Merge pull request #237 from mlin865/inward

Handle d1 scaling when using inward and update unit test for bladder

src/scaffoldmaker/utils/tubemesh.py

@@ -252,7 +252,7 @@ def extrudeSurfaceCoordinates(xSurf, d1Surf, d2Surf, d3Surf,
     :param d1Surf: Derivatives on surface around tube
     :param d2Surf: Derivatives on surface along tube
     :param d3Surf: Derivatives on surface through wall
-    :param wallThicknessList: Wall thickness for each element along tube
+    :param wallThicknessList: Wall thickness for each node along tube
     :param relativeThicknessList: Relative wall thickness for each element through wall
     :param elementsCountAround: Number of elements around tube
     :param elementsCountAlong: Number of elements along tube
@@ -292,8 +292,10 @@ def extrudeSurfaceCoordinates(xSurf, d1Surf, d2Surf, d3Surf,
             # Calculate curvature along elements around
             prevIdx = n - 1 if (n1 != 0) else (n2 + 1)*elementsCountAround - 1
             nextIdx = n + 1 if (n1 < elementsCountAround - 1) else n2*elementsCountAround
-            kappam = interp.getCubicHermiteCurvatureSimple(xSurf[prevIdx], d1Surf[prevIdx], xSurf[n], d1Surf[n], 1.0)
-            kappap = interp.getCubicHermiteCurvatureSimple(xSurf[n], d1Surf[n], xSurf[nextIdx], d1Surf[nextIdx], 0.0)
+            kappam = interp.getCubicHermiteCurvature(xSurf[prevIdx], d1Surf[prevIdx], xSurf[n], d1Surf[n],
+                                                     vector.normalise(d3Surf[n]), 1.0)
+            kappap = interp.getCubicHermiteCurvature(xSurf[n], d1Surf[n], xSurf[nextIdx], d1Surf[nextIdx],
+                                                     vector.normalise(d3Surf[n]), 0.0)
             if not transitElementList[n1] and not transitElementList[(n1-1)%elementsCountAround]:
                 curvatureAround = 0.5*(kappam + kappap)
             elif transitElementList[n1]:
@@ -336,20 +338,15 @@ def extrudeSurfaceCoordinates(xSurf, d1Surf, d2Surf, d3Surf,
                 xList.append(x)
 
                 # dx_ds1
-                factor = 1.0 + wallThickness * xi3 * curvatureAroundSurf[n]
+                factor = 1.0 - wallOutwardDisplacement * (xi3 if outward else (1.0 - xi3)) * curvatureAroundSurf[n]
                 d1 = [factor*c for c in d1Surf[n]]
                 d1List.append(d1)
 
                 # dx_ds2
-                curvature = curvatureAlong[n]
-                distance = vector.magnitude([x[i] - xSurf[n][i] for i in range(3)])
-                if outward:
-                    factor = 1.0 - curvature * distance
-                else:
-                    factor = 1.0 + curvature * distance
-                d2 = [factor*c for c in d2Surf[n]]
+                factor = 1.0 - wallOutwardDisplacement * (xi3 if outward else (1.0 - xi3)) * curvatureAlong[n]
+                d2 = [factor * c for c in d2Surf[n]]
                 d2List.append(d2)
-                curvatureList.append(curvature)
+                curvatureList.append(curvatureAlong[n])
 
                 # dx_ds3
                 d3 = [c * wallThickness * (relativeThicknessList[n3] if relativeThicknessList else 1.0/elementsCountThroughWall) for c in norm]

tests/test_bladder.py

@@ -75,10 +75,10 @@ def test_bladder1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 3.6740101958977296, delta=1.0E-8)
+        self.assertAlmostEqual(surfaceArea, 3.6692194413389085, delta=1.0E-8)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 0.02543636759208289, delta=1.0E-8)
+        self.assertAlmostEqual(volume, 0.025324264242304235, delta=1.0E-8)
         # result, flatSurfaceArea = flatSurfaceAreaField.evaluateReal(fieldcache, 1)
         # self.assertEqual(result, RESULT_OK)
         # self.assertAlmostEqual(flatSurfaceArea, 32905.65612644931, delta=1.0E-3)

tests/test_bladderurethra.py

@@ -88,10 +88,10 @@ def test_bladderurethra1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 4564.851396969593, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 4564.518506192725, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 2221.1973927759996, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 2218.8526070746825, delta=1.0E-6)
         result, flatSurfaceArea = flatSurfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
         self.assertAlmostEqual(flatSurfaceArea, 4087.7670057497376, delta=1.0E-3)

tests/test_cecum.py

@@ -70,7 +70,7 @@ def test_cecum1(self):
         self.assertTrue(coordinates.isValid())
         minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
         assertAlmostEqualList(self, minimums, [-49.01658984455258, -46.89686037622053, -2.343256155753525], 1.0E-6)
-        assertAlmostEqualList(self, maximums, [42.18085849205387, 54.902119877312636, 180.0], 1.0E-6)
+        assertAlmostEqualList(self, maximums, [42.18085849205387, 54.90211871346987, 180.0], 1.0E-6)
 
         with ChangeManager(fieldmodule):
             one = fieldmodule.createFieldConstant(1.0)
@@ -82,10 +82,10 @@ def test_cecum1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 65960.86557108756, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 65905.04907630144, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 127907.08806524028, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 127866.92887366761, delta=1.0E-6)
 
 
 if __name__ == "__main__":

tests/test_colon.py

@@ -164,10 +164,10 @@ def test_colon1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 174848.22676409548, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 174749.05868939584, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 313689.5754456567, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 314670.65237072564, delta=1.0E-6)
 
     def test_mousecolon1(self):
         """

tests/test_colonsegment.py

@@ -78,10 +78,10 @@ def test_humancolonsegment1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 21035.8818469729, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 21032.6788157990, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 39781.704358310606, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 39836.60239335828, delta=1.0E-6)
 
     def test_mousecolonsegment1(self):
         """

tests/test_esophagus.py

@@ -82,10 +82,10 @@ def test_esophagus1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 13994.064785386161, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 13952.301236699395, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 35763.04473815047, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 35523.4403218177, delta=1.0E-6)
 
         # check some annotationGroups:
         expectedSizes3d = {

tests/test_smallintestine.py

@@ -142,10 +142,10 @@ def test_smallintestine1(self):
         fieldcache = fieldmodule.createFieldcache()
         result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(surfaceArea, 143.8506801217898, delta=1.0E-6)
+        self.assertAlmostEqual(surfaceArea, 143.8501823770281, delta=1.0E-6)
         result, volume = volumeField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
-        self.assertAlmostEqual(volume, 13.608918623618687, delta=1.0E-6)
+        self.assertAlmostEqual(volume, 13.608455265457282, delta=1.0E-6)
         result, flatSurfaceArea = flatSurfaceAreaField.evaluateReal(fieldcache, 1)
         self.assertEqual(result, RESULT_OK)
         self.assertAlmostEqual(flatSurfaceArea, 144.42091907104523, delta=1.0E-3)