From c9c223d372ab44b3e73287c98236ac35605c2928 Mon Sep 17 00:00:00 2001
From: elias-soltani <egha355@aucklanduni.ac.nz>
Date: Thu, 18 Aug 2022 00:19:41 +1200
Subject: [PATCH] Add bladder markers

---
 src/scaffoldmaker/annotation/bladder_terms.py |  6 +++++
 .../meshtypes/meshtype_3d_bladderurethra1.py  | 22 ++++++++++++++++++-
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/scaffoldmaker/annotation/bladder_terms.py b/src/scaffoldmaker/annotation/bladder_terms.py
index b937bc4c..286c4fe3 100644
--- a/src/scaffoldmaker/annotation/bladder_terms.py
+++ b/src/scaffoldmaker/annotation/bladder_terms.py
@@ -16,11 +16,17 @@
     ("dorsal part of serosa of neck of urinary bladder", "ILX:0739280"),
     ("dorsal part of serosa of urethra", "ILX:0739283"),
     ("dorsal part of serosa of urinary bladder", "ILX:0739248"),
+    ("external urethral sphincter", "UBERON:0004919"),  # urinary_5
+    ("fundus of urinary bladder", "UBERON:0006082"),  # urinary_3
+    ("hypogastric nerve", "UBERON:0005303"),  # "keast_5"
     ("left hemi-bladder", "ILX:0793661"),
+    ("lumbar splanchnic nerve", "UBERON:0018683"),  # "keast_7"
     ("lumen of body of urinary bladder", "ILX:0739252"),
     ("lumen of neck of urinary bladder", "ILX:0739256"),
     ("lumen of urethra", "UBERON:0010390", "ILX:0736762"),
     ("neck of urinary bladder", "UBERON:0001258", "FMA:15912"),
+    ("pelvic splanchnic nerve", "UBERON:0018675"),  # "keast_4"
+    ("pudendal nerve", "UBERON:0011390"),  # keast_2
     ("right hemi-bladder", "ILX:0793662"),
     ("serosa of body of urinary bladder", "ILX:0739276"),
     ("serosa of neck of urinary bladder", "ILX:0739277"),
diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
index 405add15..bbbe23d4 100644
--- a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
+++ b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
@@ -8,7 +8,8 @@
 import math
 
 from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \
-    findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
+    findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString, findOrCreateFieldCoordinates
+from opencmiss.utils.zinc.finiteelement import getMaximumNodeIdentifier
 from opencmiss.zinc.element import Element
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
@@ -1163,6 +1164,25 @@ def generateBaseMesh(cls, region, options):
             bladderNodesetGroup.addNode(markerPoint)
             nodeIdentifier += 1
 
+        ################
+        # point markers
+        ################
+
+        markerTermNameBrainstemCoordinatesMap = {
+            # "pudendal nerve": [0.0, 1.0, 0.0],
+            # "pelvic splanchnic nerve": [0.0, 1.0, 0.0],
+            # "hypogastric nerve": [0.0, 1.0, 0.0],
+            # "lumbar splanchnic nerve": [0.0, 1.0, 0.0],
+            "fundus of urinary bladder": [14.6, 0.01, 23.1],
+            "external urethral sphincter": [-1.5, 6.7, 110.5],
+        }
+        bladder_coordinates = findOrCreateFieldCoordinates(fm)
+        nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1)
+        for termName, brainstemCoordinatesValues in markerTermNameBrainstemCoordinatesMap.items():
+            annotationGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term(termName))
+            annotationGroup.createMarkerNode(nodeIdentifier, bladder_coordinates, brainstemCoordinatesValues)
+            nodeIdentifier += 1
+
         fm.endChange()
         return annotationGroups