rt-utils fails on "Radiation therapy simulation head ..."
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Description
Trying to get ROI masks from this dataset: https://figshare.com/s/a5e09113f5c07b3047df
I had to use following hack in image_helper.py:
def get_slice_contour_data(series_slice: Dataset, contour_sequence: Sequence):
slice_contour_data = []
# Traverse through sequence data and get all contour data pertaining to the given slice
for contour in contour_sequence:
for contour_image in contour.ContourImageSequence:
if contour_image.ReferencedSOPInstanceUID == get_UID(series_slice.filename): #series_slice.SOPInstanceUID:
slice_contour_data.append(contour.ContourData)
return slice_contour_data
where get_UID obtaines the UID from the file name. Not sure if this means the dataset is "broken", or if this is just a real problem that is not covered by rt-utils.
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Research direction
Start in rt_utils/image_helper.py around line 253 and inspect get_slice_contour_data, comparing the referenced UID with the series slice data for the linked dataset. Verify whether the filename-derived UID is valid DICOM behavior or an rt-utils gap. Done means the dataset is handled correctly without the reported hack, with suitable regression coverage.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100