ENH: Support structure ID in file format converter.

Scripts/convert/converters.py

@@ -13,6 +13,7 @@
 
 # most-recent versions first
 version_order = [
+    'v0.2.1+2022.03.04',
     'v0.2.0+2021.08.12',
     'v0.1.1+2021.06.11',
     'v0.1.0+2020.09.18',

Scripts/convert/model.py

@@ -3,7 +3,7 @@
 import inspect
 from dataclasses import dataclass
 from pathlib import Path
-from typing import List, Tuple
+from typing import List, Tuple, Optional
 
 __all__ = ['Annotation', 'Document', 'Converter', 'versioned']
 
@@ -13,6 +13,19 @@
                  float, float, float, float,
                  float, float, float, float]
 
+@dataclass
+class Structure:
+    id: int
+    acronym: str
+
+@dataclass
+class Point:
+    position: Vector3f
+    structure: Optional[Structure] = None
+
+    def __iter__(self):
+        # enables unpacking like `x, y, z = point`
+        return iter(self.position)
 
 @dataclass
 class Annotation:
@@ -40,7 +53,7 @@ class Annotation:
     )
     """A transformation matrix storing the orientation of the slicing plane."""
 
-    points: List[Vector3f] = dataclasses.field(default_factory=list)
+    points: List[Point] = dataclasses.field(default_factory=list)
     """Control point positions for the annotation markup."""
 
 

Scripts/convert/versions/v0.0.0+2019.01.26.py

@@ -27,7 +27,7 @@ def normalize(cls, data: dict):
 
             ann.coordinate_system = 'LPS'
             ann.points = [
-                (-p['x'], -p['y'], p['z'])  # RAS → LPS conversion
+                model.Point((-p['x'], -p['y'], p['z']))  # RAS → LPS conversion
                 for p in dmark['Points']
             ]
 

Scripts/convert/versions/v0.0.0+2020.04.16.py

@@ -39,7 +39,7 @@ def normalize(cls, data: dict):
 
             ann.coordinate_system = 'LPS'
             ann.points = [
-                (-p['x'], -p['y'], p['z'])  # RAS → LPS conversion
+                model.Point((-p['x'], -p['y'], p['z']))  # RAS → LPS conversion
                 for p in dmark['Points']
             ]
 

Scripts/convert/versions/v0.0.0+2020.08.26.py

@@ -27,7 +27,7 @@ def normalize(cls, data: dict):
                 ann.coordinate_units = dmark['coordinateUnits']
 
             for point in dmark['controlPoints']:
-                ann.points.append(tuple(point['position']))
+                ann.points.append(model.Point(tuple(point['position'])))
 
             doc.annotations.append(ann)
 
@@ -50,7 +50,7 @@ def specialize(cls, doc: model.Document):
                             'label': f'MarkupsClosedCurve-{i}',
                             'description': '',
                             'associatedNodeID': 'vtkMRMLScalarVolumeNode1',
-                            'position': pt,
+                            'position': pt.position,
                             'orientation': [-1.0, -0.0, -0.0,
                                             -0.0, -1.0, -0.0,
                                             +0.0, +0.0, +1.0],

Scripts/convert/versions/v0.1.0+2020.09.18.py

@@ -29,7 +29,7 @@ def normalize(cls, data: dict):
                 ann.coordinate_units = dmark['coordinateUnits']
 
             for point in dmark['controlPoints']:
-                ann.points.append(tuple(point['position']))
+                ann.points.append(model.Point(tuple(point['position'])))
 
             doc.annotations.append(ann)
 
@@ -49,7 +49,7 @@ def specialize(cls, doc: model.Document):
                     'controlPoints': [
                         {
                             'id': str(i),
-                            'position': pt,
+                            'position': pt.position,
                             'orientation': [-1.0, -0.0, -0.0,
                                             -0.0, -1.0, -0.0,
                                             +0.0, +0.0, +1.0]

Scripts/convert/versions/v0.1.1+2021.06.11.py

@@ -29,7 +29,7 @@ def normalize(cls, data: dict):
                 ann.coordinate_units = dmark['coordinateUnits']
 
             for point in dmark['controlPoints']:
-                ann.points.append(tuple(point['position']))
+                ann.points.append(model.Point(tuple(point['position'])))
 
             doc.annotations.append(ann)
 
@@ -48,7 +48,7 @@ def specialize(cls, doc: model.Document):
                     'controlPoints': [
                         {
                             'id': str(i),
-                            'position': pt,
+                            'position': pt.position,
                             'orientation': [-1.0, -0.0, -0.0,
                                             -0.0, -1.0, -0.0,
                                             +0.0, +0.0, +1.0]

Scripts/convert/versions/v0.2.0+2021.08.12.py

@@ -29,7 +29,7 @@ def normalize(cls, data: dict):
                 ann.coordinate_units = dmark['coordinateUnits']
 
             for point in dmark['controlPoints']:
-                ann.points.append(tuple(point['position']))
+                ann.points.append(model.Point(tuple(point['position'])))
 
             doc.annotations.append(ann)
 
@@ -48,7 +48,7 @@ def specialize(cls, doc: model.Document):
                     'controlPoints': [
                         {
                             'id': str(i),
-                            'position': pt,
+                            'position': pt.position,
                             'orientation': [-1.0, -0.0, -0.0,
                                             -0.0, -1.0, -0.0,
                                             +0.0, +0.0, +1.0]

Scripts/convert/versions/v0.2.1+2022.03.04.py

@@ -0,0 +1,85 @@
+import model
+
+
+class Converter(model.Converter):
+    @classmethod
+    def normalize(cls, data: dict):
+        doc = model.Document()
+        doc.current_id = data['currentId']
+        doc.reference_view = data['referenceView']
+        doc.ontology = data['ontology']
+        doc.stepSize = data['stepSize']
+        doc.camera_position = tuple(data['cameraPosition'])
+        doc.camera_view_up = tuple(data['cameraViewUp'])
+
+        for dann in data['markups']:
+            dmark = dann['markup']
+
+            ann = model.Annotation()
+            ann.name = dann['name']
+            ann.orientation = dann['orientation']
+            ann.markup_type = dmark['type']
+
+            if ann.markup_type == 'ClosedCurve':
+                ann.representation_type = dann['representationType']
+                ann.thickness = dann['thickness']
+
+            ann.coordinate_system = dmark['coordinateSystem']
+            if 'coordinateUnits' in dmark:
+                ann.coordinate_units = dmark['coordinateUnits']
+
+            for point in dmark['controlPoints']:
+                position = tuple(point['position'])
+                structure = point.get('structure', None)
+                if structure:
+                    structure = model.Structure(
+                        structure['id'],
+                        structure['acronym'],
+                    )
+
+                ann.points.append(model.Point(position, structure))
+
+            doc.annotations.append(ann)
+
+        return doc
+
+    @classmethod
+    @model.versioned
+    def specialize(cls, doc: model.Document):
+        data = dict()
+        data['markups'] = [
+            {
+                'markup': {
+                    'type': ann.markup_type,
+                    'coordinateSystem': ann.coordinate_system,
+                    'coordinateUnits': ann.coordinate_units,
+                    'controlPoints': [
+                        {
+                            'id': str(i),
+                            'position': pt.position,
+                            'orientation': [-1.0, -0.0, -0.0,
+                                            -0.0, -1.0, -0.0,
+                                            +0.0, +0.0, +1.0],
+                            'structure': {
+                                'id': pt.structure.id,
+                                'acronym': pt.structure.acronym
+                            } if pt.structure else None
+                        }
+                        for i, pt in enumerate(ann.points, start=1)
+                    ],
+                },
+                'name': ann.name,
+                'orientation': ann.orientation,
+                'representationType': ann.representation_type,
+                'thickness': ann.thickness
+            }
+            for ann in doc.annotations
+        ]
+        data['currentId'] = doc.current_id
+        data['referenceView'] = doc.reference_view
+        data['ontology'] = doc.ontology
+        data['stepSize'] = doc.stepSize
+        data['cameraPosition'] = doc.camera_position
+        data['cameraViewUp'] = doc.camera_view_up
+
+        return data