[DAR-4924][External] Resolving issues with import & export of NifTI annotations

[JBWilkie]

Problem

This PR tackles 3 issues related to importing & exporting annotations in the NifTI format. Issue 1 is major, issues 2 & 3 are minor

• 1: NifTI annotations are being incorrectly oriented upon import and export in some situations
• 2: It is not possible to import NifTI annotations to items in dataset folders
• 3: When importing NifTI annotations as polygons, the last frame is always omitted

Solution

To tackle these problems:

• 1: We were re-orienting NifTI annotations incorrectly, and in places we didn't need to be. This PR changes the logic to be the following:

When importing NifTI annotations: If importing to a post MED_2D_VIEWER file, re-orient to LPI according to nibabel. This is the exact same logic we apply to medical file processing in the backend. Otherwise, if importing to a pre MED_2D_VIEWER file:

• If it's a NifTI dataset item: Re-orient to LPI, since all pre MED_2D_VIEWER NifTI files were re-oriented this way
• If it's a DICOM dataset item, look up current affine of the target dataset item, and re-orient the annotations based on that

When exporting NifTI annotations: Always re-orient the exported NifTI file based on the original affine of the dataset item it came from

• 2: Allow import of NifTI annotations to items in dataset folders
• 3 Resolves the issue with removing the last frame of NifTI polygon annotations

IMPORTANT NOTE: Due to what I believe were some issues in the pre MED_2D_VIEWER backend processing pipeline, we may have incorrectly stored affines and original affines for some pre MED_2D_VIEWER files. Since this is all we have to go off when re-orienting NifTI annotations, there may be issues in these cases, and we should keep an eye out for them

Changelog

Resolved issues with automatic scaling & orientation of NifTI annotations

[linear]

DAR-4924 BUG: NifTi format exports being inverted

[dorfmanrobert]

I don't think this is correct for pre MED_2D due to the volume.affine being (or expected to be at least) RAS

So this flow will try to go from RAS -> original orientation.

But really its meant to go from LPI -> original orientation. I think this is why dataobj=np.flip(volume.pixel_array, (0, 1, 2)).astype(np.int16) used to be invoked: to go from LPI to RAS, so that then this logic would make sense for pre MED_2D files

[JBWilkie]

Updated

[dorfmanrobert]

I think it might be more robust to do as_closest_canonical on img to get it to RAS, since this will only work if the Nifti annotation file is in LPI right

[JBWilkie]

Updated

[dorfmanrobert]

Having some comments on why we need these transforms for pre MED_2D would be helpful for future ref I think

[dorfmanrobert]

nice work!