def zinc_write_element_xi_marker_file(outFile, region, allMarkers, nodeIdentifier): fm = region.getFieldmodule() fm.beginChange() nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) mesh = fm.findMeshByDimension(3) cache = fm.createFieldcache() markerGroup = findOrCreateFieldGroup(fm, "marker") markerName = findOrCreateFieldStoredString(fm, name="marker_name") markerLocation = findOrCreateFieldStoredMeshLocation( fm, mesh, name="marker_location") markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup() markerTemplate = nodes.createNodetemplate() markerTemplate.defineField(markerName) markerTemplate.defineField(markerLocation) for key in allMarkers: addMarker = {"name": key + " projected", "xi": allMarkers[key]["xi"]} markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplate) cache.setNode(markerPoint) markerName.assignString(cache, addMarker["name"]) elementID = allMarkers[key]["elementID"] element = mesh.findElementByIdentifier(elementID) result = markerLocation.assignMeshLocation(cache, element, addMarker["xi"]) nodeIdentifier += 1 fm.endChange() region.writeFile(outFile) return
def _defineDataProjectionFields(self): self._dataProjectionLocationFields = [] self._dataProjectionCoordinatesFields = [] self._dataProjectionDeltaFields = [] self._dataProjectionErrorFields = [] self._dataProjectionNodeGroupFields = [] self._dataProjectionNodesetGroups = [] with ChangeManager(self._fieldmodule): datapoints = self._fieldmodule.findNodesetByFieldDomainType( Field.DOMAIN_TYPE_DATAPOINTS) for d in range(2): mesh = self._mesh[d] dataProjectionLocation = findOrCreateFieldStoredMeshLocation( self._fieldmodule, mesh, name="data_projection_location_" + mesh.getName(), managed=False) self._dataProjectionLocationFields.append( dataProjectionLocation) dataProjectionCoordinates = self._fieldmodule.createFieldEmbedded( self._modelCoordinatesField, dataProjectionLocation) dataProjectionCoordinates.setName( getUniqueFieldName( self._fieldmodule, "data_projection_coordinates_" + mesh.getName())) self._dataProjectionCoordinatesFields.append( dataProjectionCoordinates) dataProjectionDelta = dataProjectionCoordinates - self._dataCoordinatesField dataProjectionDelta.setName( getUniqueFieldName( self._fieldmodule, "data_projection_delta_" + mesh.getName())) self._dataProjectionDeltaFields.append(dataProjectionDelta) dataProjectionError = self._fieldmodule.createFieldMagnitude( dataProjectionDelta) dataProjectionError.setName( getUniqueFieldName( self._fieldmodule, "data_projection_error_" + mesh.getName())) self._dataProjectionErrorFields.append(dataProjectionError) field = self._fieldmodule.createFieldNodeGroup(datapoints) field.setName( getUniqueFieldName( self._fieldmodule, "data_projection_group_" + mesh.getName())) self._dataProjectionNodeGroupFields.append(field) self._dataProjectionNodesetGroups.append( field.getNodesetGroup()) self._dataProjectionDirectionField = findOrCreateFieldFiniteElement( self._fieldmodule, "data_projection_direction", components_count=3, component_names=["x", "y", "z"])
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'] isDefault = 'Default' in parameterSetName isMouse = 'Mouse' in parameterSetName isMean = 'mean' in parameterSetName fm = region.getFieldmodule() nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) coordinates = findOrCreateFieldCoordinates(fm) mesh = fm.findMeshByDimension(3) cache = fm.createFieldcache() 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) armCount = 3 elementLengthCentral = options['Element width central'] elementLengths = [ options['Element length along arm'], options['Element width across arm'], options['Element thickness'] ] elementsCountsAlongArms = options['Numbers of elements along arms'] elementsCount2 = 2 elementsCount3 = 1 useCrossDerivatives = False # arm group annotations for user armTerms, _ = getAutomaticArmFaceTerms(armCount) armGroups = [AnnotationGroup(region, armTerm) for armTerm in armTerms] stellateTerm = get_stellate_term( "cervicothoracic ganglion") if isMouse else ("stellate", None) stellateGroup = AnnotationGroup(region, stellateTerm) annotationGroups = [stellateGroup] + armGroups armMeshGroups = [a.getMeshGroup(mesh) for a in armGroups] stellateMeshGroup = stellateGroup.getMeshGroup(mesh) # markers with element number and xi position allMarkers = {} if isMouse: xProportion = {} xProportion['ICN'] = 0.9 xProportion['VA'] = 0.9 xProportion['DA'] = 0.9 xProportion['C8'] = 0.9 xProportion['T1'] = 0.25 xProportion['T2'] = 0.5 xProportion['T3'] = 0.75 xProportion['TST'] = 1 armNumber = {} armNumber['ICN'] = 2 armNumber['VA'] = 2 armNumber['DA'] = 3 armNumber['C8'] = 3 armNumber['T1'] = 1 armNumber['T2'] = 1 armNumber['T3'] = 1 armNumber['TST'] = 1 nerveAbbrev = list(xProportion.keys()) elementIndex = {} xi1 = {} for nerve in nerveAbbrev: elementIndex[nerve] = int( xProportion[nerve] * elementsCountsAlongArms[armNumber[nerve] - 1]) xi1[nerve] = 1 if xProportion[nerve] == 1 else xProportion[ nerve] * elementsCountsAlongArms[armNumber[nerve] - 1] - elementIndex[nerve] elementIndex[nerve] += 1 if xProportion[nerve] < 1 else 0 allMarkers = { "Inferior cardiac nerve": { "elementID": elementIndex['ICN'] + 2 * elementsCountsAlongArms[0], "xi": [xi1['ICN'], 0.0, 0.5] }, "Ventral ansa subclavia": { "elementID": elementIndex['VA'] + 2 * elementsCountsAlongArms[0] + elementsCountsAlongArms[1], "xi": [xi1['VA'], 1.0, 0.5] }, "Dorsal ansa subclavia": { "elementID": elementIndex['DA'] + 2 * (elementsCountsAlongArms[0] + elementsCountsAlongArms[1]), "xi": [xi1['DA'], 0.0, 0.5] }, "Cervical spinal nerve 8": { "elementID": elementIndex['C8'] + 2 * (elementsCountsAlongArms[0] + elementsCountsAlongArms[1]) + elementsCountsAlongArms[2], "xi": [xi1['C8'], 1.0, 0.5] }, "Thoracic spinal nerve 1": { "elementID": elementIndex['T1'], "xi": [xi1['T1'], 0.0, 0.5] }, "Thoracic spinal nerve 2": { "elementID": elementIndex['T2'], "xi": [xi1['T2'], 0.0, 0.5] }, "Thoracic spinal nerve 3": { "elementID": elementIndex['T3'], "xi": [xi1['T3'], 0.0, 0.5] }, "Thoracic sympathetic nerve trunk": { "elementID": elementIndex['TST'], "xi": [xi1['TST'], 1.0, 0.5] }, } markerGroup = findOrCreateFieldGroup(fm, "marker") markerName = findOrCreateFieldStoredString(fm, name="marker_name") markerLocation = findOrCreateFieldStoredMeshLocation( fm, mesh, name="marker_location") markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup() markerTemplateInternal = nodes.createNodetemplate() markerTemplateInternal.defineField(markerName) markerTemplateInternal.defineField(markerLocation) # Create nodes nodeIdentifier = 1 minArmAngle = 2 * math.pi / armCount halfArmArcAngleRadians = minArmAngle / 2 if not isMean: dipMultiplier = 1 for na in range(armCount): elementsCount_i = [ elementsCountsAlongArms[na], elementsCount2, elementsCount3 ] x, ds1, ds2, nWheelEdge = createArm(halfArmArcAngleRadians, elementLengths, elementLengthCentral, elementsCount_i, dipMultiplier, armCount, na) for ix in range(len(x)): if na == 0 or ix not in nWheelEdge: node = nodes.createNode(nodeIdentifier, nodetemplate) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x[ix]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, ds1[ix]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, ds2[ix]) nodeIdentifier += 1 else: x_dx_all = cls.mouseMeanMesh['meshEdits'] xyz_all = [x[0] for x in x_dx_all] dxyz = [[x[1], x[2]] for x in x_dx_all] nodeIdentifier = 1 for i, nx in enumerate(xyz_all): node = nodes.createNode(nodeIdentifier, nodetemplate) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, nx) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, dxyz[i][0]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, dxyz[i][1]) nodeIdentifier += 1 nodesCountsPerArm = [0] + [((elementsCount2 + 1) * e + 1) * 2 for e in elementsCountsAlongArms] # Create elements bicubichermitelinear = eftfactory_bicubichermitelinear( mesh, useCrossDerivatives) eft = bicubichermitelinear.createEftNoCrossDerivatives( ) #createEftBasic() elementtemplate = mesh.createElementtemplate() elementtemplate.setElementShapeType(Element.SHAPE_TYPE_CUBE) elementtemplate.defineField(coordinates, -1, eft) elementtemplateX = mesh.createElementtemplate() elementtemplateX.setElementShapeType(Element.SHAPE_TYPE_CUBE) elementIdentifier = 1 cumNodesCountsPerArm = [ sum(nodesCountsPerArm[:i + 1]) for i in range(len(nodesCountsPerArm)) ] nCentre = [ elementsCountsAlongArms[0] + 1, int(nodesCountsPerArm[1] / 2) + elementsCountsAlongArms[0] + 1 ] for na in range(armCount): for e3 in range(elementsCount3): for e2 in range(elementsCount2): for e1 in range(elementsCountsAlongArms[na]): scalefactors = None ### NODES ### no2 = (elementsCountsAlongArms[na] + 1) no3 = (elementsCount2 + 1) * no2 - 2 offset = (cumNodesCountsPerArm[na]) bni = e3 * no3 + e2 * no2 + e1 + 1 + offset if e2 == 0: if e1 == 0 and na > 0: # and na < armCount -1: # wheelSouth nWh = cumNodesCountsPerArm[na - 1] + ( 2 * elementsCountsAlongArms[na - 1]) + 2 nplUq = int( nodesCountsPerArm[na + 1] / 2 ) - elementsCountsAlongArms[ na] # unused nodes at centre and shared edge npl = int( nodesCountsPerArm[na + 1] / 2) # nodes at centre and shared edge if na < armCount - 1: cn = cumNodesCountsPerArm[ na] + elementsCountsAlongArms[na] - 2 no2 = cumNodesCountsPerArm[na] em = elementsCountsAlongArms[na] nwPrev = [ nWh, nWh + int(nodesCountsPerArm[na] / 2) ] # previous arm's edge, depends on armCount. nodeIdentifiers = [ nwPrev[0], no2 + 1, nCentre[0], no2 + em, nwPrev[1], no2 + em - 1 + nplUq, nCentre[1], bni + (4 * em) - 2 ] else: nplPrev = int( nodesCountsPerArm[na] / 2) - 2 no2 = elementsCountsAlongArms[na] - 1 no3 = int( nodesCountsPerArm[na + 1] / 2) - 3 nwPrev = [ cumNodesCountsPerArm[na - 1] + 2 * (elementsCountsAlongArms[na - 1]), cumNodesCountsPerArm[na - 1] + 2 * (elementsCountsAlongArms[na - 1]) + nplPrev ] start = cumNodesCountsPerArm[na] - 3 nodeIdentifiers = [ nwPrev[0], start, nCentre[0], start + no2, nwPrev[1], start + no3, nCentre[1], start + no2 + no3 ] elif e1 == elementsCountsAlongArms[ na] - 1: # armEnd, south if na == 0: nodeIdentifiers = [ bni, bni + no2 - 1, bni + no2, bni + no3, bni + no2 + no3 - 1, bni + no2 + no3 ] else: no3 = armCount * elementsCountsAlongArms[ na] - 1 no2 = elementsCountsAlongArms[na] if na > 1: bni -= 4 no3 -= 1 nodeIdentifiers = [ bni - 1, bni + no2 - 2, bni + no2 - 1, bni + no3 - 1, bni + no2 - 2 + no3, bni + no2 + no3 - 1 ] elif na > 0 and e1 > 0: # [na=1+, e1=1+, e2=0] for len=3+ bni -= 1 + ((armCount + 1) * (na - 1)) no2 = elementsCountsAlongArms[na] no3 = armCount * no2 - (na - 1) - 1 nodeIdentifiers = [ bni, bni + 1, bni + no2 - 1, bni + no2, bni + no3, bni + no3 + 1, bni + no2 + no3 - 1, bni + no2 + no3 ] else: nodeIdentifiers = [ bni, bni + 1, bni + no2 - 1, bni + no2, bni + no3, bni + no3 + 1, bni + no2 + no3 - 1, bni + no2 + no3 ] else: if e1 == 0 and na > 0: # and na < armCount -1: # wheelNorth if na < armCount - 1: bni -= armCount npl = int( nodesCountsPerArm[na + 1] / 2) - 2 no2 = elementsCountsAlongArms[na] nodeIdentifiers = [ nCentre[0], bni + 1, bni + no2 + 1, bni + no2 + 2, nCentre[1], bni + npl + 1, bni + npl + no2 + 1, bni + npl + no2 + 2 ] else: # last arm bni = cumNodesCountsPerArm[na] - 2 - ( armCount - elementsCountsAlongArms[na]) nodeIdentifiers = [ nCentre[0], bni + 1, 1, bni + no2, nCentre[1], bni + no3 - 2, int(nodesCountsPerArm[1] / 2) + 1, bni + no2 + no3 - armCount ] elif e1 == elementsCountsAlongArms[ na] - 1: # armEnd north if na > 0: no2 = elementsCountsAlongArms[na] nplUq = int( nodesCountsPerArm[na + 1] / 2) - 2 if na > 1: adj = na - 1 bni -= armCount * na + ( armCount - elementsCountsAlongArms[na]) + 1 if elementsCountsAlongArms[na] < 3: bni += 1 if elementsCountsAlongArms[na] > 3: bni -= elementsCountsAlongArms[ na] - 3 no2 += 1 - adj no3 = nplUq - adj nodeIdentifiers = [ bni, bni + 1, bni + no2, bni + no3, bni + no3 + 1, bni + no2 + no3 ] else: bni -= armCount nodeIdentifiers = [ bni, bni + 1, bni + no2 + 1, bni + nplUq, bni + nplUq + 1, bni + no2 + nplUq + 1 ] else: nodeIdentifiers = [ bni - 1, bni, bni + no2 - 1, bni + no3 - 1, bni + no3, bni + no2 + no3 - 1 ] elif na > 0 and e1 > 0: # [na=1+, e1=1+, e2=1] for len=3+ adj = na - 1 bni -= armCount * na + adj no2 -= adj k = armCount * elementsCountsAlongArms[na] - na nodeIdentifiers = [ bni, bni + 1, bni + no2, bni + no2 + 1, bni + k, bni + k + 1, bni + no2 + k, bni + no2 + k + 1 ] else: nodeIdentifiers = [ bni - 1, bni, bni + no2 - 1, bni + no2, bni + no3 - 1, bni + no3, bni + no2 + no3 - 1, bni + no2 + no3 ] if e1 == 0: # wheel eft1 = bicubichermitelinear.createEftNoCrossDerivatives( ) if armCount == 3: if e2 == 0: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] scaleEftNodeValueLabels( eft1, [1, 5], [ Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2 ], [1]) ns = [3, 7] else: ns = [1, 5] if na == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS2, [])]) if e2 == 0: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])]) elif na == 1: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1])]) if e2 == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS2, [1])]) elif e2 == 1: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS2, [1])]) elif na == 2: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [1])]) if e2 == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS2, [])]) elif e2 == 1: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])]) elif armCount == 4: if e2 == 0: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] scaleEftNodeValueLabels( eft1, [1, 5], [ Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2 ], [1]) ns = [3, 7] else: ns = [1, 5] if na == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS2, [])]) if e2 == 0: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])]) elif na == 1: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS2, [])]) if e2 == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS2, [1])]) else: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])]) elif na == 2: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS2, [1])]) if e2 == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])]) else: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS2, [1])]) elif na == 3: setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS2, [1])]) if e2 == 0: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS2, [])]) else: remapEftNodeValueLabel( eft1, ns, Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])]) elif e1 < (elementsCountsAlongArms[na] - 1): eft1 = eft elementtemplate1 = elementtemplate else: # rounded ends of arms. Collapse xi2 at xi1 = 1 eft1 = bicubichermitelinear.createEftNoCrossDerivatives( ) remapEftNodeValueLabel(eft1, [2, 4, 6, 8], Node.VALUE_LABEL_D_DS2, []) if e2 == 0: remapEftNodeValueLabel( eft1, [2, 6], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [])]) nodeIdentifiers = [ nodeIdentifiers[0], nodeIdentifiers[2], nodeIdentifiers[1], nodeIdentifiers[3], nodeIdentifiers[5], nodeIdentifiers[4] ] else: # e2 == 1 setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel( eft1, [4, 8], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [1])]) ln_map = [1, 2, 3, 2, 4, 5, 6, 5] remapEftLocalNodes(eft1, 6, ln_map) if eft1 is not eft: elementtemplateX.defineField(coordinates, -1, eft1) elementtemplate1 = elementtemplateX element = mesh.createElement(elementIdentifier, elementtemplate1) result = element.setNodesByIdentifier( eft1, nodeIdentifiers) result3 = element.setScaleFactors( eft1, scalefactors) if scalefactors else None # add to meshGroup stellateMeshGroup.addElement(element) armMeshGroups[na].addElement(element) elementIdentifier += 1 # annotation fiducial points if isMouse: for key in allMarkers: xi = allMarkers[key]["xi"] addMarker = {"name": key, "xi": allMarkers[key]["xi"]} markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal) nodeIdentifier += 1 cache.setNode(markerPoint) markerName.assignString(cache, addMarker["name"]) elementID = allMarkers[key]["elementID"] element = mesh.findElementByIdentifier(elementID) markerLocation.assignMeshLocation(cache, element, addMarker["xi"]) return annotationGroups
def _calculateMarkerDataLocations(self): """ Called when markerGroup exists. Find matching marker mesh locations for marker data points. Only finds matching location where there is one datapoint and one node for each name in marker group. Defines datapoint group self._markerDataLocationGroup to contain those with locations. """ self._markerDataLocationField = None self._markerDataLocationCoordinatesField = None self._markerDataDeltaField = None self._markerDataLocationGroupField = None self._markerDataLocationGroup = None if not (self._markerDataGroup and self._markerDataNameField and self._markerNodeGroup and self._markerLocationField and self._markerNameField): return markerPrefix = self._markerGroup.getName() # assume marker locations are in highest dimension mesh mesh = self.getHighestDimensionMesh() datapoints = self._fieldmodule.findNodesetByFieldDomainType( Field.DOMAIN_TYPE_DATAPOINTS) meshDimension = mesh.getDimension() fieldcache = self._fieldmodule.createFieldcache() with ChangeManager(self._fieldmodule): self._markerDataLocationField = findOrCreateFieldStoredMeshLocation( self._fieldmodule, mesh, name=markerPrefix + "_data_location_" + mesh.getName(), managed=False) self._markerDataLocationGroupField = self._fieldmodule.createFieldNodeGroup( datapoints) self._markerDataLocationGroupField.setName( getUniqueFieldName(self._fieldmodule, markerPrefix + "_data_location_group")) self._markerDataLocationGroup = self._markerDataLocationGroupField.getNodesetGroup( ) self._updateMarkerDataLocationCoordinatesField() nodetemplate = self._markerDataGroup.createNodetemplate() nodetemplate.defineField(self._markerDataLocationField) datapointIter = self._markerDataGroup.createNodeiterator() datapoint = datapointIter.next() while datapoint.isValid(): fieldcache.setNode(datapoint) name = self._markerDataNameField.evaluateString(fieldcache) # if this is the only datapoint with name: if name and findNodeWithName(self._markerDataGroup, self._markerDataNameField, name, ignore_case=True, strip_whitespace=True): node = findNodeWithName(self._markerNodeGroup, self._markerNameField, name, ignore_case=True, strip_whitespace=True) if node: fieldcache.setNode(node) element, xi = self._markerLocationField.evaluateMeshLocation( fieldcache, meshDimension) if element.isValid(): datapoint.merge(nodetemplate) fieldcache.setNode(datapoint) self._markerDataLocationField.assignMeshLocation( fieldcache, element, xi) self._markerDataLocationGroup.addNode(datapoint) datapoint = datapointIter.next() # Warn about datapoints without a location in model markerDataGroupSize = self._markerDataGroup.getSize() markerDataLocationGroupSize = self._markerDataLocationGroup.getSize() markerNodeGroupSize = self._markerNodeGroup.getSize() if self.getDiagnosticLevel() > 0: if markerDataLocationGroupSize < markerDataGroupSize: print("Warning: Only " + str(markerDataLocationGroupSize) + " of " + str(markerDataGroupSize) + " marker data points have model locations") if markerDataLocationGroupSize < markerNodeGroupSize: print("Warning: Only " + str(markerDataLocationGroupSize) + " of " + str(markerNodeGroupSize) + " marker model locations used")
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
def generateBaseMesh(cls, region, options): """ Generate the base tricubic Hermite mesh. :param region: Zinc region to define model in. Must be empty. :param options: Dict containing options. See getDefaultOptions(). :return: list of AnnotationGroup """ # set dependent outer diameter used in atria2 options['Aorta outer plus diameter'] = options[ 'LV outlet inner diameter'] + 2.0 * options[ 'LV outlet wall thickness'] elementsCountAroundAtrialSeptum = options[ 'Number of elements around atrial septum'] elementsCountAroundLeftAtriumFreeWall = options[ 'Number of elements around left atrium free wall'] elementsCountAroundLeftAtrium = elementsCountAroundLeftAtriumFreeWall + elementsCountAroundAtrialSeptum elementsCountAroundRightAtriumFreeWall = options[ 'Number of elements around right atrium free wall'] elementsCountAroundRightAtrium = elementsCountAroundRightAtriumFreeWall + elementsCountAroundAtrialSeptum useCrossDerivatives = False fm = region.getFieldmodule() coordinates = findOrCreateFieldCoordinates(fm) cache = fm.createFieldcache() mesh = fm.findMeshByDimension(3) # generate heartventriclesbase1 model and put atria1 on it ventriclesAnnotationGroups = MeshType_3d_heartventriclesbase1.generateBaseMesh( region, options) atriaAnnotationGroups = MeshType_3d_heartatria1.generateBaseMesh( region, options) annotationGroups = mergeAnnotationGroups(ventriclesAnnotationGroups, atriaAnnotationGroups) lFibrousRingGroup = findOrCreateAnnotationGroupForTerm( annotationGroups, region, get_heart_term("left fibrous ring")) rFibrousRingGroup = findOrCreateAnnotationGroupForTerm( annotationGroups, region, get_heart_term("right fibrous ring")) # annotation fiducial points 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) ############## # Create nodes ############## nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1) # discover left and right fibrous ring nodes from ventricles and atria # because nodes are iterated in identifier order, the lowest and first are on the lv outlet cfb, right and left on lower outer layers # left fibrous ring lavNodeId = [[[], []], [[], []]] # [n3][n2][n1] iter = lFibrousRingGroup.getNodesetGroup(nodes).createNodeiterator() # left fibrous ring, bottom row cfbNodeId = iter.next().getIdentifier() cfbLeftNodeId = iter.next().getIdentifier() for n1 in range(elementsCountAroundLeftAtrium): lavNodeId[0][0].append(iter.next().getIdentifier()) lavNodeId[1][0].append(cfbNodeId) lavNodeId[1][0].append(cfbLeftNodeId) for n1 in range(elementsCountAroundLeftAtriumFreeWall - 1): lavNodeId[1][0].append(iter.next().getIdentifier()) for n1 in range(elementsCountAroundAtrialSeptum - 1): lavNodeId[1][0].append(None) # no outer node on interatrial septum # left fibrous ring, top row for n1 in range(elementsCountAroundLeftAtrium): lavNodeId[0][1].append(iter.next().getIdentifier()) for n1 in range(elementsCountAroundLeftAtriumFreeWall + 1): lavNodeId[1][1].append(iter.next().getIdentifier()) for n1 in range(elementsCountAroundAtrialSeptum - 1): lavNodeId[1][1].append(None) # no outer node on interatrial septum # right fibrous ring ravNodeId = [[[], []], [[], []]] # [n3][n2][n1] iter = rFibrousRingGroup.getNodesetGroup(nodes).createNodeiterator() cfbNodeId = iter.next().getIdentifier() cfbRightNodeId = iter.next().getIdentifier() # right fibrous ring, bottom row for n1 in range(elementsCountAroundRightAtrium): ravNodeId[0][0].append(iter.next().getIdentifier()) for n1 in range(elementsCountAroundRightAtriumFreeWall - 1): ravNodeId[1][0].append(iter.next().getIdentifier()) ravNodeId[1][0].append(cfbRightNodeId) ravNodeId[1][0].append(cfbNodeId) for n1 in range(elementsCountAroundAtrialSeptum - 1): ravNodeId[1][0].append(None) # no outer node on interatrial septum # right fibrous ring, top row for n1 in range(elementsCountAroundRightAtrium): ravNodeId[0][1].append(iter.next().getIdentifier()) cfbUpperNodeId = iter.next().getIdentifier( ) # cfb from left will be first for n1 in range(elementsCountAroundRightAtriumFreeWall): ravNodeId[1][1].append(iter.next().getIdentifier()) ravNodeId[1][1].append(cfbUpperNodeId) for n1 in range(elementsCountAroundAtrialSeptum - 1): ravNodeId[1][1].append(None) # no outer node on interatrial septum #for n2 in range(2): # print('n2', n2) # print('lavNodeId[0]', lavNodeId[0][n2]) # print('lavNodeId[1]', lavNodeId[1][n2]) # print('ravNodeId[0]', ravNodeId[0][n2]) # print('ravNodeId[1]', ravNodeId[1][n2]) ################# # Create elements ################# lFibrousRingMeshGroup = lFibrousRingGroup.getMeshGroup(mesh) rFibrousRingMeshGroup = rFibrousRingGroup.getMeshGroup(mesh) elementIdentifier = getMaximumElementIdentifier(mesh) + 1 elementtemplate1 = mesh.createElementtemplate() elementtemplate1.setElementShapeType(Element.SHAPE_TYPE_CUBE) # create fibrous ring elements bicubichermitelinear = eftfactory_bicubichermitelinear( mesh, useCrossDerivatives, linearAxis=2, d_ds1=Node.VALUE_LABEL_D_DS1, d_ds2=Node.VALUE_LABEL_D_DS3) eftFibrousRing = bicubichermitelinear.createEftBasic() # left fibrous ring, starting at crux / collapsed posterior interatrial sulcus cruxElementId = None for e in range(-1, elementsCountAroundLeftAtriumFreeWall): eft1 = eftFibrousRing n1 = e nids = [ lavNodeId[0][0][n1], lavNodeId[0][0][n1 + 1], lavNodeId[0][1][n1], lavNodeId[0][1][n1 + 1], lavNodeId[1][0][n1], lavNodeId[1][0][n1 + 1], lavNodeId[1][1][n1], lavNodeId[1][1][n1 + 1] ] scalefactors = None meshGroups = [lFibrousRingMeshGroup] if e == -1: # interatrial groove straddles left and right atria, collapsed to 6 node wedge nids[0] = ravNodeId[0][0][ elementsCountAroundRightAtriumFreeWall] nids[2] = ravNodeId[0][1][ elementsCountAroundRightAtriumFreeWall] nids.pop(6) nids.pop(4) eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [1, 3], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [2, 4], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS1, []) # reverse d3 on cfb: remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [0]), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [])]) ln_map = [1, 2, 3, 4, 5, 5, 6, 6] remapEftLocalNodes(eft1, 6, ln_map) meshGroups += [rFibrousRingMeshGroup] elif e == 0: # general linear map d3 adjacent to collapsed sulcus eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] # reverse d1, d3 on cfb, left cfb: scaleEftNodeValueLabels( eft1, [6], [Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS3], [1]) remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1])]) remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [])]) elif e == 1: # reverse d1, d3 on left cfb: eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS3, [1])]) elif e == (elementsCountAroundLeftAtriumFreeWall - 1): # general linear map d3 adjacent to collapsed sulcus eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [6, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) result = elementtemplate1.defineField(coordinates, -1, eft1) element = mesh.createElement(elementIdentifier, elementtemplate1) result2 = element.setNodesByIdentifier(eft1, nids) result3 = element.setScaleFactors( eft1, scalefactors) if scalefactors else None #print('create element fibrous ring left', elementIdentifier, result, result2, result3, nids) elementIdentifier += 1 for meshGroup in meshGroups: meshGroup.addElement(element) # right fibrous ring, starting at crux / collapsed posterior interatrial sulcus for e in range(-1, elementsCountAroundRightAtriumFreeWall): eft1 = eftFibrousRing n1 = e nids = [ ravNodeId[0][0][n1], ravNodeId[0][0][n1 + 1], ravNodeId[0][1][n1], ravNodeId[0][1][n1 + 1], ravNodeId[1][0][n1], ravNodeId[1][0][n1 + 1], ravNodeId[1][1][n1], ravNodeId[1][1][n1 + 1] ] scalefactors = None meshGroups = [rFibrousRingMeshGroup] if e == -1: # interatrial groove straddles left and right atria, collapsed to 6 node wedge nids[0] = lavNodeId[0][0][ elementsCountAroundLeftAtriumFreeWall] nids[2] = lavNodeId[0][1][ elementsCountAroundLeftAtriumFreeWall] nids.pop(6) nids.pop(4) eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [1, 3], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [2, 4], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [5, 6, 7, 8], Node.VALUE_LABEL_D_DS1, []) remapEftNodeValueLabel(eft1, [5, 7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [6, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [])]) ln_map = [1, 2, 3, 4, 5, 5, 6, 6] remapEftLocalNodes(eft1, 6, ln_map) meshGroups += [lFibrousRingMeshGroup] cruxElementId = elementIdentifier elif e == 0: # general linear map d3 adjacent to collapsed crux/posterior sulcus eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [5, 7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [])]) elif e == (elementsCountAroundRightAtriumFreeWall - 2): # reverse d1, d3 on right cfb: eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS3, [1])]) elif e == (elementsCountAroundRightAtriumFreeWall - 1): # general linear map d3 adjacent to collapsed cfb/anterior sulcus eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] # reverse d1, d3 on right cfb, cfb: scaleEftNodeValueLabels( eft1, [5], [Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS3], [1]) remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1])]) remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [1])]) remapEftNodeValueLabel(eft1, [8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) result = elementtemplate1.defineField(coordinates, -1, eft1) element = mesh.createElement(elementIdentifier, elementtemplate1) result2 = element.setNodesByIdentifier(eft1, nids) result3 = element.setScaleFactors( eft1, scalefactors) if scalefactors else None #print('create element fibrous ring right', elementIdentifier, result, result2, result3, nids) elementIdentifier += 1 for meshGroup in meshGroups: meshGroup.addElement(element) # fibrous ring septum: meshGroups = [lFibrousRingMeshGroup, rFibrousRingMeshGroup] for e in range(elementsCountAroundAtrialSeptum): eft1 = eftFibrousRing nlm = e - elementsCountAroundAtrialSeptum nlp = nlm + 1 nrm = -e nrp = nrm - 1 nids = [ lavNodeId[0][0][nlm], lavNodeId[0][0][nlp], lavNodeId[0][1][nlm], lavNodeId[0][1][nlp], ravNodeId[0][0][nrm], ravNodeId[0][0][nrp], ravNodeId[0][1][nrm], ravNodeId[0][1][nrp] ] eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] if e == 0: # general linear map d3 adjacent to collapsed posterior interventricular sulcus scaleEftNodeValueLabels(eft1, [5, 6, 7, 8], [Node.VALUE_LABEL_D_DS1], [1]) scaleEftNodeValueLabels(eft1, [6, 8], [Node.VALUE_LABEL_D_DS3], [1]) remapEftNodeValueLabel(eft1, [1, 3], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [5, 7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, []), (Node.VALUE_LABEL_D_DS3, [1])]) elif e == (elementsCountAroundAtrialSeptum - 1): # general linear map d3 adjacent to cfb scaleEftNodeValueLabels(eft1, [5, 6, 7, 8], [Node.VALUE_LABEL_D_DS1], [1]) scaleEftNodeValueLabels(eft1, [5, 7], [Node.VALUE_LABEL_D_DS3], [1]) remapEftNodeValueLabel(eft1, [2, 4], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [6, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1]), (Node.VALUE_LABEL_D_DS3, [1])]) else: scaleEftNodeValueLabels( eft1, [5, 6, 7, 8], [Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS3], [1]) result = elementtemplate1.defineField(coordinates, -1, eft1) element = mesh.createElement(elementIdentifier, elementtemplate1) result2 = element.setNodesByIdentifier(eft1, nids) result3 = element.setScaleFactors( eft1, scalefactors) if scalefactors else None #print('create element fibrous ring septum', elementIdentifier, result, result2, result3, nids) elementIdentifier += 1 for meshGroup in meshGroups: meshGroup.addElement(element) # annotation fiducial points cruxElement = mesh.findElementByIdentifier(cruxElementId) cruxXi = [0.5, 0.5, 1.0] cache.setMeshLocation(cruxElement, cruxXi) result, cruxCoordinates = coordinates.evaluateReal(cache, 3) markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal) nodeIdentifier += 1 cache.setNode(markerPoint) markerName.assignString(cache, "crux of heart") markerLocation.assignMeshLocation(cache, cruxElement, cruxXi) return annotationGroups
def __init__(self, sourceRegion, targetRegion, sourceAnnotationGroups=[]): ''' Assumes targetRegion is empty. :param sourceAnnotationGroups: List of AnnotationGroup for source mesh in sourceRegion. A copy containing the refined elements is created by the MeshRefinement. ''' self._sourceRegion = sourceRegion self._sourceFm = sourceRegion.getFieldmodule() self._sourceCache = self._sourceFm.createFieldcache() self._sourceCoordinates = findOrCreateFieldCoordinates(self._sourceFm) # get range of source coordinates for octree range self._sourceFm.beginChange() sourceNodes = self._sourceFm.findNodesetByFieldDomainType( Field.DOMAIN_TYPE_NODES) minimumsField = self._sourceFm.createFieldNodesetMinimum( self._sourceCoordinates, sourceNodes) result, minimums = minimumsField.evaluateReal(self._sourceCache, 3) assert result == ZINC_OK, 'MeshRefinement failed to get minimum coordinates' maximumsField = self._sourceFm.createFieldNodesetMaximum( self._sourceCoordinates, sourceNodes) result, maximums = maximumsField.evaluateReal(self._sourceCache, 3) assert result == ZINC_OK, 'MeshRefinement failed to get maximum coordinates' xrange = [(maximums[i] - minimums[i]) for i in range(3)] edgeTolerance = 0.5 * (max(xrange)) if edgeTolerance == 0.0: edgeTolerance = 1.0 minimums = [(minimums[i] - edgeTolerance) for i in range(3)] maximums = [(maximums[i] + edgeTolerance) for i in range(3)] minimumsField = None maximumsField = None self._sourceMesh = self._sourceFm.findMeshByDimension(3) self._sourceNodes = self._sourceFm.findNodesetByFieldDomainType( Field.DOMAIN_TYPE_NODES) self._sourceElementiterator = self._sourceMesh.createElementiterator() self._octree = Octree(minimums, maximums) self._targetRegion = targetRegion self._targetFm = targetRegion.getFieldmodule() self._targetFm.beginChange() self._targetCache = self._targetFm.createFieldcache() self._targetCoordinates = findOrCreateFieldCoordinates(self._targetFm) self._targetNodes = self._targetFm.findNodesetByFieldDomainType( Field.DOMAIN_TYPE_NODES) self._nodetemplate = self._targetNodes.createNodetemplate() self._nodetemplate.defineField(self._targetCoordinates) self._targetMesh = self._targetFm.findMeshByDimension(3) self._targetBasis = self._targetFm.createElementbasis( 3, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE) self._targetEft = self._targetMesh.createElementfieldtemplate( self._targetBasis) self._targetElementtemplate = self._targetMesh.createElementtemplate() self._targetElementtemplate.setElementShapeType( Element.SHAPE_TYPE_CUBE) result = self._targetElementtemplate.defineField( self._targetCoordinates, -1, self._targetEft) self._nodeIdentifier = 1 self._elementIdentifier = 1 # prepare annotation group map self._sourceAnnotationGroups = sourceAnnotationGroups self._annotationGroups = [] self._sourceAndTargetMeshGroups = [] self._sourceAndTargetNodesetGroups = [] for sourceAnnotationGroup in sourceAnnotationGroups: targetAnnotationGroup = AnnotationGroup( self._targetRegion, sourceAnnotationGroup.getTerm()) self._annotationGroups.append(targetAnnotationGroup) # assume have only highest dimension element or node/point annotation groups: if sourceAnnotationGroup.hasMeshGroup(self._sourceMesh): self._sourceAndTargetMeshGroups.append( (sourceAnnotationGroup.getMeshGroup(self._sourceMesh), targetAnnotationGroup.getMeshGroup(self._targetMesh))) else: self._sourceAndTargetNodesetGroups.append( (sourceAnnotationGroup.getNodesetGroup(self._sourceNodes), targetAnnotationGroup.getNodesetGroup(self._targetNodes))) # prepare element -> marker point list map self.elementMarkerMap = {} sourceMarkerGroup = findOrCreateFieldGroup(self._sourceFm, "marker") sourceMarkerName = findOrCreateFieldStoredString(self._sourceFm, name="marker_name") sourceMarkerLocation = findOrCreateFieldStoredMeshLocation( self._sourceFm, self._sourceMesh, name="marker_location") sourceMarkerNodes = findOrCreateFieldNodeGroup( sourceMarkerGroup, sourceNodes).getNodesetGroup() nodeIter = sourceMarkerNodes.createNodeiterator() node = nodeIter.next() while node.isValid(): self._sourceCache.setNode(node) element, xi = sourceMarkerLocation.evaluateMeshLocation( self._sourceCache, self._sourceMesh.getDimension()) if element.isValid(): elementIdentifier = element.getIdentifier() markerName = sourceMarkerName.evaluateString(self._sourceCache) markerList = self.elementMarkerMap.get(elementIdentifier) if not markerList: markerList = [] self.elementMarkerMap[elementIdentifier] = markerList markerList.append((markerName, xi, node.getIdentifier())) node = nodeIter.next() if self.elementMarkerMap: self._targetMarkerGroup = findOrCreateFieldGroup( self._targetFm, "marker") self._targetMarkerName = findOrCreateFieldStoredString( self._targetFm, name="marker_name") self._targetMarkerLocation = findOrCreateFieldStoredMeshLocation( self._targetFm, self._targetMesh, name="marker_location") self._targetMarkerNodes = findOrCreateFieldNodeGroup( self._targetMarkerGroup, self._targetNodes).getNodesetGroup() self._targetMarkerTemplate = self._targetMarkerNodes.createNodetemplate( ) self._targetMarkerTemplate.defineField(self._targetMarkerName) self._targetMarkerTemplate.defineField(self._targetMarkerLocation)
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
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
def zinc_write_element_xi_marker_file(region, allMarkers, xiNodeInfo, regionD, nodeIdentifierStart, coordinates, outFile=[]): fm = region.getFieldmodule() if outFile: fm.beginChange() # if xiNodeInfo['nodeType'] == 'nodes': nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) mesh = fm.findMeshByDimension(3) mesh1d = fm.findMeshByDimension(1) cache = fm.createFieldcache() xiNodeName = findOrCreateFieldStoredString(fm, name=xiNodeInfo['nameStr']) xiNodeLocation = findOrCreateFieldStoredMeshLocation( fm, mesh, name="elementxi_location") xiNodeTemplate = nodes.createNodetemplate() xiNodeTemplate.defineField(xiNodeLocation) xiNodeTemplate.defineField(coordinates) xiNodeTemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1) xiNodeTemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1) xiNodeTemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1) xiNodeTemplate.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS3, 1) xiMeshGroup = AnnotationGroup( region, ('tracts_xi_elements', None)).getMeshGroup(mesh1d) nodeIdentifier = nodeIdentifierStart for key in allMarkers: xiNodeGroup = findOrCreateFieldGroup( fm, xiNodeInfo['groupName'] + '_' + key) xiNodePoints = findOrCreateFieldNodeGroup(xiNodeGroup, nodes).getNodesetGroup() addxiNode = {"name": key, "xi": allMarkers[key]["xi"]} xiNodePoint = xiNodePoints.createNode(nodeIdentifier, xiNodeTemplate) xiNodePoint.merge(xiNodeTemplate) cache.setNode(xiNodePoint) elementID = allMarkers[key]["elementID"] element = mesh.findElementByIdentifier(elementID) result = xiNodeLocation.assignMeshLocation(cache, element, addxiNode["xi"]) result = coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, list(regionD[key]['centre'])) try: result = coordinates.setNodeParameters( cache, -1, Node.VALUE_LABEL_D_DS1, 1, list(regionD[key]['axes'][0])) result = coordinates.setNodeParameters( cache, -1, Node.VALUE_LABEL_D_DS2, 1, list(regionD[key]['axes'][1])) result = coordinates.setNodeParameters( cache, -1, Node.VALUE_LABEL_D_DS3, 1, list(regionD[key]['axes'][2])) except: result = coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, [1, 0, 0]) result = coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, [0, 1, 0]) result = coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS3, 1, [0, 0, 1]) nodeIdentifier += 1 # write 1D elements between embedded nodes if True: mesh1d = fm.findMeshByDimension(1) elementIdentifier = 55555555 basis1d = fm.createElementbasis( 1, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE) eft1d = mesh1d.createElementfieldtemplate(basis1d) elementtemplate = mesh1d.createElementtemplate() elementtemplate.setElementShapeType(Element.SHAPE_TYPE_LINE) result = elementtemplate.defineField(coordinates, -1, eft1d) element = mesh1d.createElement(elementIdentifier, elementtemplate) result = element.setNodesByIdentifier( eft1d, [nodeIdentifierStart, nodeIdentifier - 1]) xiMeshGroup.addElement(element) if outFile: fm.endChange() region.writeFile(outFile) return region
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 ''' fm = region.getFieldmodule() coordinates = findOrCreateFieldCoordinates(fm) nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) 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_D_DS3, 1) mesh = fm.findMeshByDimension(3) cache = fm.createFieldcache() elementsCount1 = 2 elementsCount2 = 4 elementsCount3 = 4 # Annotation fiducial point 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) # Create nodes nodeIdentifier = 1 lNodeIds = [] d1 = [0.5, 0.0, 0.0] d2 = [0.0, 0.5, 0.0] d3 = [0.0, 0.0, 1.0] for n3 in range(elementsCount3 + 1): lNodeIds.append([]) for n2 in range(elementsCount2 + 1): lNodeIds[n3].append([]) for n1 in range(elementsCount1 + 1): lNodeIds[n3][n2].append([]) if n3 < elementsCount3: if (n1 == 0) and ((n2 == 0) or (n2 == elementsCount2)): continue else: if (n2 == 0) or (n2 == elementsCount2) or (n1 == 0): continue node = nodes.createNode(nodeIdentifier, nodetemplate) cache.setNode(node) x = [0.5 * (n1 - 1), 0.5 * (n2 - 1), 1.0 * n3] coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, d1) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, d2) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS3, 1, d3) lNodeIds[n3][n2][n1] = nodeIdentifier nodeIdentifier += 1 # Create elements mesh = fm.findMeshByDimension(3) eftfactory = eftfactory_tricubichermite(mesh, None) eftRegular = eftfactory.createEftBasic() elementtemplateRegular = mesh.createElementtemplate() elementtemplateRegular.setElementShapeType(Element.SHAPE_TYPE_CUBE) elementtemplateRegular.defineField(coordinates, -1, eftRegular) elementtemplateCustom = mesh.createElementtemplate() elementtemplateCustom.setElementShapeType(Element.SHAPE_TYPE_CUBE) lungGroup = AnnotationGroup(region, get_lung_term("lung")) leftLungGroup = AnnotationGroup(region, get_lung_term("left lung")) rightLungGroup = AnnotationGroup(region, get_lung_term("right lung")) annotationGroups = [leftLungGroup, rightLungGroup, lungGroup] lungMeshGroup = lungGroup.getMeshGroup(mesh) leftLungMeshGroup = leftLungGroup.getMeshGroup(mesh) rightLungMeshGroup = rightLungGroup.getMeshGroup(mesh) eft1 = eftfactory.createEftWedgeCollapseXi1Quadrant([1, 5]) eft2 = eftfactory.createEftWedgeCollapseXi1Quadrant([3, 7]) eft3 = eftfactory.createEftWedgeCollapseXi2Quadrant([5, 6]) eft4 = eftfactory.createEftWedgeCollapseXi2Quadrant([7, 8]) eft5 = eftfactory.createEftWedgeCollapseXi1Quadrant([5, 7]) eft6 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(8, 2) eft7 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(6, 3) elementIdentifier = 1 for e3 in range(elementsCount3): for e2 in range(elementsCount2): for e1 in range(elementsCount1): eft = eftRegular nodeIdentifiers = [ lNodeIds[e3][e2][e1], lNodeIds[e3][e2][e1 + 1], lNodeIds[e3][e2 + 1][e1], lNodeIds[e3][e2 + 1][e1 + 1], lNodeIds[e3 + 1][e2][e1], lNodeIds[e3 + 1][e2][e1 + 1], lNodeIds[e3 + 1][e2 + 1][e1], lNodeIds[e3 + 1][e2 + 1][e1 + 1] ] scalefactors = None if (e3 < elementsCount3 - 1): if (e2 == 0) and (e1 == 0): # Back wedge elements nodeIdentifiers.pop(4) nodeIdentifiers.pop(0) eft = eft1 scalefactors = [-1.0] elif (e2 == elementsCount2 - 1) and (e1 == 0): # Front wedge elements nodeIdentifiers.pop(6) nodeIdentifiers.pop(2) eft = eft2 else: if (e2 == 0) and (e1 == 1): # Top back wedge elements nodeIdentifiers.pop(5) nodeIdentifiers.pop(4) eft = eft3 elif (e2 == elementsCount2 - 1) and (e1 == 1): # Top front wedge elements nodeIdentifiers.pop(7) nodeIdentifiers.pop(6) eft = eft4 scalefactors = [-1.0] elif (e2 == 1) and (e1 == 0): # Top middle back wedge element nodeIdentifiers.pop(6) nodeIdentifiers.pop(4) eft = eft5 elif (e2 == 2) and (e1 == 0): # Top middle front wedge element nodeIdentifiers.pop(6) nodeIdentifiers.pop(4) eft = eft5 if (e2 == 0) and (e1 == 0): # Top back tetrahedron element nodeIdentifiers.pop(6) nodeIdentifiers.pop(5) nodeIdentifiers.pop(4) nodeIdentifiers.pop(0) eft = eft6 scalefactors = [-1.0] if (e2 == elementsCount2 - 1) and (e1 == 0): # Top front tetrahedron element nodeIdentifiers.pop(7) nodeIdentifiers.pop(6) nodeIdentifiers.pop(4) nodeIdentifiers.pop(2) eft = eft7 scalefactors = [-1.0] if eft is eftRegular: element = mesh.createElement(elementIdentifier, elementtemplateRegular) else: elementtemplateCustom.defineField(coordinates, -1, eft) element = mesh.createElement(elementIdentifier, elementtemplateCustom) element.setNodesByIdentifier(eft, nodeIdentifiers) if scalefactors: element.setScaleFactors(eft, scalefactors) elementIdentifier += 1 leftLungMeshGroup.addElement(element) lungMeshGroup.addElement(element) # Apex annotation point idx = elementsCount1 * elementsCount2 * ( elementsCount3 - 1) + elementsCount1 * (elementsCount2 // 2) element1 = mesh.findElementByIdentifier(idx) markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal) nodeIdentifier += 1 cache.setNode(markerPoint) markerName.assignString(cache, 'apex of left lung') markerLocation.assignMeshLocation(cache, element1, [1.0, 1.0, 1.0]) return annotationGroups