[MED-22][external] import nifti to raster layer mask annotations #725
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added 4 commits
November 20, 2023 22:26
…de paths and they seem to work as before, dropped import_format in favour of mode: mask
MED-22 Import NIFTI to raster_layer & mask annotations
Description: It is a common request to import NIFTI Masks created in external software to v7. These should be converted to Acceptance Criteria: The user should be able to import NIFTI annotations using darwin-py. |
Nathanjp91
suggested changes
Dec 13, 2023
darwin/importer/formats/nifti.py
Outdated
| @@ -177,8 +196,96 @@ def get_video_annotation( | |||
| raise Exception("If is_mpr is True, slot_names must be of length 3") | |||
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| def nifti_to_video_annotation( | |||
| volume, class_name, class_idxs, slot_names, view_idx=2, pixdims=(1, 1, 1) | |||
| def get_mask_video_annotations(volume, processed_class_map, slot_names): | |||
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Can you type annotate this? Inputs and outputs.
added 2 commits
December 15, 2023 15:24
Added a test |
Nathanjp91
approved these changes
Dec 19, 2023
Co-authored-by: Nathan Perkins <[email protected]>
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Problem
We previously supported nifti imports as polygons, this PR introduces support for nifti imports into the raster layer.
Solution
Users now have a new mode available at upload. In addition to
videoandinstanceswhich both write polygons into Darwin, users now havemaskmode which writes to the raster layer and createsmaskannotations.Changelog
We've introduced the ability to import nifti labels directly into the raster layer! This means users can perform inference off-platform or import existing annotations into a project and then annotate them using our Masks feature.