Merge pull request #23 from ArcanaFramework/dicom-read-metadata

Reworked to use "category-less" classifiers

fileformats/medimage/__init__.py

@@ -46,3 +46,53 @@
 from .surface import (
     Gifti  # noqa: F401
 )
+from .contents.imaging.modality import (  # noqa: F401
+    ImagingModality,
+    CombinedModalities,
+    DualEnergyXrayAbsorptiometry,
+    Fluoroscopy,
+    MrFluoroscopy,
+    RadioFluoroscopy,
+    MagneticResonanceImaging,
+    DiffusionTensorImaging,
+    DynamicContrast,
+    EnhancedMagneticResonanceImaging,
+    FunctionalMagneticResonanceImaging,
+    MagneticResonanceAngiography,
+    MagneticResonanceSpectroscopy,
+    NuclearMedicineImaging,
+    PositronEmissionTomography,
+    PanographicRadiograph,
+    ProjectionRadiography,
+    ComputedRadiography,
+    DigitalRadiography,
+    DualEnergySubtractionRadiograpgy,
+    Mammography,
+    ScreenFilmRadiography,
+    Stereoscopy,
+    StereotacticRadiography,
+    Spectroscopy,
+    Tomography,
+    ComputedTomography,
+    Ultrasound,
+    MRI,
+    PET,
+    CR,
+    CT,
+    DX,
+    MG,
+    MR,
+    NM,
+    PT,
+    PX,
+    RF,
+    RG,
+    US,
+)
+from .contents.imaging.derivatives import (
+    Derivative,
+    Mask
+)
+from .contents.anatomical_entity.material_anatomical_entity.anatomical_structure import (
+    Brain, SpinalCord
+)

fileformats/medimage/base.py

@@ -2,6 +2,11 @@
 import logging
 from fileformats.generic import FileSet
 from fileformats.core import hook
+from fileformats.core.mixin import WithClassifiers
+from .contents import ContentsClassifier
+from .contents.imaging.modality import ImagingModality
+from .contents.imaging.derivatives import Derivative
+from .contents.anatomical_entity.material_anatomical_entity import AnatomicalEntity
 
 logger = logging.getLogger("fileformats")
 
@@ -11,12 +16,14 @@
 # =====================================================================
 
 
-class MedicalImage(FileSet):
+class MedicalImage(WithClassifiers, FileSet):
 
     iana_mime: ty.Optional[str] = None
     INCLUDE_HDR_KEYS = None
     IGNORE_HDR_KEYS = None
     binary = True
+    allowed_classifiers = (ContentsClassifier,)
+    exclusive_classifiers = (ImagingModality, AnatomicalEntity, Derivative)
 
     @hook.extra
     def read_array(self) -> "numpy.ndarray":  # noqa

fileformats/medimage/contents/__init__.py

@@ -0,0 +1,5 @@
+from fileformats.core import Classifier
+
+
+class ContentsClassifier(Classifier):
+    pass

fileformats/medimage/contents/anatomical_entity/__init__.py

@@ -0,0 +1,5 @@
+from .. import ContentsClassifier
+
+
+class AnatomicalEntity(ContentsClassifier):
+    pass

fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/__init__.py

@@ -0,0 +1,5 @@
+from .. import AnatomicalEntity
+
+
+class MaterialAnatomicalEntity(AnatomicalEntity):
+    pass

fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/anatomical_structure.py

@@ -0,0 +1,29 @@
+from . import MaterialAnatomicalEntity
+
+
+class AnatomicalStructure(MaterialAnatomicalEntity):
+    pass
+
+
+class CardinalOrganPart(AnatomicalStructure):
+    pass
+
+
+class OrganRegion(CardinalOrganPart):
+    pass
+
+
+class OrganSegment(OrganRegion):
+    pass
+
+
+class SegmentOfNeuraxis(OrganRegion):
+    pass
+
+
+class Brain(SegmentOfNeuraxis):
+    pass
+
+
+class SpinalCord(SegmentOfNeuraxis):
+    pass

fileformats/medimage/contents/imaging/__init__.py

@@ -0,0 +1,5 @@
+from .. import ContentsClassifier
+
+
+class ImagingSpecialty(ContentsClassifier):
+    pass

fileformats/medimage/contents/imaging/derivatives.py

@@ -0,0 +1,17 @@
+from .. import ContentsClassifier
+
+
+class Derivative(ContentsClassifier):
+    """An image type that is derived from other images"""
+
+
+class Mask(Derivative):
+    """A binary image that is multiplied with a real-valued image to select sections
+    of the image for analysis"""
+
+
+class FibreOrientationDistribution(Derivative):
+    pass
+
+
+FOD = FibreOrientationDistribution

fileformats/medimage/radlex/imaging/modality.py → fileformats/medimage/contents/imaging/modality.py

@@ -1,7 +1,7 @@
-from fileformats.core import ClassifierCategory
+from .. import ContentsClassifier
 
 
-class ImagingModality(ClassifierCategory):
+class ImagingModality(ContentsClassifier):
     ontology_link = 'http://www.radlex.org/RID/RID10311'
     description = 'Form of imaging that depends on the way the image is produced'
     dicom_modality = None
@@ -144,6 +144,7 @@ class ScreenFilmRadiography(ProjectionRadiography):
     description = 'Conventional radiography'
     dicom_modality = 'RG'
 
+
 class Stereoscopy(ProjectionRadiography):
     ontology_link = 'http://www.radlex.org/RID/RID50131'
     description = None