Left atria PV annulus changes

src/scaffoldmaker/annotation/heart_terms.py

@@ -4,7 +4,7 @@
 
 # convention: preferred name, preferred id, followed by any other ids and alternative names
 heart_terms = [
-    ( "heart", "FMA:7088", "UBERON:0000948" ),
+    ( "heart", "UBERON:0000948", "FMA:7088" ),
     # ventricles
     ( "left ventricle myocardium", "FMA:9558" ),
     ( "right ventricle myocardium", "FMA:9535" ),
@@ -52,7 +52,10 @@
     ( "anterior cusp of pulmonary valve", "FMA:7249" ),
     ( "left cusp of pulmonary valve", "FMA:7247" ),
     # future: fiducial markers
-    ( "apex of heart", "FMA:7164", "UBERON:0002098")
+    ( "apex of heart", "UBERON:0002098", "FMA:7164"),
+    ( "crux of heart", "ILX:0777104", "FMA:7220" ),
+    ( "left atrium epicardium venous midpoint", "None"),  # point at centre of pulmonary vein ostia on left atrium epicardium, on anterior/ventral side for rodents
+    ( "right atrium epicardium venous midpoint", "None")  # point at centre of inferior & superior vena cavae on right atrium epicardium
     ]
 
 def get_heart_term(name : str):

src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py

@@ -54,15 +54,19 @@ def getOrderedOptionNames():
         optionNames = MeshType_3d_heartventriclesbase1.getOrderedOptionNames()
         optionNamesAtria = MeshType_3d_heartatria1.getOrderedOptionNames()
         # insert new numbers of elements from atria; others came with ventriclesbase1
-        optionNames.insert(7, 'Number of elements along vena cava inlet')
-        optionNames.insert(8, 'Number of elements over atria')
+        optionNames.insert(7, 'Number of elements along atrial appendages')
+        optionNames.insert(8, 'Number of elements along vena cava inlet')
+        optionNames.insert(9, 'Number of elements over atria')
+        optionNames.insert(10, 'Number of elements radial pulmonary vein annuli')
         # remove number of elements, unit scale and dependent options from atria options
         for key in [
+            'Number of elements along atrial appendages',
             'Number of elements along vena cava inlet',
             'Number of elements around atrial septum',
             'Number of elements around left atrium free wall',
             'Number of elements around right atrium free wall',
             'Number of elements over atria',
+            'Number of elements radial pulmonary vein annuli',
             'Unit scale',
             'Aorta outer plus diameter']:
             optionNamesAtria.remove(key)
@@ -133,6 +137,8 @@ def generateBaseMesh(cls, region, options):
         ventriclesAnnotationGroups = MeshType_3d_heartventriclesbase1.generateBaseMesh(region, options)
         atriaAnnotationGroups = MeshType_3d_heartatria1.generateBaseMesh(region, options)
         annotationGroups = mergeAnnotationGroups(ventriclesAnnotationGroups, atriaAnnotationGroups)
+        heartGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("heart"))
+        cruxGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("crux of heart"))
         lFibrousRingGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("left fibrous ring"))
         rFibrousRingGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_heart_term("right fibrous ring"))
 
@@ -211,6 +217,7 @@ def generateBaseMesh(cls, region, options):
         # Create elements
         #################
 
+        heartMeshGroup = heartGroup.getMeshGroup(mesh)
         lFibrousRingMeshGroup = lFibrousRingGroup.getMeshGroup(mesh)
         rFibrousRingMeshGroup = rFibrousRingGroup.getMeshGroup(mesh)
 
@@ -233,7 +240,7 @@ def generateBaseMesh(cls, region, options):
                 lavNodeId[0][0][n1], lavNodeId[0][0][n1 + 1], lavNodeId[0][1][n1], lavNodeId[0][1][n1 + 1],
                 lavNodeId[1][0][n1], lavNodeId[1][0][n1 + 1], lavNodeId[1][1][n1], lavNodeId[1][1][n1 + 1]]
             scalefactors = None
-            meshGroups = [ lFibrousRingMeshGroup ]
+            meshGroups = [ heartMeshGroup, lFibrousRingMeshGroup ]
 
             if e == -1:
                 # interatrial groove straddles left and right atria, collapsed to 6 node wedge
@@ -295,7 +302,7 @@ def generateBaseMesh(cls, region, options):
                 ravNodeId[0][0][n1], ravNodeId[0][0][n1 + 1], ravNodeId[0][1][n1], ravNodeId[0][1][n1 + 1],
                 ravNodeId[1][0][n1], ravNodeId[1][0][n1 + 1], ravNodeId[1][1][n1], ravNodeId[1][1][n1 + 1]]
             scalefactors = None
-            meshGroups = [ rFibrousRingMeshGroup ]
+            meshGroups = [ heartMeshGroup, rFibrousRingMeshGroup ]
 
             if e == -1:
                 # interatrial groove straddles left and right atria, collapsed to 6 node wedge
@@ -350,7 +357,7 @@ def generateBaseMesh(cls, region, options):
                 meshGroup.addElement(element)
 
         # fibrous ring septum:
-        meshGroups = [ lFibrousRingMeshGroup, rFibrousRingMeshGroup ]
+        meshGroups = [ heartMeshGroup, lFibrousRingMeshGroup, rFibrousRingMeshGroup ]
         for e in range(elementsCountAroundAtrialSeptum):
             eft1 = eftFibrousRing
             nlm = e - elementsCountAroundAtrialSeptum
@@ -391,13 +398,13 @@ def generateBaseMesh(cls, region, options):
         # annotation fiducial points
         cruxElement = mesh.findElementByIdentifier(cruxElementId)
         cruxXi = [ 0.5, 0.5, 1.0 ]
-        cache.setMeshLocation(cruxElement, cruxXi)
-        result, cruxCoordinates = coordinates.evaluateReal(cache, 3)
         markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
         nodeIdentifier += 1
         cache.setNode(markerPoint)
-        markerName.assignString(cache, "crux of heart")
+        markerName.assignString(cache, cruxGroup.getName())
         markerLocation.assignMeshLocation(cache, cruxElement, cruxXi)
+        for group in [ heartGroup, cruxGroup ]:
+            group.getNodesetGroup(nodes).addNode(markerPoint)
 
         return annotationGroups