Tube network mesh refactor

src/scaffoldmaker/annotation/uterus_terms.py

@@ -10,7 +10,7 @@
     ("dorsal top left horn", "None"),
     ("dorsal top right horn", "None"),
     ("external cervical os", "UBERON:0013760", "FMA:76836", "ILX:0736534"),
-    ("fundus", "None"),
+    ("fundus of uterus", "None"),
     ("internal cervical os", "UBERON:0013759", "FMA:17747", "ILX:0729495"),
     ("junction of left round ligament with uterus", "None"),
     ("junction of right round ligament with uterus", "None"),

src/scaffoldmaker/meshtypes/meshtype_1d_network_layout1.py

@@ -8,7 +8,7 @@
 from cmlibs.zinc.field import Field, FieldGroup
 from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils.networkmesh import NetworkMesh
+from scaffoldmaker.utils.networkmesh import NetworkMesh, pathValueLabels
 from scaffoldmaker.utils.interpolation import smoothCurveSideCrossDerivatives
 from scaffoldmaker.utils.zinc_utils import clearRegion, get_nodeset_field_parameters, \
     get_nodeset_path_ordered_field_parameters, make_nodeset_derivatives_orthogonal, \
@@ -27,7 +27,9 @@ class MeshType_1d_network_layout1(Scaffold_base):
         "Bifurcation": "1-2.1,2.2-3,2.3-4",
         "Converging bifurcation": "1-3.1,2-3.2,3.3-4",
         "Loop": "1-2-3-4-5-6-7-8-1",
-        "Sphere cube": "1.1-2.1,1.2-3.1,1.3-4.1,2.2-5.2,2.3-6.1,3.2-6.2,3.3-7.1,4.2-7.2,4.3-5.1,5.3-8.1,6.3-8.2,7.3-8.3"
+        "Sphere cube": "1.1-2.1,1.2-3.1,1.3-4.1,2.2-5.2,2.3-6.1,3.2-6.2,3.3-7.1,4.2-7.2,4.3-5.1,5.3-8.1,6.3-8.2,7.3-8.3",
+        "Trifurcation": "1-2.1,2.2-3,2.3-4,2.4-5",
+        "Trifurcation cross": "1-3.1,2-3.2,3.2-4,3.1-5"
     }
 
     @classmethod
@@ -261,10 +263,6 @@ def assignCoordinates(cls, region, options, networkMesh, functionOptions, editGr
             if not selectionMeshGroup.isValid():
                 print("Assign coordinates:  Selection contains no elements. Clear it to assign globally.")
                 return False, False
-        valueLabels = [
-            Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
-            Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
-            Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3]
 
         with ChangeManager(fieldmodule):
             # get all node parameters (from selection if any)
@@ -277,10 +275,10 @@ def assignCoordinates(cls, region, options, networkMesh, functionOptions, editGr
                 tmpMeshGroup = tmpGroup.createMeshGroup(mesh1d)
                 tmpMeshGroup.addElementsConditional(selectionGroup)
                 editNodeset = tmpGroup.getNodesetGroup(nodes)
-                _, originalNodeParameters = get_nodeset_field_parameters(editNodeset, toCoordinates, valueLabels)
+                _, originalNodeParameters = get_nodeset_field_parameters(editNodeset, toCoordinates, pathValueLabels)
                 del tmpMeshGroup
                 del tmpGroup
-            _, nodeParameters = get_nodeset_field_parameters(editNodeset, fromCoordinates, valueLabels)
+            _, nodeParameters = get_nodeset_field_parameters(editNodeset, fromCoordinates, pathValueLabels)
 
             modifyVersions = None  # default is to modify all versions
             if selectionGroup:
@@ -324,7 +322,7 @@ def assignCoordinates(cls, region, options, networkMesh, functionOptions, editGr
                         for d in range(2, 6):
                             nNodeParameters[d][v] = oNodeParameters[d][v]
 
-            set_nodeset_field_parameters(editNodeset, toCoordinates, valueLabels, nodeParameters, editGroupName)
+            set_nodeset_field_parameters(editNodeset, toCoordinates, pathValueLabels, nodeParameters, editGroupName)
             del editNodeset
 
         return False, True  # settings not changed, nodes changed