From 54dac55ff37d290621c757cd313a7e8b9c11cb68 Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Tue, 25 Nov 2025 16:43:00 -0500 Subject: [PATCH 01/22] feat: add dry run functionality to autopipeline and add sensitive dicom tags to metadata --- pixi.lock | 4 +- src/imgtools/autopipeline.py | 6 ++- src/imgtools/cli/autopipeline.py | 9 ++++ .../dicom/dicom_metadata/extractor_base.py | 9 ++++ src/imgtools/io/sample_output.py | 8 +++- .../io/writers/abstract_base_writer.py | 29 ++++++++++-- src/imgtools/io/writers/nifti_writer.py | 39 +++++++-------- src/imgtools/io/writers/numpy_writer.py | 47 ++++++++++--------- 8 files changed, 102 insertions(+), 49 deletions(-) diff --git a/pixi.lock b/pixi.lock index dc99c199..beb6a919 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11401,8 +11401,8 @@ packages: timestamp: 1733255681319 - pypi: ./ name: med-imagetools - version: 2.12.1 - sha256: 3658a851aed0a7edd1f1853978f53e8a2d37883d1c0cfbd824b5af453185cc95 + version: 2.12.2 + sha256: 2f302a82b7c1a96183e4d194850d2ea0dddf2adc509f3fd88ffbd61db42126d5 requires_dist: - structlog>=25.0,<26 - click>=8.1,<9 diff --git a/src/imgtools/autopipeline.py b/src/imgtools/autopipeline.py index e60cd64b..cc22252d 100644 --- a/src/imgtools/autopipeline.py +++ b/src/imgtools/autopipeline.py @@ -262,7 +262,7 @@ def process_one_sample( SampleNumber=idx, ) result.output_files = list(saved_files) - if not result.output_files: + if not result.output_files and not sample_output.dry_run: raise ValueError( "No output files were saved. Check the output directory." ) @@ -305,6 +305,7 @@ def __init__( spacing: tuple[float, float, float] = (0.0, 0.0, 0.0), window: float | None = None, level: float | None = None, + dry_run: bool = False, ) -> None: """ Initialize the Autopipeline. @@ -342,6 +343,8 @@ def __init__( Window level for intensity normalization, by default None level : float | None, optional Window level for intensity normalization, by default None + dry_run : bool, optional + Whether to run the pipeline in dry run mode, by default False """ self.input = SampleInput.build( directory=Path(input_directory), @@ -359,6 +362,7 @@ def __init__( filename_format=output_filename_format, existing_file_mode=existing_file_mode, extra_context={}, + dry_run=dry_run, ) transforms: list[BaseTransform] = [ diff --git a/src/imgtools/cli/autopipeline.py b/src/imgtools/cli/autopipeline.py index 57bc3c41..71e7705c 100644 --- a/src/imgtools/cli/autopipeline.py +++ b/src/imgtools/cli/autopipeline.py @@ -165,6 +165,13 @@ def parse_spacing(ctx, param, value): # type: ignore default=None, help="Path to YAML file containing ROI matching patterns." ) +@click.option( + "--dry-run", + "-d", + is_flag=True, + default=False, + help="Run the pipeline in dry run mode, by default False" +) @click.help_option( "-h", "--help", @@ -186,6 +193,7 @@ def autopipeline( roi_on_missing_regex: str, roi_match_map: Tuple[str], roi_match_yaml: Path, + dry_run: bool, ) -> None: """Core utility to process messy DICOM data into organized NIfTI files. @@ -263,6 +271,7 @@ def autopipeline( spacing=spacing, window=window, level=level, + dry_run=dry_run, ) # Run the pipeline diff --git a/src/imgtools/dicom/dicom_metadata/extractor_base.py b/src/imgtools/dicom/dicom_metadata/extractor_base.py index 4dc29213..1525c0c1 100644 --- a/src/imgtools/dicom/dicom_metadata/extractor_base.py +++ b/src/imgtools/dicom/dicom_metadata/extractor_base.py @@ -108,6 +108,15 @@ class ModalityMetadataExtractor(ABC): "SeriesInstanceUID", "StudyInstanceUID", "Modality", + # Sensitive Patient Demographics (PHI) + # These tags contain Protected Health Information (PHI) and are sensitive. + "PatientSex", + "PatientBirthDate", + "PatientAge", + "EthnicGroup", + "PatientWeight", + "PatientSize", + "AdditionalPatientHistory", # Image Geometry & Size "BodyPartExamined", "DataCollectionDiameter", diff --git a/src/imgtools/io/sample_output.py b/src/imgtools/io/sample_output.py index e92b722f..0b309669 100644 --- a/src/imgtools/io/sample_output.py +++ b/src/imgtools/io/sample_output.py @@ -131,7 +131,11 @@ class SampleOutput(BaseModel): {"dataset": "NSCLC-Radiomics", "processing_date": "2025-04-22"} ], ) - + dry_run: bool = Field( + default=False, + description="Whether to run the pipeline in dry run mode, by default False", + title="Dry Run", + ) _writer: AbstractBaseWriter | None = PrivateAttr(default=None) def model_post_init(self, __context) -> None: # type: ignore # noqa: ANN001 @@ -141,6 +145,8 @@ def model_post_init(self, __context) -> None: # type: ignore # noqa: ANN001 existing_file_mode=self.existing_file_mode, filename_format=self.filename_format, context=self.extra_context, + dry_run=self.dry_run, + create_dirs=not self.dry_run, # only create directories if not in dry run mode ) @field_validator("directory") diff --git a/src/imgtools/io/writers/abstract_base_writer.py b/src/imgtools/io/writers/abstract_base_writer.py index 3d6b7527..733d14bc 100644 --- a/src/imgtools/io/writers/abstract_base_writer.py +++ b/src/imgtools/io/writers/abstract_base_writer.py @@ -126,6 +126,10 @@ class AbstractBaseWriter(ABC, Generic[ContentType]): absolute_paths_in_index : bool, default=False If True, saves absolute paths in the index file. If False, saves paths relative to the root directory. + dry_run : bool, default=False + If True, skip the actual file I/O operations but still write to the index + and return the resolved path. Useful for previewing what would be saved + or updating the index without writing files. pattern_resolver : PatternResolver Instance used to handle filename formatting with placeholders. @@ -152,6 +156,7 @@ class AbstractBaseWriter(ABC, Generic[ContentType]): pattern_resolver: PatternResolver = field(init=False) overwrite_index: bool = field(default=False) absolute_paths_in_index: bool = field(default=False) + dry_run: bool = field(default=False) index_filename: Optional[str] = field(default=None) _checked_directories: set[str] = field(default_factory=set, init=False) @@ -212,6 +217,21 @@ def save(self, data: ContentType, **kwargs: Any) -> Path: updating them with the kwargs passed from the save method. This will help simplify repeated saves with similar context variables. + + When `self.dry_run` is True, implementations should skip file I/O operations + but still write to the index and return the resolved path. + + Parameters + ---------- + data : ContentType + The data to be saved. + **kwargs : Any + Additional context variables for filename generation and path resolution. + + Returns + ------- + Path + The resolved path where the file would be (or was) saved. """ pass @@ -612,7 +632,7 @@ def save(self, data: str, **kwargs: object) -> Path: Parameters ---------- - content : str + data : str The content to write to the file. **kwargs : Any Additional context for filename generation. @@ -625,9 +645,10 @@ def save(self, data: str, **kwargs: object) -> Path: # Resolve the output file path output_path = self.resolve_path(**kwargs) - # Write content to the file - with output_path.open(mode="w", encoding="utf-8") as f: - f.write(data) + # Write content to the file only if not in dry_run mode + if not self.dry_run: + with output_path.open(mode="w", encoding="utf-8") as f: + f.write(data) self.add_to_index(output_path, replace_existing=output_path.exists()) diff --git a/src/imgtools/io/writers/nifti_writer.py b/src/imgtools/io/writers/nifti_writer.py index f75ecaea..3e79007c 100644 --- a/src/imgtools/io/writers/nifti_writer.py +++ b/src/imgtools/io/writers/nifti_writer.py @@ -195,25 +195,26 @@ def save(self, data: sitk.Image | np.ndarray, **kwargs: object) -> Path: else: out_path = self.resolve_path(**kwargs) - if ( - out_path.exists() # check if it exists - # This will only be true if SKIP, - # OVERWRITE would have deleted the file - and self.existing_file_mode == ExistingFileMode.SKIP - ): - logger.debug("File exists, skipping.", out_path=out_path) - return out_path - - try: - sitk.WriteImage( - image, - out_path.as_posix(), - useCompression=True, - compressionLevel=self.compression_level, - ) - except Exception as e: - msg = f"Error writing image to file {out_path}: {e}" - raise NiftiWriterIOError(msg) from e + if not self.dry_run: + if ( + out_path.exists() # check if it exists + # This will only be true if SKIP, + # OVERWRITE would have deleted the file + and self.existing_file_mode == ExistingFileMode.SKIP + ): + logger.debug("File exists, skipping.", out_path=out_path) + return out_path + + try: + sitk.WriteImage( + image, + out_path.as_posix(), + useCompression=True, + compressionLevel=self.compression_level, + ) + except Exception as e: + msg = f"Error writing image to file {out_path}: {e}" + raise NiftiWriterIOError(msg) from e self.add_to_index( out_path, diff --git a/src/imgtools/io/writers/numpy_writer.py b/src/imgtools/io/writers/numpy_writer.py index 2c6e7461..3764c460 100644 --- a/src/imgtools/io/writers/numpy_writer.py +++ b/src/imgtools/io/writers/numpy_writer.py @@ -82,6 +82,8 @@ def save( ---------- data : np.ndarray | sitk.Image | dict[str, np.ndarray | sitk.Image] The data to save. Can be a single image or a dictionary of images. + **kwargs : object + Additional context for filename generation. Returns ------- @@ -95,29 +97,30 @@ def save( """ out_path = self.resolve_path(**kwargs) - if isinstance(data, (np.ndarray, sitk.Image)): - # Single image or array - array, metadata = self._to_numpy(data) - np.savez_compressed(out_path, image_array=array, **metadata) - elif isinstance(data, dict): - # Multiple images or arrays - arrays = {} - metadata = {} - for key, value in data.items(): - array, meta = self._to_numpy(value) - arrays[key] = array - for meta_key, meta_value in meta.items(): - metadata[f"{key}_{meta_key}"] = meta_value - if self.compressed: - np.savez_compressed( - out_path, allow_pickle=False, **arrays, **metadata - ) + if not self.dry_run: + if isinstance(data, (np.ndarray, sitk.Image)): + # Single image or array + array, metadata = self._to_numpy(data) + np.savez_compressed(out_path, image_array=array, **metadata) + elif isinstance(data, dict): + # Multiple images or arrays + arrays = {} + metadata = {} + for key, value in data.items(): + array, meta = self._to_numpy(value) + arrays[key] = array + for meta_key, meta_value in meta.items(): + metadata[f"{key}_{meta_key}"] = meta_value + if self.compressed: + np.savez_compressed( + out_path, allow_pickle=False, **arrays, **metadata + ) + else: + np.savez(out_path, allow_pickle=False, **arrays, **metadata) else: - np.savez(out_path, allow_pickle=False, **arrays, **metadata) - else: - raise NumpyWriterValidationError( - "Data must be a NumPy array, SimpleITK image, or a dictionary of these types." - ) + raise NumpyWriterValidationError( + "Data must be a NumPy array, SimpleITK image, or a dictionary of these types." + ) self.add_to_index( out_path, From 8c9099605c9506c7b1f1f9d8dcd429a8f2a756e5 Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Wed, 26 Nov 2025 10:42:51 -0500 Subject: [PATCH 02/22] chore: bypass existing file logic when dry_run=True --- src/imgtools/io/writers/abstract_base_writer.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/imgtools/io/writers/abstract_base_writer.py b/src/imgtools/io/writers/abstract_base_writer.py index 733d14bc..70cd46d3 100644 --- a/src/imgtools/io/writers/abstract_base_writer.py +++ b/src/imgtools/io/writers/abstract_base_writer.py @@ -352,6 +352,10 @@ def resolve_path(self, **kwargs: object) -> Path: # msg = f"Directory {out_path.parent} does not exist." # raise DirectoryNotFoundError(msg) return out_path + + if self.dry_run: # This is here so that the existing_file_mode logic is not executed in dry run mode + return out_path + match self.existing_file_mode: case ExistingFileMode.SKIP: return out_path From 37df8483ed7ef5b0529b439aab0216445294c3fa Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Wed, 26 Nov 2025 10:56:05 -0500 Subject: [PATCH 03/22] chore: ruff format --- src/imgtools/io/sample_output.py | 2 +- src/imgtools/io/writers/abstract_base_writer.py | 2 +- src/imgtools/io/writers/numpy_writer.py | 4 +++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/imgtools/io/sample_output.py b/src/imgtools/io/sample_output.py index 0b309669..cc5bc5ac 100644 --- a/src/imgtools/io/sample_output.py +++ b/src/imgtools/io/sample_output.py @@ -146,7 +146,7 @@ def model_post_init(self, __context) -> None: # type: ignore # noqa: ANN001 filename_format=self.filename_format, context=self.extra_context, dry_run=self.dry_run, - create_dirs=not self.dry_run, # only create directories if not in dry run mode + create_dirs=not self.dry_run, # only create directories if not in dry run mode ) @field_validator("directory") diff --git a/src/imgtools/io/writers/abstract_base_writer.py b/src/imgtools/io/writers/abstract_base_writer.py index 70cd46d3..0512afda 100644 --- a/src/imgtools/io/writers/abstract_base_writer.py +++ b/src/imgtools/io/writers/abstract_base_writer.py @@ -353,7 +353,7 @@ def resolve_path(self, **kwargs: object) -> Path: # raise DirectoryNotFoundError(msg) return out_path - if self.dry_run: # This is here so that the existing_file_mode logic is not executed in dry run mode + if self.dry_run: # This is here so that the existing_file_mode logic is not executed in dry run mode return out_path match self.existing_file_mode: diff --git a/src/imgtools/io/writers/numpy_writer.py b/src/imgtools/io/writers/numpy_writer.py index 3764c460..ca8bdc82 100644 --- a/src/imgtools/io/writers/numpy_writer.py +++ b/src/imgtools/io/writers/numpy_writer.py @@ -116,7 +116,9 @@ def save( out_path, allow_pickle=False, **arrays, **metadata ) else: - np.savez(out_path, allow_pickle=False, **arrays, **metadata) + np.savez( + out_path, allow_pickle=False, **arrays, **metadata + ) else: raise NumpyWriterValidationError( "Data must be a NumPy array, SimpleITK image, or a dictionary of these types." From c8a1c13aa31e84967fb8c38e4e04aac6b13b5786 Mon Sep 17 00:00:00 2001 From: Joshua Siraj <72413722+JoshuaSiraj@users.noreply.github.com> Date: Wed, 26 Nov 2025 11:33:01 -0500 Subject: [PATCH 04/22] Update src/imgtools/io/sample_output.py Co-authored-by: Katy Scott --- src/imgtools/io/sample_output.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/imgtools/io/sample_output.py b/src/imgtools/io/sample_output.py index cc5bc5ac..68df8681 100644 --- a/src/imgtools/io/sample_output.py +++ b/src/imgtools/io/sample_output.py @@ -133,7 +133,7 @@ class SampleOutput(BaseModel): ) dry_run: bool = Field( default=False, - description="Whether to run the pipeline in dry run mode, by default False", + description="Whether to run the pipeline in dry run mode, by default False. Will generate the output index listing images and specified masks with ROIs.", title="Dry Run", ) _writer: AbstractBaseWriter | None = PrivateAttr(default=None) From ce5f490b5c96101d678593ba0ecab3ead1a9ab34 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Wed, 10 Dec 2025 11:45:32 -0500 Subject: [PATCH 05/22] feat: updated snapshots for integration testing --- .../CPTAC-UCEC_CT_default | 77 ++++++++++--------- .../CPTAC-UCEC_MR_default | 3 + .../CPTAC-UCEC_PT_default | 5 ++ .../CPTAC-UCEC_RTSTRUCT_default | 2 + .../NSCLC_Radiogenomics_CT_default | 2 + .../NSCLC_Radiogenomics_PT_default | 4 + .../NSCLC_Radiogenomics_SEG_default | 2 + .../Pancreatic-CT-CBCT-SEG_CT_default | 1 + .../Pancreatic-CT-CBCT-SEG_RTDOSE_default | 1 + .../Pancreatic-CT-CBCT-SEG_RTSTRUCT_default | 1 + 10 files changed, 61 insertions(+), 37 deletions(-) diff --git a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_CT_default b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_CT_default index a4d2c4e4..6e00cd46 100644 --- a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_CT_default +++ b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_CT_default @@ -1,37 +1,40 @@ - Keyword Value - AcquisitionDate 20081209 - AcquisitionNumber 1 - AcquisitionTime 121803.711801 - ContentDate 20081209 - ContentTime 121923 - ContrastBolusAgent GASTR 25/975 & ISOVUE 370 125CC - ConvolutionKernel SOFT - DataCollectionDiameter 500.000000 - ExposureTime 600 - FrameOfReferenceUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.288215967837533272… - GantryDetectorTilt 0.000000 - ImageOrientationPatient [1.000000, 0.000000, 0.000000, 0.000000, 0.000000, - -1.000000] - ImagePositionPatient [-226.793, 18.859, -26] - InstanceCreationDate 20081209 - InstanceCreationTime 121923 - KVP 120 - Manufacturer GE MEDICAL SYSTEMS - ManufacturerModelName LightSpeed VCT - Modality CT - PatientID C3L-00947 - PatientPosition FFS - PixelSpacing [0.944824, 0.944824] - ProtocolName 6.2 ABD/PELVIS ALL WITH - ReconstructionDiameter 483.8 - RescaleIntercept -1024 - RescaleSlope 1 - RescaleType Houndsfield Unit - ScanOptions HELICAL MODE - SeriesDate 20081209 - SeriesInstanceUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.953776999629443938… - SeriesTime 121851 - SliceThickness 2.000000 - StudyDate 20081209 - StudyInstanceUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.207643928709693209… - StudyTime 121413 + Keyword Value + AcquisitionDate 20081209 + AcquisitionNumber 1 + AcquisitionTime 121803.711801 + AdditionalPatientHistory endo + ContentDate 20081209 + ContentTime 121923 + ContrastBolusAgent GASTR 25/975 & ISOVUE 370 125CC + ConvolutionKernel SOFT + DataCollectionDiameter 500.000000 + ExposureTime 600 + FrameOfReferenceUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.28821596783753327… + GantryDetectorTilt 0.000000 + ImageOrientationPatient [1.000000, 0.000000, 0.000000, 0.000000, 0.000000, + -1.000000] + ImagePositionPatient [-226.793, 18.859, -26] + InstanceCreationDate 20081209 + InstanceCreationTime 121923 + KVP 120 + Manufacturer GE MEDICAL SYSTEMS + ManufacturerModelName LightSpeed VCT + Modality CT + PatientAge 071Y + PatientID C3L-00947 + PatientPosition FFS + PatientSex F + PixelSpacing [0.944824, 0.944824] + ProtocolName 6.2 ABD/PELVIS ALL WITH + ReconstructionDiameter 483.8 + RescaleIntercept -1024 + RescaleSlope 1 + RescaleType Houndsfield Unit + ScanOptions HELICAL MODE + SeriesDate 20081209 + SeriesInstanceUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.95377699962944393… + SeriesTime 121851 + SliceThickness 2.000000 + StudyDate 20081209 + StudyInstanceUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.20764392870969320… + StudyTime 121413 diff --git a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_MR_default b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_MR_default index 82319e20..2f11159c 100644 --- a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_MR_default +++ b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_MR_default @@ -18,8 +18,11 @@ ManufacturerModelName Signa HDxt Modality MR NumberOfAverages 1.5 + PatientAge 078Y PatientID C3L-02403 PatientPosition FFS + PatientSex F + PatientWeight 74.843 PercentPhaseFieldOfView 100 PercentSampling 100 PixelBandwidth 122.07 diff --git a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_PT_default b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_PT_default index d0fe98f6..2f54074e 100644 --- a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_PT_default +++ b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_PT_default @@ -4,6 +4,7 @@ AcquisitionTerminationCondition TIME AcquisitionTime 163712 ActualFrameDuration 150000 + AdditionalPatientHistory ENDO CA AttenuationCorrectionMethod NONE, 0.000000 cm-1, CoincidenceWindowWidth 0 ContentDate 20081216 @@ -22,8 +23,12 @@ ManufacturerModelName Discovery 710 Modality PT NumberOfSlices 227 + PatientAge 071Y PatientID C3L-00947 PatientPosition HFS + PatientSex F + PatientSize 1.52 + PatientWeight 87 PixelSpacing [3.6458332538605, 3.6458332538605] ProtocolName 7.9 PTCT attenuation only MED 120-199 ReconstructionMethod VPFX diff --git a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_RTSTRUCT_default b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_RTSTRUCT_default index 9657fc57..0a79ea99 100644 --- a/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_RTSTRUCT_default +++ b/tests/snapshots/dicomshow/CPTAC-UCEC_snapshots/CPTAC-UCEC_RTSTRUCT_default @@ -5,7 +5,9 @@ ManufacturerModelName OHIF-XNAT Viewer 3.2.0 Modality RTSTRUCT NumROIs 1 + PatientAge 071Y PatientID C3L-00947 + PatientSex F ROINames ['UTERUS - 1'] ReferencedSOPUIDs [] ReferencedSeriesUID 1.3.6.1.4.1.14519.5.2.1.6450.2626.19431497777982132912… diff --git a/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_CT_default b/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_CT_default index 251e315a..cc085270 100644 --- a/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_CT_default +++ b/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_CT_default @@ -11,8 +11,10 @@ ImagePositionPatient [-182.1533203125, -314.1533203125, -67] KVP 120 Modality CT + PatientAge 078Y PatientID R01-001 PatientPosition HFS + PatientSex F PixelSpacing [0.693359375, 0.693359375] ProtocolName 01_CAP ReconstructionDiameter 355 diff --git a/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_PT_default b/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_PT_default index a1e9a306..30cb2004 100644 --- a/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_PT_default +++ b/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_PT_default @@ -17,8 +17,12 @@ Manufacturer GE MEDICAL SYSTEMS Modality PT NumberOfSlices 205 + PatientAge 078Y PatientID R01-001 PatientPosition HFS + PatientSex F + PatientSize 1.6000000238419 + PatientWeight 66 PixelSpacing [4.296875, 4.296875] ReconstructionMethod OSEM RescaleIntercept 0 diff --git a/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_SEG_default b/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_SEG_default index ae3ce4db..841f25a9 100644 --- a/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_SEG_default +++ b/tests/snapshots/dicomshow/NSCLC_Radiogenomics_snapshots/NSCLC_Radiogenomics_SEG_default @@ -7,7 +7,9 @@ Manufacturer 3D Slicer Community ManufacturerModelName https://github.com/fedorov/Reporting Modality SEG + PatientAge 078Y PatientID R01-001 + PatientSex F ROIDescriptions ['Segment No.1 is for ...'] ROINames ['Heart'] ReferencedSOPUIDs ['1.3.6.1.4.1.14519.5.2.1.4334.1501.100822413162364501… diff --git a/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_CT_default b/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_CT_default index e1a0dbf1..5af3476e 100644 --- a/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_CT_default +++ b/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_CT_default @@ -21,6 +21,7 @@ Modality CT PatientID Pancreas-CT-CB_003 PatientPosition HFS + PatientSex M PixelSpacing [1.3671875, 1.3671875] ReconstructionDiameter 700 RescaleIntercept -1000 diff --git a/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTDOSE_default b/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTDOSE_default index 2ce9e674..3e5d5cd2 100644 --- a/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTDOSE_default +++ b/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTDOSE_default @@ -16,6 +16,7 @@ ManufacturerModelName ARIA RadOnc Modality RTDOSE PatientID Pancreas-CT-CB_003 + PatientSex M PixelSpacing [2.5, 2.5] ReferencedSeriesSOPUIDs ['1.3.6.1.4.1.14519.5.2.1.30741749844713802115267821… SeriesDate 20120120 diff --git a/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTSTRUCT_default b/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTSTRUCT_default index f57a4277..2285024c 100644 --- a/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTSTRUCT_default +++ b/tests/snapshots/dicomshow/Pancreatic-CT-CBCT-SEG_snapshots/Pancreatic-CT-CBCT-SEG_RTSTRUCT_default @@ -7,6 +7,7 @@ Modality RTSTRUCT NumROIs 4 PatientID Pancreas-CT-CB_003 + PatientSex M ROINames ['Bowel_sm_CBCT', 'LUNG_L', 'LUNG_R', 'Stomach_duo_CBCT'] ReferencedSOPUIDs [] From 47567a8072f43b892691623b3fdfe432e91e1f67 Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Wed, 10 Dec 2025 14:58:24 -0500 Subject: [PATCH 06/22] chore: update lock file --- 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"test" - pixi-version: v0.47.0 + pixi-version: v0.61.0 cache: true locked: false @@ -127,10 +127,10 @@ jobs: - uses: actions/checkout@v4 - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.8.8 + uses: prefix-dev/setup-pixi@v0.9.3 with: environments: ${{ matrix.env }} - pixi-version: v0.46.0 + pixi-version: v0.61.0 cache: true locked: false # wont be the same because of the tag @@ -170,10 +170,10 @@ jobs: git config user.email github-actions[bot]@users.noreply.github.com - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.8.8 + uses: prefix-dev/setup-pixi@v0.9.3 with: environments: ${{ matrix.env }} - pixi-version: v0.46.0 + pixi-version: v0.61.0 cache: true locked: false # wont be the same because of the tag - name: Build API Reference @@ -272,10 +272,10 @@ jobs: termshot --version - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.8.8 + uses: prefix-dev/setup-pixi@v0.9.3 with: environments: "py313" - pixi-version: v0.46.0 + pixi-version: v0.61.0 cache: true locked: false activate-environment: true From 9507a17937375de321e2f8be3ed1cd61b77598ef Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Tue, 16 Dec 2025 13:21:54 -0500 Subject: [PATCH 12/22] chore: update action.yaml --- .github/actions/pytest/action.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/actions/pytest/action.yml b/.github/actions/pytest/action.yml index 7329b1b7..fa76a339 100644 --- a/.github/actions/pytest/action.yml +++ b/.github/actions/pytest/action.yml @@ -30,10 +30,10 @@ runs: - uses: actions/checkout@v4 - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.8.8 + uses: prefix-dev/setup-pixi@v0.9.3 with: environments: ${{ inputs.env }} - pixi-version: v0.47.0 + pixi-version: v0.61.0 cache: true - name: Prepare data if needed From 64958adda5e2e52a4a6be281676220dc3c2495af Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Tue, 16 Dec 2025 13:30:30 -0500 Subject: [PATCH 13/22] chore: pixi lock with version 0.61 --- pixi.lock | 14035 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a/.github/actions/pytest/action.yml b/.github/actions/pytest/action.yml index fa76a339..1beeabf0 100644 --- a/.github/actions/pytest/action.yml +++ b/.github/actions/pytest/action.yml @@ -34,7 +34,7 @@ runs: with: environments: ${{ inputs.env }} pixi-version: v0.61.0 - cache: true + cache: false - name: Prepare data if needed if: inputs.test_type == 'integration' From 91ef21a53487727d698cef7924d446b47f8858d0 Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Mon, 5 Jan 2026 11:10:13 -0500 Subject: [PATCH 16/22] chore --- .github/actions/pytest/action.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/actions/pytest/action.yml b/.github/actions/pytest/action.yml index 1beeabf0..f66cae7c 100644 --- a/.github/actions/pytest/action.yml +++ b/.github/actions/pytest/action.yml @@ -32,9 +32,8 @@ runs: - name: Install Pixi uses: prefix-dev/setup-pixi@v0.9.3 with: - environments: ${{ inputs.env }} pixi-version: v0.61.0 - cache: false + cache: true - name: Prepare data if needed if: inputs.test_type == 'integration' From f5e79b2eb7d29868165b7eb46ad8ae63772ee8df Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Mon, 5 Jan 2026 11:11:08 -0500 Subject: [PATCH 17/22] chore --- .github/actions/pytest/action.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/actions/pytest/action.yml b/.github/actions/pytest/action.yml index f66cae7c..87a5586d 100644 --- a/.github/actions/pytest/action.yml +++ b/.github/actions/pytest/action.yml @@ -32,8 +32,10 @@ runs: - name: Install Pixi uses: prefix-dev/setup-pixi@v0.9.3 with: + environments: ${{ inputs.env }} pixi-version: v0.61.0 cache: true + locked: false - name: Prepare data if needed if: inputs.test_type == 'integration' From 5e69eca5d17837315e95ef9121137304957348dc Mon Sep 17 00:00:00 2001 From: Joshua Siraj Date: Mon, 5 Jan 2026 11:27:45 -0500 Subject: [PATCH 18/22] chore --- .github/actions/pytest/action.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/actions/pytest/action.yml 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8320d5af37eb8933e5d129884ea013b2687e75b08aff5216193df3378eaea92f + md5: 8af3faf88325836e46c6cb79828e058c depends: - __glibc >=2.17,<3.0.a0 - libgcc >=14 @@ -20433,7 +20345,7 @@ packages: license: MIT license_family: MIT purls: - - pkg:pypi/zipp?source=compressed-mapping + - pkg:pypi/zipp?source=hash-mapping size: 24194 timestamp: 1764460141901 - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.2-hceb46e0_1.conda From 86bc10cc69b4855f9e233c6cb6db71a0aa24a863 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Thu, 3 Sep 2026 14:42:38 -0400 Subject: [PATCH 22/22] chore: update setup-pixi versions in ci-cd --- .github/actions/pytest/action.yml | 4 ++-- .github/workflows/main.yml | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/actions/pytest/action.yml b/.github/actions/pytest/action.yml index 5efea90e..c159849b 100644 --- a/.github/actions/pytest/action.yml +++ b/.github/actions/pytest/action.yml @@ -30,10 +30,10 @@ runs: - uses: actions/checkout@v4 - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.9.4 + uses: prefix-dev/setup-pixi@v0.10.2 with: environments: ${{ inputs.env }} - pixi-version: v0.62.2 + pixi-version: v0.66.0 cache: true locked: false diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index db7cb1c8..76bf2ef4 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -89,10 +89,10 @@ jobs: - uses: actions/checkout@v4 - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.9.4 + uses: prefix-dev/setup-pixi@v0.10.2 with: environments: "test" - pixi-version: v0.62.2 + pixi-version: v0.66.0 cache: true locked: false @@ -127,10 +127,10 @@ jobs: - uses: actions/checkout@v4 - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.9.4 + uses: prefix-dev/setup-pixi@v0.10.2 with: environments: ${{ matrix.env }} - pixi-version: v0.62.2 + pixi-version: v0.66.0 cache: true locked: false # wont be the same because of the tag @@ -170,10 +170,10 @@ jobs: git config user.email github-actions[bot]@users.noreply.github.com - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.9.4 + uses: prefix-dev/setup-pixi@v0.10.2 with: environments: ${{ matrix.env }} - pixi-version: v0.62.2 + pixi-version: v0.66.0 cache: true locked: false # wont be the same because of the tag - name: Build API Reference @@ -272,10 +272,10 @@ jobs: termshot --version - name: Install Pixi - uses: prefix-dev/setup-pixi@v0.9.4 + uses: prefix-dev/setup-pixi@v0.10.2 with: environments: "py313" - pixi-version: v0.62.2 + pixi-version: v0.66.0 cache: true locked: false activate-environment: true