[ITK-users] 8. help installing ITK (Gianluigi Caddeo) solved
Gianluigi Caddeo
ggigi78 at gmail.com
Tue Oct 7 09:12:21 EDT 2014
Hi all,
I solved my problem,
I gave the correct path to the DOXYGEN_EXECUTABLE variable.
Gg
On Tue, Oct 7, 2014 at 9:05 AM, <insight-users-request at itk.org> wrote:
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> Today's Topics:
>
> 1. [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick)
> 2. Re: [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick)
> 3. Proper chaining of filters (Jo?l Schaerer)
> 4. Re: [ITK] Proper chaining of filters (Matt McCormick)
> 5. Re: [ITK] Proper chaining of filters (Jo?l Schaerer)
> 6. 3D generalized hough transform (Pedro Morais)
> 7. vector image registration (Lianli Liu)
> 8. help installing ITK (Gianluigi Caddeo)
> 9. How to remove a tag from MetaDataDictionary? (Arnaud Gelas)
> 10. Overlap_image registration metrics (Emma Saunders)
> 11. Texture Features extraction (Marco Ulge)
> 12. Re: Texture Features extraction (Dominique T?pfer)
> 13. Re: Texture Features extraction (Marco Ulge)
> 14. Speed of ITKv4 based Gradient Descent Optimizer (Jiahui Wang)
> 15. Re: How to remove a tag from MetaDataDictionary? (Matt McCormick)
> 16. Re: Overlap_image registration metrics (Matt McCormick)
> 17. Re: [ITK] Speed of ITKv4 based Gradient Descent Optimizer
> (Andras Lasso)
> 18. Polygon inside point (Fabian Torres)
> 19. region inside points (Fabian Torres)
> 20. Re: region inside points (Gib Bogle)
> 21. Re: region inside points (Gib Bogle)
> 22. Re: region inside points (Fabian Torres)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Oct 2014 15:40:44 -0400
> From: Matt McCormick <matt.mccormick at kitware.com>
> To: "community at itk.org" <community at itk.org>, "insight-users at itk.org"
> <insight-users at itk.org>, ITK <insight-developers at itk.org>
> Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released!
> Message-ID:
> <
> CALzTN-TXyhZ2aDaA-UQoFgbg3fPPCPzYKKFpAmKvuquf1EXgrw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On behalf of the Insight Toolkit Community, we are happy to announce
> the release of ITK 4.6.1!
>
> This is a patch release that addresses critical issues. The 4.6.1
> release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK
> build errors, Python wrapping warnings, CMake configuration with
> COMPONENTS, performance and memory consumption of the ITKv4
> implementation of the mutual information matching metric, and a many
> other issues.
>
> Congratulations and thanks to everyone who contributed to this
> release. We are particularly grateful for the collaborations with the
> 3D Slicer, Debian, GDCM, and MINC communities to address these issues.
> Questions and comments are welcome on the ITK mailing lists.
>
> The release files can be downloaded from:
>
> http://itk.org/ITK/resources/software.html
>
>
> The next feature release of 4.6.0 is scheduled for June.
>
>
> Enjoy ITK!
>
>
>
> Changes from v4.6.0 to v4.6.1:
>
> Arnaud Gelas (5):
> BUG: fix gdcm version in GDCMImageIO.
> COMP: missing cast when calling gdcm::DataElement::SetByteValue
> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
> false
> BUG: split include directories into appropriate cmake variables HDF5
> BUG: missing gdcm libraries when using system GDCM
>
> Brad King (2):
> COMP: Fix vxl_config_macros usage of CMake check macros
> BUG: Fix itk_module_config for repeated calls
>
> Bradley Lowekamp (8):
> ENH: Adding License file from upstream MetaIO
> ENH: Adding script to update MetaIO from upstream
> ENH: Remove ITK MetaIO to prepare for upstream import
> COMP: Fix variable type for Set/Get macros
> BUG: Use METER of sCAL scale unit
> BUG: Use PNG_SCALE_METER for PNG sCAL unit
> BUG: Fix overflows computing size of read tiff image
> BUG: Use array delete operator for array new allocations
>
> Christopher Mullins (2):
> COMP: Allows latex to compile for ITKSoftwareGuide
> COMP: Wrap MeshBase templates
>
> David T. Chen (1):
> DOC: Fixed HistogramThresholdImageFitler
>
> Gert Wollny (1):
> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)
>
> Girish Mallya (1):
> BUG: Tests added for BinaryImageToLabelMapFilter for single-row
> images.
>
> Hans Johnson (12):
> COMP: Add tolerance for comparing floating point
> PERF: Remove non-threadable algorithm components
> PERF: Remove large foot print of PDF derivatives.
> PERF: Revert Remove large foot print of PDF derivatives.
> STYLE: Test against almost equal for floating point values
> STYLE: Non-exact floating point testing
> PERF: Distribute initialization per thread buffers
> ENH: Remove unnecessary mutable qualifier.
> STYLE: Remove comment with no meaning.
> ENH: Moved accumlator logic to main MI class
> ENH: Allow staggering of accumulations per thread.
> PERF: Zero reset thread buffers during finalize
>
> Matthew McCormick (31):
> BUG: ArchiveTestingData.py future imports must occur at the
> beginning.
> DOC: Remove Image2.cxx reference from Book 2.
> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
> DOC: Remove references to Book 1 sections from Book 2.
> DOC: Make BinaryThresholdImageFilter not floating.
> DOC: Fix Software Guide figure caption for FlipImageFilter.
> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
> DOC: Remove duplicate figure in
> LaplacianRecursiveGaussianImageFilter2.cxx.
> DOC: ImageRandomConstIteratorWithIndex table reference.
> BUG: Bump GCCXML to 2014-08-06.
> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
> BUG: Call clear instead of empty on PatchBasedDenoising
> EmptyCaches().
> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
> BUG: Fix alpha assignment for RGBA TIFF.
> BUG: Fix Nifti IO read with large images.
> BUG: Improve thread-safety and performance of
> PCAShapeSignedDistanceFunction.
> DOC: itk::statistics -> itk::Statistics.
> DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
> DOC: Fix Software Guide page overruns in
> IterativeClosestPoint{1,2}.cxx.
> BUG: TransformFileReader does not clear its TransformList.
> BUG: Prevent dangling pointer in HDF5TransformIO.
> COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
> BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform
> STYLE: Improve style in BinaryImageToLabelMapFilter.
> BUG: Fix BinaryImageToLabelMapFilter on 1D image.
> ENH: Improve precision of the joint PDF sum
> BUG: Fix BinShrinkImageFilter for different input/output image types.
> COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
> COMP: Add missing wrapping for TransformIOBaseTemplate.
> BUG: gdcm::StringFilter recognizes backslash delimiter.
> ENH: Bump ITK version to 4.6.1.
>
> MetaIO Maintainers (1):
> MetaIO (reduced)
>
> Michka Popoff (4):
> BUG: Improve SWIG version check
> BUG: Add VTK_VERSION for older VTK versions
> BUG: Update VTK minimum version (for release)
> BUG: Fix memory leak in MetaImageIO after exception
>
> Vladimir S. FONOV (1):
> BUG: Fixing incorrect MINC style inverse transform
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 1 Oct 2014 15:50:33 -0400
> From: Matt McCormick <matt.mccormick at kitware.com>
> To: "community at itk.org" <community at itk.org>, "insight-users at itk.org"
> <insight-users at itk.org>, ITK <insight-developers at itk.org>
> Subject: Re: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released!
> Message-ID:
> <
> CALzTN-S9DU8K8ACbgVP6L0ozXQGvcbnfXC7nz8iu_xqLTVtHsw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Minor correction:
>
> >
> > The next feature release of 4.6.0 is scheduled for June.
> >
>
> The next feature release of 4.7.0 is scheduled for December.
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 02 Oct 2014 11:33:06 +0200
> From: Jo?l Schaerer <joel.schaerer at laposte.net>
> To: itk <insight-users at itk.org>
> Subject: [ITK-users] Proper chaining of filters
> Message-ID: <542D1BD2.40801 at laposte.net>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hi all,
>
> I've noticed a couple times that when building a pipeline with ITK, you
> need to keep a reference to all filters before the pipeline is updated.
> This seems a little counter-intuitive to me, so I would like to better
> understand the issue and see if there is a way around it.
>
> As an example, the following code doesn't work:
>
> DilateType::Pointer dilate = DilateType::New();
> dilate->SetInput(thresh->GetOutput());
> dilate->SetKernel(kernel);
>
> dilate_filters.push_back(dilate);
> for (int i=0; i<14; ++i) {
> DilateType::Pointer temp = DilateType::New();
> temp->SetInput(dilate->GetOutput());
> temp->SetKernel(kernel);
> dilate = temp;
> }
> dilate->Update();
>
> Regions don't get propagated properly and I get the following exception
> when writing the output:
>
> C++ exception with description
>
> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290:
> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not
> fully contain requested paste IO regionPaste IO region: ImageIORegion
> (0x7fff9bb72cc0)
> Dimension: 3
> Index: 0 0 0
> Size: 0 0 0
> Largest possible region: ImageRegion (0x7fff9bb72bc0)
> Dimension: 3
> Index: [0, 0, 0]
> Size: [0, 0, 0]
> " thrown in the test body.
>
> My guess is that the filters get destroyed before they get a chance to
> be executed. If I explicitely keep references to each filter, it works:
>
> DilateType::Pointer dilate = DilateType::New();
> dilate->SetInput(thresh->GetOutput());
> dilate->SetKernel(kernel);
> // We need to keep a reference to each filter in the pipeline before
> it is updated
> std::vector<DilateType::Pointer> dilate_filters;
> dilate_filters.push_back(dilate);
> for (int i=0; i<14; ++i) {
> DilateType::Pointer temp = DilateType::New();
> temp->SetInput(dilate_filters.back()->GetOutput());
> temp->SetKernel(kernel);
> dilate = temp;
> dilate_filters.push_back(temp);
> }
> dilate_filters.back()->Update();
>
> My question is, why doesn't a filter keep a reference to the previous
> filter in the pipeline? Is there a way around this?
>
> Thanks!
>
> Jo?l
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 2 Oct 2014 10:16:08 -0400
> From: Matt McCormick <matt.mccormick at kitware.com>
> To: Jo?l Schaerer <joel.schaerer at laposte.net>
> Cc: itk <insight-users at itk.org>
> Subject: Re: [ITK-users] [ITK] Proper chaining of filters
> Message-ID:
> <CALzTN-SdcSYREtftRToGyMs9Q6=7UDerCMmMLwRYNTR5=
> v6XSg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Jo?l,
>
> Calling
>
> temp->SetInput(dilate->GetOutput());
>
> Connects the DataObject generated by dilate to the temp filter. temp
> does not increment dilate's reference count, and it would be difficult
> to do since the SetInput input is the DataObject, not the
> ProcessObject.
>
> As a consequence, at least one SmartPointer needs to be kept in scope
> as with your second example.
>
> HTH,
> Matt
>
> On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer <joel.schaerer at laposte.net>
> wrote:
> > Hi all,
> >
> > I've noticed a couple times that when building a pipeline with ITK, you
> need
> > to keep a reference to all filters before the pipeline is updated. This
> > seems a little counter-intuitive to me, so I would like to better
> understand
> > the issue and see if there is a way around it.
> >
> > As an example, the following code doesn't work:
> >
> > DilateType::Pointer dilate = DilateType::New();
> > dilate->SetInput(thresh->GetOutput());
> > dilate->SetKernel(kernel);
> >
> > dilate_filters.push_back(dilate);
> > for (int i=0; i<14; ++i) {
> > DilateType::Pointer temp = DilateType::New();
> > temp->SetInput(dilate->GetOutput());
> > temp->SetKernel(kernel);
> > dilate = temp;
> > }
> > dilate->Update();
> >
> > Regions don't get propagated properly and I get the following exception
> when
> > writing the output:
> >
> > C++ exception with description
> >
> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290:
> > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not
> > fully contain requested paste IO regionPaste IO region: ImageIORegion
> > (0x7fff9bb72cc0)
> > Dimension: 3
> > Index: 0 0 0
> > Size: 0 0 0
> > Largest possible region: ImageRegion (0x7fff9bb72bc0)
> > Dimension: 3
> > Index: [0, 0, 0]
> > Size: [0, 0, 0]
> > " thrown in the test body.
> >
> > My guess is that the filters get destroyed before they get a chance to be
> > executed. If I explicitely keep references to each filter, it works:
> >
> > DilateType::Pointer dilate = DilateType::New();
> > dilate->SetInput(thresh->GetOutput());
> > dilate->SetKernel(kernel);
> > // We need to keep a reference to each filter in the pipeline before
> it is
> > updated
> > std::vector<DilateType::Pointer> dilate_filters;
> > dilate_filters.push_back(dilate);
> > for (int i=0; i<14; ++i) {
> > DilateType::Pointer temp = DilateType::New();
> > temp->SetInput(dilate_filters.back()->GetOutput());
> > temp->SetKernel(kernel);
> > dilate = temp;
> > dilate_filters.push_back(temp);
> > }
> > dilate_filters.back()->Update();
> >
> > My question is, why doesn't a filter keep a reference to the previous
> filter
> > in the pipeline? Is there a way around this?
> >
> > Thanks!
> >
> > Jo?l
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check 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
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 02 Oct 2014 16:22:24 +0200
> From: Jo?l Schaerer <joel.schaerer at laposte.net>
> To: Matt McCormick <matt.mccormick at kitware.com>
> Cc: itk <insight-users at itk.org>
> Subject: Re: [ITK-users] [ITK] Proper chaining of filters
> Message-ID: <542D5FA0.8070903 at laposte.net>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hi Matt,
>
> Thanks for the confirmation. I was thinking there might be another
> mechanism I wasn't aware of.
>
> Jo?l
>
> On 10/02/2014 04:16 PM, Matt McCormick wrote:
> > Hi Jo?l,
> >
> > Calling
> >
> > temp->SetInput(dilate->GetOutput());
> >
> > Connects the DataObject generated by dilate to the temp filter. temp
> > does not increment dilate's reference count, and it would be difficult
> > to do since the SetInput input is the DataObject, not the
> > ProcessObject.
> >
> > As a consequence, at least one SmartPointer needs to be kept in scope
> > as with your second example.
> >
> > HTH,
> > Matt
> >
> > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer <joel.schaerer at laposte.net>
> wrote:
> >> Hi all,
> >>
> >> I've noticed a couple times that when building a pipeline with ITK, you
> need
> >> to keep a reference to all filters before the pipeline is updated. This
> >> seems a little counter-intuitive to me, so I would like to better
> understand
> >> the issue and see if there is a way around it.
> >>
> >> As an example, the following code doesn't work:
> >>
> >> DilateType::Pointer dilate = DilateType::New();
> >> dilate->SetInput(thresh->GetOutput());
> >> dilate->SetKernel(kernel);
> >>
> >> dilate_filters.push_back(dilate);
> >> for (int i=0; i<14; ++i) {
> >> DilateType::Pointer temp = DilateType::New();
> >> temp->SetInput(dilate->GetOutput());
> >> temp->SetKernel(kernel);
> >> dilate = temp;
> >> }
> >> dilate->Update();
> >>
> >> Regions don't get propagated properly and I get the following exception
> when
> >> writing the output:
> >>
> >> C++ exception with description
> >>
> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290:
> >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not
> >> fully contain requested paste IO regionPaste IO region: ImageIORegion
> >> (0x7fff9bb72cc0)
> >> Dimension: 3
> >> Index: 0 0 0
> >> Size: 0 0 0
> >> Largest possible region: ImageRegion (0x7fff9bb72bc0)
> >> Dimension: 3
> >> Index: [0, 0, 0]
> >> Size: [0, 0, 0]
> >> " thrown in the test body.
> >>
> >> My guess is that the filters get destroyed before they get a chance to
> be
> >> executed. If I explicitely keep references to each filter, it works:
> >>
> >> DilateType::Pointer dilate = DilateType::New();
> >> dilate->SetInput(thresh->GetOutput());
> >> dilate->SetKernel(kernel);
> >> // We need to keep a reference to each filter in the pipeline before
> it is
> >> updated
> >> std::vector<DilateType::Pointer> dilate_filters;
> >> dilate_filters.push_back(dilate);
> >> for (int i=0; i<14; ++i) {
> >> DilateType::Pointer temp = DilateType::New();
> >> temp->SetInput(dilate_filters.back()->GetOutput());
> >> temp->SetKernel(kernel);
> >> dilate = temp;
> >> dilate_filters.push_back(temp);
> >> }
> >> dilate_filters.back()->Update();
> >>
> >> My question is, why doesn't a filter keep a reference to the previous
> filter
> >> in the pipeline? Is there a way around this?
> >>
> >> Thanks!
> >>
> >> Jo?l
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check 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
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT)
> From: Pedro Morais <pedromorais-17 at hotmail.com>
> To: insight-users at itk.org
> Subject: [ITK-users] 3D generalized hough transform
> Message-ID: <1412267071841-7586297.post at n2.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi all,
>
> I'm wonder if ITK has an implementation of a 3D generalized hough
> transform.
> Do you have any idea?
>
> Regards,
> Pedro
>
>
>
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 2 Oct 2014 20:40:16 -0400
> From: Lianli Liu <llliu at umich.edu>
> To: "insight-users at itk.org" <insight-users at itk.org>
> Subject: [ITK-users] vector image registration
> Message-ID:
> <
> CAGKqDmfV89qpnVG5tq4bvZrc6FDHhNRHrkvWg7qEXjh_pObKsQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I wonder if ITK is supporting vector image registration now? If not, any
> suggestions to achieve this goal?
>
> Thanks!
> Lianli
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>
> ------------------------------
>
> Message: 8
> Date: Fri, 3 Oct 2014 10:05:29 +0100
> From: Gianluigi Caddeo <ggigi78 at gmail.com>
> To: insight-users at itk.org
> Subject: [ITK-users] help installing ITK
> Message-ID:
> <
> CADeTECOS-PqOswWC4H2Wo_f8eKjd24eN+eSDfRG+YK8LKF7+CA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
> during my installation on an ubuntu machine I had this problem:
>
>
>
>
>
>
> *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1:
> DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: ***
> [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: ***
> [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: ***
> [all] Errore*
> But doxygen exist and stay in my */usr/bin* directory
>
> How can I to force ITK to search doxygen in that directory?
>
> thanks a lot
>
> Gg
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 9
> Date: Mon, 6 Oct 2014 09:58:09 +0200
> From: Arnaud Gelas <arnaudgelas at gmail.com>
> To: insight-users <insight-users at itk.org>
> Cc: Mathieu Malaterre <mathieu.malaterre at gmail.com>
> Subject: [ITK-users] How to remove a tag from MetaDataDictionary?
> Message-ID:
> <
> CAK3qF+8e1kg7bN4EcM2FUYy_e3AYz-M3ZrGGwkssWz0Kvz4y2Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I am trying to write a DICOM file in which, the orientation (among others)
> has changed in my pipeline...
>
> 1- After having a look
>
> https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919
>
> It appears to me that if the orientation is in the MetaDataDictionary, it
> is saved anyway into the DICOM image, there is no way to force the ImageIO
> to recompute it from the image and save it ???
> If there is, can anyone give me a pointer?
>
> 2- Since I can't find a way to update the image orientation in
> itk::GDCMImageIO, I have been looking at removing the corresponding tag
> from the MetaDataDictionary. I could not find any method or any way to do
> it???
> If there is, can anyone give me a pointer?
>
> I wish I would not have to copy the dictionary and add if statement to
> avoid copying the direction...
>
> Thanks in advance,
> Arnaud
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> ------------------------------
>
> Message: 10
> Date: Mon, 6 Oct 2014 12:31:03 +0100
> From: Emma Saunders <emmasaunders123 at gmail.com>
> To: "insight-users at itk.org Users" <insight-users at itk.org>
> Subject: [ITK-users] Overlap_image registration metrics
> Message-ID:
> <CABQY8kQ1QoeHo_X-RJ0=fPUtBwV7-h5Qfm1bV=
> 1as4oZLo5UXQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> When computing metrics for image registration, does ITK calculated the
> metric for only the regions in the image that overlap?
>
> If so is this performed on just the initial regions that overlap or will
> this region of overlap increase during registration and thus require the
> region in which the metric is calculated to alter?
>
> Thanks for any help
>
> Emma
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>
> ------------------------------
>
> Message: 11
> Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST)
> From: Marco Ulge <marco.ulge at gmail.com>
> To: insight-users at itk.org
> Subject: [ITK-users] Texture Features extraction
> Message-ID: <1412601627242-34642.post at n7.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hello,
>
> i'm currently working on texture feature extraction and I'm following this
> examle:
> http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
> <http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures>
>
> It works fine and basically it's all i need. The only problem is that i
> need
> to able to specify an arbitrary window size (which is 3 in this example)
> but
> as soon as i try to assign it a different value this won't work anymore and
> i can't figure out why.
>
> Can anyone help me with this please?
>
> Thanks.
>
> Marco
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 06 Oct 2014 15:47:12 +0200
> From: Dominique T?pfer <dominique at toepfer-web.de>
> To: Marco Ulge <marco.ulge at gmail.com>, insight-users at itk.org
> Subject: Re: [ITK-users] Texture Features extraction
> Message-ID: <54329D60.9030004 at toepfer-web.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Marco,
>
> you probably forgot to adjust the range of the for-loops. They are
> running from 1 to size-2 so that the window will not "leave" the image
> at its boundaries.
>
> HTH
> Dominique
>
>
> On 06.10.2014 15:20, Marco Ulge wrote:
> > Hello,
> >
> > i'm currently working on texture feature extraction and I'm following
> this
> > examle:
> > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures
> > <http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures>
> >
> > It works fine and basically it's all i need. The only problem is that i
> need
> > to able to specify an arbitrary window size (which is 3 in this example)
> but
> > as soon as i try to assign it a different value this won't work anymore
> and
> > i can't figure out why.
> >
> > Can anyone help me with this please?
> >
> > Thanks.
> >
> > Marco
> >
> >
> >
> > --
> > View this message in context:
> http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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
>
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST)
> From: Marco Ulge <marco.ulge at gmail.com>
> To: insight-users at itk.org
> Subject: Re: [ITK-users] Texture Features extraction
> Message-ID: <1412605106652-34644.post at n7.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Thanks for your reply, so if i wanted to specify a window size of 5 (for
> example) i should iterate from 1 to size - 4?
>
> Thanks.
>
> Marco
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 6 Oct 2014 10:27:10 -0400
> From: Jiahui Wang <wjhzwy at gmail.com>
> To: insight-users at itk.org
> Subject: [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer
> Message-ID:
> <CAKowH=
> UPK2wK-ksA6v1vKak75aE1f3ea-de7sLQSTrGiQwxEpQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
>
> I modified ImageRegistration8.cxx to run my own rigid registration.
>
> However, I found that the processing time of ITKv4 based
> RegularStepGradientDescentOptimizer is almost 10 times more than that of
> ITKv3 based one.
>
> The program was run on the same machine. The only difference is the ITK
> libraries.
>
> Could anyone give me some suggestions to solve this issue?
>
> Thanks,
>
> JW
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>
> ------------------------------
>
> Message: 15
> Date: Mon, 6 Oct 2014 11:08:10 -0400
> From: Matt McCormick <matt.mccormick at kitware.com>
> To: Arnaud Gelas <arnaudgelas at gmail.com>
> Cc: insight-users <insight-users at itk.org>, Mathieu Malaterre
> <mathieu.malaterre at gmail.com>
> Subject: Re: [ITK-users] How to remove a tag from MetaDataDictionary?
> Message-ID:
> <
> CALzTN-TjoXUpe16JNsViVH0srU_q1oTJpVYG94G3S6a0mUD3Eg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Arnaud,
>
>
> > I am trying to write a DICOM file in which, the orientation (among
> others)
> > has changed in my pipeline...
> >
> > 1- After having a look
> >
> https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919
> >
> > It appears to me that if the orientation is in the MetaDataDictionary,
> it is
> > saved anyway into the DICOM image, there is no way to force the ImageIO
> to
> > recompute it from the image and save it ???
> > If there is, can anyone give me a pointer?
>
> If there is a Direction on the input image, it should use it [1]. But
> the DICOM tag 0020|0037 cannot be present.
>
>
> > 2- Since I can't find a way to update the image orientation in
> > itk::GDCMImageIO, I have been looking at removing the corresponding tag
> from
> > the MetaDataDictionary. I could not find any method or any way to do
> it???
> > If there is, can anyone give me a pointer?
> >
> > I wish I would not have to copy the dictionary and add if statement to
> avoid
> > copying the direction...
>
> This is the method I usually apply...
>
> Sorry for the lack of new tricks!
> Matt
>
> [1]
> https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 6 Oct 2014 11:12:52 -0400
> From: Matt McCormick <matt.mccormick at kitware.com>
> To: Emma Saunders <emmasaunders123 at gmail.com>
> Cc: "insight-users at itk.org Users" <insight-users at itk.org>
> Subject: Re: [ITK-users] Overlap_image registration metrics
> Message-ID:
> <
> CALzTN-SrbFWD0R7-GAPxxT0ssf2fzLN_bATjtHB+ZAyHYZjk+w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Emma,
>
> > When computing metrics for image registration, does ITK calculated the
> > metric for only the regions in the image that overlap?
>
> Yes. See, for example, [1].
>
> > If so is this performed on just the initial regions that overlap or
> will
> > this region of overlap increase during registration and thus require the
> > region in which the metric is calculated to alter?
>
> Yes. Ideally, as the registration progresses, the overlap increases,
> and the registration becomes progressively better.
>
> HTH,
> Matt
>
> [1]
> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312
>
>
> ------------------------------
>
> Message: 17
> Date: Mon, 6 Oct 2014 15:44:08 +0000
> From: Andras Lasso <lasso at queensu.ca>
> To: Jiahui Wang <wjhzwy at gmail.com>, "insight-users at itk.org"
> <insight-users at itk.org>
> Subject: Re: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent
> Optimizer
> Message-ID:
> <
> B6FC5543F5C41E479B8B89158B0C58FF179374D9 at MP-DUP-MBX-02.AD.QUEENSU.CA>
> Content-Type: text/plain; charset="utf-8"
>
> See this long thread about this issue:
>
> http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html
>
> 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).
>
> 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.
>
> Andras
>
> From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui
> Wang
> Sent: Monday, October 06, 2014 10:27 AM
> To: insight-users at itk.org
> Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer
>
> Dear All,
> I modified ImageRegistration8.cxx to run my own rigid registration.
>
> However, I found that the processing time of ITKv4 based
> RegularStepGradientDescentOptimizer is almost 10 times more than that of
> ITKv3 based one.
>
> The program was run on the same machine. The only difference is the ITK
> libraries.
>
> Could anyone give me some suggestions to solve this issue?
> Thanks,
> JW
>
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 18
> Date: Tue, 7 Oct 2014 15:13:06 +0800
> From: Fabian Torres <fabian.trobles at gmail.com>
> To: insight-users at itk.org
> Subject: [ITK-users] Polygon inside point
> Message-ID:
> <CALD_EpL1nDTBD7Pxb3RCjV0bo14Xy6t=
> KP5XsjnYeFWGwWbifQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all.
>
> 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.
> 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.
>
> I will be working with 2D and 3D data. Is there any class implemented in
> ITK that I can use?
>
> Thanks
>
> --
> Fabi?n Torres Robles
> Maestria en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> tel. 58081280, 0445534661338
> e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 19
> Date: Tue, 7 Oct 2014 15:38:49 +0800
> From: Fabian Torres <dae.wong at gmail.com>
> To: insight-users <insight-users at itk.org>
> Subject: [ITK-users] region inside points
> Message-ID:
> <
> CALD_Ep+OEAE8Jik0hsy8PWYGBmxTHYWoRZOoFQaP2OqT1P_GyQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all.
>
> 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.
> 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.
>
> I will be working with 2D and 3D data. Is there any class implemented in
> ITK that I can use?
>
> Thanks
> --
> Fabi?n Torres Robles
> Maestria en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> tel. 58081280, 0445534661338
> e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 20
> Date: Tue, 7 Oct 2014 07:40:40 +0000
> From: Gib Bogle <g.bogle at auckland.ac.nz>
> To: Fabian Torres <dae.wong at gmail.com>, insight-users
> <insight-users at itk.org>
> Subject: Re: [ITK-users] region inside points
> Message-ID:
> <
> BD80F91C3E2E394894ED4780703D7F9E826C670A at uxcn10-tdc06.UoA.auckland.ac.nz>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Maybe you could do something with BinaryImageDilateFilter.
> ________________________________
> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian
> Torres [dae.wong at gmail.com]
> Sent: Tuesday, 7 October 2014 8:38 p.m.
> To: insight-users
> Subject: [ITK-users] region inside points
>
> Hi all.
>
> 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.
> 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.
>
> I will be working with 2D and 3D data. Is there any class implemented in
> ITK that I can use?
>
> Thanks
> --
> Fabi?n Torres Robles
> Maestria en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> tel. 58081280, 0445534661338
> e-mail fabian.trobles at gmail.com<mailto:fabian.trobles at gmail.com>,
> dae.wong at gmail.com<mailto:dae.wong at gmail.com>
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 21
> Date: Tue, 7 Oct 2014 07:46:17 +0000
> From: Gib Bogle <g.bogle at auckland.ac.nz>
> To: Fabian Torres <dae.wong at gmail.com>, insight-users
> <insight-users at itk.org>
> Subject: Re: [ITK-users] region inside points
> Message-ID:
> <
> BD80F91C3E2E394894ED4780703D7F9E826C671B at uxcn10-tdc06.UoA.auckland.ac.nz>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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.
> ________________________________
> From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib
> Bogle [g.bogle at auckland.ac.nz]
> Sent: Tuesday, 7 October 2014 8:40 p.m.
> To: Fabian Torres; insight-users
> Subject: Re: [ITK-users] region inside points
>
> Maybe you could do something with BinaryImageDilateFilter.
> ________________________________
> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian
> Torres [dae.wong at gmail.com]
> Sent: Tuesday, 7 October 2014 8:38 p.m.
> To: insight-users
> Subject: [ITK-users] region inside points
>
> Hi all.
>
> 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.
> 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.
>
> I will be working with 2D and 3D data. Is there any class implemented in
> ITK that I can use?
>
> Thanks
> --
> Fabi?n Torres Robles
> Maestria en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> tel. 58081280, 0445534661338
> e-mail fabian.trobles at gmail.com<mailto:fabian.trobles at gmail.com>,
> dae.wong at gmail.com<mailto:dae.wong at gmail.com>
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 22
> Date: Tue, 7 Oct 2014 16:05:24 +0800
> From: Fabian Torres <dae.wong at gmail.com>
> To: Gib Bogle <g.bogle at auckland.ac.nz>
> Cc: insight-users <insight-users at itk.org>
> Subject: Re: [ITK-users] region inside points
> Message-ID:
> <
> CALD_Ep+NkNKwMdz18XLQ3ygxBAdCwK0AGFBZcNPT3MfUpC_ARA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Gib.
>
> Thanks for the quick response. The problem of using dilation and
> skeletonization is that some times the gap between pixels is big, and I
> will have to work with different and big structural elements to be sure
> that all the gaps were eliminated.
>
> I was hoping to find a class that works similar to a convex hull (it does
> not have to be convex) algorithm and then find the region surrounded by the
> hull.
>
> Thanks
>
> On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>
> > 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.
> > ------------------------------
> > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib
> > Bogle [g.bogle at auckland.ac.nz]
> > *Sent:* Tuesday, 7 October 2014 8:40 p.m.
> > *To:* Fabian Torres; insight-users
> > *Subject:* Re: [ITK-users] region inside points
> >
> > Maybe you could do something with BinaryImageDilateFilter.
> > ------------------------------
> > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of
> Fabian
> > Torres [dae.wong at gmail.com]
> > *Sent:* Tuesday, 7 October 2014 8:38 p.m.
> > *To:* insight-users
> > *Subject:* [ITK-users] region inside points
> >
> > Hi all.
> >
> > 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.
> > 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.
> >
> > I will be working with 2D and 3D data. Is there any class implemented in
> > ITK that I can use?
> >
> > Thanks
> > --
> > Fabi?n Torres Robles
> > Maestria en Ciencias en Ingenier?a Electr?nica
> > Ingenier?a en Sistemas Electr?nicos
> > tel. 58081280, 0445534661338
> > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
> >
>
>
>
> --
> Fabi?n Torres Robles
> Maestria en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> tel. 58081280, 0445534661338
> e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
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>
> Subject: Digest Footer
>
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> Insight-users at itk.org
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>
> ------------------------------
>
> End of Insight-users Digest, Vol 126, Issue 2
> *********************************************
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