- Author:
- Elias Ghadam Soltani <egha355@UoA.auckland.ac.nz>
- Date:
- 2021-01-19 16:27:59+13:00
- Desc:
- Modify ReadMe file
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/63a/rawfile/7701e5f623a4baa2e0c8cee0f628ee3bd547291e/body_add_discontinuity.py
# make outer shell of elements use version 2 of d3 & add to nodes
from opencmiss.utils.zinc.general import ChangeManager
from opencmiss.utils.zinc.finiteelement import get_element_node_identifiers
from opencmiss.zinc.context import Context
from opencmiss.zinc.field import Field
from opencmiss.zinc.node import Node
from opencmiss.zinc.result import RESULT_OK
def remapEftNodeValueLabelsVersion(eft, localNodeIndexes, valueLabels, version):
'''
Remap all uses of the given valueLabels to use the version.
:param localNodeIndexes: List of local node indexes >= 1 to remap at.
:param valueLabels: List of node value labels to be remapped.
:param version: Version >= 1
'''
functionCount = eft.getNumberOfFunctions()
for f in range(1, functionCount + 1):
termCount = eft.getFunctionNumberOfTerms(f)
for t in range(1, termCount + 1):
localNodeIndex = eft.getTermLocalNodeIndex(f, t)
valueLabel = eft.getTermNodeValueLabel(f, t)
if (localNodeIndex in localNodeIndexes) and (valueLabel in valueLabels):
result = eft.setTermNodeParameter(f, t, localNodeIndex, valueLabel, version)
#print('remap result', result)
context = Context('add_discontinuity')
logger = context.getLogger()
region = context.getDefaultRegion()
region.readFile('body_groups11.exf')
fieldmodule = region.getFieldmodule()
mesh = fieldmodule.findMeshByDimension(3)
group = fieldmodule.findFieldByName('non_core').castGroup()
elementGroup = group.getFieldElementGroup(mesh)
meshGroup = elementGroup.getMeshGroup()
print('meshGroup size', meshGroup.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
coordinates = fieldmodule.findFieldByName('coordinates').castFiniteElement()
elementtemplate = mesh.createElementtemplate()
undefineNodetemplate = nodes.createNodetemplate()
undefineNodetemplate.undefineField(coordinates)
nodetemplate = nodes.createNodetemplate()
fieldcache = fieldmodule.createFieldcache()
with ChangeManager(fieldmodule):
elementIter = meshGroup.createElementiterator()
element = elementIter.next()
localNodeIndexes = [1, 2, 3, 4]
valueLabel = Node.VALUE_LABEL_D_DS3
while element.isValid():
print('Element', element.getIdentifier())
eft = element.getElementfieldtemplate(coordinates, -1)
nodeIds = get_element_node_identifiers(element, eft)
for localNodeIndex in localNodeIndexes:
node = element.getNode(eft, localNodeIndex)
print(' Node', node.getIdentifier())
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)
#print('Results:', result0, result1, result2, result3, result4, result5)
if result3 == 0:
loggerMessageCount = logger.getNumberOfMessages()
if loggerMessageCount > 0:
for i in range(1, loggerMessageCount + 1):
print(logger.getMessageTypeAtIndex(i), logger.getMessageTextAtIndex(i))
logger.removeAllMessages()
exit()
remapEftNodeValueLabelsVersion(eft, localNodeIndexes, [ valueLabel ], 2)
result1 = elementtemplate.defineField(coordinates, -1, eft)
result2 = element.merge(elementtemplate)
result3 = element.setNodesByIdentifier(eft, nodeIds)
#print('Element merge result',result1, result2, result3)
if (result1 != RESULT_OK) or (result2 != RESULT_OK):
loggerMessageCount = logger.getNumberOfMessages()
if loggerMessageCount > 0:
for i in range(1, loggerMessageCount + 1):
print(logger.getMessageTypeAtIndex(i), logger.getMessageTextAtIndex(i))
logger.removeAllMessages()
exit()
element = elementIter.next()
region.writeFile('body_groups_discontinuity11.exf')
