def test_fit_breast2d(self):
"""
Test 2D fit with curvature penalty requiring fibre field to be set.
"""
zinc_model_file = os.path.join(here, "resources", "breast_plate.exf")
zinc_data_file = os.path.join(here, "resources", "breast_data.exf")
fitter = Fitter(zinc_model_file, zinc_data_file)
fitter.setDiagnosticLevel(1)
fitter.load()
fit1 = FitterStepFit()
fitter.addFitterStep(fit1)
self.assertEqual(2, len(fitter.getFitterSteps()))
fit1.setGroupCurvaturePenalty(None, [100.0])
# can't use a curvature penalty without a fibre field
with self.assertRaises(AssertionError) as cm:
fit1.run()
self.assertEqual(
str(cm.exception),
"Must supply a fibre field to use strain/curvature penalties "
"with mesh dimension < coordinate components.")
# set the in-built zero fibres field
fieldmodule = fitter.getFieldmodule()
zeroFibreField = fieldmodule.findFieldByName("zero fibres")
self.assertTrue(zeroFibreField.isValid())
fitter.setFibreField(zeroFibreField)
fitter.load()
# check these now as different after re-load
fieldmodule = fitter.getFieldmodule()
coordinates = fitter.getModelCoordinatesField()
self.assertEqual(coordinates.getName(), "coordinates")
self.assertEqual(fitter.getDataCoordinatesField().getName(),
"data_coordinates")
fit1.run()
# check surface area of fitted coordinates
# Note name is only prefixes with "fitted " when written with Fitter.writeModel
surfaceAreaField = createFieldMeshIntegral(coordinates,
fitter.getMesh(2),
number_of_points=4)
valid = surfaceAreaField.isValid()
self.assertTrue(surfaceAreaField.isValid())
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 104501.36293993103, delta=1.0E-1)
def test_alignMarkersFitRegularData(self):
"""
Test automatic alignment of model and data using fiducial markers.
"""
zinc_model_file = os.path.join(here, "resources", "cube_to_sphere.exf")
zinc_data_file = os.path.join(here, "resources", "cube_to_sphere_data_regular.exf")
fitter = Fitter(zinc_model_file, zinc_data_file)
fitter.setDiagnosticLevel(1)
fitter.load()
coordinates = fitter.getModelCoordinatesField()
self.assertEqual(coordinates.getName(), "coordinates")
self.assertEqual(fitter.getDataCoordinatesField().getName(), "data_coordinates")
self.assertEqual(fitter.getMarkerGroup().getName(), "marker")
#fitter.getRegion().writeFile(os.path.join(here, "resources", "km_fitgeometry1.exf"))
fieldmodule = fitter.getFieldmodule()
surfaceAreaField = createFieldMeshIntegral(coordinates, fitter.getMesh(2), number_of_points=4)
volumeField = createFieldMeshIntegral(coordinates, fitter.getMesh(3), number_of_points=3)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 6.0, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 1.0, delta=1.0E-7)
align = FitterStepAlign(fitter)
self.assertTrue(align.isAlignMarkers())
align.setAlignMarkers(True)
align.run()
#fitter.getRegion().writeFile(os.path.join(here, "resources", "km_fitgeometry2.exf"))
rotation = align.getRotation()
scale = align.getScale()
translation = align.getTranslation()
assertAlmostEqualList(self, rotation, [ -0.25*math.pi, 0.0, 0.0 ], delta=1.0E-4)
self.assertAlmostEqual(scale, 0.8047378476539072, places=5)
assertAlmostEqualList(self, translation, [ -0.5690355950594247, 1.1068454682130484e-05, -0.4023689233125251 ], delta=1.0E-6)
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 3.885618020657802, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 0.5211506471189844, delta=1.0E-6)
fit1 = FitterStepFit(fitter)
fit1.setMarkerWeight(1.0)
fit1.setCurvaturePenaltyWeight(0.1)
fit1.setNumberOfIterations(3)
fit1.setUpdateReferenceState(True)
fit1.run()
#fitter.getRegion().writeFile(os.path.join(here, "resources", "km_fitgeometry3.exf"))
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 3.1892231780263853, delta=1.0E-4)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 0.5276229458448985, delta=1.0E-4)
# test json serialisation
s = fitter.encodeSettingsJSON()
fitter2 = Fitter(zinc_model_file, zinc_data_file)
fitter2.decodeSettingsJSON(s, decodeJSONFitterSteps)
fitterSteps = fitter2.getFitterSteps()
self.assertEqual(2, len(fitterSteps))
self.assertTrue(isinstance(fitterSteps[0], FitterStepAlign))
self.assertTrue(isinstance(fitterSteps[1], FitterStepFit))
#fitter2.load()
#for fitterStep in fitterSteps:
# fitterStep.run()
s2 = fitter.encodeSettingsJSON()
self.assertEqual(s, s2)
def test_fitRegularDataGroupWeight(self):
"""
Test automatic alignment of model and data using fiducial markers.
"""
zinc_model_file = os.path.join(here, "resources", "cube_to_sphere.exf")
zinc_data_file = os.path.join(here, "resources",
"cube_to_sphere_data_regular.exf")
fitter = Fitter(zinc_model_file, zinc_data_file)
self.assertEqual(1, len(fitter.getFitterSteps())
) # there is always an initial FitterStepConfig
fitter.setDiagnosticLevel(1)
fitter.load()
coordinates = fitter.getModelCoordinatesField()
self.assertEqual(coordinates.getName(), "coordinates")
fieldmodule = fitter.getFieldmodule()
surfaceAreaField = createFieldMeshIntegral(coordinates,
fitter.getMesh(2),
number_of_points=4)
volumeField = createFieldMeshIntegral(coordinates,
fitter.getMesh(3),
number_of_points=3)
fieldcache = fieldmodule.createFieldcache()
align = FitterStepAlign()
fitter.addFitterStep(align)
self.assertEqual(2, len(fitter.getFitterSteps()))
self.assertTrue(align.setAlignMarkers(True))
align.run()
fit1 = FitterStepFit()
fitter.addFitterStep(fit1)
self.assertEqual(3, len(fitter.getFitterSteps()))
fit1.setGroupDataWeight("bottom", 0.5)
fit1.setGroupDataWeight("sides", 0.1)
groupNames = fit1.getGroupSettingsNames()
self.assertEqual(2, len(groupNames))
self.assertEqual((0.5, True, False), fit1.getGroupDataWeight("bottom"))
self.assertEqual((0.1, True, False), fit1.getGroupDataWeight("sides"))
fit1.setCurvaturePenaltyWeight(0.01)
fit1.setNumberOfIterations(3)
fit1.setUpdateReferenceState(True)
fit1.run()
dataWeightField = fieldmodule.findFieldByName(
"data_weight").castFiniteElement()
self.assertTrue(dataWeightField.isValid())
groupData = {
"bottom": (72, 0.5),
"sides": (144, 0.1),
"top": (72, 1.0)
}
mesh2d = fitter.getMesh(2)
for groupName in groupData.keys():
expectedSize, expectedWeight = groupData[groupName]
group = fieldmodule.findFieldByName(groupName).castGroup()
dataGroup = fitter.getGroupDataProjectionNodesetGroup(group)
size = dataGroup.getSize()
self.assertEqual(size, expectedSize)
dataIterator = dataGroup.createNodeiterator()
node = dataIterator.next()
while node.isValid():
fieldcache.setNode(node)
result, weight = dataWeightField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(weight, expectedWeight, delta=1.0E-10)
node = dataIterator.next()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 3.2298953613027956, delta=1.0E-4)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 0.5156233237703589, delta=1.0E-4)
def test_alignGroupsFitEllipsoidRegularData(self):
"""
Test automatic alignment of model and data using groups & fit two cubes model to ellipsoid data.
"""
zinc_model_file = os.path.join(here, "resources",
"two_cubes_hermite_nocross_groups.exf")
zinc_data_file = os.path.join(here, "resources",
"two_cubes_ellipsoid_data_regular.exf")
fitter = Fitter(zinc_model_file, zinc_data_file)
fitter.setDiagnosticLevel(1)
fitter.load()
coordinates = fitter.getModelCoordinatesField()
self.assertEqual(coordinates.getName(), "coordinates")
self.assertEqual(fitter.getDataCoordinatesField().getName(),
"data_coordinates")
fieldmodule = fitter.getFieldmodule()
# surface area includes interior surface in this case
surfaceAreaField = createFieldMeshIntegral(coordinates,
fitter.getMesh(2),
number_of_points=4)
volumeField = createFieldMeshIntegral(coordinates,
fitter.getMesh(3),
number_of_points=3)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 11.0, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 2.0, delta=1.0E-6)
activeNodeset = fitter.getActiveDataNodesetGroup()
align = FitterStepAlign()
fitter.addFitterStep(align)
self.assertEqual(2, len(fitter.getFitterSteps()))
self.assertTrue(align.setAlignGroups(True))
self.assertTrue(align.isAlignGroups())
align.run()
rotation = align.getRotation()
scale = align.getScale()
translation = align.getTranslation()
assertAlmostEqualList(self, rotation, [0.0, 0.0, 0.0], delta=1.0E-5)
self.assertAlmostEqual(scale, 1.040599599095245, places=5)
assertAlmostEqualList(
self,
translation,
[-1.0405995643008867, -0.5202997843515198, -0.5202997827678563],
delta=1.0E-6)
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 11.0 * scale * scale, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume,
2.0 * scale * scale * scale,
delta=1.0E-6)
fit1 = FitterStepFit()
fitter.addFitterStep(fit1)
self.assertEqual(3, len(fitter.getFitterSteps()))
strainPenalty, locallySet, inheritable = fit1.getGroupStrainPenalty(
None)
assertAlmostEqualList(self, strainPenalty, [0.0], delta=1.0E-7)
self.assertFalse(locallySet)
self.assertFalse(inheritable)
curvaturePenalty, locallySet, inheritable = fit1.getGroupCurvaturePenalty(
None)
assertAlmostEqualList(self, curvaturePenalty, [0.0], delta=1.0E-7)
self.assertFalse(locallySet)
self.assertFalse(inheritable)
fit1.setGroupStrainPenalty(None, [0.1])
strainPenalty, locallySet, inheritable = fit1.getGroupStrainPenalty(
None)
assertAlmostEqualList(self, strainPenalty, [0.1], delta=1.0E-7)
self.assertTrue(locallySet)
self.assertFalse(inheritable)
fit1.setGroupCurvaturePenalty(None, [0.01])
curvaturePenalty, locallySet, inheritable = fit1.getGroupCurvaturePenalty(
None)
assertAlmostEqualList(self, curvaturePenalty, [0.01], delta=1.0E-7)
self.assertTrue(locallySet)
self.assertFalse(inheritable)
# test specifying number of components:
curvaturePenalty, locallySet, inheritable = fit1.getGroupCurvaturePenalty(
None, count=5)
assertAlmostEqualList(self,
curvaturePenalty, [0.01, 0.01, 0.01, 0.01, 0.01],
delta=1.0E-7)
# group "two" strain penalty will initially fall back to default value
strainPenalty, locallySet, inheritable = fit1.getGroupStrainPenalty(
"two")
assertAlmostEqualList(self, strainPenalty, [0.1], delta=1.0E-7)
self.assertFalse(locallySet)
self.assertFalse(inheritable)
fit1.setGroupStrainPenalty(
"two", [0.1, 0.1, 0.1, 0.1, 20.0, 0.1, 0.1, 20.0, 2.0])
strainPenalty, locallySet, inheritable = fit1.getGroupStrainPenalty(
"two")
assertAlmostEqualList(self,
strainPenalty,
[0.1, 0.1, 0.1, 0.1, 20.0, 0.1, 0.1, 20.0, 2.0],
delta=1.0E-7)
self.assertTrue(locallySet)
self.assertFalse(inheritable)
fit1.setNumberOfIterations(1)
fit1.run()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 11.097773862300704, delta=1.0E-4)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 2.323461787566051, delta=1.0E-4)
# test fibre orientation field
fitter.load()
fieldmodule = fitter.getFieldmodule()
self.assertEqual(None, fitter.getFibreField())
fibreField = fieldmodule.createFieldConstant(
[0.0, 0.0, 0.25 * math.pi])
fibreField.setName("custom fibres")
fibreField.setManaged(True)
fitter.setFibreField(fibreField)
self.assertEqual(fibreField, fitter.getFibreField())
coordinates = fitter.getModelCoordinatesField()
align.run()
fit1.run()
# get end node coordinate to prove twist
nodeExpectedCoordinates = {
3: [0.8487623099139301, -0.5012613734076182, -0.5306482017126274],
6: [0.8487623092159226, 0.2617063557585618, -0.5464896371028911],
9: [0.8487623062422882, -0.2617063537282271, 0.5464896401724635],
12: [0.8487623124370356, 0.5012613792923117, 0.5306482045212996]
}
fieldcache = fieldmodule.createFieldcache()
nodes = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
for nodeIdentifier, expectedCoordinates in nodeExpectedCoordinates.items(
):
node = nodes.findNodeByIdentifier(nodeIdentifier)
self.assertEqual(RESULT_OK, fieldcache.setNode(node))
result, x = coordinates.getNodeParameters(fieldcache, -1,
Node.VALUE_LABEL_VALUE,
1, 3)
self.assertEqual(RESULT_OK, result)
assertAlmostEqualList(self, x, expectedCoordinates, delta=1.0E-6)
# test inheritance and override of penalties
fit2 = FitterStepFit()
fitter.addFitterStep(fit2)
self.assertEqual(4, len(fitter.getFitterSteps()))
strainPenalty, locallySet, inheritable = fit2.getGroupStrainPenalty(
None)
assertAlmostEqualList(self, strainPenalty, [0.1], delta=1.0E-7)
self.assertFalse(locallySet)
self.assertTrue(inheritable)
curvaturePenalty, locallySet, inheritable = fit2.getGroupCurvaturePenalty(
None)
assertAlmostEqualList(self, curvaturePenalty, [0.01], delta=1.0E-7)
self.assertFalse(locallySet)
self.assertTrue(inheritable)
fit2.setGroupCurvaturePenalty(None, None)
curvaturePenalty, locallySet, inheritable = fit2.getGroupCurvaturePenalty(
None)
assertAlmostEqualList(self, curvaturePenalty, [0.0], delta=1.0E-7)
self.assertTrue(locallySet is None)
self.assertTrue(inheritable)
strainPenalty, locallySet, inheritable = fit2.getGroupStrainPenalty(
"two")
assertAlmostEqualList(self,
strainPenalty,
[0.1, 0.1, 0.1, 0.1, 20.0, 0.1, 0.1, 20.0, 2.0],
delta=1.0E-7)
self.assertFalse(locallySet)
self.assertTrue(inheritable)
fit2.setGroupStrainPenalty("two", [0.5, 0.9, 0.2])
strainPenalty, locallySet, inheritable = fit2.getGroupStrainPenalty(
"two", count=9)
assertAlmostEqualList(self,
strainPenalty,
[0.5, 0.9, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2],
delta=1.0E-7)
self.assertTrue(locallySet)
self.assertTrue(inheritable)
# test json serialisation
s = fitter.encodeSettingsJSON()
fitter2 = Fitter(zinc_model_file, zinc_data_file)
fitter2.decodeSettingsJSON(s, decodeJSONFitterSteps)
fitterSteps = fitter2.getFitterSteps()
self.assertEqual(4, len(fitterSteps))
self.assertTrue(isinstance(fitterSteps[0], FitterStepConfig))
self.assertTrue(isinstance(fitterSteps[1], FitterStepAlign))
self.assertTrue(isinstance(fitterSteps[2], FitterStepFit))
self.assertTrue(isinstance(fitterSteps[3], FitterStepFit))
fit1 = fitterSteps[2]
strainPenalty, locallySet, inheritable = fit1.getGroupStrainPenalty(
"two")
assertAlmostEqualList(self,
strainPenalty,
[0.1, 0.1, 0.1, 0.1, 20.0, 0.1, 0.1, 20.0, 2.0],
delta=1.0E-7)
self.assertTrue(locallySet)
self.assertFalse(inheritable)
fit2 = fitterSteps[3]
curvaturePenalty, locallySet, inheritable = fit2.getGroupCurvaturePenalty(
None)
assertAlmostEqualList(self, curvaturePenalty, [0.0], delta=1.0E-7)
self.assertTrue(locallySet is None)
self.assertTrue(inheritable)
strainPenalty, locallySet, inheritable = fit2.getGroupStrainPenalty(
"two")
assertAlmostEqualList(self,
strainPenalty, [0.5, 0.9, 0.2],
delta=1.0E-7)
self.assertTrue(locallySet)
self.assertTrue(inheritable)
s2 = fitter.encodeSettingsJSON()
self.assertEqual(s, s2)
def test_alignMarkersFitRegularData(self):
"""
Test automatic alignment of model and data using fiducial markers.
"""
zinc_model_file = os.path.join(here, "resources", "cube_to_sphere.exf")
zinc_data_file = os.path.join(here, "resources",
"cube_to_sphere_data_regular.exf")
fitter = Fitter(zinc_model_file, zinc_data_file)
self.assertEqual(1, len(fitter.getFitterSteps())
) # there is always an initial FitterStepConfig
fitter.setDiagnosticLevel(1)
fitter.load()
dataScale = fitter.getDataScale()
self.assertAlmostEqual(dataScale, 1.0, delta=1.0E-7)
coordinates = fitter.getModelCoordinatesField()
self.assertEqual(coordinates.getName(), "coordinates")
self.assertEqual(fitter.getDataCoordinatesField().getName(),
"data_coordinates")
self.assertEqual(fitter.getMarkerGroup().getName(), "marker")
# fitter.getRegion().writeFile(os.path.join(here, "resources", "km_fitgeometry1.exf"))
fieldmodule = fitter.getFieldmodule()
surfaceAreaField = createFieldMeshIntegral(coordinates,
fitter.getMesh(2),
number_of_points=4)
volumeField = createFieldMeshIntegral(coordinates,
fitter.getMesh(3),
number_of_points=3)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 6.0, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 1.0, delta=1.0E-7)
activeNodeset = fitter.getActiveDataNodesetGroup()
self.assertEqual(292, activeNodeset.getSize())
groupSizes = {"bottom": 72, "sides": 144, "top": 72, "marker": 4}
for groupName, count in groupSizes.items():
self.assertEqual(
count,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName(groupName)))
align = FitterStepAlign()
fitter.addFitterStep(align)
self.assertEqual(2, len(fitter.getFitterSteps()))
self.assertTrue(align.setAlignMarkers(True))
self.assertTrue(align.isAlignMarkers())
align.run()
# fitter.getRegion().writeFile(os.path.join(here, "resources", "km_fitgeometry2.exf"))
rotation = align.getRotation()
scale = align.getScale()
translation = align.getTranslation()
assertAlmostEqualList(self,
rotation, [-0.25 * math.pi, 0.0, 0.0],
delta=1.0E-4)
self.assertAlmostEqual(scale, 0.8047378476539072, places=5)
assertAlmostEqualList(
self,
translation,
[-0.5690355950594247, 1.1068454682130484e-05, -0.4023689233125251],
delta=1.0E-6)
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 3.885618020657802, delta=1.0E-6)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 0.5211506471189844, delta=1.0E-6)
fit1 = FitterStepFit()
fitter.addFitterStep(fit1)
self.assertEqual(3, len(fitter.getFitterSteps()))
fit1.setGroupDataWeight("marker", 1.0)
fit1.setGroupCurvaturePenalty(None, [0.01])
fit1.setNumberOfIterations(3)
fit1.setUpdateReferenceState(True)
fit1.run()
# fitter.getRegion().writeFile(os.path.join(here, "resources", "km_fitgeometry3.exf"))
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 3.18921662820759, delta=1.0E-4)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 0.5276212500499845, delta=1.0E-4)
# test json serialisation
s = fitter.encodeSettingsJSON()
fitter2 = Fitter(zinc_model_file, zinc_data_file)
fitter2.decodeSettingsJSON(s, decodeJSONFitterSteps)
fitterSteps = fitter2.getFitterSteps()
self.assertEqual(3, len(fitterSteps))
self.assertTrue(isinstance(fitterSteps[0], FitterStepConfig))
self.assertTrue(isinstance(fitterSteps[1], FitterStepAlign))
self.assertTrue(isinstance(fitterSteps[2], FitterStepFit))
# fitter2.load()
# for fitterStep in fitterSteps:
# fitterStep.run()
s2 = fitter.encodeSettingsJSON()
self.assertEqual(s, s2)