def test_user_annotation_groups(self):
"""
Test user annotation group on heartatria1 scaffold with scaffold package.
"""
scaffoldPackage = ScaffoldPackage(MeshType_3d_heartatria1)
# can't add user annotation groups until generate is called()
try:
annotationGroup = scaffoldPackage.createUserAnnotationGroup()
self.assertTrue(False) # should never get here as above raises expection
except:
pass
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
fieldmodule = region.getFieldmodule()
scaffoldPackage.generate(region)
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(22, len(annotationGroups))
endocardium_of_la = scaffoldPackage.findAnnotationGroupByName('endocardium of left atrium')
self.assertTrue(isinstance(endocardium_of_la, AnnotationGroup))
self.assertFalse(scaffoldPackage.isUserAnnotationGroup(endocardium_of_la))
self.assertFalse(scaffoldPackage.deleteAnnotationGroup(endocardium_of_la)) # can't delete auto annotation groups
annotationGroup1 = scaffoldPackage.createUserAnnotationGroup()
self.assertEqual('group1', annotationGroup1.getName()) # default name
self.assertIsNone(annotationGroup1.getId())
self.assertTrue(scaffoldPackage.isUserAnnotationGroup(annotationGroup1))
self.assertEqual(-1, annotationGroup1.getDimension()) # -1 = empty
group = annotationGroup1.getGroup()
self.assertTrue(group.isValid())
mesh2d = fieldmodule.findMeshByDimension(2)
meshGroup = group.createFieldElementGroup(mesh2d).getMeshGroup()
mesh_group_add_identifier_ranges(meshGroup, [[1,2],[4,4]])
self.assertEqual(3, meshGroup.getSize())
self.assertEqual(2, annotationGroup1.getDimension())
identifier_ranges_string = identifier_ranges_to_string(mesh_group_to_identifier_ranges(meshGroup))
self.assertEqual('1-2,4', identifier_ranges_string)
annotationGroup2 = scaffoldPackage.createUserAnnotationGroup(('bob', 'BOB:1'))
self.assertEqual('bob', annotationGroup2.getName())
self.assertEqual('BOB:1', annotationGroup2.getId())
self.assertTrue(scaffoldPackage.isUserAnnotationGroup(annotationGroup2))
group = annotationGroup2.getGroup()
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodesetGroup = group.createFieldNodeGroup(nodes).getNodesetGroup()
nodeset_group_add_identifier_ranges(nodesetGroup, identifier_ranges_from_string('1,3-5,7'))
self.assertEqual(5, nodesetGroup.getSize())
self.assertEqual(0, annotationGroup2.getDimension())
identifier_ranges_string = identifier_ranges_to_string(nodeset_group_to_identifier_ranges(nodesetGroup))
self.assertEqual('1,3-5,7', identifier_ranges_string)
annotationGroup3 = scaffoldPackage.createUserAnnotationGroup()
self.assertEqual('group2', annotationGroup3.getName()) # default name
self.assertTrue(scaffoldPackage.isUserAnnotationGroup(annotationGroup3))
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(25, len(annotationGroups))
# rename group1 to fred
self.assertTrue(annotationGroup1.setName('fred'))
self.assertTrue(annotationGroup1.setId('FRED:1'))
self.assertEqual('fred', annotationGroup1.getName())
self.assertEqual('FRED:1', annotationGroup1.getId())
self.assertTrue(scaffoldPackage.deleteAnnotationGroup(annotationGroup3))
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(24, len(annotationGroups))
# test serialisation
dct = scaffoldPackage.toDict()
self.assertEqual('3D Heart Atria 1', dct['scaffoldTypeName'])
scaffoldType = Scaffolds().findScaffoldTypeByName(dct['scaffoldTypeName'])
scaffoldPackage2 = ScaffoldPackage(scaffoldType, dct)
region2 = context.createRegion()
fieldmodule2 = region2.getFieldmodule()
scaffoldPackage2.generate(region2)
annotationGroups2 = scaffoldPackage2.getAnnotationGroups()
self.assertEqual(24, len(annotationGroups2))
annotationGroup1 = scaffoldPackage2.findAnnotationGroupByName('fred')
self.assertEqual('fred', annotationGroup1.getName())
self.assertEqual('FRED:1', annotationGroup1.getId())
self.assertTrue(scaffoldPackage2.isUserAnnotationGroup(annotationGroup1))
self.assertEqual(2, annotationGroup1.getDimension())
mesh2d2 = fieldmodule2.findMeshByDimension(2)
meshGroup2 = annotationGroup1.getMeshGroup(mesh2d2)
self.assertEqual(3, meshGroup2.getSize())
identifier_ranges_string = identifier_ranges_to_string(mesh_group_to_identifier_ranges(meshGroup2))
self.assertEqual('1-2,4', identifier_ranges_string)
annotationGroup2 = scaffoldPackage2.findAnnotationGroupByName('bob')
self.assertEqual('bob', annotationGroup2.getName())
self.assertEqual('BOB:1', annotationGroup2.getId())
self.assertTrue(scaffoldPackage2.isUserAnnotationGroup(annotationGroup2))
self.assertEqual(0, annotationGroup2.getDimension())
nodes2 = fieldmodule2.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodesetGroup2 = annotationGroup2.getNodesetGroup(nodes2)
self.assertEqual(5, nodesetGroup.getSize())
identifier_ranges_string = identifier_ranges_to_string(nodeset_group_to_identifier_ranges(nodesetGroup2))
self.assertEqual('1,3-5,7', identifier_ranges_string)
def test_user_marker_points(self):
"""
Test user marker point on brainstem1 scaffold which defined "brainstem coordinates".
"""
scaffoldPackage = ScaffoldPackage(MeshType_3d_brainstem1)
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
fieldmodule = region.getFieldmodule()
mesh = fieldmodule.findMeshByDimension(3)
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
scaffoldPackage.generate(region)
# 1 higher than last node in scaffold. Make marker nodes from this number
nextNodeIdentifier = scaffoldPackage.getNextNodeIdentifier()
brainstemCoordinatesField = fieldmodule.findFieldByName("brainstem coordinates")
self.assertTrue(brainstemCoordinatesField.isValid())
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(18, len(annotationGroups))
TOL = 1.0E-6 # coarse to handle find xi tolerances
# check a built-in non-marker annotation group
ponsGroup = scaffoldPackage.findAnnotationGroupByName('pons')
self.assertFalse(ponsGroup.isMarker())
self.assertRaises(AssertionError, lambda: ponsGroup.getMarkerMaterialCoordinates())
self.assertRaises(AssertionError, lambda: ponsGroup.getMarkerLocation())
self.assertRaises(AssertionError, lambda: ponsGroup.createMarkerNode(nextNodeIdentifier))
# check a built-in marker annotation group
brainstemVentralCranialPointGroup = \
scaffoldPackage.findAnnotationGroupByName('brainstem ventral midline cranial point')
self.assertIsNotNone(brainstemVentralCranialPointGroup)
self.assertTrue(brainstemVentralCranialPointGroup.isMarker())
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = \
brainstemVentralCranialPointGroup.getMarkerMaterialCoordinates()
self.assertEqual(brainstemCoordinatesFieldOut, brainstemCoordinatesField)
assertAlmostEqualList(self, [0.0, -1.0, 8.0], brainstemCoordinatesValueOut, delta=TOL)
elementOut, xiOut = brainstemVentralCranialPointGroup.getMarkerLocation()
self.assertEqual(235, elementOut.getIdentifier())
assertAlmostEqualList(self, [1.0, 1.0, 0.0], xiOut, delta=TOL)
self.assertRaises(AssertionError, lambda: brainstemVentralCranialPointGroup.createMarkerNode(nextNodeIdentifier))
# check a non-existant annotation group
bobGroup = scaffoldPackage.findAnnotationGroupByName("bob")
self.assertIsNone(bobGroup)
# now make a marker annotation named "bob" at the default location
bobGroup = scaffoldPackage.createUserAnnotationGroup(('bob', 'BOB:1'))
self.assertTrue(scaffoldPackage.isUserAnnotationGroup(bobGroup))
self.assertFalse(bobGroup.isMarker())
node = bobGroup.createMarkerNode(nextNodeIdentifier)
bobNodeIdentifier = node.getIdentifier()
self.assertEqual(nextNodeIdentifier, bobNodeIdentifier)
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = bobGroup.getMarkerMaterialCoordinates()
self.assertIsNone(brainstemCoordinatesFieldOut)
self.assertIsNone(brainstemCoordinatesValueOut)
elementOut, xiOut = bobGroup.getMarkerLocation()
self.assertEqual(1, elementOut.getIdentifier())
assertAlmostEqualList(self, [0.0, 0.0, 0.0], xiOut, delta=TOL)
# now request brainstem coordinates and let the annotation group determine its values from element:xi
bobGroup.setMarkerMaterialCoordinates(brainstemCoordinatesField)
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = bobGroup.getMarkerMaterialCoordinates()
self.assertEqual(brainstemCoordinatesFieldOut, brainstemCoordinatesField)
# these should be precisely cos(45) but are not due to ellipse approximations
assertAlmostEqualList(self, [0.707016, -0.707198, 0], brainstemCoordinatesValueOut, delta=TOL)
# set element:xi location and check brainstem coordinates change
bobGroup.setMarkerLocation(mesh.findElementByIdentifier(33), [0.0, 0.5, 0.0])
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = bobGroup.getMarkerMaterialCoordinates()
self.assertEqual(brainstemCoordinatesFieldOut, brainstemCoordinatesField)
assertAlmostEqualList(self, [0.707016, -0.707198, 1.5], brainstemCoordinatesValueOut, delta=TOL)
# assign brainstem coordinates and check element:xi has moved
bobGroup.setMarkerMaterialCoordinates(brainstemCoordinatesField, [-0.1, -0.5, 2.2])
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = bobGroup.getMarkerMaterialCoordinates()
self.assertEqual(brainstemCoordinatesFieldOut, brainstemCoordinatesField)
assertAlmostEqualList(self, [-0.1, -0.5, 2.2], brainstemCoordinatesValueOut, delta=TOL)
elementOut, xiOut = bobGroup.getMarkerLocation()
self.assertEqual(82, elementOut.getIdentifier())
assertAlmostEqualList(self, [0.305595, 0.2, 0.485941], xiOut, delta=TOL)
# now make a marker annotation named "fred" with brainstem coordinates from the start
fredGroup = scaffoldPackage.createUserAnnotationGroup(('fred', 'FRED:1'))
# AnnotationGroup.createMarkerNode increments nextNodeIdentifier to one not used by existing node
node = fredGroup.createMarkerNode(nextNodeIdentifier, brainstemCoordinatesField, [0.5, 0.5, 4])
fredNodeIdentifier = node.getIdentifier()
self.assertEqual(nextNodeIdentifier + 1, fredNodeIdentifier)
del node
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = fredGroup.getMarkerMaterialCoordinates()
self.assertEqual(brainstemCoordinatesFieldOut, brainstemCoordinatesField)
assertAlmostEqualList(self, [0.5, 0.5, 4], brainstemCoordinatesValueOut, delta=TOL)
elementOut, xiOut = fredGroup.getMarkerLocation()
self.assertEqual(105, elementOut.getIdentifier())
assertAlmostEqualList(self, [0.346095, 1, 0.66399], xiOut, delta=TOL)
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(20, len(annotationGroups))
# test deleting a marker annotation group
scaffoldPackage.deleteAnnotationGroup(fredGroup)
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(19, len(annotationGroups))
# check node fred has gone
node = nodes.findNodeByIdentifier(fredNodeIdentifier)
self.assertFalse(node.isValid())
# re-recreate fred with just element:xi location
fredGroup = scaffoldPackage.createUserAnnotationGroup(('fred', 'FRED:1'))
element = mesh.findElementByIdentifier(105)
node = fredGroup.createMarkerNode(nextNodeIdentifier, element=element, xi=[0.346095, 1, 0.66399])
self.assertEqual(fredNodeIdentifier, node.getIdentifier())
del node
elementOut, xiOut = fredGroup.getMarkerLocation()
self.assertEqual(105, elementOut.getIdentifier())
assertAlmostEqualList(self, [0.346095, 1, 0.66399], xiOut, delta=TOL)
# check the total number of groups
annotationGroups = scaffoldPackage.getAnnotationGroups()
self.assertEqual(20, len(annotationGroups))
# test serialisation
dct = scaffoldPackage.toDict()
scaffoldType = Scaffolds().findScaffoldTypeByName(dct['scaffoldTypeName'])
scaffoldPackage2 = ScaffoldPackage(scaffoldType, dct)
region2 = context.createRegion()
fieldmodule2 = region2.getFieldmodule()
scaffoldPackage2.generate(region2)
brainstemCoordinatesField2 = fieldmodule2.findFieldByName("brainstem coordinates")
self.assertTrue(brainstemCoordinatesField2.isValid())
annotationGroups2 = scaffoldPackage2.getAnnotationGroups()
self.assertEqual(20, len(annotationGroups2))
# check user markers have been defined correctly for scaffoldPackage2
bobGroup2 = scaffoldPackage2.findAnnotationGroupByName('bob')
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = bobGroup2.getMarkerMaterialCoordinates()
self.assertEqual(brainstemCoordinatesFieldOut, brainstemCoordinatesField2)
assertAlmostEqualList(self, [-0.1, -0.5, 2.2], brainstemCoordinatesValueOut, delta=TOL)
elementOut, xiOut = bobGroup2.getMarkerLocation()
self.assertEqual(82, elementOut.getIdentifier())
assertAlmostEqualList(self, [0.305595, 0.2, 0.485941], xiOut, delta=TOL)
fredGroup2 = scaffoldPackage2.findAnnotationGroupByName('fred')
brainstemCoordinatesFieldOut, brainstemCoordinatesValueOut = fredGroup2.getMarkerMaterialCoordinates()
self.assertIsNone(brainstemCoordinatesFieldOut)
self.assertIsNone(brainstemCoordinatesValueOut)
elementOut, xiOut = fredGroup2.getMarkerLocation()
self.assertEqual(105, elementOut.getIdentifier())
assertAlmostEqualList(self, [0.346095, 1, 0.66399], xiOut, delta=TOL)