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Merged
hsorby merged 1 commit into from
Feb 13, 2025
Merged

Add new API to tests for Jacobain determinant. #42

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6 changes: 3 additions & 3 deletions src/scaffoldfitter/fitter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
from cmlibs.maths.vectorops import add, mult, sub
from cmlibs.utils.zinc.field import assignFieldParameters, createFieldFiniteElementClone, getGroupList, \
findOrCreateFieldFiniteElement, findOrCreateFieldStoredMeshLocation, getUniqueFieldName, orphanFieldByName, \
create_xi_reference_jacobian_determinant_field
create_jacobian_determinant_field
from cmlibs.utils.zinc.finiteelement import evaluate_field_nodeset_range, findNodeWithName, get_scalar_field_minimum_in_mesh
from cmlibs.utils.zinc.general import ChangeManager
from cmlibs.utils.zinc.region import write_to_buffer, read_from_buffer
Expand Down Expand Up @@ -864,7 +864,7 @@ def getLowestElementJacobian(self, mesh_group=None):
:return: Element identifier, minimum jacobian value. Values are -1, inf if there is no data or bad fields.
"""
with ChangeManager(self._fieldmodule):
jacobian = create_xi_reference_jacobian_determinant_field(self._modelCoordinatesField)
jacobian = create_jacobian_determinant_field(self._modelCoordinatesField, self._modelReferenceCoordinatesField)
result = get_scalar_field_minimum_in_mesh(jacobian, mesh_group)
del jacobian

Expand All @@ -883,7 +883,7 @@ def getLowestElementJacobianForGroup(self, group_name):
"""
group = self._fieldmodule.findFieldByName(group_name).castGroup()
if group.isValid():
mesh_group = group.getMeshGroup(self._mesh)
mesh_group = group.getMeshGroup(self.getMesh(3))
return self.getLowestElementJacobian(mesh_group)

return None, None
Expand Down
20 changes: 16 additions & 4 deletions tests/test_fitcube.py
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Expand Up @@ -429,6 +429,10 @@ def test_alignGroupsFitEllipsoidRegularData(self):
s2 = fitter.encodeSettingsJSON()
self.assertEqual(s, s2)

min_jac_el, min_jac_value = fitter.getLowestElementJacobian()
self.assertEqual(1, min_jac_el)
self.assertAlmostEqual(0.1869875394, min_jac_value)

def test_fitRegularDataGroupWeight(self):
"""
Test fitting with variable data group weights and sliding factors.
Expand Down Expand Up @@ -518,6 +522,10 @@ def test_fitRegularDataGroupWeight(self):
self.assertAlmostEqual(surfaceArea, 3.187490694645035, delta=1.0E-4)
self.assertAlmostEqual(volume, 0.5072619397447008, delta=1.0E-4)

min_jac_el, min_jac_value = fitter.getLowestElementJacobian()
self.assertEqual(1, min_jac_el)
self.assertAlmostEqual(1.0, min_jac_value)

def test_groupSettings(self):
"""
Test per-group settings, and inheritance from previous
Expand Down Expand Up @@ -572,19 +580,23 @@ def test_groupSettings(self):
activeNodeset, fitter.getFieldmodule().findFieldByName(groupName)))

groupErrors = {
"bottom": (0.47716552515635985, 0.5001722675609085),
"sides": (0.3721661947669986, 0.5000286856904854),
"top": (0.5699148581001906, 0.6755409758922845),
"marker": (0.9354143466934853, 1.224744871391589)
"bottom": (0.47716552515635985, 0.5001722675609085, math.inf),
"sides": (0.3721661947669986, 0.5000286856904854, math.inf),
"top": (0.5699148581001906, 0.6755409758922845, math.inf),
"marker": (0.9354143466934853, 1.224744871391589, math.inf)
}
for groupName, errors in groupErrors.items():
rms_error, max_error = fitter.getDataRMSAndMaximumProjectionErrorForGroup(groupName)
self.assertAlmostEqual(rms_error, errors[0], 5)
self.assertAlmostEqual(max_error, errors[1], 5)
jac_det_el, jac_det_value = fitter.getLowestElementJacobianForGroup(groupName)
self.assertAlmostEqual(jac_det_value, errors[2], 5)

rms_error, max_error = fitter.getDataRMSAndMaximumProjectionErrorForGroup('left')
self.assertEqual(None, rms_error)
self.assertEqual(None, max_error)
jac_det_el, jac_det_value = fitter.getLowestElementJacobianForGroup('left')
self.assertIsNone(jac_det_value)

# test override and inherit
config2 = FitterStepConfig()
Expand Down
3 changes: 3 additions & 0 deletions tests/test_general.py
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Expand Up @@ -75,6 +75,9 @@ def test_fit_1d_outliers(self):
rmsError, maxError = fitter.getDataRMSAndMaximumProjectionError()
self.assertAlmostEqual(rmsError, expectedRmsError, delta=TOL) # sqrt(0.12)
self.assertAlmostEqual(maxError, expectedMaxError, delta=TOL)
min_jac_el, min_jac_value = fitter.getLowestElementJacobian()
self.assertEqual(1, min_jac_el)
self.assertAlmostEqual(0.0, min_jac_value, delta=TOL)

def test_setting_group_outlier_length(self):
zinc_model_file = os.path.join(here, "resources", "nerve_trunk_model.exf")
Expand Down