enan
>>
>> On Mon, Oct 24, 2016 at 11:13 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
>> wrote:
>>>
>>> Hi D?enan,
>>>
>>> Correct me if I'm wrong, but the Import filter assumes that I have the
>>> medical image metadata (size, resolution, etc.), and the decompressed data
>>> (the C-array). However, I do not have these.
>>>
>>> All I have is a buffer buf containing the encoded image, i.e., buf is
>>> filled like so:
>>>
>>> unsigned char buf[MAX_FILE_SIZE];
>>> f = fopen("myImage.dcm", "rb");
>>> n = fread(buf, MAX_FILE_SIZE, 1, f);
>>>
>>> In other words, I'm looking for a class that can read an image from a
>>> buffer, just like ImageFileReader reads from a file. Does such a class
>>> exist?
>>>
>>> Thanks,
>>> Fijoy
>>>
>>> On Mon, Oct 24, 2016 at 10:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>>
>>>> Hi Fijoy,
>>>>
>>>> that is the job of Import filter.
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Mon, Oct 24, 2016 at 10:50 AM, Fijoy Vadakkumpadan
>>>> <tofijoy at gmail.com> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I'm wondering if ITK can decode a medical image from a buffer.
>>>>>
>>>>> For example, if I have a DICOM file read into a buffer buf using
>>>>> fread(), is there an API in ITK that I can use to get an itk::Image pointer
>>>>> from buf?
>>>>>
>>>>> Thank you,
>>>>> Fijoy
>>>>>
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From richard.beare at gmail.com  Wed Oct 26 16:17:14 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Thu, 27 Oct 2016 07:17:14 +1100
Subject: [ITK] [ITK-users] Using Python SimpleITK to Read/Write to
 BytesIO instance rather than file
In-Reply-To: <3E57C5F3-1776-4601-9CB5-FBBD0B12335C@mail.nih.gov>
References: <D43633E7.D293%yanivz@mail.nih.gov>
 <40DA95EC-BAE3-46AE-9CB0-C724B97D98AD@umail.utah.edu>
 <3E57C5F3-1776-4601-9CB5-FBBD0B12335C@mail.nih.gov>
Message-ID: <CA+V7QS9-s=_Rd9sEDnRjP7s=Y-WwqH+yGJYDKQVP--Gu-ubVsA@mail.gmail.com>

If you are trying to avoid IO, and the other packages already deal with
streams, an option may be to stream into a numpy array + a python metadata
structure, and convert that to a SimpleITK image. Obviously will be a
little messy and incur a memory overhead, but could avoid disk IO.

On Thu, Oct 27, 2016 at 2:37 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hi,
>
> Have you done a performance comparison? These other libraries may just
> download and cache the files, before doing file IO.
>
> I recall there was a URL/HTTP based ITK ImageIO, but that just downloaded
> the files and then use the actual file ImageIO. It was wrapped in a nice
> package to enable seamless passing of ?http? URLS as filename strings to
> ITK.
>
> HTH,
> Brad
>
> > On Oct 26, 2016, at 11:26 AM, Brian E Chapman <Brian.Chapman at utah.edu>
> wrote:
> >
> > Ziv,
> >
> > Thanks for your reply and the pointer to opneigtlink. Our main
> motivation is speed: just trying to save the write-to-disk/read-from-disk
> costs. Using PyDICOM we can read directly from Girder via streams and I
> believe we also can with nibabel. But ultimately our processing will be
> done with ITK and I was hoping to have SimpleITK so I was hoping to avoid
> all the challenges of reading in one format, passing to simpleitk and
> trying to keep track of all the meta data appropriately in the process.
> >
> > Brian
> >
> > ------
> > Brian E. Chapman, Ph.D.
> > Associate Professor
> > Department of Radiology and Imaging Sciences
> > University of Utah
> >
> >> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
> zivrafael.yaniv at nih.gov> wrote:
> >>
> >> Hi Brian,
> >>
> >> Currently ITK/SimpleITK do not have components for reading an image
> >> directly from a stream. We usually download, save to disk, and read from
> >> disk using the appropriate IO. We used this approach with our Jupyter
> >> notebooks where the read function either finds the data in a cache or
> >> fetches it from MIDAS into the cache and then reads it
> >> (https://github.com/InsightSoftwareConsortium/
> SimpleITK-Notebooks/blob/mast
> >> er/downloaddata.py).
> >>
> >> The challenge with streaming is that we currently don't have a protocol
> >> for interpreting the streamed data (meta-data-dictionary +
> intensity/color
> >> values). A possible solution is to use a client-server architecture with
> >> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
> >> meta-data (patient name etc.) and complete images. See the specification
> >> on their website.
> >>
> >> Out of curiosity, what is the motivation for the streaming only approach
> >> (girder -> SimpleITK -> girder)?
> >>
> >>  hope this helps
> >>    Ziv
> >>
> >>
> >>
> >>
> >>
> >> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
> >>
> >>> Hi,
> >>>
> >>> We are looking at using SimpleITK in conjunction with Girder to read
> >>> images from girder manipulate the images with a Python script and then
> >>> write the contents back up to Girder. We would prefer to do this using
> >>> Byte streams rather than saving to a local file, reading/writing to the
> >>> local file and then uploading the file to Girder, but we have not been
> >>> able to find a way within SimpleITK (within Python) to read and write
> >>> from/to streams rather than files.
> >>>
> >>> Any guidance would be appreciated.
> >>>
> >>> Brian
> >>>
> >>> _____________________________________
> >>> Powered by www.kitware.com
> >>>
> >>> Visit other Kitware open-source projects at
> >>> http://www.kitware.com/opensource/opensource.html
> >>>
> >>> Kitware offers ITK Training Courses, for more information visit:
> >>> http://www.kitware.com/products/protraining.php
> >>>
> >>> Please keep messages on-topic and check the ITK FAQ at:
> >>> http://www.itk.org/Wiki/ITK_FAQ
> >>>
> >>> Follow this link to subscribe/unsubscribe:
> >>> http://public.kitware.com/mailman/listinfo/insight-users
> >>
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
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From mustafa at inode.at  Thu Oct 27 06:48:57 2016
From: mustafa at inode.at (Mustafa Arikan)
Date: Thu, 27 Oct 2016 12:48:57 +0200
Subject: [ITK] [ITK-users] Reading a DICOM file in SimpleITK and ITK
 (spacing error)
In-Reply-To: <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>
References: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
 <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>
Message-ID: <4de1b61f-e901-39d4-8410-34ec3bd6d226@inode.at>

Hi D?enan,

this is not the problem because the spacing is not 0. And other 
frameworks like ImageJ can
read the .dcm image and save it as a .mhd image.

best regards,
Mustafa

Am 10/24/2016 um 5:01 PM schrieb D?enan Zuki?:
> Hi Mustafa,
>
> since the offending .dcm is in folder "exports", I assume some tool's 
> DICOM export is broken. Spacing should never be 0. If spacing is not 
> known, it should be set to 1. ITK has a right to complain about this. 
> Can you re-export this file, and perhaps fiddle with export settings a 
> bit?
>
> Regards,
> D?enan
>
> On Mon, Oct 24, 2016 at 6:02 AM, Mustafa Arikan <mustafa at inode.at 
> <mailto:mustafa at inode.at>> wrote:
>
>     Dear all,
>
>     reading a DICOM file (.dcm) in SimpleITK leads to following problem:
>
>>     RuntimeError: Exception thrown in SimpleITK ReadImage:
>>     c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageBase.hxx:192:
>>     itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not
>>     allowed: Spacing is [0, 0, 1]
>
>     The code looks like this:
>
>>     import SimpleITK
>>
>>     inputFileName =
>>     "D:\\workspace\\exports\\51871876-25-ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZVWGHRLQ+TNXWEN\\bscan.dcm"
>>     reader = SimpleITK.ImageSeriesReader()
>>     image= SimpleITK.ReadImage(inputFileName)
>>     reader.SetFileName ( inputFileName )
>>     imageIn = reader.Execute()
>
>     And I am getting the same error within ITK.
>
>     But opening the .dcm file with some DICOM-Viewer works.
>
>
>     thanks in advance,
>     Mustafa
>
>
>     _____________________________________
>     Powered by www.kitware.com <http://www.kitware.com>
>
>     Visit other Kitware open-source projects at
>     http://www.kitware.com/opensource/opensource.html
>     <http://www.kitware.com/opensource/opensource.html>
>
>     Kitware offers ITK Training Courses, for more information visit:
>     http://www.kitware.com/products/protraining.php
>     <http://www.kitware.com/products/protraining.php>
>
>     Please keep messages on-topic and check the ITK FAQ at:
>     http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
>     Follow this link to subscribe/unsubscribe:
>     http://public.kitware.com/mailman/listinfo/insight-users
>     <http://public.kitware.com/mailman/listinfo/insight-users>
>
>

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From blowekamp at mail.nih.gov  Thu Oct 27 09:02:33 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 27 Oct 2016 13:02:33 +0000
Subject: [ITK] [ITK-users] Reading a DICOM file in SimpleITK and ITK
 (spacing error)
In-Reply-To: <4de1b61f-e901-39d4-8410-34ec3bd6d226@inode.at>
References: <30d898e5-abaf-b47d-6fbc-b0321452bde8@inode.at>
 <CAPf2UMShOEXkZ1hRWrU6icUaoM+g+QPj5K5_A_tJdQKOqHfe-g@mail.gmail.com>
 <4de1b61f-e901-39d4-8410-34ec3bd6d226@inode.at>
Message-ID: <E3E0FCD5-D17E-4E39-A705-63E9B251783A@mail.nih.gov>

Hello,

ITK is a physical space aware image processing toolkit. It take into consideration the location, origin and SPACING when doing operations. Since an image with zero spacing has no physical size, ITK refuses to process it. From the physical perspective your image has no extent and does not exist. ITK can not process such data. Other toolkit are not physical space aware and just process pixels.

Please review the history of the file, and see where this error was introduced.

HTH,
Brad

On Oct 27, 2016, at 6:48 AM, Mustafa Arikan <mustafa at inode.at<mailto:mustafa at inode.at>> wrote:

Hi D?enan,

this is not the problem because the spacing is not 0. And other frameworks like ImageJ can
read the .dcm image and save it as a .mhd image.

best regards,
Mustafa

Am 10/24/2016 um 5:01 PM schrieb D?enan Zuki?:
Hi Mustafa,

since the offending .dcm is in folder "exports", I assume some tool's DICOM export is broken. Spacing should never be 0. If spacing is not known, it should be set to 1. ITK has a right to complain about this. Can you re-export this file, and perhaps fiddle with export settings a bit?

Regards,
D?enan

On Mon, Oct 24, 2016 at 6:02 AM, Mustafa Arikan <mustafa at inode.at<mailto:mustafa at inode.at>> wrote:

Dear all,

reading a DICOM file (.dcm) in SimpleITK leads to following problem:

RuntimeError: Exception thrown in SimpleITK ReadImage: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageBase.hxx:192:
itk::ERROR: Image(00000000163F8ED0): A spacing of 0 is not allowed: Spacing is [0, 0, 1]
<Mail Attachment.png>

The code looks like this:

import SimpleITK

inputFileName = "D:\\workspace\\exports\\<smb://workspace//exports//>51871876-25-ARTGGEANMAADQAAVSEGAJEAMD+BWSTZRRGTFTMNECYDQVUXOXNNVNTRZVWGHRLQ+TNXWEN\\bscan.dcm"
reader = SimpleITK.ImageSeriesReader()
image= SimpleITK.ReadImage(inputFileName)
reader.SetFileName ( inputFileName )
imageIn = reader.Execute()

And I am getting the same error within ITK.

But opening the .dcm file with some DICOM-Viewer works.


thanks in advance,
Mustafa

_____________________________________
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_____________________________________
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From nkwmailinglists at gmail.com  Thu Oct 27 12:57:28 2016
From: nkwmailinglists at gmail.com (Kent Williams)
Date: Thu, 27 Oct 2016 16:57:28 +0000
Subject: [ITK] [ITK-users] RandomImageSource is terrible no good not very
	random?
Message-ID: <CAA4Dnn0Zbmd4M=R3uGULL0JNkvdRbApv9taNV8SuHHByngoQfw@mail.gmail.com>

I realize that itk::RandomImageSource is not meant to be a perfect source
of randomness.  But it is pretty bad.  I was trying to generate a noise
video with ITK -- by writing out 2D Images and then combining them using
FFMPEG -- and A) for a given set of dimensions, itk::RandomImageSource
generates exactly the same image. and B) the resulting image is clearly not
that random.

I got better results (without much speed penalty) calling drand48 once per
pixel.

Link to image generated: https://flic.kr/p/Nz1p7w

#include <iostream>
#include <stdio.h>
#include <sys/types.h>
#include <unistd.h>
#include <itkImage.h>
#include <itkImageFileWriter.h>
#include <itkImageRegionIterator.h>
#include <itkRandomImageSource.h>
#include <time.h>
#include <stdlib.h>
typedef itk::Image<unsigned char,2> ImageType;
typedef itk::ImageFileWriter<ImageType> ImageFileWriter;
typedef itk::RandomImageSource<ImageType> RandomImageSource;
typedef itk::ImageRegionIterator<ImageType> Iterator;

// 1080p
//const int XSize(1920);
//const int YSize(1080);
const int XSize(1280);
const int YSize(720);

int main(int argc, char **argv) {


ImageType::SizeType imageSize;
imageSize[0] = XSize;
imageSize[1] = YSize;
// only used for the first GetBufferPointer method
ImageType::Pointer image = ImageType::New();
image->SetRegions(imageSize);
image->Allocate();

ImageFileWriter::Pointer writer = ImageFileWriter::New();
for(unsigned i = 0; i < (60*24); ++i) {
char fname[256];
sprintf(fname,"%04u.tiff", i);
writer->SetFileName(fname);
#if 0
// fill buffer with lrand48 results
unsigned char *cp = image->GetBufferPointer();
unsigned char *end = cp + (XSize * YSize);
for(; cp < end; ++cp)
*cp = lrand48();
writer->SetInput(image);
#else
srand48(getpid() + time(NULL));
RandomImageSource::Pointer rndSource = RandomImageSource::New();
rndSource->SetSize(imageSize);
writer->SetInput(rndSource->GetOutput());
#endif
writer->Update();
std::cout << i << std::endl;
}
}
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From nkwmailinglists at gmail.com  Thu Oct 27 13:00:09 2016
From: nkwmailinglists at gmail.com (Kent Williams)
Date: Thu, 27 Oct 2016 17:00:09 +0000
Subject: [ITK] [ITK-users] Output to video
Message-ID: <CAA4Dnn322yKfw6te=EGFMbUxY7kaY-XNRBNpNez6HbiOru+xpA@mail.gmail.com>

Is VTK the only way to generate a video file from a series of 2D frames?

I've not been following ITK for a while and don't know how far the library
has progressed with video output.
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From matt.mccormick at kitware.com  Thu Oct 27 13:07:26 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Oct 2016 13:07:26 -0400
Subject: [ITK] [ITK-users] Output to video
In-Reply-To: <CAA4Dnn322yKfw6te=EGFMbUxY7kaY-XNRBNpNez6HbiOru+xpA@mail.gmail.com>
References: <CAA4Dnn322yKfw6te=EGFMbUxY7kaY-XNRBNpNez6HbiOru+xpA@mail.gmail.com>
Message-ID: <CALzTN-SXASYiazVPDnOWMjhzwfDovE9dkP17uP+d7X-gF203mA@mail.gmail.com>

Hi Kent!

Yes, we have video IO now in ITK:

  https://itk.org/Insight/Doxygen/html/group__ITKVideoIO.html

Cheers,
Matt

On Thu, Oct 27, 2016 at 1:00 PM, Kent Williams
<nkwmailinglists at gmail.com> wrote:
> Is VTK the only way to generate a video file from a series of 2D frames?
>
> I've not been following ITK for a while and don't know how far the library
> has progressed with video output.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From matt.mccormick at kitware.com  Thu Oct 27 13:08:19 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 27 Oct 2016 13:08:19 -0400
Subject: [ITK] [ITK-users] RandomImageSource is terrible no good not
	very	random?
In-Reply-To: <CAA4Dnn0Zbmd4M=R3uGULL0JNkvdRbApv9taNV8SuHHByngoQfw@mail.gmail.com>
References: <CAA4Dnn0Zbmd4M=R3uGULL0JNkvdRbApv9taNV8SuHHByngoQfw@mail.gmail.com>
Message-ID: <CALzTN-QfYXuopTs=vw_gmJYV5rxRyfpot-_7CkGTqwWXcsc-WA@mail.gmail.com>

Hi Kent,

For A), the seed needs to be changed to get a different output.

HTH,
Matt

On Thu, Oct 27, 2016 at 12:57 PM, Kent Williams
<nkwmailinglists at gmail.com> wrote:
> I realize that itk::RandomImageSource is not meant to be a perfect source of
> randomness.  But it is pretty bad.  I was trying to generate a noise video
> with ITK -- by writing out 2D Images and then combining them using FFMPEG --
> and A) for a given set of dimensions, itk::RandomImageSource generates
> exactly the same image. and B) the resulting image is clearly not that
> random.
>
> I got better results (without much speed penalty) calling drand48 once per
> pixel.
>
> Link to image generated: https://flic.kr/p/Nz1p7w
>
> #include <iostream>
> #include <stdio.h>
> #include <sys/types.h>
> #include <unistd.h>
> #include <itkImage.h>
> #include <itkImageFileWriter.h>
> #include <itkImageRegionIterator.h>
> #include <itkRandomImageSource.h>
> #include <time.h>
> #include <stdlib.h>
> typedef itk::Image<unsigned char,2> ImageType;
> typedef itk::ImageFileWriter<ImageType> ImageFileWriter;
> typedef itk::RandomImageSource<ImageType> RandomImageSource;
> typedef itk::ImageRegionIterator<ImageType> Iterator;
>
> // 1080p
> //const int XSize(1920);
> //const int YSize(1080);
> const int XSize(1280);
> const int YSize(720);
>
> int main(int argc, char **argv) {
>
>
> ImageType::SizeType imageSize;
> imageSize[0] = XSize;
> imageSize[1] = YSize;
> // only used for the first GetBufferPointer method
> ImageType::Pointer image = ImageType::New();
> image->SetRegions(imageSize);
> image->Allocate();
>
> ImageFileWriter::Pointer writer = ImageFileWriter::New();
> for(unsigned i = 0; i < (60*24); ++i) {
> char fname[256];
> sprintf(fname,"%04u.tiff", i);
> writer->SetFileName(fname);
> #if 0
> // fill buffer with lrand48 results
> unsigned char *cp = image->GetBufferPointer();
> unsigned char *end = cp + (XSize * YSize);
> for(; cp < end; ++cp)
> *cp = lrand48();
> writer->SetInput(image);
> #else
> srand48(getpid() + time(NULL));
> RandomImageSource::Pointer rndSource = RandomImageSource::New();
> rndSource->SetSize(imageSize);
> writer->SetInput(rndSource->GetOutput());
> #endif
> writer->Update();
> std::cout << i << std::endl;
> }
> }
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From tofijoy at gmail.com  Thu Oct 27 13:26:03 2016
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Thu, 27 Oct 2016 13:26:03 -0400
Subject: [ITK] itk::Image serialization
Message-ID: <CAHE0P1VAiV3wSi4p3Of_o8k7rZ9YQVz5dkVA-treJ9s-TNTytA@mail.gmail.com>

Hi all,

Does ITK provide APIs to serialize and de-reserialize an itk::Image object
for the purpose of sending and receiving an image over a network?

In other words, I'm looking for APIs like this:

unsigned char* serializeImage(itk::Image::Pointer) - gives me a memory
buffer containing all image metadata and data

itk::Image::Pointer deserializeImage(unsigned char* buf) - gives me an
image object from a memory buffer created using serializeImage.

Do APIs like the above already exist?

Many thanks,
--Fijoy
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From mrguilfoyle at gmail.com  Fri Oct 28 10:11:19 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Fri, 28 Oct 2016 15:11:19 +0100
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
Message-ID: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>

Hi

SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan

This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.

Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).

Not an immediate problem as working with R 3.2.5 is ok.

The error message I get is:

In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
                                             ^
/usr/include/string.h:76:7: note: previous declaration is here
char    *strchr(const char *, int);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
                                             ^
/usr/include/string.h:86:7: note: previous declaration is here
char    *strpbrk(const char *, const char *);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
                                             ^
/usr/include/string.h:87:7: note: previous declaration is here
char    *strrchr(const char *, int);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
                                             ^
/usr/include/string.h:70:7: note: previous declaration is here
void    *memchr(const void *, int, size_t);
         ^
In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
                                             ^
/usr/include/string.h:89:7: note: previous declaration is here
char    *strstr(const char *, const char *);
         ^
5 errors generated.
make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
make: *** [all] Error 2
+ exit 1
ERROR: configuration failed for package ?SimpleITK?
* removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
Error: Command failed (1)
_____________________________________
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http://www.kitware.com/products/protraining.php

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From blowekamp at mail.nih.gov  Fri Oct 28 10:27:50 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 28 Oct 2016 14:27:50 +0000
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
Message-ID: <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>

Hello,

Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?

This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.

I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.

HTH,
Brad

[1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework

> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> 
> Hi
> 
> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
> 
> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
> 
> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
> 
> Not an immediate problem as working with R 3.2.5 is ok.
> 
> The error message I get is:
> 
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
>                                             ^
> /usr/include/string.h:76:7: note: previous declaration is here
> char    *strchr(const char *, int);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
>                                             ^
> /usr/include/string.h:86:7: note: previous declaration is here
> char    *strpbrk(const char *, const char *);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
>                                             ^
> /usr/include/string.h:87:7: note: previous declaration is here
> char    *strrchr(const char *, int);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
>                                             ^
> /usr/include/string.h:70:7: note: previous declaration is here
> void    *memchr(const void *, int, size_t);
>         ^
> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
>                                             ^
> /usr/include/string.h:89:7: note: previous declaration is here
> char    *strstr(const char *, const char *);
>         ^
> 5 errors generated.
> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> make[3]: *** [all] Error 2
> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> make: *** [all] Error 2
> + exit 1
> ERROR: configuration failed for package ?SimpleITK?
> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
> Error: Command failed (1)
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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_____________________________________
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From blowekamp at mail.nih.gov  Fri Oct 28 10:46:08 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 28 Oct 2016 14:46:08 +0000
Subject: [ITK] [ITK-dev] Problem with ImageRegistrationMethodv4 and setting
	the	VirtualDomain
Message-ID: <C6B78FD9-0FF3-497F-AB8C-2CF47747EB5D@mail.nih.gov>

Hi!

I am trying to add the VirtualDomain as an option to the SimpleITK ImageRegistrationMethod. I have does so here [1].

This method for setting the virtual domain follows the SimpleImageRegistrationTest / Example by setting the VirtualDomain on the Metric[2].

The test created in SimpleITK registers two gaussian blobs with a translation transform. The fixed image has it?s origin set to (5,100), and the FixedInitalTransform is set to a translation transform with the same 5,100 offset. This should map the 0-origined virtual domain to the same index on the fixed image, to essentially be an identity translation between then virtual domain and the fixed image when the origin and transform is take into consideration. This test fails with the following error:

MeanSquaresImageToImageMetricv4 (0x66f8930): No valid points were found during metric evaluation. For image metrics, verify that the images overlap appropriately. For instance, you can align the image centers by translation. For point-set metrics, verify that the fixed points, once transformed into the virtual domain space, actually lie within the virtual domain.

This is an indication the transforms are not being applied as I expect. My expectation of how the transforms should be applied here [3].

Digging into the code, I see that the ImageRegistrationMethod always sets the VirtualDomain here [4], to the FixedImage. This clobbers the value set directly to the Metric as in the example/test[2]. Hacking the code to use the GetCurrentLevelVirtualDomainImage() does get my one case to work.

Suggestions on how to correct this issue, or a patch are welcomed!

Thanks,
Brad


[1] http://review.source.kitware.com/#/c/21540/2
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/test/itkSimpleImageRegistrationTest.cxx#L162
[3] http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/61_Registration_Introduction_Continued.html#Version-1.1
[4] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L409-L415
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From mrguilfoyle at gmail.com  Fri Oct 28 11:36:01 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Fri, 28 Oct 2016 16:36:01 +0100
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
Message-ID: <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>

Xcode 8.1 (updated yesterday)
I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.

Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?



> On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> 
> Hello,
> 
> Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> 
> This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> 
> I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.
> 
> HTH,
> Brad
> 
> [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> 
>> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
>> 
>> Hi
>> 
>> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
>> 
>> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
>> 
>> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
>> 
>> Not an immediate problem as working with R 3.2.5 is ok.
>> 
>> The error message I get is:
>> 
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
>>                                            ^
>> /usr/include/string.h:76:7: note: previous declaration is here
>> char    *strchr(const char *, int);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
>>                                            ^
>> /usr/include/string.h:86:7: note: previous declaration is here
>> char    *strpbrk(const char *, const char *);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
>>                                            ^
>> /usr/include/string.h:87:7: note: previous declaration is here
>> char    *strrchr(const char *, int);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
>> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
>>                                            ^
>> /usr/include/string.h:70:7: note: previous declaration is here
>> void    *memchr(const void *, int, size_t);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
>>                                            ^
>> /usr/include/string.h:89:7: note: previous declaration is here
>> char    *strstr(const char *, const char *);
>>        ^
>> 5 errors generated.
>> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
>> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
>> make[3]: *** [all] Error 2
>> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
>> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
>> make: *** [all] Error 2
>> + exit 1
>> ERROR: configuration failed for package ?SimpleITK?
>> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
>> Error: Command failed (1)
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
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>> 
>> Follow this link to subscribe/unsubscribe:
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> 

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From ntustison at gmail.com  Fri Oct 28 11:48:43 2016
From: ntustison at gmail.com (Nicholas Tustison)
Date: Fri, 28 Oct 2016 08:48:43 -0700
Subject: [ITK] [ITK-dev] Problem with ImageRegistrationMethodv4 and
 setting the VirtualDomain
In-Reply-To: <C6B78FD9-0FF3-497F-AB8C-2CF47747EB5D@mail.nih.gov>
References: <C6B78FD9-0FF3-497F-AB8C-2CF47747EB5D@mail.nih.gov>
Message-ID: <5456BF25-2B4A-4B8A-95D5-9664869D30E0@gmail.com>

Hi Brad,

Thanks for looking into this.  Although specific components of the registration
framework were designed to work with a generic virtual domain image (such 
as the similarity metrics), that?s not the case for the framework in it?s entirety. 
When we wrote the image registration methods, we hard-coded various 
choices such as the use of the fixed image as the virtual domain image.  More
work would be required to generalize this.

Nick


> On Oct 28, 2016, at 7:46 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> 
> Hi!
> 
> I am trying to add the VirtualDomain as an option to the SimpleITK ImageRegistrationMethod. I have does so here [1].
> 
> This method for setting the virtual domain follows the SimpleImageRegistrationTest / Example by setting the VirtualDomain on the Metric[2].
> 
> The test created in SimpleITK registers two gaussian blobs with a translation transform. The fixed image has it?s origin set to (5,100), and the FixedInitalTransform is set to a translation transform with the same 5,100 offset. This should map the 0-origined virtual domain to the same index on the fixed image, to essentially be an identity translation between then virtual domain and the fixed image when the origin and transform is take into consideration. This test fails with the following error:
> 
> MeanSquaresImageToImageMetricv4 (0x66f8930): No valid points were found during metric evaluation. For image metrics, verify that the images overlap appropriately. For instance, you can align the image centers by translation. For point-set metrics, verify that the fixed points, once transformed into the virtual domain space, actually lie within the virtual domain.
> 
> This is an indication the transforms are not being applied as I expect. My expectation of how the transforms should be applied here [3].
> 
> Digging into the code, I see that the ImageRegistrationMethod always sets the VirtualDomain here [4], to the FixedImage. This clobbers the value set directly to the Metric as in the example/test[2]. Hacking the code to use the GetCurrentLevelVirtualDomainImage() does get my one case to work.
> 
> Suggestions on how to correct this issue, or a patch are welcomed!
> 
> Thanks,
> Brad
> 
> 
> [1] http://review.source.kitware.com/#/c/21540/2 <http://review.source.kitware.com/#/c/21540/2>
> [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/test/itkSimpleImageRegistrationTest.cxx#L162 <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/test/itkSimpleImageRegistrationTest.cxx#L162>
> [3] http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/61_Registration_Introduction_Continued.html#Version-1.1 <http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/61_Registration_Introduction_Continued.html#Version-1.1>
> [4] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L409-L415 <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L409-L415>
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From blowekamp at mail.nih.gov  Fri Oct 28 12:01:49 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 28 Oct 2016 16:01:49 +0000
Subject: [ITK] [ITK-dev] Problem with ImageRegistrationMethodv4 and
 setting the VirtualDomain
In-Reply-To: <5456BF25-2B4A-4B8A-95D5-9664869D30E0@gmail.com>
References: <C6B78FD9-0FF3-497F-AB8C-2CF47747EB5D@mail.nih.gov>
 <5456BF25-2B4A-4B8A-95D5-9664869D30E0@gmail.com>
Message-ID: <B97959B9-29EF-420D-AE2A-17D592DFC666@mail.nih.gov>

Interesting. But the InitialFixedTransform is made available. I am not sure how that could be used with out the virtual domain.

After looking at it a bit more it doesn?t look too hard. Here is my attempt at it:
http://review.source.kitware.com/#/c/21675/1

Please let know know if this is close to a usable solution.

Thanks,
Brad

On Oct 28, 2016, at 11:48 AM, Nicholas Tustison <ntustison at gmail.com<mailto:ntustison at gmail.com>> wrote:

Hi Brad,

Thanks for looking into this.  Although specific components of the registration
framework were designed to work with a generic virtual domain image (such
as the similarity metrics), that?s not the case for the framework in it?s entirety.
When we wrote the image registration methods, we hard-coded various
choices such as the use of the fixed image as the virtual domain image.  More
work would be required to generalize this.

Nick


On Oct 28, 2016, at 7:46 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:

Hi!

I am trying to add the VirtualDomain as an option to the SimpleITK ImageRegistrationMethod. I have does so here [1].

This method for setting the virtual domain follows the SimpleImageRegistrationTest / Example by setting the VirtualDomain on the Metric[2].

The test created in SimpleITK registers two gaussian blobs with a translation transform. The fixed image has it?s origin set to (5,100), and the FixedInitalTransform is set to a translation transform with the same 5,100 offset. This should map the 0-origined virtual domain to the same index on the fixed image, to essentially be an identity translation between then virtual domain and the fixed image when the origin and transform is take into consideration. This test fails with the following error:

MeanSquaresImageToImageMetricv4 (0x66f8930): No valid points were found during metric evaluation. For image metrics, verify that the images overlap appropriately. For instance, you can align the image centers by translation. For point-set metrics, verify that the fixed points, once transformed into the virtual domain space, actually lie within the virtual domain.

This is an indication the transforms are not being applied as I expect. My expectation of how the transforms should be applied here [3].

Digging into the code, I see that the ImageRegistrationMethod always sets the VirtualDomain here [4], to the FixedImage. This clobbers the value set directly to the Metric as in the example/test[2]. Hacking the code to use the GetCurrentLevelVirtualDomainImage() does get my one case to work.

Suggestions on how to correct this issue, or a patch are welcomed!

Thanks,
Brad


[1] http://review.source.kitware.com/#/c/21540/2
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/test/itkSimpleImageRegistrationTest.cxx#L162
[3] http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/61_Registration_Introduction_Continued.html#Version-1.1
[4] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L409-L415


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From ntustison at gmail.com  Fri Oct 28 12:45:24 2016
From: ntustison at gmail.com (Nicholas Tustison)
Date: Fri, 28 Oct 2016 09:45:24 -0700
Subject: [ITK] [ITK-dev] Problem with ImageRegistrationMethodv4 and
 setting the VirtualDomain
In-Reply-To: <B97959B9-29EF-420D-AE2A-17D592DFC666@mail.nih.gov>
References: <C6B78FD9-0FF3-497F-AB8C-2CF47747EB5D@mail.nih.gov>
 <5456BF25-2B4A-4B8A-95D5-9664869D30E0@gmail.com>
 <B97959B9-29EF-420D-AE2A-17D592DFC666@mail.nih.gov>
Message-ID: <BA7B9E7C-2380-4D39-AE6E-F7F345557907@gmail.com>

You?re right in that the FIxedInitialTransform is available but it could?ve simply
been an oversight on my part.  I know I tried to keep the class as general as
possible while knowing that actually exercising the virtual domain image as 
anything other than the fixed image would take more work.  I can?t remember
exactly.  The problem is that I?ve made so many significant changes to that 
class (e.g., point sets, multiple metrics, accommodating changes to the specialized
ImageRegistrationMethods), that I can?t quite remember how it has evolved 
to its current state.

At first glance, your fix looks fine to me.   It passes all the tests and so I?m 
guessing we should merge and I?ll see if ANTs has any associated hiccups
which I?m sure we can easily fix.



> On Oct 28, 2016, at 9:01 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> 
> Interesting. But the InitialFixedTransform is made available. I am not sure how that could be used with out the virtual domain.
> 
> After looking at it a bit more it doesn?t look too hard. Here is my attempt at it:
> http://review.source.kitware.com/#/c/21675/1 <http://review.source.kitware.com/#/c/21675/1>
> 
> Please let know know if this is close to a usable solution.
> 
> Thanks,
> Brad
> 
>> On Oct 28, 2016, at 11:48 AM, Nicholas Tustison <ntustison at gmail.com <mailto:ntustison at gmail.com>> wrote:
>> 
>> Hi Brad,
>> 
>> Thanks for looking into this.  Although specific components of the registration
>> framework were designed to work with a generic virtual domain image (such 
>> as the similarity metrics), that?s not the case for the framework in it?s entirety. 
>> When we wrote the image registration methods, we hard-coded various 
>> choices such as the use of the fixed image as the virtual domain image.  More
>> work would be required to generalize this.
>> 
>> Nick
>> 
>> 
>>> On Oct 28, 2016, at 7:46 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov <mailto:blowekamp at mail.nih.gov>> wrote:
>>> 
>>> Hi!
>>> 
>>> I am trying to add the VirtualDomain as an option to the SimpleITK ImageRegistrationMethod. I have does so here [1].
>>> 
>>> This method for setting the virtual domain follows the SimpleImageRegistrationTest / Example by setting the VirtualDomain on the Metric[2].
>>> 
>>> The test created in SimpleITK registers two gaussian blobs with a translation transform. The fixed image has it?s origin set to (5,100), and the FixedInitalTransform is set to a translation transform with the same 5,100 offset. This should map the 0-origined virtual domain to the same index on the fixed image, to essentially be an identity translation between then virtual domain and the fixed image when the origin and transform is take into consideration. This test fails with the following error:
>>> 
>>> MeanSquaresImageToImageMetricv4 (0x66f8930): No valid points were found during metric evaluation. For image metrics, verify that the images overlap appropriately. For instance, you can align the image centers by translation. For point-set metrics, verify that the fixed points, once transformed into the virtual domain space, actually lie within the virtual domain.
>>> 
>>> This is an indication the transforms are not being applied as I expect. My expectation of how the transforms should be applied here [3].
>>> 
>>> Digging into the code, I see that the ImageRegistrationMethod always sets the VirtualDomain here [4], to the FixedImage. This clobbers the value set directly to the Metric as in the example/test[2]. Hacking the code to use the GetCurrentLevelVirtualDomainImage() does get my one case to work.
>>> 
>>> Suggestions on how to correct this issue, or a patch are welcomed!
>>> 
>>> Thanks,
>>> Brad
>>> 
>>> 
>>> [1] http://review.source.kitware.com/#/c/21540/2 <http://review.source.kitware.com/#/c/21540/2>
>>> [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/test/itkSimpleImageRegistrationTest.cxx#L162 <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/test/itkSimpleImageRegistrationTest.cxx#L162>
>>> [3] http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/61_Registration_Introduction_Continued.html#Version-1.1 <http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/61_Registration_Introduction_Continued.html#Version-1.1>
>>> [4] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L409-L415 <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx#L409-L415>
> 

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From richard.beare at gmail.com  Fri Oct 28 17:31:43 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Sat, 29 Oct 2016 08:31:43 +1100
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
Message-ID: <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>

A while back I made an update to swig to do with the way the various R
header files were included in the swig generated code. The errors prompting
that change seemed similar to what you were seeing. Those changes have been
merged into the master swig, but probably haven't made it into a release
yet. You could try giving the superbuild a go with the "system" swig you've
built by hand, or possibly use the "swig from git" option in superbuild.
Note that this last option requires an automake installation too - the brew
version works OK.

On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> Xcode 8.1 (updated yesterday)
> I've checked both R 3.2.5 and R 3.3.1 and they both report
> LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
>
> Looking at the differences in the Rdefines.h header file  (mentioned in
> the error report) between R versions it is documented that this has been
> changed from R 3.3.0 onwards.  Several of the definitions at the top of the
> file are now prepended with Rf_ .  I don't pretend to understand the
> reasons for or implications of this but seems likely to be at least part of
> the problem?
>
>
>
> > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
> >
> > Hello,
> >
> > Do you know what version of Xcode you are using? What OS X SDK is being
> used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> >
> > This seems like it is some type of incompatibility with versions of
> Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> >
> > I am not certain what R compiler flags are passed to the SimpleITK build
> with the ?devtools? method, but some of the above may not match the way the
> old R was compiled.
> >
> > HTH,
> > Brad
> >
> > [1] http://stackoverflow.com/questions/17461196/
> determining-os-x-sdk-and-deployment-target-versions-from-framework
> >
> >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> >>
> >> Hi
> >>
> >> SimpleITK with R wrapping does not build successfully against R 3.3.1
> on OS X 10.11.6 ElCapitan
> >>
> >> This fails both using the devtools method from within R, and when
> trying to build the SuperBuild via Cmake with R wrapping turned on.
> >>
> >> Both methods work fine against the most recent prior R release
> 3.2.4-revised (subsequently relabelled 3.2.5).
> >>
> >> Not an immediate problem as working with R 3.2.5 is ok.
> >>
> >> The error message I get is:
> >>
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error:
> conflicting types for 'strchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s,
> int __c) {return ::strchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:76:7: note: previous declaration is here
> >> char    *strchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error:
> conflicting types for 'strpbrk'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1,
> const char* __s2) {return ::strpbrk(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:86:7: note: previous declaration is here
> >> char    *strpbrk(const char *, const char *);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error:
> conflicting types for 'strrchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s,
> int __c) {return ::strrchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:87:7: note: previous declaration is here
> >> char    *strrchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error:
> conflicting types for 'memchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s,
> int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> >>                                            ^
> >> /usr/include/string.h:70:7: note: previous declaration is here
> >> void    *memchr(const void *, int, size_t);
> >>        ^
> >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error:
> conflicting types for 'strstr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1,
> const char* __s2) {return ::strstr(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:89:7: note: previous declaration is here
> >> char    *strstr(const char *, const char *);
> >>        ^
> >> 5 errors generated.
> >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o]
> Error 1
> >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> >> make[3]: *** [all] Error 2
> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build]
> Error 2
> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> >> make: *** [all] Error 2
> >> + exit 1
> >> ERROR: configuration failed for package ?SimpleITK?
> >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/SimpleITK?
> >> Error: Command failed (1)
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
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From mrguilfoyle at gmail.com  Sat Oct 29 04:51:53 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Sat, 29 Oct 2016 09:51:53 +0100
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
Message-ID: <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>

Hi Richard

I've tried using the patched swig you provided several months ago and the latest swig from git option - SimpleITK compiles without error against R 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with either.  The problem previously was not failing to build but string-handling errors generated using certain R-SimpleITK functions.  As mentioned there has been a change in certain header files since 3.3.0 which presumably relates to the problem?  Happy to do any further testing you suggest.


> On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> 
> A while back I made an update to swig to do with the way the various R header files were included in the swig generated code. The errors prompting that change seemed similar to what you were seeing. Those changes have been merged into the master swig, but probably haven't made it into a release yet. You could try giving the superbuild a go with the "system" swig you've built by hand, or possibly use the "swig from git" option in superbuild. Note that this last option requires an automake installation too - the brew version works OK.
> 
> On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> Xcode 8.1 (updated yesterday)
> I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
> 
> Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?
> 
> 
> 
> > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> >
> > Hello,
> >
> > Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> >
> > This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> >
> > I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.
> >
> > HTH,
> > Brad
> >
> > [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> >
> >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> >>
> >> Hi
> >>
> >> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
> >>
> >> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
> >>
> >> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
> >>
> >> Not an immediate problem as working with R 3.2.5 is ok.
> >>
> >> The error message I get is:
> >>
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:76:7: note: previous declaration is here
> >> char    *strchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:86:7: note: previous declaration is here
> >> char    *strpbrk(const char *, const char *);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:87:7: note: previous declaration is here
> >> char    *strrchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> >>                                            ^
> >> /usr/include/string.h:70:7: note: previous declaration is here
> >> void    *memchr(const void *, int, size_t);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:89:7: note: previous declaration is here
> >> char    *strstr(const char *, const char *);
> >>        ^
> >> 5 errors generated.
> >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
> >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> >> make[3]: *** [all] Error 2
> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> >> make: *** [all] Error 2
> >> + exit 1
> >> ERROR: configuration failed for package ?SimpleITK?
> >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
> >> Error: Command failed (1)
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> 

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From richard.beare at gmail.com  Sat Oct 29 18:40:52 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Sun, 30 Oct 2016 09:40:52 +1100
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
 <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
Message-ID: <CA+V7QS_pOBXSchSsoom1K0WokKBWeqbHrW2XxdL=pvXk2XOSzw@mail.gmail.com>

I haven't been building on the mac for a while, so I'd better check it out.

On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> Hi Richard
>
> I've tried using the patched swig you provided several months ago and the
> latest swig from git option - SimpleITK compiles without error against R
> 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with
> either.  The problem previously was not failing to build but
> string-handling errors generated using certain R-SimpleITK functions.  As
> mentioned there has been a change in certain header files since 3.3.0 which
> presumably relates to the problem?  Happy to do any further testing you
> suggest.
>
>
> > On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> >
> > A while back I made an update to swig to do with the way the various R
> header files were included in the swig generated code. The errors prompting
> that change seemed similar to what you were seeing. Those changes have been
> merged into the master swig, but probably haven't made it into a release
> yet. You could try giving the superbuild a go with the "system" swig you've
> built by hand, or possibly use the "swig from git" option in superbuild.
> Note that this last option requires an automake installation too - the brew
> version works OK.
> >
> > On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > Xcode 8.1 (updated yesterday)
> > I've checked both R 3.2.5 and R 3.3.1 and they both report
> LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
> >
> > Looking at the differences in the Rdefines.h header file  (mentioned in
> the error report) between R versions it is documented that this has been
> changed from R 3.3.0 onwards.  Several of the definitions at the top of the
> file are now prepended with Rf_ .  I don't pretend to understand the
> reasons for or implications of this but seems likely to be at least part of
> the problem?
> >
> >
> >
> > > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
> > >
> > > Hello,
> > >
> > > Do you know what version of Xcode you are using? What OS X SDK is
> being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> > >
> > > This seems like it is some type of incompatibility with versions of
> Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> > >
> > > I am not certain what R compiler flags are passed to the SimpleITK
> build with the ?devtools? method, but some of the above may not match the
> way the old R was compiled.
> > >
> > > HTH,
> > > Brad
> > >
> > > [1] http://stackoverflow.com/questions/17461196/
> determining-os-x-sdk-and-deployment-target-versions-from-framework
> > >
> > >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > >>
> > >> Hi
> > >>
> > >> SimpleITK with R wrapping does not build successfully against R 3.3.1
> on OS X 10.11.6 ElCapitan
> > >>
> > >> This fails both using the devtools method from within R, and when
> trying to build the SuperBuild via Cmake with R wrapping turned on.
> > >>
> > >> Both methods work fine against the most recent prior R release
> 3.2.4-revised (subsequently relabelled 3.2.5).
> > >>
> > >> Not an immediate problem as working with R 3.2.5 is ok.
> > >>
> > >> The error message I get is:
> > >>
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error:
> conflicting types for 'strchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s,
> int __c) {return ::strchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:76:7: note: previous declaration is here
> > >> char    *strchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error:
> conflicting types for 'strpbrk'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char*
> __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:86:7: note: previous declaration is here
> > >> char    *strpbrk(const char *, const char *);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error:
> conflicting types for 'strrchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s,
> int __c) {return ::strrchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:87:7: note: previous declaration is here
> > >> char    *strrchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error:
> conflicting types for 'memchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s,
> int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> > >>                                            ^
> > >> /usr/include/string.h:70:7: note: previous declaration is here
> > >> void    *memchr(const void *, int, size_t);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error:
> conflicting types for 'strstr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1,
> const char* __s2) {return ::strstr(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:89:7: note: previous declaration is here
> > >> char    *strstr(const char *, const char *);
> > >>        ^
> > >> 5 errors generated.
> > >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o]
> Error 1
> > >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> > >> make[3]: *** [all] Error 2
> > >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build]
> Error 2
> > >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> > >> make: *** [all] Error 2
> > >> + exit 1
> > >> ERROR: configuration failed for package ?SimpleITK?
> > >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/SimpleITK?
> > >> Error: Command failed (1)
> > >> _____________________________________
> > >> Powered by www.kitware.com
> > >>
> > >> Visit other Kitware open-source projects at
> > >> http://www.kitware.com/opensource/opensource.html
> > >>
> > >> Kitware offers ITK Training Courses, for more information visit:
> > >> http://www.kitware.com/products/protraining.php
> > >>
> > >> Please keep messages on-topic and check the ITK FAQ at:
> > >> http://www.itk.org/Wiki/ITK_FAQ
> > >>
> > >> Follow this link to subscribe/unsubscribe:
> > >> http://public.kitware.com/mailman/listinfo/insight-users
> > >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
>
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From richard.beare at gmail.com  Sun Oct 30 05:04:47 2016
From: richard.beare at gmail.com (Richard Beare)
Date: Sun, 30 Oct 2016 20:04:47 +1100
Subject: [ITK] [ITK-users] SimpleITK build fail with R 3.3.1
In-Reply-To: <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
 <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
Message-ID: <CA+V7QS80v=1d8=eV1d_op5yxuSKzM5zmcpdW7N3Vb8gQfcEx5A@mail.gmail.com>

I'm seeing different failures on 3.3.1. Stuff to do with redefining length
in Rdefines.h. These problems seem to relate to sitkRArray.cxx.

It is a bit strange, but the fix for me is to add
#include <iostream>

before
#include <Rdefines.h>

in sitkRArray.cxx

This successfully builds the R package, but I get lots of link warnings
like this:

ld: warning: direct access in itk::LabelMap<itk::ShapeLabelObject<unsigned
long long, 2u> >::Graft(itk::DataObject const*) to global weak symbol
typeinfo name for itk::DataObject const* means the weak symbol cannot be
overridden at runtime. This was likely caused by different translation
units being compiled with different visibility settings.

On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> Hi Richard
>
> I've tried using the patched swig you provided several months ago and the
> latest swig from git option - SimpleITK compiles without error against R
> 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with
> either.  The problem previously was not failing to build but
> string-handling errors generated using certain R-SimpleITK functions.  As
> mentioned there has been a change in certain header files since 3.3.0 which
> presumably relates to the problem?  Happy to do any further testing you
> suggest.
>
>
> > On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> >
> > A while back I made an update to swig to do with the way the various R
> header files were included in the swig generated code. The errors prompting
> that change seemed similar to what you were seeing. Those changes have been
> merged into the master swig, but probably haven't made it into a release
> yet. You could try giving the superbuild a go with the "system" swig you've
> built by hand, or possibly use the "swig from git" option in superbuild.
> Note that this last option requires an automake installation too - the brew
> version works OK.
> >
> > On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > Xcode 8.1 (updated yesterday)
> > I've checked both R 3.2.5 and R 3.3.1 and they both report
> LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
> >
> > Looking at the differences in the Rdefines.h header file  (mentioned in
> the error report) between R versions it is documented that this has been
> changed from R 3.3.0 onwards.  Several of the definitions at the top of the
> file are now prepended with Rf_ .  I don't pretend to understand the
> reasons for or implications of this but seems likely to be at least part of
> the problem?
> >
> >
> >
> > > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
> > >
> > > Hello,
> > >
> > > Do you know what version of Xcode you are using? What OS X SDK is
> being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> > >
> > > This seems like it is some type of incompatibility with versions of
> Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> > >
> > > I am not certain what R compiler flags are passed to the SimpleITK
> build with the ?devtools? method, but some of the above may not match the
> way the old R was compiled.
> > >
> > > HTH,
> > > Brad
> > >
> > > [1] http://stackoverflow.com/questions/17461196/
> determining-os-x-sdk-and-deployment-target-versions-from-framework
> > >
> > >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
> wrote:
> > >>
> > >> Hi
> > >>
> > >> SimpleITK with R wrapping does not build successfully against R 3.3.1
> on OS X 10.11.6 ElCapitan
> > >>
> > >> This fails both using the devtools method from within R, and when
> trying to build the SuperBuild via Cmake with R wrapping turned on.
> > >>
> > >> Both methods work fine against the most recent prior R release
> 3.2.4-revised (subsequently relabelled 3.2.5).
> > >>
> > >> Not an immediate problem as working with R 3.2.5 is ok.
> > >>
> > >> The error message I get is:
> > >>
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error:
> conflicting types for 'strchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s,
> int __c) {return ::strchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:76:7: note: previous declaration is here
> > >> char    *strchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error:
> conflicting types for 'strpbrk'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char*
> __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:86:7: note: previous declaration is here
> > >> char    *strpbrk(const char *, const char *);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error:
> conflicting types for 'strrchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s,
> int __c) {return ::strrchr(__s, __c);}
> > >>                                            ^
> > >> /usr/include/string.h:87:7: note: previous declaration is here
> > >> char    *strrchr(const char *, int);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error:
> conflicting types for 'memchr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s,
> int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> > >>                                            ^
> > >> /usr/include/string.h:70:7: note: previous declaration is here
> > >> void    *memchr(const void *, int, size_t);
> > >>        ^
> > >> In file included from /private/var/folders/qy/
> 0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/
> SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-
> build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/Rdefines.h:33:
> > >> In file included from /Library/Frameworks/R.
> framework/Headers/R_ext/RS.h:27:
> > >> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error:
> conflicting types for 'strstr'
> > >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1,
> const char* __s2) {return ::strstr(__s1, __s2);}
> > >>                                            ^
> > >> /usr/include/string.h:89:7: note: previous declaration is here
> > >> char    *strstr(const char *, const char *);
> > >>        ^
> > >> 5 errors generated.
> > >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o]
> Error 1
> > >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> > >> make[3]: *** [all] Error 2
> > >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build]
> Error 2
> > >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> > >> make: *** [all] Error 2
> > >> + exit 1
> > >> ERROR: configuration failed for package ?SimpleITK?
> > >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/SimpleITK?
> > >> Error: Command failed (1)
> > >> _____________________________________
> > >> Powered by www.kitware.com
> > >>
> > >> Visit other Kitware open-source projects at
> > >> http://www.kitware.com/opensource/opensource.html
> > >>
> > >> Kitware offers ITK Training Courses, for more information visit:
> > >> http://www.kitware.com/products/protraining.php
> > >>
> > >> Please keep messages on-topic and check the ITK FAQ at:
> > >> http://www.itk.org/Wiki/ITK_FAQ
> > >>
> > >> Follow this link to subscribe/unsubscribe:
> > >> http://public.kitware.com/mailman/listinfo/insight-users
> > >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
>
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From kolin9105 at gmail.com  Sun Oct 30 14:15:05 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Mon, 31 Oct 2016 01:15:05 +0700
Subject: [ITK] [ITK-users] my problem
Message-ID: <CAEiw7u5oRqSAFZod69MuwqaBE342ufrwS_KGkACXHcORy5sYhg@mail.gmail.com>

hello everyone I am beginner in ITK.
I got  a problem in my thesis with ITK.
I find different result between using ITK and using imagej.
in itk I am working with BinaryThresholdImageFilter.
O.dcm using ITK
IM-0001-0009.jpeg using Imagej
what I have to do????
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From ivan.granata.na at gmail.com  Mon Oct 31 05:09:34 2016
From: ivan.granata.na at gmail.com (ivan)
Date: Mon, 31 Oct 2016 02:09:34 -0700 (MST)
Subject: [ITK] [ITK-users] Simple ITK Wavelet Transform ?? it is possible?
Message-ID: <1477904974504-37723.post@n7.nabble.com>

Is it possibile to apply a wavelet transform to an image in SimpleITK?
Thx



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Simple-ITK-Wavelet-Transform-it-is-possible-tp37723.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From blowekamp at mail.nih.gov  Mon Oct 31 08:54:38 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 31 Oct 2016 12:54:38 +0000
Subject: [ITK] [ITK-users] Simple ITK Wavelet Transform ?? it is
	possible?
In-Reply-To: <1477904974504-37723.post@n7.nabble.com>
References: <1477904974504-37723.post@n7.nabble.com>
Message-ID: <A2499A6A-F970-4E13-BAF5-9E83E775F9E1@mail.nih.gov>

Hello,

I am unaware of any ITK filters in ITK proper which do wavelet transforms, nor any in any remote modules.

I did find this Insight Journal article: http://www.insight-journal.org/browse/publication/155, but I haven?t used it nor do I know if it has been maintained.

If you are able to find ITK code to do the wavelets in ITK, them with a little effort a JSON description of the filter can be written to extend SimpleITK functionality.

Brad

> On Oct 31, 2016, at 5:09 AM, ivan <ivan.granata.na at gmail.com> wrote:
> 
> Is it possibile to apply a wavelet transform to an image in SimpleITK?
> Thx
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Simple-ITK-Wavelet-Transform-it-is-possible-tp37723.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Mon Oct 31 10:30:23 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 31 Oct 2016 10:30:23 -0400
Subject: [ITK] [ITK-users] my problem
In-Reply-To: <CAEiw7u5oRqSAFZod69MuwqaBE342ufrwS_KGkACXHcORy5sYhg@mail.gmail.com>
References: <CAEiw7u5oRqSAFZod69MuwqaBE342ufrwS_KGkACXHcORy5sYhg@mail.gmail.com>
Message-ID: <CAPf2UMQocNiCDckq_0_RyNm9dTf0dO8HA=cfc58MxxDhXMQ5=Q@mail.gmail.com>

Hi Meikolin,

if you gave us the input (and not just outputs), we might be able to
provide some advice.

Regards,
D?enan

On Sun, Oct 30, 2016 at 2:15 PM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> hello everyone I am beginner in ITK.
> I got  a problem in my thesis with ITK.
> I find different result between using ITK and using imagej.
> in itk I am working with BinaryThresholdImageFilter.
> O.dcm using ITK
> IM-0001-0009.jpeg using Imagej
> what I have to do????
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
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From blowekamp at mail.nih.gov  Mon Oct 31 10:41:00 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 31 Oct 2016 14:41:00 +0000
Subject: [ITK] [ITK-dev] BSpline transform IO and spline order problems
Message-ID: <0F6D6272-122C-489A-ADBF-CAA200BCF35E@mail.nih.gov>

Hello,

I recently discovered that the BSpline transforms are not serializing the order of the spline. The ITK BSplineTransform class[1] is templated over the dimension and the bspline ORDER not the output dimension (like nearly every other transform).

Currently the following strings are in the Transform factory and in ITK transform files:

"BSplineTransform_double_2_2"
?BSplineTransform_double_3_3"

"BSplineTransform_float_2_2"
?BSplineTransform_float_3_3"


The 3D one correctly get loaded as a order 3 spline but the 2D BSplineTransform get loaded with order 2!!!

I believe this a a bug, as the default template parameter for the order is 3, and that is the order almost always used.


I have a patch here to address these issue[2].


So the questions for discussions:

1) Should we correct the behavior and have the string: ?BSplineTransform_double_2_2? create a BSplineTransform<2,Order=3> now?
2) Should be keep writing these strings for order 3 splines? Order just use the new string with the addition of order? i.e. ?BSplineTransform_double_2_2_3"


Brad

[1] https://itk.org/Doxygen/html/classitk_1_1BSplineTransform.html
[2] http://review.source.kitware.com/#/c/21677/
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From blowekamp at mail.nih.gov  Mon Oct 31 11:40:03 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 31 Oct 2016 15:40:03 +0000
Subject: [ITK] [ITK-users]   SimpleITK build fail with R 3.3.1
In-Reply-To: <CA+V7QS80v=1d8=eV1d_op5yxuSKzM5zmcpdW7N3Vb8gQfcEx5A@mail.gmail.com>
References: <D7BC9943-76CA-43B1-B245-9F18E44C6813@gmail.com>
 <DF44CBC7-E1EE-42C3-A04C-6B84736718FC@mail.nih.gov>
 <E35EE205-8F41-4758-B97F-C574728BF850@gmail.com>
 <CA+V7QS-8e9vkg9m6ge7Z_u9Zi55va=WC08UkeC7wiF8iZOJ3wg@mail.gmail.com>
 <6BECC547-3CFB-42EB-B8E0-D779D3D9EF36@gmail.com>
 <CA+V7QS80v=1d8=eV1d_op5yxuSKzM5zmcpdW7N3Vb8gQfcEx5A@mail.gmail.com>
Message-ID: <36C7FF5C-A163-421A-876F-DDE10E0B0240@mail.nih.gov>

Hello,

I am build SimpleITK master with XCode 8.0, R 3.3.1 on OS X 10.11.6 with CMake 3.4.3 by comping with the SimpleITK Superbuild directory.

I get the following error:

Wrapping/R/CMakeFiles/SimpleITK_R.dir/sitkRArray.cxx.o -c /Users/blowekamp/src/SimpleITK/Wrapping/R/sitkRArray.cxx
In file included from /Users/blowekamp/src/SimpleITK/Wrapping/R/sitkRArray.cxx:23:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkImage.h:21:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkCommon.h:21:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkMacro.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/sstream:174:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ostream:138:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ios:216:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:871:34: error: too many arguments provided to function-like macro invocation
    int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
                                 ^
/Library/Frameworks/R.framework/Headers/Rinternals.h:1222:9: note: macro 'length' defined here
#define length(x)               Rf_length(x)


This patch suggested by Richard fixed it for me:
http://review.source.kitware.com/#/c/21678/

This will likely be merged into next at the end of the day.

Brad


On Oct 30, 2016, at 5:04 AM, Richard Beare <richard.beare at gmail.com<mailto:richard.beare at gmail.com>> wrote:

I'm seeing different failures on 3.3.1. Stuff to do with redefining length in Rdefines.h. These problems seem to relate to sitkRArray.cxx.

It is a bit strange, but the fix for me is to add
#include <iostream>

before
#include <Rdefines.h>

in sitkRArray.cxx

This successfully builds the R package, but I get lots of link warnings like this:


ld: warning: direct access in itk::LabelMap<itk::ShapeLabelObject<unsigned long long, 2u> >::Graft(itk::DataObject const*) to global weak symbol typeinfo name for itk::DataObject const* means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.

On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
Hi Richard

I've tried using the patched swig you provided several months ago and the latest swig from git option - SimpleITK compiles without error against R 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with either.  The problem previously was not failing to build but string-handling errors generated using certain R-SimpleITK functions.  As mentioned there has been a change in certain header files since 3.3.0 which presumably relates to the problem?  Happy to do any further testing you suggest.


> On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com<mailto:richard.beare at gmail.com>> wrote:
>
> A while back I made an update to swig to do with the way the various R header files were included in the swig generated code. The errors prompting that change seemed similar to what you were seeing. Those changes have been merged into the master swig, but probably haven't made it into a release yet. You could try giving the superbuild a go with the "system" swig you've built by hand, or possibly use the "swig from git" option in superbuild. Note that this last option requires an automake installation too - the brew version works OK.
>
> On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
> Xcode 8.1 (updated yesterday)
> I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.
>
> Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?
>
>
>
> > On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
> >
> > Hello,
> >
> > Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> >
> > This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> >
> > I am not certain what R compiler flags are passed to the SimpleITK build with the ?devtools? method, but some of the above may not match the way the old R was compiled.
> >
> > HTH,
> > Brad
> >
> > [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> >
> >> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
> >>
> >> Hi
> >>
> >> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
> >>
> >> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
> >>
> >> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
> >>
> >> Not an immediate problem as working with R 3.2.5 is ok.
> >>
> >> The error message I get is:
> >>
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:76:7: note: previous declaration is here
> >> char    *strchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:86:7: note: previous declaration is here
> >> char    *strpbrk(const char *, const char *);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
> >>                                            ^
> >> /usr/include/string.h:87:7: note: previous declaration is here
> >> char    *strrchr(const char *, int);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
> >> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
> >>                                            ^
> >> /usr/include/string.h:70:7: note: previous declaration is here
> >> void    *memchr(const void *, int, size_t);
> >>        ^
> >> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
> >> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
> >> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
> >> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
> >>                                            ^
> >> /usr/include/string.h:89:7: note: previous declaration is here
> >> char    *strstr(const char *, const char *);
> >>        ^
> >> 5 errors generated.
> >> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
> >> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
> >> make[3]: *** [all] Error 2
> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
> >> make: *** [all] Error 2
> >> + exit 1
> >> ERROR: configuration failed for package ?SimpleITK?
> >> * removing ?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK?
> >> Error: Command failed (1)
> >> _____________________________________
> >> Powered by www.kitware.com<http://www.kitware.com/>
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >
>
> _____________________________________
> Powered by www.kitware.com<http://www.kitware.com/>
>
> Visit other Kitware open-source projects at
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>
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From kolin9105 at gmail.com  Mon Oct 31 13:15:07 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 1 Nov 2016 00:15:07 +0700
Subject: [ITK] [ITK-users] My problem
Message-ID: <CAEiw7u6dT9m05m5fKOuRnMU=sUsx_xkUzB9vU4+SH+FfNdPrdw@mail.gmail.com>

I have a image with extention dcm.
When I was input the image in binaryimagethreshold.cxx I got the ouput but
when I was input image with extention jpeg with the same image the result
so far different with dcm input.
in my thesis I am just working with extention dcm not jpeg but the result I
Want what I get with  jpeg.
What I Have to do??
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From francois.budin at kitware.com  Mon Oct 31 13:47:51 2016
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 31 Oct 2016 13:47:51 -0400
Subject: [ITK] [ITK-users] My problem
In-Reply-To: <CAEiw7u6dT9m05m5fKOuRnMU=sUsx_xkUzB9vU4+SH+FfNdPrdw@mail.gmail.com>
References: <CAEiw7u6dT9m05m5fKOuRnMU=sUsx_xkUzB9vU4+SH+FfNdPrdw@mail.gmail.com>
Message-ID: <CAHwLD2W0d6_5Je=UrDOnu3VkbGNFKs3tgG_6K+245XS=gZ+DUA@mail.gmail.com>

Hello,

Have you compared the content of both your images (dcm and jpeg) and made
sure that they were exactly the same? How did you convert one into the
other? Is it possible for you to share the images with us? Maybe the
thresholds that you need to use in both your images are different if your
images are different.
Hope this helps,

Francois

On Mon, Oct 31, 2016 at 1:15 PM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> I have a image with extention dcm.
> When I was input the image in binaryimagethreshold.cxx I got the ouput but
> when I was input image with extention jpeg with the same image the result
> so far different with dcm input.
> in my thesis I am just working with extention dcm not jpeg but the result
> I Want what I get with  jpeg.
> What I Have to do??
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From fisidoro at ethz.ch  Mon Oct 31 14:08:12 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Mon, 31 Oct 2016 18:08:12 +0000
Subject: [ITK] [ITK-users] cmake build error
Message-ID: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>

Hallo,

I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on Windows 10 with Visual Studio 2015. As "current generator" I tried both "Visual Studio 14 2015" and "Visual Studio 14 2015 Win64" but I immediately get errors with cmake when configuring. Errors are:

The C compiler identification is unknown
CMake Error at CMakeLists.txt:18 (enable_language):
  No CMAKE_C_COMPILER could be found.


Compiling the C compiler identification source file "CMakeCCompilerId.c" failed.
Compiler:
Build flags:
Id flags:

The output was:
1
Microsoft (R) Build Engine version 14.0.25420.1
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 31.10.2016 18:53:27.
Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" on node 1 (default targets).
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
Done Building Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default targets) -- FAILED.

Build FAILED.

"C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default target) (1) ->
(Desktop_PlatformPrepareForBuild target) ->
  C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]

    0 Warning(s)
    1 Error(s)

Time Elapsed 00:00:00.48


Compiling the C compiler identification source file "CMakeCCompilerId.c" failed.
Compiler:
Build flags:
Id flags:

The output was:
1
Microsoft (R) Build Engine version 14.0.25420.1
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 31.10.2016 18:58:27.
Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" on node 1 (default targets).
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
Done Building Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default targets) -- FAILED.

Build FAILED.

"C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default target) (1) ->
(Desktop_PlatformPrepareForBuild target) ->
  C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]

    0 Warning(s)
    1 Error(s)


What can I do to solve the problem?

Thank you
-------------- next part --------------
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Kitware offers ITK Training Courses, for more information visit:
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From matt.mccormick at kitware.com  Mon Oct 31 14:18:42 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 31 Oct 2016 14:18:42 -0400
Subject: [ITK] [ITK-users] cmake build error
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
Message-ID: <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>

Hi Fabio,

If the command line CMake executable is used, as opposed to the GUI,
the command must be executed from a Visual Studio Command Prompt,
which adjusts the PATH environmental variable to expose the compiler.

HTH,
Matt

On Mon, Oct 31, 2016 at 2:08 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hallo,
>
>
>
> I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on Windows
> 10 with Visual Studio 2015. As ?current generator? I tried both ?Visual
> Studio 14 2015? and ?Visual Studio 14 2015 Win64? but I immediately get
> errors with cmake when configuring. Errors are:
>
>
>
> The C compiler identification is unknown
>
> CMake Error at CMakeLists.txt:18 (enable_language):
>
>   No CMAKE_C_COMPILER could be found.
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:53:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
> Time Elapsed 00:00:00.48
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:58:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the
> required version of Windows SDK or change the SDK version in the project
> property pages or by right-clicking the solution and selecting "Retarget
> solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
>
>
> What can I do to solve the problem?
>
>
>
> Thank you
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From fisidoro at ethz.ch  Mon Oct 31 14:41:56 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Mon, 31 Oct 2016 18:41:56 +0000
Subject: [ITK] [ITK-users] cmake build error
In-Reply-To: <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
 <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B40943A161805@MBX112.d.ethz.ch>

Thanks, I did it but I got the same kind of error. What else could I try?


-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Sent: Montag, 31. Oktober 2016 19:19
To: D'Isidoro Fabio
Cc: insight-users at itk.org
Subject: Re: [ITK-users] cmake build error

Hi Fabio,

If the command line CMake executable is used, as opposed to the GUI, the command must be executed from a Visual Studio Command Prompt, which adjusts the PATH environmental variable to expose the compiler.

HTH,
Matt

On Mon, Oct 31, 2016 at 2:08 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Hallo,
>
>
>
> I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on 
> Windows
> 10 with Visual Studio 2015. As ?current generator? I tried both 
> ?Visual Studio 14 2015? and ?Visual Studio 14 2015 Win64? but I 
> immediately get errors with cmake when configuring. Errors are:
>
>
>
> The C compiler identification is unknown
>
> CMake Error at CMakeLists.txt:18 (enable_language):
>
>   No CMAKE_C_COMPILER could be found.
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:53:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
> Time Elapsed 00:00:00.48
>
>
>
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
>
> Compiler:
>
> Build flags:
>
> Id flags:
>
>
>
> The output was:
>
> 1
>
> Microsoft (R) Build Engine version 14.0.25420.1
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
>
>
> Build started 31.10.2016 18:58:27.
>
> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
> on node 1 (default targets).
>
> C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
> Done Building Project
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> targets) -- FAILED.
>
>
>
> Build FAILED.
>
>
>
> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj" 
> (default
> target) (1) ->
>
> (Desktop_PlatformPrepareForBuild target) ->
>
>   C:\Program Files
> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
> error MSB8036: The Windows SDK version 8.1 was not found. Install the 
> required version of Windows SDK or change the SDK version in the 
> project property pages or by right-clicking the solution and selecting 
> "Retarget solution".
> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>
>
>
>     0 Warning(s)
>
>     1 Error(s)
>
>
>
>
>
> What can I do to solve the problem?
>
>
>
> Thank you
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

From matt.mccormick at kitware.com  Mon Oct 31 14:49:30 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 31 Oct 2016 14:49:30 -0400
Subject: [ITK] [ITK-users] cmake build error
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40943A161805@MBX112.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B40943A1617EC@MBX112.d.ethz.ch>
 <CALzTN-RJGHiYeTLPMgYJ=yqLB+zRuv65L4RbizxTC-KM0shK3g@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40943A161805@MBX112.d.ethz.ch>
Message-ID: <CALzTN-REaQ8vtx17bH86662_Zptod0VynYgDqaVWx+F2Xw8nxA@mail.gmail.com>

"The Windows SDK version 8.1 was not found. Install the required
version of Windows SDK or change the SDK version in the project
property pages or by right-clicking the solution and selecting
"Retarget solution"."

The installation of Windows SDK along with Visual Studio may have not
been successful -- Visual Studio could be re-installed or Windows SDK
can be installed on its own.

HTH,
Matt

On Mon, Oct 31, 2016 at 2:41 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
> Thanks, I did it but I got the same kind of error. What else could I try?
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 31. Oktober 2016 19:19
> To: D'Isidoro Fabio
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] cmake build error
>
> Hi Fabio,
>
> If the command line CMake executable is used, as opposed to the GUI, the command must be executed from a Visual Studio Command Prompt, which adjusts the PATH environmental variable to expose the compiler.
>
> HTH,
> Matt
>
> On Mon, Oct 31, 2016 at 2:08 PM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
>> Hallo,
>>
>>
>>
>> I downloaded ITK V4.10 and trying to build it with Cmake V3.6.2 on
>> Windows
>> 10 with Visual Studio 2015. As ?current generator? I tried both
>> ?Visual Studio 14 2015? and ?Visual Studio 14 2015 Win64? but I
>> immediately get errors with cmake when configuring. Errors are:
>>
>>
>>
>> The C compiler identification is unknown
>>
>> CMake Error at CMakeLists.txt:18 (enable_language):
>>
>>   No CMAKE_C_COMPILER could be found.
>>
>>
>>
>>
>>
>> Compiling the C compiler identification source file "CMakeCCompilerId.c"
>> failed.
>>
>> Compiler:
>>
>> Build flags:
>>
>> Id flags:
>>
>>
>>
>> The output was:
>>
>> 1
>>
>> Microsoft (R) Build Engine version 14.0.25420.1
>>
>> Copyright (C) Microsoft Corporation. All rights reserved.
>>
>>
>>
>> Build started 31.10.2016 18:53:27.
>>
>> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> on node 1 (default targets).
>>
>> C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>> Done Building Project
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> targets) -- FAILED.
>>
>>
>>
>> Build FAILED.
>>
>>
>>
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> target) (1) ->
>>
>> (Desktop_PlatformPrepareForBuild target) ->
>>
>>   C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>>
>>
>>     0 Warning(s)
>>
>>     1 Error(s)
>>
>>
>>
>> Time Elapsed 00:00:00.48
>>
>>
>>
>>
>>
>> Compiling the C compiler identification source file "CMakeCCompilerId.c"
>> failed.
>>
>> Compiler:
>>
>> Build flags:
>>
>> Id flags:
>>
>>
>>
>> The output was:
>>
>> 1
>>
>> Microsoft (R) Build Engine version 14.0.25420.1
>>
>> Copyright (C) Microsoft Corporation. All rights reserved.
>>
>>
>>
>> Build started 31.10.2016 18:58:27.
>>
>> Project "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> on node 1 (default targets).
>>
>> C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>> Done Building Project
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> targets) -- FAILED.
>>
>>
>>
>> Build FAILED.
>>
>>
>>
>> "C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj"
>> (default
>> target) (1) ->
>>
>> (Desktop_PlatformPrepareForBuild target) ->
>>
>>   C:\Program Files
>> (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5):
>> error MSB8036: The Windows SDK version 8.1 was not found. Install the
>> required version of Windows SDK or change the SDK version in the
>> project property pages or by right-clicking the solution and selecting
>> "Retarget solution".
>> [C:\ITK_build_410\CMakeFiles\3.6.2\CompilerIdC\CompilerIdC.vcxproj]
>>
>>
>>
>>     0 Warning(s)
>>
>>     1 Error(s)
>>
>>
>>
>>
>>
>> What can I do to solve the problem?
>>
>>
>>
>> Thank you
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
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From dan.muel at gmail.com  Mon Oct 31 16:49:37 2016
From: dan.muel at gmail.com (Dan Mueller)
Date: Tue, 1 Nov 2016 07:19:37 +1030
Subject: [ITK] [ITK-users] Simple ITK Wavelet Transform ?? it is
	possible?
In-Reply-To: <1477904974504-37723.post@n7.nabble.com>
References: <1477904974504-37723.post@n7.nabble.com>
Message-ID: <CAPNvZ5ZtFX5jzq+AQM3snJ0o1AR8MLF0rvyswAOax=+JiJ-LYw@mail.gmail.com>

Hi Ivan,

There is also a na?ve (ie. slow) implementation of QMF DWT here:
http://www.insight-journal.org/browse/publication/103

These filters are not wrapped in SimpleITK though...

Good luck, Dan

On 31 Oct 2016 21:05, "ivan" <ivan.granata.na at gmail.com> wrote:

> Is it possibile to apply a wavelet transform to an image in SimpleITK?
> Thx
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-users-Simple-ITK-Wavelet-Transform-it-is-possible-tp37723.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
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>
> Visit other Kitware open-source projects at
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> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
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> Please keep messages on-topic and check the ITK FAQ at:
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Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From david.paik at elucidbio.com  Mon Oct 31 19:18:21 2016
From: david.paik at elucidbio.com (David S. Paik (Elucid Bioimaging))
Date: Mon, 31 Oct 2016 23:18:21 +0000
Subject: [ITK] ITK Release 5 Wish List
Message-ID: <D12C1734-462F-447F-874C-880A797089E4@elucidbio.com>

I?d like to make contributions to https://itk.org/Wiki/ITK_Release_5/Wish_List but cannot figure out where to request a login for the wiki so that I can edit.  Can someone point me to where to sign up for an account on this wiki?

Thanks!
David

--
David S. Paik, Ph.D., Senior Director, Imaging Science
Elucid Bioimaging Inc.
225 Main Street, Suite 15 | Wenham, MA  01984  USA
Office: +1-978-468-0508
Mobile: +1-650-799-1851
Fax: +1-978-468-0527
david.paik at elucidbio.com<mailto:andrew.buckler at elucidbio.com> | www.elucidbio.com<http://www.elucidbio.com/>

This e-mail is from Elucid Bioimaging Inc., a product development and contract research company, and may contain information that is confidential or privileged. If you are not the intended recipient, do not read, copy or distribute the e-mail or any attachments. Instead, please notify the sender and delete the e-mail and any attachments. Thank you.

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