def fromDict(cls, dct, region):
'''
Instantiate from dict. See toDict()
:param region: Zinc region.
:return: AnnotationGroup
'''
assert dct['_AnnotationGroup']
name = dct['name']
ontId = dct['ontId']
dimension = dct['dimension']
identifierRangesString = dct['identifierRanges']
markerDct = dct.get('marker')
identifierRanges = identifier_ranges_from_string(
identifierRangesString)
fieldmodule = region.getFieldmodule()
with ChangeManager(fieldmodule):
annotationGroup = cls(region, (name, ontId))
annotationGroup._group.setSubelementHandlingMode(
FieldGroup.SUBELEMENT_HANDLING_MODE_FULL)
if dimension > 0:
meshGroup = annotationGroup.getMeshGroup(
fieldmodule.findMeshByDimension(dimension))
mesh_group_add_identifier_ranges(meshGroup, identifierRanges)
else:
if markerDct:
nodeIdentifier = int(identifierRanges[0][0])
annotationGroup._markerFromDict(nodeIdentifier, markerDct)
nodesetGroup = annotationGroup.getNodesetGroup(
fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES))
nodeset_group_add_identifier_ranges(nodesetGroup,
identifierRanges)
return annotationGroup
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)