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Use Resample over WarpImageFilter in Examples #809

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blowekamp opened this issue May 2, 2019 · 15 comments
Open

Use Resample over WarpImageFilter in Examples #809

blowekamp opened this issue May 2, 2019 · 15 comments
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@blowekamp
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area:Registration Issues affecting the Registration module status:Backlog Postponed without a fixed deadline

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@blowekamp
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These two filers apply deformation fields to images ( and vector images ). The same functionality now exist in the ResampleImageFilter.

Should these filters be deprecated to avoid confusion?
@blowekamp blowekamp added status:Needs info Further clarification or new data required area:Registration Issues affecting the Registration module labels May 2, 2019
@blowekamp
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@thewtex @ntustison @hjmjohnson
Any thought on these classes?

@hjmjohnson
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@blowekamp I am in favor of deprecating as long a documentation clearly expresses how to get the same results with ResampleImageFilter (Including an example refactoring).

Thanks Brad.

@blowekamp
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Here is list of examples which use the WarpImageFilter:

Filtering/WarpImageFilter1.cxx
RegistrationITKv3/DeformableRegistration10.cxx
RegistrationITKv3/DeformableRegistration16.cxx
RegistrationITKv3/DeformableRegistration17.cxx
RegistrationITKv3/DeformableRegistration2.cxx
RegistrationITKv3/DeformableRegistration3.cxx
RegistrationITKv3/DeformableRegistration5.cxx
RegistrationITKv3/DeformableRegistration9.cxx
RegistrationITKv3/LandmarkWarping2.cxx
RegistrationITKv4/DeformableRegistration10.cxx
RegistrationITKv4/DeformableRegistration16.cxx
RegistrationITKv4/DeformableRegistration17.cxx
RegistrationITKv4/DeformableRegistration2.cxx
RegistrationITKv4/DeformableRegistration3.cxx
RegistrationITKv4/DeformableRegistration5.cxx
RegistrationITKv4/DeformableRegistration9.cxx
RegistrationITKv4/LandmarkWarping2.cxx

Looks like step one is to update those examples to use the ResampleImageFilter.

@blowekamp
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We need to figure out what to do with the ITKv3 Registration examples...

@hjmjohnson
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The ITKv3 examples should definitely be deprecated, and I would recommend removing them (as they are now confusing to users who accidentally end up in that directory.

@hjmjohnson
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On second thought, perhaps we should just move them out of the "examples" directory and into a "testing" subdirectory as they may still have code coverage utility.

ITKv6 should evaluate if the ITKv3 framework is completely removed.

@blowekamp
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blowekamp commented May 2, 2019 •
edited

I agree that it is important to keep them as testing while we have the ITKv3 registration framework still there.

Tangentially related, ITKv4 registration framework now sounds old. Perhaps is would have been better to call the old one "legacy" registration framework, and just call the current one "the registration framework". I'm not sure how often it's called ITKv4 registration framework.

@hjmjohnson hjmjohnson mentioned this issue May 2, 2019
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@blowekamp blowekamp removed the status:Needs info Further clarification or new data required label May 3, 2019
@blowekamp
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It would take quite a bit of effort to fully remove the warp filters now. There are a number of filters still using them.

The examples are the important things to update now to just use the ResampleImageFilter. I'll try to knock these off little by little.

@hjmjohnson
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It would take quite a bit of effort to fully remove the warp filters now. There are a number of filters still using them.

The examples are the important things to update now to just use the ResampleImageFilter. I'll try to knock these off little by little.

@blowekamp Thanks. I appreciate the efforts.

@blowekamp blowekamp changed the title Deprecate WarpImageFilter and WarpVectorImageFilter Use Resample over WarpImageFilter in Examples May 17, 2019
@dzenanz
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dzenanz commented Jun 13, 2019

Can this now be closed? There was some work on this topic over the past month.

@blowekamp
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blowekamp commented Jun 13, 2019 •
edited

There is still quite a number of examples which should be updated.

@dzenanz
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dzenanz commented Jul 23, 2019

I just noticed compile errors in non-default module ITKFEMRegistration:
C:\Dashboard\ITK\Modules\Registration\FEM\include\itkFEMRegistrationFilter.h(166): error C2061: syntax error: identifier 'VectorInterpolateImageFunction' [C:\Dashboard\ITK-build\Modules\Registration\FEM\test\ITKFEMRegistrationTestDriver.vcxproj]. Is this on your radar @blowekamp?

@blowekamp
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Nope, I hadn't seen this before. Is it more related to one of my changes or @maekclena changes?

@dzenanz
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dzenanz commented Jul 23, 2019

Failures started on 2019-07-08. The probable culprit is 9ef036a, by @maekclena.

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stale bot commented Nov 20, 2019

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the status:Backlog Postponed without a fixed deadline label Nov 20, 2019
hjmjohnson pushed a commit to hjmjohnson/ITK that referenced this issue Nov 19, 2020
@hjmjohnson
VNL 2020-11-19 (f5c93ed9)
8d355cf 
Run the UpdateFromUpstream.sh script to extract upstream VNL
using the following shell commands.

$ git archive --prefix=upstream-vnl/ f5c93ed9 -- 
      CMakeLists.txt
      config/cmake
      core/CMakeLists.txt
      core/testlib
      core/vnl
      core/vxl_config.h.in
      core/vxl_copyright.h
      core/vxl_version.h
      v3p/CMakeLists.txt
      v3p/netlib
      vcl
 | tar x
$ git shortlog --perl-regexp --author='^((?!Kitware Robot).*)$' --no-merges --abbrev=8 --format='%h %s' a302a89b..f5c93ed9

Drew Gilliam (3):
      869d8c77 contrib/brl - update vxl_configure_file locations, and add HEADER_BINARY_DIR to vxl_add_library for appropriate BUILD_INTERFACE on targets
      38e108cf bvgl_algo - use brl_resource_file for bvgl_eulerspiral_lookup_table resource
      7437c02b bsgm_prob_pairwise_dsm bug fix - favor std::is_same over other methods for template type discovery

Hans Johnson (1):
      f5c93ed9 ENH: Add front() and back() members to vnl_vector and vnl_vector_fixed

Joseph Mundy (14):
      c320d11e templated appearance over input image type
      ad1ab6b0 modify bsgm to handle 16 bit input images
      c9e57958 added 2x processing
      a63bf124 remove debug statements
      bded9867 modified scale for 11 bits vs 8 bits
      5adc3edd restructure 16 bit dynamic range interface
      b16e0d25 added print for dynamic range setting
      7c2914c7 add comments and a few cleanups
      03ef4efe moved error checking .h to dispairity estimator .h
      5524102f add include for <limits>
      cb439258 fixed duplicate scale_0 in prob_pairwise
      596e40a9 add grid index for float data
      57f3d9b1 add .h file
      d4acae8a fix inconsistent pointset append cases

Noah Johnson (1):
      dd42c4fa ENH: vgl_io_pointset_3d (InsightSoftwareConsortium#809)

Tim Cootes (3):
      31bd3efa Added option
      f8c7778b Added line styles
      15d4a216 Added option to save separate frames

Change-Id: I444432535c0a8054edf7903eb549b2710514c730
hjmjohnson pushed a commit to hjmjohnson/ITK that referenced this issue Nov 20, 2020
@hjmjohnson
VNL 2020-11-20 (3d3e8683)
95c6f06 
Run the UpdateFromUpstream.sh script to extract upstream VNL
using the following shell commands.

$ git archive --prefix=upstream-vnl/ 3d3e8683 -- 
      CMakeLists.txt
      config/cmake
      core/CMakeLists.txt
      core/testlib
      core/vnl
      core/vxl_config.h.in
      core/vxl_copyright.h
      core/vxl_version.h
      v3p/CMakeLists.txt
      v3p/netlib
      vcl
 | tar x
$ git shortlog --perl-regexp --author='^((?!Kitware Robot).*)$' --no-merges --abbrev=8 --format='%h %s' a302a89b..3d3e8683

Drew Gilliam (3):
      869d8c77 contrib/brl - update vxl_configure_file locations, and add HEADER_BINARY_DIR to vxl_add_library for appropriate BUILD_INTERFACE on targets
      38e108cf bvgl_algo - use brl_resource_file for bvgl_eulerspiral_lookup_table resource
      7437c02b bsgm_prob_pairwise_dsm bug fix - favor std::is_same over other methods for template type discovery

Hans Johnson (2):
      f5c93ed9 ENH: Add front() and back() members to vnl_vector and vnl_vector_fixed
      3d3e8683 DOC: Grammer change in comment

Joseph Mundy (14):
      c320d11e templated appearance over input image type
      ad1ab6b0 modify bsgm to handle 16 bit input images
      c9e57958 added 2x processing
      a63bf124 remove debug statements
      bded9867 modified scale for 11 bits vs 8 bits
      5adc3edd restructure 16 bit dynamic range interface
      b16e0d25 added print for dynamic range setting
      7c2914c7 add comments and a few cleanups
      03ef4efe moved error checking .h to dispairity estimator .h
      5524102f add include for <limits>
      cb439258 fixed duplicate scale_0 in prob_pairwise
      596e40a9 add grid index for float data
      57f3d9b1 add .h file
      d4acae8a fix inconsistent pointset append cases

Noah Johnson (1):
      dd42c4fa ENH: vgl_io_pointset_3d (InsightSoftwareConsortium#809)

Tim Cootes (3):
      31bd3efa Added option
      f8c7778b Added line styles
      15d4a216 Added option to save separate frames

Change-Id: I8a2d3efb415942488161724a6a3880b3a7032e13
hjmjohnson pushed a commit to hjmjohnson/ITK that referenced this issue Nov 20, 2020
@hjmjohnson
VNL 2020-11-20 (3d3e8683)
df8f476 
Run the UpdateFromUpstream.sh script to extract upstream VNL
using the following shell commands.

$ git archive --prefix=upstream-vnl/ 3d3e8683 -- 
      CMakeLists.txt
      config/cmake
      core/CMakeLists.txt
      core/testlib
      core/vnl
      core/vxl_config.h.in
      core/vxl_copyright.h
      core/vxl_version.h
      v3p/CMakeLists.txt
      v3p/netlib
      vcl
 | tar x
$ git shortlog --perl-regexp --author='^((?!Kitware Robot).*)$' --no-merges --abbrev=8 --format='%h %s' a302a89b..3d3e8683

Drew Gilliam (3):
      869d8c77 contrib/brl - update vxl_configure_file locations, and add HEADER_BINARY_DIR to vxl_add_library for appropriate BUILD_INTERFACE on targets
      38e108cf bvgl_algo - use brl_resource_file for bvgl_eulerspiral_lookup_table resource
      7437c02b bsgm_prob_pairwise_dsm bug fix - favor std::is_same over other methods for template type discovery

Hans Johnson (2):
      f5c93ed9 ENH: Add front() and back() members to vnl_vector and vnl_vector_fixed
      3d3e8683 DOC: Grammer change in comment

Joseph Mundy (14):
      c320d11e templated appearance over input image type
      ad1ab6b0 modify bsgm to handle 16 bit input images
      c9e57958 added 2x processing
      a63bf124 remove debug statements
      bded9867 modified scale for 11 bits vs 8 bits
      5adc3edd restructure 16 bit dynamic range interface
      b16e0d25 added print for dynamic range setting
      7c2914c7 add comments and a few cleanups
      03ef4efe moved error checking .h to dispairity estimator .h
      5524102f add include for <limits>
      cb439258 fixed duplicate scale_0 in prob_pairwise
      596e40a9 add grid index for float data
      57f3d9b1 add .h file
      d4acae8a fix inconsistent pointset append cases

Noah Johnson (1):
      dd42c4fa ENH: vgl_io_pointset_3d (InsightSoftwareConsortium#809)

Tim Cootes (3):
      31bd3efa Added option
      f8c7778b Added line styles
      15d4a216 Added option to save separate frames

Change-Id: I8a2d3efb415942488161724a6a3880b3a7032e13
hjmjohnson pushed a commit to hjmjohnson/ITK that referenced this issue Nov 20, 2020
@hjmjohnson
VNL 2020-11-20 (3d3e8683)
c9b512c 
Run the UpdateFromUpstream.sh script to extract upstream VNL
using the following shell commands.

$ git archive --prefix=upstream-vnl/ 3d3e8683 -- 
      CMakeLists.txt
      config/cmake
      core/CMakeLists.txt
      core/testlib
      core/vnl
      core/vxl_config.h.in
      core/vxl_copyright.h
      core/vxl_version.h
      v3p/CMakeLists.txt
      v3p/netlib
      vcl
 | tar x
$ git shortlog --perl-regexp --author='^((?!Kitware Robot).*)$' --no-merges --abbrev=8 --format='%h %s' a302a89b..3d3e8683

Drew Gilliam (3):
      869d8c77 contrib/brl - update vxl_configure_file locations, and add HEADER_BINARY_DIR to vxl_add_library for appropriate BUILD_INTERFACE on targets
      38e108cf bvgl_algo - use brl_resource_file for bvgl_eulerspiral_lookup_table resource
      7437c02b bsgm_prob_pairwise_dsm bug fix - favor std::is_same over other methods for template type discovery

Hans Johnson (2):
      f5c93ed9 ENH: Add front() and back() members to vnl_vector and vnl_vector_fixed
      3d3e8683 DOC: Grammer change in comment

Joseph Mundy (14):
      c320d11e templated appearance over input image type
      ad1ab6b0 modify bsgm to handle 16 bit input images
      c9e57958 added 2x processing
      a63bf124 remove debug statements
      bded9867 modified scale for 11 bits vs 8 bits
      5adc3edd restructure 16 bit dynamic range interface
      b16e0d25 added print for dynamic range setting
      7c2914c7 add comments and a few cleanups
      03ef4efe moved error checking .h to dispairity estimator .h
      5524102f add include for <limits>
      cb439258 fixed duplicate scale_0 in prob_pairwise
      596e40a9 add grid index for float data
      57f3d9b1 add .h file
      d4acae8a fix inconsistent pointset append cases

Noah Johnson (1):
      dd42c4fa ENH: vgl_io_pointset_3d (InsightSoftwareConsortium#809)

Tim Cootes (3):
      31bd3efa Added option
      f8c7778b Added line styles
      15d4a216 Added option to save separate frames

Change-Id: I8a2d3efb415942488161724a6a3880b3a7032e13
hjmjohnson pushed a commit that referenced this issue Nov 21, 2020
@hjmjohnson
VNL 2020-11-20 (3d3e8683)
29caa5a 
Run the UpdateFromUpstream.sh script to extract upstream VNL
using the following shell commands.

$ git archive --prefix=upstream-vnl/ 3d3e8683 -- 
      CMakeLists.txt
      config/cmake
      core/CMakeLists.txt
      core/testlib
      core/vnl
      core/vxl_config.h.in
      core/vxl_copyright.h
      core/vxl_version.h
      v3p/CMakeLists.txt
      v3p/netlib
      vcl
 | tar x
$ git shortlog --perl-regexp --author='^((?!Kitware Robot).*)$' --no-merges --abbrev=8 --format='%h %s' a302a89b..3d3e8683

Drew Gilliam (3):
      869d8c77 contrib/brl - update vxl_configure_file locations, and add HEADER_BINARY_DIR to vxl_add_library for appropriate BUILD_INTERFACE on targets
      38e108cf bvgl_algo - use brl_resource_file for bvgl_eulerspiral_lookup_table resource
      7437c02b bsgm_prob_pairwise_dsm bug fix - favor std::is_same over other methods for template type discovery

Hans Johnson (2):
      f5c93ed9 ENH: Add front() and back() members to vnl_vector and vnl_vector_fixed
      3d3e8683 DOC: Grammer change in comment

Joseph Mundy (14):
      c320d11e templated appearance over input image type
      ad1ab6b0 modify bsgm to handle 16 bit input images
      c9e57958 added 2x processing
      a63bf124 remove debug statements
      bded9867 modified scale for 11 bits vs 8 bits
      5adc3edd restructure 16 bit dynamic range interface
      b16e0d25 added print for dynamic range setting
      7c2914c7 add comments and a few cleanups
      03ef4efe moved error checking .h to dispairity estimator .h
      5524102f add include for <limits>
      cb439258 fixed duplicate scale_0 in prob_pairwise
      596e40a9 add grid index for float data
      57f3d9b1 add .h file
      d4acae8a fix inconsistent pointset append cases

Noah Johnson (1):
      dd42c4fa ENH: vgl_io_pointset_3d (#809)

Tim Cootes (3):
      31bd3efa Added option
      f8c7778b Added line styles
      15d4a216 Added option to save separate frames

Change-Id: I8a2d3efb415942488161724a6a3880b3a7032e13
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