def getDefaultOptions(parameterSetName='Default'):
options = {}
options['Bifurcation tree'] = ScaffoldPackage(
MeshType_1d_bifurcationtree1)
options['Number of elements around root'] = 6
options['Maximum element length'] = 0.5
return options
def Scaffolds_decodeJSON(dct):
'''
Function for passing as object_hook argument to json.loads.
Constructs scaffold objects from their JSON object encoding.
'''
if ('_ScaffoldPackage' in dct):
scaffoldType = Scaffolds().findScaffoldTypeByName(dct['scaffoldTypeName'])
#print('Scaffolds_decodeJSON scaffoldType',scaffoldType.getName(), dct)
return ScaffoldPackage(scaffoldType, dct)
return dct
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.centralPathDefaultScaffoldPackages[parameterSetName])
if optionName == 'Segment profile':
if not parameterSetName:
parameterSetName = scaffoldType.getParameterSetNames()[0]
return ScaffoldPackage(scaffoldType, defaultParameterSetName = parameterSetName)
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
def getOptionScaffoldPackage(cls,
optionName,
scaffoldType,
parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + ' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Bifurcation tree':
if not parameterSetName:
parameterSetName = MeshType_1d_bifurcationtree1.getParameterSetNames(
)[0]
return ScaffoldPackage(MeshType_1d_bifurcationtree1,
defaultParameterSetName=parameterSetName)
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
def __init__(self, context, region, generator_model, parameters, material_module, scaffold_package,
scaffold_package_class):
self._context = context
self._region = region
# self._region = self._context.createRegion()
# self._region.setName('custom_scaffold')
# self._region.readFile('D:\\sparc\\tmp\\pig_scaffold.exf')
self._generator_model = generator_model
self._material_module = material_module
self._parameters = parameters.keys()
self._coordinate_field = None
_scaffold_package = scaffold_package
_scaffold_package_class = scaffold_package_class
scaffolds = Scaffolds()
self._all_scaffold_types = scaffolds.getScaffoldTypes()
scaffold_type = None
for scaffold in self._all_scaffold_types:
if scaffold == _scaffold_package[-1].getScaffoldType():
scaffold_type = scaffold
if scaffold_type is None:
raise TypeError('Scaffold Type was not found.')
scaffold_package = ScaffoldPackage(scaffold_type)
self._parameterSetName = scaffold_type.getParameterSetNames()[0]
self._scaffold_package = scaffold_package
self._scaffold = None
self._scaffold_options = None
self._temp_region = None
self._annotation_groups = None
self._scene = None
self._scaffold_is_time_aware = None
self._scaffold_fit_parameters = None
self._initialise_surface_material()
class MeshType_3d_wholebody1(Scaffold_base):
"""
Generates body coordinates using a solid cylinder of all cube elements,
with variable numbers of elements in major, minor, shell and for each section of abdomen, thorax, neck and head.
"""
cylinder1Settings = {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 3.5,
'Number of elements': 1
}
axis1 = [0, 0, 1]
axis2 = [1, 0, 0]
axis3 = [0, 1, 0]
centralPathDefaultScaffoldPackages = {
'Default': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': cylinder1Settings,
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [
[[0.0, 0.0, 0.0], setMagnitude(axis1, cylinder1Settings['Length']), setMagnitude(axis2, 0.5), [0.0, 0.0, 0.0], setMagnitude(axis3, 0.5), [0.0, 0.0, 0.0]],
[setMagnitude(axis1, cylinder1Settings['Length']), setMagnitude(axis1, cylinder1Settings['Length']), setMagnitude(axis2, 0.5), [0.0, 0.0, 0.0], setMagnitude(axis3, 0.5), [0.0, 0.0, 0.0]]
])
})
}
@staticmethod
def getName():
return '3D Whole Body 1'
@staticmethod
def getParameterSetNames():
return [
'Default',
'Human Coarse',
'Human Fine',
'Rat Coarse',
'Rat Fine'
]
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if parameterSetName == 'Default':
parameterSetName = 'Human Coarse'
centralPathOption = cls.centralPathDefaultScaffoldPackages['Default']
options = {}
options['Base parameter set'] = parameterSetName
options['Central path'] = copy.deepcopy(centralPathOption)
options['Number of elements across major'] = 6
options['Number of elements across minor'] = 6
options['Number of elements across shell'] = 1
options['Number of elements across transition'] = 1
options['Number of elements in abdomen'] = 5
options['Number of elements in thorax'] = 3
options['Number of elements in neck'] = 1
options['Number of elements in head'] = 2
options['Shell thickness proportion'] = 0.2
options['Discontinuity on the core boundary'] = True
options['Lower half'] = False
options['Use cross derivatives'] = False
options['Refine'] = False
options['Refine number of elements across major'] = 1
options['Refine number of elements along'] = 1
if 'Coarse' in parameterSetName:
pass
if 'Fine' in parameterSetName:
options['Number of elements across major'] = 10
options['Number of elements across minor'] = 10
options['Number of elements across shell'] = 1
options['Number of elements across transition'] = 1
options['Number of elements in abdomen'] = 10
options['Number of elements in thorax'] = 6
options['Number of elements in neck'] = 2
options['Number of elements in head'] = 4
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path',
'Number of elements across major',
'Number of elements across minor',
'Number of elements across shell',
'Number of elements across transition',
'Number of elements in abdomen',
'Number of elements in thorax',
'Number of elements in neck',
'Number of elements in head',
'Shell thickness proportion',
'Discontinuity on the core boundary',
'Refine',
'Refine number of elements across major',
'Refine number of elements along'
]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [MeshType_1d_path1]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.centralPathDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage('Central path', MeshType_1d_path1)
dependentChanges = False
if options['Number of elements across major'] < 4:
options['Number of elements across major'] = 4
if options['Number of elements across major'] % 2:
options['Number of elements across major'] += 1
if options['Number of elements across minor'] != options['Number of elements across major']:
options['Number of elements across minor'] = options['Number of elements across major']
dependentChanges = True
if options['Number of elements across transition'] < 1:
options['Number of elements across transition'] = 1
Rcrit = min(options['Number of elements across major']-4, options['Number of elements across minor']-4)//2
if options['Number of elements across shell'] + options['Number of elements across transition'] - 1 > Rcrit:
dependentChanges = True
options['Number of elements across shell'] = Rcrit
options['Number of elements across transition'] = 1
if options['Shell thickness proportion'] < 0.07 or options['Shell thickness proportion'] > 0.7:
options['Shell thickness proportion'] = 2*options['Number of elements across shell']/options['Number of elements across major']
if options['Number of elements in abdomen'] < 1:
options['Number of elements in abdomen'] = 1
if options['Number of elements in head'] < 1:
options['Number of elements in head'] = 1
if options['Number of elements in neck'] < 1:
options['Number of elements in neck'] = 1
if options['Number of elements in thorax'] < 1:
options['Number of elements in thorax'] = 1
return dependentChanges
@staticmethod
def generateBaseMesh(region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: List of AnnotationGroup
"""
baseParameterSetName = options['Base parameter set']
isHuman = 'Human' in baseParameterSetName
isRat = 'Rat' in baseParameterSetName
centralPath = options['Central path']
full = not options['Lower half']
elementsCountAcrossMajor = options['Number of elements across major']
if not full:
elementsCountAcrossMajor //= 2
elementsCountAcrossMinor = options['Number of elements across minor']
elementsCountAcrossShell = options['Number of elements across shell']
elementsCountAcrossTransition = options['Number of elements across transition']
elementsCountAlongAbdomen = options['Number of elements in abdomen']
elementsCountAlongHead = options['Number of elements in head']
elementsCountAlongNeck = options['Number of elements in neck']
elementsCountAlongThorax = options['Number of elements in thorax']
shellRadiusProportion = options['Shell thickness proportion']
shellProportion = 1/(1/shellRadiusProportion-1)*(elementsCountAcrossMajor/2/elementsCountAcrossShell - 1)
discontinuity = options['Discontinuity on the core boundary']
useCrossDerivatives = options['Use cross derivatives']
elementsCountAlong = elementsCountAlongAbdomen + elementsCountAlongThorax + elementsCountAlongNeck + elementsCountAlongHead
fieldmodule = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fieldmodule)
mesh = fieldmodule.findMeshByDimension(3)
bodyGroup = AnnotationGroup(region, get_body_term("body"))
coreGroup = AnnotationGroup(region, get_body_term("core"))
non_coreGroup = AnnotationGroup(region, get_body_term("non core"))
abdomenGroup = AnnotationGroup(region, get_body_term("abdomen"))
thoraxGroup = AnnotationGroup(region, get_body_term("thorax"))
neckGroup = AnnotationGroup(region, get_body_term("neck core"))
headGroup = AnnotationGroup(region, get_body_term("head core"))
annotationGroups = [bodyGroup, coreGroup, non_coreGroup, abdomenGroup, thoraxGroup, neckGroup, headGroup]
cylinderCentralPath = CylinderCentralPath(region, centralPath, elementsCountAlong)
cylinderShape = CylinderShape.CYLINDER_SHAPE_FULL
base = CylinderEnds(elementsCountAcrossMajor, elementsCountAcrossMinor, elementsCountAcrossShell,
elementsCountAcrossTransition, shellProportion,
[0.0, 0.0, 0.0], cylinderCentralPath.alongAxis[0], cylinderCentralPath.majorAxis[0],
cylinderCentralPath.minorRadii[0])
cylinder1 = CylinderMesh(fieldmodule, coordinates, elementsCountAlong, base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath, useCrossDerivatives=False)
# body coordinates
bodyCoordinates = findOrCreateFieldCoordinates(fieldmodule, name="body coordinates")
tmp_region = region.createRegion()
tmp_fieldmodule = tmp_region.getFieldmodule()
tmp_body_coordinates = findOrCreateFieldCoordinates(tmp_fieldmodule, name="body coordinates")
tmp_cylinder = CylinderMesh(tmp_fieldmodule, tmp_body_coordinates, elementsCountAlong, base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath, useCrossDerivatives=False)
sir = tmp_region.createStreaminformationRegion()
srm = sir.createStreamresourceMemory()
tmp_region.write(sir)
result, buffer = srm.getBuffer()
sir = region.createStreaminformationRegion()
srm = sir.createStreamresourceMemoryBuffer(buffer)
region.read(sir)
del srm
del sir
del tmp_body_coordinates
del tmp_fieldmodule
del tmp_region
# Groups of different parts of the body
is_body = fieldmodule.createFieldConstant(1)
bodyMeshGroup = bodyGroup.getMeshGroup(mesh)
bodyMeshGroup.addElementsConditional(is_body)
coreMeshGroup = coreGroup.getMeshGroup(mesh)
# core group
e1a = elementsCountAcrossShell
e1z = elementsCountAcrossMinor - elementsCountAcrossShell - 1
e2a = elementsCountAcrossShell
e2b = e2a + elementsCountAcrossTransition
e2z = elementsCountAcrossMajor - elementsCountAcrossShell - 1
e2y = e2z - elementsCountAcrossTransition
e1oc = elementsCountAcrossMinor - 2*elementsCountAcrossShell - 2*elementsCountAcrossTransition
e2oc = elementsCountAcrossMajor - 2*elementsCountAcrossShell - 2*elementsCountAcrossTransition
e2oCore = e2oc * e1oc + 2 * elementsCountAcrossTransition * (e2oc + e1oc)
elementsCountAround = cylinder1.getElementsCountAround()
e2oShell = elementsCountAround * elementsCountAcrossShell
e2o = e2oCore + e2oShell
elementId = cylinder1.getElementIdentifiers()
for e3 in range(elementsCountAlong):
for e2 in range(elementsCountAcrossMajor):
for e1 in range(elementsCountAcrossMinor):
coreElement = ((e2 >= e2a) and (e2 <= e2z)) and ((e1 >= e1a) and (e1 <= e1z))
if coreElement:
elementIdentifier = elementId[e3][e2][e1]
if elementIdentifier:
element = mesh.findElementByIdentifier(elementIdentifier)
coreMeshGroup.addElement(element)
is_non_core = fieldmodule.createFieldNot(coreGroup.getGroup())
non_coreMeshGroup = non_coreGroup.getMeshGroup(mesh)
non_coreMeshGroup.addElementsConditional(is_non_core)
abdomenMeshGroup = abdomenGroup.getMeshGroup(mesh)
thoraxMeshGroup = thoraxGroup.getMeshGroup(mesh)
neckMeshGroup = neckGroup.getMeshGroup(mesh)
headMeshGroup = headGroup.getMeshGroup(mesh)
meshGroups = [abdomenMeshGroup, thoraxMeshGroup, neckMeshGroup, headMeshGroup]
abdomenRange = [1, elementsCountAlongAbdomen*e2o]
thoraxRange = [abdomenRange[1]+1, abdomenRange[1]+elementsCountAlongThorax*e2o]
neckRange = [thoraxRange[1]+1, thoraxRange[1] + elementsCountAlongNeck*e2o]
headRange = [neckRange[1]+1, elementsCountAlong*e2o]
groupsRanges = [abdomenRange, thoraxRange, neckRange, headRange]
totalElements = e2o*elementsCountAlong
for elementIdentifier in range(1, totalElements+1):
element = mesh.findElementByIdentifier(elementIdentifier)
if coreMeshGroup.containsElement(element):
ri = 0
for groupRange in groupsRanges:
if (elementIdentifier >= groupRange[0]) and (elementIdentifier <= groupRange[1]):
meshGroups[ri].addElement(element)
break
ri += 1
if discontinuity:
# create discontinuity in d3 on the core boundary
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
elementtemplate = mesh.createElementtemplate()
undefineNodetemplate = nodes.createNodetemplate()
undefineNodetemplate.undefineField(coordinates)
nodetemplate = nodes.createNodetemplate()
fieldcache = fieldmodule.createFieldcache()
with ChangeManager(fieldmodule):
localNodeIndexes = [1, 2, 3, 4]
valueLabel = Node.VALUE_LABEL_D_DS3
for e3 in range(elementsCountAlong):
for e2 in range(elementsCountAcrossMajor):
for e1 in range(elementsCountAcrossMinor):
regularRowElement = (((e2 >= e2b) and (e2 <= e2y)) and ((e1 == e1a - 1) or (e1 == e1z + 1)))
non_coreFirstLayerElement = (e2 == e2a - 1) or regularRowElement or (e2 == e2z + 1)
elementIdentifier = elementId[e3][e2][e1]
if elementIdentifier and non_coreFirstLayerElement:
element = mesh.findElementByIdentifier(elementIdentifier)
eft = element.getElementfieldtemplate(coordinates, -1)
nodeIds = get_element_node_identifiers(element, eft)
for localNodeIndex in localNodeIndexes:
node = element.getNode(eft, localNodeIndex)
nodetemplate.defineFieldFromNode(coordinates, node)
versionsCount = nodetemplate.getValueNumberOfVersions(coordinates, -1, valueLabel)
if versionsCount == 1:
fieldcache.setNode(node)
result0, x = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_VALUE, 1, 3)
result0, d1 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS1, 1, 3)
result0, d2 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS2, 1, 3)
result0, d3 = coordinates.getNodeParameters(fieldcache, -1, valueLabel, 1, 3)
result1 = node.merge(undefineNodetemplate)
result2 = nodetemplate.setValueNumberOfVersions(coordinates, -1, valueLabel, 2)
result3 = node.merge(nodetemplate)
result4 = coordinates.setNodeParameters(fieldcache, -1, Node.VALUE_LABEL_VALUE, 1, x)
result4 = coordinates.setNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS1, 1, d1)
result4 = coordinates.setNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS2, 1, d2)
result4 = coordinates.setNodeParameters(fieldcache, -1, valueLabel, 1, d3)
result5 = coordinates.setNodeParameters(fieldcache, -1, valueLabel, 2, d3)
remapEftNodeValueLabelsVersion(eft, localNodeIndexes, [valueLabel], 2)
result1 = elementtemplate.defineField(coordinates, -1, eft)
result2 = element.merge(elementtemplate)
result3 = element.setNodesByIdentifier(eft, nodeIds)
else:
fieldcache = fieldmodule.createFieldcache()
# Annotation fiducial point
markerGroup = findOrCreateFieldGroup(fieldmodule, "marker")
markerName = findOrCreateFieldStoredString(fieldmodule, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(fieldmodule, mesh, name="marker_location")
markerBodyCoordinates = findOrCreateFieldCoordinates(fieldmodule, name="marker_body_coordinates")
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
markerTemplateInternal.defineField(markerBodyCoordinates)
#
middleLeft = elementsCountAcrossMinor//2
topElem = elementsCountAcrossMajor - 1
middleRight = middleLeft - 1
neckFirstElem = elementsCountAlongAbdomen+elementsCountAlongThorax
thoraxFirstElem = elementsCountAlongAbdomen
middleDown = elementsCountAcrossMajor//2 - 1
# organ landmarks groups
apexOfHeart = heart_terms.get_heart_term('apex of heart')
leftAtriumEpicardiumVenousMidpoint = heart_terms.get_heart_term('left atrium epicardium venous midpoint')
rightAtriumEpicardiumVenousMidpoint = heart_terms.get_heart_term('right atrium epicardium venous midpoint')
apexOfUrinaryBladder = bladder_terms.get_bladder_term('apex of urinary bladder')
leftUreterJunctionWithBladder = bladder_terms.get_bladder_term('left ureter junction with bladder')
rightUreterJunctionWithBladder = bladder_terms.get_bladder_term('right ureter junction with bladder')
urethraJunctionWithBladderDorsal = bladder_terms.get_bladder_term('urethra junction of dorsal bladder neck')
urethraJunctionWithBladderVentral = bladder_terms.get_bladder_term('urethra junction of ventral bladder neck')
gastroesophagalJunctionOnLesserCurvature = stomach_terms.get_stomach_term('esophagogastric junction along the lesser curvature on serosa')
limitingRidgeOnGreaterCurvature = stomach_terms.get_stomach_term('limiting ridge at the greater curvature on serosa')
pylorusOnGreaterCurvature = stomach_terms.get_stomach_term('gastroduodenal junction along the greater curvature on serosa')
junctionBetweenFundusAndBodyOnGreaterCurvature = stomach_terms.get_stomach_term("fundus-body junction along the greater curvature on serosa")
apexOfLeftLung = lung_terms.get_lung_term('apex of left lung')
ventralBaseOfLeftLung = lung_terms.get_lung_term('ventral base of left lung')
dorsalBaseOfLeftLung = lung_terms.get_lung_term('dorsal base of left lung')
apexOfRightLung = lung_terms.get_lung_term('apex of right lung')
ventralBaseOfRightLung = lung_terms.get_lung_term('ventral base of right lung')
dorsalBaseOfRightLung = lung_terms.get_lung_term('dorsal base of right lung')
laterodorsalTipOfMiddleLobeOfRightLung = lung_terms.get_lung_term('laterodorsal tip of middle lobe of right lung')
apexOfRightLungAccessoryLobe = lung_terms.get_lung_term('apex of right lung accessory lobe')
ventralBaseOfRightLungAccessoryLobe = lung_terms.get_lung_term('ventral base of right lung accessory lobe')
dorsalBaseOfRightLungAccessoryLobe = lung_terms.get_lung_term('dorsal base of right lung accessory lobe')
medialBaseOfLeftLung = lung_terms.get_lung_term("medial base of left lung")
medialBaseOfRightLung = lung_terms.get_lung_term("medial base of right lung")
brainstemDorsalMidlineCaudalPoint = brainstem_terms.get_brainstem_term('brainstem dorsal midline caudal point')
brainstemDorsalMidlineCranialPoint = brainstem_terms.get_brainstem_term('brainstem dorsal midline cranial point')
brainstemVentralMidlineCaudalPoint = brainstem_terms.get_brainstem_term('brainstem ventral midline caudal point')
brainstemVentralMidlineCranialPoint = brainstem_terms.get_brainstem_term('brainstem ventral midline cranial point')
# marker coordinates. In future we want to have only one table for all species.
if isRat:
bodyMarkerPoints = [
{"group": ("left hip joint", ''), "x": [0.367, 0.266, 0.477]},
{"group": ("right hip joint", ''), "x": [-0.367, 0.266, 0.477]},
{"group": ("left shoulder joint", ''), "x": [0.456, -0.071, 2.705]},
{"group": ("right shoulder joint", ''), "x": [-0.456, -0.071, 2.705]},
{"group": ("along left femur", ''), "x": [0.456, 0.07, 0.633]},
{"group": ("along right femur", ''), "x": [-0.456, 0.07, 0.633]},
{"group": ("along left humerus", ''), "x": [0.423, -0.173, 2.545]},
{"group": ("along right humerus", ''), "x": [-0.423, -0.173, 2.545]},
{"group": apexOfUrinaryBladder, "x": [-0.124, -0.383, 0.434]},
{"group": leftUreterJunctionWithBladder, "x": [-0.111, -0.172, 0.354]},
{"group": rightUreterJunctionWithBladder, "x": [-0.03, -0.196, 0.363]},
{"group": urethraJunctionWithBladderDorsal, "x": [-0.03, -0.26, 0.209]},
{"group": urethraJunctionWithBladderVentral, "x": [-0.037, -0.304, 0.203]},
{"group": brainstemDorsalMidlineCaudalPoint, "x": [-0.032, 0.418, 2.713]},
{"group": brainstemDorsalMidlineCranialPoint, "x": [-0.017, 0.203, 2.941]},
{"group": brainstemVentralMidlineCaudalPoint, "x": [-0.028, 0.388, 2.72]},
{"group": brainstemVentralMidlineCranialPoint, "x": [-0.019, 0.167, 2.95]},
{"group": apexOfHeart, "x": [0.096, -0.128, 1.601]},
{"group": leftAtriumEpicardiumVenousMidpoint, "x": [0.127, -0.083, 2.079]},
{"group": rightAtriumEpicardiumVenousMidpoint, "x": [0.039, -0.082, 2.075]},
{"group": apexOfLeftLung, "x": [0.172, -0.175, 2.337]},
{"group": ventralBaseOfLeftLung, "x": [0.274, -0.285, 1.602]},
{"group": dorsalBaseOfLeftLung, "x": [0.037, 0.31, 1.649]},
{"group": apexOfRightLung, "x": [-0.086, -0.096, 2.311]},
{"group": ventralBaseOfRightLung, "x": [0.14, -0.357, 1.662]},
{"group": dorsalBaseOfRightLung, "x": [-0.054, 0.304, 1.667]},
{"group": laterodorsalTipOfMiddleLobeOfRightLung, "x": [-0.258, -0.173, 2.013]},
{"group": apexOfRightLungAccessoryLobe, "x": [0.041, -0.063, 1.965]},
{"group": ventralBaseOfRightLungAccessoryLobe, "x": [0.143, -0.356, 1.66]},
{"group": dorsalBaseOfRightLungAccessoryLobe, "x": [0.121, -0.067, 1.627]},
{"group": gastroesophagalJunctionOnLesserCurvature, "x": [0.12, 0.009, 1.446]},
{"group": limitingRidgeOnGreaterCurvature, "x": [0.318, 0.097, 1.406]},
{"group": pylorusOnGreaterCurvature, "x": [0.08, -0.111, 1.443]},
]
elif isHuman:
bodyMarkerPoints = [
{"group": urethraJunctionWithBladderDorsal, "x": [-0.0071, -0.2439, 0.1798]},
{"group": urethraJunctionWithBladderVentral, "x": [-0.007, -0.2528, 0.1732]},
{"group": leftUreterJunctionWithBladder, "x": [0.1074, 0.045, 0.1728]},
{"group": rightUreterJunctionWithBladder, "x": [-0.1058, 0.0533, 0.1701]},
{"group": apexOfUrinaryBladder, "x": [0.005, 0.1286, 0.1264]},
{"group": brainstemDorsalMidlineCaudalPoint, "x": [0.0068, 0.427, 2.7389]},
{"group": brainstemDorsalMidlineCranialPoint, "x": [0.008, -0.0231, 3.0778]},
{"group": brainstemVentralMidlineCaudalPoint, "x": [0.0054, 0.3041, 2.7374]},
{"group": brainstemVentralMidlineCranialPoint, "x": [0.0025, -0.2308, 3.091]},
{"group": apexOfHeart, "x": [0.1373, -0.1855, 1.421]},
{"group": leftAtriumEpicardiumVenousMidpoint, "x": [0.0024, 0.1452, 1.8022]},
{"group": rightAtriumEpicardiumVenousMidpoint, "x": [-0.0464, 0.0373, 1.7491]},
{"group": apexOfLeftLung, "x": [0.0655, -0.0873, 2.3564]},
{"group": apexOfRightLung, "x": [-0.088, -0.0363, 2.3518]},
{"group": laterodorsalTipOfMiddleLobeOfRightLung, "x": [-0.2838, -0.0933, 1.9962]},
{"group": ventralBaseOfLeftLung, "x": [0.219, -0.2866, 1.4602]},
{"group": medialBaseOfLeftLung, "x": [0.0426, -0.0201, 1.4109]},
{"group": ventralBaseOfRightLung, "x": [-0.2302, -0.2356, 1.3926]},
{"group": medialBaseOfRightLung, "x": [-0.0363, 0.0589, 1.3984]},
{"group": dorsalBaseOfLeftLung, "x": [0.1544, 0.2603, 1.3691]},
{"group": dorsalBaseOfRightLung, "x": [0.0369, -0.2524, 0.912]},
{"group": gastroesophagalJunctionOnLesserCurvature, "x": [-0.0062, -0.3259, 0.8586]},
{"group": pylorusOnGreaterCurvature, "x": [-0.0761, -0.3189, 0.8663]},
{"group": junctionBetweenFundusAndBodyOnGreaterCurvature, "x": [0.1884, -0.1839, 0.9639]},
]
nodeIdentifier = cylinder1._endNodeIdentifier
findMarkerLocation = fieldmodule.createFieldFindMeshLocation(markerBodyCoordinates, bodyCoordinates, mesh)
findMarkerLocation.setSearchMode(FieldFindMeshLocation.SEARCH_MODE_EXACT)
for bodyMarkerPoint in bodyMarkerPoints:
markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
fieldcache.setNode(markerPoint)
markerBodyCoordinates.assignReal(fieldcache, bodyMarkerPoint["x"])
markerName.assignString(fieldcache, bodyMarkerPoint["group"][0])
element, xi = findMarkerLocation.evaluateMeshLocation(fieldcache, 3)
markerLocation.assignMeshLocation(fieldcache, element, xi)
nodeIdentifier += 1
return annotationGroups
@classmethod
def refineMesh(cls, meshRefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshRefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
assert isinstance(meshRefinement, MeshRefinement)
refineElementsCountAcrossMajor = options['Refine number of elements across major']
refineElementsCountAlong = options['Refine number of elements along']
meshRefinement.refineAllElementsCubeStandard3d(refineElementsCountAcrossMajor, refineElementsCountAlong, refineElementsCountAcrossMajor)
@classmethod
def defineFaceAnnotations(cls, region, options, annotationGroups):
"""
Add face annotation groups from the highest dimension mesh.
Must have defined faces and added subelements for highest dimension groups.
:param region: Zinc region containing model.
:param options: Dict containing options. See getDefaultOptions().
:param annotationGroups: List of annotation groups for top-level elements.
New face annotation groups are appended to this list.
"""
# create 2d surface mesh groups
fm = region.getFieldmodule()
mesh2d = fm.findMeshByDimension(2)
bodyGroup = getAnnotationGroupForTerm(annotationGroups, get_body_term("body"))
coreGroup = getAnnotationGroupForTerm(annotationGroups, get_body_term("core"))
non_coreGroup = getAnnotationGroupForTerm(annotationGroups, get_body_term("non core"))
abdomenGroup = getAnnotationGroupForTerm(annotationGroups, get_body_term("abdomen"))
thoraxGroup = getAnnotationGroupForTerm(annotationGroups, get_body_term("thorax"))
neckGroup = getAnnotationGroupForTerm(annotationGroups, get_body_term("neck core"))
skinGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_body_term("skin epidermis"))
coreBoundaryGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_body_term("core boundary"))
diaphragmGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_body_term("diaphragm"))
spinalCordGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_body_term("spinal cord"))
is_exterior = fm.createFieldIsExterior()
is_on_face_xi3_1 = fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1)
is_skin = fm.createFieldAnd(is_exterior, is_on_face_xi3_1)
skinMeshGroup = skinGroup.getMeshGroup(mesh2d)
skinMeshGroup.addElementsConditional(is_skin)
is_core_boundary = fm.createFieldAnd(coreGroup.getGroup(), non_coreGroup.getGroup())
coreBoundaryMeshGroup = coreBoundaryGroup.getMeshGroup(mesh2d)
coreBoundaryMeshGroup.addElementsConditional(is_core_boundary)
is_diaphragm = fm.createFieldAnd(abdomenGroup.getGroup(), thoraxGroup.getGroup())
diaphragmMeshGroup = diaphragmGroup.getMeshGroup(mesh2d)
diaphragmMeshGroup.addElementsConditional(is_diaphragm)
# spinal cord
coordinates = fm.findFieldByName('coordinates').castFiniteElement()
zero = fm.createFieldConstant(0)
zero_m = fm.createFieldConstant(-0.01)
zero_p = fm.createFieldConstant(0.01)
comp2 = cls.axis2.index(max(cls.axis2)) + 1
ax2_comp = fm.createFieldComponent(coordinates, comp2)
ax2_gt_zero_m = fm.createFieldGreaterThan(ax2_comp, zero_m)
ax2_lt_zero_p = fm.createFieldLessThan(ax2_comp, zero_p)
ax2_gt_zero_xi10 = fm.createFieldAnd(fm.createFieldIsOnFace(Element.FACE_TYPE_XI1_0), ax2_gt_zero_m)
ax2_lt_zero_xi10 = fm.createFieldAnd(fm.createFieldIsOnFace(Element.FACE_TYPE_XI1_0), ax2_lt_zero_p)
is_ax2_zero = fm.createFieldAnd(ax2_lt_zero_xi10, ax2_gt_zero_xi10)
comp3 = cls.axis3.index(max(cls.axis3)) + 1
ax3_comp = fm.createFieldComponent(coordinates, comp3)
ax3_positive = fm.createFieldGreaterThan(ax3_comp, zero)
is_ax2_zero_ax3_positive = fm.createFieldAnd(is_ax2_zero, ax3_positive)
is_abdomen_thorax = fm.createFieldAdd(abdomenGroup.getGroup(), thoraxGroup.getGroup())
is_abdomen_thorax_neck = fm.createFieldAdd(is_abdomen_thorax, neckGroup.getGroup())
is_abdomen_thorax_neck_boundary = fm.createFieldAnd(is_core_boundary, is_abdomen_thorax_neck)
is_spinal_cord = fm.createFieldAnd(is_ax2_zero_ax3_positive, is_abdomen_thorax_neck_boundary)
mesh1d = fm.findMeshByDimension(1)
spinalCordMeshGroup = spinalCordGroup.getMeshGroup(mesh1d)
spinalCordMeshGroup.addElementsConditional(is_spinal_cord)
class MeshType_3d_colon1(Scaffold_base):
'''
Generates a 3-D colon mesh with variable numbers
of elements around, along the central line, and through wall.
The colon is created by a function that generates a colon
segment and uses tubemesh to map the segment along a central
line profile.
'''
centralPathDefaultScaffoldPackages = {
'Human 1' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 8
},
'meshEdits' : exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ 0.0, 0.0, 0.0 ], [ -50.7, 178.2, 0.0 ], [ -24.0, -6.0, -12.0 ], [ -14.0, -1.0, -12.0 ] ],
[ [ -47.4, 188.6, 0.0 ], [ -19.3, 177.1, 0.0 ], [ -22.0, -4.0, -8.0 ], [ -4.0, 19.0, 22.0 ] ],
[ [ -4.4, 396.5, 0.0 ], [ 206.0, 40.1, 0.0 ], [ -10.0, 20.0, 8.0 ], [ -6.0, 0.0, 51.0 ] ],
[ [ 130.0, 384.1, 0.0 ], [ 130.8, -40.5, 0.0 ], [ -5.0, 4.0, 29.0 ], [ 0.0, 1.0, 24.0 ] ],
[ [ 279.4, 383.0, 0.0 ], [ 118.0, 48.7, 0.0 ], [ -2.0, 10.0, 22.0 ], [ 5.0, 25.0, -20.0 ] ],
[ [ 443.9, 390.8, 0.0 ], [ 111.3, -97.0, 0.0 ], [ 10.0, 17.0, 6.0 ], [ 1.0, -6.0, -35.0 ] ],
[ [ 475.2, 168.0, 0.0 ], [ -0.8, -112.4, 0.0 ], [ 20.0, 0.0, -20.0 ], [ 15.0, -1.0, -10.0 ] ],
[ [ 432.6, -32.3, 0.0 ], [ -90.5, -59.0, 0.0 ], [ 6.0, -9.0, -14.0 ], [ 8.0, -11.0, -13.0 ] ],
[ [ 272.4, 7.5, 0.0 ], [ -79.0, 47.4, 0.0 ], [ 1.0, -11.0, -18.0 ], [ 4.0, -12.0, -12.0 ] ] ] )
} ),
'Human 2' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 8
},
'meshEdits' : exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ 0.0, 0.0, 0.0 ], [ -34.7, 104.1, -18.1 ], [ -24.0, -6.0, -12.0 ], [ -14.0, -1.0, -12.0 ] ],
[ [ -34.5, 114.0, -18.1 ], [ 1.2, 86.6, -3.4 ], [ -22.0, -4.0, -8.0 ], [ -4.0, 19.0, 22.0 ] ],
[ [ -19.1, 218.5, 5.5 ], [ 78.7, -7.1, 94.5 ], [ -10.0, 20.0, 8.0 ], [ -6.0, 0.0, 51.0 ] ],
[ [ 82.5, 189.1, 94.2 ], [ 84.5, 7.1, 71.6 ], [ -5.0, 4.0, 29.0 ], [ 0.0, 1.0, 24.0 ] ],
[ [ 226.6, 218.7, 85.7 ], [ 95.0, 91.3, -58.5 ], [ -2.0, 10.0, 22.0 ], [ 5.0, 25.0, -20.0 ] ],
[ [ 325.5, 381.7, -57.9 ], [ 229.2, -66.7, -20.4 ], [ 10.0, 17.0, 6.0 ], [ 1.0, -6.0, -35.0 ] ],
[ [ 354.0, 105.3, -24.4 ], [ -6.3, -143.7, 20.3 ], [ 20.0, 0.0, -20.0 ], [ 15.0, -1.0, -10.0 ] ],
[ [ 296.5, -121.2, -0.6 ], [ -90.5, -59.0, 0.0 ], [ 6.0, -9.0, -14.0 ], [ 8.0, -11.0, -13.0 ] ],
[ [ 169.8, -73.4, -33.5 ], [ -72.2, 43.4, -27.4 ], [ 1.0, -11.0, -18.0 ], [ 4.0, -12.0, -12.0 ] ] ] )
} ),
'Mouse 1' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 7
},
'meshEdits' : exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ 0.0, 0.0, 0.0 ], [ 6.0, 12.0, -2.0 ], [ 2.0, 1.0, 2.0 ], [ 6.0, 0.0, 3.0 ] ],
[ [ -2.0, 11.0, -3.0 ], [ -8.0, 4.0, 9.0 ], [ 2.0, 2.0, 1.0 ], [ 0.0, 1.0, 2.0 ] ],
[ [ -3.0, 2.0, 3.0 ], [ -4.0, -8.0, 0.0 ], [ 2.0, -1.0, 2.0 ], [ 1.0, 0.0, 2.0 ] ],
[ [ -11.0, -3.0, -4.0 ], [ -8.0, -3.0, -7.0 ], [ 1.0, -2.0, 1.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -16.0, -4.0, 0.0 ], [ 4.0, -3.0, 14.0 ], [ 1.0, -3.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -7.0, -8.0, 0.0 ], [ 5.0, -1.0, -14.0 ], [ 0.0, -3.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -1.0, -6.0, -1.0 ], [ 2.0, -2.0, 9.0 ], [ 1.0, -3.0, -1.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -2.0, -14.0, 5.0 ], [ -2.0, -4.0, 2.0 ], [ 1.0, -2.0, -2.0 ], [ 0.0, 0.0, 0.5 ] ] ] )
} ),
'Mouse 2' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 4
},
'meshEdits' : exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 13.0 ], [ 0.0, -10.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 0.0, 0.0, 13.0 ], [ 0.0, 2.0, 28.0 ], [ 0.0, -10.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -14.0, -2.0, 13.0 ], [ 0.0, -3.0, -19.0 ], [ 0.0, -10.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -14.0, -1.0, -10.0 ], [ 1.0, 1.0, -17.0 ], [ 0.0, -10.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -14.0, 0.0, -28.0 ], [ 0.0, 0.0, -11.0 ], [ 0.0, -10.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ] ] )
} ),
'Pig 1' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 36
},
'meshEdits' : exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ -7.2, 83.3, -20.7 ], [ -65.2, -8.1, 7.6 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -68.5, 52.8, -9.6 ], [ -40.1, -36.1, 10.7 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -97.4, -26.3, 5.7 ], [ 18.0, -93.2, 13.7 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -56.8, -90.5, 14.1 ], [ 65.5, -41.4, 7.3 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 48.9, -100.8, 24.0 ], [ 112.2, 40.1, 19.0 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 114.8, -12.6, 38.7 ], [ 8.2, 96.1, 14.2 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 60.3, 83.5, 43.7 ], [ -108.7, 54.1, 22.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -41.2, 90.7, 56.3 ], [ -89.0, -32.4, 14.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -107.9, -9.7, 76.6 ], [ 11.1, -94.4, 11.3 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -57.3, -91.9, 81.3 ], [ 71.2, -31.2, 5.7 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 51.2, -89.4, 97.2 ], [ 99.1, 55.4, 12.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 91.6, 9.3, 103.6 ], [ 4.7, 51.2, 3.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 61.6, 111.8, 109.6 ], [ -85.2, 46.1, 2.6 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -54.6, 91.9, 129.4 ], [ -92.7, -55.0, 14.5 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -109.0, 5.6, 156.9 ], [ 23.6, -108.2, 27.7 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -59.1, -62.5, 170.8 ], [ 74.0, -20.1, 14.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 23.5, -53.2, 179.7 ], [ 84.6, 47.0, 6.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 62.3, 30.1, 187.5 ], [ -12.8, 58.0, 0.8 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 22.4, 45.2, 181.1 ], [ -23.6, -34.5, -7.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -1.9, 4.9, 180.5 ], [ -41.3, -30.9, 7.5 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -45.1, -12.6, 194.4 ], [ -40.5, -4.6, 6.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -71.7, -2.2, 197.2 ], [ -25.2, 35.8, -6.8 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -65.8, 42.1, 182.3 ], [ 26.6, 37.6, -15.6 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -14.1, 81.2, 163.5 ], [ 41.0, 10.3, -9.5 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 61.7, 86.1, 156.4 ], [ 77.9, -40.7, 8.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 92.9, 20.5, 150.3 ], [ 0.0, -73.3, -5.2 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 48.9, -65.0, 142.8 ], [ -82.8, -80.0, -1.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -54.3, -90.8, 134.0 ], [ -60.1, 26.4, -8.2 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -89.9, 11.2, 115.0 ], [ 34.9, 125.1, -27.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -17.4, 74.2, 91.1 ], [ 78.8, 19.1, -15.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 43.4, 50.2, 73.3 ], [ 30.2, -36.0, -9.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 62.4, -5.1, 63.5 ], [ 10.9, -54.2, -2.7 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 32.7, -51.7, 56.1 ], [ -38.6, -29.8, -8.1 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -38.1, -28.6, 46.8 ], [ -66.0, 83.3, -12.1 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -5.4, 32.0, 26.0 ], [ 48.1, 17.6, -21.4 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 146.6, 101.2, -41.2 ], [ 63.3, 35.3, -31.2 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ 312.3, 199.5, -123.4 ], [ 39.7, 24.3, -20.0 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ] ] )
} ),
'Pig 2': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 90.0,
'Number of elements': 3
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
[ [ 0.0, 0.0, 0.0 ], [ 30.0, 0.0, 0.0 ], [ 0.0, 1.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ],
[ [ 30.0, 0.0, 0.0 ], [ 30.0, 0.0, 0.0 ], [ 0.0, 1.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ],
[ [ 60.0, 0.0, 0.0 ], [ 30.0, 0.0, 0.0 ], [ 0.0, 1.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ],
[ [ 90.0, 0.0, 0.0 ], [ 30.0, 0.0, 0.0 ], [ 0.0, 1.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ] ] )
} ),
}
@staticmethod
def getName():
return '3D Colon 1'
@staticmethod
def getParameterSetNames():
return [
'Default',
'Human 1',
'Human 2',
'Mouse 1',
'Mouse 2',
'Pig 1',
'Pig 2']
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if 'Human 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 2']
elif 'Mouse 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Mouse 1']
elif 'Mouse 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Mouse 2']
elif 'Pig 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 1']
elif 'Pig 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 2']
else:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 1']
if 'Mouse' in parameterSetName:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName = 'Mouse 1')
elif 'Pig' in parameterSetName:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName = 'Pig 1')
else:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName = 'Human 1')
options = {
'Central path' : copy.deepcopy(centralPathOption),
'Segment profile' : segmentProfileOption,
'Number of segments': 30,
'Start phase': 0.0,
'Proximal length': 420.0,
'Transverse length': 460.0,
'Distal length': 620.0,
'Proximal inner radius': 43.5,
'Proximal tenia coli width': 10.0,
'Proximal-transverse inner radius': 33.0,
'Proximal-transverse tenia coli width': 10.0,
'Transverse-distal inner radius': 29.0,
'Transverse-distal tenia coli width': 10.0,
'Distal inner radius': 31.5,
'Distal tenia coli width': 10.0,
'Refine' : False,
'Refine number of elements around' : 1,
'Refine number of elements along' : 1,
'Refine number of elements through wall' : 1
}
if 'Human 2' in parameterSetName:
options['Proximal length'] = 180.0
options['Transverse length'] = 620.0
options['Distal length'] = 700.0
elif 'Mouse' in parameterSetName:
options['Number of segments'] = 10
options['Proximal length'] = 30.0
options['Transverse length'] = 20.0
options['Distal length'] = 25.0
options['Proximal inner radius'] = 1.0
options['Proximal tenia coli width'] = 0.5
options['Proximal-transverse inner radius'] = 0.9
options['Proximal-transverse tenia coli width'] = 0.7
options['Transverse-distal inner radius'] = 0.7
options['Transverse-distal tenia coli width'] = 1.0
options['Distal inner radius'] = 0.7
options['Distal tenia coli width'] = 1.0
elif 'Pig 1' in parameterSetName:
options['Number of segments'] = 120
options['Proximal length'] = 3000.0
options['Transverse length'] = 200.0
options['Distal length'] = 200.0
options['Proximal inner radius'] = 38.0
options['Proximal tenia coli width'] = 5.0
options['Proximal-transverse inner radius'] = 14.0
options['Proximal-transverse tenia coli width'] = 4.0
options['Transverse-distal inner radius'] = 10.5
options['Transverse-distal tenia coli width'] = 3.0
options['Distal inner radius'] = 8.0
options['Distal tenia coli width'] = 1.5
elif 'Pig 2' in parameterSetName:
options['Number of segments'] = 3
options['Proximal length'] = 30.0
options['Transverse length'] = 30.0
options['Distal length'] = 30.0
options['Proximal inner radius'] = 16.0
options['Proximal tenia coli width'] = 5.0
options['Proximal-transverse inner radius'] = 16.0
options['Proximal-transverse tenia coli width'] = 5.0
options['Transverse-distal inner radius'] = 16.0
options['Transverse-distal tenia coli width'] = 5.0
options['Distal inner radius'] = 16.0
options['Distal tenia coli width'] = 5.0
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path',
'Segment profile',
'Number of segments',
'Start phase',
'Proximal length',
'Transverse length',
'Distal length',
'Proximal inner radius',
'Proximal tenia coli width',
'Proximal-transverse inner radius',
'Proximal-transverse tenia coli width',
'Transverse-distal inner radius',
'Transverse-distal tenia coli width',
'Distal inner radius',
'Distal tenia coli width',
'Refine',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall' ]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [ MeshType_1d_path1 ]
if optionName == 'Segment profile':
return [ MeshType_3d_colonsegment1 ]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.centralPathDefaultScaffoldPackages[parameterSetName])
if optionName == 'Segment profile':
if not parameterSetName:
parameterSetName = scaffoldType.getParameterSetNames()[0]
return ScaffoldPackage(scaffoldType, defaultParameterSetName = parameterSetName)
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage('Central path', MeshType_1d_path1)
if not options['Segment profile'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Segment profile'):
options['Segment profile'] = cls.getOptionScaffoldPackage('Segment profile', MeshType_3d_colonsegment1)
for key in [
'Number of segments',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall']:
if options[key] < 1:
options[key] = 1
for key in [
'Proximal length',
'Transverse length',
'Distal length',
'Proximal inner radius',
'Proximal tenia coli width',
'Proximal-transverse inner radius',
'Proximal-transverse tenia coli width',
'Transverse-distal inner radius',
'Transverse-distal tenia coli width',
'Distal inner radius',
'Distal tenia coli width']:
if options[key] < 0.0:
options[key] = 0.0
@classmethod
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: annotationGroups
"""
centralPath = options['Central path']
segmentProfile = options['Segment profile']
segmentCount = options['Number of segments']
startPhase = options['Start phase'] % 360.0
proximalLength = options['Proximal length']
transverseLength = options['Transverse length']
proximalInnerRadius = options['Proximal inner radius']
proximalTCWidth = options['Proximal tenia coli width']
proximalTransverseInnerRadius = options['Proximal-transverse inner radius']
proximalTransverseTCWidth = options['Proximal-transverse tenia coli width']
transverseDistalInnerRadius = options['Transverse-distal inner radius']
transverseDistalTCWidth = options['Transverse-distal tenia coli width']
distalInnerRadius = options['Distal inner radius']
distalTCWidth = options['Distal tenia coli width']
segmentSettings = segmentProfile.getScaffoldSettings()
elementsCountAroundTC = segmentSettings['Number of elements around tenia coli']
elementsCountAroundHaustrum = segmentSettings['Number of elements around haustrum']
cornerInnerRadiusFactor = segmentSettings['Corner inner radius factor']
haustrumInnerRadiusFactor = segmentSettings['Haustrum inner radius factor']
segmentLengthEndDerivativeFactor = segmentSettings['Segment length end derivative factor']
segmentLengthMidDerivativeFactor = segmentSettings['Segment length mid derivative factor']
tcCount = segmentSettings['Number of tenia coli']
tcThickness = segmentSettings['Tenia coli thickness']
elementsCountAround = (elementsCountAroundTC + elementsCountAroundHaustrum)*tcCount
elementsCountAlongSegment = segmentSettings['Number of elements along segment']
elementsCountThroughWall = segmentSettings['Number of elements through wall']
wallThickness = segmentSettings['Wall thickness']
useCrossDerivatives = segmentSettings['Use cross derivatives']
useCubicHermiteThroughWall = not(segmentSettings['Use linear through wall'])
elementsCountAlong = int(elementsCountAlongSegment*segmentCount)
firstNodeIdentifier = 1
firstElementIdentifier = 1
# Central path
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cx, cd1, cd2, cd12 = extractPathParametersFromRegion(tmpRegion)
# for i in range(len(cx)):
# print(i, '[', cx[i], ',', cd1[i], ',', cd2[i], ',', cd12[i], '],')
del tmpRegion
# find arclength of colon
length = 0.0
elementsCountIn = len(cx) - 1
sd1 = interp.smoothCubicHermiteDerivativesLine(cx, cd1, fixAllDirections = True,
magnitudeScalingMode = interp.DerivativeScalingMode.HARMONIC_MEAN)
for e in range(elementsCountIn):
arcLength = interp.getCubicHermiteArcLength(cx[e], sd1[e], cx[e + 1], sd1[e + 1])
# print(e+1, arcLength)
length += arcLength
segmentLength = length / segmentCount
# print('Length = ', length)
elementAlongLength = length / elementsCountAlong
# Sample central path
sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(cx, cd1, elementsCountAlong)
sd2, sd12 = interp.interpolateSampleCubicHermite(cd2, cd12, se, sxi, ssf)
# Generate variation of radius & tc width along length
lengthList = [0.0, proximalLength, proximalLength + transverseLength, length]
innerRadiusList = [proximalInnerRadius, proximalTransverseInnerRadius,
transverseDistalInnerRadius, distalInnerRadius]
innerRadiusAlongElementList, dInnerRadiusAlongElementList = interp.sampleParameterAlongLine(lengthList,
innerRadiusList,
elementsCountAlong)
tcWidthList = [proximalTCWidth, proximalTransverseTCWidth, transverseDistalTCWidth, distalTCWidth]
tcWidthAlongElementList, dTCWidthAlongElementList = interp.sampleParameterAlongLine(lengthList,
tcWidthList,
elementsCountAlong)
# Account for reduced haustrum appearance in transverse and distal pig colon
if tcCount == 2:
haustrumInnerRadiusFactorList = [haustrumInnerRadiusFactor, haustrumInnerRadiusFactor*0.75,
haustrumInnerRadiusFactor*0.5, haustrumInnerRadiusFactor*0.2]
haustrumInnerRadiusFactorAlongElementList = \
interp.sampleParameterAlongLine(lengthList, haustrumInnerRadiusFactorList, elementsCountAlong)[0]
else:
haustrumInnerRadiusFactorAlongElementList = [haustrumInnerRadiusFactor]*(elementsCountAlong+1)
# Create annotation groups for colon sections
elementsAlongInProximal = round(proximalLength/elementAlongLength)
elementsAlongInTransverse = round(transverseLength/elementAlongLength)
elementsAlongInDistal = elementsCountAlong - elementsAlongInProximal - elementsAlongInTransverse
elementsCountAlongGroups = [elementsAlongInProximal, elementsAlongInTransverse, elementsAlongInDistal]
colonGroup = AnnotationGroup(region, get_colon_term("colon"))
if tcCount == 1:
proximalGroup = AnnotationGroup(region, get_colon_term("proximal colon"))
transverseGroup = AnnotationGroup(region, get_colon_term("transverse colon"))
distalGroup = AnnotationGroup(region, get_colon_term("distal colon"))
annotationGroupAlong = [[colonGroup, proximalGroup],
[colonGroup, transverseGroup],
[colonGroup, distalGroup]]
elif tcCount == 2:
spiralGroup = AnnotationGroup(region, get_colon_term("spiral colon"))
transverseGroup = AnnotationGroup(region, get_colon_term("transverse colon"))
distalGroup = AnnotationGroup(region, get_colon_term("distal colon"))
annotationGroupAlong = [[colonGroup, spiralGroup],
[colonGroup, transverseGroup],
[colonGroup, distalGroup]]
elif tcCount == 3:
ascendingGroup = AnnotationGroup(region, get_colon_term("ascending colon"))
transverseGroup = AnnotationGroup(region, get_colon_term("transverse colon"))
descendingGroup = AnnotationGroup(region, get_colon_term("descending colon"))
annotationGroupAlong = [[colonGroup, ascendingGroup],
[colonGroup, transverseGroup],
[colonGroup, descendingGroup]]
annotationGroupsAlong = []
for i in range(len(elementsCountAlongGroups)):
elementsCount = elementsCountAlongGroups[i]
for n in range(elementsCount):
annotationGroupsAlong.append(annotationGroupAlong[i])
annotationGroupsThroughWall = []
for i in range(elementsCountThroughWall):
annotationGroupsThroughWall.append([ ])
xExtrude = []
d1Extrude = []
d2Extrude = []
d3UnitExtrude = []
sxRefExtrudeList = []
# Create object
colonSegmentTubeMeshInnerPoints = ColonSegmentTubeMeshInnerPoints(
region, elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlongSegment,
tcCount, segmentLengthEndDerivativeFactor, segmentLengthMidDerivativeFactor,
segmentLength, wallThickness, cornerInnerRadiusFactor, haustrumInnerRadiusFactorAlongElementList,
innerRadiusAlongElementList, dInnerRadiusAlongElementList, tcWidthAlongElementList,
startPhase)
for nSegment in range(segmentCount):
# Create inner points
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, annotationGroupsAround \
= colonSegmentTubeMeshInnerPoints.getColonSegmentTubeMeshInnerPoints(nSegment)
# Project reference point for warping onto central path
start = nSegment * elementsCountAlongSegment
end = (nSegment + 1) * elementsCountAlongSegment + 1
sxRefList, sd1RefList, sd2ProjectedListRef, zRefList = \
tubemesh.getPlaneProjectionOnCentralPath(xInner, elementsCountAround, elementsCountAlongSegment,
segmentLength, sx[start:end], sd1[start:end], sd2[start:end],
sd12[start:end])
# Warp segment points
xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList = tubemesh.warpSegmentPoints(
xInner, d1Inner, d2Inner, segmentAxis, sxRefList, sd1RefList, sd2ProjectedListRef,
elementsCountAround, elementsCountAlongSegment, zRefList, innerRadiusAlongElementList[start:end],
closedProximalEnd=False)
# Store points along length
xExtrude += xWarpedList if nSegment == 0 else xWarpedList[elementsCountAround:]
d1Extrude += d1WarpedList if nSegment == 0 else d1WarpedList[elementsCountAround:]
d2Extrude += d2WarpedList if nSegment == 0 else d2WarpedList[elementsCountAround:]
d3UnitExtrude += d3WarpedUnitList if nSegment == 0 else d3WarpedUnitList[elementsCountAround:]
sxRefExtrudeList += sxRefList if nSegment == 0 else sxRefList[elementsCountAround:]
contractedWallThicknessList = colonSegmentTubeMeshInnerPoints.getContractedWallThicknessList()
# Create coordinates and derivatives
xList, d1List, d2List, d3List, curvatureList = tubemesh.getCoordinatesFromInner(xExtrude, d1Extrude,
d2Extrude, d3UnitExtrude, contractedWallThicknessList,
elementsCountAround, elementsCountAlong, elementsCountThroughWall, transitElementList)
relaxedLengthList, xiList = colonSegmentTubeMeshInnerPoints.getRelaxedLengthAndXiList()
closedProximalEnd = False
if tcThickness > 0:
tubeTCWidthList = colonSegmentTubeMeshInnerPoints.getTubeTCWidthList()
xList, d1List, d2List, d3List, annotationArrayAround = getTeniaColi(
region, xList, d1List, d2List, d3List, curvatureList, tcCount, elementsCountAroundTC,
elementsCountAroundHaustrum, elementsCountAlong, elementsCountThroughWall,
tubeTCWidthList, tcThickness, sxRefExtrudeList, annotationGroupsAround,
closedProximalEnd)
# Create flat and texture coordinates
xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture = createFlatAndTextureCoordinatesTeniaColi(
xiList, relaxedLengthList, length, wallThickness, tcCount, tcThickness,
elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlong,
elementsCountThroughWall, transitElementList, closedProximalEnd)
# Create nodes and elements
nextNodeIdentifier, nextElementIdentifier, annotationGroups = createNodesAndElementsTeniaColi(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlong, elementsCountThroughWall,
tcCount, annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd)
else:
# Create flat and texture coordinates
xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture = tubemesh.createFlatAndTextureCoordinates(
xiList, relaxedLengthList, length, wallThickness, elementsCountAround,
elementsCountAlong, elementsCountThroughWall, transitElementList)
# Create nodes and elements
nextNodeIdentifier, nextElementIdentifier, annotationGroups = tubemesh.createNodesAndElements(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAround, elementsCountAlong, elementsCountThroughWall,
annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd)
return annotationGroups
@classmethod
def refineMesh(cls, meshrefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshrefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
refineElementsCountAround = options['Refine number of elements around']
refineElementsCountAlong = options['Refine number of elements along']
refineElementsCountThroughWall = options['Refine number of elements through wall']
meshrefinement.refineAllElementsCubeStandard3d(refineElementsCountAround, refineElementsCountAlong,
refineElementsCountThroughWall)
return
def getDefaultOptions(cls, parameterSetName='Default'):
if 'Human 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 2']
elif 'Mouse 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Mouse 1']
elif 'Mouse 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Mouse 2']
elif 'Pig 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 1']
elif 'Pig 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 2']
else:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 1']
if 'Mouse' in parameterSetName:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName = 'Mouse 1')
elif 'Pig' in parameterSetName:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName = 'Pig 1')
else:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName = 'Human 1')
options = {
'Central path' : copy.deepcopy(centralPathOption),
'Segment profile' : segmentProfileOption,
'Number of segments': 30,
'Start phase': 0.0,
'Proximal length': 420.0,
'Transverse length': 460.0,
'Distal length': 620.0,
'Proximal inner radius': 43.5,
'Proximal tenia coli width': 10.0,
'Proximal-transverse inner radius': 33.0,
'Proximal-transverse tenia coli width': 10.0,
'Transverse-distal inner radius': 29.0,
'Transverse-distal tenia coli width': 10.0,
'Distal inner radius': 31.5,
'Distal tenia coli width': 10.0,
'Refine' : False,
'Refine number of elements around' : 1,
'Refine number of elements along' : 1,
'Refine number of elements through wall' : 1
}
if 'Human 2' in parameterSetName:
options['Proximal length'] = 180.0
options['Transverse length'] = 620.0
options['Distal length'] = 700.0
elif 'Mouse' in parameterSetName:
options['Number of segments'] = 10
options['Proximal length'] = 30.0
options['Transverse length'] = 20.0
options['Distal length'] = 25.0
options['Proximal inner radius'] = 1.0
options['Proximal tenia coli width'] = 0.5
options['Proximal-transverse inner radius'] = 0.9
options['Proximal-transverse tenia coli width'] = 0.7
options['Transverse-distal inner radius'] = 0.7
options['Transverse-distal tenia coli width'] = 1.0
options['Distal inner radius'] = 0.7
options['Distal tenia coli width'] = 1.0
elif 'Pig 1' in parameterSetName:
options['Number of segments'] = 120
options['Proximal length'] = 3000.0
options['Transverse length'] = 200.0
options['Distal length'] = 200.0
options['Proximal inner radius'] = 38.0
options['Proximal tenia coli width'] = 5.0
options['Proximal-transverse inner radius'] = 14.0
options['Proximal-transverse tenia coli width'] = 4.0
options['Transverse-distal inner radius'] = 10.5
options['Transverse-distal tenia coli width'] = 3.0
options['Distal inner radius'] = 8.0
options['Distal tenia coli width'] = 1.5
elif 'Pig 2' in parameterSetName:
options['Number of segments'] = 3
options['Proximal length'] = 30.0
options['Transverse length'] = 30.0
options['Distal length'] = 30.0
options['Proximal inner radius'] = 16.0
options['Proximal tenia coli width'] = 5.0
options['Proximal-transverse inner radius'] = 16.0
options['Proximal-transverse tenia coli width'] = 5.0
options['Transverse-distal inner radius'] = 16.0
options['Transverse-distal tenia coli width'] = 5.0
options['Distal inner radius'] = 16.0
options['Distal tenia coli width'] = 5.0
return options
class MeshType_3d_esophagus1(Scaffold_base):
"""
Generates a 3-D esophagus mesh with variable numbers of elements around, along the central line, and through wall.
The esophagus is created by a function that generates an elliptical tube segment and uses tubemesh to map the
segment along a central path profile.
"""
centralPathDefaultScaffoldPackages = {
'Human 1':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 4
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
], [[[7.5, 289.8, 0.0], [2.8, -33.6, 0.0], [9.9, 0.8, 0.0],
[0.1, -1.6, 0.0], [0.0, 0.0, 10.0], [0.0, 0.0, 0.0]],
[[8.9, 242.5, 0.0], [-2.6, -87.5, 0.0], [10.0, -0.3, 0.0],
[0.1, -0.6, 0.0], [0.0, 0.0, 10.0], [0.0, 0.0, 0.0]],
[[-2.5, 115.4, 0.0], [3.9, -102.0, 0.0], [10.0, 0.4, 0.0],
[-0.3, 1.9, 0.0], [0.0, 0.0, 10.0], [0.0, 0.0, 0.0]],
[[10.1, 40.3, 0.0], [17.8, -57.9, 0.0], [9.6, 2.9, 0.0],
[-1.3, 3.2, 0.0], [0.0, 0.0, 10.0], [0.0, 0.0, 0.0]],
[[28.6, -0.1, 0.0], [18.5, -22.1, 0.0], [7.7, 6.5, 0.0],
[-2.4, 3.9, 0.0], [0.0, 0.0, 10.0], [0.0, 0.0, 0.0]]]),
'userAnnotationGroups': [{
'_AnnotationGroup':
True,
'dimension':
1,
'identifierRanges':
'1',
'name':
get_esophagus_term('cervical part of esophagus')[0],
'ontId':
get_esophagus_term('cervical part of esophagus')[1]
}, {
'_AnnotationGroup':
True,
'dimension':
1,
'identifierRanges':
'2-3',
'name':
get_esophagus_term('thoracic part of esophagus')[0],
'ontId':
get_esophagus_term('thoracic part of esophagus')[1]
}, {
'_AnnotationGroup':
True,
'dimension':
1,
'identifierRanges':
'4',
'name':
get_esophagus_term('abdominal part of esophagus')[0],
'ontId':
get_esophagus_term('abdominal part of esophagus')[1]
}]
})
}
@staticmethod
def getName():
return '3D Esophagus 1'
@staticmethod
def getParameterSetNames():
return ['Default', 'Human 1']
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 1']
options = {
'Central path': copy.deepcopy(centralPathOption),
'Number of elements around': 8,
'Number of elements along': 12,
'Number of elements through wall': 4,
'Wall thickness': 5.0, # 3.0mm when relaxed
'Mucosa relative thickness': 0.35,
'Submucosa relative thickness': 0.15,
'Circular muscle layer relative thickness': 0.25,
'Longitudinal muscle layer relative thickness': 0.25,
'Use cross derivatives': False,
'Use linear through wall': True,
'Refine': False,
'Refine number of elements around': 1,
'Refine number of elements along': 1,
'Refine number of elements through wall': 1
}
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path', 'Number of elements around',
'Number of elements along', 'Number of elements through wall',
'Wall thickness', 'Mucosa relative thickness',
'Submucosa relative thickness',
'Circular muscle layer relative thickness',
'Longitudinal muscle layer relative thickness',
'Use cross derivatives', 'Use linear through wall', 'Refine',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall'
]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [MeshType_1d_path1]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls,
optionName,
scaffoldType,
parameterSetName=None):
"""
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
"""
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(
cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(
cls.centralPathDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType(
) in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage(
'Central path', MeshType_1d_path1)
if options['Number of elements through wall'] != (1 or 4):
options['Number of elements through wall'] = 4
for key in [
'Number of elements around', 'Number of elements along',
'Number of elements through wall',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall'
]:
if options[key] < 1:
options[key] = 1
if options['Wall thickness'] < 0.0:
options['Wall thickness'] = 0.0
@classmethod
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: annotationGroups
"""
centralPath = options['Central path']
elementsCountAround = options['Number of elements around']
elementsCountAlong = options['Number of elements along']
elementsCountThroughWall = options['Number of elements through wall']
wallThickness = options['Wall thickness']
mucosaRelThickness = options['Mucosa relative thickness']
submucosaRelThickness = options['Submucosa relative thickness']
circularRelThickness = options[
'Circular muscle layer relative thickness']
longitudinalRelThickness = options[
'Longitudinal muscle layer relative thickness']
useCrossDerivatives = options['Use cross derivatives']
useCubicHermiteThroughWall = not (options['Use linear through wall'])
firstNodeIdentifier = 1
firstElementIdentifier = 1
# Central path
esophagusTermsAlong = [
None, 'cervical part of esophagus', 'thoracic part of esophagus',
'abdominal part of esophagus'
]
arcLengthOfGroupsAlong = []
for i in range(len(esophagusTermsAlong)):
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cxGroup, cd1Group, cd2Group, cd3Group, cd12Group, cd13Group = \
extractPathParametersFromRegion(tmpRegion, [Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D_DS3,
Node.VALUE_LABEL_D2_DS1DS2, Node.VALUE_LABEL_D2_DS1DS3],
groupName=esophagusTermsAlong[i])
arcLength = 0.0
for e in range(len(cxGroup) - 1):
arcLength += interp.getCubicHermiteArcLength(
cxGroup[e], cd1Group[e], cxGroup[e + 1], cd1Group[e + 1])
arcLengthOfGroupsAlong.append(arcLength)
if i == 0:
cx = cxGroup
cd1 = cd1Group
cd2 = cd2Group
cd3 = cd3Group
cd12 = cd12Group
cd13 = cd13Group
del tmpRegion
# Sample central path
sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(
cx, cd1, elementsCountAlong)
sd2, sd12 = interp.interpolateSampleCubicHermite(
cd2, cd12, se, sxi, ssf)
sd3, sd13 = interp.interpolateSampleCubicHermite(
cd3, cd13, se, sxi, ssf)
centralPathLength = arcLengthOfGroupsAlong[0]
elementAlongLength = centralPathLength / elementsCountAlong
elementsCountAlongGroups = []
groupLength = 0.0
e = 0
elementsCount = 1
length = elementAlongLength
for i in range(1, len(esophagusTermsAlong)):
groupLength += arcLengthOfGroupsAlong[i]
if e == elementsCountAlong - 2:
elementsCount += 1
elementsCountAlongGroups.append(elementsCount)
else:
while length < groupLength:
elementsCount += 1
e += 1
length += elementAlongLength
# check which end is grouplength closer to
distToUpperEnd = abs(length - groupLength)
distToLowerEnd = abs(groupLength -
(length - elementsCountAlong))
if distToLowerEnd < distToUpperEnd:
elementsCount -= 1
elementsCountAlongGroups.append(elementsCount)
e -= 1
length -= elementAlongLength
else:
elementsCountAlongGroups.append(elementsCount)
elementsCount = 0
majorRadiusElementList = sd2
minorRadiusElementList = sd3
# Create annotation groups along esophagus
esophagusGroup = AnnotationGroup(region,
get_esophagus_term("esophagus"))
cervicalGroup = AnnotationGroup(
region, get_esophagus_term("cervical part of esophagus"))
thoracicGroup = AnnotationGroup(
region, get_esophagus_term("thoracic part of esophagus"))
abdominalGroup = AnnotationGroup(
region, get_esophagus_term("abdominal part of esophagus"))
annotationGroupAlong = [[esophagusGroup, cervicalGroup],
[esophagusGroup, thoracicGroup],
[esophagusGroup, abdominalGroup]]
annotationGroupsAlong = []
for i in range(len(elementsCountAlongGroups)):
elementsCount = elementsCountAlongGroups[i]
for n in range(elementsCount):
annotationGroupsAlong.append(annotationGroupAlong[i])
annotationGroupsAround = []
for i in range(elementsCountAround):
annotationGroupsAround.append([])
# Groups through wall
longitudinalMuscleGroup = AnnotationGroup(
region,
get_esophagus_term("esophagus smooth muscle longitudinal layer"))
circularMuscleGroup = AnnotationGroup(
region,
get_esophagus_term("esophagus smooth muscle circular layer"))
submucosaGroup = AnnotationGroup(
region, get_esophagus_term("submucosa of esophagus"))
mucosaGroup = AnnotationGroup(region,
get_esophagus_term("esophagus mucosa"))
if elementsCountThroughWall == 1:
relativeThicknessList = [1.0]
annotationGroupsThroughWall = [[]]
else:
relativeThicknessList = [
mucosaRelThickness, submucosaRelThickness,
circularRelThickness, longitudinalRelThickness
]
annotationGroupsThroughWall = [[mucosaGroup], [submucosaGroup],
[circularMuscleGroup],
[longitudinalMuscleGroup]]
xToSample = []
d1ToSample = []
for n2 in range(elementsCountAlong + 1):
# Create inner points
cx = [0.0, 0.0, elementAlongLength * n2]
axis1 = [vector.magnitude(majorRadiusElementList[n2]), 0.0, 0.0]
axis2 = [0.0, vector.magnitude(minorRadiusElementList[n2]), 0.0]
xInner, d1Inner = geometry.createEllipsePoints(cx,
2 * math.pi,
axis1,
axis2,
elementsCountAround,
startRadians=0.0)
xToSample += xInner
d1ToSample += d1Inner
d2ToSample = [[0.0, 0.0, elementAlongLength]
] * (elementsCountAround * (elementsCountAlong + 1))
# Sample along length
xInnerRaw = []
d2InnerRaw = []
xToWarp = []
d1ToWarp = []
d2ToWarp = []
flatWidthList = []
xiList = []
for n1 in range(elementsCountAround):
xForSamplingAlong = []
d2ForSamplingAlong = []
for n2 in range(elementsCountAlong + 1):
idx = n2 * elementsCountAround + n1
xForSamplingAlong.append(xToSample[idx])
d2ForSamplingAlong.append(d2ToSample[idx])
xSampled, d2Sampled = interp.sampleCubicHermiteCurves(
xForSamplingAlong,
d2ForSamplingAlong,
elementsCountAlong,
arcLengthDerivatives=True)[0:2]
xInnerRaw.append(xSampled)
d2InnerRaw.append(d2Sampled)
# Re-arrange sample order & calculate dx_ds1 and dx_ds3 from dx_ds2
for n2 in range(elementsCountAlong + 1):
xAround = []
d2Around = []
for n1 in range(elementsCountAround):
x = xInnerRaw[n1][n2]
d2 = d2InnerRaw[n1][n2]
xAround.append(x)
d2Around.append(d2)
d1Around = []
for n1 in range(elementsCountAround):
v1 = xAround[n1]
v2 = xAround[(n1 + 1) % elementsCountAround]
d1 = d2 = [v2[c] - v1[c] for c in range(3)]
arcLengthAround = interp.computeCubicHermiteArcLength(
v1, d1, v2, d2, True)
dx_ds1 = [c * arcLengthAround for c in vector.normalise(d1)]
d1Around.append(dx_ds1)
d1Smoothed = interp.smoothCubicHermiteDerivativesLoop(
xAround, d1Around)
xToWarp += xAround
d1ToWarp += d1Smoothed
d2ToWarp += d2Around
# Flat width and xi
flatWidth = 0.0
xiFace = []
for n1 in range(elementsCountAround):
v1 = xAround[n1]
d1 = d1Smoothed[n1]
v2 = xAround[(n1 + 1) % elementsCountAround]
d2 = d1Smoothed[(n1 + 1) % elementsCountAround]
flatWidth += interp.getCubicHermiteArcLength(v1, d1, v2, d2)
flatWidthList.append(flatWidth)
for n1 in range(elementsCountAround + 1):
xi = 1.0 / elementsCountAround * n1
xiFace.append(xi)
xiList.append(xiFace)
# Project reference point for warping onto central path
sxRefList, sd1RefList, sd2ProjectedListRef, zRefList = \
tubemesh.getPlaneProjectionOnCentralPath(xToWarp, elementsCountAround, elementsCountAlong,
centralPathLength, sx, sd1, sd2, sd12)
# Warp points
segmentAxis = [0.0, 0.0, 1.0]
closedProximalEnd = False
innerRadiusAlong = []
for n2 in range(elementsCountAlong + 1):
firstNodeAlong = xToWarp[n2 * elementsCountAround]
midptSegmentAxis = [0.0, 0.0, elementAlongLength * n2]
radius = vector.magnitude(firstNodeAlong[c] - midptSegmentAxis[c]
for c in range(3))
innerRadiusAlong.append(radius)
xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList = \
tubemesh.warpSegmentPoints(xToWarp, d1ToWarp, d2ToWarp, segmentAxis, sxRefList, sd1RefList,
sd2ProjectedListRef, elementsCountAround, elementsCountAlong,
zRefList, innerRadiusAlong, closedProximalEnd)
# Create coordinates and derivatives
transitElementList = [0] * elementsCountAround
xList, d1List, d2List, d3List, curvatureList = \
tubemesh.getCoordinatesFromInner(xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList,
[wallThickness]*(elementsCountAlong+1), relativeThicknessList,
elementsCountAround, elementsCountAlong, elementsCountThroughWall,
transitElementList)
# Create flat coordinates
xFlat, d1Flat, d2Flat = tubemesh.createFlatCoordinates(
xiList, flatWidthList, length, wallThickness,
relativeThicknessList, elementsCountAround, elementsCountAlong,
elementsCountThroughWall, transitElementList)
# Create nodes and elements
xOrgan = []
d1Organ = []
d2Organ = []
nodeIdentifier, elementIdentifier, annotationGroups = \
tubemesh.createNodesAndElements(region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat,
xOrgan, d1Organ, d2Organ, None, elementsCountAround, elementsCountAlong,
elementsCountThroughWall, annotationGroupsAround, annotationGroupsAlong,
annotationGroupsThroughWall, firstNodeIdentifier, firstElementIdentifier,
useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd)
# annotation fiducial points
fm = region.getFieldmodule()
fm.beginChange()
mesh = fm.findMeshByDimension(3)
cache = fm.createFieldcache()
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
markerNames = [
"proximodorsal midpoint on serosa of upper esophageal sphincter",
"proximoventral midpoint on serosa of upper esophageal sphincter",
"distal point of lower esophageal sphincter serosa on the greater curvature of stomach",
"distal point of lower esophageal sphincter serosa on the lesser curvature of stomach"
]
totalElements = elementIdentifier
radPerElementAround = math.pi * 2.0 / elementsCountAround
elementAroundHalfPi = int(0.25 * elementsCountAround)
xi1HalfPi = (math.pi * 0.5 - radPerElementAround *
elementAroundHalfPi) / radPerElementAround
elementAroundPi = int(0.5 * elementsCountAround)
xi1Pi = (math.pi -
radPerElementAround * elementAroundPi) / radPerElementAround
markerElementIdentifiers = [
elementsCountAround * elementsCountThroughWall -
elementAroundHalfPi, elementAroundHalfPi + 1 +
elementsCountAround * (elementsCountThroughWall - 1),
totalElements - elementsCountAround,
totalElements - elementsCountAround + elementAroundPi
]
markerXis = [[1.0 - xi1HalfPi, 0.0, 1.0], [xi1HalfPi, 0.0, 1.0],
[0.0, 1.0, 1.0], [xi1Pi, 1.0, 1.0]]
for n in range(len(markerNames)):
markerGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region, get_esophagus_term(markerNames[n]))
markerElement = mesh.findElementByIdentifier(
markerElementIdentifiers[n])
markerXi = markerXis[n]
cache.setMeshLocation(markerElement, markerXi)
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
nodeIdentifier += 1
cache.setNode(markerPoint)
markerName.assignString(cache, markerGroup.getName())
markerLocation.assignMeshLocation(cache, markerElement, markerXi)
for group in [esophagusGroup, markerGroup]:
group.getNodesetGroup(nodes).addNode(markerPoint)
fm.endChange()
return annotationGroups
@classmethod
def refineMesh(cls, meshrefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshrefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
refineElementsCountAround = options['Refine number of elements around']
refineElementsCountAlong = options['Refine number of elements along']
refineElementsCountThroughWall = options[
'Refine number of elements through wall']
meshrefinement.refineAllElementsCubeStandard3d(
refineElementsCountAround, refineElementsCountAlong,
refineElementsCountThroughWall)
return
@classmethod
def defineFaceAnnotations(cls, region, options, annotationGroups):
'''
Add face annotation groups from the highest dimension mesh.
Must have defined faces and added subelements for highest dimension groups.
:param region: Zinc region containing model.
:param options: Dict containing options. See getDefaultOptions().
:param annotationGroups: List of annotation groups for top-level elements.
New face annotation groups are appended to this list.
'''
# Create 2d surface mesh groups
fm = region.getFieldmodule()
mesh2d = fm.findMeshByDimension(2)
esophagusGroup = getAnnotationGroupForTerm(
annotationGroups, get_esophagus_term("esophagus"))
is_exterior = fm.createFieldIsExterior()
is_exterior_face_xi3_1 = fm.createFieldAnd(
is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
is_esophagus = esophagusGroup.getFieldElementGroup(mesh2d)
is_serosa = fm.createFieldAnd(is_esophagus, is_exterior_face_xi3_1)
serosa = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_esophagus_term("serosa of esophagus"))
serosa.getMeshGroup(mesh2d).addElementsConditional(is_serosa)
def test_colon1(self):
"""
Test creation of colon scaffold.
"""
parameterSetNames = MeshType_3d_colon1.getParameterSetNames()
self.assertEqual(parameterSetNames, ["Default", "Human 1", "Human 2", "Mouse 1", "Mouse 2", "Pig 1", "Pig 2"])
centralPathDefaultScaffoldPackages = {
'Test line': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 1
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2,
Node.VALUE_LABEL_D2_DS1DS2], [
[[163.7, -25.2, 12.2], [-21.7, 50.1, -18.1], [0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[117.2, 32.8, -2.6], [-64.3, 34.4, -3.9], [0.0, 0.0, 5.0], [0.0, 0.0, 0.5]]])
})
}
centralPathOption = centralPathDefaultScaffoldPackages['Test line']
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegment1, defaultParameterSetName='Human 1')
options = {
'Central path': copy.deepcopy(centralPathOption),
'Segment profile': segmentProfileOption,
'Number of segments': 3,
'Start phase': 0.0,
'Proximal length': 25.0,
'Transverse length': 25.0,
'Distal length': 25.0,
'Proximal inner radius': 20.0,
'Proximal tenia coli width': 8.0,
'Proximal-transverse inner radius': 18.0,
'Proximal-transverse tenia coli width': 6.0,
'Transverse-distal inner radius': 16.0,
'Transverse-distal tenia coli width': 5.0,
'Distal inner radius': 15.0,
'Distal tenia coli width': 5.0,
'Refine': False,
'Refine number of elements around': 1,
'Refine number of elements along': 1,
'Refine number of elements through wall': 1
}
self.assertEqual(19, len(options))
centralPath = options['Central path']
segmentProfile = options.get("Segment profile")
segmentSettings = segmentProfile.getScaffoldSettings()
self.assertEqual(8, segmentSettings.get("Number of elements around haustrum"))
self.assertEqual(0.5, segmentSettings.get("Corner inner radius factor"))
self.assertEqual(0.5, segmentSettings.get("Haustrum inner radius factor"))
self.assertEqual(0.5, segmentSettings.get("Segment length end derivative factor"))
self.assertEqual(3, segmentSettings.get("Number of tenia coli"))
self.assertEqual(1.6, segmentSettings.get("Tenia coli thickness"))
self.assertEqual(3, options.get("Number of segments"))
self.assertEqual(0.0, options.get("Start phase"))
self.assertEqual(25.0, options.get("Transverse length"))
self.assertEqual(20.0, options.get("Proximal inner radius"))
self.assertEqual(6.0, options.get("Proximal-transverse tenia coli width"))
self.assertEqual(16.0, options.get("Transverse-distal inner radius"))
self.assertEqual(5.0, options.get("Distal tenia coli width"))
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cx = extractPathParametersFromRegion(tmpRegion)[0]
self.assertEqual(2, len(cx))
assertAlmostEqualList(self, cx[0], [ 163.7, -25.2, 12.2 ], 1.0E-6)
assertAlmostEqualList(self, cx[1], [ 117.2, 32.8, -2.6 ], 1.0E-6)
del tmpRegion
annotationGroups = MeshType_3d_colon1.generateBaseMesh(region, options)
self.assertEqual(7, len(annotationGroups))
fieldmodule = region.getFieldmodule()
self.assertEqual(RESULT_OK, fieldmodule.defineAllFaces())
if annotationGroups is not None:
for annotationGroup in annotationGroups:
annotationGroup.addSubelements()
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(432, mesh3d.getSize())
mesh2d = fieldmodule.findMeshByDimension(2)
self.assertEqual(1656, mesh2d.getSize())
mesh1d = fieldmodule.findMeshByDimension(1)
self.assertEqual(2043, mesh1d.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
self.assertEqual(819, nodes.getSize())
datapoints = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums, [ 108.0250647983898, -36.876103983560014, -25.89741158325083 ], 1.0E-6)
assertAlmostEqualList(self, maximums, [ 185.46457506220003, 48.101157490744, 34.995316052158934 ], 1.0E-6)
flatCoordinates = fieldmodule.findFieldByName("flat coordinates").castFiniteElement()
self.assertTrue(flatCoordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(flatCoordinates, nodes)
assertAlmostEqualList(self, minimums, [ 0.0, 0.0, 0.0 ], 1.0E-6)
assertAlmostEqualList(self, maximums, [ 186.72988844629867, 77.4178187926561, 3.2000000000000006 ], 1.0E-6)
textureCoordinates = fieldmodule.findFieldByName("texture coordinates").castFiniteElement()
minimums, maximums = evaluateFieldNodesetRange(textureCoordinates, nodes)
assertAlmostEqualList(self, minimums, [ 0.0, 0.0, 0.0 ], 1.0E-6)
assertAlmostEqualList(self, maximums, [ 0.9812471574796385, 1.0, 2.0 ], 1.0E-6)
with ChangeManager(fieldmodule):
one = fieldmodule.createFieldConstant(1.0)
faceMeshGroup = createFaceMeshGroupExteriorOnFace(fieldmodule, Element.FACE_TYPE_XI3_1)
surfaceAreaField = fieldmodule.createFieldMeshIntegral(one, coordinates, faceMeshGroup)
surfaceAreaField.setNumbersOfPoints(4)
volumeField = fieldmodule.createFieldMeshIntegral(one, coordinates, mesh3d)
volumeField.setNumbersOfPoints(3)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 14612.416788520026, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 26826.069540921028, delta=1.0E-6)
def test_transformation(self):
"""
Test transformation of a box scaffold with scaffold package.
"""
scaffoldPackage = ScaffoldPackage(MeshType_3d_box1)
tmpScale = scaffoldPackage.getScale()
TOL = 1.0E-7
FINETOL = 1.0E-12
assertAlmostEqualList(self, tmpScale, [ 1.0, 1.0, 1.0 ], delta=FINETOL)
newScale = [ 2.0, 1.5, 0.5 ]
scaffoldPackage.setScale(newScale)
tmpScale = scaffoldPackage.getScale()
assertAlmostEqualList(self, tmpScale, newScale, delta=FINETOL)
tmpRotation = scaffoldPackage.getRotation()
assertAlmostEqualList(self, tmpRotation, [ 0.0, 0.0, 0.0 ], delta=FINETOL)
newRotation = [ 30.0, -10.0, 90.0 ]
scaffoldPackage.setRotation(newRotation)
tmpRotation = scaffoldPackage.getRotation()
assertAlmostEqualList(self, tmpRotation, newRotation, delta=FINETOL)
tmpTranslation = scaffoldPackage.getTranslation()
assertAlmostEqualList(self, tmpTranslation, [ 0.0, 0.0, 0.0 ], delta=FINETOL)
newTranslation = [ 0.5, 1.2, -0.1 ]
scaffoldPackage.setTranslation(newTranslation)
tmpTranslation = scaffoldPackage.getTranslation()
assertAlmostEqualList(self, tmpTranslation, newTranslation, delta=FINETOL)
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
scaffoldPackage.generate(region)
fieldmodule = region.getFieldmodule()
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
self.assertEqual(8, nodes.getSize())
coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums, [ 2.744244002293470e-01, 6.367511648575830e-01, -1.000000000000000e-01 ], delta=TOL)
assertAlmostEqualList(self, maximums, [ 2.455737063904887e+00, 2.184807753012208e+00, 1.724507984852172e+00 ], delta=TOL)
node = nodes.findNodeByIdentifier(8)
self.assertTrue(node.isValid())
fieldcache = fieldmodule.createFieldcache()
fieldcache.setNode(node)
result, x = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_VALUE, 1, 3)
self.assertEqual(RESULT_OK, result)
assertAlmostEqualList(self, x , [ 2.230161464134234e+00, 1.621558917869791e+00, 1.724507984852172e+00 ], delta=TOL)
# derivative magnitudes must also equal scale
result, d1 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS1, 1, 3)
self.assertEqual(RESULT_OK, result)
assertAlmostEqualList(self, d1, [ 1.705737064039425e+00, 9.848077530127952e-01, 3.472963553408093e-01 ], delta=TOL)
self.assertAlmostEqual(newScale[0], magnitude(d1), delta=TOL)
result, d2 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS2, 1, 3)
self.assertEqual(RESULT_OK, result)
assertAlmostEqualList(self, d2, [ -2.255755995328457e-01, -1.302361332111701e-01, 1.477211629352659e+00 ], delta=TOL)
self.assertAlmostEqual(newScale[1], magnitude(d2), delta=TOL)
result, d3 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS3, 1, 3)
self.assertEqual(RESULT_OK, result)
assertAlmostEqualList(self, d3, [ 2.499999998128999e-01, -4.330127019169794e-01, 0.000000000000000e+00 ], delta=TOL)
self.assertAlmostEqual(newScale[2], magnitude(d3), delta=TOL)
def test_bladder1(self):
"""
Test creation of bladder scaffold.
"""
parameterSetNames = MeshType_3d_bladder1.getParameterSetNames()
self.assertEqual(parameterSetNames, ["Default", "Cat 1", "Rat 1"])
ostiumDefaultScaffoldPackages = {
'Test ostium': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
'Number of vessels': 1,
'Number of elements across common': 2,
'Number of elements around ostium': 8,
'Number of elements along': 2,
'Number of elements through wall': 1, # not implemented for > 1
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 0.3,
'Ostium length': 0.2,
'Ostium wall thickness': 0.05,
'Ostium inter-vessel distance': 0.8,
'Ostium inter-vessel height': 0.0,
'Use linear through ostium wall': True,
'Vessel end length factor': 1.0,
'Vessel inner diameter': 0.15,
'Vessel wall thickness': 0.04,
'Vessel angle 1 degrees': 0.0,
'Vessel angle 1 spread degrees': 0.0,
'Vessel angle 2 degrees': 0.0,
'Use linear through vessel wall': True,
# 'Use cross derivatives' : False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements along': 4,
'Refine number of elements through wall': 1
},
})
}
ostiumOption = ostiumDefaultScaffoldPackages['Test ostium']
options = {
'Number of elements up neck': 8,
'Number of elements up body': 16,
'Number of elements around': 8, # should be even
'Number of elements through wall': 1,
'Number of elements around ostium': 8, # implemented for 8
'Number of elements radially on annulus': 1,
'Height': 5.0,
'Major diameter': 6.0,
'Minor diameter': 6.0,
'Bladder wall thickness': 0.05,
'Urethra diameter': 1.0,
'Ureter': copy.deepcopy(ostiumOption),
'Ostium position around': 0.15,
'Ostium position up': 0.25,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements up': 4,
'Refine number of elements through wall': 1
}
self.assertEqual(19, len(options))
ostiumSettings = ostiumOption.getScaffoldSettings()
self.assertEqual(1, ostiumSettings.get("Number of vessels"))
self.assertEqual(8, ostiumSettings.get("Number of elements around ostium"))
self.assertEqual(1, ostiumSettings.get("Number of elements through wall"))
self.assertEqual(0.3, ostiumSettings.get("Ostium diameter"))
self.assertEqual(8, options.get("Number of elements up neck"))
self.assertEqual(16, options.get("Number of elements up body"))
self.assertEqual(8, options.get("Number of elements around"))
self.assertEqual(1.0, options.get("Urethra diameter"))
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
annotationGroups = MeshType_3d_bladder1.generateBaseMesh(region, options)
self.assertEqual(3, len(annotationGroups))
fieldmodule = region.getFieldmodule()
self.assertEqual(RESULT_OK, fieldmodule.defineAllFaces())
if annotationGroups is not None:
for annotationGroup in annotationGroups:
annotationGroup.addSubelements()
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(232, mesh3d.getSize())
mesh2d = fieldmodule.findMeshByDimension(2)
self.assertEqual(936, mesh2d.getSize())
mesh1d = fieldmodule.findMeshByDimension(1)
self.assertEqual(1183, mesh1d.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
self.assertEqual(478, nodes.getSize())
datapoints = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums, [-2.996386368615517, -2.996386368615517, -6.464466094067262], 1.0E-6)
assertAlmostEqualList(self, maximums, [2.996386368615517, 2.996386368615517, 5.0], 1.0E-6)
def test_smallintestine1(self):
"""
Test creation of small intestine scaffold.
"""
parameterSetNames = MeshType_3d_smallintestine1.getParameterSetNames()
self.assertEqual(parameterSetNames, ["Default", "Cattle 1", "Mouse 1"])
centralPathDefaultScaffoldPackages = {
'Test line': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'D2 derivatives': True,
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 3
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2,
Node.VALUE_LABEL_D2_DS1DS2], [
[[-2.3, 18.5, -4.4], [-4.2, -0.8, 3.7], [0.0, 5.0, 0.0], [0.0, 0.0, 0.5]],
[[-8.6, 16.3, -0.4], [-7.1, -2.7, 1.6], [0.0, 5.0, 0.0], [0.0, 0.0, 0.5]],
[[-18.3, 12.6, -1.5], [-6.4, -1.7, -3.8], [0.0, 5.0, 0.0], [0.0, 0.0, 0.5]],
[[-15.6, 13.7, -6.1], [7.0, 2.1, -1.8], [0.0, 5.0, 0.0], [0.0, 0.0, 0.5]]])
})
}
centralPathOption = centralPathDefaultScaffoldPackages['Test line']
options = MeshType_3d_smallintestine1.getDefaultOptions("Mouse 1")
options['Central path'] = copy.deepcopy(centralPathOption)
options['Number of segments'] = 4
options['Duodenum length'] = 5.0
options['Jejunum length'] = 15.0
options['Ileum length'] = 5.0
self.assertEqual(19, len(options))
centralPath = options['Central path']
self.assertEqual(4, options.get("Number of segments"))
self.assertEqual(8, options.get("Number of elements around"))
self.assertEqual(4, options.get("Number of elements along segment"))
self.assertEqual(1, options.get("Number of elements through wall"))
self.assertEqual(5.0, options.get("Duodenum length"))
self.assertEqual(5.0, options.get("Ileum length"))
self.assertEqual(0.6, options.get("Duodenum inner radius"))
self.assertEqual(1.0, options.get("Jejunum-ileum inner radius"))
self.assertEqual(0.1, options.get("Wall thickness"))
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cx = extractPathParametersFromRegion(tmpRegion, [Node.VALUE_LABEL_VALUE])[0]
self.assertEqual(4, len(cx))
assertAlmostEqualList(self, cx[0], [-2.3, 18.5, -4.4], 1.0E-6)
assertAlmostEqualList(self, cx[2], [-18.3, 12.6, -1.5], 1.0E-6)
del tmpRegion
annotationGroups = MeshType_3d_smallintestine1.generateBaseMesh(region, options)
self.assertEqual(4, len(annotationGroups))
fieldmodule = region.getFieldmodule()
self.assertEqual(RESULT_OK, fieldmodule.defineAllFaces())
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(128, mesh3d.getSize())
mesh2d = fieldmodule.findMeshByDimension(2)
self.assertEqual(520, mesh2d.getSize())
mesh1d = fieldmodule.findMeshByDimension(1)
self.assertEqual(664, mesh1d.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
self.assertEqual(272, nodes.getSize())
datapoints = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums, [-20.06978981419564, 11.406595205949705, -7.1653294859433965], 1.0E-6)
assertAlmostEqualList(self, maximums, [-1.8300388314851923, 19.193885338090105, 0.9772071374844936], 1.0E-6)
flatCoordinates = fieldmodule.findFieldByName("flat coordinates").castFiniteElement()
self.assertTrue(flatCoordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(flatCoordinates, nodes)
assertAlmostEqualList(self, minimums, [-1.39038154442654, 0.0, 0.0], 1.0E-6)
assertAlmostEqualList(self, maximums, [4.891237158967401, 25.293706698841913, 0.1], 1.0E-6)
with ChangeManager(fieldmodule):
one = fieldmodule.createFieldConstant(1.0)
faceMeshGroup = createFaceMeshGroupExteriorOnFace(fieldmodule, Element.FACE_TYPE_XI3_1)
surfaceAreaField = fieldmodule.createFieldMeshIntegral(one, coordinates, faceMeshGroup)
surfaceAreaField.setNumbersOfPoints(4)
volumeField = fieldmodule.createFieldMeshIntegral(one, coordinates, mesh3d)
volumeField.setNumbersOfPoints(3)
flatSurfaceAreaField = fieldmodule.createFieldMeshIntegral(one, flatCoordinates, faceMeshGroup)
flatSurfaceAreaField.setNumbersOfPoints(4)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 171.27464080337143, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 16.35219225882822, delta=1.0E-6)
result, flatSurfaceArea = flatSurfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(flatSurfaceArea, 171.37026123844635, delta=1.0E-3)
class MeshType_3d_solidcylinder1(Scaffold_base):
"""
Generates a solid cylinder using a ShieldMesh of all cube elements,
with variable numbers of elements in major, minor, shell and axial directions.
"""
centralPathDefaultScaffoldPackages = {
'Cylinder 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 3.0,
'Number of elements': 3
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [
[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 2.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 3.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]]
])
})
}
@staticmethod
def getName():
return '3D Solid Cylinder 1'
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
centralPathOption = cls.centralPathDefaultScaffoldPackages['Cylinder 1']
options = {
'Central path': copy.deepcopy(centralPathOption),
'Number of elements across major': 4,
'Number of elements across minor': 4,
'Number of elements across shell': 0,
'Number of elements across transition': 1,
'Number of elements along': 1,
'Shell element thickness proportion': 1.0,
'Lower half': False,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements across major': 1,
'Refine number of elements along': 1
}
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path',
'Number of elements across major',
'Number of elements across minor',
'Number of elements across shell',
'Number of elements across transition',
'Number of elements along',
'Shell element thickness proportion',
'Lower half',
'Refine',
'Refine number of elements across major',
'Refine number of elements along'
]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [MeshType_1d_path1]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.centralPathDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage('Central path', MeshType_1d_path1)
dependentChanges = False
if options['Number of elements across major'] < 4:
options['Number of elements across major'] = 4
if options['Number of elements across major'] % 2:
options['Number of elements across major'] += 1
if options['Number of elements across minor'] < 4:
options['Number of elements across minor'] = 4
if options['Number of elements across minor'] % 2:
options['Number of elements across minor'] += 1
if options['Number of elements along'] < 1:
options['Number of elements along'] = 1
if options['Number of elements across transition'] < 1:
options['Number of elements across transition'] = 1
Rcrit = min(options['Number of elements across major']-4, options['Number of elements across minor']-4)//2
if options['Number of elements across shell'] + options['Number of elements across transition'] - 1 > Rcrit:
dependentChanges = True
options['Number of elements across shell'] = Rcrit
options['Number of elements across transition'] = 1
if options['Shell element thickness proportion'] < 0.15:
options['Shell element thickness proportion'] = 1.0
return dependentChanges
@staticmethod
def generateBaseMesh(region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: None
"""
centralPath = options['Central path']
full = not options['Lower half']
elementsCountAcrossMajor = options['Number of elements across major']
if not full:
elementsCountAcrossMajor //= 2
elementsCountAcrossMinor = options['Number of elements across minor']
elementsCountAcrossShell = options['Number of elements across shell']
elementsCountAcrossTransition = options['Number of elements across transition']
elementsCountAlong = options['Number of elements along']
shellProportion = options['Shell element thickness proportion']
useCrossDerivatives = options['Use cross derivatives']
fm = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fm)
cylinderCentralPath = CylinderCentralPath(region, centralPath, elementsCountAlong)
cylinderShape = CylinderShape.CYLINDER_SHAPE_FULL if full else CylinderShape.CYLINDER_SHAPE_LOWER_HALF
base = CylinderEnds(elementsCountAcrossMajor, elementsCountAcrossMinor, elementsCountAcrossShell,
elementsCountAcrossTransition,
shellProportion,
[0.0, 0.0, 0.0], cylinderCentralPath.alongAxis[0], cylinderCentralPath.majorAxis[0],
cylinderCentralPath.minorRadii[0])
cylinder1 = CylinderMesh(fm, coordinates, elementsCountAlong, base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath, useCrossDerivatives=False)
annotationGroup = []
return annotationGroup
@classmethod
def refineMesh(cls, meshRefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshRefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
assert isinstance(meshRefinement, MeshRefinement)
refineElementsCountAcrossMajor = options['Refine number of elements across major']
refineElementsCountAlong = options['Refine number of elements along']
meshRefinement.refineAllElementsCubeStandard3d(refineElementsCountAcrossMajor, refineElementsCountAlong, refineElementsCountAcrossMajor)
class MeshType_3d_smallintestine1(Scaffold_base):
'''
Generates a 3-D small intestine mesh with variable numbers
of elements around, along the central line, and through wall.
The small intestine is created by a function that generates
a small intestine segment and uses tubemesh to map the segment
along a central line profile.
'''
centralPathDefaultScaffoldPackages = {
'Mouse 1' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 45
},
'meshEdits' : exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ -2.3, 18.5, -4.4 ], [ -4.2, -0.8, 3.7 ], [ 0.0, 5.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -8.6, 16.3, -0.4 ], [ -7.1, -2.7, 1.6 ], [ 0.0, 5.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -18.3, 12.6, -1.5 ], [ -6.4, -1.7, -3.8 ], [ 0.0, 5.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -15.6, 13.7, -6.1 ], [ 7.0, 2.1, -1.8 ], [ 0.0, 5.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -9.3, 14.8, -4.9 ], [ 4.7, 0.7, 1.8 ], [ 0.0, 5.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -3.9, 15.7, -3.0 ], [ 4.3, 0.7, 2.0 ], [ 0.0, 5.0, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -3.4, 13.4, -2.8 ], [ -4.1, -0.7, -1.7 ], [ 0.6, -2.0, 0.3 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -7.6, 12.4, -4.6 ], [ -3.7, -0.8, -0.9 ], [ 0.0, -2.1, 0.1 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -11.6, 11.6, -5.7 ], [ -4.2, -0.7, -0.2 ], [ 0.0, -1.9, 0.1 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -16.5, 11.7, -3.9 ], [ -1.0, 0.2, 5.8 ], [ 0.3, -1.4, -0.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -12.5, 11.7, -1.4 ], [ 3.6, 0.1, 0.6 ], [ -0.1, -1.4, -0.7 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -6.8, 11.8, -0.6 ], [ 2.9, 0.0, 0.7 ], [ -0.7, -1.2, -0.9 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -6.4, 9.8, -1.6 ], [ -2.9, -0.3, -1.4 ], [ -0.9, 1.6, 0.4 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -9.5, 9.5, -2.9 ], [ -4.6, 0.0, -1.8 ], [ -0.5, 1.7, 0.7 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -14.3, 9.4, -4.6 ], [ -3.4, 0.1, -1.6 ], [ -0.1, 1.6, 0.5 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -19.0, 9.4, -2.9 ], [ 0.3, 0.2, 6.7 ], [ 0.0, 1.8, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -14.5, 9.7, 0.2 ], [ 3.6, -1.2, 1.0 ], [ 0.7, 2.2, 0.9 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -12.6, 7.7, 0.7 ], [ 0.6, -2.7, 0.2 ], [ 1.7, 0.8, 1.6 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -13.1, 3.8, 0.3 ], [ -4.0, -3.6, -1.5 ], [ 1.0, -1.1, 1.5 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -15.2, 5.1, -0.8 ], [ 6.0, 6.9, 1.8 ], [ -0.9, -0.4, 0.3 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -17.3, 6.9, -1.0 ], [ -2.5, 0.0, -0.4 ], [ -1.6, 0.0, 1.7 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -19.9, 6.8, -2.5 ], [ -1.5, -1.1, -3.4 ], [ -1.8, -0.7, 0.4 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -17.2, 6.3, -5.1 ], [ 4.0, 0.8, -1.3 ], [ -0.4, -1.3, -1.5 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -12.2, 7.8, -6.8 ], [ 4.8, 1.7, -0.3 ], [ 0.1, -0.6, -1.6 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -7.9, 9.6, -6.5 ], [ 3.7, 1.7, 0.7 ], [ 0.5, -0.6, -1.6 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -3.8, 10.3, -5.5 ], [ 3.8, -2.7, -0.1 ], [ -1.3, -0.3, -3.1 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -5.3, 7.6, -6.4 ], [ -3.5, -1.0, -1.3 ], [ -0.4, 1.1, -1.5 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -9.0, 6.4, -7.3 ], [ -3.2, -1.3, 1.9 ], [ -0.9, 0.5, -1.1 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -11.6, 4.0, -2.0 ], [ 5.6, -0.2, 4.3 ], [ -1.8, -0.3, 1.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -5.9, 5.0, -3.1 ], [ 4.1, 1.2, -1.6 ], [ 1.0, -0.3, 1.9 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -2.5, 6.0, -3.8 ], [ 3.6, 0.7, 3.2 ], [ -1.7, -1.2, 1.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -4.1, 3.2, -0.4 ], [ -3.5, -1.7, 2.6 ], [ -1.0, 0.4, -1.1 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -9.7, 1.7, 2.3 ], [ -7.9, -1.0, 1.0 ], [ -0.6, 1.0, -1.6 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -19.0, 0.6, -0.4 ], [ 0.2, 3.7, -6.8 ], [ 2.6, 0.8, 0.0 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -13.9, 2.3, -5.8 ], [ 4.4, 0.6, -1.1 ], [ 0.5, -0.1, 2.4 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -7.7, 1.2, -4.6 ], [ 3.9, -3.4, 1.5 ], [ -0.5, 0.0, 2.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -4.8, -4.0, -1.3 ], [ -4.2, -3.3, 3.1 ], [ -1.5, 2.5, 2.3 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -10.9, -6.1, -0.6 ], [ -5.3, -1.2, -0.9 ], [ -0.5, 1.9, 1.3 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -19.9, -6.4, -5.5 ], [ -0.3, 1.7, -10.5 ], [ -0.9, 2.0, 0.7 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -10.7, -3.2, -8.8 ], [ 7.8, 0.4, 0.1 ], [ -0.2, 2.1, 0.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -1.2, -1.9, -7.3 ], [ 0.8, 8.1, 2.5 ], [ -3.8, 0.1, -0.6 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -6.3, 0.5, -8.1 ], [ -9.8, -1.2, 0.5 ], [ 0.2, -1.9, -0.5 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -16.0, -0.7, -7.4 ], [ -7.6, 1.2, 1.5 ], [ -0.1, -2.0, -0.9 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -20.5, 2.3, -6.1 ], [ 3.5, 7.2, -2.9 ], [ -2.3, 0.2, -0.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -11.4, 2.6, -10.1 ], [ 10.4, 1.5, -0.2 ], [ -0.2, 1.3, -2.2 ], [ 0.0, 0.0, 0.5 ] ],
[ [ -3.8, 4.2, -7.3 ], [ 3.5, 0.9, 2.7 ], [ 0.2, 1.0, -2.6 ], [ 0.0, 0.0, 0.5 ] ] ] )
} )
}
@staticmethod
def getName():
return '3D Small Intestine 1'
@staticmethod
def getParameterSetNames():
return [
'Default',
'Mouse 1']
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
centralPathOption = cls.centralPathDefaultScaffoldPackages['Mouse 1']
options = {
'Central path': copy.deepcopy(centralPathOption),
'Number of segments': 100,
'Number of elements around': 8,
'Number of elements along segment': 4,
'Number of elements through wall': 1,
'Duodenum length': 25.0,
'Jejunum length': 240.0,
'Ileum length': 10.0,
'Duodenum inner radius': 0.6,
'Duodenum-jejunum inner radius': 1.0,
'Jejunum-ileum inner radius': 1.0,
'Ileum inner radius': 1.0,
'Wall thickness': 0.1,
'Use cross derivatives': False,
'Use linear through wall': True,
'Refine': False,
'Refine number of elements around': 1,
'Refine number of elements along': 1,
'Refine number of elements through wall': 1
}
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path',
'Number of segments',
'Number of elements around',
'Number of elements along segment',
'Number of elements through wall',
'Duodenum length',
'Jejunum length',
'Ileum length',
'Duodenum inner radius',
'Duodenum-jejunum inner radius',
'Jejunum-ileum inner radius',
'Ileum inner radius',
'Wall thickness',
'Use cross derivatives',
'Use linear through wall',
'Refine',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall' ]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [ MeshType_1d_path1 ]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.centralPathDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage('Central path', MeshType_1d_path1)
for key in [
'Number of segments',
'Number of elements around',
'Number of elements along segment',
'Number of elements through wall',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall']:
if options[key] < 1:
options[key] = 1
for key in [
'Duodenum length',
'Jejunum length',
'Ileum length',
'Duodenum inner radius',
'Duodenum-jejunum inner radius',
'Jejunum-ileum inner radius',
'Ileum inner radius',
'Wall thickness']:
if options[key] < 0.0:
options[key] = 0.0
@classmethod
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: annotationGroups
"""
centralPath = options['Central path']
segmentCount = options['Number of segments']
elementsCountAround = options['Number of elements around']
elementsCountAlongSegment = options['Number of elements along segment']
elementsCountThroughWall = options['Number of elements through wall']
duodenumLength = options['Duodenum length']
jejunumLength = options['Jejunum length']
duodenumInnerRadius = options['Duodenum inner radius']
duodenumJejunumInnerRadius = options['Duodenum-jejunum inner radius']
jejunumIleumInnerRadius = options['Jejunum-ileum inner radius']
ileumInnerRadius = options['Ileum inner radius']
wallThickness = options['Wall thickness']
useCrossDerivatives = options['Use cross derivatives']
useCubicHermiteThroughWall = not(options['Use linear through wall'])
elementsCountAlong = int(elementsCountAlongSegment*segmentCount)
startPhase = 0.0
firstNodeIdentifier = 1
firstElementIdentifier = 1
# Central path
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cx, cd1, cd2, cd12 = extractPathParametersFromRegion(tmpRegion)
# for i in range(len(cx)):
# print(i, '[', cx[i], ',', cd1[i], ',', cd2[i],',', cd12[i], '],')
del tmpRegion
# find arclength of colon
length = 0.0
elementsCountIn = len(cx) - 1
sd1 = interp.smoothCubicHermiteDerivativesLine(cx, cd1, fixAllDirections = True,
magnitudeScalingMode = interp.DerivativeScalingMode.HARMONIC_MEAN)
for e in range(elementsCountIn):
arcLength = interp.getCubicHermiteArcLength(cx[e], sd1[e], cx[e + 1], sd1[e + 1])
# print(e+1, arcLength)
length += arcLength
segmentLength = length / segmentCount
elementAlongLength = length / elementsCountAlong
# print('Length = ', length)
# Sample central path
sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(cx, cd1, elementsCountAlongSegment*segmentCount)
sd2, sd12 = interp.interpolateSampleCubicHermite(cd2, cd12, se, sxi, ssf)
# Generate variation of radius & tc width along length
lengthList = [0.0, duodenumLength, duodenumLength + jejunumLength, length]
innerRadiusList = [duodenumInnerRadius, duodenumJejunumInnerRadius, jejunumIleumInnerRadius, ileumInnerRadius]
innerRadiusSegmentList, dInnerRadiusSegmentList = interp.sampleParameterAlongLine(lengthList, innerRadiusList,
segmentCount)
# Create annotation groups for small intestine sections
elementsAlongDuodenum = round(duodenumLength / elementAlongLength)
elementsAlongJejunum = round(jejunumLength / elementAlongLength)
elementsAlongIleum = elementsCountAlong - elementsAlongDuodenum - elementsAlongJejunum
elementsCountAlongGroups = [elementsAlongDuodenum, elementsAlongJejunum, elementsAlongIleum]
smallintestineGroup = AnnotationGroup(region, get_smallintestine_term("small intestine"))
duodenumGroup = AnnotationGroup(region, get_smallintestine_term("duodenum"))
jejunumGroup = AnnotationGroup(region, get_smallintestine_term("jejunum"))
ileumGroup = AnnotationGroup(region, get_smallintestine_term("ileum"))
annotationGroupAlong = [[smallintestineGroup, duodenumGroup],
[smallintestineGroup, jejunumGroup],
[smallintestineGroup, ileumGroup]]
annotationGroupsAlong = []
for i in range(len(elementsCountAlongGroups)):
elementsCount = elementsCountAlongGroups[i]
for n in range(elementsCount):
annotationGroupsAlong.append(annotationGroupAlong[i])
annotationGroupsAround = []
for i in range(elementsCountAround):
annotationGroupsAround.append([ ])
annotationGroupsThroughWall = []
for i in range(elementsCountThroughWall):
annotationGroupsThroughWall.append([ ])
xExtrude = []
d1Extrude = []
d2Extrude = []
d3UnitExtrude = []
# Create object
smallIntestineSegmentTubeMeshInnerPoints = CylindricalSegmentTubeMeshInnerPoints(
elementsCountAround, elementsCountAlongSegment, segmentLength,
wallThickness, innerRadiusSegmentList, dInnerRadiusSegmentList, startPhase)
for nSegment in range(segmentCount):
# Create inner points
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, radiusAlongSegmentList = \
smallIntestineSegmentTubeMeshInnerPoints.getCylindricalSegmentTubeMeshInnerPoints(nSegment)
# Project reference point for warping onto central path
start = nSegment*elementsCountAlongSegment
end = (nSegment + 1)*elementsCountAlongSegment + 1
sxRefList, sd1RefList, sd2ProjectedListRef, zRefList = \
tubemesh.getPlaneProjectionOnCentralPath(xInner, elementsCountAround, elementsCountAlongSegment,
segmentLength, sx[start:end], sd1[start:end], sd2[start:end],
sd12[start:end])
# Warp segment points
xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList = tubemesh.warpSegmentPoints(
xInner, d1Inner, d2Inner, segmentAxis, sxRefList, sd1RefList, sd2ProjectedListRef,
elementsCountAround, elementsCountAlongSegment, zRefList, radiusAlongSegmentList,
closedProximalEnd=False)
# Store points along length
xExtrude = xExtrude + (xWarpedList if nSegment == 0 else xWarpedList[elementsCountAround:])
d1Extrude = d1Extrude + (d1WarpedList if nSegment == 0 else d1WarpedList[elementsCountAround:])
# Smooth d2 for nodes between segments and recalculate d3
if nSegment == 0:
d2Extrude = d2Extrude + (d2WarpedList[:-elementsCountAround])
d3UnitExtrude = d3UnitExtrude + (d3WarpedUnitList[:-elementsCountAround])
else:
xSecondFace = xWarpedList[elementsCountAround:elementsCountAround*2]
d2SecondFace = d2WarpedList[elementsCountAround:elementsCountAround*2]
for n1 in range(elementsCountAround):
nx = [xLastTwoFaces[n1], xLastTwoFaces[n1 + elementsCountAround], xSecondFace[n1]]
nd2 = [d2LastTwoFaces[n1], d2LastTwoFaces[n1 + elementsCountAround], d2SecondFace[n1]]
d2 = interp.smoothCubicHermiteDerivativesLine(nx, nd2, fixStartDerivative = True,
fixEndDerivative = True)[1]
d2Extrude.append(d2)
d3Unit = vector.normalise(vector.crossproduct3(vector.normalise(d1LastTwoFaces[n1 + elementsCountAround]),
vector.normalise(d2)))
d3UnitExtrude.append(d3Unit)
d2Extrude = d2Extrude + \
(d2WarpedList[elementsCountAround:-elementsCountAround] if nSegment < segmentCount - 1 else
d2WarpedList[elementsCountAround:])
d3UnitExtrude = d3UnitExtrude + \
(d3WarpedUnitList[elementsCountAround:-elementsCountAround] if nSegment < segmentCount - 1 else
d3WarpedUnitList[elementsCountAround:])
xLastTwoFaces = xWarpedList[-elementsCountAround*2:]
d1LastTwoFaces = d1WarpedList[-elementsCountAround*2:]
d2LastTwoFaces = d2WarpedList[-elementsCountAround*2:]
# Create coordinates and derivatives
xList, d1List, d2List, d3List, curvatureList = tubemesh.getCoordinatesFromInner(xExtrude, d1Extrude,
d2Extrude, d3UnitExtrude, [wallThickness]*(elementsCountAlong+1),
elementsCountAround, elementsCountAlong, elementsCountThroughWall, transitElementList)
flatWidthList, xiList = smallIntestineSegmentTubeMeshInnerPoints.getFlatWidthAndXiList()
# Create flat and texture coordinates
xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture = tubemesh.createFlatAndTextureCoordinates(
xiList, flatWidthList, length, wallThickness, elementsCountAround,
elementsCountAlong, elementsCountThroughWall, transitElementList)
# Create nodes and elements
nextNodeIdentifier, nextElementIdentifier, annotationGroups = tubemesh.createNodesAndElements(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAround, elementsCountAlong, elementsCountThroughWall,
annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd=False)
return annotationGroups
@classmethod
def refineMesh(cls, meshrefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshrefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
refineElementsCountAround = options['Refine number of elements around']
refineElementsCountAlong = options['Refine number of elements along']
refineElementsCountThroughWall = options['Refine number of elements through wall']
meshrefinement.refineAllElementsCubeStandard3d(refineElementsCountAround, refineElementsCountAlong,
refineElementsCountThroughWall)
return
class MeshType_3d_colon1(Scaffold_base):
'''
Generates a 3-D colon mesh with variable numbers
of elements around, along the central line, and through wall.
The colon is created by a function that generates a colon
segment and uses tubemesh to map the segment along a central
line profile.
'''
centralPathDefaultScaffoldPackages = {
'Human 1':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 8
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2
], [[[0.0, 0.0, 0.0], [-50.7, 178.2, 0.0],
[-24.0, -6.0, -12.0], [-14.0, -1.0, -12.0]],
[[-47.4, 188.6, 0.0], [-19.3, 177.1, 0.0],
[-22.0, -4.0, -8.0], [-4.0, 19.0, 22.0]],
[[-4.4, 396.5, 0.0], [206.0, 40.1, 0.0],
[-10.0, 20.0, 8.0], [-6.0, 0.0, 51.0]],
[[130.0, 384.1, 0.0], [130.8, -40.5, 0.0],
[-5.0, 4.0, 29.0], [0.0, 1.0, 24.0]],
[[279.4, 383.0, 0.0], [118.0, 48.7, 0.0],
[-2.0, 10.0, 22.0], [5.0, 25.0, -20.0]],
[[443.9, 390.8, 0.0], [111.3, -97.0, 0.0],
[10.0, 17.0, 6.0], [1.0, -6.0, -35.0]],
[[475.2, 168.0, 0.0], [-0.8, -112.4, 0.0],
[20.0, 0.0, -20.0], [15.0, -1.0, -10.0]],
[[432.6, -32.3, 0.0], [-90.5, -59.0, 0.0],
[6.0, -9.0, -14.0], [8.0, -11.0, -13.0]],
[[272.4, 7.5, 0.0], [-79.0, 47.4, 0.0],
[1.0, -11.0, -18.0], [4.0, -12.0, -12.0]]])
}),
'Human 2':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 8
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2
], [[[0.0, 0.0, 0.0], [-34.7, 104.1, -18.1],
[-24.0, -6.0, -12.0], [-14.0, -1.0, -12.0]],
[[-34.5, 114.0, -18.1], [1.2, 86.6, -3.4],
[-22.0, -4.0, -8.0], [-4.0, 19.0, 22.0]],
[[-19.1, 218.5, 5.5], [78.7, -7.1, 94.5],
[-10.0, 20.0, 8.0], [-6.0, 0.0, 51.0]],
[[82.5, 189.1, 94.2], [84.5, 7.1, 71.6], [-5.0, 4.0, 29.0],
[0.0, 1.0, 24.0]],
[[226.6, 218.7, 85.7], [95.0, 91.3, -58.5],
[-2.0, 10.0, 22.0], [5.0, 25.0, -20.0]],
[[325.5, 381.7, -57.9], [229.2, -66.7, -20.4],
[10.0, 17.0, 6.0], [1.0, -6.0, -35.0]],
[[354.0, 105.3, -24.4], [-6.3, -143.7, 20.3],
[20.0, 0.0, -20.0], [15.0, -1.0, -10.0]],
[[296.5, -121.2, -0.6], [-90.5, -59.0, 0.0],
[6.0, -9.0, -14.0], [8.0, -11.0, -13.0]],
[[169.8, -73.4, -33.5], [-72.2, 43.4, -27.4],
[1.0, -11.0, -18.0], [4.0, -12.0, -12.0]]])
}),
'Mouse 1':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 7
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2
], [[[0.0, 0.0, 0.0], [6.0, 12.0, -2.0], [2.0, 1.0, 2.0],
[6.0, 0.0, 3.0]],
[[-2.0, 11.0, -3.0], [-8.0, 4.0, 9.0], [2.0, 2.0, 1.0],
[0.0, 1.0, 2.0]],
[[-3.0, 2.0, 3.0], [-4.0, -8.0, 0.0], [2.0, -1.0, 2.0],
[1.0, 0.0, 2.0]],
[[-11.0, -3.0, -4.0], [-8.0, -3.0, -7.0], [1.0, -2.0, 1.0],
[0.0, 0.0, 0.5]],
[[-16.0, -4.0, 0.0], [4.0, -3.0, 14.0], [1.0, -3.0, 0.0],
[0.0, 0.0, 0.5]],
[[-7.0, -8.0, 0.0], [5.0, -1.0, -14.0], [0.0, -3.0, 0.0],
[0.0, 0.0, 0.5]],
[[-1.0, -6.0, -1.0], [2.0, -2.0, 9.0], [1.0, -3.0, -1.0],
[0.0, 0.0, 0.5]],
[[-2.0, -14.0, 5.0], [-2.0, -4.0, 2.0], [1.0, -2.0, -2.0],
[0.0, 0.0, 0.5]]])
}),
'Mouse 2':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 4
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2
], [[[0.0, 0.0, 0.0], [0.0, 0.0, 13.0], [0.0, -10.0, 0.0],
[0.0, 0.0, 0.5]],
[[0.0, 0.0, 13.0], [0.0, 2.0, 28.0], [0.0, -10.0, 0.0],
[0.0, 0.0, 0.5]],
[[-14.0, -2.0, 13.0], [0.0, -3.0, -19.0],
[0.0, -10.0, 0.0], [0.0, 0.0, 0.5]],
[[-14.0, -1.0, -10.0], [1.0, 1.0, -17.0],
[0.0, -10.0, 0.0], [0.0, 0.0, 0.5]],
[[-14.0, 0.0, -28.0], [0.0, 0.0, -11.0], [0.0, -10.0, 0.0],
[0.0, 0.0, 0.5]]])
}),
'Pig 1':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 1.0,
'Number of elements': 36
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2
], [[[163.7, -25.2, 12.2], [-21.7, 50.1, -18.1],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[117.2, 32.8, -2.6], [-64.3, 34.4, -3.9], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[38.8, 68.0, 2.6], [-83.9, 24.9, 14.7], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-42.8, 65.5, 15.5], [-69.9, -46.7, 10.3],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-93.1, -11.4, 30.6], [5.7, -104.4, 9.7], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-51.1, -83.7, 32.0], [69.7, -44.1, 1.0], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[43.0, -88.5, 28.5], [71.0, 41.0, -1.0], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[94.9, -5.8, 33.7], [-14.3, 60.1, 0.7], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[56.6, 72.9, 45.0], [-108.7, 54.1, 22.4], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-37.0, 64.6, 59.3], [-72.5, -33.9, 6.2], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-94.1, -15.6, 78.2], [8.5, -82.1, 13.7], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-46.1, -90.1, 82.9], [76.6, -39.9, 11.9],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[45.8, -87.7, 92.3], [99.1, 55.4, 12.9], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[110.7, 2.2, 102.2], [0.4, 61.7, 12.7], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[73.9, 58.3, 110.7], [-86.3, 19.7, 9.2], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-21.8, 25.4, 118.0], [-78.1, -83.9, 23.6],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-41.7, -49.8, 134.9], [10.8, -41.9, 18.8],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[4.0, -46.5, 133.5], [8.3, 43.8, -7.7], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[12.0, 2.6, 130.0], [27.8, 34.6, 1.5], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[67.4, 25.7, 125.9], [66.6, -38.7, -10.1],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[75.1, -21.4, 122.5], [-17.5, -31.0, 4.2],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[42.7, -66.4, 124.2], [-47.7, -41.1, -2.1],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-2.1, -88.6, 122.8], [-29.6, -5.3, -1.2],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-52.1, -78.6, 117.3], [-42.2, 33.8, -6.8],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-72.2, -6.5, 104.4], [16.8, 80.4, -10.7],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-28.6, 45.7, 90.9], [47.4, 37.5, -9.5], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[67.1, 63.6, 78.6], [77.1, -44.5, -5.2], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[89.1, -11.8, 67.7], [0.0, -73.3, -5.2], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[40.5, -79.2, 62.3], [-63.5, -36.7, -5.2],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-36.4, -80.2, 59.6], [-60.1, 26.4, -8.2],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-69.2, -19.3, 47.0], [0.0, 73.3, -5.2], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[-22.4, 39.1, 34.8], [63.5, 36.7, -5.2], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[40.6, 46.0, 32.9], [25.4, -23.1, -7.5], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[66.2, 11.0, 24.6], [13.7, -51.4, -1.8], [0.0, 0.0, 5.0],
[0.0, 0.0, 0.5]],
[[32.0, -49.3, 24.4], [-51.1, -50.1, -1.2],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-51.1, -45.3, 15.7], [-38.0, 52.2, -16.2],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]],
[[-122.9, 124.2, -36.0], [-21.3, 64.5, -18.3],
[0.0, 0.0, 5.0], [0.0, 0.0, 0.5]]])
}),
'Pig 2':
ScaffoldPackage(
MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'Length': 90.0,
'Number of elements': 3
},
'meshEdits':
exnodeStringFromNodeValues([
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2
], [[[0.0, 0.0, 0.0], [30.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 0.0]],
[[30.0, 0.0, 0.0], [30.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 0.0]],
[[60.0, 0.0, 0.0], [30.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 0.0]],
[[90.0, 0.0, 0.0], [30.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 0.0]]])
}),
}
@staticmethod
def getName():
return '3D Colon 1'
@staticmethod
def getParameterSetNames():
return [
'Default', 'Human 1', 'Human 2', 'Mouse 1', 'Mouse 2', 'Pig 1',
'Pig 2'
]
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if 'Human 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Human 2']
elif 'Mouse 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Mouse 1']
elif 'Mouse 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Mouse 2']
elif 'Pig 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 1']
elif 'Pig 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 2']
else:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Human 1']
if 'Mouse' in parameterSetName:
segmentProfileOption = ScaffoldPackage(
MeshType_3d_colonsegment1, defaultParameterSetName='Mouse 1')
elif 'Pig' in parameterSetName:
segmentProfileOption = ScaffoldPackage(
MeshType_3d_colonsegment1, defaultParameterSetName='Pig 1')
else:
segmentProfileOption = ScaffoldPackage(
MeshType_3d_colonsegment1, defaultParameterSetName='Human 1')
options = {
'Central path': copy.deepcopy(centralPathOption),
'Segment profile': segmentProfileOption,
'Number of segments': 30,
'Start phase': 0.0,
'Proximal length': 420.0,
'Transverse length': 460.0,
'Distal length': 620.0,
'Proximal inner radius': 43.5,
'Proximal tenia coli width': 10.0,
'Proximal-transverse inner radius': 33.0,
'Proximal-transverse tenia coli width': 10.0,
'Transverse-distal inner radius': 29.0,
'Transverse-distal tenia coli width': 10.0,
'Distal inner radius': 31.5,
'Distal tenia coli width': 10.0,
'Refine': False,
'Refine number of elements around': 1,
'Refine number of elements along': 1,
'Refine number of elements through wall': 1
}
if 'Human 2' in parameterSetName:
options['Proximal length'] = 180.0
options['Transverse length'] = 620.0
options['Distal length'] = 700.0
elif 'Mouse' in parameterSetName:
options['Number of segments'] = 10
options['Proximal length'] = 30.0
options['Transverse length'] = 20.0
options['Distal length'] = 25.0
options['Proximal inner radius'] = 1.0
options['Proximal tenia coli width'] = 0.5
options['Proximal-transverse inner radius'] = 0.9
options['Proximal-transverse tenia coli width'] = 0.7
options['Transverse-distal inner radius'] = 0.7
options['Transverse-distal tenia coli width'] = 1.0
options['Distal inner radius'] = 0.7
options['Distal tenia coli width'] = 1.0
elif 'Pig 1' in parameterSetName:
options['Number of segments'] = 120
options['Proximal length'] = 2610.0
options['Transverse length'] = 200.0
options['Distal length'] = 200.0
options['Proximal inner radius'] = 20.0
options['Proximal tenia coli width'] = 5.0
options['Proximal-transverse inner radius'] = 10.5
options['Proximal-transverse tenia coli width'] = 5.0
options['Transverse-distal inner radius'] = 8.0
options['Transverse-distal tenia coli width'] = 5.0
options['Distal inner radius'] = 8.0
options['Distal tenia coli width'] = 5.0
elif 'Pig 2' in parameterSetName:
options['Number of segments'] = 3
options['Proximal length'] = 30.0
options['Transverse length'] = 30.0
options['Distal length'] = 30.0
options['Proximal inner radius'] = 16.0
options['Proximal tenia coli width'] = 5.0
options['Proximal-transverse inner radius'] = 16.0
options['Proximal-transverse tenia coli width'] = 5.0
options['Transverse-distal inner radius'] = 16.0
options['Transverse-distal tenia coli width'] = 5.0
options['Distal inner radius'] = 16.0
options['Distal tenia coli width'] = 5.0
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path', 'Segment profile', 'Number of segments',
'Start phase', 'Proximal length', 'Transverse length',
'Distal length', 'Proximal inner radius',
'Proximal tenia coli width', 'Proximal-transverse inner radius',
'Proximal-transverse tenia coli width',
'Transverse-distal inner radius',
'Transverse-distal tenia coli width', 'Distal inner radius',
'Distal tenia coli width', 'Refine',
'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall'
]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [MeshType_1d_path1]
if optionName == 'Segment profile':
return [MeshType_3d_colonsegment1]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls,
optionName,
scaffoldType,
parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + ' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(
cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(
cls.centralPathDefaultScaffoldPackages[parameterSetName])
if optionName == 'Segment profile':
if not parameterSetName:
parameterSetName = scaffoldType.getParameterSetNames()[0]
return ScaffoldPackage(scaffoldType,
defaultParameterSetName=parameterSetName)
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType(
) in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage(
'Central path', MeshType_1d_path1)
if not options['Segment profile'].getScaffoldType(
) in cls.getOptionValidScaffoldTypes('Segment profile'):
options['Segment profile'] = cls.getOptionScaffoldPackage(
'Segment profile', MeshType_3d_colonsegmentteniacoli1)
for key in [
'Number of segments', 'Refine number of elements around',
'Refine number of elements along',
'Refine number of elements through wall'
]:
if options[key] < 1:
options[key] = 1
for key in [
'Proximal length', 'Transverse length', 'Distal length',
'Proximal inner radius', 'Proximal tenia coli width',
'Proximal-transverse inner radius',
'Proximal-transverse tenia coli width',
'Transverse-distal inner radius',
'Transverse-distal tenia coli width', 'Distal inner radius',
'Distal tenia coli width'
]:
if options[key] < 0.0:
options[key] = 0.0
@staticmethod
def generateBaseMesh(region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: annotationGroups
"""
centralPath = options['Central path']
segmentProfile = options['Segment profile']
segmentCount = options['Number of segments']
startPhase = options['Start phase'] % 360.0
proximalLength = options['Proximal length']
transverseLength = options['Transverse length']
distalLength = options['Distal length']
proximalInnerRadius = options['Proximal inner radius']
proximalTCWidth = options['Proximal tenia coli width']
proximalTransverseInnerRadius = options[
'Proximal-transverse inner radius']
proximalTransverseTCWidth = options[
'Proximal-transverse tenia coli width']
transverseDistalInnerRadius = options['Transverse-distal inner radius']
transverseDistalTCWidth = options['Transverse-distal tenia coli width']
distalInnerRadius = options['Distal inner radius']
distalTCWidth = options['Distal tenia coli width']
segmentSettings = segmentProfile.getScaffoldSettings()
elementsCountAroundTC = segmentSettings[
'Number of elements around tenia coli']
elementsCountAroundHaustrum = segmentSettings[
'Number of elements around haustrum']
cornerInnerRadiusFactor = segmentSettings['Corner inner radius factor']
haustrumInnerRadiusFactor = segmentSettings[
'Haustrum inner radius factor']
segmentLengthEndDerivativeFactor = segmentSettings[
'Segment length end derivative factor']
segmentLengthMidDerivativeFactor = segmentSettings[
'Segment length mid derivative factor']
tcCount = segmentSettings['Number of tenia coli']
tcThickness = segmentSettings['Tenia coli thickness']
elementsCountAround = (elementsCountAroundTC +
elementsCountAroundHaustrum) * tcCount
elementsCountAlongSegment = segmentSettings[
'Number of elements along segment']
elementsCountThroughWall = segmentSettings[
'Number of elements through wall']
wallThickness = segmentSettings['Wall thickness']
useCrossDerivatives = segmentSettings['Use cross derivatives']
useCubicHermiteThroughWall = not (
segmentSettings['Use linear through wall'])
elementsCountAlong = int(elementsCountAlongSegment * segmentCount)
firstNodeIdentifier = 1
firstElementIdentifier = 1
# Central path
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cx, cd1, cd2, cd12 = extractPathParametersFromRegion(tmpRegion)
# for i in range(len(cx)):
# print(i, '[', cx[i], ',', cd1[i], ',', cd2[i], ',', cd12[i], '],')
del tmpRegion
# find arclength of colon
length = 0.0
elementsCountIn = len(cx) - 1
sd1 = interp.smoothCubicHermiteDerivativesLine(
cx,
cd1,
fixAllDirections=True,
magnitudeScalingMode=interp.DerivativeScalingMode.HARMONIC_MEAN)
for e in range(elementsCountIn):
arcLength = interp.getCubicHermiteArcLength(
cx[e], sd1[e], cx[e + 1], sd1[e + 1])
# print(e+1, arcLength)
length += arcLength
segmentLength = length / segmentCount
# print('Length = ', length)
# Sample central path
sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(
cx, cd1, elementsCountAlongSegment * segmentCount)
sd2 = interp.interpolateSampleCubicHermite(cd2, cd12, se, sxi, ssf)[0]
# Generate variation of radius & tc width along length
lengthList = [
0.0, proximalLength, proximalLength + transverseLength, length
]
innerRadiusList = [
proximalInnerRadius, proximalTransverseInnerRadius,
transverseDistalInnerRadius, distalInnerRadius
]
innerRadiusAlongElementList, dInnerRadiusAlongElementList = interp.sampleParameterAlongLine(
lengthList, innerRadiusList, elementsCountAlong)
tcWidthList = [
proximalTCWidth, proximalTransverseTCWidth,
transverseDistalTCWidth, distalTCWidth
]
tcWidthAlongElementList, dTCWidthAlongElementList = interp.sampleParameterAlongLine(
lengthList, tcWidthList, elementsCountAlong)
xExtrude = []
d1Extrude = []
d2Extrude = []
d3UnitExtrude = []
# Create object
colonSegmentTubeMeshInnerPoints = ColonSegmentTubeMeshInnerPoints(
region, elementsCountAroundTC, elementsCountAroundHaustrum,
elementsCountAlongSegment, tcCount,
segmentLengthEndDerivativeFactor, segmentLengthMidDerivativeFactor,
segmentLength, wallThickness, cornerInnerRadiusFactor,
haustrumInnerRadiusFactor, innerRadiusAlongElementList,
dInnerRadiusAlongElementList, tcWidthAlongElementList, startPhase)
for nSegment in range(segmentCount):
# Create inner points
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, annotationGroups, annotationArray, \
faceMidPointsZ = colonSegmentTubeMeshInnerPoints.getColonSegmentTubeMeshInnerPoints(nSegment)
# Warp segment points
xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList = tubemesh.warpSegmentPoints(
xInner, d1Inner, d2Inner, segmentAxis, segmentLength, sx, sd1,
sd2, elementsCountAround, elementsCountAlongSegment, nSegment,
faceMidPointsZ)
# Store points along length
xExtrude = xExtrude + (xWarpedList if nSegment == 0 else
xWarpedList[elementsCountAround:])
d1Extrude = d1Extrude + (d1WarpedList if nSegment == 0 else
d1WarpedList[elementsCountAround:])
d2Extrude = d2Extrude + (d2WarpedList if nSegment == 0 else
d2WarpedList[elementsCountAround:])
d3UnitExtrude = d3UnitExtrude + (
d3WarpedUnitList
if nSegment == 0 else d3WarpedUnitList[elementsCountAround:])
contractedWallThicknessList = colonSegmentTubeMeshInnerPoints.getContractedWallThicknessList(
)
# Create coordinates and derivatives
xList, d1List, d2List, d3List, curvatureList = tubemesh.getCoordinatesFromInner(
xExtrude, d1Extrude, d2Extrude, d3UnitExtrude,
contractedWallThicknessList, elementsCountAround,
elementsCountAlong, elementsCountThroughWall, transitElementList)
relaxedLengthList, xiList = colonSegmentTubeMeshInnerPoints.getRelaxedLengthAndXiList(
)
if tcThickness > 0:
tubeTCWidthList = colonSegmentTubeMeshInnerPoints.getTubeTCWidthList(
)
xList, d1List, d2List, d3List, annotationGroups, annotationArray = getTeniaColi(
region, xList, d1List, d2List, d3List, curvatureList, tcCount,
elementsCountAroundTC, elementsCountAroundHaustrum,
elementsCountAlong, elementsCountThroughWall, tubeTCWidthList,
tcThickness, sx, annotationGroups, annotationArray)
# Create flat and texture coordinates
xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture = createFlatAndTextureCoordinatesTeniaColi(
xiList, relaxedLengthList, length, wallThickness, tcCount,
tcThickness, elementsCountAroundTC,
elementsCountAroundHaustrum, elementsCountAlong,
elementsCountThroughWall, transitElementList)
# Create nodes and elements
nextNodeIdentifier, nextElementIdentifier, annotationGroups = createNodesAndElementsTeniaColi(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat,
xTexture, d1Texture, d2Texture, elementsCountAroundTC,
elementsCountAroundHaustrum, elementsCountAlong,
elementsCountThroughWall, tcCount, annotationGroups,
annotationArray, firstNodeIdentifier, firstElementIdentifier,
useCubicHermiteThroughWall, useCrossDerivatives)
else:
# Create flat and texture coordinates
xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture = tubemesh.createFlatAndTextureCoordinates(
xiList, relaxedLengthList, length, wallThickness,
elementsCountAround, elementsCountAlong,
elementsCountThroughWall, transitElementList)
# Create nodes and elements
nextNodeIdentifier, nextElementIdentifier, annotationGroups = tubemesh.createNodesAndElements(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat,
xTexture, d1Texture, d2Texture, elementsCountAround,
elementsCountAlong, elementsCountThroughWall, annotationGroups,
annotationArray, firstNodeIdentifier, firstElementIdentifier,
useCubicHermiteThroughWall, useCrossDerivatives)
return annotationGroups
@classmethod
def generateMesh(cls, region, options):
"""
Generate base or refined mesh.
:param region: Zinc region to create mesh in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: list of AnnotationGroup for mesh.
"""
if not options['Refine']:
return cls.generateBaseMesh(region, options)
refineElementsCountAround = options['Refine number of elements around']
refineElementsCountAlong = options['Refine number of elements along']
refineElementsCountThroughWall = options[
'Refine number of elements through wall']
baseRegion = region.createRegion()
baseAnnotationGroups = cls.generateBaseMesh(baseRegion, options)
meshrefinement = MeshRefinement(baseRegion, region,
baseAnnotationGroups)
meshrefinement.refineAllElementsCubeStandard3d(
refineElementsCountAround, refineElementsCountAlong,
refineElementsCountThroughWall)
return meshrefinement.getAnnotationGroups()
class MeshType_3d_brainstem1(Scaffold_base):
"""
Generates a tapered cylinder for the brainstem based on
solid cylinder mesh, with variable numbers of elements
in major, minor and length directions. Regions of the
brainstem are annotated.
"""
centralPathDefaultScaffoldPackages = {
'Brainstem 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 3.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
], [[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 2.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 3.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 4.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 5.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 6.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 7.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 8.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.0, 0.0], [0.0, 0.0, 0.0]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '2',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
}),
'Cat 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 3.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
],
[
# [ [0.0,1.0,-5.0], [0.0,0.0,4.5], [5.0,0.0,0.0], [1.0,0.0,0.0], [0.0,2.4,0.0], [0.0,2.2,0.0] ],
# [ [0.0,1.0,-0.5], [0.0,0.0,4.5], [6.0,0.0,0.0], [1.0,0.0,0.0], [0.0,4.0,0.0], [0.0,1.1,0.0] ],
# [ [0.0,1.0, 4.0], [0.0,0.0,4.5], [7.0,0.0,0.0], [1.0,0.0,0.0], [0.0,4.5,0.0], [0.0,0.8,0.0] ],
# [ [0.0,1.0, 8.5], [0.0,0.0,4.5], [8.0,0.0,0.0], [1.0,0.0,0.0], [0.0,5.5,0.0], [0.0,0.8,0.0] ],
# [ [0.0,1.0,13.0], [0.0,0.0,4.5], [9.0,0.0,0.0], [1.0,0.0,0.0], [0.0,6.0,0.0], [0.0,0.2,0.0] ]
[[0.0, 10.7, -12.3], [0.0, -3.8, 3.1], [4.8, 0.0, 0.0],
[-0.7, 0.0, 0.0], [-0.0, 2.2, 2.6], [0.0, 0.5, 0.1]],
[[0.0, 6.8, -8.8], [0.0, -4.0, 3.9], [4.5, 0.0, 0.0],
[0.1, 0.0, 0.0], [-0.0, 2.7, 2.7], [0.0, 0.5, 0.1]],
[[0.0, 2.8, -4.5], [0.0, -3.5, 4.2], [5.0, 0.0, 0.0],
[1.2, 0.0, 0.0], [-0.0, 3.2, 2.8], [0.0, 0.5, 0.0]],
[[0.0, -0.2, -0.5], [0.0, -2.8, 3.8], [6.8, 0.0, 0.0],
[0.8, 0.0, 0.0], [-0.0, 3.8, 2.8], [0.0, 0.6, -0.4]],
[[0.0, -2.8, 3.0], [0.0, -1.9, 4.1], [6.8, 0.0, 0.0],
[-0.6, 0.0, 0.0], [-0.0, 4.5, 2.0], [0.0, 0.3, -0.1]],
[[0.0, -3.8, 7.5], [0.0, -2.7, 4.6], [5.5, 0.0, 0.0],
[-0.2, 0.0, 0.0], [-0.0, 4.3, 2.5], [0.0, -1.0, 1.0]],
[[0.0, -8.2, 11.5], [0.0, -5.9, 3.2], [6.8, 0.0, 0.0],
[2.8, 0.0, 0.0], [-0.0, 2.3, 4.2], [0.0, -3.1, 2.4]]
]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '2',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
}),
'Human 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
],
[[[0.0, 18.9, -50.7], [0.0, -3.2, 15.4], [7.8, 0.0, 0.0],
[0.5, 0.0, 0.0], [-0.0, 6.1, 1.3], [0.0, 0.8, 1.7]],
[[0.0, 14.6, -36.3], [0.0, -5.4, 13.3], [8.5, 0.0, 0.0],
[0.9, 0.0, 0.0], [-0.0, 7.2, 2.9], [0.0, 1.4, 1.6]],
[[0.0, 8.3, -24.1], [0.0, -6.4, 12.5], [9.6, 0.0, 0.0],
[4.4, 0.0, 0.0], [-0.0, 8.9, 4.6], [0.0, 1.3, 0.5]],
[[0.0, 1.8, -11.4], [0.0, -5.3, 13.3], [17.4, 0.0, 0.0],
[5.3, 0.0, 0.0], [-0.0, 9.8, 3.9], [0.0, 2.6, -0.2]],
[[0.0, -2.3, 2.4], [0.0, -3.9, 13.2], [20.2, 0.0, 0.0],
[-0.4, 0.0, 0.0], [-0.0, 14.1, 4.2], [0.0, 2.2, -0.5]],
[[0.0, -6.0, 15.0], [0.0, -2.6, 12.9], [16.8, 0.0, 0.0],
[-2.4, 0.0, 0.0], [-0.0, 14.4, 2.9], [0.0, 0.2, -1.9]],
[[0.0, -7.5, 28.0], [0.0, -0.4, 13.1], [15.3, 0.0, 0.0],
[-0.6, 0.0, 0.0], [-0.0, 14.5, 0.4], [0.0, 0.0, -3.1]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
}),
'Mouse 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
],
[([[0.0, 1.5, -3.4], [0.0, -0.1, 1.1], [1.4, 0.0, 0.0],
[-0.1, 0.0, 0.0], [0.0, 1.0, 0.1], [0.0, 0.1, 0.9]]),
([[0.0, 1.0, -2.3], [0.0, -0.8, 1.0], [1.3, 0.0, 0.0],
[0.0, 0.0, 0.0], [0.0, 0.8, 0.7], [0.0, 0.0, 0.6]]),
([[0.0, -0.1, -1.6], [0.0, -1.2, 0.8], [1.5, 0.0, 0.0],
[0.4, 0.0, 0.0], [0.0, 0.7, 1.0], [0.0, 0.1, 0.1]]),
([[0.0, -1.2, -0.7], [0.0, -0.7, 1.2], [2.0, 0.0, 0.0],
[0.2, 0.0, 0.0], [0.0, 1.2, 0.7], [0.0, 0.1, -0.1]]),
([[0.0, -1.5, 0.5], [0.0, 0.1, 1.4], [2.0, 0.0, 0.0],
[-0.1, 0.0, 0.0], [0.0, 1.4, -0.1], [0.0, 0.1, -0.1]]),
([[0.0, -1.1, 1.9], [0.0, -0.3, 1.4], [1.6, 0.0, 0.0],
[-0.1, 0.0, 0.0], [0.0, 1.5, 0.3], [0.0, -0.3, 0.3]]),
([[0.0, -2.1, 3.1], [0.0, -1.3, 0.8], [2.0, 0.0, 0.0],
[0.8, 0.0, 0.0], [0.0, 0.7, 1.2], [0.0, -0.8, 0.7]])]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
}),
'Rat 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
],
[[[0.0, 2.9, -5.4], [0.0, 0.5, 1.7], [1.9, 0.0, 0.0],
[-0.2, 0.0, 0.0], [0.0, 1.3, -0.4], [-0.0, 0.2, 1.3]],
[[0.0, 2.7, -3.5], [0.0, -0.9, 2.0], [1.8, 0.0, 0.0],
[0.0, 0.0, 0.0], [-0.0, 1.4, 0.6], [-0.0, 0.0, 0.8]],
[[0.0, 1.1, -1.8], [0.0, -1.4, 1.7], [2.0, 0.0, 0.0],
[0.5, 0.0, 0.0], [-0.0, 1.3, 1.1], [0.0, 0.1, 0.2]],
[[0.0, -0.1, -0.2], [0.0, -1.1, 1.5], [2.7, 0.0, 0.0],
[0.3, 0.0, 0.0], [-0.0, 1.5, 1.1], [0.0, 0.2, -0.2]],
[[0.0, -1.1, 1.2], [0.0, -0.7, 1.6], [2.7, 0.0, 0.0],
[-0.2, 0.0, 0.0], [-0.0, 1.8, 0.8], [0.0, 0.1, -0.1]],
[[0.0, -1.5, 3.0], [0.0, -1.1, 1.9], [2.2, 0.0, 0.0],
[-0.1, 0.0, 0.0], [-0.0, 1.7, 1.0], [0.0, -0.4, 0.4]],
[[0.0, -3.3, 4.6], [0.0, -2.4, 1.3], [2.7, 0.0, 0.0],
[1.1, 0.0, 0.0], [-0.0, 0.9, 1.7], [0.0, -1.2, 1.0]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
}),
'Pig 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
],
[([[0.0, 25.6, -29.3], [0.0, -5.4, 3.5], [4.8, 0.0, 0.0],
[-0.7, 0.0, 0.0], [0.0, 1.8, 2.9], [0.0, 1.1, 1.4]]),
([[0.0, 19.5, -25.3], [0.0, -6.7, 4.8], [5.7, 0.0, 0.0],
[2.5, 0.0, 0.0], [0.0, 2.8, 4.0], [0.0, 0.8, 0.7]]),
([[0.0, 12.2, -19.9], [0.0, -6.7, 5.4], [10.1, 0.0, 0.0],
[3.0, 0.0, 0.0], [0.0, 3.3, 4.2], [0.0, 1.5, 0.5]]),
([[0.0, 6.0, -14.5], [0.0, -5.5, 6.3], [12.9, -0.2, -0.2],
[0.7, 0.0, 0.0], [0.1, 5.7, 4.9], [0.0, 2.0, -0.6]]),
([[0.0, 1.5, -7.4], [0.0, -2.8, 7.0], [11.4, 0.0, 0.0],
[-0.3, 0.2, 0.0], [0.0, 7.4, 3.0], [-0.2, 2.4, -1.2]]),
([[0.0, 0.1, -1.0], [0.0, -1.5, 6.9], [11.2, 0.3, 0.1],
[-0.5, 0.1, 0.1], [-0.3, 11.3, 2.5], [-0.1, 1.5, -0.2]
]),
([[0.0, -1.5, 6.6], [0.0, -2.0, 7.4], [10.3, 0.2, 0.0],
[-1.3, -0.2, -0.0], [-0.2, 9.4, 2.5], [0.2, -2.3, 0.9]])
]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
}),
'Sheep 1':
ScaffoldPackage(
MeshType_1d_path1,
{
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits':
exnodeStringFromNodeValues( # dimensional.
[
Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3
],
[([[0.0, 21.3, -33.2], [0.0, -7.5, 6.0], [4.8, 0.0, 0.0],
[4.8, -0.0, -0.0], [0.0, 2.8, 3.5], [0.0, 3.2, 1.3]]),
([[0.0, 14.5, -26.7], [0.0, -6.1, 7.2], [8.5, -0.0, -0.0],
[2.6, 0.0, 0.0], [0.0, 4.9, 4.1], [-0.0, 1.1, 0.1]]),
([[0.0, 9.2, -19.0], [0.0, -5.2, 7.2], [10.1, 0.0, 0.0],
[1.1, -0.1, -0.0], [0.0, 5.0, 3.6], [0.1, 0.4, -0.6]]),
([[0.0, 4.0, -12.2], [0.0, -3.5, 7.0], [10.8, -0.2, -0.1],
[-0.4, 0.2, 0.0], [0.1, 5.7, 2.9], [-0.1, 0.8, -1.4]]),
([[0.0, 2.1, -5.5], [0.0, -1.2, 7.6], [9.4, 0.3, 0.1],
[0.1, 0.2, 0.1], [-0.2, 6.6, 1.0], [-0.2, 2.2, -0.3]]),
([[0.0, 1.9, 2.9], [0.0, -2.1, 8.8], [11.2, 0.2, 0.1],
[3.3, -0.1, -0.0], [-0.2, 10.4, 2.5], [0.1, 0.3, 2.0]]),
([[0.0, -2.3, 11.4], [0.0, -6.2, 8.1], [16.2, 0.1, 0.0],
[6.7, -0.2, -0.0], [-0.0, 6.7, 5.1], [0.3, -7.7, 3.2]])
]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
}, {
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}
]
})
}
@staticmethod
def getName():
return '3D Brainstem 1'
@staticmethod
def getParameterSetNames():
return [
'Default', 'Cat 1', 'Human 1', 'Mouse 1', 'Rat 1', 'Pig 1',
'Sheep 1'
]
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if parameterSetName == 'Default':
parameterSetName = 'Human 1'
if 'Cat 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Cat 1']
if 'Human 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Human 1']
if 'Mouse 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Mouse 1']
if 'Rat 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Rat 1']
if 'Pig 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 1']
if 'Sheep 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages[
'Sheep 1']
options = {
'Base parameter set': parameterSetName,
'Central path': copy.deepcopy(centralPathOption),
'Number of elements across major': 6,
'Number of elements across minor': 6,
'Number of elements along': 8,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements across major and minor': 1,
'Refine number of elements along': 1
}
return options
@staticmethod
def getOrderedOptionNames():
return [
'Central path', 'Number of elements across major',
'Number of elements across minor', 'Number of elements along',
'Refine', 'Refine number of elements across major and minor',
'Refine number of elements along'
]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Central path':
return [MeshType_1d_path1]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Central path':
return list(cls.centralPathDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), \
cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls,
optionName,
scaffoldType,
parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + \
' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Central path':
if not parameterSetName:
parameterSetName = list(
cls.centralPathDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(
cls.centralPathDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Central path'].getScaffoldType(
) in cls.getOptionValidScaffoldTypes('Central path'):
options['Central path'] = cls.getOptionScaffoldPackage(
'Central path', MeshType_1d_path1)
dependentChanges = False
if options['Number of elements across major'] < 4:
options['Number of elements across major'] = 4
if options['Number of elements across major'] % 2:
options['Number of elements across major'] += 1
if options['Number of elements across minor'] < 4:
options['Number of elements across minor'] = 4
if options['Number of elements across minor'] % 2:
options['Number of elements across minor'] += 1
if options['Number of elements along'] < 2:
options['Number of elements along'] = 2
return dependentChanges
@classmethod
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: None
"""
parameterSetName = options['Base parameter set']
isCat = 'Cat 1' in parameterSetName
isHuman = 'Human 1' in parameterSetName
isMouse = 'Mouse 1' in parameterSetName
isRat = 'Rat 1' in parameterSetName
isPig = 'Pig 1' in parameterSetName
isSheep = 'Sheep 1' in parameterSetName
centralPath = options['Central path']
brainstemPath = cls.centralPathDefaultScaffoldPackages['Brainstem 1']
elementsCountAcrossMajor = options['Number of elements across major']
elementsCountAcrossMinor = options['Number of elements across minor']
elementsCountAlong = options['Number of elements along']
# Cross section at Z axis
halfBrainStem = False
if halfBrainStem:
elementsCountAcrossMajor //= 2
elementsPerLayer = (
(elementsCountAcrossMajor - 2) *
elementsCountAcrossMinor) + (2 * (elementsCountAcrossMinor - 2))
fm = region.getFieldmodule()
cache = fm.createFieldcache()
coordinates = findOrCreateFieldCoordinates(fm)
mesh = fm.findMeshByDimension(3)
# Annotation groups
brainstemGroup = AnnotationGroup(region,
get_brainstem_term('brainstem'))
brainstemMeshGroup = brainstemGroup.getMeshGroup(mesh)
midbrainGroup = AnnotationGroup(region, get_brainstem_term('midbrain'))
midbrainMeshGroup = midbrainGroup.getMeshGroup(mesh)
ponsGroup = AnnotationGroup(region, get_brainstem_term('pons'))
ponsMeshGroup = ponsGroup.getMeshGroup(mesh)
medullaGroup = AnnotationGroup(region,
get_brainstem_term('medulla oblongata'))
medullaMeshGroup = medullaGroup.getMeshGroup(mesh)
annotationGroups = [
brainstemGroup, midbrainGroup, ponsGroup, medullaGroup
]
annotationGroupAlong = [[brainstemGroup, midbrainGroup],
[brainstemGroup, ponsGroup],
[brainstemGroup, medullaGroup]]
# point markers
# centralCanal = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
# get_brainstem_term('central canal of spinal cord'))
# cerebralAqueduct = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
# get_brainstem_term('cerebral aqueduct'))
# foramenCaecum = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
# get_brainstem_term('foramen caecum of medulla oblongata'))
dorsalMidCaudalGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem dorsal midline caudal point'))
ventralMidCaudalGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem ventral midline caudal point'))
dorsalMidCranGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem dorsal midline cranial point'))
ventralMidCranGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem ventral midline cranial point'))
dorsalMidMedullaPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem dorsal midline pons-medulla junction'))
ventralMidMedullaPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem ventral midline pons-medulla junction'))
dorsalMidMidbrainPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem dorsal midline midbrain-pons junction'))
ventralMidMidbrainPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem ventral midline midbrain-pons junction'))
#######################
# CREATE MAIN BODY MESH
#######################
cylinderShape = CylinderShape.CYLINDER_SHAPE_FULL if not halfBrainStem else CylinderShape.CYLINDER_SHAPE_LOWER_HALF
# Body coordinates
cylinderCentralPath = CylinderCentralPath(region, centralPath,
elementsCountAlong)
base = CylinderEnds(elementsCountAcrossMajor,
elementsCountAcrossMinor,
centre=[0.0, 0.0, 0.0],
alongAxis=cylinderCentralPath.alongAxis[0],
majorAxis=cylinderCentralPath.majorAxis[0],
minorRadius=cylinderCentralPath.minorRadii[0])
cylinder1 = CylinderMesh(fm,
coordinates,
elementsCountAlong,
base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath,
useCrossDerivatives=False)
brainstem_coordinates = findOrCreateFieldCoordinates(
fm, name="brainstem coordinates")
# Brain coordinates
tmp_region = region.createRegion()
tmp_fm = tmp_region.getFieldmodule()
tmp_brainstem_coordinates = findOrCreateFieldCoordinates(
tmp_fm, name="brainstem coordinates")
cylinderCentralPath1 = CylinderCentralPath(tmp_region, brainstemPath,
elementsCountAlong)
base1 = CylinderEnds(elementsCountAcrossMajor,
elementsCountAcrossMinor,
centre=[0.0, 0.0, 0.0],
alongAxis=cylinderCentralPath1.alongAxis[0],
majorAxis=cylinderCentralPath1.majorAxis[0],
minorRadius=cylinderCentralPath1.minorRadii[0])
cylinder2 = CylinderMesh(tmp_fm,
tmp_brainstem_coordinates,
elementsCountAlong,
base1,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath1,
useCrossDerivatives=False)
# Write two coordinates
sir = tmp_region.createStreaminformationRegion()
srm = sir.createStreamresourceMemory()
tmp_region.write(sir)
result, buffer = srm.getBuffer()
sir = region.createStreaminformationRegion()
srm = sir.createStreamresourceMemoryBuffer(buffer)
region.read(sir)
del srm
del sir
del tmp_fm
del tmp_brainstem_coordinates
del tmp_region
# Annotating groups
iRegionBoundaries = [
int(6 * elementsCountAlong / 15),
int(13 * elementsCountAlong / 15)
]
for elementIdentifier in range(1, mesh.getSize() + 1):
element = mesh.findElementByIdentifier(elementIdentifier)
brainstemMeshGroup.addElement(element)
if elementIdentifier > (iRegionBoundaries[-1] * elementsPerLayer):
midbrainMeshGroup.addElement(element)
elif (elementIdentifier >
(iRegionBoundaries[0] * elementsPerLayer)) and (
elementIdentifier <=
(iRegionBoundaries[-1] * elementsPerLayer)):
ponsMeshGroup.addElement(element)
else:
medullaMeshGroup.addElement(element)
################
# point markers
################
pointMarkers = [
{
"group": dorsalMidCaudalGroup,
"marker_brainstem_coordinates": [0.0, 1.0, 0.0]
},
{
"group": ventralMidCaudalGroup,
"marker_brainstem_coordinates": [0.0, -1.0, 0.0]
},
{
"group": dorsalMidCranGroup,
"marker_brainstem_coordinates": [0.0, 1.0, 8.0]
},
{
"group": ventralMidCranGroup,
"marker_brainstem_coordinates": [0.0, -1.0, 8.0]
},
{
"group": dorsalMidMedullaPonsJunction,
"marker_brainstem_coordinates": [0.0, 1.0, 3.0]
},
{
"group": ventralMidMedullaPonsJunction,
"marker_brainstem_coordinates": [0.0, -1.0, 3.0]
},
{
"group": dorsalMidMidbrainPonsJunction,
"marker_brainstem_coordinates": [0.0, 1.0, 6.0]
},
{
"group": ventralMidMidbrainPonsJunction,
"marker_brainstem_coordinates": [0.0, -1.0, 6.0]
},
]
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerBrainstemCoordinates = findOrCreateFieldCoordinates(
fm, name="marker_body_coordinates")
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
markerTemplateInternal.defineField(markerBrainstemCoordinates)
cache = fm.createFieldcache()
brainstemNodesetGroup = brainstemGroup.getNodesetGroup(nodes)
nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1)
findMarkerLocation = fm.createFieldFindMeshLocation(
markerBrainstemCoordinates, brainstem_coordinates, mesh)
findMarkerLocation.setSearchMode(
FieldFindMeshLocation.SEARCH_MODE_EXACT)
for pointMarker in pointMarkers:
group = pointMarker["group"]
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
cache.setNode(markerPoint)
markerBrainstemCoordinates.assignReal(
cache, pointMarker["marker_brainstem_coordinates"])
markerName.assignString(cache, group.getName())
element, xi = findMarkerLocation.evaluateMeshLocation(cache, 3)
markerLocation.assignMeshLocation(cache, element, xi)
group.getNodesetGroup(nodes).addNode(markerPoint)
brainstemNodesetGroup.addNode(markerPoint)
nodeIdentifier += 1
return annotationGroups
@classmethod
def refineMesh(cls, meshRefinement, options):
"""
Refine source mesh into separate region, with change of basis.
:param meshRefinement: MeshRefinement, which knows source and target region.
:param options: Dict containing options. See getDefaultOptions().
"""
assert isinstance(meshRefinement, MeshRefinement)
refineElementsCountAcrossMajor = options[
'Refine number of elements across major and minor']
refineElementsCountAlong = options['Refine number of elements along']
meshRefinement.refineAllElementsCubeStandard3d(
refineElementsCountAcrossMajor, refineElementsCountAlong,
refineElementsCountAcrossMajor)
@classmethod
def defineFaceAnnotations(cls, region, options, annotationGroups):
"""
Add face annotation groups from the 1D mesh.
:param region: Zinc region containing model.
:param options: Dict containing options. See getDefaultOptions().
:param annotationGroups: List of annotation groups for ventral-level elements.
New point annotation groups are appended to this list.
"""
# create groups
fm = region.getFieldmodule()
mesh2d = fm.findMeshByDimension(2)
is_exterior = fm.createFieldIsExterior()
is_exterior_face_xi1 = fm.createFieldOr(
fm.createFieldAnd(is_exterior,
fm.createFieldIsOnFace(Element.FACE_TYPE_XI1_0)),
fm.createFieldAnd(is_exterior,
fm.createFieldIsOnFace(Element.FACE_TYPE_XI1_1)))
is_exterior_face_xi2 = fm.createFieldOr(
fm.createFieldAnd(is_exterior,
fm.createFieldIsOnFace(Element.FACE_TYPE_XI2_0)),
fm.createFieldAnd(is_exterior,
fm.createFieldIsOnFace(Element.FACE_TYPE_XI2_1)))
is_exterior_face_xi3 = fm.createFieldOr(
fm.createFieldAnd(is_exterior,
fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0)),
fm.createFieldAnd(is_exterior,
fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1)))
# external regions
groupNames = ['brainstem', 'midbrain', 'medulla oblongata', 'pons']
for groupName in groupNames:
subGroup = AnnotationGroup(region, get_brainstem_term(groupName))
issub = subGroup.getFieldElementGroup(mesh2d)
is_subface_ext = fm.createFieldOr(
fm.createFieldAnd(issub, is_exterior_face_xi1),
fm.createFieldAnd(issub, is_exterior_face_xi3))
subFaceGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(groupName + ' exterior'))
subFaceGroup.getMeshGroup(mesh2d).addElementsConditional(
is_subface_ext)
# brainstem interface
groupNames = [
'brainstem-spinal cord interface', 'thalamus-brainstem interface'
]
for groupName in groupNames:
subGroupName = 'midbrain' if groupName == 'thalamus-brainstem interface' else 'medulla oblongata'
subGroup = AnnotationGroup(region,
get_brainstem_term(subGroupName))
issub = subGroup.getFieldElementGroup(mesh2d)
is_subface_ext = fm.createFieldAnd(issub, is_exterior_face_xi2)
subFaceGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region, get_brainstem_term(groupName))
subFaceGroup.getMeshGroup(mesh2d).addElementsConditional(
is_subface_ext)
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)
class MeshType_3d_bladder1(Scaffold_base):
'''
3-D bladder scaffold.
'''
ostiumDefaultScaffoldPackages = {
'Ostium Cat 1': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
'Number of vessels': 1,
'Number of elements across common': 2,
'Number of elements around ostium': 8,
'Number of elements along': 2,
'Number of elements through wall': 1, # not implemented for > 1
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 0.3,
'Ostium length': 0.2,
'Ostium wall thickness': 0.05,
'Ostium inter-vessel distance': 0.8,
'Ostium inter-vessel height': 0.0,
'Use linear through ostium wall': True,
'Vessel end length factor': 1.0,
'Vessel inner diameter': 0.15,
'Vessel wall thickness': 0.04,
'Vessel angle 1 degrees': 0.0,
'Vessel angle 1 spread degrees': 0.0,
'Vessel angle 2 degrees': 0.0,
'Use linear through vessel wall': True,
# 'Use cross derivatives': False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements along': 4,
'Refine number of elements through wall': 1
},
}),
'Ostium Rat 1': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
'Number of vessels': 1,
'Number of elements across common': 2,
'Number of elements around ostium': 8,
'Number of elements along': 1,
'Number of elements through wall': 1, # not implemented for > 1
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 0.15,
'Ostium length': 0.05,
'Ostium wall thickness': 0.02,
'Ostium inter-vessel distance': 0.8,
'Ostium inter-vessel height': 0.0,
'Use linear through ostium wall': True,
'Vessel end length factor': 1.0,
'Vessel inner diameter': 0.04,
'Vessel wall thickness': 0.01,
'Vessel angle 1 degrees': 0.0,
'Vessel angle 1 spread degrees': 0.0,
'Vessel angle 2 degrees': 0.0,
'Use linear through vessel wall': True,
# 'Use cross derivatives': False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements along': 4,
'Refine number of elements through wall': 1
},
})
}
@staticmethod
def getName():
return '3D Bladder 1'
@staticmethod
def getParameterSetNames():
return [
'Default',
'Cat 1',
'Rat 1']
@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if 'Rat' in parameterSetName:
ostiumOption = cls.ostiumDefaultScaffoldPackages['Ostium Rat 1']
else:
ostiumOption = cls.ostiumDefaultScaffoldPackages['Ostium Cat 1']
options = {
'Number of elements up neck': 6,
'Number of elements up body': 8,
'Number of elements around': 8, # should be even
'Number of elements through wall': 1,
'Number of elements around ostium': 8, # implemented for 8
'Number of elements radially on annulus': 1,
'Height': 5.0,
'Major diameter': 6.0,
'Minor diameter': 6.0,
'Bladder wall thickness': 0.05,
'Urethra diameter': 1.0,
'Ureter': copy.deepcopy(ostiumOption),
'Ostium position around': 0.55, # should be on the dorsal part
'Ostium position up': 0.55,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements up': 4,
'Refine number of elements through wall': 1
}
if 'Rat' in parameterSetName:
options['Number of elements around'] = 16 # should be even
options['Height'] = 3.0
options['Major diameter'] = 5.0
options['Minor diameter'] = 3.0
options['Bladder wall thickness'] = 0.02
options['Urethra diameter'] = 0.7
options['Ostium position around'] = 0.65 # should be on the dorsal part
options['Ostium position up'] = 0.75
return options
@staticmethod
def getOrderedOptionNames():
return [
'Number of elements up neck',
'Number of elements up body',
'Number of elements around',
'Number of elements through wall',
'Number of elements radially on annulus',
'Height',
'Major diameter',
'Minor diameter',
'Bladder wall thickness',
'Urethra diameter',
'Ostium position around',
'Ostium position up',
'Ureter',
'Use cross derivatives',
'Refine',
'Refine number of elements around',
'Refine number of elements up',
'Refine number of elements through wall'
]
@classmethod
def getOptionValidScaffoldTypes(cls, optionName):
if optionName == 'Ureter':
return [MeshType_3d_ostium1]
return []
@classmethod
def getOptionScaffoldTypeParameterSetNames(cls, optionName, scaffoldType):
if optionName == 'Ureter':
return list(cls.ostiumDefaultScaffoldPackages.keys())
assert scaffoldType in cls.getOptionValidScaffoldTypes(optionName), cls.__name__ + '.getOptionScaffoldTypeParameterSetNames. ' + \
'Invalid option \'' + optionName + '\' scaffold type ' + scaffoldType.getName()
return scaffoldType.getParameterSetNames()
@classmethod
def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=None):
'''
:param parameterSetName: Name of valid parameter set for option Scaffold, or None for default.
:return: ScaffoldPackage.
'''
if parameterSetName:
assert parameterSetName in cls.getOptionScaffoldTypeParameterSetNames(optionName, scaffoldType), \
'Invalid parameter set ' + str(parameterSetName) + ' for scaffold ' + str(scaffoldType.getName()) + ' in option ' + str(optionName) + ' of scaffold ' + cls.getName()
if optionName == 'Ureter':
if not parameterSetName:
parameterSetName = list(cls.ostiumDefaultScaffoldPackages.keys())[0]
return copy.deepcopy(cls.ostiumDefaultScaffoldPackages[parameterSetName])
assert False, cls.__name__ + '.getOptionScaffoldPackage: Option ' + optionName + ' is not a scaffold'
@classmethod
def checkOptions(cls, options):
if not options['Ureter'].getScaffoldType() in cls.getOptionValidScaffoldTypes('Ureter'):
options['Ureter'] = cls.getOptionScaffoldPackage('Ureter', MeshType_3d_ostium1)
if (options['Number of elements up neck'] < 4):
options['Number of elements up neck'] = 4
if (options['Number of elements up body'] < 4):
options['Number of elements up body'] = 4
if (options['Number of elements around'] < 8):
options['Number of elements around'] = 8
elif (options['Number of elements around'] % 2) == 1:
options['Number of elements around'] += 1
if (options['Number of elements through wall'] != 1):
options['Number of elements through wall'] = 1
if(options['Number of elements radially on annulus'] > 2):
options['Number of elements radially on annulus'] = 2
if (options['Major diameter'] < options['Minor diameter']):
options['Major diameter'] = options['Minor diameter']
@classmethod
def generateBaseMesh(cls, region, options):
'''
Generate the base bicubic Hermite mesh.
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: list of AnnotationGroup
'''
elementsCountUpNeck = options['Number of elements up neck']
elementsCountUpBody = options['Number of elements up body']
elementsCountAround = options['Number of elements around']
height = options['Height']
majorDiameter = options['Major diameter']
minorDiameter = options['Minor diameter']
radius = 0.5 * options['Urethra diameter']
bladderWallThickness = options['Bladder wall thickness']
useCrossDerivatives = options['Use cross derivatives']
elementsCountAroundOstium = options['Number of elements around ostium']
elementsCountAnnulusRadially = options['Number of elements radially on annulus']
ostiumPositionAround = options['Ostium position around']
ostiumPositionUp = options['Ostium position up']
ostiumOptions = options['Ureter']
ostiumDefaultOptions = ostiumOptions.getScaffoldSettings()
fm = region.getFieldmodule()
fm.beginChange()
coordinates = findOrCreateFieldCoordinates(fm)
cache = fm.createFieldcache()
mesh = fm.findMeshByDimension(3)
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplateApex = nodes.createNodetemplate()
nodetemplateApex.defineField(coordinates)
nodetemplateApex.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1)
nodetemplateApex.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1)
nodetemplateApex.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1)
if useCrossDerivatives:
nodetemplate = nodes.createNodetemplate()
nodetemplate.defineField(coordinates)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D2_DS1DS2, 1)
else:
nodetemplate = nodetemplateApex
eftfactory = eftfactory_bicubichermitelinear(mesh, useCrossDerivatives)
eft = eftfactory.createEftBasic()
elementtemplate = mesh.createElementtemplate()
elementtemplate.setElementShapeType(Element.SHAPE_TYPE_CUBE)
elementtemplate.defineField(coordinates, -1, eft)
neckGroup = AnnotationGroup(region, get_bladder_term("neck of urinary bladder"))
bodyGroup = AnnotationGroup(region, get_bladder_term("dome of the bladder"))
urinaryBladderGroup = AnnotationGroup(region, get_bladder_term("urinary bladder"))
annotationGroups = [neckGroup, bodyGroup, urinaryBladderGroup]
neckMeshGroup = neckGroup.getMeshGroup(mesh)
bodyMeshGroup = bodyGroup.getMeshGroup(mesh)
urinaryBladderMeshGroup = urinaryBladderGroup.getMeshGroup(mesh)
# create nodes
# create neck of the bladder
nodeIdentifier = 1
radiansPerElementAround = 2.0*math.pi/elementsCountAround
radiansPerElementUpNeck = (math.pi/4)/elementsCountUpNeck
# create lower part of the ellipsoidal
neckHeight = height - height * math.cos(math.pi / 4)
ellipsoidal_x = []
ellipsoidal_d1 = []
ellipsoidal_d2 = []
for n2 in range(0, elementsCountUpNeck+1):
radiansUp = n2 * radiansPerElementUpNeck
cosRadiansUp = math.cos(radiansUp)
sinRadiansUp = math.sin(radiansUp)
majorRadius = 0.5 * majorDiameter * sinRadiansUp
minorRadius = 0.5 * minorDiameter * sinRadiansUp
if n2 == 0:
for n1 in range(elementsCountAround):
radiansAround = n1 * radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
x = [
-majorRadius * sinRadiansAround,
minorRadius * cosRadiansAround,
-height - neckHeight
]
dx_ds1 = [
-majorRadius * cosRadiansAround * radiansPerElementAround,
minorRadius * -sinRadiansAround * radiansPerElementAround,
0.0
]
dx_ds2 = [
-0.5 * majorDiameter * sinRadiansAround * cosRadiansUp * radiansPerElementUpNeck,
0.5 * minorDiameter * cosRadiansAround * cosRadiansUp * radiansPerElementUpNeck,
height * sinRadiansUp * radiansPerElementUpNeck
]
ellipsoidal_x.append(x)
ellipsoidal_d1.append(dx_ds1)
ellipsoidal_d2.append(dx_ds2)
else:
for n1 in range(elementsCountAround):
neckHeight = height - height * math.cos(math.pi/4)
radiansAround = n1 * radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
x = [
-majorRadius * sinRadiansAround,
minorRadius * cosRadiansAround,
-height - neckHeight + n2 * 2 * neckHeight / elementsCountUpNeck
]
dx_ds1 = [
-majorRadius * cosRadiansAround * radiansPerElementAround,
minorRadius * -sinRadiansAround * radiansPerElementAround,
0.0
]
dx_ds2 = [
-0.5 * majorDiameter * sinRadiansAround * cosRadiansUp * radiansPerElementUpNeck,
0.5 * minorDiameter * cosRadiansAround * cosRadiansUp * radiansPerElementUpNeck,
height * sinRadiansUp * radiansPerElementUpNeck
]
ellipsoidal_x.append(x)
ellipsoidal_d1.append(dx_ds1)
ellipsoidal_d2.append(dx_ds2)
# create tube nodes
radiansPerElementAround = 2.0 * math.pi / elementsCountAround
tube_x = []
tube_d1 = []
tube_d2 = []
for n2 in range(0, elementsCountUpNeck + 1):
radiansUp = n2 * radiansPerElementUpNeck
cosRadiansUp = math.cos(radiansUp)
sinRadiansUp = math.sin(radiansUp)
if n2 == 0:
for n1 in range(elementsCountAround):
radiansAround = n1 * radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
x = [
-radius * sinRadiansAround,
radius * cosRadiansAround,
-height - neckHeight
]
dx_ds1 = [
-radiansPerElementAround * radius * cosRadiansAround,
radiansPerElementAround * radius * -sinRadiansAround,
0.0
]
dx_ds2 = [0, 0, height / (2 * elementsCountUpNeck)]
tube_x.append(x)
tube_d1.append(dx_ds1)
tube_d2.append(dx_ds2)
else:
for n1 in range(elementsCountAround):
neckHeight = height - height* math.cos(math.pi/4)
radiansAround = n1 * radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
x = [
-radius * sinRadiansAround,
radius * cosRadiansAround,
-height - neckHeight + n2 * 2 * neckHeight / elementsCountUpNeck
]
dx_ds1 = [
-radiansPerElementAround * radius * cosRadiansAround,
radiansPerElementAround * radius * -sinRadiansAround,
0.0
]
dx_ds2 = [0, 0, height / elementsCountUpNeck]
tube_x.append(x)
tube_d1.append(dx_ds1)
tube_d2.append(dx_ds2)
# interpolation between the lower part of the ellipsoidal and the tube
m1 = 0
z_bottom = ellipsoidal_x[-1][2]
z_top = ellipsoidal_x[0][2]
delta_z = z_top - z_bottom
interpolatedNodes = []
interpolatedNodes_d1 = []
interpolatedNodes_d2 = []
for n2 in range(elementsCountUpNeck+1):
xi = 1.0 - (ellipsoidal_x[m1][2] - z_bottom) / delta_z
for n1 in range(elementsCountAround):
phi_inner, _, phi_outer, _ = getCubicHermiteBasis(xi)
x = [(phi_inner*tube_x[m1][c] + phi_outer*ellipsoidal_x[m1][c]) for c in range(3)]
d1 = [(phi_inner*tube_d1[m1][c] + phi_outer*ellipsoidal_d1[m1][c]) for c in range(3)]
d2 = [(phi_inner*tube_d2[m1][c] + phi_outer*ellipsoidal_d2[m1][c]) for c in range(3)]
interpolatedNodes.append(x)
interpolatedNodes_d1.append(d1)
interpolatedNodes_d2.append(d2)
m1 += 1
# smoothing the derivatives
sd2Raw = []
for n1 in range(elementsCountAround):
lineSmoothingNodes = []
lineSmoothingNodes_d2 = []
for n2 in range(elementsCountUpNeck+1):
lineSmoothingNodes.append(interpolatedNodes[n1 + n2 * elementsCountAround])
lineSmoothingNodes_d2.append(interpolatedNodes_d2[n1 + n2 * elementsCountAround])
sd2 = smoothCubicHermiteDerivativesLine(lineSmoothingNodes, lineSmoothingNodes_d2,
fixAllDirections=False,
fixStartDerivative=True, fixEndDerivative=True,
fixStartDirection=False, fixEndDirection=False)
sd2Raw.append(sd2)
# re-arrange the derivatives order
d2RearrangedList = []
for n2 in range(elementsCountUpNeck+1):
for n1 in range(elementsCountAround):
d2 = sd2Raw[n1][n2]
d2RearrangedList.append(d2)
# create tracksurface at the outer layer of the neck
nodesOnTrackSurface = []
nodesOnTrackSurface_d1 = []
nodesOnTrackSurface_d2 = []
for n2 in range(elementsCountUpNeck+1):
for n1 in range(elementsCountAround):
if (n1 <= elementsCountAround / 2):
nodesOnTrackSurface.append(interpolatedNodes[n2 * elementsCountAround + n1])
nodesOnTrackSurface_d1.append(interpolatedNodes_d1[n2 * elementsCountAround + n1])
nodesOnTrackSurface_d2.append(d2RearrangedList[n2 * elementsCountAround + n1])
# nodes and derivatives of the neck of the bladder
listOuterNeck_x = []
listOuterNeck_d1 = []
listOuterNeck_d2 = []
elementsCount1 = elementsCountAround // 2
elementsCount2 = elementsCountUpNeck
tracksurfaceOstium1 = TrackSurface(elementsCount1, elementsCount2, nodesOnTrackSurface, nodesOnTrackSurface_d1,
nodesOnTrackSurface_d2)
ostium1Position = tracksurfaceOstium1.createPositionProportion(ostiumPositionAround, ostiumPositionUp)
ostium1Position.xi1 = 1.0
ostium1Position.xi2 = 1.0
ostiumElementPositionAround = ostium1Position.e1
ostiumElementPositionUp = ostium1Position.e2
for n2 in range(len(interpolatedNodes)):
listOuterNeck_x.append(interpolatedNodes[n2])
listOuterNeck_d1.append(interpolatedNodes_d1[n2])
listOuterNeck_d2.append(d2RearrangedList[n2])
# create body of the bladder
radiansPerElementAround = 2.0 * math.pi / elementsCountAround
radiansPerElementUpBody = (3 * math.pi / 4) / elementsCountUpBody
# create regular rows
listOuterBody_x = []
listOuterBody_d1 = []
listOuterBody_d2 = []
for n2 in range(1, elementsCountUpBody):
radiansUp = (math.pi / 4) + n2 * radiansPerElementUpBody
cosRadiansUp = math.cos(radiansUp)
sinRadiansUp = math.sin(radiansUp)
majorRadius = 0.5 * majorDiameter * sinRadiansUp
minorRadius = 0.5 * minorDiameter * sinRadiansUp
for n1 in range(elementsCountAround):
radiansAround = n1 * radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
x = [
-majorRadius * sinRadiansAround,
minorRadius * cosRadiansAround,
-height * cosRadiansUp
]
dx_ds1 = [
-majorRadius * cosRadiansAround * radiansPerElementAround,
minorRadius * -sinRadiansAround * radiansPerElementAround,
0.0
]
dx_ds2 = [
-0.5 * majorDiameter * sinRadiansAround * cosRadiansUp * radiansPerElementUpBody,
0.5 * minorDiameter * cosRadiansAround * cosRadiansUp * radiansPerElementUpBody,
height*sinRadiansUp * radiansPerElementUpBody
]
listOuterBody_x.append(x)
listOuterBody_d1.append(dx_ds1)
listOuterBody_d2.append(dx_ds2)
# create outer apex node
outerApexNode_x = []
outerApexNode_d1 = []
outerApexNode_d2 = []
x = [0.0, 0.0, height]
dx_ds1 = [height*radiansPerElementUpBody/2, 0.0, 0.0]
dx_ds2 = [0.0, height*radiansPerElementUpBody/2, 0.0]
outerApexNode_x.append(x)
outerApexNode_d1.append(dx_ds1)
outerApexNode_d2.append(dx_ds2)
# set nodes of outer layer of the bladder
listTotalOuter_x = listOuterNeck_x + listOuterBody_x + outerApexNode_x
listTotalOuter_d1 = listOuterNeck_d1 + listOuterBody_d1 + outerApexNode_d1
listTotalOuter_d2 = listOuterNeck_d2 + listOuterBody_d2 + outerApexNode_d2
outerLayer_x = []
outerLayer_d1 = []
outerLayer_d2 = []
for n2 in range(len(listTotalOuter_x)):
if (n2 != (ostiumElementPositionUp + 1) * elementsCountAround + ostiumElementPositionAround + 1) and\
(n2 != (ostiumElementPositionUp + 1) * elementsCountAround + elementsCountAround - ostiumElementPositionAround - 1):
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, listTotalOuter_x[n2])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, listTotalOuter_d1[n2])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, listTotalOuter_d2[n2])
nodeIdentifier += 1
outerLayer_x.append(listTotalOuter_x[n2])
outerLayer_d1.append(listTotalOuter_d1[n2])
outerLayer_d2.append(listTotalOuter_d2[n2])
# create and set nodes of inner layer of the bladder
listTotalInner_x = []
listTotalInner_d1 = []
listTotalInner_d2 = []
for n2 in range(elementsCountUpNeck + elementsCountUpBody):
loop_x = [listTotalOuter_x[n2 * elementsCountAround + n1] for n1 in range(elementsCountAround)]
loop_d1 = [listTotalOuter_d1[n2 * elementsCountAround + n1] for n1 in range(elementsCountAround)]
loop_d2 = [listTotalOuter_d2[n2 * elementsCountAround + n1] for n1 in range(elementsCountAround)]
for n1 in range(elementsCountAround):
x, d1, _, _ = interp.projectHermiteCurvesThroughWall(loop_x, loop_d1, loop_d2, n1,
-bladderWallThickness, loop=True)
listTotalInner_x.append(x)
listTotalInner_d1.append(d1)
listInner_d2 = []
for n2 in range(elementsCountAround):
nx = [listTotalOuter_x[n1 * elementsCountAround + n2] for n1 in range(elementsCountUpNeck + elementsCountUpBody)]
nd1 = [listTotalOuter_d1[n1 * elementsCountAround + n2] for n1 in range(elementsCountUpNeck + elementsCountUpBody)]
nd2 = [listTotalOuter_d2[n1 * elementsCountAround + n2] for n1 in range(elementsCountUpNeck + elementsCountUpBody)]
for n1 in range(elementsCountUpNeck + elementsCountUpBody):
_, d2, _, _ = interp.projectHermiteCurvesThroughWall(nx, nd2, nd1, n1,
bladderWallThickness, loop=False)
listInner_d2.append(d2)
# re-arrange the derivatives order
for n2 in range(elementsCountUpNeck + elementsCountUpBody):
for n1 in range(elementsCountAround):
rearranged_d2 = listInner_d2[n1 * (elementsCountUpNeck + elementsCountUpBody) + n2]
listTotalInner_d2.append(rearranged_d2)
innerLayer_x = []
innerLayer_d1 = []
innerLayer_d2 = []
for n2 in range(len(listTotalInner_x)):
if (n2 != (ostiumElementPositionUp + 1) * elementsCountAround + ostiumElementPositionAround + 1) and \
(n2 != (ostiumElementPositionUp + 1) * elementsCountAround + elementsCountAround - ostiumElementPositionAround - 1):
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, listTotalInner_x[n2])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, listTotalInner_d1[n2])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, listTotalInner_d2[n2])
nodeIdentifier += 1
innerLayer_x.append(listTotalInner_x[n2])
innerLayer_d1.append(listTotalInner_d1[n2])
innerLayer_d2.append(listTotalInner_d2[n2])
# create inner apex node
x = [0.0, 0.0, height - bladderWallThickness]
dx_ds1 = [height*radiansPerElementUpBody/2, 0.0, 0.0]
dx_ds2 = [0.0, height*radiansPerElementUpBody/2, 0.0]
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, dx_ds1)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, dx_ds2)
listTotalInner_x.append(x)
listTotalInner_d1.append(dx_ds1)
listTotalInner_d2.append(dx_ds2)
innerLayer_x.append(x)
innerLayer_d1.append(dx_ds1)
innerLayer_d2.append(dx_ds2)
nodeIdentifier += 1
# create ureters on the surface
elementIdentifier = 1
# ureter 1
centerUreter1_x, centerUreter1_d1, centerUreter1_d2 = tracksurfaceOstium1.evaluateCoordinates(ostium1Position, derivatives=True)
td1, td2, td3 = calculate_surface_axes(centerUreter1_d1, centerUreter1_d2, [1.0, 0.0, 0.0])
m1 = ostiumElementPositionUp * elementsCountAround + ostiumElementPositionAround
ureter1StartCornerx = listOuterNeck_x[m1]
v1 = [(ureter1StartCornerx[c] - centerUreter1_x[c]) for c in range(3)]
ostium1Direction = vector.crossproduct3(td3, v1)
nodeIdentifier, elementIdentifier, (o1_x, o1_d1, o1_d2, _, o1_NodeId, o1_Positions) = \
generateOstiumMesh(region, ostiumDefaultOptions, tracksurfaceOstium1, ostium1Position, ostium1Direction,
startNodeIdentifier=nodeIdentifier, startElementIdentifier=elementIdentifier)
# ureter 2
tracksurfaceOstium2 = tracksurfaceOstium1.createMirrorX()
ostium2Position = TrackSurfacePosition(elementsCountAround - ostiumElementPositionAround, ostiumElementPositionUp - 1, 0.0, 1.0)
centerUreter2_x, centerUreter2_d1, centerUreter2_d2 = tracksurfaceOstium2.evaluateCoordinates(ostium2Position, derivatives =True)
ad1, ad2, ad3 = calculate_surface_axes(centerUreter2_d1, centerUreter2_d2, [1.0, 0.0, 0.0])
if elementsCountAroundOstium == 4:
m2 = ostiumElementPositionUp * elementsCountAround + elementsCountAround - ostiumElementPositionAround - 1
else:
m2 = ostiumElementPositionUp * elementsCountAround + elementsCountAround - ostiumElementPositionAround - 2
ureter2StartCornerx = listOuterNeck_x[m2]
v2 = [(ureter2StartCornerx[c] - centerUreter2_x[c]) for c in range(3)]
ostium2Direction = vector.crossproduct3(ad3, v2)
nodeIdentifier, elementIdentifier, (o2_x, o2_d1, o2_d2, _, o2_NodeId, o2_Positions) = \
generateOstiumMesh(region, ostiumDefaultOptions, tracksurfaceOstium2, ostium2Position, ostium2Direction,
startNodeIdentifier=nodeIdentifier, startElementIdentifier=elementIdentifier)
# create annulus mesh around ostium
endPoints1_x = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endPoints1_d1 = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endPoints1_d2 = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endNode1_Id = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endDerivativesMap = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endPoints2_x = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endPoints2_d1 = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endPoints2_d2 = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
endNode2_Id = [[None] * elementsCountAroundOstium, [None] * elementsCountAroundOstium]
nodeCountsEachWallLayer = (elementsCountUpNeck + elementsCountUpBody) * elementsCountAround - 1
for n3 in range(2):
n1 = 0
endNode1_Id[n3][n1] = ((1 - n3) * nodeCountsEachWallLayer) + (ostiumElementPositionUp * elementsCountAround) + ostiumElementPositionAround + 1
endNode1_Id[n3][n1 + 1] = endNode1_Id[n3][n1] + elementsCountAround
endNode1_Id[n3][n1 + 2] = endNode1_Id[n3][n1 + 1] + elementsCountAround - 2
endNode1_Id[n3][n1 + 3] = endNode1_Id[n3][n1 + 2] + 1
endNode1_Id[n3][n1 + 4] = endNode1_Id[n3][n1 + 3] + 1
endNode1_Id[n3][n1 + 5] = endNode1_Id[n3][n1 + 1] + 1
endNode1_Id[n3][n1 + 6] = endNode1_Id[n3][n1] + 2
endNode1_Id[n3][n1 + 7] = endNode1_Id[n3][n1] + 1
if ostiumElementPositionAround == 0:
endNode2_Id[n3][n1] = ((1 - n3) * nodeCountsEachWallLayer) + (ostiumElementPositionUp * elementsCountAround)\
+ elementsCountAround - ostiumElementPositionAround - 1
endNode2_Id[n3][n1 + 1] = endNode2_Id[n3][n1] + elementsCountAround - 1
endNode2_Id[n3][n1 + 2] = endNode2_Id[n3][n1 + 1] + elementsCountAround - 1
endNode2_Id[n3][n1 + 3] = endNode2_Id[n3][n1 + 2] + 1
endNode2_Id[n3][n1 + 4] = endNode2_Id[n3][n1 + 3] - elementsCountAround + 1
endNode2_Id[n3][n1 + 5] = endNode2_Id[n3][n1 + 4] - elementsCountAround + 2
endNode2_Id[n3][n1 + 6] = endNode2_Id[n3][n1 + 5] - elementsCountAround
endNode2_Id[n3][n1 + 7] = endNode2_Id[n3][n1] + 1
else:
endNode2_Id[n3][n1] = ((1 - n3) * nodeCountsEachWallLayer) + (ostiumElementPositionUp * elementsCountAround)\
+ elementsCountAround - ostiumElementPositionAround - 1
endNode2_Id[n3][n1 + 1] = endNode2_Id[n3][n1] + elementsCountAround - 1
endNode2_Id[n3][n1 + 2] = endNode2_Id[n3][n1 + 1] + elementsCountAround - 1
endNode2_Id[n3][n1 + 3] = endNode2_Id[n3][n1 + 2] + 1
endNode2_Id[n3][n1 + 4] = endNode2_Id[n3][n1 + 3] + 1
endNode2_Id[n3][n1 + 5] = endNode2_Id[n3][n1 + 1] + 1
endNode2_Id[n3][n1 + 6] = endNode2_Id[n3][n1] + 2
endNode2_Id[n3][n1 + 7] = endNode2_Id[n3][n1] + 1
for n3 in range(2):
for n1 in range(elementsCountAroundOstium):
nc1 = endNode1_Id[n3][n1] - (1 - n3) * nodeCountsEachWallLayer - 1
endPoints1_x[n3][n1] = innerLayer_x[nc1]
endPoints1_d1[n3][n1] = innerLayer_d1[nc1]
endPoints1_d2[n3][n1] = [innerLayer_d2[nc1][c] for c in range(3)]
nc2 = endNode2_Id[n3][n1] - (1 - n3) * nodeCountsEachWallLayer - 1
endPoints2_x[n3][n1] = innerLayer_x[nc2]
endPoints2_d1[n3][n1] = innerLayer_d1[nc2]
endPoints2_d2[n3][n1] = innerLayer_d2[nc2]
for n1 in range(elementsCountAroundOstium):
if n1 == 0:
endDerivativesMap[0][n1] = ((-1, 0, 0), (-1, -1, 0), None, (0, 1, 0))
endDerivativesMap[1][n1] = ((-1, 0, 0), (-1, -1, 0), None, (0, 1, 0))
elif n1 == 1:
endDerivativesMap[0][n1] = ((0, 1, 0), (-1, 0, 0), None)
endDerivativesMap[1][n1] = ((0, 1, 0), (-1, 0, 0), None)
elif n1 == 2:
endDerivativesMap[0][n1] = ((0, 1, 0), (-1, 1, 0), None, (1, 0, 0))
endDerivativesMap[1][n1] = ((0, 1, 0), (-1, 1, 0), None, (1, 0, 0))
elif n1 == 3:
endDerivativesMap[0][n1] = ((1, 0, 0), (0, 1, 0), None)
endDerivativesMap[1][n1] = ((1, 0, 0), (0, 1, 0), None)
elif n1 == 4:
endDerivativesMap[0][n1] = ((1, 0, 0), (1, 1, 0), None, (0, -1, 0))
endDerivativesMap[1][n1] = ((1, 0, 0), (1, 1, 0), None, (0, -1, 0))
elif n1 == 5:
endDerivativesMap[0][n1] = ((0, -1, 0), (1, 0, 0), None)
endDerivativesMap[1][n1] = ((0, -1, 0), (1, 0, 0), None)
elif n1 == 6:
endDerivativesMap[0][n1] = ((0, -1, 0), (1, -1, 0), None, (-1, 0, 0))
endDerivativesMap[1][n1] = ((0, -1, 0), (1, -1, 0), None, (-1, 0, 0))
else:
endDerivativesMap[0][n1] = ((-1, 0, 0), (0, -1, 0), None)
endDerivativesMap[1][n1] = ((-1, 0, 0), (0, -1, 0), None)
nodeIdentifier, elementIdentifier = createAnnulusMesh3d(
nodes, mesh, nodeIdentifier, elementIdentifier,
o1_x, o1_d1, o1_d2, None, o1_NodeId, None,
endPoints1_x, endPoints1_d1, endPoints1_d2, None, endNode1_Id, endDerivativesMap,
elementsCountRadial=elementsCountAnnulusRadially, meshGroups=[neckMeshGroup, urinaryBladderMeshGroup])
nodeIdentifier, elementIdentifier = createAnnulusMesh3d(
nodes, mesh, nodeIdentifier, elementIdentifier,
o2_x, o2_d1, o2_d2, None, o2_NodeId, None,
endPoints2_x, endPoints2_d1, endPoints2_d2, None, endNode2_Id, endDerivativesMap,
elementsCountRadial=elementsCountAnnulusRadially, meshGroups=[neckMeshGroup, urinaryBladderMeshGroup])
# create elements
for e3 in range(1):
newl = (e3 + 1) * ((elementsCountUpNeck + elementsCountUpBody) * elementsCountAround - 1)
# create bladder neck elements
for e2 in range(elementsCountUpNeck):
for e1 in range(elementsCountAround):
if e2 == ostiumElementPositionUp:
if (e1 == ostiumElementPositionAround or e1 == ostiumElementPositionAround + 1):
pass
elif (e1 == elementsCountAround - ostiumElementPositionAround - 2 or e1 == elementsCountAround - 1 - ostiumElementPositionAround):
pass
else:
bni1 = e2 * elementsCountAround + e1 + 1
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround + 1
if e1 < ostiumElementPositionAround:
bni3 = bni1 + elementsCountAround
bni4 = bni2 + elementsCountAround
elif (ostiumElementPositionAround + 1 < e1 < elementsCountAround - ostiumElementPositionAround - 2):
bni3 = bni1 + elementsCountAround - 1
bni4 = bni2 + elementsCountAround - 1
elif e1 > elementsCountAround - ostiumElementPositionAround - 1:
bni3 = bni1 + elementsCountAround - 2
if e1 == elementsCountAround - 1:
bni4 = bni2 + elementsCountAround
else:
bni4 = bni2 + elementsCountAround - 2
element = mesh.createElement(elementIdentifier, elementtemplate)
nodeIdentifiers = [bni1 + newl, bni2 + newl, bni3 + newl, bni4 + newl,
bni1, bni2, bni3, bni4]
result = element.setNodesByIdentifier(eft, nodeIdentifiers)
neckMeshGroup.addElement(element)
urinaryBladderMeshGroup.addElement(element)
elementIdentifier += 1
elif e2 == ostiumElementPositionUp + 1:
if (e1 == ostiumElementPositionAround or e1 == ostiumElementPositionAround + 1):
pass
elif (e1 == elementsCountAround - ostiumElementPositionAround - 2 or e1 == elementsCountAround - 1 - ostiumElementPositionAround):
pass
else:
if e1 < ostiumElementPositionAround:
bni1 = e2 * elementsCountAround + e1 + 1
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround + 1
bni3 = bni1 + elementsCountAround - 2
bni4 = bni2 + elementsCountAround - 2
elif (ostiumElementPositionAround + 1 < e1 < elementsCountAround - ostiumElementPositionAround - 2):
bni1 = e2 * elementsCountAround + e1
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround
bni3 = bni1 + elementsCountAround - 1
bni4 = bni2 + elementsCountAround - 1
elif e1 > elementsCountAround - ostiumElementPositionAround - 1:
bni1 = e2 * elementsCountAround + e1 - 1
bni3 = bni1 + elementsCountAround
if e1 == elementsCountAround - 1:
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround + 1
bni4 = bni2 + elementsCountAround - 2
else:
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround - 1
bni4 = bni2 + elementsCountAround
element = mesh.createElement(elementIdentifier, elementtemplate)
nodeIdentifiers = [bni1 + newl, bni2 + newl, bni3 + newl, bni4 + newl,
bni1, bni2, bni3, bni4]
result = element.setNodesByIdentifier(eft, nodeIdentifiers)
neckMeshGroup.addElement(element)
urinaryBladderMeshGroup.addElement(element)
elementIdentifier += 1
elif e2 > ostiumElementPositionUp + 1:
element = mesh.createElement(elementIdentifier, elementtemplate)
bni1 = e2 * elementsCountAround + e1 - 1
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround - 1
bni3 = bni1 + elementsCountAround
bni4 = bni2 + elementsCountAround
nodeIdentifiers = [bni1 + newl, bni2 + newl, bni3 + newl, bni4 + newl,
bni1, bni2, bni3, bni4]
result = element.setNodesByIdentifier(eft, nodeIdentifiers)
neckMeshGroup.addElement(element)
urinaryBladderMeshGroup.addElement(element)
elementIdentifier += 1
else:
element = mesh.createElement(elementIdentifier, elementtemplate)
bni1 = e2 * elementsCountAround + e1 + 1
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround + 1
bni3 = bni1 + elementsCountAround
bni4 = bni2 + elementsCountAround
nodeIdentifiers = [bni1 + newl, bni2 + newl, bni3 + newl, bni4 + newl,
bni1, bni2, bni3, bni4]
result = element.setNodesByIdentifier(eft, nodeIdentifiers)
neckMeshGroup.addElement(element)
urinaryBladderMeshGroup.addElement(element)
elementIdentifier += 1
# create bladder body elements
for e2 in range(elementsCountUpNeck, (elementsCountUpNeck + elementsCountUpBody - 1)):
for e1 in range(elementsCountAround):
element = mesh.createElement(elementIdentifier, elementtemplate)
bni1 = e2 * elementsCountAround + e1 - 1
bni2 = e2 * elementsCountAround + (e1 + 1) % elementsCountAround - 1
bni3 = bni1 + elementsCountAround
bni4 = bni2 + elementsCountAround
nodeIdentifiers = [bni1 + newl, bni2 + newl, bni3 + newl, bni4 + newl,
bni1, bni2, bni3, bni4]
result = element.setNodesByIdentifier(eft, nodeIdentifiers)
bodyMeshGroup.addElement(element)
urinaryBladderMeshGroup.addElement(element)
elementIdentifier += 1
# create apex elements
bni3 = (elementsCountUpNeck + elementsCountUpBody) * elementsCountAround - 1
elementtemplateApex = mesh.createElementtemplate()
elementtemplateApex.setElementShapeType(Element.SHAPE_TYPE_CUBE)
for e1 in range(elementsCountAround):
va = e1
vb = (e1 + 1) % elementsCountAround
eftApex = eftfactory.createEftShellPoleTop(va, vb)
elementtemplateApex.defineField(coordinates, -1, eftApex)
# redefine field in template for changes to eftApex:
element = mesh.createElement(elementIdentifier, elementtemplateApex)
bni1 = bni3 - elementsCountAround + e1
bni2 = bni3 - elementsCountAround + (e1 + 1) % elementsCountAround
nodeIdentifiers = [bni1 + newl, bni2 + newl, bni3 + newl, bni1, bni2, bni3]
result = element.setNodesByIdentifier(eftApex, nodeIdentifiers)
bodyMeshGroup.addElement(element)
urinaryBladderMeshGroup.addElement(element)
elementIdentifier += 1
fm.endChange()
return annotationGroups
@classmethod
def refineMesh(cls, meshrefinement, options):
assert isinstance(meshrefinement, MeshRefinement)
refineElementsCountAround = options['Refine number of elements around']
refineElementsCountUp = options['Refine number of elements up']
refineElementsCountThroughWall = options['Refine number of elements through wall']
element = meshrefinement._sourceElementiterator.next()
while element.isValid():
numberInXi1 = refineElementsCountAround
numberInXi2 = refineElementsCountUp
numberInXi3 = refineElementsCountThroughWall
meshrefinement.refineElementCubeStandard3d(element, numberInXi1, numberInXi2, numberInXi3)
element = meshrefinement._sourceElementiterator.next()
@classmethod
def defineFaceAnnotations(cls, region, options, annotationGroups):
"""
Add face annotation groups from the highest dimension mesh.
Must have defined faces and added subelements for highest dimension groups.
:param region: Zinc region containing model.
:param options: Dict containing options. See getDefaultOptions().
:param annotationGroups: List of annotation groups for top-level elements.
New face annotation groups are appended to this list.
"""
# create 2d surface mesh groups
fm = region.getFieldmodule()
neckGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("neck of urinary bladder"))
bodyGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("dome of the bladder"))
urinaryBladderGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("urinary bladder"))
mesh2d = fm.findMeshByDimension(2)
is_exterior = fm.createFieldIsExterior()
is_exterior_face_xi3_1 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
is_exterior_face_xi3_0 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0))
is_body = bodyGroup.getFieldElementGroup(mesh2d)
is_body_serosa = fm.createFieldAnd(is_body, is_exterior_face_xi3_1)
is_body_lumen = fm.createFieldAnd(is_body, is_exterior_face_xi3_0)
is_neck = neckGroup.getFieldElementGroup(mesh2d)
is_neck_serosa = fm.createFieldAnd(is_neck, is_exterior_face_xi3_1)
is_neck_lumen = fm.createFieldAnd(is_neck, is_exterior_face_xi3_0)
serosaOfBody = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("serosa of body of urinary bladder"))
serosaOfBody.getMeshGroup(mesh2d).addElementsConditional(is_body_serosa)
lumenOfBody = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("lumen of body of urinary bladder"))
lumenOfBody.getMeshGroup(mesh2d).addElementsConditional(is_body_lumen)
SerosaOfNeck =findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("serosa of neck of urinary bladder"))
SerosaOfNeck.getMeshGroup(mesh2d).addElementsConditional(is_neck_serosa)
lumenOfNeck = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("lumen of neck of urinary bladder"))
lumenOfNeck.getMeshGroup(mesh2d).addElementsConditional(is_neck_lumen)
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)