How to read linear transform from C++ CLI

Development
1

Slicer used to write .h5 or .tfm files when a transform needed to be passed to a CLI:

<transform type="linear" fileExtensions=".tfm,.h5,.hdf5,.mat,.txt">
  <longflag>transform0</longflag>
  <description>...</description>
  <label>rigid transform 0</label>
  <channel>input</channel>
</transform>

but now a CLI gets --transform0 C:/Temp/Slicer/BDBAI_AAAAAAAABFECHIFA.mrml#vtkMRMLLinearTransformNode1 which itk::TransformFileReader cannot read. How to force Slicer to write an ITK-readable transform?

2

Which Slicer version does this? Many CLI modules uses transforms with ITK readers - do they work correctly?

3

1aa2f026195e7f8206748867cca4a6fc46197f7c from 2018-01-27

4

Are you using the “force executable” setting in Settings->Modules?

5

@dzenanz Many CLI modules uses transforms with ITK readers - do they work correctly?

For example, “Resample Scalar/Vector/DWI volume” module works correctly for me, writing the transform to .h5 file.

Full command line

Resample Scalar/Vector/DWI Volume command line:

C:/D/S4R/Slicer-build/lib/Slicer-4.9/cli-modules/Release/ResampleScalarVectorDWIVolume.exe --Reference C:/Users/msliv/AppData/Local/Temp/Slicer/CCCEE_vtkMRMLScalarVolumeNodeB.nrrd --transformationFile C:/Users/msliv/AppData/Local/Temp/Slicer/CCCEE_vtkMRMLLinearTransformNodeE.h5 --hfieldtype h-Field --interpolation linear --transform_order output-to-input --image_center input --spacing 0,0,0 --size 0,0,0 --direction_matrix 0,0,0,0,0,0,0,0,0 --number_of_thread 0 --default_pixel_value 0 --window_function c --spline_order 3 --transform_matrix 1,0,0,0,1,0,0,0,1,0,0,0 --transform a C:/Users/msliv/AppData/Local/Temp/Slicer/CCCEE_vtkMRMLScalarVolumeNodeB.nrrd C:/Users/msliv/AppData/Local/Temp/Slicer/CCCEE_vtkMRMLScalarVolumeNodeD.nrrd

It uses this XML:

<transform fileExtensions=".h5">
  <name>transformationFile</name>
  <label>Transform Node</label>
  <flag>-f</flag>
  <longflag>--transformationFile</longflag>
  <default/>
  <channel>input</channel>
</transform>

You can add the few missing tags to your XML file (name, default, flag) and see if it makes a difference.

1 Like
6

After changing the fileExtensions=".tfm,.h5,.hdf5,.mat,.txt" into fileExtensions=".tfm" and recompiling the problem went away. Then I changed back into the original, and the transforms are still being written normally (as .tfm files). Perhaps changes to CMake code made the difference. I explicitly added this (trying to fix an unrelated linking error with tests):

find_package(SlicerExecutionModel REQUIRED)
include(${SlicerExecutionModel_USE_FILE})

set(MABMIS_ITK_COMPONENTS
  ITKIOImageBase
  ITKTransform
  ITKIOTransformBase
  ITKIOXML
  )
find_package(ITK 4.6 COMPONENTS ${MABMIS_ITK_COMPONENTS} REQUIRED)
set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt
include(${ITK_USE_FILE})

find_package(Slicer)
include(${Slicer_USE_FILE})

But why would any of this make a difference?

@ihnorton Disabling “Prefer executable CLIs” passes the images via pointer, but does not seem to affect transforms.

7

Are you running CLI a executable or shared library?

8

Sorry for the noise, I was on the phone and didn’t see the full thread.

9

I think you need to force recompilation after you change the module description XML. I noticed in the past that XML file changes did not take effect with a simple build.