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Add sub-scaffolds #47

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merged 14 commits into from
Apr 9, 2019
Merged

Add sub-scaffolds #47

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171484a
Add scaffold package for nested scaffolds with edits
rchristie Mar 27, 2019
5c48636
More scaffold package methods
rchristie Mar 29, 2019
b48baaa
Make colon central path ScaffoldPackage option
rchristie Apr 2, 2019
244bc70
Restore colon checking haustra options
rchristie Apr 3, 2019
9d2510f
Use common functions to find or create fields
rchristie Apr 3, 2019
0980224
Remove import * for zinc_utils
rchristie Apr 4, 2019
80966f1
Tidy vector, matrix utils imports and use
rchristie Apr 4, 2019
4e538b9
Tidy tubemesh imports and use
rchristie Apr 4, 2019
3cf8225
Tidy interpolation imports and use
rchristie Apr 4, 2019
4af8c45
Tidy geometry imports
rchristie Apr 4, 2019
0245811
Tidy eft_utils imports
rchristie Apr 4, 2019
c35ac70
Store meshEdits in group 'meshEdits'
rchristie Apr 9, 2019
b65c7f9
Deprecate MeshType functions for Scaffold
rchristie Apr 9, 2019
cc07ebe
Remove @author and date tags
rchristie Apr 9, 2019
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130 changes: 130 additions & 0 deletions scaffoldmaker/meshtypes/meshtype_1d_path1.py
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Original file line number Diff line number Diff line change
@@ -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.zinc_utils import *
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 = 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
11 changes: 2 additions & 9 deletions scaffoldmaker/meshtypes/meshtype_2d_plate1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from __future__ import division
import math
from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
from scaffoldmaker.utils.zinc_utils import *
from opencmiss.zinc.element import Element, Elementbasis
from opencmiss.zinc.field import Field
from opencmiss.zinc.node import Node
Expand Down Expand Up @@ -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 = getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)

nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplate = nodes.createNodetemplate()
Expand Down
11 changes: 2 additions & 9 deletions scaffoldmaker/meshtypes/meshtype_2d_platehole1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import math
from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
from scaffoldmaker.utils.zinc_utils import *
from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
from opencmiss.zinc.field import Field
from opencmiss.zinc.node import Node
Expand Down Expand Up @@ -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 = getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)

nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplate = nodes.createNodetemplate()
Expand Down
10 changes: 2 additions & 8 deletions scaffoldmaker/meshtypes/meshtype_2d_sphere1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from __future__ import division
import math
from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
from scaffoldmaker.utils.zinc_utils import *
from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
from opencmiss.zinc.field import Field
from opencmiss.zinc.node import Node
Expand Down Expand Up @@ -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 = getOrCreateCoordinateField(fm)

nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplateApex = nodes.createNodetemplate()
Expand Down
10 changes: 2 additions & 8 deletions scaffoldmaker/meshtypes/meshtype_2d_tube1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from __future__ import division
import math
from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
from scaffoldmaker.utils.zinc_utils import *
from opencmiss.zinc.element import Element, Elementbasis
from opencmiss.zinc.field import Field
from opencmiss.zinc.node import Node
Expand Down Expand Up @@ -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 = getOrCreateCoordinateField(fm)
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Make same changes to meshtype_3d_boxhole1.py, meshtyple_3d_sphereshellseptum1.py, meshtype_3d_stomachhuman1.py, meshtype_3d_tube1.py, meshtype_3d_tubeseptum1.py


nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplate = nodes.createNodetemplate()
Expand Down
10 changes: 2 additions & 8 deletions scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.zinc_utils import *
from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
from opencmiss.zinc.field import Field
from opencmiss.zinc.node import Node
Expand Down Expand Up @@ -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 = getOrCreateCoordinateField(fm)

nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplate = nodes.createNodetemplate()
Expand Down
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