Add properties and methods to SR content items and templates

src/highdicom/base.py

@@ -108,7 +108,7 @@ def __init__(
         required by the corresponding Information Object Definition (IOD).
         Additional optional attributes can subsequently be added to the dataset.
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         if transfer_syntax_uid is None:
             transfer_syntax_uid = ImplicitVRLittleEndian
@@ -279,36 +279,3 @@ def copy_specimen_information(self, dataset: Dataset) -> None:
 
         """
         self._copy_root_attributes_of_module(dataset, 'Image', 'Specimen')
-
-    @classmethod
-    def from_dataset(cls, dataset: Dataset) -> 'SOPClass':
-        try:
-            inst = cls(
-                study_instance_uid=dataset.StudyInstanceUID,
-                series_instance_uid=dataset.SeriesInstanceUID,
-                series_number=dataset.SeriesNumber,
-                sop_instance_uid=dataset.SOPInstanceUID,
-                sop_class_uid=dataset.SOPClassUID,
-                instance_number=dataset.InstanceNumber,
-                manufacturer=dataset.Manufacturer,
-                modality=dataset.Modality,
-                transfer_syntax_uid=dataset.file_meta.TransferSyntaxUID,
-                patient_id=dataset.PatientID,
-                patient_name=dataset.PatientName,
-                patient_birth_date=dataset.PatientBirthDate,
-                patient_sex=dataset.PatientSex,
-                accession_number=dataset.AccessionNumber,
-                study_id=dataset.StudyID,
-                study_date=dataset.StudyDate,
-                study_time=dataset.StudyTime,
-                referring_physician_name=dataset.ReferringPhysicianName
-            )
-        except AttributeError as error:
-            raise AttributeError(
-                'Required attribute missing: {}'.format(error)
-            )
-        if inst.SOPClassUID != dataset.SOPClassUID:
-            raise AttributeError(
-                'Incorrect SOP Class UID for type "{}".'.format(cls.__name__)
-            )
-        return inst

src/highdicom/coding_schemes.py

@@ -63,7 +63,7 @@ def __init__(
         resources: Sequence[pydicom.sr.coding.CodingSchemeResourceItem], optional
             one or more resources related to the scheme
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         self.CodingSchemeDesignator = str(designator)
         if name is not None:

src/highdicom/content.py

@@ -51,7 +51,7 @@ def __init__(
             Name and actual value of the parameters with which the algorithm
             was invoked
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         item = Dataset()
         item.AlgorithmName = name
@@ -313,7 +313,7 @@ def __init__(
             Type of identifier of the entity that created the examined specimen
             (required if `issuer_of_specimen_id` is a Unique Entity ID)
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         if issuer_of_identifier_type is None:
             self.LocalNamespaceEntityID = issuer_of_identifier
@@ -341,7 +341,7 @@ def __init__(
         procedure: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Procedure used to collect the examined specimen
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         item = CodeContentItem(
             name=codes.SCT.SpecimenCollection,
@@ -377,7 +377,7 @@ def __init__(
         issuer_of_parent_specimen_id: highdicom.IssuerOfIdentifier, optional
             Issuer who created the parent specimen
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         # CID 8110
         method_item = CodeContentItem(
@@ -426,7 +426,7 @@ def __init__(
         substances: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]]
             Substances used to stain examined specimen(s)
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         # CID 8112
         for s in substances:
@@ -481,7 +481,7 @@ def __init__(
         embedding_medium: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional
             Embedding medium used during processing
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         specimen_identifier_item = TextContentItem(
             name=codes.DCM.SpecimenIdentifier,
@@ -572,7 +572,7 @@ def __init__(
         issuer_of_specimen_id: highdicom.IssuerOfIdentifier, optional
             Description of the issuer of the specimen identifier
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         self.SpecimenIdentifier = specimen_id
         self.SpecimenUID = specimen_uid

src/highdicom/frame.py

@@ -323,28 +323,7 @@ def decode_frame(
     ds.HighBit = bits_stored - 1
 
     if UID(file_meta.TransferSyntaxUID).is_encapsulated:
-        if (transfer_syntax_uid == JPEGBaseline and
-                photometric_interpretation == 'RGB'):
-            # RGB color images, which were not transformed into YCbCr color
-            # space upon JPEG compression, need to be handled separately.
-            # Pillow assumes that images were transformed into YCbCr color
-            # space prior to JPEG compression. However, with photometric
-            # interpretation RGB, no color transformation was performed.
-            # Setting the value of "mode" to YCbCr signals Pillow to not
-            # apply any color transformation upon decompression.
-            image = Image.open(BytesIO(value))
-            color_mode = 'YCbCr'
-            image.tile = [(
-                'jpeg',
-                image.tile[0][1],
-                image.tile[0][2],
-                (color_mode, ''),
-            )]
-            image.mode = color_mode
-            image.rawmode = color_mode
-            return np.asarray(image)
-        else:
-            ds.PixelData = encapsulate(frames=[value])
+        ds.PixelData = encapsulate(frames=[value])
     else:
         ds.PixelData = value
 

src/highdicom/sc/sop.py

@@ -172,7 +172,7 @@ def __init__(
             Additional keyword arguments that will be passed to the constructor
             of `highdicom.base.SOPClass`
 
-        """  # noqa
+        """  # noqa: E501
         supported_transfer_syntaxes = {
             ImplicitVRLittleEndian,
             ExplicitVRLittleEndian,

src/highdicom/seg/content.py

@@ -82,7 +82,7 @@ def __init__(
         must have consecutive segment numbers, starting at 1 for the first
         segment added.
 
-        """  # noqa
+        """  # noqa: E501
         super().__init__()
         if segment_number < 1:
             raise ValueError("Segment number must be a positive integer")
@@ -291,7 +291,7 @@ def __init__(
 
         else:
             raise ValueError(
-                f'Unknown coordinate system "{self._coordinat_system}"'
+                f'Unknown coordinate system "{self._coordinate_system}"'
             )
 
     def get_plane_positions_of_image(

src/highdicom/seg/sop.py

@@ -196,7 +196,7 @@ def __init__(
         the same frame of reference as `source_images`.
 
 
-        """  # noqa
+        """  # noqa: E501
         if len(source_images) == 0:
             raise ValueError('At least one source image is required.')
         self._source_images = source_images
@@ -535,7 +535,7 @@ def add_segments(
         one segment can be encoded by `pixel_array` and hence only one item is
         permitted in `segment_descriptions`.
 
-        """  # noqa
+        """  # noqa: E501
         if pixel_array.ndim == 2:
             pixel_array = pixel_array[np.newaxis, ...]
         if pixel_array.ndim != 3:

src/highdicom/seg/utils.py

@@ -26,7 +26,7 @@ def iter_segments(dataset: Dataset) -> Iterator:
     AttributeError
         When data set does not contain Content Sequence attribute.
 
-    """  # noqa
+    """  # noqa: E501
     if not hasattr(dataset, 'PixelData'):
         raise AttributeError(
             'Data set does not contain a Pixel Data attribute.'

src/highdicom/spatial.py

@@ -52,11 +52,9 @@ class ImageToReferenceTransformer(object):
     >>>     image_orientation=[1.0, 0.0, 0.0, 0.0, 1.0, 0.0],
     >>>     pixel_spacing=[0.5, 0.5]
     >>> )
-    >>>
     >>> # Use the transformer to convert coordinates
     >>> image_coords = np.array([[0.0, 10.0], [5.0, 5.0]])
     >>> ref_coords = transformer(image_coords)
-    >>>
     >>> print(ref_coords)
     >>> # [[56.  39.2  1. ]
     >>> #  [58.5 36.7  1. ]]

src/highdicom/sr/__init__.py

@@ -9,7 +9,6 @@
     SourceImageForSegmentation,
     SourceImageForRegion,
     SourceSeriesForSegmentation,
-    QualitativeEvaluation,
     RealWorldValueMap,
     ReferencedSegment,
     ReferencedSegmentationFrame,
@@ -18,10 +17,12 @@
 from highdicom.sr.enum import (
     GraphicTypeValues,
     GraphicTypeValues3D,
+    PlanarROITypes,
     PixelOriginInterpretationValues,
     RelationshipTypeValues,
     TemporalRangeTypeValues,
     ValueTypeValues,
+    VolumetricROITypes,
 )
 from highdicom.sr.sop import (
     EnhancedSR,
@@ -32,6 +33,7 @@
     AlgorithmIdentification,
     DeviceObserverIdentifyingAttributes,
     ImageLibrary,
+    ImageLibraryEntryDescriptors,
     LanguageOfContentItemAndDescendants,
     Measurement,
     MeasurementProperties,
@@ -44,6 +46,7 @@
     ObservationContext,
     PersonObserverIdentifyingAttributes,
     PlanarROIMeasurementsAndQualitativeEvaluations,
+    QualitativeEvaluation,
     SubjectContext,
     SubjectContextDevice,
     SubjectContextFetus,
@@ -108,6 +111,7 @@
     'GraphicTypeValues3D',
     'ImageContentItem',
     'ImageLibrary',
+    'ImageLibraryEntryDescriptors',
     'ImageRegion',
     'ImageRegion3D',
     'LanguageOfContentItemAndDescendants',
@@ -124,6 +128,7 @@
     'ObservationContext',
     'PersonObserverIdentifyingAttributes',
     'PlanarROIMeasurementsAndQualitativeEvaluations',
+    'PlanarROITypes',
     'PixelOriginInterpretationValues',
     'PnameContentItem',
     'QualitativeEvaluation',
@@ -152,4 +157,5 @@
     'ValueTypeValues',
     'VolumeSurface',
     'VolumetricROIMeasurementsAndQualitativeEvaluations',
+    'VolumetricROITypes',
 ]

src/highdicom/sr/coding.py

@@ -47,6 +47,9 @@ def __init__(
             self.CodingSchemeVersion = str(scheme_version)
         # TODO: Enhanced Code Sequence Macro Attributes
 
+    def __hash__(self) -> int:
+        return hash(self.scheme_designator + self.value)
+
     def __eq__(self, other: Any) -> bool:
         """Compares `self` and `other` for equality.
 
@@ -109,3 +112,43 @@ def scheme_designator(self) -> str:
     def scheme_version(self) -> str:
         """Union[str, None]: version of the coding scheme (if specified)"""
         return getattr(self, 'CodingSchemeVersion', None)
+
+    @classmethod
+    def from_dataset(cls, dataset: Dataset) -> 'CodedConcept':
+        """Construct a CodedConcept from an existing dataset.
+
+        Parameters
+        ----------
+        dataset: pydicom.dataset.Dataset
+            Dataset representing a coded concept.
+
+        Returns
+        -------
+        highdicom.sr.coding.CodedConcept:
+            Coded concept representation of the dataset.
+
+        Raises
+        ------
+        TypeError:
+            If the passed dataset is not a pydicom dataset.
+        AttributeError:
+            If the dataset does not contain the required elements for a
+            coded concept.
+
+        """
+        if not isinstance(dataset, Dataset):
+            raise TypeError(
+                'Dataset must be a pydicom.dataset.Dataset.'
+            )
+        for kw in ['CodeValue', 'CodeMeaning', 'CodingSchemeDesignator']:
+            if not hasattr(dataset, kw):
+                raise AttributeError(
+                    'Dataset does not contain the following attribute '
+                    f'required for coded concepts: {kw}.'
+                )
+        return cls(
+            value=dataset.CodeValue,
+            scheme_designator=dataset.CodingSchemeDesignator,
+            meaning=dataset.CodeMeaning,
+            scheme_version=getattr(dataset, 'CodingSchemeVersion', None)
+        )