Rename to CMLibs

README.rst

@@ -1,7 +1,7 @@
 Scaffold Maker
 ==============
 
-Anatomical scaffold generator using OpenCMISS-Zinc.
+Anatomical scaffold generator using Zinc.
 Install with::
 
   pip install scaffoldmaker
@@ -14,8 +14,8 @@ For developing scaffolds::
 
 Requires the following Python libraries to be installed.
 
-* opencmiss.zinc
-* opencmiss.utils
+* cmlibs.zinc
+* cmlibs.utils
 
 We recommend installing scaffoldmaker into a virtual python environment.
 See `python virtual environment documentation <https://docs.python.org/3/library/venv.html>`__ for information on virtual environments.

docs/index.rst

@@ -1,7 +1,7 @@
-*scaffoldmaker library*
-=======================
+ScaffoldMaker library
+=====================
 
-The *scaffoldmaker library* contains scripts for programmatically generating anatomical scaffolds for a range of organs and other structures, and includes utility code for building common geometric shapes, annotation, and refinement. The scripts generate the scaffold model in the data structures of the underlying *OpenCMISS-Zinc library*, and through the Zinc API clients can interrogate the model or export it for subsequent use.
+The *scaffoldmaker library* contains scripts for programmatically generating anatomical scaffolds for a range of organs and other structures, and includes utility code for building common geometric shapes, annotation, and refinement. The scripts generate the scaffold model in the data structures of the underlying *Zinc library*, and through the Zinc API clients can interrogate the model or export it for subsequent use.
 
 Most users will make scaffolds using the ABI Mapping Tools' **Scaffold Creator** user interface for this library, and its documentation gives a good introduction to anatomical scaffolds and some common features of them.
 

setup.py

@@ -25,9 +25,9 @@ def readfile(filename, split=False):
 # into the 'requirements.txt' file.
 requires = [
     # minimal requirements listing
-    "opencmiss.maths",
-    "opencmiss.utils >= 0.3",
-    "opencmiss.zinc >= 3.10.2",
+    "cmlibs.maths",
+    "cmlibs.utils >= 0.3",
+    "cmlibs.zinc >= 3.99",
     "scipy",
     "numpy",
 ]
@@ -36,7 +36,7 @@ def readfile(filename, split=False):
 setup(
     name="scaffoldmaker",
     version="0.8.1",
-    description="Python client for generating anatomical scaffolds using OpenCMISS-Zinc",
+    description="Python client for generating anatomical scaffolds using Zinc",
     long_description="\n".join(readme) + source_license,
     long_description_content_type="text/x-rst",
     classifiers=[

src/scaffoldmaker/annotation/annotationgroup.py

@@ -3,16 +3,16 @@
 """
 import sys
 
-from opencmiss.utils.zinc.general import ChangeManager
-from opencmiss.utils.zinc.field import find_or_create_field_coordinates, find_or_create_field_group, \
+from cmlibs.utils.zinc.general import ChangeManager
+from cmlibs.utils.zinc.field import find_or_create_field_coordinates, find_or_create_field_group, \
     find_or_create_field_stored_mesh_location, find_or_create_field_stored_string
-from opencmiss.zinc.element import Element, Mesh
-from opencmiss.zinc.field import Field, FieldFiniteElement, FieldGroup, FieldStoredMeshLocation, FieldStoredString, \
+from cmlibs.zinc.element import Element, Mesh
+from cmlibs.zinc.field import Field, FieldFiniteElement, FieldGroup, FieldStoredMeshLocation, FieldStoredString, \
     FieldFindMeshLocation
-from opencmiss.zinc.fieldcache import Fieldcache
-from opencmiss.zinc.fieldmodule import Fieldmodule
-from opencmiss.zinc.node import Node
-from opencmiss.zinc.result import RESULT_OK
+from cmlibs.zinc.fieldcache import Fieldcache
+from cmlibs.zinc.fieldmodule import Fieldmodule
+from cmlibs.zinc.node import Node
+from cmlibs.zinc.result import RESULT_OK
 from scaffoldmaker.utils.zinc_utils import get_highest_dimension_mesh, get_next_unused_node_identifier, \
     group_get_highest_dimension, identifier_ranges_from_string, identifier_ranges_to_string, \
     mesh_group_add_identifier_ranges, mesh_group_to_identifier_ranges, \

src/scaffoldmaker/meshtypes/meshtype_1d_bifurcationtree1.py

@@ -5,12 +5,12 @@
 from __future__ import division
 from math import cos, radians, sin
 
-from opencmiss.maths.vectorops import add, cross, magnitude, mult, normalize, sub
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFiniteElement
-from opencmiss.utils.zinc.general import ChangeManager
-from opencmiss.zinc.element import Element, Elementbasis
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.maths.vectorops import add, cross, magnitude, mult, normalize, sub
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFiniteElement
+from cmlibs.utils.zinc.general import ChangeManager
+from cmlibs.zinc.element import Element, Elementbasis
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 

src/scaffoldmaker/meshtypes/meshtype_1d_path1.py

@@ -4,11 +4,11 @@
 
 from __future__ import division
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup
-from opencmiss.utils.zinc.general import ChangeManager
-from opencmiss.zinc.element import Element, Elementbasis
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup
+from cmlibs.utils.zinc.general import ChangeManager
+from cmlibs.zinc.element import Element, Elementbasis
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.interpolation import smoothCubicHermiteCrossDerivativesLine

src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py

@@ -4,10 +4,10 @@
 
 from __future__ import division
 
-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 cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element, Elementbasis
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 

src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py

@@ -9,10 +9,10 @@
 
 import math
 
-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 cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
 

src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py

@@ -6,10 +6,10 @@
 
 import math
 
-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 cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 

src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py

@@ -6,10 +6,10 @@
 
 import math
 
-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 cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element, Elementbasis
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
 

src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcation1.py

@@ -6,10 +6,10 @@
 
 import math
 
-from opencmiss.maths.vectorops import cross, mult, normalize, sub
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.maths.vectorops import cross, mult, normalize, sub
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.bifurcation import get_tube_bifurcation_connection_elements_counts, \
     make_tube_bifurcation_points, make_tube_bifurcation_elements_2d

src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcationtree1.py

@@ -5,9 +5,9 @@
 from __future__ import division
 import math
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.meshtype_1d_bifurcationtree1 import MeshType_1d_bifurcationtree1
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.scaffoldpackage import ScaffoldPackage

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -7,10 +7,10 @@
 import copy
 import math
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm
 from scaffoldmaker.annotation.bladder_terms import get_bladder_term
 from scaffoldmaker.meshtypes.meshtype_3d_ostium1 import MeshType_3d_ostium1, generateOstiumMesh

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

@@ -7,11 +7,11 @@
 import copy
 import math
 
-from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \
+from cmlibs.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \
     findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, \
     getAnnotationGroupForTerm
 from scaffoldmaker.annotation.bladder_terms import get_bladder_term

src/scaffoldmaker/meshtypes/meshtype_3d_box1.py

@@ -4,10 +4,10 @@
 
 from __future__ import division
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.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

src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py

@@ -9,10 +9,10 @@
 
 import math
 
-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 cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate
+from cmlibs.zinc.field import Field
+from cmlibs.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

src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py

@@ -6,13 +6,13 @@
 
 import copy
 
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.node import Node
-from opencmiss.zinc.field import FieldFindMeshLocation
-from opencmiss.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, \
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.node import Node
+from cmlibs.zinc.field import FieldFindMeshLocation
+from cmlibs.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, \
     findOrCreateFieldStoredString
-from opencmiss.utils.zinc.general import ChangeManager
-from opencmiss.utils.zinc.finiteelement import getMaximumNodeIdentifier
+from cmlibs.utils.zinc.general import ChangeManager
+from cmlibs.utils.zinc.finiteelement import getMaximumNodeIdentifier
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm
 from scaffoldmaker.annotation.brainstem_terms import get_brainstem_term
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base

src/scaffoldmaker/meshtypes/meshtype_3d_cecum1.py

@@ -7,8 +7,8 @@
 import copy
 import math
 
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
 from scaffoldmaker.annotation.colon_terms import get_colon_term
 from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion

src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py

@@ -6,8 +6,8 @@
 
 import copy
 
-from opencmiss.zinc.node import Node
-from opencmiss.zinc.element import Element
+from cmlibs.zinc.node import Node
+from cmlibs.zinc.element import Element
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm
 from scaffoldmaker.annotation.colon_terms import get_colon_term
 from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion

src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

@@ -8,10 +8,10 @@
 import copy
 import math
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, mergeAnnotationGroups, \
     findOrCreateAnnotationGroupForTerm, findAnnotationGroupByName, getAnnotationGroupForTerm
 from scaffoldmaker.annotation.colon_terms import get_colon_term

src/scaffoldmaker/meshtypes/meshtype_3d_esophagus1.py

@@ -6,11 +6,11 @@
 
 import copy
 import math
-from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldStoredString, \
+from cmlibs.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldStoredString, \
     findOrCreateFieldStoredMeshLocation, findOrCreateFieldNodeGroup
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm, \
     findOrCreateAnnotationGroupForTerm
 from scaffoldmaker.annotation.esophagus_terms import get_esophagus_term

src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py

@@ -4,12 +4,12 @@
 
 from __future__ import division
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \
     findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
-from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm, mergeAnnotationGroups
 from scaffoldmaker.annotation.heart_terms import get_heart_term
 from scaffoldmaker.meshtypes.meshtype_3d_heartatria1 import MeshType_3d_heartatria1

src/scaffoldmaker/meshtypes/meshtype_3d_heart2.py

@@ -4,7 +4,7 @@
 
 from __future__ import division
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
 from scaffoldmaker.annotation.annotationgroup import mergeAnnotationGroups
 from scaffoldmaker.meshtypes.meshtype_3d_heartatria2 import MeshType_3d_heartatria2
 from scaffoldmaker.meshtypes.meshtype_3d_heartventriclesbase2 import MeshType_3d_heartventriclesbase2

src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialroot1.py

@@ -7,11 +7,11 @@
 
 import math
 
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier
-from opencmiss.zinc.element import Element, Elementbasis
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier
+from cmlibs.zinc.element import Element, Elementbasis
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup
 from scaffoldmaker.annotation.heart_terms import get_heart_term
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base

src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialvalve1.py

@@ -8,12 +8,12 @@
 
 import math
 
-from opencmiss.maths.vectorops import eulerToRotationMatrix3
-from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.utils.zinc.general import ChangeManager
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
+from cmlibs.maths.vectorops import eulerToRotationMatrix3
+from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
+from cmlibs.utils.zinc.general import ChangeManager
+from cmlibs.zinc.element import Element
+from cmlibs.zinc.field import Field
+from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.eft_utils import setEftScaleFactorIds