def exfile_to_OpenCMISS(nodeFilename, elementFilename, coordinateField, region, meshUserNumber,
dimension=2, interpolation='linear'):
"""Convert an exnode and exelem files to a morphic mesh.
Only Linear lagrange elements supported.
Keyword arguments:
nodeFilename -- exnode filename
elementFilename -- exelem filename
coordinateField -- the field to read in
dimension -- dimension of mesh to read in
interpolation -- the interpolation of the mesh to read in
"""
# Load exfiles
exnode = exfile.Exnode(nodeFilename)
exelem = exfile.Exelem(elementFilename, dimension)
totalNumberOfNodes = len(exnode.nodeids)
totalNumberOfElements = len(exelem.elements)
# Start the creation of a manually generated mesh in the region
mesh = iron.Mesh()
mesh.CreateStart(meshUserNumber, region, dimension)
mesh.NumberOfComponentsSet(1)
mesh.NumberOfElementsSet(totalNumberOfElements)
# Define nodes for the mesh
nodes = iron.Nodes()
nodes.CreateStart(region, totalNumberOfNodes)
nodes.UserNumbersAllSet(exnode.nodeids)
nodes.CreateFinish()
elements = iron.MeshElements()
meshComponentNumber = 1
elements.CreateStart(mesh, meshComponentNumber, basis)
elemNums = []
for elem in exelem.elements:
elemNums.append(elem.number)
elements.UserNumbersAllSet(elemNums)
for elem_idx, elem in enumerate(exelem.elements):
elements.NodesSet(elem_idx+1, elem.nodes)
elements.CreateFinish()
mesh.CreateFinish()
coordinates, node_ids = extract_exfile_coordinates(nodeFilename, coordinateField, interpolation)
return mesh, coordinates, node_ids
decompositionUserNumber, geometricFieldUserNumber, equationsSetUserNumber,
equationsSetFieldUserNumber, independentFieldUserNumber,
dependentFieldUserNumber, problemUserNumber, fibreFieldUserNumber,
materialFieldUserNumber, deformedFieldUserNumber, strainFieldUserNumber,
cellMLUserNumber, cellMLModelsFieldUserNumber,
cellMLParametersFieldUserNumber, cellMLIntermediateFieldUserNumber) = range(
1, 22)
# longitudinal elements, circumferential elements, transmural elements
elems = [8, 8, 2]
"""
cmd = '. ./matlab_batcher.sh benchmark_ellipse_linear ['+str(elems[0])+','+str(elems[1])+','+str(elems[2])+']'
if not os.path.exists("ellipse_benchmark_lin_"+str(elems[2])+"-"+str(elems[1])+"-"+str(elems[0])+".exnode"):
os.system(cmd)
"""
inputNodes = exfile.Exnode("ellipse_benchmark_lin_" + str(elems[2]) + "-" +
str(elems[1]) + "-" + str(elems[0]) + ".exnode")
inputElems = exfile.Exelem("ellipse_benchmark_lin_" + str(elems[2]) + "-" +
str(elems[1]) + "-" + str(elems[0]) + ".exelem")
num_apex_elem = elems[1] * elems[2]
# Set up region and CS
[numOfCompNodes, compNodeNum, CS,
region] = BasicSetUp(regionUserNumber, coordinateSystemUserNumber)
# Set up tricubic Hermite basis functions
[linearBasis, colBasis] = BasisFunction(linearBasisUserNumber,
numOfXi,
option,
collapsed=True)
# Set up mesh
def exfile_to_morphic(nodeFilename, elementFilename, coordinateField,
dimension=2, interpolation='linear'):
"""Convert an exnode and exelem files to a morphic mesh.
Only Linear lagrange elements supported.
Keyword arguments:
nodeFilename -- exnode filename
elementFilename -- exelem filename
coordinateField -- the field to read in
dimension -- dimension of mesh to read in
"""
# Create morphic mesh
mesh = morphic.Mesh()
# Load exfiles
exnode = exfile.Exnode(nodeFilename)
exelem = exfile.Exelem(elementFilename, dimension)
# Add nodes
if interpolation == 'linear':
derivatives = [1]
elif interpolation == 'hermite':
derivatives = range(1,9)
for node_num in exnode.nodeids:
coordinates = []
for component in range(1, 4):
component_name = ["x", "y", "z"][component - 1]
componentValues = []
for derivative_idx, derivative in enumerate(derivatives):
componentValues.append(exnode.node_value(coordinateField,
component_name, node_num,
derivative))
coordinates.append(componentValues)
mesh.add_stdnode(node_num, coordinates, group='_default')
print 'Morhpic node added', node_num, coordinates
if dimension == 2:
if interpolation == 'linear':
element_interpolation = ['L1', 'L1']
if interpolation == 'quadratic':
element_interpolation = ['L2', 'L2']
elif dimension == 3:
if interpolation == 'linear':
element_interpolation = ['L1', 'L1', 'L1']
if interpolation == 'quadratic':
element_interpolation = ['L2', 'L2', 'L2']
if interpolation == 'hermite':
element_interpolation = ['H3', 'H3', 'H3']
# Add elements
for elem in exelem.elements:
mesh.add_element(elem.number, element_interpolation, elem.nodes)
print 'Morphic element added', elem.number
# Generate the mesh
mesh.generate(True)
return mesh
# The number of data points which are digitised from the heart segments
# fix interior nodes so that fitting only applies to surface
# If start iteration > 1, read in geometry from a previous fit iteration
numberOfDataPoints = 2513
numberOfIterations = 1
fixInterior = True
zeroTolerance = 0.00001
hermite = True
# Set Sobolev smoothing parameters
tau = 0.00005
kappa = 0.00001
iteration = 1
if iteration > 1:
exfileMesh = True
exnode = exfile.Exnode("DeformedGeometry" + str(iteration - 1) +
".part0.exnode")
exelem = exfile.Exelem("UndeformedGeometry.part0.exelem")
else:
exfileMesh = False
print "other parameters setted up "
#=================================================================
#
#=================================================================
(coordinateSystemUserNumber, regionUserNumber, basisUserNumber,
generatedMeshUserNumber, meshUserNumber, decompositionUserNumber,
geometricFieldUserNumber, equationsSetFieldUserNumber,
dependentFieldUserNumber, independentFieldUserNumber,
dataPointFieldUserNumber, materialFieldUserNumber, analyticFieldUserNumber,
dependentDataFieldUserNumber, dataPointsUserNumber, dataProjectionUserNumber,
equationsSetUserNumber, problemUserNumber) = range(1, 19)