def testGetNextVersionValue(self):
val1 = Annotationelement().getNextVersionValue()
val2 = Annotationelement().getNextVersionValue()
assert val2 > val1
Annotationelement().versionId = None
val3 = Annotationelement().getNextVersionValue()
assert val3 > val2
def testBoundingBox(self):
bbox = Annotationelement()._boundingBox(
{'points': [[1, -2, 3], [-4, 5, -6], [7, -8, 9]]})
assert bbox == {
'lowx': -4,
'lowy': -8,
'lowz': -6,
'highx': 7,
'highy': 5,
'highz': 9,
'details': 3,
'size': ((7 + 4)**2 + (8 + 5)**2)**0.5
}
bbox = Annotationelement()._boundingBox({'center': [1, -2, 3]})
assert bbox == {
'lowx': 0.5,
'lowy': -2.5,
'lowz': 3,
'highx': 1.5,
'highy': -1.5,
'highz': 3,
'details': 1,
'size': 2**0.5
}
bbox = Annotationelement()._boundingBox({
'center': [1, -2, 3],
'radius': 4
})
assert bbox == {
'lowx': -3,
'lowy': -6,
'lowz': 3,
'highx': 5,
'highy': 2,
'highz': 3,
'details': 4,
'size': 8 * 2**0.5
}
bbox = Annotationelement()._boundingBox({
'center': [1, -2, 3],
'width': 2,
'height': 4
})
assert bbox == {
'lowx': 0,
'lowy': -4,
'lowz': 3,
'highx': 2,
'highy': 0,
'highz': 3,
'details': 4,
'size': (2**2 + 4**2)**0.5
}
bbox = Annotationelement()._boundingBox({
'center': [1, -2, 3],
'width': 2,
'height': 4,
'rotation': math.pi * 0.25
})
assert bbox['size'] == pytest.approx(4, 1.0e-4)
def testOverlayBounds(self, server, admin, fsAssetstore):
file = utilities.uploadExternalFile('sample_image.ptif', admin, fsAssetstore)
itemId = str(file['itemId'])
# test no transform
lowx, highx, lowy, highy = Annotationelement()._overlayBounds({
'type': 'image', 'girderId': itemId
})
assert lowx == 0
assert lowy == 0
assert highx == 58368
assert highy == 12288
# test offset
lowx, highx, lowy, highy = Annotationelement()._overlayBounds({
'type': 'image', 'girderId': itemId,
'transform': {'xoffset': 500, 'yoffset': 1000}
})
assert lowx == 500
assert lowy == 1000
assert highx == 58868
assert highy == 13288
# test affine matrix, scale to 50%
lowx, highx, lowy, highy = Annotationelement()._overlayBounds({
'type': 'image', 'girderId': itemId,
'transform': {
'matrix': [[0.5, 0], [0, 0.5]]
}
})
assert lowx == 0
assert lowy == 0
assert highx == 58368 / 2
assert highy == 12288 / 2
# test transform and scaling
lowx, highx, lowy, highy = Annotationelement()._overlayBounds({
'type': 'image', 'girderId': itemId,
'transform': {
'xoffset': 500,
'yoffset': 1000,
'matrix': [[0.5, 0], [0, 0.5]]
}
})
assert lowx == 500
assert lowy == 1000
assert highx == (58368 / 2) + 500
assert highy == (12288 / 2) + 1000
def testRemoveElements(self, admin):
publicFolder = utilities.namedFolder(admin, 'Public')
item = Item().createItem('sample', admin, publicFolder)
annot = Annotation().createAnnotation(item, admin, sampleAnnotation)
assert len(Annotation().load(
annot['_id'], user=admin)['annotation']['elements']) == 1
Annotationelement().removeElements(annot)
assert len(Annotation().load(
annot['_id'], user=admin)['annotation']['elements']) == 0
def testOverlayBoundingBox(self, server, admin, fsAssetstore):
file = utilities.uploadExternalFile('sample_image.ptif', admin, fsAssetstore)
itemId = str(file['itemId'])
bbox = Annotationelement()._boundingBox(
{'type': 'image', 'girderId': itemId})
assert bbox == {
'lowx': 0, 'lowy': 0, 'lowz': 0,
'highx': 58368, 'highy': 12288, 'highz': 0,
'details': 1,
'size': (58368**2 + 12288**2)**0.5}
def testGetElementsByCentroids(self, admin):
publicFolder = utilities.namedFolder(admin, 'Public')
item = Item().createItem('sample', admin, publicFolder)
largeSample = makeLargeSampleAnnotation()
# Use a copy of largeSample so we don't just have a reference to it
annot = Annotation().createAnnotation(item, admin, largeSample.copy())
# Clear existing element data, the get elements
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {'centroids': True})
assert '_elementQuery' in annot
assert len(annot['annotation']['elements']) == len(largeSample['elements']) # 7707
assert annot['_elementQuery']['centroids'] is True
assert 'props' in annot['_elementQuery']
elements = annot['annotation']['elements']
assert isinstance(elements[0], list)
def testGetElements(self, admin):
publicFolder = utilities.namedFolder(admin, 'Public')
item = Item().createItem('sample', admin, publicFolder)
largeSample = makeLargeSampleAnnotation()
# Use a copy of largeSample so we don't just have a reference to it
annot = Annotation().createAnnotation(item, admin, largeSample.copy())
# Clear existing element data, the get elements
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot)
assert '_elementQuery' in annot
assert len(annot['annotation']['elements']) == len(largeSample['elements']) # 7707
assert 'centroids' not in annot['_elementQuery']
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {'limit': 100})
assert '_elementQuery' in annot
assert annot['_elementQuery']['count'] == len(largeSample['elements'])
assert annot['_elementQuery']['returned'] == 100
assert len(annot['annotation']['elements']) == 100
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {
'left': 3000, 'right': 4000, 'top': 4500, 'bottom': 6500})
assert len(annot['annotation']['elements']) == 157
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {
'left': 3000, 'right': 4000, 'top': 4500, 'bottom': 6500,
'minimumSize': 16})
assert len(annot['annotation']['elements']) == 39
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {'maxDetails': 300})
assert len(annot['annotation']['elements']) == 75
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {
'maxDetails': 300, 'sort': 'size', 'sortdir': -1})
elements = annot['annotation']['elements']
assert (elements[0]['width'] * elements[0]['height'] >
elements[-1]['width'] * elements[-1]['height'])
annot.pop('elements', None)
annot.pop('_elementQuery', None)
Annotationelement().getElements(annot, {
'maxDetails': 300, 'sort': 'size', 'sortdir': 1})
elements = annot['annotation']['elements']
assert (elements[0]['width'] * elements[0]['height'] <
elements[-1]['width'] * elements[-1]['height'])
def testInitialize(self):
# initialize should be called as we fetch the model
assert Annotationelement().name == 'annotationelement'
