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Merged
rchristie merged 2 commits into from
Jun 5, 2025
Merged

Add cleanup function #44

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78340ec
Add field cleanup function
rchristie Apr 8, 2025
74eac9d
Merge remote-tracking branch 'abi/main' into cleanup
rchristie Jun 5, 2025
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30 changes: 23 additions & 7 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_jacobian_determinant_field)
find_or_create_field_stored_mesh_location, getUniqueFieldName, orphanFieldByName, 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.group import match_fitting_group_names
Expand Down Expand Up @@ -117,6 +117,15 @@ def __init__(self, zincModelFileName: str=None, zincDataFileName: str=None, regi
fitterStep = FitterStepConfig()
self.addFitterStep(fitterStep)

def cleanup(self):
self._fitterSteps = []
self._clearFields()
self._rawDataRegion = None
self._fieldmodule = None
self._region = None
self._logger = None
self._context = None

def decodeSettingsJSON(self, s: str, decoder):
"""
Define Fitter from JSON serialisation output by encodeSettingsJSON.
Expand Down Expand Up @@ -410,7 +419,7 @@ def _defineCommonDataFields(self):
with ChangeManager(self._fieldmodule):
mesh = self.getHighestDimensionMesh()
datapoints = self._fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
self._dataHostLocationField = findOrCreateFieldStoredMeshLocation(
self._dataHostLocationField = find_or_create_field_stored_mesh_location(
self._fieldmodule, mesh, "data_location_" + mesh.getName(), managed=False)
self._dataHostCoordinatesField = self._fieldmodule.createFieldEmbedded(
self._modelCoordinatesField, self._dataHostLocationField)
Expand Down Expand Up @@ -973,6 +982,8 @@ def _calculateMarkerDataLocations(self):
markerDataLocationGroupSize = self._markerDataLocationGroup.getSize()
markerNodeGroupSize = self._markerNodeGroup.getSize()
if self.getDiagnosticLevel() > 0:
print(str(markerDataLocationGroupSize) + " of " + str(markerDataGroupSize) +
" marker data points have model locations")
if markerDataLocationGroupSize < markerDataGroupSize:
print("Warning: Only " + str(markerDataLocationGroupSize) +
" of " + str(markerDataGroupSize) + " marker data points have model locations")
Expand Down Expand Up @@ -1259,6 +1270,8 @@ def calculateGroupDataProjections(self, fieldcache, group, dataGroup, meshGroup,
nodeIter = dataGroup.createNodeiterator()
node = nodeIter.next()
dataProportionCounter = 0.5
pointsProjected = 0
outlierPointsRemoved = 0
while node.isValid():
dataProportionCounter += dataProportion
if dataProportionCounter >= 1.0:
Expand All @@ -1277,18 +1290,21 @@ def calculateGroupDataProjections(self, fieldcache, group, dataGroup, meshGroup,
dataProjectionLengths.append((node.getIdentifier(), projectionLength))
if (outlierLength <= 0.0) or (projectionLength <= outlierLength):
dataProjectionNodesetGroup.addNode(node)
pointsProjected += 1
else:
outlierPointsRemoved += 1
node = nodeIter.next()
if outlierLength < 0.0:
relativeOutlierLength = (1.0 + outlierLength) * maximumProjectionLength
for nodeIdentifier, projectionLength in dataProjectionLengths:
if projectionLength > relativeOutlierLength:
node = dataGroup.findNodeByIdentifier(nodeIdentifier)
dataProjectionNodesetGroup.removeNode(node)
pointsProjected = dataProjectionNodesetGroup.getSize() - sizeBefore
if pointsProjected < dataGroup.getSize():
if self.getDiagnosticLevel() > 0:
print("Warning: Only " + str(pointsProjected) + " of " + str(dataGroup.getSize()) +
" data points projected for group " + groupName)
pointsProjected -= 1
outlierPointsRemoved += 1
if self.getDiagnosticLevel() > 0:
print(str(pointsProjected) + " of " + str(dataGroup.getSize()) + " data points projected for group " +
groupName + "; " + str(outlierPointsRemoved) + " outliers removed")
# add to active group
self._activeDataNodesetGroup.addNodesConditional(self._dataProjectionNodeGroupFields[meshDimension - 1])
return
Expand Down
1 change: 0 additions & 1 deletion tests/test_general.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,6 @@ def test_fit_projection_subgroup(self):
zinc_data_file_name = os.path.join(here, "resources", "nerve_path_data.exf")
if i == 0:
# use fitter with model and data files
region = None
fitter = Fitter(zinc_model_file_name, zinc_data_file_name)
fitter.setDiagnosticLevel(1)
fitter.load()
Expand Down