Release Notes

1.1.11 [2022-03-30]

Fixes:

Fixed import statement for HierarchyCurator to use direct class import from flywheel_gear_toolkit.utils.curator
Updated ROICurator initialization to properly pass keyword arguments to parent HierarchyCurator class
Added explicit configuration of multi and depth_first attributes in ROICurator.__init__() to ensure correct curator behavior
Fixed instantiation of ROICurator to use keyword argument syntax (fw=fw)

Fixes:

Fixed handling of ROI metadata with alternate UID field names (StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID)
Added error handling for non-DICOM zip members during ROI matching
Added error handling for directory entries in zip files
Fixed DICOM file matching to support both zipped and unzipped files

Maintenance:

Refactored get_roi_dicom_file() to separate zipped and unzipped DICOM matching logic into match_zipped_dicom_member() and match_unzipped_dicom() methods
Removed unnecessary copy.deepcopy() call in acquire_rois()
Added NotZip exception class for handling uncompressed DICOM files
Improved error logging for invalid container types and DICOM loading failures

Maintenance:

Fixes:

Fixed Docker image name from flywheel/export_roi to flywheel/export-rois in manifest configuration

Enhancements:

Added filtering to process only dicom type files when searching for ROI references

Fixes:

Fixed typo in acquisition label key ("scquisition" to "acquisition") in utils/MyCurator.py:317
Added fallback logic to check alternative DICOM UID field names (studyInstanceUid/StudyInstanceUID, seriesInstanceUid/SeriesInstanceUID, sopInstanceUid/SOPInstanceUID) for improved compatibility
Fixed iteration logic bug where for OHIF_KEY in session_info: was changed to if OHIF_KEY in session_info: in utils/MyCurator.py:546
Fixed typo in warning message from "mathing" to "matching" in utils/MyCurator.py:659
Added copy.deepcopy() to prevent mutation of container dictionaries during processing

Maintenance:

Standardized all CSV output column names to lowercase format (Group → group, Project → project, X min → x min, etc.) throughout codebase
Enhanced debug logging with additional context messages in file/acquisition/session processing paths
Improved warning message to include series UID value when multiple matches found

Documentation:

Updated README.md to reflect lowercase column naming convention for all Flywheel location columns and ROI information columns

Fixes:

Fixed uninitialized variable bug in ROICurator.get_ohif_viewer_data() by ensuring output_dict is initialized before the loop
Fixed potential issue in run.py by extracting project_id before calling fw.get_project() for better code clarity

Maintenance:

Refactored Dockerfile to copy entire utils directory instead of individual files
Added utils/__init__.py to make utils a proper Python package
Removed unused mapping_class.py module

Enhancements:

Added DICOM member filename extraction for each exported ROI, enabling precise identification of the raw DICOM file within zip archives
Implemented support for exporting ROIs from both ohifViewer and roi metadata namespaces
Added comprehensive ROI statistics export including area, count, voxel values (min, max, mean, standard deviation, variance)
Implemented hierarchical path reconstruction for ROIs, providing complete Flywheel location context (group, project, subject, session, acquisition)
Added file type detection for DICOM and NIFTI formats based on file extensions

Documentation:

Added comprehensive README with gear description, usage instructions, and detailed output column specifications
Documented DICOM classifier prerequisite and performance implications

Maintenance:

Added initial Dockerfile based on python:3.7 runtime
Implemented custom ROICurator class extending flywheel_gear_toolkit.utils.curator.HierarchyCurator
Implemented custom MyWalker class extending flywheel_gear_toolkit.utils.walker.Walker
Added support for flywheel-gear-toolkit and pydicom libraries
Implemented DICOM zip archive member matching using Study, Series, and SOP Instance UIDs