def test_alignFixedRandomData(self):
"""
Test alignment of model and data to known transformations.
"""
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)
fitter.setDiagnosticLevel(1)
fitter.load()
dataScale = fitter.getDataScale()
self.assertAlmostEqual(dataScale, 1.0, delta=1.0E-7)
self.assertEqual(fitter.getModelCoordinatesField().getName(),
"coordinates")
self.assertEqual(fitter.getDataCoordinatesField().getName(),
"data_coordinates")
self.assertEqual(fitter.getMarkerGroup().getName(), "marker")
bottomCentre1 = fitter.evaluateNodeGroupMeanCoordinates("bottom",
"coordinates",
isData=False)
sidesCentre1 = fitter.evaluateNodeGroupMeanCoordinates("sides",
"coordinates",
isData=False)
topCentre1 = fitter.evaluateNodeGroupMeanCoordinates("top",
"coordinates",
isData=False)
assertAlmostEqualList(self,
bottomCentre1, [0.5, 0.5, 0.0],
delta=1.0E-7)
assertAlmostEqualList(self,
sidesCentre1, [0.5, 0.5, 0.5],
delta=1.0E-7)
assertAlmostEqualList(self, topCentre1, [0.5, 0.5, 1.0], delta=1.0E-7)
align = FitterStepAlign()
fitter.addFitterStep(align)
align.setScale(1.1)
align.setTranslation([0.1, -0.2, 0.3])
align.setRotation([math.pi / 4.0, math.pi / 8.0, math.pi / 2.0])
self.assertFalse(align.isAlignMarkers())
align.run()
rotation = align.getRotation()
scale = align.getScale()
translation = align.getTranslation()
rotationMatrix = getRotationMatrix(rotation)
transformationMatrix = [v * scale for v in rotationMatrix]
bottomCentre2Expected, sidesCentre2Expected, topCentre2Expected = transformCoordinatesList(
[bottomCentre1, sidesCentre1, topCentre1], transformationMatrix,
translation)
bottomCentre2 = fitter.evaluateNodeGroupMeanCoordinates("bottom",
"coordinates",
isData=False)
sidesCentre2 = fitter.evaluateNodeGroupMeanCoordinates("sides",
"coordinates",
isData=False)
topCentre2 = fitter.evaluateNodeGroupMeanCoordinates("top",
"coordinates",
isData=False)
assertAlmostEqualList(self,
bottomCentre2,
bottomCentre2Expected,
delta=1.0E-7)
assertAlmostEqualList(self,
sidesCentre2,
sidesCentre2Expected,
delta=1.0E-7)
assertAlmostEqualList(self,
topCentre2,
topCentre2Expected,
delta=1.0E-7)
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())
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("bottom")))
self.assertEqual(
144,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("sides")))
self.assertEqual(
72,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("top")))
self.assertEqual(
4,
getNodesetConditionalSize(
activeNodeset,
fitter.getFieldmodule().findFieldByName("marker")))
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.setMarkerWeight(1.0)
fit1.setCurvaturePenaltyWeight(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)