pydicom-seg
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razorx89
Python package for DICOM-SEG medical segmentation file reading and writing
If I install Jupyter Notebook after having installed pydicom-seg it returns this dependency error: ERROR: pip's dependency resolver does not currently take into account all the packages that are installed....
Hi, While trying to load a DICOM structure file (`dataset.Modality == RTSTRUCT`), I get an error saying: `ValueError: DICOM dataset is not a DICOM-SEG storage` After digging into the code...
We can replace poetry with [poetry-core](https://github.com/python-poetry/poetry-core) as the build backend so that we can use a more lightweight tool than poetry to build this package (such as [`build`](https://pypa-build.readthedocs.io/en/stable/)).
Hello, I am converting a DICOM Seg file, which contains no empty slices (No mask annotations). After I have converted it into nifti format, I got a segmentation mask which...
Currently, only segments with a positive mask get copied to the `SegmentSequence`: https://github.com/razorx89/pydicom-seg/blob/ee1aba7923b39014baa9653a016f5061d682f749/pydicom_seg/writer.py#L165-L170 However, the DICOM standard says "Segment Number (0062,0004) shall be unique within each Instance, start at a...
https://github.com/razorx89/pydicom-seg/blob/ee1aba7923b39014baa9653a016f5061d682f749/pyproject.toml#L21
In import_hierarchy in writer_utils, the FrameOfReferenceUID may be imported if a reference series was passed. However, in the __init__ method of SegmentationDataset, after the import_hierarchy is called, FrameOfReferenceUID is always...
pydicom-seg considers the ClinicalTrialSeriesID and ClinicalTrialTimePointID fields as mandatory according to the code in copy_segmentation_template in writer_utils.py . But based on the info here https://dicom.innolitics.com/ciods/segmentation/clinical-trial-study these fields are optional, both...
[pydicom v3.0.0 Release Notes](https://github.com/pydicom/pydicom/blob/main/doc/release_notes/v3.0.0.rst) indicates the removal of `_storage_sopclass_uids` (and replace with `uid`) which being import in both `segmentation_dataset` and `reader`. And `_storage_sopclass_uids` is [deprecated since v2.3.0](https://github.com/pydicom/pydicom/blob/v2.3.0/pydicom/_storage_sopclass_uids.py). Will it be...
