ENH: Cell Locator 0.2.0

- Update slicer-application-properties.cmake
- Update current version in CHANGES.md
- Update the current annotation file format version to match release.
    - Add corresponding converter to the file conversion script.
    - Add entry to AnnotationFileFormat.md

Applications/CellLocatorApp/slicer-application-properties.cmake

@@ -7,7 +7,7 @@ set(VERSION_MAJOR
   0
   )
 set(VERSION_MINOR
-  1
+  2
   )
 set(VERSION_PATCH
   0

CHANGES.md

@@ -4,6 +4,14 @@
 
 Features:
 
+Fixes:
+
+Documentation:
+
+## Cell Locator 0.2.0 2021-08-12
+
+Features:
+
 - Created script to convert between Cell Locator file formats. [#181](https://github.com/BICCN/cell-locator/pull/181), [#182](https://github.com/BICCN/cell-locator/pull/182)
 
 Fixes:

Documentation/developer_guide/AnnotationFileFormat.md

@@ -10,6 +10,10 @@ We mean it.
 
 ## Versions
 
+## 0.2.0 (2021-08-11)
+
+Unchanged from 0.1.1; this version synchronizes the file format and cell locator release.
+
 ## 0.1.1 (2021-06-11)
 
 Removed the `"measurements"` key from markups.

Modules/Scripted/Home/Home.py

@@ -284,7 +284,7 @@ def setMetadata(self, data):
 class AnnotationManager:
   """Manage serialization and bookkeeping for a collection of annotations."""
 
-  FORMAT_VERSION = '0.1.1+2021.06.11'
+  FORMAT_VERSION = '0.2.0+2021.08.12'
 
   DefaultReferenceView = 'Coronal'
   DefaultOntology = 'Structure'

Scripts/convert/converters.py

@@ -13,6 +13,7 @@
 
 # most-recent versions first
 version_order = [
+    'v0.2.0+2021.08.12',
     'v0.1.1+2021.06.11',
     'v0.1.0+2020.09.18',
     'v0.0.0+2020.08.26',

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

@@ -0,0 +1,73 @@
+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']:
+                ann.points.append(tuple(point['position']))
+
+            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,
+                            'orientation': [-1.0, -0.0, -0.0,
+                                            -0.0, -1.0, -0.0,
+                                            +0.0, +0.0, +1.0]
+                        }
+                        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