Add new API for getting Jacobian information about model. #41
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src/scaffoldfitter/fitter.py
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| """ | ||
| with ChangeManager(self._fieldmodule): | ||
| jacobian = calculate_jacobian(self._modelCoordinatesField) | ||
| report = report_on_lowest_value(jacobian, mesh_group if mesh_group else None) |
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Add following line within context manager:
del jacobian
so no notification about field ever existing.
Note I'd also prefer mesh_3d to be discovered here and a mesh or mesh_group passed to the function creating the jacobian field.
src/scaffoldfitter/fitter.py
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| @@ -852,6 +853,37 @@ def getDataRMSAndMaximumProjectionErrorForGroup(self, groupName): | |||
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| return None, None | |||
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| def getModelWorstElementJacobianInfo(self, mesh_group=None): | |||
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getLowestElementJacobian(self, mesh_group=None)
Add comment that a value <= 0.0 is bad, either zero or negative volume / left-handed coordinates.
src/scaffoldfitter/fitter.py
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| :param group_name: Name of group to make calculation over. | ||
| :return: Element identifier, minimum jacobian value. | ||
| """ | ||
| with ChangeManager(self._fieldmodule): |
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ChangeManager is redundant here.
src/scaffoldfitter/fitter.py
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| return report | ||
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| def getModelWorstElementJacobianInfoForGroup(self, group_name): |
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getLowestElementJacobianForGroupName
src/scaffoldfitter/fitter.py
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| If the group_name is not a valid group name then None, None is returned. | ||
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| :param group_name: Name of group to make calculation over. | ||
| :return: Element identifier, minimum jacobian value. |
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Need to note returns -1, inf if failed to evaluate, but this is at odds with returning None, None below.
src/scaffoldfitter/fitter.py
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| """ | ||
| group = self._fieldmodule.findFieldByName(group_name).castGroup() | ||
| if group.isValid(): | ||
| return self.getLowestElementJacobian(group) |
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Need to get mesh group for highest dimension mesh and pass it here; it doesn't a group field.
src/scaffoldfitter/fitter.py
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| from cmlibs.utils.zinc.general import ChangeManager | ||
| from cmlibs.utils.zinc.field import get_element_jacobian_field, get_scalar_field_minimum_in_mesh |
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Might be some changes to name and locations of these cmlibs.utils.
| :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) |
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needs reference coordinate field argument:
jacobian = create_jacobian_determinant_field(self._modelCoordinatesField, self._modelReferenceCoordinatesField)
also do a test evaluation in any test. in test_fitcube.py test_alignMarkersFitRegularData
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