Merge pull request #148 from zekh167/bladder_ILX

Bladder ilx
ABI-Software · Jun 15, 2021 · de77f0a · de77f0a
2 parents d69842d + 37e54f0
commit de77f0a
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/src/scaffoldmaker/annotation/bladder_terms.py b/src/scaffoldmaker/annotation/bladder_terms.py
@@ -6,11 +6,11 @@
 bladder_terms = [
     ("bladder lumen", "UBERON:0009958"),
     ("dome of the bladder", "ILX:0738433"),
-    ("dorsal part of bladder lumen", "None"),
+    ("dorsal part of urinary bladder lumen", "ILX:0777128"),
     ("dorsal part of lumen of body of urinary bladder", "ILX:0739250"),
     ("dorsal part of lumen of neck of urinary bladder", "ILX:0739255"),
     ("dorsal part of lumen of urethra", "ILX:0739260"),
-    ("dorsal part of bladder", "None"),
+    ("dorsal part of bladder", "ILX:0778155"),
     ("dorsal part of urethra", "ILX:0739258"),
     ("dorsal part of serosa of body of urinary bladder", "ILX:0739278"),
     ("dorsal part of serosa of neck of urinary bladder", "ILX:0739280"),
@@ -27,21 +27,21 @@
     ("ureter", "UBERON:0000056", "ILX:0728080"),
     ("urethra", "UBERON:0000057", "ILX:0733022"),
     ("urinary bladder", "UBERON:0001255", "FMA:15900"),
-    ("ventral part of bladder lumen", "None"),
+    ("ventral part of urinary bladder lumen", "ILX:0777129"),
     ("ventral part of lumen of body of urinary bladder", "ILX:0739251"),
     ("ventral part of lumen of neck of urinary bladder", "ILX:0739257"),
     ("ventral part of lumen of urethra", "ILX:0739261"),
     ("ventral part of serosa of body of urinary bladder", "ILX:0739279"),
     ("ventral part of serosa of neck of urinary bladder", "ILX:0739281"),
     ("ventral part of serosa of urethra", "ILX:0739306"),
     ("ventral part of serosa of urinary bladder", "ILX:0739249"),
-    ("ventral part of bladder", "None"),
+    ("ventral part of bladder", "ILX:0778156 "),
     ("ventral part of urethra", "ILX:0739259"),
     ("apex of urinary bladder", "ILX:0774405"),
-    ("left ureter junction with bladder", "None"),
-    ("right ureter junction with bladder", "None"),
-    ("urethra junction with bladder dorsal", "None"),
-    ("urethra junction with bladder ventral", "None")
+    ("left ureter junction with bladder", "ILX:0778142"),
+    ("right ureter junction with bladder", "ILX:0778143"),
+    ("urethra junction of dorsal bladder neck", "ILX:0778154"),
+    ("urethra junction of ventral bladder neck", "ILX:0738410")
 ]
 
 def get_bladder_term(name : str):

diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
@@ -896,8 +896,8 @@ def generateBaseMesh(cls, region, options):
         apexGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("apex of urinary bladder"))
         leftUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("left ureter junction with bladder"))
         rightUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("right ureter junction with bladder"))
-        dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder dorsal"))
-        ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder ventral"))
+        dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction of dorsal bladder neck"))
+        ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction of ventral bladder neck"))
 
         idx1 = 1
         xi1 = [0.0, 0.0, 0.0]
@@ -1017,11 +1017,11 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
         serosaOfBladder_ventral.getMeshGroup(mesh2d).addElementsConditional(is_bladder_serosa_ventral)
 
         is_bladder_lumen_dorsal = fm.createFieldAnd(is_urinaryBladder_lumen, is_dorsal_bladder)
-        lumenOfBladder_dorsal = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("dorsal part of bladder lumen"))
+        lumenOfBladder_dorsal = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("dorsal part of urinary bladder lumen"))
         lumenOfBladder_dorsal.getMeshGroup(mesh2d).addElementsConditional(is_bladder_lumen_dorsal)
 
         is_bladder_lumen_ventral = fm.createFieldAnd(is_urinaryBladder_lumen, is_ventral_bladder)
-        lumenOfBladder_ventral = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("ventral part of bladder lumen"))
+        lumenOfBladder_ventral = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("ventral part of urinary bladder lumen"))
         lumenOfBladder_ventral.getMeshGroup(mesh2d).addElementsConditional(is_bladder_lumen_ventral)
 
         is_body_serosa_dorsal = fm.createFieldAnd(is_body_serosa, is_dorsal_bladder)