-
Notifications
You must be signed in to change notification settings - Fork 43
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1385 from girder/annotation-to-geojson
Add a utility function to yield annotations as geojson.
- Loading branch information
Showing
6 changed files
with
251 additions
and
4 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
159 changes: 159 additions & 0 deletions
159
girder_annotation/girder_large_image_annotation/utils/__init__.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| import json | ||
| import math | ||
|
|
||
|
|
||
| class AnnotationGeoJSON: | ||
| """ | ||
| Generate GeoJSON for an annotation via an iterator. | ||
| """ | ||
|
|
||
| def __init__(self, annotationId, asFeatures=False, mustConvert=False): | ||
| """ | ||
| Return an itertor for converting an annotation into geojson. | ||
| :param annotatioId: the id of the annotation. No permissions checks | ||
| are performed. | ||
| :param asFeatures: if False, return a geojson string. If True, return | ||
| the features of the geojson. This can be wrapped in | ||
| `{'type': 'FeatureCollection', 'features: [...output...]}` | ||
| to make it a full geojson object. | ||
| :param mustConvert: if True, raise an exception if any annotation | ||
| elements cannot be converted. Otherwise, skip those elements. | ||
| """ | ||
| from ..models.annotation import Annotation | ||
| from ..models.annotationelement import Annotationelement | ||
|
|
||
| self._id = annotationId | ||
| self.annotation = Annotation().load(id=self._id, force=True, getElements=False) | ||
| self.elemIterator = Annotationelement().yieldElements(self.annotation) | ||
| self.stage = 'header' | ||
| self.first = self.annotation['annotation'] | ||
| self.asFeatures = asFeatures | ||
| self.mustConvert = mustConvert | ||
|
|
||
| def __iter__(self): | ||
| from ..models.annotationelement import Annotationelement | ||
|
|
||
| self.elemIterator = Annotationelement().yieldElements(self.annotation) | ||
| self.stage = 'header' | ||
| return self | ||
|
|
||
| def __next__(self): | ||
| if self.stage == 'header': | ||
| self.stage = 'firstelement' | ||
| if not self.asFeatures: | ||
| return '{"type":"FeatureCollection","features":[' | ||
| if self.stage == 'done': | ||
| raise StopIteration | ||
| try: | ||
| while True: | ||
| element = next(self.elemIterator) | ||
| result = self.elementToGeoJSON(element) | ||
| if result is not None: | ||
| break | ||
| if self.mustConvert: | ||
| msg = f'Element of type {element["type"]} cannot be represented as geojson' | ||
| raise Exception(msg) | ||
| prefix = '' | ||
| if self.stage == 'firstelement': | ||
| result['properties']['annotation'] = self.first | ||
| self.stage = 'elements' | ||
| else: | ||
| prefix = ',' | ||
| if not self.asFeatures: | ||
| return prefix + json.dumps(result, separators=(',', ':')) | ||
| return result | ||
| except StopIteration: | ||
| self.stage = 'done' | ||
| if not self.asFeatures: | ||
| return ']}' | ||
| raise | ||
|
|
||
| def rotate(self, r, cx, cy, x, y, z): | ||
| if not r: | ||
| return [x + cx, y + cy, z] | ||
| cosr = math.cos(r) | ||
| sinr = math.sin(r) | ||
| x -= cx | ||
| y -= cy | ||
| return [x * cosr - y * sinr + cx, x * sinr + y * sinr + cy, z] | ||
|
|
||
| def circleType(self, element, geom, prop): | ||
| x, y, z = element['center'] | ||
| r = element['radius'] | ||
| geom['type'] = 'Polygon' | ||
| geom['coordinates'] = [[ | ||
| [x - r, y - r, z], | ||
| [x + r, y - r, z], | ||
| [x + r, y + r, z], | ||
| [x - r, y + r, z], | ||
| [x - r, y - r, z], | ||
| ]] | ||
|
|
||
| def ellipseType(self, element, geom, prop): | ||
| return self.rectangleType(element, geom, prop) | ||
|
|
||
| def pointType(self, element, geom, prop): | ||
| geom['type'] = 'Point' | ||
| geom['coordinates'] = element['center'] | ||
|
|
||
| def polylineType(self, element, geom, prop): | ||
| if element['closed']: | ||
| geom['type'] = 'Polygon' | ||
| geom['coordinates'] = [element['points'][:]] | ||
| geom['coordinates'][0].append(geom['coordinates'][0][0]) | ||
| if element.get('holes'): | ||
| for hole in element['holes']: | ||
| hole = hole[:] | ||
| hole.append(hole[0]) | ||
| geom['coordinates'].append(hole) | ||
| else: | ||
| geom['type'] = 'LineString' | ||
| geom['coordinates'] = element['points'] | ||
|
|
||
| def rectangleType(self, element, geom, prop): | ||
| x, y, z = element['center'] | ||
| width = element['width'] | ||
| height = element['height'] | ||
| rotation = element.get('rotation', 0) | ||
| left = x - width / 2 | ||
| right = x + width / 2 | ||
| top = y - height / 2 | ||
| bottom = y + height / 2 | ||
|
|
||
| geom['type'] = 'Polygon' | ||
| geom['coordinates'] = [[ | ||
| self.rotate(rotation, x, y, left, top, z), | ||
| self.rotate(rotation, x, y, right, top, z), | ||
| self.rotate(rotation, x, y, right, bottom, z), | ||
| self.rotate(rotation, x, y, left, bottom, z), | ||
| self.rotate(rotation, x, y, left, top, z), | ||
| ]] | ||
|
|
||
| # not represented | ||
| # heatmap, griddata, image, pixelmap, arrow, rectanglegrid | ||
| # heatmap could be MultiPoint, griddata could be rectangle with lots of | ||
| # properties, image and pixelmap could be rectangle with the image id as a | ||
| # property, arrow and rectangelgrid aren't really supported | ||
|
|
||
| def elementToGeoJSON(self, element): | ||
| elemType = element.get('type', '') | ||
| funcName = elemType + 'Type' | ||
| if not hasattr(self, funcName): | ||
| return None | ||
| result = { | ||
| 'type': 'Feature', | ||
| 'geometry': {}, | ||
| 'properties': { | ||
| k: v if k != 'id' else str(v) | ||
| for k, v in element.items() if k in { | ||
| 'id', 'label', 'group', 'user', 'lineColor', 'lineWidth', | ||
| 'fillColor', 'radius', 'width', 'height', 'rotation', | ||
| 'normal', | ||
| } | ||
| }, | ||
| } | ||
| getattr(self, funcName)(element, result['geometry'], result['properties']) | ||
| if result['geometry']['type'].lower() != element['type']: | ||
| result['properties']['type'] = element['type'] | ||
| return result |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters