Model point count changing after transformation

pieper · December 16, 2022, 4:13pm

It sounds like dependency walker is a red herring.

I agree with @lassoan first step would be to explore fixing the module.

Then we could explore these platform / environment specific issues if they haven’t gone away.

muratmaga · December 16, 2022, 6:18pm

@jcfr is any of the extension developers are on this forum?

lassoan · December 16, 2022, 8:17pm

It is a trivial change (just skip the cleaning step if corresponding points are used). If you test it locally and send a pull request then we can get it merged quickly. Both @jcfr and @Sam_Horvath seem to have commit rights to the extension.

smrolfe · December 16, 2022, 9:13pm

When it does run on Linux and Mac, the output point number is equal to the reduced point number generated by vtkCleanPolyData, not the input mesh, so I suspect it may not actually be generating the point-to-point results.

jcfr · December 16, 2022, 10:34pm

It is a trivial change (just skip the cleaning step if corresponding points are used).

See ModelToModelDistance: Skip cleaning if corresponding_point_to_point mode is set by jcfr · Pull Request #12 · NIRALUser/3DMetricTools · GitHub

@smrolfe Let me know if that addresses the issue.

smrolfe · December 20, 2022, 6:35am

Thanks @jcfr it looks like this should fix the issue. I just tried to build the extension to test, but am having a problem with the ITK/VTK builds, which are failing with errors:

2>Performing download step (git clone) for ‘VTK’
2>Cloning into ‘VTK’…
3>Performing download step (git clone) for ‘ITKv4’
3>Cloning into ‘ITKv4’…
3>fatal: repository ‘http://itk.org/ITK.git/’ not found
2>fatal: repository ‘VTK / VTK · GitLab’ not found

This looks like errors I’ve gotten when building Slicer behind our firewall with USE_GIT_PROTOCOL enabled, but I’ve checked that it’s disabled for this extension build.

muratmaga · December 22, 2022, 7:38pm

We can build other extensions, but this seems to fail for us. Can anyone else have this issue?
@lassoan @jcfr @pieper

jcfr · December 22, 2022, 9:11pm

Since we focus our effort on building the extension against Slicer and not into supporting building the project as a standalone project, I suggest you configure the extension directly passing Slicer_DIR.

After removing the content of the build directory, there are two ways:

start cmake-gui, add an entry called Slicer_DIR pointing to the C:/path/to/Slicer-Release/Slicer-build
directly from the command-line with cmake -DSlicer_DIR:PATH=C:/path/to/Slicer-Release/Slicer-build -S C:/path/to/3DMetricTools -B C:/path/to/3DMetricTools-Release

If using a single config generator (e.g Unix Makefiles), specify CMAKE_BUILD_TYPE to Release.

Background

Setting reasonable default during the first configuration is the approach we have been using for most extension intended to be build as either a Slicer extension or an independent

This is explained by the following logic:

github.com

NIRALUser/3DMetricTools/blob/ff114ebc86603773bb32a96b08ccab7713c7e57e/CMakeLists.txt#L4-L17


      
          set(_msg "Setting C++ standard")
          message(STATUS "${_msg}")
          if(NOT DEFINED CMAKE_CXX_STANDARD)
            if(DEFINED Qt5_DIR OR DEFINED Slicer_DIR)
              set(CMAKE_CXX_STANDARD 17)
            elseif("${3DMetricTools_VTK_VERSION_MAJOR}" STREQUAL "8")
              set(CMAKE_CXX_STANDARD 11)
            else()
              set(CMAKE_CXX_STANDARD 98)
            endif()
          endif()
          set(CMAKE_CXX_STANDARD_REQUIRED ON)
          set(CMAKE_CXX_EXTENSIONS OFF)
          message(STATUS "${_msg} - C++${CMAKE_CXX_STANDARD}")

github.com

NIRALUser/3DMetricTools/blob/ff114ebc86603773bb32a96b08ccab7713c7e57e/CMakeLists.txt#L45-L61


      
          set(_default OFF)
          set(_reason "${EXTENSION_NAME}_BUILD_SLICER_EXTENSION is ON")
          if(NOT DEFINED ${EXTENSION_NAME}_BUILD_SLICER_EXTENSION AND DEFINED Slicer_DIR)
            set(_default ON)
            set(_reason "Slicer_DIR is SET")
          endif()
          
          
option(${EXTENSION_NAME}_BUILD_SLICER_EXTENSION "Build as a Slicer Extension" ${_default})
          
          
set(_msg "Checking if building as a Slicer extension")
          message(STATUS ${_msg})
          if(${EXTENSION_NAME}_BUILD_SLICER_EXTENSION)
            message(STATUS "${_msg} - yes (${_reason})")
          else()
            message(STATUS "${_msg} - no (${EXTENSION_NAME}_BUILD_SLICER_EXTENSION is OFF)")
          endif()
          mark_as_superbuild(${EXTENSION_NAME}_BUILD_SLICER_EXTENSION:BOOL)

smrolfe · December 23, 2022, 7:28am

Thanks @jcfr I’m using the instructions in the extensions documentation which includes adding the Slicer_DIR variable, so this has not resolved the git-related error. Is there anything else that might cause this? I did not get this error when I built Slicer.

smrolfe · December 23, 2022, 7:32am

I also got the following error on configuring:

CMake Error at C:/Program Files/CMake/share/cmake-3.23/Modules/FindQt4.cmake:1314 (message):
Found unsuitable Qt version “5.9.7” from
C:/Users/srolfe/Anaconda3/Library/bin/qmake.exe, this code requires Qt 4.x
Call Stack (most recent call first):
Common.cmake:28 (find_package)
SuperBuild.cmake:12 (include)
CMakeLists.txt:53 (include)

which I resolved this by getting QT 4.8 and setting the QT_QMAKE_EXECUTABLE. This took care of the error, but I’m wondering if this issue is expected or if using the requested version of Qt might be causing a problem?

jcfr · December 23, 2022, 2:08pm

To move forward:

Make sure you download the source from NIRALUser/3DMetricTools and not from juliettepera/3DMetricTools. See [1]
Clear build directory
Attempt to configure setting Slicer_DIR first

[1]: To avoid confusion, we have been trying to reach out to the owner of the “root” fork without success. See Re-fork repositories to avoid confusion · Issue #10 · NIRALUser/3DMetricTools · GitHub

smrolfe · December 23, 2022, 6:42pm

I rebuilt from NIRALUser/3DMetricTools, set Slicer_DIR and Qt5_DIR before configuring, and its now building correctly.

@jcfr I tested the fix in ModelToModelDistance: Skip cleaning if corresponding_point_to_point mode is set by jcfr · Pull Request #12 · NIRALUser/3DMetricTools · GitHub and it resolves the issue with the point count changing.

jcfr · December 23, 2022, 6:55pm

Thanks for testing, changes have been integrated in NIRALUser/3DMetricTools and fixed extension ModelToModelDistance is expected to be published tomorrow for Slicer 5.2 and Preview.

@smrolfe If you need the updated extension to be published before that, let me know and I can manually take care of it.

smrolfe · December 23, 2022, 7:21pm

Thanks @jcfr! Tomorrow works for me.

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Model point count changing after transformation

Background

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