[DAR-4140][External] Fixed NifTI import orientation

[JBWilkie]

Problem

Currently, the NifTI importer attempts to apply the LPI orientation to annotations to be imported, since all uploaded NifTI / DICOM files are transformed to LPI. However, the used function (apply_orientation()) flips all 3 axes. Why? The LPI orientation can be represented by [-1, -1, -1], which we feed into the function as the target orientation. However, that function just flips an axis if the corresponding value in the above 3-element array is -1, and doesn't flip if not. This means that for any input orientation not in RAS, at least one axis will be flipped incorrectly

Solution

Simplify the process_nifti function so that:

• 1: All incoming files are first transformed to RAS, regardless of the state of legacy
• 2: The target orientation is applied to the file

Changelog

Resolved orientation issue when importing annotations in the NifTI format

[linear]

DAR-4140 BUG: Inistro reports that imported annotations are flipped/not consistent with what they see in their viewer