From 8877595ba7f2684d39994ca4c6572e6121e48cca Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 15 Jan 2024 14:40:23 +1100
Subject: [PATCH] touching up classifiers

---
 fileformats/medimage/__init__.py              |  9 +++---
 fileformats/medimage/base.py                  |  4 +++
 .../__init__.py                               |  0
 .../anatomical_entity/anatomical_set.py       |  0
 .../immaterial_anatomical_entity.py           |  0
 .../material_anatomical_entity/__init__.py    |  5 ++++
 .../anatomical_structure.py                   | 29 +++++++++++++++++++
 fileformats/medimage/contents/derivatives.py  |  6 ----
 .../medimage/contents/imaging/derivatives.py  | 17 +++++++++++
 9 files changed, 60 insertions(+), 10 deletions(-)
 rename fileformats/medimage/contents/{anatomical => anatomical_entity}/__init__.py (100%)
 create mode 100644 fileformats/medimage/contents/anatomical_entity/anatomical_set.py
 create mode 100644 fileformats/medimage/contents/anatomical_entity/immaterial_anatomical_entity.py
 create mode 100644 fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/__init__.py
 create mode 100644 fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/anatomical_structure.py
 delete mode 100644 fileformats/medimage/contents/derivatives.py
 create mode 100644 fileformats/medimage/contents/imaging/derivatives.py

diff --git a/fileformats/medimage/__init__.py b/fileformats/medimage/__init__.py
index 4bc47f5..ca8becb 100644
--- a/fileformats/medimage/__init__.py
+++ b/fileformats/medimage/__init__.py
@@ -46,9 +46,6 @@
 from .surface import (
     Gifti  # noqa: F401
 )
-from .contents.anatomical import (
-    AnatomicalEntity  # noqa: F401
-)
 from .contents.imaging.modality import (  # noqa: F401
     ImagingModality,
     CombinedModalities,
@@ -92,6 +89,10 @@
     RG,
     US,
 )
-from .contents.derivatives import (
+from .contents.imaging.derivatives import (
+    Derivative,
     Mask
 )
+from .contents.anatomical_entity.material_anatomical_entity.anatomical_structure import (
+    Brain, SpinalCord
+)
\ No newline at end of file
diff --git a/fileformats/medimage/base.py b/fileformats/medimage/base.py
index d5a8958..93910ad 100644
--- a/fileformats/medimage/base.py
+++ b/fileformats/medimage/base.py
@@ -4,6 +4,9 @@
 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")
 
@@ -20,6 +23,7 @@ class MedicalImage(WithClassifiers, FileSet):
     IGNORE_HDR_KEYS = None
     binary = True
     allowed_classifiers = (ContentsClassifier,)
+    exclusive_classifiers = (ImagingModality, AnatomicalEntity, Derivative)
 
     @hook.extra
     def read_array(self) -> "numpy.ndarray":  # noqa
diff --git a/fileformats/medimage/contents/anatomical/__init__.py b/fileformats/medimage/contents/anatomical_entity/__init__.py
similarity index 100%
rename from fileformats/medimage/contents/anatomical/__init__.py
rename to fileformats/medimage/contents/anatomical_entity/__init__.py
diff --git a/fileformats/medimage/contents/anatomical_entity/anatomical_set.py b/fileformats/medimage/contents/anatomical_entity/anatomical_set.py
new file mode 100644
index 0000000..e69de29
diff --git a/fileformats/medimage/contents/anatomical_entity/immaterial_anatomical_entity.py b/fileformats/medimage/contents/anatomical_entity/immaterial_anatomical_entity.py
new file mode 100644
index 0000000..e69de29
diff --git a/fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/__init__.py b/fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/__init__.py
new file mode 100644
index 0000000..33a255c
--- /dev/null
+++ b/fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/__init__.py
@@ -0,0 +1,5 @@
+from .. import AnatomicalEntity
+
+
+class MaterialAnatomicalEntity(AnatomicalEntity):
+    pass
diff --git a/fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/anatomical_structure.py b/fileformats/medimage/contents/anatomical_entity/material_anatomical_entity/anatomical_structure.py
new file mode 100644
index 0000000..f1068b5
--- /dev/null
+++ b/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
diff --git a/fileformats/medimage/contents/derivatives.py b/fileformats/medimage/contents/derivatives.py
deleted file mode 100644
index 82f6051..0000000
--- a/fileformats/medimage/contents/derivatives.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from . import ContentsClassifier
-
-
-class Mask(ContentsClassifier):
-    """A binary image that is multiplied with a real-valued image to select sections
-    of the image for analysis"""
diff --git a/fileformats/medimage/contents/imaging/derivatives.py b/fileformats/medimage/contents/imaging/derivatives.py
new file mode 100644
index 0000000..f3480d5
--- /dev/null
+++ b/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