Merge pull request #18 from MGHComputationalPathology/feature/even_mo…

…re_seg_tests

Feature/even more seg tests

docs/usage.rst

@@ -79,6 +79,7 @@ Derive a Segmentation image from a series of single-frame Computed Tomography
         sop_instance_uid=generate_uid(),
         instance_number=1,
         manufacturer='Manufacturer',
+        manufacturer_model_name='Model',
         software_versions='v1',
         device_serial_number='Device XYZ',
         manufacturer_model_name='The best one'
@@ -147,6 +148,7 @@ Derive a Segmentation image from a multi-frame Slide Microscopy (SM) image:
         sop_instance_uid=generate_uid(),
         instance_number=1,
         manufacturer='Manufacturer',
+        manufacturer_model_name='Model',
         software_versions='v1',
         device_serial_number='Device XYZ'
     )

src/highdicom/base.py

@@ -16,7 +16,7 @@
 from pydicom.valuerep import DA, DT, TM
 
 from highdicom.sr.coding import CodingSchemeIdentificationItem
-from highdicom.enum import ContentQualifications
+from highdicom.enum import ContentQualificationValues
 from highdicom.version import __version__
 from highdicom._iods import IOD_MODULE_MAP
 from highdicom._modules import MODULE_ATTRIBUTE_MAP
@@ -174,7 +174,9 @@ def __init__(
         self.ContentDate = DA(datetime.now().date())
         self.ContentTime = TM(datetime.now().time())
         if content_qualification is not None:
-            content_qualification = ContentQualifications(content_qualification)
+            content_qualification = ContentQualificationValues(
+                content_qualification
+            )
             self.ContentQualification = content_qualification.value
         if coding_schemes is not None:
             self.CodingSchemeIdentificationSequence = []

src/highdicom/content.py

@@ -10,9 +10,8 @@
 
 from highdicom.enum import (
     CoordinateSystemNames,
-    UniversalEntityIDTypes,
+    UniversalEntityIDTypeValues,
 )
-from highdicom.seg.enum import SegmentAlgorithmTypes
 from highdicom.sr.coding import CodedConcept
 from highdicom.sr.value_types import (
     CodeContentItem,
@@ -277,15 +276,15 @@ def __init__(
             self,
             issuer_of_identifier: str,
             issuer_of_identifier_type: Optional[
-                Union[str, UniversalEntityIDTypes]
+                Union[str, UniversalEntityIDTypeValues]
             ] = None
         ):
         """
         Parameters
         ----------
         issuer_of_identifier: str
             Identifier of the entity that created the examined specimen
-        issuer_of_identifier_type: Union[str, highdicom.enum.UniversalEntityIDTypes], optional
+        issuer_of_identifier_type: Union[str, highdicom.enum.UniversalEntityIDTypeValues], optional
             Type of identifier of the entity that created the examined specimen
             (required if `issuer_of_specimen_id` is a Unique Entity ID)
 
@@ -295,7 +294,7 @@ def __init__(
             self.LocalNamespaceEntityID = issuer_of_identifier
         else:
             self.UniversalEntityID = issuer_of_identifier
-            issuer_of_identifier_type = UniversalEntityIDTypes(
+            issuer_of_identifier_type = UniversalEntityIDTypeValues(
                 issuer_of_identifier_type
             )
             self.UniversalEntityIDType = issuer_of_identifier_type.value

src/highdicom/enum.py

@@ -10,7 +10,7 @@ class CoordinateSystemNames(Enum):
     SLIDE = 'SLIDE'
 
 
-class ContentQualifications(Enum):
+class ContentQualificationValues(Enum):
 
     """Enumerated values for Content Qualification attribute."""
 
@@ -19,7 +19,7 @@ class ContentQualifications(Enum):
     SERVICE = 'SERVICE'
 
 
-class DimensionOrganizationTypes(Enum):
+class DimensionOrganizationTypeValues(Enum):
 
     """Enumerated values for Dimension Organization Type attribute."""
 
@@ -29,7 +29,7 @@ class DimensionOrganizationTypes(Enum):
     TILED_SPARSE = 'TILED_SPARSE'
 
 
-class PhotometricInterpretations(Enum):
+class PhotometricInterpretationValues(Enum):
 
     """Enumerated values for Photometric Interpretation attribute."""
 
@@ -44,23 +44,23 @@ class PhotometricInterpretations(Enum):
     YBR_RCT = 'YBR_RCT'
 
 
-class Lateralities(Enum):
+class LateralityValues(Enum):
 
     """Enumerated values for Laterality attribute."""
 
     R = 'R'
     L = 'L'
 
 
-class AnatomicalOrientationTypes(Enum):
+class AnatomicalOrientationTypeValues(Enum):
 
     """Enumerated values for Anatomical Orientation Type attribute."""
 
     BIPED = 'BIPED'
     QUADRUPED = 'QUADRUPED'
 
 
-class PatientOrientationsBiped(Enum):
+class PatientOrientationValuesBiped(Enum):
 
     """Enumerated values for Patient Orientation attribute
     if Anatomical Orientation Type attribute has value ``"BIPED"``.
@@ -74,7 +74,7 @@ class PatientOrientationsBiped(Enum):
     F = 'F'
 
 
-class PatientOrientationsQuadruped(Enum):
+class PatientOrientationValuesQuadruped(Enum):
 
     """Enumerated values for Patient Orientation attribute
     if Anatomical Orientation Type attribute has value ``"QUADRUPED"``.
@@ -95,7 +95,7 @@ class PatientOrientationsQuadruped(Enum):
     PL = 'PL'
 
 
-class UniversalEntityIDTypes(Enum):
+class UniversalEntityIDTypeValues(Enum):
 
     """Enumerated values for Universal Entity ID Type attribute."""
 

src/highdicom/sc/enum.py

@@ -2,7 +2,7 @@
 from enum import Enum
 
 
-class ConversionTypes(Enum):
+class ConversionTypeValues(Enum):
 
     """Enumerated values for attribute Conversion Type."""
 

src/highdicom/sc/sop.py

@@ -15,14 +15,14 @@
     SpecimenDescription,
 )
 from highdicom.enum import (
-    AnatomicalOrientationTypes,
+    AnatomicalOrientationTypeValues,
     CoordinateSystemNames,
-    Lateralities,
-    PhotometricInterpretations,
-    PatientOrientationsBiped,
-    PatientOrientationsQuadruped,
+    LateralityValues,
+    PhotometricInterpretationValues,
+    PatientOrientationValuesBiped,
+    PatientOrientationValuesQuadruped,
 )
-from highdicom.sc.enum import ConversionTypes
+from highdicom.sc.enum import ConversionTypeValues
 from highdicom.sr.coding import CodedConcept
 
 
@@ -38,7 +38,10 @@ class SCImage(SOPClass):
     def __init__(
             self,
             pixel_array: np.ndarray,
-            photometric_interpretation: Union[str, PhotometricInterpretations],
+            photometric_interpretation: Union[
+                str,
+                PhotometricInterpretationValues
+            ],
             bits_allocated: int,
             coordinate_system: Union[str, CoordinateSystemNames],
             study_instance_uid: str,
@@ -57,19 +60,22 @@ def __init__(
             study_time: Optional[Union[str, datetime.time]] = None,
             referring_physician_name: Optional[str] = None,
             pixel_spacing: Optional[Tuple[int, int]] = None,
-            laterality: Optional[Union[str, Lateralities]] = None,
+            laterality: Optional[Union[str, LateralityValues]] = None,
             patient_orientation: Optional[
                 Union[
                     Tuple[str, str],
-                    Tuple[PatientOrientationsBiped, PatientOrientationsBiped],
                     Tuple[
-                        PatientOrientationsQuadruped,
-                        PatientOrientationsQuadruped,
+                        PatientOrientationValuesBiped,
+                        PatientOrientationValuesBiped,
+                    ],
+                    Tuple[
+                        PatientOrientationValuesQuadruped,
+                        PatientOrientationValuesQuadruped,
                     ]
                 ]
             ] = None,
             anatomical_orientation_type: Optional[
-                Union[str, AnatomicalOrientationTypes]
+                Union[str, AnatomicalOrientationTypeValues]
             ] = None,
             container_identifier: Optional[str] = None,
             issuer_of_container_identifier: Optional[IssuerOfIdentifier] = None,
@@ -86,7 +92,7 @@ def __init__(
             Array of unsigned integer pixel values representing a single-frame
             image; either a 2D grayscale image or a 3D color image
             (RGB color space)
-        photometric_interpretation: Union[str, highdicom.enum.PhotometricInterpretations]
+        photometric_interpretation: Union[str, highdicom.enum.PhotometricInterpretationValues]
             Interpretation of pixel data; either ``"MONOCHROME1"`` or
             ``"MONOCHROME2"`` for 2D grayscale images or ``"RGB"`` or
             ``"YBR_FULL"`` for 3D color images
@@ -130,14 +136,14 @@ def __init__(
         pixel_spacing: Tuple[int, int], optional
             Physical spacing in millimeter between pixels along the row and
             column dimension
-        laterality: Union[str, highdicom.enum.Lateralities], optional
+        laterality: Union[str, highdicom.enum.LateralityValues], optional
             Laterality of the examined body part (required if
             `coordinate_system` is ``"PATIENT"``)
         patient_orientation:
-                Union[Tuple[str, str], Tuple[highdicom.enum.PatientOrientationsBiped, highdicom.enum.PatientOrientationsBiped], Tuple[highdicom.enum.PatientOrientationsQuadruped, highdicom.enum.PatientOrientationsQuadruped]], optional
+                Union[Tuple[str, str], Tuple[highdicom.enum.PatientOrientationValuesBiped, highdicom.enum.PatientOrientationValuesBiped], Tuple[highdicom.enum.PatientOrientationValuesQuadruped, highdicom.enum.PatientOrientationValuesQuadruped]], optional
             Orientation of the patient along the row and column axes of the
             image (required if `coordinate_system` is ``"PATIENT"``)
-        anatomical_orientation_type: Union[str, highdicom.enum.AnatomicalOrientationTypes], optional
+        anatomical_orientation_type: Union[str, highdicom.enum.AnatomicalOrientationTypeValues], optional
             Type of anatomical orientation of patient relative to image (may be
             provide if `coordinate_system` is ``"PATIENT"`` and patient is
             an animal)
@@ -190,28 +196,31 @@ def __init__(
                 )
 
             # General Series
-            laterality = Lateralities(laterality)
+            laterality = LateralityValues(laterality)
             self.Laterality = laterality.value
 
             # General Image
             if anatomical_orientation_type is not None:
-                anatomical_orientation_type = AnatomicalOrientationTypes(
+                anatomical_orientation_type = AnatomicalOrientationTypeValues(
                     anatomical_orientation_type
                 )
                 self.AnatomicalOrientationType = \
                     anatomical_orientation_type.value
             else:
-                anatomical_orientation_type = AnatomicalOrientationTypes.BIPED
+                anatomical_orientation_type = \
+                    AnatomicalOrientationTypeValues.BIPED
 
-            if anatomical_orientation_type == AnatomicalOrientationTypes.BIPED:
+            row_orientation, col_orientation = patient_orientation
+            if (anatomical_orientation_type ==
+                    AnatomicalOrientationTypeValues.BIPED):
                 patient_orientation = [
-                    PatientOrientationsBiped(patient_orientation[0]).value,
-                    PatientOrientationsBiped(patient_orientation[1]).value,
+                    PatientOrientationValuesBiped(row_orientation).value,
+                    PatientOrientationValuesBiped(col_orientation).value,
                 ]
             else:
                 patient_orientation = [
-                    PatientOrientationsQuadruped(patient_orientation[0]).value,
-                    PatientOrientationsQuadruped(patient_orientation[1]).value,
+                    PatientOrientationValuesQuadruped(row_orientation).value,
+                    PatientOrientationValuesQuadruped(col_orientation).value,
                 ]
             self.PatientOrientation = patient_orientation
 
@@ -239,7 +248,7 @@ def __init__(
             self.SpecimenDescriptionSequence = specimen_descriptions
 
         # SC Equipment
-        self.ConversionType = ConversionTypes.DI.value
+        self.ConversionType = ConversionTypeValues.DI.value
 
         # SC Image
         now = datetime.datetime.now()
@@ -263,15 +272,15 @@ def __init__(
         self.HighBit = self.BitsAllocated - 1
         self.BitsStored = self.BitsAllocated
         self.PixelRepresentation = 0
-        photometric_interpretation = PhotometricInterpretations(
+        photometric_interpretation = PhotometricInterpretationValues(
             photometric_interpretation
         )
         if pixel_array.ndim == 3:
             accepted_interpretations = (
-                PhotometricInterpretations.RGB.value,
-                PhotometricInterpretations.YBR_FULL.value,
-                PhotometricInterpretations.YBR_FULL_422.value,
-                PhotometricInterpretations.YBR_PARTIAL_420.value,
+                PhotometricInterpretationValues.RGB.value,
+                PhotometricInterpretationValues.YBR_FULL.value,
+                PhotometricInterpretationValues.YBR_FULL_422.value,
+                PhotometricInterpretationValues.YBR_PARTIAL_420.value,
             )
             if photometric_interpretation.value not in accepted_interpretations:
                 raise ValueError(
@@ -293,8 +302,8 @@ def __init__(
             self.PlanarConfiguration = 0
         elif pixel_array.ndim == 2:
             accepted_interpretations = (
-                PhotometricInterpretations.MONOCHROME1.value,
-                PhotometricInterpretations.MONOCHROME2.value,
+                PhotometricInterpretationValues.MONOCHROME1.value,
+                PhotometricInterpretationValues.MONOCHROME2.value,
             )
             if photometric_interpretation.value not in accepted_interpretations:
                 raise ValueError(

src/highdicom/seg/content.py

@@ -9,7 +9,7 @@
 
 from highdicom.content import AlgorithmIdentificationSequence
 from highdicom.enum import CoordinateSystemNames
-from highdicom.seg.enum import SegmentAlgorithmTypes
+from highdicom.seg.enum import SegmentAlgorithmTypeValues
 from highdicom.sr.coding import CodedConcept
 
 
@@ -23,7 +23,7 @@ def __init__(
             segment_label: str,
             segmented_property_category: Union[Code, CodedConcept],
             segmented_property_type: Union[Code, CodedConcept],
-            algorithm_type: Union[SegmentAlgorithmTypes, str],
+            algorithm_type: Union[SegmentAlgorithmTypeValues, str],
             algorithm_identification: AlgorithmIdentificationSequence,
             tracking_uid: Optional[str] = None,
             tracking_id: Optional[str] = None,
@@ -49,7 +49,7 @@ def __init__(
             Property the segment represents,
             e.g. ``Code("108369006", "SCT", "Neoplasm")``
             (see CID 7151 Segmentation Property Types)
-        algorithm_type: Union[str, highdicom.seg.enum.SegmentAlgorithmTypes]
+        algorithm_type: Union[str, highdicom.seg.enum.SegmentAlgorithmTypeValues]
             Type of algorithm
         algorithm_identification: AlgorithmIdentificationSequence, optional
             Information useful for identification of the algorithm, such
@@ -87,7 +87,8 @@ def __init__(
                 segmented_property_type.scheme_version
             ),
         ]
-        self.SegmentAlgorithmType = SegmentAlgorithmTypes(algorithm_type).value
+        algorithm_type = SegmentAlgorithmTypeValues(algorithm_type)
+        self.SegmentAlgorithmType = algorithm_type.value
         self.SegmentAlgorithmName = algorithm_identification[0].AlgorithmName
         self.SegmentationAlgorithmIdentificationSequence = \
             algorithm_identification