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[External] Add multi-segment nifti export support #1082

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[External] Add multi-segment nifti export support #1082

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071bd28
Add multi-segment nifti export support
Jo-Byr Jul 3, 2025
b83955c
Fix pixel offset in test data and add tests
Jo-Byr Jul 9, 2025
5afdfce
Add multi-label nifti import test
Jo-Byr Jul 10, 2025
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13 changes: 12 additions & 1 deletion darwin/exporter/formats/nifti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,13 +58,18 @@ class Volume:
primary_plane: str


# Unique ID and file suffix for the "All segments" volume
multi_segments_label = "0"
multi_segments_name = "Segments"


def export(
annotation_files: Iterable[dt.AnnotationFile],
output_dir: Path,
) -> None:
"""
Exports the given ``AnnotationFile``\\s into nifti format inside of the given
``output_dir``. Deletes everything within ``output_dir/masks`` before writting to it.
``output_dir``. Deletes everything within ``output_dir/masks`` before writing to it.

Parameters
----------
Expand Down Expand Up @@ -146,6 +151,8 @@ def export(
for ann in slot_annotations
if ann.annotation_class.annotation_type == "mask"
}
# Add a unique ID for the "All segments" volume
mask_id_to_classname[multi_segments_label] = multi_segments_name
raster_output_volumes = build_output_volumes(
slot,
class_names_to_export=list(mask_id_to_classname.values()),
Expand Down Expand Up @@ -497,6 +504,10 @@ def populate_output_volumes_from_raster_layer(
volume[class_name].pixel_array = np.where(
multilabel_volume == global_id, 1, volume[class_name].pixel_array
)
elif mask_id == multi_segments_label:
# Unique ID for "All segments":
volume = output_volumes[series_instance_uid]
volume[multi_segments_name].pixel_array = multilabel_volume

return volume

Expand Down
259 changes: 259 additions & 0 deletions tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/darwin.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,259 @@
{
"version": "2.0",
"schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/2.0/schema.json",
"item": {
"name": "axial_RPI_pixdim_1.0_1.0_1.0.dcm",
"path": "/",
"source_info": {
"item_id": "0197ee1d-591e-a61b-82e2-e6f1e5c30cf2",
"dataset": {
"name": "dicom_test_data_new",
"slug": "dicom_test_data_new",
"dataset_management_url": "https://darwin.v7labs.com/datasets/1856922/dataset-management"
},
"team": {
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"slug": "v7-john"
},
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},
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{
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"pixdim": "(1.0, 1.0, 1.0)",
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},
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}
}
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Binary file added tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/ground_truth.nii.gz
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