Move most zinc_utils to opencmiss.utils

README.rst

@@ -6,3 +6,8 @@ Anatomical scaffold generator using OpenCMISS-Zinc.
 For the interim, install with the following command::
 
     pip install -e .
+
+Requires the following Python libraries to be installed:
+
+- opencmiss.zinc (manual install from opencmiss.org)
+- github.com/OpenCMISS-Bindings/opencmiss.utils

setup.py

@@ -19,7 +19,8 @@ def readfile(filename, split=False):
 # into the 'requirements.txt' file.
 requires = [
     # minimal requirements listing
-    "opencmiss.utils @ https://api.github.com/repos/OpenCMISS-Bindings/opencmiss.utils/tarball/master",
+    "opencmiss.utils >= 0.2",
+    "opencmiss.zinc",  # not yet on pypi - need manual install from opencmiss.org
     "ZincPythonTools @ https://api.github.com/repos/OpenCMISS-Bindings/ZincPythonTools/tarball/master",
     "scipy",
     "numpy",
@@ -28,7 +29,7 @@ def readfile(filename, split=False):
 
 setup(
     name="scaffoldmaker",
-    version="0.1.2",
+    version="0.1.3",
     description="Python client for generating anatomical scaffolds using OpenCMISS-Zinc",
     long_description="\n".join(readme) + source_license,
     classifiers=[

src/scaffoldmaker/meshtypes/meshtype_1d_path1.py

@@ -4,11 +4,11 @@
 
 from __future__ import division
 import math
-from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils import zinc_utils
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 class MeshType_1d_path1(Scaffold_base):
     '''
@@ -56,7 +56,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)
+        coordinates = findOrCreateFieldCoordinates(fm, components_count=coordinateDimensions)
         cache = fm.createFieldcache()
 
         #################

src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py

@@ -4,11 +4,11 @@
 
 from __future__ import division
 import math
-from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils import zinc_utils
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 class MeshType_2d_plate1(Scaffold_base):
     '''
@@ -61,7 +61,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)
+        coordinates = findOrCreateFieldCoordinates(fm, components_count=coordinateDimensions)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py

@@ -7,12 +7,12 @@
 
 from __future__ import division
 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.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
 
 class MeshType_2d_platehole1(Scaffold_base):
     '''
@@ -78,7 +78,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm, componentsCount=coordinateDimensions)
+        coordinates = findOrCreateFieldCoordinates(fm, components_count=coordinateDimensions)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py

@@ -4,11 +4,11 @@
 
 from __future__ import division
 import math
-from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils import zinc_utils
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 class MeshType_2d_sphere1(Scaffold_base):
     '''
@@ -54,7 +54,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+        coordinates = findOrCreateFieldCoordinates(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplateApex = nodes.createNodetemplate()

src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py

@@ -4,11 +4,11 @@
 
 from __future__ import division
 import math
-from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils import zinc_utils
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 class MeshType_2d_tube1(Scaffold_base):
     '''
@@ -54,7 +54,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+        coordinates = findOrCreateFieldCoordinates(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

src/scaffoldmaker/meshtypes/meshtype_3d_box1.py

@@ -4,13 +4,13 @@
 
 from __future__ import division
 import math
-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 import zinc_utils
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
+from scaffoldmaker.utils.meshrefinement import MeshRefinement
 
 class MeshType_3d_box1(Scaffold_base):
     '''
@@ -73,7 +73,7 @@ def generateBaseMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+        coordinates = findOrCreateFieldCoordinates(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py

@@ -7,13 +7,13 @@
 
 from __future__ import division
 import math
-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.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
+from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
+from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
+from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
 
 class MeshType_3d_boxhole1(Scaffold_base):
     '''
@@ -77,7 +77,7 @@ def generateMesh(region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+        coordinates = findOrCreateFieldCoordinates(fm)
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
         nodetemplate = nodes.createNodetemplate()

src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py

@@ -13,7 +13,7 @@
 from scaffoldmaker.utils import interpolation as interp
 from scaffoldmaker.utils import tubemesh
 from scaffoldmaker.utils import vector
-from scaffoldmaker.utils import zinc_utils
+from scaffoldmaker.utils.zinc_utils import exnodeStringFromNodeValues
 from opencmiss.zinc.node import Node
 
 class MeshType_3d_colon1(Scaffold_base):
@@ -32,7 +32,7 @@ class MeshType_3d_colon1(Scaffold_base):
                 'Length' : 1.0,
                 'Number of elements' : 8
                 },
-            'meshEdits' : zinc_utils.exnodeStringFromNodeValues(
+            'meshEdits' : exnodeStringFromNodeValues(
                 [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2  ], [
                 [ [   0.0,   0.0, 0.0 ], [ -50.7,  178.2, 0.0 ], [ -24.0,  -6.0, -12.0 ], [ -14.0,  -1.0, -12.0 ] ],
                 [ [ -47.4, 188.6, 0.0 ], [ -19.3,  177.1, 0.0 ], [ -22.0,  -4.0,  -8.0 ], [  -4.0,  19.0,  22.0 ] ],
@@ -50,7 +50,7 @@ class MeshType_3d_colon1(Scaffold_base):
                 'Length' : 1.0,
                 'Number of elements' : 8
                 },
-            'meshEdits' : zinc_utils.exnodeStringFromNodeValues(
+            'meshEdits' : exnodeStringFromNodeValues(
                 [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
                 [ [   0.0,   0.0,    0.0 ], [ -34.7,  104.1, -18.1 ], [ -24.0,  -6.0, -12.0 ], [ -14.0,  -1.0, -12.0 ] ],
                 [ [ -34.5,  114.0, -18.1 ], [   1.2,   86.6,  -3.4 ], [ -22.0,  -4.0,  -8.0 ], [  -4.0,  19.0,  22.0 ] ],
@@ -68,7 +68,7 @@ class MeshType_3d_colon1(Scaffold_base):
                 'Length' : 1.0,
                 'Number of elements' : 7
                 },
-            'meshEdits' : zinc_utils.exnodeStringFromNodeValues(
+            'meshEdits' : exnodeStringFromNodeValues(
                 [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
                 [ [   0.0,   0.0,  0.0 ], [  6.0, 12.0,  -2.0 ], [ 2.0,  1.0,  2.0 ], [ 6.0, 0.0, 3.0 ] ],
                 [ [  -2.0,  11.0, -3.0 ], [ -8.0,  4.0,   9.0 ], [ 2.0,  2.0,  1.0 ], [ 0.0, 1.0, 2.0 ] ],
@@ -85,7 +85,7 @@ class MeshType_3d_colon1(Scaffold_base):
                 'Length' : 1.0,
                 'Number of elements' : 4
                 },
-            'meshEdits' : zinc_utils.exnodeStringFromNodeValues(
+            'meshEdits' : exnodeStringFromNodeValues(
                 [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
                 [ [   0.0,  0.0,   0.0 ], [  0.0,  0.0,  13.0 ], [  0.0, -10.0,  0.0 ], [ 0.0, 0.0, 0.5 ] ],
                 [ [   0.0,  0.0,  13.0 ], [  0.0,  2.0,  28.0 ], [  0.0, -10.0,  0.0 ], [ 0.0, 0.0, 0.5 ] ],
@@ -99,7 +99,7 @@ class MeshType_3d_colon1(Scaffold_base):
                 'Length' : 1.0,
                 'Number of elements' : 36
                 },
-            'meshEdits' : zinc_utils.exnodeStringFromNodeValues(
+            'meshEdits' : exnodeStringFromNodeValues(
                 [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
                 [ [  163.7, -25.2,  12.2 ], [  -21.7,   50.1, -18.1 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],
                 [ [  117.2,  32.8,  -2.6 ], [  -64.3,   34.4,  -3.9 ], [ 0.0, 0.0, 5.0 ], [ 0.0, 0.0, 0.5 ] ],

src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

@@ -6,6 +6,10 @@
 """
 
 import math
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldTextureCoordinates
+from opencmiss.zinc.element import Element, Elementbasis
+from opencmiss.zinc.field import Field
+from opencmiss.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.eftfactory_bicubichermitelinear import eftfactory_bicubichermitelinear
@@ -16,10 +20,6 @@
 from scaffoldmaker.utils import interpolation as interp
 from scaffoldmaker.utils import tubemesh
 from scaffoldmaker.utils import vector
-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_3d_colonsegment1(Scaffold_base):
     '''
@@ -1466,7 +1466,7 @@ def createNodesAndElementsTeniaColi(region,
     fm = region.getFieldmodule()
     fm.beginChange()
     cache = fm.createFieldcache()
-    coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+    coordinates = findOrCreateFieldCoordinates(fm)
 
     nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
     nodetemplate = nodes.createNodetemplate()
@@ -1507,7 +1507,7 @@ def createNodesAndElementsTeniaColi(region,
     elementtemplate2.defineField(coordinates, -1, eft2)
 
     # Create flat coordinates field
-    flatCoordinates = zinc_utils.getOrCreateFlatCoordinateField(fm)
+    flatCoordinates = findOrCreateFieldCoordinates(fm, name="flat coordinates")
     flatNodetemplate1 = nodes.createNodetemplate()
     flatNodetemplate1.defineField(flatCoordinates)
     flatNodetemplate1.setValueNumberOfVersions(flatCoordinates, -1, Node.VALUE_LABEL_VALUE, 1)
@@ -1552,7 +1552,7 @@ def createNodesAndElementsTeniaColi(region,
     flatElementtemplate5.defineField(flatCoordinates, -1, eftTexture7)
 
     # Create texture coordinates field
-    textureCoordinates = zinc_utils.getOrCreateTextureCoordinateField(fm)
+    textureCoordinates = findOrCreateFieldTextureCoordinates(fm)
     textureNodetemplate1 = nodes.createNodetemplate()
     textureNodetemplate1.defineField(textureCoordinates)
     textureNodetemplate1.setValueNumberOfVersions(textureCoordinates, -1, Node.VALUE_LABEL_VALUE, 1)

src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py

@@ -4,17 +4,19 @@
 
 from __future__ import division
 import math
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \
+    findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
+from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier
+from opencmiss.zinc.element import Element
+from opencmiss.zinc.field import Field
+from opencmiss.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findAnnotationGroupByName
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.meshtypes.meshtype_3d_heartatria1 import MeshType_3d_heartatria1
 from scaffoldmaker.meshtypes.meshtype_3d_heartventriclesbase1 import MeshType_3d_heartventriclesbase1
 from scaffoldmaker.utils.eft_utils import remapEftLocalNodes, remapEftNodeValueLabel, scaleEftNodeValueLabels, setEftScaleFactorIds
 from scaffoldmaker.utils.eftfactory_bicubichermitelinear import eftfactory_bicubichermitelinear
-from scaffoldmaker.utils import zinc_utils
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
 
 class MeshType_3d_heart1(Scaffold_base):
     '''
@@ -120,9 +122,11 @@ def generateBaseMesh(cls, region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+        coordinates = findOrCreateFieldCoordinates(fm)
         cache = fm.createFieldcache()
 
+        mesh = fm.findMeshByDimension(3)
+
         # generate heartventriclesbase1 model and put atria1 on it
         annotationGroups = MeshType_3d_heartventriclesbase1.generateBaseMesh(region, options)
         annotationGroups += MeshType_3d_heartatria1.generateBaseMesh(region, options)
@@ -131,13 +135,13 @@ def generateBaseMesh(cls, region, options):
         annotationGroups += [ lFibrousRingGroup, rFibrousRingGroup ]
 
         # 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')
+        fiducialGroup = findOrCreateFieldGroup(fm, 'fiducial')
+        fiducialCoordinates = findOrCreateFieldCoordinates(fm, 'fiducial_coordinates')
+        fiducialLabel = findOrCreateFieldStoredString(fm, name='fiducial_label')
+        fiducialElementXi = findOrCreateFieldStoredMeshLocation(fm, mesh, name='fiducial_element_xi')
 
         datapoints = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
-        fiducialPoints = zinc_utils.getOrCreateNodesetGroup(fiducialGroup, datapoints)
+        fiducialPoints = findOrCreateFieldNodeGroup(fiducialGroup, datapoints).getNodesetGroup()
         datapointTemplateInternal = datapoints.createNodetemplate()
         datapointTemplateInternal.defineField(fiducialCoordinates)
         datapointTemplateInternal.defineField(fiducialLabel)
@@ -207,12 +211,10 @@ def generateBaseMesh(cls, region, options):
         # Create elements
         #################
 
-        mesh = fm.findMeshByDimension(3)
-
         lFibrousRingMeshGroup = lFibrousRingGroup.getMeshGroup(mesh)
         rFibrousRingMeshGroup = rFibrousRingGroup.getMeshGroup(mesh)
 
-        elementIdentifier = startElementIdentifier = zinc_utils.getMaximumElementIdentifier(mesh) + 1
+        elementIdentifier = getMaximumElementIdentifier(mesh) + 1
 
         elementtemplate1 = mesh.createElementtemplate()
         elementtemplate1.setElementShapeType(Element.SHAPE_TYPE_CUBE)

src/scaffoldmaker/meshtypes/meshtype_3d_heart2.py

@@ -4,11 +4,11 @@
 
 from __future__ import division
 import math
+from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findAnnotationGroupByName
 from scaffoldmaker.meshtypes.meshtype_3d_heartatria2 import MeshType_3d_heartatria2
 from scaffoldmaker.meshtypes.meshtype_3d_heartventriclesbase2 import MeshType_3d_heartventriclesbase2
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils import zinc_utils
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
 
 class MeshType_3d_heart2(Scaffold_base):
@@ -78,7 +78,7 @@ def generateBaseMesh(cls, region, options):
 
         fm = region.getFieldmodule()
         fm.beginChange()
-        coordinates = zinc_utils.getOrCreateCoordinateField(fm)
+        coordinates = findOrCreateFieldCoordinates(fm)
         cache = fm.createFieldcache()
 
         # generate heartventriclesbase2 model and put atria2 on it