Apply zinc group changes

setup.py

@@ -25,17 +25,17 @@ def readfile(filename, split=False):
 # into the 'requirements.txt' file.
 requires = [
     # minimal requirements listing
-    "cmlibs.maths",
-    "cmlibs.utils",
-    "cmlibs.zinc",
+    "cmlibs.maths >= 0.3",
+    "cmlibs.utils >= 0.6",
+    "cmlibs.zinc >= 4.0",
     "scipy",
     "numpy",
 ]
 source_license = readfile("LICENSE")
 
 setup(
     name="scaffoldmaker",
-    version="0.9.0",
+    version="0.10.0",
     description="Python client for generating anatomical scaffolds using Zinc",
     long_description="\n".join(readme) + source_license,
     long_description_content_type="text/x-rst",

src/scaffoldmaker/annotation/annotationgroup.py

@@ -6,17 +6,17 @@
 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 cmlibs.utils.zinc.finiteelement import get_highest_dimension_mesh, get_next_unused_node_identifier
+from cmlibs.utils.zinc.group import group_get_highest_dimension, \
+    identifier_ranges_from_string, identifier_ranges_to_string, \
+    mesh_group_add_identifier_ranges, mesh_group_to_identifier_ranges, \
+    nodeset_group_add_identifier_ranges, nodeset_group_to_identifier_ranges
 from cmlibs.zinc.element import Element, Mesh
 from cmlibs.zinc.field import Field, FieldFiniteElement, FieldGroup, FieldStoredMeshLocation, FieldStoredString, \
     FieldFindMeshLocation
 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, \
-    nodeset_group_add_identifier_ranges, nodeset_group_to_identifier_ranges
 
 
 class AnnotationGroup(object):
@@ -75,7 +75,7 @@ def toDict(self):
         identifierRanges = []
         if dimension > 0:
             mesh = fieldmodule.findMeshByDimension(dimension)
-            meshGroup = self._group.getFieldElementGroup(mesh).getMeshGroup()
+            meshGroup = self._group.getMeshGroup(mesh)
             if meshGroup.isValid():
                 identifierRanges = mesh_group_to_identifier_ranges(meshGroup)
         else:
@@ -84,7 +84,7 @@ def toDict(self):
                     identifierRanges = [[self._markerIdentifier, self._markerIdentifier]]
             else:
                 nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
-                nodesetGroup = self._group.getFieldNodeGroup(nodes).getNodesetGroup()
+                nodesetGroup = self._group.getNodesetGroup(nodes)
                 if nodesetGroup.isValid():
                     identifierRanges = nodeset_group_to_identifier_ranges(nodesetGroup)
         dct = {
@@ -438,18 +438,8 @@ def setName(self, name):
             fieldcache.setNode(markerNode)
             markerName.assignString(fieldcache, name)
         else:
-            with ChangeManager(fieldmodule):
-                if RESULT_OK != self._group.setName(name):
-                    return False
-                # workaround for zinc issue: must rename subelement groups
-                for dimension in range(3, 0, -1):
-                    mesh = fieldmodule.findMeshByDimension(dimension)
-                    elementGroup = self._group.getFieldElementGroup(mesh)
-                    if elementGroup.isValid():
-                        elementGroup.setName(name + '.' + mesh.getName())
-                nodeGroup = self._group.getFieldNodeGroup(nodes)
-                if nodeGroup.isValid():
-                    nodeGroup.setName(name + '.' + nodes.getName())
+            if RESULT_OK != self._group.setName(name):
+                return False
         self._name = name
         return True
 
@@ -488,55 +478,37 @@ def getDimension(self):
         """
         return group_get_highest_dimension(self._group)
 
-    def getFieldElementGroup(self, mesh):
-        """
-        :param mesh: The Zinc mesh to manage a sub group of.
-        :return: The Zinc element group field for mesh in this AnnotationGroup.
-        """
-        elementGroup = self._group.getFieldElementGroup(mesh)
-        if not elementGroup.isValid():
-            elementGroup = self._group.createFieldElementGroup(mesh)
-        return elementGroup
-
-    def getFieldNodeGroup(self, nodeset):
-        """
-        :param nodeset: The Zinc nodeset to manage a sub group of.
-        :return: The Zinc node group field for nodeset in this AnnotationGroup.
-        """
-        nodeGroup = self._group.getFieldNodeGroup(nodeset)
-        if not nodeGroup.isValid():
-            nodeGroup = self._group.createFieldNodeGroup(nodeset)
-        return nodeGroup
-
     def getMeshGroup(self, mesh):
         """
+        Get or create mesh group.
         :param mesh: The Zinc mesh to manage a sub group of.
         :return: The Zinc meshGroup for adding elements of mesh in this AnnotationGroup.
         """
-        return self.getFieldElementGroup(mesh).getMeshGroup()
+        return self._group.getOrCreateMeshGroup(mesh)
 
     def hasMeshGroup(self, mesh):
         """
         :param mesh: The Zinc mesh to query a sub group of.
         :return: True if MeshGroup for mesh exists and is not empty, otherwise False.
         """
-        elementGroup = self._group.getFieldElementGroup(mesh)
-        return elementGroup.isValid() and (elementGroup.getMeshGroup().getSize() > 0)
+        meshGroup = self._group.getMeshGroup(mesh)
+        return meshGroup.isValid() and (meshGroup.getSize() > 0)
 
     def getNodesetGroup(self, nodeset):
         """
+        Get or create nodeset group.
         :param nodeset: The Zinc nodeset to manage a sub group of.
         :return: The Zinc nodesetGroup for adding nodes from nodeset in this AnnotationGroup.
         """
-        return self.getFieldNodeGroup(nodeset).getNodesetGroup()
+        return self._group.getOrCreateNodesetGroup(nodeset)
 
     def hasNodesetGroup(self, nodeset):
         """
         :param nodeset: The Zinc nodeset to query a sub group of.
         :return: True if NodesetGroup for nodeset exists and is not empty, otherwise False.
         """
-        nodeGroup = self._group.getFieldNodeGroup(nodeset)
-        return nodeGroup.isValid() and (nodeGroup.getNodesetGroup().getSize() > 0)
+        nodesetGroup = self._group.getNodesetGroup(nodeset)
+        return nodesetGroup.isValid() and (nodesetGroup.getSize() > 0)
 
     def addSubelements(self):
         """
@@ -546,11 +518,10 @@ def addSubelements(self):
         fm = self._group.getFieldmodule()
         for dimension in range(1, 4):
             mesh = fm.findMeshByDimension(dimension)
-            elementGroup = self._group.getFieldElementGroup(mesh)
-            if elementGroup.isValid():
-                meshGroup = elementGroup.getMeshGroup()
+            meshGroup = self._group.getMeshGroup(mesh)
+            if meshGroup.isValid():
                 #print('Mesh group:', self._name, ', size', meshGroup.getSize())
-                meshGroup.addElementsConditional(elementGroup)  # use FieldElementGroup as conditional field
+                meshGroup.addElementsConditional(self._group)  # use whole group as conditional field
 
 
 def findAnnotationGroupByName(annotationGroups: list, name: str):

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -872,11 +872,11 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         is_exterior_face_xi3_1 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
         is_exterior_face_xi3_0 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0))
 
-        is_body = bodyGroup.getFieldElementGroup(mesh2d)
+        is_body = bodyGroup.getGroup()
         is_body_serosa = fm.createFieldAnd(is_body, is_exterior_face_xi3_1)
         is_body_lumen = fm.createFieldAnd(is_body, is_exterior_face_xi3_0)
 
-        is_neck = neckGroup.getFieldElementGroup(mesh2d)
+        is_neck = neckGroup.getGroup()
         is_neck_serosa = fm.createFieldAnd(is_neck, is_exterior_face_xi3_1)
         is_neck_lumen = fm.createFieldAnd(is_neck, is_exterior_face_xi3_0)
 

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

@@ -7,7 +7,7 @@
 import copy
 import math
 
-from cmlibs.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \
+from cmlibs.utils.zinc.field import findOrCreateFieldGroup, \
     findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
 from cmlibs.zinc.element import Element
 from cmlibs.zinc.field import Field
@@ -632,7 +632,7 @@ def generateBaseMesh(cls, region, options):
         markerLocation = findOrCreateFieldStoredMeshLocation(fm, mesh, name="marker_location")
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
-        markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup()
+        markerPoints = markerGroup.getOrCreateNodesetGroup(nodes)
         markerTemplateInternal = nodes.createNodetemplate()
         markerTemplateInternal.defineField(markerName)
         markerTemplateInternal.defineField(markerLocation)
@@ -649,12 +649,12 @@ def generateBaseMesh(cls, region, options):
 
         tmpGroup = tmpFieldmodule.findFieldByName("urinary bladder").castGroup()
         cx_bladder, cd1_bladder, cd2_bladder, cd12_bladder = get_nodeset_path_field_parameters(
-            tmpGroup.getFieldNodeGroup(tmpNodes).getNodesetGroup(), tmpCoordinates,
+            tmpGroup.getNodesetGroup(tmpNodes), tmpCoordinates,
             [Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2])
 
         tmpGroup = tmpFieldmodule.findFieldByName("urethra").castGroup()
         cx_urethra, cd1_urethra, cd2_urethra, cd12_urethra = get_nodeset_path_field_parameters(
-            tmpGroup.getFieldNodeGroup(tmpNodes).getNodesetGroup(), tmpCoordinates,
+            tmpGroup.getNodesetGroup(tmpNodes), tmpCoordinates,
             [Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2])
 
         del tmpGroup
@@ -1208,20 +1208,20 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         is_exterior_face_xi3_1 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
         is_exterior_face_xi3_0 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0))
 
-        is_body = bodyGroup.getFieldElementGroup(mesh2d)
+        is_body = bodyGroup.getGroup()
         is_body_serosa = fm.createFieldAnd(is_body, is_exterior_face_xi3_1)
         is_body_lumen = fm.createFieldAnd(is_body, is_exterior_face_xi3_0)
 
-        is_neck = neckGroup.getFieldElementGroup(mesh2d)
+        is_neck = neckGroup.getGroup()
         is_neck_serosa = fm.createFieldAnd(is_neck, is_exterior_face_xi3_1)
         is_neck_lumen = fm.createFieldAnd(is_neck, is_exterior_face_xi3_0)
 
-        is_urinaryBladder = urinaryBladderGroup.getFieldElementGroup(mesh2d)
+        is_urinaryBladder = urinaryBladderGroup.getGroup()
         is_urinaryBladder_serosa = fm.createFieldAnd(is_urinaryBladder, is_exterior_face_xi3_1)
         is_urinaryBladder_lumen = fm.createFieldAnd(is_urinaryBladder, is_exterior_face_xi3_0)
 
-        is_dorsal_bladder = bladderDorsalGroup.getFieldElementGroup(mesh2d)
-        is_ventral_bladder = bladderVentralGroup.getFieldElementGroup(mesh2d)
+        is_dorsal_bladder = bladderDorsalGroup.getGroup()
+        is_ventral_bladder = bladderVentralGroup.getGroup()
 
         serosaOfUrinaryBladder = \
             findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("serosa of urinary bladder"))
@@ -1324,12 +1324,12 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
                                                             get_bladder_term("ventral part of urethra"))
             urethraDorsalGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("dorsal part of urethra"))
 
-            is_urethra = urethraGroup.getFieldElementGroup(mesh2d)
+            is_urethra = urethraGroup.getGroup()
             is_urethra_serosa = fm.createFieldAnd(is_urethra, is_exterior_face_xi3_1)
             is_urethra_lumen = fm.createFieldAnd(is_urethra, is_exterior_face_xi3_0)
 
-            is_dorsal_urethra = urethraDorsalGroup.getFieldElementGroup(mesh2d)
-            is_ventral_urethra = urethraVentralGroup.getFieldElementGroup(mesh2d)
+            is_dorsal_urethra = urethraDorsalGroup.getGroup()
+            is_ventral_urethra = urethraVentralGroup.getGroup()
 
             serosaOfUrethra = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
                                                                  get_bladder_term("serosa of urethra"))

src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py

@@ -8,9 +8,7 @@
 
 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 cmlibs.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldStoredString
 from cmlibs.utils.zinc.general import ChangeManager
 from cmlibs.utils.zinc.finiteelement import getMaximumNodeIdentifier
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm
@@ -626,7 +624,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         groupNames = ['brainstem', 'midbrain', 'medulla oblongata', 'pons']
         for groupName in groupNames:
             subGroup = AnnotationGroup(region, get_brainstem_term(groupName))
-            issub = subGroup.getFieldElementGroup(mesh2d)
+            issub = subGroup.getGroup()
             is_subface_ext = fm.createFieldOr(fm.createFieldAnd(issub, is_exterior_face_xi1), fm.createFieldAnd(issub, is_exterior_face_xi3))
             subFaceGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_brainstem_term(groupName + ' exterior'))
             subFaceGroup.getMeshGroup(mesh2d).addElementsConditional(is_subface_ext)
@@ -636,7 +634,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         for groupName in groupNames:
             subGroupName = 'midbrain' if groupName == 'thalamus-brainstem interface' else 'medulla oblongata'
             subGroup = AnnotationGroup(region, get_brainstem_term(subGroupName))
-            issub = subGroup.getFieldElementGroup(mesh2d)
+            issub = subGroup.getGroup()
             is_subface_ext = fm.createFieldAnd(issub, is_exterior_face_xi2)
             subFaceGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
                                                               get_brainstem_term(groupName))

src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py

@@ -673,7 +673,7 @@ def generateBaseMesh(cls, region, options):
 
         for termName in colonTermsAlong:
             tmpGroup = tmpFieldmodule.findFieldByName(termName).castGroup() if termName else None
-            tmpNodeset = tmpGroup.getFieldNodeGroup(tmpNodes).getNodesetGroup() if tmpGroup else tmpNodes
+            tmpNodeset = tmpGroup.getNodesetGroup(tmpNodes) if tmpGroup else tmpNodes
 
             cxGroup, cd1Group, cd2Group, cd3Group, cd12Group, cd13Group = get_nodeset_path_field_parameters(
                 tmpNodeset, tmpCoordinates,
@@ -959,7 +959,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         is_exterior = fm.createFieldIsExterior()
         is_exterior_face_xi3_1 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
         is_exterior_face_xi3_0 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0))
-        is_colon = colonGroup.getFieldElementGroup(mesh2d)
+        is_colon = colonGroup.getGroup()
         is_serosa = fm.createFieldAnd(is_colon, is_exterior_face_xi3_1)
         serosa = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_colon_term("serosa of colon"))
         serosa.getMeshGroup(mesh2d).addElementsConditional(is_serosa)

src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

@@ -424,7 +424,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         is_exterior = fm.createFieldIsExterior()
         is_exterior_face_xi3_1 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
         is_exterior_face_xi3_0 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0))
-        is_colon = colonGroup.getFieldElementGroup(mesh2d)
+        is_colon = colonGroup.getGroup()
         is_serosa = fm.createFieldAnd(is_colon, is_exterior_face_xi3_1)
         serosa = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_colon_term("serosa of colon"))
         serosa.getMeshGroup(mesh2d).addElementsConditional(is_serosa)

src/scaffoldmaker/meshtypes/meshtype_3d_esophagus1.py

@@ -7,7 +7,7 @@
 import copy
 import math
 from cmlibs.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldStoredString, \
-    findOrCreateFieldStoredMeshLocation, findOrCreateFieldNodeGroup
+    findOrCreateFieldStoredMeshLocation
 from cmlibs.zinc.element import Element
 from cmlibs.zinc.field import Field
 from cmlibs.zinc.node import Node
@@ -214,7 +214,7 @@ def generateBaseMesh(cls, region, options):
 
         for termName in esophagusTermsAlong:
             tmpGroup = tmpFieldmodule.findFieldByName(termName).castGroup() if termName else None
-            tmpNodeset = tmpGroup.getFieldNodeGroup(tmpNodes).getNodesetGroup() if tmpGroup else tmpNodes
+            tmpNodeset = tmpGroup.getNodesetGroup(tmpNodes) if tmpGroup else tmpNodes
 
             cxGroup, cd1Group, cd2Group, cd3Group, cd12Group, cd13Group = get_nodeset_path_field_parameters(
                 tmpNodeset, tmpCoordinates,
@@ -457,7 +457,7 @@ def generateBaseMesh(cls, region, options):
         markerLocation = findOrCreateFieldStoredMeshLocation(fm, mesh, name="marker_location")
 
         nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
-        markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup()
+        markerPoints = markerGroup.getOrCreateNodesetGroup(nodes)
         markerTemplateInternal = nodes.createNodetemplate()
         markerTemplateInternal.defineField(markerName)
         markerTemplateInternal.defineField(markerLocation)
@@ -535,7 +535,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         is_exterior = fm.createFieldIsExterior()
         is_exterior_face_xi3_1 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
         is_exterior_face_xi3_0 = fm.createFieldAnd(is_exterior, fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_0))
-        is_esophagus = esophagusGroup.getFieldElementGroup(mesh2d)
+        is_esophagus = esophagusGroup.getGroup()
         is_serosa = fm.createFieldAnd(is_esophagus, is_exterior_face_xi3_1)
         serosa = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_esophagus_term("serosa of esophagus"))
         serosa.getMeshGroup(mesh2d).addElementsConditional(is_serosa)