From 448351fde9000a2a8723834cb3216ac4f3c4006f Mon Sep 17 00:00:00 2001 From: Chris Bridge Date: Wed, 19 May 2021 12:39:44 +0000 Subject: [PATCH] Fix import PR docstrings (#72) * Fix all sphinx warnings * Removed all unnecessary modules from doc content tree, fixed all docstrings to match * Fix unused import --- docs/package.rst | 128 ------------------------ src/highdicom/base.py | 2 +- src/highdicom/content.py | 32 +++--- src/highdicom/sc/sop.py | 4 +- src/highdicom/seg/__init__.py | 4 + src/highdicom/seg/content.py | 18 ++-- src/highdicom/seg/sop.py | 14 +-- src/highdicom/sr/coding.py | 2 +- src/highdicom/sr/content.py | 48 ++++----- src/highdicom/sr/sop.py | 8 +- src/highdicom/sr/templates.py | 172 ++++++++++++++++---------------- src/highdicom/sr/utils.py | 22 ++-- src/highdicom/sr/value_types.py | 92 ++++++++--------- src/highdicom/utils.py | 4 +- tests/test_content.py | 2 +- tests/test_sc.py | 4 +- tests/test_seg.py | 8 +- tests/test_sr.py | 12 +-- tests/test_utils.py | 2 +- 19 files changed, 227 insertions(+), 351 deletions(-) diff --git a/docs/package.rst b/docs/package.rst index 04083eea..39806c79 100644 --- a/docs/package.rst +++ b/docs/package.rst @@ -23,15 +23,6 @@ highdicom.color module :undoc-members: :show-inheritance: -highdicom.content module -++++++++++++++++++++++++ - -.. automodule:: highdicom.content - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - highdicom.enum module +++++++++++++++++++++ @@ -68,15 +59,6 @@ highdicom.spatial module :undoc-members: :show-inheritance: -highdicom.uid module -++++++++++++++++++++++ - -.. automodule:: highdicom.uid - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - highdicom.utils module ++++++++++++++++++++++ @@ -99,16 +81,6 @@ highdicom.legacy package :show-inheritance: -highdicom.legacy.sop module -+++++++++++++++++++++++++++ - -.. automodule:: highdicom.legacy.sop - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - - .. _highdicom-seg-subpackage: highdicom.seg package @@ -120,33 +92,6 @@ highdicom.seg package :undoc-members: :show-inheritance: -highdicom.seg.content module -++++++++++++++++++++++++++++ - -.. automodule:: highdicom.seg.content - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.seg.enum module -+++++++++++++++++++++++++ - -.. automodule:: highdicom.seg.enum - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.seg.sop module -++++++++++++++++++++++++ - -.. automodule:: highdicom.seg.sop - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - highdicom.seg.utils module ++++++++++++++++++++++++++ @@ -167,42 +112,6 @@ highdicom.sr package :undoc-members: :show-inheritance: -highdicom.sr.coding module -++++++++++++++++++++++++++ - -.. automodule:: highdicom.sr.coding - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.sr.content module -+++++++++++++++++++++++++++ - -.. automodule:: highdicom.sr.content - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.sr.enum module -++++++++++++++++++++++++ - -.. automodule:: highdicom.sr.enum - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.sr.sop module -+++++++++++++++++++++++ - -.. automodule:: highdicom.sr.sop - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - highdicom.sr.utils module +++++++++++++++++++++++++ @@ -212,25 +121,6 @@ highdicom.sr.utils module :undoc-members: :show-inheritance: -highdicom.sr.templates module -+++++++++++++++++++++++++++++ - -.. automodule:: highdicom.sr.templates - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.sr.value\_types module -++++++++++++++++++++++++++++++++ - -.. automodule:: highdicom.sr.value_types - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - - .. _highdicom-sc-subpackage: highdicom.sc package @@ -241,21 +131,3 @@ highdicom.sc package :special-members: __call__ :undoc-members: :show-inheritance: - -highdicom.sc.enum module -+++++++++++++++++++++++++ - -.. automodule:: highdicom.sc.enum - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: - -highdicom.sc.sop module -++++++++++++++++++++++++ - -.. automodule:: highdicom.sc.sop - :members: - :special-members: __call__ - :undoc-members: - :show-inheritance: diff --git a/src/highdicom/base.py b/src/highdicom/base.py index 87cea3f1..18548cae 100644 --- a/src/highdicom/base.py +++ b/src/highdicom/base.py @@ -93,7 +93,7 @@ def __init__( Name of the referring physician content_qualification: Union[str, highdicom.enum.ContentQualificationValues], optional Indicator of content qualification - coding_schemes: Sequence[highdicom.sr.coding.CodingSchemeIdentificationItem], optional + coding_schemes: Sequence[highdicom.sr.CodingSchemeIdentificationItem], optional private or public coding schemes that are not part of the DICOM standard series_description: str, optional diff --git a/src/highdicom/content.py b/src/highdicom/content.py index 626dd2d9..ce878302 100644 --- a/src/highdicom/content.py +++ b/src/highdicom/content.py @@ -41,7 +41,7 @@ def __init__( ---------- name: str Name of the algorithm - family: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + family: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Kind of algorithm family version: str Version of the algorithm @@ -175,7 +175,7 @@ def __eq__(self, other: Any) -> bool: Parameters ---------- - other: highdicom.content.PlanePositionSequence + other: highdicom.PlanePositionSequence Plane position of other image that should be compared Returns @@ -255,7 +255,7 @@ def __eq__(self, other: Any) -> bool: Parameters ---------- - other: highdicom.content.PlaneOrientationSequence + other: highdicom.PlaneOrientationSequence Plane position of other image that should be compared Returns @@ -338,7 +338,7 @@ def __init__( """ Parameters ---------- - procedure: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + procedure: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Procedure used to collect the examined specimen """ # noqa @@ -368,13 +368,13 @@ def __init__( """ Parameters ---------- - method: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + method: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Method used to sample the examined specimen from a parent specimen parent_specimen_id: str Identifier of the parent specimen - parent_specimen_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + parent_specimen_type: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Type of the parent specimen - issuer_of_parent_specimen_id: highdicom.content.IssuerOfIdentifier, optional + issuer_of_parent_specimen_id: highdicom.IssuerOfIdentifier, optional Issuer who created the parent specimen """ # noqa @@ -423,7 +423,7 @@ def __init__( """ Parameters ---------- - substances: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]] + substances: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]] Substances used to stain examined specimen(s) """ # noqa @@ -467,18 +467,18 @@ def __init__( ---------- specimen_id: str Identifier of the processed specimen - processing_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + processing_type: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Type of processing - processing_procedure: Union[highdicom.content.SpecimenCollection, highdicom.content.SpecimenSampling, highdicom.content.SpecimenStaining] + processing_procedure: Union[highdicom.SpecimenCollection, highdicom.SpecimenSampling, highdicom.SpecimenStaining] Procedure used during processing processing_datetime: datetime.datetime, optional Datetime of processing - processing_description: Union[str, pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional + processing_description: Union[str, pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional Description of processing - issuer_of_specimen_id: highdicom.content.IssuerOfIdentifier, optional - fixative: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional + issuer_of_specimen_id: highdicom.IssuerOfIdentifier, optional + fixative: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional Fixative used during processing - embedding_medium: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional + embedding_medium: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional Embedding medium used during processing """ # noqa @@ -566,10 +566,10 @@ def __init__( provided either in form of text or in form of spatial x, y, z coordinates specifying the position (offset) relative to the three-dimensional slide coordinate system - specimen_preparation_steps: Sequence[highdicom.content.SpecimenPreparationStep], optional + specimen_preparation_steps: Sequence[highdicom.SpecimenPreparationStep], optional Steps that were applied during the preparation of the examined specimen in the laboratory prior to image acquisition - issuer_of_specimen_id: highdicom.content.IssuerOfIdentifier, optional + issuer_of_specimen_id: highdicom.IssuerOfIdentifier, optional Description of the issuer of the specimen identifier """ # noqa diff --git a/src/highdicom/sc/sop.py b/src/highdicom/sc/sop.py index 9e53118a..1bc5553b 100644 --- a/src/highdicom/sc/sop.py +++ b/src/highdicom/sc/sop.py @@ -158,9 +158,9 @@ def __init__( container_identifier: str, optional Identifier of the container holding the specimen (required if `coordinate_system` is ``"SLIDE"``) - issuer_of_container_identifier: highdicom.content.IssuerOfIdentifier, optional + issuer_of_container_identifier: highdicom.IssuerOfIdentifier, optional Issuer of `container_identifier` - specimen_descriptions: Sequence[highdicom.content.SpecimenDescriptions], optional + specimen_descriptions: Sequence[highdicom.SpecimenDescriptions], optional Description of each examined specimen (required if `coordinate_system` is ``"SLIDE"``) transfer_syntax_uid: str, optional diff --git a/src/highdicom/seg/__init__.py b/src/highdicom/seg/__init__.py index 89f627a3..a71c68c4 100644 --- a/src/highdicom/seg/__init__.py +++ b/src/highdicom/seg/__init__.py @@ -7,6 +7,10 @@ SpatialLocationsPreservedValues, SegmentsOverlapValues, ) +from highdicom.seg.content import ( + SegmentDescription, + DimensionIndexSequence, +) from highdicom.seg import utils SOP_CLASS_UIDS = { diff --git a/src/highdicom/seg/content.py b/src/highdicom/seg/content.py index 52ddf504..99f5fc06 100644 --- a/src/highdicom/seg/content.py +++ b/src/highdicom/seg/content.py @@ -47,32 +47,32 @@ def __init__( Number of the segment. segment_label: str Label of the segment - segmented_property_category: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + segmented_property_category: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Category of the property the segment represents, e.g. ``Code("49755003", "SCT", "Morphologically Abnormal Structure")`` (see `CID 7150 `_ "Segmentation Property Categories") - segmented_property_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept] + segmented_property_type: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept] Property the segment represents, e.g. ``Code("108369006", "SCT", "Neoplasm")`` (see `CID 7151 `_ "Segmentation Property Types") - algorithm_type: Union[str, highdicom.seg.enum.SegmentAlgorithmTypeValues] + algorithm_type: Union[str, highdicom.seg.SegmentAlgorithmTypeValues] Type of algorithm - algorithm_identification: highdicom.content.AlgorithmIdentificationSequence, optional + algorithm_identification: highdicom.AlgorithmIdentificationSequence, optional Information useful for identification of the algorithm, such as its name or version. Required unless the algorithm type is `MANUAL` tracking_uid: str, optional Unique tracking identifier (universally unique) tracking_id: str, optional Tracking identifier (unique only with the domain of use) - anatomic_regions: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]], optional + anatomic_regions: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]], optional Anatomic region(s) into which segment falls, e.g. ``Code("41216001", "SCT", "Prostate")`` (see `CID 4 `_ "Anatomic Region", `CID 4031 `_ "Common Anatomic Regions", as as well as other CIDs for domain-specific anatomic regions) - primary_anatomic_structures: Sequence[Union[highdicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]], optional + primary_anatomic_structures: Sequence[Union[highdicom.sr.Code, highdicom.sr.CodedConcept]], optional Anatomic structure(s) the segment represents (see CIDs for domain-specific primary anatomic structures) @@ -307,7 +307,7 @@ def get_plane_positions_of_image( Returns ------- - List[PlanePositionSequence] + List[highdicom.PlanePositionSequence] Plane position of each frame in the image """ @@ -348,7 +348,7 @@ def get_plane_positions_of_series( Returns ------- - List[PlanePositionSequence] + List[highdicom.PlanePositionSequence] Plane position of each frame in the image """ @@ -376,7 +376,7 @@ def get_index_values( Parameters ---------- - plane_positions: Sequence[PlanePositionSequence] + plane_positions: Sequence[highdicom.PlanePositionSequence] Plane position of frames in a multi-frame image or in a series of single-frame images diff --git a/src/highdicom/seg/sop.py b/src/highdicom/seg/sop.py index a81286b3..976bc649 100644 --- a/src/highdicom/seg/sop.py +++ b/src/highdicom/seg/sop.py @@ -113,9 +113,9 @@ def __init__( the column dimension, which are defined in the three-dimensional slide coordinate system by the direction cosines encoded by the *Image Orientation (Slide)* attribute). - segmentation_type: Union[str, highdicom.seg.enum.SegmentationTypeValues] + segmentation_type: Union[str, highdicom.seg.SegmentationTypeValues] Type of segmentation, either ``"BINARY"`` or ``"FRACTIONAL"`` - segment_descriptions: Sequence[highdicom.seg.content.SegmentDescription] + segment_descriptions: Sequence[highdicom.seg.SegmentDescription] Description of each segment encoded in `pixel_array`. In the case of pixel arrays with multiple integer values, the segment description with the corresponding segment number is used to describe each segment. @@ -135,7 +135,7 @@ def __init__( application) that creates the instance software_versions: Union[str, Tuple[str]] Version(s) of the software that creates the instance - fractional_type: Union[str, highdicom.seg.enum.SegmentationFractionalTypeValues], optional + fractional_type: Union[str, highdicom.seg.SegmentationFractionalTypeValues], optional Type of fractional segmentation that indicates how pixel data should be interpreted max_fractional_value: int, optional @@ -156,12 +156,12 @@ def __init__( Physical spacing of image pixels in `pixel_array`. If ``None``, it will be assumed that the segmentation image has the same pixel measures as the source image(s). - plane_orientation: highdicom.content.PlaneOrientationSequence, optional + plane_orientation: highdicom.PlaneOrientationSequence, optional Orientation of planes in `pixel_array` relative to axes of three-dimensional patient or slide coordinate space. If ``None``, it will be assumed that the segmentation image as the same plane orientation as the source image(s). - plane_positions: Sequence[highdicom.content.PlanePositionSequence], optional + plane_positions: Sequence[highdicom.PlanePositionSequence], optional Position of each plane in `pixel_array` in the three-dimensional patient or slide coordinate space. If ``None``, it will be assumed that the segmentation image has the @@ -467,12 +467,12 @@ def add_segments( the column dimension, which are defined in the three-dimensional slide coordinate system by the direction cosines encoded by the *Image Orientation (Slide)* attribute). - segment_descriptions: Sequence[highdicom.seg.content.SegmentDescription] + segment_descriptions: Sequence[highdicom.seg.SegmentDescription] Description of each segment encoded in `pixel_array`. In the case of pixel arrays with multiple integer values, the segment description with the corresponding segment number is used to describe each segment. - plane_positions: Sequence[highdicom.content.PlanePositionSequence], optional + plane_positions: Sequence[highdicom.PlanePositionSequence], optional Position of each plane in `pixel_array` relative to the three-dimensional patient or slide coordinate system. diff --git a/src/highdicom/sr/coding.py b/src/highdicom/sr/coding.py index be41f928..a64a2378 100644 --- a/src/highdicom/sr/coding.py +++ b/src/highdicom/sr/coding.py @@ -52,7 +52,7 @@ def __eq__(self, other: Any) -> bool: Parameters ---------- - other: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + other: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] code Returns diff --git a/src/highdicom/sr/content.py b/src/highdicom/sr/content.py index 9cdd6198..ca084a0a 100644 --- a/src/highdicom/sr/content.py +++ b/src/highdicom/sr/content.py @@ -110,9 +110,9 @@ def __init__( ---------- value: Union[int, float], optional offset in time from a particular event of significance - unit: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + unit: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional unit of time, e.g., "Days" or "Seconds" - event_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + event_type: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional type of event to which offset is relative, e.g., "Baseline" or "Enrollment" @@ -204,7 +204,7 @@ def from_source_image( Returns ------- - highdicom.sr.content.SourceImageForMeasurement + highdicom.sr.SourceImageForMeasurement Content item representing a reference to the image dataset """ @@ -286,7 +286,7 @@ def from_source_image( Returns ------- - highdicom.sr.content.SourceImageForRegion + highdicom.sr.SourceImageForRegion Content item representing a reference to the image dataset """ @@ -368,7 +368,7 @@ def from_source_image( Returns ------- - highdicom.sr.content.SourceImageForSegmentation + highdicom.sr.SourceImageForSegmentation Content item representing a reference to the image dataset """ @@ -424,7 +424,7 @@ def from_source_image( Returns ------- - highdicom.sr.content.SourceSeriesForSegmentation + highdicom.sr.SourceSeriesForSegmentation Content item representing a reference to the image dataset """ @@ -452,21 +452,21 @@ def __init__( """ Parameters ---------- - graphic_type: Union[highdicom.sr.enum.GraphicTypeValues, str] + graphic_type: Union[highdicom.sr.GraphicTypeValues, str] name of the graphic type graphic_data: numpy.ndarray array of ordered spatial coordinates, where each row of the array represents a (column, row) coordinate pair source_image: highdicom.sr.template.SourceImageForRegion source image to which `graphic_data` relates - pixel_origin_interpretation: Union[highdicom.sr.enum.PixelOriginInterpretationValues, str], optional + pixel_origin_interpretation: Union[highdicom.sr.PixelOriginInterpretationValues, str], optional whether pixel coordinates specified by `graphic_data` are defined relative to the total pixel matrix - (``highdicom.sr.enum.PixelOriginInterpretationValues.VOLUME``) or + (``highdicom.sr.PixelOriginInterpretationValues.VOLUME``) or relative to an individual frame - (``highdicom.sr.enum.PixelOriginInterpretationValues.FRAME``) + (``highdicom.sr.PixelOriginInterpretationValues.FRAME``) of the source image - (default: ``highdicom.sr.enum.PixelOriginInterpretationValues.VOLUME``) + (default: ``highdicom.sr.PixelOriginInterpretationValues.VOLUME``) """ # noqa graphic_type = GraphicTypeValues(graphic_type) @@ -516,7 +516,7 @@ def __init__( """ Parameters ---------- - graphic_type: Union[highdicom.sr.enum.GraphicTypeValues3D, str] + graphic_type: Union[highdicom.sr.GraphicTypeValues3D, str] name of the graphic type graphic_data: numpy.ndarray array of ordered spatial coordinates, where each row of the array @@ -566,16 +566,16 @@ def __init__( """ Parameters ---------- - graphic_type: Union[highdicom.sr.enum.GraphicTypeValues3D, str] + graphic_type: Union[highdicom.sr.GraphicTypeValues3D, str] name of the graphic type graphic_data: Sequence[Sequence[int]] ordered set of (row, column, frame) coordinate pairs frame_of_reference_uid: str unique identifier of the frame of reference within which the coordinates are defined - source_images: Sequence[highdicom.sr.content.SourceImageForSegmentation], optional + source_images: Sequence[highdicom.sr.SourceImageForSegmentation], optional source images for segmentation - source_series: highdicom.sr.content.SourceSeriesForSegmentation, optional + source_series: highdicom.sr.SourceSeriesForSegmentation, optional source series for segmentation Note @@ -660,7 +660,7 @@ def from_source_value_map( Returns ------- - highdicom.sr.content.RealWorldValueMap + highdicom.sr.RealWorldValueMap Content item representing a reference to the image dataset """ @@ -686,13 +686,13 @@ def __init__( """ Parameters ---------- - anatomic_location: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + anatomic_location: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] coded anatomic location (region or structure) - laterality: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + laterality: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded laterality (see `CID 244 `_ "Laterality" for options) - topographical_modifier: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + topographical_modifier: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded modifier of anatomic location """ # noqa @@ -757,7 +757,7 @@ def __init__( number of the segment to which the refernce applies frame_number: int number of the frame to which the reference applies - source_image: highdicom.sr.content.SourceImageForSegmentation + source_image: highdicom.sr.SourceImageForSegmentation source image for segmentation """ @@ -801,7 +801,7 @@ def from_segmentation( Returns ------- - highdicom.sr.content.ReferencedSegment + highdicom.sr.ReferencedSegment Content item representing a reference to the segment Notes @@ -940,9 +940,9 @@ def __init__( frame_numbers: Sequence[int], optional numbers of the frames to which the reference applies (in case a segmentation instance is referenced) - source_images: Sequence[highdicom.sr.content.SourceImageForSegmentation], optional + source_images: Sequence[highdicom.sr.SourceImageForSegmentation], optional source images for segmentation - source_series: highdicom.sr.content.SourceSeriesForSegmentation, optional + source_series: highdicom.sr.SourceSeriesForSegmentation, optional source series for segmentation Note @@ -1010,7 +1010,7 @@ def from_segmentation( Returns ------- - highdicom.sr.content.ReferencedSegment + highdicom.sr.ReferencedSegment Content item representing a reference to the segment Notes diff --git a/src/highdicom/sr/sop.py b/src/highdicom/sr/sop.py index 060b3965..69fd260b 100644 --- a/src/highdicom/sr/sop.py +++ b/src/highdicom/sr/sop.py @@ -96,7 +96,7 @@ def __init__( verifying_organization: str, optional Name of the organization that verfied the SR document (required if `is_verified`) - performed_procedure_codes: List[highdicom.sr.coding.CodedConcept], optional + performed_procedure_codes: List[highdicom.sr.CodedConcept], optional Codes of the performed procedures that resulted in the SR document requested_procedures: List[pydicom.dataset.Dataset], optional Requested procedures that are being fullfilled by creation of the @@ -423,7 +423,7 @@ def __init__( verifying_organization: str, optional Name of the organization that verfied the SR document (required if `is_verified`) - performed_procedure_codes: List[highdicom.sr.coding.CodedConcept], optional + performed_procedure_codes: List[highdicom.sr.CodedConcept], optional Codes of the performed procedures that resulted in the SR document requested_procedures: List[pydicom.dataset.Dataset], optional Requested procedures that are being fullfilled by creation of the @@ -551,7 +551,7 @@ def __init__( verifying_organization: str, optional Name of the organization that verfied the SR document (required if `is_verified`) - performed_procedure_codes: List[highdicom.sr.coding.CodedConcept], optional + performed_procedure_codes: List[highdicom.sr.CodedConcept], optional Codes of the performed procedures that resulted in the SR document requested_procedures: List[pydicom.dataset.Dataset] Requested procedures that are being fullfilled by creation of the @@ -679,7 +679,7 @@ def __init__( verifying_organization: str, optional Name of the organization that verfied the SR document (required if `is_verified`) - performed_procedure_codes: List[highdicom.sr.coding.CodedConcept], optional + performed_procedure_codes: List[highdicom.sr.CodedConcept], optional Codes of the performed procedures that resulted in the SR document requested_procedures: List[pydicom.dataset.Dataset] Requested procedures that are being fullfilled by creation of the diff --git a/src/highdicom/sr/templates.py b/src/highdicom/sr/templates.py index 34c660d3..804a1d6d 100644 --- a/src/highdicom/sr/templates.py +++ b/src/highdicom/sr/templates.py @@ -178,7 +178,7 @@ def __init__( ---------- time_point: str actual value representation of the time point - time_point_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + time_point_type: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded type of time point, e.g., "Baseline" or "Posttreatment" (see `CID 6146 `_ "Time Point Types" for options) @@ -193,7 +193,7 @@ def __init__( identifier of a specific time point in a time series, which is unique within an appropriate local context and specific to a particular protocol using the same value for different subjects - temporal_offset_from_event: highdicom.sr.content.LongitudinalTemporalOffsetFromEvent, optional + temporal_offset_from_event: highdicom.sr.LongitudinalTemporalOffsetFromEvent, optional offset in time from a particular event of significance, e.g., the baseline of an imaging study or enrollment into a clinical trial @@ -279,7 +279,7 @@ def __init__( Parameters ---------- - values: Sequence[highdicom.sr.value_types.NumContentItem] + values: Sequence[highdicom.sr.NumContentItem] reference values of the population of measurements, e.g., its mean or standard deviation (see `CID 226 `_ @@ -342,7 +342,7 @@ def __init__( Parameters ---------- - values: Sequence[highdicom.sr.value_types.NumContentItem] + values: Sequence[highdicom.sr.NumContentItem] reference values of the normal range, e.g., its upper and lower bound (see `CID 223 `_ @@ -400,23 +400,23 @@ def __init__( Parameters ---------- - normality: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + normality: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional the extend to which the measurement is considered normal or abnormal (see `CID 222 `_ "Normality Codes" for options) - level_of_significance: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + level_of_significance: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional the extend to which the measurement is considered normal or abnormal (see `CID 220 `_ "Level of Significance" for options) - selection_status: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + selection_status: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional how the measurement value was selected or computed from a set of available values (see `CID 224 `_ "Selection Method" for options) - measurement_statistical_properties: highdicom.sr.templates.MeasurementStatisticalProperties, optional + measurement_statistical_properties: highdicom.sr.MeasurementStatisticalProperties, optional statistical properties of a reference population for a measurement and/or the position of a measurement in such a reference population - normal_range_properties: highdicom.sr.templates.NormalRangeProperties, optional + normal_range_properties: highdicom.sr.NormalRangeProperties, optional statistical properties of a reference population for a measurement and/or the position of a measurement in such a reference population upper_measurement_uncertainty: Union[int, float], optional @@ -522,9 +522,9 @@ def __init__( login name of the person organization_name: str, optional name of the person's organization - role_in_organization: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + role_in_organization: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional role of the person within the organization - role_in_procedure: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + role_in_procedure: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional role of the person in the reported procedure """ # noqa @@ -697,11 +697,11 @@ def __init__( Parameters ---------- - observer_type: highdicom.sr.coding.CodedConcept + observer_type: highdicom.sr.CodedConcept type of observer (see `CID 270 `_ "Observer Type" for options) - observer_identifying_attributes: Union[highdicom.sr.templates.PersonObserverIdentifyingAttributes, highdicom.sr.templates.DeviceObserverIdentifyingAttributes] + observer_identifying_attributes: Union[highdicom.sr.PersonObserverIdentifyingAttributes, highdicom.sr.DeviceObserverIdentifyingAttributes] observer identifying attributes """ # noqa @@ -794,7 +794,7 @@ def __init__( container_identifier: str, optional identifier of the container holding the speciment (e.g., a glass slide) - specimen_type: highdicom.sr.coding.CodedConcept, optional + specimen_type: highdicom.sr.CodedConcept, optional type of the specimen (see `CID 8103 `_ "Anatomic Pathology Specimen Types" for options) @@ -954,11 +954,11 @@ def __init__( Parameters ---------- - subject_class: highdicom.sr.coding.CodedConcept + subject_class: highdicom.sr.CodedConcept type of subject if the subject of the report is not the patient (see `CID 271 `_ "Observation Subject Class" for options) - subject_class_specific_context: Union[highdicom.sr.templates.SubjectContextFetus, highdicom.sr.templates.SubjectContextSpecimen, highdicom.sr.templates.SubjectContextDevice], optional + subject_class_specific_context: Union[highdicom.sr.SubjectContextFetus, highdicom.sr.SubjectContextSpecimen, highdicom.sr.SubjectContextDevice], optional additional context information specific to `subject_class` """ # noqa @@ -992,12 +992,12 @@ def __init__( Parameters ---------- - observer_person_context: [highdicom.sr.templates.ObserverContext, None], optional + observer_person_context: [highdicom.sr.ObserverContext, None], optional description of the person that reported the observation - observer_device_context: highdicom.sr.templates.ObserverContext, optional + observer_device_context: highdicom.sr.ObserverContext, optional description of the device that was involved in reporting the observation - subject_context: highdicom.sr.templates.SubjectContext, optional + subject_context: highdicom.sr.SubjectContext, optional description of the imaging subject in case it is not the patient for which the report is generated (e.g., a pathology specimen in a whole-slide microscopy image, a fetus in an ultrasound image, or @@ -1043,7 +1043,7 @@ def __init__(self, language: CodedConcept): Parameters ---------- - language: highdicom.sr.coding.CodedConcept + language: highdicom.sr.CodedConcept language used for content items included in report """ @@ -1084,45 +1084,45 @@ def __init__( Parameters ---------- - name: highdicom.sr.coding.CodedConcept + name: highdicom.sr.CodedConcept Name of the measurement (see `CID 7469 `_ "Generic Intensity and Size Measurements" and `CID 7468 `_ "Texture Measurements" for options) - tracking_identifier: highdicom.sr.templates.TrackingIdentifier, optional + tracking_identifier: highdicom.sr.TrackingIdentifier, optional Identifier for tracking measurements value: Union[int, float], optional Numeric measurement value - unit: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + unit: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional Unit of the numeric measurement value (see `CID 7181 `_ "Abstract Multi-dimensional Image Model Component Units" for options) - qualifier: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + qualifier: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional Qualification of numeric measurement value or as an alternative qualitative description - algorithm_id: highdicom.sr.templates.AlgorithmIdentification, optional + algorithm_id: highdicom.sr.AlgorithmIdentification, optional Identification of algorithm used for making measurements - derivation: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + derivation: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional How the value was computed (see `CID 7464 `_ "General Region of Interest Measurement Modifiers" for options) - finding_sites: Sequence[highdicom.sr.content.FindingSite], optional + finding_sites: Sequence[highdicom.sr.FindingSite], optional Coded description of one or more anatomic locations corresonding to the image region from which measurement was taken - method: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + method: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional Measurement method (see `CID 6147 `_ "Response Criteria" for options) - properties: highdicom.sr.templates.MeasurementProperties, optional + properties: highdicom.sr.MeasurementProperties, optional Measurement properties, including evaluations of its normality and/or significance, its relationship to a reference population, and an indication of its selection from a set of measurements - referenced_images: Sequence[highdicom.sr.content.SourceImageForMeasurement], optional + referenced_images: Sequence[highdicom.sr.SourceImageForMeasurement], optional Referenced images which were used as sources for the measurement - referenced_real_world_value_map: highdicom.sr.content.RealWorldValueMap, optional + referenced_real_world_value_map: highdicom.sr.RealWorldValueMap, optional Referenced real world value map for referenced source images """ # noqa @@ -1232,28 +1232,28 @@ def __init__( Parameters ---------- - tracking_identifier: highdicom.sr.templates.TrackingIdentifier + tracking_identifier: highdicom.sr.TrackingIdentifier Identifier for tracking measurements - referenced_real_world_value_map: highdicom.sr.content.RealWorldValueMap, optional + referenced_real_world_value_map: highdicom.sr.RealWorldValueMap, optional Referenced real world value map for region of interest - time_point_context: highdicom.sr.templates.TimePointContext, optional + time_point_context: highdicom.sr.TimePointContext, optional Description of the time point context - finding_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + finding_type: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional Type of object that was measured, e.g., organ or tumor - method: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + method: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded measurement method (see `CID 6147 `_ "Response Criteria" for options) - algorithm_id: highdicom.sr.templates.AlgorithmIdentification, optional + algorithm_id: highdicom.sr.AlgorithmIdentification, optional identification of algorithm used for making measurements - finding_sites: Sequence[highdicom.sr.content.FindingSite], optional + finding_sites: Sequence[highdicom.sr.FindingSite], optional Coded description of one or more anatomic locations corresonding to the image region from which measurement was taken session: str, optional Description of the session - measurements: Sequence[highdicom.sr.templates.Measurement], optional + measurements: Sequence[highdicom.sr.Measurement], optional Numeric measurements - qualitative_evaluations: Sequence[highdicom.sr.value_types.CodeContentItem], optional + qualitative_evaluations: Sequence[highdicom.sr.CodeContentItem], optional Coded name-value pairs that describe measurements in qualitative terms @@ -1398,37 +1398,37 @@ def __init__( Parameters ---------- - tracking_identifier: highdicom.sr.templates.TrackingIdentifier + tracking_identifier: highdicom.sr.TrackingIdentifier identifier for tracking measurements - referenced_regions: Union[Sequence[highdicom.sr.content.ImageRegion], Sequence[highdicom.sr.content.ImageRegion3D]], optional + referenced_regions: Union[Sequence[highdicom.sr.ImageRegion], Sequence[highdicom.sr.ImageRegion3D]], optional regions of interest in source image(s) - referenced_segment: Union[highdicom.sr.content.ReferencedSegment, highdicom.sr.content.ReferencedSegmentationFrame], optional + referenced_segment: Union[highdicom.sr.ReferencedSegment, highdicom.sr.ReferencedSegmentationFrame], optional segmentation for region of interest in source image referenced_volume_surface: hidicom.sr.content.VolumeSurface, optional surface segmentation for region of interest in source image - referenced_real_world_value_map: highdicom.sr.content.RealWorldValueMap, optional + referenced_real_world_value_map: highdicom.sr.RealWorldValueMap, optional referenced real world value map for region of interest - time_point_context: highdicom.sr.templates.TimePointContext, optional + time_point_context: highdicom.sr.TimePointContext, optional description of the time point context - finding_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + finding_type: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional type of object that was measured, e.g., organ or tumor - method: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + method: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded measurement method (see `CID 6147 `_ "Response Criteria" for options) - algorithm_id: highdicom.sr.templates.AlgorithmIdentification, optional + algorithm_id: highdicom.sr.AlgorithmIdentification, optional identification of algorithm used for making measurements - finding_sites: Sequence[highdicom.sr.content.FindingSite], optional + finding_sites: Sequence[highdicom.sr.FindingSite], optional Coded description of one or more anatomic locations corresonding to the image region from which measurement was taken session: str, optional description of the session - measurements: Sequence[highdicom.sr.templates.Measurement], optional + measurements: Sequence[highdicom.sr.Measurement], optional numeric measurements - qualitative_evaluations: Sequence[highdicom.sr.value_types.CodeContentItem], optional + qualitative_evaluations: Sequence[highdicom.sr.CodeContentItem], optional coded name-value (question-answer) pairs that describe the measurements in qualitative terms - geometric_purpose: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + geometric_purpose: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional geometric interpretation of region of interest (see `CID 219 `_ "Geometry Graphical Representation" for options) @@ -1544,35 +1544,35 @@ def __init__( Parameters ---------- - tracking_identifier: highdicom.sr.templates.TrackingIdentifier + tracking_identifier: highdicom.sr.TrackingIdentifier identifier for tracking measurements - referenced_region: Union[highdicom.sr.content.ImageRegion, highdicom.sr.content.ImageRegion3D], optional + referenced_region: Union[highdicom.sr.ImageRegion, highdicom.sr.ImageRegion3D], optional region of interest in source image - referenced_segment: highdicom.sr.content.ReferencedSegmentationFrame, optional + referenced_segment: highdicom.sr.ReferencedSegmentationFrame, optional segmentation for region of interest in source image - referenced_real_world_value_map: highdicom.sr.content.RealWorldValueMap, optional + referenced_real_world_value_map: highdicom.sr.RealWorldValueMap, optional referenced real world value map for region of interest - time_point_context: highdicom.sr.templates.TimePointContext, optional + time_point_context: highdicom.sr.TimePointContext, optional description of the time point context - finding_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + finding_type: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional type of object that was measured, e.g., organ or tumor - method: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + method: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded measurement method (see `CID 6147 `_ "Response Criteria" for options) - algorithm_id: highdicom.sr.templates.AlgorithmIdentification, optional + algorithm_id: highdicom.sr.AlgorithmIdentification, optional identification of algorithm used for making measurements - finding_sites: Sequence[highdicom.sr.content.FindingSite], optional + finding_sites: Sequence[highdicom.sr.FindingSite], optional Coded description of one or more anatomic locations corresonding to the image region from which measurement was taken session: str, optional description of the session - measurements: Sequence[highdicom.sr.templates.Measurement], optional + measurements: Sequence[highdicom.sr.Measurement], optional measurements for a region of interest - qualitative_evaluations: Sequence[highdicom.sr.value_types.CodeContentItem], optional + qualitative_evaluations: Sequence[highdicom.sr.CodeContentItem], optional coded name-value (question-answer) pairs that describe the measurements in qualitative terms for a region of interest - geometric_purpose: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + geometric_purpose: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional geometric interpretation of region of interest (see `CID 219 `_ "Geometry Graphical Representation" for options) @@ -1649,37 +1649,37 @@ def __init__( Parameters ---------- - tracking_identifier: highdicom.sr.templates.TrackingIdentifier + tracking_identifier: highdicom.sr.TrackingIdentifier identifier for tracking measurements - referenced_regions: Union[Sequence[highdicom.sr.content.ImageRegion], Sequence[highdicom.sr.content.ImageRegion3D]], optional + referenced_regions: Union[Sequence[highdicom.sr.ImageRegion], Sequence[highdicom.sr.ImageRegion3D]], optional regions of interest in source image(s) - referenced_volume_surface: highdicom.sr.content.VolumeSurface, optional + referenced_volume_surface: highdicom.sr.VolumeSurface, optional volume of interest in source image(s) - referenced_segment: highdicom.sr.content.ReferencedSegment, optional + referenced_segment: highdicom.sr.ReferencedSegment, optional segmentation for region of interest in source image - referenced_real_world_value_map: highdicom.sr.content.RealWorldValueMap, optional + referenced_real_world_value_map: highdicom.sr.RealWorldValueMap, optional referenced real world value map for region of interest - time_point_context: highdicom.sr.templates.TimePointContext, optional + time_point_context: highdicom.sr.TimePointContext, optional description of the time point context - finding_type: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + finding_type: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional type of object that was measured, e.g., organ or tumor - method: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + method: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded measurement method (see `CID 6147 `_ "Response Criteria" for options) - algorithm_id: highdicom.sr.templates.AlgorithmIdentification, optional + algorithm_id: highdicom.sr.AlgorithmIdentification, optional identification of algorithm used for making measurements - finding_sites: Sequence[highdicom.sr.content.FindingSite], optional + finding_sites: Sequence[highdicom.sr.FindingSite], optional Coded description of one or more anatomic locations corresonding to the image region from which measurement was taken session: str, optional description of the session - measurements: Sequence[highdicom.sr.templates.Measurement], optional + measurements: Sequence[highdicom.sr.Measurement], optional measurements for a volume of interest - qualitative_evaluations: Sequence[highdicom.sr.value_types.CodeContentItem], optional + qualitative_evaluations: Sequence[highdicom.sr.CodeContentItem], optional coded name-value (question-answer) pairs that describe the measurements in qualitative terms for a volume of interest - geometric_purpose: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + geometric_purpose: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional geometric interpretation of region of interest (see `CID 219 `_ "Geometry Graphical Representation" for options) @@ -1726,16 +1726,16 @@ def __init__( Parameters ---------- - derivation: Sequence[highdicom.sr.coding.CodedConcept] + derivation: Sequence[highdicom.sr.CodedConcept] methods for derivation of measurements from multiple ROIs measurements (see `CID 7465 `_ "Measurements Derived From Multiple ROI Measurements" for options) - measurement_groups: Union[Sequence[highdicom.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations], Sequence[highdicom.sr.templates.VolumetricROIMeasurementsAndQualitativeEvaluations]] + measurement_groups: Union[Sequence[highdicom.sr.PlanarROIMeasurementsAndQualitativeEvaluations], Sequence[highdicom.sr.VolumetricROIMeasurementsAndQualitativeEvaluations]] one or more groups of either planar or volumetric ROI measurements and qualitative evaluations - measurement_properties: highdicom.sr.templates.MeasurementProperties, optional + measurement_properties: highdicom.sr.MeasurementProperties, optional measurement properties, including evaluations of its normality and/or significance, its relationship to a reference population, and an indication of its selection from a set of measurements @@ -1800,24 +1800,24 @@ def __init__( Parameters ---------- - observation_context: highdicom.sr.templates.ObservationContext + observation_context: highdicom.sr.ObservationContext description of the observation context - procedure_reported: Union[Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], Sequence[Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code]]] + procedure_reported: Union[Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], Sequence[Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code]]] one or more coded description(s) of the procedure (see `CID 100 `_ "Quantitative Diagnostic Imaging Procedures" for options) - imaging_measurements: Sequence[Union[highdicom.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations, highdicom.sr.templates.VolumetricROIMeasurementsAndQualitativeEvaluations, highdicom.sr.templates.MeasurementsAndQualitativeEvaluations]], optional + imaging_measurements: Sequence[Union[highdicom.sr.PlanarROIMeasurementsAndQualitativeEvaluations, highdicom.sr.VolumetricROIMeasurementsAndQualitativeEvaluations, highdicom.sr.MeasurementsAndQualitativeEvaluations]], optional measurements and qualitative evaluations of images or regions within images - derived_imaging_measurements: Sequence[highdicom.sr.templates.MeasurementsDerivedFromMultipleROIMeasurements], optional + derived_imaging_measurements: Sequence[highdicom.sr.MeasurementsDerivedFromMultipleROIMeasurements], optional measurements derived from other measurements of images or regions within images qualitative evaluations of images - title: highdicom.sr.coding.CodedConcept, optional + title: highdicom.sr.CodedConcept, optional title of the report (see `CID 7021 `_ "Measurement Report Document Titles" for options) - language_of_content_item_and_descendants: highdicom.sr.templates.LanguageOfContentItemAndDescendants, optional + language_of_content_item_and_descendants: highdicom.sr.LanguageOfContentItemAndDescendants, optional specification of the language of report content items (defaults to English) diff --git a/src/highdicom/sr/utils.py b/src/highdicom/sr/utils.py index 7da33843..ea1b1172 100644 --- a/src/highdicom/sr/utils.py +++ b/src/highdicom/sr/utils.py @@ -23,14 +23,14 @@ def find_content_items( ---------- dataset: pydicom.dataset.Dataset SR document instance - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional Coded name that items should have - value_type: Union[highdicom.sr.enum.ValueTypeValues, str], optional + value_type: Union[highdicom.sr.ValueTypeValues, str], optional Type of value that items should have - (e.g. ``highdicom.sr.enum.ValueTypeValues.CONTAINER``) - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + (e.g. ``highdicom.sr.ValueTypeValues.CONTAINER``) + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional Type of relationship that items should have with its parent - (e.g. ``highdicom.sr.enum.RelationshipTypeValues.CONTAINS``) + (e.g. ``highdicom.sr.RelationshipTypeValues.CONTAINS``) recursive: bool, optional Whether search should be performed recursively, i.e. whether contained child content items should also be queried @@ -121,14 +121,14 @@ def search_tree( def get_coded_name(item: Dataset) -> CodedConcept: """Gets the concept name of a SR Content Item. - Parameter - --------- + Parameters + ---------- item: pydicom.dataset.Dataset Content Item Returns ------- - highdicom.sr.coding.CodedConcept + highdicom.sr.CodedConcept Concept name """ @@ -150,14 +150,14 @@ def get_coded_name(item: Dataset) -> CodedConcept: def get_coded_value(item: Dataset) -> CodedConcept: """Gets the value of a SR Content Item with Value Type CODE. - Parameter - --------- + Parameters + ---------- item: pydicom.dataset.Dataset Content Item Returns ------- - highdicom.sr.coding.CodedConcept + highdicom.sr.CodedConcept Value """ diff --git a/src/highdicom/sr/value_types.py b/src/highdicom/sr/value_types.py index c47810d5..1641204a 100644 --- a/src/highdicom/sr/value_types.py +++ b/src/highdicom/sr/value_types.py @@ -36,11 +36,11 @@ def __init__( """ Parameters ---------- - value_type: Union[str, highdicom.sr.enum.ValueTypeValues] + value_type: Union[str, highdicom.sr.ValueTypeValues] type of value encoded in a content item - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] coded name or an enumerated item representing a coded name - relationship_type: Union[str, highdicom.sr.enum.RelationshipTypeValues], optional + relationship_type: Union[str, highdicom.sr.RelationshipTypeValues], optional type of relationship with parent content item """ # noqa @@ -66,13 +66,13 @@ def __setattr__(self, name: str, value: Any) -> None: @property def name(self) -> CodedConcept: - """CodedConcept: coded name of the content item""" + """highdicom.sr.CodedConcept: coded name of the content item""" return self.ConceptNameCodeSequence[0] @property def value_type(self) -> str: """str: type of the content item - (see `highdicom.sr.value_types.ValueTypeValues`) + (see `highdicom.sr.ValueTypeValues`) """ return self.ValueType @@ -80,7 +80,7 @@ def value_type(self) -> str: @property def relationship_type(self) -> str: """str: type of relationship the content item has with its parent - (see `highdicom.sr.enum.RelationshipTypeValues`) + (see `highdicom.sr.RelationshipTypeValues`) """ return getattr(self, 'RelationshipType', None) @@ -112,7 +112,7 @@ def get_nodes(self) -> 'ContentSequence': Returns ------- - highdicom.sr.value_types.ContentSequence[highdicom.sr.value_types.ContentItem] + highdicom.sr.ContentSequence[highdicom.sr.ContentItem] matched content items """ @@ -126,7 +126,7 @@ def append(self, item: ContentItem) -> None: Parameters ---------- - item: highdicom.sr.value_types.ContentItem + item: highdicom.sr.ContentItem content item """ @@ -143,7 +143,7 @@ def extend(self, items: Sequence[ContentItem]) -> None: Parameters ---------- - items: Sequence[highdicom.sr.value_types.ContentItem] + items: Sequence[highdicom.sr.ContentItem] content items """ @@ -157,7 +157,7 @@ def insert(self, position: int, item: ContentItem) -> None: ---------- position: int index position - item: highdicom.sr.value_types.ContentItem + item: highdicom.sr.ContentItem content item """ @@ -185,11 +185,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name - value: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + value: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] coded value or an enumerated item representing a coded value - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -220,11 +220,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: Union[str, pydicom.valuerep.PersonName] name of the person - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -249,11 +249,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: str description of the concept in free text - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -278,11 +278,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: Union[str, datetime.time, pydicom.valuerep.TM] time - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -307,11 +307,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: Union[str, datetime.date, pydicom.valuerep.DA] date - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -336,11 +336,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: Union[str, datetime.datetime, pydicom.valuerep.DT] datetime - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -365,11 +365,11 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: Union[pydicom.uid.UID, str] unique identifier - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -396,19 +396,19 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name value: Union[int, float], optional numeric value - unit: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + unit: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional coded units of measurement (see `CID 7181 `_ "Abstract Multi-dimensional Image Model Component Units") - qualifier: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code], optional + qualifier: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code], optional qualification of numeric value or as an alternative to numeric value, e.g., reason for absence of numeric value (see `CID 42 `_ "Numeric Value Qualifier" for options) - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item Note @@ -469,7 +469,7 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name is_content_continous: bool, optional whether contained content items are logically linked in a @@ -510,13 +510,13 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name referenced_sop_class_uid: Union[pydicom.uid.UID, str] SOP Class UID of the referenced object referenced_sop_instance_uid: Union[pydicom.uid.UID, str] SOP Instance UID of the referenced object - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -551,7 +551,7 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name referenced_sop_class_uid: Union[pydicom.uid.UID, str] SOP Class UID of the referenced image object @@ -563,7 +563,7 @@ def __init__( referenced_segment_numbers: Union[int, Sequence[int]], optional number of segment(s) to which the refernce applies in case of a segmentation image - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -607,22 +607,22 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name - graphic_type: Union[highdicom.sr.enum.GraphicTypeValues, str] + graphic_type: Union[highdicom.sr.GraphicTypeValues, str] name of the graphic type graphic_data: numpy.ndarray[numpy.int] array of ordered spatial coordinates, where each row of the array represents a (column, row) coordinate pair - pixel_origin_interpretation: Union[highdicom.sr.enum.PixelOriginInterpretationValues, str] + pixel_origin_interpretation: Union[highdicom.sr.PixelOriginInterpretationValues, str] whether pixel coordinates specified by `graphic_data` are defined relative to the total pixel matrix - (``highdicom.sr.enum.PixelOriginInterpretationValues.VOLUME``) or + (``highdicom.sr.PixelOriginInterpretationValues.VOLUME``) or relative to an individual frame - (``highdicom.sr.enum.PixelOriginInterpretationValues.FRAME``) + (``highdicom.sr.PixelOriginInterpretationValues.FRAME``) fiducial_uid: Union[pydicom.uid.UID, str, None], optional unique identifier for the content item - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -702,9 +702,9 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name - graphic_type: Union[highdicom.sr.enum.GraphicTypeValues3D, str] + graphic_type: Union[highdicom.sr.GraphicTypeValues3D, str] name of the graphic type graphic_data: numpy.ndarray[numpy.float] array of spatial coordinates, where each row of the array @@ -714,7 +714,7 @@ def __init__( coordinates are defined fiducial_uid: str, optional unique identifier for the content item - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa @@ -775,9 +775,9 @@ def __init__( """ Parameters ---------- - name: Union[highdicom.sr.coding.CodedConcept, pydicom.sr.coding.Code] + name: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code] concept name - temporal_range_type: Union[highdicom.sr.enum.TemporalRangeTypeValues, str] + temporal_range_type: Union[highdicom.sr.TemporalRangeTypeValues, str] name of the temporal range type referenced_sample_positions: Sequence[int], optional one-based relative sample position of acquired time points @@ -786,7 +786,7 @@ def __init__( seconds after start of the acquisition of the time series referenced_date_time: Sequence[datetime.datetime], optional absolute time points - relationship_type: Union[highdicom.sr.enum.RelationshipTypeValues, str], optional + relationship_type: Union[highdicom.sr.RelationshipTypeValues, str], optional type of relationship with parent content item """ # noqa diff --git a/src/highdicom/utils.py b/src/highdicom/utils.py index eea35425..a1dd8cff 100644 --- a/src/highdicom/utils.py +++ b/src/highdicom/utils.py @@ -103,7 +103,7 @@ def compute_plane_position_tiled_full( Returns ------- - highdicom.content.PlanePositionSequence + highdicom.PlanePositionSequence Positon of the plane in the slide coordinate system Raises @@ -160,7 +160,7 @@ def compute_plane_position_slide_per_frame( Returns ------- - List[highdicom.content.PlanePositionSequence] + List[highdicom.PlanePositionSequence] Plane Position Sequence per frame Raises diff --git a/tests/test_content.py b/tests/test_content.py index fe1f068c..65efa1b3 100644 --- a/tests/test_content.py +++ b/tests/test_content.py @@ -2,7 +2,7 @@ import pytest -from highdicom.content import ( +from highdicom import ( PixelMeasuresSequence, PlaneOrientationSequence, PlanePositionSequence, diff --git a/tests/test_sc.py b/tests/test_sc.py index cd6a065e..e416f117 100644 --- a/tests/test_sc.py +++ b/tests/test_sc.py @@ -6,8 +6,8 @@ from pydicom import dcmread from pydicom.uid import generate_uid, RLELossless -from highdicom.content import SpecimenDescription -from highdicom.sc.sop import SCImage +from highdicom import SpecimenDescription +from highdicom.sc import SCImage class TestSCImage(unittest.TestCase): diff --git a/tests/test_seg.py b/tests/test_seg.py index 428ac8ec..41542422 100644 --- a/tests/test_seg.py +++ b/tests/test_seg.py @@ -15,23 +15,23 @@ RLELossless, ) -from highdicom.content import ( +from highdicom import ( AlgorithmIdentificationSequence, PlanePositionSequence, PixelMeasuresSequence, PlaneOrientationSequence, ) from highdicom.enum import CoordinateSystemNames -from highdicom.seg.content import ( +from highdicom.seg import ( DimensionIndexSequence, SegmentDescription, ) -from highdicom.seg.enum import ( +from highdicom.seg import ( SegmentAlgorithmTypeValues, SegmentsOverlapValues, SegmentationTypeValues, ) -from highdicom.seg.sop import Segmentation +from highdicom.seg import Segmentation from highdicom.seg.utils import iter_segments diff --git a/tests/test_sr.py b/tests/test_sr.py index c600078f..549b7702 100644 --- a/tests/test_sr.py +++ b/tests/test_sr.py @@ -14,8 +14,8 @@ from pydicom.uid import generate_uid, UID from pydicom.valuerep import DA, DS, DT, TM -from highdicom.sr.coding import CodedConcept -from highdicom.sr.content import ( +from highdicom.sr import CodedConcept +from highdicom.sr import ( FindingSite, ImageRegion, ImageRegion3D, @@ -29,14 +29,14 @@ SourceSeriesForSegmentation, VolumeSurface, ) -from highdicom.sr.enum import ( +from highdicom.sr import ( GraphicTypeValues, GraphicTypeValues3D, RelationshipTypeValues, ValueTypeValues, ) from highdicom.sr.utils import find_content_items -from highdicom.sr.value_types import ( +from highdicom.sr import ( CodeContentItem, ContainerContentItem, CompositeContentItem, @@ -50,12 +50,12 @@ TimeContentItem, UIDRefContentItem, ) -from highdicom.sr.sop import ( +from highdicom.sr import ( ComprehensiveSR, Comprehensive3DSR, EnhancedSR, ) -from highdicom.sr.templates import ( +from highdicom.sr import ( AlgorithmIdentification, DeviceObserverIdentifyingAttributes, Measurement, diff --git a/tests/test_utils.py b/tests/test_utils.py index 01921c47..e65221e5 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,6 +1,6 @@ import pytest -from highdicom.content import PlanePositionSequence +from highdicom import PlanePositionSequence from highdicom.enum import CoordinateSystemNames from highdicom.utils import compute_plane_position_tiled_full