Rescale derivatives for annulus mesh

src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py

@@ -43,6 +43,7 @@ def getName():
     def getParameterSetNames():
         return [
             'Default',
+            'Cattle 1',
             'Human 1',
             'Mouse 1',
             'Pig 1']
@@ -78,7 +79,19 @@ def getDefaultOptions(parameterSetName='Default'):
             'Refine number of elements along segment' : 1,
             'Refine number of elements through wall' : 1
         }
-        if 'Mouse' in parameterSetName:
+        if 'Cattle' in parameterSetName:
+            options['Start inner radius'] = 10.5
+            options['End inner radius'] = 10.5
+            options['Corner inner radius factor'] = 0.0
+            options['Haustrum inner radius factor'] = 0.0
+            options['Segment length end derivative factor'] = 0.0
+            options['Segment length mid derivative factor'] = 0.0
+            options['Number of tenia coli'] = 1
+            options['Start tenia coli width'] = 3.0
+            options['End tenia coli width'] = 3.0
+            options['Tenia coli thickness'] = 0.0
+            options['Wall thickness'] = 3.02
+        elif 'Mouse' in parameterSetName:
             options['Start inner radius'] = 0.94
             options['End inner radius'] = 0.94
             options['Corner inner radius factor'] = 0.0

src/scaffoldmaker/utils/eft_utils.py

@@ -117,13 +117,13 @@ def scaleEftNodeValueLabels(eft, localNodeIndexes, valueLabels, addScaleFactorIn
                     scaleFactorIndexes += addScaleFactorIndexes
                     eft.setTermScaling(f, t, scaleFactorIndexes)
 
-def setEftScaleFactorIds(eft, generalScaleFactorIds, nodeScaleFactorIds):
+def setEftScaleFactorIds(eft, globalScaleFactorIds, nodeScaleFactorIds):
     '''
     Set general followed by node scale factor identifiers.
     '''
-    eft.setNumberOfLocalScaleFactors(len(generalScaleFactorIds) + len(nodeScaleFactorIds))
+    eft.setNumberOfLocalScaleFactors(len(globalScaleFactorIds) + len(nodeScaleFactorIds))
     s = 1
-    for id in generalScaleFactorIds:
+    for id in globalScaleFactorIds:
         eft.setScaleFactorType(s, Elementfieldtemplate.SCALE_FACTOR_TYPE_GLOBAL_GENERAL)
         eft.setScaleFactorIdentifier(s, id)
         s += 1

tests/test_bladder.py

@@ -87,7 +87,7 @@ def test_bladder1(self):
         self.assertTrue(region.isValid())
 
         annotationGroups = MeshType_3d_bladder1.generateBaseMesh(region, options)
-        self.assertEqual(2, len(annotationGroups))
+        self.assertEqual(3, len(annotationGroups))
         fieldmodule = region.getFieldmodule()
         self.assertEqual(RESULT_OK, fieldmodule.defineAllFaces())
         if annotationGroups is not None:

tests/test_cecum.py

@@ -79,10 +79,10 @@ def test_cecum1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 65960.02821062482, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 65959.34314511667, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 127893.74708048582, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 127894.8597203706, delta=1.0E-6)
 
 if __name__ == "__main__":
     unittest.main()

tests/test_colon.py

@@ -21,7 +21,7 @@ def test_colon1(self):
         Test creation of colon scaffold.
         """
         parameterSetNames = MeshType_3d_colon1.getParameterSetNames()
-        self.assertEqual(parameterSetNames, ["Default", "Human 1", "Human 2", "Mouse 1", "Mouse 2", "Pig 1", "Pig 2"])
+        self.assertEqual(parameterSetNames, ["Default", "Cattle 1", "Human 1", "Human 2", "Mouse 1", "Mouse 2", "Pig 1", "Pig 2"])
         centralPathDefaultScaffoldPackages = {
             'Test line': ScaffoldPackage(MeshType_1d_path1, {
                 'scaffoldSettings': {
@@ -112,14 +112,14 @@ def test_colon1(self):
         coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement()
         self.assertTrue(coordinates.isValid())
         minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
-        assertAlmostEqualList(self, minimums, [ 108.0250647983898, -36.876103983560014,  -25.89741158325083 ], 1.0E-6)
-        assertAlmostEqualList(self, maximums, [ 185.46457506220003, 48.101157490744, 34.995316052158934 ], 1.0E-6)
+        assertAlmostEqualList(self, minimums, [ 108.03959866945482, -36.876103983560014, -25.93217903595996 ], 1.0E-6)
+        assertAlmostEqualList(self, maximums, [ 185.43446761757468, 48.07433517752282, 34.995316052158934 ], 1.0E-6)
 
         flatCoordinates = fieldmodule.findFieldByName("flat coordinates").castFiniteElement()
         self.assertTrue(flatCoordinates.isValid())
         minimums, maximums = evaluateFieldNodesetRange(flatCoordinates, nodes)
         assertAlmostEqualList(self, minimums, [ 0.0, 0.0, 0.0 ], 1.0E-6)
-        assertAlmostEqualList(self, maximums, [ 186.72988844629867, 77.4178187926561, 3.2000000000000006 ], 1.0E-6)
+        assertAlmostEqualList(self, maximums, [ 186.72988844629867, 75.79769125771575, 3.2000000000000006 ], 1.0E-6)
 
         textureCoordinates = fieldmodule.findFieldByName("texture coordinates").castFiniteElement()
         minimums, maximums = evaluateFieldNodesetRange(textureCoordinates, nodes)
@@ -136,10 +136,10 @@ def test_colon1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 14612.416788520026, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 14623.340352853866, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 26826.069540921028, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 26869.74823158621, delta=1.0E-6)
 
     def test_mousecolon1(self):
         """
@@ -175,7 +175,7 @@ def test_mousecolon1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, flatSurfaceArea = flatSurfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(flatSurfaceArea, 652.2383326727861, delta=1.0E-6)
+        self.assertAlmostEqual(flatSurfaceArea, 629.440514706522, delta=1.0E-6)
         result, textureSurfaceArea = textureSurfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
         self.assertAlmostEqual(textureSurfaceArea, 1.0, delta=1.0E-6)

tests/test_colonsegment.py

@@ -16,7 +16,7 @@ def test_humancolonsegment1(self):
         Test creation of human colon segment scaffold.
         """
         parameterSetNames = MeshType_3d_colonsegment1.getParameterSetNames()
-        self.assertEqual(parameterSetNames, [ "Default", "Human 1", "Mouse 1", "Pig 1" ])
+        self.assertEqual(parameterSetNames, [ "Default", "Cattle 1", "Human 1", "Mouse 1", "Pig 1" ])
         options = MeshType_3d_colonsegment1.getDefaultOptions("Human 1")
         self.assertEqual(27, len(options))
         self.assertEqual(0.0, options.get("Start phase"))