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 decodeJSONFitterSteps(fitter: Fitter, dct):
"""
Function for passing as decoder to Fitter.decodeSettingsJSON().
Constructs scaffold objects from their JSON object encoding.
Used as object_hook argument to json.loads as a lambda function
to pass fitter:
lambda dct: decodeJSONFitterSteps(fitter, dct)
:param fitter: Owning Fitter object for new FitterSteps.
"""
for FitterStepType in [FitterStepAlign, FitterStepConfig, FitterStepFit]:
if FitterStepType.getJsonTypeId() in dct:
if (FitterStepType is FitterStepConfig) and (len(
fitter.getFitterSteps()) == 1):
fitterStep = fitter.getInitialFitterStepConfig()
else:
fitterStep = FitterStepType()
fitter.addFitterStep(fitterStep)
fitterStep.decodeSettingsJSONDict(dct)
return fitterStep
return dct
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_preAlignment(self):
"""
Test prealignment step to ensure models at different translation, scale and rotation all return close
to same aligned model.
"""
zinc_model_file = os.path.join(here, "resources", "cube_to_sphere.exf")
zinc_data_file = os.path.join(here, "resources",
"cube_to_sphere_data_random.exf")
fitter = Fitter(zinc_model_file, zinc_data_file)
self.assertEqual(1, len(fitter.getFitterSteps()))
fitter.setDiagnosticLevel(1)
# Rotation, scale, translation
transformationList = [
[[0.0, 0.0, 0.0], 1.0, [0.0, 0.0, 0.0]],
[[math.pi * 20 / 180, 0.0, 0.0], 1.0, [0.0, 0.0, 0.0]],
[[math.pi * 135 / 180, 0.0, 0.0], 1.0, [0.0, 0.0, 0.0]],
[[math.pi * 250 / 180, math.pi * -45 / 180, 0.0], 1.0,
[0.0, 0.0, 0.0]],
[[math.pi * 45 / 180, math.pi * 45 / 180, math.pi * 45 / 180], 1.0,
[0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0], 0.05, [0.0, 0.0, 0.0]],
[[math.pi * 70 / 180, math.pi * 10 / 180, math.pi * -300 / 180],
0.2, [0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0], 1.0, [15.0, 15.0, 15.0]],
[[0.0, 0.0, 0.0], 20.0, [50.0, 0.0, 10.0]],
[[math.pi * 90 / 180, math.pi * 200 / 180, math.pi * 5 / 180], 1.0,
[-10.0, -20.0, 100.0]],
[[math.pi * -45 / 180, math.pi * 120 / 180, math.pi * 10 / 180],
500.0, [100.0, 100.0, 100.0]]
]
expectedAlignedNodes = [
[
-0.5690355951820659, 1.1070979208244695e-05,
-0.40236892417087866
],
[
-1.1077595833408616e-05, -0.5690355904946871,
-0.4023689227447479
],
[1.1066291829453512e-05, 0.5690355885654408, -0.4023689255966489],
[0.569035583878062, -1.1072908454692232e-05, -0.4023689241705181],
[-0.5690355951822816, 1.1072995806778281e-05, 0.4023689241678401],
[-1.107759604912495e-05, -0.5690355884780887, 0.40236892559397086],
[1.10662916138482e-05, 0.5690355905820392, 0.4023689227420698],
[0.5690355838778464, -1.1070891856158648e-05, 0.4023689241682007]
]
align = FitterStepAlign()
fitter.addFitterStep(align)
self.assertTrue(align.setAlignMarkers(True))
self.assertTrue(align.isAlignMarkers())
for i in range(len(transformationList)):
fitter.load()
fieldmodule = fitter.getFieldmodule()
fieldcache = fieldmodule.createFieldcache()
modelCoordinates = fitter.getModelCoordinatesField()
rotation = transformationList[i][0]
scale = transformationList[i][1]
translation = transformationList[i][2]
modelCoordinatesTransformed = createFieldsTransformations(
modelCoordinates, rotation, scale, translation)[0]
fieldassignment = modelCoordinates.createFieldassignment(
modelCoordinatesTransformed)
fieldassignment.assign()
align.run()
nodeset = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
for nodeIdentifier in range(1, 9):
node = nodeset.findNodeByIdentifier(nodeIdentifier)
fieldcache.setNode(node)
result, x = modelCoordinates.getNodeParameters(
fieldcache, -1, Node.VALUE_LABEL_VALUE, 1, 3)
assertAlmostEqualList(self,
x,
expectedAlignedNodes[nodeIdentifier - 1],
delta=1.0E-3)
def test_groupSettings(self):
"""
Test per-group settings, and inheritance from previous
"""
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)
config1 = fitter.getInitialFitterStepConfig()
groupNames = config1.getGroupSettingsNames()
self.assertEqual(0, len(groupNames))
self.assertEqual((1.0, False, False),
config1.getGroupDataProportion("sides"))
config1.setGroupDataProportion("sides", -0.1)
groupNames = config1.getGroupSettingsNames()
self.assertEqual(1, len(groupNames))
self.assertEqual((0.0, True, False),
config1.getGroupDataProportion("sides"))
config1.setGroupDataProportion("sides", 0.25)
config1.setGroupDataProportion("sides", "A")
config1.setGroupDataProportion("top", 0.4)
groupNames = config1.getGroupSettingsNames()
self.assertEqual(2, len(groupNames))
self.assertTrue("sides" in groupNames)
self.assertTrue("top" in groupNames)
self.assertEqual((0.25, True, False),
config1.getGroupDataProportion("sides"))
self.assertEqual((0.4, True, False),
config1.getGroupDataProportion("top"))
self.assertEqual((1.0, False, False),
config1.getGroupDataProportion("bottom"))
config1.setGroupDataProportion("bottom", 0.1)
self.assertEqual((0.1, True, False),
config1.getGroupDataProportion("bottom"))
groupNames = config1.getGroupSettingsNames()
self.assertEqual(3, len(groupNames))
# setting a non-inheriting value to None clears it:
config1.setGroupDataProportion("bottom", None)
self.assertEqual((1.0, False, False),
config1.getGroupDataProportion("bottom"))
groupNames = config1.getGroupSettingsNames()
self.assertEqual(2, len(groupNames))
config1.setGroupDataProportion("bottom", 0.12)
self.assertEqual((0.12, True, False),
config1.getGroupDataProportion("bottom"))
groupNames = config1.getGroupSettingsNames()
self.assertEqual(3, len(groupNames))
config1.clearGroupDataProportion("bottom")
self.assertEqual((1.0, False, False),
config1.getGroupDataProportion("bottom"))
groupNames = config1.getGroupSettingsNames()
self.assertEqual(2, len(groupNames))
self.assertTrue("sides" in groupNames)
self.assertTrue("top" in groupNames)
fitter.load()
activeNodeset = fitter.getActiveDataNodesetGroup()
self.assertEqual(141, activeNodeset.getSize())
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("bottom")))
self.assertEqual(
36,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("sides")))
self.assertEqual(
29,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("top")))
self.assertEqual(
4,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("marker")))
# test override and inherit
config2 = FitterStepConfig()
fitter.addFitterStep(config2)
config2.setGroupDataProportion("top", None)
groupNames = config2.getGroupSettingsNames()
self.assertEqual(1, len(groupNames))
self.assertTrue("top" in groupNames)
self.assertEqual((0.25, False, True),
config2.getGroupDataProportion("sides"))
# test that the reset proportion has setLocally None
self.assertEqual((1.0, None, True),
config2.getGroupDataProportion("top"))
config2.run()
activeNodeset = fitter.getActiveDataNodesetGroup()
self.assertEqual(184, activeNodeset.getSize())
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("bottom")))
self.assertEqual(
36,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("sides")))
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("top")))
self.assertEqual(
4,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("marker")))
# test inherit through 2 previous configs and cancel/None in config2
config3 = FitterStepConfig()
fitter.addFitterStep(config3)
groupNames = config3.getGroupSettingsNames()
self.assertEqual(0, len(groupNames))
self.assertEqual((0.25, False, True),
config3.getGroupDataProportion("sides"))
self.assertEqual((1.0, False, False),
config3.getGroupDataProportion("top"))
config3.run()
activeNodeset = fitter.getActiveDataNodesetGroup()
self.assertEqual(184, activeNodeset.getSize())
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("bottom")))
self.assertEqual(
36,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("sides")))
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("top")))
self.assertEqual(
4,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("marker")))
del config1
del config2
del config3
# 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))
config1, config2, config3 = fitterSteps
self.assertTrue(isinstance(config1, FitterStepConfig))
self.assertTrue(isinstance(config2, FitterStepConfig))
self.assertTrue(isinstance(config3, FitterStepConfig))
groupNames = config1.getGroupSettingsNames()
self.assertEqual(2, len(groupNames))
self.assertTrue("sides" in groupNames)
self.assertTrue("top" in groupNames)
self.assertEqual((0.25, True, False),
config1.getGroupDataProportion("sides"))
self.assertEqual((0.4, True, False),
config1.getGroupDataProportion("top"))
self.assertEqual((1.0, False, False),
config1.getGroupDataProportion("bottom"))
groupNames = config2.getGroupSettingsNames()
self.assertEqual(1, len(groupNames))
self.assertTrue("top" in groupNames)
self.assertEqual((0.25, False, True),
config2.getGroupDataProportion("sides"))
self.assertEqual((1.0, None, True),
config2.getGroupDataProportion("top"))
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)
class GeometricFitModel(object):
"""
Geometric fit model adding visualisations to github.com/ABI-Software/scaffoldfitter
"""
def __init__(self, inputZincModelFile, inputZincDataFile, location,
identifier):
"""
:param location: Path to folder for mapclient step name.
"""
self._fitter = Fitter(inputZincModelFile, inputZincDataFile)
#self._fitter.setDiagnosticLevel(1)
self._location = os.path.join(location, identifier)
self._identifier = identifier
self._initGraphicsModules()
self._settings = {
"displayAxes": True,
"displayMarkerDataPoints": True,
"displayMarkerDataNames": False,
"displayMarkerDataProjections": True,
"displayMarkerPoints": True,
"displayMarkerNames": False,
"displayDataPoints": True,
"displayDataProjections": True,
"displayDataProjectionPoints": True,
"displayNodePoints": False,
"displayNodeNumbers": False,
"displayNodeDerivatives": False,
"displayNodeDerivativeLabels": nodeDerivativeLabels[0:3],
"displayElementNumbers": False,
"displayElementAxes": False,
"displayLines": True,
"displayLinesExterior": False,
"displaySurfaces": True,
"displaySurfacesExterior": True,
"displaySurfacesTranslucent": True,
"displaySurfacesWireframe": False
}
self._loadSettings()
self._fitter.load()
def _initGraphicsModules(self):
context = self._fitter.getContext()
self._materialmodule = context.getMaterialmodule()
with ChangeManager(self._materialmodule):
self._materialmodule.defineStandardMaterials()
solid_blue = self._materialmodule.createMaterial()
solid_blue.setName("solid_blue")
solid_blue.setManaged(True)
solid_blue.setAttributeReal3(Material.ATTRIBUTE_AMBIENT,
[0.0, 0.2, 0.6])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE,
[0.0, 0.7, 1.0])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.1, 0.1, 0.1])
solid_blue.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
trans_blue = self._materialmodule.createMaterial()
trans_blue.setName("trans_blue")
trans_blue.setManaged(True)
trans_blue.setAttributeReal3(Material.ATTRIBUTE_AMBIENT,
[0.0, 0.2, 0.6])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE,
[0.0, 0.7, 1.0])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.1, 0.1, 0.1])
trans_blue.setAttributeReal(Material.ATTRIBUTE_ALPHA, 0.3)
trans_blue.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
glyphmodule = context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
tessellationmodule = context.getTessellationmodule()
defaultTessellation = tessellationmodule.getDefaultTessellation()
defaultTessellation.setRefinementFactors([12])
def _getFitSettingsFileName(self):
return self._location + "-settings.json"
def _getDisplaySettingsFileName(self):
return self._location + "-display-settings.json"
def _loadSettings(self):
try:
with open(self._getFitSettingsFileName(), "r") as f:
self._fitter.decodeSettingsJSON(f.read(),
decodeJSONFitterSteps)
except:
pass
try:
with open(self._getDisplaySettingsFileName(), "r") as f:
savedSettings = json.loads(f.read())
self._settings.update(savedSettings)
except:
pass
def _saveSettings(self):
with open(self._getFitSettingsFileName(), "w") as f:
f.write(self._fitter.encodeSettingsJSON())
with open(self._getDisplaySettingsFileName(), "w") as f:
f.write(json.dumps(self._settings, sort_keys=False, indent=4))
def getOutputModelFileName(self):
return self._location + ".exf"
def done(self):
self._saveSettings()
fitterSteps = self._fitter.getFitterSteps()
for fitterStep in fitterSteps:
if not fitterStep.hasRun():
fitterStep.run()
self._fitter.writeModel(self.getOutputModelFileName())
def getIdentifier(self):
return self._identifier
def getContext(self):
return self._fitter.getContext()
def getFitter(self):
return self._fitter
def getRegion(self):
return self._fitter.getRegion()
def getScene(self):
return self._fitter.getRegion().getScene()
def _getVisibility(self, graphicsName):
return self._settings[graphicsName]
def _setVisibility(self, graphicsName, show):
self._settings[graphicsName] = show
graphics = self.getScene().findGraphicsByName(graphicsName)
graphics.setVisibilityFlag(show)
def isDisplayAxes(self):
return self._getVisibility("displayAxes")
def setDisplayAxes(self, show):
self._setVisibility("displayAxes", show)
def isDisplayElementNumbers(self):
return self._getVisibility("displayElementNumbers")
def setDisplayElementNumbers(self, show):
self._setVisibility("displayElementNumbers", show)
def isDisplayLines(self):
return self._getVisibility("displayLines")
def setDisplayLines(self, show):
self._setVisibility("displayLines", show)
def isDisplayLinesExterior(self):
return self._settings["displayLinesExterior"]
def setDisplayLinesExterior(self, isExterior):
self._settings["displayLinesExterior"] = isExterior
lines = self.getScene().findGraphicsByName("displayLines")
lines.setExterior(self.isDisplayLinesExterior())
def isDisplayNodeDerivatives(self):
return self._getVisibility("displayNodeDerivatives")
def setDisplayNodeDerivatives(self, show):
self._settings["displayNodeDerivatives"] = show
scene = self.getScene()
for nodeDerivativeLabel in nodeDerivativeLabels:
graphics = scene.findGraphicsByName("displayNodeDerivatives" +
nodeDerivativeLabel)
graphics.setVisibilityFlag(
show
and self.isDisplayNodeDerivativeLabels(nodeDerivativeLabel))
def isDisplayNodeDerivativeLabels(self, nodeDerivativeLabel):
"""
:param nodeDerivativeLabel: Label from nodeDerivativeLabels ("D1", "D2" ...)
"""
return nodeDerivativeLabel in self._settings[
"displayNodeDerivativeLabels"]
def setDisplayNodeDerivativeLabels(self, nodeDerivativeLabel, show):
"""
:param nodeDerivativeLabel: Label from nodeDerivativeLabels ("D1", "D2" ...)
"""
shown = nodeDerivativeLabel in self._settings[
"displayNodeDerivativeLabels"]
if show:
if not shown:
# keep in same order as nodeDerivativeLabels
nodeDerivativeLabels = []
for label in nodeDerivativeLabels:
if (label == nodeDerivativeLabel
) or self.isDisplayNodeDerivativeLabels(label):
nodeDerivativeLabels.append(label)
self._settings[
"displayNodeDerivativeLabels"] = nodeDerivativeLabels
else:
if shown:
self._settings["displayNodeDerivativeLabels"].remove(
nodeDerivativeLabel)
graphics = self.getScene().findGraphicsByName(
"displayNodeDerivatives" + nodeDerivativeLabel)
graphics.setVisibilityFlag(show and self.isDisplayNodeDerivatives())
def isDisplayMarkerDataPoints(self):
return self._getVisibility("displayMarkerDataPoints")
def setDisplayMarkerDataPoints(self, show):
self._setVisibility("displayMarkerDataPoints", show)
def isDisplayMarkerDataNames(self):
return self._getVisibility("displayMarkerDataNames")
def setDisplayMarkerDataNames(self, show):
self._setVisibility("displayMarkerDataNames", show)
def isDisplayMarkerDataProjections(self):
return self._getVisibility("displayMarkerDataProjections")
def setDisplayMarkerDataProjections(self, show):
self._setVisibility("displayMarkerDataProjections", show)
def isDisplayMarkerPoints(self):
return self._getVisibility("displayMarkerPoints")
def setDisplayMarkerPoints(self, show):
self._setVisibility("displayMarkerPoints", show)
def isDisplayMarkerNames(self):
return self._getVisibility("displayMarkerNames")
def setDisplayMarkerNames(self, show):
self._setVisibility("displayMarkerNames", show)
def isDisplayDataPoints(self):
return self._getVisibility("displayDataPoints")
def setDisplayDataPoints(self, show):
self._setVisibility("displayDataPoints", show)
def isDisplayDataProjections(self):
return self._getVisibility("displayDataProjections")
def setDisplayDataProjections(self, show):
self._setVisibility("displayDataProjections", show)
def isDisplayDataProjectionPoints(self):
return self._getVisibility("displayDataProjectionPoints")
def setDisplayDataProjectionPoints(self, show):
self._setVisibility("displayDataProjectionPoints", show)
def isDisplayNodeNumbers(self):
return self._getVisibility("displayNodeNumbers")
def setDisplayNodeNumbers(self, show):
self._setVisibility("displayNodeNumbers", show)
def isDisplayNodePoints(self):
return self._getVisibility("displayNodePoints")
def setDisplayNodePoints(self, show):
self._setVisibility("displayNodePoints", show)
def isDisplaySurfaces(self):
return self._getVisibility("displaySurfaces")
def setDisplaySurfaces(self, show):
self._setVisibility("displaySurfaces", show)
def isDisplaySurfacesExterior(self):
return self._settings["displaySurfacesExterior"]
def setDisplaySurfacesExterior(self, isExterior):
self._settings["displaySurfacesExterior"] = isExterior
surfaces = self.getScene().findGraphicsByName("displaySurfaces")
surfaces.setExterior(self.isDisplaySurfacesExterior() if (
self._fitter.getHighestDimensionMesh().getDimension() == 3
) else False)
def isDisplaySurfacesTranslucent(self):
return self._settings["displaySurfacesTranslucent"]
def setDisplaySurfacesTranslucent(self, isTranslucent):
self._settings["displaySurfacesTranslucent"] = isTranslucent
surfaces = self.getScene().findGraphicsByName("displaySurfaces")
surfacesMaterial = self._materialmodule.findMaterialByName(
"trans_blue" if isTranslucent else "solid_blue")
surfaces.setMaterial(surfacesMaterial)
def isDisplaySurfacesWireframe(self):
return self._settings["displaySurfacesWireframe"]
def setDisplaySurfacesWireframe(self, isWireframe):
self._settings["displaySurfacesWireframe"] = isWireframe
surfaces = self.getScene().findGraphicsByName("displaySurfaces")
surfaces.setRenderPolygonMode(
Graphics.RENDER_POLYGON_MODE_WIREFRAME
if isWireframe else Graphics.RENDER_POLYGON_MODE_SHADED)
def isDisplayElementAxes(self):
return self._getVisibility("displayElementAxes")
def setDisplayElementAxes(self, show):
self._setVisibility("displayElementAxes", show)
def needPerturbLines(self):
"""
Return if solid surfaces are drawn with lines, requiring perturb lines to be activated.
"""
region = self.getRegion()
if region is None:
return False
mesh2d = region.getFieldmodule().findMeshByDimension(2)
if mesh2d.getSize() == 0:
return False
return self.isDisplayLines() and self.isDisplaySurfaces(
) and not self.isDisplaySurfacesTranslucent()
def createGraphics(self):
fieldmodule = self._fitter.getFieldmodule()
mesh = self._fitter.getHighestDimensionMesh()
meshDimension = mesh.getDimension()
modelCoordinates = self._fitter.getModelCoordinatesField()
componentsCount = modelCoordinates.getNumberOfComponents()
# prepare fields and calculate axis and glyph scaling
with ChangeManager(fieldmodule):
# fields in same order as nodeDerivativeLabels
nodeDerivativeFields = [
fieldmodule.createFieldNodeValue(modelCoordinates, derivative,
1)
for derivative in [
Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D2_DS1DS3, Node.VALUE_LABEL_D2_DS2DS3,
Node.VALUE_LABEL_D3_DS1DS2DS3
]
]
elementDerivativesField = fieldmodule.createFieldConcatenate([
fieldmodule.createFieldDerivative(modelCoordinates, d + 1)
for d in range(meshDimension)
])
cmiss_number = fieldmodule.findFieldByName("cmiss_number")
markerNodeGroup, markerLocation, markerCoordinates, markerName = self._fitter.getMarkerModelFields(
)
# get sizing for axes
axesScale = 1.0
nodes = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
minX, maxX = evaluateFieldNodesetRange(modelCoordinates, nodes)
if componentsCount == 1:
maxRange = maxX - minX
else:
maxRange = maxX[0] - minX[0]
for c in range(1, componentsCount):
maxRange = max(maxRange, maxX[c] - minX[c])
if maxRange > 0.0:
while axesScale * 10.0 < maxRange:
axesScale *= 10.0
while axesScale * 0.1 > maxRange:
axesScale *= 0.1
# fixed width glyph size is based on average element size in all dimensions
mesh1d = fieldmodule.findMeshByDimension(1)
meanLineLength = 0.0
lineCount = mesh1d.getSize()
if lineCount > 0:
one = fieldmodule.createFieldConstant(1.0)
sumLineLength = fieldmodule.createFieldMeshIntegral(
one, modelCoordinates, mesh1d)
cache = fieldmodule.createFieldcache()
result, totalLineLength = sumLineLength.evaluateReal(cache, 1)
glyphWidth = 0.1 * totalLineLength / lineCount
del cache
del sumLineLength
del one
if (lineCount == 0) or (glyphWidth == 0.0):
# use function of coordinate range if no elements
if componentsCount == 1:
maxScale = maxX - minX
else:
first = True
for c in range(componentsCount):
scale = maxX[c] - minX[c]
if first or (scale > maxScale):
maxScale = scale
first = False
if maxScale == 0.0:
maxScale = 1.0
glyphWidth = 0.01 * maxScale
glyphWidthSmall = 0.25 * glyphWidth
# make graphics
scene = self._fitter.getRegion().getScene()
with ChangeManager(scene):
scene.removeAllGraphics()
axes = scene.createGraphicsPoints()
pointattr = axes.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_AXES_XYZ)
pointattr.setBaseSize([axesScale, axesScale, axesScale])
pointattr.setLabelText(1, " " + str(axesScale))
axes.setMaterial(self._materialmodule.findMaterialByName("grey50"))
axes.setName("displayAxes")
axes.setVisibilityFlag(self.isDisplayAxes())
# marker points, projections
markerGroup = self._fitter.getMarkerGroup()
markerDataGroup, markerDataCoordinates, markerDataName = self._fitter.getMarkerDataFields(
)
markerDataLocation, markerDataLocationCoordinates, markerDataDelta = self._fitter.getMarkerDataLocationFields(
)
markerNodeGroup, markerLocation, markerCoordinates, markerName = self._fitter.getMarkerModelFields(
)
markerDataLocationGroupField = self._fitter.getMarkerDataLocationGroupField(
)
markerDataPoints = scene.createGraphicsPoints()
markerDataPoints.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if markerDataLocationGroupField:
markerDataPoints.setSubgroupField(markerDataLocationGroupField)
elif markerGroup:
markerDataPoints.setSubgroupField(markerGroup)
if markerDataCoordinates:
markerDataPoints.setCoordinateField(markerDataCoordinates)
pointattr = markerDataPoints.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_CROSS)
markerDataPoints.setMaterial(
self._materialmodule.findMaterialByName("yellow"))
markerDataPoints.setName("displayMarkerDataPoints")
markerDataPoints.setVisibilityFlag(
self.isDisplayMarkerDataPoints())
markerDataNames = scene.createGraphicsPoints()
markerDataNames.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if markerDataLocationGroupField:
markerDataNames.setSubgroupField(markerDataLocationGroupField)
elif markerGroup:
markerDataPoints.setSubgroupField(markerGroup)
if markerDataCoordinates:
markerDataNames.setCoordinateField(markerDataCoordinates)
pointattr = markerDataNames.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
if markerDataName:
pointattr.setLabelField(markerDataName)
markerDataNames.setMaterial(
self._materialmodule.findMaterialByName("yellow"))
markerDataNames.setName("displayMarkerDataNames")
markerDataNames.setVisibilityFlag(self.isDisplayMarkerDataNames())
markerDataProjections = scene.createGraphicsPoints()
markerDataProjections.setFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
if markerDataLocationGroupField:
markerDataProjections.setSubgroupField(
markerDataLocationGroupField)
elif markerGroup:
markerDataPoints.setSubgroupField(markerGroup)
if markerDataCoordinates:
markerDataProjections.setCoordinateField(markerDataCoordinates)
pointAttr = markerDataProjections.getGraphicspointattributes()
pointAttr.setGlyphShapeType(Glyph.SHAPE_TYPE_LINE)
pointAttr.setBaseSize([0.0, 1.0, 1.0])
pointAttr.setScaleFactors([1.0, 0.0, 0.0])
if markerDataDelta:
pointAttr.setOrientationScaleField(markerDataDelta)
markerDataProjections.setMaterial(
self._materialmodule.findMaterialByName("magenta"))
markerDataProjections.setName("displayMarkerDataProjections")
markerDataProjections.setVisibilityFlag(
self.isDisplayMarkerDataProjections())
markerPoints = scene.createGraphicsPoints()
markerPoints.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
if markerGroup:
markerPoints.setSubgroupField(markerGroup)
if markerCoordinates:
markerPoints.setCoordinateField(markerCoordinates)
pointattr = markerPoints.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_CROSS)
markerPoints.setMaterial(
self._materialmodule.findMaterialByName("white"))
markerPoints.setName("displayMarkerPoints")
markerPoints.setVisibilityFlag(self.isDisplayMarkerPoints())
markerNames = scene.createGraphicsPoints()
markerNames.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
if markerGroup:
markerNames.setSubgroupField(markerGroup)
if markerCoordinates:
markerNames.setCoordinateField(markerCoordinates)
pointattr = markerNames.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
if markerName:
pointattr.setLabelField(markerName)
markerNames.setMaterial(
self._materialmodule.findMaterialByName("white"))
markerNames.setName("displayMarkerNames")
markerNames.setVisibilityFlag(self.isDisplayMarkerNames())
# data points, projections and projection points
meshDimension = 2
dataCoordinates = self._fitter.getDataCoordinatesField()
dataProjectionCoordinates = self._fitter.getDataProjectionCoordinatesField(
meshDimension)
dataProjectionDelta = self._fitter.getDataProjectionDeltaField(
meshDimension)
dataProjectionError = self._fitter.getDataProjectionErrorField(
meshDimension)
dataPoints = scene.createGraphicsPoints()
dataPoints.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if dataCoordinates:
dataPoints.setCoordinateField(dataCoordinates)
pointattr = dataPoints.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_CROSS)
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
#pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_POINT)
#dataPoints.setRenderPointSize(2.0);
dataPoints.setMaterial(
self._materialmodule.findMaterialByName("grey50"))
dataPoints.setName("displayDataPoints")
dataPoints.setVisibilityFlag(self.isDisplayDataPoints())
dataProjections = scene.createGraphicsPoints()
dataProjections.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if dataCoordinates:
dataProjections.setCoordinateField(dataCoordinates)
#dataProjections.setSubgroupField(self._activeDataPointGroupField)
pointAttr = dataProjections.getGraphicspointattributes()
pointAttr.setGlyphShapeType(Glyph.SHAPE_TYPE_LINE)
pointAttr.setBaseSize([0.0, 1.0, 1.0])
pointAttr.setScaleFactors([1.0, 0.0, 0.0])
if dataProjectionDelta:
pointAttr.setOrientationScaleField(dataProjectionDelta)
if dataProjectionError:
dataProjections.setDataField(dataProjectionError)
spectrummodule = scene.getSpectrummodule()
spectrum = spectrummodule.getDefaultSpectrum()
dataProjections.setSpectrum(spectrum)
dataProjections.setName("displayDataProjections")
dataPoints.setVisibilityFlag(self.isDisplayDataProjections())
dataProjectionPoints = scene.createGraphicsPoints()
dataProjectionPoints.setFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
if dataProjectionCoordinates:
dataProjectionPoints.setCoordinateField(
dataProjectionCoordinates)
pointattr = dataProjectionPoints.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_CROSS)
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
#pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_POINT)
#dataPoints.setRenderPointSize(2.0);
dataProjectionPoints.setMaterial(
self._materialmodule.findMaterialByName("grey50"))
dataProjectionPoints.setName("displayDataProjectionPoints")
dataProjectionPoints.setVisibilityFlag(
self.isDisplayDataProjectionPoints())
nodePoints = scene.createGraphicsPoints()
nodePoints.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodePoints.setCoordinateField(modelCoordinates)
pointattr = nodePoints.getGraphicspointattributes()
pointattr.setBaseSize([glyphWidth, glyphWidth, glyphWidth])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_SPHERE)
nodePoints.setMaterial(
self._materialmodule.findMaterialByName("white"))
nodePoints.setName("displayNodePoints")
nodePoints.setVisibilityFlag(self.isDisplayNodePoints())
nodeNumbers = scene.createGraphicsPoints()
nodeNumbers.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodeNumbers.setCoordinateField(modelCoordinates)
pointattr = nodeNumbers.getGraphicspointattributes()
pointattr.setLabelField(cmiss_number)
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
nodeNumbers.setMaterial(
self._materialmodule.findMaterialByName("green"))
nodeNumbers.setName("displayNodeNumbers")
nodeNumbers.setVisibilityFlag(self.isDisplayNodeNumbers())
# names in same order as nodeDerivativeLabels "D1", "D2", "D3", "D12", "D13", "D23", "D123" and nodeDerivativeFields
nodeDerivativeMaterialNames = [
"gold", "silver", "green", "cyan", "magenta", "yellow", "blue"
]
derivativeScales = [1.0, 1.0, 1.0, 0.5, 0.5, 0.5, 0.25]
for i in range(len(nodeDerivativeLabels)):
nodeDerivativeLabel = nodeDerivativeLabels[i]
nodeDerivatives = scene.createGraphicsPoints()
nodeDerivatives.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodeDerivatives.setCoordinateField(modelCoordinates)
pointattr = nodeDerivatives.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_ARROW_SOLID)
pointattr.setOrientationScaleField(nodeDerivativeFields[i])
pointattr.setBaseSize([0.0, glyphWidth, glyphWidth])
pointattr.setScaleFactors([derivativeScales[i], 0.0, 0.0])
material = self._materialmodule.findMaterialByName(
nodeDerivativeMaterialNames[i])
nodeDerivatives.setMaterial(material)
nodeDerivatives.setSelectedMaterial(material)
nodeDerivatives.setName("displayNodeDerivatives" +
nodeDerivativeLabel)
nodeDerivatives.setVisibilityFlag(
self.isDisplayNodeDerivatives() and
self.isDisplayNodeDerivativeLabels(nodeDerivativeLabel))
elementNumbers = scene.createGraphicsPoints()
elementNumbers.setFieldDomainType(
Field.DOMAIN_TYPE_MESH_HIGHEST_DIMENSION)
elementNumbers.setCoordinateField(modelCoordinates)
pointattr = elementNumbers.getGraphicspointattributes()
pointattr.setLabelField(cmiss_number)
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
elementNumbers.setMaterial(
self._materialmodule.findMaterialByName("cyan"))
elementNumbers.setName("displayElementNumbers")
elementNumbers.setVisibilityFlag(self.isDisplayElementNumbers())
elementAxes = scene.createGraphicsPoints()
elementAxes.setFieldDomainType(
Field.DOMAIN_TYPE_MESH_HIGHEST_DIMENSION)
elementAxes.setCoordinateField(modelCoordinates)
pointattr = elementAxes.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_AXES_123)
pointattr.setOrientationScaleField(elementDerivativesField)
if meshDimension == 1:
pointattr.setBaseSize([0.0, 2 * glyphWidth, 2 * glyphWidth])
pointattr.setScaleFactors([0.25, 0.0, 0.0])
elif meshDimension == 2:
pointattr.setBaseSize([0.0, 0.0, 2 * glyphWidth])
pointattr.setScaleFactors([0.25, 0.25, 0.0])
else:
pointattr.setBaseSize([0.0, 0.0, 0.0])
pointattr.setScaleFactors([0.25, 0.25, 0.25])
elementAxes.setMaterial(
self._materialmodule.findMaterialByName("yellow"))
elementAxes.setName("displayElementAxes")
elementAxes.setVisibilityFlag(self.isDisplayElementAxes())
lines = scene.createGraphicsLines()
lines.setCoordinateField(modelCoordinates)
lines.setExterior(self.isDisplayLinesExterior())
lines.setName("displayLines")
lines.setVisibilityFlag(self.isDisplayLines())
surfaces = scene.createGraphicsSurfaces()
surfaces.setCoordinateField(modelCoordinates)
surfaces.setRenderPolygonMode(
Graphics.RENDER_POLYGON_MODE_WIREFRAME if self.
isDisplaySurfacesWireframe(
) else Graphics.RENDER_POLYGON_MODE_SHADED)
surfaces.setExterior(self.isDisplaySurfacesExterior() if (
meshDimension == 3) else False)
surfacesMaterial = self._materialmodule.findMaterialByName(
"trans_blue" if self.isDisplaySurfacesTranslucent(
) else "solid_blue")
surfaces.setMaterial(surfacesMaterial)
surfaces.setName("displaySurfaces")
surfaces.setVisibilityFlag(self.isDisplaySurfaces())
def autorangeSpectrum(self):
scene = self._fitter.getRegion().getScene()
spectrummodule = scene.getSpectrummodule()
spectrum = spectrummodule.getDefaultSpectrum()
spectrum.autorange(scene, Scenefilter())
# === Align Utilities ===
def rotateModel(self, axis, angle):
quat = vectorops.axisAngleToQuaternion(axis, angle)
mat1 = vectorops.rotmx(quat)
mat2 = vectorops.eulerToRotationMatrix3(
self._alignSettings["euler_angles"])
if self.isAlignMirror():
mat2[0] = vectorops.mult(mat2[0], -1.0)
newmat = vectorops.matrixmult(mat1, mat2)
if self.isAlignMirror():
newmat[0] = vectorops.mult(newmat[0], -1.0)
self._alignSettings["euler_angles"] = vectorops.rotationMatrix3ToEuler(
newmat)
self._applyAlignSettings()
def scaleModel(self, factor):
self._alignSettings["scale"] *= factor
self._applyAlignSettings()
def translateModel(self, relativeOffset):
self._alignSettings["offset"] = vectorops.add(
self._alignSettings["offset"], relativeOffset)
self._applyAlignSettings()
def _autorangeSpectrum(self):
scene = self.getScene()
spectrummodule = scene.getSpectrummodule()
spectrum = spectrummodule.getDefaultSpectrum()
scenefiltermodule = scene.getScenefiltermodule()
scenefilter = scenefiltermodule.getDefaultScenefilter()
spectrum.autorange(scene, scenefilter)
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)