def createEftTetrahedronXi1Zero(self, nodeScaleFactorOffset0, nodeScaleFactorOffset1): ''' Create a bicubic hermite linear element field for a solid tetrahedron for the apex of cecum, with xi1 and xi3 collapsed on xi2 = 0, and xi3 collapsed on xi1 = 0, xi2 = 1. Each collapsed node on xi2 = 0 has 3 scale factors giving the cos, sin coefficients of the radial line from global derivatives, plus the arc subtended by the element in radians, so the circumferential direction is rounded. Need to create a new template for each sector around axis giving common nodeScaleFactorOffset values on common faces. Suggestion is to start at 0 and add 10000 for each radial line around axis. :param nodeScaleFactorOffset0: offset of node scale factors at axis on xi1=0 :param nodeScaleFactorOffset1: offset of node scale factors at axis on xi1=1 :return: Element field template ''' # start with full bicubic hermite linear eft = self._mesh.createElementfieldtemplate(self._basis) for n in [2, 3, 6, 7]: eft.setFunctionNumberOfTerms(n * 4 + 4, 0) # GRC: allow scale factor identifier for global -1.0 to be prescribed setEftScaleFactorIds(eft, [1], [ nodeScaleFactorOffset0 + 1, nodeScaleFactorOffset0 + 2, nodeScaleFactorOffset0 + 3, nodeScaleFactorOffset1 + 1, nodeScaleFactorOffset1 + 2, nodeScaleFactorOffset1 + 3 ]) # remap parameters on xi2 = 0 before collapsing nodes remapEftNodeValueLabel(eft, [1, 2, 5, 6], Node.VALUE_LABEL_D_DS1, []) for layer in range(2): soAround = 1 ln = layer * 4 + 1 # 2 terms for d/dxi2 via general linear map: remapEftNodeValueLabel(eft, [ln], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [soAround + 1]), (Node.VALUE_LABEL_D_DS2, [soAround + 2])]) # 2 terms for cross derivative 1 2 to correct circular apex: cos(theta).phi, -sin(theta).phi remapEftNodeValueLabel( eft, [ln], Node.VALUE_LABEL_D2_DS1DS2, [(Node.VALUE_LABEL_D_DS1, [soAround + 2, soAround + 3]), (Node.VALUE_LABEL_D_DS2, [1, soAround + 1, soAround + 3])]) ln = layer * 4 + 2 # 2 terms for d/dxi2 via general linear map: remapEftNodeValueLabel(eft, [ln], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [soAround + 4]), (Node.VALUE_LABEL_D_DS2, [soAround + 5])]) # 2 terms for cross derivative 1 2 to correct circular apex: cos(theta).phi, -sin(theta).phi remapEftNodeValueLabel( eft, [ln], Node.VALUE_LABEL_D2_DS1DS2, [(Node.VALUE_LABEL_D_DS1, [soAround + 5, soAround + 6]), (Node.VALUE_LABEL_D_DS2, [1, soAround + 4, soAround + 6])]) ln_map = [1, 1, 2, 3, 1, 1, 2, 4] remapEftLocalNodes(eft, 4, ln_map) assert eft.validate( ), 'eftfactory_bicubichermitelinear.createEftTetrahedronXi1Zero: Failed to validate eft' return eft
def createEftWedgeXi1Zero(self): ''' Create a basic bicubic hermite linear element template for elements along boundary of tenia coli where nodes on xi1 = 0 are collapsed. :return: Element field template ''' eft = self.createEftBasic() ln_map = [1, 2, 3, 4, 1, 5, 3, 6] remapEftLocalNodes(eft, 6, ln_map) assert eft.validate( ), 'eftfactory_tricubichermite.createEftWedgeXi1Zero: Failed to validate eft' return eft
def createEftWedgeXi1ZeroOpenTube(self): ''' Create a basic bicubic hermite linear element template for elements along boundary of tenia coli where nodes on xi1 = 0 are collapsed where a tube is opened on xi1 = 1 for a flat preparation. :return: Element field template ''' eft = self.createEftBasic() for n in [1, 3, 5, 7]: ln = n + 1 eft.setTermNodeParameter(n * 4 + 1, 1, ln, Node.VALUE_LABEL_VALUE, 2) eft.setTermNodeParameter(n * 4 + 2, 1, ln, Node.VALUE_LABEL_D_DS1, 2) eft.setTermNodeParameter(n * 4 + 3, 1, ln, Node.VALUE_LABEL_D_DS2, 2) if self._useCrossDerivatives: eft.setTermNodeParameter(n * 4 + 4, 1, ln, Node.VALUE_LABEL_D2_DS1DS2, 2) ln_map = [1, 2, 3, 4, 1, 5, 3, 6] remapEftLocalNodes(eft, 6, ln_map) assert eft.validate( ), 'eftfactory_tricubichermite.createEftWedgeXi1ZeroOpenTube: Failed to validate eft' return eft
def createEftShellPoleBottom(self, nodeScaleFactorOffset0, nodeScaleFactorOffset1): ''' Create a bicubic hermite linear element field for closing bottom pole of a shell. Element is collapsed in xi1 on xi2 = 0. Each collapsed node has 3 scale factors giving the cos, sin coefficients of the radial line from global derivatives, plus the arc subtended by the element in radians, so the pole can be rounded. Need to create a new template for each sector around pole giving common nodeScaleFactorOffset values on common faces. Suggestion is to start at 0 and add 100 for each radial line around pole. :param nodeScaleFactorOffset0: offset of node scale factors at pole on xi1=0 :param nodeScaleFactorOffset1: offset of node scale factors at pole on xi1=1 :return: Element field template ''' # start with full bicubic hermite linear to remap D2_DS1DS2 at pole eft = self._mesh.createElementfieldtemplate(self._basis) if not self._useCrossDerivatives: for n in [2, 3, 6, 7]: eft.setFunctionNumberOfTerms(n * 4 + 4, 0) # GRC: allow scale factor identifier for global -1.0 to be prescribed setEftScaleFactorIds(eft, [1], [ nodeScaleFactorOffset0 + 1, nodeScaleFactorOffset0 + 2, nodeScaleFactorOffset0 + 3, nodeScaleFactorOffset1 + 1, nodeScaleFactorOffset1 + 2, nodeScaleFactorOffset1 + 3, nodeScaleFactorOffset0 + 1, nodeScaleFactorOffset0 + 2, nodeScaleFactorOffset0 + 3, nodeScaleFactorOffset1 + 1, nodeScaleFactorOffset1 + 2, nodeScaleFactorOffset1 + 3 ]) # remap parameters before collapsing nodes remapEftNodeValueLabel(eft, [1, 2, 5, 6], Node.VALUE_LABEL_D_DS1, []) for layer in range(2): so = layer * 6 + 1 ln = layer * 4 + 1 # 2 terms for d/dxi2 via general linear map: remapEftNodeValueLabel(eft, [ln], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [so + 1]), (Node.VALUE_LABEL_D_DS2, [so + 2])]) # 2 terms for cross derivative 1 2 to correct circular pole: -sin(theta).phi, cos(theta).phi remapEftNodeValueLabel( eft, [ln], Node.VALUE_LABEL_D2_DS1DS2, [(Node.VALUE_LABEL_D_DS1, [so + 2, so + 3]), (Node.VALUE_LABEL_D_DS2, [1, so + 1, so + 3])]) ln = layer * 4 + 2 # 2 terms for d/dxi2 via general linear map: remapEftNodeValueLabel(eft, [ln], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [so + 4]), (Node.VALUE_LABEL_D_DS2, [so + 5])]) # 2 terms for cross derivative 1 2 to correct circular pole: -sin(theta).phi, cos(theta).phi remapEftNodeValueLabel( eft, [ln], Node.VALUE_LABEL_D2_DS1DS2, [(Node.VALUE_LABEL_D_DS1, [so + 5, so + 6]), (Node.VALUE_LABEL_D_DS2, [1, so + 4, so + 6])]) ln_map = [1, 1, 2, 3, 4, 4, 5, 6] remapEftLocalNodes(eft, 6, ln_map) assert eft.validate( ), 'eftfactory_tricubichermite.createEftShellPoleBottom: Failed to validate eft' return eft
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 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 createEftWedgeCollapseXi2Quadrant(self, collapseNodes): ''' Create a bicubic hermite linear element field for a wedge element collapsed in xi2. :param collapseNodes: As the element can be collapsed in xi2 at either ends of xi1 or xi3, collapseNodes are the local indices of nodes whose d1 (for elements collapse at either ends of xi1) or d3 (for elements collapse at either ends of xi3) are remapped with d2 before collapsing the nodes. :return: Element field template ''' eft = self.createEftBasic() valid = True if collapseNodes in [[1, 2], [3, 4]]: # xi3 = 0 nodes = [1, 2, 3, 4] remapEftNodeValueLabel(eft, nodes, Node.VALUE_LABEL_D_DS2, []) ln_map = [1, 2, 1, 2, 3, 4, 5, 6] elif collapseNodes in [[5, 6], [7, 8]]: # xi3 = 1 nodes = [5, 6, 7, 8] remapEftNodeValueLabel(eft, nodes, Node.VALUE_LABEL_D_DS2, []) ln_map = [1, 2, 3, 4, 5, 6, 5, 6] elif collapseNodes in [[3, 7]]: nodes = [1, 3, 5, 7] # remap parameters on xi1 = 0 before collapsing nodes if collapseNodes == [3, 7]: remapEftNodeValueLabel(eft, nodes, Node.VALUE_LABEL_D_DS2, []) remapEftNodeValueLabel(eft, collapseNodes, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [])]) else: valid = False ln_map = [1, 2, 1, 3, 4, 5, 4, 6] elif collapseNodes in [[2, 6], [4, 8]]: nodes = [2, 4, 6, 8] # remap parameters on xi1 = 1 before collapsing nodes if collapseNodes == [2, 6]: remapEftNodeValueLabel(eft, nodes, Node.VALUE_LABEL_D_DS2, []) remapEftNodeValueLabel(eft, collapseNodes, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [])]) elif collapseNodes == [4, 8]: setEftScaleFactorIds(eft, [1], []) remapEftNodeValueLabel(eft, collapseNodes, Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [1])]) remapEftNodeValueLabel(eft, nodes, Node.VALUE_LABEL_D_DS2, []) else: valid = False ln_map = [1, 2, 3, 2, 4, 5, 6, 5] else: valid = False if not valid: assert False, "createEftWedgeCollapseXi2Quadrant. Not implemented for collapse nodes " + str( collapseNodes) # zero cross derivative parameters remapEftNodeValueLabel(eft, nodes, Node.VALUE_LABEL_D2_DS1DS2, []) remapEftLocalNodes(eft, 6, ln_map) if not eft.validate(): print( 'eftfactory_bicubichermitelinear.createEftWedgeCollapseXi2Quadrant: Failed to validate eft for collapseNodes', collapseNodes) return eft
def generateBaseMesh(cls, region, options, baseCentre=[0.0, 0.0, 0.0], axisSide1=[0.0, -1.0, 0.0], axisUp=[0.0, 0.0, 1.0]): """ Generate the base bicubic-linear Hermite mesh. See also generateMesh(). Optional extra parameters allow centre and axes to be set. :param region: Zinc region to define model in. Must be empty. :param options: Dict containing options. See getDefaultOptions(). :param baseCentre: Centre of valve on ventriculo-arterial junction. :param axisSide: Unit vector in first side direction where angle around starts. :param axisUp: Unit vector in outflow direction of valve. :return: list of AnnotationGroup """ unitScale = options['Unit scale'] outerHeight = unitScale * options['Outer height'] innerDepth = unitScale * options['Inner depth'] cuspHeight = unitScale * options['Cusp height'] innerRadius = unitScale * 0.5 * options['Inner diameter'] sinusRadialDisplacement = unitScale * options[ 'Sinus radial displacement'] wallThickness = unitScale * options['Wall thickness'] cuspThickness = unitScale * options['Cusp thickness'] aorticNotPulmonary = options['Aortic not pulmonary'] useCrossDerivatives = False fm = region.getFieldmodule() fm.beginChange() coordinates = zinc_utils.getOrCreateCoordinateField(fm) cache = fm.createFieldcache() if aorticNotPulmonary: arterialRootGroup = AnnotationGroup(region, 'root of aorta', FMANumber=3740, lyphID='Lyph ID unknown') cuspGroups = [ AnnotationGroup(region, 'posterior cusp of aortic valve', FMANumber=7253, lyphID='Lyph ID unknown'), AnnotationGroup(region, 'right cusp of aortic valve', FMANumber=7252, lyphID='Lyph ID unknown'), AnnotationGroup(region, 'left cusp of aortic valve', FMANumber=7251, lyphID='Lyph ID unknown') ] else: arterialRootGroup = AnnotationGroup(region, 'root of pulmonary trunk', FMANumber=8612, lyphID='Lyph ID unknown') cuspGroups = [ AnnotationGroup(region, 'right cusp of pulmonary valve', FMANumber=7250, lyphID='Lyph ID unknown'), AnnotationGroup(region, 'anterior cusp of pulmonary valve', FMANumber=7249, lyphID='Lyph ID unknown'), AnnotationGroup(region, 'left cusp of pulmonary valve', FMANumber=7247, lyphID='Lyph ID unknown') ] allGroups = [arterialRootGroup ] # groups that all elements in scaffold will go in annotationGroups = allGroups + cuspGroups # annotation fiducial points fiducialGroup = zinc_utils.getOrCreateGroupField(fm, 'fiducial') fiducialCoordinates = zinc_utils.getOrCreateCoordinateField( fm, 'fiducial_coordinates') fiducialLabel = zinc_utils.getOrCreateLabelField(fm, 'fiducial_label') #fiducialElementXi = zinc_utils.getOrCreateElementXiField(fm, 'fiducial_element_xi') datapoints = fm.findNodesetByFieldDomainType( Field.DOMAIN_TYPE_DATAPOINTS) fiducialPoints = zinc_utils.getOrCreateNodesetGroup( fiducialGroup, datapoints) datapointTemplateExternal = datapoints.createNodetemplate() datapointTemplateExternal.defineField(fiducialCoordinates) datapointTemplateExternal.defineField(fiducialLabel) ################# # Create nodes ################# 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) # most nodes in this scaffold do not have a DS3 derivative nodetemplateLinearS3 = nodes.createNodetemplate() nodetemplateLinearS3.defineField(coordinates) nodetemplateLinearS3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1) nodetemplateLinearS3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1) nodetemplateLinearS3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1) # several only have a DS1 derivative nodetemplateLinearS2S3 = nodes.createNodetemplate() nodetemplateLinearS2S3.defineField(coordinates) nodetemplateLinearS2S3.setValueNumberOfVersions( coordinates, -1, Node.VALUE_LABEL_VALUE, 1) nodetemplateLinearS2S3.setValueNumberOfVersions( coordinates, -1, Node.VALUE_LABEL_D_DS1, 1) nodeIdentifier = max(1, zinc_utils.getMaximumNodeIdentifier(nodes) + 1) elementsCountAround = 6 radiansPerElementAround = 2.0 * math.pi / elementsCountAround axisSide2 = vector.crossproduct3(axisUp, axisSide1) outerRadius = innerRadius + wallThickness cuspOuterLength2 = 0.5 * getApproximateEllipsePerimeter( innerRadius, cuspHeight) cuspOuterWallArcLength = cuspOuterLength2 * innerRadius / ( innerRadius + cuspHeight) noduleOuterAxialArcLength = cuspOuterLength2 - cuspOuterWallArcLength noduleOuterRadialArcLength = innerRadius cuspOuterWalld1 = interp.interpolateLagrangeHermiteDerivative( [innerRadius, outerHeight + innerDepth - cuspHeight], [0.0, 0.0], [-innerRadius, 0.0], 0.0) sin60 = math.sin(math.pi / 3.0) cuspThicknessLowerFactor = 4.5 # GRC fudge factor cuspInnerLength2 = 0.5 * getApproximateEllipsePerimeter( innerRadius - cuspThickness / sin60, cuspHeight - cuspThicknessLowerFactor * cuspThickness) noduleInnerAxialArcLength = cuspInnerLength2 * ( cuspHeight - cuspThicknessLowerFactor * cuspThickness) / ( innerRadius - cuspThickness / sin60 + cuspHeight - cuspThicknessLowerFactor * cuspThickness) noduleInnerRadialArcLength = innerRadius - cuspThickness / math.tan( math.pi / 3.0) nMidCusp = 0 if aorticNotPulmonary else 1 # lower points ix, id1 = createCirclePoints( [(baseCentre[c] - axisUp[c] * innerDepth) for c in range(3)], [axisSide1[c] * innerRadius for c in range(3)], [axisSide2[c] * innerRadius for c in range(3)], elementsCountAround) ox, od1 = getSemilunarValveSinusPoints(baseCentre, axisSide1, axisSide2, outerRadius, sinusRadialDisplacement, startMidCusp=aorticNotPulmonary) lowerx, lowerd1 = [ix, ox], [id1, od1] # upper points topCentre = [(baseCentre[c] + axisUp[c] * outerHeight) for c in range(3)] # twice as many on inner: ix, id1 = createCirclePoints( topCentre, [axisSide1[c] * innerRadius for c in range(3)], [axisSide2[c] * innerRadius for c in range(3)], elementsCountAround * 2) # tweak inner points so elements attached to cusps are narrower cuspRadiansFactor = 0.25 # GRC fudge factor midDerivativeFactor = 1.0 + 0.5 * (1.0 - cuspRadiansFactor ) # GRC test compromise cuspAttachmentRadians = cuspRadiansFactor * radiansPerElementAround cuspAttachmentRadialDisplacement = wallThickness * 0.333 # GRC fudge factor cuspAttachmentRadius = innerRadius - cuspAttachmentRadialDisplacement for cusp in range(3): n1 = cusp * 2 - 1 + nMidCusp n2 = n1 * 2 id1[n2 + 2] = [2.0 * d for d in id1[n2 + 2]] # side 1 radiansAround = n1 * radiansPerElementAround + cuspAttachmentRadians rcosRadiansAround = cuspAttachmentRadius * math.cos(radiansAround) rsinRadiansAround = cuspAttachmentRadius * math.sin(radiansAround) ix[n2 + 1] = [(topCentre[c] + rcosRadiansAround * axisSide1[c] + rsinRadiansAround * axisSide2[c]) for c in range(3)] id1[n2 + 1] = interp.interpolateLagrangeHermiteDerivative( ix[n2 + 1], ix[n2 + 2], id1[n2 + 2], 0.0) # side 2 n1 = ((cusp + 1) * 2 - 1 + nMidCusp) % elementsCountAround n2 = n1 * 2 radiansAround = n1 * radiansPerElementAround - cuspAttachmentRadians rcosRadiansAround = cuspAttachmentRadius * math.cos(radiansAround) rsinRadiansAround = cuspAttachmentRadius * math.sin(radiansAround) ix[n2 - 1] = [(topCentre[c] + rcosRadiansAround * axisSide1[c] + rsinRadiansAround * axisSide2[c]) for c in range(3)] id1[n2 - 1] = interp.interpolateHermiteLagrangeDerivative( ix[n2 - 2], id1[n2 - 2], ix[n2 - 1], 1.0) ox, od1 = createCirclePoints( topCentre, [axisSide1[c] * outerRadius for c in range(3)], [axisSide2[c] * outerRadius for c in range(3)], elementsCountAround) upperx, upperd1 = [ix, ox], [id1, od1] # get lower and upper derivative 2 zero = [0.0, 0.0, 0.0] upperd2factor = outerHeight upd2 = [d * upperd2factor for d in axisUp] lowerOuterd2 = interp.smoothCubicHermiteDerivativesLine( [lowerx[1][nMidCusp], upperx[1][nMidCusp]], [upd2, upd2], fixStartDirection=True, fixEndDerivative=True)[0] lowerd2factor = 2.0 * (outerHeight + innerDepth) - upperd2factor lowerInnerd2 = [d * lowerd2factor for d in axisUp] lowerd2 = [[lowerInnerd2] * elementsCountAround, [lowerOuterd2] * elementsCountAround ] # some lowerd2[0] to be fitted below upperd2 = [[upd2] * (elementsCountAround * 2), [upd2] * elementsCountAround] # get lower and upper derivative 1 or 2 pointing to/from cusps for n1 in range(elementsCountAround): radiansAround = n1 * radiansPerElementAround cosRadiansAround = math.cos(radiansAround) sinRadiansAround = math.sin(radiansAround) if (n1 % 2) == nMidCusp: lowerd2[0][n1] = [ -cuspOuterWallArcLength * (cosRadiansAround * axisSide1[c] + sinRadiansAround * axisSide2[c]) for c in range(3) ] else: upperd1[0][n1 * 2] = [ (cuspOuterWalld1[0] * (cosRadiansAround * axisSide1[c] + sinRadiansAround * axisSide2[c]) + cuspOuterWalld1[1] * axisUp[c]) for c in range(3) ] # inner wall and mid sinus points; only every second one is used sinusDepth = innerDepth - cuspThicknessLowerFactor * cuspThickness # GRC test sinusCentre = [(baseCentre[c] - sinusDepth * axisUp[c]) for c in range(3)] sinusx, sinusd1 = createCirclePoints( sinusCentre, [axisSide1[c] * innerRadius for c in range(3)], [axisSide2[c] * innerRadius for c in range(3)], elementsCountAround) # get sinusd2, parallel to lower inclined lines sd2 = interp.smoothCubicHermiteDerivativesLine( [[innerRadius, -sinusDepth], [innerRadius, outerHeight]], [[wallThickness + sinusRadialDisplacement, innerDepth], [0.0, upperd2factor]], fixStartDirection=True, fixEndDerivative=True)[0] sinusd2 = [None] * elementsCountAround for cusp in range(3): n1 = cusp * 2 + nMidCusp radiansAround = n1 * radiansPerElementAround cosRadiansAround = math.cos(radiansAround) sinRadiansAround = math.sin(radiansAround) sinusd2[n1] = [(sd2[0] * (cosRadiansAround * axisSide1[c] + sinRadiansAround * axisSide2[c]) + sd2[1] * axisUp[c]) for c in range(3)] # get points on arc between mid sinus and upper cusp points arcx = [] arcd1 = [] scaled1 = 2.5 # GRC fudge factor for cusp in range(3): n1 = cusp * 2 + nMidCusp n1m = n1 - 1 n1p = (n1 + 1) % elementsCountAround n2m = n1m * 2 + 1 n2p = n1p * 2 - 1 ax, ad1 = interp.sampleCubicHermiteCurves( [upperx[0][n2m], sinusx[n1]], [[-scaled1 * d for d in upperd2[0][n2m]], [scaled1 * d for d in sinusd1[n1]]], elementsCountOut=2, addLengthStart=0.5 * vector.magnitude(upperd2[0][n2m]), lengthFractionStart=0.5, addLengthEnd=0.5 * vector.magnitude(sinusd1[n1]), lengthFractionEnd=0.5, arcLengthDerivatives=False)[0:2] arcx.append(ax[1]) arcd1.append(ad1[1]) ax, ad1 = interp.sampleCubicHermiteCurves( [ sinusx[n1], upperx[0][n2p], ], [[scaled1 * d for d in sinusd1[n1]], [scaled1 * d for d in upperd2[0][n2p]]], elementsCountOut=2, addLengthStart=0.5 * vector.magnitude(sinusd1[n1]), lengthFractionStart=0.5, addLengthEnd=0.5 * vector.magnitude(upperd2[0][n2p]), lengthFractionEnd=0.5, arcLengthDerivatives=False)[0:2] arcx.append(ax[1]) arcd1.append(ad1[1]) if nMidCusp == 0: arcx.append(arcx.pop(0)) arcd1.append(arcd1.pop(0)) # cusp nodule points noduleCentre = [(baseCentre[c] + axisUp[c] * (cuspHeight - innerDepth)) for c in range(3)] nodulex = [[], []] noduled1 = [[], []] noduled2 = [[], []] noduled3 = [[], []] cuspRadialThickness = cuspThickness / sin60 for i in range(3): nodulex[0].append(noduleCentre) n1 = i * 2 + nMidCusp radiansAround = n1 * radiansPerElementAround cosRadiansAround = math.cos(radiansAround) sinRadiansAround = math.sin(radiansAround) nodulex[1].append([(noduleCentre[c] + cuspRadialThickness * (cosRadiansAround * axisSide1[c] + sinRadiansAround * axisSide2[c])) for c in range(3)]) n1 = i * 2 - 1 + nMidCusp radiansAround = n1 * radiansPerElementAround cosRadiansAround = math.cos(radiansAround) sinRadiansAround = math.sin(radiansAround) noduled1[0].append([ noduleOuterRadialArcLength * (cosRadiansAround * axisSide1[c] + sinRadiansAround * axisSide2[c]) for c in range(3) ]) noduled1[1].append( vector.setMagnitude(noduled1[0][i], noduleInnerRadialArcLength)) n1 = i * 2 + 1 + nMidCusp radiansAround = n1 * radiansPerElementAround cosRadiansAround = math.cos(radiansAround) sinRadiansAround = math.sin(radiansAround) noduled2[0].append([ noduleOuterRadialArcLength * (cosRadiansAround * axisSide1[c] + sinRadiansAround * axisSide2[c]) for c in range(3) ]) noduled2[1].append( vector.setMagnitude(noduled2[0][i], noduleInnerRadialArcLength)) noduled3[0].append( [noduleOuterAxialArcLength * axisUp[c] for c in range(3)]) noduled3[1].append( [noduleInnerAxialArcLength * axisUp[c] for c in range(3)]) # Create nodes lowerNodeId = [[], []] for n3 in range(2): for n1 in range(elementsCountAround): node = nodes.createNode(nodeIdentifier, nodetemplateLinearS3) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, lowerx[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, lowerd1[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, lowerd2[n3][n1]) lowerNodeId[n3].append(nodeIdentifier) nodeIdentifier += 1 sinusNodeId = [] for n1 in range(elementsCountAround): if (n1 % 2) != nMidCusp: sinusNodeId.append(None) continue node = nodes.createNode(nodeIdentifier, nodetemplateLinearS3) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, sinusx[n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, sinusd1[n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, sinusd2[n1]) sinusNodeId.append(nodeIdentifier) nodeIdentifier += 1 arcNodeId = [] for n1 in range(elementsCountAround): node = nodes.createNode(nodeIdentifier, nodetemplateLinearS2S3) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, arcx[n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, arcd1[n1]) arcNodeId.append(nodeIdentifier) nodeIdentifier += 1 noduleNodeId = [[], []] for n3 in range(2): for n1 in range(3): node = nodes.createNode(nodeIdentifier, nodetemplate) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, nodulex[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, noduled1[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, noduled2[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS3, 1, noduled3[n3][n1]) noduleNodeId[n3].append(nodeIdentifier) nodeIdentifier += 1 upperNodeId = [[], []] for n3 in range(2): for n1 in range(len(upperx[n3])): node = nodes.createNode(nodeIdentifier, nodetemplateLinearS3) cache.setNode(node) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, upperx[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, upperd1[n3][n1]) coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, upperd2[n3][n1]) upperNodeId[n3].append(nodeIdentifier) nodeIdentifier += 1 ################# # Create elements ################# mesh = fm.findMeshByDimension(3) allMeshGroups = [allGroup.getMeshGroup(mesh) for allGroup in allGroups] cuspMeshGroups = [ cuspGroup.getMeshGroup(mesh) for cuspGroup in cuspGroups ] linearHermiteLinearBasis = fm.createElementbasis( 3, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE) linearHermiteLinearBasis.setFunctionType( 2, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE) hermiteLinearLinearBasis = fm.createElementbasis( 3, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE) hermiteLinearLinearBasis.setFunctionType( 1, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE) bicubichermitelinear = eftfactory_bicubichermitelinear( mesh, useCrossDerivatives) eftDefault = bicubichermitelinear.createEftNoCrossDerivatives() elementIdentifier = max( 1, zinc_utils.getMaximumElementIdentifier(mesh) + 1) elementtemplate1 = mesh.createElementtemplate() elementtemplate1.setElementShapeType(Element.SHAPE_TYPE_CUBE) # wall elements for cusp in range(3): n1 = cusp * 2 - 1 + nMidCusp n2 = n1 * 2 for e in range(6): eft1 = None scalefactors = None if (e == 0) or (e == 5): # 6 node linear-hermite-linear collapsed wedge element expanding from zero width on outer wall of root, attaching to vertical part of cusp eft1 = mesh.createElementfieldtemplate( linearHermiteLinearBasis) # switch mappings to use DS2 instead of default DS1 remapEftNodeValueLabel(eft1, [1, 2, 3, 4, 5, 6, 7, 8], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [])]) if e == 0: nids = [ lowerNodeId[0][n1], arcNodeId[n1], upperNodeId[0][n2], upperNodeId[0][n2 + 1], lowerNodeId[1][n1], upperNodeId[1][n1] ] setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] remapEftNodeValueLabel(eft1, [2], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])]) else: nids = [ arcNodeId[n1 + 1], lowerNodeId[0][n1 - 4], upperNodeId[0][n2 + 3], upperNodeId[0][n2 - 8], lowerNodeId[1][n1 - 4], upperNodeId[1][n1 - 4] ] remapEftNodeValueLabel(eft1, [1], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])]) ln_map = [1, 2, 3, 4, 5, 5, 6, 6] remapEftLocalNodes(eft1, 6, ln_map) elif (e == 1) or (e == 4): # 6 node hermite-linear-linear collapsed wedge element on lower wall eft1 = mesh.createElementfieldtemplate( hermiteLinearLinearBasis) if e == 1: nids = [ lowerNodeId[0][n1], lowerNodeId[0][n1 + 1], arcNodeId[n1], sinusNodeId[n1 + 1], lowerNodeId[1][n1], lowerNodeId[1][n1 + 1] ] else: nids = [ lowerNodeId[0][n1 + 1], lowerNodeId[0][n1 - 4], sinusNodeId[n1 + 1], arcNodeId[n1 + 1], lowerNodeId[1][n1 + 1], lowerNodeId[1][n1 - 4] ] ln_map = [1, 2, 3, 4, 5, 6, 5, 6] remapEftLocalNodes(eft1, 6, ln_map) else: # 8 node elements with wedges on two sides if e == 2: eft1 = bicubichermitelinear.createEftNoCrossDerivatives( ) setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] nids = [ arcNodeId[n1], sinusNodeId[n1 + 1], upperNodeId[0][n2 + 1], upperNodeId[0][n2 + 2], lowerNodeId[1][n1], lowerNodeId[1][n1 + 1], upperNodeId[1][n1], upperNodeId[1][n1 + 1] ] remapEftNodeValueLabel(eft1, [1], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])]) else: eft1 = eftDefault nids = [ sinusNodeId[n1 + 1], arcNodeId[n1 + 1], upperNodeId[0][n2 + 2], upperNodeId[0][n2 + 3], lowerNodeId[1][n1 + 1], lowerNodeId[1][n1 - 4], upperNodeId[1][n1 + 1], upperNodeId[1][n1 - 4] ] remapEftNodeValueLabel(eft1, [2], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])]) result = elementtemplate1.defineField(coordinates, -1, eft1) element = mesh.createElement(elementIdentifier, elementtemplate1) result2 = element.setNodesByIdentifier(eft1, nids) if scalefactors: result3 = element.setScaleFactors(eft1, scalefactors) else: result3 = 7 #print('create arterial root wall', cusp, e, 'element',elementIdentifier, result, result2, result3, nids) elementIdentifier += 1 for meshGroup in allMeshGroups: meshGroup.addElement(element) # cusps (leaflets) for cusp in range(3): n1 = cusp * 2 - 1 + nMidCusp n2 = n1 * 2 meshGroups = allMeshGroups + [cuspMeshGroups[cusp]] for e in range(2): eft1 = bicubichermitelinear.createEftNoCrossDerivatives() setEftScaleFactorIds(eft1, [1], []) scalefactors = [-1.0] if e == 0: nids = [ lowerNodeId[0][n1], lowerNodeId[0][n1 + 1], upperNodeId[0][n2], noduleNodeId[0][cusp], arcNodeId[n1], sinusNodeId[n1 + 1], upperNodeId[0][n2 + 1], noduleNodeId[1][cusp] ] remapEftNodeValueLabel(eft1, [4, 8], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1])]) remapEftNodeValueLabel(eft1, [4, 8], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])]) remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS2, [1])]) remapEftNodeValueLabel(eft1, [7], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1])]) else: nids = [ lowerNodeId[0][n1 + 1], lowerNodeId[0][n1 - 4], noduleNodeId[0][cusp], upperNodeId[0][n2 - 8], sinusNodeId[n1 + 1], arcNodeId[n1 + 1], noduleNodeId[1][cusp], upperNodeId[0][n2 + 3] ] remapEftNodeValueLabel(eft1, [3, 7], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [])]) remapEftNodeValueLabel(eft1, [3, 7], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS2, [])]) remapEftNodeValueLabel(eft1, [4, 8], Node.VALUE_LABEL_D_DS1, [(Node.VALUE_LABEL_D_DS1, [1])]) remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS2, [1])]) remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])]) result = elementtemplate1.defineField(coordinates, -1, eft1) element = mesh.createElement(elementIdentifier, elementtemplate1) result2 = element.setNodesByIdentifier(eft1, nids) if scalefactors: result3 = element.setScaleFactors(eft1, scalefactors) else: result3 = 7 #print('create semilunar cusp', cusp, e, 'element',elementIdentifier, result, result2, result3, nids) elementIdentifier += 1 for meshGroup in meshGroups: meshGroup.addElement(element) # create annotation points datapoint = fiducialPoints.createNode(-1, datapointTemplateExternal) cache.setNode(datapoint) fiducialCoordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, noduleCentre) fiducialLabel.assignString( cache, 'aortic valve ctr' if aorticNotPulmonary else 'pulmonary valve ctr') fm.endChange() return annotationGroups