<div dir="ltr">Hi all,<br><br>I solved my problem,<br>I gave the correct path to the DOXYGEN_EXECUTABLE variable.<br><br>Gg<br><div><br><div><div><br><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 7, 2014 at 9:05 AM, <span dir="ltr"><<a href="mailto:insight-users-request@itk.org" target="_blank">insight-users-request@itk.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send Insight-users mailing list submissions to<br>
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When replying, please edit your Subject line so it is more specific<br>
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<br>
Today's Topics:<br>
<br>
1. [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick)<br>
2. Re: [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick)<br>
3. Proper chaining of filters (Jo?l Schaerer)<br>
4. Re: [ITK] Proper chaining of filters (Matt McCormick)<br>
5. Re: [ITK] Proper chaining of filters (Jo?l Schaerer)<br>
6. 3D generalized hough transform (Pedro Morais)<br>
7. vector image registration (Lianli Liu)<br>
8. help installing ITK (Gianluigi Caddeo)<br>
9. How to remove a tag from MetaDataDictionary? (Arnaud Gelas)<br>
10. Overlap_image registration metrics (Emma Saunders)<br>
11. Texture Features extraction (Marco Ulge)<br>
12. Re: Texture Features extraction (Dominique T?pfer)<br>
13. Re: Texture Features extraction (Marco Ulge)<br>
14. Speed of ITKv4 based Gradient Descent Optimizer (Jiahui Wang)<br>
15. Re: How to remove a tag from MetaDataDictionary? (Matt McCormick)<br>
16. Re: Overlap_image registration metrics (Matt McCormick)<br>
17. Re: [ITK] Speed of ITKv4 based Gradient Descent Optimizer<br>
(Andras Lasso)<br>
18. Polygon inside point (Fabian Torres)<br>
19. region inside points (Fabian Torres)<br>
20. Re: region inside points (Gib Bogle)<br>
21. Re: region inside points (Gib Bogle)<br>
22. Re: region inside points (Fabian Torres)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 1 Oct 2014 15:40:44 -0400<br>
From: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
To: "<a href="mailto:community@itk.org">community@itk.org</a>" <<a href="mailto:community@itk.org">community@itk.org</a>>, "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>"<br>
<<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>>, ITK <<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>><br>
Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released!<br>
Message-ID:<br>
<<a href="mailto:CALzTN-TXyhZ2aDaA-UQoFgbg3fPPCPzYKKFpAmKvuquf1EXgrw@mail.gmail.com">CALzTN-TXyhZ2aDaA-UQoFgbg3fPPCPzYKKFpAmKvuquf1EXgrw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
On behalf of the Insight Toolkit Community, we are happy to announce<br>
the release of ITK 4.6.1!<br>
<br>
This is a patch release that addresses critical issues. The 4.6.1<br>
release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK<br>
build errors, Python wrapping warnings, CMake configuration with<br>
COMPONENTS, performance and memory consumption of the ITKv4<br>
implementation of the mutual information matching metric, and a many<br>
other issues.<br>
<br>
Congratulations and thanks to everyone who contributed to this<br>
release. We are particularly grateful for the collaborations with the<br>
3D Slicer, Debian, GDCM, and MINC communities to address these issues.<br>
Questions and comments are welcome on the ITK mailing lists.<br>
<br>
The release files can be downloaded from:<br>
<br>
<a href="http://itk.org/ITK/resources/software.html" target="_blank">http://itk.org/ITK/resources/software.html</a><br>
<br>
<br>
The next feature release of 4.6.0 is scheduled for June.<br>
<br>
<br>
Enjoy ITK!<br>
<br>
<br>
<br>
Changes from v4.6.0 to v4.6.1:<br>
<br>
Arnaud Gelas (5):<br>
BUG: fix gdcm version in GDCMImageIO.<br>
COMP: missing cast when calling gdcm::DataElement::SetByteValue<br>
BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false<br>
BUG: split include directories into appropriate cmake variables HDF5<br>
BUG: missing gdcm libraries when using system GDCM<br>
<br>
Brad King (2):<br>
COMP: Fix vxl_config_macros usage of CMake check macros<br>
BUG: Fix itk_module_config for repeated calls<br>
<br>
Bradley Lowekamp (8):<br>
ENH: Adding License file from upstream MetaIO<br>
ENH: Adding script to update MetaIO from upstream<br>
ENH: Remove ITK MetaIO to prepare for upstream import<br>
COMP: Fix variable type for Set/Get macros<br>
BUG: Use METER of sCAL scale unit<br>
BUG: Use PNG_SCALE_METER for PNG sCAL unit<br>
BUG: Fix overflows computing size of read tiff image<br>
BUG: Use array delete operator for array new allocations<br>
<br>
Christopher Mullins (2):<br>
COMP: Allows latex to compile for ITKSoftwareGuide<br>
COMP: Wrap MeshBase templates<br>
<br>
David T. Chen (1):<br>
DOC: Fixed HistogramThresholdImageFitler<br>
<br>
Gert Wollny (1):<br>
COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)<br>
<br>
Girish Mallya (1):<br>
BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.<br>
<br>
Hans Johnson (12):<br>
COMP: Add tolerance for comparing floating point<br>
PERF: Remove non-threadable algorithm components<br>
PERF: Remove large foot print of PDF derivatives.<br>
PERF: Revert Remove large foot print of PDF derivatives.<br>
STYLE: Test against almost equal for floating point values<br>
STYLE: Non-exact floating point testing<br>
PERF: Distribute initialization per thread buffers<br>
ENH: Remove unnecessary mutable qualifier.<br>
STYLE: Remove comment with no meaning.<br>
ENH: Moved accumlator logic to main MI class<br>
ENH: Allow staggering of accumulations per thread.<br>
PERF: Zero reset thread buffers during finalize<br>
<br>
Matthew McCormick (31):<br>
BUG: ArchiveTestingData.py future imports must occur at the beginning.<br>
DOC: Remove Image2.cxx reference from Book 2.<br>
DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.<br>
DOC: Remove references to Book 1 sections from Book 2.<br>
DOC: Make BinaryThresholdImageFilter not floating.<br>
DOC: Fix Software Guide figure caption for FlipImageFilter.<br>
DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.<br>
DOC: Remove duplicate figure in<br>
LaplacianRecursiveGaussianImageFilter2.cxx.<br>
DOC: ImageRandomConstIteratorWithIndex table reference.<br>
BUG: Bump GCCXML to 2014-08-06.<br>
BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.<br>
BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().<br>
BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.<br>
BUG: Fix alpha assignment for RGBA TIFF.<br>
BUG: Fix Nifti IO read with large images.<br>
BUG: Improve thread-safety and performance of<br>
PCAShapeSignedDistanceFunction.<br>
DOC: itk::statistics -> itk::Statistics.<br>
DOC: Remove duplicate text in LaplacianRecursiveGaussian example.<br>
DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.<br>
BUG: TransformFileReader does not clear its TransformList.<br>
BUG: Prevent dangling pointer in HDF5TransformIO.<br>
COMP: Fix missing prefix in ITKv3ImageRegistration20Test.<br>
BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform<br>
STYLE: Improve style in BinaryImageToLabelMapFilter.<br>
BUG: Fix BinaryImageToLabelMapFilter on 1D image.<br>
ENH: Improve precision of the joint PDF sum<br>
BUG: Fix BinShrinkImageFilter for different input/output image types.<br>
COMP: Fix transform type for ITKv3/IterativeClosestPoint2.<br>
COMP: Add missing wrapping for TransformIOBaseTemplate.<br>
BUG: gdcm::StringFilter recognizes backslash delimiter.<br>
ENH: Bump ITK version to 4.6.1.<br>
<br>
MetaIO Maintainers (1):<br>
MetaIO (reduced)<br>
<br>
Michka Popoff (4):<br>
BUG: Improve SWIG version check<br>
BUG: Add VTK_VERSION for older VTK versions<br>
BUG: Update VTK minimum version (for release)<br>
BUG: Fix memory leak in MetaImageIO after exception<br>
<br>
Vladimir S. FONOV (1):<br>
BUG: Fixing incorrect MINC style inverse transform<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 1 Oct 2014 15:50:33 -0400<br>
From: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
To: "<a href="mailto:community@itk.org">community@itk.org</a>" <<a href="mailto:community@itk.org">community@itk.org</a>>, "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>"<br>
<<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>>, ITK <<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>><br>
Subject: Re: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released!<br>
Message-ID:<br>
<<a href="mailto:CALzTN-S9DU8K8ACbgVP6L0ozXQGvcbnfXC7nz8iu_xqLTVtHsw@mail.gmail.com">CALzTN-S9DU8K8ACbgVP6L0ozXQGvcbnfXC7nz8iu_xqLTVtHsw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Minor correction:<br>
<br>
><br>
> The next feature release of 4.6.0 is scheduled for June.<br>
><br>
<br>
The next feature release of 4.7.0 is scheduled for December.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 02 Oct 2014 11:33:06 +0200<br>
From: Jo?l Schaerer <<a href="mailto:joel.schaerer@laposte.net">joel.schaerer@laposte.net</a>><br>
To: itk <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: [ITK-users] Proper chaining of filters<br>
Message-ID: <<a href="mailto:542D1BD2.40801@laposte.net">542D1BD2.40801@laposte.net</a>><br>
Content-Type: text/plain; charset=utf-8; format=flowed<br>
<br>
Hi all,<br>
<br>
I've noticed a couple times that when building a pipeline with ITK, you<br>
need to keep a reference to all filters before the pipeline is updated.<br>
This seems a little counter-intuitive to me, so I would like to better<br>
understand the issue and see if there is a way around it.<br>
<br>
As an example, the following code doesn't work:<br>
<br>
DilateType::Pointer dilate = DilateType::New();<br>
dilate->SetInput(thresh->GetOutput());<br>
dilate->SetKernel(kernel);<br>
<br>
dilate_filters.push_back(dilate);<br>
for (int i=0; i<14; ++i) {<br>
DilateType::Pointer temp = DilateType::New();<br>
temp->SetInput(dilate->GetOutput());<br>
temp->SetKernel(kernel);<br>
dilate = temp;<br>
}<br>
dilate->Update();<br>
<br>
Regions don't get propagated properly and I get the following exception<br>
when writing the output:<br>
<br>
C++ exception with description<br>
"/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290:<br>
itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not<br>
fully contain requested paste IO regionPaste IO region: ImageIORegion<br>
(0x7fff9bb72cc0)<br>
Dimension: 3<br>
Index: 0 0 0<br>
Size: 0 0 0<br>
Largest possible region: ImageRegion (0x7fff9bb72bc0)<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [0, 0, 0]<br>
" thrown in the test body.<br>
<br>
My guess is that the filters get destroyed before they get a chance to<br>
be executed. If I explicitely keep references to each filter, it works:<br>
<br>
DilateType::Pointer dilate = DilateType::New();<br>
dilate->SetInput(thresh->GetOutput());<br>
dilate->SetKernel(kernel);<br>
// We need to keep a reference to each filter in the pipeline before<br>
it is updated<br>
std::vector<DilateType::Pointer> dilate_filters;<br>
dilate_filters.push_back(dilate);<br>
for (int i=0; i<14; ++i) {<br>
DilateType::Pointer temp = DilateType::New();<br>
temp->SetInput(dilate_filters.back()->GetOutput());<br>
temp->SetKernel(kernel);<br>
dilate = temp;<br>
dilate_filters.push_back(temp);<br>
}<br>
dilate_filters.back()->Update();<br>
<br>
My question is, why doesn't a filter keep a reference to the previous<br>
filter in the pipeline? Is there a way around this?<br>
<br>
Thanks!<br>
<br>
Jo?l<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 2 Oct 2014 10:16:08 -0400<br>
From: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
To: Jo?l Schaerer <<a href="mailto:joel.schaerer@laposte.net">joel.schaerer@laposte.net</a>><br>
Cc: itk <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] [ITK] Proper chaining of filters<br>
Message-ID:<br>
<CALzTN-SdcSYREtftRToGyMs9Q6=7UDerCMmMLwRYNTR5=<a href="mailto:v6XSg@mail.gmail.com">v6XSg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Hi Jo?l,<br>
<br>
Calling<br>
<br>
temp->SetInput(dilate->GetOutput());<br>
<br>
Connects the DataObject generated by dilate to the temp filter. temp<br>
does not increment dilate's reference count, and it would be difficult<br>
to do since the SetInput input is the DataObject, not the<br>
ProcessObject.<br>
<br>
As a consequence, at least one SmartPointer needs to be kept in scope<br>
as with your second example.<br>
<br>
HTH,<br>
Matt<br>
<br>
On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer <<a href="mailto:joel.schaerer@laposte.net">joel.schaerer@laposte.net</a>> wrote:<br>
> Hi all,<br>
><br>
> I've noticed a couple times that when building a pipeline with ITK, you need<br>
> to keep a reference to all filters before the pipeline is updated. This<br>
> seems a little counter-intuitive to me, so I would like to better understand<br>
> the issue and see if there is a way around it.<br>
><br>
> As an example, the following code doesn't work:<br>
><br>
> DilateType::Pointer dilate = DilateType::New();<br>
> dilate->SetInput(thresh->GetOutput());<br>
> dilate->SetKernel(kernel);<br>
><br>
> dilate_filters.push_back(dilate);<br>
> for (int i=0; i<14; ++i) {<br>
> DilateType::Pointer temp = DilateType::New();<br>
> temp->SetInput(dilate->GetOutput());<br>
> temp->SetKernel(kernel);<br>
> dilate = temp;<br>
> }<br>
> dilate->Update();<br>
><br>
> Regions don't get propagated properly and I get the following exception when<br>
> writing the output:<br>
><br>
> C++ exception with description<br>
> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290:<br>
> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not<br>
> fully contain requested paste IO regionPaste IO region: ImageIORegion<br>
> (0x7fff9bb72cc0)<br>
> Dimension: 3<br>
> Index: 0 0 0<br>
> Size: 0 0 0<br>
> Largest possible region: ImageRegion (0x7fff9bb72bc0)<br>
> Dimension: 3<br>
> Index: [0, 0, 0]<br>
> Size: [0, 0, 0]<br>
> " thrown in the test body.<br>
><br>
> My guess is that the filters get destroyed before they get a chance to be<br>
> executed. If I explicitely keep references to each filter, it works:<br>
><br>
> DilateType::Pointer dilate = DilateType::New();<br>
> dilate->SetInput(thresh->GetOutput());<br>
> dilate->SetKernel(kernel);<br>
> // We need to keep a reference to each filter in the pipeline before it is<br>
> updated<br>
> std::vector<DilateType::Pointer> dilate_filters;<br>
> dilate_filters.push_back(dilate);<br>
> for (int i=0; i<14; ++i) {<br>
> DilateType::Pointer temp = DilateType::New();<br>
> temp->SetInput(dilate_filters.back()->GetOutput());<br>
> temp->SetKernel(kernel);<br>
> dilate = temp;<br>
> dilate_filters.push_back(temp);<br>
> }<br>
> dilate_filters.back()->Update();<br>
><br>
> My question is, why doesn't a filter keep a reference to the previous filter<br>
> in the pipeline? Is there a way around this?<br>
><br>
> Thanks!<br>
><br>
> Jo?l<br>
> _____________________________________<br>
> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
><br>
> Visit other Kitware open-source projects at<br>
> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
><br>
> Kitware offers ITK Training Courses, for more information visit:<br>
> <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
><br>
> Please keep messages on-topic and check the ITK FAQ at:<br>
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> Follow this link to subscribe/unsubscribe:<br>
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<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 02 Oct 2014 16:22:24 +0200<br>
From: Jo?l Schaerer <<a href="mailto:joel.schaerer@laposte.net">joel.schaerer@laposte.net</a>><br>
To: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
Cc: itk <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] [ITK] Proper chaining of filters<br>
Message-ID: <<a href="mailto:542D5FA0.8070903@laposte.net">542D5FA0.8070903@laposte.net</a>><br>
Content-Type: text/plain; charset=utf-8; format=flowed<br>
<br>
Hi Matt,<br>
<br>
Thanks for the confirmation. I was thinking there might be another<br>
mechanism I wasn't aware of.<br>
<br>
Jo?l<br>
<br>
On 10/02/2014 04:16 PM, Matt McCormick wrote:<br>
> Hi Jo?l,<br>
><br>
> Calling<br>
><br>
> temp->SetInput(dilate->GetOutput());<br>
><br>
> Connects the DataObject generated by dilate to the temp filter. temp<br>
> does not increment dilate's reference count, and it would be difficult<br>
> to do since the SetInput input is the DataObject, not the<br>
> ProcessObject.<br>
><br>
> As a consequence, at least one SmartPointer needs to be kept in scope<br>
> as with your second example.<br>
><br>
> HTH,<br>
> Matt<br>
><br>
> On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer <<a href="mailto:joel.schaerer@laposte.net">joel.schaerer@laposte.net</a>> wrote:<br>
>> Hi all,<br>
>><br>
>> I've noticed a couple times that when building a pipeline with ITK, you need<br>
>> to keep a reference to all filters before the pipeline is updated. This<br>
>> seems a little counter-intuitive to me, so I would like to better understand<br>
>> the issue and see if there is a way around it.<br>
>><br>
>> As an example, the following code doesn't work:<br>
>><br>
>> DilateType::Pointer dilate = DilateType::New();<br>
>> dilate->SetInput(thresh->GetOutput());<br>
>> dilate->SetKernel(kernel);<br>
>><br>
>> dilate_filters.push_back(dilate);<br>
>> for (int i=0; i<14; ++i) {<br>
>> DilateType::Pointer temp = DilateType::New();<br>
>> temp->SetInput(dilate->GetOutput());<br>
>> temp->SetKernel(kernel);<br>
>> dilate = temp;<br>
>> }<br>
>> dilate->Update();<br>
>><br>
>> Regions don't get propagated properly and I get the following exception when<br>
>> writing the output:<br>
>><br>
>> C++ exception with description<br>
>> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290:<br>
>> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not<br>
>> fully contain requested paste IO regionPaste IO region: ImageIORegion<br>
>> (0x7fff9bb72cc0)<br>
>> Dimension: 3<br>
>> Index: 0 0 0<br>
>> Size: 0 0 0<br>
>> Largest possible region: ImageRegion (0x7fff9bb72bc0)<br>
>> Dimension: 3<br>
>> Index: [0, 0, 0]<br>
>> Size: [0, 0, 0]<br>
>> " thrown in the test body.<br>
>><br>
>> My guess is that the filters get destroyed before they get a chance to be<br>
>> executed. If I explicitely keep references to each filter, it works:<br>
>><br>
>> DilateType::Pointer dilate = DilateType::New();<br>
>> dilate->SetInput(thresh->GetOutput());<br>
>> dilate->SetKernel(kernel);<br>
>> // We need to keep a reference to each filter in the pipeline before it is<br>
>> updated<br>
>> std::vector<DilateType::Pointer> dilate_filters;<br>
>> dilate_filters.push_back(dilate);<br>
>> for (int i=0; i<14; ++i) {<br>
>> DilateType::Pointer temp = DilateType::New();<br>
>> temp->SetInput(dilate_filters.back()->GetOutput());<br>
>> temp->SetKernel(kernel);<br>
>> dilate = temp;<br>
>> dilate_filters.push_back(temp);<br>
>> }<br>
>> dilate_filters.back()->Update();<br>
>><br>
>> My question is, why doesn't a filter keep a reference to the previous filter<br>
>> in the pipeline? Is there a way around this?<br>
>><br>
>> Thanks!<br>
>><br>
>> Jo?l<br>
>> _____________________________________<br>
>> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>><br>
>> Visit other Kitware open-source projects at<br>
>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>><br>
>> Kitware offers ITK Training Courses, for more information visit:<br>
>> <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
>><br>
>> Please keep messages on-topic and check the ITK FAQ at:<br>
>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>><br>
>> Follow this link to subscribe/unsubscribe:<br>
>> <a href="http://public.kitware.com/mailman/listinfo/insight-users" target="_blank">http://public.kitware.com/mailman/listinfo/insight-users</a><br>
>> _______________________________________________<br>
>> Community mailing list<br>
>> <a href="mailto:Community@itk.org">Community@itk.org</a><br>
>> <a href="http://public.kitware.com/mailman/listinfo/community" target="_blank">http://public.kitware.com/mailman/listinfo/community</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT)<br>
From: Pedro Morais <<a href="mailto:pedromorais-17@hotmail.com">pedromorais-17@hotmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK-users] 3D generalized hough transform<br>
Message-ID: <<a href="mailto:1412267071841-7586297.post@n2.nabble.com">1412267071841-7586297.post@n2.nabble.com</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi all,<br>
<br>
I'm wonder if ITK has an implementation of a 3D generalized hough transform.<br>
Do you have any idea?<br>
<br>
Regards,<br>
Pedro<br>
<br>
<br>
<br>
--<br>
View this message in context: <a href="http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html</a><br>
Sent from the ITK Insight Users mailing list archive at Nabble.com.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Thu, 2 Oct 2014 20:40:16 -0400<br>
From: Lianli Liu <<a href="mailto:llliu@umich.edu">llliu@umich.edu</a>><br>
To: "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: [ITK-users] vector image registration<br>
Message-ID:<br>
<<a href="mailto:CAGKqDmfV89qpnVG5tq4bvZrc6FDHhNRHrkvWg7qEXjh_pObKsQ@mail.gmail.com">CAGKqDmfV89qpnVG5tq4bvZrc6FDHhNRHrkvWg7qEXjh_pObKsQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I wonder if ITK is supporting vector image registration now? If not, any<br>
suggestions to achieve this goal?<br>
<br>
Thanks!<br>
Lianli<br>
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<br>
Message: 8<br>
Date: Fri, 3 Oct 2014 10:05:29 +0100<br>
From: Gianluigi Caddeo <<a href="mailto:ggigi78@gmail.com">ggigi78@gmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK-users] help installing ITK<br>
Message-ID:<br>
<<a href="mailto:CADeTECOS-PqOswWC4H2Wo_f8eKjd24eN%2BeSDfRG%2BYK8LKF7%2BCA@mail.gmail.com">CADeTECOS-PqOswWC4H2Wo_f8eKjd24eN+eSDfRG+YK8LKF7+CA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
during my installation on an ubuntu machine I had this problem:<br>
<br>
<br>
<br>
<br>
<br>
<br>
*[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1:<br>
DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: ***<br>
[Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: ***<br>
[Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: ***<br>
[all] Errore*<br>
But doxygen exist and stay in my */usr/bin* directory<br>
<br>
How can I to force ITK to search doxygen in that directory?<br>
<br>
thanks a lot<br>
<br>
Gg<br>
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<br>
Message: 9<br>
Date: Mon, 6 Oct 2014 09:58:09 +0200<br>
From: Arnaud Gelas <<a href="mailto:arnaudgelas@gmail.com">arnaudgelas@gmail.com</a>><br>
To: insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Cc: Mathieu Malaterre <<a href="mailto:mathieu.malaterre@gmail.com">mathieu.malaterre@gmail.com</a>><br>
Subject: [ITK-users] How to remove a tag from MetaDataDictionary?<br>
Message-ID:<br>
<<a href="mailto:CAK3qF%2B8e1kg7bN4EcM2FUYy_e3AYz-M3ZrGGwkssWz0Kvz4y2Q@mail.gmail.com">CAK3qF+8e1kg7bN4EcM2FUYy_e3AYz-M3ZrGGwkssWz0Kvz4y2Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I am trying to write a DICOM file in which, the orientation (among others)<br>
has changed in my pipeline...<br>
<br>
1- After having a look<br>
<a href="https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919" target="_blank">https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919</a><br>
<br>
It appears to me that if the orientation is in the MetaDataDictionary, it<br>
is saved anyway into the DICOM image, there is no way to force the ImageIO<br>
to recompute it from the image and save it ???<br>
If there is, can anyone give me a pointer?<br>
<br>
2- Since I can't find a way to update the image orientation in<br>
itk::GDCMImageIO, I have been looking at removing the corresponding tag<br>
from the MetaDataDictionary. I could not find any method or any way to do<br>
it???<br>
If there is, can anyone give me a pointer?<br>
<br>
I wish I would not have to copy the dictionary and add if statement to<br>
avoid copying the direction...<br>
<br>
Thanks in advance,<br>
Arnaud<br>
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<br>
Message: 10<br>
Date: Mon, 6 Oct 2014 12:31:03 +0100<br>
From: Emma Saunders <<a href="mailto:emmasaunders123@gmail.com">emmasaunders123@gmail.com</a>><br>
To: "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a> Users" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: [ITK-users] Overlap_image registration metrics<br>
Message-ID:<br>
<CABQY8kQ1QoeHo_X-RJ0=fPUtBwV7-h5Qfm1bV=<a href="mailto:1as4oZLo5UXQ@mail.gmail.com">1as4oZLo5UXQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello all,<br>
<br>
When computing metrics for image registration, does ITK calculated the<br>
metric for only the regions in the image that overlap?<br>
<br>
If so is this performed on just the initial regions that overlap or will<br>
this region of overlap increase during registration and thus require the<br>
region in which the metric is calculated to alter?<br>
<br>
Thanks for any help<br>
<br>
Emma<br>
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<br>
Message: 11<br>
Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST)<br>
From: Marco Ulge <<a href="mailto:marco.ulge@gmail.com">marco.ulge@gmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK-users] Texture Features extraction<br>
Message-ID: <<a href="mailto:1412601627242-34642.post@n7.nabble.com">1412601627242-34642.post@n7.nabble.com</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hello,<br>
<br>
i'm currently working on texture feature extraction and I'm following this<br>
examle:<br>
<a href="http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures" target="_blank">http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures</a><br>
<<a href="http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures" target="_blank">http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures</a>><br>
<br>
It works fine and basically it's all i need. The only problem is that i need<br>
to able to specify an arbitrary window size (which is 3 in this example) but<br>
as soon as i try to assign it a different value this won't work anymore and<br>
i can't figure out why.<br>
<br>
Can anyone help me with this please?<br>
<br>
Thanks.<br>
<br>
Marco<br>
<br>
<br>
<br>
--<br>
View this message in context: <a href="http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html" target="_blank">http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html</a><br>
Sent from the ITK - Users mailing list archive at Nabble.com.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 12<br>
Date: Mon, 06 Oct 2014 15:47:12 +0200<br>
From: Dominique T?pfer <<a href="mailto:dominique@toepfer-web.de">dominique@toepfer-web.de</a>><br>
To: Marco Ulge <<a href="mailto:marco.ulge@gmail.com">marco.ulge@gmail.com</a>>, <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: Re: [ITK-users] Texture Features extraction<br>
Message-ID: <<a href="mailto:54329D60.9030004@toepfer-web.de">54329D60.9030004@toepfer-web.de</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Hi Marco,<br>
<br>
you probably forgot to adjust the range of the for-loops. They are<br>
running from 1 to size-2 so that the window will not "leave" the image<br>
at its boundaries.<br>
<br>
HTH<br>
Dominique<br>
<br>
<br>
On <a href="tel:06.10.2014%2015" value="+390610201415">06.10.2014 15</a>:20, Marco Ulge wrote:<br>
> Hello,<br>
><br>
> i'm currently working on texture feature extraction and I'm following this<br>
> examle:<br>
> <a href="http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures" target="_blank">http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures</a><br>
> <<a href="http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures" target="_blank">http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures</a>><br>
><br>
> It works fine and basically it's all i need. The only problem is that i need<br>
> to able to specify an arbitrary window size (which is 3 in this example) but<br>
> as soon as i try to assign it a different value this won't work anymore and<br>
> i can't figure out why.<br>
><br>
> Can anyone help me with this please?<br>
><br>
> Thanks.<br>
><br>
> Marco<br>
><br>
><br>
><br>
> --<br>
> View this message in context: <a href="http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html" target="_blank">http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html</a><br>
> Sent from the ITK - Users mailing list archive at Nabble.com.<br>
> _____________________________________<br>
> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
><br>
> Visit other Kitware open-source projects at<br>
> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
><br>
> Kitware offers ITK Training Courses, for more information visit:<br>
> <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
><br>
> Please keep messages on-topic and check the ITK FAQ at:<br>
> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
><br>
> Follow this link to subscribe/unsubscribe:<br>
> <a href="http://public.kitware.com/mailman/listinfo/insight-users" target="_blank">http://public.kitware.com/mailman/listinfo/insight-users</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 13<br>
Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST)<br>
From: Marco Ulge <<a href="mailto:marco.ulge@gmail.com">marco.ulge@gmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: Re: [ITK-users] Texture Features extraction<br>
Message-ID: <<a href="mailto:1412605106652-34644.post@n7.nabble.com">1412605106652-34644.post@n7.nabble.com</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Thanks for your reply, so if i wanted to specify a window size of 5 (for<br>
example) i should iterate from 1 to size - 4?<br>
<br>
Thanks.<br>
<br>
Marco<br>
<br>
<br>
<br>
--<br>
View this message in context: <a href="http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html" target="_blank">http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html</a><br>
Sent from the ITK - Users mailing list archive at Nabble.com.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 14<br>
Date: Mon, 6 Oct 2014 10:27:10 -0400<br>
From: Jiahui Wang <<a href="mailto:wjhzwy@gmail.com">wjhzwy@gmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer<br>
Message-ID:<br>
<CAKowH=<a href="mailto:UPK2wK-ksA6v1vKak75aE1f3ea-de7sLQSTrGiQwxEpQ@mail.gmail.com">UPK2wK-ksA6v1vKak75aE1f3ea-de7sLQSTrGiQwxEpQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear All,<br>
<br>
I modified ImageRegistration8.cxx to run my own rigid registration.<br>
<br>
However, I found that the processing time of ITKv4 based<br>
RegularStepGradientDescentOptimizer is almost 10 times more than that of<br>
ITKv3 based one.<br>
<br>
The program was run on the same machine. The only difference is the ITK<br>
libraries.<br>
<br>
Could anyone give me some suggestions to solve this issue?<br>
<br>
Thanks,<br>
<br>
JW<br>
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------------------------------<br>
<br>
Message: 15<br>
Date: Mon, 6 Oct 2014 11:08:10 -0400<br>
From: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
To: Arnaud Gelas <<a href="mailto:arnaudgelas@gmail.com">arnaudgelas@gmail.com</a>><br>
Cc: insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>>, Mathieu Malaterre<br>
<<a href="mailto:mathieu.malaterre@gmail.com">mathieu.malaterre@gmail.com</a>><br>
Subject: Re: [ITK-users] How to remove a tag from MetaDataDictionary?<br>
Message-ID:<br>
<<a href="mailto:CALzTN-TjoXUpe16JNsViVH0srU_q1oTJpVYG94G3S6a0mUD3Eg@mail.gmail.com">CALzTN-TjoXUpe16JNsViVH0srU_q1oTJpVYG94G3S6a0mUD3Eg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Hi Arnaud,<br>
<br>
<br>
> I am trying to write a DICOM file in which, the orientation (among others)<br>
> has changed in my pipeline...<br>
><br>
> 1- After having a look<br>
> <a href="https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919" target="_blank">https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919</a><br>
><br>
> It appears to me that if the orientation is in the MetaDataDictionary, it is<br>
> saved anyway into the DICOM image, there is no way to force the ImageIO to<br>
> recompute it from the image and save it ???<br>
> If there is, can anyone give me a pointer?<br>
<br>
If there is a Direction on the input image, it should use it [1]. But<br>
the DICOM tag 0020|0037 cannot be present.<br>
<br>
<br>
> 2- Since I can't find a way to update the image orientation in<br>
> itk::GDCMImageIO, I have been looking at removing the corresponding tag from<br>
> the MetaDataDictionary. I could not find any method or any way to do it???<br>
> If there is, can anyone give me a pointer?<br>
><br>
> I wish I would not have to copy the dictionary and add if statement to avoid<br>
> copying the direction...<br>
<br>
This is the method I usually apply...<br>
<br>
Sorry for the lack of new tricks!<br>
Matt<br>
<br>
[1] <a href="https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828" target="_blank">https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 16<br>
Date: Mon, 6 Oct 2014 11:12:52 -0400<br>
From: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
To: Emma Saunders <<a href="mailto:emmasaunders123@gmail.com">emmasaunders123@gmail.com</a>><br>
Cc: "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a> Users" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] Overlap_image registration metrics<br>
Message-ID:<br>
<<a href="mailto:CALzTN-SrbFWD0R7-GAPxxT0ssf2fzLN_bATjtHB%2BZAyHYZjk%2Bw@mail.gmail.com">CALzTN-SrbFWD0R7-GAPxxT0ssf2fzLN_bATjtHB+ZAyHYZjk+w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Hi Emma,<br>
<br>
> When computing metrics for image registration, does ITK calculated the<br>
> metric for only the regions in the image that overlap?<br>
<br>
Yes. See, for example, [1].<br>
<br>
> If so is this performed on just the initial regions that overlap or will<br>
> this region of overlap increase during registration and thus require the<br>
> region in which the metric is calculated to alter?<br>
<br>
Yes. Ideally, as the registration progresses, the overlap increases,<br>
and the registration becomes progressively better.<br>
<br>
HTH,<br>
Matt<br>
<br>
[1] <a href="http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312" target="_blank">http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 17<br>
Date: Mon, 6 Oct 2014 15:44:08 +0000<br>
From: Andras Lasso <<a href="mailto:lasso@queensu.ca">lasso@queensu.ca</a>><br>
To: Jiahui Wang <<a href="mailto:wjhzwy@gmail.com">wjhzwy@gmail.com</a>>, "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>"<br>
<<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent<br>
Optimizer<br>
Message-ID:<br>
<<a href="mailto:B6FC5543F5C41E479B8B89158B0C58FF179374D9@MP-DUP-MBX-02.AD.QUEENSU.CA">B6FC5543F5C41E479B8B89158B0C58FF179374D9@MP-DUP-MBX-02.AD.QUEENSU.CA</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
See this long thread about this issue:<br>
<a href="http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html" target="_blank">http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html</a><br>
<br>
Short summary: There were some performance regressions in mutual information metric computation, threading, etc. that have been recently fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more accurate optimizer, but if you adjust the number of samples and stopping condition then usually the registration time only increases by about 30-50% (and you might get better quality results).<br>
<br>
You can see all the changes that have been done in 3D Slicer and BRAINS repositories to go from a 10x-100x slowdown to an approximately equivalent registration speed with ITKv4 compared to ITKv3.<br>
<br>
Andras<br>
<br>
From: Community [mailto:<a href="mailto:community-bounces@itk.org">community-bounces@itk.org</a>] On Behalf Of Jiahui Wang<br>
Sent: Monday, October 06, 2014 10:27 AM<br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer<br>
<br>
Dear All,<br>
I modified ImageRegistration8.cxx to run my own rigid registration.<br>
<br>
However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one.<br>
<br>
The program was run on the same machine. The only difference is the ITK libraries.<br>
<br>
Could anyone give me some suggestions to solve this issue?<br>
Thanks,<br>
JW<br>
<br>
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Message: 18<br>
Date: Tue, 7 Oct 2014 15:13:06 +0800<br>
From: Fabian Torres <<a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK-users] Polygon inside point<br>
Message-ID:<br>
<CALD_EpL1nDTBD7Pxb3RCjV0bo14Xy6t=<a href="mailto:KP5XsjnYeFWGwWbifQ@mail.gmail.com">KP5XsjnYeFWGwWbifQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all.<br>
<br>
I have an image that represents some pixels over the surface of an object.<br>
Pixels in the surface have value of 1 while any other pixel has value of 0.<br>
The pixels are not a continuous line, there are some gaps between pixels. I<br>
want to know the region surrounded by the white pixels in my image.<br>
<br>
I will be working with 2D and 3D data. Is there any class implemented in<br>
ITK that I can use?<br>
<br>
Thanks<br>
<br>
--<br>
Fabi?n Torres Robles<br>
Maestria en Ciencias en Ingenier?a Electr?nica<br>
Ingenier?a en Sistemas Electr?nicos<br>
tel. 58081280, 0445534661338<br>
e-mail <a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>, <a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a><br>
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Message: 19<br>
Date: Tue, 7 Oct 2014 15:38:49 +0800<br>
From: Fabian Torres <<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>><br>
To: insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: [ITK-users] region inside points<br>
Message-ID:<br>
<<a href="mailto:CALD_Ep%2BOEAE8Jik0hsy8PWYGBmxTHYWoRZOoFQaP2OqT1P_GyQ@mail.gmail.com">CALD_Ep+OEAE8Jik0hsy8PWYGBmxTHYWoRZOoFQaP2OqT1P_GyQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all.<br>
<br>
I have an image that represents some pixels over the surface of an object.<br>
Pixels in the surface have value of 1 while any other pixel has value of 0.<br>
The pixels are not a continuous line, there are some gaps between pixels. I<br>
want to know the region surrounded by the white pixels in my image.<br>
<br>
I will be working with 2D and 3D data. Is there any class implemented in<br>
ITK that I can use?<br>
<br>
Thanks<br>
--<br>
Fabi?n Torres Robles<br>
Maestria en Ciencias en Ingenier?a Electr?nica<br>
Ingenier?a en Sistemas Electr?nicos<br>
tel. 58081280, 0445534661338<br>
e-mail <a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>, <a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a><br>
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Message: 20<br>
Date: Tue, 7 Oct 2014 07:40:40 +0000<br>
From: Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>><br>
To: Fabian Torres <<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>>, insight-users<br>
<<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] region inside points<br>
Message-ID:<br>
<<a href="mailto:BD80F91C3E2E394894ED4780703D7F9E826C670A@uxcn10-tdc06.UoA.auckland.ac.nz">BD80F91C3E2E394894ED4780703D7F9E826C670A@uxcn10-tdc06.UoA.auckland.ac.nz</a>><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Maybe you could do something with BinaryImageDilateFilter.<br>
________________________________<br>
From: Insight-users [<a href="mailto:insight-users-bounces@itk.org">insight-users-bounces@itk.org</a>] on behalf of Fabian Torres [<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>]<br>
Sent: Tuesday, 7 October 2014 8:38 p.m.<br>
To: insight-users<br>
Subject: [ITK-users] region inside points<br>
<br>
Hi all.<br>
<br>
I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0.<br>
The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image.<br>
<br>
I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use?<br>
<br>
Thanks<br>
--<br>
Fabi?n Torres Robles<br>
Maestria en Ciencias en Ingenier?a Electr?nica<br>
Ingenier?a en Sistemas Electr?nicos<br>
tel. 58081280, 0445534661338<br>
e-mail <a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a><mailto:<a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>>, <a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a><mailto:<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>><br>
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Message: 21<br>
Date: Tue, 7 Oct 2014 07:46:17 +0000<br>
From: Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>><br>
To: Fabian Torres <<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>>, insight-users<br>
<<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] region inside points<br>
Message-ID:<br>
<<a href="mailto:BD80F91C3E2E394894ED4780703D7F9E826C671B@uxcn10-tdc06.UoA.auckland.ac.nz">BD80F91C3E2E394894ED4780703D7F9E826C671B@uxcn10-tdc06.UoA.auckland.ac.nz</a>><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization.<br>
________________________________<br>
From: Insight-users [<a href="mailto:insight-users-bounces@itk.org">insight-users-bounces@itk.org</a>] on behalf of Gib Bogle [<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>]<br>
Sent: Tuesday, 7 October 2014 8:40 p.m.<br>
To: Fabian Torres; insight-users<br>
Subject: Re: [ITK-users] region inside points<br>
<br>
Maybe you could do something with BinaryImageDilateFilter.<br>
________________________________<br>
From: Insight-users [<a href="mailto:insight-users-bounces@itk.org">insight-users-bounces@itk.org</a>] on behalf of Fabian Torres [<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>]<br>
Sent: Tuesday, 7 October 2014 8:38 p.m.<br>
To: insight-users<br>
Subject: [ITK-users] region inside points<br>
<br>
Hi all.<br>
<br>
I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0.<br>
The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image.<br>
<br>
I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use?<br>
<br>
Thanks<br>
--<br>
Fabi?n Torres Robles<br>
Maestria en Ciencias en Ingenier?a Electr?nica<br>
Ingenier?a en Sistemas Electr?nicos<br>
tel. 58081280, 0445534661338<br>
e-mail <a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a><mailto:<a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>>, <a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a><mailto:<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>><br>
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Message: 22<br>
Date: Tue, 7 Oct 2014 16:05:24 +0800<br>
From: Fabian Torres <<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>><br>
To: Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>><br>
Cc: insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK-users] region inside points<br>
Message-ID:<br>
<<a href="mailto:CALD_Ep%2BNkNKwMdz18XLQ3ygxBAdCwK0AGFBZcNPT3MfUpC_ARA@mail.gmail.com">CALD_Ep+NkNKwMdz18XLQ3ygxBAdCwK0AGFBZcNPT3MfUpC_ARA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Gib.<br>
<br>
Thanks for the quick response. The problem of using dilation and<br>
skeletonization is that some times the gap between pixels is big, and I<br>
will have to work with different and big structural elements to be sure<br>
that all the gaps were eliminated.<br>
<br>
I was hoping to find a class that works similar to a convex hull (it does<br>
not have to be convex) algorithm and then find the region surrounded by the<br>
hull.<br>
<br>
Thanks<br>
<br>
On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>> wrote:<br>
<br>
> Sorry, I misread your post Fabian - I read it as you wanting the region<br>
> _surrounding_ the white pixels. But dilate might be usable to fill the<br>
> gaps, followed by skeletonization.<br>
> ------------------------------<br>
> *From:* Insight-users [<a href="mailto:insight-users-bounces@itk.org">insight-users-bounces@itk.org</a>] on behalf of Gib<br>
> Bogle [<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>]<br>
> *Sent:* Tuesday, 7 October 2014 8:40 p.m.<br>
> *To:* Fabian Torres; insight-users<br>
> *Subject:* Re: [ITK-users] region inside points<br>
><br>
> Maybe you could do something with BinaryImageDilateFilter.<br>
> ------------------------------<br>
> *From:* Insight-users [<a href="mailto:insight-users-bounces@itk.org">insight-users-bounces@itk.org</a>] on behalf of Fabian<br>
> Torres [<a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a>]<br>
> *Sent:* Tuesday, 7 October 2014 8:38 p.m.<br>
> *To:* insight-users<br>
> *Subject:* [ITK-users] region inside points<br>
><br>
> Hi all.<br>
><br>
> I have an image that represents some pixels over the surface of an<br>
> object. Pixels in the surface have value of 1 while any other pixel has<br>
> value of 0.<br>
> The pixels are not a continuous line, there are some gaps between pixels.<br>
> I want to know the region surrounded by the white pixels in my image.<br>
><br>
> I will be working with 2D and 3D data. Is there any class implemented in<br>
> ITK that I can use?<br>
><br>
> Thanks<br>
> --<br>
> Fabi?n Torres Robles<br>
> Maestria en Ciencias en Ingenier?a Electr?nica<br>
> Ingenier?a en Sistemas Electr?nicos<br>
> tel. 58081280, 0445534661338<br>
> e-mail <a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>, <a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a><br>
><br>
<br>
<br>
<br>
--<br>
Fabi?n Torres Robles<br>
Maestria en Ciencias en Ingenier?a Electr?nica<br>
Ingenier?a en Sistemas Electr?nicos<br>
tel. 58081280, 0445534661338<br>
e-mail <a href="mailto:fabian.trobles@gmail.com">fabian.trobles@gmail.com</a>, <a href="mailto:dae.wong@gmail.com">dae.wong@gmail.com</a><br>
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</blockquote></div><br></div></div></div></div></div></div>