The process_nifti function forces the annotations to be oriented as LPI. However, this function is used internally for model integrations running inference on medical volumes. This is an issue as medical BE changes are being made that allow some DICOM files to be stored in orientations that are not LPI. So, we want to allow the model integrations to pass process_nifti a custom orientation.
Solution
We add an argument to process_nifti that defaults to LPI (which is what it was before, although there was a typo in the actual value -- typo wasn't affecting the output though). This means model integrations can use it with custom orientations, but the public darwin-py api is unaffected.
linear[bot]
commented
4 months ago
Problem
The
process_niftifunction forces the annotations to be oriented as LPI. However, this function is used internally for model integrations running inference on medical volumes. This is an issue as medical BE changes are being made that allow some DICOM files to be stored in orientations that are not LPI. So, we want to allow the model integrations to passprocess_niftia custom orientation.Solution
We add an argument to
process_niftithat defaults to LPI (which is what it was before, although there was a typo in the actual value -- typo wasn't affecting the output though). This means model integrations can use it with custom orientations, but the public darwin-py api is unaffected.