From maudette at odu.edu  Mon Mar  2 14:45:23 2015
From: maudette at odu.edu (Audette, Michel A.)
Date: Mon, 2 Mar 2015 19:45:23 +0000
Subject: [ITK-users] possible to get a closest-point map from a distance map
	in ITK?
Message-ID: <22EC75E8215562428ACADFA35877A25A26187E3F@JANEWAY.ts.odu.edu>

Dear ITK users,



a student of mine would like to use the ITK implementation of distance maps in a way where the point label of the closest initial boundary is propagated throughout, i.e. a closest boundary point map. Is there something like this implemented already in ITK? I would like to use something like this to produce a spatially varying distance threshold.



Thanks for your kind support.



Michel



Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
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From richard.beare at gmail.com  Mon Mar  2 15:37:06 2015
From: richard.beare at gmail.com (Richard Beare)
Date: Tue, 3 Mar 2015 07:37:06 +1100
Subject: [ITK-users] possible to get a closest-point map from a distance
 map in ITK?
In-Reply-To: <22EC75E8215562428ACADFA35877A25A26187E3F@JANEWAY.ts.odu.edu>
References: <22EC75E8215562428ACADFA35877A25A26187E3F@JANEWAY.ts.odu.edu>
Message-ID: <CA+V7QS_c146Vz_wO9+Do+qFAhCeWPFjJXEVUWTH=i5PPOEJ1cw@mail.gmail.com>

I've written a set of label erosion and dilation filters that might do what
you're after. I've also got some spatially varying morphology filters, but
have't put them on the insight journal. The label erode dilate filters
aren't outputing the distance map, so they aren't exactly what you want,
but they use the same kind of computation internally. Thus you could use
them in conjunction with the parabolic distance transforms to get labels
and distances.

https://github.com/richardbeare/LabelErodeDilate.git
https://github.com/richardbeare/parabolicMorphology.git

The insight journal article.

http://hdl.handle.net/10380/3399


I can provide more details about the spatially variant stuff if it is of
interest. Note that it only works with binary images, and simply weights
the input image.

On Tue, Mar 3, 2015 at 6:45 AM, Audette, Michel A. <maudette at odu.edu> wrote:

>  Dear ITK users,
>
>
>
> a student of mine would like to use the ITK implementation of distance
> maps in a way where the point label of the closest initial boundary is
> propagated throughout, i.e. a closest boundary point map. Is there
> something like this implemented already in ITK? I would like to use
> something like this to produce a spatially varying distance threshold.
>
>
>
> Thanks for your kind support.
>
>
>
> Michel
>
>
> Michel Audette, Ph.D.
> Assistant Professor,
> Department of Modeling, Simulation and Visualization Engineering,
> Old Dominion University,
> Norfolk, VA.
>
> _____________________________________
> 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 88.vikram at gmail.com  Tue Mar  3 02:19:40 2015
From: 88.vikram at gmail.com (Vikram Venkatraghavan)
Date: Tue, 3 Mar 2015 12:49:40 +0530
Subject: [ITK-users] Reading a very large image
Message-ID: <CANcPDb8t-GR0sbt4O=8yj42yERbgxAXWZfi-N4y0u6WJRLdOOg@mail.gmail.com>

Hello,

I am relatively new to ITK. I am trying to read a very large TIFF image
using the IO streaming functionality in ITK. I am reading a very small
portion of the image and I still end up getting memory allocation error. I
get the feeling, the code is trying to read the entire image at once, even
after specifying the region to read. Can someone please tell what is wrong
the following code snippet ?

typedef itk::RGBPixel< unsigned char >  RGBPixelType;
typedef itk::Image< RGBPixelType, 2 >   RGB2DImageType;
typedef itk::ImageFileReader<RGB2DImageType> RGBReaderType;

itk::TIFFImageIO::Pointer tiffIO = itk::TIFFImageIO::New();
tiffIO->SetPixelType(itk::ImageIOBase::RGBA);

RGB2DImageType::SizeType sz;
RGB2DImageType::IndexType idx;
sz[0]=128; sz[1]=128;
idx[0]=0; idx[1]=0;

itk::ImageIORegion region(2);
region.SetSize(0,sz[0]);
region.SetSize(1,sz[1]);
region.SetIndex(0,idx[0]);
region.SetIndex(1,idx[1]);
tiffIO->SetIORegion(region);

RGBReaderType::Pointer reader = RGBReaderType::New();
reader->SetFileName("V:\\TiFF_Image.tiff");
reader->SetImageIO(tiffIO);
reader->SetUseStreaming(1);
reader->Update();

Thanks in advance.

Regards,
Vikram
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From lluna.nova at gmail.com  Tue Mar  3 04:35:14 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Tue, 3 Mar 2015 10:35:14 +0100
Subject: [ITK-users] Reading a very large image
In-Reply-To: <CANcPDb8t-GR0sbt4O=8yj42yERbgxAXWZfi-N4y0u6WJRLdOOg@mail.gmail.com>
References: <CANcPDb8t-GR0sbt4O=8yj42yERbgxAXWZfi-N4y0u6WJRLdOOg@mail.gmail.com>
Message-ID: <CALAZn4gVUS_PMbem0xKGcQeuaaamg9QSD0to-vYaWo+=pgZ=-g@mail.gmail.com>

Hello Vikram,


I followed the same road a few months ago, read the kind and insightful
answer of Bradley here:
http://public.kitware.com/pipermail/community/2014-November/007678.html

tl; dr
@Bradley is working on streaming the tiff reader, but it isn't ready yet
(right? I apologize for not having had the time to test it). So indeed,
your reader is reading the whole image. Try using mha instead if possible.


2015-03-03 8:19 GMT+01:00 Vikram Venkatraghavan <88.vikram at gmail.com>:

> Hello,
>
> I am relatively new to ITK. I am trying to read a very large TIFF image
> using the IO streaming functionality in ITK. I am reading a very small
> portion of the image and I still end up getting memory allocation error. I
> get the feeling, the code is trying to read the entire image at once, even
> after specifying the region to read. Can someone please tell what is wrong
> the following code snippet ?
>
> typedef itk::RGBPixel< unsigned char >  RGBPixelType;
> typedef itk::Image< RGBPixelType, 2 >   RGB2DImageType;
> typedef itk::ImageFileReader<RGB2DImageType> RGBReaderType;
>
> itk::TIFFImageIO::Pointer tiffIO = itk::TIFFImageIO::New();
> tiffIO->SetPixelType(itk::ImageIOBase::RGBA);
>
> RGB2DImageType::SizeType sz;
> RGB2DImageType::IndexType idx;
> sz[0]=128; sz[1]=128;
> idx[0]=0; idx[1]=0;
>
> itk::ImageIORegion region(2);
> region.SetSize(0,sz[0]);
> region.SetSize(1,sz[1]);
> region.SetIndex(0,idx[0]);
> region.SetIndex(1,idx[1]);
> tiffIO->SetIORegion(region);
>
> RGBReaderType::Pointer reader = RGBReaderType::New();
> reader->SetFileName("V:\\TiFF_Image.tiff");
> reader->SetImageIO(tiffIO);
> reader->SetUseStreaming(1);
> reader->Update();
>
> Thanks in advance.
>
> Regards,
> Vikram
>
> _____________________________________
> 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 Mar  3 09:27:11 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 3 Mar 2015 09:27:11 -0500
Subject: [ITK-users] Reading a very large image
In-Reply-To: <CALAZn4gVUS_PMbem0xKGcQeuaaamg9QSD0to-vYaWo+=pgZ=-g@mail.gmail.com>
References: <CANcPDb8t-GR0sbt4O=8yj42yERbgxAXWZfi-N4y0u6WJRLdOOg@mail.gmail.com>
 <CALAZn4gVUS_PMbem0xKGcQeuaaamg9QSD0to-vYaWo+=pgZ=-g@mail.gmail.com>
Message-ID: <B360B595-4E02-47B7-B115-C4FD215D0876@mail.nih.gov>

Hello Vikram,

Unfortunately TIFFImageIO doesn't support streaming. So your code will try to load the whole things.

Perhaps you can find a machine with a large amount of memory and convert the TIFF to a mha file to perform ITK streaming processing on?

However, even if TIFFImageIO supported streaming your code would still try to read the largest possible region.

The ImageIORegion::SetIORegion is not a method that really should be used for IO streaming. For reading images the ITK pipeline architecture will take care of it automatically, by only reading the requested region. For writing the SetNumberOfStreamingDivisions methods can be set to sequentially write a region, and the ImageFileWriter::SetIORegion, can be use to only update a sub-region in the output.

I would strongly urge to read Section 8.3 of the new ITK Software guide[1][2], a couple of times. You need to be comfortable processing images with the LargestPossibleRegion being different than the buffered region. As well as know that just calling Update, is the same thing as calling UpdateLargestPossibleRegion

Consider the following changes:

1) Remove the manual setup of the ImageIO, just let the factory take care of it.
2) Replace the Update call with: SetRequestedRegion(region) followed by PropagateRequestedRegion(). ( This will not cause memory allocation or reading. It'll just determine what the ImageIO can read).
3) Print the output, of the image reader. Noting the LargestPossibleRegion, BufferedRegion and the RequestedRegion.

Hope that gets you started,
Brad


[1] http://www.itk.org/ITK/resources/software.html
[2] http://www.amazon.com/ITK-Software-Guide-Book-Introduction/dp/1930934270/ref=sr_1_1?ie=UTF8&qid=1425392002&sr=8-1&keywords=ITK+Software


Pol,

Yes, I did a bit of work on the TIFFImageIO for the 4.7 ITK release, to improve performance (~3-5X) and add support for the TIFF tags in the meta-data dictionary. This took a good bit of time, and just improving the read performance was sufficient for my project, and I didn't need streaming. It would certainly be nice to add streaming, but I haven't gotten around to it. Letting me know it's important to people certainly helps prioritize :)

Brad


On Mar 3, 2015, at 4:35 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:

> Hello Vikram,
> 
> 
> I followed the same road a few months ago, read the kind and insightful answer of Bradley here: http://public.kitware.com/pipermail/community/2014-November/007678.html
> 
> tl; dr
> @Bradley is working on streaming the tiff reader, but it isn't ready yet (right? I apologize for not having had the time to test it). So indeed, your reader is reading the whole image. Try using mha instead if possible.
> 
> 
> 2015-03-03 8:19 GMT+01:00 Vikram Venkatraghavan <88.vikram at gmail.com>:
> Hello,
> 
> I am relatively new to ITK. I am trying to read a very large TIFF image using the IO streaming functionality in ITK. I am reading a very small portion of the image and I still end up getting memory allocation error. I get the feeling, the code is trying to read the entire image at once, even after specifying the region to read. Can someone please tell what is wrong the following code snippet ?
> 
> typedef itk::RGBPixel< unsigned char >  RGBPixelType;
> typedef itk::Image< RGBPixelType, 2 >   RGB2DImageType;
> typedef itk::ImageFileReader<RGB2DImageType> RGBReaderType;
> 
> itk::TIFFImageIO::Pointer tiffIO = itk::TIFFImageIO::New();
> tiffIO->SetPixelType(itk::ImageIOBase::RGBA);
> 
> RGB2DImageType::SizeType sz;
> RGB2DImageType::IndexType idx;
> sz[0]=128; sz[1]=128;
> idx[0]=0; idx[1]=0;
> 
> itk::ImageIORegion region(2);
> region.SetSize(0,sz[0]);
> region.SetSize(1,sz[1]);
> region.SetIndex(0,idx[0]);
> region.SetIndex(1,idx[1]);
> tiffIO->SetIORegion(region);
> 
> RGBReaderType::Pointer reader = RGBReaderType::New();
> reader->SetFileName("V:\\TiFF_Image.tiff");
> reader->SetImageIO(tiffIO);
> reader->SetUseStreaming(1);
> reader->Update();
> 
> Thanks in advance.
> 
> Regards,
> Vikram
> 
> _____________________________________
> 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 majcjc at gmail.com  Tue Mar  3 11:23:29 2015
From: majcjc at gmail.com (Lin M)
Date: Tue, 3 Mar 2015 11:23:29 -0500
Subject: [ITK-users] find_package(ITK) and find_package(VTK) problems in
	CMake
Message-ID: <CALmrq1a8zSQzPXmkHC7zkjmtbntoVpfKJ5=aJRWLhzBGuXV=4Q@mail.gmail.com>

Hi guys,

I met a strange problem when I try to use ITK and VTK in my projects. If I
only use find_package( VTK required ) cmake will find all the right .h and
.lib files and add them to the project, but if I use both find_package(ITK)
and find_package(VTK), then some of the .h and .lib of VTK just disappeared
in my VS projects. Does anyone have some suggestions for that? Thank you
very much!

My CMakeLists.txt is written as below:

...
...
# QT FILES
FIND_PACKAGE( Qt5Widgets )
FIND_PACKAGE( Qt5Xml )
FIND_PACKAGE( Qt5Core )

# ITK FILES
FIND_PACKAGE( ITK REQUIRED )
INCLUDE( ${ITK_USE_FILE} )

# VTK FILES
FIND_PACKAGE( VTK REQUIRED )
NCLUDE( ${VTK_USE_FILE} )

...
...
TARGET_LINK_LIBRARIES( ${PROJECT_NAME}
   ${Qt5Widgets_LIBRARIES}
   ${Qt5Xml_LIBRARIES}
   ${Qt5Core_LIBRARIES}
   ${VTK_LIBRARIES}
   ${ITK_LIBRARIES}
   )


Best,
Lin
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From jlg145 at pitt.edu  Tue Mar  3 17:00:36 2015
From: jlg145 at pitt.edu (Grimm, Jonathan Louis)
Date: Tue, 3 Mar 2015 22:00:36 +0000
Subject: [ITK-users] Position on Image Registration and Analysis
Message-ID: <1425420037101.94853@pitt.edu>

The Laboratory of Ocular Biomechanics at the University of Pittsburgh is seeking candidates for a position on image analysis and soft tissue biomechanics. Although our preference is for a post-doctoral fellow, strong candidates without a PhD will be considered.?


More information provided in the link.


http://ocularbiomechanics.org/pdfs/PostDocAd-ITK_WithImages_27Feb.pdf<http://ocularbiomechanics.com/pdfs/PostDocAd-ITK_WithImages_27Feb.pdf>
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From zeinsalah at gmail.com  Wed Mar  4 05:25:52 2015
From: zeinsalah at gmail.com (Zein Salah)
Date: Wed, 4 Mar 2015 11:25:52 +0100
Subject: [ITK-users] Filling the region inside a closed contour
Message-ID: <CADiSopNMtXi+0uxOFLa=dJ7fq+aLUOpHJ_6X+7p3EeqX=JCr=g@mail.gmail.com>

Hi,

I want to fill the region surrounded by a closed contour in a 2d
itk image. I have been doing this using a reverse flood-filling procedure.
I am wondering is itk has a more efficient/robust mechanism for
doing this.

BTW, 2d-coordinates of the point on the contour are also stored in a
vector if this helps.

thanks,
Zeno

From blowekamp at mail.nih.gov  Wed Mar  4 09:30:39 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 4 Mar 2015 09:30:39 -0500
Subject: [ITK-users] possible to get a closest-point map from a distance
	map in ITK?
In-Reply-To: <CA+V7QS_c146Vz_wO9+Do+qFAhCeWPFjJXEVUWTH=i5PPOEJ1cw@mail.gmail.com>
References: <22EC75E8215562428ACADFA35877A25A26187E3F@JANEWAY.ts.odu.edu>
 <CA+V7QS_c146Vz_wO9+Do+qFAhCeWPFjJXEVUWTH=i5PPOEJ1cw@mail.gmail.com>
Message-ID: <564311ED-2E71-4B12-919B-C36B78084AF8@mail.nih.gov>

Richard,

You have some nice additional morphological filters in those repositories. I have been meaning to give them a try.

Given that you have Insight Journal articles for them, have you considered making them more readily available to the community by adding and converting them into Remote modules for ITK?

Brad

On Mar 2, 2015, at 3:37 PM, Richard Beare <richard.beare at gmail.com> wrote:

> I've written a set of label erosion and dilation filters that might do what you're after. I've also got some spatially varying morphology filters, but have't put them on the insight journal. The label erode dilate filters aren't outputing the distance map, so they aren't exactly what you want, but they use the same kind of computation internally. Thus you could use them in conjunction with the parabolic distance transforms to get labels and distances.
> 
> https://github.com/richardbeare/LabelErodeDilate.git
> https://github.com/richardbeare/parabolicMorphology.git
> 
> The insight journal article.
> 
> http://hdl.handle.net/10380/3399
> 
> 
> I can provide more details about the spatially variant stuff if it is of interest. Note that it only works with binary images, and simply weights the input image.
> 
> On Tue, Mar 3, 2015 at 6:45 AM, Audette, Michel A. <maudette at odu.edu> wrote:
> Dear ITK users,
> 
>  
> a student of mine would like to use the ITK implementation of distance maps in a way where the point label of the closest initial boundary is propagated throughout, i.e. a closest boundary point map. Is there something like this implemented already in ITK? I would like to use something like this to produce a spatially varying distance threshold.
> 
>  
> Thanks for your kind support.
> 
>  
> Michel
> 
>  
> Michel Audette, Ph.D.
> Assistant Professor,
> Department of Modeling, Simulation and Visualization Engineering,
> Old Dominion University,
> Norfolk, VA.
> 
> _____________________________________
> 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 blowekamp at mail.nih.gov  Wed Mar  4 09:28:44 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 4 Mar 2015 09:28:44 -0500
Subject: [ITK-users] Filling the region inside a closed contour
In-Reply-To: <CADiSopNMtXi+0uxOFLa=dJ7fq+aLUOpHJ_6X+7p3EeqX=JCr=g@mail.gmail.com>
References: <CADiSopNMtXi+0uxOFLa=dJ7fq+aLUOpHJ_6X+7p3EeqX=JCr=g@mail.gmail.com>
Message-ID: <D8323013-16B2-4F6B-93F7-641009764B18@mail.nih.gov>

Hello,

The turn-key solution would the to use the BinaryFillholeImageFilter[1]. There may be a solution which uses connected components and the LabelMap framework to determine the regions separated by the contour. Then there are a variety of conditional flood fill conditional iterators that could be used [2].

Lastly if I could make the assumption that the contour didn't touch the boarder, I'd write a threaded filter which uses a scan-line iterator which would alternate between an inside  and outside state based on encountering the input contour and wrote the output image accordingly.

You have options. The "best" or most "efficient" or most "robust" method can only be determine with experimentation and quantification for your problem.

Brad

[1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryFillholeImageFilter.html
[2] http://www.itk.org/Doxygen/html/classitk_1_1ShapedFloodFilledFunctionConditionalConstIterator.html

On Mar 4, 2015, at 5:25 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi,
> 
> I want to fill the region surrounded by a closed contour in a 2d
> itk image. I have been doing this using a reverse flood-filling procedure.
> I am wondering is itk has a more efficient/robust mechanism for
> doing this.
> 
> BTW, 2d-coordinates of the point on the contour are also stored in a
> vector if this helps.
> 
> thanks,
> Zeno
> _____________________________________
> 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 lchauvin at bwh.harvard.edu  Wed Mar  4 14:11:15 2015
From: lchauvin at bwh.harvard.edu (Laurent Chauvin)
Date: Wed, 4 Mar 2015 14:11:15 -0500
Subject: [ITK-users] 1 DOF Optimizer
Message-ID: <CAPGPba+PwNCvCjs26p4QumNOBBkS5-CC+o=DCBA7GxeNHwuYpQ@mail.gmail.com>

Hello,

I'm trying to develop a registration algorithm, and in order to do that, I
need an optimizer but I couldn't find this kind in ITK.
I need to specificy a plane, and rotate this plane around one given axis,
on 360 degrees (with a step of 1 degree for example), and calculate some
energy function for each step and find the minimum.
360 degrees avoid to find local minima only.

Do you know if such optimizer already exists ?

Thank you very much.
-Laurent
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From blowekamp at mail.nih.gov  Wed Mar  4 14:21:12 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 4 Mar 2015 14:21:12 -0500
Subject: [ITK-users] 1 DOF Optimizer
In-Reply-To: <CAPGPba+PwNCvCjs26p4QumNOBBkS5-CC+o=DCBA7GxeNHwuYpQ@mail.gmail.com>
References: <CAPGPba+PwNCvCjs26p4QumNOBBkS5-CC+o=DCBA7GxeNHwuYpQ@mail.gmail.com>
Message-ID: <210B4188-70F4-4E95-97D1-527CC3162EC8@mail.nih.gov>

Hello Laurent,

You can configure the ExhaustiveOptimizer to do that [1], [2].

Brad

[1] http://www.itk.org/Doxygen46/html/classitk_1_1ExhaustiveOptimizer.html
[2] http://www.itk.org/Doxygen46/html/classitk_1_1ExhaustiveOptimizerv4.html

On Mar 4, 2015, at 2:11 PM, Laurent Chauvin <lchauvin at bwh.harvard.edu> wrote:

> Hello,
> 
> I'm trying to develop a registration algorithm, and in order to do that, I need an optimizer but I couldn't find this kind in ITK.
> I need to specificy a plane, and rotate this plane around one given axis, on 360 degrees (with a step of 1 degree for example), and calculate some energy function for each step and find the minimum.
> 360 degrees avoid to find local minima only.
> 
> Do you know if such optimizer already exists ?
> 
> Thank you very much.
> -Laurent
> _____________________________________
> 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 lchauvin at bwh.harvard.edu  Wed Mar  4 14:24:45 2015
From: lchauvin at bwh.harvard.edu (Laurent Chauvin)
Date: Wed, 4 Mar 2015 14:24:45 -0500
Subject: [ITK-users] 1 DOF Optimizer
In-Reply-To: <210B4188-70F4-4E95-97D1-527CC3162EC8@mail.nih.gov>
References: <CAPGPba+PwNCvCjs26p4QumNOBBkS5-CC+o=DCBA7GxeNHwuYpQ@mail.gmail.com>
 <210B4188-70F4-4E95-97D1-527CC3162EC8@mail.nih.gov>
Message-ID: <CAPGPbaJ511Vc0r19AbJzJ513sV+70GwecDpQOJFB=9euFj1ZqQ@mail.gmail.com>

Thank you Bradley, I will have a look at it.

-Laurent

On Wed, Mar 4, 2015 at 2:21 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello Laurent,
>
> You can configure the ExhaustiveOptimizer to do that [1], [2].
>
> Brad
>
> [1] http://www.itk.org/Doxygen46/html/classitk_1_1ExhaustiveOptimizer.html
> [2]
> http://www.itk.org/Doxygen46/html/classitk_1_1ExhaustiveOptimizerv4.html
>
> On Mar 4, 2015, at 2:11 PM, Laurent Chauvin <lchauvin at bwh.harvard.edu>
> wrote:
>
> > Hello,
> >
> > I'm trying to develop a registration algorithm, and in order to do that,
> I need an optimizer but I couldn't find this kind in ITK.
> > I need to specificy a plane, and rotate this plane around one given
> axis, on 360 degrees (with a step of 1 degree for example), and calculate
> some energy function for each step and find the minimum.
> > 360 degrees avoid to find local minima only.
> >
> > Do you know if such optimizer already exists ?
> >
> > Thank you very much.
> > -Laurent
> > _____________________________________
> > 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
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
>
>


-- 
Laurent Chauvin, MS
Surgical Navigation and Robotics Laboratory, Radiology Department
Brigham And Women's Hospital, Harvard Medical School
http://wiki.ncigt.org/index.php/User:Lchauvin
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From tejasm at gmail.com  Wed Mar  4 14:40:33 2015
From: tejasm at gmail.com (tejas9090)
Date: Wed, 4 Mar 2015 12:40:33 -0700 (MST)
Subject: [ITK-users] ITK Ver 4.5 memory leak in HDF5 library
Message-ID: <1425498033934-7586961.post@n2.nabble.com>

Hi, 

Apologies if this topic has been posted before but I could not find an
answer for this. 

I am using Visual Leak Detector with my VC++/VS2012 code which uses ITK 4.5.
The output shows some memory leaks at program exit in the HDF5 library.
Sample memory leak output from VLD shown below. 

Does anyone know if this is a genuine leak and if there is way to fix this? 

Thank you in advance, 
TJ 


Visual Visual Leak Detector Version 2.4RC2 installed. 
    Outputting the report to the debugger and to
C:\MyProject\Algorithm\AlgorithmBuild\Driver\memory_leak_report.txt 
WARNING: Visual Leak Detector detected memory leaks! 
---------- Block 1035319 at 0x0069C2C0: 8 bytes ---------- 
  Leak Hash: 0x83CD32EA, Count: 1, Total 8 bytes 
  Call Stack (TID 296): 
    f:\dd\vctools\crt_bld\self_x86\crt\src\dbgmalloc.c (55):
MSVCR110D.dll!malloc 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5fl.c
(241): (Module name unavailable)!H5FL_reg_init + 0xA bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5fl.c
(382): (Module name unavailable)!H5FL_reg_malloc + 0x9 bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5fl.c
(458): (Module name unavailable)!H5FL_reg_calloc + 0x9 bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5e.c
(464): (Module name unavailable)!H5E_register_class + 0xA bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5e.c
(238): (Module name unavailable)!H5E_init_interface + 0x16 bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5e.c
(147): (Module name unavailable)!H5E_init + 0x1F bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5.c
(170): (Module name unavailable)!H5_init_library + 0x5 bytes 
    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5i.c
(1131): (Module name unavailable)!H5Iget_type + 0x1F bytes 
   
C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\c++\src\h5idcomponent.cpp
(317): (Module name unavailable)!H5::IdComponent::p_valid_id + 0x9 bytes 
   
C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\c++\src\h5dataspace.cpp
(608): (Module name unavailable)!H5::DataSpace::close + 0xC bytes 
   
C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\c++\src\h5dataspace.cpp
(633): (Module name unavailable)!H5::DataSpace::~DataSpace + 0x8 bytes 
    0x108DE98D (File and line number not available): (Module name
unavailable)!`dynamic atexit destructor for 'H5::DataSpace::ALL'' + 0xD
bytes 
    f:\dd\vctools\crt_bld\self_x86\crt\src\crtdll.c (416): (Module name
unavailable)!_CRT_INIT 
    f:\dd\vctools\crt_bld\self_x86\crt\src\crtdll.c (522): (Module name
unavailable)!__DllMainCRTStartup + 0x11 bytes 
    f:\dd\vctools\crt_bld\self_x86\crt\src\crtdll.c (472): (Module name
unavailable)!_DllMainCRTStartup + 0x11 bytes 
    0x772999A0 (File and line number not available):
ntdll.dll!RtlQueryEnvironmentVariable + 0x241 bytes 
    0x772BAD1E (File and line number not available):
ntdll.dll!LdrRemoveLoadAsDataTable + 0x5D5 bytes 
    0x772A12D1 (File and line number not available): ntdll.dll!LdrUnloadDll
+ 0x4A bytes 
    0x76CF2D2C (File and line number not available):
KERNELBASE.dll!FreeLibrary + 0x15 bytes 
    C:\MyProject\Algorithm\driver\loadccmdll_w.cpp (112):
Driver.exe!ATMAlgo_W::FreeDll + 0x12 bytes 
    C:\MyProject\Algorithm\driver\loadruncc_w.cpp (28): Driver.exe!Clean 
    C:\MyProject\Algorithm\driver\main.cpp (207): Driver.exe!main 
    f:\dd\vctools\crt_bld\self_x86\crt\src\crtexe.c (536):
Driver.exe!__tmainCRTStartup + 0x19 bytes 
    f:\dd\vctools\crt_bld\self_x86\crt\src\crtexe.c (377):
Driver.exe!mainCRTStartup 
    0x764A338A (File and line number not available):
kernel32.dll!BaseThreadInitThunk + 0x12 bytes 
    0x77299F72 (File and line number not available):
ntdll.dll!RtlInitializeExceptionChain + 0x63 bytes 
    0x77299F45 (File and line number not available):
ntdll.dll!RtlInitializeExceptionChain + 0x36 bytes 
  Data: 
    C0 CA BF 10    00 00 00 00     




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View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Ver-4-5-memory-leak-in-HDF5-library-tp7586961.html
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From blowekamp at mail.nih.gov  Wed Mar  4 14:53:18 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 4 Mar 2015 14:53:18 -0500
Subject: [ITK-users] ITK Ver 4.5 memory leak in HDF5 library
In-Reply-To: <1425498033934-7586961.post@n2.nabble.com>
References: <1425498033934-7586961.post@n2.nabble.com>
Message-ID: <C74D017A-13AF-420D-8CA6-E2DB1492C665@mail.nih.gov>

Hello,

Thanks for reporting this!

We don't have any HDF5 suppressions for the valgrind memory defect checking we run each night.

Is there a minimal program which exhibits this behavior on Windows?

Brad

On Mar 4, 2015, at 2:40 PM, tejas9090 <tejasm at gmail.com> wrote:

> Hi, 
> 
> Apologies if this topic has been posted before but I could not find an
> answer for this. 
> 
> I am using Visual Leak Detector with my VC++/VS2012 code which uses ITK 4.5.
> The output shows some memory leaks at program exit in the HDF5 library.
> Sample memory leak output from VLD shown below. 
> 
> Does anyone know if this is a genuine leak and if there is way to fix this? 
> 
> Thank you in advance, 
> TJ 
> 
> 
> Visual Visual Leak Detector Version 2.4RC2 installed. 
>    Outputting the report to the debugger and to
> C:\MyProject\Algorithm\AlgorithmBuild\Driver\memory_leak_report.txt 
> WARNING: Visual Leak Detector detected memory leaks! 
> ---------- Block 1035319 at 0x0069C2C0: 8 bytes ---------- 
>  Leak Hash: 0x83CD32EA, Count: 1, Total 8 bytes 
>  Call Stack (TID 296): 
>    f:\dd\vctools\crt_bld\self_x86\crt\src\dbgmalloc.c (55):
> MSVCR110D.dll!malloc 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5fl.c
> (241): (Module name unavailable)!H5FL_reg_init + 0xA bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5fl.c
> (382): (Module name unavailable)!H5FL_reg_malloc + 0x9 bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5fl.c
> (458): (Module name unavailable)!H5FL_reg_calloc + 0x9 bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5e.c
> (464): (Module name unavailable)!H5E_register_class + 0xA bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5e.c
> (238): (Module name unavailable)!H5E_init_interface + 0x16 bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5e.c
> (147): (Module name unavailable)!H5E_init + 0x1F bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5.c
> (170): (Module name unavailable)!H5_init_library + 0x5 bytes 
>    C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\src\h5i.c
> (1131): (Module name unavailable)!H5Iget_type + 0x1F bytes 
> 
> C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\c++\src\h5idcomponent.cpp
> (317): (Module name unavailable)!H5::IdComponent::p_valid_id + 0x9 bytes 
> 
> C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\c++\src\h5dataspace.cpp
> (608): (Module name unavailable)!H5::DataSpace::close + 0xC bytes 
> 
> C:\MyProject\tp\itk4_5\modules\thirdparty\hdf5\src\itkhdf5\c++\src\h5dataspace.cpp
> (633): (Module name unavailable)!H5::DataSpace::~DataSpace + 0x8 bytes 
>    0x108DE98D (File and line number not available): (Module name
> unavailable)!`dynamic atexit destructor for 'H5::DataSpace::ALL'' + 0xD
> bytes 
>    f:\dd\vctools\crt_bld\self_x86\crt\src\crtdll.c (416): (Module name
> unavailable)!_CRT_INIT 
>    f:\dd\vctools\crt_bld\self_x86\crt\src\crtdll.c (522): (Module name
> unavailable)!__DllMainCRTStartup + 0x11 bytes 
>    f:\dd\vctools\crt_bld\self_x86\crt\src\crtdll.c (472): (Module name
> unavailable)!_DllMainCRTStartup + 0x11 bytes 
>    0x772999A0 (File and line number not available):
> ntdll.dll!RtlQueryEnvironmentVariable + 0x241 bytes 
>    0x772BAD1E (File and line number not available):
> ntdll.dll!LdrRemoveLoadAsDataTable + 0x5D5 bytes 
>    0x772A12D1 (File and line number not available): ntdll.dll!LdrUnloadDll
> + 0x4A bytes 
>    0x76CF2D2C (File and line number not available):
> KERNELBASE.dll!FreeLibrary + 0x15 bytes 
>    C:\MyProject\Algorithm\driver\loadccmdll_w.cpp (112):
> Driver.exe!ATMAlgo_W::FreeDll + 0x12 bytes 
>    C:\MyProject\Algorithm\driver\loadruncc_w.cpp (28): Driver.exe!Clean 
>    C:\MyProject\Algorithm\driver\main.cpp (207): Driver.exe!main 
>    f:\dd\vctools\crt_bld\self_x86\crt\src\crtexe.c (536):
> Driver.exe!__tmainCRTStartup + 0x19 bytes 
>    f:\dd\vctools\crt_bld\self_x86\crt\src\crtexe.c (377):
> Driver.exe!mainCRTStartup 
>    0x764A338A (File and line number not available):
> kernel32.dll!BaseThreadInitThunk + 0x12 bytes 
>    0x77299F72 (File and line number not available):
> ntdll.dll!RtlInitializeExceptionChain + 0x63 bytes 
>    0x77299F45 (File and line number not available):
> ntdll.dll!RtlInitializeExceptionChain + 0x36 bytes 
>  Data: 
>    C0 CA BF 10    00 00 00 00     
> 
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Ver-4-5-memory-leak-in-HDF5-library-tp7586961.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From tejasm at gmail.com  Wed Mar  4 15:01:55 2015
From: tejasm at gmail.com (tejas9090)
Date: Wed, 4 Mar 2015 13:01:55 -0700 (MST)
Subject: [ITK-users] ITK Ver 4.5 memory leak in HDF5 library
In-Reply-To: <C74D017A-13AF-420D-8CA6-E2DB1492C665@mail.nih.gov>
References: <1425498033934-7586961.post@n2.nabble.com>
 <C74D017A-13AF-420D-8CA6-E2DB1492C665@mail.nih.gov>
Message-ID: <1425499315444-7586963.post@n2.nabble.com>

Hello Brad,

Thank you for the quick response. Unfortunately I don't have a minimal
program to reproduce this leak.
To be honest I am new to ITK and am using some inherited code (which tends
to be quite large). When I ran this program through Visual Leak Detector, I
came across a whole bunch of these leaks in the same part of the ITK code.
Was hoping somebody else would have come across the same and possibly new
why this might be happening.

Thank you,
TJ





--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Ver-4-5-memory-leak-in-HDF5-library-tp7586961p7586963.html
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From matt.mccormick at kitware.com  Wed Mar  4 15:07:20 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 4 Mar 2015 15:07:20 -0500
Subject: [ITK-users] [ITK]  ITK Ver 4.5 memory leak in HDF5 library
In-Reply-To: <1425499315444-7586963.post@n2.nabble.com>
References: <1425498033934-7586961.post@n2.nabble.com>
 <C74D017A-13AF-420D-8CA6-E2DB1492C665@mail.nih.gov>
 <1425499315444-7586963.post@n2.nabble.com>
Message-ID: <CALzTN-Ri0OEop4a+NQa_q7Dz8-J-OOfOkSJdm9CFDtMpnwQMnw@mail.gmail.com>

Hi TJ,

I have experienced some reported memory leaks and memory errors from
the valgrind tool using ITK's HDF5 library.  However, this was with
some custom code outside of the ITK image IO context.  As far as I
could tell, though, they were false positives.

HTH,
Matt

On Wed, Mar 4, 2015 at 3:01 PM, tejas9090 <tejasm at gmail.com> wrote:
> Hello Brad,
>
> Thank you for the quick response. Unfortunately I don't have a minimal
> program to reproduce this leak.
> To be honest I am new to ITK and am using some inherited code (which tends
> to be quite large). When I ran this program through Visual Leak Detector, I
> came across a whole bunch of these leaks in the same part of the ITK code.
> Was hoping somebody else would have come across the same and possibly new
> why this might be happening.
>
> Thank you,
> TJ
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Ver-4-5-memory-leak-in-HDF5-library-tp7586961p7586963.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

From tejasm at gmail.com  Wed Mar  4 16:02:48 2015
From: tejasm at gmail.com (tejas9090)
Date: Wed, 4 Mar 2015 14:02:48 -0700 (MST)
Subject: [ITK-users] [ITK]  ITK Ver 4.5 memory leak in HDF5 library
In-Reply-To: <CALzTN-Ri0OEop4a+NQa_q7Dz8-J-OOfOkSJdm9CFDtMpnwQMnw@mail.gmail.com>
References: <1425498033934-7586961.post@n2.nabble.com>
 <C74D017A-13AF-420D-8CA6-E2DB1492C665@mail.nih.gov>
 <1425499315444-7586963.post@n2.nabble.com>
 <CALzTN-Ri0OEop4a+NQa_q7Dz8-J-OOfOkSJdm9CFDtMpnwQMnw@mail.gmail.com>
Message-ID: <1425502968082-7586965.post@n2.nabble.com>

Matt, thanks!



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From matt.mccormick at kitware.com  Wed Mar  4 22:44:28 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 4 Mar 2015 22:44:28 -0500
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-T1eqY-cmf75H8-WJ5pyOZ67_afA_Nu4vPJdhSrypUvsg@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/covpn37cs306pbu11gl42gdlo5c


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/events/cnbf68nke70rp5ttt6plcp232n0


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Wed Mar  4 23:31:10 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 4 Mar 2015 23:31:10 -0500
Subject: [ITK-users] find_package(ITK) and find_package(VTK) problems in
	CMake
In-Reply-To: <CALmrq1a8zSQzPXmkHC7zkjmtbntoVpfKJ5=aJRWLhzBGuXV=4Q@mail.gmail.com>
References: <CALmrq1a8zSQzPXmkHC7zkjmtbntoVpfKJ5=aJRWLhzBGuXV=4Q@mail.gmail.com>
Message-ID: <CALzTN-Q57ikKKfTLkv2u7nGPh8OAWCaad=6MYkTPTytj3rBBaw@mail.gmail.com>

Hi Lin,

Please try using VTK 6.2rc1 or newer.

Thanks,
Matt

On Tue, Mar 3, 2015 at 11:23 AM, Lin M <majcjc at gmail.com> wrote:
> Hi guys,
>
> I met a strange problem when I try to use ITK and VTK in my projects. If I
> only use find_package( VTK required ) cmake will find all the right .h and
> .lib files and add them to the project, but if I use both find_package(ITK)
> and find_package(VTK), then some of the .h and .lib of VTK just disappeared
> in my VS projects. Does anyone have some suggestions for that? Thank you
> very much!
>
> My CMakeLists.txt is written as below:
>
> ...
> ...
> # QT FILES
> FIND_PACKAGE( Qt5Widgets )
> FIND_PACKAGE( Qt5Xml )
> FIND_PACKAGE( Qt5Core )
>
> # ITK FILES
> FIND_PACKAGE( ITK REQUIRED )
> INCLUDE( ${ITK_USE_FILE} )
>
> # VTK FILES
> FIND_PACKAGE( VTK REQUIRED )
> NCLUDE( ${VTK_USE_FILE} )
>
> ...
> ...
> TARGET_LINK_LIBRARIES( ${PROJECT_NAME}
>   ${Qt5Widgets_LIBRARIES}
>   ${Qt5Xml_LIBRARIES}
>   ${Qt5Core_LIBRARIES}
>   ${VTK_LIBRARIES}
>   ${ITK_LIBRARIES}
>   )
>
>
> Best,
> Lin
>
> _____________________________________
> 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 lassi.paavolainen at jyu.fi  Mon Mar  9 06:11:55 2015
From: lassi.paavolainen at jyu.fi (Paavolainen, Lassi)
Date: Mon, 9 Mar 2015 10:11:55 +0000
Subject: [ITK-users] Memory leak in Python wrapped Image GetPixel method?
Message-ID: <BB43A6B0CAEAFC439640CD9D13607DC24E61B922@mbs1.ad.jyu.fi>

Hi,

I noticed that GetPixel method in itk.Image object eats memory in Python wrapped code. I think I've seen some Python wrapping memory issues years ago but nothing as simple as this. Here is a simple test script:
import sys
import itk
reader = itk.ImageFileReader.IUC2.New()
reader.SetFileName(sys.argv[1])
reader.Update()
img = reader.GetOutput()
size = img.GetLargestPossibleRegion().GetSize()
for i in range(100):
	for x in range(size[0]):
		for y in range(size[1]):
			value = img.GetPixel((x,y))
	print "Done with iteration %d"%(i+1)

When I run it with 1 MB image, it end up taking 1.5 GB of memory. After spending lots of time on debugging a bigger bunch of code I realized that the GetPixel method was to blame. Can anyone reproduce it? I'm using ITK 4.6.1

Cheers,
Lassi

From matt.mccormick at kitware.com  Mon Mar  9 14:22:24 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 9 Mar 2015 14:22:24 -0400
Subject: [ITK-users] Memory leak in Python wrapped Image GetPixel method?
In-Reply-To: <BB43A6B0CAEAFC439640CD9D13607DC24E61B922@mbs1.ad.jyu.fi>
References: <BB43A6B0CAEAFC439640CD9D13607DC24E61B922@mbs1.ad.jyu.fi>
Message-ID: <CALzTN-TzYRkFGZkYfx3XhnjZQNEhZ+PkxhmuZiOxRr-TTzrdbg@mail.gmail.com>

Hi Lassi,

Thanks for investigating and reporting the issue!

I have created an issue in the Issue Tracker to keep track of it:

  https://issues.itk.org/jira/browse/ITK-3352

Matt

On Mon, Mar 9, 2015 at 6:11 AM, Paavolainen, Lassi
<lassi.paavolainen at jyu.fi> wrote:
> Hi,
>
> I noticed that GetPixel method in itk.Image object eats memory in Python wrapped code. I think I've seen some Python wrapping memory issues years ago but nothing as simple as this. Here is a simple test script:
> import sys
> import itk
> reader = itk.ImageFileReader.IUC2.New()
> reader.SetFileName(sys.argv[1])
> reader.Update()
> img = reader.GetOutput()
> size = img.GetLargestPossibleRegion().GetSize()
> for i in range(100):
>         for x in range(size[0]):
>                 for y in range(size[1]):
>                         value = img.GetPixel((x,y))
>         print "Done with iteration %d"%(i+1)
>
> When I run it with 1 MB image, it end up taking 1.5 GB of memory. After spending lots of time on debugging a bigger bunch of code I realized that the GetPixel method was to blame. Can anyone reproduce it? I'm using ITK 4.6.1
>
> Cheers,
> Lassi
> _____________________________________
> 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 lassi.paavolainen at jyu.fi  Mon Mar  9 15:59:26 2015
From: lassi.paavolainen at jyu.fi (Paavolainen, Lassi)
Date: Mon, 9 Mar 2015 19:59:26 +0000
Subject: [ITK-users] Memory leak in Python wrapped Image GetPixel method?
In-Reply-To: <CALzTN-TzYRkFGZkYfx3XhnjZQNEhZ+PkxhmuZiOxRr-TTzrdbg@mail.gmail.com>
References: <BB43A6B0CAEAFC439640CD9D13607DC24E61B922@mbs1.ad.jyu.fi>,
 <CALzTN-TzYRkFGZkYfx3XhnjZQNEhZ+PkxhmuZiOxRr-TTzrdbg@mail.gmail.com>
Message-ID: <BB43A6B0CAEAFC439640CD9D13607DC24E61BB11@mbs1.ad.jyu.fi>

Hi Matt,

Seems its an issue with local environment. Here is also for the list what I replied to Gaetan:
"This is interesting. I'm using ITK 4.6.1 with swig that comes with it. I now tested with 3.20 that has been built long time ago with swig 1.9 (if I remember correctly). The same thing. So the conclusion is that it must be something local as I'm sure I've done something similar over the years many times.

Next is to try to find out what on my environment causes this."

To add to that, I ran 30 iterations using valgrind. Here is the report:
==8603== HEAP SUMMARY:
==8603==     in use at exit: 478,066,856 bytes in 483,719 blocks
==8603==   total heap usage: 657,312 allocs, 173,593 frees, 787,087,705 bytes allocated
==8603== 
==8603== LEAK SUMMARY:
==8603==    definitely lost: 0 bytes in 0 blocks
==8603==    indirectly lost: 0 bytes in 0 blocks
==8603==      possibly lost: 20,224 bytes in 34 blocks
==8603==    still reachable: 478,046,632 bytes in 483,685 blocks
==8603==         suppressed: 0 bytes in 0 blocks

So almost 500 MB is in heap but still reachable when the program exits.

Lassi

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, March 09, 2015 20:22
To: Paavolainen, Lassi
Cc: insight-users at itk.org; Ga?tan Lehmann; Michka Popoff
Subject: Re: [ITK-users] Memory leak in Python wrapped Image GetPixel method?

Hi Lassi,

Thanks for investigating and reporting the issue!

I have created an issue in the Issue Tracker to keep track of it:

  https://issues.itk.org/jira/browse/ITK-3352

Matt

On Mon, Mar 9, 2015 at 6:11 AM, Paavolainen, Lassi
<lassi.paavolainen at jyu.fi> wrote:
> Hi,
>
> I noticed that GetPixel method in itk.Image object eats memory in Python wrapped code. I think I've seen some Python wrapping memory issues years ago but nothing as simple as this. Here is a simple test script:
> import sys
> import itk
> reader = itk.ImageFileReader.IUC2.New()
> reader.SetFileName(sys.argv[1])
> reader.Update()
> img = reader.GetOutput()
> size = img.GetLargestPossibleRegion().GetSize()
> for i in range(100):
>         for x in range(size[0]):
>                 for y in range(size[1]):
>                         value = img.GetPixel((x,y))
>         print "Done with iteration %d"%(i+1)
>
> When I run it with 1 MB image, it end up taking 1.5 GB of memory. After spending lots of time on debugging a bigger bunch of code I realized that the GetPixel method was to blame. Can anyone reproduce it? I'm using ITK 4.6.1
>
> Cheers,
> Lassi
> _____________________________________
> 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 gabrielgimenez85 at gmail.com  Mon Mar  9 19:40:48 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Mon, 9 Mar 2015 16:40:48 -0700 (MST)
Subject: [ITK-users] Mattes Mutual Information Speed with 3D Images
Message-ID: <1425944448336-7586972.post@n2.nabble.com>

Hello everyone... 

I'm working on a genetic optimizer for Rigid 3D Registration. 

The fitness of each individual is calculated using Mattes Mutual
Information, the execution time of the metric is high ... (30 seconds on
average). This makes the registration too slow. 

Any recommendations? could improve the performance metrics?other most
appropriate metric? 

Regards!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-Speed-with-3D-Images-tp7586972.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From gabrielgimenez85 at gmail.com  Mon Mar  9 19:02:21 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Mon, 9 Mar 2015 16:02:21 -0700 (MST)
Subject: [ITK-users] Mattes Mutual Information Speed with 3D Images
Message-ID: <1425942141529-7586971.post@n2.nabble.com>

Hello everyone...

I'm working on a genetic optimizer for Rigid 3D Registration. 

The fitness of each individual is calculated using Mattes Mutual
Information, the execution time of the metric is high ... (30 seconds on
average). This makes the registration too slow.

Any recommendations? could improve the performance metrics? otherwise most
appropriate metric?

Regards!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-Speed-with-3D-Images-tp7586971.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From arnaudgelas at gmail.com  Tue Mar 10 05:30:01 2015
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Tue, 10 Mar 2015 10:30:01 +0100
Subject: [ITK-users] apply color map to a label map with overlapping label
	objects?
Message-ID: <F13813D5-49FB-498A-9C61-4EF125255472@gmail.com>

Hi all,

I would like to colorize one label map with overlapping label objects. I know there is itk::LabelMapOverlayImageFilter but would it work on such a case? (could be wrong, but based on the code it does not seem so)

Thanks
Arnaud

From blowekamp at mail.nih.gov  Tue Mar 10 08:59:24 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 10 Mar 2015 08:59:24 -0400
Subject: [ITK-users] [ITK] Mattes Mutual Information Speed with 3D Images
In-Reply-To: <1425942141529-7586971.post@n2.nabble.com>
References: <1425942141529-7586971.post@n2.nabble.com>
Message-ID: <6DB0A858-9B7D-4A6A-832A-2E86661C7611@mail.nih.gov>

Hello,

Unfortunately, I can help much because of lack of information.

I can tell you I just wrote SimpleITK registration code which uses Mattes Mutual Information, Versor Rigid Transform, with a Regular Step Gradient Descent optimizer . The sampling percentage for the metric is 0.2, and the volumes are about 60^3 each. This is able to do the registration in about 8 iterations in 0.3 seconds.

Brad

On Mar 9, 2015, at 7:02 PM, Gabriel A. Gim?nez <gabrielgimenez85 at gmail.com> wrote:

> Hello everyone...
> 
> I'm working on a genetic optimizer for Rigid 3D Registration. 
> 
> The fitness of each individual is calculated using Mattes Mutual
> Information, the execution time of the metric is high ... (30 seconds on
> average). This makes the registration too slow.
> 
> Any recommendations? could improve the performance metrics? otherwise most
> appropriate metric?
> 
> Regards!
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-Speed-with-3D-Images-tp7586971.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From gabrielgimenez85 at gmail.com  Tue Mar 10 09:03:41 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Tue, 10 Mar 2015 10:03:41 -0300
Subject: [ITK-users] [ITK] Mattes Mutual Information Speed with 3D Images
In-Reply-To: <6DB0A858-9B7D-4A6A-832A-2E86661C7611@mail.nih.gov>
References: <1425942141529-7586971.post@n2.nabble.com>
 <6DB0A858-9B7D-4A6A-832A-2E86661C7611@mail.nih.gov>
Message-ID: <CAHpGi9d1L=r=NwDyWwtYoS0ytdjUPFYHCGO1m2NGLeVibTn5nQ@mail.gmail.com>

Hi! thanks for your answer...

I use images of RIRE BD (http://www.insight-journal.org/rire/), my initial
tests I make with package training_001 (CT - MR_PD). Following
recommendation here is my configuration:


         metric->SetNumberOfHistogramBins( 50 );
         double samplingPercentage = 0.002;
         registration->SetMetricSamplingPercentage( samplingPercentage );
         RegistrationType::MetricSamplingStrategyType  samplingStrategy  =

               RegistrationType::REGULAR;

Unfortunately, the results were not good ... the average execution time
remains the same (25 ~ 30 seconds). With a population size equal to 50, the
execution time of an iteration is in the order of 25 minutes, very slow for
me ...

These are the image data:

Fixed Image:

ObjectType = Image

NDims = 3

BinaryDataByteOrderMSB = True

AnatomicalOrientation = LPH

ElementSpacing = 0.653595 0.653595 4.000000

*DimSize = 512 512 29*

ElementType = MET_SHORT

ElementDataFile = image.bin


Moving Image:

ObjectType = Image

NDims = 3

BinaryDataByteOrderMSB = True

AnatomicalOrientation = LPH

ElementSpacing = 1.250000 1.250000 4.000000

*DimSize = 256 256 26*

ElementType = MET_SHORT

ElementDataFile = image.bin



Thanks and regards!


2015-03-10 9:59 GMT-03:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> Hello,
>
> Unfortunately, I can help much because of lack of information.
>
> I can tell you I just wrote SimpleITK registration code which uses Mattes
> Mutual Information, Versor Rigid Transform, with a Regular Step Gradient
> Descent optimizer . The sampling percentage for the metric is 0.2, and the
> volumes are about 60^3 each. This is able to do the registration in about 8
> iterations in 0.3 seconds.
>
> Brad
>
> On Mar 9, 2015, at 7:02 PM, Gabriel A. Gim?nez <gabrielgimenez85 at gmail.com>
> wrote:
>
> > Hello everyone...
> >
> > I'm working on a genetic optimizer for Rigid 3D Registration.
> >
> > The fitness of each individual is calculated using Mattes Mutual
> > Information, the execution time of the metric is high ... (30 seconds on
> > average). This makes the registration too slow.
> >
> > Any recommendations? could improve the performance metrics? otherwise
> most
> > appropriate metric?
> >
> > Regards!
> >
> >
> >
> > --
> > View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-Speed-with-3D-Images-tp7586971.html
> > Sent from the ITK Insight Users mailing list archive at Nabble.com.
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
>
>


-- 
*Gabriel Alberto Gim?nez.*
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From bill.lorensen at gmail.com  Tue Mar 10 09:09:54 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 10 Mar 2015 09:09:54 -0400
Subject: [ITK-users] [ITK] Mattes Mutual Information Speed with 3D Images
In-Reply-To: <CAHpGi9d1L=r=NwDyWwtYoS0ytdjUPFYHCGO1m2NGLeVibTn5nQ@mail.gmail.com>
References: <1425942141529-7586971.post@n2.nabble.com>
 <6DB0A858-9B7D-4A6A-832A-2E86661C7611@mail.nih.gov>
 <CAHpGi9d1L=r=NwDyWwtYoS0ytdjUPFYHCGO1m2NGLeVibTn5nQ@mail.gmail.com>
Message-ID: <CADZJ4hOkhen6wzSYZuvagUbDFH2dk3_eiJD-eGAd2BQKAxhBdA@mail.gmail.com>

Are ITK and your app built Release?

On Tue, Mar 10, 2015 at 9:03 AM, Gabriel A. Gim?nez
<gabrielgimenez85 at gmail.com> wrote:
> Hi! thanks for your answer...
>
> I use images of RIRE BD (http://www.insight-journal.org/rire/), my initial
> tests I make with package training_001 (CT - MR_PD). Following
> recommendation here is my configuration:
>
>
>          metric->SetNumberOfHistogramBins( 50 );
>          double samplingPercentage = 0.002;
>          registration->SetMetricSamplingPercentage( samplingPercentage );
>          RegistrationType::MetricSamplingStrategyType  samplingStrategy  =
>
> RegistrationType::REGULAR;
>
> Unfortunately, the results were not good ... the average execution time
> remains the same (25 ~ 30 seconds). With a population size equal to 50, the
> execution time of an iteration is in the order of 25 minutes, very slow for
> me ...
>
> These are the image data:
>
> Fixed Image:
>
> ObjectType = Image
>
> NDims = 3
>
> BinaryDataByteOrderMSB = True
>
> AnatomicalOrientation = LPH
>
> ElementSpacing = 0.653595 0.653595 4.000000
>
> DimSize = 512 512 29
>
> ElementType = MET_SHORT
>
> ElementDataFile = image.bin
>
>
> Moving Image:
>
> ObjectType = Image
>
> NDims = 3
>
> BinaryDataByteOrderMSB = True
>
> AnatomicalOrientation = LPH
>
> ElementSpacing = 1.250000 1.250000 4.000000
>
> DimSize = 256 256 26
>
> ElementType = MET_SHORT
>
> ElementDataFile = image.bin
>
>
>
> Thanks and regards!
>
>
> 2015-03-10 9:59 GMT-03:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>
>> Hello,
>>
>> Unfortunately, I can help much because of lack of information.
>>
>> I can tell you I just wrote SimpleITK registration code which uses Mattes
>> Mutual Information, Versor Rigid Transform, with a Regular Step Gradient
>> Descent optimizer . The sampling percentage for the metric is 0.2, and the
>> volumes are about 60^3 each. This is able to do the registration in about 8
>> iterations in 0.3 seconds.
>>
>> Brad
>>
>> On Mar 9, 2015, at 7:02 PM, Gabriel A. Gim?nez
>> <gabrielgimenez85 at gmail.com> wrote:
>>
>> > Hello everyone...
>> >
>> > I'm working on a genetic optimizer for Rigid 3D Registration.
>> >
>> > The fitness of each individual is calculated using Mattes Mutual
>> > Information, the execution time of the metric is high ... (30 seconds on
>> > average). This makes the registration too slow.
>> >
>> > Any recommendations? could improve the performance metrics? otherwise
>> > most
>> > appropriate metric?
>> >
>> > Regards!
>> >
>> >
>> >
>> > --
>> > View this message in context:
>> > http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-Speed-with-3D-Images-tp7586971.html
>> > Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> > _______________________________________________
>> > Community mailing list
>> > Community at itk.org
>> > http://public.kitware.com/mailman/listinfo/community
>>
>
>
>
> --
> Gabriel Alberto Gim?nez.
>
> _____________________________________
> 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
>



-- 
Unpaid intern in BillsBasement at noware dot com

From chiara.magliaro at googlemail.com  Tue Mar 10 09:26:53 2015
From: chiara.magliaro at googlemail.com (Chiara Magliaro)
Date: Tue, 10 Mar 2015 14:26:53 +0100
Subject: [ITK-users] read an image stack .tif
Message-ID: <CAE=VBDFjCOMmUhGrY1NDL4mzJ3RH5qNB7Ng9j+UMYFSNwAeezw@mail.gmail.com>

Hi all,

i'd like to read a tiff file, stocking an image stack and see the different
images composing the stack. Is there any irk class to do this?
Thanks in advance

Best regards
Chiara

-- 
Chiara Magliaro
PhD Student
Research Center "E. Piaggio" - University of Pisa
Largo Lucio Lazzarino 1, 56122 Pisa, Italy
Tel. 0039 0502217061 - Fax. 0039 0502217051
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From grothausmann.roman at mh-hannover.de  Tue Mar 10 10:14:58 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Tue, 10 Mar 2015 15:14:58 +0100
Subject: [ITK-users] Help needed to implement 64-bit "label" image in
 ITK-Snap for global watershed segmentation mode
In-Reply-To: <547C5A89.9090905@mh-hannover.de>
References: <547C5A89.9090905@mh-hannover.de>
Message-ID: <54FEFC62.7000105@mh-hannover.de>

Dear mailing list members,


To ease further development and possible help, my extensions to ITK-Snap 
(Click'n'Join and a global dynamic watershed segmentation mode) are now 
available on github: https://github.com/romangrothausmann/itksnap.git

The branch rel_3.0+gdWS contains the changes needed for ITK-Snap v3.0, 
rel_3.2+gdWS for ITK-Snap v3.2 and master+gdWS for the newest development. For 
this branch there is also a PR (https://github.com/pyushkevich/itksnap/pull/1) 
with a short description and two screen shots, a documentation (article in the 
MIDAS journal) is on the way.

One point on the ToDo list I would need help on is the realization of the 
join-srouce-image being 64-bit (itk::IdentifierType) and possibly coloured with 
itk::ScalarToRGBPixelFunctor. Other things I tried are those reported before/below.
So if someone has any idea how to realize this or would like to take part in 
further development, please let me know.

Thanks for any help or hints.
Roman


On 01/12/14 13:09, Dr. Roman Grothausmann wrote:
> Dear mailing list members,
>
>
> How can I modify the ColorLabelTableDisplayMappingPolicy to accept also images
> containing labels of long unsigned int, i.e. the output of the
> itkWatershedImageFilter?
> It seems that this image type only causes problems for:
> m_RGBAFilter[i]->SetInput(wrapper->GetSlice(i));
> i.e. m_RGBAFilter can only handle short but the slice from the output of a
> itkWatershedImageFilter is of type long.
> I tried to incorporate a CastImageFilter (see below, as the loss of precision
> does not matter for the colouring), but that cannot be updated because the input
> region size is [0,0] at that position of the pipeline:
>
>
>      typedef itk::Image<typename TWrapperTraits::ComponentType, 2> JsrcImageType;
>      typedef itk::Image<LabelType, 2> LabelInputSliceType;
>      typedef itk::CastImageFilter<JsrcImageType, LabelInputSliceType> CIFType;
>      typename CIFType::Pointer cif;
>      cif = CIFType::New();
>      wrapper->GetSlice(i)->Print(std::cerr);
>      cif->SetInput(dynamic_cast<JsrcImageType *>(wrapper->GetSlice(i)));
>      //cif->InPlaceOff();
>      cif->Print(std::cerr);
>      std::cerr << "cif->Update" << std::endl;
>      //cif->UpdateLargestPossibleRegion();
>      cif->Update(); ////crashes as input region size is [0,0]
>      cif->GetOutput()->Print(std::cerr);
>      m_RGBAFilter[i]->SetInput(cif->GetOutput());
>
>
> I wonder if there is a better place to do the casting but e.g.
> Logic/Slicing/IRISSlicer.txx didn't seem more promising to me.
>
> Or how could I create a new ColorLabelTableDisplayMappingPolicy2 that would
> handle long?
> It seems that the typedef itk::Image<LabelType, 2> InputSliceType; in
> DisplayMappingPolicy.h is not used, i.e. changing it to use long for labels has
> no effect.
>
> Setting the Label type globally to long in SNAPCommon.h:
> typedef itk::IdentifierType LabelType;
> confuses Qt.
>
> Any help or hints how I can handle this type mismatch are very welcome
> Thanks,
> Roman
>

-- 
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. +49 511 532-9574

From lluna.nova at gmail.com  Tue Mar 10 12:02:24 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Tue, 10 Mar 2015 17:02:24 +0100
Subject: [ITK-users] read an image stack .tif
In-Reply-To: <CAE=VBDFjCOMmUhGrY1NDL4mzJ3RH5qNB7Ng9j+UMYFSNwAeezw@mail.gmail.com>
References: <CAE=VBDFjCOMmUhGrY1NDL4mzJ3RH5qNB7Ng9j+UMYFSNwAeezw@mail.gmail.com>
Message-ID: <CALAZn4gsQg6fza+qxmxs0J6ru=vWw=wNb+zXN4WSJS60O9xJ3w@mail.gmail.com>

Yes, there is.

How are the images stacked? Are we talking about a volume? If so, read it
normally with a reader with a dimension of 3. Check the reader example:
http://itk.org/Wiki/ITK/Examples/IO/ImageFileReader

You'll have to change the Dimension to 3 and remove the visualization part.

If you only want to visualize, you could use Fiji for this.

Pol

2015-03-10 14:26 GMT+01:00 Chiara Magliaro <chiara.magliaro at googlemail.com>:

> Hi all,
>
> i'd like to read a tiff file, stocking an image stack and see the
> different images composing the stack. Is there any irk class to do this?
> Thanks in advance
>
> Best regards
> Chiara
>
> --
> Chiara Magliaro
> PhD Student
> Research Center "E. Piaggio" - University of Pisa
> Largo Lucio Lazzarino 1, 56122 Pisa, Italy
> Tel. 0039 0502217061 - Fax. 0039 0502217051
>
> _____________________________________
> 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 janschepers1 at gmail.com  Tue Mar 10 12:14:24 2015
From: janschepers1 at gmail.com (Jan Schepers)
Date: Tue, 10 Mar 2015 17:14:24 +0100
Subject: [ITK-users] Question about itkCenteredVersorTransformInitializer
Message-ID: <CAHcrnz8v8D5HV2hU4=nPNakWM_ocFh2=UY-t-TO8hSQt45Azng@mail.gmail.com>

Hello,

in the method InitializeTransform the rotation matrix is computed as
follows:
MovingMatrixType rotationMatrix = movingPrincipalAxis *
fixedPrincipalAxis.GetInverse();

This doesn't work for me. If I change it to
MovingMatrixType rotationMatrix =
movingPrincipalAxis.GetInverse() * fixedPrincipalAxis;
then I get the results that I expected. Strangely, both rotation matrices
are not even each other's inverse.

Did anyone experience the same problem?

Best regards,
Jan
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From blowekamp at mail.nih.gov  Tue Mar 10 12:56:32 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 10 Mar 2015 12:56:32 -0400
Subject: [ITK-users] Question about itkCenteredVersorTransformInitializer
In-Reply-To: <CAHcrnz8v8D5HV2hU4=nPNakWM_ocFh2=UY-t-TO8hSQt45Azng@mail.gmail.com>
References: <CAHcrnz8v8D5HV2hU4=nPNakWM_ocFh2=UY-t-TO8hSQt45Azng@mail.gmail.com>
Message-ID: <9D59DDE4-7748-4804-95BD-D2244A2E9EC6@mail.nih.gov>

Hello Jan,

Please remember that the ITK registration framework ( and initializers ) produce a transform which maps points from the fixed image to the moving image. My first guess is that you are applying the transform in the wrong direction.

Brad

On Mar 10, 2015, at 12:14 PM, Jan Schepers <janschepers1 at gmail.com> wrote:

> Hello,
> 
> in the method InitializeTransform the rotation matrix is computed as follows:
> MovingMatrixType rotationMatrix = movingPrincipalAxis * fixedPrincipalAxis.GetInverse();
> 
> This doesn't work for me. If I change it to 
> MovingMatrixType rotationMatrix = movingPrincipalAxis.GetInverse() * fixedPrincipalAxis;
> then I get the results that I expected. Strangely, both rotation matrices are not even each other's inverse.
> 
> Did anyone experience the same problem?
> 
> Best regards,
> Jan
> _____________________________________
> 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 amghanem at gmail.com  Tue Mar 10 16:18:25 2015
From: amghanem at gmail.com (amghanem)
Date: Tue, 10 Mar 2015 13:18:25 -0700 (MST)
Subject: [ITK-users] error exception occurred during SingleMethodExecute
Message-ID: <1426018705093-35316.post@n7.nabble.com>

Hi,

I am working on Osirix plugin and when the following code run, ITK generate
the following runtime error


 itk::ERROR: MultiThreader(0x79f1400): Exception occurred during
SingleMethodExecute
ITK180/Modules/Core/Common/include/itkImageSource.hxx:300:
itk::ERROR: ImageToImageFilter(0x126df1a0): Subclass should override this
method!!!
The signature of ThreadedGenerateData() has been changed in ITK v4 to use
the new ThreadIdType.
ImageToImageFilter::ThreadedGenerateData() might need to be updated to used
it.

  the version of ITK that used by osirix is 4.1


 

thanks,



const     unsigned int        Dimension       = 3;
   
    
    typedef float                              PixelType;
    typedef itk::Image< PixelType, Dimension > ImageType;
    
    
    typedef itk::SymmetricSecondRankTensor< double, Dimension >
HessianPixelType;
    typedef itk::Image< HessianPixelType, Dimension >          
HessianImageType;
    typedef itk::HessianToObjectnessMeasureImageFilter< HessianImageType,
ImageType > ObjectnessFilterType;
    ObjectnessFilterType::Pointer objectnessFilter =
ObjectnessFilterType::New();
    //objectnessFilter->SetBrightObject( false );
    objectnessFilter->SetBrightObject( true );
    objectnessFilter->SetScaleObjectnessMeasure( false );
    objectnessFilter->SetAlpha( 0.5 );
    objectnessFilter->SetBeta( 1.0 );
    objectnessFilter->SetGamma( 5.0 );
    objectnessFilter->SetObjectDimension(1); //vessels
    
    typedef itk::MultiScaleHessianBasedMeasureImageFilter< ImageType,
HessianImageType, ImageType > MultiScaleEnhancementFilterType;
    MultiScaleEnhancementFilterType::Pointer multiScaleEnhancementFilter =
MultiScaleEnhancementFilterType::New();
    multiScaleEnhancementFilter->SetInput( importFilter->GetOutput() );
    multiScaleEnhancementFilter->SetHessianToMeasureFilter( objectnessFilter
);
    multiScaleEnhancementFilter->SetSigmaStepMethodToEquispaced();
    multiScaleEnhancementFilter->SetSigmaMinimum( 0.2 );
    multiScaleEnhancementFilter->SetSigmaMaximum( 2 );
    multiScaleEnhancementFilter->SetNumberOfSigmaSteps( 2);
    multiScaleEnhancementFilter->SetGenerateHessianOutput(true);
    multiScaleEnhancementFilter->SetGenerateScalesOutput(false);
    
 

    try
    {
        multiScaleEnhancementFilter->Update();
    }
    catch( itk::ExceptionObject & excep )
    {
        NSString * erro = [[ NSString alloc]
initWithCString:excep.GetDescription()];
      
        NSLog(erro);
        return 1;
    }

    float*
enhanceOutput=multiScaleEnhancementFilter->GetOutput()->GetBufferPointer();



--
View this message in context: http://itk-users.7.n7.nabble.com/error-exception-occurred-during-SingleMethodExecute-tp35316.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Wed Mar 11 08:56:07 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 11 Mar 2015 08:56:07 -0400
Subject: [ITK-users] [ITK] error exception occurred during
	SingleMethodExecute
In-Reply-To: <1426018705093-35316.post@n7.nabble.com>
References: <1426018705093-35316.post@n7.nabble.com>
Message-ID: <656320A1-1E8F-45B6-8C3D-1EE5168C0941@mail.nih.gov>

Hello,

I think you have a build and include path problem and are mixing up using different versions of ITK headers. Or perhaps some how using an old version of the these filters.

Brad

On Mar 10, 2015, at 4:18 PM, amghanem <amghanem at gmail.com> wrote:

> Hi,
> 
> I am working on Osirix plugin and when the following code run, ITK generate
> the following runtime error
> 
> 
> itk::ERROR: MultiThreader(0x79f1400): Exception occurred during
> SingleMethodExecute
> ITK180/Modules/Core/Common/include/itkImageSource.hxx:300:
> itk::ERROR: ImageToImageFilter(0x126df1a0): Subclass should override this
> method!!!
> The signature of ThreadedGenerateData() has been changed in ITK v4 to use
> the new ThreadIdType.
> ImageToImageFilter::ThreadedGenerateData() might need to be updated to used
> it.
> 
>  the version of ITK that used by osirix is 4.1
> 
> 
> 
> 
> thanks,
> 
> 
> 
> const     unsigned int        Dimension       = 3;
> 
> 
>    typedef float                              PixelType;
>    typedef itk::Image< PixelType, Dimension > ImageType;
> 
> 
>    typedef itk::SymmetricSecondRankTensor< double, Dimension >
> HessianPixelType;
>    typedef itk::Image< HessianPixelType, Dimension >          
> HessianImageType;
>    typedef itk::HessianToObjectnessMeasureImageFilter< HessianImageType,
> ImageType > ObjectnessFilterType;
>    ObjectnessFilterType::Pointer objectnessFilter =
> ObjectnessFilterType::New();
>    //objectnessFilter->SetBrightObject( false );
>    objectnessFilter->SetBrightObject( true );
>    objectnessFilter->SetScaleObjectnessMeasure( false );
>    objectnessFilter->SetAlpha( 0.5 );
>    objectnessFilter->SetBeta( 1.0 );
>    objectnessFilter->SetGamma( 5.0 );
>    objectnessFilter->SetObjectDimension(1); //vessels
> 
>    typedef itk::MultiScaleHessianBasedMeasureImageFilter< ImageType,
> HessianImageType, ImageType > MultiScaleEnhancementFilterType;
>    MultiScaleEnhancementFilterType::Pointer multiScaleEnhancementFilter =
> MultiScaleEnhancementFilterType::New();
>    multiScaleEnhancementFilter->SetInput( importFilter->GetOutput() );
>    multiScaleEnhancementFilter->SetHessianToMeasureFilter( objectnessFilter
> );
>    multiScaleEnhancementFilter->SetSigmaStepMethodToEquispaced();
>    multiScaleEnhancementFilter->SetSigmaMinimum( 0.2 );
>    multiScaleEnhancementFilter->SetSigmaMaximum( 2 );
>    multiScaleEnhancementFilter->SetNumberOfSigmaSteps( 2);
>    multiScaleEnhancementFilter->SetGenerateHessianOutput(true);
>    multiScaleEnhancementFilter->SetGenerateScalesOutput(false);
> 
> 
> 
>    try
>    {
>        multiScaleEnhancementFilter->Update();
>    }
>    catch( itk::ExceptionObject & excep )
>    {
>        NSString * erro = [[ NSString alloc]
> initWithCString:excep.GetDescription()];
> 
>        NSLog(erro);
>        return 1;
>    }
> 
>    float*
> enhanceOutput=multiScaleEnhancementFilter->GetOutput()->GetBufferPointer();
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/error-exception-occurred-during-SingleMethodExecute-tp35316.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From amghanem at gmail.com  Wed Mar 11 10:25:57 2015
From: amghanem at gmail.com (amghanem)
Date: Wed, 11 Mar 2015 07:25:57 -0700 (MST)
Subject: [ITK-users] [ITK] error exception occurred during
 SingleMethodExecute
In-Reply-To: <656320A1-1E8F-45B6-8C3D-1EE5168C0941@mail.nih.gov>
References: <1426018705093-35316.post@n7.nabble.com>
 <656320A1-1E8F-45B6-8C3D-1EE5168C0941@mail.nih.gov>
Message-ID: <1426083957973-35318.post@n7.nabble.com>

Thanks Brad,
I used the ITK library which integrated with Osirix so I think, There is no
headers library version conflict.

 



--
View this message in context: http://itk-users.7.n7.nabble.com/error-exception-occurred-during-SingleMethodExecute-tp35316p35318.html
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From matt.mccormick at kitware.com  Wed Mar 11 13:21:21 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 11 Mar 2015 13:21:21 -0400
Subject: [ITK-users] [ITK] error exception occurred during
	SingleMethodExecute
In-Reply-To: <1426083957973-35318.post@n7.nabble.com>
References: <1426018705093-35316.post@n7.nabble.com>
 <656320A1-1E8F-45B6-8C3D-1EE5168C0941@mail.nih.gov>
 <1426083957973-35318.post@n7.nabble.com>
Message-ID: <CALzTN-SXji2t2NCjao584PGw49NM1SD6T-8CxJ_JivXcf6cgBg@mail.gmail.com>

Hi,

You will need to run the code in a debugger to see which class is
causing the issue.

It is likely related to the use of "ThreadIdType" in the
ThreadedGenerateData method signature.

HTH,
Matt

On Wed, Mar 11, 2015 at 10:25 AM, amghanem <amghanem at gmail.com> wrote:
> Thanks Brad,
> I used the ITK library which integrated with Osirix so I think, There is no
> headers library version conflict.
>
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/error-exception-occurred-during-SingleMethodExecute-tp35316p35318.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From matimontg at gmail.com  Wed Mar 11 18:32:17 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Mar 2015 19:32:17 -0300
Subject: [ITK-users] Registration in SimpleITK
Message-ID: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>

Hi,

is it possible to do registration in SimpleITK? I mean, something like in
this example:
http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup

Thanks,

Matias,
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From blowekamp at mail.nih.gov  Wed Mar 11 18:46:07 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 11 Mar 2015 18:46:07 -0400
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
Message-ID: <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>

Hello Matias,

Currently there is SimpleITK 0.9b01 [1] out with the registration framework.

With it you can do things like this:
http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
or
http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html

Please give it a try and let us know how it work for you.

Enjoy,
Brad

[1] http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release

On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi,
> 
> is it possible to do registration in SimpleITK? I mean, something like in this example:
> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
> 
> Thanks,
> 
> Matias,
> _____________________________________
> 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 matimontg at gmail.com  Wed Mar 11 18:54:41 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Mar 2015 19:54:41 -0300
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
Message-ID: <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>

Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't
aware of this new Beta release
Thanks,
Matias.

On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello Matias,
>
> Currently there is SimpleITK 0.9b01 [1] out with the registration
> framework.
>
> With it you can do things like this:
>
> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
> or
>
> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>
> Please give it a try and let us know how it work for you.
>
> Enjoy,
> Brad
>
> [1]
> http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>
> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> Hi,
>
> is it possible to do registration in SimpleITK? I mean, something like in
> this example:
>
> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>
> Thanks,
>
> Matias,
> _____________________________________
> 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 matimontg at gmail.com  Wed Mar 11 19:31:48 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Mar 2015 20:31:48 -0300
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
Message-ID: <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>

My project is using 64 bits and some DLL I use as well, I've ran into
issues when using the beta version because is 32 bits. I guess I'll wait
until the final release is done.
Thanks,
Matias.

On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com>
wrote:

> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't
> aware of this new Beta release
> Thanks,
> Matias.
>
> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello Matias,
>>
>> Currently there is SimpleITK 0.9b01 [1] out with the registration
>> framework.
>>
>> With it you can do things like this:
>>
>> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
>> or
>>
>> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>>
>> Please give it a try and let us know how it work for you.
>>
>> Enjoy,
>> Brad
>>
>> [1]
>> http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>>
>> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>> Hi,
>>
>> is it possible to do registration in SimpleITK? I mean, something like in
>> this example:
>>
>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>>
>> Thanks,
>>
>> Matias,
>> _____________________________________
>> 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 blowekamp at mail.nih.gov  Wed Mar 11 19:56:56 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 11 Mar 2015 19:56:56 -0400
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
 <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
Message-ID: <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>

Hello,

If you are willing to compile it yourself you can get it to work with just a little bit of effort.

Compile the SimpleITK superbuild with shared libraries enabled. Do the usual installation of SimpleITK from the super build [1], this will install the SimpleITK python library into your site-packages. However, this libraries also depends on all the SimpleITK an ITK dlls (not installed or packaged), these should be in the superbuild's bin directory. These need to be in your run-time path when importing SimpleITK. This can be done either by modifying you PATH environment variable you copying them to the appropriate place ( which may depend on the python environment, and there are likely several alternatives).

Brad

[1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Python_installation

On Mar 11, 2015, at 7:31 PM, Matias Montroull <matimontg at gmail.com> wrote:

> 
> My project is using 64 bits and some DLL I use as well, I've ran into issues when using the beta version because is 32 bits. I guess I'll wait until the final release is done.
> Thanks,
> Matias.
> 
> On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com> wrote:
> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't aware of this new Beta release
> Thanks,
> Matias.
> 
> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello Matias,
> 
> Currently there is SimpleITK 0.9b01 [1] out with the registration framework.
> 
> With it you can do things like this:
> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
> or
> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
> 
> Please give it a try and let us know how it work for you.
> 
> Enjoy,
> Brad
> 
> [1] http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
> 
> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com> wrote:
> 
>> Hi,
>> 
>> is it possible to do registration in SimpleITK? I mean, something like in this example:
>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>> 
>> Thanks,
>> 
>> Matias,
>> _____________________________________
>> 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 camargo at lncc.br  Thu Mar 12 14:56:53 2015
From: camargo at lncc.br (Eduardo - LNCC)
Date: Thu, 12 Mar 2015 15:56:53 -0300
Subject: [ITK-users] abs function ambigous in Mac OS X 10.9
Message-ID: <CAPQEPqSeBkFobc0qd34+OpiMbTPoPdr3LLVnFaxOXF1Er2xqiQ@mail.gmail.com>

Hi,

I am trying compile ITK 3.20 in the Mac OS X 10.9.5 I received the erro
below and I don't figure out what have happened. Someboy can help me?


[  1%] Built target itksys
[  6%] Built target itkjpeg8
[ 11%] Built target itkjpeg12
[ 16%] Built target itkjpeg16
[ 17%] Built target itkzlib
[ 18%] Built target itkpng
[ 18%] Built target itkmkg3states
[ 21%] Built target itktiff
[ 23%] Built target itkopenjpeg
[ 25%] Built target ITKMetaIO
[ 28%] Built target ITKNrrdIO
[ 28%] Built target ITKEXPAT
[ 28%] Built target ITKznz
[ 28%] Built target ITKniftiio
[ 29%] Built target ITKDICOMParser
[ 30%] Built target itkvcl
[ 51%] Built target itkv3p_netlib
[ 51%] Built target itktestlib
[ 69%] Built target itkvnl
[ 74%] Built target itkvnl_algo
[ 76%] Built target itkNetlibSlatec
[ 80%] Built target itkgdcm
[ 82%] Built target itkvnl_inst
[ 88%] Built target ITKCommon
[ 91%] Built target ITKNumerics
[ 91%] Built target ITKBasicFilters
[ 91%] Built target ITKStatistics
[ 91%] Built target ITKAlgorithms
[ 91%] Built target ITKSpatialObject
[ 96%] Built target ITKIO
[ 96%] Building CXX object
Code/IO/CMakeFiles/itkTestDriver.dir/itkTestDriver.o
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:20:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkMacro.h:42:
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:86:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double e
 VCL_STATIC_CONST_INIT_FLOAT_DECL(2.7182818284590452354);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:87:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double log2e
 VCL_STATIC_CONST_INIT_FLOAT_DECL(1.4426950408889634074);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:88:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double log10e
VCL_STATIC_CONST_INIT_FLOAT_DECL(0.43429448190325182765);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:89:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double ln2
 VCL_STATIC_CONST_INIT_FLOAT_DECL(0.69314718055994530942);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:90:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double ln10
VCL_STATIC_CONST_INIT_FLOAT_DECL(2.30258509299404568402);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:91:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double pi
VCL_STATIC_CONST_INIT_FLOAT_DECL(3.14159265358979323846);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:92:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double pi_over_2
 VCL_STATIC_CONST_INIT_FLOAT_DECL(1.57079632679489661923);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:93:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double pi_over_4
 VCL_STATIC_CONST_INIT_FLOAT_DECL(0.78539816339744830962);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:94:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double one_over_pi
 VCL_STATIC_CONST_INIT_FLOAT_DECL(0.31830988618379067154);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:95:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double two_over_pi
 VCL_STATIC_CONST_INIT_FLOAT_DECL(0.63661977236758134308);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:96:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double two_over_sqrtpi
 VCL_STATIC_CONST_INIT_FLOAT_DECL(1.12837916709551257390);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:97:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double one_over_sqrt2pi
VCL_STATIC_CONST_INIT_FLOAT_DECL(0.39894228040143267794);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:98:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double sqrt2
 VCL_STATIC_CONST_INIT_FLOAT_DECL(1.41421356237309504880);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:99:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double sqrt1_2
 VCL_STATIC_CONST_INIT_FLOAT_DECL(0.70710678118654752440);
                                   ^
          ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:102:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double eps
VCL_STATIC_CONST_INIT_FLOAT_DECL(2.2204460492503131e-16);
                                   ^
         ~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:103:36:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const double sqrteps
VCL_STATIC_CONST_INIT_FLOAT_DECL(1.490116119384766e-08);
                                   ^
         ~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:105:35:
warning: in-class initializer for static data member of type 'const float'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const float float_eps
 VCL_STATIC_CONST_INIT_FLOAT_DECL(1.192092896e-07f);
                                  ^
        ~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:106:35:
warning: in-class initializer for static data member of type 'const float'
is a GNU extension [-Wgnu-static-float-init]
  static VNL_DLL_DATA const float float_sqrteps
 VCL_STATIC_CONST_INIT_FLOAT_DECL(3.4526698307e-4f);
                                  ^
        ~~~~~~~~~~~~~~~~
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:35:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkImage.h:20:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkImageBase.h:25:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkImageRegion.h:27:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkContinuousIndex.h:20:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkPoint.h:23:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkVector.h:23:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_vector_ref.h:20:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_vector.h:20:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_c_vector.h:25:
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:340:22:
warning: in-class initializer for static data member of type 'const float'
is a GNU extension [-Wgnu-static-float-init]
  static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F);
                     ^                                     ~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:342:22:
warning: in-class initializer for static data member of type 'const float'
is a GNU extension [-Wgnu-static-float-init]
  static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F);
                     ^                                    ~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:344:22:
warning: in-class initializer for static data member of type 'const float'
is a GNU extension [-Wgnu-static-float-init]
  static const float maxval
VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F);
                     ^
~~~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:363:23:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0);
                      ^                                     ~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:365:23:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0);
                      ^                                    ~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:367:23:
warning: in-class initializer for static data member of type 'const double'
is a GNU extension [-Wgnu-static-float-init]
  static const double maxval
VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308);
                      ^
~~~~~~~~~~~~~~~~~~~~~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:386:28:
warning: in-class initializer for static data member of type 'const long
double' is a GNU extension [-Wgnu-static-float-init]
  static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0);
                           ^                                     ~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:388:28:
warning: in-class initializer for static data member of type 'const long
double' is a GNU extension [-Wgnu-static-float-init]
  static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0);
                           ^                                    ~~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:390:28:
warning: in-class initializer for static data member of type 'const long
double' is a GNU extension [-Wgnu-static-float-init]
  static const long double maxval
VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308);
                           ^
~~~~~~~~~~~~~~~~~~~~~~~
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:939:16:
error: call to 'abs' is ambiguous
        return abs(__c.real());
               ^~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:294:1:
note: in instantiation of function template specialization
'std::__1::norm<unsigned int>' requested here
ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE(unsigned int);
^
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:287:17:
note: expanded from macro 'ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE'
    return std::norm(pixel);                                             \
                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
note: candidate function
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
{return  labs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
{return llabs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
note: candidate function
abs(float __x) _NOEXCEPT {return fabsf(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
note: candidate function
abs(double __x) _NOEXCEPT {return fabs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
note: candidate function
abs(long double __x) _NOEXCEPT {return fabsl(__x);}
^
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:941:16:
error: call to 'abs' is ambiguous
        return abs(__c.imag());
               ^~~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
note: candidate function
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
{return  labs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
{return llabs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
note: candidate function
abs(float __x) _NOEXCEPT {return fabsf(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
note: candidate function
abs(double __x) _NOEXCEPT {return fabs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
note: candidate function
abs(long double __x) _NOEXCEPT {return fabsl(__x);}
^
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:939:16:
error: call to 'abs' is ambiguous
        return abs(__c.real());
               ^~~
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:298:1:
note: in instantiation of function template specialization
'std::__1::norm<unsigned long>' requested here
ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE(unsigned long);
^
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:287:17:
note: expanded from macro 'ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE'
    return std::norm(pixel);                                             \
                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
note: candidate function
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
{return  labs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
{return llabs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
note: candidate function
abs(float __x) _NOEXCEPT {return fabsf(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
note: candidate function
abs(double __x) _NOEXCEPT {return fabs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
note: candidate function
abs(long double __x) _NOEXCEPT {return fabsl(__x);}
^
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
In file included from
/Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:941:16:
error: call to 'abs' is ambiguous
        return abs(__c.imag());
               ^~~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
note: candidate function
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
{return  labs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
{return llabs(__x);}
                                           ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
note: candidate function
abs(float __x) _NOEXCEPT {return fabsf(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
note: candidate function
abs(double __x) _NOEXCEPT {return fabs(__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
note: candidate function
abs(long double __x) _NOEXCEPT {return fabsl(__x);}
^
27 warnings and 4 errors generated.
make[2]: *** [Code/IO/CMakeFiles/itkTestDriver.dir/itkTestDriver.o] Error 1
make[1]: *** [Code/IO/CMakeFiles/itkTestDriver.dir/all] Error 2
make: *** [all] Error 2

Atenciosamente,


Eduardo Camargo, M.Sc.

Analista de Sistemas
Instituto Nacional de Ci?ncia e Tecnologia em
Medicina Assistida por Computa??o Cient?fica
INCT-MACC  http://macc.lncc.br
Laborat?rio Nacional de Computa??o Cient?fica
LNCC - http://www.lncc.br
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From gabrielgimenez85 at gmail.com  Thu Mar 12 15:24:05 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Thu, 12 Mar 2015 16:24:05 -0300
Subject: [ITK-users] [ITK] Mattes Mutual Information Speed with 3D Images
In-Reply-To: <CAHpGi9ex98XndayvNo2gbe-udBf0Kx_inRSxGdXxKqAW9Orejw@mail.gmail.com>
References: <1425942141529-7586971.post@n2.nabble.com>
 <069517FAB08E5D4C80ABEB86CB55A1AB4CEF83A8@BHMF314A.SIRONA.ORG>
 <CAHpGi9c3rEf75VO0gCDPSVXSje1HKC52cfiesz97rbuK3NmaVg@mail.gmail.com>
 <069517FAB08E5D4C80ABEB86CB55A1AB4CEFB491@BHMF314A.SIRONA.ORG>
 <CAHpGi9cenGtFDo3Dx5K8Giy3S=ad7dy3djww+UrmuGccLHim_A@mail.gmail.com>
 <069517FAB08E5D4C80ABEB86CB55A1AB4CEFB4C3@BHMF314A.SIRONA.ORG>
 <CAHpGi9ex98XndayvNo2gbe-udBf0Kx_inRSxGdXxKqAW9Orejw@mail.gmail.com>
Message-ID: <CAHpGi9fJoQPyv0OeeDq2aMhvrkbvXTOecZcZyw4FtyYn+zKDnQ@mail.gmail.com>

Hi!

I debug the code of the MMI implementation and the bottleneck is in in this
part:

*itkImageToImageMetricv4GetValueAndDerivativeThreader.hxx:*

template< typename TImageToImageMetricv4 >
void
ImageToImageMetricv4GetValueAndDerivativeThreader<
ThreadedIndexedContainerPartitioner, TImageToImageMetricv4 >
::*ThreadedExecution* ( const DomainType & indexSubRange,
                      const ThreadIdType threadId )
{
  //Initialize per thread buffers and variables.
  this->m_Associate->InitializeThread( threadId );

  typename TImageToImageMetricv4::VirtualPointSetType::ConstPointer
virtualSampledPointSet = this->m_Associate->GetVirtualSampledPointSet();
  typedef typename
TImageToImageMetricv4::VirtualPointSetType::MeshTraits::PointIdentifier
ElementIdentifierType;
  const ElementIdentifierType begin = indexSubRange[0];
  const ElementIdentifierType end   = indexSubRange[1];
  VirtualIndexType virtualIndex;
  typename VirtualImageType::ConstPointer virtualImage =
this->m_Associate->GetVirtualImage();
 * for( ElementIdentifierType i = begin; i <= end; ++i )*
*    {*
*    const VirtualPointType & virtualPoint =
virtualSampledPointSet->GetPoint( i );*
*    virtualImage->TransformPhysicalPointToIndex( virtualPoint,
virtualIndex );*
*    this->ProcessVirtualPoint( virtualIndex, virtualPoint, threadId );*
*    }*
  //Finalize per thread actions
  this->m_Associate->FinalizeThread( threadId );
}

The "for" statement takes a long time to finish running... and I think the
default multithreaded is 2...I tried to raise this value through seter
"SetMaximumNumberOfThreads()" but did not notice substantial improvements
in performance ..

However, when set build-type to "release" instead "debug" the performance
is much better (2 ~ 3 sec.) but without reaching to the order of
milliseconds....would I like it to be.

I could not do the test with the ITK 3D Slicer (my OS is of 32-bits only).

What do you think? can further improve performance?

Thanks and regards!












2015-03-11 9:37 GMT-03:00 Gabriel A. Gim?nez <gabrielgimenez85 at gmail.com>:

> Ok...I understand...,I'll try...and I commented the results....
>
> Thanks in advance!
>
> 2015-03-11 9:26 GMT-03:00 Braun Tim <Tim.Braun at sirona.com>:
>
>  Yes, exactly. If you compile ITK e.g. with Visual Studio, you can set
>> the compile profile either to ?debug?, which is slow but allows the
>> debugger to stop at breakpoints etc, and ?release?, which is much faster
>> due to enabled optimizations but cannot be debugged easily.. If you have
>> trouble compiling ITK, there are some good youtube tutorials around
>> covering this topic.
>>
>>
>>
>> *Von:* Gabriel A. Gim?nez [mailto:gabrielgimenez85 at gmail.com]
>> *Gesendet:* Mittwoch, 11. M?rz 2015 13:21
>>
>> *An:* Braun Tim
>> *Betreff:* Re: [ITK] [ITK-users] Mattes Mutual Information Speed with 3D
>> Images
>>
>>
>>
>> Hi! thank you very much for your answer!
>>
>> I'll try the alternatives do you recommend me...,I do not understand the
>> execution mode "Release" ? it is a compile option?
>>
>>
>>
>> Regards!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 2015-03-11 6:18 GMT-03:00 Braun Tim <Tim.Braun at sirona.com>:
>>
>> Hi Gabriel,
>>
>>
>>
>> this is several orders of magnitude slower than it should be, so I assume
>> there is something weird going on. Applying the metric should take a couple
>> of milliseconds, not longer. Did you compile ITK from source yourself? Then
>> you should be able to use the ?DEBUG? configuration to trace into the
>> metric evaluation and find out what the performance bottleneck is ? that?s
>> probably faster than empirical testing.. Running the algorithm must be done
>> in release mode, of course. Another option would be to try the ITK Slicer
>> program, which contains the Brainsfit algorithm which uses MMI for
>> registration ? here, you can try different parameters and check the
>> runtime..
>>
>>
>>
>> cheers, Tim
>>
>>
>>
>>
>>
>> *Von:* Gabriel A. Gim?nez [mailto:gabrielgimenez85 at gmail.com]
>> *Gesendet:* Dienstag, 10. M?rz 2015 13:33
>> *An:* Braun Tim
>> *Betreff:* Re: [ITK] [ITK-users] Mattes Mutual Information Speed with 3D
>> Images
>>
>>
>>
>> Hi Braun, thanks for your answer...
>>
>>
>>
>> I use images of RIRE BD (http://www.insight-journal.org/rire/), my
>> initial tests I make with package training_001 (CT - MR_PD). Following your
>> recommendation here is my configuration:
>>
>>
>>
>>
>>
>>          metric->SetNumberOfHistogramBins( 50 );
>>
>>          double samplingPercentage = 0.002;
>>
>>          registration->SetMetricSamplingPercentage( samplingPercentage );
>>
>>          RegistrationType::MetricSamplingStrategyType  samplingStrategy  =
>>
>>
>>                  RegistrationType::REGULAR;
>>
>>
>>
>> Unfortunately, the results were not good ... the average execution time
>> remains the same (25 ~ 30 seconds). With a population size equal to 50, the
>> execution time of an iteration is in the order of 25 minutes, very slow for
>> me ...
>>
>>
>>
>> These are the image data:
>>
>>
>>
>>  Fixed Image:
>>
>>   ObjectType = Image
>>
>>   NDims = 3
>>
>>   BinaryDataByteOrderMSB = True
>>
>>   AnatomicalOrientation = LPH
>>
>>   ElementSpacing = 0.653595 0.653595 4.000000
>>
>>   *DimSize = 512 512 29*
>>
>>   ElementType = MET_SHORT
>>
>>   ElementDataFile = image.bin
>>
>>
>>
>> Moving Image:
>>
>>   ObjectType = Image
>>
>>   NDims = 3
>>
>>   BinaryDataByteOrderMSB = True
>>
>>   AnatomicalOrientation = LPH
>>
>>   ElementSpacing = 1.250000 1.250000 4.000000
>>
>>   *DimSize = 256 256 26*
>>
>>   ElementType = MET_SHORT
>>
>>   ElementDataFile = image.bin
>>
>>
>>
>>
>>
>> Thanks and regards!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 2015-03-10 5:51 GMT-03:00 Braun Tim <Tim.Braun at sirona.com>:
>>
>> Hi Gabriel,
>>
>> the easiest way to speed up the metric calculation I can think of
>> (without having more detailed information about your setup) is to reduce
>> the numbers of samples used to build the MMI histogram estimates. For 256^3
>> Voxel Volumes, we typically use a value of 0.002. You can set the sampling
>> percentage in the registration method that manages the metric and the
>> optimizer:
>>
>>
>> registrationMethod->SetMetricSamplingStrategy(ImageRegistrationMethodTypev4::REGULAR);
>>         registrationMethod->SetMetricSamplingPercentage(0.002);
>>
>> Another way to speed up calculation would be to reduce the resolution of
>> the registered volumes - which is somewhat similar to reducing the sampling
>> percentage, but has memory benefits and might reduce aliasing..
>>
>>
>> Hope that helps!
>>
>> Cheers,
>> Tim
>>
>> -----Urspr?ngliche Nachricht-----
>> Von: Community [mailto:community-bounces at itk.org] Im Auftrag von Gabriel
>> A. Gim?nez
>> Gesendet: Dienstag, 10. M?rz 2015 00:02
>> An: insight-users at itk.org
>> Betreff: [ITK] [ITK-users] Mattes Mutual Information Speed with 3D Images
>>
>>
>> Hello everyone...
>>
>> I'm working on a genetic optimizer for Rigid 3D Registration.
>>
>> The fitness of each individual is calculated using Mattes Mutual
>> Information, the execution time of the metric is high ... (30 seconds on
>> average). This makes the registration too slow.
>>
>> Any recommendations? could improve the performance metrics? otherwise
>> most appropriate metric?
>>
>> Regards!
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-Speed-with-3D-Images-tp7586971.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
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>> http://www.kitware.com/products/protraining.php
>>
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>>
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>>
>>
>>
>> -----------------------------------------------------------------------------------------------------------
>> Sirona Dental Systems GmbH * HRB 24948 *
>> Vorsitzender des Aufsichtsrats: Dr. Erich Blum *
>> Sirona Dental Services GmbH * HRB 25817 *
>> Geschaeftsfuehrung: Rainer Berthan * Michael Geil *
>> Sitz der Gesellschaften: Bensheim * Registergericht: AG Darmstadt *
>>
>> ------------------------------------------------------------------------------------------------------------
>> Diese E-Mail ist ausschliesslich fuer den angesprochenen Adressaten
>> bestimmt und kann vertrauliche Informationen beinhalten.
>> --
>> This e-mail is intended only for the designated recipient(s). It may
>> contain confidential or proprietary information.
>>
>> ------------------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>>
>> --
>>
>> *Gabriel Alberto Gim?nez.*
>>
>>
>>
>>
>> -----------------------------------------------------------------------------------------------------------
>> Sirona Dental Systems GmbH ? HRB 24948 ?
>>
>> Vorsitzender des Aufsichtsrats: Dr. Erich Blum ?
>> Sirona Dental Services GmbH ? HRB 25817 ?
>> Gesch?ftsf?hrung: Rainer Berthan ? Michael Geil ?
>> Sitz der Gesellschaften: Bensheim ? Registergericht: AG Darmstadt ?
>>
>> ------------------------------------------------------------------------------------------------------------
>> Diese E-Mail ist ausschliesslich fuer den angesprochenen Adressaten
>> bestimmt und kann vertrauliche Informationen beinhalten.
>> --
>> This e-mail is intended only for the designated recipient(s). It may
>> contain confidential or proprietary information.
>>
>> ------------------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>>
>> --
>>
>> *Gabriel Alberto Gim?nez.*
>>
>
>
>
> --
> *Gabriel Alberto Gim?nez.*
>



-- 
*Gabriel Alberto Gim?nez.*
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From matt.mccormick at kitware.com  Thu Mar 12 16:11:12 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 12 Mar 2015 16:11:12 -0400
Subject: [ITK-users] abs function ambigous in Mac OS X 10.9
In-Reply-To: <CAPQEPqSeBkFobc0qd34+OpiMbTPoPdr3LLVnFaxOXF1Er2xqiQ@mail.gmail.com>
References: <CAPQEPqSeBkFobc0qd34+OpiMbTPoPdr3LLVnFaxOXF1Er2xqiQ@mail.gmail.com>
Message-ID: <CALzTN-S9CAXmwzDwFnOfKToPcrKB+kMrFRWa8q-h=5as=toAsg@mail.gmail.com>

Hello,

This issue has been addressed in ITKv4.  Please use ITKv4 or backport
a patch to the "release-3.20" Git branch and share it it with the
list.

Thanks,
Matt

On Thu, Mar 12, 2015 at 2:56 PM, Eduardo - LNCC <camargo at lncc.br> wrote:
> Hi,
>
> I am trying compile ITK 3.20 in the Mac OS X 10.9.5 I received the erro
> below and I don't figure out what have happened. Someboy can help me?
>
>
> [  1%] Built target itksys
> [  6%] Built target itkjpeg8
> [ 11%] Built target itkjpeg12
> [ 16%] Built target itkjpeg16
> [ 17%] Built target itkzlib
> [ 18%] Built target itkpng
> [ 18%] Built target itkmkg3states
> [ 21%] Built target itktiff
> [ 23%] Built target itkopenjpeg
> [ 25%] Built target ITKMetaIO
> [ 28%] Built target ITKNrrdIO
> [ 28%] Built target ITKEXPAT
> [ 28%] Built target ITKznz
> [ 28%] Built target ITKniftiio
> [ 29%] Built target ITKDICOMParser
> [ 30%] Built target itkvcl
> [ 51%] Built target itkv3p_netlib
> [ 51%] Built target itktestlib
> [ 69%] Built target itkvnl
> [ 74%] Built target itkvnl_algo
> [ 76%] Built target itkNetlibSlatec
> [ 80%] Built target itkgdcm
> [ 82%] Built target itkvnl_inst
> [ 88%] Built target ITKCommon
> [ 91%] Built target ITKNumerics
> [ 91%] Built target ITKBasicFilters
> [ 91%] Built target ITKStatistics
> [ 91%] Built target ITKAlgorithms
> [ 91%] Built target ITKSpatialObject
> [ 96%] Built target ITKIO
> [ 96%] Building CXX object
> Code/IO/CMakeFiles/itkTestDriver.dir/itkTestDriver.o
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:20:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkMacro.h:42:
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:86:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double e
> VCL_STATIC_CONST_INIT_FLOAT_DECL(2.7182818284590452354);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:87:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double log2e
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.4426950408889634074);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:88:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double log10e
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.43429448190325182765);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:89:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double ln2
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.69314718055994530942);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:90:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double ln10
> VCL_STATIC_CONST_INIT_FLOAT_DECL(2.30258509299404568402);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:91:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double pi
> VCL_STATIC_CONST_INIT_FLOAT_DECL(3.14159265358979323846);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:92:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double pi_over_2
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.57079632679489661923);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:93:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double pi_over_4
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.78539816339744830962);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:94:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double one_over_pi
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.31830988618379067154);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:95:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double two_over_pi
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.63661977236758134308);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:96:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double two_over_sqrtpi
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.12837916709551257390);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:97:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double one_over_sqrt2pi
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.39894228040143267794);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:98:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double sqrt2
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.41421356237309504880);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:99:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double sqrt1_2
> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.70710678118654752440);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:102:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double eps
> VCL_STATIC_CONST_INIT_FLOAT_DECL(2.2204460492503131e-16);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:103:36:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const double sqrteps
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.490116119384766e-08);
>                                    ^
> ~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:105:35:
> warning: in-class initializer for static data member of type 'const float'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const float float_eps
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.192092896e-07f);
>                                   ^
> ~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_math.h:106:35:
> warning: in-class initializer for static data member of type 'const float'
> is a GNU extension [-Wgnu-static-float-init]
>   static VNL_DLL_DATA const float float_sqrteps
> VCL_STATIC_CONST_INIT_FLOAT_DECL(3.4526698307e-4f);
>                                   ^
> ~~~~~~~~~~~~~~~~
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:35:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkImage.h:20:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkImageBase.h:25:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkImageRegion.h:27:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkContinuousIndex.h:20:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkPoint.h:23:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkVector.h:23:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_vector_ref.h:20:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_vector.h:20:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_c_vector.h:25:
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:340:22:
> warning: in-class initializer for static data member of type 'const float'
> is a GNU extension [-Wgnu-static-float-init]
>   static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F);
>                      ^                                     ~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:342:22:
> warning: in-class initializer for static data member of type 'const float'
> is a GNU extension [-Wgnu-static-float-init]
>   static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F);
>                      ^                                    ~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:344:22:
> warning: in-class initializer for static data member of type 'const float'
> is a GNU extension [-Wgnu-static-float-init]
>   static const float maxval
> VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F);
>                      ^
> ~~~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:363:23:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0);
>                       ^                                     ~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:365:23:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0);
>                       ^                                    ~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:367:23:
> warning: in-class initializer for static data member of type 'const double'
> is a GNU extension [-Wgnu-static-float-init]
>   static const double maxval
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308);
>                       ^
> ~~~~~~~~~~~~~~~~~~~~~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:386:28:
> warning: in-class initializer for static data member of type 'const long
> double' is a GNU extension [-Wgnu-static-float-init]
>   static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0);
>                            ^                                     ~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:388:28:
> warning: in-class initializer for static data member of type 'const long
> double' is a GNU extension [-Wgnu-static-float-init]
>   static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0);
>                            ^                                    ~~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Utilities/vxl/core/vnl/vnl_numeric_traits.h:390:28:
> warning: in-class initializer for static data member of type 'const long
> double' is a GNU extension [-Wgnu-static-float-init]
>   static const long double maxval
> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308);
>                            ^
> ~~~~~~~~~~~~~~~~~~~~~~~
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:939:16:
> error: call to 'abs' is ambiguous
>         return abs(__c.real());
>                ^~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:294:1:
> note: in instantiation of function template specialization
> 'std::__1::norm<unsigned int>' requested here
> ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE(unsigned int);
> ^
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:287:17:
> note: expanded from macro 'ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE'
>     return std::norm(pixel);                                             \
>                 ^
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
> note: candidate function
> int      abs(int) __pure2;
>          ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
> {return  labs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
> {return llabs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
> note: candidate function
> abs(float __x) _NOEXCEPT {return fabsf(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
> note: candidate function
> abs(double __x) _NOEXCEPT {return fabs(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
> note: candidate function
> abs(long double __x) _NOEXCEPT {return fabsl(__x);}
> ^
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:941:16:
> error: call to 'abs' is ambiguous
>         return abs(__c.imag());
>                ^~~
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
> note: candidate function
> int      abs(int) __pure2;
>          ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
> {return  labs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
> {return llabs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
> note: candidate function
> abs(float __x) _NOEXCEPT {return fabsf(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
> note: candidate function
> abs(double __x) _NOEXCEPT {return fabs(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
> note: candidate function
> abs(long double __x) _NOEXCEPT {return fabsl(__x);}
> ^
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:939:16:
> error: call to 'abs' is ambiguous
>         return abs(__c.real());
>                ^~~
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:298:1:
> note: in instantiation of function template specialization
> 'std::__1::norm<unsigned long>' requested here
> ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE(unsigned long);
> ^
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkDefaultConvertPixelTraits.h:287:17:
> note: expanded from macro 'ITK_DEFAULTCONVERTTRAITS_COMPLEX_TYPE'
>     return std::norm(pixel);                                             \
>                 ^
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
> note: candidate function
> int      abs(int) __pure2;
>          ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
> {return  labs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
> {return llabs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
> note: candidate function
> abs(float __x) _NOEXCEPT {return fabsf(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
> note: candidate function
> abs(double __x) _NOEXCEPT {return fabs(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
> note: candidate function
> abs(long double __x) _NOEXCEPT {return fabsl(__x);}
> ^
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/IO/itkTestDriver.cxx:33:
> In file included from
> /Users/hemolab/Documents/workspace/libs/InsightToolkit-3.16.0/Code/Common/itkNumericTraits.h:32:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:941:16:
> error: call to 'abs' is ambiguous
>         return abs(__c.imag());
>                ^~~
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:129:6:
> note: candidate function
> int      abs(int) __pure2;
>          ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:159:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long      abs(     long __x) _NOEXCEPT
> {return  labs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:161:44:
> note: candidate function
> inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT
> {return llabs(__x);}
>                                            ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:1:
> note: candidate function
> abs(float __x) _NOEXCEPT {return fabsf(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:1:
> note: candidate function
> abs(double __x) _NOEXCEPT {return fabs(__x);}
> ^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:1:
> note: candidate function
> abs(long double __x) _NOEXCEPT {return fabsl(__x);}
> ^
> 27 warnings and 4 errors generated.
> make[2]: *** [Code/IO/CMakeFiles/itkTestDriver.dir/itkTestDriver.o] Error 1
> make[1]: *** [Code/IO/CMakeFiles/itkTestDriver.dir/all] Error 2
> make: *** [all] Error 2
>
> Atenciosamente,
>
>
> Eduardo Camargo, M.Sc.
>
> Analista de Sistemas
> Instituto Nacional de Ci?ncia e Tecnologia em
> Medicina Assistida por Computa??o Cient?fica
> INCT-MACC  http://macc.lncc.br
> Laborat?rio Nacional de Computa??o Cient?fica
> LNCC - http://www.lncc.br
>
> _____________________________________
> 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 gaetan.lehmann at gmail.com  Thu Mar 12 17:49:05 2015
From: gaetan.lehmann at gmail.com (Gaetan Lehmann)
Date: Thu, 12 Mar 2015 22:49:05 +0100
Subject: [ITK-users] apply color map to a label map with overlapping
	label objects?
In-Reply-To: <F13813D5-49FB-498A-9C61-4EF125255472@gmail.com>
References: <F13813D5-49FB-498A-9C61-4EF125255472@gmail.com>
Message-ID: <CAGmO4ixxCBDhgcKNr27nNpUrPp16_Pwdjzee6fdm_wuXg6E3bg@mail.gmail.com>

Hi Arnaud,

Converting a label map with overlapping objects to an image usually works
quite badly, and itk::LabelMapOverlayImageFilter is no exception.
The overlapping zones must be removed first, for example with
itk::UniqueLableMapFilter.

This may not be what you want though. What would you expect as output for
the overlapping objects?

Regards,

Ga?tan

2015-03-10 10:30 GMT+01:00 Arnaud Gelas <arnaudgelas at gmail.com>:

> Hi all,
>
> I would like to colorize one label map with overlapping label objects. I
> know there is itk::LabelMapOverlayImageFilter but would it work on such a
> case? (could be wrong, but based on the code it does not seem so)
>
> Thanks
> Arnaud
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From matimontg at gmail.com  Thu Mar 12 19:26:47 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Thu, 12 Mar 2015 20:26:47 -0300
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
 <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
 <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>
Message-ID: <CAKKNfuJH+6-WbbY1Z16MSpjKbNdgh9rXyQ9nRKxbYMfV_ZR6Ng@mail.gmail.com>

Hi Brad, thanks for the explanation. I'm using C#, would that be the same
process?

On Wed, Mar 11, 2015 at 8:56 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> If you are willing to compile it yourself you can get it to work with just
> a little bit of effort.
>
> Compile the SimpleITK superbuild with shared libraries enabled. Do the
> usual installation of SimpleITK from the super build [1], this will install
> the SimpleITK python library into your site-packages. However, this
> libraries also depends on all the SimpleITK an ITK dlls (not installed or
> packaged), these should be in the superbuild's bin directory. These need to
> be in your run-time path when importing SimpleITK. This can be done either
> by modifying you PATH environment variable you copying them to the
> appropriate place ( which may depend on the python environment, and there
> are likely several alternatives).
>
> Brad
>
> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Python_installation
>
> On Mar 11, 2015, at 7:31 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
>
> My project is using 64 bits and some DLL I use as well, I've ran into
> issues when using the beta version because is 32 bits. I guess I'll wait
> until the final release is done.
> Thanks,
> Matias.
>
> On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com>
> wrote:
>
>> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't
>> aware of this new Beta release
>> Thanks,
>> Matias.
>>
>> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
>> > wrote:
>>
>>> Hello Matias,
>>>
>>> Currently there is SimpleITK 0.9b01 [1] out with the registration
>>> framework.
>>>
>>> With it you can do things like this:
>>>
>>> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
>>> or
>>>
>>> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>>>
>>> Please give it a try and let us know how it work for you.
>>>
>>> Enjoy,
>>> Brad
>>>
>>> [1]
>>> http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>>>
>>> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>
>>> is it possible to do registration in SimpleITK? I mean, something like
>>> in this example:
>>>
>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>>>
>>> Thanks,
>>>
>>> Matias,
>>> _____________________________________
>>> 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 blowekamp at mail.nih.gov  Thu Mar 12 20:50:30 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 12 Mar 2015 20:50:30 -0400
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <CAKKNfuJH+6-WbbY1Z16MSpjKbNdgh9rXyQ9nRKxbYMfV_ZR6Ng@mail.gmail.com>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
 <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
 <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>
 <CAKKNfuJH+6-WbbY1Z16MSpjKbNdgh9rXyQ9nRKxbYMfV_ZR6Ng@mail.gmail.com>
Message-ID: <DED8DC80-12C5-401C-B33C-DEE020623AC8@mail.nih.gov>

Hello,

Yes, it is more or less the same process. Grab all the ITK and SimpleITK dlls from the bin directories and place them in your path.

The SimpleITK Superbuild INSTALL target will actually install ITK and SimpleITK's core libraries correctly in to the CMake specified path. The installation target for the superbuild project just doesn't install the target languages ( every language has at least one own way of doing things that CMake does not know about ). You could use this to install all the needed dlls into a defined path. Then just grab the CSharp dll for your project and that should work too.

Also I worked on the explicit instantiation in SimpleITK today. I was able to reduce the size of the .o files on Linux by 30% by explicitly instantiating about 20 classes with their used templates. This is expected to resolve the linking and packaging issues on windows. So a solution is forth coming.

Brad

On Mar 12, 2015, at 7:26 PM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi Brad, thanks for the explanation. I'm using C#, would that be the same process?
> 
> On Wed, Mar 11, 2015 at 8:56 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> If you are willing to compile it yourself you can get it to work with just a little bit of effort.
> 
> Compile the SimpleITK superbuild with shared libraries enabled. Do the usual installation of SimpleITK from the super build [1], this will install the SimpleITK python library into your site-packages. However, this libraries also depends on all the SimpleITK an ITK dlls (not installed or packaged), these should be in the superbuild's bin directory. These need to be in your run-time path when importing SimpleITK. This can be done either by modifying you PATH environment variable you copying them to the appropriate place ( which may depend on the python environment, and there are likely several alternatives).
> 
> Brad
> 
> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Python_installation
> 
> On Mar 11, 2015, at 7:31 PM, Matias Montroull <matimontg at gmail.com> wrote:
> 
>> 
>> My project is using 64 bits and some DLL I use as well, I've ran into issues when using the beta version because is 32 bits. I guess I'll wait until the final release is done.
>> Thanks,
>> Matias.
>> 
>> On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com> wrote:
>> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't aware of this new Beta release
>> Thanks,
>> Matias.
>> 
>> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Hello Matias,
>> 
>> Currently there is SimpleITK 0.9b01 [1] out with the registration framework.
>> 
>> With it you can do things like this:
>> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
>> or
>> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>> 
>> Please give it a try and let us know how it work for you.
>> 
>> Enjoy,
>> Brad
>> 
>> [1] http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>> 
>> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com> wrote:
>> 
>>> Hi,
>>> 
>>> is it possible to do registration in SimpleITK? I mean, something like in this example:
>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>>> 
>>> Thanks,
>>> 
>>> Matias,
>>> _____________________________________
>>> 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 lassi.paavolainen at jyu.fi  Fri Mar 13 07:42:54 2015
From: lassi.paavolainen at jyu.fi (Paavolainen, Lassi)
Date: Fri, 13 Mar 2015 11:42:54 +0000
Subject: [ITK-users] Memory leak in Python wrapped Image GetPixel method?
In-Reply-To: <BB43A6B0CAEAFC439640CD9D13607DC24E61BB11@mbs1.ad.jyu.fi>
References: <BB43A6B0CAEAFC439640CD9D13607DC24E61B922@mbs1.ad.jyu.fi>,
 <CALzTN-TzYRkFGZkYfx3XhnjZQNEhZ+PkxhmuZiOxRr-TTzrdbg@mail.gmail.com>,
 <BB43A6B0CAEAFC439640CD9D13607DC24E61BB11@mbs1.ad.jyu.fi>
Message-ID: <BB43A6B0CAEAFC439640CD9D13607DC24E622058@mbs1.ad.jyu.fi>

In case it makes any difference, I can see the same issue with freshly installed another computer. Though both have pretty much the same environment (updated Ubuntu 14.04, Python 2.7.6). The freshly installed machine is using ITK 4.7.1, but as said I can see the same problem with ITK 4.6 and 3.20.

Would be nice to hear if anyone with similar setup is able to reproduce the issue.

Lassi

________________________________________
From: Insight-users [insight-users-bounces at itk.org] on behalf of Paavolainen, Lassi [lassi.paavolainen at jyu.fi]
Sent: Monday, March 09, 2015 21:59
To: Matt McCormick
Cc: insight-users at itk.org
Subject: Re: [ITK-users] Memory leak in Python wrapped Image GetPixel method?

Hi Matt,

Seems its an issue with local environment. Here is also for the list what I replied to Gaetan:
"This is interesting. I'm using ITK 4.6.1 with swig that comes with it. I now tested with 3.20 that has been built long time ago with swig 1.9 (if I remember correctly). The same thing. So the conclusion is that it must be something local as I'm sure I've done something similar over the years many times.

Next is to try to find out what on my environment causes this."

To add to that, I ran 30 iterations using valgrind. Here is the report:
==8603== HEAP SUMMARY:
==8603==     in use at exit: 478,066,856 bytes in 483,719 blocks
==8603==   total heap usage: 657,312 allocs, 173,593 frees, 787,087,705 bytes allocated
==8603==
==8603== LEAK SUMMARY:
==8603==    definitely lost: 0 bytes in 0 blocks
==8603==    indirectly lost: 0 bytes in 0 blocks
==8603==      possibly lost: 20,224 bytes in 34 blocks
==8603==    still reachable: 478,046,632 bytes in 483,685 blocks
==8603==         suppressed: 0 bytes in 0 blocks

So almost 500 MB is in heap but still reachable when the program exits.

Lassi

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, March 09, 2015 20:22
To: Paavolainen, Lassi
Cc: insight-users at itk.org; Ga?tan Lehmann; Michka Popoff
Subject: Re: [ITK-users] Memory leak in Python wrapped Image GetPixel method?

Hi Lassi,

Thanks for investigating and reporting the issue!

I have created an issue in the Issue Tracker to keep track of it:

  https://issues.itk.org/jira/browse/ITK-3352

Matt

On Mon, Mar 9, 2015 at 6:11 AM, Paavolainen, Lassi
<lassi.paavolainen at jyu.fi> wrote:
> Hi,
>
> I noticed that GetPixel method in itk.Image object eats memory in Python wrapped code. I think I've seen some Python wrapping memory issues years ago but nothing as simple as this. Here is a simple test script:
> import sys
> import itk
> reader = itk.ImageFileReader.IUC2.New()
> reader.SetFileName(sys.argv[1])
> reader.Update()
> img = reader.GetOutput()
> size = img.GetLargestPossibleRegion().GetSize()
> for i in range(100):
>         for x in range(size[0]):
>                 for y in range(size[1]):
>                         value = img.GetPixel((x,y))
>         print "Done with iteration %d"%(i+1)
>
> When I run it with 1 MB image, it end up taking 1.5 GB of memory. After spending lots of time on debugging a bigger bunch of code I realized that the GetPixel method was to blame. Can anyone reproduce it? I'm using ITK 4.6.1
>
> Cheers,
> Lassi
> _____________________________________
> 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 lluna.nova at gmail.com  Mon Mar 16 07:37:23 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Mon, 16 Mar 2015 12:37:23 +0100
Subject: [ITK-users] Splitting and repasting a volume with overlap
Message-ID: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>

Hello everyone,

We need to split a volume into pieces, overlaped by a certain amount, do
some computation and then repaste them.

The computation requires the pieces' region indexes to be set to zero. The
original volume might not have index at zero, but be a subregion itself.

What is the best way to achieve this?

I've thought of the following pipeline:

1. imageRegionSplitterSlowDimension
2. Store the index and size of each region
3. manually increase the size of each region (and modify index)
4. crop with the largestPossibleRegion of the original volume (to prevent
requesting more than available)
iterate over regions:
      5. extractImageFilter
      6. disconnect pipeline for each region
      7. reset indexes
      8. perform computation
      9. crop with the regions in step 1 to remove the added overlap
      10. restore indexes
11. pasteImageFilter

I'll have to think of a smart way to deal with the index restore/cropping
of steps 9 and 10.

I somehow feel somebody will have already dealt with this... And there's
certainly a better way to do it.
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From ds_prakash at rediffmail.com  Mon Mar 16 08:48:44 2015
From: ds_prakash at rediffmail.com (Surya Prakash)
Date: 16 Mar 2015 12:48:44 -0000
Subject: [ITK-users] =?utf-8?q?big_image?=
Message-ID: <20150316124844.23818.qmail@f4mail-235-154.rediffmail.com>

hello,
I have very large, 50k x 50k images assume. How I can read part of an image.

Thanks & regards
Prakash
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From blowekamp at mail.nih.gov  Mon Mar 16 09:00:00 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 16 Mar 2015 09:00:00 -0400
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
Message-ID: <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>

Hello,

The RegionOfInterestImageFilter[1] is very similar to the ExtractImageFilter, but returns an image whose starting index is always zeros.

The process you described is remarkable close to what occur in each filter for the multi-threading process.  Also what occurs in the StreamingImageFilter is very similar, but just copies the region.

As you didn't mention you motivation for chunking the data this way be it for threading or memory requirements, I can't fully advise. 

Brad


[1 ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213


On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:

> Hello everyone,
> 
> We need to split a volume into pieces, overlaped by a certain amount, do some computation and then repaste them.
> 
> The computation requires the pieces' region indexes to be set to zero. The original volume might not have index at zero, but be a subregion itself.
> 
> What is the best way to achieve this?
> 
> I've thought of the following pipeline:
> 
> 1. imageRegionSplitterSlowDimension
> 2. Store the index and size of each region
> 3. manually increase the size of each region (and modify index)
> 4. crop with the largestPossibleRegion of the original volume (to prevent requesting more than available)
> iterate over regions:
>       5. extractImageFilter
>       6. disconnect pipeline for each region
>       7. reset indexes
>       8. perform computation
>       9. crop with the regions in step 1 to remove the added overlap
>       10. restore indexes
> 11. pasteImageFilter
> 
> I'll have to think of a smart way to deal with the index restore/cropping of steps 9 and 10.
> 
> I somehow feel somebody will have already dealt with this... And there's certainly a better way to do it.
> _____________________________________
> 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  Mon Mar 16 09:05:02 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 16 Mar 2015 09:05:02 -0400
Subject: [ITK-users] big image
In-Reply-To: <20150316124844.23818.qmail@f4mail-235-154.rediffmail.com>
References: <20150316124844.23818.qmail@f4mail-235-154.rediffmail.com>
Message-ID: <26A3491B-B64F-43E8-9708-A366E27549D8@mail.nih.gov>

Hello Surya,

What file format do you have?

You may find this article helpful:
http://www.kitware.com/media/html/IOStreamingInITK.htm

The currently support formats for streaming io input include HDF5, JPEG2000, MRC, SCIFIO, VTK, NIFTI and MetaIO. I myself have personally extensively used MetaImageIO, and MRC, and a little VTK.

Brad

On Mar 16, 2015, at 8:48 AM, Surya Prakash <ds_prakash at rediffmail.com> wrote:

> hello,
> I have very large, 50k x 50k images assume. How I can read part of an image.
> 
> Thanks & regards
> Prakash
> 
> Get your own FREE website, FREE domain & FREE mobile app with Company email.  
> Know More >
> _____________________________________
> 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 lluna.nova at gmail.com  Mon Mar 16 09:25:49 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Mon, 16 Mar 2015 14:25:49 +0100
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
Message-ID: <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>

Hello Bradley,

Thank you for your answer and suggestion.

Answering your question: It's not for multi-threading purposes, I have to
split the image due to memory limitations.

I would use extractImage directly and do streaming, but the client and the
low-level libraries might not work correctly if I do that. I have to
provide itk images disconnected from the pipeline and with proper indexes
and sizes.

The RegionOfInterestImageFilter would have the same memory footprint, and
it would still be tricky to compute the regions of interest, due to the
overlapping.


2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> Hello,
>
> The RegionOfInterestImageFilter[1] is very similar to the
> ExtractImageFilter, but returns an image whose starting index is always
> zeros.
>
> The process you described is remarkable close to what occur in each filter
> for the multi-threading process.  Also what occurs in the
> StreamingImageFilter is very similar, but just copies the region.
>
> As you didn't mention you motivation for chunking the data this way be it
> for threading or memory requirements, I can't fully advise.
>
> Brad
>
>
> [1 ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> [2]
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>
>
> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
>
> > Hello everyone,
> >
> > We need to split a volume into pieces, overlaped by a certain amount, do
> some computation and then repaste them.
> >
> > The computation requires the pieces' region indexes to be set to zero.
> The original volume might not have index at zero, but be a subregion itself.
> >
> > What is the best way to achieve this?
> >
> > I've thought of the following pipeline:
> >
> > 1. imageRegionSplitterSlowDimension
> > 2. Store the index and size of each region
> > 3. manually increase the size of each region (and modify index)
> > 4. crop with the largestPossibleRegion of the original volume (to
> prevent requesting more than available)
> > iterate over regions:
> >       5. extractImageFilter
> >       6. disconnect pipeline for each region
> >       7. reset indexes
> >       8. perform computation
> >       9. crop with the regions in step 1 to remove the added overlap
> >       10. restore indexes
> > 11. pasteImageFilter
> >
> > I'll have to think of a smart way to deal with the index
> restore/cropping of steps 9 and 10.
> >
> > I somehow feel somebody will have already dealt with this... And there's
> certainly a better way to do it.
> > _____________________________________
> > 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
>
>

2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> Hello,
>
> The RegionOfInterestImageFilter[1] is very similar to the
> ExtractImageFilter, but returns an image whose starting index is always
> zeros.
>
> The process you described is remarkable close to what occur in each filter
> for the multi-threading process.  Also what occurs in the
> StreamingImageFilter is very similar, but just copies the region.
>
> As you didn't mention you motivation for chunking the data this way be it
> for threading or memory requirements, I can't fully advise.
>
> Brad
>
>
> [1 ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> [2]
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>
>
> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
>
> > Hello everyone,
> >
> > We need to split a volume into pieces, overlaped by a certain amount, do
> some computation and then repaste them.
> >
> > The computation requires the pieces' region indexes to be set to zero.
> The original volume might not have index at zero, but be a subregion itself.
> >
> > What is the best way to achieve this?
> >
> > I've thought of the following pipeline:
> >
> > 1. imageRegionSplitterSlowDimension
> > 2. Store the index and size of each region
> > 3. manually increase the size of each region (and modify index)
> > 4. crop with the largestPossibleRegion of the original volume (to
> prevent requesting more than available)
> > iterate over regions:
> >       5. extractImageFilter
> >       6. disconnect pipeline for each region
> >       7. reset indexes
> >       8. perform computation
> >       9. crop with the regions in step 1 to remove the added overlap
> >       10. restore indexes
> > 11. pasteImageFilter
> >
> > I'll have to think of a smart way to deal with the index
> restore/cropping of steps 9 and 10.
> >
> > I somehow feel somebody will have already dealt with this... And there's
> certainly a better way to do it.
> > _____________________________________
> > 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 Gordian.Kabelitz at medma.uni-heidelberg.de  Mon Mar 16 08:59:23 2015
From: Gordian.Kabelitz at medma.uni-heidelberg.de (Kabelitz, Gordian)
Date: Mon, 16 Mar 2015 13:59:23 +0100
Subject: [ITK-users] Examples for ITK-based 2D/3D registration
Message-ID: <5E843F0B86B47846B72559B57A54F96217BE836658@MBX02.ad.uni-heidelberg.de>

Hello,

I am interested in 2D/3D medical image registration using ITK. Currently I am looking for some good examples for a 2D/3D registration based on CT and conventional x-ray images.
Is there a recommended tutorial or framework in addition to ITK? I am familiar with the registration examples from [1]. IMHO these are not useful for my topic. I am interested in all the possibilities for optimizing the registration process the ITK can provide.
I would appreciate it if someone can give me a hint. I already checked the documentation center for ITK [3].

Bonus question:
Is the extended ITK-based Framework for Intensity-based 2D/3D-Registration [2] from 2009 included in the ITK?

Thanks in advance.

Regards,
 Gordian Kabelitz

[1]: http://www.itk.org/Doxygen47/html/examples.html
[2]: https://ibia.umit.at/ResearchGroup/Phil/web/Simple2D3DRegistrationFramework.html
[3]: www.itk.org/Wiki/ITK/Documentation<http://www.itk.org/Wiki/ITK/Documentation>




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From ds_prakash at rediffmail.com  Mon Mar 16 08:38:14 2015
From: ds_prakash at rediffmail.com (Surya Prakash)
Date: 16 Mar 2015 12:38:14 -0000
Subject: [ITK-users] =?utf-8?q?connected_threshold?=
Message-ID: <20150316123814.27479.qmail@f4mail-235-189.rediffmail.com>

Hello,
I am making an interactive region growing application using connectedThreshold. Seed point etc I want to collect interactively. After collecting the inputs, I will execute something like this.

smoothing->SetInput( reader->GetOutput() );
connectedThreshold->SetInput( smoothing->GetOutput() );

As it is not possible to read big images, I will read portion of the data and give it to 'smoothing', by passing the 'Reader'. Please help me with some sample. I am using the 'ConnectedThresholdImageFilter sample.



Thanks & regards
Prakash
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From ds_prakash at rediffmail.com  Mon Mar 16 15:23:45 2015
From: ds_prakash at rediffmail.com (ds_prakash)
Date: 16 Mar 2015 19:23:45 -0000
Subject: [ITK-users] =?utf-8?q?multiple_seeds?=
Message-ID: <20150316192345.1345.qmail@f4mail-235-145.rediffmail.com>

hello ALL,
Is it possible to give multiple seed pixels to ConnectedThresholdImageFilter? I also want the output of regions grown corresponding to all seeds in a single output file.

Thanks
Prakash
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From scapegoat.sarthak at gmail.com  Mon Mar 16 10:15:03 2015
From: scapegoat.sarthak at gmail.com (Scapegoat Sarthak)
Date: Mon, 16 Mar 2015 10:15:03 -0400
Subject: [ITK-users] Error while reading Unknown Image Information
Message-ID: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>

Hi All,

I am trying to read information from different images using the Unknown
Image Type Example (http://itk.org/Wiki/ITK/Examples/IO/ReadUnknownImageType)
but I am getting an Access violation error. The three main lines of code
(which compile without issues) I am using are:

itk::ImageIOBase::Pointer imageIO =
itk::ImageIOFactory::CreateImageIO(argv[3], itk::ImageIOFactory::ReadMode );
imageIO->SetFileName(std::string(argv[3]));
imageIO->ReadImageInformation();

I am getting the error in the second line. I am using CMake to generate
project files as described in the example so the include directories and
libraries are all taken care of. I tried to read different files (.nii,
.dcm, .png, .jpg) but all of them give the same error.

Any suggestions regarding what I am doing wrong?

Thanks in advance,
Sarthak
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From lluna.nova at gmail.com  Mon Mar 16 10:16:05 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Mon, 16 Mar 2015 15:16:05 +0100
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
Message-ID: <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>

Mmh, I believe I misread the RegionOfInterestImageFilter documentation,
confusing dimension with size. That should work.

I still have the computation of the splitting regions problem to handle,
but maybe with this filter is easier than with the ExtractImageFilter. Or
maybe it just removes step 7?

Is there a way to ease the repasting back to the original region with it?
How should I use the physical space index?

2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:

> Hello Bradley,
>
> Thank you for your answer and suggestion.
>
> Answering your question: It's not for multi-threading purposes, I have to
> split the image due to memory limitations.
>
> I would use extractImage directly and do streaming, but the client and the
> low-level libraries might not work correctly if I do that. I have to
> provide itk images disconnected from the pipeline and with proper indexes
> and sizes.
>
> The RegionOfInterestImageFilter would have the same memory footprint, and
> it would still be tricky to compute the regions of interest, due to the
> overlapping.
>
>
>
> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>
>> Hello,
>>
>> The RegionOfInterestImageFilter[1] is very similar to the
>> ExtractImageFilter, but returns an image whose starting index is always
>> zeros.
>>
>> The process you described is remarkable close to what occur in each
>> filter for the multi-threading process.  Also what occurs in the
>> StreamingImageFilter is very similar, but just copies the region.
>>
>> As you didn't mention you motivation for chunking the data this way be it
>> for threading or memory requirements, I can't fully advise.
>>
>> Brad
>>
>>
>> [1 ]
>> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>> [2]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>>
>>
>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>> wrote:
>>
>> > Hello everyone,
>> >
>> > We need to split a volume into pieces, overlaped by a certain amount,
>> do some computation and then repaste them.
>> >
>> > The computation requires the pieces' region indexes to be set to zero.
>> The original volume might not have index at zero, but be a subregion itself.
>> >
>> > What is the best way to achieve this?
>> >
>> > I've thought of the following pipeline:
>> >
>> > 1. imageRegionSplitterSlowDimension
>> > 2. Store the index and size of each region
>> > 3. manually increase the size of each region (and modify index)
>> > 4. crop with the largestPossibleRegion of the original volume (to
>> prevent requesting more than available)
>> > iterate over regions:
>> >       5. extractImageFilter
>> >       6. disconnect pipeline for each region
>> >       7. reset indexes
>> >       8. perform computation
>> >       9. crop with the regions in step 1 to remove the added overlap
>> >       10. restore indexes
>> > 11. pasteImageFilter
>> >
>> > I'll have to think of a smart way to deal with the index
>> restore/cropping of steps 9 and 10.
>> >
>> > I somehow feel somebody will have already dealt with this... And
>> there's certainly a better way to do it.
>> > _____________________________________
>> > 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
>>
>>
>
> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>
>> Hello,
>>
>> The RegionOfInterestImageFilter[1] is very similar to the
>> ExtractImageFilter, but returns an image whose starting index is always
>> zeros.
>>
>> The process you described is remarkable close to what occur in each
>> filter for the multi-threading process.  Also what occurs in the
>> StreamingImageFilter is very similar, but just copies the region.
>>
>> As you didn't mention you motivation for chunking the data this way be it
>> for threading or memory requirements, I can't fully advise.
>>
>> Brad
>>
>>
>> [1 ]
>> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>> [2]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>>
>>
>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>> wrote:
>>
>> > Hello everyone,
>> >
>> > We need to split a volume into pieces, overlaped by a certain amount,
>> do some computation and then repaste them.
>> >
>> > The computation requires the pieces' region indexes to be set to zero.
>> The original volume might not have index at zero, but be a subregion itself.
>> >
>> > What is the best way to achieve this?
>> >
>> > I've thought of the following pipeline:
>> >
>> > 1. imageRegionSplitterSlowDimension
>> > 2. Store the index and size of each region
>> > 3. manually increase the size of each region (and modify index)
>> > 4. crop with the largestPossibleRegion of the original volume (to
>> prevent requesting more than available)
>> > iterate over regions:
>> >       5. extractImageFilter
>> >       6. disconnect pipeline for each region
>> >       7. reset indexes
>> >       8. perform computation
>> >       9. crop with the regions in step 1 to remove the added overlap
>> >       10. restore indexes
>> > 11. pasteImageFilter
>> >
>> > I'll have to think of a smart way to deal with the index
>> restore/cropping of steps 9 and 10.
>> >
>> > I somehow feel somebody will have already dealt with this... And
>> there's certainly a better way to do it.
>> > _____________________________________
>> > 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  Mon Mar 16 10:20:24 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 16 Mar 2015 10:20:24 -0400
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
Message-ID: <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>

You may find this method useful:

http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20

Brad

On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:

> Mmh, I believe I misread the RegionOfInterestImageFilter documentation, confusing dimension with size. That should work.
> 
> I still have the computation of the splitting regions problem to handle, but maybe with this filter is easier than with the ExtractImageFilter. Or maybe it just removes step 7?
> 
> Is there a way to ease the repasting back to the original region with it? How should I use the physical space index?
> 
> 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
> Hello Bradley,
> 
> Thank you for your answer and suggestion.
> 
> Answering your question: It's not for multi-threading purposes, I have to split the image due to memory limitations. 
> 
> I would use extractImage directly and do streaming, but the client and the low-level libraries might not work correctly if I do that. I have to provide itk images disconnected from the pipeline and with proper indexes and sizes.
> 
> The RegionOfInterestImageFilter would have the same memory footprint, and it would still be tricky to compute the regions of interest, due to the overlapping.
> 
> 
> 
> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> Hello,
> 
> The RegionOfInterestImageFilter[1] is very similar to the ExtractImageFilter, but returns an image whose starting index is always zeros.
> 
> The process you described is remarkable close to what occur in each filter for the multi-threading process.  Also what occurs in the StreamingImageFilter is very similar, but just copies the region.
> 
> As you didn't mention you motivation for chunking the data this way be it for threading or memory requirements, I can't fully advise.
> 
> Brad
> 
> 
> [1 ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> [2] https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> 
> 
> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
> 
> > Hello everyone,
> >
> > We need to split a volume into pieces, overlaped by a certain amount, do some computation and then repaste them.
> >
> > The computation requires the pieces' region indexes to be set to zero. The original volume might not have index at zero, but be a subregion itself.
> >
> > What is the best way to achieve this?
> >
> > I've thought of the following pipeline:
> >
> > 1. imageRegionSplitterSlowDimension
> > 2. Store the index and size of each region
> > 3. manually increase the size of each region (and modify index)
> > 4. crop with the largestPossibleRegion of the original volume (to prevent requesting more than available)
> > iterate over regions:
> >       5. extractImageFilter
> >       6. disconnect pipeline for each region
> >       7. reset indexes
> >       8. perform computation
> >       9. crop with the regions in step 1 to remove the added overlap
> >       10. restore indexes
> > 11. pasteImageFilter
> >
> > I'll have to think of a smart way to deal with the index restore/cropping of steps 9 and 10.
> >
> > I somehow feel somebody will have already dealt with this... And there's certainly a better way to do it.
> > _____________________________________
> > 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
> 
> 
> 
> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> Hello,
> 
> The RegionOfInterestImageFilter[1] is very similar to the ExtractImageFilter, but returns an image whose starting index is always zeros.
> 
> The process you described is remarkable close to what occur in each filter for the multi-threading process.  Also what occurs in the StreamingImageFilter is very similar, but just copies the region.
> 
> As you didn't mention you motivation for chunking the data this way be it for threading or memory requirements, I can't fully advise.
> 
> Brad
> 
> 
> [1 ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> [2] https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> 
> 
> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
> 
> > Hello everyone,
> >
> > We need to split a volume into pieces, overlaped by a certain amount, do some computation and then repaste them.
> >
> > The computation requires the pieces' region indexes to be set to zero. The original volume might not have index at zero, but be a subregion itself.
> >
> > What is the best way to achieve this?
> >
> > I've thought of the following pipeline:
> >
> > 1. imageRegionSplitterSlowDimension
> > 2. Store the index and size of each region
> > 3. manually increase the size of each region (and modify index)
> > 4. crop with the largestPossibleRegion of the original volume (to prevent requesting more than available)
> > iterate over regions:
> >       5. extractImageFilter
> >       6. disconnect pipeline for each region
> >       7. reset indexes
> >       8. perform computation
> >       9. crop with the regions in step 1 to remove the added overlap
> >       10. restore indexes
> > 11. pasteImageFilter
> >
> > I'll have to think of a smart way to deal with the index restore/cropping of steps 9 and 10.
> >
> > I somehow feel somebody will have already dealt with this... And there's certainly a better way to do it.
> > _____________________________________
> > 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  Mon Mar 16 10:46:00 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 16 Mar 2015 10:46:00 -0400
Subject: [ITK-users] Examples for ITK-based 2D/3D registration
In-Reply-To: <5E843F0B86B47846B72559B57A54F96217BE836658@MBX02.ad.uni-heidelberg.de>
References: <5E843F0B86B47846B72559B57A54F96217BE836658@MBX02.ad.uni-heidelberg.de>
Message-ID: <CALzTN-QQjvfGujLBW8-82epLmVsTgxwQnc3WP3JSbU9-HFDw0Q@mail.gmail.com>

Hi Gordian,

Hopefully you came across this example that uses the
RayCastInterpolateImageFunction [1].

Regarding the reference from 2009, to the best of my knowledge it has
not been integrated into the toolkit. To help that process along,
first find its associated article in the Insight Journal [2].  Next,
organize the code into an ITKv4 External module.  Finally, submit it
as a Remote Module [4]. Of course, adding documentation along the way
will help others in your situation.

Thanks,
Matt


[1] http://www.itk.org/Doxygen/html/Examples_2Filtering_2DigitallyReconstructedRadiograph1_8cxx-example.html

[2] http://insight-journal.org

[3] http://www.kitware.com/blog/home/post/557

[4] http://www.itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules

On Mon, Mar 16, 2015 at 8:59 AM, Kabelitz, Gordian
<Gordian.Kabelitz at medma.uni-heidelberg.de> wrote:
> Hello,
>
> I am interested in 2D/3D medical image registration using ITK. Currently I
> am looking for some good examples for a 2D/3D registration based on CT and
> conventional x-ray images.
> Is there a recommended tutorial or framework in addition to ITK? I am
> familiar with the registration examples from [1]. IMHO these are not useful
> for my topic. I am interested in all the possibilities for optimizing the
> registration process the ITK can provide.
> I would appreciate it if someone can give me a hint. I already checked the
> documentation center for ITK [3].
>
> Bonus question:
> Is the extended ITK-based Framework for Intensity-based 2D/3D-Registration
> [2] from 2009 included in the ITK?
>
> Thanks in advance.
>
> Regards,
> Gordian Kabelitz
>
> [1]: http://www.itk.org/Doxygen47/html/examples.html
> [2]:
> https://ibia.umit.at/ResearchGroup/Phil/web/Simple2D3DRegistrationFramework.html
> [3]: www.itk.org/Wiki/ITK/Documentation
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Mon Mar 16 10:50:09 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 16 Mar 2015 10:50:09 -0400
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
Message-ID: <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>

Hi Sarthak,

You may also find this example [1] informative.

To investigate the access violation error, use try{}catch{} statements
as found in the examples (use it around your
imageIO->ReadImageInformation; statement). Also, run the code in a
debugger.

Hope this helps,
Matt


[1] http://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html?highlight=read

On Mon, Mar 16, 2015 at 10:15 AM, Scapegoat Sarthak
<scapegoat.sarthak at gmail.com> wrote:
> Hi All,
>
> I am trying to read information from different images using the Unknown
> Image Type Example
> (http://itk.org/Wiki/ITK/Examples/IO/ReadUnknownImageType) but I am getting
> an Access violation error. The three main lines of code (which compile
> without issues) I am using are:
>
> itk::ImageIOBase::Pointer imageIO =
> itk::ImageIOFactory::CreateImageIO(argv[3], itk::ImageIOFactory::ReadMode );
> imageIO->SetFileName(std::string(argv[3]));
> imageIO->ReadImageInformation();
>
> I am getting the error in the second line. I am using CMake to generate
> project files as described in the example so the include directories and
> libraries are all taken care of. I tried to read different files (.nii,
> .dcm, .png, .jpg) but all of them give the same error.
>
> Any suggestions regarding what I am doing wrong?
>
> Thanks in advance,
> Sarthak
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Mon Mar 16 11:05:30 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 16 Mar 2015 11:05:30 -0400
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
Message-ID: <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>

Hi Pol,

As a side note, limitation of memory usage is built into the streaming
pipeline design of ITK.  All computation of appropriate regions should
occur if the filters are implemented correctly.  To take advantage of
streaming, place the StreamingImageFilter [1] at the end of your
pipeline. To use less memory, set the ReleaseDataFlagOn() [2] on the
component filters.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1StreamingImageFilter.html

[2] http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae732e9163879ae559ccd0b5957141f97

On Mon, Mar 16, 2015 at 10:20 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> You may find this method useful:
>
> http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
>
> Brad
>
> On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
>
> Mmh, I believe I misread the RegionOfInterestImageFilter documentation,
> confusing dimension with size. That should work.
>
> I still have the computation of the splitting regions problem to handle, but
> maybe with this filter is easier than with the ExtractImageFilter. Or maybe
> it just removes step 7?
>
> Is there a way to ease the repasting back to the original region with it?
> How should I use the physical space index?
>
> 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
>>
>> Hello Bradley,
>>
>> Thank you for your answer and suggestion.
>>
>> Answering your question: It's not for multi-threading purposes, I have to
>> split the image due to memory limitations.
>>
>> I would use extractImage directly and do streaming, but the client and the
>> low-level libraries might not work correctly if I do that. I have to provide
>> itk images disconnected from the pipeline and with proper indexes and sizes.
>>
>> The RegionOfInterestImageFilter would have the same memory footprint, and
>> it would still be tricky to compute the regions of interest, due to the
>> overlapping.
>>
>>
>>
>> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>>>
>>> Hello,
>>>
>>> The RegionOfInterestImageFilter[1] is very similar to the
>>> ExtractImageFilter, but returns an image whose starting index is always
>>> zeros.
>>>
>>> The process you described is remarkable close to what occur in each
>>> filter for the multi-threading process.  Also what occurs in the
>>> StreamingImageFilter is very similar, but just copies the region.
>>>
>>> As you didn't mention you motivation for chunking the data this way be it
>>> for threading or memory requirements, I can't fully advise.
>>>
>>> Brad
>>>
>>>
>>> [1
>>> ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>>> [2]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>>>
>>>
>>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>>> wrote:
>>>
>>> > Hello everyone,
>>> >
>>> > We need to split a volume into pieces, overlaped by a certain amount,
>>> > do some computation and then repaste them.
>>> >
>>> > The computation requires the pieces' region indexes to be set to zero.
>>> > The original volume might not have index at zero, but be a subregion itself.
>>> >
>>> > What is the best way to achieve this?
>>> >
>>> > I've thought of the following pipeline:
>>> >
>>> > 1. imageRegionSplitterSlowDimension
>>> > 2. Store the index and size of each region
>>> > 3. manually increase the size of each region (and modify index)
>>> > 4. crop with the largestPossibleRegion of the original volume (to
>>> > prevent requesting more than available)
>>> > iterate over regions:
>>> >       5. extractImageFilter
>>> >       6. disconnect pipeline for each region
>>> >       7. reset indexes
>>> >       8. perform computation
>>> >       9. crop with the regions in step 1 to remove the added overlap
>>> >       10. restore indexes
>>> > 11. pasteImageFilter
>>> >
>>> > I'll have to think of a smart way to deal with the index
>>> > restore/cropping of steps 9 and 10.
>>> >
>>> > I somehow feel somebody will have already dealt with this... And
>>> > there's certainly a better way to do it.
>>> > _____________________________________
>>> > 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
>>>
>>
>>
>> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>>>
>>> Hello,
>>>
>>> The RegionOfInterestImageFilter[1] is very similar to the
>>> ExtractImageFilter, but returns an image whose starting index is always
>>> zeros.
>>>
>>> The process you described is remarkable close to what occur in each
>>> filter for the multi-threading process.  Also what occurs in the
>>> StreamingImageFilter is very similar, but just copies the region.
>>>
>>> As you didn't mention you motivation for chunking the data this way be it
>>> for threading or memory requirements, I can't fully advise.
>>>
>>> Brad
>>>
>>>
>>> [1
>>> ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>>> [2]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>>>
>>>
>>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>>> wrote:
>>>
>>> > Hello everyone,
>>> >
>>> > We need to split a volume into pieces, overlaped by a certain amount,
>>> > do some computation and then repaste them.
>>> >
>>> > The computation requires the pieces' region indexes to be set to zero.
>>> > The original volume might not have index at zero, but be a subregion itself.
>>> >
>>> > What is the best way to achieve this?
>>> >
>>> > I've thought of the following pipeline:
>>> >
>>> > 1. imageRegionSplitterSlowDimension
>>> > 2. Store the index and size of each region
>>> > 3. manually increase the size of each region (and modify index)
>>> > 4. crop with the largestPossibleRegion of the original volume (to
>>> > prevent requesting more than available)
>>> > iterate over regions:
>>> >       5. extractImageFilter
>>> >       6. disconnect pipeline for each region
>>> >       7. reset indexes
>>> >       8. perform computation
>>> >       9. crop with the regions in step 1 to remove the added overlap
>>> >       10. restore indexes
>>> > 11. pasteImageFilter
>>> >
>>> > I'll have to think of a smart way to deal with the index
>>> > restore/cropping of steps 9 and 10.
>>> >
>>> > I somehow feel somebody will have already dealt with this... And
>>> > there's certainly a better way to do it.
>>> > _____________________________________
>>> > 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 scapegoat.sarthak at gmail.com  Mon Mar 16 11:18:06 2015
From: scapegoat.sarthak at gmail.com (scap3y)
Date: Mon, 16 Mar 2015 08:18:06 -0700 (MST)
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
Message-ID: <1426519086520-7587013.post@n2.nabble.com>

Hi Matt,

Thanks for your reply.

I have been using VS 2012. The thing is, the first statement works, so
try{}catch{} isn't able to find anything. As soon as the program hits
imageIO->SetFileName() statement, everything breaks. In the debugger mode,
it throws the Access violation error and the imageIO is basically an
uninitialized pointer (see image).

<http://itk-insight-users.2283740.n2.nabble.com/file/n7587013/itk-imageIO_error.png> 

I have also tried with a raw image but I am getting the same error.

Thanks,
Sarthak


Matt McCormick-2 wrote
> Hi Sarthak,
> 
> You may also find this example [1] informative.
> 
> To investigate the access violation error, use try{}catch{} statements
> as found in the examples (use it around your
> imageIO->ReadImageInformation; statement). Also, run the code in a
> debugger.
> 
> Hope this helps,
> Matt
> 
> 
> [1]
> http://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html?highlight=read
> 
> On Mon, Mar 16, 2015 at 10:15 AM, Scapegoat Sarthak
> &lt;

> scapegoat.sarthak@

> &gt; wrote:
>> Hi All,
> [snip!]
>>
> _____________________________________
> 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 sebastian.ordas at gmail.com  Mon Mar 16 15:03:31 2015
From: sebastian.ordas at gmail.com (Sebastian Ordas)
Date: Mon, 16 Mar 2015 16:03:31 -0300
Subject: [ITK-users] [ITK]  multiple seeds
In-Reply-To: <20150316192345.1345.qmail@f4mail-235-145.rediffmail.com>
References: <20150316192345.1345.qmail@f4mail-235-145.rediffmail.com>
Message-ID: <55072903.90108@gmail.com>

Hi Prakash,

sure, you can: use the method:

AddSeed 
<http://www.itk.org/Doxygen45/html/classitk_1_1ConnectedThresholdImageFilter.html#a78e36efbaf11e9c463691d3fcb71a814>(const 
IndexType 
<http://www.itk.org/Doxygen45/html/classitk_1_1ConnectedThresholdImageFilter.html#a42a387acce282985067e70f642ec00f0> 
& seed);

The output will correspond to the combined effect of all input seeds.

hope that helps,
sebastian

On 16/03/2015 04:23 p.m., ds_prakash wrote:
> hello ALL,
> Is it possible to give multiple seed pixels to 
> ConnectedThresholdImageFilter? I also want the output of regions grown 
> corresponding to all seeds in a single output file.
>
> Thanks
> Prakash
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm at Middle?> 
>
>
> Get your own *FREE* website, *FREE* domain & *FREE* mobile app with 
> Company email.
> 	*Know More >* 
> <http://track.rediff.com/click?url=___http://businessemail.rediff.com?sc_cid=sign-1-10-13___&cmp=host&lnk=sign-1-10-13&nsrv1=host> 
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

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From matt.mccormick at kitware.com  Mon Mar 16 16:33:00 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 16 Mar 2015 16:33:00 -0400
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <1426519086520-7587013.post@n2.nabble.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
Message-ID: <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>

Hi Sarthak,

You will need to check that CreateImageIO does not generate a null
pointer.  If none of the registered ImageIO classes can read the given
file path, it will return a null pointer [1].

HTH,
Matt

[1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOFactory.cxx;h=638775873847ad8c4017a85f0992de9f4dee7161;hb=HEAD#l63

On Mon, Mar 16, 2015 at 11:18 AM, scap3y <scapegoat.sarthak at gmail.com> wrote:
> Hi Matt,
>
> Thanks for your reply.
>
> I have been using VS 2012. The thing is, the first statement works, so
> try{}catch{} isn't able to find anything. As soon as the program hits
> imageIO->SetFileName() statement, everything breaks. In the debugger mode,
> it throws the Access violation error and the imageIO is basically an
> uninitialized pointer (see image).
>
> <http://itk-insight-users.2283740.n2.nabble.com/file/n7587013/itk-imageIO_error.png>
>
> I have also tried with a raw image but I am getting the same error.
>
> Thanks,
> Sarthak
>
>
> Matt McCormick-2 wrote
>> Hi Sarthak,
>>
>> You may also find this example [1] informative.
>>
>> To investigate the access violation error, use try{}catch{} statements
>> as found in the examples (use it around your
>> imageIO->ReadImageInformation; statement). Also, run the code in a
>> debugger.
>>
>> Hope this helps,
>> Matt
>>
>>
>> [1]
>> http://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html?highlight=read
>>
>> On Mon, Mar 16, 2015 at 10:15 AM, Scapegoat Sarthak
>> &lt;
>
>> scapegoat.sarthak@
>
>> &gt; wrote:
>>> Hi All,
>> [snip!]
>>>
>> _____________________________________
>> 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
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Error-while-reading-Unknown-Image-Information-tp7587007p7587013.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From ds_prakash at rediffmail.com  Tue Mar 17 06:54:22 2015
From: ds_prakash at rediffmail.com (Surya Prakash)
Date: 17 Mar 2015 10:54:22 -0000
Subject: [ITK-users] =?utf-8?q?providing_data?=
Message-ID: <20150317105422.15641.qmail@f4mail-235-154.rediffmail.com>

Hello,
I am developing an application using ITK. I have data in an Arry pointed to by a 'float *'. I am aware of data sizes. How I can provide this array to 'ConnectedThresholdImageFilter' or for that matter to any filter.

Thanks
Prakash
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From matt.mccormick at kitware.com  Tue Mar 17 07:01:50 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 17 Mar 2015 07:01:50 -0400
Subject: [ITK-users] providing data
In-Reply-To: <20150317105422.15641.qmail@f4mail-235-154.rediffmail.com>
References: <20150317105422.15641.qmail@f4mail-235-154.rediffmail.com>
Message-ID: <CALzTN-Su-j0mZen-vLMRrmbxx7fsFt9BcJkc_0WSN7Y82Ldk=A@mail.gmail.com>

Hi Prakash,

The ImportImageFilter [1] can be used to import a pixel buffer into an
itk::Image data structure.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1ImportImageFilter.html

On Tue, Mar 17, 2015 at 6:54 AM, Surya Prakash <ds_prakash at rediffmail.com>
wrote:

> Hello,
> I am developing an application using ITK. I have data in an Arry pointed
> to by a 'float *'. I am aware of data sizes. How I can provide this array
> to 'ConnectedThresholdImageFilter' or for that matter to any filter.
>
> Thanks
> Prakash
>
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm at Middle?>
> Get your own *FREE* website, *FREE* domain & *FREE* mobile app with
> Company email.
> *Know More >*
> <http://track.rediff.com/click?url=___http://businessemail.rediff.com?sc_cid=sign-1-10-13___&cmp=host&lnk=sign-1-10-13&nsrv1=host>
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From scapegoat.sarthak at gmail.com  Tue Mar 17 09:14:34 2015
From: scapegoat.sarthak at gmail.com (scap3y)
Date: Tue, 17 Mar 2015 06:14:34 -0700 (MST)
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
 <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
Message-ID: <1426598074586-7587018.post@n2.nabble.com>

Hi Matt,

Thanks for your reply.

I am checking for a null pointer like this:

*if ( imageIO )
{
  imageIO->SetFileName(argv[3]);
  imageIO->ReadImageInformation();
}
else
{
  std::cout <<"Could not read the input image information from '" << argv[3]
<< "'\n";
} *

And it is going into the "else" loop after the CreateImageIO step. What I am
not able to understand is that why is this the case. Does CreateImageIO have
restrictions? If so, what are they? I have tried reading 2D images in JPG,
PNG, DCM, NII formats and 3D images in DCM and NII formats. It fails in all
of them. 

Best, 
Sarthak


Matt McCormick-2 wrote
> Hi Sarthak,
> 
> You will need to check that CreateImageIO does not generate a null
> pointer.  If none of the registered ImageIO classes can read the given
> file path, it will return a null pointer [1].
> 
> HTH,
> Matt
> 
> [1]
> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOFactory.cxx;h=638775873847ad8c4017a85f0992de9f4dee7161;hb=HEAD#l63
> 
> On Mon, Mar 16, 2015 at 11:18 AM, scap3y &lt;

> scapegoat.sarthak@

> &gt; wrote:
>> Hi Matt,
>>
>> Thanks for your reply.
> [snip!]
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users





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From matt.mccormick at kitware.com  Tue Mar 17 09:27:02 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 17 Mar 2015 09:27:02 -0400
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <1426598074586-7587018.post@n2.nabble.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
 <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
 <1426598074586-7587018.post@n2.nabble.com>
Message-ID: <CALzTN-T_qPq7X1dp6PSKHcA6q16wk346v_usPYFSOQgyS=RmiA@mail.gmail.com>

Hi Sarthak,

It looks like a good improvement.

The ImageIO's classes for the different file formats must be
registered to the factory.  When using CMake to configure your
project, this is done automatically.  When not using CMake, it must be
done manually.  Are you using CMake to configure your project?

HTH,
Matt

On Tue, Mar 17, 2015 at 9:14 AM, scap3y <scapegoat.sarthak at gmail.com> wrote:
> Hi Matt,
>
> Thanks for your reply.
>
> I am checking for a null pointer like this:
>
> *if ( imageIO )
> {
>   imageIO->SetFileName(argv[3]);
>   imageIO->ReadImageInformation();
> }
> else
> {
>   std::cout <<"Could not read the input image information from '" << argv[3]
> << "'\n";
> } *
>
> And it is going into the "else" loop after the CreateImageIO step. What I am
> not able to understand is that why is this the case. Does CreateImageIO have
> restrictions? If so, what are they? I have tried reading 2D images in JPG,
> PNG, DCM, NII formats and 3D images in DCM and NII formats. It fails in all
> of them.
>
> Best,
> Sarthak
>
>
> Matt McCormick-2 wrote
>> Hi Sarthak,
>>
>> You will need to check that CreateImageIO does not generate a null
>> pointer.  If none of the registered ImageIO classes can read the given
>> file path, it will return a null pointer [1].
>>
>> HTH,
>> Matt
>>
>> [1]
>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOFactory.cxx;h=638775873847ad8c4017a85f0992de9f4dee7161;hb=HEAD#l63
>>
>> On Mon, Mar 16, 2015 at 11:18 AM, scap3y &lt;
>
>> scapegoat.sarthak@
>
>> &gt; wrote:
>>> Hi Matt,
>>>
>>> Thanks for your reply.
>> [snip!]
>>> 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
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Error-while-reading-Unknown-Image-Information-tp7587007p7587018.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From sebastian.ordas at gmail.com  Tue Mar 17 09:28:46 2015
From: sebastian.ordas at gmail.com (Sebastian Ordas)
Date: Tue, 17 Mar 2015 10:28:46 -0300
Subject: [ITK-users] providing data
In-Reply-To: <20150317105422.15641.qmail@f4mail-235-154.rediffmail.com>
References: <20150317105422.15641.qmail@f4mail-235-154.rediffmail.com>
Message-ID: <55082C0E.7000508@gmail.com>

you can interate over your array and set seeds to 
ConnectedThresholdImageFilter one by one

On 17/03/2015 07:54 a.m., Surya Prakash wrote:
> Hello,
> I am developing an application using ITK. I have data in an Arry 
> pointed to by a 'float *'. I am aware of data sizes. How I can provide 
> this array to 'ConnectedThresholdImageFilter' or for that matter to 
> any filter.
>
> Thanks
> Prakash
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm at Middle?> 
>
>
> Get your own *FREE* website, *FREE* domain & *FREE* mobile app with 
> Company email.
> 	*Know More >* 
> <http://track.rediff.com/click?url=___http://businessemail.rediff.com?sc_cid=sign-1-10-13___&cmp=host&lnk=sign-1-10-13&nsrv1=host> 
>
>

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From sebastian.ordas at gmail.com  Tue Mar 17 09:32:20 2015
From: sebastian.ordas at gmail.com (Sebastian Ordas)
Date: Tue, 17 Mar 2015 10:32:20 -0300
Subject: [ITK-users] providing data
In-Reply-To: <55082C0E.7000508@gmail.com>
References: <20150317105422.15641.qmail@f4mail-235-154.rediffmail.com>
 <55082C0E.7000508@gmail.com>
Message-ID: <55082CE4.8070202@gmail.com>

sorry Prakash , I misunderstood your problem.
do as Matt suggested using the ImportImageFilter

On 17/03/2015 10:28 a.m., Sebastian Ordas wrote:
> you can interate over your array and set seeds to 
> ConnectedThresholdImageFilter one by one
>
> On 17/03/2015 07:54 a.m., Surya Prakash wrote:
>> Hello,
>> I am developing an application using ITK. I have data in an Arry 
>> pointed to by a 'float *'. I am aware of data sizes. How I can 
>> provide this array to 'ConnectedThresholdImageFilter' or for that 
>> matter to any filter.
>>
>> Thanks
>> Prakash
>> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm at Middle?> 
>>
>>
>> Get your own *FREE* website, *FREE* domain & *FREE* mobile app with 
>> Company email.
>> 	*Know More >* 
>> <http://track.rediff.com/click?url=___http://businessemail.rediff.com?sc_cid=sign-1-10-13___&cmp=host&lnk=sign-1-10-13&nsrv1=host> 
>>
>>
>

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From scapegoat.sarthak at gmail.com  Tue Mar 17 09:53:28 2015
From: scapegoat.sarthak at gmail.com (scap3y)
Date: Tue, 17 Mar 2015 06:53:28 -0700 (MST)
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <CALzTN-T_qPq7X1dp6PSKHcA6q16wk346v_usPYFSOQgyS=RmiA@mail.gmail.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
 <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
 <1426598074586-7587018.post@n2.nabble.com>
 <CALzTN-T_qPq7X1dp6PSKHcA6q16wk346v_usPYFSOQgyS=RmiA@mail.gmail.com>
Message-ID: <1426600408388-7587022.post@n2.nabble.com>

Hi Matt,

Thanks for your reply.

I am indeed using CMake for configuring my project (I don't think I have
used anything else since the past 3-odd years; I am a huge CMake fan). Could
you give me the details on how to do the registration for the different file
formats?

Much appreciated,
Sarthak


Matt McCormick-2 wrote
> Hi Sarthak,
> 
> It looks like a good improvement.
> 
> The ImageIO's classes for the different file formats must be
> registered to the factory.  When using CMake to configure your
> project, this is done automatically.  When not using CMake, it must be
> done manually.  Are you using CMake to configure your project?
> 
> HTH,
> Matt
> 
> On Tue, Mar 17, 2015 at 9:14 AM, scap3y &lt;

> scapegoat.sarthak@

> &gt; wrote:
>> Hi Matt,
> [snip!]
> _____________________________________
> 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 Mar 17 10:49:21 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 17 Mar 2015 10:49:21 -0400
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <1426600408388-7587022.post@n2.nabble.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
 <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
 <1426598074586-7587018.post@n2.nabble.com>
 <CALzTN-T_qPq7X1dp6PSKHcA6q16wk346v_usPYFSOQgyS=RmiA@mail.gmail.com>
 <1426600408388-7587022.post@n2.nabble.com>
Message-ID: <CALzTN-TzhdKjKSzOB-jQuaK66VkihEh_nXBPWdjSWRcqg6ErMw@mail.gmail.com>

Hi Sarthak,

To perform manual registration call the static RegisterOneFactory()
method on the ImageIO class.  See, e.g.,

 http://www.itk.org/Doxygen/html/classitk_1_1VTKImageIOFactory.html#abd26950373ca63c737794504f09bb18a

HTH,
Matt

On Tue, Mar 17, 2015 at 9:53 AM, scap3y <scapegoat.sarthak at gmail.com> wrote:
> Hi Matt,
>
> Thanks for your reply.
>
> I am indeed using CMake for configuring my project (I don't think I have
> used anything else since the past 3-odd years; I am a huge CMake fan). Could
> you give me the details on how to do the registration for the different file
> formats?
>
> Much appreciated,
> Sarthak
>
>
> Matt McCormick-2 wrote
>> Hi Sarthak,
>>
>> It looks like a good improvement.
>>
>> The ImageIO's classes for the different file formats must be
>> registered to the factory.  When using CMake to configure your
>> project, this is done automatically.  When not using CMake, it must be
>> done manually.  Are you using CMake to configure your project?
>>
>> HTH,
>> Matt
>>
>> On Tue, Mar 17, 2015 at 9:14 AM, scap3y &lt;
>
>> scapegoat.sarthak@
>
>> &gt; wrote:
>>> Hi Matt,
>> [snip!]
>> _____________________________________
>> 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
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Error-while-reading-Unknown-Image-Information-tp7587007p7587022.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From scapegoat.sarthak at gmail.com  Tue Mar 17 11:10:36 2015
From: scapegoat.sarthak at gmail.com (scap3y)
Date: Tue, 17 Mar 2015 08:10:36 -0700 (MST)
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <CALzTN-TzhdKjKSzOB-jQuaK66VkihEh_nXBPWdjSWRcqg6ErMw@mail.gmail.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
 <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
 <1426598074586-7587018.post@n2.nabble.com>
 <CALzTN-T_qPq7X1dp6PSKHcA6q16wk346v_usPYFSOQgyS=RmiA@mail.gmail.com>
 <1426600408388-7587022.post@n2.nabble.com>
 <CALzTN-TzhdKjKSzOB-jQuaK66VkihEh_nXBPWdjSWRcqg6ErMw@mail.gmail.com>
Message-ID: <1426605036611-7587024.post@n2.nabble.com>

Hi Matt,

Thanks for your reply.

I am hesitant to do this since I just want to read image properties
automatically. Doing a manual registration seems like an overkill and to be
honest seems to mitigate the main idea behind problem in the first place. In
any case, this shouldn't be required if I am using CMake to configure the
project, correct? I am using a pretty standard CMakeLists file for attaching
ITK includes and libraries to my project (taken from the previously
mentioned example). Since the ImageIOFactory should be automatically
registered, I am confused regarding what I am doing wrong.

Best,
Sarthak


Matt McCormick-2 wrote
> Hi Sarthak,
> 
> To perform manual registration call the static RegisterOneFactory()
> method on the ImageIO class.  See, e.g.,
> 
> 
> http://www.itk.org/Doxygen/html/classitk_1_1VTKImageIOFactory.html#abd26950373ca63c737794504f09bb18a
> 
> HTH,
> Matt
> 
> On Tue, Mar 17, 2015 at 9:53 AM, scap3y &lt;

> scapegoat.sarthak@

> &gt; wrote:
> [snip!]
> _____________________________________
> 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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Sent from the ITK Insight Users mailing list archive at Nabble.com.

From scapegoat.sarthak at gmail.com  Tue Mar 17 11:26:11 2015
From: scapegoat.sarthak at gmail.com (scap3y)
Date: Tue, 17 Mar 2015 08:26:11 -0700 (MST)
Subject: [ITK-users] Error while reading Unknown Image Information
In-Reply-To: <1426605036611-7587024.post@n2.nabble.com>
References: <CANbSmSdgbDBgdtmiKavUj-H-yGwsT6GACYMaWhY3S4ffD2PzfQ@mail.gmail.com>
 <CALzTN-S81FQ1A6YSL5SkZ1qvizgAwpRV_4c=1fnmG78pFOX8wA@mail.gmail.com>
 <1426519086520-7587013.post@n2.nabble.com>
 <CALzTN-Qhqh2Z0Q9R9y5=cQZ8fUyidAFk7+VD1nuBdUyW-Z3h_g@mail.gmail.com>
 <1426598074586-7587018.post@n2.nabble.com>
 <CALzTN-T_qPq7X1dp6PSKHcA6q16wk346v_usPYFSOQgyS=RmiA@mail.gmail.com>
 <1426600408388-7587022.post@n2.nabble.com>
 <CALzTN-TzhdKjKSzOB-jQuaK66VkihEh_nXBPWdjSWRcqg6ErMw@mail.gmail.com>
 <1426605036611-7587024.post@n2.nabble.com>
Message-ID: <1426605971241-7587025.post@n2.nabble.com>

Hi Matt,

This is probably the stupidest thing. I solved the issue by removing
"itkImageIOBase.h" and "itkImageIOFactory.h". No idea why this is the
reason. 

Thanks for all the help,
Sarthak



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From lluna.nova at gmail.com  Tue Mar 17 12:33:29 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Tue, 17 Mar 2015 17:33:29 +0100
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
Message-ID: <CALAZn4jETaK6y6L7=Uf-T2EaYBPE5Z2H350j-spYiLw_4sc3Ew@mail.gmail.com>

Indeed, that simplifies the pasting. Good suggestion!

2015-03-16 15:20 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> You may find this method useful:
>
>
> http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
>
> Brad
>
> On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> wrote:
>
> Mmh, I believe I misread the RegionOfInterestImageFilter documentation,
> confusing dimension with size. That should work.
>
> I still have the computation of the splitting regions problem to handle,
> but maybe with this filter is easier than with the ExtractImageFilter. Or
> maybe it just removes step 7?
>
> Is there a way to ease the repasting back to the original region with it?
> How should I use the physical space index?
>
> 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
>
>> Hello Bradley,
>>
>> Thank you for your answer and suggestion.
>>
>> Answering your question: It's not for multi-threading purposes, I have to
>> split the image due to memory limitations.
>>
>> I would use extractImage directly and do streaming, but the client and
>> the low-level libraries might not work correctly if I do that. I have to
>> provide itk images disconnected from the pipeline and with proper indexes
>> and sizes.
>>
>> The RegionOfInterestImageFilter would have the same memory footprint, and
>> it would still be tricky to compute the regions of interest, due to the
>> overlapping.
>>
>>
>>
>> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>>
>>> Hello,
>>>
>>> The RegionOfInterestImageFilter[1] is very similar to the
>>> ExtractImageFilter, but returns an image whose starting index is always
>>> zeros.
>>>
>>> The process you described is remarkable close to what occur in each
>>> filter for the multi-threading process.  Also what occurs in the
>>> StreamingImageFilter is very similar, but just copies the region.
>>>
>>> As you didn't mention you motivation for chunking the data this way be
>>> it for threading or memory requirements, I can't fully advise.
>>>
>>> Brad
>>>
>>>
>>> [1 ]
>>> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>>> [2]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>>>
>>>
>>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>>> wrote:
>>>
>>> > Hello everyone,
>>> >
>>> > We need to split a volume into pieces, overlaped by a certain amount,
>>> do some computation and then repaste them.
>>> >
>>> > The computation requires the pieces' region indexes to be set to zero.
>>> The original volume might not have index at zero, but be a subregion itself.
>>> >
>>> > What is the best way to achieve this?
>>> >
>>> > I've thought of the following pipeline:
>>> >
>>> > 1. imageRegionSplitterSlowDimension
>>> > 2. Store the index and size of each region
>>> > 3. manually increase the size of each region (and modify index)
>>> > 4. crop with the largestPossibleRegion of the original volume (to
>>> prevent requesting more than available)
>>> > iterate over regions:
>>> >       5. extractImageFilter
>>> >       6. disconnect pipeline for each region
>>> >       7. reset indexes
>>> >       8. perform computation
>>> >       9. crop with the regions in step 1 to remove the added overlap
>>> >       10. restore indexes
>>> > 11. pasteImageFilter
>>> >
>>> > I'll have to think of a smart way to deal with the index
>>> restore/cropping of steps 9 and 10.
>>> >
>>> > I somehow feel somebody will have already dealt with this... And
>>> there's certainly a better way to do it.
>>> > _____________________________________
>>> > 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
>>>
>>>
>>
>> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>>
>>> Hello,
>>>
>>> The RegionOfInterestImageFilter[1] is very similar to the
>>> ExtractImageFilter, but returns an image whose starting index is always
>>> zeros.
>>>
>>> The process you described is remarkable close to what occur in each
>>> filter for the multi-threading process.  Also what occurs in the
>>> StreamingImageFilter is very similar, but just copies the region.
>>>
>>> As you didn't mention you motivation for chunking the data this way be
>>> it for threading or memory requirements, I can't fully advise.
>>>
>>> Brad
>>>
>>>
>>> [1 ]
>>> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>>> [2]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>>>
>>>
>>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>>> wrote:
>>>
>>> > Hello everyone,
>>> >
>>> > We need to split a volume into pieces, overlaped by a certain amount,
>>> do some computation and then repaste them.
>>> >
>>> > The computation requires the pieces' region indexes to be set to zero.
>>> The original volume might not have index at zero, but be a subregion itself.
>>> >
>>> > What is the best way to achieve this?
>>> >
>>> > I've thought of the following pipeline:
>>> >
>>> > 1. imageRegionSplitterSlowDimension
>>> > 2. Store the index and size of each region
>>> > 3. manually increase the size of each region (and modify index)
>>> > 4. crop with the largestPossibleRegion of the original volume (to
>>> prevent requesting more than available)
>>> > iterate over regions:
>>> >       5. extractImageFilter
>>> >       6. disconnect pipeline for each region
>>> >       7. reset indexes
>>> >       8. perform computation
>>> >       9. crop with the regions in step 1 to remove the added overlap
>>> >       10. restore indexes
>>> > 11. pasteImageFilter
>>> >
>>> > I'll have to think of a smart way to deal with the index
>>> restore/cropping of steps 9 and 10.
>>> >
>>> > I somehow feel somebody will have already dealt with this... And
>>> there's certainly a better way to do it.
>>> > _____________________________________
>>> > 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 lluna.nova at gmail.com  Tue Mar 17 13:13:02 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Tue, 17 Mar 2015 18:13:02 +0100
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
 <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
Message-ID: <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>

Hello Matt,

As I've told Bradley, I can't use streaming as-is because I need overlap
between chunks and because the low-level library would need a proper itk
image with correct size, region, etc.
which I guess it wouldn't be provided by streaming.

But most definetely, right now I use 'streaming' by using the ExtractFilter
at the end. I believe that streams too. I was actually more interested in
having a filter/object that computes the splits for me. I've implemented
it, but it's far from perfect. For example, it broke when the input image
had a non-zero index. (It's fixed now, but still, I'm sure the itk's
Splitter filter does a better job, if only could I have overlap ;))

I guess the way to go would be to take the splitter (probably
ImageRegionSplitterMultidimensional now that I look at it) and extend it to
support overlap. If I do it, I'll let you know in case it is of interest to
anyone. For now I'll stick to my class.

Cheers,

Pol

2015-03-16 16:05 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Pol,
>
> As a side note, limitation of memory usage is built into the streaming
> pipeline design of ITK.  All computation of appropriate regions should
> occur if the filters are implemented correctly.  To take advantage of
> streaming, place the StreamingImageFilter [1] at the end of your
> pipeline. To use less memory, set the ReleaseDataFlagOn() [2] on the
> component filters.
>
> HTH,
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1StreamingImageFilter.html
>
> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae732e9163879ae559ccd0b5957141f97
>
> On Mon, Mar 16, 2015 at 10:20 AM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
> > You may find this method useful:
> >
> >
> http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
> >
> > Brad
> >
> > On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> wrote:
> >
> > Mmh, I believe I misread the RegionOfInterestImageFilter documentation,
> > confusing dimension with size. That should work.
> >
> > I still have the computation of the splitting regions problem to handle,
> but
> > maybe with this filter is easier than with the ExtractImageFilter. Or
> maybe
> > it just removes step 7?
> >
> > Is there a way to ease the repasting back to the original region with it?
> > How should I use the physical space index?
> >
> > 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
> >>
> >> Hello Bradley,
> >>
> >> Thank you for your answer and suggestion.
> >>
> >> Answering your question: It's not for multi-threading purposes, I have
> to
> >> split the image due to memory limitations.
> >>
> >> I would use extractImage directly and do streaming, but the client and
> the
> >> low-level libraries might not work correctly if I do that. I have to
> provide
> >> itk images disconnected from the pipeline and with proper indexes and
> sizes.
> >>
> >> The RegionOfInterestImageFilter would have the same memory footprint,
> and
> >> it would still be tricky to compute the regions of interest, due to the
> >> overlapping.
> >>
> >>
> >>
> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> >>>
> >>> Hello,
> >>>
> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >>> ExtractImageFilter, but returns an image whose starting index is always
> >>> zeros.
> >>>
> >>> The process you described is remarkable close to what occur in each
> >>> filter for the multi-threading process.  Also what occurs in the
> >>> StreamingImageFilter is very similar, but just copies the region.
> >>>
> >>> As you didn't mention you motivation for chunking the data this way be
> it
> >>> for threading or memory requirements, I can't fully advise.
> >>>
> >>> Brad
> >>>
> >>>
> >>> [1
> >>> ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >>> [2]
> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >>>
> >>>
> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >>> wrote:
> >>>
> >>> > Hello everyone,
> >>> >
> >>> > We need to split a volume into pieces, overlaped by a certain amount,
> >>> > do some computation and then repaste them.
> >>> >
> >>> > The computation requires the pieces' region indexes to be set to
> zero.
> >>> > The original volume might not have index at zero, but be a subregion
> itself.
> >>> >
> >>> > What is the best way to achieve this?
> >>> >
> >>> > I've thought of the following pipeline:
> >>> >
> >>> > 1. imageRegionSplitterSlowDimension
> >>> > 2. Store the index and size of each region
> >>> > 3. manually increase the size of each region (and modify index)
> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >>> > prevent requesting more than available)
> >>> > iterate over regions:
> >>> >       5. extractImageFilter
> >>> >       6. disconnect pipeline for each region
> >>> >       7. reset indexes
> >>> >       8. perform computation
> >>> >       9. crop with the regions in step 1 to remove the added overlap
> >>> >       10. restore indexes
> >>> > 11. pasteImageFilter
> >>> >
> >>> > I'll have to think of a smart way to deal with the index
> >>> > restore/cropping of steps 9 and 10.
> >>> >
> >>> > I somehow feel somebody will have already dealt with this... And
> >>> > there's certainly a better way to do it.
> >>> > _____________________________________
> >>> > 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
> >>>
> >>
> >>
> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> >>>
> >>> Hello,
> >>>
> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >>> ExtractImageFilter, but returns an image whose starting index is always
> >>> zeros.
> >>>
> >>> The process you described is remarkable close to what occur in each
> >>> filter for the multi-threading process.  Also what occurs in the
> >>> StreamingImageFilter is very similar, but just copies the region.
> >>>
> >>> As you didn't mention you motivation for chunking the data this way be
> it
> >>> for threading or memory requirements, I can't fully advise.
> >>>
> >>> Brad
> >>>
> >>>
> >>> [1
> >>> ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >>> [2]
> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >>>
> >>>
> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >>> wrote:
> >>>
> >>> > Hello everyone,
> >>> >
> >>> > We need to split a volume into pieces, overlaped by a certain amount,
> >>> > do some computation and then repaste them.
> >>> >
> >>> > The computation requires the pieces' region indexes to be set to
> zero.
> >>> > The original volume might not have index at zero, but be a subregion
> itself.
> >>> >
> >>> > What is the best way to achieve this?
> >>> >
> >>> > I've thought of the following pipeline:
> >>> >
> >>> > 1. imageRegionSplitterSlowDimension
> >>> > 2. Store the index and size of each region
> >>> > 3. manually increase the size of each region (and modify index)
> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >>> > prevent requesting more than available)
> >>> > iterate over regions:
> >>> >       5. extractImageFilter
> >>> >       6. disconnect pipeline for each region
> >>> >       7. reset indexes
> >>> >       8. perform computation
> >>> >       9. crop with the regions in step 1 to remove the added overlap
> >>> >       10. restore indexes
> >>> > 11. pasteImageFilter
> >>> >
> >>> > I'll have to think of a smart way to deal with the index
> >>> > restore/cropping of steps 9 and 10.
> >>> >
> >>> > I somehow feel somebody will have already dealt with this... And
> >>> > there's certainly a better way to do it.
> >>> > _____________________________________
> >>> > Powered by www.kitware.com
> >>> >
> >>> > Visit other Kitware open-source projects at
> >>> > http://www.kitware.com/opensource/opensource.html
> >>> >
> >>> > Kitware offers ITK Training Courses, for more information visit:
> >>> > http://www.kitware.com/products/protraining.php
> >>> >
> >>> > Please keep messages on-topic and check the ITK FAQ at:
> >>> > http://www.itk.org/Wiki/ITK_FAQ
> >>> >
> >>> > Follow this link to subscribe/unsubscribe:
> >>> > http://public.kitware.com/mailman/listinfo/insight-users
> >>>
> >>
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
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From matt.mccormick at kitware.com  Tue Mar 17 15:22:17 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 17 Mar 2015 15:22:17 -0400
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
 <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
 <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
Message-ID: <CALzTN-RsWQ=S9B_yHt7VwsxGOaM1HXeVhscZFvyEySgXD7j-QQ@mail.gmail.com>

Hi Pol,

You may already be aware of this, but the chunks will overlap if you
implement a GenerateInputRequestedRegion() method on your filter that
pads the output RequestedRegion.

HTH,
Matt

On Tue, Mar 17, 2015 at 1:13 PM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
> Hello Matt,
>
> As I've told Bradley, I can't use streaming as-is because I need overlap
> between chunks and because the low-level library would need a proper itk
> image with correct size, region, etc.
> which I guess it wouldn't be provided by streaming.
>
> But most definetely, right now I use 'streaming' by using the ExtractFilter
> at the end. I believe that streams too. I was actually more interested in
> having a filter/object that computes the splits for me. I've implemented it,
> but it's far from perfect. For example, it broke when the input image had a
> non-zero index. (It's fixed now, but still, I'm sure the itk's Splitter
> filter does a better job, if only could I have overlap ;))
>
> I guess the way to go would be to take the splitter (probably
> ImageRegionSplitterMultidimensional now that I look at it) and extend it to
> support overlap. If I do it, I'll let you know in case it is of interest to
> anyone. For now I'll stick to my class.
>
> Cheers,
>
> Pol
>
> 2015-03-16 16:05 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hi Pol,
>>
>> As a side note, limitation of memory usage is built into the streaming
>> pipeline design of ITK.  All computation of appropriate regions should
>> occur if the filters are implemented correctly.  To take advantage of
>> streaming, place the StreamingImageFilter [1] at the end of your
>> pipeline. To use less memory, set the ReleaseDataFlagOn() [2] on the
>> component filters.
>>
>> HTH,
>> Matt
>>
>> [1] http://www.itk.org/Doxygen/html/classitk_1_1StreamingImageFilter.html
>>
>> [2]
>> http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae732e9163879ae559ccd0b5957141f97
>>
>> On Mon, Mar 16, 2015 at 10:20 AM, Bradley Lowekamp
>> <blowekamp at mail.nih.gov> wrote:
>> > You may find this method useful:
>> >
>> >
>> > http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
>> >
>> > Brad
>> >
>> > On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>> > wrote:
>> >
>> > Mmh, I believe I misread the RegionOfInterestImageFilter documentation,
>> > confusing dimension with size. That should work.
>> >
>> > I still have the computation of the splitting regions problem to handle,
>> > but
>> > maybe with this filter is easier than with the ExtractImageFilter. Or
>> > maybe
>> > it just removes step 7?
>> >
>> > Is there a way to ease the repasting back to the original region with
>> > it?
>> > How should I use the physical space index?
>> >
>> > 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
>> >>
>> >> Hello Bradley,
>> >>
>> >> Thank you for your answer and suggestion.
>> >>
>> >> Answering your question: It's not for multi-threading purposes, I have
>> >> to
>> >> split the image due to memory limitations.
>> >>
>> >> I would use extractImage directly and do streaming, but the client and
>> >> the
>> >> low-level libraries might not work correctly if I do that. I have to
>> >> provide
>> >> itk images disconnected from the pipeline and with proper indexes and
>> >> sizes.
>> >>
>> >> The RegionOfInterestImageFilter would have the same memory footprint,
>> >> and
>> >> it would still be tricky to compute the regions of interest, due to the
>> >> overlapping.
>> >>
>> >>
>> >>
>> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>> >>>
>> >>> Hello,
>> >>>
>> >>> The RegionOfInterestImageFilter[1] is very similar to the
>> >>> ExtractImageFilter, but returns an image whose starting index is
>> >>> always
>> >>> zeros.
>> >>>
>> >>> The process you described is remarkable close to what occur in each
>> >>> filter for the multi-threading process.  Also what occurs in the
>> >>> StreamingImageFilter is very similar, but just copies the region.
>> >>>
>> >>> As you didn't mention you motivation for chunking the data this way be
>> >>> it
>> >>> for threading or memory requirements, I can't fully advise.
>> >>>
>> >>> Brad
>> >>>
>> >>>
>> >>> [1
>> >>>
>> >>> ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>> >>> [2]
>> >>>
>> >>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>> >>>
>> >>>
>> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>> >>> wrote:
>> >>>
>> >>> > Hello everyone,
>> >>> >
>> >>> > We need to split a volume into pieces, overlaped by a certain
>> >>> > amount,
>> >>> > do some computation and then repaste them.
>> >>> >
>> >>> > The computation requires the pieces' region indexes to be set to
>> >>> > zero.
>> >>> > The original volume might not have index at zero, but be a subregion
>> >>> > itself.
>> >>> >
>> >>> > What is the best way to achieve this?
>> >>> >
>> >>> > I've thought of the following pipeline:
>> >>> >
>> >>> > 1. imageRegionSplitterSlowDimension
>> >>> > 2. Store the index and size of each region
>> >>> > 3. manually increase the size of each region (and modify index)
>> >>> > 4. crop with the largestPossibleRegion of the original volume (to
>> >>> > prevent requesting more than available)
>> >>> > iterate over regions:
>> >>> >       5. extractImageFilter
>> >>> >       6. disconnect pipeline for each region
>> >>> >       7. reset indexes
>> >>> >       8. perform computation
>> >>> >       9. crop with the regions in step 1 to remove the added overlap
>> >>> >       10. restore indexes
>> >>> > 11. pasteImageFilter
>> >>> >
>> >>> > I'll have to think of a smart way to deal with the index
>> >>> > restore/cropping of steps 9 and 10.
>> >>> >
>> >>> > I somehow feel somebody will have already dealt with this... And
>> >>> > there's certainly a better way to do it.
>> >>> > _____________________________________
>> >>> > 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
>> >>>
>> >>
>> >>
>> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>> >>>
>> >>> Hello,
>> >>>
>> >>> The RegionOfInterestImageFilter[1] is very similar to the
>> >>> ExtractImageFilter, but returns an image whose starting index is
>> >>> always
>> >>> zeros.
>> >>>
>> >>> The process you described is remarkable close to what occur in each
>> >>> filter for the multi-threading process.  Also what occurs in the
>> >>> StreamingImageFilter is very similar, but just copies the region.
>> >>>
>> >>> As you didn't mention you motivation for chunking the data this way be
>> >>> it
>> >>> for threading or memory requirements, I can't fully advise.
>> >>>
>> >>> Brad
>> >>>
>> >>>
>> >>> [1
>> >>>
>> >>> ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>> >>> [2]
>> >>>
>> >>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
>> >>>
>> >>>
>> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
>> >>> wrote:
>> >>>
>> >>> > Hello everyone,
>> >>> >
>> >>> > We need to split a volume into pieces, overlaped by a certain
>> >>> > amount,
>> >>> > do some computation and then repaste them.
>> >>> >
>> >>> > The computation requires the pieces' region indexes to be set to
>> >>> > zero.
>> >>> > The original volume might not have index at zero, but be a subregion
>> >>> > itself.
>> >>> >
>> >>> > What is the best way to achieve this?
>> >>> >
>> >>> > I've thought of the following pipeline:
>> >>> >
>> >>> > 1. imageRegionSplitterSlowDimension
>> >>> > 2. Store the index and size of each region
>> >>> > 3. manually increase the size of each region (and modify index)
>> >>> > 4. crop with the largestPossibleRegion of the original volume (to
>> >>> > prevent requesting more than available)
>> >>> > iterate over regions:
>> >>> >       5. extractImageFilter
>> >>> >       6. disconnect pipeline for each region
>> >>> >       7. reset indexes
>> >>> >       8. perform computation
>> >>> >       9. crop with the regions in step 1 to remove the added overlap
>> >>> >       10. restore indexes
>> >>> > 11. pasteImageFilter
>> >>> >
>> >>> > I'll have to think of a smart way to deal with the index
>> >>> > restore/cropping of steps 9 and 10.
>> >>> >
>> >>> > I somehow feel somebody will have already dealt with this... And
>> >>> > there's certainly a better way to do it.
>> >>> > _____________________________________
>> >>> > 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 aamundarain at ceit.es  Wed Mar 18 07:43:49 2015
From: aamundarain at ceit.es (Amundarain, Aiert)
Date: Wed, 18 Mar 2015 11:43:49 +0000
Subject: [ITK-users] ITK dicom reader wrong spacing
Message-ID: <DB3PR02MB107D01405D11A9D546358A4BE000@DB3PR02MB107.eurprd02.prod.outlook.com>

I have a DICOM Image serie that itk does not read properly. The x,y,z spacing are incorrect and the return value is the default one (1,1,1).

If I read this DICOM Image serie using vtk (vtkDICOMImageReader), the reading is correct.

Both softwares are developed by kitware but the results are different.



Is is possible to read the dicom files using ITK without using the gdcm library?



Thank you.

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From lluna.nova at gmail.com  Wed Mar 18 08:58:06 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Wed, 18 Mar 2015 13:58:06 +0100
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALzTN-RsWQ=S9B_yHt7VwsxGOaM1HXeVhscZFvyEySgXD7j-QQ@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
 <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
 <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
 <CALzTN-RsWQ=S9B_yHt7VwsxGOaM1HXeVhscZFvyEySgXD7j-QQ@mail.gmail.com>
Message-ID: <CALAZn4i5roSC+YO3UCONDcCTOstAX-7bJWyNfrLYPW9pF7RQbA@mail.gmail.com>

Hello matt,

I wasn't aware of that possibility, thanks for the heads up!It doesn't
apply to our case becaues I haven't created a filter but rather a class
that takes a region and gives me the splitted regions that later on I feed
to an extract filter (or the copy algorithm Bradley pointed out to repaste
the results back). Creating a filter doesn't really fit well, the
'low-level' is based on machine learning so it trains and then predicts,
and it requires several minutes depending on the size of the image etc. I
didn't judge appropriate to create a Filter out of it.

Could you elaborate a little bit on what you were proposing? Let's say I
have a set of preprocessing filters, my processing and a set of
postprocessing filters. The output would be a set of connected components.
The volume doesn't necessarily fit in memory (specially the processing) so
we have to stream. Because the chunks need to overlap, are you saying that
I could place,  in the pipeline, a Filter that is derived from the
StreamingImageFilter that re-implements GeneratInputRequestedRegion() to
have an overlap of 30 voxels, and that would should do it? where should I
place such a filter and how does interact with the pre/post-processing?

I will re-read the article on streaming, but maybe it would help me if you
pinpoint the particularities of the approach you suggested.

Cheers,

Pol




2015-03-17 20:22 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Pol,
>
> You may already be aware of this, but the chunks will overlap if you
> implement a GenerateInputRequestedRegion() method on your filter that
> pads the output RequestedRegion.
>
> HTH,
> Matt
>
> On Tue, Mar 17, 2015 at 1:13 PM, Pol Mons? Purt? <lluna.nova at gmail.com>
> wrote:
> > Hello Matt,
> >
> > As I've told Bradley, I can't use streaming as-is because I need overlap
> > between chunks and because the low-level library would need a proper itk
> > image with correct size, region, etc.
> > which I guess it wouldn't be provided by streaming.
> >
> > But most definetely, right now I use 'streaming' by using the
> ExtractFilter
> > at the end. I believe that streams too. I was actually more interested in
> > having a filter/object that computes the splits for me. I've implemented
> it,
> > but it's far from perfect. For example, it broke when the input image
> had a
> > non-zero index. (It's fixed now, but still, I'm sure the itk's Splitter
> > filter does a better job, if only could I have overlap ;))
> >
> > I guess the way to go would be to take the splitter (probably
> > ImageRegionSplitterMultidimensional now that I look at it) and extend it
> to
> > support overlap. If I do it, I'll let you know in case it is of interest
> to
> > anyone. For now I'll stick to my class.
> >
> > Cheers,
> >
> > Pol
> >
> > 2015-03-16 16:05 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> >>
> >> Hi Pol,
> >>
> >> As a side note, limitation of memory usage is built into the streaming
> >> pipeline design of ITK.  All computation of appropriate regions should
> >> occur if the filters are implemented correctly.  To take advantage of
> >> streaming, place the StreamingImageFilter [1] at the end of your
> >> pipeline. To use less memory, set the ReleaseDataFlagOn() [2] on the
> >> component filters.
> >>
> >> HTH,
> >> Matt
> >>
> >> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1StreamingImageFilter.html
> >>
> >> [2]
> >>
> http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae732e9163879ae559ccd0b5957141f97
> >>
> >> On Mon, Mar 16, 2015 at 10:20 AM, Bradley Lowekamp
> >> <blowekamp at mail.nih.gov> wrote:
> >> > You may find this method useful:
> >> >
> >> >
> >> >
> http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
> >> >
> >> > Brad
> >> >
> >> > On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >> > wrote:
> >> >
> >> > Mmh, I believe I misread the RegionOfInterestImageFilter
> documentation,
> >> > confusing dimension with size. That should work.
> >> >
> >> > I still have the computation of the splitting regions problem to
> handle,
> >> > but
> >> > maybe with this filter is easier than with the ExtractImageFilter. Or
> >> > maybe
> >> > it just removes step 7?
> >> >
> >> > Is there a way to ease the repasting back to the original region with
> >> > it?
> >> > How should I use the physical space index?
> >> >
> >> > 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
> >> >>
> >> >> Hello Bradley,
> >> >>
> >> >> Thank you for your answer and suggestion.
> >> >>
> >> >> Answering your question: It's not for multi-threading purposes, I
> have
> >> >> to
> >> >> split the image due to memory limitations.
> >> >>
> >> >> I would use extractImage directly and do streaming, but the client
> and
> >> >> the
> >> >> low-level libraries might not work correctly if I do that. I have to
> >> >> provide
> >> >> itk images disconnected from the pipeline and with proper indexes and
> >> >> sizes.
> >> >>
> >> >> The RegionOfInterestImageFilter would have the same memory footprint,
> >> >> and
> >> >> it would still be tricky to compute the regions of interest, due to
> the
> >> >> overlapping.
> >> >>
> >> >>
> >> >>
> >> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov
> >:
> >> >>>
> >> >>> Hello,
> >> >>>
> >> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >> >>> ExtractImageFilter, but returns an image whose starting index is
> >> >>> always
> >> >>> zeros.
> >> >>>
> >> >>> The process you described is remarkable close to what occur in each
> >> >>> filter for the multi-threading process.  Also what occurs in the
> >> >>> StreamingImageFilter is very similar, but just copies the region.
> >> >>>
> >> >>> As you didn't mention you motivation for chunking the data this way
> be
> >> >>> it
> >> >>> for threading or memory requirements, I can't fully advise.
> >> >>>
> >> >>> Brad
> >> >>>
> >> >>>
> >> >>> [1
> >> >>>
> >> >>> ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >> >>> [2]
> >> >>>
> >> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >> >>>
> >> >>>
> >> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> > Hello everyone,
> >> >>> >
> >> >>> > We need to split a volume into pieces, overlaped by a certain
> >> >>> > amount,
> >> >>> > do some computation and then repaste them.
> >> >>> >
> >> >>> > The computation requires the pieces' region indexes to be set to
> >> >>> > zero.
> >> >>> > The original volume might not have index at zero, but be a
> subregion
> >> >>> > itself.
> >> >>> >
> >> >>> > What is the best way to achieve this?
> >> >>> >
> >> >>> > I've thought of the following pipeline:
> >> >>> >
> >> >>> > 1. imageRegionSplitterSlowDimension
> >> >>> > 2. Store the index and size of each region
> >> >>> > 3. manually increase the size of each region (and modify index)
> >> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >> >>> > prevent requesting more than available)
> >> >>> > iterate over regions:
> >> >>> >       5. extractImageFilter
> >> >>> >       6. disconnect pipeline for each region
> >> >>> >       7. reset indexes
> >> >>> >       8. perform computation
> >> >>> >       9. crop with the regions in step 1 to remove the added
> overlap
> >> >>> >       10. restore indexes
> >> >>> > 11. pasteImageFilter
> >> >>> >
> >> >>> > I'll have to think of a smart way to deal with the index
> >> >>> > restore/cropping of steps 9 and 10.
> >> >>> >
> >> >>> > I somehow feel somebody will have already dealt with this... And
> >> >>> > there's certainly a better way to do it.
> >> >>> > _____________________________________
> >> >>> > 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
> >> >>>
> >> >>
> >> >>
> >> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov
> >:
> >> >>>
> >> >>> Hello,
> >> >>>
> >> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >> >>> ExtractImageFilter, but returns an image whose starting index is
> >> >>> always
> >> >>> zeros.
> >> >>>
> >> >>> The process you described is remarkable close to what occur in each
> >> >>> filter for the multi-threading process.  Also what occurs in the
> >> >>> StreamingImageFilter is very similar, but just copies the region.
> >> >>>
> >> >>> As you didn't mention you motivation for chunking the data this way
> be
> >> >>> it
> >> >>> for threading or memory requirements, I can't fully advise.
> >> >>>
> >> >>> Brad
> >> >>>
> >> >>>
> >> >>> [1
> >> >>>
> >> >>> ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >> >>> [2]
> >> >>>
> >> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >> >>>
> >> >>>
> >> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> > Hello everyone,
> >> >>> >
> >> >>> > We need to split a volume into pieces, overlaped by a certain
> >> >>> > amount,
> >> >>> > do some computation and then repaste them.
> >> >>> >
> >> >>> > The computation requires the pieces' region indexes to be set to
> >> >>> > zero.
> >> >>> > The original volume might not have index at zero, but be a
> subregion
> >> >>> > itself.
> >> >>> >
> >> >>> > What is the best way to achieve this?
> >> >>> >
> >> >>> > I've thought of the following pipeline:
> >> >>> >
> >> >>> > 1. imageRegionSplitterSlowDimension
> >> >>> > 2. Store the index and size of each region
> >> >>> > 3. manually increase the size of each region (and modify index)
> >> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >> >>> > prevent requesting more than available)
> >> >>> > iterate over regions:
> >> >>> >       5. extractImageFilter
> >> >>> >       6. disconnect pipeline for each region
> >> >>> >       7. reset indexes
> >> >>> >       8. perform computation
> >> >>> >       9. crop with the regions in step 1 to remove the added
> overlap
> >> >>> >       10. restore indexes
> >> >>> > 11. pasteImageFilter
> >> >>> >
> >> >>> > I'll have to think of a smart way to deal with the index
> >> >>> > restore/cropping of steps 9 and 10.
> >> >>> >
> >> >>> > I somehow feel somebody will have already dealt with this... And
> >> >>> > there's certainly a better way to do it.
> >> >>> > _____________________________________
> >> >>> > 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 blowekamp at mail.nih.gov  Wed Mar 18 09:14:53 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 18 Mar 2015 09:14:53 -0400
Subject: [ITK-users] Splitting and repasting a volume with overlap
In-Reply-To: <CALAZn4i5roSC+YO3UCONDcCTOstAX-7bJWyNfrLYPW9pF7RQbA@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
 <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
 <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
 <CALzTN-RsWQ=S9B_yHt7VwsxGOaM1HXeVhscZFvyEySgXD7j-QQ@mail.gmail.com>
 <CALAZn4i5roSC+YO3UCONDcCTOstAX-7bJWyNfrLYPW9pF7RQbA@mail.gmail.com>
Message-ID: <01DFDABC-9640-47CF-A2EA-4019A1C8A5F4@mail.nih.gov>

Hello Pol,

I believe I have already suggested reading the latest ITK Software Guide, and the section "How To Write a Filter" which details how the pipeline works. This will cover the GenerateInputRequestedRegion method and how it interacts with the Pipeline and it critical for understanding the pipeline. Your case really does sound like the ITK pipeline, and would benefit as being a filter. You described your output as "connected components", I am not sure if that is a image or another reduced structure. Does the output represent the whole thing in a compact fashion or does it represent a small part which can also be streamed?

The may add more complications to your situation but it may be the right fit. I have written a external module "itkStreamingSinc"[1], which provides a base class for algorithms which are both streamed and threaded. I have used it for things like computing bounding boxes and image statistics on images which are hundreds of gigabytes in an out of core fashion. I have also wanted to write one which produces a an itk RLE LabelObject. It works good for algorithms that can consume a chunk and produce a reduced structure.

Hope that helps,
Brad

[1] https://github.com/blowekamp/itkStreamingSinc



On Mar 18, 2015, at 8:58 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:

> Hello matt,
> 
> I wasn't aware of that possibility, thanks for the heads up!It doesn't apply to our case becaues I haven't created a filter but rather a class that takes a region and gives me the splitted regions that later on I feed to an extract filter (or the copy algorithm Bradley pointed out to repaste the results back). Creating a filter doesn't really fit well, the 'low-level' is based on machine learning so it trains and then predicts, and it requires several minutes depending on the size of the image etc. I didn't judge appropriate to create a Filter out of it. 
> 
> Could you elaborate a little bit on what you were proposing? Let's say I have a set of preprocessing filters, my processing and a set of postprocessing filters. The output would be a set of connected components. The volume doesn't necessarily fit in memory (specially the processing) so we have to stream. Because the chunks need to overlap, are you saying that I could place,  in the pipeline, a Filter that is derived from the StreamingImageFilter that re-implements GeneratInputRequestedRegion() to have an overlap of 30 voxels, and that would should do it? where should I place such a filter and how does interact with the pre/post-processing?
> 
> I will re-read the article on streaming, but maybe it would help me if you pinpoint the particularities of the approach you suggested.
> 
> Cheers,
> 
> Pol
> 
> 
> 
> 
> 2015-03-17 20:22 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> Hi Pol,
> 
> You may already be aware of this, but the chunks will overlap if you
> implement a GenerateInputRequestedRegion() method on your filter that
> pads the output RequestedRegion.
> 
> HTH,
> Matt
> 
> On Tue, Mar 17, 2015 at 1:13 PM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
> > Hello Matt,
> >
> > As I've told Bradley, I can't use streaming as-is because I need overlap
> > between chunks and because the low-level library would need a proper itk
> > image with correct size, region, etc.
> > which I guess it wouldn't be provided by streaming.
> >
> > But most definetely, right now I use 'streaming' by using the ExtractFilter
> > at the end. I believe that streams too. I was actually more interested in
> > having a filter/object that computes the splits for me. I've implemented it,
> > but it's far from perfect. For example, it broke when the input image had a
> > non-zero index. (It's fixed now, but still, I'm sure the itk's Splitter
> > filter does a better job, if only could I have overlap ;))
> >
> > I guess the way to go would be to take the splitter (probably
> > ImageRegionSplitterMultidimensional now that I look at it) and extend it to
> > support overlap. If I do it, I'll let you know in case it is of interest to
> > anyone. For now I'll stick to my class.
> >
> > Cheers,
> >
> > Pol
> >
> > 2015-03-16 16:05 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> >>
> >> Hi Pol,
> >>
> >> As a side note, limitation of memory usage is built into the streaming
> >> pipeline design of ITK.  All computation of appropriate regions should
> >> occur if the filters are implemented correctly.  To take advantage of
> >> streaming, place the StreamingImageFilter [1] at the end of your
> >> pipeline. To use less memory, set the ReleaseDataFlagOn() [2] on the
> >> component filters.
> >>
> >> HTH,
> >> Matt
> >>
> >> [1] http://www.itk.org/Doxygen/html/classitk_1_1StreamingImageFilter.html
> >>
> >> [2]
> >> http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae732e9163879ae559ccd0b5957141f97
> >>
> >> On Mon, Mar 16, 2015 at 10:20 AM, Bradley Lowekamp
> >> <blowekamp at mail.nih.gov> wrote:
> >> > You may find this method useful:
> >> >
> >> >
> >> > http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
> >> >
> >> > Brad
> >> >
> >> > On Mar 16, 2015, at 10:16 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >> > wrote:
> >> >
> >> > Mmh, I believe I misread the RegionOfInterestImageFilter documentation,
> >> > confusing dimension with size. That should work.
> >> >
> >> > I still have the computation of the splitting regions problem to handle,
> >> > but
> >> > maybe with this filter is easier than with the ExtractImageFilter. Or
> >> > maybe
> >> > it just removes step 7?
> >> >
> >> > Is there a way to ease the repasting back to the original region with
> >> > it?
> >> > How should I use the physical space index?
> >> >
> >> > 2015-03-16 14:25 GMT+01:00 Pol Mons? Purt? <lluna.nova at gmail.com>:
> >> >>
> >> >> Hello Bradley,
> >> >>
> >> >> Thank you for your answer and suggestion.
> >> >>
> >> >> Answering your question: It's not for multi-threading purposes, I have
> >> >> to
> >> >> split the image due to memory limitations.
> >> >>
> >> >> I would use extractImage directly and do streaming, but the client and
> >> >> the
> >> >> low-level libraries might not work correctly if I do that. I have to
> >> >> provide
> >> >> itk images disconnected from the pipeline and with proper indexes and
> >> >> sizes.
> >> >>
> >> >> The RegionOfInterestImageFilter would have the same memory footprint,
> >> >> and
> >> >> it would still be tricky to compute the regions of interest, due to the
> >> >> overlapping.
> >> >>
> >> >>
> >> >>
> >> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> >> >>>
> >> >>> Hello,
> >> >>>
> >> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >> >>> ExtractImageFilter, but returns an image whose starting index is
> >> >>> always
> >> >>> zeros.
> >> >>>
> >> >>> The process you described is remarkable close to what occur in each
> >> >>> filter for the multi-threading process.  Also what occurs in the
> >> >>> StreamingImageFilter is very similar, but just copies the region.
> >> >>>
> >> >>> As you didn't mention you motivation for chunking the data this way be
> >> >>> it
> >> >>> for threading or memory requirements, I can't fully advise.
> >> >>>
> >> >>> Brad
> >> >>>
> >> >>>
> >> >>> [1
> >> >>>
> >> >>> ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >> >>> [2]
> >> >>>
> >> >>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >> >>>
> >> >>>
> >> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> > Hello everyone,
> >> >>> >
> >> >>> > We need to split a volume into pieces, overlaped by a certain
> >> >>> > amount,
> >> >>> > do some computation and then repaste them.
> >> >>> >
> >> >>> > The computation requires the pieces' region indexes to be set to
> >> >>> > zero.
> >> >>> > The original volume might not have index at zero, but be a subregion
> >> >>> > itself.
> >> >>> >
> >> >>> > What is the best way to achieve this?
> >> >>> >
> >> >>> > I've thought of the following pipeline:
> >> >>> >
> >> >>> > 1. imageRegionSplitterSlowDimension
> >> >>> > 2. Store the index and size of each region
> >> >>> > 3. manually increase the size of each region (and modify index)
> >> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >> >>> > prevent requesting more than available)
> >> >>> > iterate over regions:
> >> >>> >       5. extractImageFilter
> >> >>> >       6. disconnect pipeline for each region
> >> >>> >       7. reset indexes
> >> >>> >       8. perform computation
> >> >>> >       9. crop with the regions in step 1 to remove the added overlap
> >> >>> >       10. restore indexes
> >> >>> > 11. pasteImageFilter
> >> >>> >
> >> >>> > I'll have to think of a smart way to deal with the index
> >> >>> > restore/cropping of steps 9 and 10.
> >> >>> >
> >> >>> > I somehow feel somebody will have already dealt with this... And
> >> >>> > there's certainly a better way to do it.
> >> >>> > _____________________________________
> >> >>> > 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
> >> >>>
> >> >>
> >> >>
> >> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
> >> >>>
> >> >>> Hello,
> >> >>>
> >> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >> >>> ExtractImageFilter, but returns an image whose starting index is
> >> >>> always
> >> >>> zeros.
> >> >>>
> >> >>> The process you described is remarkable close to what occur in each
> >> >>> filter for the multi-threading process.  Also what occurs in the
> >> >>> StreamingImageFilter is very similar, but just copies the region.
> >> >>>
> >> >>> As you didn't mention you motivation for chunking the data this way be
> >> >>> it
> >> >>> for threading or memory requirements, I can't fully advise.
> >> >>>
> >> >>> Brad
> >> >>>
> >> >>>
> >> >>> [1
> >> >>>
> >> >>> ]http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >> >>> [2]
> >> >>>
> >> >>> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >> >>>
> >> >>>
> >> >>> On Mar 16, 2015, at 7:37 AM, Pol Mons? Purt? <lluna.nova at gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> > Hello everyone,
> >> >>> >
> >> >>> > We need to split a volume into pieces, overlaped by a certain
> >> >>> > amount,
> >> >>> > do some computation and then repaste them.
> >> >>> >
> >> >>> > The computation requires the pieces' region indexes to be set to
> >> >>> > zero.
> >> >>> > The original volume might not have index at zero, but be a subregion
> >> >>> > itself.
> >> >>> >
> >> >>> > What is the best way to achieve this?
> >> >>> >
> >> >>> > I've thought of the following pipeline:
> >> >>> >
> >> >>> > 1. imageRegionSplitterSlowDimension
> >> >>> > 2. Store the index and size of each region
> >> >>> > 3. manually increase the size of each region (and modify index)
> >> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >> >>> > prevent requesting more than available)
> >> >>> > iterate over regions:
> >> >>> >       5. extractImageFilter
> >> >>> >       6. disconnect pipeline for each region
> >> >>> >       7. reset indexes
> >> >>> >       8. perform computation
> >> >>> >       9. crop with the regions in step 1 to remove the added overlap
> >> >>> >       10. restore indexes
> >> >>> > 11. pasteImageFilter
> >> >>> >
> >> >>> > I'll have to think of a smart way to deal with the index
> >> >>> > restore/cropping of steps 9 and 10.
> >> >>> >
> >> >>> > I somehow feel somebody will have already dealt with this... And
> >> >>> > there's certainly a better way to do it.
> >> >>> > _____________________________________
> >> >>> > 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 blowekamp at mail.nih.gov  Thu Mar 19 09:17:44 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 19 Mar 2015 09:17:44 -0400
Subject: [ITK-users] [ITK]  Registration in SimpleITK
In-Reply-To: <DED8DC80-12C5-401C-B33C-DEE020623AC8@mail.nih.gov>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
 <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
 <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>
 <CAKKNfuJH+6-WbbY1Z16MSpjKbNdgh9rXyQ9nRKxbYMfV_ZR6Ng@mail.gmail.com>
 <DED8DC80-12C5-401C-B33C-DEE020623AC8@mail.nih.gov>
Message-ID: <E1635A96-C13E-4CD1-BDB1-0FC151A022E2@mail.nih.gov>

Hello,

Binaries for the current master are on the dashboard and now include the CSharp for windows 64. You can find more information about downloading nightly binaries here:
http://www.itk.org/Wiki/SimpleITK/GettingStarted#Nightly_binaries

Brad

On Mar 12, 2015, at 8:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:

> Hello,
> 
> Yes, it is more or less the same process. Grab all the ITK and SimpleITK dlls from the bin directories and place them in your path.
> 
> The SimpleITK Superbuild INSTALL target will actually install ITK and SimpleITK's core libraries correctly in to the CMake specified path. The installation target for the superbuild project just doesn't install the target languages ( every language has at least one own way of doing things that CMake does not know about ). You could use this to install all the needed dlls into a defined path. Then just grab the CSharp dll for your project and that should work too.
> 
> Also I worked on the explicit instantiation in SimpleITK today. I was able to reduce the size of the .o files on Linux by 30% by explicitly instantiating about 20 classes with their used templates. This is expected to resolve the linking and packaging issues on windows. So a solution is forth coming.
> 
> Brad
> 
> On Mar 12, 2015, at 7:26 PM, Matias Montroull <matimontg at gmail.com> wrote:
> 
>> Hi Brad, thanks for the explanation. I'm using C#, would that be the same process?
>> 
>> On Wed, Mar 11, 2015 at 8:56 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Hello,
>> 
>> If you are willing to compile it yourself you can get it to work with just a little bit of effort.
>> 
>> Compile the SimpleITK superbuild with shared libraries enabled. Do the usual installation of SimpleITK from the super build [1], this will install the SimpleITK python library into your site-packages. However, this libraries also depends on all the SimpleITK an ITK dlls (not installed or packaged), these should be in the superbuild's bin directory. These need to be in your run-time path when importing SimpleITK. This can be done either by modifying you PATH environment variable you copying them to the appropriate place ( which may depend on the python environment, and there are likely several alternatives).
>> 
>> Brad
>> 
>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Python_installation
>> 
>> On Mar 11, 2015, at 7:31 PM, Matias Montroull <matimontg at gmail.com> wrote:
>> 
>>> 
>>> My project is using 64 bits and some DLL I use as well, I've ran into issues when using the beta version because is 32 bits. I guess I'll wait until the final release is done.
>>> Thanks,
>>> Matias.
>>> 
>>> On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com> wrote:
>>> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't aware of this new Beta release
>>> Thanks,
>>> Matias.
>>> 
>>> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>> Hello Matias,
>>> 
>>> Currently there is SimpleITK 0.9b01 [1] out with the registration framework.
>>> 
>>> With it you can do things like this:
>>> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
>>> or
>>> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>>> 
>>> Please give it a try and let us know how it work for you.
>>> 
>>> Enjoy,
>>> Brad
>>> 
>>> [1] http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>>> 
>>> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> is it possible to do registration in SimpleITK? I mean, something like in this example:
>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>>>> 
>>>> Thanks,
>>>> 
>>>> Matias,
>>>> _____________________________________
>>>> 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

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From matt.mccormick at kitware.com  Thu Mar 19 16:20:06 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 19 Mar 2015 16:20:06 -0400
Subject: [ITK-users] ITK dicom reader wrong spacing
In-Reply-To: <DB3PR02MB107D01405D11A9D546358A4BE000@DB3PR02MB107.eurprd02.prod.outlook.com>
References: <DB3PR02MB107D01405D11A9D546358A4BE000@DB3PR02MB107.eurprd02.prod.outlook.com>
Message-ID: <CALzTN-Q7Oo8D2-fzGOXGavmzY61FDcqarxm-49PAS2dhJZQ9ww@mail.gmail.com>

Hi Aiert,

It is possible to use DCMTK instead of GDCM.  Turn on
Module_ITKIODCMTK in your CMake configuration.  See the
itkDCMTKSeriesReadImageWriter.cxx test for example usage.

HTH,
Matt

On Wed, Mar 18, 2015 at 7:43 AM, Amundarain, Aiert <aamundarain at ceit.es> wrote:
> I have a DICOM Image serie that itk does not read properly. The x,y,z
> spacing are incorrect and the return value is the default one (1,1,1).
>
> If I read this DICOM Image serie using vtk (vtkDICOMImageReader), the
> reading is correct.
>
> Both softwares are developed by kitware but the results are different.
>
>
>
> Is is possible to read the dicom files using ITK without using the gdcm
> library?
>
>
>
> Thank you.
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From audrey.istace at imavie.fr  Mon Mar 23 11:11:13 2015
From: audrey.istace at imavie.fr (AI)
Date: Mon, 23 Mar 2015 08:11:13 -0700 (MST)
Subject: [ITK-users] itk - Writing dicom files from single 3D file
Message-ID: <1427123473731-7587034.post@n2.nabble.com>

Hello,

I would like to write Dicom files from a nifti image files using
DCMTKImageIO. In the code below, I read a nifti file using
itkImageFileReader, and then try to write dicom files using
itkImageSeriesWriter. I was not able to do it, probably because of the
SetMetaDataDictionaryArray method, that I don?t know how to use since I
don?t read dicom series as input. Can you help me with that ?

Thank you very much,

Audrey

#include "itkDCMTKImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"

int main(int argc, char *argv[])
{
               typedef signed short                                            
PixelType;
               const unsigned int                                              
Dimension = 3;
               typedef itk::Image< PixelType, Dimension >                      
ImageType;
               typedef itk::Image< PixelType, 2 >                              
OutputImageType;
               typedef itk::ImageFileReader< ImageType >                       
ReaderType;
               typedef itk::DCMTKImageIO                                       
ImageIOType;
               typedef itk::NumericSeriesFileNames                             
NamesGeneratorType;
               typedef itk::ImageSeriesWriter< ImageType, OutputImageType >    
WriterType;
               
               ImageIOType::Pointer dcmtkIO = ImageIOType::New();
               NamesGeneratorType::Pointer namesGenerator =
NamesGeneratorType::New();
               ReaderType::Pointer reader = ReaderType::New();
               WriterType::Pointer writer = WriterType::New();
               
               reader->SetFileName( "../../out.nii" );
               reader->Update();
               
               
               
               itksys::SystemTools::MakeDirectory( "../../OutputDicom/" );
               
               std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
               namesGenerator->SetSeriesFormat (seriesFormat.c_str());
               namesGenerator->SetStartIndex (1);
               namesGenerator->SetEndIndex (166);
               
               
               writer->SetInput( reader->GetOutput() );
               writer->SetImageIO( dcmtkIO );
               writer->SetFileNames( namesGenerator->GetFileNames() );
//           writer->SetMetaDataDictionaryArray(
reader->GetMetaDataDictionaryArray() );
               writer->Update();
}




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files-from-single-3D-file-tp7587034.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From majcjc at gmail.com  Mon Mar 23 12:10:43 2015
From: majcjc at gmail.com (Lin M)
Date: Mon, 23 Mar 2015 12:10:43 -0400
Subject: [ITK-users] Computational time of fast marching
Message-ID: <CALmrq1ZSQDQWemX+hPOvS1K-tRu4ToQjPCPcp+24ZcF8s7Gvtg@mail.gmail.com>

Hi guys.

I'm using fast marching to compute the distance map, but the time of
computation is much slower than I expected. Is it normal to cost about
250secs for a 512*512*365 image? I'm using the released mode.

My process is like this:
1. initialize a binary image (alive image) where segmented target is set to
1, the rest is set to 0
2. initialize the trial image where the neighbourhood of alive image is set
to 1, the rest is set to 0
3. give the two images to the adaptor and set the alive value and the trial
value both to 1
4. run fast marching

Do you have any ideas about that or some suggestions to improve the
performance. Thank you very much!

Best,
Lin
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From majcjc at gmail.com  Mon Mar 23 12:18:44 2015
From: majcjc at gmail.com (Lin M)
Date: Mon, 23 Mar 2015 12:18:44 -0400
Subject: [ITK-users] Computational time of fast marching
In-Reply-To: <CALmrq1ZSQDQWemX+hPOvS1K-tRu4ToQjPCPcp+24ZcF8s7Gvtg@mail.gmail.com>
References: <CALmrq1ZSQDQWemX+hPOvS1K-tRu4ToQjPCPcp+24ZcF8s7Gvtg@mail.gmail.com>
Message-ID: <CALmrq1Y2RrM92yHGQWJAa3U55pafSG7WyM_Ek_0_8DF8yoC2vw@mail.gmail.com>

I'm using a i7-4650U 8G machine.

On Mon, Mar 23, 2015 at 12:10 PM, Lin M <majcjc at gmail.com> wrote:

> Hi guys.
>
> I'm using fast marching to compute the distance map, but the time of
> computation is much slower than I expected. Is it normal to cost about
> 250secs for a 512*512*365 image? I'm using the released mode.
>
> My process is like this:
> 1. initialize a binary image (alive image) where segmented target is set
> to 1, the rest is set to 0
> 2. initialize the trial image where the neighbourhood of alive image is
> set to 1, the rest is set to 0
> 3. give the two images to the adaptor and set the alive value and the
> trial value both to 1
> 4. run fast marching
>
> Do you have any ideas about that or some suggestions to improve the
> performance. Thank you very much!
>
> Best,
> Lin
>
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From matimontg at gmail.com  Tue Mar 24 11:10:32 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 12:10:32 -0300
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <1427123473731-7587034.post@n2.nabble.com>
References: <1427123473731-7587034.post@n2.nabble.com>
Message-ID: <CAKKNfuJa_BsNJkgfz+uHcvDidp=K-xLtrp5nSJn-m1bcvapGNw@mail.gmail.com>

I'm able to write individual slices from a mha or mhd file, is that the
same as nifti file? if so, I can send you the code, I think it's a
copy/paste from one of the examples out there.

On Mon, Mar 23, 2015 at 12:11 PM, AI <audrey.istace at imavie.fr> wrote:

> Hello,
>
> I would like to write Dicom files from a nifti image files using
> DCMTKImageIO. In the code below, I read a nifti file using
> itkImageFileReader, and then try to write dicom files using
> itkImageSeriesWriter. I was not able to do it, probably because of the
> SetMetaDataDictionaryArray method, that I don?t know how to use since I
> don?t read dicom series as input. Can you help me with that ?
>
> Thank you very much,
>
> Audrey
>
> #include "itkDCMTKImageIO.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageFileReader.h"
> #include "itkImageSeriesWriter.h"
>
> int main(int argc, char *argv[])
> {
>                typedef signed short
> PixelType;
>                const unsigned int
> Dimension = 3;
>                typedef itk::Image< PixelType, Dimension >
> ImageType;
>                typedef itk::Image< PixelType, 2 >
> OutputImageType;
>                typedef itk::ImageFileReader< ImageType >
> ReaderType;
>                typedef itk::DCMTKImageIO
> ImageIOType;
>                typedef itk::NumericSeriesFileNames
> NamesGeneratorType;
>                typedef itk::ImageSeriesWriter< ImageType, OutputImageType >
> WriterType;
>
>                ImageIOType::Pointer dcmtkIO = ImageIOType::New();
>                NamesGeneratorType::Pointer namesGenerator =
> NamesGeneratorType::New();
>                ReaderType::Pointer reader = ReaderType::New();
>                WriterType::Pointer writer = WriterType::New();
>
>                reader->SetFileName( "../../out.nii" );
>                reader->Update();
>
>
>
>                itksys::SystemTools::MakeDirectory( "../../OutputDicom/" );
>
>                std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
>                namesGenerator->SetSeriesFormat (seriesFormat.c_str());
>                namesGenerator->SetStartIndex (1);
>                namesGenerator->SetEndIndex (166);
>
>
>                writer->SetInput( reader->GetOutput() );
>                writer->SetImageIO( dcmtkIO );
>                writer->SetFileNames( namesGenerator->GetFileNames() );
> //           writer->SetMetaDataDictionaryArray(
> reader->GetMetaDataDictionaryArray() );
>                writer->Update();
> }
>
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files-from-single-3D-file-tp7587034.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From matimontg at gmail.com  Tue Mar 24 11:17:43 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 12:17:43 -0300
Subject: [ITK-users] [ITK] Registration in SimpleITK
In-Reply-To: <E1635A96-C13E-4CD1-BDB1-0FC151A022E2@mail.nih.gov>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
 <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
 <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>
 <CAKKNfuJH+6-WbbY1Z16MSpjKbNdgh9rXyQ9nRKxbYMfV_ZR6Ng@mail.gmail.com>
 <DED8DC80-12C5-401C-B33C-DEE020623AC8@mail.nih.gov>
 <E1635A96-C13E-4CD1-BDB1-0FC151A022E2@mail.nih.gov>
Message-ID: <CAKKNfuLEu9=W4G8Buj2QyZo7VB_ubo=1j2zd3x-Qzqfn_dXz=w@mail.gmail.com>

Hi Bradley, so if I would like to download the Csharp DLL files, I need to
go to the link you posted? for example, I can download:
VS9-Win32-pkg-py2.7-csharp-java-master
<https://open.cdash.org/buildSummary.php?buildid=3741479>
[image: Files] <https://open.cdash.org/viewFiles.php?buildid=3741479>[image:
info]
?
Thanks, I'm new to the dashboard.
Matias.

On Thu, Mar 19, 2015 at 10:17 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> Binaries for the current master are on the dashboard and now include the
> CSharp for windows 64. You can find more information about downloading
> nightly binaries here:
> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Nightly_binaries
>
> Brad
>
> On Mar 12, 2015, at 8:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
> Hello,
>
> Yes, it is more or less the same process. Grab all the ITK and SimpleITK
> dlls from the bin directories and place them in your path.
>
> The SimpleITK Superbuild INSTALL target will actually install ITK and
> SimpleITK's core libraries correctly in to the CMake specified path. The
> installation target for the superbuild project just doesn't install the
> target languages ( every language has at least one own way of doing things
> that CMake does not know about ). You could use this to install all the
> needed dlls into a defined path. Then just grab the CSharp dll for your
> project and that should work too.
>
> Also I worked on the explicit instantiation in SimpleITK today. I was able
> to reduce the size of the .o files on Linux by 30% by explicitly
> instantiating about 20 classes with their used templates. This is expected
> to resolve the linking and packaging issues on windows. So a solution is
> forth coming.
>
> Brad
>
> On Mar 12, 2015, at 7:26 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> Hi Brad, thanks for the explanation. I'm using C#, would that be the same
> process?
>
> On Wed, Mar 11, 2015 at 8:56 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello,
>>
>> If you are willing to compile it yourself you can get it to work with
>> just a little bit of effort.
>>
>> Compile the SimpleITK superbuild with shared libraries enabled. Do the
>> usual installation of SimpleITK from the super build [1], this will install
>> the SimpleITK python library into your site-packages. However, this
>> libraries also depends on all the SimpleITK an ITK dlls (not installed or
>> packaged), these should be in the superbuild's bin directory. These need to
>> be in your run-time path when importing SimpleITK. This can be done either
>> by modifying you PATH environment variable you copying them to the
>> appropriate place ( which may depend on the python environment, and there
>> are likely several alternatives).
>>
>> Brad
>>
>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Python_installation
>>
>> On Mar 11, 2015, at 7:31 PM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>>
>> My project is using 64 bits and some DLL I use as well, I've ran into
>> issues when using the beta version because is 32 bits. I guess I'll wait
>> until the final release is done.
>> Thanks,
>> Matias.
>>
>> On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>>> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but
>>> wasn't aware of this new Beta release
>>> Thanks,
>>> Matias.
>>>
>>> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <
>>> blowekamp at mail.nih.gov> wrote:
>>>
>>>> Hello Matias,
>>>>
>>>> Currently there is SimpleITK 0.9b01 [1] out with the registration
>>>> framework.
>>>>
>>>> With it you can do things like this:
>>>>
>>>> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
>>>> or
>>>>
>>>> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>>>>
>>>> Please give it a try and let us know how it work for you.
>>>>
>>>> Enjoy,
>>>> Brad
>>>>
>>>> [1]
>>>> http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>>>>
>>>> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> is it possible to do registration in SimpleITK? I mean, something like
>>>> in this example:
>>>>
>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>>>>
>>>> Thanks,
>>>>
>>>> Matias,
>>>> _____________________________________
>>>> 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
>
>
>
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From blowekamp at mail.nih.gov  Tue Mar 24 11:22:06 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 24 Mar 2015 11:22:06 -0400
Subject: [ITK-users] [ITK] Registration in SimpleITK
In-Reply-To: <CAKKNfuLEu9=W4G8Buj2QyZo7VB_ubo=1j2zd3x-Qzqfn_dXz=w@mail.gmail.com>
References: <CAKKNfuJu8-6Uv69+rdgkAZvC90mpAjp5v3j6cAkObH8qPnJC-A@mail.gmail.com>
 <C263D9FD-DAAD-4A1C-BD9E-F942CA0C5449@mail.nih.gov>
 <CAKKNfuLoJwo_U4xPj+A60x24=QcUQ+Jcp1TgKhNxsZancq2K=w@mail.gmail.com>
 <CAKKNfu+ChzbTeKpdovNdjHdfXPNnPR_CgCCmDBxDgR3Z-SmbYQ@mail.gmail.com>
 <F4A0C9AE-5FC1-4D9C-A788-266BB343EE20@mail.nih.gov>
 <CAKKNfuJH+6-WbbY1Z16MSpjKbNdgh9rXyQ9nRKxbYMfV_ZR6Ng@mail.gmail.com>
 <DED8DC80-12C5-401C-B33C-DEE020623AC8@mail.nih.gov>
 <E1635A96-C13E-4CD1-BDB1-0FC151A022E2@mail.nih.gov>
 <CAKKNfuLEu9=W4G8Buj2QyZo7VB_ubo=1j2zd3x-Qzqfn_dXz=w@mail.gmail.com>
Message-ID: <1AB9A9D9-03DC-4478-9EC1-B6682B5581B5@mail.nih.gov>

The link you provided is for windows 32. You said you wanted windows 64, its here:
https://open.cdash.org/viewFiles.php?buildid=3741847

Brad

On Mar 24, 2015, at 11:17 AM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi Bradley, so if I would like to download the Csharp DLL files, I need to go to the link you posted? for example, I can download: 
> VS9-Win32-pkg-py2.7-csharp-java-master
> ?
> Thanks, I'm new to the dashboard.
> Matias.
> 
> On Thu, Mar 19, 2015 at 10:17 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> Binaries for the current master are on the dashboard and now include the CSharp for windows 64. You can find more information about downloading nightly binaries here:
> http://www.itk.org/Wiki/SimpleITK/GettingStarted#Nightly_binaries
> 
> Brad
> 
> On Mar 12, 2015, at 8:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 
>> Hello,
>> 
>> Yes, it is more or less the same process. Grab all the ITK and SimpleITK dlls from the bin directories and place them in your path.
>> 
>> The SimpleITK Superbuild INSTALL target will actually install ITK and SimpleITK's core libraries correctly in to the CMake specified path. The installation target for the superbuild project just doesn't install the target languages ( every language has at least one own way of doing things that CMake does not know about ). You could use this to install all the needed dlls into a defined path. Then just grab the CSharp dll for your project and that should work too.
>> 
>> Also I worked on the explicit instantiation in SimpleITK today. I was able to reduce the size of the .o files on Linux by 30% by explicitly instantiating about 20 classes with their used templates. This is expected to resolve the linking and packaging issues on windows. So a solution is forth coming.
>> 
>> Brad
>> 
>> On Mar 12, 2015, at 7:26 PM, Matias Montroull <matimontg at gmail.com> wrote:
>> 
>>> Hi Brad, thanks for the explanation. I'm using C#, would that be the same process?
>>> 
>>> On Wed, Mar 11, 2015 at 8:56 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>> Hello,
>>> 
>>> If you are willing to compile it yourself you can get it to work with just a little bit of effort.
>>> 
>>> Compile the SimpleITK superbuild with shared libraries enabled. Do the usual installation of SimpleITK from the super build [1], this will install the SimpleITK python library into your site-packages. However, this libraries also depends on all the SimpleITK an ITK dlls (not installed or packaged), these should be in the superbuild's bin directory. These need to be in your run-time path when importing SimpleITK. This can be done either by modifying you PATH environment variable you copying them to the appropriate place ( which may depend on the python environment, and there are likely several alternatives).
>>> 
>>> Brad
>>> 
>>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Python_installation
>>> 
>>> On Mar 11, 2015, at 7:31 PM, Matias Montroull <matimontg at gmail.com> wrote:
>>> 
>>>> 
>>>> My project is using 64 bits and some DLL I use as well, I've ran into issues when using the beta version because is 32 bits. I guess I'll wait until the final release is done.
>>>> Thanks,
>>>> Matias.
>>>> 
>>>> On Wed, Mar 11, 2015 at 7:54 PM, Matias Montroull <matimontg at gmail.com> wrote:
>>>> Thanks Bradley, I'll give it a try. I downloaded version 0.8.1 but wasn't aware of this new Beta release
>>>> Thanks,
>>>> Matias.
>>>> 
>>>> On Wed, Mar 11, 2015 at 7:46 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>> Hello Matias,
>>>> 
>>>> Currently there is SimpleITK 0.9b01 [1] out with the registration framework.
>>>> 
>>>> With it you can do things like this:
>>>> http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/56_VH_Registration1.html
>>>> or
>>>> http://www.itk.org/SimpleITKDoxygen/html/ImageRegistrationMethod2_8py-example.html
>>>> 
>>>> Please give it a try and let us know how it work for you.
>>>> 
>>>> Enjoy,
>>>> Brad
>>>> 
>>>> [1] http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release
>>>> 
>>>> On Mar 11, 2015, at 6:32 PM, Matias Montroull <matimontg at gmail.com> wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> is it possible to do registration in SimpleITK? I mean, something like in this example:
>>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Insight/Examples/Registration/ImageRegistration2.cxx?view=markup
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Matias,
>>>>> _____________________________________
>>>>> 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
> 
> 

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From audrey.istace at imavie.fr  Tue Mar 24 11:57:35 2015
From: audrey.istace at imavie.fr (AI)
Date: Tue, 24 Mar 2015 08:57:35 -0700 (MST)
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <CAKKNfuJa_BsNJkgfz+uHcvDidp=K-xLtrp5nSJn-m1bcvapGNw@mail.gmail.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CAKKNfuJa_BsNJkgfz+uHcvDidp=K-xLtrp5nSJn-m1bcvapGNw@mail.gmail.com>
Message-ID: <DBXPR04MB493AFDD5831E2B0AD1DCA0BE60A0@DBXPR04MB493.eurprd04.prod.outlook.com>

Hi Matias,

Thank you for your answer.
If your code is working with DCMTKImageIO and not GDCMImageIO, I would be happy to see it.
For me it works using gdcm but not using dcmtk (compilation is ok, but no dicom is written in my output directory after execution), and I would like to use dcmtk.

De : Matias Montroull [via ITK Insight Users] [mailto:ml-node+s2283740n7587037h21 at n2.nabble.com]
Envoy? : mardi 24 mars 2015 16:11
? : Audrey Istace
Objet : Re: [ITK-users] itk - Writing dicom files from single 3D file

I'm able to write individual slices from a mha or mhd file, is that the same as nifti file? if so, I can send you the code, I think it's a copy/paste from one of the examples out there.

On Mon, Mar 23, 2015 at 12:11 PM, AI <[hidden email]</user/SendEmail.jtp?type=node&node=7587037&i=0>> wrote:
Hello,

I would like to write Dicom files from a nifti image files using
DCMTKImageIO. In the code below, I read a nifti file using
itkImageFileReader, and then try to write dicom files using
itkImageSeriesWriter. I was not able to do it, probably because of the
SetMetaDataDictionaryArray method, that I don?t know how to use since I
don?t read dicom series as input. Can you help me with that ?

Thank you very much,

Audrey

#include "itkDCMTKImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"

int main(int argc, char *argv[])
{
               typedef signed short
PixelType;
               const unsigned int
Dimension = 3;
               typedef itk::Image< PixelType, Dimension >
ImageType;
               typedef itk::Image< PixelType, 2 >
OutputImageType;
               typedef itk::ImageFileReader< ImageType >
ReaderType;
               typedef itk::DCMTKImageIO
ImageIOType;
               typedef itk::NumericSeriesFileNames
NamesGeneratorType;
               typedef itk::ImageSeriesWriter< ImageType, OutputImageType >
WriterType;

               ImageIOType::Pointer dcmtkIO = ImageIOType::New();
               NamesGeneratorType::Pointer namesGenerator =
NamesGeneratorType::New();
               ReaderType::Pointer reader = ReaderType::New();
               WriterType::Pointer writer = WriterType::New();

               reader->SetFileName( "../../out.nii" );
               reader->Update();



               itksys::SystemTools::MakeDirectory( "../../OutputDicom/" );

               std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
               namesGenerator->SetSeriesFormat (seriesFormat.c_str());
               namesGenerator->SetStartIndex (1);
               namesGenerator->SetEndIndex (166);


               writer->SetInput( reader->GetOutput() );
               writer->SetImageIO( dcmtkIO );
               writer->SetFileNames( namesGenerator->GetFileNames() );
//           writer->SetMetaDataDictionaryArray(
reader->GetMetaDataDictionaryArray() );
               writer->Update();
}




--
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Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
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:
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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

Follow this link to subscribe/unsubscribe:
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From matimontg at gmail.com  Tue Mar 24 12:08:13 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 13:08:13 -0300
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <DBXPR04MB493AFDD5831E2B0AD1DCA0BE60A0@DBXPR04MB493.eurprd04.prod.outlook.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CAKKNfuJa_BsNJkgfz+uHcvDidp=K-xLtrp5nSJn-m1bcvapGNw@mail.gmail.com>
 <DBXPR04MB493AFDD5831E2B0AD1DCA0BE60A0@DBXPR04MB493.eurprd04.prod.outlook.com>
Message-ID: <CAKKNfu++VGSVT-_2nX_wy+EsDvVu5qrLxM5M-Mhcke5Oq+ZiUw@mail.gmail.com>

Al, the code I have is using GDCM:
typedef itk::GDCMImageIO ImageIOType;

On Tue, Mar 24, 2015 at 12:57 PM, AI <audrey.istace at imavie.fr> wrote:

> Hi Matias,
>
> Thank you for your answer.
> If your code is working with DCMTKImageIO and not GDCMImageIO, I would be
> happy to see it.
> For me it works using gdcm but not using dcmtk (compilation is ok, but no
> dicom is written in my output directory after execution), and I would like
> to use dcmtk.
>
> De : Matias Montroull [via ITK Insight Users] [mailto:
> ml-node+s2283740n7587037h21 at n2.nabble.com]
> Envoy? : mardi 24 mars 2015 16:11
> ? : Audrey Istace
> Objet : Re: [ITK-users] itk - Writing dicom files from single 3D file
>
> I'm able to write individual slices from a mha or mhd file, is that the
> same as nifti file? if so, I can send you the code, I think it's a
> copy/paste from one of the examples out there.
>
> On Mon, Mar 23, 2015 at 12:11 PM, AI <[hidden
> email]</user/SendEmail.jtp?type=node&node=7587037&i=0>> wrote:
> Hello,
>
> I would like to write Dicom files from a nifti image files using
> DCMTKImageIO. In the code below, I read a nifti file using
> itkImageFileReader, and then try to write dicom files using
> itkImageSeriesWriter. I was not able to do it, probably because of the
> SetMetaDataDictionaryArray method, that I don?t know how to use since I
> don?t read dicom series as input. Can you help me with that ?
>
> Thank you very much,
>
> Audrey
>
> #include "itkDCMTKImageIO.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageFileReader.h"
> #include "itkImageSeriesWriter.h"
>
> int main(int argc, char *argv[])
> {
>                typedef signed short
> PixelType;
>                const unsigned int
> Dimension = 3;
>                typedef itk::Image< PixelType, Dimension >
> ImageType;
>                typedef itk::Image< PixelType, 2 >
> OutputImageType;
>                typedef itk::ImageFileReader< ImageType >
> ReaderType;
>                typedef itk::DCMTKImageIO
> ImageIOType;
>                typedef itk::NumericSeriesFileNames
> NamesGeneratorType;
>                typedef itk::ImageSeriesWriter< ImageType, OutputImageType >
> WriterType;
>
>                ImageIOType::Pointer dcmtkIO = ImageIOType::New();
>                NamesGeneratorType::Pointer namesGenerator =
> NamesGeneratorType::New();
>                ReaderType::Pointer reader = ReaderType::New();
>                WriterType::Pointer writer = WriterType::New();
>
>                reader->SetFileName( "../../out.nii" );
>                reader->Update();
>
>
>
>                itksys::SystemTools::MakeDirectory( "../../OutputDicom/" );
>
>                std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
>                namesGenerator->SetSeriesFormat (seriesFormat.c_str());
>                namesGenerator->SetStartIndex (1);
>                namesGenerator->SetEndIndex (166);
>
>
>                writer->SetInput( reader->GetOutput() );
>                writer->SetImageIO( dcmtkIO );
>                writer->SetFileNames( namesGenerator->GetFileNames() );
> //           writer->SetMetaDataDictionaryArray(
> reader->GetMetaDataDictionaryArray() );
>                writer->Update();
> }
>
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files-from-single-3D-file-tp7587034.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com<http://www.kitware.com>
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> _____________________________________
> Powered by www.kitware.com<http://www.kitware.com>
>
> Visit other Kitware open-source projects at
> 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
>
> ________________________________
> If you reply to this email, your message will be added to the discussion
> below:
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From audrey.istace at imavie.fr  Tue Mar 24 12:12:38 2015
From: audrey.istace at imavie.fr (AI)
Date: Tue, 24 Mar 2015 09:12:38 -0700 (MST)
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <CAKKNfu++VGSVT-_2nX_wy+EsDvVu5qrLxM5M-Mhcke5Oq+ZiUw@mail.gmail.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CAKKNfuJa_BsNJkgfz+uHcvDidp=K-xLtrp5nSJn-m1bcvapGNw@mail.gmail.com>
 <DBXPR04MB493AFDD5831E2B0AD1DCA0BE60A0@DBXPR04MB493.eurprd04.prod.outlook.com>
 <CAKKNfu++VGSVT-_2nX_wy+EsDvVu5qrLxM5M-Mhcke5Oq+ZiUw@mail.gmail.com>
Message-ID: <DBXPR04MB493DF7D990A8588D3CEE492E60A0@DBXPR04MB493.eurprd04.prod.outlook.com>

Thank you.
If someone has already writen dicom files using itkDCMTKImageIO.h, please help me !

De : Matias Montroull [via ITK Insight Users] [mailto:ml-node+s2283740n7587041h45 at n2.nabble.com]
Envoy? : mardi 24 mars 2015 17:09
? : Audrey Istace
Objet : Re: [ITK-users] itk - Writing dicom files from single 3D file

Al, the code I have is using GDCM:
typedef itk::GDCMImageIO ImageIOType;

On Tue, Mar 24, 2015 at 12:57 PM, AI <[hidden email]</user/SendEmail.jtp?type=node&node=7587041&i=0>> wrote:
Hi Matias,

Thank you for your answer.
If your code is working with DCMTKImageIO and not GDCMImageIO, I would be happy to see it.
For me it works using gdcm but not using dcmtk (compilation is ok, but no dicom is written in my output directory after execution), and I would like to use dcmtk.

De : Matias Montroull [via ITK Insight Users] [mailto:[hidden email]</user/SendEmail.jtp?type=node&node=7587041&i=1>]
Envoy? : mardi 24 mars 2015 16:11
? : Audrey Istace
Objet : Re: [ITK-users] itk - Writing dicom files from single 3D file

I'm able to write individual slices from a mha or mhd file, is that the same as nifti file? if so, I can send you the code, I think it's a copy/paste from one of the examples out there.
On Mon, Mar 23, 2015 at 12:11 PM, AI <[hidden email]</user/SendEmail.jtp?type=node&node=7587037&i=0>> wrote:
Hello,

I would like to write Dicom files from a nifti image files using
DCMTKImageIO. In the code below, I read a nifti file using
itkImageFileReader, and then try to write dicom files using
itkImageSeriesWriter. I was not able to do it, probably because of the
SetMetaDataDictionaryArray method, that I don?t know how to use since I
don?t read dicom series as input. Can you help me with that ?

Thank you very much,

Audrey

#include "itkDCMTKImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"

int main(int argc, char *argv[])
{
               typedef signed short
PixelType;
               const unsigned int
Dimension = 3;
               typedef itk::Image< PixelType, Dimension >
ImageType;
               typedef itk::Image< PixelType, 2 >
OutputImageType;
               typedef itk::ImageFileReader< ImageType >
ReaderType;
               typedef itk::DCMTKImageIO
ImageIOType;
               typedef itk::NumericSeriesFileNames
NamesGeneratorType;
               typedef itk::ImageSeriesWriter< ImageType, OutputImageType >
WriterType;

               ImageIOType::Pointer dcmtkIO = ImageIOType::New();
               NamesGeneratorType::Pointer namesGenerator =
NamesGeneratorType::New();
               ReaderType::Pointer reader = ReaderType::New();
               WriterType::Pointer writer = WriterType::New();

               reader->SetFileName( "../../out.nii" );
               reader->Update();



               itksys::SystemTools::MakeDirectory( "../../OutputDicom/" );

               std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
               namesGenerator->SetSeriesFormat (seriesFormat.c_str());
               namesGenerator->SetStartIndex (1);
               namesGenerator->SetEndIndex (166);


               writer->SetInput( reader->GetOutput() );
               writer->SetImageIO( dcmtkIO );
               writer->SetFileNames( namesGenerator->GetFileNames() );
//           writer->SetMetaDataDictionaryArray(
reader->GetMetaDataDictionaryArray() );
               writer->Update();
}




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From matt.mccormick at kitware.com  Tue Mar 24 12:43:50 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 24 Mar 2015 12:43:50 -0400
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <1427123473731-7587034.post@n2.nabble.com>
References: <1427123473731-7587034.post@n2.nabble.com>
Message-ID: <CALzTN-QmuHpsFZ9ZiDyZ3X+uO2Xz0g0zb5SSkf+NsoJ1ac53BQ@mail.gmail.com>

Hi,

DCMTKImageIO not serialize or de-serialize DICOM tags to / from its
MetaDataDictionaryArray currently like GDCM does.

HTH,
Matt

On Mon, Mar 23, 2015 at 11:11 AM, AI <audrey.istace at imavie.fr> wrote:
> Hello,
>
> I would like to write Dicom files from a nifti image files using
> DCMTKImageIO. In the code below, I read a nifti file using
> itkImageFileReader, and then try to write dicom files using
> itkImageSeriesWriter. I was not able to do it, probably because of the
> SetMetaDataDictionaryArray method, that I don?t know how to use since I
> don?t read dicom series as input. Can you help me with that ?
>
> Thank you very much,
>
> Audrey
>
> #include "itkDCMTKImageIO.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageFileReader.h"
> #include "itkImageSeriesWriter.h"
>
> int main(int argc, char *argv[])
> {
>                typedef signed short
> PixelType;
>                const unsigned int
> Dimension = 3;
>                typedef itk::Image< PixelType, Dimension >
> ImageType;
>                typedef itk::Image< PixelType, 2 >
> OutputImageType;
>                typedef itk::ImageFileReader< ImageType >
> ReaderType;
>                typedef itk::DCMTKImageIO
> ImageIOType;
>                typedef itk::NumericSeriesFileNames
> NamesGeneratorType;
>                typedef itk::ImageSeriesWriter< ImageType, OutputImageType >
> WriterType;
>
>                ImageIOType::Pointer dcmtkIO = ImageIOType::New();
>                NamesGeneratorType::Pointer namesGenerator =
> NamesGeneratorType::New();
>                ReaderType::Pointer reader = ReaderType::New();
>                WriterType::Pointer writer = WriterType::New();
>
>                reader->SetFileName( "../../out.nii" );
>                reader->Update();
>
>
>
>                itksys::SystemTools::MakeDirectory( "../../OutputDicom/" );
>
>                std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
>                namesGenerator->SetSeriesFormat (seriesFormat.c_str());
>                namesGenerator->SetStartIndex (1);
>                namesGenerator->SetEndIndex (166);
>
>
>                writer->SetInput( reader->GetOutput() );
>                writer->SetImageIO( dcmtkIO );
>                writer->SetFileNames( namesGenerator->GetFileNames() );
> //           writer->SetMetaDataDictionaryArray(
> reader->GetMetaDataDictionaryArray() );
>                writer->Update();
> }
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files-from-single-3D-file-tp7587034.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
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> http://www.kitware.com/products/protraining.php
>
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> http://www.itk.org/Wiki/ITK_FAQ
>
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From matimontg at gmail.com  Tue Mar 24 13:45:16 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 14:45:16 -0300
Subject: [ITK-users] ImageSeriesWriter | SimpleITK
Message-ID: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>

Hi,

I'm looking for an example on how to convert an mhd or mha image into
slices. I downloaded SimpleITK V0.9 Beta and was playing around with the
new ImageSeriesWriter class but can't figure out how to do it.
Do I need to declare a VectorString?
Thanks,

Matias.
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From blowekamp at mail.nih.gov  Tue Mar 24 13:50:43 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 24 Mar 2015 13:50:43 -0400
Subject: [ITK-users] ImageSeriesWriter | SimpleITK
In-Reply-To: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>
References: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>
Message-ID: <0ED4F886-5DA7-408C-A834-E372D8C77564@mail.nih.gov>

Yes, it you should use the VectorString SimpleITK for CSharp has for the fileNames argument.

If you are having trouble please provide a small example, and what the error/problem is.

Brad

On Mar 24, 2015, at 1:45 PM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi,
> 
> I'm looking for an example on how to convert an mhd or mha image into slices. I downloaded SimpleITK V0.9 Beta and was playing around with the new ImageSeriesWriter class but can't figure out how to do it.
> Do I need to declare a VectorString?
> Thanks,
> 
> Matias.

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From matimontg at gmail.com  Tue Mar 24 13:56:12 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 14:56:12 -0300
Subject: [ITK-users] ImageSeriesWriter | SimpleITK
In-Reply-To: <0ED4F886-5DA7-408C-A834-E372D8C77564@mail.nih.gov>
References: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>
 <0ED4F886-5DA7-408C-A834-E372D8C77564@mail.nih.gov>
Message-ID: <CAKKNfuJRAayrOtNVZagQtSDfGHLOjDYVyubL6OKUcwjvXWc+TQ@mail.gmail.com>

Bradley,

Here's what I'm testing now (I'm trying to write a series of slices from a
mha file)


            ImageFileReader imgreader = new ImageFileReader();
            imgreader.SetFileName(path_pacientes + nombre_paciente +
@"\Fusion\" + "resultado.mha");
            itk.simple.Image imgtest = imgreader.Execute();
            ImageSeriesWriter SeriesWriter = new ImageSeriesWriter();
            VectorString vs = new VectorString();

//Here's where I struggle...
            vs.Add(path_pacientes + nombre_paciente +
@"\Fusion\SalidaTest\imagen%03d.dcm"); //Is this rthe right way to include
a vector of strings?
            SeriesWriter.SetFileNames(vs);


On Tue, Mar 24, 2015 at 2:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Yes, it you should use the VectorString SimpleITK for CSharp has for the
> fileNames argument.
>
> If you are having trouble please provide a small example, and what the
> error/problem is.
>
> Brad
>
> On Mar 24, 2015, at 1:45 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> Hi,
>
> I'm looking for an example on how to convert an mhd or mha image into
> slices. I downloaded SimpleITK V0.9 Beta and was playing around with the
> new ImageSeriesWriter class but can't figure out how to do it.
> Do I need to declare a VectorString?
> Thanks,
>
> Matias.
>
>
>
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From blowekamp at mail.nih.gov  Tue Mar 24 14:12:47 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 24 Mar 2015 14:12:47 -0400
Subject: [ITK-users] ImageSeriesWriter | SimpleITK
In-Reply-To: <CAKKNfuJRAayrOtNVZagQtSDfGHLOjDYVyubL6OKUcwjvXWc+TQ@mail.gmail.com>
References: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>
 <0ED4F886-5DA7-408C-A834-E372D8C77564@mail.nih.gov>
 <CAKKNfuJRAayrOtNVZagQtSDfGHLOjDYVyubL6OKUcwjvXWc+TQ@mail.gmail.com>
Message-ID: <1C0358A6-56D5-4D38-B21F-A875F85E09E3@mail.nih.gov>

Hello,

On Mar 24, 2015, at 1:56 PM, Matias Montroull <matimontg at gmail.com> wrote:

> //Here's where I struggle...
>             vs.Add(path_pacientes + nombre_paciente + @"\Fusion\SalidaTest\imagen%03d.dcm"); //Is this rthe right way to include a vector of strings


No that is not the write way. You actually need to create the list for file names. You needs something closer to what's here in the C++ test [1] but converted to CSharp. The length of the list must match the z size of the images.

Many languages have convenient generator expressions or list comprehensions, which seems more natural than C printf formatting and the perils associated with it.

The long way to do it is just write a little for loop, something like:

for (i=0; i < img.GetSize()[2], ++i)
	vs.Add( "name {0}.ext".Format(i))

Brad

[1] https://github.com/SimpleITK/SimpleITK/blob/master/Testing/Unit/IOTests.cxx#L123-L152

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From matimontg at gmail.com  Tue Mar 24 17:19:04 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 18:19:04 -0300
Subject: [ITK-users] ImageSeriesWriter | SimpleITK
In-Reply-To: <1C0358A6-56D5-4D38-B21F-A875F85E09E3@mail.nih.gov>
References: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>
 <0ED4F886-5DA7-408C-A834-E372D8C77564@mail.nih.gov>
 <CAKKNfuJRAayrOtNVZagQtSDfGHLOjDYVyubL6OKUcwjvXWc+TQ@mail.gmail.com>
 <1C0358A6-56D5-4D38-B21F-A875F85E09E3@mail.nih.gov>
Message-ID: <CAKKNfuJuBODVqa3t=jmO30e8H+p-2URBMgxv5U02iKq5Af=bHw@mail.gmail.com>

Thanks Bradley,

So, I did this:

      ImageFileReader imgreader = new ImageFileReader();
            imgreader.SetFileName(path_pacientes + nombre_paciente +
@"\Fusion\" + "resultado.mha");
            itk.simple.Image imgtest = imgreader.Execute();
            ImageSeriesWriter SeriesWriter = new ImageSeriesWriter();
            VectorString vs = new VectorString();
            for (int i=0; i < imgtest.GetSize()[2]; ++i)
            {
                vs.Add("imagen {0}.dcm");
            }

            SeriesWriter.SetFileNames(vs);
            SeriesWriter.Execute(imgtest, vs, false);

And I only get one file name (imagen {0}.dcm), am I missing something? (I
wasn't able to do this: "name {0}.ext".Format(i))

Thanks,

Matias.

On Tue, Mar 24, 2015 at 3:12 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> On Mar 24, 2015, at 1:56 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> //Here's where I struggle...
>             vs.Add(path_pacientes + nombre_paciente +
> @"\Fusion\SalidaTest\imagen%03d.dcm"); //Is this rthe right way to include
> a vector of strings
>
>
>
> No that is not the write way. You actually need to create the list for
> file names. You needs something closer to what's here in the C++ test [1]
> but converted to CSharp. The length of the list must match the z size of
> the images.
>
> Many languages have convenient generator expressions or list
> comprehensions, which seems more natural than C printf formatting and the
> perils associated with it.
>
> The long way to do it is just write a little for loop, something like:
>
> for (i=0; i < img.GetSize()[2], ++i)
> vs.Add( "name {0}.ext".Format(i))
>
> Brad
>
> [1]
> https://github.com/SimpleITK/SimpleITK/blob/master/Testing/Unit/IOTests.cxx#L123-L152
>
>
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From matimontg at gmail.com  Tue Mar 24 17:25:20 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 24 Mar 2015 18:25:20 -0300
Subject: [ITK-users] ImageSeriesWriter | SimpleITK
In-Reply-To: <CAKKNfuJuBODVqa3t=jmO30e8H+p-2URBMgxv5U02iKq5Af=bHw@mail.gmail.com>
References: <CAKKNfu+2244q3pZ=0xriGL=mUJz5HfnopCpsG7=SsBWHU2Uz+A@mail.gmail.com>
 <0ED4F886-5DA7-408C-A834-E372D8C77564@mail.nih.gov>
 <CAKKNfuJRAayrOtNVZagQtSDfGHLOjDYVyubL6OKUcwjvXWc+TQ@mail.gmail.com>
 <1C0358A6-56D5-4D38-B21F-A875F85E09E3@mail.nih.gov>
 <CAKKNfuJuBODVqa3t=jmO30e8H+p-2URBMgxv5U02iKq5Af=bHw@mail.gmail.com>
Message-ID: <CAKKNfuL_KQvEws+KTHR=VcL6FsHuAq70Fs7cGS42GikKx_LvKQ@mail.gmail.com>

Sorry... I figured out:

here's the code that works, I missed to add the images using "i" as the
variable that changes in every iteration as well as specifying the full
path to the directory in the Add method

            ImageFileReader imgreader = new ImageFileReader();
            imgreader.SetFileName(path_pacientes + nombre_paciente +
@"\Fusion\" + "resultado.mha");
            itk.simple.Image imgtest = imgreader.Execute();
            ImageSeriesWriter SeriesWriter = new ImageSeriesWriter();
            VectorString vs = new VectorString();
            for (int i=0; i < imgtest.GetSize()[2]; ++i)
            {
                vs.Add(path_pacientes + nombre_paciente + @"\Fusion\Test\"
+ "imagen" + i + ".dcm");
            }

            SeriesWriter.SetFileNames(vs);

            SeriesWriter.Execute(imgtest, vs, false);

Thanks for all your help!

Matias.

On Tue, Mar 24, 2015 at 6:19 PM, Matias Montroull <matimontg at gmail.com>
wrote:

> Thanks Bradley,
>
> So, I did this:
>
>       ImageFileReader imgreader = new ImageFileReader();
>             imgreader.SetFileName(path_pacientes + nombre_paciente +
> @"\Fusion\" + "resultado.mha");
>             itk.simple.Image imgtest = imgreader.Execute();
>             ImageSeriesWriter SeriesWriter = new ImageSeriesWriter();
>             VectorString vs = new VectorString();
>             for (int i=0; i < imgtest.GetSize()[2]; ++i)
>             {
>                 vs.Add("imagen {0}.dcm");
>             }
>
>             SeriesWriter.SetFileNames(vs);
>             SeriesWriter.Execute(imgtest, vs, false);
>
> And I only get one file name (imagen {0}.dcm), am I missing something? (I
> wasn't able to do this: "name {0}.ext".Format(i))
>
> Thanks,
>
> Matias.
>
> On Tue, Mar 24, 2015 at 3:12 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello,
>>
>> On Mar 24, 2015, at 1:56 PM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>> //Here's where I struggle...
>>             vs.Add(path_pacientes + nombre_paciente +
>> @"\Fusion\SalidaTest\imagen%03d.dcm"); //Is this rthe right way to include
>> a vector of strings
>>
>>
>>
>> No that is not the write way. You actually need to create the list for
>> file names. You needs something closer to what's here in the C++ test [1]
>> but converted to CSharp. The length of the list must match the z size of
>> the images.
>>
>> Many languages have convenient generator expressions or list
>> comprehensions, which seems more natural than C printf formatting and the
>> perils associated with it.
>>
>> The long way to do it is just write a little for loop, something like:
>>
>> for (i=0; i < img.GetSize()[2], ++i)
>> vs.Add( "name {0}.ext".Format(i))
>>
>> Brad
>>
>> [1]
>> https://github.com/SimpleITK/SimpleITK/blob/master/Testing/Unit/IOTests.cxx#L123-L152
>>
>>
>
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From audrey.istace at imavie.fr  Wed Mar 25 03:49:59 2015
From: audrey.istace at imavie.fr (Audrey Istace)
Date: Wed, 25 Mar 2015 07:49:59 +0000
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <CALzTN-QmuHpsFZ9ZiDyZ3X+uO2Xz0g0zb5SSkf+NsoJ1ac53BQ@mail.gmail.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CALzTN-QmuHpsFZ9ZiDyZ3X+uO2Xz0g0zb5SSkf+NsoJ1ac53BQ@mail.gmail.com>
Message-ID: <DBXPR04MB493E31F66AE83836449F5AAE60B0@DBXPR04MB493.eurprd04.prod.outlook.com>

Hi Matt,

Thank you for answering.
I am not sure to understand. Does that mean that I cannot write dicom files using DCMTKImageIO (or any other itk DCMTK class) ?

-----Message d'origine-----
De?: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Envoy??: mardi 24 mars 2015 17:44
??: Audrey Istace
Cc?: insight-users at itk.org
Objet?: Re: [ITK-users] itk - Writing dicom files from single 3D file

Hi,

DCMTKImageIO not serialize or de-serialize DICOM tags to / from its MetaDataDictionaryArray currently like GDCM does.

HTH,
Matt

On Mon, Mar 23, 2015 at 11:11 AM, AI <audrey.istace at imavie.fr> wrote:
> Hello,
>
> I would like to write Dicom files from a nifti image files using 
> DCMTKImageIO. In the code below, I read a nifti file using 
> itkImageFileReader, and then try to write dicom files using 
> itkImageSeriesWriter. I was not able to do it, probably because of the 
> SetMetaDataDictionaryArray method, that I don?t know how to use since 
> I don?t read dicom series as input. Can you help me with that ?
>
> Thank you very much,
>
> Audrey
>
> #include "itkDCMTKImageIO.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageFileReader.h"
> #include "itkImageSeriesWriter.h"
>
> int main(int argc, char *argv[])
> {
>                typedef signed short
> PixelType;
>                const unsigned int
> Dimension = 3;
>                typedef itk::Image< PixelType, Dimension > ImageType;
>                typedef itk::Image< PixelType, 2 > OutputImageType;
>                typedef itk::ImageFileReader< ImageType > ReaderType;
>                typedef itk::DCMTKImageIO ImageIOType;
>                typedef itk::NumericSeriesFileNames NamesGeneratorType;
>                typedef itk::ImageSeriesWriter< ImageType, 
> OutputImageType > WriterType;
>
>                ImageIOType::Pointer dcmtkIO = ImageIOType::New();
>                NamesGeneratorType::Pointer namesGenerator = 
> NamesGeneratorType::New();
>                ReaderType::Pointer reader = ReaderType::New();
>                WriterType::Pointer writer = WriterType::New();
>
>                reader->SetFileName( "../../out.nii" );
>                reader->Update();
>
>
>
>                itksys::SystemTools::MakeDirectory( 
> "../../OutputDicom/" );
>
>                std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
>                namesGenerator->SetSeriesFormat (seriesFormat.c_str());
>                namesGenerator->SetStartIndex (1);
>                namesGenerator->SetEndIndex (166);
>
>
>                writer->SetInput( reader->GetOutput() );
>                writer->SetImageIO( dcmtkIO );
>                writer->SetFileNames( namesGenerator->GetFileNames() );
> //           writer->SetMetaDataDictionaryArray(
> reader->GetMetaDataDictionaryArray() );
>                writer->Update();
> }
>
>
>
>
> --
> View this message in context: 
> http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files
> -from-single-3D-file-tp7587034.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From matt.mccormick at kitware.com  Wed Mar 25 10:02:38 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 25 Mar 2015 10:02:38 -0400
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <DBXPR04MB493E31F66AE83836449F5AAE60B0@DBXPR04MB493.eurprd04.prod.outlook.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CALzTN-QmuHpsFZ9ZiDyZ3X+uO2Xz0g0zb5SSkf+NsoJ1ac53BQ@mail.gmail.com>
 <DBXPR04MB493E31F66AE83836449F5AAE60B0@DBXPR04MB493.eurprd04.prod.outlook.com>
Message-ID: <CALzTN-RUm8nngNrdCK6dwf9TVN7EKQsEDUX+9ndpxvaY+NnOoA@mail.gmail.com>

Hi Audrey,

It means that it is more difficult (than usual) to write DICOM images
with the correct metadata.

HTH,
Matt

On Wed, Mar 25, 2015 at 3:49 AM, Audrey Istace <audrey.istace at imavie.fr> wrote:
> Hi Matt,
>
> Thank you for answering.
> I am not sure to understand. Does that mean that I cannot write dicom files using DCMTKImageIO (or any other itk DCMTK class) ?
>
> -----Message d'origine-----
> De : Matt McCormick [mailto:matt.mccormick at kitware.com]
> Envoy? : mardi 24 mars 2015 17:44
> ? : Audrey Istace
> Cc : insight-users at itk.org
> Objet : Re: [ITK-users] itk - Writing dicom files from single 3D file
>
> Hi,
>
> DCMTKImageIO not serialize or de-serialize DICOM tags to / from its MetaDataDictionaryArray currently like GDCM does.
>
> HTH,
> Matt
>
> On Mon, Mar 23, 2015 at 11:11 AM, AI <audrey.istace at imavie.fr> wrote:
>> Hello,
>>
>> I would like to write Dicom files from a nifti image files using
>> DCMTKImageIO. In the code below, I read a nifti file using
>> itkImageFileReader, and then try to write dicom files using
>> itkImageSeriesWriter. I was not able to do it, probably because of the
>> SetMetaDataDictionaryArray method, that I don?t know how to use since
>> I don?t read dicom series as input. Can you help me with that ?
>>
>> Thank you very much,
>>
>> Audrey
>>
>> #include "itkDCMTKImageIO.h"
>> #include "itkNumericSeriesFileNames.h"
>> #include "itkImageFileReader.h"
>> #include "itkImageSeriesWriter.h"
>>
>> int main(int argc, char *argv[])
>> {
>>                typedef signed short
>> PixelType;
>>                const unsigned int
>> Dimension = 3;
>>                typedef itk::Image< PixelType, Dimension > ImageType;
>>                typedef itk::Image< PixelType, 2 > OutputImageType;
>>                typedef itk::ImageFileReader< ImageType > ReaderType;
>>                typedef itk::DCMTKImageIO ImageIOType;
>>                typedef itk::NumericSeriesFileNames NamesGeneratorType;
>>                typedef itk::ImageSeriesWriter< ImageType,
>> OutputImageType > WriterType;
>>
>>                ImageIOType::Pointer dcmtkIO = ImageIOType::New();
>>                NamesGeneratorType::Pointer namesGenerator =
>> NamesGeneratorType::New();
>>                ReaderType::Pointer reader = ReaderType::New();
>>                WriterType::Pointer writer = WriterType::New();
>>
>>                reader->SetFileName( "../../out.nii" );
>>                reader->Update();
>>
>>
>>
>>                itksys::SystemTools::MakeDirectory(
>> "../../OutputDicom/" );
>>
>>                std::string seriesFormat = "../../OutputDicom/IM%d.dcm";
>>                namesGenerator->SetSeriesFormat (seriesFormat.c_str());
>>                namesGenerator->SetStartIndex (1);
>>                namesGenerator->SetEndIndex (166);
>>
>>
>>                writer->SetInput( reader->GetOutput() );
>>                writer->SetImageIO( dcmtkIO );
>>                writer->SetFileNames( namesGenerator->GetFileNames() );
>> //           writer->SetMetaDataDictionaryArray(
>> reader->GetMetaDataDictionaryArray() );
>>                writer->Update();
>> }
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files
>> -from-single-3D-file-tp7587034.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users

From matimontg at gmail.com  Wed Mar 25 18:17:51 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 25 Mar 2015 19:17:51 -0300
Subject: [ITK-users] SimpleITK | ImagePositionPatient and origins
Message-ID: <CAKKNfuLDeKg4nSPnXkbphYwRyA8FQUtHFcxwTBLWi+aSTsL9Yg@mail.gmail.com>

Hi,

I was testing the new ImageSeriesWriter in the new SimpleITK 0.9 Beta and
for some reason it's not copying the Image Position Patient information
when writing the slices.

any ideas why this happens?

Here's my code:
  ImageFileReader imgreader_resultado = new ImageFileReader();
            imgreader_resultado.SetFileName(path_pacientes +
nombre_paciente + @"\Fusion\" + "resultado.mha");
            itk.simple.Image imgresultado = imgreader_resultado.Execute();
            ImageSeriesWriter SeriesWriter_resultado = new
ImageSeriesWriter();
            VectorString vs_resultado = new VectorString();
            for (int i = 0; i < imgresultado.GetSize()[2]; ++i)
            {
                vs_resultado.Add(path_pacientes + nombre_paciente +
@"\Fusion\Resultado\" + "imagen" + i + ".dcm");
            }

            SeriesWriter_resultado.SetFileNames(vs_resultado);

            if (!Directory.Exists(path_pacientes + nombre_paciente +
@"\Fusion\Resultado")) //Si se abri? el plan y nunca se hizo registraci?n
previamente, se crea el directorio Registraci?n
            {
                Directory.CreateDirectory(path_pacientes + nombre_paciente
+ @"\Fusion\Resultado");
            }

            SeriesWriter_resultado.Execute(imgresultado, vs_resultado,
false);

Thank you,

Matias.
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From JohannesWeber at gmx.at  Thu Mar 26 05:24:22 2015
From: JohannesWeber at gmx.at (JohannesWeber at gmx.at)
Date: Thu, 26 Mar 2015 10:24:22 +0100
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
	value
Message-ID: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>

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From blowekamp at mail.nih.gov  Thu Mar 26 08:36:27 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 26 Mar 2015 08:36:27 -0400
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
	value
In-Reply-To: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
References: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
Message-ID: <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>

Hello,

If you have a 3D image and you are visiting a neighborhood of size 20^3, you are doing 8000 visits per pixel there is no way to make this efficient. You have a big O algorithm problem.

The Neighborhood iterator would be a the more ITK way of doing what you are trying to do [1] [2]. But that's is not the order of efficiency improvement you need.

You need to revise your algorithm so you only visit each pixel once. Perhaps with region growing and queues, or auxiliary images to keep track of the current distance or other data.

Hope that helps,
Brad

[1] http://www.itk.org/Doxygen/html/classitk_1_1NeighborhoodIterator.html
[2] http://itk.org/Wiki/ITK/Examples/Iterators/NeighborhoodIterator

On Mar 26, 2015, at 5:24 AM, JohannesWeber at gmx.at wrote:

> Hello everyone,
>  
> I have the following problem: after calculating the distance map (e.g. with DanielssonDistanceMapImageFilter) I am getting rid of most of the voxels (= setting 0) after calculating a so called distance ridge (kind of a skeleton). Now I want for every voxel of this distance ridge that it is a center voxel for a spherical neighborhood with the radius equal to the distance value of the voxel, and all voxels included in this sphere are set to the distance value of the voxel of the distance ridge (the center voxel of the sphere). So that means the neighborhoods can become big, e.g. radius of 10, or 20 voxels. The problem is here the performance... I implemented it somehow, but the performance nowhere near it should be.
> e.g. going through the image with a neighborhood iterator and vor every voxel bigger than 0 creating a neighborhood with the radius with the distance value of this voxel that seems to take very long alone to create and indexing the neighborhood.
> another approach I tried is to extract all the voxels of the distance ridge, iterate through them and calculate for every ridge voxel the region and iterate through the region doing proper calculations:
>  
> for (int rp = 0; rp < nRidgePoints; rp++)
>     {
>         ImageType::IndexType s1Index;
>         const int i = ridgePointsIndex[0][rp];
>         const int j = ridgePointsIndex[1][rp];
>         const int k = ridgePointsIndex[2][rp];
>         const float r = ridgePointsValues[rp];
> 
>         rSquared = (int) ((r * r) + 0.5f);
>         rInt = (int) r;
>         if(rInt < r) rInt++;
>         iStart = i - rInt;
>         if(iStart < 0) iStart = 0;
>         iStop = i + rInt;
>         if(iStop >= imageSize[0]) iStop = imageSize[0] - 1;
>         jStart = j - rInt;
>         if(jStart < 0) jStart = 0;
>         jStop = j + rInt;
>         if(jStop >= imageSize[1]) jStop = imageSize[1] - 1;
>         kStart = k - rInt;
>         if(kStart < 0) kStart = 0;
>         kStop = k + rInt;
>         if(kStop >= imageSize[2]) kStop = imageSize[2] - 1;
>         ImageType::IndexType index;
>         ImageType::SizeType size;
>         index[0] = iStart;
>         index[1] = jStart;
>         index[2] = kStart;
>         size[0] = iStop - iStart + 1;
>         size[1] = jStop - jStart + 1;
>         size[2] = kStop - kStart + 1;
>         ImageType::RegionType region;
>         region.SetIndex(index);
>         region.SetSize(size);
>         ImageRegionIteratorWithIndexType iteratorWithIndex (distanceRidge, region);
>     
>         for (iteratorWithIndex.GoToBegin(); !iteratorWithIndex.IsAtEnd(); iteratorWithIndex++)
>         {
>             s1Index = iteratorWithIndex.GetIndex();
>             r1SquaredK = (s1Index[0] - i) * (s1Index[0] - i);
>             r1SquaredJK = r1SquaredK + (s1Index[1] - j) * (s1Index[1] - j);
>             if(r1SquaredJK <= rSquared)
>             {
>                 r1Squared = r1SquaredJK + (s1Index[2] - k) * (s1Index[2] - k);
>                 if (r1Squared <= rSquared)
>                 {                    
>                     s1 = iteratorWithIndex.Get();
>                     if (rSquared > s1)
>                     {
>                         iteratorWithIndex.Set(rSquared);                        
>                     }
>                 }               
>             }
>         }
>         
>     }
>  
> so every approach I tried until now is very slow comparing to other implementations of the algorithm I want to do... would maybe spatial objects help me somehow? But I do not really understand how they work...
> thanks for your help!
>  
> greetings,
> Johannes
> _____________________________________
> 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 Mar 26 08:47:13 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 26 Mar 2015 08:47:13 -0400
Subject: [ITK-users] ITK dicom reader wrong spacing
In-Reply-To: <DB3PR02MB10777098396AF26937C7CEBBE080@DB3PR02MB107.eurprd02.prod.outlook.com>
References: <DB3PR02MB107D01405D11A9D546358A4BE000@DB3PR02MB107.eurprd02.prod.outlook.com>
 <CALzTN-Q7Oo8D2-fzGOXGavmzY61FDcqarxm-49PAS2dhJZQ9ww@mail.gmail.com>
 <DB3PR02MB10777098396AF26937C7CEBBE080@DB3PR02MB107.eurprd02.prod.outlook.com>
Message-ID: <CALzTN-QCsq+Z=sLgxOieFM+qa2izcjbRok+9Ki+OPi63+EE5zg@mail.gmail.com>

Hi Aiert,

VolView uses a different, custom method for loading DICOM series than
ITK-SNAP and Slicer.

Spacing in DICOM is tricky -- spacing and spacing-like information is
specified in many different tags. To find the tag that you are looking
for gdcmdump and similar tools can be used to inspect the tags.

HTH,
Matt

On Thu, Mar 26, 2015 at 8:18 AM, Amundarain, Aiert <aamundarain at ceit.es> wrote:
> Hi Matt.
>
> I have tried the solution you suggested but the final result is the same. I tried opening the dicom series in ITK-SNAP and Slicer with similar result. However, Volview loads the DICOM series properly. Do you know the difference among those programs when they load DICOM Series? all the programs are based in ITK.
>
> Thank you
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: jueves, 19 de marzo de 2015 21:20
> To: Amundarain, Aiert
> Cc: Insight-users at itk.org
> Subject: Re: [ITK-users] ITK dicom reader wrong spacing
>
> Hi Aiert,
>
> It is possible to use DCMTK instead of GDCM.  Turn on Module_ITKIODCMTK in your CMake configuration.  See the itkDCMTKSeriesReadImageWriter.cxx test for example usage.
>
> HTH,
> Matt
>
> On Wed, Mar 18, 2015 at 7:43 AM, Amundarain, Aiert <aamundarain at ceit.es> wrote:
>> I have a DICOM Image serie that itk does not read properly. The x,y,z
>> spacing are incorrect and the return value is the default one (1,1,1).
>>
>> If I read this DICOM Image serie using vtk (vtkDICOMImageReader), the
>> reading is correct.
>>
>> Both softwares are developed by kitware but the results are different.
>>
>>
>>
>> Is is possible to read the dicom files using ITK without using the
>> gdcm library?
>>
>>
>>
>> Thank you.
>>
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>

From blowekamp at mail.nih.gov  Thu Mar 26 09:12:28 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 26 Mar 2015 09:12:28 -0400
Subject: [ITK-users] SimpleITK | ImagePositionPatient and origins
In-Reply-To: <CAKKNfuLDeKg4nSPnXkbphYwRyA8FQUtHFcxwTBLWi+aSTsL9Yg@mail.gmail.com>
References: <CAKKNfuLDeKg4nSPnXkbphYwRyA8FQUtHFcxwTBLWi+aSTsL9Yg@mail.gmail.com>
Message-ID: <369AD1DD-ABBC-4F3B-BFD7-0ECAB831EC94@mail.nih.gov>

Hello,

Can you please create a JIRA ticket to track this issue?

https://issues.itk.org/jira/browse/SIMPLEITK

Thank you,
Brad

On Mar 25, 2015, at 6:17 PM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi,
> 
> I was testing the new ImageSeriesWriter in the new SimpleITK 0.9 Beta and for some reason it's not copying the Image Position Patient information when writing the slices.
> 
> any ideas why this happens?
> 
> Here's my code:
>   ImageFileReader imgreader_resultado = new ImageFileReader();
>             imgreader_resultado.SetFileName(path_pacientes + nombre_paciente + @"\Fusion\" + "resultado.mha");
>             itk.simple.Image imgresultado = imgreader_resultado.Execute();
>             ImageSeriesWriter SeriesWriter_resultado = new ImageSeriesWriter();
>             VectorString vs_resultado = new VectorString();
>             for (int i = 0; i < imgresultado.GetSize()[2]; ++i)
>             {
>                 vs_resultado.Add(path_pacientes + nombre_paciente + @"\Fusion\Resultado\" + "imagen" + i + ".dcm");
>             }
> 
>             SeriesWriter_resultado.SetFileNames(vs_resultado);
>             
>             if (!Directory.Exists(path_pacientes + nombre_paciente + @"\Fusion\Resultado")) //Si se abri? el plan y nunca se hizo registraci?n previamente, se crea el directorio Registraci?n
>             {
>                 Directory.CreateDirectory(path_pacientes + nombre_paciente + @"\Fusion\Resultado");
>             }
> 
>             SeriesWriter_resultado.Execute(imgresultado, vs_resultado, false);
> 
> Thank you,
> 
> Matias.
> _____________________________________
> 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 matimontg at gmail.com  Thu Mar 26 09:38:12 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Thu, 26 Mar 2015 10:38:12 -0300
Subject: [ITK-users] SimpleITK | ImagePositionPatient and origins
In-Reply-To: <369AD1DD-ABBC-4F3B-BFD7-0ECAB831EC94@mail.nih.gov>
References: <CAKKNfuLDeKg4nSPnXkbphYwRyA8FQUtHFcxwTBLWi+aSTsL9Yg@mail.gmail.com>
 <369AD1DD-ABBC-4F3B-BFD7-0ECAB831EC94@mail.nih.gov>
Message-ID: <CAKKNfuLC0bjjT5iHtNM8ku6p2ahL+pRQkgSjQTedvsLLX7WnxA@mail.gmail.com>

Hi Brad, I just created a JIRA issue:
https://issues.itk.org/jira/browse/SIMPLEITK-627
Regards,
Matias.

On Thu, Mar 26, 2015 at 10:12 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> Can you please create a JIRA ticket to track this issue?
>
> https://issues.itk.org/jira/browse/SIMPLEITK
>
> Thank you,
> Brad
>
> On Mar 25, 2015, at 6:17 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> > Hi,
> >
> > I was testing the new ImageSeriesWriter in the new SimpleITK 0.9 Beta
> and for some reason it's not copying the Image Position Patient information
> when writing the slices.
> >
> > any ideas why this happens?
> >
> > Here's my code:
> >   ImageFileReader imgreader_resultado = new ImageFileReader();
> >             imgreader_resultado.SetFileName(path_pacientes +
> nombre_paciente + @"\Fusion\" + "resultado.mha");
> >             itk.simple.Image imgresultado =
> imgreader_resultado.Execute();
> >             ImageSeriesWriter SeriesWriter_resultado = new
> ImageSeriesWriter();
> >             VectorString vs_resultado = new VectorString();
> >             for (int i = 0; i < imgresultado.GetSize()[2]; ++i)
> >             {
> >                 vs_resultado.Add(path_pacientes + nombre_paciente +
> @"\Fusion\Resultado\" + "imagen" + i + ".dcm");
> >             }
> >
> >             SeriesWriter_resultado.SetFileNames(vs_resultado);
> >
> >             if (!Directory.Exists(path_pacientes + nombre_paciente +
> @"\Fusion\Resultado")) //Si se abri? el plan y nunca se hizo registraci?n
> previamente, se crea el directorio Registraci?n
> >             {
> >                 Directory.CreateDirectory(path_pacientes +
> nombre_paciente + @"\Fusion\Resultado");
> >             }
> >
> >             SeriesWriter_resultado.Execute(imgresultado, vs_resultado,
> false);
> >
> > Thank you,
> >
> > Matias.
> > _____________________________________
> > 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 mihail.isakov at googlemail.com  Thu Mar 26 15:30:32 2015
From: mihail.isakov at googlemail.com (Mihail Isakov)
Date: Thu, 26 Mar 2015 20:30:32 +0100
Subject: [ITK-users] SimpleITK | ImagePositionPatient and origins
In-Reply-To: <CAKKNfuLC0bjjT5iHtNM8ku6p2ahL+pRQkgSjQTedvsLLX7WnxA@mail.gmail.com>
References: <CAKKNfuLDeKg4nSPnXkbphYwRyA8FQUtHFcxwTBLWi+aSTsL9Yg@mail.gmail.com>
 <369AD1DD-ABBC-4F3B-BFD7-0ECAB831EC94@mail.nih.gov>
 <CAKKNfuLC0bjjT5iHtNM8ku6p2ahL+pRQkgSjQTedvsLLX7WnxA@mail.gmail.com>
Message-ID: <CAJYHnF+kfLTu=4ub_+d8mYqDcXjsDSLE+MbjxZif9aUqP+4mwQ@mail.gmail.com>

Hi, just guessing ... and it is also applicable to many other DICOM
read/write questions here ...There are dozens of DICOM media storage
classes (secondary capture, MR, CT, enhanced MR, US and so on ) and
they have different sets of tags, many of them are conditional, it is
very very complicated with DICOM... so complicated that 100% compliant
files are rare .. most likely by default "secondary capture" is taken
and it doesn't have image postion patient and image orientation
patient... Check 0002|0002 (MediaStorageSOPClassUID) and  0008|0016
(SOPClassUID). To set particular IOD something like this can work
(with GDCM, don't know how does it work with ITK metadata dictionary,
i gave it up and did it with pure GDCM for a while)

gdcm::ImageWriter writer;
gdcm::Image   & image  = writer.GetImage();
gdcm::DataSet & ds = writer.GetFile().GetDataSet();
gdcm::Attribute<0x0008,0x0016, gdcm::VR::UI> asop;
asop.SetValue("1.2.840.10008.5.1.4.1.1.4"); // MR Image IOD Modules
ds.Replace(asop.GetAsDataElement());

without warranty, try to ask GDCM developers and DICOM people

So far GDCM is trying the best to be DICOM correct..


Regards,
Mihail

"1.2.840.10008.1.3.10" , "Basic Directory IOD Modules"
"1.2.840.10008.5.1.4.1.1.1" , "CR Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.1.1" , "Digital X Ray Image IOD Modules" //
DX IOD (see B.5.1.1)
"1.2.840.10008.5.1.4.1.1.1.1.1" , "Digital X Ray Image IOD Modules" //
DX IOD (see B.5.1.1)
"1.2.840.10008.5.1.4.1.1.1.2" , "Digital Mammography X Ray Image IOD
Modules" // (see B.5.1.2)
"1.2.840.10008.5.1.4.1.1.1.2.1" , "Digital Mammography X Ray Image IOD
Modules"// (see B.5.1.2)
"1.2.840.10008.5.1.4.1.1.1.3" , "Digital Intra Oral X Ray Image IOD
Modules" // (see B.5.1.3)
"1.2.840.10008.5.1.4.1.1.1.3.1" , "Digital Intra Oral X Ray Image IOD
Modules" // (see B.5.1.3)
"1.2.840.10008.5.1.4.1.1.2" , "CT Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.2.1" , "Enhanced CT Image IOD Modules" // (see B.5.1.7)
"1.2.840.10008.5.1.4.1.1.3.1" , "US Multi Frame Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.4" , "MR Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.4.1" , "Enhanced MR Image IOD Modules" // (see B.5.1.6)
"1.2.840.10008.5.1.4.1.1.4.2" , "MR Spectroscopy IOD Modules"
"1.2.840.10008.5.1.4.1.1.4.3" , "Enhanced MR Color Image"
"1.2.840.10008.5.1.4.1.1.6.1" , "US Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.6.2" , "Enhanced US Volume"
"1.2.840.10008.5.1.4.1.1.7" , "SC Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.7.1" , "Multi Frame Single Bit SC Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.7.2" , "Multi Frame Grayscale Byte SC Image
IOD Modules"
"1.2.840.10008.5.1.4.1.1.7.3" , "Multi Frame Grayscale Word SC Image
IOD Modules"
"1.2.840.10008.5.1.4.1.1.7.4" , "Multi Frame True Color SC Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.9.1.1" , "12 Lead ECG IOD Modules"
"1.2.840.10008.5.1.4.1.1.9.1.2" , "General ECG IOD Modules"
"1.2.840.10008.5.1.4.1.1.9.1.3" , "Ambulatory ECG IOD Modules"
"1.2.840.10008.5.1.4.1.1.9.2.1" , "Hemodynamic IOD Modules"
"1.2.840.10008.5.1.4.1.1.9.3.1" , "Basic Cardiac EP IOD Modules" //
Cardiac Electrophysiology Waveform
"1.2.840.10008.5.1.4.1.1.9.4.1" , "Basic Voice Audio IOD Modules"
"1.2.840.10008.5.1.4.1.1.9.4.2" , "General Audio Waveform"
"1.2.840.10008.5.1.4.1.1.9.5.1" , "Arterial Pulse Waveform"
"1.2.840.10008.5.1.4.1.1.9.6.1" , "Respiratory Waveform"
"1.2.840.10008.5.1.4.1.1.11.1" , "Grayscale Softcopy Presentation
State IOD Modules"
"1.2.840.10008.5.1.4.1.1.11.2" , "Color Softcopy Presentation State"
"1.2.840.10008.5.1.4.1.1.11.3" , "Pseudo-Color Softcopy Presentation State"
"1.2.840.10008.5.1.4.1.1.11.4" , "Blending Softcopy Presentation State"
"1.2.840.10008.5.1.4.1.1.11.5" , "IOD defined in PS 3.3"
"1.2.840.10008.5.1.4.1.1.12.1" , "X Ray Angiographic Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.12.1.1" , "Enhanced X Ray Angiographic Image
IOD Modules"
"1.2.840.10008.5.1.4.1.1.12.2" , "XRF Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.12.2.1" , "Enhanced X Ray RF Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.13.1.1" , "X Ray 3D Angiographic Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.13.1.2" , "X-Ray 3D Craniofacial Image"
"1.2.840.10008.5.1.4.1.1.13.1.3" , "IOD defined in PS 3.3"
"1.2.840.10008.5.1.4.1.1.20" , "NM Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.66" , "Raw Data IOD Modules"
"1.2.840.10008.5.1.4.1.1.66.1" , "Spatial Registration IOD Modules"
"1.2.840.10008.5.1.4.1.1.66.2" , "Spatial Fiducials IOD Modules"
"1.2.840.10008.5.1.4.1.1.66.3" , "Deformable Spatial Registration"
"1.2.840.10008.5.1.4.1.1.66.4" , "Segmentation IOD Modules"
"1.2.840.10008.5.1.4.1.1.66.5" , "Surface Segmentation"
"1.2.840.10008.5.1.4.1.1.67" , "Real World Value Mapping"
"1.2.840.10008.5.1.4.1.1.77.1.1" , "VL Endoscopic Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.77.1.1.1" , "Video Endoscopic Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.77.1.2" , "VL Microscopic Image"
"1.2.840.10008.5.1.4.1.1.77.1.2.1" , "Video Microscopic Image"
"1.2.840.10008.5.1.4.1.1.77.1.3" , "VL Slide-Coordinates Microscopic Image"
"1.2.840.10008.5.1.4.1.1.77.1.4" , "VL Photographic Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.77.1.4.1" , "Video Photographic Image"
"1.2.840.10008.5.1.4.1.1.77.1.5.1" , "Ophthalmic Photography 8 Bit Image"
"1.2.840.10008.5.1.4.1.1.77.1.5.2" , "Ophthalmic Photography 16 Bit Image"
"1.2.840.10008.5.1.4.1.1.77.1.5.3" , "Stereometric Relationship"
"1.2.840.10008.5.1.4.1.1.77.1.5.4" , "Ophthalmic Tomography Image"
"1.2.840.10008.5.1.4.1.1.78.1" , "Lensometry Measurements"
"1.2.840.10008.5.1.4.1.1.78.2" , "Autorefraction Measurements"
"1.2.840.10008.5.1.4.1.1.78.3" , "Keratometry Measurements"
"1.2.840.10008.5.1.4.1.1.78.4" , "Subjective Refraction Measurements"
"1.2.840.10008.5.1.4.1.1.78.5" , "Visual Acuity Measurements"
"1.2.840.10008.5.1.4.1.1.78.6" , "Spectacle Prescription Report"
"1.2.840.10008.5.1.4.1.1.79.1" , "Macular Grid Thickness and Volume Report"
"1.2.840.10008.5.1.4.1.1.88.11" , "Basic Text SR IOD Modules"
"1.2.840.10008.5.1.4.1.1.88.22" , "Enhanced SR IOD Modules"
"1.2.840.10008.5.1.4.1.1.88.33" , "Comprehensive SR IOD Modules"
"1.2.840.10008.5.1.4.1.1.88.40" , "Procedure Log"
"1.2.840.10008.5.1.4.1.1.88.50" , "Mammography CAD SR IOD Modules"
"1.2.840.10008.5.1.4.1.1.88.59" , "Key Object Selection Document IOD Modules"
"1.2.840.10008.5.1.4.1.1.88.65" , "Chest CAD SR IOD"
"1.2.840.10008.5.1.4.1.1.88.67" , "X Ray Radiation Dose SR IOD Modules"
"1.2.840.10008.5.1.4.1.1.88.69" , "Colon CAD SR IOD"
"1.2.840.10008.5.1.4.1.1.104.1" , "Encapsulated PDF IOD Modules"
"1.2.840.10008.5.1.4.1.1.104.2" , "Encapsulated CDA IOD Modules"
"1.2.840.10008.5.1.4.1.1.128" , "PET Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.130" , "IOD defined in PS 3.3"
"1.2.840.10008.5.1.4.1.1.131" , "Basic Structured Display IOD"
"1.2.840.10008.5.1.4.1.1.481.1" , "RT Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.2" , "RT Dose IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.3" , "RT Structure Set IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.4" , "RT Beams Treatment Record IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.5" , "RT Plan IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.6" , "RT Brachy Treatment Record IOD Modules"
 "1.2.840.10008.5.1.4.1.1.481.7" , "RT Treatment Summary Record IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.8" , "RT Ion Plan IOD Modules"
"1.2.840.10008.5.1.4.1.1.481.9" , "RT Ion Beams Treatment Record IOD Modules"
"1.2.840.10008.5.1.4.38.1" , "Hanging Protocol IOD Modules"
"1.2.840.10008.5.1.4.39.1" , "Color Palette IOD"
// Deprecated:
"1.2.840.10008.3.1.2.3.3" , "Modality Performed Procedure Step IOD Modules"
"1.2.840.10008.5.1.4.1.1.5" , "NM Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.6" , "US Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.3" , "US Multi Frame Image IOD Modules"
"1.2.840.10008.5.1.4.1.1.12.3" , "" // XRayAngiographicBiplaneImageStorage
// private:
 "1.3.12.2.1107.5.9.1" , "Siemens Non-image IOD Modules" // CSA
Non-Image Storage

On Thu, Mar 26, 2015 at 2:38 PM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi Brad, I just created a JIRA issue:
> https://issues.itk.org/jira/browse/SIMPLEITK-627
> Regards,
> Matias.
>
> On Thu, Mar 26, 2015 at 10:12 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>>
>> Hello,
>>
>> Can you please create a JIRA ticket to track this issue?
>>
>> https://issues.itk.org/jira/browse/SIMPLEITK
>>
>> Thank you,
>> Brad
>>
>> On Mar 25, 2015, at 6:17 PM, Matias Montroull <matimontg at gmail.com> wrote:
>>
>> > Hi,
>> >
>> > I was testing the new ImageSeriesWriter in the new SimpleITK 0.9 Beta
>> > and for some reason it's not copying the Image Position Patient information
>> > when writing the slices.
>> >
>> > any ideas why this happens?
>> >
>> > Here's my code:
>> >   ImageFileReader imgreader_resultado = new ImageFileReader();
>> >             imgreader_resultado.SetFileName(path_pacientes +
>> > nombre_paciente + @"\Fusion\" + "resultado.mha");
>> >             itk.simple.Image imgresultado =
>> > imgreader_resultado.Execute();
>> >             ImageSeriesWriter SeriesWriter_resultado = new
>> > ImageSeriesWriter();
>> >             VectorString vs_resultado = new VectorString();
>> >             for (int i = 0; i < imgresultado.GetSize()[2]; ++i)
>> >             {
>> >                 vs_resultado.Add(path_pacientes + nombre_paciente +
>> > @"\Fusion\Resultado\" + "imagen" + i + ".dcm");
>> >             }
>> >
>> >             SeriesWriter_resultado.SetFileNames(vs_resultado);
>> >
>> >             if (!Directory.Exists(path_pacientes + nombre_paciente +
>> > @"\Fusion\Resultado")) //Si se abri? el plan y nunca se hizo registraci?n
>> > previamente, se crea el directorio Registraci?n
>> >             {
>> >                 Directory.CreateDirectory(path_pacientes +
>> > nombre_paciente + @"\Fusion\Resultado");
>> >             }
>> >
>> >             SeriesWriter_resultado.Execute(imgresultado, vs_resultado,
>> > false);
>> >
>> > Thank you,
>> >
>> > Matias.
>> > _____________________________________
>> > 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 richard.beare at gmail.com  Thu Mar 26 17:02:54 2015
From: richard.beare at gmail.com (Richard Beare)
Date: Fri, 27 Mar 2015 08:02:54 +1100
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
	value
In-Reply-To: <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>
References: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
 <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>
Message-ID: <CA+V7QS9VvP--rCTztACp9S51KSDOxdJSjw2hXg1pSW-dMZqV6g@mail.gmail.com>

This isn't a complete solution, but might give you some ideas.

The part about using the skeleton points, which are distance transform
voxels, as the source for the radius, can be implemented using spatially
variant morphology. I have a short publication about doing this efficiently
with parabolic functions. However this doesn't propagate the voxel value,
only producing a mask. I have thought about combining with label dilation,
to propagate a label value, but haven't done it yet.

A queue based approach to something similar is discussed in:
"Labelled reconstruction of binary objects: a vector propagation
algorithm", buckley and lagerstrom

On Thu, Mar 26, 2015 at 11:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> If you have a 3D image and you are visiting a neighborhood of size 20^3,
> you are doing 8000 visits per pixel there is no way to make this efficient.
> You have a big O algorithm problem.
>
> The Neighborhood iterator would be a the more ITK way of doing what you
> are trying to do [1] [2]. But that's is not the order of efficiency
> improvement you need.
>
> You need to revise your algorithm so you only visit each pixel once.
> Perhaps with region growing and queues, or auxiliary images to keep track
> of the current distance or other data.
>
> Hope that helps,
> Brad
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1NeighborhoodIterator.html
> [2] http://itk.org/Wiki/ITK/Examples/Iterators/NeighborhoodIterator
>
> On Mar 26, 2015, at 5:24 AM, JohannesWeber at gmx.at wrote:
>
> Hello everyone,
>
> I have the following problem: after calculating the distance map (e.g.
> with DanielssonDistanceMapImageFilter) I am getting rid of most of the
> voxels (= setting 0) after calculating a so called distance ridge (kind of
> a skeleton). Now I want for every voxel of this distance ridge that it is a
> center voxel for a spherical neighborhood with the radius equal to the
> distance value of the voxel, and all voxels included in this sphere are set
> to the distance value of the voxel of the distance ridge (the center voxel
> of the sphere). So that means the neighborhoods can become big, e.g. radius
> of 10, or 20 voxels. The problem is here the performance... I implemented
> it somehow, but the performance nowhere near it should be.
> e.g. going through the image with a neighborhood iterator and vor every
> voxel bigger than 0 creating a neighborhood with the radius with the
> distance value of this voxel that seems to take very long alone to create
> and indexing the neighborhood.
> another approach I tried is to extract all the voxels of the distance
> ridge, iterate through them and calculate for every ridge voxel the region
> and iterate through the region doing proper calculations:
>
>  for (int rp = 0; rp < nRidgePoints; rp++)
>     {
>         ImageType::IndexType s1Index;
>         const int i = ridgePointsIndex[0][rp];
>         const int j = ridgePointsIndex[1][rp];
>         const int k = ridgePointsIndex[2][rp];
>         const float r = ridgePointsValues[rp];
>
>         rSquared = (int) ((r * r) + 0.5f);
>         rInt = (int) r;
>         if(rInt < r) rInt++;
>         iStart = i - rInt;
>         if(iStart < 0) iStart = 0;
>         iStop = i + rInt;
>         if(iStop >= imageSize[0]) iStop = imageSize[0] - 1;
>         jStart = j - rInt;
>         if(jStart < 0) jStart = 0;
>         jStop = j + rInt;
>         if(jStop >= imageSize[1]) jStop = imageSize[1] - 1;
>         kStart = k - rInt;
>         if(kStart < 0) kStart = 0;
>         kStop = k + rInt;
>         if(kStop >= imageSize[2]) kStop = imageSize[2] - 1;
>         ImageType::IndexType index;
>         ImageType::SizeType size;
>         index[0] = iStart;
>         index[1] = jStart;
>         index[2] = kStart;
>         size[0] = iStop - iStart + 1;
>         size[1] = jStop - jStart + 1;
>         size[2] = kStop - kStart + 1;
>         ImageType::RegionType region;
>         region.SetIndex(index);
>         region.SetSize(size);
>         ImageRegionIteratorWithIndexType iteratorWithIndex (distanceRidge,
> region);
>
>         for (iteratorWithIndex.GoToBegin(); !iteratorWithIndex.IsAtEnd();
> iteratorWithIndex++)
>         {
>             s1Index = iteratorWithIndex.GetIndex();
>             r1SquaredK = (s1Index[0] - i) * (s1Index[0] - i);
>             r1SquaredJK = r1SquaredK + (s1Index[1] - j) * (s1Index[1] - j);
>             if(r1SquaredJK <= rSquared)
>             {
>                 r1Squared = r1SquaredJK + (s1Index[2] - k) * (s1Index[2] -
> k);
>                 if (r1Squared <= rSquared)
>                 {
>                     s1 = iteratorWithIndex.Get();
>                     if (rSquared > s1)
>                     {
>                         iteratorWithIndex.Set(rSquared);
>
>                     }
>                 }
>             }
>         }
>
>     }
>
> so every approach I tried until now is very slow comparing to other
> implementations of the algorithm I want to do... would maybe spatial
> objects help me somehow? But I do not really understand how they work...
> thanks for your help!
>
> greetings,
> Johannes
>  _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From richard.beare at gmail.com  Thu Mar 26 18:47:10 2015
From: richard.beare at gmail.com (Richard Beare)
Date: Fri, 27 Mar 2015 09:47:10 +1100
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
	value
In-Reply-To: <CA+V7QS9VvP--rCTztACp9S51KSDOxdJSjw2hXg1pSW-dMZqV6g@mail.gmail.com>
References: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
 <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>
 <CA+V7QS9VvP--rCTztACp9S51KSDOxdJSjw2hXg1pSW-dMZqV6g@mail.gmail.com>
Message-ID: <CA+V7QS9vrfspjf4zbvhECdy1-YieKYypX7n7M9E5e3-_83Ma1w@mail.gmail.com>

Here's another option - I haven't thought it through completely so could be
far from the mark, but I think it is close.

consider the following:

A - input mask
B - distance transform of mask (positive values inside the mask)
C - ridge lines in B (sort of skeleton)

You are aiming to create an image of spheres, centres on voxels in C, with
size set by the "brightness" at centre location in C.

Suppose you can create the spatially variant dilation by a sphere using the
parabolic tools I mentioned in the previous message - that gives you
another mask:

D - spatially variant dilation of C

Now invert C and take the distance transform to give E.
take a distance transform of D and add to E, then mask by D. The idea here
is that if you add two distance transforms together you end up with a flat
surface, at least in the case where the second DT is computed from peaks in
the first.

The result should be a sort of tube, of varying thickness, where the voxel
value corresponds to the tube thickness (possibly with a uniform offset).
Note that I don't think you will see sphere corresponding to the brightest
skeleton points using this approach, but the result may be useful for your
application.


Also, a couple of notes regarding the direct approach.

If you use neighbourhoods, which is the appropriate ITK structure, then
avoid visiting all voxels with the neighbourhood iterator. Use a standard
single voxel iterator to find the skeleton voxels, then move the
neighbourhood iterator to that location.

There are also some optimizations you can use if you do some checks of the
change in sphere size between neighbours. If the spheres were all
identically sized then it is feasible to construct lists of voxels that are
not in common between neighbouring spheres, and just visit those, which is
a big saving. Much trickier when the sizes aren't the same, but I'd guess
that for a given skeleton there'd be a relatively small number of
combinations of neighbouring sizes.



On Fri, Mar 27, 2015 at 8:02 AM, Richard Beare <richard.beare at gmail.com>
wrote:

> This isn't a complete solution, but might give you some ideas.
>
> The part about using the skeleton points, which are distance transform
> voxels, as the source for the radius, can be implemented using spatially
> variant morphology. I have a short publication about doing this efficiently
> with parabolic functions. However this doesn't propagate the voxel value,
> only producing a mask. I have thought about combining with label dilation,
> to propagate a label value, but haven't done it yet.
>
> A queue based approach to something similar is discussed in:
> "Labelled reconstruction of binary objects: a vector propagation
> algorithm", buckley and lagerstrom
>
> On Thu, Mar 26, 2015 at 11:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
> > wrote:
>
>> Hello,
>>
>> If you have a 3D image and you are visiting a neighborhood of size 20^3,
>> you are doing 8000 visits per pixel there is no way to make this efficient.
>> You have a big O algorithm problem.
>>
>> The Neighborhood iterator would be a the more ITK way of doing what you
>> are trying to do [1] [2]. But that's is not the order of efficiency
>> improvement you need.
>>
>> You need to revise your algorithm so you only visit each pixel once.
>> Perhaps with region growing and queues, or auxiliary images to keep track
>> of the current distance or other data.
>>
>> Hope that helps,
>> Brad
>>
>> [1] http://www.itk.org/Doxygen/html/classitk_1_1NeighborhoodIterator.html
>> [2] http://itk.org/Wiki/ITK/Examples/Iterators/NeighborhoodIterator
>>
>> On Mar 26, 2015, at 5:24 AM, JohannesWeber at gmx.at wrote:
>>
>> Hello everyone,
>>
>> I have the following problem: after calculating the distance map (e.g.
>> with DanielssonDistanceMapImageFilter) I am getting rid of most of the
>> voxels (= setting 0) after calculating a so called distance ridge (kind of
>> a skeleton). Now I want for every voxel of this distance ridge that it is a
>> center voxel for a spherical neighborhood with the radius equal to the
>> distance value of the voxel, and all voxels included in this sphere are set
>> to the distance value of the voxel of the distance ridge (the center voxel
>> of the sphere). So that means the neighborhoods can become big, e.g. radius
>> of 10, or 20 voxels. The problem is here the performance... I implemented
>> it somehow, but the performance nowhere near it should be.
>> e.g. going through the image with a neighborhood iterator and vor every
>> voxel bigger than 0 creating a neighborhood with the radius with the
>> distance value of this voxel that seems to take very long alone to create
>> and indexing the neighborhood.
>> another approach I tried is to extract all the voxels of the distance
>> ridge, iterate through them and calculate for every ridge voxel the region
>> and iterate through the region doing proper calculations:
>>
>>  for (int rp = 0; rp < nRidgePoints; rp++)
>>     {
>>         ImageType::IndexType s1Index;
>>         const int i = ridgePointsIndex[0][rp];
>>         const int j = ridgePointsIndex[1][rp];
>>         const int k = ridgePointsIndex[2][rp];
>>         const float r = ridgePointsValues[rp];
>>
>>         rSquared = (int) ((r * r) + 0.5f);
>>         rInt = (int) r;
>>         if(rInt < r) rInt++;
>>         iStart = i - rInt;
>>         if(iStart < 0) iStart = 0;
>>         iStop = i + rInt;
>>         if(iStop >= imageSize[0]) iStop = imageSize[0] - 1;
>>         jStart = j - rInt;
>>         if(jStart < 0) jStart = 0;
>>         jStop = j + rInt;
>>         if(jStop >= imageSize[1]) jStop = imageSize[1] - 1;
>>         kStart = k - rInt;
>>         if(kStart < 0) kStart = 0;
>>         kStop = k + rInt;
>>         if(kStop >= imageSize[2]) kStop = imageSize[2] - 1;
>>         ImageType::IndexType index;
>>         ImageType::SizeType size;
>>         index[0] = iStart;
>>         index[1] = jStart;
>>         index[2] = kStart;
>>         size[0] = iStop - iStart + 1;
>>         size[1] = jStop - jStart + 1;
>>         size[2] = kStop - kStart + 1;
>>         ImageType::RegionType region;
>>         region.SetIndex(index);
>>         region.SetSize(size);
>>         ImageRegionIteratorWithIndexType iteratorWithIndex
>> (distanceRidge, region);
>>
>>         for (iteratorWithIndex.GoToBegin(); !iteratorWithIndex.IsAtEnd();
>> iteratorWithIndex++)
>>         {
>>             s1Index = iteratorWithIndex.GetIndex();
>>             r1SquaredK = (s1Index[0] - i) * (s1Index[0] - i);
>>             r1SquaredJK = r1SquaredK + (s1Index[1] - j) * (s1Index[1] -
>> j);
>>             if(r1SquaredJK <= rSquared)
>>             {
>>                 r1Squared = r1SquaredJK + (s1Index[2] - k) * (s1Index[2]
>> - k);
>>                 if (r1Squared <= rSquared)
>>                 {
>>                     s1 = iteratorWithIndex.Get();
>>                     if (rSquared > s1)
>>                     {
>>                         iteratorWithIndex.Set(rSquared);
>>
>>                     }
>>                 }
>>             }
>>         }
>>
>>     }
>>
>> so every approach I tried until now is very slow comparing to other
>> implementations of the algorithm I want to do... would maybe spatial
>> objects help me somehow? But I do not really understand how they work...
>> thanks for your help!
>>
>> greetings,
>> Johannes
>>  _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From matt.mccormick at kitware.com  Fri Mar 27 00:43:51 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 27 Mar 2015 00:43:51 -0400
Subject: [ITK-users] Updated Gerrit Code Review!
Message-ID: <CALzTN-T+AMw-8RGe1c5Owi0pZuHh1O7CLtmwjzEHz+kc_GU=Rg@mail.gmail.com>

As previously noted, we now have an updated Gerrit Code Review instance!  See

  http://review.source.kitware.com

This was a major upgrade from version 2.2.2 to version 2.10.1.


This update was required for a change in authentication mechanism. Our
Gerrit instance previously only had support for OpenID authentication.
However, Google has dropped support for OpenID.

The updated instance uses GitHub OAuth2 authentication. Community
members now login with their GitHub account [1]. If an existing user's
GitHub account has one of their email addresses registered with their
previous Gerrit account, their old Gerrit account will automatically
be associated with their GitHub login.

In the future, we will also add support for patch submission via
GitHub pull requests.


The upgraded Gerrit instance also bring brings many new features.
Here are some highlights:

- There is a new user interface. When existing users log in, they will
be presented with the option to stay with the old user interface or
migrate to the new user interface. Interface choice can be changed in
Settings -> Preferences. The new interface contains a number of
usability and presentation improvements. For example, it is now easier
to see and step through patches in a branch.

- There are now a number of ways to download a change including patch
files and archives. Note that the "Checkout" line has changed slightly
in that it checks out 'FETCH_HEAD' instead of a named branch with '-b
topic-name'. It is still possible to modify the line pasted in your
terminal by replacing 'FETCH_HEAD' with '-b topic-name'. This new
default prevents the proliferation of branches in a reviewer's
repository and it prevents confusion of new reviewers when they try to
checkout a branch with the same name as an existing branch.

- A number of new preferences are available for the diff view.

- There are many other user interface enhancements.


We have also greatly improved how our patch robots builds occur and
their capabilities. This will be discussed in another thread.


To discuss more about Gerrit and learn more about how to participate
in ITK, join us tomorrow on the Hangout [2]

[1] http://www.itk.org/Wiki/ITK/Git/Account

[2]  https://plus.google.com/u/1/events/cv779d1fdghhko68eef25a9e30c

From audrey.istace at imavie.fr  Fri Mar 27 08:57:18 2015
From: audrey.istace at imavie.fr (AI)
Date: Fri, 27 Mar 2015 05:57:18 -0700 (MST)
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <CALzTN-RUm8nngNrdCK6dwf9TVN7EKQsEDUX+9ndpxvaY+NnOoA@mail.gmail.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CALzTN-QmuHpsFZ9ZiDyZ3X+uO2Xz0g0zb5SSkf+NsoJ1ac53BQ@mail.gmail.com>
 <DBXPR04MB493E31F66AE83836449F5AAE60B0@DBXPR04MB493.eurprd04.prod.outlook.com>
 <CALzTN-RUm8nngNrdCK6dwf9TVN7EKQsEDUX+9ndpxvaY+NnOoA@mail.gmail.com>
Message-ID: <1427461038272-7587063.post@n2.nabble.com>

Hi Matt,

I saw in the source code that MetaData was not handled at all in
itkDCMTKImageIO, whereas it is handled in itkGDCMImageIO. Is that why I
can't write dicom files with DCMTK as easily as I can using GDCM ?

Do you know if itkDCMTKImageIO will be improved in future itk versions ?

Thank you,

Audrey



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itk-Writing-dicom-files-from-single-3D-file-tp7587034p7587063.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Fri Mar 27 09:33:34 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 27 Mar 2015 09:33:34 -0400
Subject: [ITK-users] possible to get a closest-point map from a distance
	map in ITK?
In-Reply-To: <CA+V7QS8aOwcWnK3s8ZPCUEJgHiMjq5Q0oKPW+ia4qY_9F3Ng5g@mail.gmail.com>
References: <22EC75E8215562428ACADFA35877A25A26187E3F@JANEWAY.ts.odu.edu>
 <CA+V7QS_c146Vz_wO9+Do+qFAhCeWPFjJXEVUWTH=i5PPOEJ1cw@mail.gmail.com>
 <564311ED-2E71-4B12-919B-C36B78084AF8@mail.nih.gov>
 <CA+V7QS8aOwcWnK3s8ZPCUEJgHiMjq5Q0oKPW+ia4qY_9F3Ng5g@mail.gmail.com>
Message-ID: <A590A3D8-E582-4067-8A6A-FFA7DD918590@mail.nih.gov>

Hello,

Sorry for the delay in following up with this!

Here is some information about how to create a module for your code:
http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/ConstructITKModule/index.html

Please note that for a remote module it should not begin with the "ITK" prefix. Here is also some policy related info to:
http://www.itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules

Please let us know if you need help. I think many people would appreciate getting easier access to these advanced morphology algorithms.

Brad

On Mar 4, 2015, at 3:19 PM, Richard Beare <richard.beare at gmail.com> wrote:

> Good thought - I haven't looked into that. Is it easy to do? My ITK efforts are lagging due to lack of time at present, I'm afraid.
> 
> On Thu, Mar 5, 2015 at 1:30 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Richard,
> 
> You have some nice additional morphological filters in those repositories. I have been meaning to give them a try.
> 
> Given that you have Insight Journal articles for them, have you considered making them more readily available to the community by adding and converting them into Remote modules for ITK?
> 
> Brad
> 
> On Mar 2, 2015, at 3:37 PM, Richard Beare <richard.beare at gmail.com> wrote:
> 
>> I've written a set of label erosion and dilation filters that might do what you're after. I've also got some spatially varying morphology filters, but have't put them on the insight journal. The label erode dilate filters aren't outputing the distance map, so they aren't exactly what you want, but they use the same kind of computation internally. Thus you could use them in conjunction with the parabolic distance transforms to get labels and distances.
>> 
>> https://github.com/richardbeare/LabelErodeDilate.git
>> https://github.com/richardbeare/parabolicMorphology.git
>> 
>> The insight journal article.
>> 
>> http://hdl.handle.net/10380/3399
>> 
>> 
>> I can provide more details about the spatially variant stuff if it is of interest. Note that it only works with binary images, and simply weights the input image.
>> 
>> On Tue, Mar 3, 2015 at 6:45 AM, Audette, Michel A. <maudette at odu.edu> wrote:
>> Dear ITK users,
>> 
>>  
>> a student of mine would like to use the ITK implementation of distance maps in a way where the point label of the closest initial boundary is propagated throughout, i.e. a closest boundary point map. Is there something like this implemented already in ITK? I would like to use something like this to produce a spatially varying distance threshold.
>> 
>>  
>> Thanks for your kind support.
>> 
>>  
>> Michel
>> 
>>  
>> Michel Audette, Ph.D.
>> Assistant Professor,
>> Department of Modeling, Simulation and Visualization Engineering,
>> Old Dominion University,
>> Norfolk, VA.
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

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From matt.mccormick at kitware.com  Fri Mar 27 09:59:51 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 27 Mar 2015 09:59:51 -0400
Subject: [ITK-users] itk - Writing dicom files from single 3D file
In-Reply-To: <1427461038272-7587063.post@n2.nabble.com>
References: <1427123473731-7587034.post@n2.nabble.com>
 <CALzTN-QmuHpsFZ9ZiDyZ3X+uO2Xz0g0zb5SSkf+NsoJ1ac53BQ@mail.gmail.com>
 <DBXPR04MB493E31F66AE83836449F5AAE60B0@DBXPR04MB493.eurprd04.prod.outlook.com>
 <CALzTN-RUm8nngNrdCK6dwf9TVN7EKQsEDUX+9ndpxvaY+NnOoA@mail.gmail.com>
 <1427461038272-7587063.post@n2.nabble.com>
Message-ID: <CALzTN-QGn8fKMcqjAcNVWyxC1+jD4GMpY+vUiLkEscR72qPrZQ@mail.gmail.com>

Hi Audrey,

> I saw in the source code that MetaData was not handled at all in
> itkDCMTKImageIO, whereas it is handled in itkGDCMImageIO. Is that why I
> can't write dicom files with DCMTK as easily as I can using GDCM ?

Yes.

> Do you know if itkDCMTKImageIO will be improved in future itk versions ?

There are not any active plans of which I am aware. However,
contributions are welcome [1].

Thanks,
Matt

[1] http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html

From seidel at cvrti.utah.edu  Fri Mar 27 10:16:12 2015
From: seidel at cvrti.utah.edu (Thomas Seidel)
Date: Fri, 27 Mar 2015 08:16:12 -0600
Subject: [ITK-users] How to Calculate Hessian Matrix from Gradient Image?
Message-ID: <D13AC24C.B38C7%seidel@cvrti.utah.edu>

Hi all,

I would like to calculate the hessian matrix and get an output of type
SymmetricSecondRankTensor pixel from a gradient image.

The irk HessianRecursiveGaussianImageFilter uses as input an intensity
image.
However, I would like to implement a method for vessel detection based on
the following algorithm:

1. GradientImageFilter
2. GradientVectorFlowImageFilter
3. get the hessian Matrix from 2. (this is my problem)
4. Hessian3DToVesselnessImageFilter


How can I get from the vector field in 2. to the hessian matrix I need for
3.?

Thanks for your help,
Thomas


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From blowekamp at mail.nih.gov  Fri Mar 27 11:02:46 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 27 Mar 2015 11:02:46 -0400
Subject: [ITK-users] How to Calculate Hessian Matrix from Gradient Image?
In-Reply-To: <D13AC24C.B38C7%seidel@cvrti.utah.edu>
References: <D13AC24C.B38C7%seidel@cvrti.utah.edu>
Message-ID: <99977733-F928-4D49-AF1D-F86EDA34612D@mail.nih.gov>

Hello,

I don't think there is going to be anything turnkey to do what you want.

I'd looking to writing a custom filter for this specialized task. You can either base it off the the HessianRecursiveGaussianImageFilter [1] , which utilizes filters per-component and adaptors.

Or do a discrite approach along the lines of something I have done here [2]. 

Hope that helps,
Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/1ce0e5dd3b2d9c7a7a9353dfb8b728ada8d71320/Modules/Filtering/ImageFeature/include/itkHessianRecursiveGaussianImageFilter.hxx#L187-L368
[2] https://github.com/blowekamp/itkLocalDiscreteHessian/blob/30aa775494c20eaf9e085781ae233e0511773758/include/itkHessianImageFilter.hxx#L132-L174

On Mar 27, 2015, at 10:16 AM, Thomas Seidel <seidel at cvrti.utah.edu> wrote:

> Hi all,
> 
> I would like to calculate the hessian matrix and get an output of type SymmetricSecondRankTensor pixel from a gradient image.
> 
> The irk HessianRecursiveGaussianImageFilter uses as input an intensity image.
> However, I would like to implement a method for vessel detection based on the following algorithm:
> 
> 1. GradientImageFilter
> 2. GradientVectorFlowImageFilter
> 3. get the hessian Matrix from 2. (this is my problem)
> 4. Hessian3DToVesselnessImageFilter
> 
> 
> How can I get from the vector field in 2. to the hessian matrix I need for 3.?
> 
> Thanks for your help,
> Thomas
> _____________________________________
> 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  Fri Mar 27 15:24:21 2015
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Fri, 27 Mar 2015 19:24:21 +0000
Subject: [ITK-users] NLM Pill Image Recognition - Request for Information
Message-ID: <D13B26A4.1D69%yanivz@mail.nih.gov>

Dear colleagues,

Please excuse this slightly off topic mail.

I would like to bring to your attention the following request for information which may be of interest to some in the community.

The National Library of Medicine (NLM) has issued a call for participation in a Pill Image Recognition (PIR) Request for Information (RFI). Unidentified and misidentified prescription pills present challenges for individuals and professionals. Unidentified pills can be found by family members, health professionals, educators, and law enforcement. The nine out of 10 US citizens over age 65 who take more than one prescription pill can be prone to misidentifying those pills. This PIR RFI is a pilot for a forthcoming PIR Challenge whose goal is to develop smart phone apps that individuals can use to take pictures of prescription pills and then search for and retrieve pill images and associated data of likely matches in an NLM database. NLM anticipates that respondents will include professionals and students, individually or in teams, in computer vision and computer graphics working on content-based image retrieval.

Instructions for responding to the RFI are at http://pir.nlm.nih.gov/pilot/instructions.html

The deadline for submissions to this RFI is Friday, May 15, 2015.

Questions and comments are welcome at pir at nlm.nih.gov.

     best regards
          Ziv

--
Ziv Yaniv, PhD,
Office of High Performance Computing and Communications
National Library of Medicine
National Institutes of Health
Bldg. 38A, Room B1N30D
8600 Rockville Pike,
Bethesda, MD, 20894
Phone:+1-301-435-6633
Email: zivyaniv at nih.gov


From wumengda at gmail.com  Fri Mar 27 22:45:28 2015
From: wumengda at gmail.com (Wei Xiong)
Date: Sat, 28 Mar 2015 03:45:28 +0100
Subject: [ITK-users] from: Wei Xiong
Message-ID: <BE7126AD-C5FA-4C74-A8E9-4B5D79EB74D6@nixvoip.com.br>

Hi


http://ARMOIRIES-BOIS.COM/hunt.php?greatest=y68cvbe7b7pzkc





wumengda at gmail.com

Sent from my iPhone

From matimontg at gmail.com  Sat Mar 28 08:57:00 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 28 Mar 2015 09:57:00 -0300
Subject: [ITK-users] SimpleITK | chnage Window Levels on an image
Message-ID: <CAKKNfuK5bxyPtGOTEyC0iWR5Ao7YBGnf-EfKvbadsp1QUjscfQ@mail.gmail.com>

Hi,

I would like to change the window width and window center of an image using
ITK.

I guess it may be simple but I can't find the filter that would do that.

Thanks,

Matias.
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From zivrafael.yaniv at nih.gov  Sat Mar 28 10:47:50 2015
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Sat, 28 Mar 2015 14:47:50 +0000
Subject: [ITK-users] SimpleITK | chnage Window Levels on an image
In-Reply-To: <CAKKNfuK5bxyPtGOTEyC0iWR5Ao7YBGnf-EfKvbadsp1QUjscfQ@mail.gmail.com>
References: <CAKKNfuK5bxyPtGOTEyC0iWR5Ao7YBGnf-EfKvbadsp1QUjscfQ@mail.gmail.com>
Message-ID: <B2DE09A5824F4746A0528DAB608EF520018383B9@msgb10.nih.gov>

The filter is:

itk::IntensityWindowingImageFilter


         Ziv
________________________________
From: Matias Montroull [matimontg at gmail.com]
Sent: Saturday, March 28, 2015 8:57 AM
To: insight-users at itk.org Users
Subject: [ITK-users] SimpleITK | chnage Window Levels on an image

Hi,

I would like to change the window width and window center of an image using ITK.

I guess it may be simple but I can't find the filter that would do that.

Thanks,

Matias.

From matimontg at gmail.com  Sat Mar 28 10:55:18 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 28 Mar 2015 11:55:18 -0300
Subject: [ITK-users] SimpleITK | chnage Window Levels on an image
In-Reply-To: <B2DE09A5824F4746A0528DAB608EF520018383B9@msgb10.nih.gov>
References: <CAKKNfuK5bxyPtGOTEyC0iWR5Ao7YBGnf-EfKvbadsp1QUjscfQ@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF520018383B9@msgb10.nih.gov>
Message-ID: <CAKKNfu+0tAgWO43U1e9FLT6-fTs1E_StJ+d1ADoS3rgx4Q1StA@mail.gmail.com>

Thanks Yaniv,

So if I would like to set the Levels of an image to let's say: WC 120 and
WW 40, how should I use the variables below to do so?

  filter->SetWindowMinimum(?);
  filter->SetWindowMaximum(?);

I guess the above sentence just defines the range of the levels and
not the actual level


Thank you,


Matias.


On Sat, Mar 28, 2015 at 11:47 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
zivrafael.yaniv at nih.gov> wrote:

> The filter is:
>
> itk::IntensityWindowingImageFilter
>
>
>          Ziv
> ________________________________
> From: Matias Montroull [matimontg at gmail.com]
> Sent: Saturday, March 28, 2015 8:57 AM
> To: insight-users at itk.org Users
> Subject: [ITK-users] SimpleITK | chnage Window Levels on an image
>
> Hi,
>
> I would like to change the window width and window center of an image
> using ITK.
>
> I guess it may be simple but I can't find the filter that would do that.
>
> Thanks,
>
> Matias.
>
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From zivrafael.yaniv at nih.gov  Sat Mar 28 11:22:32 2015
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Sat, 28 Mar 2015 15:22:32 +0000
Subject: [ITK-users] SimpleITK | chnage Window Levels on an image
In-Reply-To: <CAKKNfu+0tAgWO43U1e9FLT6-fTs1E_StJ+d1ADoS3rgx4Q1StA@mail.gmail.com>
References: <CAKKNfuK5bxyPtGOTEyC0iWR5Ao7YBGnf-EfKvbadsp1QUjscfQ@mail.gmail.com>
 <B2DE09A5824F4746A0528DAB608EF520018383B9@msgb10.nih.gov>,
 <CAKKNfu+0tAgWO43U1e9FLT6-fTs1E_StJ+d1ADoS3rgx4Q1StA@mail.gmail.com>
Message-ID: <B2DE09A5824F4746A0528DAB608EF520018383D2@msgb10.nih.gov>

My understanding is that you want to set the window and level. You can do this directly using the SetWindowLevel method:

http://www.itk.org/Doxygen/html/classitk_1_1IntensityWindowingImageFilter.html#ad99d5bd667dd23391ff3e2b2db1ce92d

      Ziv

________________________________
From: Matias Montroull [matimontg at gmail.com]
Sent: Saturday, March 28, 2015 10:55 AM
To: Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
Cc: insight-users at itk.org Users
Subject: Re: [ITK-users] SimpleITK | chnage Window Levels on an image

Thanks Yaniv,

So if I would like to set the Levels of an image to let's say: WC 120 and WW 40, how should I use the variables below to do so?


  filter->SetWindowMinimum(?);
  filter->SetWindowMaximum(?);


I guess the above sentence just defines the range of the levels and not the actual level


Thank you,


Matias.

On Sat, Mar 28, 2015 at 11:47 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov<mailto:zivrafael.yaniv at nih.gov>> wrote:
The filter is:

itk::IntensityWindowingImageFilter


         Ziv
________________________________
From: Matias Montroull [matimontg at gmail.com<mailto:matimontg at gmail.com>]
Sent: Saturday, March 28, 2015 8:57 AM
To: insight-users at itk.org<mailto:insight-users at itk.org> Users
Subject: [ITK-users] SimpleITK | chnage Window Levels on an image

Hi,

I would like to change the window width and window center of an image using ITK.

I guess it may be simple but I can't find the filter that would do that.

Thanks,

Matias.


From gabrielgimenez85 at gmail.com  Sat Mar 28 19:09:59 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Sat, 28 Mar 2015 16:09:59 -0700 (MST)
Subject: [ITK-users] Resample and Directions in Image Registration
Message-ID: <1427584199821-7587074.post@n2.nabble.com>

Hello everyone,
I am confused with some concepts ...

In the munual (version 4.6) of ITK it is mentioned about ResamplingFilter
(page 129):

*"Probably the most important thing to keep in mind when resampling images
is that the transform
is used to map points from the output image space into the input image
space."*

This mean that the parameters are passed to filter mapped points from the
output image to the input image, right?

Then in the chapter about registration mentioned (page 174) :

*"The Transform that is optimized in the ITK registration framework is the
one that maps points
from the physical space of the fixed image into the physical space of the
moving image"*

This indicates that the transformation parameters mapped points from the
fixed image to moving image ( In the example ?Hello World Registration" this
is observed ), right ? 

During the resampling, at the end of registration for the resulting image,
this is done:

*resampler->SetTransform( registration->GetOutput()->Get() );*

*Why this? should not be pass to the filter the opposite transformation?*

I've read much... but I still very confusing concepts like these...
(physical spaces, grid/pixel spaces, directions of the transformations,
etc...)

Thanks in advance ...









--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Resample-and-Directions-in-Image-Registration-tp7587074.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From lluna.nova at gmail.com  Sat Mar 28 19:44:14 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Sun, 29 Mar 2015 00:44:14 +0100
Subject: [ITK-users] itk and const-correctness
Message-ID: <CALAZn4gkYYvbx1Z0MZOH6L79bsGR4b2cx+B4TL83Mj4pxP7WNg@mail.gmail.com>

Hello all,

What is the preferred way to achieve const-correctness in ITK?

I've stumbled with this 2010 post:
http://itk-insight-users.2283740.n2.nabble.com/itk-SmartPointer-problem-making-code-const-correct-td5109890.html

which suggests using raw pointers as arguments and pass ::Pointer in
practice. Like the first function of
http://www.itk.org/Wiki/ITK/Examples/Utilities/PassImageToFunction with

  myStandardPointer(image);


Is that still the case in 2014?

Cheers,

Pol
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From blowekamp at mail.nih.gov  Sat Mar 28 22:49:23 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Sat, 28 Mar 2015 22:49:23 -0400
Subject: [ITK-users] itk and const-correctness
In-Reply-To: <CALAZn4gkYYvbx1Z0MZOH6L79bsGR4b2cx+B4TL83Mj4pxP7WNg@mail.gmail.com>
References: <CALAZn4gkYYvbx1Z0MZOH6L79bsGR4b2cx+B4TL83Mj4pxP7WNg@mail.gmail.com>
Message-ID: <041919CE-D608-4D99-B7EC-2FA83841E278@mail.nih.gov>

Hello Pol,

I don't think anything has changed on this front [1]. So this is still the case for 2014 and 2015. ITK's style is to be more explicit with conversions than implicit and this is consistent with that philosophy.

Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkSmartPointer.h

On Mar 28, 2015, at 7:44 PM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:

> Hello all,
> 
> What is the preferred way to achieve const-correctness in ITK?
> 
> I've stumbled with this 2010 post: http://itk-insight-users.2283740.n2.nabble.com/itk-SmartPointer-problem-making-code-const-correct-td5109890.html
> 
> which suggests using raw pointers as arguments and pass ::Pointer in practice. Like the first function of http://www.itk.org/Wiki/ITK/Examples/Utilities/PassImageToFunction with 
>   myStandardPointer(image);
> 
> Is that still the case in 2014? 
> 
> Cheers,
> 
> Pol
> 
>  
> _____________________________________
> 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  Sun Mar 29 10:47:02 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 29 Mar 2015 10:47:02 -0400
Subject: [ITK-users] Resample and Directions in Image Registration
In-Reply-To: <1427584199821-7587074.post@n2.nabble.com>
References: <1427584199821-7587074.post@n2.nabble.com>
Message-ID: <CALzTN-SjQF9eg9sSkZXQ7p5HJE8sDCfckkOyeNKqv4KSN8Ewmw@mail.gmail.com>

Hi Gabriel,

> In the munual (version 4.6) of ITK it is mentioned about ResamplingFilter
> (page 129):
>
> *"Probably the most important thing to keep in mind when resampling images
> is that the transform
> is used to map points from the output image space into the input image
> space."*
>
> This mean that the parameters are passed to filter mapped points from the
> output image to the input image, right?

Correct.

> Then in the chapter about registration mentioned (page 174) :
>
> *"The Transform that is optimized in the ITK registration framework is the
> one that maps points
> from the physical space of the fixed image into the physical space of the
> moving image"*
>
> This indicates that the transformation parameters mapped points from the
> fixed image to moving image ( In the example ?Hello World Registration" this
> is observed ), right ?

Yes. These are consistent. The resampled output image is sampled on
the grid of points in physical space where the fixed image is sampled.

HTH,
Matt

From gabrielgimenez85 at gmail.com  Sun Mar 29 17:25:58 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Sun, 29 Mar 2015 14:25:58 -0700 (MST)
Subject: [ITK-users] Resample and Directions in Image Registration
In-Reply-To: <CALzTN-SjQF9eg9sSkZXQ7p5HJE8sDCfckkOyeNKqv4KSN8Ewmw@mail.gmail.com>
References: <1427584199821-7587074.post@n2.nabble.com>
 <CALzTN-SjQF9eg9sSkZXQ7p5HJE8sDCfckkOyeNKqv4KSN8Ewmw@mail.gmail.com>
Message-ID: <1427664358535-7587078.post@n2.nabble.com>

Hi Matt, thanks for your answer...It is now clear to me ...

Matt! another question please ... what is the normal runtime of Mattes
Mutual Information Metric with 3D images? It is normal to be in the range of
2.5 to 4 seconds? I use CT and MR images ... and this is my configuration:

samplingPercentage = 0.002;
samplingStrategy  = RegistrationType::REGULAR;
NumberOfHistogramBins = 50 

thank you very much!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Resample-and-Directions-in-Image-Registration-tp7587074p7587078.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Sun Mar 29 18:07:09 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 29 Mar 2015 18:07:09 -0400
Subject: [ITK-users] Resample and Directions in Image Registration
In-Reply-To: <1427664358535-7587078.post@n2.nabble.com>
References: <1427584199821-7587074.post@n2.nabble.com>
 <CALzTN-SjQF9eg9sSkZXQ7p5HJE8sDCfckkOyeNKqv4KSN8Ewmw@mail.gmail.com>
 <1427664358535-7587078.post@n2.nabble.com>
Message-ID: <CALzTN-SmhSTnAcirM3+760fSXSm+3VJeVUaKtrFCfnabhsVCqA@mail.gmail.com>

Hi Gabriel,

> Hi Matt, thanks for your answer...It is now clear to me ...

Great!

> Matt! another question please ... what is the normal runtime of Mattes
> Mutual Information Metric with 3D images? It is normal to be in the range of
> 2.5 to 4 seconds? I use CT and MR images ... and this is my configuration:
>
> samplingPercentage = 0.002;
> samplingStrategy  = RegistrationType::REGULAR;
> NumberOfHistogramBins = 50

I do not know offhand what the expected computation time is, but I
would not be surprised if it was that slow on 3D images.

Matt

From JohannesWeber at gmx.at  Mon Mar 30 03:51:42 2015
From: JohannesWeber at gmx.at (Johannes Weber)
Date: Mon, 30 Mar 2015 09:51:42 +0200
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
 value
In-Reply-To: <CA+V7QS9vrfspjf4zbvhECdy1-YieKYypX7n7M9E5e3-_83Ma1w@mail.gmail.com>
References: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
 <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>
 <CA+V7QS9VvP--rCTztACp9S51KSDOxdJSjw2hXg1pSW-dMZqV6g@mail.gmail.com>,
 <CA+V7QS9vrfspjf4zbvhECdy1-YieKYypX7n7M9E5e3-_83Ma1w@mail.gmail.com>
Message-ID: <trinity-6290c9a7-cd86-4d67-a57d-b1c5be14a1e5-1427701901996@3capp-gmx-bs54>

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From richard.beare at gmail.com  Mon Mar 30 04:52:03 2015
From: richard.beare at gmail.com (Richard Beare)
Date: Mon, 30 Mar 2015 19:52:03 +1100
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
 value
In-Reply-To: <trinity-6290c9a7-cd86-4d67-a57d-b1c5be14a1e5-1427701901996@3capp-gmx-bs54>
References: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
 <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>
 <CA+V7QS9VvP--rCTztACp9S51KSDOxdJSjw2hXg1pSW-dMZqV6g@mail.gmail.com>
 <CA+V7QS9vrfspjf4zbvhECdy1-YieKYypX7n7M9E5e3-_83Ma1w@mail.gmail.com>
 <trinity-6290c9a7-cd86-4d67-a57d-b1c5be14a1e5-1427701901996@3capp-gmx-bs54>
Message-ID: <CA+V7QS_EkiJvPiggdv+ddf=cQ4v5wj7Jga=4ejSySuDRsquYqA@mail.gmail.com>

I guess the obvious common traps need to be checked - confirm you are in
Release mode. Things like neighbourhood iterators can be very expensive in
debug mode. Also, the neighbourhood iterator will be doing some sort of
edge of image safety check, which your other code may not be doing (I
haven't checked). The neighbourhood iterator isn't, I guess, really
designed to be resized every time it is used. Normally you set it up once
and apply it lots of times. I've no clue as to how expensive the
initialisation is, but it may pay to keep a structure containing iterators
that you've already allocated so that you can pick the right one and move
it.

It may turn out that the design is really bad for your problem, with
performance being destroyed by the creation phase, that isn't an issue in
the normal use case. Continuing to use it will give you edge safety and
dimension independence, but I guess you'll need to address the issue of
initialization by being clever about the reuse of iterators.

One way to do that would be to use a pass to record the location and value
of all of the skeleton points, sort them by brightness, then visit in order
so that neighbourhoods can be reused without resizing. This assumes, of
course that the skeletons contain much fewer voxels than the image.


On Mon, Mar 30, 2015 at 6:51 PM, Johannes Weber <JohannesWeber at gmx.at>
wrote:

> thank you for your answers!
>
> I tried out following idea of yours: "If you use neighbourhoods, which is
> the appropriate ITK structure, then avoid visiting all voxels with the
> neighbourhood iterator. Use a standard single voxel iterator to find the
> skeleton voxels, then move the neighbourhood iterator to that location."
> this is fast until I use the SetRadius method of the neighborhood
> iterator... it goes up form about 2 seconds to 1 minute.
>  for(iterator.GoToBegin(); !iterator.IsAtEnd(); iterator++)
>     {
>         if(iterator.Get() > 0)
>         {
>             neighborhoodIterator.SetLocation(iterator.GetIndex());
>             radius.Fill( (int) iterator.Get());
>             neighborhoodIterator.SetRadius(radius);
>         }
>     }
>
> Than I implemented what I want to do by direct accessing the image array:
> float * imgArray = distanceRidge->GetBufferPointer();
>
> and for every ridge point (value > 0) in the image I go through the
> desired region with 3 for loops:
>
>  for (int i1 = iStart; i1 <= iStop; i1++)
>         {
>             r1SquaredK = (i1 - i) * (i1 - i);
>             for (int j1 = jStart; j1 <= jStop; j1++)
>             {
>                 r1SquaredJK = r1SquaredK + (j1 - j) * (j1 - j);
>                 if(r1SquaredJK <= rSquared)
>                 {
>                     for (int k1 = kStart; k1 <= kStop; k1++)
>                     {
>                         r1Squared = r1SquaredJK + (k1 - k) * (k1 - k);
>                         if (r1Squared <= rSquared)
>                         {
>                             s1 = imgArray[i1 + imageSize[0] * (j1 +
> imageSize[1] * k1)];
>                             if(rSquared > s1)
>                             {
>                                 imgArray[i1 + imageSize[0] * (j1 +
> imageSize[1] * k1)] = rSquared;
>                             }
>                         }
>                     }
>                 }
>             }
>         }
>
> and this works fine! and it is really fast! with this approach I am
> getting there where I want to be.
> I am doing the same with the neighborhood iterator, or I also tried out
> doing it with a image region iterator and instead of going through the
> desired region with 3 for loops I always set the region of the iterator
> (see my first email).
> So what I am asking myself is now, if it is so much faster using directly
> the flat array where the image data is saved... is it also a proper way to
> do it like this? and is there a different way of implementing this, which
> is as fast as with flat array but using iterators from ITK or other
> functions/options from ITK?
>
> *Gesendet:* Freitag, 27. M?rz 2015 um 00:47 Uhr
> *Von:* "Richard Beare" <richard.beare at gmail.com>
> *An:* Richard.Beare at ieee.org
> *Cc:* "Johannes Weber" <JohannesWeber at gmx.at>, "Insight Users" <
> insight-users at itk.org>
> *Betreff:* Re: [ITK-users] setting big spherical neighborhoods to center
> voxel value
>        Here's another option - I haven't thought it through completely so
> could be far from the mark, but I think it is close.
>
> consider the following:
>
>  A - input mask
> B - distance transform of mask (positive values inside the mask)
> C - ridge lines in B (sort of skeleton)
>
> You are aiming to create an image of spheres, centres on voxels in C, with
> size set by the "brightness" at centre location in C.
>
> Suppose you can create the spatially variant dilation by a sphere using
> the parabolic tools I mentioned in the previous message - that gives you
> another mask:
>
> D - spatially variant dilation of C
>
> Now invert C and take the distance transform to give E.
> take a distance transform of D and add to E, then mask by D. The idea here
> is that if you add two distance transforms together you end up with a flat
> surface, at least in the case where the second DT is computed from peaks in
> the first.
>
> The result should be a sort of tube, of varying thickness, where the voxel
> value corresponds to the tube thickness (possibly with a uniform offset).
> Note that I don't think you will see sphere corresponding to the brightest
> skeleton points using this approach, but the result may be useful for your
> application.
>
>
> Also, a couple of notes regarding the direct approach.
>
> If you use neighbourhoods, which is the appropriate ITK structure, then
> avoid visiting all voxels with the neighbourhood iterator. Use a standard
> single voxel iterator to find the skeleton voxels, then move the
> neighbourhood iterator to that location.
>
>
>  There are also some optimizations you can use if you do some checks of
> the change in sphere size between neighbours. If the spheres were all
> identically sized then it is feasible to construct lists of voxels that are
> not in common between neighbouring spheres, and just visit those, which is
> a big saving. Much trickier when the sizes aren't the same, but I'd guess
> that for a given skeleton there'd be a relatively small number of
> combinations of neighbouring sizes.
>
>
>
> On Fri, Mar 27, 2015 at 8:02 AM, Richard Beare <richard.beare at gmail.com>
> wrote:
>>
>> This isn't a complete solution, but might give you some ideas.
>>
>> The part about using the skeleton points, which are distance transform
>> voxels, as the source for the radius, can be implemented using spatially
>> variant morphology. I have a short publication about doing this efficiently
>> with parabolic functions. However this doesn't propagate the voxel value,
>> only producing a mask. I have thought about combining with label dilation,
>> to propagate a label value, but haven't done it yet.
>>
>> A queue based approach to something similar is discussed in:
>> "Labelled reconstruction of binary objects: a vector propagation
>> algorithm", buckley and lagerstrom
>>
>> On Thu, Mar 26, 2015 at 11:36 PM, Bradley Lowekamp <
>> blowekamp at mail.nih.gov> wrote:
>>>
>>> Hello,
>>>
>>> If you have a 3D image and you are visiting a neighborhood of size 20^3,
>>> you are doing 8000 visits per pixel there is no way to make this efficient.
>>> You have a big O algorithm problem.
>>>
>>> The Neighborhood iterator would be a the more ITK way of doing what you
>>> are trying to do [1] [2]. But that's is not the order of efficiency
>>> improvement you need.
>>>
>>> You need to revise your algorithm so you only visit each pixel once.
>>> Perhaps with region growing and queues, or auxiliary images to keep track
>>> of the current distance or other data.
>>>
>>> Hope that helps,
>>> Brad
>>>
>>> [1]
>>> http://www.itk.org/Doxygen/html/classitk_1_1NeighborhoodIterator.html
>>> [2] http://itk.org/Wiki/ITK/Examples/Iterators/NeighborhoodIterator
>>>
>>> On Mar 26, 2015, at 5:24 AM, JohannesWeber at gmx.at wrote:
>>>
>>>
>>>  Hello everyone,
>>>
>>> I have the following problem: after calculating the distance map (e.g.
>>> with DanielssonDistanceMapImageFilter) I am getting rid of most of the
>>> voxels (= setting 0) after calculating a so called distance ridge (kind of
>>> a skeleton). Now I want for every voxel of this distance ridge that it is a
>>> center voxel for a spherical neighborhood with the radius equal to the
>>> distance value of the voxel, and all voxels included in this sphere are set
>>> to the distance value of the voxel of the distance ridge (the center voxel
>>> of the sphere). So that means the neighborhoods can become big, e.g. radius
>>> of 10, or 20 voxels. The problem is here the performance... I implemented
>>> it somehow, but the performance nowhere near it should be.
>>> e.g. going through the image with a neighborhood iterator and vor every
>>> voxel bigger than 0 creating a neighborhood with the radius with the
>>> distance value of this voxel that seems to take very long alone to create
>>> and indexing the neighborhood.
>>> another approach I tried is to extract all the voxels of the distance
>>> ridge, iterate through them and calculate for every ridge voxel the region
>>> and iterate through the region doing proper calculations:
>>>
>>>  for (int rp = 0; rp < nRidgePoints; rp++)
>>>     {
>>>         ImageType::IndexType s1Index;
>>>         const int i = ridgePointsIndex[0][rp];
>>>         const int j = ridgePointsIndex[1][rp];
>>>         const int k = ridgePointsIndex[2][rp];
>>>         const float r = ridgePointsValues[rp];
>>>
>>>         rSquared = (int) ((r * r) + 0.5f);
>>>         rInt = (int) r;
>>>         if(rInt < r) rInt++;
>>>         iStart = i - rInt;
>>>         if(iStart < 0) iStart = 0;
>>>         iStop = i + rInt;
>>>         if(iStop >= imageSize[0]) iStop = imageSize[0] - 1;
>>>         jStart = j - rInt;
>>>         if(jStart < 0) jStart = 0;
>>>         jStop = j + rInt;
>>>         if(jStop >= imageSize[1]) jStop = imageSize[1] - 1;
>>>         kStart = k - rInt;
>>>         if(kStart < 0) kStart = 0;
>>>         kStop = k + rInt;
>>>         if(kStop >= imageSize[2]) kStop = imageSize[2] - 1;
>>>         ImageType::IndexType index;
>>>         ImageType::SizeType size;
>>>         index[0] = iStart;
>>>         index[1] = jStart;
>>>         index[2] = kStart;
>>>         size[0] = iStop - iStart + 1;
>>>         size[1] = jStop - jStart + 1;
>>>         size[2] = kStop - kStart + 1;
>>>         ImageType::RegionType region;
>>>         region.SetIndex(index);
>>>         region.SetSize(size);
>>>         ImageRegionIteratorWithIndexType iteratorWithIndex
>>> (distanceRidge, region);
>>>
>>>         for (iteratorWithIndex.GoToBegin();
>>> !iteratorWithIndex.IsAtEnd(); iteratorWithIndex++)
>>>         {
>>>             s1Index = iteratorWithIndex.GetIndex();
>>>             r1SquaredK = (s1Index[0] - i) * (s1Index[0] - i);
>>>             r1SquaredJK = r1SquaredK + (s1Index[1] - j) * (s1Index[1] -
>>> j);
>>>             if(r1SquaredJK <= rSquared)
>>>             {
>>>                 r1Squared = r1SquaredJK + (s1Index[2] - k) * (s1Index[2]
>>> - k);
>>>                 if (r1Squared <= rSquared)
>>>                 {
>>>                     s1 = iteratorWithIndex.Get();
>>>                     if (rSquared > s1)
>>>                     {
>>>                         iteratorWithIndex.Set(rSquared);
>>>
>>>                     }
>>>                 }
>>>             }
>>>         }
>>>
>>>     }
>>>
>>> so every approach I tried until now is very slow comparing to other
>>> implementations of the algorithm I want to do... would maybe spatial
>>> objects help me somehow? But I do not really understand how they work...
>>> thanks for your help!
>>>
>>> greetings,
>>> Johannes
>>>   _____________________________________
>>> 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 grothausmann.roman at mh-hannover.de  Mon Mar 30 05:25:25 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 30 Mar 2015 11:25:25 +0200
Subject: [ITK-users] automated splitting and pasting of volumes for use in
	external programs
In-Reply-To: <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
 <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
 <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
Message-ID: <55191685.9020706@mh-hannover.de>

Dear mailing list members,


A dataset I work on is too big to load completely into itksnap for manual 
adjustment of the automatic pre-segementation with watersheds. The full 
resolution is needed, so I cannot work with a re-sampled version. The only 
possible easy solution I see at the moment is to split up the 3D image into 
smaller blocks of sizes as equal as possible, do the itsnap interaction, and 
finally paste all blocks of the resulting segmentation back together.
Would itkImageRegionSplitterMultidimensional be the right filter for the 
splitting of blocks as equal in size as possible?
Is there a "logger" like e.g. itkXMLFileOutputWindow (as used in 
itkStreamingImageFilterTest2.cxx) that could be used to store the regions 
corresponding to each block-file to use that for itkPasteImageFilter to combine 
these blocks later again?
Not needed now, but perhaps lager: Is there some nice way to handle overlaps in 
this case that is already implemented in itk, something like 
itkImageRegionSplitterMultidimensional::SetOverlap()?

Many thanks for any help or hints.
Roman

On 17/03/15 18:13, Pol Mons? Purt? wrote:
> I guess the way to go would be to take the splitter (probably
> ImageRegionSplitterMultidimensional now that I look at it) and extend it to
> support overlap. If I do it, I'll let you know in case it is of interest to
> anyone. For now I'll stick to my class.


-- 
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. +49 511 532-9574

From lluna.nova at gmail.com  Mon Mar 30 05:50:39 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Mon, 30 Mar 2015 11:50:39 +0200
Subject: [ITK-users] registering ROI
Message-ID: <CALAZn4jNC9BTg0wXcgpribtd9jqRHcnDcP5_koZtdXddB9cE_w@mail.gmail.com>

Hello all,

tl; dr

How can I reset the index of two labelObjects' bounding box generated from
a ROIExtractor output to the original image's LargestPossibleRegion()
coordinate system?

--

I need to apply a series of (non-itk) operations on a ShapeLabelObject
present in a small ROI of the image with the purpose of dividing it in two.
I was using ROI filter because among other things I want the Indexes to be
referred to the ROI so it is less complex to refer to the voxels'
coordinates.

But afterwards I need the original Index so that the GetBoundingBox() of
the two generated label objects returns a region that refers to the
original image repectively, while maintaining the size (probably index
offset shift) of the new labelobject.

I could do as for now and store the roi and then do something like
(roi.getIndex() + obj->GetBoudingBox().GetIndex() ) to create a shifted
bounding box, but maybe there is a better way to do it, as read in the
documentation:

The origin coordinates of the output images will be computed in such a way
that if mapped to physical space, the output image will overlay the input
image with perfect registration. In other words, a registration process
between the output image and the input image will return an identity
transform.

So how could I remap to the original "physical space"? I don't know to what
does that phrase refer to, but it sounds like it's exactly what I am trying
to do.

I've looked into SetRequestedRegion also as an alternative, but that would
not give me indexes relative to roi, so I would have to substract them
right before the operations, which might be an option too, but I believe
things get complicated if I do that.

Cheers,

Pol
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From blowekamp at mail.nih.gov  Mon Mar 30 07:15:19 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 30 Mar 2015 07:15:19 -0400
Subject: [ITK-users] [ITK]  registering ROI
In-Reply-To: <CALAZn4jNC9BTg0wXcgpribtd9jqRHcnDcP5_koZtdXddB9cE_w@mail.gmail.com>
References: <CALAZn4jNC9BTg0wXcgpribtd9jqRHcnDcP5_koZtdXddB9cE_w@mail.gmail.com>
Message-ID: <B997F0A8-1591-4B64-8A3D-8391CB693954@mail.nih.gov>

Hello,

Since you have done the ROI extraction with ITK, then the physical location of each pixel has been maintained. Use the ROI Image's TransformIndexToPhysicalPoint method[1], then use your original image's TransformPhysicalPointToIndex method[2]. This would be the most generalized and robust method which the documentation refers too. You could use it to validate your optimized approach.

Yes, alternatively you can use the RegionOfInterestImageFilter ( I believe ) to extract a region which has a non-zero starting index, and is the same indexing and the input image. Alternatively you can use the pipeline and rely on the streaming to produce the regions, but then you have to deal with the fact that the buffered region is different than the largest possible region. There are many possibilities on what to do here.

Hope that helps,
Brad

[1] http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#ab003313ba1a078d89a832dc0a35d2efa
[2] http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25

On Mar 30, 2015, at 5:50 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:

> Hello all,
> 
> tl; dr
> 
> How can I reset the index of two labelObjects' bounding box generated from a ROIExtractor output to the original image's LargestPossibleRegion() coordinate system?
> 
> --
> 
> I need to apply a series of (non-itk) operations on a ShapeLabelObject present in a small ROI of the image with the purpose of dividing it in two. I was using ROI filter because among other things I want the Indexes to be referred to the ROI so it is less complex to refer to the voxels' coordinates.
> 
> But afterwards I need the original Index so that the GetBoundingBox() of the two generated label objects returns a region that refers to the original image repectively, while maintaining the size (probably index offset shift) of the new labelobject.
> 
> I could do as for now and store the roi and then do something like (roi.getIndex() + obj->GetBoudingBox().GetIndex() ) to create a shifted bounding box, but maybe there is a better way to do it, as read in the documentation:
> 
> The origin coordinates of the output images will be computed in such a way that if mapped to physical space, the output image will overlay the input image with perfect registration. In other words, a registration process between the output image and the input image will return an identity transform.
> 
> So how could I remap to the original "physical space"? I don't know to what does that phrase refer to, but it sounds like it's exactly what I am trying to do.
> 
> I've looked into SetRequestedRegion also as an alternative, but that would not give me indexes relative to roi, so I would have to substract them right before the operations, which might be an option too, but I believe things get complicated if I do that.
> 
> Cheers,
> 
> Pol
> 
> 
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From blowekamp at mail.nih.gov  Mon Mar 30 09:06:55 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 30 Mar 2015 09:06:55 -0400
Subject: [ITK-users] setting big spherical neighborhoods to center voxel
	value
In-Reply-To: <CA+V7QS_EkiJvPiggdv+ddf=cQ4v5wj7Jga=4ejSySuDRsquYqA@mail.gmail.com>
References: <trinity-96d7d929-9773-4fee-ade0-a844c457fe58-1427361862740@3capp-gmx-bs36>
 <6E34D00A-F187-4E5E-A2E4-6F490D8CE87C@mail.nih.gov>
 <CA+V7QS9VvP--rCTztACp9S51KSDOxdJSjw2hXg1pSW-dMZqV6g@mail.gmail.com>
 <CA+V7QS9vrfspjf4zbvhECdy1-YieKYypX7n7M9E5e3-_83Ma1w@mail.gmail.com>
 <trinity-6290c9a7-cd86-4d67-a57d-b1c5be14a1e5-1427701901996@3capp-gmx-bs54>
 <CA+V7QS_EkiJvPiggdv+ddf=cQ4v5wj7Jga=4ejSySuDRsquYqA@mail.gmail.com>
Message-ID: <4F13082D-A19A-4BF2-B720-9418E39C2510@mail.nih.gov>

Hello,

Yes please check the obvious things first.

Recently I had similar requirements for an algorithm; I needed to iterate over a sparse set of neighborhoods. I ended up creating ImageScanlineImageIterators for each neighborhood. You may want to try the approach here [1] ( apologize of not having more comments there). If it works for you, I'd be quite interested if the performance comparison.

HTH,
Brad


[1] https://github.com/blowekamp/itkSuperPixel/blob/d63741c87067376f0a1e5651a7f96964974c724b/include/itkSLICImageFilter.hxx#L238-L277


On Mar 30, 2015, at 4:52 AM, Richard Beare <richard.beare at gmail.com> wrote:

> I guess the obvious common traps need to be checked - confirm you are in Release mode. Things like neighbourhood iterators can be very expensive in debug mode. Also, the neighbourhood iterator will be doing some sort of edge of image safety check, which your other code may not be doing (I haven't checked). The neighbourhood iterator isn't, I guess, really designed to be resized every time it is used. Normally you set it up once and apply it lots of times. I've no clue as to how expensive the initialisation is, but it may pay to keep a structure containing iterators that you've already allocated so that you can pick the right one and move it.
> 
> It may turn out that the design is really bad for your problem, with performance being destroyed by the creation phase, that isn't an issue in the normal use case. Continuing to use it will give you edge safety and dimension independence, but I guess you'll need to address the issue of initialization by being clever about the reuse of iterators.
> 
> One way to do that would be to use a pass to record the location and value of all of the skeleton points, sort them by brightness, then visit in order so that neighbourhoods can be reused without resizing. This assumes, of course that the skeletons contain much fewer voxels than the image.
> 
> 
> On Mon, Mar 30, 2015 at 6:51 PM, Johannes Weber <JohannesWeber at gmx.at> wrote:
> thank you for your answers!
>  
> I tried out following idea of yours: "If you use neighbourhoods, which is the appropriate ITK structure, then avoid visiting all voxels with the neighbourhood iterator. Use a standard single voxel iterator to find the skeleton voxels, then move the neighbourhood iterator to that location."
> this is fast until I use the SetRadius method of the neighborhood iterator... it goes up form about 2 seconds to 1 minute.
> for(iterator.GoToBegin(); !iterator.IsAtEnd(); iterator++)
>     {
>         if(iterator.Get() > 0)
>         {
>             neighborhoodIterator.SetLocation(iterator.GetIndex());
>             radius.Fill( (int) iterator.Get());
>             neighborhoodIterator.SetRadius(radius);
>         }
>     }
>  
> Than I implemented what I want to do by direct accessing the image array:
> float * imgArray = distanceRidge->GetBufferPointer();
>  
> and for every ridge point (value > 0) in the image I go through the desired region with 3 for loops:
>  
> for (int i1 = iStart; i1 <= iStop; i1++)
>         {
>             r1SquaredK = (i1 - i) * (i1 - i);
>             for (int j1 = jStart; j1 <= jStop; j1++)
>             {
>                 r1SquaredJK = r1SquaredK + (j1 - j) * (j1 - j);
>                 if(r1SquaredJK <= rSquared)
>                 {
>                     for (int k1 = kStart; k1 <= kStop; k1++)
>                     {                       
>                         r1Squared = r1SquaredJK + (k1 - k) * (k1 - k);
>                         if (r1Squared <= rSquared)
>                         {                            
>                             s1 = imgArray[i1 + imageSize[0] * (j1 + imageSize[1] * k1)];
>                             if(rSquared > s1)
>                             {
>                                 imgArray[i1 + imageSize[0] * (j1 + imageSize[1] * k1)] = rSquared;                                
>                             }                            
>                         }
>                     }
>                 }
>             }            
>         }
>  
> and this works fine! and it is really fast! with this approach I am getting there where I want to be.
> I am doing the same with the neighborhood iterator, or I also tried out doing it with a image region iterator and instead of going through the desired region with 3 for loops I always set the region of the iterator (see my first email).
> So what I am asking myself is now, if it is so much faster using directly the flat array where the image data is saved... is it also a proper way to do it like this? and is there a different way of implementing this, which is as fast as with flat array but using iterators from ITK or other functions/options from ITK?
>  
> Gesendet: Freitag, 27. M?rz 2015 um 00:47 Uhr
> Von: "Richard Beare" <richard.beare at gmail.com>
> An: Richard.Beare at ieee.org
> Cc: "Johannes Weber" <JohannesWeber at gmx.at>, "Insight Users" <insight-users at itk.org>
> Betreff: Re: [ITK-users] setting big spherical neighborhoods to center voxel value
> Here's another option - I haven't thought it through completely so could be far from the mark, but I think it is close.
>  
> consider the following:
>  
> A - input mask
> B - distance transform of mask (positive values inside the mask)
> C - ridge lines in B (sort of skeleton)
>  
> You are aiming to create an image of spheres, centres on voxels in C, with size set by the "brightness" at centre location in C.
>  
> Suppose you can create the spatially variant dilation by a sphere using the parabolic tools I mentioned in the previous message - that gives you another mask:
>  
> D - spatially variant dilation of C
>  
> Now invert C and take the distance transform to give E.
> take a distance transform of D and add to E, then mask by D. The idea here is that if you add two distance transforms together you end up with a flat surface, at least in the case where the second DT is computed from peaks in the first. 
>  
> The result should be a sort of tube, of varying thickness, where the voxel value corresponds to the tube thickness (possibly with a uniform offset). Note that I don't think you will see sphere corresponding to the brightest skeleton points using this approach, but the result may be useful for your application.
> 
>  
> Also, a couple of notes regarding the direct approach.
>  
> If you use neighbourhoods, which is the appropriate ITK structure, then avoid visiting all voxels with the neighbourhood iterator. Use a standard single voxel iterator to find the skeleton voxels, then move the neighbourhood iterator to that location.
>  
>  
> There are also some optimizations you can use if you do some checks of the change in sphere size between neighbours. If the spheres were all identically sized then it is feasible to construct lists of voxels that are not in common between neighbouring spheres, and just visit those, which is a big saving. Much trickier when the sizes aren't the same, but I'd guess that for a given skeleton there'd be a relatively small number of combinations of neighbouring sizes.
>  
>  
>  
> On Fri, Mar 27, 2015 at 8:02 AM, Richard Beare <richard.beare at gmail.com> wrote:
> This isn't a complete solution, but might give you some ideas.
>  
> The part about using the skeleton points, which are distance transform voxels, as the source for the radius, can be implemented using spatially variant morphology. I have a short publication about doing this efficiently with parabolic functions. However this doesn't propagate the voxel value, only producing a mask. I have thought about combining with label dilation, to propagate a label value, but haven't done it yet.
>  
> A queue based approach to something similar is discussed in:
> "Labelled reconstruction of binary objects: a vector propagation algorithm", buckley and lagerstrom 
>  
> On Thu, Mar 26, 2015 at 11:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
>  
> If you have a 3D image and you are visiting a neighborhood of size 20^3, you are doing 8000 visits per pixel there is no way to make this efficient. You have a big O algorithm problem.
>  
> The Neighborhood iterator would be a the more ITK way of doing what you are trying to do [1] [2]. But that's is not the order of efficiency improvement you need.
>  
> You need to revise your algorithm so you only visit each pixel once. Perhaps with region growing and queues, or auxiliary images to keep track of the current distance or other data.
>  
> Hope that helps,
> Brad
>  
> [1] http://www.itk.org/Doxygen/html/classitk_1_1NeighborhoodIterator.html
> [2] http://itk.org/Wiki/ITK/Examples/Iterators/NeighborhoodIterator
>  
> On Mar 26, 2015, at 5:24 AM, JohannesWeber at gmx.at wrote:
>  
> Hello everyone,
>  
> I have the following problem: after calculating the distance map (e.g. with DanielssonDistanceMapImageFilter) I am getting rid of most of the voxels (= setting 0) after calculating a so called distance ridge (kind of a skeleton). Now I want for every voxel of this distance ridge that it is a center voxel for a spherical neighborhood with the radius equal to the distance value of the voxel, and all voxels included in this sphere are set to the distance value of the voxel of the distance ridge (the center voxel of the sphere). So that means the neighborhoods can become big, e.g. radius of 10, or 20 voxels. The problem is here the performance... I implemented it somehow, but the performance nowhere near it should be.
> e.g. going through the image with a neighborhood iterator and vor every voxel bigger than 0 creating a neighborhood with the radius with the distance value of this voxel that seems to take very long alone to create and indexing the neighborhood.
> another approach I tried is to extract all the voxels of the distance ridge, iterate through them and calculate for every ridge voxel the region and iterate through the region doing proper calculations:
>  
> for (int rp = 0; rp < nRidgePoints; rp++)
>     {
>         ImageType::IndexType s1Index;
>         const int i = ridgePointsIndex[0][rp];
>         const int j = ridgePointsIndex[1][rp];
>         const int k = ridgePointsIndex[2][rp];
>         const float r = ridgePointsValues[rp];
> 
>         rSquared = (int) ((r * r) + 0.5f);
>         rInt = (int) r;
>         if(rInt < r) rInt++;
>         iStart = i - rInt;
>         if(iStart < 0) iStart = 0;
>         iStop = i + rInt;
>         if(iStop >= imageSize[0]) iStop = imageSize[0] - 1;
>         jStart = j - rInt;
>         if(jStart < 0) jStart = 0;
>         jStop = j + rInt;
>         if(jStop >= imageSize[1]) jStop = imageSize[1] - 1;
>         kStart = k - rInt;
>         if(kStart < 0) kStart = 0;
>         kStop = k + rInt;
>         if(kStop >= imageSize[2]) kStop = imageSize[2] - 1;
>         ImageType::IndexType index;
>         ImageType::SizeType size;
>         index[0] = iStart;
>         index[1] = jStart;
>         index[2] = kStart;
>         size[0] = iStop - iStart + 1;
>         size[1] = jStop - jStart + 1;
>         size[2] = kStop - kStart + 1;
>         ImageType::RegionType region;
>         region.SetIndex(index);
>         region.SetSize(size);
>         ImageRegionIteratorWithIndexType iteratorWithIndex (distanceRidge, region);
>     
>         for (iteratorWithIndex.GoToBegin(); !iteratorWithIndex.IsAtEnd(); iteratorWithIndex++)
>         {
>             s1Index = iteratorWithIndex.GetIndex();
>             r1SquaredK = (s1Index[0] - i) * (s1Index[0] - i);
>             r1SquaredJK = r1SquaredK + (s1Index[1] - j) * (s1Index[1] - j);
>             if(r1SquaredJK <= rSquared)
>             {
>                 r1Squared = r1SquaredJK + (s1Index[2] - k) * (s1Index[2] - k);
>                 if (r1Squared <= rSquared)
>                 {                    
>                     s1 = iteratorWithIndex.Get();
>                     if (rSquared > s1)
>                     {
>                         iteratorWithIndex.Set(rSquared);                        
>                     }
>                 }               
>             }
>         }
>         
>     }
>  
> so every approach I tried until now is very slow comparing to other implementations of the algorithm I want to do... would maybe spatial objects help me somehow? But I do not really understand how they work...
> thanks for your help!
>  
> greetings,
> Johannes
> _____________________________________
> 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 lluna.nova at gmail.com  Mon Mar 30 09:53:20 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Mon, 30 Mar 2015 15:53:20 +0200
Subject: [ITK-users] [ITK]  registering ROI
In-Reply-To: <B997F0A8-1591-4B64-8A3D-8391CB693954@mail.nih.gov>
References: <CALAZn4jNC9BTg0wXcgpribtd9jqRHcnDcP5_koZtdXddB9cE_w@mail.gmail.com>
 <B997F0A8-1591-4B64-8A3D-8391CB693954@mail.nih.gov>
Message-ID: <CALAZn4i4nTcVWWyUsU3Von=MX=NVL8J0xwxQLsRaQ_Kog9hSSA@mail.gmail.com>

Hello Bradley,

Great, I'll try out the first approach you suggested.

Alternativelly, if I still have the RegionType roi at hand, how could I use
it to my advantatge using setRegions of the output image? Something that
does the reverse of RegionOfInterestImageFilter.

And what about the approach of changing the BoundingBox's index of the
labelObject?

--

On a side note, I am confused by your second paragraph, in my case:

Since you have done the ROI extraction with ITK


and


> you can use the RegionOfInterestImageFilter
>

are the same thing.

I indeed used the filter to extract the ROI, the indices are re-computed so
they start to [0,0,0], not with the same indexing as the first image as you
said (and that's what I want, so all good here ;)). Maybe you were
referring to the physical point?

Cheers,

Pol





2015-03-30 13:15 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> Hello,
>
> Since you have done the ROI extraction with ITK, then the physical
> location of each pixel has been maintained. Use the ROI Image's
> TransformIndexToPhysicalPoint method[1], then use your original image's
> TransformPhysicalPointToIndex method[2]. This would be the most generalized
> and robust method which the documentation refers too. You could use it to
> validate your optimized approach.
>
> Yes, alternatively you can use the RegionOfInterestImageFilter ( I believe
> ) to extract a region which has a non-zero starting index, and is the same
> indexing and the input image. Alternatively you can use the pipeline and
> rely on the streaming to produce the regions, but then you have to deal
> with the fact that the buffered region is different than the largest
> possible region. There are many possibilities on what to do here.
>
> Hope that helps,
> Brad
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#ab003313ba1a078d89a832dc0a35d2efa
> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25
>
> On Mar 30, 2015, at 5:50 AM, Pol Mons? Purt? <lluna.nova at gmail.com> wrote:
>
> > Hello all,
> >
> > tl; dr
> >
> > How can I reset the index of two labelObjects' bounding box generated
> from a ROIExtractor output to the original image's LargestPossibleRegion()
> coordinate system?
> >
> > --
> >
> > I need to apply a series of (non-itk) operations on a ShapeLabelObject
> present in a small ROI of the image with the purpose of dividing it in two.
> I was using ROI filter because among other things I want the Indexes to be
> referred to the ROI so it is less complex to refer to the voxels'
> coordinates.
> >
> > But afterwards I need the original Index so that the GetBoundingBox() of
> the two generated label objects returns a region that refers to the
> original image repectively, while maintaining the size (probably index
> offset shift) of the new labelobject.
> >
> > I could do as for now and store the roi and then do something like
> (roi.getIndex() + obj->GetBoudingBox().GetIndex() ) to create a shifted
> bounding box, but maybe there is a better way to do it, as read in the
> documentation:
> >
> > The origin coordinates of the output images will be computed in such a
> way that if mapped to physical space, the output image will overlay the
> input image with perfect registration. In other words, a registration
> process between the output image and the input image will return an
> identity transform.
> >
> > So how could I remap to the original "physical space"? I don't know to
> what does that phrase refer to, but it sounds like it's exactly what I am
> trying to do.
> >
> > I've looked into SetRequestedRegion also as an alternative, but that
> would not give me indexes relative to roi, so I would have to substract
> them right before the operations, which might be an option too, but I
> believe things get complicated if I do that.
> >
> > Cheers,
> >
> > Pol
> >
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
>
>
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From matt.mccormick at kitware.com  Mon Mar 30 10:02:27 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 30 Mar 2015 10:02:27 -0400
Subject: [ITK-users] automated splitting and pasting of volumes for use
 in external programs
In-Reply-To: <55191685.9020706@mh-hannover.de>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>
 <0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>
 <CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>
 <CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>
 <BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>
 <CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>
 <CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>
 <55191685.9020706@mh-hannover.de>
Message-ID: <CALzTN-QFB9dp9CTKyNyZW43QS_eAOLq=4ygfux23Jm+xoUGGwg@mail.gmail.com>

Hi Roman,

You probably want to use the streaming capabilities of the ITK
pipeline.  This is covered in more detailed in the ITK Software Guide.
The pipeline internally uses ImageRegionSplitter classes. Overlaps are
handled by propagation of the RequestedRegion throughout the pipeline.
To monitor the changes in the regions, use the
PipelineMonitorImageFilter [1].

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html

On Mon, Mar 30, 2015 at 5:25 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
> Dear mailing list members,
>
>
> A dataset I work on is too big to load completely into itksnap for manual
> adjustment of the automatic pre-segementation with watersheds. The full
> resolution is needed, so I cannot work with a re-sampled version. The only
> possible easy solution I see at the moment is to split up the 3D image into
> smaller blocks of sizes as equal as possible, do the itsnap interaction, and
> finally paste all blocks of the resulting segmentation back together.
> Would itkImageRegionSplitterMultidimensional be the right filter for the
> splitting of blocks as equal in size as possible?
> Is there a "logger" like e.g. itkXMLFileOutputWindow (as used in
> itkStreamingImageFilterTest2.cxx) that could be used to store the regions
> corresponding to each block-file to use that for itkPasteImageFilter to
> combine these blocks later again?
> Not needed now, but perhaps lager: Is there some nice way to handle overlaps
> in this case that is already implemented in itk, something like
> itkImageRegionSplitterMultidimensional::SetOverlap()?
>
> Many thanks for any help or hints.
> Roman
>
> On 17/03/15 18:13, Pol Mons? Purt? wrote:
>>
>> I guess the way to go would be to take the splitter (probably
>> ImageRegionSplitterMultidimensional now that I look at it) and extend it
>> to
>> support overlap. If I do it, I'll let you know in case it is of interest
>> to
>> anyone. For now I'll stick to my class.
>
>
>
> --
> 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. +49 511 532-9574
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From matt.mccormick at kitware.com  Mon Mar 30 10:49:03 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 30 Mar 2015 10:49:03 -0400
Subject: [ITK-users] Updates to Gerrit Robot Builds
Message-ID: <CALzTN-TxwQoin2jU8b9-nv4BEtE15ssMj-5tW3j3R97yVhnQRg@mail.gmail.com>

Hi folks,

Along with our recent Gerrit upgrade, we have also re-worked and
greatly improved the robot builds for proposed patches. The new system
uses the Gerrit Trigger plugin for Jenkins. Two Jenkins instances
currently will create robot builds, one on the Azure cloud for Linux
and Windows builds [1] and one at Kitware for MacOSX builds.

Improvements include:

- More builds executors with a more reliable uptime. The Azure builds
will now spin up and spin down on demand, and they stay up more
reliably. We now have two full-time MacOSX build executors.

- MacOSX builds are now running the latest version of XCode and
generating fully green build results.

- Remote Module submissions will have their module enabled during submission.

- Builds report when they are finished and add a +1 or -1 Verified
status automatically. It is much more useful to know when the builds
finish as opposed to when the builds start. The notification makes is
easier to know at a glance whether a patch builds cleanly. Links are
included to filtered CDash build results.  Links are also included to
the Jenkins jobs on Azure, which has a useful link to the full console
output.

- New and more extensive build controls. The following comments will
initiate builds:

  request build: all
  request build: windows
  request build: osx
  request build: linux
  request build: python

The 'request build: all' comment will generate Windows, MacOSX, and
Linux builds. The 'request build: python' comment will initiate builds
with Python wrapping.  These commands have been added and will be
updated on the Git development wiki page [2]

Happy testing :-),
Matt

[1] http://itkjenkins.cloudapp.net

[2] http://www.itk.org/Wiki/ITK/Git/Develop

From majcjc at gmail.com  Mon Mar 30 12:24:48 2015
From: majcjc at gmail.com (Lin M)
Date: Mon, 30 Mar 2015 12:24:48 -0400
Subject: [ITK-users] What's the difference between
	itkFastMarchingImageFilterBase and itkFastMarchingImageFilter?
Message-ID: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>

Hi all,

I'm wondering what's the difference between itkFastMarchingImageFilterBase
and itkFastMarchingImageFilter.

I'm currently using itkFastMarchingImageFilterBase on a 3D image
(512*512*365) whose computational time is much slower than I expected
(about 250secs). I'm trying to find a way to improve that but I really
don't have a clue now. Can you give me some suggestions about that? Thank
you very much!

Best,
Lin
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From blowekamp at mail.nih.gov  Mon Mar 30 13:15:31 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 30 Mar 2015 13:15:31 -0400
Subject: [ITK-users] What's the difference between
	itkFastMarchingImageFilterBase and itkFastMarchingImageFilter?
In-Reply-To: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>
References: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>
Message-ID: <5377FDCD-B8C2-475A-9E6E-80FAC10A05FF@mail.nih.gov>

Hello,

The itkFastMarchingImageFilterBase, is new and more generalized with a support for generalized stopping criteria and a base infrastructure that can run on quad-edge meshes. The plain itkFastMarchingImageFilter is a bit faster but missing some features and flexibility.

HTH,
Brad


On Mar 30, 2015, at 12:24 PM, Lin M <majcjc at gmail.com> wrote:

> Hi all,
> 
> I'm wondering what's the difference between itkFastMarchingImageFilterBase and itkFastMarchingImageFilter.
> 
> I'm currently using itkFastMarchingImageFilterBase on a 3D image (512*512*365) whose computational time is much slower than I expected (about 250secs). I'm trying to find a way to improve that but I really don't have a clue now. Can you give me some suggestions about that? Thank you very much!
> 
> Best,
> Lin
> _____________________________________
> 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 majcjc at gmail.com  Mon Mar 30 13:47:38 2015
From: majcjc at gmail.com (Lin M)
Date: Mon, 30 Mar 2015 13:47:38 -0400
Subject: [ITK-users] What's the difference between
 itkFastMarchingImageFilterBase and itkFastMarchingImageFilter?
In-Reply-To: <5377FDCD-B8C2-475A-9E6E-80FAC10A05FF@mail.nih.gov>
References: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>
 <5377FDCD-B8C2-475A-9E6E-80FAC10A05FF@mail.nih.gov>
Message-ID: <CALmrq1Z98Eo4yOSSSV_w2kXx0iGghb9kseJ752MYNT+pRk=dWA@mail.gmail.com>

Hi Brad,

Thank you for your reply! Do you think it's normal to take about 250 secs
on a 512*512*365 image to compute the result?

I followed the example from here
http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2FastMarching_2CreateDistanceMapFromSeeds_2Code_8cxx-example.html#_a2

I'm using a i7-860 16G 64bit win8 machine.

Best,
Lin

On Mon, Mar 30, 2015 at 1:15 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> The itkFastMarchingImageFilterBase, is new and more generalized with a
> support for generalized stopping criteria and a base infrastructure that
> can run on quad-edge meshes. The plain itkFastMarchingImageFilter is a bit
> faster but missing some features and flexibility.
>
> HTH,
> Brad
>
>
> On Mar 30, 2015, at 12:24 PM, Lin M <majcjc at gmail.com> wrote:
>
> Hi all,
>
> I'm wondering what's the difference between itkFastMarchingImageFilterBase
> and itkFastMarchingImageFilter.
>
> I'm currently using itkFastMarchingImageFilterBase on a 3D image
> (512*512*365) whose computational time is much slower than I expected
> (about 250secs). I'm trying to find a way to improve that but I really
> don't have a clue now. Can you give me some suggestions about that? Thank
> you very much!
>
> Best,
> Lin
> _____________________________________
> 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 bill.lorensen at gmail.com  Mon Mar 30 13:57:05 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 30 Mar 2015 10:57:05 -0700
Subject: [ITK-users] What's the difference between
 itkFastMarchingImageFilterBase and itkFastMarchingImageFilter?
In-Reply-To: <CALmrq1Z98Eo4yOSSSV_w2kXx0iGghb9kseJ752MYNT+pRk=dWA@mail.gmail.com>
References: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>
 <5377FDCD-B8C2-475A-9E6E-80FAC10A05FF@mail.nih.gov>
 <CALmrq1Z98Eo4yOSSSV_w2kXx0iGghb9kseJ752MYNT+pRk=dWA@mail.gmail.com>
Message-ID: <CADZJ4hMiUxwtqQ7nezMW1rv9O3KK3yDn8uzyA6q6R2ZG1x3y0g@mail.gmail.com>

Is your windows build a Release build or Debug build?

On Mon, Mar 30, 2015 at 10:47 AM, Lin M <majcjc at gmail.com> wrote:
> Hi Brad,
>
> Thank you for your reply! Do you think it's normal to take about 250 secs on
> a 512*512*365 image to compute the result?
>
> I followed the example from here
> http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2FastMarching_2CreateDistanceMapFromSeeds_2Code_8cxx-example.html#_a2
>
> I'm using a i7-860 16G 64bit win8 machine.
>
> Best,
> Lin
>
> On Mon, Mar 30, 2015 at 1:15 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>>
>> Hello,
>>
>> The itkFastMarchingImageFilterBase, is new and more generalized with a
>> support for generalized stopping criteria and a base infrastructure that can
>> run on quad-edge meshes. The plain itkFastMarchingImageFilter is a bit
>> faster but missing some features and flexibility.
>>
>> HTH,
>> Brad
>>
>>
>> On Mar 30, 2015, at 12:24 PM, Lin M <majcjc at gmail.com> wrote:
>>
>> Hi all,
>>
>> I'm wondering what's the difference between itkFastMarchingImageFilterBase
>> and itkFastMarchingImageFilter.
>>
>> I'm currently using itkFastMarchingImageFilterBase on a 3D image
>> (512*512*365) whose computational time is much slower than I expected (about
>> 250secs). I'm trying to find a way to improve that but I really don't have a
>> clue now. Can you give me some suggestions about that? Thank you very much!
>>
>> Best,
>> Lin
>> _____________________________________
>> 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
>



-- 
Unpaid intern in BillsBasement at noware dot com

From majcjc at gmail.com  Mon Mar 30 14:00:49 2015
From: majcjc at gmail.com (Lin M)
Date: Mon, 30 Mar 2015 14:00:49 -0400
Subject: [ITK-users] What's the difference between
 itkFastMarchingImageFilterBase and itkFastMarchingImageFilter?
In-Reply-To: <CADZJ4hMiUxwtqQ7nezMW1rv9O3KK3yDn8uzyA6q6R2ZG1x3y0g@mail.gmail.com>
References: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>
 <5377FDCD-B8C2-475A-9E6E-80FAC10A05FF@mail.nih.gov>
 <CALmrq1Z98Eo4yOSSSV_w2kXx0iGghb9kseJ752MYNT+pRk=dWA@mail.gmail.com>
 <CADZJ4hMiUxwtqQ7nezMW1rv9O3KK3yDn8uzyA6q6R2ZG1x3y0g@mail.gmail.com>
Message-ID: <CALmrq1brzFY7PzkVc40t1ncAZHPiwfVb=MJDHOLNj4hHaxbCFg@mail.gmail.com>

Hi Bill,

It's a Release build.

Best,
Lin

On Mon, Mar 30, 2015 at 1:57 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> Is your windows build a Release build or Debug build?
>
> On Mon, Mar 30, 2015 at 10:47 AM, Lin M <majcjc at gmail.com> wrote:
> > Hi Brad,
> >
> > Thank you for your reply! Do you think it's normal to take about 250
> secs on
> > a 512*512*365 image to compute the result?
> >
> > I followed the example from here
> >
> http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2FastMarching_2CreateDistanceMapFromSeeds_2Code_8cxx-example.html#_a2
> >
> > I'm using a i7-860 16G 64bit win8 machine.
> >
> > Best,
> > Lin
> >
> > On Mon, Mar 30, 2015 at 1:15 PM, Bradley Lowekamp <
> blowekamp at mail.nih.gov>
> > wrote:
> >>
> >> Hello,
> >>
> >> The itkFastMarchingImageFilterBase, is new and more generalized with a
> >> support for generalized stopping criteria and a base infrastructure
> that can
> >> run on quad-edge meshes. The plain itkFastMarchingImageFilter is a bit
> >> faster but missing some features and flexibility.
> >>
> >> HTH,
> >> Brad
> >>
> >>
> >> On Mar 30, 2015, at 12:24 PM, Lin M <majcjc at gmail.com> wrote:
> >>
> >> Hi all,
> >>
> >> I'm wondering what's the difference between
> itkFastMarchingImageFilterBase
> >> and itkFastMarchingImageFilter.
> >>
> >> I'm currently using itkFastMarchingImageFilterBase on a 3D image
> >> (512*512*365) whose computational time is much slower than I expected
> (about
> >> 250secs). I'm trying to find a way to improve that but I really don't
> have a
> >> clue now. Can you give me some suggestions about that? Thank you very
> much!
> >>
> >> Best,
> >> Lin
> >> _____________________________________
> >> 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
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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From blowekamp at mail.nih.gov  Mon Mar 30 14:32:02 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 30 Mar 2015 14:32:02 -0400
Subject: [ITK-users] What's the difference between
	itkFastMarchingImageFilterBase and itkFastMarchingImageFilter?
In-Reply-To: <CALmrq1brzFY7PzkVc40t1ncAZHPiwfVb=MJDHOLNj4hHaxbCFg@mail.gmail.com>
References: <CALmrq1brb4ZqsD7bkfTpZQeanAswcyj8ZnD1Nut4PVGKwwBKCQ@mail.gmail.com>
 <5377FDCD-B8C2-475A-9E6E-80FAC10A05FF@mail.nih.gov>
 <CALmrq1Z98Eo4yOSSSV_w2kXx0iGghb9kseJ752MYNT+pRk=dWA@mail.gmail.com>
 <CADZJ4hMiUxwtqQ7nezMW1rv9O3KK3yDn8uzyA6q6R2ZG1x3y0g@mail.gmail.com>
 <CALmrq1brzFY7PzkVc40t1ncAZHPiwfVb=MJDHOLNj4hHaxbCFg@mail.gmail.com>
Message-ID: <F5A2D816-92EA-4CA4-B248-DA61ABE0D360@mail.nih.gov>

Hello,

I just completed a quick performance test in SimpleITK:

In [1]: import SimpleITK as sitk

In [2]: print sitk.Version()
SimpleITK Version: 0.9.0b01
Compiled: Feb 19 2015 00:47:16


In [3]: img = sitk.Image(512,515,365,sitk.sitkFloat32)

In [4]: img += 1

In [5]: %timeit -n 1 -r 1 sitk.FastMarchingBase( img, [[10,10,10]])
1 loops, best of 1: 4min 1s per loop

In [6]: %timeit -n 1 -r 1 sitk.FastMarching( img, [[10,10,10]])
1 loops, best of 1: 5min per loop


Your time does strike me as slow but it is on par with what I got on my i7 MacBook Pro. I recall previous experiments yielding the non-Base as the clear winner. This constant image is a convoluted example and may not reflect real world performance.

Perhaps you can improve the stopping citera,  so as to not compute more that needed.

HTH,
Brad

On Mar 30, 2015, at 2:00 PM, Lin M <majcjc at gmail.com> wrote:

> Hi Bill,
> 
> It's a Release build. 
> 
> Best,
> Lin
> 
> On Mon, Mar 30, 2015 at 1:57 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Is your windows build a Release build or Debug build?
> 
> On Mon, Mar 30, 2015 at 10:47 AM, Lin M <majcjc at gmail.com> wrote:
> > Hi Brad,
> >
> > Thank you for your reply! Do you think it's normal to take about 250 secs on
> > a 512*512*365 image to compute the result?
> >
> > I followed the example from here
> > http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2FastMarching_2CreateDistanceMapFromSeeds_2Code_8cxx-example.html#_a2
> >
> > I'm using a i7-860 16G 64bit win8 machine.
> >
> > Best,
> > Lin
> >
> > On Mon, Mar 30, 2015 at 1:15 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> > wrote:
> >>
> >> Hello,
> >>
> >> The itkFastMarchingImageFilterBase, is new and more generalized with a
> >> support for generalized stopping criteria and a base infrastructure that can
> >> run on quad-edge meshes. The plain itkFastMarchingImageFilter is a bit
> >> faster but missing some features and flexibility.
> >>
> >> HTH,
> >> Brad
> >>
> >>
> >> On Mar 30, 2015, at 12:24 PM, Lin M <majcjc at gmail.com> wrote:
> >>
> >> Hi all,
> >>
> >> I'm wondering what's the difference between itkFastMarchingImageFilterBase
> >> and itkFastMarchingImageFilter.
> >>
> >> I'm currently using itkFastMarchingImageFilterBase on a 3D image
> >> (512*512*365) whose computational time is much slower than I expected (about
> >> 250secs). I'm trying to find a way to improve that but I really don't have a
> >> clue now. Can you give me some suggestions about that? Thank you very much!
> >>
> >> Best,
> >> Lin
> >> _____________________________________
> >> 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
> >
> 
> 
> 
> --
> Unpaid intern in BillsBasement at noware dot com
> 

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From lluna.nova at gmail.com  Mon Mar 30 17:02:38 2015
From: lluna.nova at gmail.com (=?UTF-8?B?UG9sIE1vbnPDsyBQdXJ0w60=?=)
Date: Mon, 30 Mar 2015 23:02:38 +0200
Subject: [ITK-users] Region of two labelObjects
Message-ID: <CALAZn4gy47P+8mjwNXXeBfLJiyYCmkG6_saftJvrYodkZCmHLA@mail.gmail.com>

Hello all,

I have two label objects, how can I merge the two BoundingBoxes together so
I know the necessary size of the image? (other than creating it myself by
searching max/min of each dimension)

How come LabelMap doesn't resize automatically when objects are added? It
could.

template< typename TImageType >
void labelObjects2Image(ShapeLabelObjectType* labelObject1,
                   ShapeLabelObjectType* labelObject2,
                   typename TImageType::Pointer& labelMapImage){

typedef itk::ShapeLabelObject< typename TImageType::PixelType,
TImageType::ImageDimension > ShapeLabelObjectType;
typedef itk::LabelMap< ShapeLabelObjectType > LabelMapType;
typedef itk::LabelMapToLabelImageFilter< LabelMapType, TImageType >
Label2VolumeFilter;

*--> region = labelObject1->GetBoundingBox() "+"
labelObject2->GetBoundingBox()*

auto segLabelMap = LabelMapType::New();
segLabelMap->SetRegions(region);
segLabelMap->Allocate();

segLabelMap->AddLabelObject(labelObject1);
segLabelMap->AddLabelObject(labelObject2);

auto label2volume = Label2VolumeFilter::New();

label2volume->SetInput(segLabelMap);

label2volume->Update();
labelMapImage = label2volume->GetOutput();

}

Cheers,

Pol
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From gabrielgimenez85 at gmail.com  Mon Mar 30 20:05:49 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Mon, 30 Mar 2015 20:05:49 -0400
Subject: [ITK-users] Resample and Directions in Image Registration
In-Reply-To: <CALzTN-SmhSTnAcirM3+760fSXSm+3VJeVUaKtrFCfnabhsVCqA@mail.gmail.com>
References: <1427584199821-7587074.post@n2.nabble.com>
 <CALzTN-SjQF9eg9sSkZXQ7p5HJE8sDCfckkOyeNKqv4KSN8Ewmw@mail.gmail.com>
 <1427664358535-7587078.post@n2.nabble.com>
 <CALzTN-SmhSTnAcirM3+760fSXSm+3VJeVUaKtrFCfnabhsVCqA@mail.gmail.com>
Message-ID: <CAHpGi9fBKBWwzqgTiz=QpwcOTndmaabR4c3ynrc0sE9kP5z0Zw@mail.gmail.com>

Thanks Matt!! ;-)
El 29/03/2015 18:07, "Matt McCormick" <matt.mccormick at kitware.com> escribi?:

> Hi Gabriel,
>
> > Hi Matt, thanks for your answer...It is now clear to me ...
>
> Great!
>
> > Matt! another question please ... what is the normal runtime of Mattes
> > Mutual Information Metric with 3D images? It is normal to be in the
> range of
> > 2.5 to 4 seconds? I use CT and MR images ... and this is my
> configuration:
> >
> > samplingPercentage = 0.002;
> > samplingStrategy  = RegistrationType::REGULAR;
> > NumberOfHistogramBins = 50
>
> I do not know offhand what the expected computation time is, but I
> would not be surprised if it was that slow on 3D images.
>
> Matt
>
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From lchauvin at bwh.harvard.edu  Tue Mar 31 10:21:50 2015
From: lchauvin at bwh.harvard.edu (Laurent Chauvin)
Date: Tue, 31 Mar 2015 10:21:50 -0400
Subject: [ITK-users] Constrain a transform for optimizer
Message-ID: <CAPGPbaJMkRuUisZQ2eTBF2TUao5gO-LaVX0A0d96NZwaG=YfLQ@mail.gmail.com>

Hello ITK users,

I'm trying to use a Levenberg-Marquardt optimizer to find a point in a
plane (based on a cost function).
For now I create a itk::TranslationTransform< double, 3 > and set it to the
Levenberg-Marquardt optmizer.

However, I know the point I'm looking for is included in a plane.

I was wondering if there is a way to constrain the transform to only check
points in the plane (to avoid looking for points out of the plane to speed
up the optimization process) ?

Thank you very much.

-- 
Laurent Chauvin, MS
Surgical Navigation and Robotics Laboratory, Radiology Department
Brigham And Women's Hospital, Harvard Medical School
http://wiki.ncigt.org/index.php/User:Lchauvin
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From grothausmann.roman at mh-hannover.de  Tue Mar 31 15:10:44 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Tue, 31 Mar 2015 21:10:44 +0200
Subject: [ITK-users] automated splitting and pasting of volumes for use
 in external programs
In-Reply-To: <CALzTN-QFB9dp9CTKyNyZW43QS_eAOLq=4ygfux23Jm+xoUGGwg@mail.gmail.com>
References: <CALAZn4jwxiVBXv2PJaWTHUHdb=sP3FQ+48EeD1W31PzMdgu1pA@mail.gmail.com>	<0B31CB6B-D4D0-48B1-A019-775E1E09E686@mail.nih.gov>	<CALAZn4iHhgAmJF+kTR5M0wBgCpwTC-j+CjNExGcQWD-PM_a39Q@mail.gmail.com>	<CALAZn4hJm2tNT=TZXyQLqaV0Kfin=mw78vornifwX0CKmCq8CQ@mail.gmail.com>	<BF5A6B99-194F-49BC-A115-9B53E2779E73@mail.nih.gov>	<CALzTN-Qre04UwY9TG8GiQOAOvd+rrLqv7+U+_UqREzCLa6i3PA@mail.gmail.com>	<CALAZn4jFBTk6Vf7Grrn5kHDy=Z0CZt3W3kT9WwTqs-Ln7wBPEw@mail.gmail.com>	<55191685.9020706@mh-hannover.de>
 <CALzTN-QFB9dp9CTKyNyZW43QS_eAOLq=4ygfux23Jm+xoUGGwg@mail.gmail.com>
Message-ID: <551AF134.4080804@mh-hannover.de>

Dear Matt,


Thanks for Your quick reply. If I got Your hint right, You suggest writing my 
own filter (that e.g. does the writing of the chunk to a file) and put an 
itkStreamingImageFilter after it supplying it with the # of chunks and the type 
of splitter. If I understand the ITK Software Guide correctly, such a filter 
needs to be threaded, i.e. have a ThreadedGenerateData.
I tried that with a simple AddFilter that should just add a constant according 
to the chunk number to the region it is supposed to process (files attached). 
However it stops due to region miss-matches. I can't see why. With just 
GenerateData it seems like it is not streaming, according to the 
PipelineMonitorImageFilter.
What would be the correct way to go?

Many thanks for looking into this.
Roman

On 30/03/15 16:02, Matt McCormick wrote:
> Hi Roman,
>
> You probably want to use the streaming capabilities of the ITK
> pipeline.  This is covered in more detailed in the ITK Software Guide.
> The pipeline internally uses ImageRegionSplitter classes. Overlaps are
> handled by propagation of the RequestedRegion throughout the pipeline.
> To monitor the changes in the regions, use the
> PipelineMonitorImageFilter [1].
>
> HTH,
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html
>
> On Mon, Mar 30, 2015 at 5:25 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Dear mailing list members,
>>
>>
>> A dataset I work on is too big to load completely into itksnap for manual
>> adjustment of the automatic pre-segementation with watersheds. The full
>> resolution is needed, so I cannot work with a re-sampled version. The only
>> possible easy solution I see at the moment is to split up the 3D image into
>> smaller blocks of sizes as equal as possible, do the itsnap interaction, and
>> finally paste all blocks of the resulting segmentation back together.
>> Would itkImageRegionSplitterMultidimensional be the right filter for the
>> splitting of blocks as equal in size as possible?
>> Is there a "logger" like e.g. itkXMLFileOutputWindow (as used in
>> itkStreamingImageFilterTest2.cxx) that could be used to store the regions
>> corresponding to each block-file to use that for itkPasteImageFilter to
>> combine these blocks later again?
>> Not needed now, but perhaps lager: Is there some nice way to handle overlaps
>> in this case that is already implemented in itk, something like
>> itkImageRegionSplitterMultidimensional::SetOverlap()?
>>
>> Many thanks for any help or hints.
>> Roman
>>
>> On 17/03/15 18:13, Pol Mons? Purt? wrote:
>>>
>>> I guess the way to go would be to take the splitter (probably
>>> ImageRegionSplitterMultidimensional now that I look at it) and extend it
>>> to
>>> support overlap. If I do it, I'll let you know in case it is of interest
>>> to
>>> anyone. For now I'll stick to my class.
>>
>>
>>
>> --
>> 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. +49 511 532-9574
>> _____________________________________
>> 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

-- 
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. +49 511 532-9574
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From gabrielgimenez85 at gmail.com  Tue Mar 31 23:52:03 2015
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Tue, 31 Mar 2015 20:52:03 -0700 (MST)
Subject: [ITK-users] Working with RIRE Datasets
Message-ID: <1427860323074-7587099.post@n2.nabble.com>

Hi! how are you?

I'm trying to use RIRE datasets..., for example: 

In the RIRE terminology we say "From CT to MR", this means that the "moving
image" is the CT image and the fixed image is the MR image. Then, I need a
transformation "T"  to apply to the CT test points for the comparison with
the "ground truth"...I'm not wrong about this?

But my problem is that the ITK provides a transformation that maps poins of
the fixed (MR) image on the moving image (CT) , I guess I need to get the
inverse transformation...is that possible? I'm misunderstanding something?

I hope you can help me...I need to test my implementation, thank you in
advance.

Regards,



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