Merge branch 'main' of github.com:ABI-Software/scaffoldmaker

setup.py

@@ -27,7 +27,7 @@ def readfile(filename, split=False):
     # minimal requirements listing
     "cmlibs.maths >= 0.3",
     "cmlibs.utils >= 0.6",
-    "cmlibs.zinc >= 4.0",
+    "cmlibs.zinc >= 4.1",
     "scipy",
     "numpy",
 ]

src/scaffoldmaker/annotation/cecum_terms.py

@@ -4,7 +4,13 @@
 
 # convention: preferred name, preferred id, followed by any other ids and alternative names
 cecum_terms = [
-    ("caecum", "UBERON:0001153", "FMA:14541", "ILX:0732270")
+    ("caecum", "UBERON:0001153", "FMA:14541", "ILX:0732270"),
+    ("cecum mucosa", "UBERON:0000314", "FMA:14998", "ILX:0723957"),
+    ("circular muscle layer of cecum", "ILX:0774843"),
+    ("ileum part of cecum", "None"),
+    ("longitudinal muscle layer of cecum", "ILX:0776047"),
+    ("serosa of cecum", "ILX:0773223"),
+    ("submucosa of cecum", "UBERON:0004927", "FMA:14999", "ILX:0725500")
     ]
 
 

src/scaffoldmaker/annotation/smallintestine_terms.py

@@ -5,16 +5,22 @@
 # convention: preferred name, preferred id, followed by any other ids and alternative names
 smallintestine_terms = [
     ("circular-longitudinal muscle interface of first segment of the duodenum along the gastric-omentum attachment", "ILX:0793090"),
+    ("circular muscle layer of ileum", "ILX:0776561"),
     ("circular muscle layer of small intestine", "ILX:0772669"),
     ("duodenum", "UBERON:0002114", "FMA:7206", "ILX:0726125"),
+    ("ileocecal junction", "UBERON:0001073", "FMA:11338", "ILX:0730012"),
     ("ileum", "UBERON:0002116", "FMA:7208", "ILX:0728151"),
     ("jejunum", "UBERON:0002115", "FMA:7207", "ILX:0724224"),
+    ("longitudinal muscle layer of ileum", "ILX:0770304"),
     ("longitudinal muscle layer of small intestine", "ILX:0772125"),
     ("luminal surface of duodenum", "ILX:0793121"),
+    ("mucosa of ileum", "ILX:0770578"),
     ("mucosa of small intestine", "UBERON:0001204", "FMA:14933", "ILX:0770578"),
     ("serosa of duodenum", "UBERON:0003336", "FMA:14948", "ILX:0732373"),
+    ("serosa of ileum", "ILX:0774472"),
     ("serosa of small intestine", "UBERON:0001206", "FMA:14938", "ILX:0727465"),
     ("small intestine", "UBERON:0002108", "FMA:7200", "ILX:0726770"),
+    ("submucosa of ileum", "UBERON:0004946", "FMA:14957", "ILX:0734297"),
     ("submucosa of small intestine", "UBERON:0001205", "FMA:14934", "ILX:0735609")
     ]
 

src/scaffoldmaker/annotation/stomach_terms.py

@@ -23,13 +23,15 @@
     ("distal point of lower esophageal sphincter serosa on the greater curvature of stomach", "ILX:0793179"),
     ("distal point of lower esophageal sphincter serosa on the lesser curvature of stomach", "ILX:0793180"),
     ("dorsal stomach", "ILX:0793086"),
+    ("duodenum part of stomach", "None"),
     ("esophagogastric junction", "UBERON:0007650", "FMA: 9434", "ILX:0733910"),
     ("esophagogastric junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793098"),
     ("esophagogastric junction along the greater curvature on luminal surface", "ILX:0793099"),
     ("esophagogastric junction along the greater curvature on serosa", "ILX:0793100"),
     ("esophagogastric junction along the lesser curvature on circular-longitudinal muscle interface", "ILX:0793101"),
     ("esophagogastric junction along the lesser curvature on luminal surface", "ILX:0793102"),
     ("esophagogastric junction along the lesser curvature on serosa", "ILX:0793103"),
+    ("esophagus part of stomach", "None"),
     ("forestomach-glandular stomach junction", "UBERON:0012270", "ILX:0729974"),
     ("fundus of stomach", "UBERON:0001160", " FMA:14559", "ILX:0724443"),
     ("fundus-body junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793104"),

src/scaffoldmaker/meshtypes/meshtype_1d_network_layout1.py

@@ -143,7 +143,7 @@ def generateBaseMesh(cls, region, options):
                     cd2[nodeIndexes[ln]].append(d2)
                     cd13[nodeIndexes[ln]].append(mult(d1Unit, edgeAngle * tubeRadius))
             # fix the one node out of order:
-            for d in [cd1[4], cd2[4]]:
+            for d in [cd1[4], cd2[4], cd13[4]]:
                 d[0:2] = [d[1], d[0]]
             for n in range(8):
                 node = nodes.findNodeByIdentifier(n + 1)

src/scaffoldmaker/meshtypes/meshtype_2d_tubenetwork1.py

@@ -81,7 +81,7 @@ def getOptionScaffoldPackage(cls, optionName, scaffoldType, parameterSetName=Non
     @classmethod
     def checkOptions(cls, options):
         if not options["Network layout"].getScaffoldType() in cls.getOptionValidScaffoldTypes("Network layout"):
-            options["Network layout"] = cls.getOptionScaffoldPackage("Network layout")
+            options["Network layout"] = cls.getOptionScaffoldPackage("Network layout", MeshType_1d_network_layout1)
         elementsCountAround = options["Elements count around"]
         if options["Elements count around"] < 4:
             options["Elements count around"] = 4

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -573,7 +573,7 @@ def generateBaseMesh(cls, region, options):
             bladderCoordinatesFieldName, elementsCountAround, elementsCountAlongBladder, elementsCountThroughWall,
             annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
             firstNodeIdentifier, firstElementIdentifier,
-            useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd=True)
+            useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd=True)[0:3]
 
         bladderCoordinates = fm.findFieldByName(bladderCoordinatesFieldName)
 
@@ -1335,7 +1335,7 @@ def getBladderCoordinates(elementsCountAlongDome, elementsCountAlongNeck, elemen
     xList, d1List, d2List, d3List, curvatureList = \
         tubemesh.extrudeSurfaceCoordinates(xInner, d1Inner, d2Inner, d3Inner, wallThicknessList, relativeThicknessList,
                                          elementsCountAround, elementsCountAlongBladder, elementsCountThroughWall,
-                                         transitElementList, outward=False)
+                                         transitElementList, outward=False)[0:5]
 
     # Deal with multiple nodes at the start point for closed proximal end
     n = elementsCountAround * (elementsCountThroughWall + 1)

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

@@ -884,14 +884,12 @@ def generateBaseMesh(cls, region, options):
         transitElementList = [0] * elementsCountAround
 
         relativeThicknessList = []
-        xList, d1List, d2List, d3List, curvatureList = tubemesh.extrudeSurfaceCoordinates(xWarpedList, d1WarpedList,
-                                                                                        d2WarpedList, d3WarpedUnitList,
-                                                                                        wallThicknessList,
-                                                                                        relativeThicknessList,
-                                                                                        elementsCountAround,
-                                                                                        elementsCountAlong,
-                                                                                        elementsCountThroughWall,
-                                                                                        transitElementList, outward=True)
+        xList, d1List, d2List, d3List, curvatureList = \
+            tubemesh.extrudeSurfaceCoordinates(xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList,
+                                               wallThicknessList, relativeThicknessList, elementsCountAround,
+                                               elementsCountAlong, elementsCountThroughWall, transitElementList,
+                                               outward=True)[0:5]
+
         # Call the derivatives from the transition list to be replaced in the d2List
         idx = elementsCountAlongBladder * elementsCountAround
         for n2 in range(elementsCountThroughWall + 1):
@@ -1045,7 +1043,7 @@ def generateBaseMesh(cls, region, options):
             elementsCountAround, elementsCountAlong, elementsCountThroughWall,
             annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
             firstNodeIdentifier, firstElementIdentifier,
-            useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd=True)
+            useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd=True)[0:3]
 
         if includeUreter:
             annotationGroups.append(ureterGroup)