From bill.lorensen at gmail.com  Fri Jul  1 10:23:56 2016
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 1 Jul 2016 10:23:56 -0400
Subject: [ITK] [ITK-dev] core/vnl/tests/test_container_interface.cxx
	appeared today
Message-ID: <CADZJ4hMn02fZS8fB6cPiDu7ACd4cXtxCLw0FSqjngAYWPR1JdQ@mail.gmail.com>

After an update today, the filke
core/vnl/tests/test_container_interface.cxx
appeared in my top level ITK directory

Was this checked in my accident?

Bill
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From matt.mccormick at kitware.com  Fri Jul  1 13:38:55 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 1 Jul 2016 13:38:55 -0400
Subject: [ITK] [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo
In-Reply-To: <C3D62BAE-8248-4854-93E1-27B7D49386EC@gmail.com>
References: <1465709590989.57546@sphic.org.cn>
 <C3D62BAE-8248-4854-93E1-27B7D49386EC@gmail.com>
Message-ID: <CALzTN-QV1jfHv4jEHhA-=F6uO+TRs5xSHuxv1PjRjOH7COwpYA@mail.gmail.com>

Hi Zhuangming Shen,

This patch was created to address the issue:

  http://review.source.kitware.com/#/c/21286/

Could you please verify that it has fixed your issue? It will included
in the 4.10.1 release.

Thanks,
Matt

On Mon, Jun 27, 2016 at 4:25 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Hi
>
> thanks for reporting this. I also could reproduce the warnings.
> I opened a bug for this here so we can keep track of it:
> https://issues.itk.org/jira/browse/ITK-3448
>
> The same error was also reported on the mailing list yesterday.
> If you just want to hide the warning you can use:
>
> import warnings
> warnings.simplefilter(?ignore", Warning)
>
> If you need to use QuadEdgeMeshCellTraitsInfo with Python,
> somebody will need to fix this. I already gave it a shot, but
> this may take some time. Not sure I will be able to look at
> this until next week.
>
> Thanks
>
> Michka
>
>
>
>> On 12 Jun 2016, at 07:33, ??? <zhuangming.shen at sphic.org.cn> wrote:
>>
>> Hi all,
>>
>> When I used python-supported ITK 4.10.0 to get the types of itk.QuadEdgeMeshCellTraitsInfo for the first time, I got two warnings
>>
>> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
>> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
>> <itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
>> Options:
>>
>>
>> If I run itk.QuadEdgeMeshCellTraitsInfo.GetTypes() again or use ITK 4.9.1 instead, it just displays
>>
>> <itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
>> Options:
>>
>>
>> So what's the problem? What is the unknown parameter? Has someone met this issue? Thanks.
>>
>>
>> Regards,
>>
>> Zhuangming Shen
>>
>>
>>
>>
>>
>>
>>
>> _____________________________________
>> 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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>
> Visit other Kitware open-source projects at
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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:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From matt.mccormick at kitware.com  Fri Jul  1 13:56:17 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 1 Jul 2016 13:56:17 -0400
Subject: [ITK] [ITK-dev] core/vnl/tests/test_container_interface.cxx
 appeared today
In-Reply-To: <CADZJ4hMn02fZS8fB6cPiDu7ACd4cXtxCLw0FSqjngAYWPR1JdQ@mail.gmail.com>
References: <CADZJ4hMn02fZS8fB6cPiDu7ACd4cXtxCLw0FSqjngAYWPR1JdQ@mail.gmail.com>
Message-ID: <CALzTN-TVXhbbL9H5U_5DSBz5K3q7g6q31pGHZ41wOmoQoxjHEA@mail.gmail.com>

Hi Bill,

Good catch. Yes, the file was accidentally added in a recent VNL
subtree merge.  Here is a patch:

  http://review.source.kitware.com/#/c/21294/

Thanks,
Matt

On Fri, Jul 1, 2016 at 10:23 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> After an update today, the filke
> core/vnl/tests/test_container_interface.cxx
> appeared in my top level ITK directory
>
> Was this checked in my accident?
>
> Bill
> _______________________________________________
> 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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From marcus.hanwell at kitware.com  Fri Jul  1 14:10:27 2016
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Fri, 1 Jul 2016 14:10:27 -0400
Subject: [ITK] [ITK-dev] ITK Python wrapping issue with GCC 6.1.1
Message-ID: <CAMkPkZV-RW11Pfi9DqT-GVKUF3-stK1TKWHXJUgYKR8QoTPPPw@mail.gmail.com>

I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am
seeing a compile error:

Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _
wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?:
Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi
ng function for call to ?itk::TriangleHelper<itk::Point<double, 2u> >::TriangleH
elper()?
      result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
                                                                ^
In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO
bject.h:21:0,
                from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject
.h:31,
                from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman
d.h:21,
                from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3,
                from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325
8:
/home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note
: candidate: itk::TriangleHelper<TPoint>::TriangleHelper(const itk::TriangleHelp
er<TPoint>&) [with TPoint = itk::Point<double, 2u>] <deleted>
  ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper);

Is my GCC too new? It only seems to be happening with the wrapping,
this is on Linux. I can post more details if it helps.
_______________________________________________
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From matt.mccormick at kitware.com  Fri Jul  1 14:54:22 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 1 Jul 2016 14:54:22 -0400
Subject: [ITK] [ITK-dev]   ITK Python wrapping issue with GCC 6.1.1
In-Reply-To: <CAMkPkZV-RW11Pfi9DqT-GVKUF3-stK1TKWHXJUgYKR8QoTPPPw@mail.gmail.com>
References: <CAMkPkZV-RW11Pfi9DqT-GVKUF3-stK1TKWHXJUgYKR8QoTPPPw@mail.gmail.com>
Message-ID: <CALzTN-RjOuCrP0VBD1VExCwxVT=9_92yrGNBkkmVuaE5WRfWUw@mail.gmail.com>

Hi Marcus,

Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is
having issues.  There is now an issue to track this:

  https://issues.itk.org/jira/browse/ITK-3450

Thanks,
Matt

On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell
<marcus.hanwell at kitware.com> wrote:
> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am
> seeing a compile error:
>
> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _
> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?:
> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi
> ng function for call to ?itk::TriangleHelper<itk::Point<double, 2u> >::TriangleH
> elper()?
>       result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
>                                                                 ^
> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO
> bject.h:21:0,
>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject
> .h:31,
>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman
> d.h:21,
>                 from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3,
>                 from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325
> 8:
> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note
> : candidate: itk::TriangleHelper<TPoint>::TriangleHelper(const itk::TriangleHelp
> er<TPoint>&) [with TPoint = itk::Point<double, 2u>] <deleted>
>   ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper);
>
> Is my GCC too new? It only seems to be happening with the wrapping,
> this is on Linux. I can post more details if it helps.
> _______________________________________________
> 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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From marcus.hanwell at kitware.com  Fri Jul  1 15:01:10 2016
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Fri, 1 Jul 2016 15:01:10 -0400
Subject: [ITK] [ITK-dev]   ITK Python wrapping issue with GCC 6.1.1
In-Reply-To: <CALzTN-RjOuCrP0VBD1VExCwxVT=9_92yrGNBkkmVuaE5WRfWUw@mail.gmail.com>
References: <CAMkPkZV-RW11Pfi9DqT-GVKUF3-stK1TKWHXJUgYKR8QoTPPPw@mail.gmail.com>
 <CALzTN-RjOuCrP0VBD1VExCwxVT=9_92yrGNBkkmVuaE5WRfWUw@mail.gmail.com>
Message-ID: <CAMkPkZVt9pLAUxrZPYohyqD3YeiqE52zZmaLJvpV5H9eM0_oEA@mail.gmail.com>

Matt, thanks for the confirmation, sorry I didn't spot it in the issue
tracker. I will monitor the bug.

On Fri, Jul 1, 2016 at 2:54 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Marcus,
>
> Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is
> having issues.  There is now an issue to track this:
>
>   https://issues.itk.org/jira/browse/ITK-3450
>
> Thanks,
> Matt
>
> On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell
> <marcus.hanwell at kitware.com> wrote:
>> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am
>> seeing a compile error:
>>
>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _
>> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?:
>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi
>> ng function for call to ?itk::TriangleHelper<itk::Point<double, 2u> >::TriangleH
>> elper()?
>>       result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
>>                                                                 ^
>> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO
>> bject.h:21:0,
>>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject
>> .h:31,
>>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman
>> d.h:21,
>>                 from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3,
>>                 from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325
>> 8:
>> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note
>> : candidate: itk::TriangleHelper<TPoint>::TriangleHelper(const itk::TriangleHelp
>> er<TPoint>&) [with TPoint = itk::Point<double, 2u>] <deleted>
>>   ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper);
>>
>> Is my GCC too new? It only seems to be happening with the wrapping,
>> this is on Linux. I can post more details if it helps.
>> _______________________________________________
>> 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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From noreply at insightsoftwareconsortium.org  Fri Jul  1 16:34:04 2016
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Fri,  1 Jul 2016 16:34:04 -0400 (EDT)
Subject: [ITK] [ITK-users] New Submission: Performance Benchmarking the
	Insight	Toolkit
Message-ID: <20160701203404.F35403D6207E@insight-journal.org>

Hello,

A new submission has been added to the Insight Journal.

Title: Performance Benchmarking the Insight Toolkit
Authors: McCormick M., Kang H.J., Barre S.
Abstract: This document describes a module for the Insight Toolkit (ITK) to assist in performance
benchmarking and a suite of benchmarks for the toolkit. These resources provide metrics to quantify
software computational performance. This is a pre-requisite to improve performance either through
algorithmic advancements or better utilization of hardware resources.
Computational performance is quantified by reducing factors that confound timing measurements and
by estimating measurement variance. New classes are presented that increase operating system process
priority to minimize the impact of other processes running on the system. System hardware characteristics
are extracted and displayed. The influence of hard disk input/output on runtime measurements is
removed in the suite of benchmarks. Additionally, the number of threads used by each benchmark can be
specified. These benchmarks consist of common analysis pipelines and run on 3D magnetic resonance
brain image data so realistic performance is quantified. Benchmarks can be executed with multiple iterations,
and timing statistics are recorded in tab separated value (.tsv) files, which are easily stored or
processed for further analysis and visualization.
This paper is accompanied with the source code, input data, parameters and output data that the authors
used for validating the algorithm described in this paper. This adheres to the fundamental principle
that scientific publications must facilitate reproducibility of the reported results.

Download and review this publication at: http://hdl.handle.net/10380/3557

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ .
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From noreply at insightsoftwareconsortium.org  Fri Jul  1 17:29:44 2016
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Fri,  1 Jul 2016 17:29:44 -0400 (EDT)
Subject: [ITK] [ITK-users] New Submission: OpenCL accelerated GPU
	binary	morphology image filters for ITK
Message-ID: <20160701212944.EF55F3D62059@insight-journal.org>

Hello,

A new submission has been added to the Insight Journal.

Title: OpenCL accelerated GPU binary morphology image filters for ITK
Authors: Bardosi Z.
Abstract: Binary morphological operations are fundamental tools in image processing but the processing time scales with the number of pixels thus making them expensive operations on the CPU for larger 3D datasets that typically appear in medical imaging. Since erosion and dilatation are special neighborhood operators, each pixel in the output depends only on the neighborhood region which makes them fit for massive GPU parallelization. This document introduces a new ITK module that implements generic (OpenCL based) GPU accelerated binary morphology image filters for erosion and dilatation. The filter can be executed within the standard ITKGPU pipeline.

Download and review this publication at: http://hdl.handle.net/10380/3525

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From jmerkow at gmail.com  Sun Jul  3 16:36:38 2016
From: jmerkow at gmail.com (Jameson Merkow)
Date: Sun, 3 Jul 2016 13:36:38 -0700
Subject: [ITK] [ITK-users] Reading an image from a file object
	with	SimpleITK+Python
Message-ID: <CAHWMK+iAYci1JwrNDhftkahmcnMP=AjZtpO5=RF7_fj44L2iAw@mail.gmail.com>

Hello all,

Is there a way to read an image with SimpleITK+Python from a file object
(as opposed to a string/filename)? I cannot find anything in the Doxygen or
otherwise to do this.

Here is a toy example:

    import cStringIO
    import SimpleITK as sitk
    dcmfn="test.dcm"
    with open(dcmfn,'rb') as data:
        body = data.read()
        strio=cStringIO.StringIO(body)
        img=sitk.ReadImage(strio)
        strio.close()



--Jameson
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From mrguilfoyle at gmail.com  Sun Jul  3 21:11:43 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Mon, 4 Jul 2016 02:11:43 +0100
Subject: [ITK] [ITK-users] LabelStatisticsImageFilter in 3D
Message-ID: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>

Hi

Using SimpleITK I'm trying to get statistics for a grayscale image segmentation for which I have a binary mask.  Both image and mask are 3D volumes

I have converted my binary mask to a Label map and then tried to apply the LabelStatisticsImageFilter, however I get the following exception:

Pixel type: 32-bit float is not supported in 3D

I've tried casting the intensity image to unsigned int, Float 64 etc... none of them work.  It seems to be the 3D that is the issue.  Is this filter defined for 3D images?  There is nothing I have found in the documentation/source to suggest not.

Thanks
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From ocuadrosl at gmail.com  Mon Jul  4 16:57:31 2016
From: ocuadrosl at gmail.com (Oscar Cuadros Linares)
Date: Mon, 4 Jul 2016 13:57:31 -0700
Subject: [ITK] [ITK-users] 3D registration - teeth image
Message-ID: <CAMxqLnRf9N3pwDdoTPpcET5Z6SGDepJex+2eV=hD4r6mQoA_Sw@mail.gmail.com>

Hi guys

I have to register two 3D images of teeth (screenshots attached).
I tested several approaches, such as: affine registration, rigid
registration,
mattes and mean square metric, etc.
When I use moments centering I get an error (Too many samples map outside
moving
image buffer)   and when I use geometric centering I do not get error, but
the result (resampler)
is exactly the same moving image. Any sugestions

Thank you so much
Oscar
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From zhuangming.shen at sphic.org.cn  Mon Jul  4 20:15:01 2016
From: zhuangming.shen at sphic.org.cn (=?gb2312?B?yfLXr8P3?=)
Date: Tue, 5 Jul 2016 00:15:01 +0000
Subject: [ITK] [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo
In-Reply-To: <CALzTN-QV1jfHv4jEHhA-=F6uO+TRs5xSHuxv1PjRjOH7COwpYA@mail.gmail.com>
References: <1465709590989.57546@sphic.org.cn>
 <C3D62BAE-8248-4854-93E1-27B7D49386EC@gmail.com>,
 <CALzTN-QV1jfHv4jEHhA-=F6uO+TRs5xSHuxv1PjRjOH7COwpYA@mail.gmail.com>
Message-ID: <1467677701042.44519@sphic.org.cn>

Hi Matt and Michka,

Thank you for your prompt response. I have verified the issue has been fixed. Thanks again.


Regards,

Zhuangming Shen
________________________________________
From: Matt McCormick <matt.mccormick at kitware.com>
Sent: Saturday, July 2, 2016 1:38 AM
To: Michka Popoff
Cc: ???; insight-users at itk.org
Subject: Re: [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo

Hi Zhuangming Shen,

This patch was created to address the issue:

  http://review.source.kitware.com/#/c/21286/

Could you please verify that it has fixed your issue? It will included
in the 4.10.1 release.

Thanks,
Matt

On Mon, Jun 27, 2016 at 4:25 PM, Michka Popoff <michkapopoff at gmail.com> wrote:
> Hi
>
> thanks for reporting this. I also could reproduce the warnings.
> I opened a bug for this here so we can keep track of it:
> https://issues.itk.org/jira/browse/ITK-3448
>
> The same error was also reported on the mailing list yesterday.
> If you just want to hide the warning you can use:
>
> import warnings
> warnings.simplefilter(?ignore", Warning)
>
> If you need to use QuadEdgeMeshCellTraitsInfo with Python,
> somebody will need to fix this. I already gave it a shot, but
> this may take some time. Not sure I will be able to look at
> this until next week.
>
> Thanks
>
> Michka
>
>
>
>> On 12 Jun 2016, at 07:33, ??? <zhuangming.shen at sphic.org.cn> wrote:
>>
>> Hi all,
>>
>> When I used python-supported ITK 4.10.0 to get the types of itk.QuadEdgeMeshCellTraitsInfo for the first time, I got two warnings
>>
>> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
>> Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface'
>> <itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
>> Options:
>>
>>
>> If I run itk.QuadEdgeMeshCellTraitsInfo.GetTypes() again or use ITK 4.9.1 instead, it just displays
>>
>> <itkTemplate itk::QuadEdgeMeshCellTraitsInfo>
>> Options:
>>
>>
>> So what's the problem? What is the unknown parameter? Has someone met this issue? Thanks.
>>
>>
>> Regards,
>>
>> Zhuangming Shen
>>
>>
>>
>>
>>
>>
>>
>> _____________________________________
>> 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 piotpia124 at student.polsl.pl  Tue Jul  5 02:46:09 2016
From: piotpia124 at student.polsl.pl (Piotr Piasecki)
Date: Tue, 05 Jul 2016 08:46:09 +0200
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
Message-ID: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>

 Dear Sir or Madam.

 I am a student in Biomedical Engineering at the Silesian University of 
 Technology. During my studies I worked with ITK and SimpleITK in C#. I 
 want to use them in my current project, but I have an important 
 question. After loading and processing a series of .dcm files I lost 
 information about the patient and study to which they belong, and that 
 they belong to one series. How can I keep this information?

 I will be very grateful for any answer.

 Best regards.

 Peter.
_____________________________________
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From 2389127171 at qq.com  Tue Jul  5 04:38:32 2016
From: 2389127171 at qq.com (=?ISO-8859-1?B?WVlERGFsZ28=?=)
Date: Tue, 5 Jul 2016 16:38:32 +0800
Subject: [ITK] [ITK-users] The method base on Karl Krissian 'Model Based
	Detection	of Tubular Structures in 3D Images'
Message-ID: <tencent_53AEAEF213A38F0B531C0D41@qq.com>

Hi,
Now I am working on the detection of tube structure; But it is hard for a freshman to deal with the code.
so is there anyone konw how to implement it and can you give a code for studying?


Best wishes
Even
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From tevain at telecom-paristech.fr  Tue Jul  5 04:56:02 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Tue, 5 Jul 2016 10:56:02 +0200 (CEST)
Subject: [ITK] [ITK-users]   3D registration - teeth image
In-Reply-To: <CAMxqLnRf9N3pwDdoTPpcET5Z6SGDepJex+2eV=hD4r6mQoA_Sw@mail.gmail.com>
References: <CAMxqLnRf9N3pwDdoTPpcET5Z6SGDepJex+2eV=hD4r6mQoA_Sw@mail.gmail.com>
Message-ID: <828117311.21362941.1467708962631.JavaMail.zimbra@enst.fr>

Hi Oscar,

The error you are receiving means that your images don't overlap with the initial transformation in the physical space. 
You have to set a better transformation initialization.
You should take a look to the itk CenteredTransformInitializer ( https://itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html#a3284b1aabf2690889aa7435676fc7893 ), or the versor version of it, if you're using a transform with versor for rotation.
This will help setting a good starting position.

HTH,

Tim


----- Mail original -----
De: "Oscar Cuadros Linares" <ocuadrosl at gmail.com>
?: insight-users at itk.org
Envoy?: Lundi 4 Juillet 2016 22:57:31
Objet: [ITK] [ITK-users] 3D registration - teeth image

Hi guys 

I have to register two 3D images of teeth (screenshots attached). 
I tested several approaches, such as: affine registration, rigid registration, 
mattes and mean square metric, etc. 
When I use moments centering I get an error (Too many samples map outside moving 
image buffer) and when I use geometric centering I do not get error, but the result (resampler) 
is exactly the same moving image. Any sugestions 

Thank you so much 
Oscar 


_____________________________________
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From blowekamp at mail.nih.gov  Tue Jul  5 09:33:18 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 5 Jul 2016 13:33:18 +0000
Subject: [ITK] [ITK-users] Reading an image from a file
	object	with	SimpleITK+Python
In-Reply-To: <CAHWMK+iAYci1JwrNDhftkahmcnMP=AjZtpO5=RF7_fj44L2iAw@mail.gmail.com>
References: <CAHWMK+iAYci1JwrNDhftkahmcnMP=AjZtpO5=RF7_fj44L2iAw@mail.gmail.com>
Message-ID: <A6474A91-C8F6-4E98-8AC8-63D4E963690A@mail.nih.gov>

Hello,

SimpleITK does not currently support this low level interface. I am not aware of an ITK ImageIO that directly support reading am image from a C FILE object either.

You may find a lower level IO library such as GDCM or jpeg which can support this type of feature, but I have not tried it myself.

HTH,
Brad

> On Jul 3, 2016, at 4:36 PM, Jameson Merkow <jmerkow at gmail.com> wrote:
> 
> Hello all,
> 
> Is there a way to read an image with SimpleITK+Python from a file object (as opposed to a string/filename)? I cannot find anything in the Doxygen or otherwise to do this.
> 
> Here is a toy example:
> 
>     import cStringIO
>     import SimpleITK as sitk
>     dcmfn="test.dcm"
>     with open(dcmfn,'rb') as data:
>         body = data.read()
>         strio=cStringIO.StringIO(body)
>         img=sitk.ReadImage(strio)
>         strio.close()
> 
> 
> 
> --Jameson
> _____________________________________
> 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 Jul  5 09:45:16 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 5 Jul 2016 09:45:16 -0400
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
Message-ID: <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>

Hi Piotr,

if you want to carry over metadata from input image to output image, you
should save the metadata dictionary in a way similar to this:

itk::MetaDataDictionary metadata;

template< typename TImage >
itk::SmartPointer<TImage> readImage(std::string fileName)
{
    typedef itk::ImageFileReader<TImage> ReaderType;
    typename ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(fileName.c_str());
    try
    {
        reader->Update();
        metadata = reader->GetMetaDataDictionary();
        return reader->GetOutput();
    }
    catch (itk::ExceptionObject & error)
    {
        std::cerr << "Error: " << error << std::endl;
        return NULL;
    }
}

template< typename TImage >
void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
{
    image->SetMetaDataDictionary(metadata); //full metadata
    typedef itk::ImageFileWriter<TImage> WriterType;
    typename WriterType::Pointer writer = WriterType::New();
    writer->SetFileName(fileName.c_str());
    writer->SetInput(image);
    try
    {
        writer->Update();
    }
    catch (itk::ExceptionObject & error)
    {
        std::cerr << "Error: " << error << std::endl;
    }
}

On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <piotpia124 at student.polsl.pl>
wrote:

> Dear Sir or Madam.
>
> I am a student in Biomedical Engineering at the Silesian University of
> Technology. During my studies I worked with ITK and SimpleITK in C#. I want
> to use them in my current project, but I have an important question. After
> loading and processing a series of .dcm files I lost information about the
> patient and study to which they belong, and that they belong to one series.
> How can I keep this information?
>
> I will be very grateful for any answer.
>
> Best regards.
>
> Peter.
> _____________________________________
> 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 zivrafael.yaniv at nih.gov  Tue Jul  5 10:43:57 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Tue, 5 Jul 2016 14:43:57 +0000
Subject: [ITK] [ITK-users] LabelStatisticsImageFilter in 3D
In-Reply-To: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>
References: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>
Message-ID: <D3A13FDD.B84B%yanivz@mail.nih.gov>

Hi Mathew,

As I haven?t seen your code I cannot pinpoint the issue, but it is not the
dimension of the image.

The following SimpleITK code does what I believe you are asking for (image
is available here - https://midas3.kitware.com/midas/item/317034):

import SimpleITK as sitk

image = sitk.ReadImage("training_001_ct.mha")

# HU values for bone are 700 and up
segmented_image = image>700

# segmented label for the threshold operation is 1 (0 for everything else).
# the LabelIntensityStatisticsImageFilter also works with multiple labels
and not just a binary segmentation.
segmented_label = 1

lisf = sitk.LabelIntensityStatisticsImageFilter()
lisf.Execute(segmented_image, image)

print("mean HU value: {0:.2f}".format(lisf.GetMean(segmented_label)))

     hope this helped

             Ziv






On 7/3/16, 9:11 PM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:

>Hi
>
>Using SimpleITK I'm trying to get statistics for a grayscale image
>segmentation for which I have a binary mask.  Both image and mask are 3D
>volumes
>
>I have converted my binary mask to a Label map and then tried to apply
>the LabelStatisticsImageFilter, however I get the following exception:
>
>Pixel type: 32-bit float is not supported in 3D
>
>I've tried casting the intensity image to unsigned int, Float 64 etc...
>none of them work.  It seems to be the 3D that is the issue.  Is this
>filter defined for 3D images?  There is nothing I have found in the
>documentation/source to suggest not.
>
>Thanks
>_____________________________________
>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 Jul  5 14:11:27 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 5 Jul 2016 14:11:27 -0400
Subject: [ITK] [ITK-dev] Patches for 4.10.1
Message-ID: <CALzTN-TkyRSnW5=k3Crn4tO9u0kwBA1a=ckLqFaijN6HaZPeSQ@mail.gmail.com>

Hi,

Looking to the ITK 4.10.1 bugfix release, the following patches are in the
release branch:


Bradley Lowekamp (4):
      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

Hans Johnson (1):
      COMP: Add long long usage for HDF5

Hastings Greer (1):
      BUG: ITK-3448 Wrap itkQuadEdgeCellTraitsInfo more specifically

Matthew McCormick (3):
      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

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


The following patches will be added:

BUG: remove lsqr because of license issues ITK 1160
http://review.source.kitware.com/#/c/21296/

BUG: ResampleImageFilter honor isInside output of the transform method
http://review.source.kitware.com/#/c/21295/


Are there any others that have been missed?

Thanks,
Matt
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From mrguilfoyle at gmail.com  Tue Jul  5 21:37:00 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Wed, 6 Jul 2016 02:37:00 +0100
Subject: [ITK] [ITK-users] R-SimpleITK LabelStatisticsImageFilter 3D
	Error
In-Reply-To: <D3A13FDD.B84B%yanivz@mail.nih.gov>
References: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>
 <D3A13FDD.B84B%yanivz@mail.nih.gov>
Message-ID: <3F8EFACD-CA13-4B07-86D5-67951C421476@gmail.com>

Ziv: thanks for the reply.

I'm using the R wrapped version of SimpleITK

I've run the equivalent of your example:

library('SimpleITK')
image = ReadImage('training_001_ct.mha')

segmented_image = image>700

lisf = LabelIntensityStatisticsImageFilter()
lisf$Execute(segmented_image, image)

Unfortunately I'm getting the same error as for my own scripts:

Warning message:
In f(...) :
  Exception thrown in SimpleITK Show: /ITK/SITK/Source-Current/Build-290516/ITK-prefix/include/ITK-4.10/itkImageFileWriter.hxx:290:
itk::ERROR: ImageFileWriter(0x10c05cbc0): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff5fbf6cd8)
  Dimension: 2
  Index: 0 0 
  Size: 0 0 
Largest possible region: ImageRegion (0x7fff5fbf6d70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]

I have a feeling that this is a problem with the LabelIntensityStatisticsImageFilter being templated over 2D and 3D images and when it is instantiated it is defaulting to the 2D?  Previously using Python wrapped ITK (i.e. not SimpleITK) when I declared these filters I would give it a 2D or 3D image type but this is not possible in SimpleITK.

However, if this is working for you in Python-SimpleITK maybe it is an issue peculiar to the R wrapping?

Any further suggestions would be appreciated

Cheers

> On 5 Jul 2016, at 15:43, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> 
> Hi Mathew,
> 
> As I haven?t seen your code I cannot pinpoint the issue, but it is not the
> dimension of the image.
> 
> The following SimpleITK code does what I believe you are asking for (image
> is available here - https://midas3.kitware.com/midas/item/317034):
> 
> import SimpleITK as sitk
> 
> image = sitk.ReadImage("training_001_ct.mha")
> 
> # HU values for bone are 700 and up
> segmented_image = image>700
> 
> # segmented label for the threshold operation is 1 (0 for everything else).
> # the LabelIntensityStatisticsImageFilter also works with multiple labels
> and not just a binary segmentation.
> segmented_label = 1
> 
> lisf = sitk.LabelIntensityStatisticsImageFilter()
> lisf.Execute(segmented_image, image)
> 
> print("mean HU value: {0:.2f}".format(lisf.GetMean(segmented_label)))
> 
>     hope this helped
> 
>             Ziv
> 
> 
> 
> 
> 
> 
> On 7/3/16, 9:11 PM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:
> 
>> Hi
>> 
>> Using SimpleITK I'm trying to get statistics for a grayscale image
>> segmentation for which I have a binary mask.  Both image and mask are 3D
>> volumes
>> 
>> I have converted my binary mask to a Label map and then tried to apply
>> the LabelStatisticsImageFilter, however I get the following exception:
>> 
>> Pixel type: 32-bit float is not supported in 3D
>> 
>> I've tried casting the intensity image to unsigned int, Float 64 etc...
>> none of them work.  It seems to be the 3D that is the issue.  Is this
>> filter defined for 3D images?  There is nothing I have found in the
>> documentation/source to suggest not.
>> 
>> Thanks
>> _____________________________________
>> 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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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From weiehome at sina.com  Wed Jul  6 05:25:01 2016
From: weiehome at sina.com (weiehome at sina.com)
Date: Wed, 6 Jul 2016 17:25:01 +0800
Subject: [ITK] question regarding simpleitk java wrapper
Message-ID: <201607061725003293645@sina.com>

Hi, 

Is there a possible way i can create an itk image in java just like in c++ :

Image itkImage = new Image();
itkImage.setOrgin( ... );
itkImage.setSpacing( ... );
itkImage.setRegion( ... );
itkImage.fill(0);

It seems in java i can get itk Image object either by reading files or from filters?

Regards, Tommi


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From blowekamp at mail.nih.gov  Wed Jul  6 08:26:43 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 6 Jul 2016 12:26:43 +0000
Subject: [ITK] [ITK-users] R-SimpleITK LabelStatisticsImageFilter 3D
	Error
In-Reply-To: <3F8EFACD-CA13-4B07-86D5-67951C421476@gmail.com>
References: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>
 <D3A13FDD.B84B%yanivz@mail.nih.gov>
 <3F8EFACD-CA13-4B07-86D5-67951C421476@gmail.com>
Message-ID: <B4553C98-8583-4841-894B-6DBFF3AB9274@mail.nih.gov>

Hello,

Did you compile R SimpleITK from a very recent version of the SimpleITK master branch from git?

There have been a lot of improvements for the R wrapping, and required improvement with SWIG too. This looks like an problem that has been fixed related R reference counting. 

SimpleITK is smart enough to know when to call the 3D or 2D version of a filter. It also knows the pixel types of the inputs and calls the correct template combinations for the ITK filter automatically. When the filter is not instantiated with the pixel types passed to it will give an error message as the original poster of this thread got.

HTH,
Brad

> On Jul 5, 2016, at 9:37 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> 
> Ziv: thanks for the reply.
> 
> I'm using the R wrapped version of SimpleITK
> 
> I've run the equivalent of your example:
> 
> library('SimpleITK')
> image = ReadImage('training_001_ct.mha')
> 
> segmented_image = image>700
> 
> lisf = LabelIntensityStatisticsImageFilter()
> lisf$Execute(segmented_image, image)
> 
> Unfortunately I'm getting the same error as for my own scripts:
> 
> Warning message:
> In f(...) :
>  Exception thrown in SimpleITK Show: /ITK/SITK/Source-Current/Build-290516/ITK-prefix/include/ITK-4.10/itkImageFileWriter.hxx:290:
> itk::ERROR: ImageFileWriter(0x10c05cbc0): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff5fbf6cd8)
>  Dimension: 2
>  Index: 0 0 
>  Size: 0 0 
> Largest possible region: ImageRegion (0x7fff5fbf6d70)
>  Dimension: 2
>  Index: [0, 0]
>  Size: [0, 0]
> 
> I have a feeling that this is a problem with the LabelIntensityStatisticsImageFilter being templated over 2D and 3D images and when it is instantiated it is defaulting to the 2D?  Previously using Python wrapped ITK (i.e. not SimpleITK) when I declared these filters I would give it a 2D or 3D image type but this is not possible in SimpleITK.
> 
> However, if this is working for you in Python-SimpleITK maybe it is an issue peculiar to the R wrapping?
> 
> Any further suggestions would be appreciated
> 
> Cheers
> 
>> On 5 Jul 2016, at 15:43, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
>> 
>> Hi Mathew,
>> 
>> As I haven?t seen your code I cannot pinpoint the issue, but it is not the
>> dimension of the image.
>> 
>> The following SimpleITK code does what I believe you are asking for (image
>> is available here - https://midas3.kitware.com/midas/item/317034):
>> 
>> import SimpleITK as sitk
>> 
>> image = sitk.ReadImage("training_001_ct.mha")
>> 
>> # HU values for bone are 700 and up
>> segmented_image = image>700
>> 
>> # segmented label for the threshold operation is 1 (0 for everything else).
>> # the LabelIntensityStatisticsImageFilter also works with multiple labels
>> and not just a binary segmentation.
>> segmented_label = 1
>> 
>> lisf = sitk.LabelIntensityStatisticsImageFilter()
>> lisf.Execute(segmented_image, image)
>> 
>> print("mean HU value: {0:.2f}".format(lisf.GetMean(segmented_label)))
>> 
>>    hope this helped
>> 
>>            Ziv
>> 
>> 
>> 
>> 
>> 
>> 
>> On 7/3/16, 9:11 PM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> Using SimpleITK I'm trying to get statistics for a grayscale image
>>> segmentation for which I have a binary mask.  Both image and mask are 3D
>>> volumes
>>> 
>>> I have converted my binary mask to a Label map and then tried to apply
>>> the LabelStatisticsImageFilter, however I get the following exception:
>>> 
>>> Pixel type: 32-bit float is not supported in 3D
>>> 
>>> I've tried casting the intensity image to unsigned int, Float 64 etc...
>>> none of them work.  It seems to be the 3D that is the issue.  Is this
>>> filter defined for 3D images?  There is nothing I have found in the
>>> documentation/source to suggest not.
>>> 
>>> Thanks
>>> _____________________________________
>>> 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:
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 blowekamp at mail.nih.gov  Wed Jul  6 09:00:03 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 6 Jul 2016 13:00:03 +0000
Subject: [ITK] question regarding simpleitk java wrapper
In-Reply-To: <201607061725003293645@sina.com>
References: <201607061725003293645@sina.com>
Message-ID: <4C245F08-B5B7-4540-9818-C45F0D0F57F0@mail.nih.gov>

Hello,

You can create it in a similar way to C++. The constructor does have required arguments to specify its size and pixel type.. You need to look at the Doxygen for the API documentation [1]. Also the SimpleITK Image will automatically allocated and initialized the data to 0 unlike an ITK image.

It would look something like the

   Image img2 = new Image( 10, 10, PixelIDValueEnum.sitkInt16 );

    VectorDouble origin = new VectorDouble(img2.getDimension());
    origin.set( 0, 1.0);
    origin.set( 1, 2.0);
    img2.setOrigin(origin);

    System.out.format("%s", img2.toString());

HTH,
Brad

[1] https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html

On Jul 6, 2016, at 5:25 AM, weiehome at sina.com<mailto:weiehome at sina.com> wrote:

Hi,

Is there a possible way i can create an itk image in java just like in c++ :

Image itkImage = new Image();
itkImage.setOrgin( ... );
itkImage.setSpacing( ... );
itkImage.setRegion( ... );
itkImage.fill(0);

It seems in java i can get itk Image object either by reading files or from filters?

Regards, Tommi


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

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From mrguilfoyle at gmail.com  Wed Jul  6 09:47:29 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Wed, 6 Jul 2016 14:47:29 +0100
Subject: [ITK] [ITK-users] R-SimpleITK LabelStatisticsImageFilter 3D
	Error
In-Reply-To: <B4553C98-8583-4841-894B-6DBFF3AB9274@mail.nih.gov>
References: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>
 <D3A13FDD.B84B%yanivz@mail.nih.gov>
 <3F8EFACD-CA13-4B07-86D5-67951C421476@gmail.com>
 <B4553C98-8583-4841-894B-6DBFF3AB9274@mail.nih.gov>
Message-ID: <CAC5Ld0DoYYBRdUzjZ_FdWBUmA=6Cw7UrUQvj8Mw3F0U_+P601g@mail.gmail.com>

Hi

Compiled from a git around two months ago.

In fact, though the error report suggests a fatal problem, the code I
posted does work in as much as I can use the filter to get the label
statistics.  I don't know if the warning that comes up impacts on the
filter function - I have not found a problem thus far.  When I get a
chance I'll recompile a more recent version and check the errors
again.

Thanks

On 6 July 2016 at 13:26, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Hello,
>
> Did you compile R SimpleITK from a very recent version of the SimpleITK master branch from git?
>
> There have been a lot of improvements for the R wrapping, and required improvement with SWIG too. This looks like an problem that has been fixed related R reference counting.
>
> SimpleITK is smart enough to know when to call the 3D or 2D version of a filter. It also knows the pixel types of the inputs and calls the correct template combinations for the ITK filter automatically. When the filter is not instantiated with the pixel types passed to it will give an error message as the original poster of this thread got.
>
> HTH,
> Brad
>
>> On Jul 5, 2016, at 9:37 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
>>
>> Ziv: thanks for the reply.
>>
>> I'm using the R wrapped version of SimpleITK
>>
>> I've run the equivalent of your example:
>>
>> library('SimpleITK')
>> image = ReadImage('training_001_ct.mha')
>>
>> segmented_image = image>700
>>
>> lisf = LabelIntensityStatisticsImageFilter()
>> lisf$Execute(segmented_image, image)
>>
>> Unfortunately I'm getting the same error as for my own scripts:
>>
>> Warning message:
>> In f(...) :
>>  Exception thrown in SimpleITK Show: /ITK/SITK/Source-Current/Build-290516/ITK-prefix/include/ITK-4.10/itkImageFileWriter.hxx:290:
>> itk::ERROR: ImageFileWriter(0x10c05cbc0): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff5fbf6cd8)
>>  Dimension: 2
>>  Index: 0 0
>>  Size: 0 0
>> Largest possible region: ImageRegion (0x7fff5fbf6d70)
>>  Dimension: 2
>>  Index: [0, 0]
>>  Size: [0, 0]
>>
>> I have a feeling that this is a problem with the LabelIntensityStatisticsImageFilter being templated over 2D and 3D images and when it is instantiated it is defaulting to the 2D?  Previously using Python wrapped ITK (i.e. not SimpleITK) when I declared these filters I would give it a 2D or 3D image type but this is not possible in SimpleITK.
>>
>> However, if this is working for you in Python-SimpleITK maybe it is an issue peculiar to the R wrapping?
>>
>> Any further suggestions would be appreciated
>>
>> Cheers
>>
>>> On 5 Jul 2016, at 15:43, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
>>>
>>> Hi Mathew,
>>>
>>> As I haven?t seen your code I cannot pinpoint the issue, but it is not the
>>> dimension of the image.
>>>
>>> The following SimpleITK code does what I believe you are asking for (image
>>> is available here - https://midas3.kitware.com/midas/item/317034):
>>>
>>> import SimpleITK as sitk
>>>
>>> image = sitk.ReadImage("training_001_ct.mha")
>>>
>>> # HU values for bone are 700 and up
>>> segmented_image = image>700
>>>
>>> # segmented label for the threshold operation is 1 (0 for everything else).
>>> # the LabelIntensityStatisticsImageFilter also works with multiple labels
>>> and not just a binary segmentation.
>>> segmented_label = 1
>>>
>>> lisf = sitk.LabelIntensityStatisticsImageFilter()
>>> lisf.Execute(segmented_image, image)
>>>
>>> print("mean HU value: {0:.2f}".format(lisf.GetMean(segmented_label)))
>>>
>>>    hope this helped
>>>
>>>            Ziv
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 7/3/16, 9:11 PM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> Using SimpleITK I'm trying to get statistics for a grayscale image
>>>> segmentation for which I have a binary mask.  Both image and mask are 3D
>>>> volumes
>>>>
>>>> I have converted my binary mask to a Label map and then tried to apply
>>>> the LabelStatisticsImageFilter, however I get the following exception:
>>>>
>>>> Pixel type: 32-bit float is not supported in 3D
>>>>
>>>> I've tried casting the intensity image to unsigned int, Float 64 etc...
>>>> none of them work.  It seems to be the 3D that is the issue.  Is this
>>>> filter defined for 3D images?  There is nothing I have found in the
>>>> documentation/source to suggest not.
>>>>
>>>> Thanks
>>>> _____________________________________
>>>> 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:
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 mrguilfoyle at gmail.com  Wed Jul  6 09:55:45 2016
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Wed, 6 Jul 2016 14:55:45 +0100
Subject: [ITK] [ITK-users] R-SimpleITK memory management
Message-ID: <CAC5Ld0CH-8pOQJrH+-=AoUatYmVn7+A-+Murw0hEcoPdZd238w@mail.gmail.com>

I'm processing a large number of CT scans using R wrapped SimpleITK
(some filtering and then registration before a segmentation).   I'm
running R within RStudio on OS X 10.11

I'm running into memory problems with long processing runs.  Though in
the R loops I reassign new images to the same R variable the
underlying C++ objects do not seem to get deleted but accumulate on
each loop - I can see steadily rising memory usage in Activity Monitor
until R/RStudio crashes.  I have tried explicitly deleting the
temporary images during each loop and calling the R garbage collector
(gc()), but it doesn't seem to have an effect.  If I restart the R
session then the memory is cleared.

My understanding was that the C++ objects would get garbage collected
once all pointers are removed but this doesn't seem to happen.  Is
there a method to explicitly delete the C++ image objects so I can
manage the memory usage myself?

Cheers
_____________________________________
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 zivrafael.yaniv at nih.gov  Wed Jul  6 10:34:11 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 6 Jul 2016 14:34:11 +0000
Subject: [ITK] [ITK-users] R-SimpleITK LabelStatisticsImageFilter 3D
	Error
In-Reply-To: <CAC5Ld0DoYYBRdUzjZ_FdWBUmA=6Cw7UrUQvj8Mw3F0U_+P601g@mail.gmail.com>
References: <6ECF75BD-4C2B-4FE4-BD6D-FFFDC7A414BD@gmail.com>
 <D3A13FDD.B84B%yanivz@mail.nih.gov>
 <3F8EFACD-CA13-4B07-86D5-67951C421476@gmail.com>
 <B4553C98-8583-4841-894B-6DBFF3AB9274@mail.nih.gov>
 <CAC5Ld0DoYYBRdUzjZ_FdWBUmA=6Cw7UrUQvj8Mw3F0U_+P601g@mail.gmail.com>
Message-ID: <D3A28C32.B8BC%yanivz@mail.nih.gov>

Hi Mathew,

This is an issue with the fact that some filters return a zero sized image
for some method calls. The default behavior of R is to attempt to display
this variable (showing a zero size image crashes). You have two options
either assign to a dummy variable or wrap with ?invisible?. Following code
works in R:

library(SimpleITK)

image <- ReadImage("training_001_ct.mha")
segmented_image <- image>700
segmented_label <- 1
lisf <- LabelIntensityStatisticsImageFilter()
ignore_me <- lisf$Execute(segmented_image, image)
# or
invisible(lisf$Execute(segmented_image, image))

cat(lisf$GetMean(segmented_label))
cat(ignore_me$GetSize())


Finally, with regard to building and installing SimpleITK, we now have a
one liner (assuming you have git, Cmake and a working compiler and have
devtools installed in your R environment):

devtools::install_github("SimpleITK/SimpleITKRInstaller",
args=c('--configure-vars="MAKEJ=6"'))


Please set the number of cores according to what you have (we used 6 for
the example).

       regards
          Ziv
 



On 7/6/16, 9:47 AM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:

>Hi
>
>Compiled from a git around two months ago.
>
>In fact, though the error report suggests a fatal problem, the code I
>posted does work in as much as I can use the filter to get the label
>statistics.  I don't know if the warning that comes up impacts on the
>filter function - I have not found a problem thus far.  When I get a
>chance I'll recompile a more recent version and check the errors
>again.
>
>Thanks
>
>On 6 July 2016 at 13:26, Lowekamp, Bradley (NIH/NLM/LHC) [C]
><blowekamp at mail.nih.gov> wrote:
>> Hello,
>>
>> Did you compile R SimpleITK from a very recent version of the SimpleITK
>>master branch from git?
>>
>> There have been a lot of improvements for the R wrapping, and required
>>improvement with SWIG too. This looks like an problem that has been
>>fixed related R reference counting.
>>
>> SimpleITK is smart enough to know when to call the 3D or 2D version of
>>a filter. It also knows the pixel types of the inputs and calls the
>>correct template combinations for the ITK filter automatically. When the
>>filter is not instantiated with the pixel types passed to it will give
>>an error message as the original poster of this thread got.
>>
>> HTH,
>> Brad
>>
>>> On Jul 5, 2016, at 9:37 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>>wrote:
>>>
>>> Ziv: thanks for the reply.
>>>
>>> I'm using the R wrapped version of SimpleITK
>>>
>>> I've run the equivalent of your example:
>>>
>>> library('SimpleITK')
>>> image = ReadImage('training_001_ct.mha')
>>>
>>> segmented_image = image>700
>>>
>>> lisf = LabelIntensityStatisticsImageFilter()
>>> lisf$Execute(segmented_image, image)
>>>
>>> Unfortunately I'm getting the same error as for my own scripts:
>>>
>>> Warning message:
>>> In f(...) :
>>>  Exception thrown in SimpleITK Show:
>>>/ITK/SITK/Source-Current/Build-290516/ITK-prefix/include/ITK-4.10/itkIma
>>>geFileWriter.hxx:290:
>>> itk::ERROR: ImageFileWriter(0x10c05cbc0): Largest possible region does
>>>not fully contain requested paste IO regionPaste IO region:
>>>ImageIORegion (0x7fff5fbf6cd8)
>>>  Dimension: 2
>>>  Index: 0 0
>>>  Size: 0 0
>>> Largest possible region: ImageRegion (0x7fff5fbf6d70)
>>>  Dimension: 2
>>>  Index: [0, 0]
>>>  Size: [0, 0]
>>>
>>> I have a feeling that this is a problem with the
>>>LabelIntensityStatisticsImageFilter being templated over 2D and 3D
>>>images and when it is instantiated it is defaulting to the 2D?
>>>Previously using Python wrapped ITK (i.e. not SimpleITK) when I
>>>declared these filters I would give it a 2D or 3D image type but this
>>>is not possible in SimpleITK.
>>>
>>> However, if this is working for you in Python-SimpleITK maybe it is an
>>>issue peculiar to the R wrapping?
>>>
>>> Any further suggestions would be appreciated
>>>
>>> Cheers
>>>
>>>> On 5 Jul 2016, at 15:43, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
>>>><zivrafael.yaniv at nih.gov> wrote:
>>>>
>>>> Hi Mathew,
>>>>
>>>> As I haven?t seen your code I cannot pinpoint the issue, but it is
>>>>not the
>>>> dimension of the image.
>>>>
>>>> The following SimpleITK code does what I believe you are asking for
>>>>(image
>>>> is available here - https://midas3.kitware.com/midas/item/317034):
>>>>
>>>> import SimpleITK as sitk
>>>>
>>>> image = sitk.ReadImage("training_001_ct.mha")
>>>>
>>>> # HU values for bone are 700 and up
>>>> segmented_image = image>700
>>>>
>>>> # segmented label for the threshold operation is 1 (0 for everything
>>>>else).
>>>> # the LabelIntensityStatisticsImageFilter also works with multiple
>>>>labels
>>>> and not just a binary segmentation.
>>>> segmented_label = 1
>>>>
>>>> lisf = sitk.LabelIntensityStatisticsImageFilter()
>>>> lisf.Execute(segmented_image, image)
>>>>
>>>> print("mean HU value: {0:.2f}".format(lisf.GetMean(segmented_label)))
>>>>
>>>>    hope this helped
>>>>
>>>>            Ziv
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 7/3/16, 9:11 PM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> Using SimpleITK I'm trying to get statistics for a grayscale image
>>>>> segmentation for which I have a binary mask.  Both image and mask
>>>>>are 3D
>>>>> volumes
>>>>>
>>>>> I have converted my binary mask to a Label map and then tried to
>>>>>apply
>>>>> the LabelStatisticsImageFilter, however I get the following
>>>>>exception:
>>>>>
>>>>> Pixel type: 32-bit float is not supported in 3D
>>>>>
>>>>> I've tried casting the intensity image to unsigned int, Float 64
>>>>>etc...
>>>>> none of them work.  It seems to be the 3D that is the issue.  Is this
>>>>> filter defined for 3D images?  There is nothing I have found in the
>>>>> documentation/source to suggest not.
>>>>>
>>>>> Thanks
>>>>> _____________________________________
>>>>> 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 bakkari.abdelkhalek at hotmail.fr  Wed Jul  6 11:11:35 2016
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Wed, 6 Jul 2016 16:11:35 +0100
Subject: [ITK] Manual 3d image segmentation using itk
Message-ID: <DUB126-W779BDA0691573D1ACAB88833A0@phx.gbl>




Hi,
I would like to ask if you could help me  with a code source related to Manual interactive 3d image segmentation using itk as described in the video below :
https://www.youtube.com/watch?v=7wCC2NaVLjs

Thank you in advance.

Best regards,


Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland


 		 	   		  
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From zivrafael.yaniv at nih.gov  Wed Jul  6 11:23:37 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 6 Jul 2016 15:23:37 +0000
Subject: [ITK] [ITK-users] R-SimpleITK memory management
In-Reply-To: <CAC5Ld0CH-8pOQJrH+-=AoUatYmVn7+A-+Murw0hEcoPdZd238w@mail.gmail.com>
References: <CAC5Ld0CH-8pOQJrH+-=AoUatYmVn7+A-+Murw0hEcoPdZd238w@mail.gmail.com>
Message-ID: <D3A29778.B8DD%yanivz@mail.nih.gov>

Hi Mathew,

Can you provide a concise example so that we can recreate the problem? I
tried the trivial thing with the code we were previously discussing, just
repeatedly running it in a loop and the memory useage is as expected,
doesn?t change after initial run, code below:

library(SimpleITK)
library(pryr)

for(i in 1:100)
{
  print(mem_used())
  image <- ReadImage("training_001_ct.mha")
  segmented_image <- image>700
  segmented_label <- 1
  lisf <- LabelIntensityStatisticsImageFilter()
  invisible(lisf$Execute(segmented_image, image))
  print(mem_used())
}

When I ran this in R studio the memory usage was higher, but still
consistent. Apparently R studio also keeps a reference to every object
created on the command line (Hadly Wickham?s book on Advanced R, memory
management http://adv-r.had.co.nz/memory.html).


    Ziv




On 7/6/16, 9:55 AM, "Mathew Guilfoyle" <mrguilfoyle at gmail.com> wrote:

>I'm processing a large number of CT scans using R wrapped SimpleITK
>(some filtering and then registration before a segmentation).   I'm
>running R within RStudio on OS X 10.11
>
>I'm running into memory problems with long processing runs.  Though in
>the R loops I reassign new images to the same R variable the
>underlying C++ objects do not seem to get deleted but accumulate on
>each loop - I can see steadily rising memory usage in Activity Monitor
>until R/RStudio crashes.  I have tried explicitly deleting the
>temporary images during each loop and calling the R garbage collector
>(gc()), but it doesn't seem to have an effect.  If I restart the R
>session then the memory is cleared.
>
>My understanding was that the C++ objects would get garbage collected
>once all pointers are removed but this doesn't seem to happen.  Is
>there a method to explicitly delete the C++ image objects so I can
>manage the memory usage myself?
>
>Cheers
>_____________________________________
>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:
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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From matt.mccormick at kitware.com  Wed Jul  6 11:42:51 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 6 Jul 2016 11:42:51 -0400
Subject: [ITK] Manual 3d image segmentation using itk
In-Reply-To: <DUB126-W779BDA0691573D1ACAB88833A0@phx.gbl>
References: <DUB126-W779BDA0691573D1ACAB88833A0@phx.gbl>
Message-ID: <CALzTN-SPZkfP1rqEFz8mqhg9gBNgbbdkfJY5wRPR5b5oaVjvuw@mail.gmail.com>

Hi,

You may want to investigate the open source, ITK-based ITK-SNAP project,
which has similiar functionality.

HTH,
Matt

On Wed, Jul 6, 2016 at 11:11 AM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Hi,
>
> I would like to ask if you could help me  with a code source related
> to Manual interactive 3d image segmentation using itk as described in the
> video below :
> https://www.youtube.com/watch?v=7wCC2NaVLjs
>
> Thank you in advance.
>
> Best regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From dzenanz at gmail.com  Wed Jul  6 14:34:29 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 6 Jul 2016 14:34:29 -0400
Subject: [ITK] [ITK-users]  Manual 3d image segmentation using itk
In-Reply-To: <CALzTN-SPZkfP1rqEFz8mqhg9gBNgbbdkfJY5wRPR5b5oaVjvuw@mail.gmail.com>
References: <DUB126-W779BDA0691573D1ACAB88833A0@phx.gbl>
 <CALzTN-SPZkfP1rqEFz8mqhg9gBNgbbdkfJY5wRPR5b5oaVjvuw@mail.gmail.com>
Message-ID: <CAPf2UMRacN_fVwSGmBZ+9Thgw+mLwwPdPmUnmm_hftsLfNj+fg@mail.gmail.com>

Hi Abdelkhalek,

Slicer <https://www.slicer.org/>'s editor module has a graph-cut "effect"
which is quite similar to what the video shows.

Regards,
D?enan

On Wed, Jul 6, 2016 at 11:42 AM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi,
>
> You may want to investigate the open source, ITK-based ITK-SNAP project,
> which has similiar functionality.
>
> HTH,
> Matt
>
> On Wed, Jul 6, 2016 at 11:11 AM, Abdelkhalek Bakkari <
> bakkari.abdelkhalek at hotmail.fr> wrote:
>
>> Hi,
>>
>> I would like to ask if you could help me  with a code source related
>> to Manual interactive 3d image segmentation using itk as described in the
>> video below :
>> https://www.youtube.com/watch?v=7wCC2NaVLjs
>>
>> Thank you in advance.
>>
>> Best regards,
>>
>>
>> Abdelkhalek Bakkari
>> Ph.D candidate in Computer Science
>> Institute of Applied Computer Science
>> Lodz University of Technology, Poland
>>
>>
>>
>> _______________________________________________
>> 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
>
>
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From weiehome at sina.com  Thu Jul  7 05:21:42 2016
From: weiehome at sina.com (weiehome at sina.com)
Date: Thu, 7 Jul 2016 17:21:42 +0800
Subject: [ITK] question regarding simpleitk java wrapper
References: <201607061725003293645@sina.com>, 
 <4C245F08-B5B7-4540-9818-C45F0D0F57F0@mail.nih.gov>
Message-ID: <2016070717214197101712@sina.com>

Hi, Bradley

Thank you ! But how can i fill it with metadata information?
In c++, i can set metadatas manually using raw pointer to MetadataDictionary instance to achieve it, but in JAVA, it seems there is no such way of setting Image Metadata?

One function i found is CopyInformation(), however it requires Given input image has to be as same dimension as output one.
What i want is followings: 
1.First read dicoms volume data (CTs) from a folder recursively using SeriesReader
2. then convert all 3d volumes into my own data structure, then serialize it into bytes and passed to some remote server.
consider 1-2 steps are data import steps.
when exporting the data from remote server, i do :
3.read the bytes and deserialize bytes into self-defined image data structure.
4.convert data structure into itk image(3d)
remember when i do import, i actually extract all dicom tags i needed and put finally into data structure. 
So the question is how can i use Simpleitk java to read self-defined structure to recontruct dicom images including pixel data and metadata.
 
Best Regards,
Tom    



weiehome at sina.com
 
From: Lowekamp, Bradley (NIH/NLM/LHC) [C]
Date: 2016-07-06 21:00
To: weiehome at sina.com
CC: community at itk.org
Subject: Re: [ITK] question regarding simpleitk java wrapper
Hello, 

You can create it in a similar way to C++. The constructor does have required arguments to specify its size and pixel type.. You need to look at the Doxygen for the API documentation [1]. Also the SimpleITK Image will automatically allocated and initialized the data to 0 unlike an ITK image.

It would look something like the 

   Image img2 = new Image( 10, 10, PixelIDValueEnum.sitkInt16 );

    VectorDouble origin = new VectorDouble(img2.getDimension());
    origin.set( 0, 1.0);
    origin.set( 1, 2.0);
    img2.setOrigin(origin);

    System.out.format("%s", img2.toString());

HTH,
Brad

[1] https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html

On Jul 6, 2016, at 5:25 AM, weiehome at sina.com wrote:

Hi, 

Is there a possible way i can create an itk image in java just like in c++ :

Image itkImage = new Image();
itkImage.setOrgin( ... );
itkImage.setSpacing( ... );
itkImage.setRegion( ... );
itkImage.fill(0);

It seems in java i can get itk Image object either by reading files or from filters?

Regards, Tommi


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http://public.kitware.com/mailman/listinfo/community

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From piotpia124 at student.polsl.pl  Thu Jul  7 08:35:12 2016
From: piotpia124 at student.polsl.pl (Piotr Piasecki)
Date: Thu, 7 Jul 2016 14:35:12 +0200
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
Message-ID: <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>

Hi D?enan,

thank you for your help and for this example. Unfortunately, I have not
found method GetMetaDataDictionary() in SimpleITK in C# (I found only
GetMetaDataKeys() and GetMetaData(string key)). Also, I have not found a
method SetMetaDataDictionary or any other that allows me to assign DICOM
tags.

My short piece of code looks like this:

static public void ReadImage()
        {
            sitk.ImageFileReader reader = new sitk.ImageFileReader();
            reader.SetFileName(@".\DICOM_TEST\original.dcm");
            var image = reader.Execute();

            sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
            writer.SetFileName(@".\DICOM_TEST\modified.dcm");
            writer.Execute(image);
        }

Another problem is that your example describes only loading and saving a
single .dcm file. What if I have to process a whole series of files using
sitk.ImageSeriesReader and sitk.ImageSeriesWriter?

Regards,

Peter.

2016-07-05 15:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:

> Hi Piotr,
>
> if you want to carry over metadata from input image to output image, you
> should save the metadata dictionary in a way similar to this:
>
> itk::MetaDataDictionary metadata;
>
> template< typename TImage >
> itk::SmartPointer<TImage> readImage(std::string fileName)
> {
>     typedef itk::ImageFileReader<TImage> ReaderType;
>     typename ReaderType::Pointer reader = ReaderType::New();
>     reader->SetFileName(fileName.c_str());
>     try
>     {
>         reader->Update();
>         metadata = reader->GetMetaDataDictionary();
>         return reader->GetOutput();
>     }
>     catch (itk::ExceptionObject & error)
>     {
>         std::cerr << "Error: " << error << std::endl;
>         return NULL;
>     }
> }
>
> template< typename TImage >
> void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
> {
>     image->SetMetaDataDictionary(metadata); //full metadata
>     typedef itk::ImageFileWriter<TImage> WriterType;
>     typename WriterType::Pointer writer = WriterType::New();
>     writer->SetFileName(fileName.c_str());
>     writer->SetInput(image);
>     try
>     {
>         writer->Update();
>     }
>     catch (itk::ExceptionObject & error)
>     {
>         std::cerr << "Error: " << error << std::endl;
>     }
> }
>
> On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <
> piotpia124 at student.polsl.pl> wrote:
>
>> Dear Sir or Madam.
>>
>> I am a student in Biomedical Engineering at the Silesian University of
>> Technology. During my studies I worked with ITK and SimpleITK in C#. I want
>> to use them in my current project, but I have an important question. After
>> loading and processing a series of .dcm files I lost information about the
>> patient and study to which they belong, and that they belong to one series.
>> How can I keep this information?
>>
>> I will be very grateful for any answer.
>>
>> Best regards.
>>
>> Peter.
>> _____________________________________
>> 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 Jul  7 08:45:27 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 7 Jul 2016 08:45:27 -0400
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
 <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
Message-ID: <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>

Hi Piotr,

instead of ImageReader->GetMetaDataDictionary() call
ImageSeriesReader->GetMetaDataDictionary(). Also, the image format you are
writing to needs to be able to support metadata (e.g. .mha, .nrrd, DICOM),
otherwise the metadata is lost (.nii, .jpg, .bmp etc).

But for writing DICOM, the process might be somewhat different from what I
described in the first email. Definitely different if you want metadata
copied slice for slice from input to output - in this case some metadata
needs to be changed anyway, such as flag that this is a derived image and
not an original image coming out of a scanner.

I suppose that MetaDataDictionary class is not wrapped. You can then loop
through all the keys and copy them and their content one by one.

Regards

On Thu, Jul 7, 2016 at 8:35 AM, Piotr Piasecki <piotpia124 at student.polsl.pl>
wrote:

> Hi D?enan,
>
> thank you for your help and for this example. Unfortunately, I have not
> found method GetMetaDataDictionary() in SimpleITK in C# (I found only
> GetMetaDataKeys() and GetMetaData(string key)). Also, I have not found a
> method SetMetaDataDictionary or any other that allows me to assign DICOM
> tags.
>
> My short piece of code looks like this:
>
> static public void ReadImage()
>         {
>             sitk.ImageFileReader reader = new sitk.ImageFileReader();
>             reader.SetFileName(@".\DICOM_TEST\original.dcm");
>             var image = reader.Execute();
>
>             sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
>             writer.SetFileName(@".\DICOM_TEST\modified.dcm");
>             writer.Execute(image);
>         }
>
> Another problem is that your example describes only loading and saving a
> single .dcm file. What if I have to process a whole series of files using
> sitk.ImageSeriesReader and sitk.ImageSeriesWriter?
>
> Regards,
>
> Peter.
>
> 2016-07-05 15:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
>
>> Hi Piotr,
>>
>> if you want to carry over metadata from input image to output image, you
>> should save the metadata dictionary in a way similar to this:
>>
>> itk::MetaDataDictionary metadata;
>>
>> template< typename TImage >
>> itk::SmartPointer<TImage> readImage(std::string fileName)
>> {
>>     typedef itk::ImageFileReader<TImage> ReaderType;
>>     typename ReaderType::Pointer reader = ReaderType::New();
>>     reader->SetFileName(fileName.c_str());
>>     try
>>     {
>>         reader->Update();
>>         metadata = reader->GetMetaDataDictionary();
>>         return reader->GetOutput();
>>     }
>>     catch (itk::ExceptionObject & error)
>>     {
>>         std::cerr << "Error: " << error << std::endl;
>>         return NULL;
>>     }
>> }
>>
>> template< typename TImage >
>> void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
>> {
>>     image->SetMetaDataDictionary(metadata); //full metadata
>>     typedef itk::ImageFileWriter<TImage> WriterType;
>>     typename WriterType::Pointer writer = WriterType::New();
>>     writer->SetFileName(fileName.c_str());
>>     writer->SetInput(image);
>>     try
>>     {
>>         writer->Update();
>>     }
>>     catch (itk::ExceptionObject & error)
>>     {
>>         std::cerr << "Error: " << error << std::endl;
>>     }
>> }
>>
>> On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <
>> piotpia124 at student.polsl.pl> wrote:
>>
>>> Dear Sir or Madam.
>>>
>>> I am a student in Biomedical Engineering at the Silesian University of
>>> Technology. During my studies I worked with ITK and SimpleITK in C#. I want
>>> to use them in my current project, but I have an important question. After
>>> loading and processing a series of .dcm files I lost information about the
>>> patient and study to which they belong, and that they belong to one series.
>>> How can I keep this information?
>>>
>>> I will be very grateful for any answer.
>>>
>>> Best regards.
>>>
>>> Peter.
>>> _____________________________________
>>> 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  Thu Jul  7 09:48:48 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 7 Jul 2016 09:48:48 -0400
Subject: [ITK] [ITK-dev]   ITK Python wrapping issue with GCC 6.1.1
In-Reply-To: <CAMkPkZVt9pLAUxrZPYohyqD3YeiqE52zZmaLJvpV5H9eM0_oEA@mail.gmail.com>
References: <CAMkPkZV-RW11Pfi9DqT-GVKUF3-stK1TKWHXJUgYKR8QoTPPPw@mail.gmail.com>
 <CALzTN-RjOuCrP0VBD1VExCwxVT=9_92yrGNBkkmVuaE5WRfWUw@mail.gmail.com>
 <CAMkPkZVt9pLAUxrZPYohyqD3YeiqE52zZmaLJvpV5H9eM0_oEA@mail.gmail.com>
Message-ID: <CALzTN-RDAdmaH_5vktX2YPuN2cygUp7xYDqrWNn5ynzfxU7rFw@mail.gmail.com>

Following up, this issue was addressed in this patch:

  http://review.source.kitware.com/#/c/21311/

which will be included in the 4.10.1 release.

On Fri, Jul 1, 2016 at 3:01 PM, Marcus D. Hanwell
<marcus.hanwell at kitware.com> wrote:
> Matt, thanks for the confirmation, sorry I didn't spot it in the issue
> tracker. I will monitor the bug.
>
> On Fri, Jul 1, 2016 at 2:54 PM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>> Hi Marcus,
>>
>> Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is
>> having issues.  There is now an issue to track this:
>>
>>   https://issues.itk.org/jira/browse/ITK-3450
>>
>> Thanks,
>> Matt
>>
>> On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell
>> <marcus.hanwell at kitware.com> wrote:
>>> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am
>>> seeing a compile error:
>>>
>>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _
>>> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?:
>>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi
>>> ng function for call to ?itk::TriangleHelper<itk::Point<double, 2u> >::TriangleH
>>> elper()?
>>>       result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
>>>                                                                 ^
>>> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO
>>> bject.h:21:0,
>>>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject
>>> .h:31,
>>>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman
>>> d.h:21,
>>>                 from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3,
>>>                 from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325
>>> 8:
>>> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note
>>> : candidate: itk::TriangleHelper<TPoint>::TriangleHelper(const itk::TriangleHelp
>>> er<TPoint>&) [with TPoint = itk::Point<double, 2u>] <deleted>
>>>   ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper);
>>>
>>> Is my GCC too new? It only seems to be happening with the wrapping,
>>> this is on Linux. I can post more details if it helps.
>>> _______________________________________________
>>> 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
_______________________________________________
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://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From matt.mccormick at kitware.com  Thu Jul  7 09:49:20 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 7 Jul 2016 09:49:20 -0400
Subject: [ITK] [ITK-users] Build errors in python wrapping of 4.10.0
In-Reply-To: <CAL1JtzDwp5dx-yKpk52OxTg6h0gLt_xMg-c0ZUCpkF_cJ3hk2A@mail.gmail.com>
References: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>
 <D452B2C7-BD65-426B-BC46-A10C642DB70A@gmail.com>
 <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu>
 <CAL1JtzDwp5dx-yKpk52OxTg6h0gLt_xMg-c0ZUCpkF_cJ3hk2A@mail.gmail.com>
Message-ID: <CALzTN-SDR+fm7nRtcoPMDEWDRirhdi5rJR7Rcpx933w4PT-hEQ@mail.gmail.com>

Following up, this issue was addressed in this patch:

  http://review.source.kitware.com/#/c/21311/

which will be included in the 4.10.1 release.

On Thu, Jun 30, 2016 at 11:55 AM, Christopher Mullins
<christopherrmullins at gmail.com> wrote:
> Hi all,
>
> Thanks for the help on this.  I've been traveling and haven't had much time
> to investigate, but I believe Michka is correct.  It looks like the build is
> successful with the -std=c++98 flag, and only one test fails [1].  I'll test
> the python wrapping and report back if anything terrible happens -- if not
> I'll bump the AUR PKGBUILD.  Thanks again,
>
> Chris
>
> [1] https://open.cdash.org/buildSummary.php?buildid=4435570
>
> On Wed, Jun 15, 2016 at 5:22 PM, Johnson, Hans J <hans-johnson at uiowa.edu>
> wrote:
>>
>> I?m trying to reproduce now.
>>
>> Hans
>>
>>
>> --
>>
>>
>> On 6/15/16, 4:12 PM, "Insight-users on behalf of Michka Popoff"
>> <insight-users-bounces at itk.org on behalf of michkapopoff at gmail.com> wrote:
>>
>> >Hi
>> >
>> >I think this bug is not known. I had a look and could reproduce it with
>> > gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X.
>> >GCC 6 is using c++14 by default, but even with c++11 you would probably
>> > get the problem.
>> >The problem is also there with the latest commit from the master branch.
>> >
>> >Please note that we probably never tested Python Wrappings with c++11,
>> > even not speaking of c++14.
>> >
>> >The problem seems to have appeared with this patch:
>>
>> > >https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395
>> >
>> >I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy
>> > constructor, and was able to compile
>> >with gcc 6. But it may just a side effect of that patch which is now only
>> > appearing with c++ >= 11.
>> >It is weird that the problem seems to be only for the itkTriangleHelper
>> > class.
>> >
>> >I will have to look what is the difference in the files generated for
>> > swig and what is exactly failing,
>> >though I do not know how long it will take me. I hope I can do this this
>> > weekend.
>> >
>> >Thanks
>> >
>> >Michka
>> >
>> >
>> >> On 09 Jun 2016, at 16:14, Christopher Mullins
>> >> <christopherrmullins at gmail.com> wrote:
>> >>
>> >> Hi all,
>> >>
>> >> Apparently my subscription to this list has lapsed and my first email
>> >> was rejected (despite receiving the list in my inbox every day).  Sorry if
>> >> there's a double post.
>> >>
>> >> I'm getting the following build errors when building ITK 4.10.0 with
>> >> the WRAP_PYTHON option ON[1], [3].  Is this a known issue, or is there a
>> >> configuration setting I've set improperly?
>> >>
>> >> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There
>> >> are no warnings. See all output details for this machine here [2], and
>> >> please let me know if I can provide any others.
>> >>
>> >> The faster I fix this the faster I'll feel comfortable updating the
>> >> Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer.
>> >>
>> >> Thanks,
>> >> Chris
>> >>
>> >>
>> >>
>> >> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379
>> >> [2] https://open.cdash.org/buildSummary.php?buildid=4403379
>> >>
>> >> [3] To save you a click, and for the sake of archiving, the error is:
>> >>
>> >> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:
>> >> In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*,
>> >> PyObject*)':
>> >> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65:
>> >> error: no matching function for call to
>> >> 'itk::TriangleHelper<itk::Point<double, 2u> >::TriangleHelper()' result =
>> >> (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
>> >> _____________________________________
>> >> 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

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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

Follow this link to subscribe/unsubscribe:
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From piotpia124 at student.polsl.pl  Thu Jul  7 09:49:56 2016
From: piotpia124 at student.polsl.pl (Piotr Piasecki)
Date: Thu, 7 Jul 2016 15:49:56 +0200
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
 <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
 <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>
Message-ID: <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>

Hello Again

I found the information, that in SimpleITK the MetaDataDictionary interface
is only part of the Image class. Currently it provides a read only
interface, with the GetMetaDataKeys(), and GetMetaData(key) methods. This
get method only returns the type of data in the dictionary converted to a
string.

The required method would be Image::SetMetaData(key,value). But
unfortunately I do not see this method, so I think that this is still not
implemented. The only what I need is to keep information that my files
belong to one series of images, which belongs to one patient and study (
not necessarily the same study or series as the original).

Regards.

Peter.


2016-07-07 14:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:

> Hi Piotr,
>
> instead of ImageReader->GetMetaDataDictionary() call
> ImageSeriesReader->GetMetaDataDictionary(). Also, the image format you are
> writing to needs to be able to support metadata (e.g. .mha, .nrrd, DICOM),
> otherwise the metadata is lost (.nii, .jpg, .bmp etc).
>
> But for writing DICOM, the process might be somewhat different from what I
> described in the first email. Definitely different if you want metadata
> copied slice for slice from input to output - in this case some metadata
> needs to be changed anyway, such as flag that this is a derived image and
> not an original image coming out of a scanner.
>
> I suppose that MetaDataDictionary class is not wrapped. You can then loop
> through all the keys and copy them and their content one by one.
>
> Regards
>
> On Thu, Jul 7, 2016 at 8:35 AM, Piotr Piasecki <
> piotpia124 at student.polsl.pl> wrote:
>
>> Hi D?enan,
>>
>> thank you for your help and for this example. Unfortunately, I have not
>> found method GetMetaDataDictionary() in SimpleITK in C# (I found only
>> GetMetaDataKeys() and GetMetaData(string key)). Also, I have not found a
>> method SetMetaDataDictionary or any other that allows me to assign DICOM
>> tags.
>>
>> My short piece of code looks like this:
>>
>> static public void ReadImage()
>>         {
>>             sitk.ImageFileReader reader = new sitk.ImageFileReader();
>>             reader.SetFileName(@".\DICOM_TEST\original.dcm");
>>             var image = reader.Execute();
>>
>>             sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
>>             writer.SetFileName(@".\DICOM_TEST\modified.dcm");
>>             writer.Execute(image);
>>         }
>>
>> Another problem is that your example describes only loading and saving a
>> single .dcm file. What if I have to process a whole series of files
>> using sitk.ImageSeriesReader and sitk.ImageSeriesWriter?
>>
>> Regards,
>>
>> Peter.
>>
>> 2016-07-05 15:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
>>
>>> Hi Piotr,
>>>
>>> if you want to carry over metadata from input image to output image, you
>>> should save the metadata dictionary in a way similar to this:
>>>
>>> itk::MetaDataDictionary metadata;
>>>
>>> template< typename TImage >
>>> itk::SmartPointer<TImage> readImage(std::string fileName)
>>> {
>>>     typedef itk::ImageFileReader<TImage> ReaderType;
>>>     typename ReaderType::Pointer reader = ReaderType::New();
>>>     reader->SetFileName(fileName.c_str());
>>>     try
>>>     {
>>>         reader->Update();
>>>         metadata = reader->GetMetaDataDictionary();
>>>         return reader->GetOutput();
>>>     }
>>>     catch (itk::ExceptionObject & error)
>>>     {
>>>         std::cerr << "Error: " << error << std::endl;
>>>         return NULL;
>>>     }
>>> }
>>>
>>> template< typename TImage >
>>> void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
>>> {
>>>     image->SetMetaDataDictionary(metadata); //full metadata
>>>     typedef itk::ImageFileWriter<TImage> WriterType;
>>>     typename WriterType::Pointer writer = WriterType::New();
>>>     writer->SetFileName(fileName.c_str());
>>>     writer->SetInput(image);
>>>     try
>>>     {
>>>         writer->Update();
>>>     }
>>>     catch (itk::ExceptionObject & error)
>>>     {
>>>         std::cerr << "Error: " << error << std::endl;
>>>     }
>>> }
>>>
>>> On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <
>>> piotpia124 at student.polsl.pl> wrote:
>>>
>>>> Dear Sir or Madam.
>>>>
>>>> I am a student in Biomedical Engineering at the Silesian University of
>>>> Technology. During my studies I worked with ITK and SimpleITK in C#. I want
>>>> to use them in my current project, but I have an important question. After
>>>> loading and processing a series of .dcm files I lost information about the
>>>> patient and study to which they belong, and that they belong to one series.
>>>> How can I keep this information?
>>>>
>>>> I will be very grateful for any answer.
>>>>
>>>> Best regards.
>>>>
>>>> Peter.
>>>> _____________________________________
>>>> 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  Thu Jul  7 09:57:47 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 7 Jul 2016 09:57:47 -0400
Subject: [ITK] [ITK-dev] LSQR (and related VNL code) Licensing Issues -
	fix	lost
In-Reply-To: <CAPG4jkQoqgXfo9R3cqA8fM1but1O9GKOW_A0zDBYagx4n-ijRA@mail.gmail.com>
References: <CAPG4jkQoqgXfo9R3cqA8fM1but1O9GKOW_A0zDBYagx4n-ijRA@mail.gmail.com>
Message-ID: <CALzTN-Qu_yWRwUBArYgcBmnzHxjk4dNxCJZzCmcGo7uO3vpbiQ@mail.gmail.com>

Following up, this issue was addressed in this patch:

  http://review.source.kitware.com/#/c/21296/

and pushed upstream here:

  https://github.com/vxl/vxl/pull/337

It will be included in the ITK 4.10.1 release.

On Fri, Jul 1, 2016 at 4:45 AM, Tom Vercauteren <tom.vercauteren at m4x.org> wrote:
> Dear all,
>
> Sorry for the cross-posting but this refers to an issue linking both ITK and
> VNL.
>
> In 2010, we identified a licensing issue with some code from vnl and at the
> time Luis Ibanez fixed it from the ITK side:
> https://issues.itk.org/jira/browse/HISTITK-1160
>
> Luis notably rewrote the LSQR code:
> https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg
> http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/
> https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg
>
> It seems that this effort was not backported to VXL and was subsequently
> lost when moving to ITK 4:
> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg
>
> It would be great if someone could look into this (important) licensing
> issue.
>
> For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a
> standalone github repo here:
> https://github.com/tvercaut/LSQR-cpp
>
> I have also added a comment in the ITK and VXL bug trackers:
> https://issues.itk.org/jira/browse/HISTITK-1160
> https://github.com/vxl/vxl/issues/332
>
> Best wishes,
> Tom
>
> _______________________________________________
> 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

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

Kitware offers ITK Training Courses, for more information visit:
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From blowekamp at mail.nih.gov  Thu Jul  7 10:01:27 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 7 Jul 2016 14:01:27 +0000
Subject: [ITK] [ITK-dev] LSQR (and related VNL code) Licensing Issues
	-	fix	lost
In-Reply-To: <CALzTN-Qu_yWRwUBArYgcBmnzHxjk4dNxCJZzCmcGo7uO3vpbiQ@mail.gmail.com>
References: <CAPG4jkQoqgXfo9R3cqA8fM1but1O9GKOW_A0zDBYagx4n-ijRA@mail.gmail.com>
 <CALzTN-Qu_yWRwUBArYgcBmnzHxjk4dNxCJZzCmcGo7uO3vpbiQ@mail.gmail.com>
Message-ID: <09B7458A-8DC2-4616-9038-0068115F14C4@mail.nih.gov>

Matt,

This patch looks like it is the source of a number of valgrind defects on the ITK dashboard that need to be addressed.

https://open.cdash.org/viewDynamicAnalysisFile.php?id=3934294

Brad

> On Jul 7, 2016, at 9:57 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
> Following up, this issue was addressed in this patch:
> 
>  http://review.source.kitware.com/#/c/21296/
> 
> and pushed upstream here:
> 
>  https://github.com/vxl/vxl/pull/337
> 
> It will be included in the ITK 4.10.1 release.
> 
> On Fri, Jul 1, 2016 at 4:45 AM, Tom Vercauteren <tom.vercauteren at m4x.org> wrote:
>> Dear all,
>> 
>> Sorry for the cross-posting but this refers to an issue linking both ITK and
>> VNL.
>> 
>> In 2010, we identified a licensing issue with some code from vnl and at the
>> time Luis Ibanez fixed it from the ITK side:
>> https://issues.itk.org/jira/browse/HISTITK-1160
>> 
>> Luis notably rewrote the LSQR code:
>> https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg
>> http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/
>> https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg
>> 
>> It seems that this effort was not backported to VXL and was subsequently
>> lost when moving to ITK 4:
>> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg
>> 
>> It would be great if someone could look into this (important) licensing
>> issue.
>> 
>> For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a
>> standalone github repo here:
>> https://github.com/tvercaut/LSQR-cpp
>> 
>> I have also added a comment in the ITK and VXL bug trackers:
>> https://issues.itk.org/jira/browse/HISTITK-1160
>> https://github.com/vxl/vxl/issues/332
>> 
>> Best wishes,
>> Tom
>> 
>> _______________________________________________
>> 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:
> http://public.kitware.com/mailman/listinfo/insight-developers

_______________________________________________
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Kitware offers ITK Training Courses, for more information visit:
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From dzenanz at gmail.com  Thu Jul  7 10:11:21 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 7 Jul 2016 10:11:21 -0400
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
 <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
 <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>
 <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>
Message-ID: <CAPf2UMSzuqpCaq1=1X3dZtLE1RRmfpVDEe_sZCShp3JDYyrb4A@mail.gmail.com>

If SimpleITK does not provide write access to meta-data dictionary, you can
indicate patient, study and series in the filename by specially formatting
it.

Hopefully Brad can provide more useful advice.

Regards

On Thu, Jul 7, 2016 at 9:49 AM, Piotr Piasecki <piotpia124 at student.polsl.pl>
wrote:

> Hello Again
>
> I found the information, that in SimpleITK the MetaDataDictionary
> interface is only part of the Image class. Currently it provides a read
> only interface, with the GetMetaDataKeys(), and GetMetaData(key) methods.
> This get method only returns the type of data in the dictionary converted
> to a string.
>
> The required method would be Image::SetMetaData(key,value). But
> unfortunately I do not see this method, so I think that this is still not
> implemented. The only what I need is to keep information that my files
> belong to one series of images, which belongs to one patient and study (
> not necessarily the same study or series as the original).
>
> Regards.
>
> Peter.
>
>
>
> 2016-07-07 14:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
>
>> Hi Piotr,
>>
>> instead of ImageReader->GetMetaDataDictionary() call
>> ImageSeriesReader->GetMetaDataDictionary(). Also, the image format you are
>> writing to needs to be able to support metadata (e.g. .mha, .nrrd, DICOM),
>> otherwise the metadata is lost (.nii, .jpg, .bmp etc).
>>
>> But for writing DICOM, the process might be somewhat different from what
>> I described in the first email. Definitely different if you want metadata
>> copied slice for slice from input to output - in this case some metadata
>> needs to be changed anyway, such as flag that this is a derived image and
>> not an original image coming out of a scanner.
>>
>> I suppose that MetaDataDictionary class is not wrapped. You can then loop
>> through all the keys and copy them and their content one by one.
>>
>> Regards
>>
>> On Thu, Jul 7, 2016 at 8:35 AM, Piotr Piasecki <
>> piotpia124 at student.polsl.pl> wrote:
>>
>>> Hi D?enan,
>>>
>>> thank you for your help and for this example. Unfortunately, I have not
>>> found method GetMetaDataDictionary() in SimpleITK in C# (I found only
>>> GetMetaDataKeys() and GetMetaData(string key)). Also, I have not found a
>>> method SetMetaDataDictionary or any other that allows me to assign DICOM
>>> tags.
>>>
>>> My short piece of code looks like this:
>>>
>>> static public void ReadImage()
>>>         {
>>>             sitk.ImageFileReader reader = new sitk.ImageFileReader();
>>>             reader.SetFileName(@".\DICOM_TEST\original.dcm");
>>>             var image = reader.Execute();
>>>
>>>             sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
>>>             writer.SetFileName(@".\DICOM_TEST\modified.dcm");
>>>             writer.Execute(image);
>>>         }
>>>
>>> Another problem is that your example describes only loading and saving a
>>> single .dcm file. What if I have to process a whole series of files
>>> using sitk.ImageSeriesReader and sitk.ImageSeriesWriter?
>>>
>>> Regards,
>>>
>>> Peter.
>>>
>>> 2016-07-05 15:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com>:
>>>
>>>> Hi Piotr,
>>>>
>>>> if you want to carry over metadata from input image to output image,
>>>> you should save the metadata dictionary in a way similar to this:
>>>>
>>>> itk::MetaDataDictionary metadata;
>>>>
>>>> template< typename TImage >
>>>> itk::SmartPointer<TImage> readImage(std::string fileName)
>>>> {
>>>>     typedef itk::ImageFileReader<TImage> ReaderType;
>>>>     typename ReaderType::Pointer reader = ReaderType::New();
>>>>     reader->SetFileName(fileName.c_str());
>>>>     try
>>>>     {
>>>>         reader->Update();
>>>>         metadata = reader->GetMetaDataDictionary();
>>>>         return reader->GetOutput();
>>>>     }
>>>>     catch (itk::ExceptionObject & error)
>>>>     {
>>>>         std::cerr << "Error: " << error << std::endl;
>>>>         return NULL;
>>>>     }
>>>> }
>>>>
>>>> template< typename TImage >
>>>> void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
>>>> {
>>>>     image->SetMetaDataDictionary(metadata); //full metadata
>>>>     typedef itk::ImageFileWriter<TImage> WriterType;
>>>>     typename WriterType::Pointer writer = WriterType::New();
>>>>     writer->SetFileName(fileName.c_str());
>>>>     writer->SetInput(image);
>>>>     try
>>>>     {
>>>>         writer->Update();
>>>>     }
>>>>     catch (itk::ExceptionObject & error)
>>>>     {
>>>>         std::cerr << "Error: " << error << std::endl;
>>>>     }
>>>> }
>>>>
>>>> On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <
>>>> piotpia124 at student.polsl.pl> wrote:
>>>>
>>>>> Dear Sir or Madam.
>>>>>
>>>>> I am a student in Biomedical Engineering at the Silesian University of
>>>>> Technology. During my studies I worked with ITK and SimpleITK in C#. I want
>>>>> to use them in my current project, but I have an important question. After
>>>>> loading and processing a series of .dcm files I lost information about the
>>>>> patient and study to which they belong, and that they belong to one series.
>>>>> How can I keep this information?
>>>>>
>>>>> I will be very grateful for any answer.
>>>>>
>>>>> Best regards.
>>>>>
>>>>> Peter.
>>>>> _____________________________________
>>>>> 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

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From christopherrmullins at gmail.com  Thu Jul  7 10:38:10 2016
From: christopherrmullins at gmail.com (Christopher Mullins)
Date: Thu, 7 Jul 2016 10:38:10 -0400
Subject: [ITK] [ITK-users] Build errors in python wrapping of 4.10.0
In-Reply-To: <CALzTN-SDR+fm7nRtcoPMDEWDRirhdi5rJR7Rcpx933w4PT-hEQ@mail.gmail.com>
References: <CAL1JtzBgoYx3k7xn_pff9s5M9AGLFuKE0ZQJb4Wen0BkAHkzNA@mail.gmail.com>
 <D452B2C7-BD65-426B-BC46-A10C642DB70A@gmail.com>
 <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu>
 <CAL1JtzDwp5dx-yKpk52OxTg6h0gLt_xMg-c0ZUCpkF_cJ3hk2A@mail.gmail.com>
 <CALzTN-SDR+fm7nRtcoPMDEWDRirhdi5rJR7Rcpx933w4PT-hEQ@mail.gmail.com>
Message-ID: <CAL1JtzCbbM_2dXA+5BSD-uSJG7yyjJKr7h53DUAd7TJWd8gcJA@mail.gmail.com>

Thank you very much!

Chris

On Thu, Jul 7, 2016 at 9:49 AM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Following up, this issue was addressed in this patch:
>
>   http://review.source.kitware.com/#/c/21311/
>
> which will be included in the 4.10.1 release.
>
> On Thu, Jun 30, 2016 at 11:55 AM, Christopher Mullins
> <christopherrmullins at gmail.com> wrote:
> > Hi all,
> >
> > Thanks for the help on this.  I've been traveling and haven't had much
> time
> > to investigate, but I believe Michka is correct.  It looks like the
> build is
> > successful with the -std=c++98 flag, and only one test fails [1].  I'll
> test
> > the python wrapping and report back if anything terrible happens -- if
> not
> > I'll bump the AUR PKGBUILD.  Thanks again,
> >
> > Chris
> >
> > [1] https://open.cdash.org/buildSummary.php?buildid=4435570
> >
> > On Wed, Jun 15, 2016 at 5:22 PM, Johnson, Hans J <hans-johnson at uiowa.edu
> >
> > wrote:
> >>
> >> I?m trying to reproduce now.
> >>
> >> Hans
> >>
> >>
> >> --
> >>
> >>
> >> On 6/15/16, 4:12 PM, "Insight-users on behalf of Michka Popoff"
> >> <insight-users-bounces at itk.org on behalf of michkapopoff at gmail.com>
> wrote:
> >>
> >> >Hi
> >> >
> >> >I think this bug is not known. I had a look and could reproduce it with
> >> > gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X.
> >> >GCC 6 is using c++14 by default, but even with c++11 you would probably
> >> > get the problem.
> >> >The problem is also there with the latest commit from the master
> branch.
> >> >
> >> >Please note that we probably never tested Python Wrappings with c++11,
> >> > even not speaking of c++14.
> >> >
> >> >The problem seems to have appeared with this patch:
> >>
> >> > >
> https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395
> >> >
> >> >I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy
> >> > constructor, and was able to compile
> >> >with gcc 6. But it may just a side effect of that patch which is now
> only
> >> > appearing with c++ >= 11.
> >> >It is weird that the problem seems to be only for the itkTriangleHelper
> >> > class.
> >> >
> >> >I will have to look what is the difference in the files generated for
> >> > swig and what is exactly failing,
> >> >though I do not know how long it will take me. I hope I can do this
> this
> >> > weekend.
> >> >
> >> >Thanks
> >> >
> >> >Michka
> >> >
> >> >
> >> >> On 09 Jun 2016, at 16:14, Christopher Mullins
> >> >> <christopherrmullins at gmail.com> wrote:
> >> >>
> >> >> Hi all,
> >> >>
> >> >> Apparently my subscription to this list has lapsed and my first email
> >> >> was rejected (despite receiving the list in my inbox every day).
> Sorry if
> >> >> there's a double post.
> >> >>
> >> >> I'm getting the following build errors when building ITK 4.10.0 with
> >> >> the WRAP_PYTHON option ON[1], [3].  Is this a known issue, or is
> there a
> >> >> configuration setting I've set improperly?
> >> >>
> >> >> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2.
> There
> >> >> are no warnings. See all output details for this machine here [2],
> and
> >> >> please let me know if I can provide any others.
> >> >>
> >> >> The faster I fix this the faster I'll feel comfortable updating the
> >> >> Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can
> offer.
> >> >>
> >> >> Thanks,
> >> >> Chris
> >> >>
> >> >>
> >> >>
> >> >> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379
> >> >> [2] https://open.cdash.org/buildSummary.php?buildid=4403379
> >> >>
> >> >> [3] To save you a click, and for the sake of archiving, the error is:
> >> >>
> >> >>
> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:
> >> >> In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*,
> >> >> PyObject*)':
> >> >>
> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65:
> >> >> error: no matching function for call to
> >> >> 'itk::TriangleHelper<itk::Point<double, 2u> >::TriangleHelper()'
> result =
> >> >> (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
> >> >> _____________________________________
> >> >> 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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_____________________________________
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From zivrafael.yaniv at nih.gov  Thu Jul  7 10:43:39 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Thu, 7 Jul 2016 14:43:39 +0000
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
 <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
 <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>
 <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>
Message-ID: <D3A3DB17.B966%yanivz@mail.nih.gov>

Hello Peter,

We are actually working on adding the set method for the upcoming release, which will be out shortly. One issue that we do want to point out, which likely you are aware of but just in case, you have to indicate in the Image Type tag ( (0008,0008) that this is a derived image. Please see the DICOM standard (http://dicom.nema.org/medical/dicom/current/output/pdf/part03.pdf), section  C.7.6.1.1.2 for the details.

        regards
             Ziv


From: Piotr Piasecki <piotpia124 at student.polsl.pl<mailto:piotpia124 at student.polsl.pl>>
Date: Thursday, July 7, 2016 at 9:49 AM
To: D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>>, Bradley Lowekamp <brad at lowekamp.net<mailto:brad at lowekamp.net>>, "insight-users at itk.org<mailto:insight-users at itk.org>" <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [ITK-users] Lost Patient, Study and Series DICOM tags

Hello Again

I found the information, that in SimpleITK the MetaDataDictionary interface is only part of the Image class. Currently it provides a read only interface, with the GetMetaDataKeys(), and GetMetaData(key) methods. This get method only returns the type of data in the dictionary converted to a string.

The required method would be Image::SetMetaData(key,value). But unfortunately I do not see this method, so I think that this is still not implemented. The only what I need is to keep information that my files belong to one series of images, which belongs to one patient and study ( not necessarily the same study or series as the original).

Regards.

Peter.


2016-07-07 14:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>>:
Hi Piotr,

instead of ImageReader->GetMetaDataDictionary() call ImageSeriesReader->GetMetaDataDictionary(). Also, the image format you are writing to needs to be able to support metadata (e.g. .mha, .nrrd, DICOM), otherwise the metadata is lost (.nii, .jpg, .bmp etc).

But for writing DICOM, the process might be somewhat different from what I described in the first email. Definitely different if you want metadata copied slice for slice from input to output - in this case some metadata needs to be changed anyway, such as flag that this is a derived image and not an original image coming out of a scanner.

I suppose that MetaDataDictionary class is not wrapped. You can then loop through all the keys and copy them and their content one by one.

Regards

On Thu, Jul 7, 2016 at 8:35 AM, Piotr Piasecki <piotpia124 at student.polsl.pl<mailto:piotpia124 at student.polsl.pl>> wrote:
Hi D?enan,

thank you for your help and for this example. Unfortunately, I have not found method GetMetaDataDictionary() in SimpleITK in C# (I found only GetMetaDataKeys() and GetMetaData(string key)). Also, I have not found a method SetMetaDataDictionary or any other that allows me to assign DICOM tags.

My short piece of code looks like this:

static public void ReadImage()
        {
            sitk.ImageFileReader reader = new sitk.ImageFileReader();
            reader.SetFileName(@".\DICOM_TEST\original.dcm");
            var image = reader.Execute();

            sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
            writer.SetFileName(@".\DICOM_TEST\modified.dcm");
            writer.Execute(image);
        }

Another problem is that your example describesonly loading and saving a single .dcm file.What if I have to process a whole series of files using sitk.ImageSeriesReader and sitk.ImageSeriesWriter?

Regards,

Peter.

2016-07-05 15:45 GMT+02:00 D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>>:
Hi Piotr,

if you want to carry over metadata from input image to output image, you should save the metadata dictionary in a way similar to this:

itk::MetaDataDictionary metadata;

template< typename TImage >
itk::SmartPointer<TImage> readImage(std::string fileName)
{
    typedef itk::ImageFileReader<TImage> ReaderType;
    typename ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(fileName.c_str());
    try
    {
        reader->Update();
        metadata = reader->GetMetaDataDictionary();
        return reader->GetOutput();
    }
    catch (itk::ExceptionObject & error)
    {
        std::cerr << "Error: " << error << std::endl;
        return NULL;
    }
}

template< typename TImage >
void writeImage(itk::SmartPointer<TImage> image, std::string fileName)
{
    image->SetMetaDataDictionary(metadata); //full metadata
    typedef itk::ImageFileWriter<TImage> WriterType;
    typename WriterType::Pointer writer = WriterType::New();
    writer->SetFileName(fileName.c_str());
    writer->SetInput(image);
    try
    {
        writer->Update();
    }
    catch (itk::ExceptionObject & error)
    {
        std::cerr << "Error: " << error << std::endl;
    }
}

On Tue, Jul 5, 2016 at 2:46 AM, Piotr Piasecki <piotpia124 at student.polsl.pl<mailto:piotpia124 at student.polsl.pl>> wrote:
Dear Sir or Madam.

I am a student in Biomedical Engineering at the Silesian University of Technology. During my studies I worked with ITK and SimpleITK in C#. I want to use them in my current project, but I have an important question. After loading and processing a series of .dcm files I lost information about the patient and study to which they belong, and that they belong to one series. How can I keep this information?

I will be very grateful for any answer.

Best regards.

Peter.
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From matt.mccormick at kitware.com  Thu Jul  7 10:57:16 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 7 Jul 2016 10:57:16 -0400
Subject: [ITK] [ITK-dev] LSQR (and related VNL code) Licensing Issues -
	fix	lost
In-Reply-To: <09B7458A-8DC2-4616-9038-0068115F14C4@mail.nih.gov>
References: <CAPG4jkQoqgXfo9R3cqA8fM1but1O9GKOW_A0zDBYagx4n-ijRA@mail.gmail.com>
 <CALzTN-Qu_yWRwUBArYgcBmnzHxjk4dNxCJZzCmcGo7uO3vpbiQ@mail.gmail.com>
 <09B7458A-8DC2-4616-9038-0068115F14C4@mail.nih.gov>
Message-ID: <CALzTN-SBhjJ7MOx3J5f-a-vLvkQKGmBfbo3X6B5ZoqFV9uu-ww@mail.gmail.com>

Hi,

Yes, these will be fixed in a follow-up patch.

Thanks,
Matt

On Thu, Jul 7, 2016 at 10:01 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Matt,
>
> This patch looks like it is the source of a number of valgrind defects on the ITK dashboard that need to be addressed.
>
> https://open.cdash.org/viewDynamicAnalysisFile.php?id=3934294
>
> Brad
>
>> On Jul 7, 2016, at 9:57 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>
>> Following up, this issue was addressed in this patch:
>>
>>  http://review.source.kitware.com/#/c/21296/
>>
>> and pushed upstream here:
>>
>>  https://github.com/vxl/vxl/pull/337
>>
>> It will be included in the ITK 4.10.1 release.
>>
>> On Fri, Jul 1, 2016 at 4:45 AM, Tom Vercauteren <tom.vercauteren at m4x.org> wrote:
>>> Dear all,
>>>
>>> Sorry for the cross-posting but this refers to an issue linking both ITK and
>>> VNL.
>>>
>>> In 2010, we identified a licensing issue with some code from vnl and at the
>>> time Luis Ibanez fixed it from the ITK side:
>>> https://issues.itk.org/jira/browse/HISTITK-1160
>>>
>>> Luis notably rewrote the LSQR code:
>>> https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg
>>> http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/
>>> https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg
>>>
>>> It seems that this effort was not backported to VXL and was subsequently
>>> lost when moving to ITK 4:
>>> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg
>>>
>>> It would be great if someone could look into this (important) licensing
>>> issue.
>>>
>>> For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a
>>> standalone github repo here:
>>> https://github.com/tvercaut/LSQR-cpp
>>>
>>> I have also added a comment in the ITK and VXL bug trackers:
>>> https://issues.itk.org/jira/browse/HISTITK-1160
>>> https://github.com/vxl/vxl/issues/332
>>>
>>> Best wishes,
>>> Tom
>>>
>>> _______________________________________________
>>> 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:
>> http://public.kitware.com/mailman/listinfo/insight-developers
>
_______________________________________________
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From matt.mccormick at kitware.com  Thu Jul  7 11:50:05 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 7 Jul 2016 11:50:05 -0400
Subject: [ITK] [ITK-dev] Gerrit robot builds offline
Message-ID: <CALzTN-R-Vf6xvtyYpdOGa474Jcq+3GQgNAijcfv5eH63HMakQQ@mail.gmail.com>

Hi,

Our Gerrit robot builds will be down for at least one day for
infrastructure changes.

Matt
_______________________________________________
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From zivrafael.yaniv at nih.gov  Thu Jul  7 12:32:41 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Thu, 7 Jul 2016 16:32:41 +0000
Subject: [ITK] question regarding simpleitk java wrapper
In-Reply-To: <2016070717214197101712@sina.com>
References: <201607061725003293645@sina.com>
 <4C245F08-B5B7-4540-9818-C45F0D0F57F0@mail.nih.gov>
 <2016070717214197101712@sina.com>
Message-ID: <D3A3F9DB.B9D4%yanivz@mail.nih.gov>

Hello Tom,

We are currently working on adding a Set method for data in the metadata dictionary of SimpleITK images. This should be out shortly.

With regard to the second question, "how can i use Simpleitk java to read self-defined structure to recontruct dicom images including pixel data and metadata.? If the image is in your self defined data structure then SimpleITK can?t do a thing, we only work with SimpleITK images. If you have a SimpleITK image object which you filled with intensity data+spacing data + size data + direction data, you will be able to update its meta-data dictionary once we add the Set method for the meta-data dictionary and then you can save it as a DICOM series.

hope this clarified things
             Ziv

From: "weiehome at sina.com<mailto:weiehome at sina.com>" <weiehome at sina.com<mailto:weiehome at sina.com>>
Date: Thursday, July 7, 2016 at 5:21 AM
To: "Lowekamp, Bradley (NIH/NLM/LHC) [C]" <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>
Cc: "community at itk.org<mailto:community at itk.org>" <community at itk.org<mailto:community at itk.org>>
Subject: Re: [ITK] question regarding simpleitk java wrapper

Hi, Bradley

Thank you ! But how can i fill it with metadata information?
In c++, i can set metadatas manually using raw pointer to MetadataDictionary instance to achieve it, but in JAVA, it seems there is no such way of setting Image Metadata?

One function i found is CopyInformation(), however it requires Given input image has to be as same dimension as output one.
What i want is followings:
1.First read dicoms volume data (CTs) from a folder recursively using SeriesReader
2. then convert all 3d volumes into my own data structure, then serialize it into bytes and passed to some remote server.
consider 1-2 steps are data import steps.
when exporting the data from remote server, i do :
3.read the bytes and deserialize bytes into self-defined image data structure.
4.convert data structure into itk image(3d)
remember when i do import, i actually extract all dicom tags i needed and put finally into data structure.
So the question is how can i use Simpleitk java to read self-defined structure to recontruct dicom images including pixel data and metadata.

Best Regards,
Tom

________________________________
weiehome at sina.com<mailto:weiehome at sina.com>

From: Lowekamp, Bradley (NIH/NLM/LHC) [C]<mailto:blowekamp at mail.nih.gov>
Date: 2016-07-06 21:00
To: weiehome at sina.com<mailto:weiehome at sina.com>
CC: community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK] question regarding simpleitk java wrapper
Hello,

You can create it in a similar way to C++. The constructor does have required arguments to specify its size and pixel type.. You need to look at the Doxygen for the API documentation [1]. Also the SimpleITK Image will automatically allocated and initialized the data to 0 unlike an ITK image.

It would look something like the

   Image img2 = new Image( 10, 10, PixelIDValueEnum.sitkInt16 );

    VectorDouble origin = new VectorDouble(img2.getDimension());
    origin.set( 0, 1.0);
    origin.set( 1, 2.0);
    img2.setOrigin(origin);

    System.out.format("%s", img2.toString());

HTH,
Brad

[1] https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html

On Jul 6, 2016, at 5:25 AM, weiehome at sina.com<mailto:weiehome at sina.com> wrote:

Hi,

Is there a possible way i can create an itk image in java just like in c++ :

Image itkImage = new Image();
itkImage.setOrgin( ... );
itkImage.setSpacing( ... );
itkImage.setRegion( ... );
itkImage.fill(0);

It seems in java i can get itk Image object either by reading files or from filters?

Regards, Tommi


_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
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From weiehome at sina.com  Fri Jul  8 02:31:44 2016
From: weiehome at sina.com (weiehome at sina.com)
Date: Fri, 8 Jul 2016 14:31:44 +0800
Subject: [ITK] question regarding simpleitk java wrapper
References: <201607061725003293645@sina.com>, 
 <4C245F08-B5B7-4540-9818-C45F0D0F57F0@mail.nih.gov>, 
 <2016070717214197101712@sina.com>, 
 <D3A3F9DB.B9D4%yanivz@mail.nih.gov>
Message-ID: <201607081431432051741@sina.com>

Thanks! Can't wait to see the new release. Set method for metadata is exactly what i want.



weiehome at sina.com
 
From: Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
Date: 2016-07-08 00:32
To: weiehome at sina.com; Lowekamp, Bradley (NIH/NLM/LHC) [C]
CC: community at itk.org
Subject: Re: [ITK] question regarding simpleitk java wrapper
Hello Tom,

We are currently working on adding a Set method for data in the metadata dictionary of SimpleITK images. This should be out shortly.

With regard to the second question, "how can i use Simpleitk java to read self-defined structure to recontruct dicom images including pixel data and metadata.? If the image is in your self defined data structure then SimpleITK can?t do a thing, we only work with SimpleITK images. If you have a SimpleITK image object which you filled with intensity data+spacing data + size data + direction data, you will be able to update its meta-data dictionary once we add the Set method for the meta-data dictionary and then you can save it as a DICOM series.

hope this clarified things
             Ziv

From: "weiehome at sina.com" <weiehome at sina.com>
Date: Thursday, July 7, 2016 at 5:21 AM
To: "Lowekamp, Bradley (NIH/NLM/LHC) [C]" <blowekamp at mail.nih.gov>
Cc: "community at itk.org" <community at itk.org>
Subject: Re: [ITK] question regarding simpleitk java wrapper

Hi, Bradley

Thank you ! But how can i fill it with metadata information?
In c++, i can set metadatas manually using raw pointer to MetadataDictionary instance to achieve it, but in JAVA, it seems there is no such way of setting Image Metadata?

One function i found is CopyInformation(), however it requires Given input image has to be as same dimension as output one.
What i want is followings: 
1.First read dicoms volume data (CTs) from a folder recursively using SeriesReader
2. then convert all 3d volumes into my own data structure, then serialize it into bytes and passed to some remote server.
consider 1-2 steps are data import steps.
when exporting the data from remote server, i do :
3.read the bytes and deserialize bytes into self-defined image data structure.
4.convert data structure into itk image(3d)
remember when i do import, i actually extract all dicom tags i needed and put finally into data structure. 
So the question is how can i use Simpleitk java to read self-defined structure to recontruct dicom images including pixel data and metadata.
 
Best Regards,
Tom    



weiehome at sina.com
 
From: Lowekamp, Bradley (NIH/NLM/LHC) [C]
Date: 2016-07-06 21:00
To: weiehome at sina.com
CC: community at itk.org
Subject: Re: [ITK] question regarding simpleitk java wrapper
Hello, 

You can create it in a similar way to C++. The constructor does have required arguments to specify its size and pixel type.. You need to look at the Doxygen for the API documentation [1]. Also the SimpleITK Image will automatically allocated and initialized the data to 0 unlike an ITK image.

It would look something like the 

   Image img2 = new Image( 10, 10, PixelIDValueEnum.sitkInt16 );

    VectorDouble origin = new VectorDouble(img2.getDimension());
    origin.set( 0, 1.0);
    origin.set( 1, 2.0);
    img2.setOrigin(origin);

    System.out.format("%s", img2.toString());

HTH,
Brad

[1] https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html

On Jul 6, 2016, at 5:25 AM, weiehome at sina.com wrote:

Hi, 

Is there a possible way i can create an itk image in java just like in c++ :

Image itkImage = new Image();
itkImage.setOrgin( ... );
itkImage.setSpacing( ... );
itkImage.setRegion( ... );
itkImage.fill(0);

It seems in java i can get itk Image object either by reading files or from filters?

Regards, Tommi


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

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From blowekamp at mail.nih.gov  Fri Jul  8 10:22:53 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 8 Jul 2016 14:22:53 +0000
Subject: [ITK] [ITK-dev] lhcp-rh6 turned on shared libraries
Message-ID: <6A861DE4-BE9D-41C5-A1B6-E0051E2353A8@mail.nih.gov>

Hi,

I have gone ahead an turned on BUILC_SHARED_LIBS for the lhcp-rh6 builds. Let us see if the transform dynamic_cast issue occurs any place else.

Brad
_______________________________________________
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http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From piotpia124 at student.polsl.pl  Fri Jul  8 14:41:45 2016
From: piotpia124 at student.polsl.pl (Piotr Piasecki)
Date: Fri, 8 Jul 2016 20:41:45 +0200
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <D3A3DB17.B966%yanivz@mail.nih.gov>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
 <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
 <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>
 <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>
 <D3A3DB17.B966%yanivz@mail.nih.gov>
Message-ID: <CACTtAODYL-eiRVBU+2k0PvACy3Juvrzt=oqJ4ngSBQWruOkQvw@mail.gmail.com>

I know that GDCM library (or its elements) is used in some cases in ITK. If
SimpleITK does not provide write access to dicom tags whether is it
possible to use GDCM wrapped in C# to do this? I can imagine a scenario in
which I'll use SimpleITK to process image, and GDCM to replace specified
tags.

Is it possible? If so, I would ask for help person skilled in using GDCM in
C#. Are there any examples of how to do such a thing?
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From brad at lowekamp.net  Fri Jul  8 14:53:03 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Fri, 8 Jul 2016 14:53:03 -0400
Subject: [ITK] [ITK-users] Lost Patient, Study and Series DICOM tags
In-Reply-To: <CACTtAODYL-eiRVBU+2k0PvACy3Juvrzt=oqJ4ngSBQWruOkQvw@mail.gmail.com>
References: <950a17346e556728857382ebf5cb79e4@poczta.student.polsl.pl>
 <CAPf2UMT+U7UCwMObcu+Xyj1vyMN9N5kM+qtxkvbfKfP6_BYy-A@mail.gmail.com>
 <CACTtAOCyOCguwNK3-_YD+mdnUxaD3sZe38tuD-y2e9WPud0vog@mail.gmail.com>
 <CAPf2UMRGmdaSC=5Zx7JDi97SFCnaQryu-W-M-MQ_uM-nnWkdDw@mail.gmail.com>
 <CACTtAODcp0apHLAq6dZ+xP3zz3N_7Z5oq6=JPzQ+c6eyVftyow@mail.gmail.com>
 <D3A3DB17.B966%yanivz@mail.nih.gov>
 <CACTtAODYL-eiRVBU+2k0PvACy3Juvrzt=oqJ4ngSBQWruOkQvw@mail.gmail.com>
Message-ID: <7E31C0B1-801D-4BC6-AFA5-AAAB36EDA3B9@lowekamp.net>

Hello,

We have just merged the topic which adds the ?SetMetaData? method to the SimpleITK Image interface into the ?next? development branch of SimpleITK [1]. We expect for this to shortly be merged into the master branch after nightly testing. We are also creating an example which uses it for writing a modified DICOM file.

There should be nightly binaries that follow shortly there after for CSharp [2]. This may meet your needs.

Directly using GDCM is a sensible way to go for more control over DICOM IO. I have not done what you propose, but I expect it is possible. You would likely need some lower level buffer access as is done here[3].

HTH,
Brad

[1] https://github.com/SimpleITK/SimpleITK/commit/69865add060e87c175c7f212c7bdddab11e127ab
[2] https://itk.org/Wiki/SimpleITK/GettingStarted#Nightly_binaries
[3] https://itk.org/SimpleITKDoxygen/html/CSharp_2ImageGetBuffer_8cs-example.html

> On Jul 8, 2016, at 2:41 PM, Piotr Piasecki <piotpia124 at student.polsl.pl> wrote:
> 
> I know that GDCM library (or its elements) is used in some cases in ITK. If SimpleITK does not provide write access to dicom tags whether is it possible to use GDCM wrapped in C# to do this? I can imagine a scenario in which I'll use SimpleITK to process image, and GDCM to replace specified tags.
> 
> Is it possible? If so, I would ask for help person skilled in using GDCM in C#. Are there any examples of how to do such a thing?
> _____________________________________
> 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
> 
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From vladimir.fonov at gmail.com  Fri Jul  8 17:58:11 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 8 Jul 2016 17:58:11 -0400
Subject: [ITK] [ITK-dev] patch to build ITK 3.20.1 with gcc 5.3
Message-ID: <578021F3.3080202@gmail.com>

Hello,

I recently came across an issue with building old version of itk (3.20.1 
) on Ubuntu 16.04, gcc version 5.3.1 Attached find a patch to fix the error.


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
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From matt.mccormick at kitware.com  Sat Jul  9 09:50:43 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 9 Jul 2016 09:50:43 -0400
Subject: [ITK] [ITK-dev]   patch to build ITK 3.20.1 with gcc 5.3
In-Reply-To: <578021F3.3080202@gmail.com>
References: <578021F3.3080202@gmail.com>
Message-ID: <CALzTN-QyK21den9roazCgu2aR2Qns2-gDDx2M0j8eLVtu95TYw@mail.gmail.com>

Hi Vlad,

Thank you! Pushed to the release-3.20 Git branch:

  https://itk.org/gitweb?p=ITK.git;a=commit;h=529bcc7ddc6f523db52d82e4bb91418da737559b

Matt

On Fri, Jul 8, 2016 at 5:58 PM, Vladimir S. FONOV
<vladimir.fonov at gmail.com> wrote:
> Hello,
>
> I recently came across an issue with building old version of itk (3.20.1 )
> on Ubuntu 16.04, gcc version 5.3.1 Attached find a patch to fix the error.
>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.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://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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From marcus.hanwell at kitware.com  Sun Jul 10 06:38:49 2016
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Sun, 10 Jul 2016 06:38:49 -0400
Subject: [ITK] [ITK-dev]   ITK Python wrapping issue with GCC 6.1.1
In-Reply-To: <CALzTN-RDAdmaH_5vktX2YPuN2cygUp7xYDqrWNn5ynzfxU7rFw@mail.gmail.com>
References: <CAMkPkZV-RW11Pfi9DqT-GVKUF3-stK1TKWHXJUgYKR8QoTPPPw@mail.gmail.com>
 <CALzTN-RjOuCrP0VBD1VExCwxVT=9_92yrGNBkkmVuaE5WRfWUw@mail.gmail.com>
 <CAMkPkZVt9pLAUxrZPYohyqD3YeiqE52zZmaLJvpV5H9eM0_oEA@mail.gmail.com>
 <CALzTN-RDAdmaH_5vktX2YPuN2cygUp7xYDqrWNn5ynzfxU7rFw@mail.gmail.com>
Message-ID: <CAMkPkZUCQF85fn2WKU_DiiPjVBFpaA=f0X0XshWsJuf4-QZqjw@mail.gmail.com>

Thanks Matt, everything compiles for me locally, and in my initial
testing seems to work well too.

On Thu, Jul 7, 2016 at 9:48 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Following up, this issue was addressed in this patch:
>
>   http://review.source.kitware.com/#/c/21311/
>
> which will be included in the 4.10.1 release.
>
> On Fri, Jul 1, 2016 at 3:01 PM, Marcus D. Hanwell
> <marcus.hanwell at kitware.com> wrote:
>> Matt, thanks for the confirmation, sorry I didn't spot it in the issue
>> tracker. I will monitor the bug.
>>
>> On Fri, Jul 1, 2016 at 2:54 PM, Matt McCormick
>> <matt.mccormick at kitware.com> wrote:
>>> Hi Marcus,
>>>
>>> Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is
>>> having issues.  There is now an issue to track this:
>>>
>>>   https://issues.itk.org/jira/browse/ITK-3450
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell
>>> <marcus.hanwell at kitware.com> wrote:
>>>> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am
>>>> seeing a compile error:
>>>>
>>>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _
>>>> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?:
>>>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi
>>>> ng function for call to ?itk::TriangleHelper<itk::Point<double, 2u> >::TriangleH
>>>> elper()?
>>>>       result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2();
>>>>                                                                 ^
>>>> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO
>>>> bject.h:21:0,
>>>>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject
>>>> .h:31,
>>>>                 from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman
>>>> d.h:21,
>>>>                 from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3,
>>>>                 from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325
>>>> 8:
>>>> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note
>>>> : candidate: itk::TriangleHelper<TPoint>::TriangleHelper(const itk::TriangleHelp
>>>> er<TPoint>&) [with TPoint = itk::Point<double, 2u>] <deleted>
>>>>   ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper);
>>>>
>>>> Is my GCC too new? It only seems to be happening with the wrapping,
>>>> this is on Linux. I can post more details if it helps.
>>>> _______________________________________________
>>>> 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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From abou_zeid_wassim at hotmail.com  Mon Jul 11 10:27:19 2016
From: abou_zeid_wassim at hotmail.com (wassim bouzeid)
Date: Mon, 11 Jul 2016 14:27:19 +0000
Subject: [ITK] Translation parameters not obtained properly
 MultiResImageRegistration3.cxx
Message-ID: <DUB117-W12D070717FF3604FBEA79D63F0@phx.gbl>

Hi Everyone,

I have a T1.nii image and I am applying to the same image a translation in (X,Y,Z) by (20, 0, 0) mm. Then I am passing these two images (T1.nii and T1transformed.nii) as an input to MultiResImageRegistration3.cxx.

Below is the results that I obtained from this example which shows a translation in Y and Z that I have not applied. When I overlapped the registrated image to T1.nii image, they look perfectly aligned.
 Translation X = 20.0094
 Translation Y = 3.26976
 Translation Z = 9.65584
 Iterations    = 47
 Metric value  = -0.644247

Can anyone explain why I am having this shift in Y and Z, though that my shift is 0 in both direction.

Thanks in advance,
Sam









 		 	   		  
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From dzenanz at gmail.com  Mon Jul 11 11:47:19 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 11 Jul 2016 11:47:19 -0400
Subject: [ITK] Translation parameters not obtained properly
	MultiResImageRegistration3.cxx
In-Reply-To: <DUB117-W12D070717FF3604FBEA79D63F0@phx.gbl>
References: <DUB117-W12D070717FF3604FBEA79D63F0@phx.gbl>
Message-ID: <CAPf2UMQL=1jy_ygYU_aMs0MKUFtY+bs0u+T8EYo8m=LXBNsq3A@mail.gmail.com>

Hi Abu Zeid,

the most likely explanation is that you made a mistake somewhere. However,
we cannot be certain without your original, translated and registered
images. Can you share those?

Regards,
D?enan

On Mon, Jul 11, 2016 at 10:27 AM, wassim bouzeid <
abou_zeid_wassim at hotmail.com> wrote:

> Hi Everyone,
>
> I have a T1.nii image and I am applying to the same image a translation in
> (X,Y,Z) by (20, 0, 0) mm. Then I am passing these two images (T1.nii and
> T1transformed.nii) as an input to MultiResImageRegistration3.cxx.
>
> Below is the results that I obtained from this example which shows a
> translation in Y and Z that I have not applied. When I overlapped the
> registrated image to T1.nii image, they look perfectly aligned.
>  Translation X = 20.0094
>  Translation Y = 3.26976
>  Translation Z = 9.65584
>  Iterations    = 47
>  Metric value  = -0.644247
>
> Can anyone explain why I am having this shift in Y and Z, though that my
> shift is 0 in both direction.
>
> Thanks in advance,
> Sam
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From sami.koho at gmail.com  Tue Jul 12 05:29:34 2016
From: sami.koho at gmail.com (Sami Koho)
Date: Tue, 12 Jul 2016 12:29:34 +0300
Subject: [ITK] [ITK-users] SimpleITK landmark based initialisation (and
	image	visualisation)
Message-ID: <21BECCEC-1354-4E9A-B08F-D36BFE535407@gmail.com>

Hi,

I was thinking of adding a manual landmark based initialisation to my image registration method, as the automatic initialiser does not reliably work in my current application. I?m registering correlative microscopy images with very large shift and rotation between moving and fixed images ? usually the moving image also covers only a small part of the area shown in the fixed image. By specifying the initial offset and rotation manually, registration works nicely, but this is a bit cumbersome, because I have to figure out the approximate offsets first.

The problem is that I do not seem to have the sitk.LandmarkBasedTransformInitializer() available in my SimpleITK version. It was used in the notebook http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/67_Registration_Semiautomatic_Homework.html. I have SimpleITK 0.9.1 (Compiled Sep 28 2015) that I have installed on Anaconda according to the Wiki instructions. I am using Python 2.7. Would I possibly need some other version of SimpleITK? How could I get it? 

Alternatively, is there some other simple method for calculating a spatial transformation from control point pairs in SimpleITK? I can of course do that in Numpy, but I wouldn?t like to overly complicate things.

Another question, in the notebook above you are using a visualisation module named ?gui" to show nice interactive plots, from which it is possible to make landmark selections as well. Is that by chance publicly available somewhere?  

Best,

Sami


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From zivrafael.yaniv at nih.gov  Tue Jul 12 10:18:37 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Tue, 12 Jul 2016 14:18:37 +0000
Subject: [ITK] [ITK-users] SimpleITK landmark based initialisation (and
 image visualisation)
In-Reply-To: <21BECCEC-1354-4E9A-B08F-D36BFE535407@gmail.com>
References: <21BECCEC-1354-4E9A-B08F-D36BFE535407@gmail.com>
Message-ID: <D3AA6958.BA32%yanivz@mail.nih.gov>

Hello Sami,

We are just about to release the latest version of SimpleITK which includes the LandmarkBasedTransformInitializer. This will happen in the next couple of weeks.

For an immediate solution, you can build the toolkit?s master branch for anaconda using the conda recipe found on my github:

git clone https://github.com/zivy/conda-recipes.git
cd conda-recipes
git checkout simpleitkMaster
cd python
conda build simpleitk

Then just install the package you built. This build process is for people who want to stay on the cutting edge, in between official releases (the master branch is our stable branch so you should be fine).

     regards
              Ziv

From: Sami Koho <sami.koho at gmail.com<mailto:sami.koho at gmail.com>>
Date: Tuesday, July 12, 2016 at 5:29 AM
To: insight-users <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: [ITK-users] SimpleITK landmark based initialisation (and image visualisation)

Hi,

I was thinking of adding a manual landmark based initialisation to my image registration method, as the automatic initialiser does not reliably work in my current application. I?m registering correlative microscopy images with very large shift and rotation between moving and fixed images ? usually the moving image also covers only a small part of the area shown in the fixed image. By specifying the initial offset and rotation manually, registration works nicely, but this is a bit cumbersome, because I have to figure out the approximate offsets first.

The problem is that I do not seem to have the sitk.LandmarkBasedTransformInitializer() available in my SimpleITK version. It was used in the notebook http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/67_Registration_Semiautomatic_Homework.html. I have SimpleITK 0.9.1 (Compiled Sep 28 2015) that I have installed on Anaconda according to the Wiki instructions. I am using Python 2.7. Would I possibly need some other version of SimpleITK? How could I get it?

Alternatively, is there some other simple method for calculating a spatial transformation from control point pairs in SimpleITK? I can of course do that in Numpy, but I wouldn?t like to overly complicate things.

Another question, in the notebook above you are using a visualisation module named ?gui" to show nice interactive plots, from which it is possible to make landmark selections as well. Is that by chance publicly available somewhere?

Best,

Sami


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From sg.ele.eng at gmail.com  Tue Jul 12 16:54:25 2016
From: sg.ele.eng at gmail.com (Sara Gh)
Date: Tue, 12 Jul 2016 16:54:25 -0400
Subject: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the
 Axial View
In-Reply-To: <1561329490.15991909.1467020401395.JavaMail.zimbra@enst.fr>
References: <CACjcMuasgTMj+=-BFO_vLUT6kWE73FBA6PewcLSFZNFm4Se7Sg@mail.gmail.com>
 <1561329490.15991909.1467020401395.JavaMail.zimbra@enst.fr>
Message-ID: <CACjcMuZg68OPEM=rTA2jyCQUCL7YP2JnGpwsE6pdnev+-fOJKQ@mail.gmail.com>

Hello Tim,

Thank you for your helpful email and sorry for late reply.

Yes, that's right. The size of resampled imageC should be 256x68x256 and
imageC should be rotated -pi/2 around the X axis.
Now, my first question is: Can I use the direction of imageA as
the OutputDirection instead of using Euler3DTransform? Something like this:

# Direction of imageA: (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
# Direction of imageC: (1.0, 0.0, 0.0, 0.0, -0.0, 1.0, 0.0, -1.0, -0.0)
resample = sitk.ResampleImageFilter()
resample.SetTransform(sitk.Transform(3, sitk.sitkIdentity))
resample.SetReferenceImage(imageC)
resample.SetOutputDirection(imageA.GetDirection())
resample.SetOutputOrigin(imageA.GetOrigin())
spacingCA = [spacingC[0],spacingC[2],spacingC[1]]
resample.SetOutputSpacing(spacingCA)
sizeC = imageC.GetSize()
sizeCA = [sizeC[0], sizeC[2], sizeC[1]]
resample.SetSize(sizeCA)
imageCA=resample.Execute(imageC)
sitk.Show(imageCA)

Second, I think I haven't set the correct OutputOrigin for the resampled
image because when I compare imageCA with the axial view of imageC
(calculated by ImageJ > Stacks> Orthogonal Views), it seems that the
resulted imageCA is the translated version of the correct axial view.

I have read the ITK guide chapter 2.9 about transformation and resampling
processes but it is still vague to me how one should calculate/select the
correct origin for the output image. I would be thankful if you could refer
me to any other resources that could be helpful to me in this regard.

Thank you in advance.

Best regards,
Sara


On Mon, Jun 27, 2016 at 5:40 AM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> Hello,
>
> First of all, it depends on the patient position in the data, but usually
> the X axis describe the left/right direction, the Y axis the
> anterior/posterior direction and the Z axis the top/bottom one.
> So I would expect the resampled imageC size to be 256x68x256 rather than
> 68x256x256.
>
> Then, I think you should try to transform your imageC to be in the imageA
> orientation. Let say the imageA have a LPS coordinate system.
> If the imageC :
> -first direction represents the axis going from the patient's right to the
> patient's left
> -second direction represents the axis going from the patient's top to the
> patient's bottom
> -third direction represents the axis going from the patient's front to the
> patient's rear
> Then you should rotate the imageC by a -pi/2 angle around the X axis.
>
> You could use the Euler3DTransform to get this rotation.
> Then you feed the resample filter with this transform, plus the needed
> parameters (origin, spacing, size,...), and you should be able to have your
> resampled data.
> Just be sure to fully understand the transformation you're making (I
> recommend the ResampleImageFilter part of the ITK guide which is quite
> useful).
>
> HTH,
>
> Tim
>
>
> ----- Mail original -----
> De: "Sara Gh" <sg.ele.eng at gmail.com>
> ?: insight-users at itk.org
> Envoy?: Dimanche 26 Juin 2016 07:57:16
> Objet: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the
> Axial      View
>
> Hello experts,
>
> I have two MRI scans: Axial and Coronal
> # imageA : Axial MRI scan, size : 256x256x56 (256mmx256mmx168mm) ,
> spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 )
> # imageC : Coronal MRI scan, size : 256x256x68 (256mmx256mmx204mm) ,
> spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 )
>
> I am trying to view Coronal image from the axial view i.e. resampling
> Coronal image using the direction of Axial image. Here is my code:
>
> resample = sitk.ResampleImageFilter()
> resample.SetReferenceImage(imageC)
> resample.SetOutputDirection(imageA.GetDirection())
> resample.SetOutputOrigin(imageA.GetOrigin())
> imageCA = resample.Execute(imageC)
> sitk.Show(imageCA)
>
> # Result: imageCA: size : 256x256x68 (256mmx256mmx204mm), spacing: 1,1,3
>
> I believe I have missed something because, in my idea, the size of
> resampled coronal image (imageCA) should be 68x256x256 ( 204mmx256mmx256mm)
> with the spacing [3,1,1] .
>
> I also tried to set the OutputSpacing to [3,1,1], but the size of the
> imageCA changes to 256x256x68 (768mmx256mmx68mm).
>
> I would be thankful if someone could help me in this regard.
>
> Best regards,
> Sara Gh
>
> _____________________________________
> 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
>



-- 
Sara Gharabaghi, Ph.D. Student
Graduate Research Assistant
Advanced Visual Data Analysis (AViDA) Lab
Biomedical Imaging Lab
Wright State University
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From lnicola at dend.ro  Wed Jul 13 05:12:14 2016
From: lnicola at dend.ro (=?UTF-8?Q?Lauren=C8=9Biu=20Nicola?=)
Date: Wed, 13 Jul 2016 12:12:14 +0300
Subject: [ITK] Threading issues
Message-ID: <1468401134.3088708.664867785.4970C5A2@webmail.messagingengine.com>

Hi,
 
This is a bit of a shot in the dark asking this, but we're working on a
project that uses a library based on ITK (OTB). We noticed two issues:
 
1. We've seen processes with a single remaining thread that's stuck in
   pthread_join().
2. We're getting some segfaults in libpthread.so:
 
[Jul13 09:42] otbApplicationL[37610]: segfault at 7ff2f27fc9d0 ip
00007ff3375c2e61 sp 00007ffd9ef0d620 error 4 in libpthread-
2.17.so[7ff3375ba000+16000]
[  +0.002159] otbApplicationL[31064]: segfault at 2d3 ip
00007fd3bf636e61 sp 00007fff2446f210 error 4 in libpthread-
2.17.so[7fd3bf62e000+16000]
[  +0.007911] otbApplicationL[10366]: segfault at 7feb000008cc ip
00007febeaa15e61 sp 00007ffe34bb1e10 error 4 in libpthread-
2.17.so[7febeaa0d000+16000]
[Jul13 09:44] maccs-processin[39138]: segfault at 7f6b713979d0 ip
00007f6b767cae61 sp 00007ffe09fe6410 error 4 in libpthread-
2.17.so[7f6b767c2000+16000]
[  +0.000092] otbApplicationL[22007]: segfault at 2d0 ip
00007f06a6541e61 sp 00007fffb4299660 error 4 in libpthread-
2.17.so[7f06a6539000+16000]
[  +0.000384] otbApplicationL[33830]: segfault at 100001626 ip
00007f37c1f90e61 sp 00007fff8a0f44d0 error 4 in libpthread-
2.17.so[7f37c1f88000+16000]
 
My theory is that 2d0 is an offset into a NULL pthread struct, but I
couldn't find the definition of that structure (pthread_t is an
opaque handle).
 
I suspect that the two issues are related. The weird part is that those
segfaults tend to happen for multiple processes at the same time. The
system was probably loaded, but I don't think it was an OOM situation.
 
Right now we're on ITK 4.9.1. Is there anyone else who encountered this
or knows about recent ITK fixes related to multithreading?
 
Regards,
Laurentiu Nicola
 
(gdb) bt
#  0x00007f0d74650ef7 in pthread_join () from /usr/lib64/libpthread.so.0
#1  0x00007f0d74dd1cca in
#itk::MultiThreader::SpawnWaitForSingleMethodThread
#(this=this at entry=0x2411670, threadHandle=<optimized out>)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
    BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreaderPThrea-
    ds.cxx:239
#2  0x00007f0d74dd244b in itk::MultiThreader::WaitForSingleMethodThread
#(this=this at entry=0x2411670, threadHandle=<optimized out>)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
    BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:480
#3  0x00007f0d74dd2f7d in itk::MultiThreader::SingleMethodExecute
#(this=0x2411670) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
#BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:389
#4  0x00007f0d7cedb87d in itk::ImageSource<otb::VectorImage<float, 2u>
#>::GenerateData (this=0x23fff10) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/install/otb-
#install/usr/include/ITK-4.8/itkImageSource.hxx:254
#5  0x00007f0d74dcdc00 in itk::ProcessObject::UpdateOutputData
#(this=0x23fff10) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
#BUILD/ITK/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1739
#6  0x00007f0d74dcdcc0 in itk::ProcessObject::UpdateOutputData
#(this=0x23e9b00) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
#BUILD/ITK/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1700
#7  0x00007f0d4af29368 in
#otb::StreamingImageVirtualWriter<otb::VectorImage<float, 2u>
#>::GenerateData (this=0x23e9700)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
    5.0/Modules/Core/Streaming/include/otbStreamingImageVirtualWrit-
    er.txx:248
#8  0x00007f0d4af1c8ce in
#otb::StreamingImageVirtualWriter<otb::VectorImage<float, 2u> >::Update
#(this=0x23e9700)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
    5.0/Modules/Core/Streaming/include/otbStreamingImageVirtualWrit-
    er.txx:156
#9  0x00007f0d4af11aad in otb::PersistentFilterStreamingDecorator<otb::-
#PersistentShrinkImageFilter<otb::VectorImage<float, 2u>,
#otb::VectorImage<float, 2u> > >::GenerateData (this=0x2466c20)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
    5.0/Modules/Core/Streaming/include/otbPersistentFilterStreamingDeco-
    rator.txx:52
#10 0x00007f0d4af1f4be in otb::Wrapper::Quicklook::DoExecute
#(this=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Applications/AppImageUtils/app/otbQuicklook.cxx:272
#11 0x00007f0d7d2026c8 in otb::Wrapper::Application::Execute
#(this=this at entry=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplicatio-
#n.cxx:223
#12 0x00007f0d7d202789 in
#otb::Wrapper::Application::ExecuteAndWriteOutput
#(this=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplicatio-
#n.cxx:230
#13 0x00007f0d7d60b2c9 in
#otb::Wrapper::CommandLineLauncher::ExecuteAndWriteOutput
#(this=0x2366aa0) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLaunche-
#r.cxx:158
#14 0x00000000004034a8 in main (argc=<optimized out>, argv=<optimized
#out>) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/CommandLine/src/otbApplicationLauncherCommandLin-
#e.cxx:299
 
(gdb) info threads
  Id   Target Id         Frame
* 1??? Thread 0x7f0d63055880 (LWP 21145) "otbApplicationL"
  0x00007f0d74650ef7 in pthread_join () from /usr/lib64/libpthread.so.0
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From tevain at telecom-paristech.fr  Wed Jul 13 05:54:55 2016
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Wed, 13 Jul 2016 11:54:55 +0200 (CEST)
Subject: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the
 Axial View
In-Reply-To: <CACjcMuZg68OPEM=rTA2jyCQUCL7YP2JnGpwsE6pdnev+-fOJKQ@mail.gmail.com>
References: <CACjcMuasgTMj+=-BFO_vLUT6kWE73FBA6PewcLSFZNFm4Se7Sg@mail.gmail.com>
 <1561329490.15991909.1467020401395.JavaMail.zimbra@enst.fr>
 <CACjcMuZg68OPEM=rTA2jyCQUCL7YP2JnGpwsE6pdnev+-fOJKQ@mail.gmail.com>
Message-ID: <553598682.26391964.1468403695421.JavaMail.zimbra@enst.fr>

Hi Sara,

The origin of an image is the point in world coordinates where the image "start" (from lower indexes to higher ones), not to be confused with the origin of the reference frame, which is [0,0,0]. When dealing with geometry, a drawing is often helpful to know what happens to the image origin during transformation.

And yes, you could do it through direction modification, that's just a bit more complicated.
Since modifing direction means transforming the reference frame, you have to compute where and which point will be the new origin of the imageC.

Sticking with the previous hypothesis on imageC position, the "true" origin of imageC (origin of imageCA) is the point:
-last in the original Y imageC direction
-first in the original X imageC direction
-first in the original Z imageC direction

So if the original origin of imageC is [0,0,0], this point will be [0,SizeC[1]*SpacingC[1],0].
Then this "true" origin will be modified by the rotation of the frame. In your case , -pi/2, giving [0,0,-SizeC[1]*SpacingC[1]].
Put this as the output origin and you should be fine.
Of course, is the original origin of imageC isn't [0,0,0], you should compute the new point accordingly.

For general matters, it should be noted that this works because the default rotation center is also the reference frame origin (i.e. [0,0,0])

HTH,

Tim



----- Mail original -----
De: "Sara Gh" <sg.ele.eng at gmail.com>
?: "Timothee Evain" <tevain at telecom-paristech.fr>
Cc: insight-users at itk.org
Envoy?: Mardi 12 Juillet 2016 22:54:25
Objet: Re: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the Axial View

Hello Tim,

Thank you for your helpful email and sorry for late reply.

Yes, that's right. The size of resampled imageC should be 256x68x256 and
imageC should be rotated -pi/2 around the X axis.
Now, my first question is: Can I use the direction of imageA as
the OutputDirection instead of using Euler3DTransform? Something like this:

# Direction of imageA: (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
# Direction of imageC: (1.0, 0.0, 0.0, 0.0, -0.0, 1.0, 0.0, -1.0, -0.0)
resample = sitk.ResampleImageFilter()
resample.SetTransform(sitk.Transform(3, sitk.sitkIdentity))
resample.SetReferenceImage(imageC)
resample.SetOutputDirection(imageA.GetDirection())
resample.SetOutputOrigin(imageA.GetOrigin())
spacingCA = [spacingC[0],spacingC[2],spacingC[1]]
resample.SetOutputSpacing(spacingCA)
sizeC = imageC.GetSize()
sizeCA = [sizeC[0], sizeC[2], sizeC[1]]
resample.SetSize(sizeCA)
imageCA=resample.Execute(imageC)
sitk.Show(imageCA)

Second, I think I haven't set the correct OutputOrigin for the resampled
image because when I compare imageCA with the axial view of imageC
(calculated by ImageJ > Stacks> Orthogonal Views), it seems that the
resulted imageCA is the translated version of the correct axial view.

I have read the ITK guide chapter 2.9 about transformation and resampling
processes but it is still vague to me how one should calculate/select the
correct origin for the output image. I would be thankful if you could refer
me to any other resources that could be helpful to me in this regard.

Thank you in advance.

Best regards,
Sara


On Mon, Jun 27, 2016 at 5:40 AM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> Hello,
>
> First of all, it depends on the patient position in the data, but usually
> the X axis describe the left/right direction, the Y axis the
> anterior/posterior direction and the Z axis the top/bottom one.
> So I would expect the resampled imageC size to be 256x68x256 rather than
> 68x256x256.
>
> Then, I think you should try to transform your imageC to be in the imageA
> orientation. Let say the imageA have a LPS coordinate system.
> If the imageC :
> -first direction represents the axis going from the patient's right to the
> patient's left
> -second direction represents the axis going from the patient's top to the
> patient's bottom
> -third direction represents the axis going from the patient's front to the
> patient's rear
> Then you should rotate the imageC by a -pi/2 angle around the X axis.
>
> You could use the Euler3DTransform to get this rotation.
> Then you feed the resample filter with this transform, plus the needed
> parameters (origin, spacing, size,...), and you should be able to have your
> resampled data.
> Just be sure to fully understand the transformation you're making (I
> recommend the ResampleImageFilter part of the ITK guide which is quite
> useful).
>
> HTH,
>
> Tim
>
>
> ----- Mail original -----
> De: "Sara Gh" <sg.ele.eng at gmail.com>
> ?: insight-users at itk.org
> Envoy?: Dimanche 26 Juin 2016 07:57:16
> Objet: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the
> Axial      View
>
> Hello experts,
>
> I have two MRI scans: Axial and Coronal
> # imageA : Axial MRI scan, size : 256x256x56 (256mmx256mmx168mm) ,
> spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 )
> # imageC : Coronal MRI scan, size : 256x256x68 (256mmx256mmx204mm) ,
> spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 )
>
> I am trying to view Coronal image from the axial view i.e. resampling
> Coronal image using the direction of Axial image. Here is my code:
>
> resample = sitk.ResampleImageFilter()
> resample.SetReferenceImage(imageC)
> resample.SetOutputDirection(imageA.GetDirection())
> resample.SetOutputOrigin(imageA.GetOrigin())
> imageCA = resample.Execute(imageC)
> sitk.Show(imageCA)
>
> # Result: imageCA: size : 256x256x68 (256mmx256mmx204mm), spacing: 1,1,3
>
> I believe I have missed something because, in my idea, the size of
> resampled coronal image (imageCA) should be 68x256x256 ( 204mmx256mmx256mm)
> with the spacing [3,1,1] .
>
> I also tried to set the OutputSpacing to [3,1,1], but the size of the
> imageCA changes to 256x256x68 (768mmx256mmx68mm).
>
> I would be thankful if someone could help me in this regard.
>
> Best regards,
> Sara Gh
>
> _____________________________________
> 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://public.kitware.com/mailman/listinfo/community
>



-- 
Sara Gharabaghi, Ph.D. Student
Graduate Research Assistant
Advanced Visual Data Analysis (AViDA) Lab
Biomedical Imaging Lab
Wright State University
_____________________________________
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From julien.jomier at kitware.com  Wed Jul 13 09:12:31 2016
From: julien.jomier at kitware.com (Julien Jomier)
Date: Wed, 13 Jul 2016 15:12:31 +0200
Subject: [ITK] [ITK-users] ANN: CMake Course - October 10 in Lyon, France
Message-ID: <cfb32f8e-b403-3571-5949-0170d542c582@kitware.com>

Kitware will be holding a CMake training course on October 10, 2016 at 
Kitware's office in Lyon, France. This one-day course will cover CMake, 
CTest, CPack and CDash.

Visit our website for more information and registration details (early 
registration and student discounts available):

    http://training.kitware.fr/browse/129

Note that the course will be taught in English. If you have any 
questions, please contact me directly or training at kitware.fr.

We are looking forward to seeing you in Lyon,
Julien
-- 
Kitware SAS
26 rue Louis Gu?rin
69100 Villeurbanne, France
http://www.kitware.eu
_____________________________________
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From brad at lowekamp.net  Wed Jul 13 20:35:13 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Wed, 13 Jul 2016 19:35:13 -0500
Subject: [ITK] Threading issues
In-Reply-To: <1468401134.3088708.664867785.4970C5A2@webmail.messagingengine.com>
References: <1468401134.3088708.664867785.4970C5A2@webmail.messagingengine.com>
Message-ID: <AEE05289-8701-449F-838E-F1F2FA72A1C1@mail.nih.gov>

Hello,

My guess it something is clobbering the stack. Does this occur with all of itk or just a specific filter? 

> On Jul 13, 2016, at 4:12 AM, Lauren?iu Nicola <lnicola at dend.ro> wrote:
> 
> Hi,
>  
> This is a bit of a shot in the dark asking this, but we're working on a project that uses a library based on ITK (OTB). We noticed two issues:
>  
> 1. We've seen processes with a single remaining thread that's stuck in pthread_join().
> 2. We're getting some segfaults in libpthread.so:
>  
> [Jul13 09:42] otbApplicationL[37610]: segfault at 7ff2f27fc9d0 ip 00007ff3375c2e61 sp 00007ffd9ef0d620 error 4 in libpthread-2.17.so[7ff3375ba000+16000]
> [  +0.002159] otbApplicationL[31064]: segfault at 2d3 ip 00007fd3bf636e61 sp 00007fff2446f210 error 4 in libpthread-2.17.so[7fd3bf62e000+16000]
> [  +0.007911] otbApplicationL[10366]: segfault at 7feb000008cc ip 00007febeaa15e61 sp 00007ffe34bb1e10 error 4 in libpthread-2.17.so[7febeaa0d000+16000]
> [Jul13 09:44] maccs-processin[39138]: segfault at 7f6b713979d0 ip 00007f6b767cae61 sp 00007ffe09fe6410 error 4 in libpthread-2.17.so[7f6b767c2000+16000]
> [  +0.000092] otbApplicationL[22007]: segfault at 2d0 ip 00007f06a6541e61 sp 00007fffb4299660 error 4 in libpthread-2.17.so[7f06a6539000+16000]
> [  +0.000384] otbApplicationL[33830]: segfault at 100001626 ip 00007f37c1f90e61 sp 00007fff8a0f44d0 error 4 in libpthread-2.17.so[7f37c1f88000+16000]
>  
> My theory is that 2d0 is an offset into a NULL pthread struct, but I couldn't find the definition of that structure (pthread_t is an opaque handle).
>  
> I suspect that the two issues are related. The weird part is that those segfaults tend to happen for multiple processes at the same time. The system was probably loaded, but I don't think it was an OOM situation.
>  
> Right now we're on ITK 4.9.1. Is there anyone else who encountered this or knows about recent ITK fixes related to multithreading?
>  
> Regards,
> Laurentiu Nicola
>  
> (gdb) bt
> #0  0x00007f0d74650ef7 in pthread_join () from /usr/lib64/libpthread.so.0
> #1  0x00007f0d74dd1cca in itk::MultiThreader::SpawnWaitForSingleMethodThread (this=this at entry=0x2411670, threadHandle=<optimized out>)
>     at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreaderPThreads.cxx:239
> #2  0x00007f0d74dd244b in itk::MultiThreader::WaitForSingleMethodThread (this=this at entry=0x2411670, threadHandle=<optimized out>)
>     at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:480
> #3  0x00007f0d74dd2f7d in itk::MultiThreader::SingleMethodExecute (this=0x2411670) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:389
> #4  0x00007f0d7cedb87d in itk::ImageSource<otb::VectorImage<float, 2u> >::GenerateData (this=0x23fff10) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/install/otb-install/usr/include/ITK-4.8/itkImageSource.hxx:254
> #5  0x00007f0d74dcdc00 in itk::ProcessObject::UpdateOutputData (this=0x23fff10) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-BUILD/ITK/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1739
> #6  0x00007f0d74dcdcc0 in itk::ProcessObject::UpdateOutputData (this=0x23e9b00) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-BUILD/ITK/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1700
> #7  0x00007f0d4af29368 in otb::StreamingImageVirtualWriter<otb::VectorImage<float, 2u> >::GenerateData (this=0x23e9700)
>     at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Core/Streaming/include/otbStreamingImageVirtualWriter.txx:248
> #8  0x00007f0d4af1c8ce in otb::StreamingImageVirtualWriter<otb::VectorImage<float, 2u> >::Update (this=0x23e9700)
>     at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Core/Streaming/include/otbStreamingImageVirtualWriter.txx:156
> #9  0x00007f0d4af11aad in otb::PersistentFilterStreamingDecorator<otb::PersistentShrinkImageFilter<otb::VectorImage<float, 2u>, otb::VectorImage<float, 2u> > >::GenerateData (this=0x2466c20)
>     at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Core/Streaming/include/otbPersistentFilterStreamingDecorator.txx:52
> #10 0x00007f0d4af1f4be in otb::Wrapper::Quicklook::DoExecute (this=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Applications/AppImageUtils/app/otbQuicklook.cxx:272
> #11 0x00007f0d7d2026c8 in otb::Wrapper::Application::Execute (this=this at entry=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplication.cxx:223
> #12 0x00007f0d7d202789 in otb::Wrapper::Application::ExecuteAndWriteOutput (this=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplication.cxx:230
> #13 0x00007f0d7d60b2c9 in otb::Wrapper::CommandLineLauncher::ExecuteAndWriteOutput (this=0x2366aa0) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLauncher.cxx:158
> #14 0x00000000004034a8 in main (argc=<optimized out>, argv=<optimized out>) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0/Modules/Wrappers/CommandLine/src/otbApplicationLauncherCommandLine.cxx:299
>  
> (gdb) info threads
>   Id   Target Id         Frame 
> * 1    Thread 0x7f0d63055880 (LWP 21145) "otbApplicationL" 0x00007f0d74650ef7 in pthread_join () from /usr/lib64/libpthread.so.0
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
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From brad at lowekamp.net  Wed Jul 13 23:03:40 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Wed, 13 Jul 2016 22:03:40 -0500
Subject: [ITK] SimpleITK 0.10 Release Candidate 1
Message-ID: <3136CBFF-D3A7-456F-80DC-567AE5EA0686@mail.nih.gov>

Hello,

We are pleased to announce the SimpleITK 0.10 Release Candidate 1 is available!

The binaries are available for download from Source Forge:

https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10rc1/

The latest versions of ?pip? is recommended to install the downloaded binary wheel for Python. Python eggs are not longer being distributed.

You are encouraged to checkout SimpleITK?s master branch in the git repository for testing building the source code.

Key Improvements:
* The R language bindings have received extensive improvements and bug fixes.
* Added Image::SetMetaData method
* Added LandmarkBasedTransformInitializer
* Added MultiLableSTAPLEImageFilter
* Default sitk::Show support for Fiji over ImageJ
* Moved third-party packages Lua, gtest, virtualenv from source code to Superbuild projects
* Added Forbid Download option
* Enabled each language wrapping to be an independent project dependent on SimpleITK C++ interface and libraries.
* Lua languages bindings now compile as a loadable module
* Many CMake build improvements to default configurations
* CMake version 3.3 is now required

Enjoy!
Brad

From dzenanz at gmail.com  Thu Jul 14 10:47:07 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 14 Jul 2016 10:47:07 -0400
Subject: [ITK] [ITK-users] Help needed to get the Mean Squared Error and
 Mutual Information values of two volumes
In-Reply-To: <1279017441.3214342.1468486988479.JavaMail.yahoo@mail.yahoo.com>
References: <1279017441.3214342.1468486988479.JavaMail.yahoo.ref@mail.yahoo.com>
 <1279017441.3214342.1468486988479.JavaMail.yahoo@mail.yahoo.com>
Message-ID: <CAPf2UMRj3PD0+Vqrm6+J8c1vtjdvz0tg6Y9NSP+CNvBJnPJEGg@mail.gmail.com>

Hi Ibraheem,

the signature
<https://itk.org/Doxygen/html/classitk_1_1MutualInformationImageToImageMetric.html>
of GetValue method is:
MeasureType GetValue (const ParametersType &parameters) const override;
which means that you need to give transform parameters to get a value. What
you might want is create an identity transform and pass that in.

Regards,
D?enan

On Thu, Jul 14, 2016 at 5:03 AM, ibraheem aldhamari via Insight-users <
insight-users at itk.org> wrote:

> Dear users,
> I am trying to get the values of Mean Squared Error and Mutual Information
> of two images. The input is two volumes: Imga and Imgb. Both have
> the same data type, size, spacing and origin. Here is my code :
>
>     typedef itk::MeanSquaresImageToImageMetric < Img_Tuc,Img_Tuc > SDF_T;
>
>     typedef itk::MutualInformationImageToImageMetric < Img_Tuc,Img_Tuc> MIF_T;
>
>     // Squared Difference
>
>        SDF_T::Pointer SD_F = SDF_T::New();
>
>        SD_F->SetFixedImage( Imga->GetOutput(0));
>
>        SD_F->SetMovingImage( Imgb->GetOutput(0));
>
>        float SD=SD_F->GetValue()  ;
>
>        cout<<"SD Result = " << SD <<endl;
>
>    //Mutual Information
>
>        MIF_T::Pointer MI_F = MIF_T::New();
>
>        MI_F->SetFixedImage (Imga->GetOutput(0));
>
>        MI_F->SetMovingImage(Imgb->GetOutput(0));
>
>        float MI=MI_F->GetValue() ;
>
>        cout<<"MI Result = " << MI <<endl;
>
>
>  but I keep getting these errors:
>
>  error: no matching function for call to 'itk::MeanSquaresImageToImageMetric<itk::Image<unsigned char, 3u>, itk::Image<unsigned char, 3u> >::GetValue()'
>
>         float SD=SD_F->GetValue()  ;                               ^
>
> error: no matching function for call to 'itk::MutualInformationImageToImageMetric<itk::Image<unsigned char, 3u>, itk::Image<unsigned char, 3u> >::GetValue()'
>         float MI=MI_F->GetValue() ;                                ^
>
> Could you please suggest a correction.
>
> Have a nice day!
>
> Ibraheem
>
>
> _____________________________________
> 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 kolin9105 at gmail.com  Thu Jul 14 13:49:23 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Fri, 15 Jul 2016 00:49:23 +0700
Subject: [ITK] [ITK-users] my problem
Message-ID: <CAEiw7u4CvyVeuw9uWzARH2Fd7Ek92YRQQhdCvbOqQ-iRSnaXCw@mail.gmail.com>

hello every one I am so confused until now I haven't find the correct
answer  about  , what is the advantage  seedX and seedY in confidence
connected filter ???
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From dzenanz at gmail.com  Thu Jul 14 16:54:14 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 14 Jul 2016 16:54:14 -0400
Subject: [ITK] [ITK-users] my problem
In-Reply-To: <CAEiw7u4CvyVeuw9uWzARH2Fd7Ek92YRQQhdCvbOqQ-iRSnaXCw@mail.gmail.com>
References: <CAEiw7u4CvyVeuw9uWzARH2Fd7Ek92YRQQhdCvbOqQ-iRSnaXCw@mail.gmail.com>
Message-ID: <CAPf2UMQg0NJDTekLf3FyKu5OTcOfK6-r=T2CVG4RNmRPmni3vA@mail.gmail.com>

Hi Meikolin,

there is no "advantage" to seeds, it is how confidence connected filter
operates. It finds all voxels which are connected to the provided seeds
with a certain confidence. So seeds are starting points.

Regards,
D?enan

On Thu, Jul 14, 2016 at 1:49 PM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> hello every one I am so confused until now I haven't find the correct
> answer  about  , what is the advantage  seedX and seedY in confidence
> connected filter ???
>
> _____________________________________
> 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

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From lnicola at dend.ro  Fri Jul 15 04:36:31 2016
From: lnicola at dend.ro (=?UTF-8?Q?Lauren=C8=9Biu=20Nicola?=)
Date: Fri, 15 Jul 2016 11:36:31 +0300
Subject: [ITK] Threading issues
In-Reply-To: <AEE05289-8701-449F-838E-F1F2FA72A1C1@mail.nih.gov>
References: <1468401134.3088708.664867785.4970C5A2@webmail.messagingengine.com>
 <AEE05289-8701-449F-838E-F1F2FA72A1C1@mail.nih.gov>
Message-ID: <1468571791.902001.667012561.5805671A@webmail.messagingengine.com>

On Thu, Jul 14, 2016, at 03:35, Bradley Lowekamp wrote:
>
> Hello,
>
> My guess it something is clobbering the stack. Does this occur with
> all of itk or just a specific filter?
 
It might be. In the meanwhile, I ran one of the affected applications
under Valgrind memcheck and helgrind, but found nothing relevant. Same
with the Clang sanitizers, although that was with a newer version of ITK
and OTB, because of build system troubles.
 
At least two of three instances I'm aware of involved (different
implementations of) resampling filters.
 
I'll add that the machine in cause has ECC ram and no errors were
reported by the system.
 
Laurentiu
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From dzenanz at gmail.com  Fri Jul 15 10:34:29 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 15 Jul 2016 10:34:29 -0400
Subject: [ITK] [ITK-users] my problem
In-Reply-To: <CAEiw7u4PTQ=BMtwOVBOWnJXY5sfe_wiAPyD55asCiz42Rz1CWA@mail.gmail.com>
References: <CAEiw7u4CvyVeuw9uWzARH2Fd7Ek92YRQQhdCvbOqQ-iRSnaXCw@mail.gmail.com>
 <CAPf2UMQg0NJDTekLf3FyKu5OTcOfK6-r=T2CVG4RNmRPmni3vA@mail.gmail.com>
 <CAEiw7u4PTQ=BMtwOVBOWnJXY5sfe_wiAPyD55asCiz42Rz1CWA@mail.gmail.com>
Message-ID: <CAPf2UMR=seuwcaVks4sDdah7GA1vGaRAcv2xYmpK-qj7k8EU3A@mail.gmail.com>

Hi Meikolin,

it is not clear to me what your problem is. Can you give some images (what
you get, what you want, where you put the seeds) and explain a bit more
what you did code-wise? Otherwise I would have to guess.

Regards,
D?enan

On Fri, Jul 15, 2016 at 3:26 AM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> thanks before sir..
> I have one problem in my thesis.
> I have a image of brain tumor,I can find the tumor and the skull using
> confidence connected segmentation, but I just wanna need the tumor no the
> skull. I just wanna one picture no full head to analyzed.
> can you help me sir??
> please sir..
>
> On Fri, Jul 15, 2016 at 3:54 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Meikolin,
>>
>> there is no "advantage" to seeds, it is how confidence connected filter
>> operates. It finds all voxels which are connected to the provided seeds
>> with a certain confidence. So seeds are starting points.
>>
>> Regards,
>> D?enan
>>
>> On Thu, Jul 14, 2016 at 1:49 PM, meikolin saimara <kolin9105 at gmail.com>
>> wrote:
>>
>>> hello every one I am so confused until now I haven't find the correct
>>> answer  about  , what is the advantage  seedX and seedY in confidence
>>> connected filter ???
>>>
>>> _____________________________________
>>> 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 ocuadrosl at gmail.com  Fri Jul 15 18:04:58 2016
From: ocuadrosl at gmail.com (Oscar Cuadros Linares)
Date: Fri, 15 Jul 2016 15:04:58 -0700
Subject: [ITK] [ITK-users] region of interest size problem
Message-ID: <57895E0A.7010108@gmail.com>

Hi Guys

I am trying to extract a region of interest (ROI) from a 3D tomography
I am using the filter  "itkRegionOfInterestImageFilter.h". The issue is
that the filter changes the original size of the input image.
According the documentation, the output image has the same
dimension of the input image. But size of the output image
is the size of the selected region (ROI).
My code is based on this example:
https://itk.org/Wiki/ITK/Examples/ImageProcessing/RegionOfInterestImageFilter

Thank you for your suggestions
Oscar

_____________________________________
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From dzenanz at gmail.com  Sat Jul 16 13:52:54 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 16 Jul 2016 13:52:54 -0400
Subject: [ITK] [ITK-users]   region of interest size problem
In-Reply-To: <57895E0A.7010108@gmail.com>
References: <57895E0A.7010108@gmail.com>
Message-ID: <CAPf2UMRVJL5sMqdri82pSzf1XxuGwDUZ4TE1vqLCpc7O2=gNPA@mail.gmail.com>

Hi Oscar,

the output dimension is the same: 3D input produces 3D output, 2D input
produces 2D output etc. But the point of RoI filter is to get an image
which is only a part of the input image, and in that respect the filter is
working correctly. What did you expect to happen? If you want only part of
the image be processed, set its RequestedRegion to something smaller than
LargestPossibleRegion.

Regards,
D?enan

On Fri, Jul 15, 2016 at 6:04 PM, Oscar Cuadros Linares <ocuadrosl at gmail.com>
wrote:

> Hi Guys
>
> I am trying to extract a region of interest (ROI) from a 3D tomography
> I am using the filter  "itkRegionOfInterestImageFilter.h". The issue is
> that the filter changes the original size of the input image.
> According the documentation, the output image has the same
> dimension of the input image. But size of the output image
> is the size of the selected region (ROI).
> My code is based on this example:
>
> https://itk.org/Wiki/ITK/Examples/ImageProcessing/RegionOfInterestImageFilter
>
> Thank you for your suggestions
> Oscar
>
> _____________________________________
> 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 zhuangming.shen at sphic.org.cn  Mon Jul 18 05:00:56 2016
From: zhuangming.shen at sphic.org.cn (=?gb2312?B?yfLXr8P3?=)
Date: Mon, 18 Jul 2016 09:00:56 +0000
Subject: [ITK] [ITK-users] Deformable registration question
Message-ID: <1468832456487.30276@sphic.org.cn>

Hi all,


I have two questions.

1) Has itk::BSplineTransformInitializer been wrapped to python-supported ITK?

2) Which deformable registration algorithms in ITK can deal with multi-modal image registration such as CT-MR registration?

Thanks.



Regards,


Zhuangming Shen
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Please keep messages on-topic and check the ITK FAQ at:
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From dzenanz at gmail.com  Mon Jul 18 09:04:44 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 18 Jul 2016 09:04:44 -0400
Subject: [ITK] [ITK-users] Deformable registration question
In-Reply-To: <1468832456487.30276@sphic.org.cn>
References: <1468832456487.30276@sphic.org.cn>
Message-ID: <CAPf2UMQ-ZRn=2+2T9PiaA0PUkt9631NNZnmO03W-yA=UOnGLAA@mail.gmail.com>

Hi Shen,

2) for multi-modal registration you need to use one variant of mutual
information registration metric. All the other parts of the registration
framework should be applicable.

Regards,
D?enan

On Mon, Jul 18, 2016 at 5:00 AM, ??? <zhuangming.shen at sphic.org.cn> wrote:

> Hi all,
>
>
> I have two questions.
>
> 1) Has itk::BSplineTransformInitializer been wrapped to python-supported
> ITK?
>
> 2) Which deformable registration algorithms in ITK can deal with
> multi-modal image registration such as CT-MR registration?
>
> Thanks.
>
>
>
> Regards,
>
>
> Zhuangming Shen
>
> _____________________________________
> 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  Mon Jul 18 10:02:55 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 18 Jul 2016 10:02:55 -0400
Subject: [ITK] [ITK-users] my problem
In-Reply-To: <CAEiw7u7C04YvocOFZ1B5D2VeydWAibHN3cra2eu1srFoEEi=yw@mail.gmail.com>
References: <CAEiw7u4CvyVeuw9uWzARH2Fd7Ek92YRQQhdCvbOqQ-iRSnaXCw@mail.gmail.com>
 <CAPf2UMQg0NJDTekLf3FyKu5OTcOfK6-r=T2CVG4RNmRPmni3vA@mail.gmail.com>
 <CAEiw7u4PTQ=BMtwOVBOWnJXY5sfe_wiAPyD55asCiz42Rz1CWA@mail.gmail.com>
 <CAPf2UMR=seuwcaVks4sDdah7GA1vGaRAcv2xYmpK-qj7k8EU3A@mail.gmail.com>
 <CAEiw7u50bcFet5vf_1rC+QwQUi8C0_qHDgzQbYWikCTczrJkvw@mail.gmail.com>
 <CAPf2UMSaOFg0eRaKFrSVvcLB9q77-Extu__+=mN6RBaiyjT-9A@mail.gmail.com>
 <CAEiw7u7C04YvocOFZ1B5D2VeydWAibHN3cra2eu1srFoEEi=yw@mail.gmail.com>
Message-ID: <CAPf2UMRP_h=euLhspVEt7c6wsu7Kqv4dGYFCvOHUOJC5tS=BsQ@mail.gmail.com>

There is a paper
<http://www.insight-journal.org/download/viewpdf/859/4/download> which goes
along with the source code, which give more description as well as how to
call the filter.

On Mon, Jul 18, 2016 at 9:55 AM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> I just have tried how to compile the code.  I am confused how to use it.
>
> but I have problem to use that because the skull stripping approaches need
> data sheet of brain.
> I just want send one image in my thesis no more.
> I am sorry sir I am beginner in ITK.
>
>
> On Mon, Jul 18, 2016 at 8:02 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Have you tried some skull stripping approaches? One example is this:
>> http://www.insight-journal.org/browse/publication/859
>>
>> Also, something similar to what you are trying to do already exists:
>> http://volbrain.upv.es
>>
>> Regards
>>
>> On Mon, Jul 18, 2016 at 4:34 AM, meikolin saimara <kolin9105 at gmail.com>
>> wrote:
>>
>>> oke I will explain to you what I want to do in my thesis.
>>> in my thesis I want to build web service to analyze large of brain tumor.
>>> the steps are  client send one image of brain which one will be analyzed
>>> after that server will be processed the image without being noticed by
>>> client.
>>> in server using command prompt to analyzed the image. after that the
>>> result will be showed to Client.
>>>
>>> now my problem is I can't remove outside the skull with itk in my server.
>>> if outside the skull Can't be removed so the itk program will enter
>>> pixel of  the skull mixed the tumor.
>>> first image is before processed and second image is after processed.
>>> in confidence connected uses the seedX is 100 and the seedY 75.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Fri, Jul 15, 2016 at 9:34 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>>> Hi Meikolin,
>>>>
>>>> it is not clear to me what your problem is. Can you give some images
>>>> (what you get, what you want, where you put the seeds) and explain a bit
>>>> more what you did code-wise? Otherwise I would have to guess.
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Fri, Jul 15, 2016 at 3:26 AM, meikolin saimara <kolin9105 at gmail.com>
>>>> wrote:
>>>>
>>>>> thanks before sir..
>>>>> I have one problem in my thesis.
>>>>> I have a image of brain tumor,I can find the tumor and the skull using
>>>>> confidence connected segmentation, but I just wanna need the tumor no the
>>>>> skull. I just wanna one picture no full head to analyzed.
>>>>> can you help me sir??
>>>>> please sir..
>>>>>
>>>>> On Fri, Jul 15, 2016 at 3:54 AM, D?enan Zuki? <dzenanz at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Meikolin,
>>>>>>
>>>>>> there is no "advantage" to seeds, it is how confidence connected
>>>>>> filter operates. It finds all voxels which are connected to the provided
>>>>>> seeds with a certain confidence. So seeds are starting points.
>>>>>>
>>>>>> Regards,
>>>>>> D?enan
>>>>>>
>>>>>> On Thu, Jul 14, 2016 at 1:49 PM, meikolin saimara <
>>>>>> kolin9105 at gmail.com> wrote:
>>>>>>
>>>>>>> hello every one I am so confused until now I haven't find the
>>>>>>> correct  answer  about  , what is the advantage  seedX and seedY in
>>>>>>> confidence connected filter ???
>>>>>>>
>>>>>>> _____________________________________
>>>>>>> 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  Mon Jul 18 10:31:20 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 18 Jul 2016 10:31:20 -0400
Subject: [ITK] [ITK-users] my problem
In-Reply-To: <CAEiw7u544Cyg2Fa0kYGYMRMkaTMBzPGDP8GgbLYddwQRP-M7dg@mail.gmail.com>
References: <CAEiw7u4CvyVeuw9uWzARH2Fd7Ek92YRQQhdCvbOqQ-iRSnaXCw@mail.gmail.com>
 <CAPf2UMQg0NJDTekLf3FyKu5OTcOfK6-r=T2CVG4RNmRPmni3vA@mail.gmail.com>
 <CAEiw7u4PTQ=BMtwOVBOWnJXY5sfe_wiAPyD55asCiz42Rz1CWA@mail.gmail.com>
 <CAPf2UMR=seuwcaVks4sDdah7GA1vGaRAcv2xYmpK-qj7k8EU3A@mail.gmail.com>
 <CAEiw7u50bcFet5vf_1rC+QwQUi8C0_qHDgzQbYWikCTczrJkvw@mail.gmail.com>
 <CAPf2UMSaOFg0eRaKFrSVvcLB9q77-Extu__+=mN6RBaiyjT-9A@mail.gmail.com>
 <CAEiw7u7C04YvocOFZ1B5D2VeydWAibHN3cra2eu1srFoEEi=yw@mail.gmail.com>
 <CAPf2UMRP_h=euLhspVEt7c6wsu7Kqv4dGYFCvOHUOJC5tS=BsQ@mail.gmail.com>
 <CAEiw7u544Cyg2Fa0kYGYMRMkaTMBzPGDP8GgbLYddwQRP-M7dg@mail.gmail.com>
Message-ID: <CAPf2UMQ7SbEdac95TFnQxJNrYXcRk3aryxwsoLR-X1+6Sins_Q@mail.gmail.com>

The image you sent before is a 2D image, and you should do some 2D skull
stripping (e.g. this
<https://www.researchgate.net/publication/264042031_Skull_Stripping_of_MRI_Using_Clustering_and_2D_Region_Growing_Method>
).

Also, can you try to keep the conversation on the mailing list so other
people can benefit from it in the future?

Regards,
D?enan

On Mon, Jul 18, 2016 at 10:23 AM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> thanks before sir,
> I have read this before but I don't about dataset.
> how about my image what I send before??
> can you remove the skull??
>
> On Mon, Jul 18, 2016 at 9:02 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> There is a paper
>> <http://www.insight-journal.org/download/viewpdf/859/4/download> which
>> goes along with the source code, which give more description as well as how
>> to call the filter.
>>
>> On Mon, Jul 18, 2016 at 9:55 AM, meikolin saimara <kolin9105 at gmail.com>
>> wrote:
>>
>>> I just have tried how to compile the code.  I am confused how to use
>>> it.
>>> but I have problem to use that because the skull stripping approaches
>>> need data sheet of brain.
>>> I just want send one image in my thesis no more.
>>> I am sorry sir I am beginner in ITK.
>>>
>>>
>>> On Mon, Jul 18, 2016 at 8:02 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>>> Have you tried some skull stripping approaches? One example is this:
>>>> http://www.insight-journal.org/browse/publication/859
>>>>
>>>> Also, something similar to what you are trying to do already exists:
>>>> http://volbrain.upv.es
>>>>
>>>> Regards
>>>>
>>>> On Mon, Jul 18, 2016 at 4:34 AM, meikolin saimara <kolin9105 at gmail.com>
>>>> wrote:
>>>>
>>>>> oke I will explain to you what I want to do in my thesis.
>>>>> in my thesis I want to build web service to analyze large of brain
>>>>> tumor.
>>>>> the steps are  client send one image of brain which one will be
>>>>> analyzed after that server will be processed the image without being
>>>>> noticed by client.
>>>>> in server using command prompt to analyzed the image. after that the
>>>>> result will be showed to Client.
>>>>>
>>>>> now my problem is I can't remove outside the skull with itk in my
>>>>> server.
>>>>> if outside the skull Can't be removed so the itk program will enter
>>>>> pixel of  the skull mixed the tumor.
>>>>> first image is before processed and second image is after processed.
>>>>> in confidence connected uses the seedX is 100 and the seedY 75.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Jul 15, 2016 at 9:34 PM, D?enan Zuki? <dzenanz at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Meikolin,
>>>>>>
>>>>>> it is not clear to me what your problem is. Can you give some images
>>>>>> (what you get, what you want, where you put the seeds) and explain a bit
>>>>>> more what you did code-wise? Otherwise I would have to guess.
>>>>>>
>>>>>> Regards,
>>>>>> D?enan
>>>>>>
>>>>>> On Fri, Jul 15, 2016 at 3:26 AM, meikolin saimara <
>>>>>> kolin9105 at gmail.com> wrote:
>>>>>>
>>>>>>> thanks before sir..
>>>>>>> I have one problem in my thesis.
>>>>>>> I have a image of brain tumor,I can find the tumor and the skull
>>>>>>> using confidence connected segmentation, but I just wanna need the tumor no
>>>>>>> the skull. I just wanna one picture no full head to analyzed.
>>>>>>> can you help me sir??
>>>>>>> please sir..
>>>>>>>
>>>>>>> On Fri, Jul 15, 2016 at 3:54 AM, D?enan Zuki? <dzenanz at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Meikolin,
>>>>>>>>
>>>>>>>> there is no "advantage" to seeds, it is how confidence connected
>>>>>>>> filter operates. It finds all voxels which are connected to the provided
>>>>>>>> seeds with a certain confidence. So seeds are starting points.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>> D?enan
>>>>>>>>
>>>>>>>> On Thu, Jul 14, 2016 at 1:49 PM, meikolin saimara <
>>>>>>>> kolin9105 at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> hello every one I am so confused until now I haven't find the
>>>>>>>>> correct  answer  about  , what is the advantage  seedX and seedY in
>>>>>>>>> confidence connected filter ???
>>>>>>>>>
>>>>>>>>> _____________________________________
>>>>>>>>> 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 ocuadrosl at gmail.com  Mon Jul 18 15:01:41 2016
From: ocuadrosl at gmail.com (Oscar Cuadros Linares)
Date: Mon, 18 Jul 2016 12:01:41 -0700
Subject: [ITK] [ITK-users]   region of interest size problem
In-Reply-To: <CAPf2UMRVJL5sMqdri82pSzf1XxuGwDUZ4TE1vqLCpc7O2=gNPA@mail.gmail.com>
References: <57895E0A.7010108@gmail.com>
 <CAPf2UMRVJL5sMqdri82pSzf1XxuGwDUZ4TE1vqLCpc7O2=gNPA@mail.gmail.com>
Message-ID: <CAMxqLnS7k_5oc2UsUkocqV-BAsv1zhX25Jm+wBMD36B3=07sPQ@mail.gmail.com>

Hi D?enan Zuki?

Thank you for your reply.
I know that a 3D input produces a 3D output. I will try to explain better
my issue.
I have a 3D image and I want to get to a ROI (200x200x100 size) from that
image.
But the output image has to keep the original information, especially the
region size.
(400x400x550 in my case). The problem is that the output image is
200x200x100 size
and not 400x400x550 like the input image.

Thank you so much.
Oscar



On Sat, Jul 16, 2016 at 10:52 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Oscar,
>
> the output dimension is the same: 3D input produces 3D output, 2D input
> produces 2D output etc. But the point of RoI filter is to get an image
> which is only a part of the input image, and in that respect the filter is
> working correctly. What did you expect to happen? If you want only part of
> the image be processed, set its RequestedRegion to something smaller than
> LargestPossibleRegion.
>
> Regards,
> D?enan
>
> On Fri, Jul 15, 2016 at 6:04 PM, Oscar Cuadros Linares <
> ocuadrosl at gmail.com> wrote:
>
>> Hi Guys
>>
>> I am trying to extract a region of interest (ROI) from a 3D tomography
>> I am using the filter  "itkRegionOfInterestImageFilter.h". The issue is
>> that the filter changes the original size of the input image.
>> According the documentation, the output image has the same
>> dimension of the input image. But size of the output image
>> is the size of the selected region (ROI).
>> My code is based on this example:
>>
>> https://itk.org/Wiki/ITK/Examples/ImageProcessing/RegionOfInterestImageFilter
>>
>> Thank you for your suggestions
>> Oscar
>>
>> _____________________________________
>> 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
>>
>
>


-- 
Oscar Cuadros Linares
Computer Science
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From dzenanz at gmail.com  Mon Jul 18 15:15:19 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 18 Jul 2016 15:15:19 -0400
Subject: [ITK] [ITK-users]   region of interest size problem
In-Reply-To: <CAMxqLnS7k_5oc2UsUkocqV-BAsv1zhX25Jm+wBMD36B3=07sPQ@mail.gmail.com>
References: <57895E0A.7010108@gmail.com>
 <CAPf2UMRVJL5sMqdri82pSzf1XxuGwDUZ4TE1vqLCpc7O2=gNPA@mail.gmail.com>
 <CAMxqLnS7k_5oc2UsUkocqV-BAsv1zhX25Jm+wBMD36B3=07sPQ@mail.gmail.com>
Message-ID: <CAPf2UMRV+Bhgh5FVmjyZbvQp3Xg7fQW32UPteYOWEGC2=jSVgA@mail.gmail.com>

Hi Oscar,

if you want to copy part of the image, and have the rest be filled with
zeroes, you should:

   1. create a new image
   2. copy information from the source image
   3. set regions using source's region
   4. allocate(true)
   5. use PasteImageFilter
   <https://itk.org/Doxygen/html/classitk_1_1PasteImageFilter.html> to copy
   a portion of source to the new image

Does this answer your question?

Regards,
D?enan

On Mon, Jul 18, 2016 at 3:01 PM, Oscar Cuadros Linares <ocuadrosl at gmail.com>
wrote:

> Hi D?enan Zuki?
>
> Thank you for your reply.
> I know that a 3D input produces a 3D output. I will try to explain better
> my issue.
> I have a 3D image and I want to get to a ROI (200x200x100 size) from that
> image.
> But the output image has to keep the original information, especially the
> region size.
> (400x400x550 in my case). The problem is that the output image is
> 200x200x100 size
> and not 400x400x550 like the input image.
>
> Thank you so much.
> Oscar
>
>
>
> On Sat, Jul 16, 2016 at 10:52 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Oscar,
>>
>> the output dimension is the same: 3D input produces 3D output, 2D input
>> produces 2D output etc. But the point of RoI filter is to get an image
>> which is only a part of the input image, and in that respect the filter is
>> working correctly. What did you expect to happen? If you want only part of
>> the image be processed, set its RequestedRegion to something smaller than
>> LargestPossibleRegion.
>>
>> Regards,
>> D?enan
>>
>> On Fri, Jul 15, 2016 at 6:04 PM, Oscar Cuadros Linares <
>> ocuadrosl at gmail.com> wrote:
>>
>>> Hi Guys
>>>
>>> I am trying to extract a region of interest (ROI) from a 3D tomography
>>> I am using the filter  "itkRegionOfInterestImageFilter.h". The issue is
>>> that the filter changes the original size of the input image.
>>> According the documentation, the output image has the same
>>> dimension of the input image. But size of the output image
>>> is the size of the selected region (ROI).
>>> My code is based on this example:
>>>
>>> https://itk.org/Wiki/ITK/Examples/ImageProcessing/RegionOfInterestImageFilter
>>>
>>> Thank you for your suggestions
>>> Oscar
>>>
>>> _____________________________________
>>> 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
>>>
>>
>>
>
>
> --
> Oscar Cuadros Linares
> Computer Science
>
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From anton.delehony at gmail.com  Mon Jul 18 17:06:54 2016
From: anton.delehony at gmail.com (Anton Delehony)
Date: Mon, 18 Jul 2016 17:06:54 -0400
Subject: [ITK] [ITK-users] simpleITK C# bspline registation
Message-ID: <CAB8ojqT+zENo1oMqAnYEf42DT4COChJTU-kHMFA+GVNAzCf+aw@mail.gmail.com>

Hi all,



I noticed that the output of my registration is exactly as the moving
image, which means that the code below is not correct, but not sure where
is the mistake. I think it has to do with the transform initializer....



Thanks,



AD



              // Read input static

             itk.simple.ImageFileReader reader1 = new
itk.simple.ImageFileReader();

             reader1.SetFileName(args[0]);

             Image static = reader1.Execute();

             // Read input moving

             itk.simple.ImageFileReader reader2 = new
itk.simple.ImageFileReader();

             reader2.SetFileName(args[0]);

             Image moving = reader2.Execute();



            //registation

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

            R.SetMetricAsMattesMutualInformation(50);

            R.SetMetricSamplingPercentage(30.0);

            R.SetInterpolator(itk.simple.InterpolatorEnum.sitkLinear);

            R.SetOptimizerAsLBFGSB();

            itk.simple.BSplineTransform transform = new
itk.simple.BSplineTransform(3);

            R.SetInitialTransform( transform);

            itk.simple.Transform trans_f = R.Execute(static, moving);

            //resample image

            itk.simple.ResampleImageFilter resample = new
itk.simple.ResampleImageFilter();

            resample.SetReferenceImage(static);

            resample.SetTransform(trans_f);


resample.SetInterpolator(itk.simple.InterpolatorEnum.sitkBSpline);

            itk.simple.Image registered = resample.Execute(moving);
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From zivrafael.yaniv at nih.gov  Mon Jul 18 20:30:33 2016
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Tue, 19 Jul 2016 00:30:33 +0000
Subject: [ITK] [ITK-users] simpleITK C# bspline registation
In-Reply-To: <CAB8ojqT+zENo1oMqAnYEf42DT4COChJTU-kHMFA+GVNAzCf+aw@mail.gmail.com>
References: <CAB8ojqT+zENo1oMqAnYEf42DT4COChJTU-kHMFA+GVNAzCf+aw@mail.gmail.com>
Message-ID: <B2DE09A5824F4746A0528DAB608EF520150D81B6@msgb10.nih.gov>

Hello Anton,

Yes, likely you are correct. Right now your code initializes using the identity transform and as far as I remember your B-spline grid doesn't physically overlap with your images (maybe it does, but this would be by chance).
What is a bit surprising is that you did not get an error with regard to too many samples outside the domain (indicating no overlap between images - so I am a bit puzzled as it means your images do overlap sufficiently).

This scenario is rare in practice and usually only happens when you are registering temporal data such as 3D volumes from a 4D CT dataset. Please see the following Jupyter Python notebook for an example on setting things up https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/master/65_Registration_FFD.ipynb . It will be easy for you to translate it to C#.


You will also likely need to initialize your registration by performing a registration using a global transformation (rigid/affine) and only then a local registration (FFD).

One last thing, there is a bug in the code in the line: R.SetMetricSamplingPercentage(30.0);

This is a 300% sampling. The expected values are in (0.0,1.0].


          hope this helps
                  Ziv

________________________________
From: Anton Delehony [anton.delehony at gmail.com]
Sent: Monday, July 18, 2016 5:06 PM
To: insight-users at itk.org
Subject: [ITK-users] simpleITK C# bspline registation

Hi all,

I noticed that the output of my registration is exactly as the moving image, which means that the code below is not correct, but not sure where is the mistake. I think it has to do with the transform initializer....

Thanks,

AD

              // Read input static
             itk.simple.ImageFileReader reader1 = new itk.simple.ImageFileReader();
             reader1.SetFileName(args[0]);
             Image static = reader1.Execute();
             // Read input moving
             itk.simple.ImageFileReader reader2 = new itk.simple.ImageFileReader();
             reader2.SetFileName(args[0]);
             Image moving = reader2.Execute();

            //registation
            itk.simple.ImageRegistrationMethod R = new itk.simple.ImageRegistrationMethod();
            R.SetMetricAsMattesMutualInformation(50);
            R.SetMetricSamplingPercentage(30.0);
            R.SetInterpolator(itk.simple.InterpolatorEnum.sitkLinear);
            R.SetOptimizerAsLBFGSB();
            itk.simple.BSplineTransform transform = new itk.simple.BSplineTransform(3);
            R.SetInitialTransform( transform);
            itk.simple.Transform trans_f = R.Execute(static, moving);
            //resample image
            itk.simple.ResampleImageFilter resample = new itk.simple.ResampleImageFilter();
            resample.SetReferenceImage(static);
            resample.SetTransform(trans_f);
            resample.SetInterpolator(itk.simple.InterpolatorEnum.sitkBSpline);
            itk.simple.Image registered = resample.Execute(moving);

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From matt.mccormick at kitware.com  Mon Jul 18 22:45:14 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 18 Jul 2016 22:45:14 -0400
Subject: [ITK] [ITK-users] Deformable registration question
In-Reply-To: <CAPf2UMQ-ZRn=2+2T9PiaA0PUkt9631NNZnmO03W-yA=UOnGLAA@mail.gmail.com>
References: <1468832456487.30276@sphic.org.cn>
 <CAPf2UMQ-ZRn=2+2T9PiaA0PUkt9631NNZnmO03W-yA=UOnGLAA@mail.gmail.com>
Message-ID: <CALzTN-S5tw1yziWMo31L-QhZyhe7sBaVcZCre=M75ZodjyG=sQ@mail.gmail.com>

Hi,

For 1) here is a patch that will add wrapping support for
itk::BSplineTransformInitializer:

  http://review.source.kitware.com/#/c/21341/

HTH,
Matt

On Mon, Jul 18, 2016 at 9:04 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Shen,
>
> 2) for multi-modal registration you need to use one variant of mutual
> information registration metric. All the other parts of the registration
> framework should be applicable.
>
> Regards,
> D?enan
>
> On Mon, Jul 18, 2016 at 5:00 AM, ??? <zhuangming.shen at sphic.org.cn> wrote:
>>
>> Hi all,
>>
>>
>> I have two questions.
>>
>> 1) Has itk::BSplineTransformInitializer been wrapped to python-supported
>> ITK?
>>
>> 2) Which deformable registration algorithms in ITK can deal with
>> multi-modal image registration such as CT-MR registration?
>>
>> Thanks.
>>
>>
>>
>> Regards,
>>
>>
>> Zhuangming Shen
>>
>>
>> _____________________________________
>> 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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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 kolin9105 at gmail.com  Tue Jul 19 01:40:51 2016
From: kolin9105 at gmail.com (meikolin saimara)
Date: Tue, 19 Jul 2016 12:40:51 +0700
Subject: [ITK] [ITK-users] (no subject)
Message-ID: <CAEiw7u70pTxVoBuiar2o0ZbheJE8kNMjof7EqgqqJUQ6tzfi2w@mail.gmail.com>

hello every one..
I have a problem in my thesis I want to remove the skull but I didn't.
I have a Image 2D.
how to remove it???
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From manuel.grizonnet at cnes.fr  Tue Jul 19 06:15:10 2016
From: manuel.grizonnet at cnes.fr (Manuel GRIZONNET)
Date: Tue, 19 Jul 2016 12:15:10 +0200
Subject: [ITK] [ITK-dev] Compilation issue with ITK master branch (related
	to vcl)
Message-ID: <578DFDAE.9060504@cnes.fr>

Hi all,

I've got a compilation error in the ORFEO ToolBox (which depend on ITK) 
when I tried to compile the library with ITK master branch. You can see 
the compilation error ('vcl_config_manual.h' file not found) on OTB 
dashboard:

http://dash.orfeo-toolbox.org/viewBuildError.php?buildid=237391 
<http://dash.orfeo-toolbox.org/viewBuildError.php?buildid=237391>

The compilation failed since around mid-June (ITK master branch is 
updated once a week on this platform):

http://dash.orfeo-toolbox.org/buildSummary.php?buildid=237391

I read that there was ongoing work on vcl but I do not know if the error 
is related to my configuration of ITK or if recent modifications in VCL 
changes will imply modifications in OTB.

Thanks in advance for your help.

Best regards,

Manuel

-- 
Manuel GRIZONNET

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From matt.mccormick at kitware.com  Tue Jul 19 13:12:40 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 19 Jul 2016 13:12:40 -0400
Subject: [ITK] [ITK-dev] Compilation issue with ITK master branch
 (related to vcl)
In-Reply-To: <578DFDAE.9060504@cnes.fr>
References: <578DFDAE.9060504@cnes.fr>
Message-ID: <CALzTN-SgJN=iv0soaNP_pXe52fxs2MiQYtJ4A5ohKwFJTfs4-w@mail.gmail.com>

Hi Manuel,

Thanks for bringing attention to this.

A patch is here:

  http://review.source.kitware.com/#/c/21345/

and upstream:

  https://github.com/vxl/vxl/pull/345

HTH,
Matt

On Tue, Jul 19, 2016 at 6:15 AM, Manuel GRIZONNET
<manuel.grizonnet at cnes.fr> wrote:
> Hi all,
>
> I've got a compilation error in the ORFEO ToolBox (which depend on ITK) when
> I tried to compile the library with ITK master branch. You can see the
> compilation error ('vcl_config_manual.h' file not found) on OTB dashboard:
>
> http://dash.orfeo-toolbox.org/viewBuildError.php?buildid=237391
> <http://dash.orfeo-toolbox.org/viewBuildError.php?buildid=237391>
>
> The compilation failed since around mid-June (ITK master branch is updated
> once a week on this platform):
>
> http://dash.orfeo-toolbox.org/buildSummary.php?buildid=237391
>
> I read that there was ongoing work on vcl but I do not know if the error is
> related to my configuration of ITK or if recent modifications in VCL changes
> will imply modifications in OTB.
>
> Thanks in advance for your help.
>
> Best regards,
>
> Manuel
>
> --
> Manuel GRIZONNET
>
> _______________________________________________
> 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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From blowekamp at mail.nih.gov  Wed Jul 20 16:25:09 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 20 Jul 2016 20:25:09 +0000
Subject: [ITK] [ITK-dev] VCL install issues
Message-ID: <F921FD41-9F4A-441D-A876-29CE7CD71E1C@mail.nih.gov>

Hello,

I can getting the following missing header error when using and installed ITK from master:

[ 37%] Generating src/sitkComplexToPhaseImageFilter.cxx
In file included from /tmp/SimpleITK/Code/Explicit/src/sitkExplicitITKImageRegion.cxx:19:
In file included from /tmp/SimpleITK/Code/Explicit/include/sitkExplicitITKImageRegion.h:21:
In file included from /usr/local/include/ITK-4.11/itkImageRegion.h:31:
In file included from /usr/local/include/ITK-4.11/itkRegion.h:31:
In file included from /usr/local/include/ITK-4.11/itkObject.h:31:
In file included from /usr/local/include/ITK-4.11/itkLightObject.h:25:
In file included from /usr/local/include/ITK-4.11/itkAtomicInt.h:38:
In file included from /usr/local/include/ITK-4.11/itkConceptChecking.h:32:
In file included from /usr/local/include/ITK-4.11/itkNumericTraits.h:51:
In file included from /usr/local/include/ITK-4.11/vcl_limits.h:5:
/usr/local/include/ITK-4.11/vcl_compiler.h:121:10: fatal error: 'vcl_config_manual.h' file not found
#include <vcl_config_manual.h>
         ^

Here is the DockerFile I was working with:

== DockerFile ==

FROM ubuntu:14.04

RUN \
  apt-get update && \
  apt-get -y upgrade && \
  apt-get install -y build-essential clang git curl swig python-dev

RUN \
    curl -O https://cmake.org/files/v3.6/cmake-3.6.0-Linux-x86_64.sh && \
    umask 022 && echo "y\n" | bash cmake-3.6.0-Linux-x86_64.sh --prefix=/usr/local  --exclude-subdir

WORKDIR /tmp/

RUN \
    git clone https://itk.org/ITK.git && \
    cd ITK && \
    git checkout master && \
    mkdir bld

RUN \
    cd ITK/bld && \
    CC=clang CXX=clang++ cmake \
       -DBUILD_SHARED_LIBS:BOOL=ON \
       -DUSE_COMPILER_HIDDEN_VISIBILITY:BOOL=OFF \
       -DBUILD_TESTING:BOOL=OFF \
       -DModule_ITKReview:BOOL=ON \
       .. && \
    make -j $(nproc) install && \
    ldconfig



RUN \
    git clone https://itk.org/SimpleITK.git && \
    cd SimpleITK && \
    git checkout master && \
    mkdir bld

RUN \
    cd SimpleITK/bld && \
    CC=clang CXX=clang++ cmake \
      -DBUILD_SHARED_LIBS:BOOL=ON \
      -DWRAP_LUA:BOOL=OFF \
      -DWRAP_PYTHON:BOOL=ON \
      -DUSE_SYSTEM_SWIG:BOOL=ON \
      -DUSE_SYSTEM_ITK:BOOL=ON \
      -DBUILD_TESTING:BOOL=OFF \
      ../SuperBuild && \
    make -j $(nproc)

== end ==

Thanks,
Brad

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From tossin at gmail.com  Wed Jul 20 19:09:53 2016
From: tossin at gmail.com (Evan Kao)
Date: Wed, 20 Jul 2016 16:09:53 -0700
Subject: [ITK] [ITK-users] Target Machine type error when trying to build
	64-bit	ITK using VS2015
Message-ID: <CAEhu9hDVDp4XY4uB9za_Vj14m8KJFfox4d61G-j1nnziP7R0KA@mail.gmail.com>

Hello all,

This may be more of a Visual Studio issue than an ITK issue, but I was
wondering if anyone else found a way around this.  I'm trying to build ITK
4.10.0 on a Windows 7 64-bit machine with Python (2.7 64-bit) wrapping
using Visual Studio 2015.  I should add I'm not familiar with either CMake,
ITK, or Visual Studio so I could be missing something obvious.

I keep getting the following error for multiple *.obj files:
x64\Release\*.obj : fatal error LNK1112: module machine type 'x64'
conflicts with target machine type 'X86'

I noticed that CMake generates vxproj files for only Win32 by default.
Then the files are modified by Visual Studio when switching the platform to
x64 and selecting "Clean Solution", which adds the following lines, among
others:
    <ProjectConfiguration Include="Release|x64">
      <Configuration>Release</Configuration>
      <Platform>x64</Platform>

However, many individual sub-projects are still not updated to account for
x64 configurations.  I took a look at the Advanced CMAKE variables in the
CMake GUI, but had no idea what to modify (everything seems to target
Win32).

Is there a way to configure CMake to generate x64 files?  If not, does
anyone know how to correctly configure ITK on x64 platforms in VS2015?

Thanks,
Evan Kao
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http://www.itk.org/Wiki/ITK_FAQ

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From dzenanz at gmail.com  Wed Jul 20 20:00:37 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 20 Jul 2016 20:00:37 -0400
Subject: [ITK] [ITK-users] Target Machine type error when trying to
 build 64-bit ITK using VS2015
In-Reply-To: <CAEhu9hDVDp4XY4uB9za_Vj14m8KJFfox4d61G-j1nnziP7R0KA@mail.gmail.com>
References: <CAEhu9hDVDp4XY4uB9za_Vj14m8KJFfox4d61G-j1nnziP7R0KA@mail.gmail.com>
Message-ID: <CAPf2UMQ3_wK8RFDX_FRrQVNQ1Z7+=o4WxXdYZdz=Ciq7XjwrUw@mail.gmail.com>

Hi Evan,

you need to select "Visual Studio 14 2015 Win64" as the generator:
[image: Inline image 3]

The result of this should be that you only have x64 platform in Visual
Studio:
[image: Inline image 2]

Regards,
D?enan

On Wed, Jul 20, 2016 at 7:09 PM, Evan Kao <tossin at gmail.com> wrote:

> Hello all,
>
> This may be more of a Visual Studio issue than an ITK issue, but I was
> wondering if anyone else found a way around this.  I'm trying to build ITK
> 4.10.0 on a Windows 7 64-bit machine with Python (2.7 64-bit) wrapping
> using Visual Studio 2015.  I should add I'm not familiar with either CMake,
> ITK, or Visual Studio so I could be missing something obvious.
>
> I keep getting the following error for multiple *.obj files:
> x64\Release\*.obj : fatal error LNK1112: module machine type 'x64'
> conflicts with target machine type 'X86'
>
> I noticed that CMake generates vxproj files for only Win32 by default.
> Then the files are modified by Visual Studio when switching the platform to
> x64 and selecting "Clean Solution", which adds the following lines, among
> others:
>     <ProjectConfiguration Include="Release|x64">
>       <Configuration>Release</Configuration>
>       <Platform>x64</Platform>
>
> However, many individual sub-projects are still not updated to account for
> x64 configurations.  I took a look at the Advanced CMAKE variables in the
> CMake GUI, but had no idea what to modify (everything seems to target
> Win32).
>
> Is there a way to configure CMake to generate x64 files?  If not, does
> anyone know how to correctly configure ITK on x64 platforms in VS2015?
>
> Thanks,
> Evan Kao
>
> _____________________________________
> 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 zhuangming.shen at sphic.org.cn  Thu Jul 21 03:06:15 2016
From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=)
Date: Thu, 21 Jul 2016 07:06:15 +0000
Subject: [ITK] [ITK-users] Deformable registration question
In-Reply-To: <CALzTN-S5tw1yziWMo31L-QhZyhe7sBaVcZCre=M75ZodjyG=sQ@mail.gmail.com>
References: <1468832456487.30276@sphic.org.cn>
 <CAPf2UMQ-ZRn=2+2T9PiaA0PUkt9631NNZnmO03W-yA=UOnGLAA@mail.gmail.com>,
 <CALzTN-S5tw1yziWMo31L-QhZyhe7sBaVcZCre=M75ZodjyG=sQ@mail.gmail.com>
Message-ID: <1469084775272.2605@sphic.org.cn>

Hi Matt and D?enan,

Thanks for your prompt replies. Would you please also add python wrapping supports for the three classes below? As a result, I can use B-spline registration under ITKv4 registration framework. Thanks in advance.

(1) itk::LBFGSBOptimizerv4
(2) itk::LBFGSOptimizerv4
(3) itk::TransformToDisplacementFieldFilter

Regards,

Zhuangming Shen
________________________________________
From: Matt McCormick <matt.mccormick at kitware.com>
Sent: Tuesday, July 19, 2016 10:45 AM
To: D?enan Zuki?
Cc: ???; insight-users at itk.org
Subject: Re: [ITK-users] Deformable registration question

Hi,

For 1) here is a patch that will add wrapping support for
itk::BSplineTransformInitializer:

  http://review.source.kitware.com/#/c/21341/

HTH,
Matt

On Mon, Jul 18, 2016 at 9:04 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Shen,
>
> 2) for multi-modal registration you need to use one variant of mutual
> information registration metric. All the other parts of the registration
> framework should be applicable.
>
> Regards,
> D?enan
>
> On Mon, Jul 18, 2016 at 5:00 AM, ??? <zhuangming.shen at sphic.org.cn> wrote:
>>
>> Hi all,
>>
>>
>> I have two questions.
>>
>> 1) Has itk::BSplineTransformInitializer been wrapped to python-supported
>> ITK?
>>
>> 2) Which deformable registration algorithms in ITK can deal with
>> multi-modal image registration such as CT-MR registration?
>>
>> Thanks.
>>
>>
>>
>> Regards,
>>
>>
>> Zhuangming Shen
>>
>>
>> _____________________________________
>> 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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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 grothausmann.roman at mh-hannover.de  Thu Jul 21 06:41:56 2016
From: grothausmann.roman at mh-hannover.de (Grothausmann, Roman Dr.)
Date: Thu, 21 Jul 2016 12:41:56 +0200
Subject: [ITK] [ITK-users] streaming TileImageFilter for arbitrary number of
	inputs
In-Reply-To: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
References: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
Message-ID: <e5200ab0-4548-093d-4f01-afa79099cf5a@mh-hannover.de>

Dear mailing list members,


Based on the examples for TileImageFilter I've created a working CLI to append 
an arbitrary number of inputs 
(https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx).
As there is an example that does not apply Update and DisconnectPipeline on the 
readers 
(https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2) 

I changed my code such that a reader instance is created for each input in a 
for-loop:
https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9

However, the update from the writer seems not to propagate to the readers 
whether streaming or not. Can the TileImageFilter not stream in such a case or 
are further modifications necessary?

Thanks for any help or hints
Roman


On 18/08/14 17:01, Michka Popoff wrote:
> Hi
>
> Going the way described in the CreateVolume example is the way to go.
>
> Why did you uncomment the DisconnectPipeline() call and Update() call in the for
> loop ? They need to stay there, else you will always use the last image.
> That?s why you see the same image, the single update call will be triggered at
> the end of the script and read only one image.
>
> You don?t need to call tileFilter->Update(), you can remove this line. The
> writer->Update() will take care of the pipeline update.
> As a bonus, you may wrap your writer->Update() call, to fetch errors at the end
> of the pipeline:
>
> try
> {
> writer->Update();
> }
> catch( itk::ExceptionObject & error )
> {
> std::cerr << "Error: " << error << std::endl;
> return EXIT_FAILURE;
> }
>
> I made a little Python prototype, the syntax is a little bit different than in
> C++ but it gives you the main idea.
>
> Michka
>

-- 
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
_____________________________________
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 c.spanakis83 at gmail.com  Thu Jul 21 08:25:25 2016
From: c.spanakis83 at gmail.com (Constantinus Spanakis)
Date: Thu, 21 Jul 2016 15:25:25 +0300
Subject: [ITK] Passing parameters in image transform
Message-ID: <CAOZihbcoiLHPqTGFBmbRQAn42qNME_vEywYv5b86u5460sK_RA@mail.gmail.com>

Hello. I try to do image registration between two images, called fixedImage
and movingImage using firstly rigid transform and then affine transform.

After I finish the rigid registration, I want to use the movingImage, after
it gets transformed due to rigid registration,  and use the NEW movingImage
as the movingimage input of the affine registration. Does the following
code do the trick?


rigidTransform->SetParameters(registration->GetLastTransformParameters());
resample->SetTransform(rigidTransform);
resample->SetInput(movingImageReader->GetOutput());

resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
resample->SetOutputOrigin(fixedImage->GetOrigin());
resample->SetOutputSpacing(fixedImage->GetSpacing());
resample->SetOutputDirection(fixedImage->GetDirection());

registration->SetMovingImage(resample->GetOutput());
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From blowekamp at mail.nih.gov  Thu Jul 21 09:41:20 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 21 Jul 2016 13:41:20 +0000
Subject: [ITK] [ITK-users] streaming TileImageFilter for arbitrary
 number of	inputs
In-Reply-To: <e5200ab0-4548-093d-4f01-afa79099cf5a@mh-hannover.de>
References: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
 <e5200ab0-4548-093d-4f01-afa79099cf5a@mh-hannover.de>
Message-ID: <C266AAD9-184A-47A3-B9E6-A099BA3804E0@mail.nih.gov>

Hello,

The TileImageFilter does not fully stream [1]. The filter also has some odd behavior, and other older implementation details. If you are going to work on a streaming pipelines it is best practice to examine the filters to determine how the Requested regions behave.

However, there is no reason that the TileImageFilter algorithm couldn?t support streaming. It is just a matter of code and a bunch of testing. A contribution for this issue would be welcomed! Also this filter is in need a refactoring and bring it up to several other best practices. There are several issue with the current implementation that would cause it not to work correctly with a streaming pipeline, and cause excessive execution.

You can also use the PipelieMoniotorImageFilter to record and print the pipeline interaction during Update [2]. This information helps with debugging and diagnosing problems, but if the pipeline is mis-behaving ( as the TileImageFilter may ), the information may not be correct.

I have tried similar streaming with the JoinSeriesImageFilter. However I ran into many problems with having hundreds of ImageIO being utilized at the same time. There were problems with having too many files open at the same time along with ImageIO libraries that couldn?t handle single threaded access to multiple files.

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136
[2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html

> On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr. <grothausmann.roman at mh-hannover.de> wrote:
> 
> Dear mailing list members,
> 
> 
> Based on the examples for TileImageFilter I've created a working CLI to append an arbitrary number of inputs (https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx).
> As there is an example that does not apply Update and DisconnectPipeline on the readers (https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2) 
> I changed my code such that a reader instance is created for each input in a for-loop:
> https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9
> 
> However, the update from the writer seems not to propagate to the readers whether streaming or not. Can the TileImageFilter not stream in such a case or are further modifications necessary?
> 
> Thanks for any help or hints
> Roman
> 
> 
> On 18/08/14 17:01, Michka Popoff wrote:
>> Hi
>> 
>> Going the way described in the CreateVolume example is the way to go.
>> 
>> Why did you uncomment the DisconnectPipeline() call and Update() call in the for
>> loop ? They need to stay there, else you will always use the last image.
>> That?s why you see the same image, the single update call will be triggered at
>> the end of the script and read only one image.
>> 
>> You don?t need to call tileFilter->Update(), you can remove this line. The
>> writer->Update() will take care of the pipeline update.
>> As a bonus, you may wrap your writer->Update() call, to fetch errors at the end
>> of the pipeline:
>> 
>> try
>> {
>> writer->Update();
>> }
>> catch( itk::ExceptionObject & error )
>> {
>> std::cerr << "Error: " << error << std::endl;
>> return EXIT_FAILURE;
>> }
>> 
>> I made a little Python prototype, the syntax is a little bit different than in
>> C++ but it gives you the main idea.
>> 
>> Michka
>> 
> 
> -- 
> 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
> _____________________________________
> 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

From dzenanz at gmail.com  Thu Jul 21 11:43:54 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 21 Jul 2016 11:43:54 -0400
Subject: [ITK] Passing parameters in image transform
In-Reply-To: <CAOZihbcoiLHPqTGFBmbRQAn42qNME_vEywYv5b86u5460sK_RA@mail.gmail.com>
References: <CAOZihbcoiLHPqTGFBmbRQAn42qNME_vEywYv5b86u5460sK_RA@mail.gmail.com>
Message-ID: <CAPf2UMSswKNkNOdT94CptQt74pH+a6ES-treUiYW6GBQtpt1oA@mail.gmail.com>

It looks like it should. Maybe you could have new instance of registration
class, to prevent loop dependency. Anyway, it is best to try :D

On Thu, Jul 21, 2016 at 8:25 AM, Constantinus Spanakis <
c.spanakis83 at gmail.com> wrote:

> Hello. I try to do image registration between two images, called
> fixedImage and movingImage using firstly rigid transform and then affine
> transform.
>
> After I finish the rigid registration, I want to use the movingImage,
> after it gets transformed due to rigid registration,  and use the NEW
> movingImage as the movingimage input of the affine registration. Does the
> following code do the trick?
>
>
> rigidTransform->SetParameters(registration->GetLastTransformParameters());
> resample->SetTransform(rigidTransform);
> resample->SetInput(movingImageReader->GetOutput());
>
> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
> resample->SetOutputOrigin(fixedImage->GetOrigin());
> resample->SetOutputSpacing(fixedImage->GetSpacing());
> resample->SetOutputDirection(fixedImage->GetDirection());
>
> registration->SetMovingImage(resample->GetOutput());
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From matt.mccormick at kitware.com  Thu Jul 21 11:49:17 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 21 Jul 2016 11:49:17 -0400
Subject: [ITK] Passing parameters in image transform
In-Reply-To: <CAPf2UMSswKNkNOdT94CptQt74pH+a6ES-treUiYW6GBQtpt1oA@mail.gmail.com>
References: <CAOZihbcoiLHPqTGFBmbRQAn42qNME_vEywYv5b86u5460sK_RA@mail.gmail.com>
 <CAPf2UMSswKNkNOdT94CptQt74pH+a6ES-treUiYW6GBQtpt1oA@mail.gmail.com>
Message-ID: <CALzTN-S1+2aFHjsWGaf8TZ0zc42QfvJhKiKUQQvSHynPeq8-mw@mail.gmail.com>

The itk::CompositeTransform:

  https://itk.org/Doxygen/html/classitk_1_1CompositeTransform.html

was designed for this use case. It can be used in this way in the
ITKv4 registration framework.

HTH,
Matt

On Thu, Jul 21, 2016 at 11:43 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> It looks like it should. Maybe you could have new instance of registration
> class, to prevent loop dependency. Anyway, it is best to try :D
>
> On Thu, Jul 21, 2016 at 8:25 AM, Constantinus Spanakis
> <c.spanakis83 at gmail.com> wrote:
>>
>> Hello. I try to do image registration between two images, called
>> fixedImage and movingImage using firstly rigid transform and then affine
>> transform.
>>
>> After I finish the rigid registration, I want to use the movingImage,
>> after it gets transformed due to rigid registration,  and use the NEW
>> movingImage as the movingimage input of the affine registration. Does the
>> following code do the trick?
>>
>>
>> rigidTransform->SetParameters(registration->GetLastTransformParameters());
>> resample->SetTransform(rigidTransform);
>> resample->SetInput(movingImageReader->GetOutput());
>>
>> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
>> resample->SetOutputOrigin(fixedImage->GetOrigin());
>> resample->SetOutputSpacing(fixedImage->GetSpacing());
>> resample->SetOutputDirection(fixedImage->GetDirection());
>>
>> registration->SetMovingImage(resample->GetOutput());
>>
>> _______________________________________________
>> 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 matt.mccormick at kitware.com  Thu Jul 21 13:15:04 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 21 Jul 2016 13:15:04 -0400
Subject: [ITK] [ITK-dev] VCL install issues
In-Reply-To: <F921FD41-9F4A-441D-A876-29CE7CD71E1C@mail.nih.gov>
References: <F921FD41-9F4A-441D-A876-29CE7CD71E1C@mail.nih.gov>
Message-ID: <CALzTN-QJeighBCPvv4kdJgK6mdCZ=jUx64rLjyo4gMb9ibwpqw@mail.gmail.com>

Hi Brad,

This patch should address those issues.

  http://review.source.kitware.com/#/c/21345/

HTH,
Matt

On Wed, Jul 20, 2016 at 4:25 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Hello,
>
> I can getting the following missing header error when using and installed
> ITK from master:
>
> [ 37%] Generating src/sitkComplexToPhaseImageFilter.cxx
> In file included from
> /tmp/SimpleITK/Code/Explicit/src/sitkExplicitITKImageRegion.cxx:19:
> In file included from
> /tmp/SimpleITK/Code/Explicit/include/sitkExplicitITKImageRegion.h:21:
> In file included from /usr/local/include/ITK-4.11/itkImageRegion.h:31:
> In file included from /usr/local/include/ITK-4.11/itkRegion.h:31:
> In file included from /usr/local/include/ITK-4.11/itkObject.h:31:
> In file included from /usr/local/include/ITK-4.11/itkLightObject.h:25:
> In file included from /usr/local/include/ITK-4.11/itkAtomicInt.h:38:
> In file included from /usr/local/include/ITK-4.11/itkConceptChecking.h:32:
> In file included from /usr/local/include/ITK-4.11/itkNumericTraits.h:51:
> In file included from /usr/local/include/ITK-4.11/vcl_limits.h:5:
> /usr/local/include/ITK-4.11/vcl_compiler.h:121:10: fatal error:
> 'vcl_config_manual.h' file not found
> #include <vcl_config_manual.h>
>          ^
>
> Here is the DockerFile I was working with:
>
> == DockerFile ==
>
> FROM ubuntu:14.04
>
> RUN \
>   apt-get update && \
>   apt-get -y upgrade && \
>   apt-get install -y build-essential clang git curl swig python-dev
>
> RUN \
>     curl -O https://cmake.org/files/v3.6/cmake-3.6.0-Linux-x86_64.sh && \
>     umask 022 && echo "y\n" | bash cmake-3.6.0-Linux-x86_64.sh
> --prefix=/usr/local  --exclude-subdir
>
> WORKDIR /tmp/
>
> RUN \
>     git clone https://itk.org/ITK.git && \
>     cd ITK && \
>     git checkout master && \
>     mkdir bld
>
> RUN \
>     cd ITK/bld && \
>     CC=clang CXX=clang++ cmake \
>        -DBUILD_SHARED_LIBS:BOOL=ON \
>        -DUSE_COMPILER_HIDDEN_VISIBILITY:BOOL=OFF \
>        -DBUILD_TESTING:BOOL=OFF \
>        -DModule_ITKReview:BOOL=ON \
>        .. && \
>     make -j $(nproc) install && \
>     ldconfig
>
>
>
> RUN \
>     git clone https://itk.org/SimpleITK.git && \
>     cd SimpleITK && \
>     git checkout master && \
>     mkdir bld
>
> RUN \
>     cd SimpleITK/bld && \
>     CC=clang CXX=clang++ cmake \
>       -DBUILD_SHARED_LIBS:BOOL=ON \
>       -DWRAP_LUA:BOOL=OFF \
>       -DWRAP_PYTHON:BOOL=ON \
>       -DUSE_SYSTEM_SWIG:BOOL=ON \
>       -DUSE_SYSTEM_ITK:BOOL=ON \
>       -DBUILD_TESTING:BOOL=OFF \
>       ../SuperBuild && \
>     make -j $(nproc)
>
> == end ==
>
> Thanks,
> Brad
>
>
> _______________________________________________
> 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:
http://public.kitware.com/mailman/listinfo/insight-developers

From c.spanakis83 at gmail.com  Fri Jul 22 05:33:07 2016
From: c.spanakis83 at gmail.com (Constantinus Spanakis)
Date: Fri, 22 Jul 2016 12:33:07 +0300
Subject: [ITK] Passing parameters in image transform
In-Reply-To: <CALzTN-S1+2aFHjsWGaf8TZ0zc42QfvJhKiKUQQvSHynPeq8-mw@mail.gmail.com>
References: <CAOZihbcoiLHPqTGFBmbRQAn42qNME_vEywYv5b86u5460sK_RA@mail.gmail.com>
 <CAPf2UMSswKNkNOdT94CptQt74pH+a6ES-treUiYW6GBQtpt1oA@mail.gmail.com>
 <CALzTN-S1+2aFHjsWGaf8TZ0zc42QfvJhKiKUQQvSHynPeq8-mw@mail.gmail.com>
Message-ID: <CAOZihbd8=ZjknGyO_BbnVG0kYVadmRkp+O-ELbwh5G_0qHZbeQ@mail.gmail.com>

I have a new question. I have a typedef
itk::ImageRegistrationMethod<FixedImageType, MovingImageType >
 RegistrationType; Then I create a pointer RegistrationType::Pointer
registration=RegistrationType::New();
In the registration pointer i set the optimization method, the metric and
the fixedImage and the movingImage, the transform method and a few other
parameters. After I finish the rigid registration, then I set to the very
same registration pointer the affine transform. Will the registration
pointer continue automatically the registration (by executing the
registration ->Update()) starting from the result of the previous
registration or must I manually reset the movingImage parameter?

Thank you in advance

On Thu, Jul 21, 2016 at 6:49 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> The itk::CompositeTransform:
>
>   https://itk.org/Doxygen/html/classitk_1_1CompositeTransform.html
>
> was designed for this use case. It can be used in this way in the
> ITKv4 registration framework.
>
> HTH,
> Matt
>
> On Thu, Jul 21, 2016 at 11:43 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> > It looks like it should. Maybe you could have new instance of
> registration
> > class, to prevent loop dependency. Anyway, it is best to try :D
> >
> > On Thu, Jul 21, 2016 at 8:25 AM, Constantinus Spanakis
> > <c.spanakis83 at gmail.com> wrote:
> >>
> >> Hello. I try to do image registration between two images, called
> >> fixedImage and movingImage using firstly rigid transform and then affine
> >> transform.
> >>
> >> After I finish the rigid registration, I want to use the movingImage,
> >> after it gets transformed due to rigid registration,  and use the NEW
> >> movingImage as the movingimage input of the affine registration. Does
> the
> >> following code do the trick?
> >>
> >>
> >>
> rigidTransform->SetParameters(registration->GetLastTransformParameters());
> >> resample->SetTransform(rigidTransform);
> >> resample->SetInput(movingImageReader->GetOutput());
> >>
> >> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
> >> resample->SetOutputOrigin(fixedImage->GetOrigin());
> >> resample->SetOutputSpacing(fixedImage->GetSpacing());
> >> resample->SetOutputDirection(fixedImage->GetDirection());
> >>
> >> registration->SetMovingImage(resample->GetOutput());
> >>
> >> _______________________________________________
> >> 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 grothausmann.roman at mh-hannover.de  Fri Jul 22 06:00:26 2016
From: grothausmann.roman at mh-hannover.de (Grothausmann, Roman Dr.)
Date: Fri, 22 Jul 2016 12:00:26 +0200
Subject: [ITK] [ITK-users] streaming TileImageFilter for arbitrary
 number of inputs
In-Reply-To: <C266AAD9-184A-47A3-B9E6-A099BA3804E0@mail.nih.gov>
References: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
 <e5200ab0-4548-093d-4f01-afa79099cf5a@mh-hannover.de>
 <C266AAD9-184A-47A3-B9E6-A099BA3804E0@mail.nih.gov>
Message-ID: <dc7cf545-5ca9-669b-53fb-6ad8fe2222f8@mh-hannover.de>

Many thanks Brad for Your detailed reply. I understand now the problems 
concerning streaming TileImageFilter.
However I still wonder why my non-streaming version also does not work any more 
after moving the creation of reader instances into the for-loop:
https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50

Is this construct inappropriate for the TileImageFilter?
Why does it work for:
https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2

On 21/07/16 15:41, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
> Hello,
>
> The TileImageFilter does not fully stream [1]. The filter also has some odd
> behavior, and other older implementation details. If you are going to work on
> a streaming pipelines it is best practice to examine the filters to determine
> how the Requested regions behave.
>
> However, there is no reason that the TileImageFilter algorithm couldn?t
> support streaming. It is just a matter of code and a bunch of testing. A
> contribution for this issue would be welcomed! Also this filter is in need a
> refactoring and bring it up to several other best practices. There are
> several issue with the current implementation that would cause it not to work
> correctly with a streaming pipeline, and cause excessive execution.
>
> You can also use the PipelieMoniotorImageFilter to record and print the
> pipeline interaction during Update [2]. This information helps with debugging
> and diagnosing problems, but if the pipeline is mis-behaving ( as the
> TileImageFilter may ), the information may not be correct.
>
> I have tried similar streaming with the JoinSeriesImageFilter. However I ran
> into many problems with having hundreds of ImageIO being utilized at the same
> time. There were problems with having too many files open at the same time
> along with ImageIO libraries that couldn?t handle single threaded access to
> multiple files.
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136
>
>
[2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html
>
>> On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr.
>> <grothausmann.roman at mh-hannover.de> wrote:
>>
>> Dear mailing list members,
>>
>>
>> Based on the examples for TileImageFilter I've created a working CLI to
>> append an arbitrary number of inputs
>> (https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx).
>>
>>
As there is an example that does not apply Update and DisconnectPipeline on the 
readers 
(https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2) 

>> I changed my code such that a reader instance is created for each input in
>> a for-loop:
>> https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9
>>
>>
>>
However, the update from the writer seems not to propagate to the readers 
whether streaming or not. Can the TileImageFilter not stream in such a case or 
are further modifications necessary?
>>
>> Thanks for any help or hints Roman
>>
>>
>> On 18/08/14 17:01, Michka Popoff wrote:
>>> Hi
>>>
>>> Going the way described in the CreateVolume example is the way to go.
>>>
>>> Why did you uncomment the DisconnectPipeline() call and Update() call in
>>> the for loop ? They need to stay there, else you will always use the last
>>> image. That?s why you see the same image, the single update call will be
>>> triggered at the end of the script and read only one image.
>>>
>>> You don?t need to call tileFilter->Update(), you can remove this line.
>>> The writer->Update() will take care of the pipeline update. As a bonus,
>>> you may wrap your writer->Update() call, to fetch errors at the end of
>>> the pipeline:
>>>
>>> try { writer->Update(); } catch( itk::ExceptionObject & error ) {
>>> std::cerr << "Error: " << error << std::endl; return EXIT_FAILURE; }
>>>
>>> I made a little Python prototype, the syntax is a little bit different
>>> than in C++ but it gives you the main idea.
>>>
>>> Michka
>>>
>>
>> -- 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 _____________________________________ 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
>

-- 
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
_____________________________________
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

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From blowekamp at mail.nih.gov  Fri Jul 22 08:49:03 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 22 Jul 2016 12:49:03 +0000
Subject: [ITK] [ITK-users] streaming TileImageFilter for arbitrary
 number of inputs
In-Reply-To: <dc7cf545-5ca9-669b-53fb-6ad8fe2222f8@mh-hannover.de>
References: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
 <e5200ab0-4548-093d-4f01-afa79099cf5a@mh-hannover.de>
 <C266AAD9-184A-47A3-B9E6-A099BA3804E0@mail.nih.gov>
 <dc7cf545-5ca9-669b-53fb-6ad8fe2222f8@mh-hannover.de>
Message-ID: <EF0AFB4E-01FE-416F-99E8-5C6F7626A9C0@mail.nih.gov>

Hi,

Who is holding the pointer to the newly created ImageFileReader outside of the loop? For that type of operation I?ll frequently just stash smart pointers into a std::vector or list.

Regarding the example, look at the scope of the smart pointers with respect to the execution of the pipeline.

HTH,
Brad


> On Jul 22, 2016, at 6:00 AM, Grothausmann, Roman Dr. <grothausmann.roman at mh-hannover.de> wrote:
> 
> Many thanks Brad for Your detailed reply. I understand now the problems concerning streaming TileImageFilter.
> However I still wonder why my non-streaming version also does not work any more after moving the creation of reader instances into the for-loop:
> https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50
> 
> Is this construct inappropriate for the TileImageFilter?
> Why does it work for:
> https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2
> 
> On 21/07/16 15:41, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>> Hello,
>> 
>> The TileImageFilter does not fully stream [1]. The filter also has some odd
>> behavior, and other older implementation details. If you are going to work on
>> a streaming pipelines it is best practice to examine the filters to determine
>> how the Requested regions behave.
>> 
>> However, there is no reason that the TileImageFilter algorithm couldn?t
>> support streaming. It is just a matter of code and a bunch of testing. A
>> contribution for this issue would be welcomed! Also this filter is in need a
>> refactoring and bring it up to several other best practices. There are
>> several issue with the current implementation that would cause it not to work
>> correctly with a streaming pipeline, and cause excessive execution.
>> 
>> You can also use the PipelieMoniotorImageFilter to record and print the
>> pipeline interaction during Update [2]. This information helps with debugging
>> and diagnosing problems, but if the pipeline is mis-behaving ( as the
>> TileImageFilter may ), the information may not be correct.
>> 
>> I have tried similar streaming with the JoinSeriesImageFilter. However I ran
>> into many problems with having hundreds of ImageIO being utilized at the same
>> time. There were problems with having too many files open at the same time
>> along with ImageIO libraries that couldn?t handle single threaded access to
>> multiple files.
>> 
>> [1]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136
>> 
>> 
> [2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html
>> 
>>> On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr.
>>> <grothausmann.roman at mh-hannover.de> wrote:
>>> 
>>> Dear mailing list members,
>>> 
>>> 
>>> Based on the examples for TileImageFilter I've created a working CLI to
>>> append an arbitrary number of inputs
>>> (https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx).
>>> 
>>> 
> As there is an example that does not apply Update and DisconnectPipeline on the readers (https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2) 
>>> I changed my code such that a reader instance is created for each input in
>>> a for-loop:
>>> https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9
>>> 
>>> 
>>> 
> However, the update from the writer seems not to propagate to the readers whether streaming or not. Can the TileImageFilter not stream in such a case or are further modifications necessary?
>>> 
>>> Thanks for any help or hints Roman
>>> 
>>> 
>>> On 18/08/14 17:01, Michka Popoff wrote:
>>>> Hi
>>>> 
>>>> Going the way described in the CreateVolume example is the way to go.
>>>> 
>>>> Why did you uncomment the DisconnectPipeline() call and Update() call in
>>>> the for loop ? They need to stay there, else you will always use the last
>>>> image. That?s why you see the same image, the single update call will be
>>>> triggered at the end of the script and read only one image.
>>>> 
>>>> You don?t need to call tileFilter->Update(), you can remove this line.
>>>> The writer->Update() will take care of the pipeline update. As a bonus,
>>>> you may wrap your writer->Update() call, to fetch errors at the end of
>>>> the pipeline:
>>>> 
>>>> try { writer->Update(); } catch( itk::ExceptionObject & error ) {
>>>> std::cerr << "Error: " << error << std::endl; return EXIT_FAILURE; }
>>>> 
>>>> I made a little Python prototype, the syntax is a little bit different
>>>> than in C++ but it gives you the main idea.
>>>> 
>>>> Michka
>>>> 
>>> 
>>> -- 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 _____________________________________ 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
>> 
> 
> -- 
> 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

_____________________________________
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  Fri Jul 22 09:00:42 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 22 Jul 2016 09:00:42 -0400
Subject: [ITK] [ITK-dev] c:\.git\hooks
Message-ID: <CAPf2UMQM0-CbYewp8syEba1Jm8qXANNH3pK1F0YK5By+Rch63g@mail.gmail.com>

Hi everybody,

occasionally, a folder "C:\.git\hooks" appears on my computer. Since I use
TortoiseGit, this is very annoying because right-click context menu of
entire C: drive thinks it is under version control. I filed a bug
<https://gitlab.com/tortoisegit/tortoisegit/issues/2801> report, but
support people think that git hooks in some of my projects (almost all
instances of ITK, VTK and Slicer builds) are causing this behavior. Did
anyone else encounter this or something similar?

Regards,
D?enan
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From brad.king at kitware.com  Fri Jul 22 09:14:25 2016
From: brad.king at kitware.com (Brad King)
Date: Fri, 22 Jul 2016 09:14:25 -0400
Subject: [ITK] [ITK-dev] c:\.git\hooks
In-Reply-To: <CAPf2UMQM0-CbYewp8syEba1Jm8qXANNH3pK1F0YK5By+Rch63g@mail.gmail.com>
References: <CAPf2UMQM0-CbYewp8syEba1Jm8qXANNH3pK1F0YK5By+Rch63g@mail.gmail.com>
Message-ID: <e2da9f41-8aa4-01fd-a02d-08a3b3c40214@kitware.com>

On 07/22/2016 09:00 AM, D?enan Zuki? wrote:
> occasionally, a folder "C:\.git\hooks" appears on my computer.
[snip]
> but support people think that git hooks in some of my projects
> (almost all instances of ITK, VTK and Slicer builds) are causing
> this behavior. Did anyone else encounter this or something similar?

Dig through our Utilities/SetupForDevelopment.sh scripts (or equivalent
in each project) and the scripts it invokes.  See if running any of
them causes this to happen.  Otherwise check whether running CMake on
each project causes it in case there is any attempt to install hooks
that way.

You'll likely have to diligently check for the folder after each step
of working with each project until you figure out which one causes it.

-Brad

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

Kitware offers ITK Training Courses, for more information visit:
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From blowekamp at mail.nih.gov  Fri Jul 22 09:31:01 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 22 Jul 2016 13:31:01 +0000
Subject: [ITK] [ITK-dev] Use Vcvarsall.bat in CTest script
Message-ID: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov>

Hello,

I am finally wanting to start using ninja with some of my windows builds. It seems the critical thing is to invoke the appropriate Vcvarsall.bat file before the cmake configuration. 

Currently I am just using a ctest script  with ctest_run_script to drive my dashboard nightly dashboard scripts. How can I invoke the bat file and then get a ctest command in a sub-process?

Currently I have something like this:

foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
         message( "Starting to execute script: ${NEXT_SCRIPT}..." )
    ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
endforeach()

And I want something like the following so that the NEXT_SCRIPT with have the correct environment:

foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
     message( "Starting to execute script: ${NEXT_SCRIPT}...? )
     NEW PROCESS
	RUN Vcvarsall.bat 
        ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
endforeach()



My googling skills are not finding a solution that is as simple as I would expect it to be.

Thank you for the help with this simple question!
Brad


_______________________________________________
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From matt.mccormick at kitware.com  Fri Jul 22 10:38:26 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 22 Jul 2016 10:38:26 -0400
Subject: [ITK] Passing parameters in image transform
In-Reply-To: <CAOZihbd8=ZjknGyO_BbnVG0kYVadmRkp+O-ELbwh5G_0qHZbeQ@mail.gmail.com>
References: <CAOZihbcoiLHPqTGFBmbRQAn42qNME_vEywYv5b86u5460sK_RA@mail.gmail.com>
 <CAPf2UMSswKNkNOdT94CptQt74pH+a6ES-treUiYW6GBQtpt1oA@mail.gmail.com>
 <CALzTN-S1+2aFHjsWGaf8TZ0zc42QfvJhKiKUQQvSHynPeq8-mw@mail.gmail.com>
 <CAOZihbd8=ZjknGyO_BbnVG0kYVadmRkp+O-ELbwh5G_0qHZbeQ@mail.gmail.com>
Message-ID: <CALzTN-QjjrTAJZY0P74yfMq2oWPv81CPAkKWuJoDZNQX1EgZUA@mail.gmail.com>

Hi,

The parameters of the registration method can be adjusted as desired. See

  ITK/Examples/RegistrationITKv4

for a few examples.

HTH,
Matt

On Fri, Jul 22, 2016 at 5:33 AM, Constantinus Spanakis
<c.spanakis83 at gmail.com> wrote:
> I have a new question. I have a typedef
> itk::ImageRegistrationMethod<FixedImageType, MovingImageType >
> RegistrationType; Then I create a pointer RegistrationType::Pointer
> registration=RegistrationType::New();
> In the registration pointer i set the optimization method, the metric and
> the fixedImage and the movingImage, the transform method and a few other
> parameters. After I finish the rigid registration, then I set to the very
> same registration pointer the affine transform. Will the registration
> pointer continue automatically the registration (by executing the
> registration ->Update()) starting from the result of the previous
> registration or must I manually reset the movingImage parameter?
>
> Thank you in advance
>
> On Thu, Jul 21, 2016 at 6:49 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> The itk::CompositeTransform:
>>
>>   https://itk.org/Doxygen/html/classitk_1_1CompositeTransform.html
>>
>> was designed for this use case. It can be used in this way in the
>> ITKv4 registration framework.
>>
>> HTH,
>> Matt
>>
>> On Thu, Jul 21, 2016 at 11:43 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>> > It looks like it should. Maybe you could have new instance of
>> > registration
>> > class, to prevent loop dependency. Anyway, it is best to try :D
>> >
>> > On Thu, Jul 21, 2016 at 8:25 AM, Constantinus Spanakis
>> > <c.spanakis83 at gmail.com> wrote:
>> >>
>> >> Hello. I try to do image registration between two images, called
>> >> fixedImage and movingImage using firstly rigid transform and then
>> >> affine
>> >> transform.
>> >>
>> >> After I finish the rigid registration, I want to use the movingImage,
>> >> after it gets transformed due to rigid registration,  and use the NEW
>> >> movingImage as the movingimage input of the affine registration. Does
>> >> the
>> >> following code do the trick?
>> >>
>> >>
>> >>
>> >> rigidTransform->SetParameters(registration->GetLastTransformParameters());
>> >> resample->SetTransform(rigidTransform);
>> >> resample->SetInput(movingImageReader->GetOutput());
>> >>
>> >> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
>> >> resample->SetOutputOrigin(fixedImage->GetOrigin());
>> >> resample->SetOutputSpacing(fixedImage->GetSpacing());
>> >> resample->SetOutputDirection(fixedImage->GetDirection());
>> >>
>> >> registration->SetMovingImage(resample->GetOutput());
>> >>
>> >> _______________________________________________
>> >> 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 amirhossein.jaberzadeh at gmail.com  Fri Jul 22 11:27:51 2016
From: amirhossein.jaberzadeh at gmail.com (Amir Jaberzadeh)
Date: Fri, 22 Jul 2016 11:27:51 -0400
Subject: [ITK] [ITK-users] Insight journal dataset upload error
Message-ID: <CANWh7-CWHKsddVWuwFzk_hoR2DEM9FhN5E+UNdyGYsqWHdki8A@mail.gmail.com>

Dear all,

I am submitting an insight journal paper, while uploading my example
dataset, it is not possible to upload a file larger than 10 MB. I would
like to upload a 89 MB zip file and attaching them one by one was the only
solution I could find so far.

I appreciate your help in advance,
Amir
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From tossin at gmail.com  Fri Jul 22 12:42:14 2016
From: tossin at gmail.com (Evan Kao)
Date: Fri, 22 Jul 2016 09:42:14 -0700
Subject: [ITK] [ITK-users] Target Machine type error when trying to
 build 64-bit ITK using VS2015
In-Reply-To: <CAPf2UMQ3_wK8RFDX_FRrQVNQ1Z7+=o4WxXdYZdz=Ciq7XjwrUw@mail.gmail.com>
References: <CAEhu9hDVDp4XY4uB9za_Vj14m8KJFfox4d61G-j1nnziP7R0KA@mail.gmail.com>
 <CAPf2UMQ3_wK8RFDX_FRrQVNQ1Z7+=o4WxXdYZdz=Ciq7XjwrUw@mail.gmail.com>
Message-ID: <CAEhu9hBLEcMRYesUjzBBurb+dSiWJn8sRWKE38un5TQ+DozDvg@mail.gmail.com>

Thanks D?enan, that was really helpful.  I was able to build it
successfully.

- Evan

On Wed, Jul 20, 2016 at 5:00 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Evan,
>
> you need to select "Visual Studio 14 2015 Win64" as the generator:
> [image: Inline image 3]
>
> The result of this should be that you only have x64 platform in Visual
> Studio:
> [image: Inline image 2]
>
> Regards,
> D?enan
>
> On Wed, Jul 20, 2016 at 7:09 PM, Evan Kao <tossin at gmail.com> wrote:
>
>> Hello all,
>>
>> This may be more of a Visual Studio issue than an ITK issue, but I was
>> wondering if anyone else found a way around this.  I'm trying to build ITK
>> 4.10.0 on a Windows 7 64-bit machine with Python (2.7 64-bit) wrapping
>> using Visual Studio 2015.  I should add I'm not familiar with either CMake,
>> ITK, or Visual Studio so I could be missing something obvious.
>>
>> I keep getting the following error for multiple *.obj files:
>> x64\Release\*.obj : fatal error LNK1112: module machine type 'x64'
>> conflicts with target machine type 'X86'
>>
>> I noticed that CMake generates vxproj files for only Win32 by default.
>> Then the files are modified by Visual Studio when switching the platform to
>> x64 and selecting "Clean Solution", which adds the following lines, among
>> others:
>>     <ProjectConfiguration Include="Release|x64">
>>       <Configuration>Release</Configuration>
>>       <Platform>x64</Platform>
>>
>> However, many individual sub-projects are still not updated to account
>> for x64 configurations.  I took a look at the Advanced CMAKE variables
>> in the CMake GUI, but had no idea what to modify (everything seems to
>> target Win32).
>>
>> Is there a way to configure CMake to generate x64 files?  If not, does
>> anyone know how to correctly configure ITK on x64 platforms in VS2015?
>>
>> Thanks,
>> Evan Kao
>>
>> _____________________________________
>> 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 jchris.fillionr at kitware.com  Fri Jul 22 14:17:37 2016
From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin)
Date: Fri, 22 Jul 2016 14:17:37 -0400
Subject: [ITK] [ITK-dev] Use Vcvarsall.bat in CTest script
In-Reply-To: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov>
References: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov>
Message-ID: <CANLz8R7JH=7zLNWGrv9_JXpGYGD2rF+iNecvnNYjJW4On1s0_g@mail.gmail.com>

Hi Brad,

If you create a .bat file like the following, it should work as expected:

call "C:\Program Files (x86)\Microsoft Visual Studio
9.0\VC\bin\vcvarsx86_amd64.bat"

call "C:\path\to\ctest.exe -S C:\path\to\script"

Hth
Jc

On Fri, Jul 22, 2016 at 9:31 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> I am finally wanting to start using ninja with some of my windows builds.
> It seems the critical thing is to invoke the appropriate Vcvarsall.bat file
> before the cmake configuration.
>
> Currently I am just using a ctest script  with ctest_run_script to drive
> my dashboard nightly dashboard scripts. How can I invoke the bat file and
> then get a ctest command in a sub-process?
>
> Currently I have something like this:
>
> foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
>          message( "Starting to execute script: ${NEXT_SCRIPT}..." )
>     ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
> endforeach()
>
> And I want something like the following so that the NEXT_SCRIPT with have
> the correct environment:
>
> foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
>      message( "Starting to execute script: ${NEXT_SCRIPT}...? )
>      NEW PROCESS
>         RUN Vcvarsall.bat
>         ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
> endforeach()
>
>
>
> My googling skills are not finding a solution that is as simple as I would
> expect it to be.
>
> Thank you for the help with this simple question!
> Brad
>
>
> _______________________________________________
> 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 blowekamp at mail.nih.gov  Fri Jul 22 15:07:18 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 22 Jul 2016 19:07:18 +0000
Subject: [ITK] [ITK-dev] Use Vcvarsall.bat in CTest script
In-Reply-To: <CANLz8R7JH=7zLNWGrv9_JXpGYGD2rF+iNecvnNYjJW4On1s0_g@mail.gmail.com>
References: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov>
 <CANLz8R7JH=7zLNWGrv9_JXpGYGD2rF+iNecvnNYjJW4On1s0_g@mail.gmail.com>
Message-ID: <31FA8F28-9C6F-47C2-91CC-A257ABA14B4A@mail.nih.gov>

Generating that bat file on the fly would not be too bad.

I am imagining adding something like the following line to the beginning of the nightly ctest scripts:

# BAT:  "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\vcvarsx86_amd64.bat"

Which tells my script to generate your suggested bat file.


Thanks JC!



On Jul 22, 2016, at 2:17 PM, Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com<mailto:jchris.fillionr at kitware.com>> wrote:

Hi Brad,

If you create a .bat file like the following, it should work as expected:

call "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\vcvarsx86_amd64.bat"

call "C:\path\to\ctest.exe -S C:\path\to\script"

Hth
Jc

On Fri, Jul 22, 2016 at 9:31 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
Hello,

I am finally wanting to start using ninja with some of my windows builds. It seems the critical thing is to invoke the appropriate Vcvarsall.bat file before the cmake configuration.

Currently I am just using a ctest script  with ctest_run_script to drive my dashboard nightly dashboard scripts. How can I invoke the bat file and then get a ctest command in a sub-process?

Currently I have something like this:

foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
         message( "Starting to execute script: ${NEXT_SCRIPT}..." )
    ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
endforeach()

And I want something like the following so that the NEXT_SCRIPT with have the correct environment:

foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
     message( "Starting to execute script: ${NEXT_SCRIPT}...? )
     NEW PROCESS
        RUN Vcvarsall.bat
        ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
endforeach()



My googling skills are not finding a solution that is as simple as I would expect it to be.

Thank you for the help with this simple question!
Brad


_______________________________________________
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From jchris.fillionr at kitware.com  Fri Jul 22 16:17:43 2016
From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin)
Date: Fri, 22 Jul 2016 16:17:43 -0400
Subject: [ITK] [ITK-dev] Use Vcvarsall.bat in CTest script
In-Reply-To: <31FA8F28-9C6F-47C2-91CC-A257ABA14B4A@mail.nih.gov>
References: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov>
 <CANLz8R7JH=7zLNWGrv9_JXpGYGD2rF+iNecvnNYjJW4On1s0_g@mail.gmail.com>
 <31FA8F28-9C6F-47C2-91CC-A257ABA14B4A@mail.nih.gov>
Message-ID: <CANLz8R5LtFK_5757hcBMfBGdP52Orf+qgBjjLByiOdKeQ4Wcug@mail.gmail.com>

Or you could also have a .bat file that would take two params:
* path to vcvars batch file
* command invoking ctest

You could then invoke cmd.exe using execute_process and give the bat file +
arguments

Jc


On Fri, Jul 22, 2016 at 3:07 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Generating that bat file on the fly would not be too bad.
>
> I am imagining adding something like the following line to the beginning
> of the nightly ctest scripts:
>
> # BAT:  "C:\Program Files (x86)\Microsoft Visual Studio
> 9.0\VC\bin\vcvarsx86_amd64.bat"
>
> Which tells my script to generate your suggested bat file.
>
>
> Thanks JC!
>
>
>
> On Jul 22, 2016, at 2:17 PM, Jean-Christophe Fillion-Robin <
> jchris.fillionr at kitware.com> wrote:
>
> Hi Brad,
>
> If you create a .bat file like the following, it should work as expected:
>
> call "C:\Program Files (x86)\Microsoft Visual Studio
> 9.0\VC\bin\vcvarsx86_amd64.bat"
>
> call "C:\path\to\ctest.exe -S C:\path\to\script"
>
> Hth
> Jc
>
> On Fri, Jul 22, 2016 at 9:31 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov> wrote:
>
>> Hello,
>>
>> I am finally wanting to start using ninja with some of my windows builds.
>> It seems the critical thing is to invoke the appropriate Vcvarsall.bat file
>> before the cmake configuration.
>>
>> Currently I am just using a ctest script  with ctest_run_script to drive
>> my dashboard nightly dashboard scripts. How can I invoke the bat file and
>> then get a ctest command in a sub-process?
>>
>> Currently I have something like this:
>>
>> foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
>>          message( "Starting to execute script: ${NEXT_SCRIPT}..." )
>>     ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
>> endforeach()
>>
>> And I want something like the following so that the NEXT_SCRIPT with have
>> the correct environment:
>>
>> foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS )
>>      message( "Starting to execute script: ${NEXT_SCRIPT}...? )
>>      NEW PROCESS
>>         RUN Vcvarsall.bat
>>         ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} )
>> endforeach()
>>
>>
>>
>> My googling skills are not finding a solution that is as simple as I
>> would expect it to be.
>>
>> Thank you for the help with this simple question!
>> Brad
>>
>>
>> _______________________________________________
>> 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
>>
>
>
>
> --
> +1 919 869 8849
>
>
>


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From aharr8 at uwo.ca  Sun Jul 24 08:26:13 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Sun, 24 Jul 2016 08:26:13 -0400
Subject: [ITK] [ITK-users] Fwd: MeanSquaresImageToImageMetricv4 with
 unsigned char PixelType results in error C2440
In-Reply-To: <CAJ0LxQKR_4jandBaCeN1cqoEyh711yCC++h3TXE26d6uOVbcUw@mail.gmail.com>
References: <CAJ0LxQKR_4jandBaCeN1cqoEyh711yCC++h3TXE26d6uOVbcUw@mail.gmail.com>
Message-ID: <CAJ0LxQ+57NjNc7Wijxnb8C6uVrWhAxOvfWBZfc3r2T6HSCi+yw@mail.gmail.com>

Hello,
I am attempting to build the example in section 3.6.4 of the 2nd volume
Insight Toolkit user guide to read unsigned char data rather than float.  I
have narrowed the error I?m getting down to the
MeanSquaresImageToImageMetricv4, and the error I?m getting is:

error C2440: ?initializing?: cannot convert from
?itk::Concept::Detail::UniqueType_bool<false>? to
?itk::Concept::Detail::UniqueType_bool<true>?

I am using Visual Studio 2013 and ITK 4.10.0, any ideas on how to fix this
would be helpful. I read the Microsoft Compiler Error documentation but
didn?t really understand it.

--

AH


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From matt.mccormick at kitware.com  Sun Jul 24 21:05:36 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 24 Jul 2016 21:05:36 -0400
Subject: [ITK] [ITK-users] Fwd: MeanSquaresImageToImageMetricv4 with
 unsigned char PixelType results in error C2440
In-Reply-To: <CAJ0LxQ+57NjNc7Wijxnb8C6uVrWhAxOvfWBZfc3r2T6HSCi+yw@mail.gmail.com>
References: <CAJ0LxQKR_4jandBaCeN1cqoEyh711yCC++h3TXE26d6uOVbcUw@mail.gmail.com>
 <CAJ0LxQ+57NjNc7Wijxnb8C6uVrWhAxOvfWBZfc3r2T6HSCi+yw@mail.gmail.com>
Message-ID: <CALzTN-R5hXbfEoT0FjYyuXXpVMFX+s-MboPCPG6hjpQSPt51fQ@mail.gmail.com>

Hi Andrew,

This itk::ConceptCheck [1] says that the pixel values must be float to
be used in itk::MeanSquaresImageToImageMetricv4 -- use an
itk::CastImageFilter to change the pixel type.

HTH,
Matt

[1] https://itk.org/Wiki/ITK/Proposals:Concept_Checking

On Sun, Jul 24, 2016 at 8:26 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
> Hello,
> I am attempting to build the example in section 3.6.4 of the 2nd volume
> Insight Toolkit user guide to read unsigned char data rather than float.  I
> have narrowed the error I?m getting down to the
> MeanSquaresImageToImageMetricv4, and the error I?m getting is:
>
> error C2440: ?initializing?: cannot convert from
> ?itk::Concept::Detail::UniqueType_bool<false>? to
> ?itk::Concept::Detail::UniqueType_bool<true>?
>
> I am using Visual Studio 2013 and ITK 4.10.0, any ideas on how to fix this
> would be helpful. I read the Microsoft Compiler Error documentation but
> didn?t really understand it.
>
> --
>
> AH
>
>
> -----------------------------------------------------------------------------------------------
>
> This email and any attachments thereto may contain private, confidential,
> and privileged materials for the sole use of the intended recipient. Any
> reviewing, copying, or distribution of this email (or any attachments
> thereto) by other than the intended recipient is strictly prohibited. If you
> are not the intended recipient, please contact the sender immediately and
> permanently destroy this email and any attachments thereto.
>
>
>
> _____________________________________
> 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 grothausmann.roman at mh-hannover.de  Mon Jul 25 08:07:30 2016
From: grothausmann.roman at mh-hannover.de (Grothausmann, Roman Dr.)
Date: Mon, 25 Jul 2016 14:07:30 +0200
Subject: [ITK] [ITK-users] streaming TileImageFilter for arbitrary
 number of inputs
In-Reply-To: <EF0AFB4E-01FE-416F-99E8-5C6F7626A9C0@mail.nih.gov>
References: <E41A3C04-73C1-40C8-9435-CCCD7E08D927@gmail.com>
 <e5200ab0-4548-093d-4f01-afa79099cf5a@mh-hannover.de>
 <C266AAD9-184A-47A3-B9E6-A099BA3804E0@mail.nih.gov>
 <dc7cf545-5ca9-669b-53fb-6ad8fe2222f8@mh-hannover.de>
 <EF0AFB4E-01FE-416F-99E8-5C6F7626A9C0@mail.nih.gov>
Message-ID: <eae31d35-1aaf-15af-5284-5472a91464a0@mh-hannover.de>

Many thanks Brad for the hint of the smart pointer scope and storing it in 
std::vector, at least the non-SDI version now works as expected.

On 22/07/16 14:49, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
> Hi,
>
> Who is holding the pointer to the newly created ImageFileReader outside of
> the loop? For that type of operation I?ll frequently just stash smart
> pointers into a std::vector or list.
>
> Regarding the example, look at the scope of the smart pointers with respect
> to the execution of the pipeline.
>
> HTH, Brad
>
>
>> On Jul 22, 2016, at 6:00 AM, Grothausmann, Roman Dr.
>> <grothausmann.roman at mh-hannover.de> wrote:
>>
>> Many thanks Brad for Your detailed reply. I understand now the problems
>> concerning streaming TileImageFilter. However I still wonder why my
>> non-streaming version also does not work any more after moving the creation
>> of reader instances into the for-loop:
>> https://github.com/romangrothausmann/ITK-CLIs/blob/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9/tile.cxx#L46-L50
>>
>>
>>
Is this construct inappropriate for the TileImageFilter?
>> Why does it work for:
>> https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2
>>
>>
>>
On 21/07/16 15:41, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>>> Hello,
>>>
>>> The TileImageFilter does not fully stream [1]. The filter also has some
>>> odd behavior, and other older implementation details. If you are going to
>>> work on a streaming pipelines it is best practice to examine the filters
>>> to determine how the Requested regions behave.
>>>
>>> However, there is no reason that the TileImageFilter algorithm couldn?t
>>> support streaming. It is just a matter of code and a bunch of testing. A
>>> contribution for this issue would be welcomed! Also this filter is in
>>> need a refactoring and bring it up to several other best practices. There
>>> are several issue with the current implementation that would cause it not
>>> to work correctly with a streaming pipeline, and cause excessive
>>> execution.
>>>
>>> You can also use the PipelieMoniotorImageFilter to record and print the
>>> pipeline interaction during Update [2]. This information helps with
>>> debugging and diagnosing problems, but if the pipeline is mis-behaving (
>>> as the TileImageFilter may ), the information may not be correct.
>>>
>>> I have tried similar streaming with the JoinSeriesImageFilter. However I
>>> ran into many problems with having hundreds of ImageIO being utilized at
>>> the same time. There were problems with having too many files open at the
>>> same time along with ImageIO libraries that couldn?t handle single
>>> threaded access to multiple files.
>>>
>>> [1]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageGrid/include/itkTileImageFilter.hxx#L125-L136
>>>
>>>
>>
>>>
[2] https://itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html
>>>
>>>> On Jul 21, 2016, at 6:41 AM, Grothausmann, Roman Dr.
>>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>
>>>> Dear mailing list members,
>>>>
>>>>
>>>> Based on the examples for TileImageFilter I've created a working CLI
>>>> to append an arbitrary number of inputs
>>>> (https://github.com/romangrothausmann/ITK-CLIs/blob/4fdf5778022598dcf83fb38e6002df72bd67bef3/tile.cxx).
>>>>
>>>>
>>
>>>>
As there is an example that does not apply Update and DisconnectPipeline on the 
readers 
(https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2AppendTwo3DVolumes_2Code_8cxx-example.html#_a2) 

>>>> I changed my code such that a reader instance is created for each input
>>>> in a for-loop:
>>>> https://github.com/romangrothausmann/ITK-CLIs/commit/ebfc0aea37d28cbbf2bb22c3f56be52453cebde9
>>>>
>>>>
>>>>
>>
>>>>
However, the update from the writer seems not to propagate to the readers 
whether streaming or not. Can the TileImageFilter not stream in such a case or 
are further modifications necessary?
>>>>
>>>> Thanks for any help or hints Roman
>>>>
>>>>
>>>> On 18/08/14 17:01, Michka Popoff wrote:
>>>>> Hi
>>>>>
>>>>> Going the way described in the CreateVolume example is the way to
>>>>> go.
>>>>>
>>>>> Why did you uncomment the DisconnectPipeline() call and Update() call
>>>>> in the for loop ? They need to stay there, else you will always use
>>>>> the last image. That?s why you see the same image, the single update
>>>>> call will be triggered at the end of the script and read only one
>>>>> image.
>>>>>
>>>>> You don?t need to call tileFilter->Update(), you can remove this
>>>>> line. The writer->Update() will take care of the pipeline update. As
>>>>> a bonus, you may wrap your writer->Update() call, to fetch errors at
>>>>> the end of the pipeline:
>>>>>
>>>>> try { writer->Update(); } catch( itk::ExceptionObject & error ) {
>>>>> std::cerr << "Error: " << error << std::endl; return EXIT_FAILURE; }
>>>>>
>>>>> I made a little Python prototype, the syntax is a little bit
>>>>> different than in C++ but it gives you the main idea.
>>>>>
>>>>> Michka
>>>>>
>>>>
>>>> -- 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 _____________________________________ 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
>>>
>>
>> -- 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
>

-- 
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 dzenanz at gmail.com  Mon Jul 25 11:31:53 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 25 Jul 2016 11:31:53 -0400
Subject: [ITK] [ITK-dev] c:\.git\hooks
In-Reply-To: <e2da9f41-8aa4-01fd-a02d-08a3b3c40214@kitware.com>
References: <CAPf2UMQM0-CbYewp8syEba1Jm8qXANNH3pK1F0YK5By+Rch63g@mail.gmail.com>
 <e2da9f41-8aa4-01fd-a02d-08a3b3c40214@kitware.com>
Message-ID: <CAPf2UMRazm0Vok4taepo3ZyRgJqjvczgAWfzSnW8+pawbeCYTA@mail.gmail.com>

I ran all the SetupForDevelopment scripts in ITK git folder. The C:/.git
folder was not created. Thanks for suggestion though.

This problem is not annoying enough because it is easy to solve by deleting
C:/.git folder. I will not spend more time randomly examining everything
git-related. If somebody else comes forward with the same problem then we
might be able to determine what we have in common and narrow down the
problem to perhaps make it reasonably tractable.

So if anyone runs into this, don't be shy!

On Fri, Jul 22, 2016 at 9:14 AM, Brad King <brad.king at kitware.com> wrote:

> On 07/22/2016 09:00 AM, D?enan Zuki? wrote:
> > occasionally, a folder "C:\.git\hooks" appears on my computer.
> [snip]
> > but support people think that git hooks in some of my projects
> > (almost all instances of ITK, VTK and Slicer builds) are causing
> > this behavior. Did anyone else encounter this or something similar?
>
> Dig through our Utilities/SetupForDevelopment.sh scripts (or equivalent
> in each project) and the scripts it invokes.  See if running any of
> them causes this to happen.  Otherwise check whether running CMake on
> each project causes it in case there is any attempt to install hooks
> that way.
>
> You'll likely have to diligently check for the folder after each step
> of working with each project until you figure out which one causes it.
>
> -Brad
>
>
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From dzenanz at gmail.com  Tue Jul 26 09:15:06 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 26 Jul 2016 09:15:06 -0400
Subject: [ITK] [ITK-users] Image spacing
In-Reply-To: <CAEiw7u6iH9gEMDmoA9nbCnbGg-EJ_fMW_g=u8JNzig4W+Y_gmg@mail.gmail.com>
References: <CAPf2UMR6u75FQjF_wjcrucasktW4=60KcG5=e1gmDou9E2OTFw@mail.gmail.com>
 <CAEiw7u6iH9gEMDmoA9nbCnbGg-EJ_fMW_g=u8JNzig4W+Y_gmg@mail.gmail.com>
Message-ID: <CAPf2UMRDRH8cOm0kGruGQzmsYLELvejs+2fq4njqW=MGpFUQEw@mail.gmail.com>

Hi Meikolin,

sp is a ImageType::SpacingType variable which is assigned on the line
before.

If you couldn't deduce that, you should really try going through ITK
software guide <https://itk.org/ItkSoftwareGuide.pdf>. Spacing is described
in chapter about data representation
<https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html>,
section "Defining Origin and Spacing".

Regards,
D?enan

On Tue, Jul 26, 2016 at 4:21 AM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> what is sp [0] and sp [1] sir??
>
> On Mon, Jul 25, 2016 at 8:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Meikolin,
>>
>> you have image spacing, which gives you the size of one pixel/voxel:
>> sp=image->GetSpacing();
>> pixelSize=sp[0]*sp[1]; //square millimeters
>>
>> Regards,
>> D?enan
>>
>> On Mon, Jul 25, 2016 at 3:10 AM, meikolin saimara <kolin9105 at gmail.com>
>> wrote:
>>
>>> maybe one pixel =   .......Square millimeters???
>>>
>>>
>>> On Mon, Jul 25, 2016 at 1:45 PM, meikolin saimara <kolin9105 at gmail.com>
>>> wrote:
>>>
>>>> sir I have question ??
>>>> after we got number of pixel and large of the pixel...
>>>> I want to know how we can get the large of the pixel I mean the formula
>>>> for it not the source code
>>>> maybe can you give me some journal for it.
>>>>
>>>>
>
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From aharr8 at uwo.ca  Tue Jul 26 13:43:28 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Tue, 26 Jul 2016 13:43:28 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
Message-ID: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>

Hello,
I am attempting to use the CastImageFilter to convert between unsigned char
and float image types, and am getting a System.AccessViolationException at
runtime.  I have seen reference to this being caused by referring to a
pointer that is out of scope, but in this case both the image and the cast
filter are delcared in the same method, so I?m not sure how it can be going
out of scope.  I can include the header and definition files if that would
be helpful.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
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From brad at lowekamp.net  Tue Jul 26 19:09:52 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Tue, 26 Jul 2016 19:09:52 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
Message-ID: <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>

Hello,

The most common mistake here would be forgetting to call Allocate on your image. Beyond that sharing your code would be helpful. 

Brad

> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
> 
> Hello,
> I am attempting to use the CastImageFilter to convert between unsigned char and float image types, and am getting a System.AccessViolationException at runtime.  I have seen reference to this being caused by referring to a pointer that is out of scope, but in this case both the image and the cast filter are delcared in the same method, so I?m not sure how it can be going out of scope.  I can include the header and definition files if that would be helpful.
> --
> 
> AH
> 
> 
> 
> -----------------------------------------------------------------------------------------------
> 
> This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.
> 
> _____________________________________
> 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 blowekamp at mail.nih.gov  Tue Jul 26 23:28:36 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 27 Jul 2016 03:28:36 +0000
Subject: [ITK] SimpleITK 0.10 Release Candidate 2
Message-ID: <DA2915A530468E47B3C4845298E6EB03833FB317@msgb06.nih.gov>


Hi!

We are pleased to announce the SimpleITK 0.10 Release Candidate 2 is now available! The release is expected to follow shortly.

There have been many improvements to better support wrapping for R. SimpleITK for R needs to be compiled from the source. 

The Python Java and CSharp binaries are available for download from Source Forge:

https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10rc2/


The latest versions of ?pip? is recommended to install the downloaded binary wheel for Python. Python eggs are no longer being distributed.

You are encouraged to checkout SimpleITK?s master branch in the git repository for testing building from the source code.

Also we have packages for the Anaconda Python distributions in the SimpleITK group and under the ?dev" label. These packages can be installed with the following command:

$ conda install -c https://conda.anaconda.org/simpleitk/label/dev SimpleITK

Since the 0.10rc1, there have been a number of configuration and fixes to support gcc 6.1. Additionally, new examples and updated documentation. Please see the git long for further information

Key Improvements since 0.9.1:
* The R language bindings have received extensive improvements and bug fixes.
* Added Image::SetMetaData method
* Added LandmarkBasedTransformInitializer
* Added MultiLableSTAPLEImageFilter
* Default sitk::Show support for Fiji over ImageJ
* Moved third-party packages Lua, gtest, virtualenv from source code to Superbuild projects
* Added Forbid Download option
* Enabled each language wrapping to be an independent project dependent on SimpleITK C++ interface and libraries.
* Lua languages bindings now compile as a loadable module
* Many CMake build improvements to default configurations
* CMake version 3.3 is now required

Enjoy!
Brad

From dzenanz at gmail.com  Wed Jul 27 14:37:34 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 27 Jul 2016 14:37:34 -0400
Subject: [ITK] [ITK-users] Image spacing
In-Reply-To: <CAEiw7u6STEsK9JDQXZeyXYc8OFbtdPxaknWpySwKYb7CLSNFqg@mail.gmail.com>
References: <CAPf2UMR6u75FQjF_wjcrucasktW4=60KcG5=e1gmDou9E2OTFw@mail.gmail.com>
 <CAEiw7u6iH9gEMDmoA9nbCnbGg-EJ_fMW_g=u8JNzig4W+Y_gmg@mail.gmail.com>
 <CAPf2UMRDRH8cOm0kGruGQzmsYLELvejs+2fq4njqW=MGpFUQEw@mail.gmail.com>
 <CAEiw7u6STEsK9JDQXZeyXYc8OFbtdPxaknWpySwKYb7CLSNFqg@mail.gmail.com>
Message-ID: <CAPf2UMTT0Dt0PMBaBhggTkeF1VuYLDHaLRfL1YBj=5ZM6Z7TYg@mail.gmail.com>

That depends on you image. Try this
<https://itk.org/ITKExamples/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.html>
example with your image.

Regards

On Wed, Jul 27, 2016 at 1:27 PM, meikolin saimara <kolin9105 at gmail.com>
wrote:

> what is the value of sp[0 ] and sp[1] sir??
>
> On Tue, Jul 26, 2016 at 8:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Meikolin,
>>
>> sp is a ImageType::SpacingType variable which is assigned on the line
>> before.
>>
>> If you couldn't deduce that, you should really try going through ITK
>> software guide <https://itk.org/ItkSoftwareGuide.pdf>. Spacing is
>> described in chapter about data representation
>> <https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html>,
>> section "Defining Origin and Spacing".
>>
>> Regards,
>> D?enan
>>
>> On Tue, Jul 26, 2016 at 4:21 AM, meikolin saimara <kolin9105 at gmail.com>
>> wrote:
>>
>>> what is sp [0] and sp [1] sir??
>>>
>>> On Mon, Jul 25, 2016 at 8:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>>> Hi Meikolin,
>>>>
>>>> you have image spacing, which gives you the size of one pixel/voxel:
>>>> sp=image->GetSpacing();
>>>> pixelSize=sp[0]*sp[1]; //square millimeters
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Mon, Jul 25, 2016 at 3:10 AM, meikolin saimara <kolin9105 at gmail.com>
>>>> wrote:
>>>>
>>>>> maybe one pixel =   .......Square millimeters???
>>>>>
>>>>>
>>>>> On Mon, Jul 25, 2016 at 1:45 PM, meikolin saimara <kolin9105 at gmail.com
>>>>> > wrote:
>>>>>
>>>>>> sir I have question ??
>>>>>> after we got number of pixel and large of the pixel...
>>>>>> I want to know how we can get the large of the pixel I mean the
>>>>>> formula for it not the source code
>>>>>> maybe can you give me some journal for it.
>>>>>>
>>>>>>
>>>
>>
>
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From aharr8 at uwo.ca  Wed Jul 27 15:54:39 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 27 Jul 2016 15:54:39 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
Message-ID: <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>

Thanks for getting back to me, after conferring with a colleague I tried
using the output of the cast filter directly in the subsequent pipeline
rather than writing it to a new image object of the filter's output type. I
got the same error doing that, and also got the same error just running
Update() on the cast filter, which leads me to believe I'm doing something
wrong in setting up the cast filter.  I'm attaching my code for the class
I'm writing, hope it's something simple I'm doing wrong. Currently it's
throwing the exception at line 85 when the registration transform
initializer is activated.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net> wrote:

> Hello,
>
> The most common mistake here would be forgetting to call Allocate on your
> image. Beyond that sharing your code would be helpful.
>
> Brad
>
> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
> Hello,
> I am attempting to use the CastImageFilter to convert between unsigned
> char and float image types, and am getting a
> System.AccessViolationException at runtime.  I have seen reference to this
> being caused by referring to a pointer that is out of scope, but in this
> case both the image and the cast filter are delcared in the same method, so
> I?m not sure how it can be going out of scope.  I can include the header
> and definition files if that would be helpful.
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> _____________________________________
> 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  Wed Jul 27 17:16:45 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 27 Jul 2016 17:16:45 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
Message-ID: <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>

Hi Andrew,

I think that line 62 of .cpp should be:
castFilter->Update();
I don't see the pipeline updated elsewhere.

Regards,
D?enan

On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Thanks for getting back to me, after conferring with a colleague I tried
> using the output of the cast filter directly in the subsequent pipeline
> rather than writing it to a new image object of the filter's output type. I
> got the same error doing that, and also got the same error just running
> Update() on the cast filter, which leads me to believe I'm doing something
> wrong in setting up the cast filter.  I'm attaching my code for the class
> I'm writing, hope it's something simple I'm doing wrong. Currently it's
> throwing the exception at line 85 when the registration transform
> initializer is activated.
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net>
> wrote:
>
>> Hello,
>>
>> The most common mistake here would be forgetting to call Allocate on your
>> image. Beyond that sharing your code would be helpful.
>>
>> Brad
>>
>> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>
>> Hello,
>> I am attempting to use the CastImageFilter to convert between unsigned
>> char and float image types, and am getting a
>> System.AccessViolationException at runtime.  I have seen reference to this
>> being caused by referring to a pointer that is out of scope, but in this
>> case both the image and the cast filter are delcared in the same method, so
>> I?m not sure how it can be going out of scope.  I can include the header
>> and definition files if that would be helpful.
>>
>> --
>>
>> AH
>>
>>
>>
>> -----------------------------------------------------------------------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> _____________________________________
>> 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 aharr8 at uwo.ca  Wed Jul 27 20:26:08 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 27 Jul 2016 20:26:08 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
 <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
Message-ID: <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>

Thanks D?enan, as I said in my previous email running Update() on the
castFilter pointer returns the same error.  I did put in a try/catch block
to update it though.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Wed, Jul 27, 2016 at 5:16 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Andrew,
>
> I think that line 62 of .cpp should be:
> castFilter->Update();
> I don't see the pipeline updated elsewhere.
>
> Regards,
> D?enan
>
> On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
>> Thanks for getting back to me, after conferring with a colleague I tried
>> using the output of the cast filter directly in the subsequent pipeline
>> rather than writing it to a new image object of the filter's output type. I
>> got the same error doing that, and also got the same error just running
>> Update() on the cast filter, which leads me to believe I'm doing something
>> wrong in setting up the cast filter.  I'm attaching my code for the class
>> I'm writing, hope it's something simple I'm doing wrong. Currently it's
>> throwing the exception at line 85 when the registration transform
>> initializer is activated.
>>
>> --
>>
>> AH
>>
>>
>>
>> -----------------------------------------------------------------------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net>
>> wrote:
>>
>>> Hello,
>>>
>>> The most common mistake here would be forgetting to call Allocate on
>>> your image. Beyond that sharing your code would be helpful.
>>>
>>> Brad
>>>
>>> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>
>>> Hello,
>>> I am attempting to use the CastImageFilter to convert between unsigned
>>> char and float image types, and am getting a
>>> System.AccessViolationException at runtime.  I have seen reference to this
>>> being caused by referring to a pointer that is out of scope, but in this
>>> case both the image and the cast filter are delcared in the same method, so
>>> I?m not sure how it can be going out of scope.  I can include the header
>>> and definition files if that would be helpful.
>>>
>>> --
>>>
>>> AH
>>>
>>>
>>>
>>> -----------------------------------------------------------------------------------------------
>>>
>>> *This email and any attachments thereto may contain private,
>>> confidential, and privileged materials for the sole use of the intended
>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>> attachments thereto) by other than the intended recipient is strictly
>>> prohibited. If you are not the intended recipient, please contact the
>>> sender immediately and permanently destroy this email and any attachments
>>> thereto.*
>>>
>>> _____________________________________
>>> 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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>>
>
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From hebennink at gmail.com  Thu Jul 28 04:37:35 2016
From: hebennink at gmail.com (Edwin Bennink)
Date: Thu, 28 Jul 2016 10:37:35 +0200
Subject: [ITK] [ITK-users] In-place extraction of N-1 dimensional images
	from N	dimensional images
Message-ID: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>

Hello,

I am working on an ITK/VTK viewer for visualizing 3D+time image data. The
data is represented by 4D images in ITK (x,y,z,t). I would like to be able
to access the 3D data in VTK without copying it, since that would slow down
scrolling through time in large datasets. I noticed that, although in-place
extraction should be possible, the ExtractImageFilter 'says no' to in-place
extraction when the input and output dimensions differ. Does anyone know a
way to achieve my goal using existing ITK functions? For example, if there
would be some way of reducing the dimension of 'flat' images, i.e. 3D
(Nx,Ny,1) to 2D (Nx, Ny), then I could still use the ExtractImageFilter.

Best,
Edwin
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From noreply at insightsoftwareconsortium.org  Thu Jul 28 05:13:18 2016
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Thu, 28 Jul 2016 05:13:18 -0400 (EDT)
Subject: [ITK] [ITK-users] New Submission: A new implementation
	of	itk::ImageToImageFilter for efficient parallelization
	of	image processing algorithms using Intel Threading Building Blocks
Message-ID: <20160728091318.B625A3D6205E@insight-journal.org>

Hello,

A new submission has been added to the Insight Journal.

Title: A new implementation of itk::ImageToImageFilter for efficient parallelization of image processing algorithms using Intel Threading Building Blocks
Authors: Jaberzadeh A., Scherrer B., Warfield S.
Abstract: Modern medical imaging makes use of high performance computing to accelerate image acquisition, image reconstruction, image visualization and image analysis. Software libraries that provide implementations of key medical imaging algorithms need to efficiently exploit modern CPU architectures. In particular, workstations with small numbers of cores are being replaced by very high core count architectures, and by many integrated core architectures, which offer acceleration by vectorization and multi-threading.

The Insight Toolkit (ITK) is the premier open source implementation of medical imaging algorithms, with a generic design for image processing filters that allows for many developers to rapidly incorporate these algorithms in to new applications.  While ITK filters benefit from a generic, platform independent multithreading capability,  the current implementation is difficult to exploit to achieve very high performance. Specifically, ITK relies on a static decomposition of the image into subsets of equal size which can be highly inefficient. Threads that terminate early due to uneven work throughout  the image finish early and do not contribute further to the processing of more complex regions, leading to idle computational resources and longer execution times. Performance is also difficult to coordinate across multiple algorithms, as the ITK filter assumes each filter operates independently but the global implementation has an impact across filters.  

In this work, we propose a novel, simple to use, high performance multithreading capability for ITK that accelerates the itk::ImageToImageFilter. We utilise a workpile data decomposition strategy, and leave the task of optimal job scheduling on CPU cores to the library called Threading Building Blocks (TBB). We demonstrate the efficacy of multi-threading with TBB in comparison to the itk::Multithreader class, through three simple example image analysis algorithms. 

Our implementation provides a new multi-threaded itk::ImageToImageFilter that can be conveniently reused to provide simple and efficient multi-threaded code across applications and algorithm libraries. Our new implementation is distributed as open-source software to the  community and is straightforward to adopt.

Download and review this publication at: http://hdl.handle.net/10380/3560

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ .
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From dzenanz at gmail.com  Thu Jul 28 08:29:46 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 28 Jul 2016 08:29:46 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
 <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
 <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>
Message-ID: <CAPf2UMR3cWPOOCehyqgVLcoGcbit8OPXJJKMvR3irH70OEcrcQ@mail.gmail.com>

Have you tried calling Update on the import filter? That might be the
problem. Cast filter is simple and non-special, I doubt it is the problem.

On Wed, Jul 27, 2016 at 8:26 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Thanks D?enan, as I said in my previous email running Update() on the
> castFilter pointer returns the same error.  I did put in a try/catch block
> to update it though.
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Wed, Jul 27, 2016 at 5:16 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Andrew,
>>
>> I think that line 62 of .cpp should be:
>> castFilter->Update();
>> I don't see the pipeline updated elsewhere.
>>
>> Regards,
>> D?enan
>>
>> On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>
>>> Thanks for getting back to me, after conferring with a colleague I tried
>>> using the output of the cast filter directly in the subsequent pipeline
>>> rather than writing it to a new image object of the filter's output type. I
>>> got the same error doing that, and also got the same error just running
>>> Update() on the cast filter, which leads me to believe I'm doing something
>>> wrong in setting up the cast filter.  I'm attaching my code for the class
>>> I'm writing, hope it's something simple I'm doing wrong. Currently it's
>>> throwing the exception at line 85 when the registration transform
>>> initializer is activated.
>>>
>>> --
>>>
>>> AH
>>>
>>>
>>>
>>> -----------------------------------------------------------------------------------------------
>>>
>>> *This email and any attachments thereto may contain private,
>>> confidential, and privileged materials for the sole use of the intended
>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>> attachments thereto) by other than the intended recipient is strictly
>>> prohibited. If you are not the intended recipient, please contact the
>>> sender immediately and permanently destroy this email and any attachments
>>> thereto.*
>>>
>>> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> The most common mistake here would be forgetting to call Allocate on
>>>> your image. Beyond that sharing your code would be helpful.
>>>>
>>>> Brad
>>>>
>>>> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>
>>>> Hello,
>>>> I am attempting to use the CastImageFilter to convert between unsigned
>>>> char and float image types, and am getting a
>>>> System.AccessViolationException at runtime.  I have seen reference to this
>>>> being caused by referring to a pointer that is out of scope, but in this
>>>> case both the image and the cast filter are delcared in the same method, so
>>>> I?m not sure how it can be going out of scope.  I can include the header
>>>> and definition files if that would be helpful.
>>>>
>>>> --
>>>>
>>>> AH
>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------------------------------------
>>>>
>>>> *This email and any attachments thereto may contain private,
>>>> confidential, and privileged materials for the sole use of the intended
>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>> attachments thereto) by other than the intended recipient is strictly
>>>> prohibited. If you are not the intended recipient, please contact the
>>>> sender immediately and permanently destroy this email and any attachments
>>>> thereto.*
>>>>
>>>> _____________________________________
>>>> 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  Thu Jul 28 08:40:51 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 28 Jul 2016 08:40:51 -0400
Subject: [ITK] [ITK-users] In-place extraction of N-1 dimensional images
 from N dimensional images
In-Reply-To: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>
References: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>
Message-ID: <CAPf2UMSz32cPe-F4WmVp4mzvBX3U0nnu1-GFXbPb9BZZtdjHEw@mail.gmail.com>

Hi Edwin,

you should be able to achieve your goal using import image filter
<http://www.vtk.org/doc/nightly/html/classvtkImageImport.html#details>. ITK
has import image filter too
<https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html>, so you
can decide in which library to do dimensional reduction.

Regards,
D?enan

On Thu, Jul 28, 2016 at 4:37 AM, Edwin Bennink <hebennink at gmail.com> wrote:

> Hello,
>
> I am working on an ITK/VTK viewer for visualizing 3D+time image data. The
> data is represented by 4D images in ITK (x,y,z,t). I would like to be able
> to access the 3D data in VTK without copying it, since that would slow down
> scrolling through time in large datasets. I noticed that, although in-place
> extraction should be possible, the ExtractImageFilter 'says no' to in-place
> extraction when the input and output dimensions differ. Does anyone know a
> way to achieve my goal using existing ITK functions? For example, if there
> would be some way of reducing the dimension of 'flat' images, i.e. 3D
> (Nx,Ny,1) to 2D (Nx, Ny), then I could still use the ExtractImageFilter.
>
> Best,
> Edwin
>
> _____________________________________
> 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 brad at lowekamp.net  Thu Jul 28 09:01:57 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Thu, 28 Jul 2016 09:01:57 -0400
Subject: [ITK] [ITK-users]
	itk::CastImageFilter	causes	AccessViolationException
In-Reply-To: <CAPf2UMR3cWPOOCehyqgVLcoGcbit8OPXJJKMvR3irH70OEcrcQ@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
 <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
 <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>
 <CAPf2UMR3cWPOOCehyqgVLcoGcbit8OPXJJKMvR3irH70OEcrcQ@mail.gmail.com>
Message-ID: <673C89C9-8EAE-47FE-B38A-8762FDE10734@lowekamp.net>

Hello,

I noticed you are using type int for you imageSiize. How big is your image? You may be overflowing when computing the number of pixels.

I don?t think you have provided a stack trace of when the error occurs. That would be helpful too.

Brad

> On Jul 28, 2016, at 8:29 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> 
> Have you tried calling Update on the import filter? That might be the problem. Cast filter is simple and non-special, I doubt it is the problem.
> 
> On Wed, Jul 27, 2016 at 8:26 PM, Andrew Harris <aharr8 at uwo.ca <mailto:aharr8 at uwo.ca>> wrote:
> Thanks D?enan, as I said in my previous email running Update() on the castFilter pointer returns the same error.  I did put in a try/catch block to update it though. 
> 
> --
> 
> AH
> 
> 
> 
> -----------------------------------------------------------------------------------------------
> 
> This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.
> 
> 
> On Wed, Jul 27, 2016 at 5:16 PM, D?enan Zuki? <dzenanz at gmail.com <mailto:dzenanz at gmail.com>> wrote:
> Hi Andrew,
> 
> I think that line 62 of .cpp should be:
> castFilter->Update();
> I don't see the pipeline updated elsewhere.
> 
> Regards,
> D?enan
> 
> On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca <mailto:aharr8 at uwo.ca>> wrote:
> Thanks for getting back to me, after conferring with a colleague I tried using the output of the cast filter directly in the subsequent pipeline rather than writing it to a new image object of the filter's output type. I got the same error doing that, and also got the same error just running Update() on the cast filter, which leads me to believe I'm doing something wrong in setting up the cast filter.  I'm attaching my code for the class I'm writing, hope it's something simple I'm doing wrong. Currently it's throwing the exception at line 85 when the registration transform initializer is activated.
> 
> --
> 
> AH
> 
> 
> 
> -----------------------------------------------------------------------------------------------
> 
> This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.
> 
> 
> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net <mailto:brad at lowekamp.net>> wrote:
> Hello,
> 
> The most common mistake here would be forgetting to call Allocate on your image. Beyond that sharing your code would be helpful. 
> 
> Brad
> 
> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca <mailto:aharr8 at uwo.ca>> wrote:
> 
>> Hello,
>> I am attempting to use the CastImageFilter to convert between unsigned char and float image types, and am getting a System.AccessViolationException at runtime.  I have seen reference to this being caused by referring to a pointer that is out of scope, but in this case both the image and the cast filter are delcared in the same method, so I?m not sure how it can be going out of scope.  I can include the header and definition files if that would be helpful.
>> --
>> 
>> AH
>> 
>> 
>> 
>> -----------------------------------------------------------------------------------------------
>> 
>> This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.
>> 
>> _____________________________________
>> 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:
> http://public.kitware.com/mailman/listinfo/insight-users <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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Kitware offers ITK Training Courses, for more information visit:
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From aharr8 at uwo.ca  Thu Jul 28 10:24:33 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Thu, 28 Jul 2016 10:24:33 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <673C89C9-8EAE-47FE-B38A-8762FDE10734@lowekamp.net>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
 <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
 <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>
 <CAPf2UMR3cWPOOCehyqgVLcoGcbit8OPXJJKMvR3irH70OEcrcQ@mail.gmail.com>
 <673C89C9-8EAE-47FE-B38A-8762FDE10734@lowekamp.net>
Message-ID: <CAJ0LxQLG23=OHLoWAKiqPuAjq_nky=NkUyLU0pnE2ne5sv_MxA@mail.gmail.com>

Thanks all for getting back to me.  I put in a call to update the
importFilter and upon debugging found that the image variable is getting
the correct size settings and number of elements (or at least it is the
same as the importFilter finds).  I tried casting the imageSize to unsigned
int and got the same numbers throughout, and still had the exception at
castImage->Update().  Here is the stack trace at the exception:

> BING_Andrew.exe!std::_Transform<unsigned char const *,float
*,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
_First, unsigned char* _Last, float* _Dest,
itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 950 + 0x9
bytes C++
  BING_Andrew.exe!std::_Transform1<unsigned char const *,float
*,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
_First, unsigned char* _Last, float* _Dest,
itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func,
std::random_access_iterator_tag __unnamed004,
std::random_access_iterator_tag __unnamed005) Line 988 + 0x2b bytes C++
  BING_Andrew.exe!std::_Transform1<unsigned char const *,float
*,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
_First, unsigned char* _Last, float* _Dest,
itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func,
std::integral_constant<bool,0> __unnamed004) Line 1012 + 0x6d bytes C++
  BING_Andrew.exe!std::transform<unsigned char const *,float
*,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
_First, unsigned char* _Last, float* _Dest,
itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 1026 +
0x48 bytes C++
  BING_Andrew.exe!itk::ImageAlgorithm::CopyHelper<unsigned
char,float>(unsigned char* first, unsigned char* last, float* result) Line
213 + 0x14 bytes C++
  BING_Andrew.exe!itk::ImageAlgorithm::DispatchedCopy<itk::Image<unsigned
char,3>,itk::Image<float,3> >(itk::Image<unsigned char,3>* inImage,
itk::Image<float,3>* outImage, itk::ImageRegion<3>& inRegion,
itk::ImageRegion<3>& outRegion, std::integral_constant<bool,1>
__unnamed004) Line 136 + 0x12 bytes C++
  BING_Andrew.exe!itk::ImageAlgorithm::Copy<unsigned
char,float,3>(itk::Image<unsigned char,3>* inImage, itk::Image<float,3>*
outImage, itk::ImageRegion<3>& inRegion, itk::ImageRegion<3>& outRegion)
Line 113 C++
  BING_Andrew.exe!itk::CastImageFilter<itk::Image<unsigned
char,3>,itk::Image<float,3> >::ThreadedGenerateData(itk::ImageRegion<3>&
outputRegionForThread, unsigned int threadId) Line 73 + 0x13 bytes C++
  [External Code]
  BING_Andrew.exe!itk::ImageSource<itk::Image<float,3>
>::ThreaderCallback(void* arg) Line 316 C++
  BING_Andrew.exe!itk::MultiThreader::SingleMethodProxy(void * arg)  Line
437 + 0xe bytes C++
  msvcr120d.dll!03573651()
  [Frames below may be incorrect and/or missing, no symbols loaded for
msvcr120d.dll]
  msvcr120d.dll!03573861()
  kernel32.dll!74c738f4()
  ntdll.dll!776d5de3()
  ntdll.dll!776d5dae()

I'm attaching this as a txt file also because the formatting looks a little
weird in my email client, it might be easier to read as plain text.  One
other thing I forgot to mention, the window generated by the exception has
the following text as well:
Additional information: Attempted to read or write protected memory. This
is often an indication that other memory is corrupt.

Thanks again for the help.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Thu, Jul 28, 2016 at 9:01 AM, Bradley Lowekamp <brad at lowekamp.net> wrote:

> Hello,
>
> I noticed you are using type int for you imageSiize. How big is your
> image? You may be overflowing when computing the number of pixels.
>
> I don?t think you have provided a stack trace of when the error occurs.
> That would be helpful too.
>
> Brad
>
> On Jul 28, 2016, at 8:29 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
> Have you tried calling Update on the import filter? That might be the
> problem. Cast filter is simple and non-special, I doubt it is the problem.
>
> On Wed, Jul 27, 2016 at 8:26 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
>> Thanks D?enan, as I said in my previous email running Update() on the
>> castFilter pointer returns the same error.  I did put in a try/catch block
>> to update it though.
>>
>> --
>>
>> AH
>>
>>
>>
>> -----------------------------------------------------------------------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> On Wed, Jul 27, 2016 at 5:16 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>>> Hi Andrew,
>>>
>>> I think that line 62 of .cpp should be:
>>> castFilter->Update();
>>> I don't see the pipeline updated elsewhere.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>
>>>> Thanks for getting back to me, after conferring with a colleague I
>>>> tried using the output of the cast filter directly in the subsequent
>>>> pipeline rather than writing it to a new image object of the filter's
>>>> output type. I got the same error doing that, and also got the same error
>>>> just running Update() on the cast filter, which leads me to believe I'm
>>>> doing something wrong in setting up the cast filter.  I'm attaching my code
>>>> for the class I'm writing, hope it's something simple I'm doing wrong.
>>>> Currently it's throwing the exception at line 85 when the registration
>>>> transform initializer is activated.
>>>>
>>>> --
>>>>
>>>> AH
>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------------------------------------
>>>>
>>>> *This email and any attachments thereto may contain private,
>>>> confidential, and privileged materials for the sole use of the intended
>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>> attachments thereto) by other than the intended recipient is strictly
>>>> prohibited. If you are not the intended recipient, please contact the
>>>> sender immediately and permanently destroy this email and any attachments
>>>> thereto.*
>>>>
>>>> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net>
>>>> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> The most common mistake here would be forgetting to call Allocate on
>>>>> your image. Beyond that sharing your code would be helpful.
>>>>>
>>>>> Brad
>>>>>
>>>>> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>>
>>>>> Hello,
>>>>> I am attempting to use the CastImageFilter to convert between unsigned
>>>>> char and float image types, and am getting a
>>>>> System.AccessViolationException at runtime.  I have seen reference to this
>>>>> being caused by referring to a pointer that is out of scope, but in this
>>>>> case both the image and the cast filter are delcared in the same method, so
>>>>> I?m not sure how it can be going out of scope.  I can include the header
>>>>> and definition files if that would be helpful.
>>>>>
>>>>> --
>>>>>
>>>>> AH
>>>>>
>>>>>
>>>>>
>>>>> -----------------------------------------------------------------------------------------------
>>>>>
>>>>> *This email and any attachments thereto may contain private,
>>>>> confidential, and privileged materials for the sole use of the intended
>>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>>> attachments thereto) by other than the intended recipient is strictly
>>>>> prohibited. If you are not the intended recipient, please contact the
>>>>> sender immediately and permanently destroy this email and any attachments
>>>>> thereto.*
>>>>>
>>>>> _____________________________________
>>>>> 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
>
>
>
-------------- next part --------------
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URL: <http://public.kitware.com/pipermail/community/attachments/20160728/05223905/attachment-0001.html>
-------------- next part --------------
>	BING_Andrew.exe!std::_Transform<unsigned char const *,float *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char* _First, unsigned char* _Last, float* _Dest, itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 950 + 0x9 bytes	C++
 	BING_Andrew.exe!std::_Transform1<unsigned char const *,float *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char* _First, unsigned char* _Last, float* _Dest, itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func, std::random_access_iterator_tag __unnamed004, std::random_access_iterator_tag __unnamed005) Line 988 + 0x2b bytes	C++
 	BING_Andrew.exe!std::_Transform1<unsigned char const *,float *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char* _First, unsigned char* _Last, float* _Dest, itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func, std::integral_constant<bool,0> __unnamed004) Line 1012 + 0x6d bytes	C++
 	BING_Andrew.exe!std::transform<unsigned char const *,float *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char* _First, unsigned char* _Last, float* _Dest, itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 1026 + 0x48 bytes	C++
 	BING_Andrew.exe!itk::ImageAlgorithm::CopyHelper<unsigned char,float>(unsigned char* first, unsigned char* last, float* result) Line 213 + 0x14 bytes	C++
 	BING_Andrew.exe!itk::ImageAlgorithm::DispatchedCopy<itk::Image<unsigned char,3>,itk::Image<float,3> >(itk::Image<unsigned char,3>* inImage, itk::Image<float,3>* outImage, itk::ImageRegion<3>& inRegion, itk::ImageRegion<3>& outRegion, std::integral_constant<bool,1> __unnamed004) Line 136 + 0x12 bytes	C++
 	BING_Andrew.exe!itk::ImageAlgorithm::Copy<unsigned char,float,3>(itk::Image<unsigned char,3>* inImage, itk::Image<float,3>* outImage, itk::ImageRegion<3>& inRegion, itk::ImageRegion<3>& outRegion) Line 113	C++
 	BING_Andrew.exe!itk::CastImageFilter<itk::Image<unsigned char,3>,itk::Image<float,3> >::ThreadedGenerateData(itk::ImageRegion<3>& outputRegionForThread, unsigned int threadId) Line 73 + 0x13 bytes	C++
 	[External Code]	
 	BING_Andrew.exe!itk::ImageSource<itk::Image<float,3> >::ThreaderCallback(void* arg) Line 316	C++
 	BING_Andrew.exe!itk::MultiThreader::SingleMethodProxy(void * arg)  Line 437 + 0xe bytes	C++
 	msvcr120d.dll!03573651() 	
 	[Frames below may be incorrect and/or missing, no symbols loaded for msvcr120d.dll]	
 	msvcr120d.dll!03573861() 	
 	kernel32.dll!74c738f4() 	
 	ntdll.dll!776d5de3() 	
 	ntdll.dll!776d5dae() 	
-------------- next part --------------
_____________________________________
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 dzenanz at gmail.com  Thu Jul 28 11:13:30 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 28 Jul 2016 11:13:30 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <CAJ0LxQLG23=OHLoWAKiqPuAjq_nky=NkUyLU0pnE2ne5sv_MxA@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
 <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
 <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>
 <CAPf2UMR3cWPOOCehyqgVLcoGcbit8OPXJJKMvR3irH70OEcrcQ@mail.gmail.com>
 <673C89C9-8EAE-47FE-B38A-8762FDE10734@lowekamp.net>
 <CAJ0LxQLG23=OHLoWAKiqPuAjq_nky=NkUyLU0pnE2ne5sv_MxA@mail.gmail.com>
Message-ID: <CAPf2UMS-tbRm5HSCEjK9yrtUL1Nt8gWnQit9upQ8uGV+2-CMVg@mail.gmail.com>

I would focus on the input array now. The cast filter is perhaps accessing
elements past the end of the input array. Try passing a smaller number for
Z size and see whether that solves the crash (access violation).

On Thu, Jul 28, 2016 at 10:24 AM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Thanks all for getting back to me.  I put in a call to update the
> importFilter and upon debugging found that the image variable is getting
> the correct size settings and number of elements (or at least it is the
> same as the importFilter finds).  I tried casting the imageSize to unsigned
> int and got the same numbers throughout, and still had the exception at
> castImage->Update().  Here is the stack trace at the exception:
>
> > BING_Andrew.exe!std::_Transform<unsigned char const *,float
> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
> _First, unsigned char* _Last, float* _Dest,
> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 950 + 0x9
> bytes C++
>   BING_Andrew.exe!std::_Transform1<unsigned char const *,float
> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
> _First, unsigned char* _Last, float* _Dest,
> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func,
> std::random_access_iterator_tag __unnamed004,
> std::random_access_iterator_tag __unnamed005) Line 988 + 0x2b bytes C++
>   BING_Andrew.exe!std::_Transform1<unsigned char const *,float
> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
> _First, unsigned char* _Last, float* _Dest,
> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func,
> std::integral_constant<bool,0> __unnamed004) Line 1012 + 0x6d bytes C++
>   BING_Andrew.exe!std::transform<unsigned char const *,float
> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
> _First, unsigned char* _Last, float* _Dest,
> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 1026 +
> 0x48 bytes C++
>   BING_Andrew.exe!itk::ImageAlgorithm::CopyHelper<unsigned
> char,float>(unsigned char* first, unsigned char* last, float* result) Line
> 213 + 0x14 bytes C++
>   BING_Andrew.exe!itk::ImageAlgorithm::DispatchedCopy<itk::Image<unsigned
> char,3>,itk::Image<float,3> >(itk::Image<unsigned char,3>* inImage,
> itk::Image<float,3>* outImage, itk::ImageRegion<3>& inRegion,
> itk::ImageRegion<3>& outRegion, std::integral_constant<bool,1>
> __unnamed004) Line 136 + 0x12 bytes C++
>   BING_Andrew.exe!itk::ImageAlgorithm::Copy<unsigned
> char,float,3>(itk::Image<unsigned char,3>* inImage, itk::Image<float,3>*
> outImage, itk::ImageRegion<3>& inRegion, itk::ImageRegion<3>& outRegion)
> Line 113 C++
>   BING_Andrew.exe!itk::CastImageFilter<itk::Image<unsigned
> char,3>,itk::Image<float,3> >::ThreadedGenerateData(itk::ImageRegion<3>&
> outputRegionForThread, unsigned int threadId) Line 73 + 0x13 bytes C++
>   [External Code]
>   BING_Andrew.exe!itk::ImageSource<itk::Image<float,3>
> >::ThreaderCallback(void* arg) Line 316 C++
>   BING_Andrew.exe!itk::MultiThreader::SingleMethodProxy(void * arg)  Line
> 437 + 0xe bytes C++
>   msvcr120d.dll!03573651()
>   [Frames below may be incorrect and/or missing, no symbols loaded for
> msvcr120d.dll]
>   msvcr120d.dll!03573861()
>   kernel32.dll!74c738f4()
>   ntdll.dll!776d5de3()
>   ntdll.dll!776d5dae()
>
> I'm attaching this as a txt file also because the formatting looks a
> little weird in my email client, it might be easier to read as plain text.
> One other thing I forgot to mention, the window generated by the exception
> has the following text as well:
> Additional information: Attempted to read or write protected memory. This
> is often an indication that other memory is corrupt.
>
> Thanks again for the help.
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Thu, Jul 28, 2016 at 9:01 AM, Bradley Lowekamp <brad at lowekamp.net>
> wrote:
>
>> Hello,
>>
>> I noticed you are using type int for you imageSiize. How big is your
>> image? You may be overflowing when computing the number of pixels.
>>
>> I don?t think you have provided a stack trace of when the error occurs.
>> That would be helpful too.
>>
>> Brad
>>
>> On Jul 28, 2016, at 8:29 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>> Have you tried calling Update on the import filter? That might be the
>> problem. Cast filter is simple and non-special, I doubt it is the problem.
>>
>> On Wed, Jul 27, 2016 at 8:26 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>
>>> Thanks D?enan, as I said in my previous email running Update() on the
>>> castFilter pointer returns the same error.  I did put in a try/catch block
>>> to update it though.
>>>
>>> --
>>>
>>> AH
>>>
>>>
>>>
>>> -----------------------------------------------------------------------------------------------
>>>
>>> *This email and any attachments thereto may contain private,
>>> confidential, and privileged materials for the sole use of the intended
>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>> attachments thereto) by other than the intended recipient is strictly
>>> prohibited. If you are not the intended recipient, please contact the
>>> sender immediately and permanently destroy this email and any attachments
>>> thereto.*
>>>
>>> On Wed, Jul 27, 2016 at 5:16 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>>> Hi Andrew,
>>>>
>>>> I think that line 62 of .cpp should be:
>>>> castFilter->Update();
>>>> I don't see the pipeline updated elsewhere.
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>
>>>>> Thanks for getting back to me, after conferring with a colleague I
>>>>> tried using the output of the cast filter directly in the subsequent
>>>>> pipeline rather than writing it to a new image object of the filter's
>>>>> output type. I got the same error doing that, and also got the same error
>>>>> just running Update() on the cast filter, which leads me to believe I'm
>>>>> doing something wrong in setting up the cast filter.  I'm attaching my code
>>>>> for the class I'm writing, hope it's something simple I'm doing wrong.
>>>>> Currently it's throwing the exception at line 85 when the registration
>>>>> transform initializer is activated.
>>>>>
>>>>> --
>>>>>
>>>>> AH
>>>>>
>>>>>
>>>>>
>>>>> -----------------------------------------------------------------------------------------------
>>>>>
>>>>> *This email and any attachments thereto may contain private,
>>>>> confidential, and privileged materials for the sole use of the intended
>>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>>> attachments thereto) by other than the intended recipient is strictly
>>>>> prohibited. If you are not the intended recipient, please contact the
>>>>> sender immediately and permanently destroy this email and any attachments
>>>>> thereto.*
>>>>>
>>>>> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net>
>>>>> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> The most common mistake here would be forgetting to call Allocate on
>>>>>> your image. Beyond that sharing your code would be helpful.
>>>>>>
>>>>>> Brad
>>>>>>
>>>>>> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>>>
>>>>>> Hello,
>>>>>> I am attempting to use the CastImageFilter to convert between
>>>>>> unsigned char and float image types, and am getting a
>>>>>> System.AccessViolationException at runtime.  I have seen reference to this
>>>>>> being caused by referring to a pointer that is out of scope, but in this
>>>>>> case both the image and the cast filter are delcared in the same method, so
>>>>>> I?m not sure how it can be going out of scope.  I can include the header
>>>>>> and definition files if that would be helpful.
>>>>>>
>>>>>> --
>>>>>>
>>>>>> AH
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------------------------------------------------------------------------
>>>>>>
>>>>>> *This email and any attachments thereto may contain private,
>>>>>> confidential, and privileged materials for the sole use of the intended
>>>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>>>> attachments thereto) by other than the intended recipient is strictly
>>>>>> prohibited. If you are not the intended recipient, please contact the
>>>>>> sender immediately and permanently destroy this email and any attachments
>>>>>> thereto.*
>>>>>>
>>>>>> _____________________________________
>>>>>> 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 amirhossein.jaberzadeh at gmail.com  Thu Jul 28 11:40:49 2016
From: amirhossein.jaberzadeh at gmail.com (Amir Jaberzadeh)
Date: Thu, 28 Jul 2016 11:40:49 -0400
Subject: [ITK] [ITK-users] Insight journal dataset upload error
Message-ID: <CANWh7-AnDoDoBJVxD_Mt1w4qSUsLq+SX_WzfCqXx+JpbYFehbw@mail.gmail.com>

Dear all,

I am submitting an insight journal paper, while uploading my example
dataset, it is not possible to upload a file larger than 10 MB. I would
like to upload a 89 MB zip file and attaching them one by one was the only
solution I could find so far.

I appreciate your help in advance,
Amir
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From aharr8 at uwo.ca  Thu Jul 28 12:59:13 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Thu, 28 Jul 2016 12:59:13 -0400
Subject: [ITK] [ITK-users] itk::CastImageFilter
	causes	AccessViolationException
In-Reply-To: <CAPf2UMS-tbRm5HSCEjK9yrtUL1Nt8gWnQit9upQ8uGV+2-CMVg@mail.gmail.com>
References: <CAJ0LxQLUXVm6W_Df7jTJCQNT80YQ85sJtN1NhOuarSigTm3ysQ@mail.gmail.com>
 <C039B2D8-33DE-4BE8-8677-9731576801FD@mail.nih.gov>
 <CAJ0LxQLZLscNFCQX4gXhgw3S+RGfxeAFdrPhNXx+MwCxktHbmQ@mail.gmail.com>
 <CAPf2UMRshiLM0Eb2mR0qPdRDrWTemReaX_phMCm4k2JiNZ7xtw@mail.gmail.com>
 <CAJ0LxQ+hMmm0EmywnMENZG5+xe1F6Q+XR6Om21PVqefHZJtC6A@mail.gmail.com>
 <CAPf2UMR3cWPOOCehyqgVLcoGcbit8OPXJJKMvR3irH70OEcrcQ@mail.gmail.com>
 <673C89C9-8EAE-47FE-B38A-8762FDE10734@lowekamp.net>
 <CAJ0LxQLG23=OHLoWAKiqPuAjq_nky=NkUyLU0pnE2ne5sv_MxA@mail.gmail.com>
 <CAPf2UMS-tbRm5HSCEjK9yrtUL1Nt8gWnQit9upQ8uGV+2-CMVg@mail.gmail.com>
Message-ID: <CAJ0LxQ+zoeKK+N1fsLxpBYkC3+4DO1TjFspuZU4OGBLh0syqgA@mail.gmail.com>

Thanks all for the help, I wrote a for loop to do the same task and got the
same error, and upon investigating it turns out the program I am building
upon was passing the incorrect dimensions for the image buffer. Turns out
this is a PEBKAC error.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Thu, Jul 28, 2016 at 11:13 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> I would focus on the input array now. The cast filter is perhaps accessing
> elements past the end of the input array. Try passing a smaller number for
> Z size and see whether that solves the crash (access violation).
>
> On Thu, Jul 28, 2016 at 10:24 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
>> Thanks all for getting back to me.  I put in a call to update the
>> importFilter and upon debugging found that the image variable is getting
>> the correct size settings and number of elements (or at least it is the
>> same as the importFilter finds).  I tried casting the imageSize to unsigned
>> int and got the same numbers throughout, and still had the exception at
>> castImage->Update().  Here is the stack trace at the exception:
>>
>> > BING_Andrew.exe!std::_Transform<unsigned char const *,float
>> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
>> _First, unsigned char* _Last, float* _Dest,
>> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 950 + 0x9
>> bytes C++
>>   BING_Andrew.exe!std::_Transform1<unsigned char const *,float
>> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
>> _First, unsigned char* _Last, float* _Dest,
>> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func,
>> std::random_access_iterator_tag __unnamed004,
>> std::random_access_iterator_tag __unnamed005) Line 988 + 0x2b bytes C++
>>   BING_Andrew.exe!std::_Transform1<unsigned char const *,float
>> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
>> _First, unsigned char* _Last, float* _Dest,
>> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func,
>> std::integral_constant<bool,0> __unnamed004) Line 1012 + 0x6d bytes C++
>>   BING_Andrew.exe!std::transform<unsigned char const *,float
>> *,itk::ImageAlgorithm::StaticCast<unsigned char,float> >(unsigned char*
>> _First, unsigned char* _Last, float* _Dest,
>> itk::ImageAlgorithm::StaticCast<unsigned char,float> _Func) Line 1026 +
>> 0x48 bytes C++
>>   BING_Andrew.exe!itk::ImageAlgorithm::CopyHelper<unsigned
>> char,float>(unsigned char* first, unsigned char* last, float* result) Line
>> 213 + 0x14 bytes C++
>>   BING_Andrew.exe!itk::ImageAlgorithm::DispatchedCopy<itk::Image<unsigned
>> char,3>,itk::Image<float,3> >(itk::Image<unsigned char,3>* inImage,
>> itk::Image<float,3>* outImage, itk::ImageRegion<3>& inRegion,
>> itk::ImageRegion<3>& outRegion, std::integral_constant<bool,1>
>> __unnamed004) Line 136 + 0x12 bytes C++
>>   BING_Andrew.exe!itk::ImageAlgorithm::Copy<unsigned
>> char,float,3>(itk::Image<unsigned char,3>* inImage, itk::Image<float,3>*
>> outImage, itk::ImageRegion<3>& inRegion, itk::ImageRegion<3>& outRegion)
>> Line 113 C++
>>   BING_Andrew.exe!itk::CastImageFilter<itk::Image<unsigned
>> char,3>,itk::Image<float,3> >::ThreadedGenerateData(itk::ImageRegion<3>&
>> outputRegionForThread, unsigned int threadId) Line 73 + 0x13 bytes C++
>>   [External Code]
>>   BING_Andrew.exe!itk::ImageSource<itk::Image<float,3>
>> >::ThreaderCallback(void* arg) Line 316 C++
>>   BING_Andrew.exe!itk::MultiThreader::SingleMethodProxy(void * arg)
>>  Line 437 + 0xe bytes C++
>>   msvcr120d.dll!03573651()
>>   [Frames below may be incorrect and/or missing, no symbols loaded for
>> msvcr120d.dll]
>>   msvcr120d.dll!03573861()
>>   kernel32.dll!74c738f4()
>>   ntdll.dll!776d5de3()
>>   ntdll.dll!776d5dae()
>>
>> I'm attaching this as a txt file also because the formatting looks a
>> little weird in my email client, it might be easier to read as plain text.
>> One other thing I forgot to mention, the window generated by the exception
>> has the following text as well:
>> Additional information: Attempted to read or write protected memory. This
>> is often an indication that other memory is corrupt.
>>
>> Thanks again for the help.
>>
>> --
>>
>> AH
>>
>>
>>
>> -----------------------------------------------------------------------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> On Thu, Jul 28, 2016 at 9:01 AM, Bradley Lowekamp <brad at lowekamp.net>
>> wrote:
>>
>>> Hello,
>>>
>>> I noticed you are using type int for you imageSiize. How big is your
>>> image? You may be overflowing when computing the number of pixels.
>>>
>>> I don?t think you have provided a stack trace of when the error occurs.
>>> That would be helpful too.
>>>
>>> Brad
>>>
>>> On Jul 28, 2016, at 8:29 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>> Have you tried calling Update on the import filter? That might be the
>>> problem. Cast filter is simple and non-special, I doubt it is the problem.
>>>
>>> On Wed, Jul 27, 2016 at 8:26 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>
>>>> Thanks D?enan, as I said in my previous email running Update() on the
>>>> castFilter pointer returns the same error.  I did put in a try/catch block
>>>> to update it though.
>>>>
>>>> --
>>>>
>>>> AH
>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------------------------------------
>>>>
>>>> *This email and any attachments thereto may contain private,
>>>> confidential, and privileged materials for the sole use of the intended
>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>> attachments thereto) by other than the intended recipient is strictly
>>>> prohibited. If you are not the intended recipient, please contact the
>>>> sender immediately and permanently destroy this email and any attachments
>>>> thereto.*
>>>>
>>>> On Wed, Jul 27, 2016 at 5:16 PM, D?enan Zuki? <dzenanz at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Andrew,
>>>>>
>>>>> I think that line 62 of .cpp should be:
>>>>> castFilter->Update();
>>>>> I don't see the pipeline updated elsewhere.
>>>>>
>>>>> Regards,
>>>>> D?enan
>>>>>
>>>>> On Wed, Jul 27, 2016 at 3:54 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>>
>>>>>> Thanks for getting back to me, after conferring with a colleague I
>>>>>> tried using the output of the cast filter directly in the subsequent
>>>>>> pipeline rather than writing it to a new image object of the filter's
>>>>>> output type. I got the same error doing that, and also got the same error
>>>>>> just running Update() on the cast filter, which leads me to believe I'm
>>>>>> doing something wrong in setting up the cast filter.  I'm attaching my code
>>>>>> for the class I'm writing, hope it's something simple I'm doing wrong.
>>>>>> Currently it's throwing the exception at line 85 when the registration
>>>>>> transform initializer is activated.
>>>>>>
>>>>>> --
>>>>>>
>>>>>> AH
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------------------------------------------------------------------------
>>>>>>
>>>>>> *This email and any attachments thereto may contain private,
>>>>>> confidential, and privileged materials for the sole use of the intended
>>>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>>>> attachments thereto) by other than the intended recipient is strictly
>>>>>> prohibited. If you are not the intended recipient, please contact the
>>>>>> sender immediately and permanently destroy this email and any attachments
>>>>>> thereto.*
>>>>>>
>>>>>> On Tue, Jul 26, 2016 at 7:09 PM, Bradley Lowekamp <brad at lowekamp.net>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> The most common mistake here would be forgetting to call Allocate on
>>>>>>> your image. Beyond that sharing your code would be helpful.
>>>>>>>
>>>>>>> Brad
>>>>>>>
>>>>>>> On Jul 26, 2016, at 1:43 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>>>>
>>>>>>> Hello,
>>>>>>> I am attempting to use the CastImageFilter to convert between
>>>>>>> unsigned char and float image types, and am getting a
>>>>>>> System.AccessViolationException at runtime.  I have seen reference to this
>>>>>>> being caused by referring to a pointer that is out of scope, but in this
>>>>>>> case both the image and the cast filter are delcared in the same method, so
>>>>>>> I?m not sure how it can be going out of scope.  I can include the header
>>>>>>> and definition files if that would be helpful.
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> AH
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>> *This email and any attachments thereto may contain private,
>>>>>>> confidential, and privileged materials for the sole use of the intended
>>>>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>>>>> attachments thereto) by other than the intended recipient is strictly
>>>>>>> prohibited. If you are not the intended recipient, please contact the
>>>>>>> sender immediately and permanently destroy this email and any attachments
>>>>>>> thereto.*
>>>>>>>
>>>>>>> _____________________________________
>>>>>>> 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 dzenanz at gmail.com  Thu Jul 28 13:06:11 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 28 Jul 2016 13:06:11 -0400
Subject: [ITK] [ITK-users] In-place extraction of N-1 dimensional images
 from N dimensional images
In-Reply-To: <0089D58A-9C8D-443F-AC63-90A9E43E1B8B@kcl.ac.uk>
References: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>
 <CAPf2UMSz32cPe-F4WmVp4mzvBX3U0nnu1-GFXbPb9BZZtdjHEw@mail.gmail.com>
 <0089D58A-9C8D-443F-AC63-90A9E43E1B8B@kcl.ac.uk>
Message-ID: <CAPf2UMQ=WTWnJMW5tXvXgPGs=+=DJyCPEtA1VO5Lt5OqK0n8OQ@mail.gmail.com>

Hi Toby,

Extract filter could theoretically run in place only when the extraction
region differs from largest possible region only along the slowest changing
index. To make this possible, ExtractImageFilter should
override CanRunInPlace() which it inherits from InPlaceImageFilter and
implement this theoretical check. Of course, other changes will be required
to make it function properly.

Regards,
D?enan

On Thu, Jul 28, 2016 at 9:23 AM, Wood, Tobias <tobias.wood at kcl.ac.uk> wrote:

> Hello D?enan,
>
> I have had the same problem as Edwin with ExtractImageFilter, but in a
> different context. Eventually I gave up and accepted the speed/memory
> penalty of copying the 3D volumes out of the 4D series. Is there really no
> way in ITK to get a temporary ?view? of a subregion for processing, without
> resorting to referencing the raw arrays?
>
> Thanks,
> Toby
>
> On 28/07/2016, 13:40, "Insight-users on behalf of D?enan Zuki?" <
> insight-users-bounces at itk.org on behalf of dzenanz at gmail.com> wrote:
>
>
>     Hi Edwin,
>
>
>     you should be able to achieve your goal using
>     import image filter <
> http://www.vtk.org/doc/nightly/html/classvtkImageImport.html#details>.
> ITK has import image filter
>     too <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html>,
> so you can decide in which library to do dimensional reduction.
>
>
>     Regards,
>     D?enan
>
>
>     On Thu, Jul 28, 2016 at 4:37 AM, Edwin Bennink
>     <hebennink at gmail.com> wrote:
>
>     Hello,
>
>
>     I am working on an ITK/VTK viewer for visualizing 3D+time image data.
> The data is represented by 4D images in ITK (x,y,z,t). I would like to be
> able to access the 3D data in VTK without copying it, since that would slow
> down scrolling through time in large
>      datasets. I noticed that, although in-place extraction should be
> possible, the ExtractImageFilter 'says no' to in-place extraction when the
> input and output dimensions differ. Does anyone know a way to achieve my
> goal using existing ITK functions? For example,
>      if there would be some way of reducing the dimension of 'flat'
> images, i.e. 3D (Nx,Ny,1) to 2D (Nx, Ny), then I could still use the
> ExtractImageFilter.
>
>
>     Best,
>     Edwin
>
>
>     _____________________________________
>     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
>
>
>
>
>
>
>
>
>
>
>
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From blowekamp at mail.nih.gov  Thu Jul 28 13:24:44 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 28 Jul 2016 17:24:44 +0000
Subject: [ITK] [ITK-users] In-place extraction of N-1 dimensional images
 from N dimensional images
In-Reply-To: <CAPf2UMQ=WTWnJMW5tXvXgPGs=+=DJyCPEtA1VO5Lt5OqK0n8OQ@mail.gmail.com>
References: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>
 <CAPf2UMSz32cPe-F4WmVp4mzvBX3U0nnu1-GFXbPb9BZZtdjHEw@mail.gmail.com>
 <0089D58A-9C8D-443F-AC63-90A9E43E1B8B@kcl.ac.uk>
 <CAPf2UMQ=WTWnJMW5tXvXgPGs=+=DJyCPEtA1VO5Lt5OqK0n8OQ@mail.gmail.com>
Message-ID: <B3E10953-41D3-4A02-9F50-171E465884D5@mail.nih.gov>

Hello,

I think the missing features to implement this proper is one step lower that the ExtractImageFilter, rather in the ImportImageContainer. The container would need to support presenting one buffer, but holding the whole buffer someplace. Also the ability to share buffers between images is not supported either. When filters are run ?InPlace? the output steals the buffer from the input, so there is no buffer sharing. This is essentially adding different ?view? to a buffer.

I had been concerned about the performance of the ExtractImageFilter filter previously. If I recall correctly I update the filter to use the ImageAlgorithm::Copy method and improved the performance by something like 100x for some test cases. You could profile the filter run with the default number of thread and with just 1 thread to determine how best to run it. Also you would need to veriify that the pipeline is executing as expected and efficiently. If this still does not meet your timing requirements you?d likely be better off just writing a function to create a ImportImageContainer with your ?view?, and manage the memory yourself. This would bypass the pipeline.

HTH,
Brad

On Jul 28, 2016, at 1:06 PM, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:

Hi Toby,

Extract filter could theoretically run in place only when the extraction region differs from largest possible region only along the slowest changing index. To make this possible, ExtractImageFilter should override CanRunInPlace() which it inherits from InPlaceImageFilter and implement this theoretical check. Of course, other changes will be required to make it function properly.

Regards,
D?enan

On Thu, Jul 28, 2016 at 9:23 AM, Wood, Tobias <tobias.wood at kcl.ac.uk<mailto:tobias.wood at kcl.ac.uk>> wrote:
Hello D?enan,

I have had the same problem as Edwin with ExtractImageFilter, but in a different context. Eventually I gave up and accepted the speed/memory penalty of copying the 3D volumes out of the 4D series. Is there really no way in ITK to get a temporary ?view? of a subregion for processing, without resorting to referencing the raw arrays?

Thanks,
Toby

On 28/07/2016, 13:40, "Insight-users on behalf of D?enan Zuki?" <insight-users-bounces at itk.org<mailto:insight-users-bounces at itk.org> on behalf of dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:


    Hi Edwin,


    you should be able to achieve your goal using
    import image filter <http://www.vtk.org/doc/nightly/html/classvtkImageImport.html#details>. ITK has import image filter
    too <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html>, so you can decide in which library to do dimensional reduction.


    Regards,
    D?enan


    On Thu, Jul 28, 2016 at 4:37 AM, Edwin Bennink
    <hebennink at gmail.com<mailto:hebennink at gmail.com>> wrote:

    Hello,


    I am working on an ITK/VTK viewer for visualizing 3D+time image data. The data is represented by 4D images in ITK (x,y,z,t). I would like to be able to access the 3D data in VTK without copying it, since that would slow down scrolling through time in large
     datasets. I noticed that, although in-place extraction should be possible, the ExtractImageFilter 'says no' to in-place extraction when the input and output dimensions differ. Does anyone know a way to achieve my goal using existing ITK functions? For example,
     if there would be some way of reducing the dimension of 'flat' images, i.e. 3D (Nx,Ny,1) to 2D (Nx, Ny), then I could still use the ExtractImageFilter.


    Best,
    Edwin


    _____________________________________
    Powered by www.kitware.com<http://www.kitware.com/> <http://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:
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_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

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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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_____________________________________
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

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From tobias.wood at kcl.ac.uk  Thu Jul 28 09:23:36 2016
From: tobias.wood at kcl.ac.uk (Wood, Tobias)
Date: Thu, 28 Jul 2016 13:23:36 +0000
Subject: [ITK] [ITK-users] In-place extraction of N-1 dimensional images
 from N dimensional images
In-Reply-To: <CAPf2UMSz32cPe-F4WmVp4mzvBX3U0nnu1-GFXbPb9BZZtdjHEw@mail.gmail.com>
References: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>
 <CAPf2UMSz32cPe-F4WmVp4mzvBX3U0nnu1-GFXbPb9BZZtdjHEw@mail.gmail.com>
Message-ID: <0089D58A-9C8D-443F-AC63-90A9E43E1B8B@kcl.ac.uk>

Hello D?enan,

I have had the same problem as Edwin with ExtractImageFilter, but in a different context. Eventually I gave up and accepted the speed/memory penalty of copying the 3D volumes out of the 4D series. Is there really no way in ITK to get a temporary ?view? of a subregion for processing, without resorting to referencing the raw arrays?

Thanks,
Toby

On 28/07/2016, 13:40, "Insight-users on behalf of D?enan Zuki?" <insight-users-bounces at itk.org on behalf of dzenanz at gmail.com> wrote:

    
    Hi Edwin,
    
    
    you should be able to achieve your goal using 
    import image filter <http://www.vtk.org/doc/nightly/html/classvtkImageImport.html#details>. ITK has import image filter 
    too <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html>, so you can decide in which library to do dimensional reduction.
    
    
    Regards,
    D?enan
    
    
    On Thu, Jul 28, 2016 at 4:37 AM, Edwin Bennink 
    <hebennink at gmail.com> wrote:
    
    Hello,
    
    
    I am working on an ITK/VTK viewer for visualizing 3D+time image data. The data is represented by 4D images in ITK (x,y,z,t). I would like to be able to access the 3D data in VTK without copying it, since that would slow down scrolling through time in large
     datasets. I noticed that, although in-place extraction should be possible, the ExtractImageFilter 'says no' to in-place extraction when the input and output dimensions differ. Does anyone know a way to achieve my goal using existing ITK functions? For example,
     if there would be some way of reducing the dimension of 'flat' images, i.e. 3D (Nx,Ny,1) to 2D (Nx, Ny), then I could still use the ExtractImageFilter.
    
    
    Best,
    Edwin
    
    
    _____________________________________
    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

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 amirhossein.jaberzadeh at gmail.com  Thu Jul 28 22:24:11 2016
From: amirhossein.jaberzadeh at gmail.com (Amir Jaberzadeh)
Date: Thu, 28 Jul 2016 22:24:11 -0400
Subject: [ITK] Insight journal dataset upload error
Message-ID: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>

Dear all,

I am submitting an insight journal paper and while uploading my example
dataset, it is not possible to upload a file larger than 10 MB. I would
like to upload all as zip file and attaching them one by one does not seem
right.

I appreciate your help in advance,
Amir
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From dzenanz at gmail.com  Fri Jul 29 09:57:08 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 29 Jul 2016 09:57:08 -0400
Subject: [ITK] Insight journal dataset upload error
In-Reply-To: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>
References: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>
Message-ID: <CAPf2UMSOKfBA+2QeaEC=tUAs3BvgDpooeBurY=njy6y+TMFJhA@mail.gmail.com>

Hi Amir,

I don't know whether IJ's size limit can be circumvented or lifted, but you
can upload a large dataset to either Girder <https://data.kitware.com/> or
Midas <https://midas3.kitware.com/> and then add a hyperlink to
Insight-Journal.

Regards,
D?enan

On Thu, Jul 28, 2016 at 10:24 PM, Amir Jaberzadeh <
amirhossein.jaberzadeh at gmail.com> wrote:

> Dear all,
>
> I am submitting an insight journal paper and while uploading my example
> dataset, it is not possible to upload a file larger than 10 MB. I would
> like to upload all as zip file and attaching them one by one does not seem
> right.
>
> I appreciate your help in advance,
> Amir
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From matt.mccormick at kitware.com  Fri Jul 29 11:56:20 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 29 Jul 2016 11:56:20 -0400
Subject: [ITK] Insight journal dataset upload error
In-Reply-To: <CAPf2UMSOKfBA+2QeaEC=tUAs3BvgDpooeBurY=njy6y+TMFJhA@mail.gmail.com>
References: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>
 <CAPf2UMSOKfBA+2QeaEC=tUAs3BvgDpooeBurY=njy6y+TMFJhA@mail.gmail.com>
Message-ID: <CALzTN-Qx64gjLcEEKX0Ny7_ow4AyEQ07xK=E1t0QkqON5Xzmsw@mail.gmail.com>

Hi Amir,

As Dzenan mentioned, until the size limit is increased, your data
could be added here:

  https://midas3.kitware.com/midas/folder/10393

After you sign up with an account on midas3.kitware.com and join the
"ITK" community, let us know, and we will add upload permissions to
your account.

Thanks,
Matt

On Fri, Jul 29, 2016 at 9:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Amir,
>
> I don't know whether IJ's size limit can be circumvented or lifted, but you
> can upload a large dataset to either Girder or Midas and then add a
> hyperlink to Insight-Journal.
>
> Regards,
> D?enan
>
> On Thu, Jul 28, 2016 at 10:24 PM, Amir Jaberzadeh
> <amirhossein.jaberzadeh at gmail.com> wrote:
>>
>> Dear all,
>>
>> I am submitting an insight journal paper and while uploading my example
>> dataset, it is not possible to upload a file larger than 10 MB. I would like
>> to upload all as zip file and attaching them one by one does not seem right.
>>
>> I appreciate your help in advance,
>> Amir
>>
>> _______________________________________________
>> 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 amirhossein.jaberzadeh at gmail.com  Fri Jul 29 12:08:23 2016
From: amirhossein.jaberzadeh at gmail.com (Amir Jaberzadeh)
Date: Fri, 29 Jul 2016 12:08:23 -0400
Subject: [ITK] Insight journal dataset upload error
In-Reply-To: <CALzTN-Qx64gjLcEEKX0Ny7_ow4AyEQ07xK=E1t0QkqON5Xzmsw@mail.gmail.com>
References: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>
 <CAPf2UMSOKfBA+2QeaEC=tUAs3BvgDpooeBurY=njy6y+TMFJhA@mail.gmail.com>
 <CALzTN-Qx64gjLcEEKX0Ny7_ow4AyEQ07xK=E1t0QkqON5Xzmsw@mail.gmail.com>
Message-ID: <CANWh7-CUQXNqk0r9CudfKg=JWfRpncurY_2U-yeVOnk+=u-kng@mail.gmail.com>

Thanks Matt and D?enan

I have joined with name: Amir Jaberzadeh to the ITK community.
By the way, I can't find a way to add a hyperlink to my Insight-Journal.
What I did so far is to create a txt file and write the link into it and
upload that txt file.

Bests,
Amire

On Fri, Jul 29, 2016 at 11:56 AM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Amir,
>
> As Dzenan mentioned, until the size limit is increased, your data
> could be added here:
>
>   https://midas3.kitware.com/midas/folder/10393
>
> After you sign up with an account on midas3.kitware.com and join the
> "ITK" community, let us know, and we will add upload permissions to
> your account.
>
> Thanks,
> Matt
>
> On Fri, Jul 29, 2016 at 9:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> > Hi Amir,
> >
> > I don't know whether IJ's size limit can be circumvented or lifted, but
> you
> > can upload a large dataset to either Girder or Midas and then add a
> > hyperlink to Insight-Journal.
> >
> > Regards,
> > D?enan
> >
> > On Thu, Jul 28, 2016 at 10:24 PM, Amir Jaberzadeh
> > <amirhossein.jaberzadeh at gmail.com> wrote:
> >>
> >> Dear all,
> >>
> >> I am submitting an insight journal paper and while uploading my example
> >> dataset, it is not possible to upload a file larger than 10 MB. I would
> like
> >> to upload all as zip file and attaching them one by one does not seem
> right.
> >>
> >> I appreciate your help in advance,
> >> Amir
> >>
> >> _______________________________________________
> >> 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  Fri Jul 29 12:17:50 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 29 Jul 2016 12:17:50 -0400
Subject: [ITK] Insight journal dataset upload error
In-Reply-To: <CANWh7-CUQXNqk0r9CudfKg=JWfRpncurY_2U-yeVOnk+=u-kng@mail.gmail.com>
References: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>
 <CAPf2UMSOKfBA+2QeaEC=tUAs3BvgDpooeBurY=njy6y+TMFJhA@mail.gmail.com>
 <CALzTN-Qx64gjLcEEKX0Ny7_ow4AyEQ07xK=E1t0QkqON5Xzmsw@mail.gmail.com>
 <CANWh7-CUQXNqk0r9CudfKg=JWfRpncurY_2U-yeVOnk+=u-kng@mail.gmail.com>
Message-ID: <CALzTN-SndG2Zd8Vw+CwpKCx4uTEppvu38hQdBShoogVBc+_vig@mail.gmail.com>

Hi Amir,

Great, thanks.  Your account now has upload permissions.

A link in a text file works, or a link in the article text would work too.

Also, we now have improved documentation on how to package your code
into an ITK module [1].  This uses the content-addressed CMake
ExternalData storage system, which is a useful way to distribute
testing data [2].

Thanks,
Matt

[1] https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1430009

[2] https://blog.kitware.com/cmake-externaldata-using-large-files-with-distributed-version-control/

On Fri, Jul 29, 2016 at 12:08 PM, Amir Jaberzadeh
<amirhossein.jaberzadeh at gmail.com> wrote:
> Thanks Matt and D?enan
>
> I have joined with name: Amir Jaberzadeh to the ITK community.
> By the way, I can't find a way to add a hyperlink to my Insight-Journal.
> What I did so far is to create a txt file and write the link into it and
> upload that txt file.
>
> Bests,
> Amire
>
> On Fri, Jul 29, 2016 at 11:56 AM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>>
>> Hi Amir,
>>
>> As Dzenan mentioned, until the size limit is increased, your data
>> could be added here:
>>
>>   https://midas3.kitware.com/midas/folder/10393
>>
>> After you sign up with an account on midas3.kitware.com and join the
>> "ITK" community, let us know, and we will add upload permissions to
>> your account.
>>
>> Thanks,
>> Matt
>>
>> On Fri, Jul 29, 2016 at 9:57 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>> > Hi Amir,
>> >
>> > I don't know whether IJ's size limit can be circumvented or lifted, but
>> > you
>> > can upload a large dataset to either Girder or Midas and then add a
>> > hyperlink to Insight-Journal.
>> >
>> > Regards,
>> > D?enan
>> >
>> > On Thu, Jul 28, 2016 at 10:24 PM, Amir Jaberzadeh
>> > <amirhossein.jaberzadeh at gmail.com> wrote:
>> >>
>> >> Dear all,
>> >>
>> >> I am submitting an insight journal paper and while uploading my example
>> >> dataset, it is not possible to upload a file larger than 10 MB. I would
>> >> like
>> >> to upload all as zip file and attaching them one by one does not seem
>> >> right.
>> >>
>> >> I appreciate your help in advance,
>> >> Amir
>> >>
>> >> _______________________________________________
>> >> 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 amirhossein.jaberzadeh at gmail.com  Fri Jul 29 12:56:54 2016
From: amirhossein.jaberzadeh at gmail.com (Amir Jaberzadeh)
Date: Fri, 29 Jul 2016 12:56:54 -0400
Subject: [ITK] Insight journal dataset upload error
In-Reply-To: <CALzTN-SndG2Zd8Vw+CwpKCx4uTEppvu38hQdBShoogVBc+_vig@mail.gmail.com>
References: <CANWh7-C14xGcp81y+ODN9eNj4AmKAbc-JCjzGvo00-Gp-ipxKg@mail.gmail.com>
 <CAPf2UMSOKfBA+2QeaEC=tUAs3BvgDpooeBurY=njy6y+TMFJhA@mail.gmail.com>
 <CALzTN-Qx64gjLcEEKX0Ny7_ow4AyEQ07xK=E1t0QkqON5Xzmsw@mail.gmail.com>
 <CANWh7-CUQXNqk0r9CudfKg=JWfRpncurY_2U-yeVOnk+=u-kng@mail.gmail.com>
 <CALzTN-SndG2Zd8Vw+CwpKCx4uTEppvu38hQdBShoogVBc+_vig@mail.gmail.com>
Message-ID: <CANWh7-BXRcvrTidZBeTzH38B+AjQ2rDCGjKzmpHLpDVRf_-_RQ@mail.gmail.com>

Hi Matt,

I tried to follow a similar convention and made a folder
TBBImageToImageFilter/test and uploaded my dataset there.
Then shared the link by a text file.

I will follow up by reading the documentation for creating an ITK module.

Have a good day,
Amir

On Fri, Jul 29, 2016 at 12:17 PM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Amir,
>
> Great, thanks.  Your account now has upload permissions.
>
> A link in a text file works, or a link in the article text would work too.
>
> Also, we now have improved documentation on how to package your code
> into an ITK module [1].  This uses the content-addressed CMake
> ExternalData storage system, which is a useful way to distribute
> testing data [2].
>
> Thanks,
> Matt
>
> [1]
> https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1430009
>
> [2]
> https://blog.kitware.com/cmake-externaldata-using-large-files-with-distributed-version-control/
>
> On Fri, Jul 29, 2016 at 12:08 PM, Amir Jaberzadeh
> <amirhossein.jaberzadeh at gmail.com> wrote:
> > Thanks Matt and D?enan
> >
> > I have joined with name: Amir Jaberzadeh to the ITK community.
> > By the way, I can't find a way to add a hyperlink to my Insight-Journal.
> > What I did so far is to create a txt file and write the link into it and
> > upload that txt file.
> >
> > Bests,
> > Amire
> >
> > On Fri, Jul 29, 2016 at 11:56 AM, Matt McCormick
> > <matt.mccormick at kitware.com> wrote:
> >>
> >> Hi Amir,
> >>
> >> As Dzenan mentioned, until the size limit is increased, your data
> >> could be added here:
> >>
> >>   https://midas3.kitware.com/midas/folder/10393
> >>
> >> After you sign up with an account on midas3.kitware.com and join the
> >> "ITK" community, let us know, and we will add upload permissions to
> >> your account.
> >>
> >> Thanks,
> >> Matt
> >>
> >> On Fri, Jul 29, 2016 at 9:57 AM, D?enan Zuki? <dzenanz at gmail.com>
> wrote:
> >> > Hi Amir,
> >> >
> >> > I don't know whether IJ's size limit can be circumvented or lifted,
> but
> >> > you
> >> > can upload a large dataset to either Girder or Midas and then add a
> >> > hyperlink to Insight-Journal.
> >> >
> >> > Regards,
> >> > D?enan
> >> >
> >> > On Thu, Jul 28, 2016 at 10:24 PM, Amir Jaberzadeh
> >> > <amirhossein.jaberzadeh at gmail.com> wrote:
> >> >>
> >> >> Dear all,
> >> >>
> >> >> I am submitting an insight journal paper and while uploading my
> example
> >> >> dataset, it is not possible to upload a file larger than 10 MB. I
> would
> >> >> like
> >> >> to upload all as zip file and attaching them one by one does not seem
> >> >> right.
> >> >>
> >> >> I appreciate your help in advance,
> >> >> Amir
> >> >>
> >> >> _______________________________________________
> >> >> 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 blowekamp at mail.nih.gov  Fri Jul 29 14:43:59 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 29 Jul 2016 18:43:59 +0000
Subject: [ITK] [ANNOUNCE] SimpleITK 0.10.0 Release
Message-ID: <660C990B-C30F-47FC-928F-B9176B2C9CBD@mail.nih.gov>


We are pleased to announce the release of SimpleITK 0.10.0!

As with all SimpleITK releases, we have a variety of binaries available. This includes fresh Python Wheels for MS Windows, GNU Linux and Apple OS X, along with Java and CSharp binaries for MS Windows. Additionally, binaries for the Python distribution Anaconda are available.

This release features major improvements to the build infrastructure, improved support for R, better downloads with pip and many new features!


Information on how to get started and download the binaries: https://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/

Release Doxygen Documentation: https://www.itk.org/SimpleITKDoxygen010/html/index.html

Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.10.0_Release

Key Improvements
* The R language bindings have received extensive improvements and bug fixes.
* Added Image::SetMetaData method
* Added LandmarkBasedTransformInitializer
* Added MultiLableSTAPLEImageFilter
* Show now prefers Fiji over the basic ImageJ
* Refactored Wrapping directory into separate languages (paths have changed!)
* Separated Lua, GTest, and virtualenv into SuperBuild dependencies
* Added SITK_FORBID_DOWNLOADS option
* Enabled each language wrapping to be an independent project dependent on the SimpleITK C++ interface and libraries.
* Many CMake build improvements to default configurations such as visibility, and link library interfaces
* Support for gcc 6.1 and compatibility with c++14
* CMake version 3.3 is now required


Python
* Update your pip version!
* Added manylinux1 wheels (PEP 513) 
* SimpleITK_PYTHON_THREADS enabled by default to better support multi-threading in Python
* No egg binary distributions, wheels fully support the standard platforms
* Python 2.7 is no longer packaged for 64-bit windows
* Avoid linking against libpython.so to improve compatibility and portability

Lua
* Lua languages bindings now compile as a loadable module
* Created Lua rockspec builder (https://github.com/SimpleITK/SimpleITKLuaRock)
* Can be used in Lua Torch

R
* Fix issues with the bracket operator preserving physical location
* Created script to generate R man pages
* Disabled return Self value from functions
* Create simplified R Installer (https://github.com/SimpleITK/SimpleITKRInstaller)


Enjoy!

Brad

From tobias.wood at kcl.ac.uk  Fri Jul 29 12:28:52 2016
From: tobias.wood at kcl.ac.uk (Wood, Tobias)
Date: Fri, 29 Jul 2016 16:28:52 +0000
Subject: [ITK] [ITK-users] In-place extraction of N-1 dimensional images
 from N dimensional images
In-Reply-To: <B3E10953-41D3-4A02-9F50-171E465884D5@mail.nih.gov>
References: <CAJbB22GozQHOk0U+6FTmXV05NL3XEg8ddN--RjkyVMYLu7BEDg@mail.gmail.com>
 <CAPf2UMSz32cPe-F4WmVp4mzvBX3U0nnu1-GFXbPb9BZZtdjHEw@mail.gmail.com>
 <0089D58A-9C8D-443F-AC63-90A9E43E1B8B@kcl.ac.uk>
 <CAPf2UMQ=WTWnJMW5tXvXgPGs=+=DJyCPEtA1VO5Lt5OqK0n8OQ@mail.gmail.com>
 <B3E10953-41D3-4A02-9F50-171E465884D5@mail.nih.gov>
Message-ID: <F3DEFE55-6A9F-4CD2-8A50-5A6051E127BE@kcl.ac.uk>

Thanks for the technical details Brad.

I am going to plead lack of time (and understanding of ITK internals) here, and keep my code as-is. Maybe for the future some time.

Best wishes,
Toby

On 28/07/2016, 18:24, "Lowekamp, Bradley (NIH/NLM/LHC) [C]" <blowekamp at mail.nih.gov> wrote:

    
    
    
    Hello,
    
    
    I think the missing features to implement this proper is one step lower that the ExtractImageFilter, rather in the ImportImageContainer. The container would need to support presenting one buffer, but holding the whole buffer someplace. Also the
     ability to share buffers between images is not supported either. When filters are run ?InPlace? the output steals the buffer from the input, so there is no buffer sharing. This is essentially adding different ?view? to a buffer.
    
    
    I had been concerned about the performance of the ExtractImageFilter filter previously. If I recall correctly I update the filter to use the ImageAlgorithm::Copy method and improved the performance by something like 100x for some test cases. You
     could profile the filter run with the default number of thread and with just 1 thread to determine how best to run it. Also you would need to veriify that the pipeline is executing as expected and efficiently. If this still does not meet your timing requirements
     you?d likely be better off just writing a function to create a ImportImageContainer with your ?view?, and manage the memory yourself. This would bypass the pipeline. 
    
    
    HTH,
    Brad
    
    
    On Jul 28, 2016, at 1:06 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
    
    Hi Toby,
    
    
    Extract filter could theoretically run in place only when the extraction region differs from largest possible region only along the slowest changing index. To make this possible, ExtractImageFilter should override CanRunInPlace() which it inherits from InPlaceImageFilter
     and implement this theoretical check. Of course, other changes will be required to make it function properly.
    
    
    Regards,
    D?enan
    
    
    On Thu, Jul 28, 2016 at 9:23 AM, Wood, Tobias 
    <tobias.wood at kcl.ac.uk> wrote:
    
    Hello D?enan,
    
    I have had the same problem as Edwin with ExtractImageFilter, but in a different context. Eventually I gave up and accepted the speed/memory penalty of copying the 3D volumes out of the 4D series. Is there really no way in ITK to get a temporary ?view? of a
     subregion for processing, without resorting to referencing the raw arrays?
    
    Thanks,
    Toby
    
    On 28/07/2016, 13:40, "Insight-users on behalf of D?enan Zuki?" <insight-users-bounces at itk.org on behalf of
    dzenanz at gmail.com> wrote:
    
    
        Hi Edwin,
    
    
        you should be able to achieve your goal using
        import image filter <http://www.vtk.org/doc/nightly/html/classvtkImageImport.html#details>. ITK has import image filter
        too <https://itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html>, so you can decide in which library to do dimensional reduction.
    
    
        Regards,
        D?enan
    
    
        On Thu, Jul 28, 2016 at 4:37 AM, Edwin Bennink
        <hebennink at gmail.com> wrote:
    
        Hello,
    
    
        I am working on an ITK/VTK viewer for visualizing 3D+time image data. The data is represented by 4D images in ITK (x,y,z,t). I would like to be able to access the 3D data in VTK without copying it, since that would slow down scrolling through time in large
         datasets. I noticed that, although in-place extraction should be possible, the ExtractImageFilter 'says no' to in-place extraction when the input and output dimensions differ. Does anyone know a way to achieve my goal using existing ITK functions? For
     example,
         if there would be some way of reducing the dimension of 'flat' images, i.e. 3D (Nx,Ny,1) to 2D (Nx, Ny), then I could still use the ExtractImageFilter.
    
    
        Best,
        Edwin
    
    
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    _____________________________________
    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
    
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Visit other Kitware open-source projects at
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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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Follow this link to subscribe/unsubscribe:
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From matthew.brett at gmail.com  Sat Jul 30 17:25:18 2016
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 30 Jul 2016 22:25:18 +0100
Subject: [ITK] SimpleITK Python wheels?
Message-ID: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>

Hi,

Sorry if this came up before - but I would really like to use
SimpleITK for a course I'm teaching in a month or so, and I noticed
that you only have Windows wheels at the moment.

I'm very experienced with building OSX and the new manylinux wheels,
and so I wonder if I can help with building those, so they can be
uploaded to pypi?

Cheers,

Matthew

From matt.mccormick at kitware.com  Sat Jul 30 17:35:49 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 30 Jul 2016 17:35:49 -0400
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
Message-ID: <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>

Hi Matthew,

The just-released SimpleITK 0.10.0 has OSX and manylinux wheels in
addition to Windows wheels.

We are working on improved wheel support in SimpleITK and also
hopefully ITK, VTK, symengine, pyne, matplotlib... with the
scikit-build project:

  https://github.com/scikit-build/scikit-build

We made many strides since the 2016 SciPy conference. Additional
community collaboration and contributions are welcome :-).

Thanks,
Matt

On Sat, Jul 30, 2016 at 5:25 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Hi,
>
> Sorry if this came up before - but I would really like to use
> SimpleITK for a course I'm teaching in a month or so, and I noticed
> that you only have Windows wheels at the moment.
>
> I'm very experienced with building OSX and the new manylinux wheels,
> and so I wonder if I can help with building those, so they can be
> uploaded to pypi?
>
> Cheers,
>
> Matthew
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From matthew.brett at gmail.com  Sat Jul 30 17:45:58 2016
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 30 Jul 2016 22:45:58 +0100
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
Message-ID: <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>

Hi,

On Sat, Jul 30, 2016 at 10:35 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Matthew,
>
> The just-released SimpleITK 0.10.0 has OSX and manylinux wheels in
> addition to Windows wheels.

Ah - yes - I saw 0.10.0 - but the only wheels on pypi are Windows
wheels - unless I'm looking at the wrong page:

https://pypi.python.org/pypi/SimpleITK/0.10.0

I couldn't see any 0.10.0 wheels at
https://itk.org/SimpleITKDoxygen/html/PyDownloadPage.html or
http://www.simpleitk.org//SimpleITK/resources/software.html .

I did try installing the 0.9.1 wheel via the sourceforge address, but
that failed at the download step, so I had to download manually.

I would really help if the wheels were up on pypi - it's generally
very reliable and fast, and it's where people are expecting to find
them.

> We are working on improved wheel support in SimpleITK and also
> hopefully ITK, VTK, symengine, pyne, matplotlib... with the
> scikit-build project:
>
>   https://github.com/scikit-build/scikit-build
>
> We made many strides since the 2016 SciPy conference. Additional
> community collaboration and contributions are welcome :-).

Good to know - thanks for the pointer.

Here is my current machinery for building and testing manylinux and
OSX wheels : https://github.com/matthew-brett/multibuild - it's
currently in use for numpy, scipy, matplotlib, pandas, h5py and
others,

Cheers,

Matthew

From matt.mccormick at kitware.com  Sat Jul 30 18:08:46 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 30 Jul 2016 18:08:46 -0400
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
 <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
Message-ID: <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>

On Sat, Jul 30, 2016 at 5:45 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Hi,
>
> On Sat, Jul 30, 2016 at 10:35 PM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>> Hi Matthew,
>>
>> The just-released SimpleITK 0.10.0 has OSX and manylinux wheels in
>> addition to Windows wheels.
>
> Ah - yes - I saw 0.10.0 - but the only wheels on pypi are Windows
> wheels - unless I'm looking at the wrong page:
>
> https://pypi.python.org/pypi/SimpleITK/0.10.0
>
> I couldn't see any 0.10.0 wheels at
> https://itk.org/SimpleITKDoxygen/html/PyDownloadPage.html or
> http://www.simpleitk.org//SimpleITK/resources/software.html .

The wheels are currently on Sourceforge -- we will work on getting
them on PyPI and updating the documentation:

  https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Python/


> I did try installing the 0.9.1 wheel via the sourceforge address, but
> that failed at the download step, so I had to download manually.
>
> I would really help if the wheels were up on pypi - it's generally
> very reliable and fast, and it's where people are expecting to find
> them.
>
>> We are working on improved wheel support in SimpleITK and also
>> hopefully ITK, VTK, symengine, pyne, matplotlib... with the
>> scikit-build project:
>>
>>   https://github.com/scikit-build/scikit-build
>>
>> We made many strides since the 2016 SciPy conference. Additional
>> community collaboration and contributions are welcome :-).
>
> Good to know - thanks for the pointer.
>
> Here is my current machinery for building and testing manylinux and
> OSX wheels : https://github.com/matthew-brett/multibuild - it's
> currently in use for numpy, scipy, matplotlib, pandas, h5py and
> others,

Very cool! Hopefully we can re-use and build upon it.

Thanks,
Matt

From brad at lowekamp.net  Sat Jul 30 18:22:13 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Sat, 30 Jul 2016 18:22:13 -0400
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
 <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
 <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>
Message-ID: <29A0B0AE-5D9D-4EDC-8866-BE9B802E0E08@mail.nih.gov>

Hello,

Thank you for your interest with SimpleITK. 

You can read how to install with pip here:
https://itk.org/Wiki/SimpleITK/GettingStarted#Generic_Distribution

For some reason I believe audit wheel changed the version from 0.10.0 to 0.10.0.0:

https://pypi.python.org/pypi/SimpleITK/0.10.0.0

I need to look into the further. 

The problem with the OS X wheels is that they are too big for pipy at about 75mb. These are still fat binaries of i386 and x86_64. I have not check what pip would do with just a x86_64 wheel but with a fat Python version. 

HTH,
Brad

> On Jul 30, 2016, at 6:08 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
>> On Sat, Jul 30, 2016 at 5:45 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
>> Hi,
>> 
>> On Sat, Jul 30, 2016 at 10:35 PM, Matt McCormick
>> <matt.mccormick at kitware.com> wrote:
>>> Hi Matthew,
>>> 
>>> The just-released SimpleITK 0.10.0 has OSX and manylinux wheels in
>>> addition to Windows wheels.
>> 
>> Ah - yes - I saw 0.10.0 - but the only wheels on pypi are Windows
>> wheels - unless I'm looking at the wrong page:
>> 
>> https://pypi.python.org/pypi/SimpleITK/0.10.0
>> 
>> I couldn't see any 0.10.0 wheels at
>> https://itk.org/SimpleITKDoxygen/html/PyDownloadPage.html or
>> http://www.simpleitk.org//SimpleITK/resources/software.html .
> 
> The wheels are currently on Sourceforge -- we will work on getting
> them on PyPI and updating the documentation:
> 
>  https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Python/
> 
> 
>> I did try installing the 0.9.1 wheel via the sourceforge address, but
>> that failed at the download step, so I had to download manually.
>> 
>> I would really help if the wheels were up on pypi - it's generally
>> very reliable and fast, and it's where people are expecting to find
>> them.
>> 
>>> We are working on improved wheel support in SimpleITK and also
>>> hopefully ITK, VTK, symengine, pyne, matplotlib... with the
>>> scikit-build project:
>>> 
>>>  https://github.com/scikit-build/scikit-build
>>> 
>>> We made many strides since the 2016 SciPy conference. Additional
>>> community collaboration and contributions are welcome :-).
>> 
>> Good to know - thanks for the pointer.
>> 
>> Here is my current machinery for building and testing manylinux and
>> OSX wheels : https://github.com/matthew-brett/multibuild - it's
>> currently in use for numpy, scipy, matplotlib, pandas, h5py and
>> others,
> 
> Very cool! Hopefully we can re-use and build upon it.
> 
> Thanks,
> Matt

From matthew.brett at gmail.com  Sat Jul 30 19:26:53 2016
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sun, 31 Jul 2016 00:26:53 +0100
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <29A0B0AE-5D9D-4EDC-8866-BE9B802E0E08@mail.nih.gov>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
 <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
 <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>
 <29A0B0AE-5D9D-4EDC-8866-BE9B802E0E08@mail.nih.gov>
Message-ID: <CAH6Pt5p7jVM+SkZNZfFYyZYtDoqS7mwdSNn6uMh_LcuC4C18tg@mail.gmail.com>

Hi,

On Sat, Jul 30, 2016 at 11:22 PM, Bradley Lowekamp <brad at lowekamp.net> wrote:
> Hello,
>
> Thank you for your interest with SimpleITK.
>
> You can read how to install with pip here:
> https://itk.org/Wiki/SimpleITK/GettingStarted#Generic_Distribution
>
> For some reason I believe audit wheel changed the version from 0.10.0 to 0.10.0.0:

> https://pypi.python.org/pypi/SimpleITK/0.10.0.0

That is strange - maybe worth a bug report to auditwheel?  Is that in
the wheel metadata - I see the filenames are correct.  How did you
upload the wheels - with twine?

> I need to look into the further.
>
> The problem with the OS X wheels is that they are too big for pipy at about 75mb. These are still fat binaries of i386 and x86_64. I have not check what pip would do with just a x86_64 wheel but with a fat Python version.

I think the pypi maintainers would be OK with increasing the upload
size for you if you asked them - I remember matplotlib discussing this
with them a while ago (they were a tad over 50M at the time).

But - I think it's also completely reasonable to drop off the i386
architecture and claim (via the wheel filename) that it's a fat wheel
- I built and uploaded an h5py wheel about a year ago for which the
i386 execution was segfaulting, but no-one noticed.  I doubt anyone
using SimpleITK would use the i386 architecture in the fat wheel
either.

Cheers,

Matthew

From brad at lowekamp.net  Sat Jul 30 22:28:09 2016
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Sat, 30 Jul 2016 22:28:09 -0400
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <CAH6Pt5p7jVM+SkZNZfFYyZYtDoqS7mwdSNn6uMh_LcuC4C18tg@mail.gmail.com>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
 <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
 <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>
 <29A0B0AE-5D9D-4EDC-8866-BE9B802E0E08@mail.nih.gov>
 <CAH6Pt5p7jVM+SkZNZfFYyZYtDoqS7mwdSNn6uMh_LcuC4C18tg@mail.gmail.com>
Message-ID: <D339D74E-DFBF-4658-921E-1DB7C65FCD56@lowekamp.net>

That is awesome you are looking to use SimpleITK in a course!  If you have not found them yet, we have some Jupyter notebooks which may be of help:

http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/

They contain a variety of introductory and advanced topics which may be of use.

There are more comments below.


> On Jul 30, 2016, at 7:26 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> 
> Hi,
> 
> On Sat, Jul 30, 2016 at 11:22 PM, Bradley Lowekamp <brad at lowekamp.net> wrote:
>> Hello,
>> 
>> Thank you for your interest with SimpleITK.
>> 
>> You can read how to install with pip here:
>> https://itk.org/Wiki/SimpleITK/GettingStarted#Generic_Distribution
>> 
>> For some reason I believe audit wheel changed the version from 0.10.0 to 0.10.0.0:
> 
>> https://pypi.python.org/pypi/SimpleITK/0.10.0.0
> 
> That is strange - maybe worth a bug report to auditwheel?  Is that in
> the wheel metadata - I see the filenames are correct.  How did you
> upload the wheels - with twine?

I need to investigate it more. The filename was consistent with 0.10.0.0. I didn?t think anything of it until I made the release and uploaded the files with twine. Then like you I could not find them. I tries renaming them with 0.10.0, but I guess the versions in the wheel metadata.

> 
>> I need to look into the further.
>> 
>> The problem with the OS X wheels is that they are too big for pipy at about 75mb. These are still fat binaries of i386 and x86_64. I have not check what pip would do with just a x86_64 wheel but with a fat Python version.
> 
> I think the pypi maintainers would be OK with increasing the upload
> size for you if you asked them - I remember matplotlib discussing this
> with them a while ago (they were a tad over 50M at the time).
> 
> But - I think it's also completely reasonable to drop off the i386
> architecture and claim (via the wheel filename) that it's a fat wheel
> - I built and uploaded an h5py wheel about a year ago for which the
> i386 execution was segfaulting, but no-one noticed.  I doubt anyone
> using SimpleITK would use the i386 architecture in the fat wheel
> either.

Do you know the way to contact the pypi maintainers to make this request?

Brad
> 
> Cheers,
> 
> Matthew
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From matthew.brett at gmail.com  Sat Jul 30 22:45:30 2016
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sun, 31 Jul 2016 03:45:30 +0100
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <D339D74E-DFBF-4658-921E-1DB7C65FCD56@lowekamp.net>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
 <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
 <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>
 <29A0B0AE-5D9D-4EDC-8866-BE9B802E0E08@mail.nih.gov>
 <CAH6Pt5p7jVM+SkZNZfFYyZYtDoqS7mwdSNn6uMh_LcuC4C18tg@mail.gmail.com>
 <D339D74E-DFBF-4658-921E-1DB7C65FCD56@lowekamp.net>
Message-ID: <CAH6Pt5oqysmyaLvUwSh8LPJtUt4qh_qxy6Zz7ozk2k3rG+bfpA@mail.gmail.com>

Hi,

On Sun, Jul 31, 2016 at 3:28 AM, Bradley Lowekamp <brad at lowekamp.net> wrote:
> That is awesome you are looking to use SimpleITK in a course!  If you have not found them yet, we have some Jupyter notebooks which may be of help:
>
> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/
>
> They contain a variety of introductory and advanced topics which may be of use.
>
> There are more comments below.
>
>
>> On Jul 30, 2016, at 7:26 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
>>
>> Hi,
>>
>> On Sat, Jul 30, 2016 at 11:22 PM, Bradley Lowekamp <brad at lowekamp.net> wrote:
>>> Hello,
>>>
>>> Thank you for your interest with SimpleITK.
>>>
>>> You can read how to install with pip here:
>>> https://itk.org/Wiki/SimpleITK/GettingStarted#Generic_Distribution
>>>
>>> For some reason I believe audit wheel changed the version from 0.10.0 to 0.10.0.0:
>>
>>> https://pypi.python.org/pypi/SimpleITK/0.10.0.0
>>
>> That is strange - maybe worth a bug report to auditwheel?  Is that in
>> the wheel metadata - I see the filenames are correct.  How did you
>> upload the wheels - with twine?
>
> I need to investigate it more. The filename was consistent with 0.10.0.0. I didn?t think anything of it until I made the release and uploaded the files with twine. Then like you I could not find them. I tries renaming them with 0.10.0, but I guess the versions in the wheel metadata.
>

I see that the filenames inside the wheel match the original version:

$ unzip SimpleITK-0.10.0-cp27-cp27m-manylinux1_i686.whl
Archive:  SimpleITK-0.10.0-cp27-cp27m-manylinux1_i686.whl
  inflating: SimpleITK-0.10.0.0.data/purelib/SimpleITK/__init__.py
  inflating: SimpleITK-0.10.0.0.data/purelib/SimpleITK/SimpleITK.py
  inflating: SimpleITK-0.10.0.0.data/purelib/SimpleITK/_SimpleITK.so
  inflating: SimpleITK-0.10.0.0.dist-info/DESCRIPTION.rst
  inflating: SimpleITK-0.10.0.0.dist-info/metadata.json
  inflating: SimpleITK-0.10.0.0.dist-info/top_level.txt
  inflating: SimpleITK-0.10.0.0.dist-info/WHEEL
  inflating: SimpleITK-0.10.0.0.dist-info/METADATA
  inflating: SimpleITK-0.10.0.0.dist-info/RECORD

In SimpleITK-0.10.0.0.dist-info/METADATA there is:

Version: 0.10.0.0

but I don't know if that is where twine gets the version number - I
had assumed (and have some vague feeling I had evidence) that the
version comes from the file name, but maybe you have refuted that.

It is possible to make another release of binary files with the same
version, using the "build-tag" feature - see
https://github.com/h5py/h5py/issues/731#issuecomment-230826012 .  I
wonder whether you could just delete the 0.10.0.0 release, rebuild the
wheels with the correct version number, and then re-upload the
manylinux files to the 0.10.0 release, with an increment to the build
tag number, as in something like:

SimpleITK-1-0.10.0-cp27-cp27m-manylinux1_i686.whl

etc (see https://gist.github.com/matthew-brett/1b2e76d0f4993c1ff6c1ed4d16a7384d).

If it really is an auditwheel bug, it would be good to nail that down...

> Do you know the way to contact the pypi maintainers to make this request?

How about emailing the `wheel-builders` mailing list at a first pass -
I think the relevant people are on there:

https://mail.python.org/mailman/listinfo/wheel-builders

Cheers,

Matthew

From matt.mccormick at kitware.com  Sun Jul 31 19:12:14 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 31 Jul 2016 19:12:14 -0400
Subject: [ITK] SimpleITK Python wheels?
In-Reply-To: <D339D74E-DFBF-4658-921E-1DB7C65FCD56@lowekamp.net>
References: <CAH6Pt5oMVLJ0zyknfwVR9ako9wSFVYMf2A_bzHToG4AyV-=vVg@mail.gmail.com>
 <CALzTN-ShTvDJSQPEKo_WHvVm8x7tpyT_WyM+-1oZ-7Hc0yvQKg@mail.gmail.com>
 <CAH6Pt5ov=9ta=Qk6WHFCicS8AVKdKF0ZnBanYqUgcUpwSduKmg@mail.gmail.com>
 <CALzTN-TGDXtp1JZP047M3btTwTd6L1pHaHb88HVztUYmxEQy=w@mail.gmail.com>
 <29A0B0AE-5D9D-4EDC-8866-BE9B802E0E08@mail.nih.gov>
 <CAH6Pt5p7jVM+SkZNZfFYyZYtDoqS7mwdSNn6uMh_LcuC4C18tg@mail.gmail.com>
 <D339D74E-DFBF-4658-921E-1DB7C65FCD56@lowekamp.net>
Message-ID: <CALzTN-SdKQ4YuNdLqNO0yh_c4pY31qQLY+oPnrXA8dDr-8fU3Q@mail.gmail.com>

>>> The problem with the OS X wheels is that they are too big for pipy at about 75mb. These are still fat binaries of i386 and x86_64. I have not check what pip would do with just a x86_64 wheel but with a fat Python version.
>>
>> I think the pypi maintainers would be OK with increasing the upload
>> size for you if you asked them - I remember matplotlib discussing this
>> with them a while ago (they were a tad over 50M at the time).
>>
>> But - I think it's also completely reasonable to drop off the i386
>> architecture and claim (via the wheel filename) that it's a fat wheel
>> - I built and uploaded an h5py wheel about a year ago for which the
>> i386 execution was segfaulting, but no-one noticed.  I doubt anyone
>> using SimpleITK would use the i386 architecture in the fat wheel
>> either.
>
> Do you know the way to contact the pypi maintainers to make this request?

I added that request here:

  https://sourceforge.net/p/pypi/support-requests/415/

Part of the answer was that an increased size could be possible when
Warehouse goes live, and it is now live.

So, it would be worthwhile trying to upload to warehouse as described here:

  https://mail.python.org/pipermail/distutils-sig/2016-June/029083.html

although the upload URL has recently been changed to
https://upload.pypi.org/legacy/ per

  https://mail.python.org/pipermail/distutils-sig/2016-July/029332.html

If it does not work, then a ping on the issue or distutils-sig may help.

HTH,
Matt

From matt.mccormick at kitware.com  Sun Jul 31 19:29:21 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 31 Jul 2016 19:29:21 -0400
Subject: [ITK] [ITK-users] Import itk always takes ages and results in
	warnings
In-Reply-To: <CAO8H67PRxGby0gt0ZzSUYMU0O=e+C1Gw1Pj4zvXSMsLs4+7esg@mail.gmail.com>
References: <CAO8H67PxXkXJgLSoKST2gOdfH2jRYmuL4D0hkE9RUVU-FGGU3A@mail.gmail.com>
 <A651064C-2610-47EF-9DDE-914666F048D1@gmail.com>
 <CAO8H67PRxGby0gt0ZzSUYMU0O=e+C1Gw1Pj4zvXSMsLs4+7esg@mail.gmail.com>
Message-ID: <CALzTN-RMaiAr0m37rOFpxM4CqX4SMFLqcYk3gPNTBnX_fPujEw@mail.gmail.com>

Hi JP,

The ITK Python import time was increased by a factor of two in 4.10.0
compared to 4.9.0 by hiding symbols in the generated libraries. The
next release of ITK will improve the import time by a factor of ten in
some cases because the lazy loading has been fixed [1]. Instructions
to try out the development version can be found here [2].

HTH,
Matt

[1] http://review.source.kitware.com/#/c/21305/

[2] https://itk.org/Wiki/ITK/Git/Download

On Tue, Jun 28, 2016 at 4:59 AM,  <cervellone at gmail.com> wrote:
> Dear Michka
> Thank you for your reply.
>
> I will take that into consideration when building ITK next time.
> Unfortunately there is little comprehensive guide to what all those options
> in cmake really mean or do, so id rather build more than less.
> Also VTK is pretty heavy in term of modules, and I have the impression that
> it is noticeably faster.
> Best
> JP
>
> On Mon, Jun 27, 2016 at 10:03 PM, Michka Popoff <michkapopoff at gmail.com>
> wrote:
>>
>> Hi
>>
>> to reduce the import time, one solution would be to reduce the number of
>> wrapped modules
>> and types (and image/vector dimensions). If you re-build ITK by disabling
>> the things you
>> don?t need, there will be less things to load.
>>
>> I have some ideas on how to improve the import situation but never came to
>> it, so
>> not sure anybody has been working intensively on that.
>>
>> For the warnings, we need to fix them in ITK.
>> The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is.
>>
>> If you want to hide the warnings, you can use (like for other python
>> warnings):
>>
>> import warnings
>> warnings.simplefilter(?ignore", Warning)
>>
>> You can reset the filter after the import.
>>
>> That should to it.
>>
>>
>> Michka
>>
>> > On 26 Jun 2016, at 22:07, cervellone at gmail.com wrote:
>> >
>> > Hello all,
>> >
>> > Is there a way to speed up the import of itk in an application and the
>> > suppression of the warnings I get every time I run the python script ?
>> >
>> > Thank you all
>> > JP
>> >
>> >
>> > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo<
>> > 3,float,float,unsigned long,unsigned long,unsigned
>> > char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned
>> > long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned
>> > long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned
>> > long,unsigned long,bool,bool,true > > >,std::set< unsigned long
>> > >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >'
>> > in template 'itk::CellInterface'
>> >
>> >
>> > _____________________________________
>> > 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
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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:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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