Error loading supported file formats with volume_loader

[tbirdso]

Overview

A user reported an error in which they were not able to load data with the volume_loader operator.

Investigation

• Verify image loading with each type of sample data
  • NRRD
  • MetaImage
  • NIFTI
• Investigate and address any observed loading issues

EDIT: Updated to reflect we are not sure what file type was failing. The error occurred while trying to set up the volume_rendering_xr application with custom data.

[rbridgewaterML]

Noting: I received an unclear message, File is not a supported volume format MRI_headerless.nrrd after using a headerless NRRD (As apparently NRRDs with attached headers are known to have issues, which might be good to document as well)

[AndreasHeumann]

The loader in currently supports NRRD data with detached header (https://teem.sourceforge.net/nrrd/format.html#detached) only. I agree that this is not documented clearly.
There are no know issues with the MetaImage and NIFTI loaders.

[tbirdso]

Results from my local testing:

Unexpected Behavior

• Compressed .nhdr volume fails to load with error: "NRRD unexpected value for encoding: gzip"
• Uncompressed .nhdr volume loads, but rendering appears incorrect.
  

Verified Behavior

• .mhd + .raw loads without error
• .nii.gz loads without error
• .mha load error: "File is not a supported volume format"
• nrrd load error: "File is not a supported volume format"

Test Procedure

I tested in the volume_rendering app (which makes use of VolumeLoaderOp and VolumeRenderOp) as follows:

1. Verify default app build/run behavior with ./dev_container build_and_run volume_rendering
2. Launch the HoloHub container:

./dev_container launch

3. Use the ITK Python package to convert .mhd sample data to other supported formats under test:

pip install itk
pushd data/volume_rendering
python -c "import itk; image = itk.imread('highResCT.mha'); itk.imwrite(image, 'highResCT.<output-format>, compression=<True/False>)"
popd

4. Try running the volume_rendering app with the density image in the given file type:

/workspace/holohub$ /workspace/holohub/build/applications/volume_rendering/volume_rendering  --mask /workspace/holohub/data/volume_rendering/smoothmasks.seg.mhd --config /workspace/holohub/data/volume_rendering/config.json --density /workspace/holohub/data/volume_rendering/highResCT.<file-format>

Followup Notes

• I see that we may have used uncompressed, detached-header NRRD files elsewhere (see bonsai). It looks like we have an implicit NRRD requirement that data is uncompressed. @AndreasHeumann do you know whether there may be additional constraints or underlying assumptions for NRRD volume loading, such as maybe expecting a uint8 type on load?
• My recommendation is that we continue to direct users towards detached-header .mhd and compressed .nii.gz volumes for now. It is OK to not support all possible medical volume types in VolumeLoaderOp so long as external conversion tools are available.

[AndreasHeumann]

I see that we may have used uncompressed, detached-header NRRD files elsewhere (see [bonsai](https://klacansky.com/open- scivis-datasets/)). It looks like we have an implicit NRRD requirement that data is uncompressed. @AndreasHeumann do you know whether there may be additional constraints or underlying assumptions for NRRD volume loading, such as maybe expecting a uint8 type on load?

Uncompressed data is supported, but the loader is only checking for gz:

https://github.com/nvidia-holoscan/holohub/blob/main/operators/volume_loader/nrrd_loader.cpp#L81

Should be a simple fix to also add gzip which is a valid value as mentioned in the spec:
https://teem.sourceforge.net/nrrd/format.html#encoding

All types except 64 bit types ([u]int64 and float64) are supported: https://teem.sourceforge.net/nrrd/format.html#type.

There are other limitations

• txt, hex and bz2 encodings are not supported
• big endian is not supported
• linespkip and byteskip is not supported