Add sub-scaffolds

scaffoldmaker/meshtypes/meshtype_1d_path1.py

@@ -0,0 +1,130 @@
+"""
+Generates a 1-D path mesh.
+"""
+
+from __future__ import division
+import math
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils import zinc_utils
+from opencmiss.zinc.element import Element, Elementbasis
+from opencmiss.zinc.field import Field
+from opencmiss.zinc.node import Node
+
+class MeshType_1d_path1(Scaffold_base):
+    '''
+    classdocs
+    '''
+    @staticmethod
+    def getName():
+        return '1D Path 1'
+
+    @staticmethod
+    def getDefaultOptions(parameterSetName='Default'):
+        return {
+            'Coordinate dimensions' : 3,
+            'Length' : 1.0,
+            'Number of elements' : 1
+        }
+
+    @staticmethod
+    def getOrderedOptionNames():
+        return [
+            'Coordinate dimensions',
+            'Length',
+            'Number of elements'
+        ]
+
+    @staticmethod
+    def checkOptions(options):
+        if (options['Coordinate dimensions'] < 1) :
+            options['Coordinate dimensions'] = 1
+        elif (options['Coordinate dimensions'] > 3) :
+            options['Coordinate dimensions'] = 3
+        if (options['Number of elements'] < 1) :
+            options['Number of elements'] = 1
+
+    @staticmethod
+    def generateMesh(region, options):
+        """
+        :param region: Zinc region to define model in. Must be empty.
+        :param options: Dict containing options. See getDefaultOptions().
+        :return: None
+        """
+        coordinateDimensions = options['Coordinate dimensions']
+        length = options['Length']
+        elementsCount = options['Number of elements']
+
+        fm = region.getFieldmodule()
+        fm.beginChange()
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)
+        cache = fm.createFieldcache()
+
+        #################
+        # 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)
+
+        nodeIdentifier = 1
+        x = [ 0.0, 0.0, 0.0 ]
+        dx_ds1 = [ length/elementsCount, 0.0, 0.0 ]
+        for n in range(elementsCount + 1):
+            x[0] = length*n/elementsCount
+            node = nodes.createNode(nodeIdentifier, nodetemplate)
+            cache.setNode(node)
+            coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, x)
+            coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, dx_ds1)
+            nodeIdentifier = nodeIdentifier + 1
+
+        #################
+        # Create elements
+        #################
+
+        mesh = fm.findMeshByDimension(1)
+        cubicHermiteBasis = fm.createElementbasis(1, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE)
+        eft = mesh.createElementfieldtemplate(cubicHermiteBasis)
+        elementtemplate = mesh.createElementtemplate()
+        elementtemplate.setElementShapeType(Element.SHAPE_TYPE_LINE)
+        result = elementtemplate.defineField(coordinates, -1, eft)
+
+        elementIdentifier = 1
+        for e in range(elementsCount):
+            element = mesh.createElement(elementIdentifier, elementtemplate)
+            element.setNodesByIdentifier(eft, [ e + 1, e + 2 ])
+            elementIdentifier = elementIdentifier + 1
+
+        fm.endChange()
+
+
+def extractPathParametersFromRegion(region):
+    '''
+    Returns parameters of all nodes in region in identifier order.
+    Assumes nodes in region have field coordinates (1 to 3 components).
+    Currently limited to nodes with exactly value and d_ds1, same as path 1 scaffold.
+    :return: cx, cd1 (all padded with zeroes to 3 components)
+    '''
+    fm = region.getFieldmodule()
+    coordinates = fm.findFieldByName('coordinates').castFiniteElement()
+    componentsCount = coordinates.getNumberOfComponents()
+    assert componentsCount in [ 1, 2, 3 ], 'extractPathParametersFromRegion.  Invalid coordinates number of components'
+    cache = fm.createFieldcache()
+    cx = []
+    cd1 = []
+    nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
+    nodeIter = nodes.createNodeiterator()
+    node = nodeIter.next()
+    while node.isValid():
+        cache.setNode(node)
+        result, x  = coordinates.getNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, componentsCount)
+        result, d1 = coordinates.getNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, componentsCount)
+        for c in range(componentsCount, 3):
+            x.append(0.0)
+            d1.append(0.0)
+        cx.append(x)
+        cd1.append(d1)
+        node = nodeIter.next()
+    return cx, cd1

scaffoldmaker/meshtypes/meshtype_2d_plate1.py

@@ -5,6 +5,7 @@
 from __future__ import division
 import math
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils import zinc_utils
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -60,15 +61,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = fm.createFieldFiniteElement(coordinateDimensions)
-        coordinates.setName('coordinates')
-        coordinates.setManaged(True)
-        coordinates.setTypeCoordinate(True)
-        coordinates.setCoordinateSystemType(Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
-        coordinates.setComponentName(1, 'x')
-        coordinates.setComponentName(2, 'y')
-        if coordinateDimensions == 3:
-            coordinates.setComponentName(3, 'z')
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

scaffoldmaker/meshtypes/meshtype_2d_platehole1.py

@@ -9,6 +9,7 @@
 import math
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
+from scaffoldmaker.utils import zinc_utils
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -77,15 +78,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = fm.createFieldFiniteElement(coordinateDimensions)
-        coordinates.setName('coordinates')
-        coordinates.setManaged(True)
-        coordinates.setTypeCoordinate(True)
-        coordinates.setCoordinateSystemType(Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
-        coordinates.setComponentName(1, 'x')
-        coordinates.setComponentName(2, 'y')
-        if coordinateDimensions == 3:
-            coordinates.setComponentName(3, 'z')
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

scaffoldmaker/meshtypes/meshtype_2d_sphere1.py

@@ -5,6 +5,7 @@
 from __future__ import division
 import math
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils import zinc_utils
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -53,14 +54,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = fm.createFieldFiniteElement(3)
-        coordinates.setName('coordinates')
-        coordinates.setManaged(True)
-        coordinates.setTypeCoordinate(True)
-        coordinates.setCoordinateSystemType(Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
-        coordinates.setComponentName(1, 'x')
-        coordinates.setComponentName(2, 'y')
-        coordinates.setComponentName(3, 'z')
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplateApex = nodes.createNodetemplate()

scaffoldmaker/meshtypes/meshtype_2d_tube1.py

@@ -5,6 +5,7 @@
 from __future__ import division
 import math
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils import zinc_utils
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -53,14 +54,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = fm.createFieldFiniteElement(3)
-        coordinates.setName('coordinates')
-        coordinates.setManaged(True)
-        coordinates.setTypeCoordinate(True)
-        coordinates.setCoordinateSystemType(Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
-        coordinates.setComponentName(1, 'x')
-        coordinates.setComponentName(2, 'y')
-        coordinates.setComponentName(3, 'z')
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

scaffoldmaker/meshtypes/meshtype_3d_box1.py

@@ -7,7 +7,7 @@
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
-from scaffoldmaker.utils.zinc_utils import *
+from scaffoldmaker.utils import zinc_utils
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -73,7 +73,7 @@ def generateBaseMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = getOrCreateCoordinateField(fm)
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py

@@ -10,6 +10,7 @@
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
 from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
+from scaffoldmaker.utils import zinc_utils
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -76,14 +77,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = fm.createFieldFiniteElement(3)
-        coordinates.setName('coordinates')
-        coordinates.setManaged(True)
-        coordinates.setTypeCoordinate(True)
-        coordinates.setCoordinateSystemType(Field.COORDINATE_SYSTEM_TYPE_RECTANGULAR_CARTESIAN)
-        coordinates.setComponentName(1, 'x')
-        coordinates.setComponentName(2, 'y')
-        coordinates.setComponentName(3, 'z')
+        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()