def _stepsAddFitClicked(self):
"""
Add a new fit step.
"""
self._currentFitterStep = FitterStepFit()
self._fitter.addFitterStep(self._currentFitterStep) # Future: , lastFitterStep
self._buildStepsList()
def _stepsAddConfigClicked(self):
"""
Add a new config step.
"""
self._currentFitterStep = FitterStepConfig()
self._fitter.addFitterStep(self._currentFitterStep) # Future: , lastFitterStep
self._buildStepsList()
def _stepsAddAlignClicked(self):
"""
Add a new align step.
"""
self._currentFitterStep = FitterStepAlign()
self._fitter.addFitterStep(self._currentFitterStep) # Future: , lastFitterStep
self._buildStepsList()
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)
class GeometricFitWidget(QtGui.QWidget):
"""
User interface for github.com/ABI-Software/scaffoldfitter
"""
def __init__(self, model, parent=None):
"""
"""
super(GeometricFitWidget, self).__init__(parent)
self._ui = Ui_GeometricFitWidget()
self._ui.setupUi(self)
self._ui.alignmentsceneviewerwidget.setContext(model.getContext())
self._ui.alignmentsceneviewerwidget.setModel(model)
self._model = model
self._fitter = self._model.getFitter()
self._region = self._fitter.getRegion()
self._scene = self._region.getScene()
self._currentFitterStep = None # Current FitterStep being edited; None = Fitter config
self._ui.alignmentsceneviewerwidget.graphicsInitialized.connect(
self._graphicsInitialized)
self._callback = None
self._setupConfigWidgets()
self._updateGeneralWidgets()
self._updateConfigWidgets()
self._updateDisplayWidgets()
self._makeConnections()
def _graphicsInitialized(self):
"""
Callback for when SceneviewerWidget is initialised
"""
self._sceneChanged()
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
sceneviewer.setTransparencyMode(sceneviewer.TRANSPARENCY_MODE_SLOW)
self._autoPerturbLines()
sceneviewer.viewAll()
def _sceneChanged(self):
"""
Set custom scene from model.
"""
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
self._model.createGraphics()
sceneviewer.setScene(self._model.getScene())
self._refreshGraphics()
def _refreshGraphics(self):
"""
Autorange spectrum and force redraw of graphics.
"""
self._model.autorangeSpectrum()
self._ui.alignmentsceneviewerwidget.paintGL()
def _makeConnections(self):
self._makeConnectionsGeneral()
self._makeConnectionsDisplay()
self._makeConnectionsConfig()
self._makeConnectionsAlign()
self._makeConnectionsFit()
def registerDoneExecution(self, callback):
self._callback = callback
def _autoPerturbLines(self):
"""
Enable scene viewer perturb lines iff solid surfaces are drawn with lines.
Call whenever lines, surfaces or translucency changes
"""
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
sceneviewer.setPerturbLinesFlag(self._model.needPerturbLines())
# === general widgets ===
def _makeConnectionsGeneral(self):
self._ui.stepsAddAlign_pushButton.clicked.connect(
self._stepsAddAlignClicked)
self._ui.stepsAddFit_pushButton.clicked.connect(
self._stepsAddFitClicked)
self._ui.stepsDelete_pushButton.clicked.connect(
self._stepsDeleteClicked)
self._ui.steps_listView.clicked[QtCore.QModelIndex].connect(
self._stepsListItemClicked)
self._ui.done_pushButton.clicked.connect(self._doneClicked)
self._ui.viewAll_pushButton.clicked.connect(self._viewAllClicked)
def _updateGeneralWidgets(self):
self._ui.identifier_label.setText("Identifier: " +
self._model.getIdentifier())
self._buildStepsList()
def _stepsAddAlignClicked(self):
"""
Add a new align step.
"""
self._currentFitterStep = FitterStepAlign(self._fitter)
self._buildStepsList()
def _stepsAddFitClicked(self):
"""
Add a new fit step.
"""
self._currentFitterStep = FitterStepFit(self._fitter)
self._buildStepsList()
def _stepsDeleteClicked(self):
"""
Delete the currently selected step, except for config.
Select next step after, or before if none.
"""
destroyFitterStep = self._currentFitterStep
if destroyFitterStep:
if destroyFitterStep.hasRun():
# Undo to before step being destroyed
fitterSteps = self._fitter.getFitterSteps()
currentIndex = fitterSteps.index(self._currentFitterStep)
self._fitter.load()
self._sceneChanged()
for index in range(currentIndex):
fitterSteps[index].run()
self._refreshGraphics()
for index in range(currentIndex, len(fitterSteps)):
fitterSteps[index].setHasRun(False)
self._currentFitterStep = self._fitter.getNextFitterStep(
self._currentFitterStep)
destroyFitterStep.destroy()
self._buildStepsList()
def _stepsListItemClicked(self, modelIndex):
"""
Changes current step and possibly changes checked/run status.
"""
model = modelIndex.model()
item = model.itemFromIndex(modelIndex)
isChecked = item.checkState() == QtCore.Qt.Checked
self._currentFitterStep = item.data()
if self._currentFitterStep:
fitterSteps = self._fitter.getFitterSteps()
currentIndex = fitterSteps.index(self._currentFitterStep)
#print("currentIndex", currentIndex, isChecked)
if (not self._currentFitterStep.hasRun()) and isChecked:
for index in range(currentIndex + 1):
step = fitterSteps[index]
if not step.hasRun():
step.run()
self._refreshStepItem(step)
self._refreshGraphics()
elif self._currentFitterStep.hasRun() and (not isChecked):
self._fitter.load()
self._sceneChanged()
for index in range(currentIndex):
fitterSteps[index].run()
self._refreshGraphics()
for index in range(currentIndex, len(fitterSteps)):
step = fitterSteps[index]
if step.hasRun():
step.setHasRun(False)
self._refreshStepItem(step)
self._updateFitterStepWidgets()
def _buildStepsList(self):
"""
Fill the graphics list view with the list of graphics for current region/scene
"""
self._stepsItems = QtGui.QStandardItemModel(self._ui.steps_listView)
selectedIndex = None
fitter = self._model.getFitter()
# fitter configuration appears as first step called "Config"
item = QtGui.QStandardItem("Config")
item.setData(None)
item.setCheckable(False)
item.setEditable(False)
self._stepsItems.appendRow(item)
selectedIndex = self._stepsItems.indexFromItem(item)
for step in fitter.getFitterSteps():
name = None
isAlign = isinstance(step, FitterStepAlign)
isFit = isinstance(step, FitterStepFit)
assert isAlign or isFit, "GeometricFitWidget. Unknown FitterStep type"
name = "Align" if isAlign else "Fit"
item = QtGui.QStandardItem(name)
item.setData(step)
item.setCheckable(True)
item.setEditable(False)
item.setCheckState(
QtCore.Qt.Checked if step.hasRun() else QtCore.Qt.Unchecked)
self._stepsItems.appendRow(item)
if step == self._currentFitterStep:
selectedIndex = self._stepsItems.indexFromItem(item)
self._ui.steps_listView.setModel(self._stepsItems)
self._ui.steps_listView.setCurrentIndex(selectedIndex)
self._ui.steps_listView.show()
self._updateFitterStepWidgets()
def _refreshStepItem(self, step):
"""
Update check state and selection of step in steps list view.
:param stepIndex: Row index of item in step items.
"""
item = self._stepsItems.item(
self._fitter.getFitterSteps().index(step) + 1)
item.setCheckState(
QtCore.Qt.Checked if step.hasRun() else QtCore.Qt.Unchecked)
step = item.data()
if step == self._currentFitterStep:
self._ui.steps_listView.setCurrentIndex(
self._stepsItems.indexFromItem(item))
def _updateFitterStepWidgets(self):
"""
Update and display widgets for currentFitterStep
"""
if self._currentFitterStep is None:
self._ui.config_groupBox.show()
self._ui.align_groupBox.hide()
self._ui.fit_groupBox.hide()
elif isinstance(self._currentFitterStep, FitterStepAlign):
self._updateAlignWidgets()
self._ui.config_groupBox.hide()
self._ui.align_groupBox.show()
self._ui.fit_groupBox.hide()
else: # elif isinstance(self._currentFitterStep, FitterStepFit):
self._updateFitWidgets()
self._ui.config_groupBox.hide()
self._ui.align_groupBox.hide()
self._ui.fit_groupBox.show()
self._ui.stepsDelete_pushButton.setEnabled(
self._currentFitterStep is not None)
def _doneClicked(self):
self._model.done()
self._ui.dockWidget.setFloating(False)
self._callback()
def _viewAllClicked(self):
self._ui.alignmentsceneviewerwidget.viewAll()
# === display widgets ===
def _makeConnectionsDisplay(self):
self._ui.displayAxes_checkBox.clicked.connect(self._displayAxesClicked)
self._ui.displayMarkerDataPoints_checkBox.clicked.connect(
self._displayMarkerDataPointsClicked)
self._ui.displayMarkerDataNames_checkBox.clicked.connect(
self._displayMarkerDataNamesClicked)
self._ui.displayMarkerDataProjections_checkBox.clicked.connect(
self._displayMarkerDataProjectionsClicked)
self._ui.displayMarkerPoints_checkBox.clicked.connect(
self._displayMarkerPointsClicked)
self._ui.displayMarkerNames_checkBox.clicked.connect(
self._displayMarkerNamesClicked)
self._ui.displayDataPoints_checkBox.clicked.connect(
self._displayDataPointsClicked)
self._ui.displayDataProjections_checkBox.clicked.connect(
self._displayDataProjectionsClicked)
self._ui.displayDataProjectionPoints_checkBox.clicked.connect(
self._displayDataProjectionPointsClicked)
self._ui.displayNodePoints_checkBox.clicked.connect(
self._displayNodePointsClicked)
self._ui.displayNodeNumbers_checkBox.clicked.connect(
self._displayNodeNumbersClicked)
self._ui.displayNodeDerivativeLabelsD1_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD1Clicked)
self._ui.displayNodeDerivativeLabelsD2_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD2Clicked)
self._ui.displayNodeDerivativeLabelsD3_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD3Clicked)
self._ui.displayNodeDerivativeLabelsD12_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD12Clicked)
self._ui.displayNodeDerivativeLabelsD13_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD13Clicked)
self._ui.displayNodeDerivativeLabelsD23_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD23Clicked)
self._ui.displayNodeDerivativeLabelsD123_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD123Clicked)
self._ui.displayNodeDerivatives_checkBox.clicked.connect(
self._displayNodeDerivativesClicked)
self._ui.displayElementAxes_checkBox.clicked.connect(
self._displayElementAxesClicked)
self._ui.displayElementNumbers_checkBox.clicked.connect(
self._displayElementNumbersClicked)
self._ui.displayLines_checkBox.clicked.connect(
self._displayLinesClicked)
self._ui.displayLinesExterior_checkBox.clicked.connect(
self._displayLinesExteriorClicked)
self._ui.displaySurfaces_checkBox.clicked.connect(
self._displaySurfacesClicked)
self._ui.displaySurfacesExterior_checkBox.clicked.connect(
self._displaySurfacesExteriorClicked)
self._ui.displaySurfacesTranslucent_checkBox.clicked.connect(
self._displaySurfacesTranslucentClicked)
self._ui.displaySurfacesWireframe_checkBox.clicked.connect(
self._displaySurfacesWireframeClicked)
def _updateDisplayWidgets(self):
"""
Update display widgets to display settings for model graphics display.
"""
self._ui.displayAxes_checkBox.setChecked(self._model.isDisplayAxes())
self._ui.displayMarkerDataPoints_checkBox.setChecked(
self._model.isDisplayMarkerDataPoints())
self._ui.displayMarkerDataNames_checkBox.setChecked(
self._model.isDisplayMarkerDataNames())
self._ui.displayMarkerDataProjections_checkBox.setChecked(
self._model.isDisplayMarkerDataProjections())
self._ui.displayMarkerPoints_checkBox.setChecked(
self._model.isDisplayMarkerPoints())
self._ui.displayMarkerNames_checkBox.setChecked(
self._model.isDisplayMarkerNames())
self._ui.displayDataPoints_checkBox.setChecked(
self._model.isDisplayDataPoints())
self._ui.displayDataProjections_checkBox.setChecked(
self._model.isDisplayDataProjections())
self._ui.displayDataProjectionPoints_checkBox.setChecked(
self._model.isDisplayDataProjectionPoints())
self._ui.displayNodePoints_checkBox.setChecked(
self._model.isDisplayNodePoints())
self._ui.displayNodeNumbers_checkBox.setChecked(
self._model.isDisplayNodeNumbers())
self._ui.displayNodeDerivativeLabelsD1_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D1"))
self._ui.displayNodeDerivativeLabelsD2_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D2"))
self._ui.displayNodeDerivativeLabelsD3_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D3"))
self._ui.displayNodeDerivativeLabelsD12_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D12"))
self._ui.displayNodeDerivativeLabelsD13_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D13"))
self._ui.displayNodeDerivativeLabelsD23_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D23"))
self._ui.displayNodeDerivativeLabelsD123_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D123"))
self._ui.displayNodeDerivatives_checkBox.setChecked(
self._model.isDisplayNodeDerivatives())
self._ui.displayElementNumbers_checkBox.setChecked(
self._model.isDisplayElementNumbers())
self._ui.displayElementAxes_checkBox.setChecked(
self._model.isDisplayElementAxes())
self._ui.displayLines_checkBox.setChecked(self._model.isDisplayLines())
self._ui.displayLinesExterior_checkBox.setChecked(
self._model.isDisplayLinesExterior())
self._ui.displaySurfaces_checkBox.setChecked(
self._model.isDisplaySurfaces())
self._ui.displaySurfacesExterior_checkBox.setChecked(
self._model.isDisplaySurfacesExterior())
self._ui.displaySurfacesTranslucent_checkBox.setChecked(
self._model.isDisplaySurfacesTranslucent())
self._ui.displaySurfacesWireframe_checkBox.setChecked(
self._model.isDisplaySurfacesWireframe())
def _displayAxesClicked(self):
self._model.setDisplayAxes(self._ui.displayAxes_checkBox.isChecked())
def _displayMarkerDataPointsClicked(self):
self._model.setDisplayMarkerDataPoints(
self._ui.displayMarkerDataPoints_checkBox.isChecked())
def _displayMarkerDataNamesClicked(self):
self._model.setDisplayMarkerDataNames(
self._ui.displayMarkerDataNames_checkBox.isChecked())
def _displayMarkerDataProjectionsClicked(self):
self._model.setDisplayMarkerDataProjections(
self._ui.displayMarkerDataProjections_checkBox.isChecked())
def _displayMarkerPointsClicked(self):
self._model.setDisplayMarkerPoints(
self._ui.displayMarkerPoints_checkBox.isChecked())
def _displayMarkerNamesClicked(self):
self._model.setDisplayMarkerNames(
self._ui.displayMarkerNames_checkBox.isChecked())
def _displayDataPointsClicked(self):
self._model.setDisplayDataPoints(
self._ui.displayDataPoints_checkBox.isChecked())
def _displayDataProjectionsClicked(self):
self._model.setDisplayDataProjections(
self._ui.displayDataProjections_checkBox.isChecked())
def _displayDataProjectionPointsClicked(self):
self._model.setDisplayDataProjectionPoints(
self._ui.displayDataProjectionPoints_checkBox.isChecked())
def _displayNodePointsClicked(self):
self._model.setDisplayNodePoints(
self._ui.displayNodePoints_checkBox.isChecked())
def _displayNodeNumbersClicked(self):
self._model.setDisplayNodeNumbers(
self._ui.displayNodeNumbers_checkBox.isChecked())
def _displayNodeDerivativesClicked(self):
self._model.setDisplayNodeDerivatives(
self._ui.displayNodeDerivatives_checkBox.isChecked())
def _displayNodeDerivativeLabelsD1Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D1", self._ui.displayNodeDerivativeLabelsD1_checkBox.isChecked())
def _displayNodeDerivativeLabelsD2Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D2", self._ui.displayNodeDerivativeLabelsD2_checkBox.isChecked())
def _displayNodeDerivativeLabelsD3Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D3", self._ui.displayNodeDerivativeLabelsD3_checkBox.isChecked())
def _displayNodeDerivativeLabelsD12Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D12",
self._ui.displayNodeDerivativeLabelsD12_checkBox.isChecked())
def _displayNodeDerivativeLabelsD13Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D13",
self._ui.displayNodeDerivativeLabelsD13_checkBox.isChecked())
def _displayNodeDerivativeLabelsD23Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D23",
self._ui.displayNodeDerivativeLabelsD23_checkBox.isChecked())
def _displayNodeDerivativeLabelsD123Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D123",
self._ui.displayNodeDerivativeLabelsD123_checkBox.isChecked())
def _displayElementAxesClicked(self):
self._model.setDisplayElementAxes(
self._ui.displayElementAxes_checkBox.isChecked())
def _displayElementNumbersClicked(self):
self._model.setDisplayElementNumbers(
self._ui.displayElementNumbers_checkBox.isChecked())
def _displayLinesClicked(self):
self._model.setDisplayLines(self._ui.displayLines_checkBox.isChecked())
self._autoPerturbLines()
def _displayLinesExteriorClicked(self):
self._model.setDisplayLinesExterior(
self._ui.displayLinesExterior_checkBox.isChecked())
def _displaySurfacesClicked(self):
self._model.setDisplaySurfaces(
self._ui.displaySurfaces_checkBox.isChecked())
self._autoPerturbLines()
def _displaySurfacesExteriorClicked(self):
self._model.setDisplaySurfacesExterior(
self._ui.displaySurfacesExterior_checkBox.isChecked())
def _displaySurfacesTranslucentClicked(self):
self._model.setDisplaySurfacesTranslucent(
self._ui.displaySurfacesTranslucent_checkBox.isChecked())
self._autoPerturbLines()
def _displaySurfacesWireframeClicked(self):
self._model.setDisplaySurfacesWireframe(
self._ui.displaySurfacesWireframe_checkBox.isChecked())
# === config widgets ===
def _setupConfigWidgets(self):
"""
Set up config widgets and display values from fitter object.
"""
self._ui.configModelCoordinates_fieldChooser.setRegion(self._region)
self._ui.configModelCoordinates_fieldChooser.setNullObjectName("-")
self._ui.configModelCoordinates_fieldChooser.setConditional(
fieldIsManagedCoordinates)
self._ui.configDataCoordinates_fieldChooser.setRegion(self._region)
self._ui.configDataCoordinates_fieldChooser.setNullObjectName("-")
self._ui.configDataCoordinates_fieldChooser.setConditional(
fieldIsManagedCoordinates)
self._ui.configMarkerGroup_fieldChooser.setRegion(self._region)
self._ui.configMarkerGroup_fieldChooser.setNullObjectName("-")
self._ui.configMarkerGroup_fieldChooser.setConditional(
fieldIsManagedGroup)
def _updateConfigWidgets(self):
"""
Update config widgets to display settings for Fitter.
"""
self._ui.configModelCoordinates_fieldChooser.setField(
self._fitter.getModelCoordinatesField())
self._ui.configDataCoordinates_fieldChooser.setField(
self._fitter.getDataCoordinatesField())
self._ui.configMarkerGroup_fieldChooser.setField(
self._fitter.getMarkerGroup())
def _makeConnectionsConfig(self):
self._ui.configModelCoordinates_fieldChooser.currentIndexChanged.connect(
self._configModelCoordinatesFieldChanged)
self._ui.configDataCoordinates_fieldChooser.currentIndexChanged.connect(
self._configDataCoordinatesFieldChanged)
self._ui.configMarkerGroup_fieldChooser.currentIndexChanged.connect(
self._configMarkerGroupChanged)
def _configModelCoordinatesFieldChanged(self, index):
"""
Callback for change in model coordinates field chooser widget.
"""
field = self._ui.configModelCoordinates_fieldChooser.getField()
if field:
self._fitter.setModelCoordinatesField(field)
def _configDataCoordinatesFieldChanged(self, index):
"""
Callback for change in data coordinates field chooser widget.
"""
field = self._ui.configDataCoordinates_fieldChooser.getField()
if field:
self._fitter.setDataCoordinatesField(field)
def _configMarkerGroupChanged(self, index):
"""
Callback for change in marker group field chooser widget.
"""
group = self._ui.configMarkerGroup_fieldChooser.getField()
if group:
self._fitter.setMarkerGroup(group)
# === align widgets ===
def _makeConnectionsAlign(self):
self._ui.alignMarkers_checkBox.clicked.connect(
self._alignMarkersClicked)
self._ui.alignRotation_lineEdit.editingFinished.connect(
self._alignRotationEntered)
self._ui.alignScale_lineEdit.editingFinished.connect(
self._alignScaleEntered)
self._ui.alignTranslation_lineEdit.editingFinished.connect(
self._alignTranslationEntered)
def _getAlign(self):
align = self._currentFitterStep
assert isinstance(align, FitterStepAlign)
return align
def _updateAlignWidgets(self):
"""
Update align widgets to display parameters from current align step.
"""
align = self._getAlign()
realFormat = "{:.4g}"
self._ui.alignMarkers_checkBox.setCheckState(
QtCore.Qt.Checked if align.isAlignMarkers(
) else QtCore.Qt.Unchecked)
self._ui.alignRotation_lineEdit.setText(", ".join(
realFormat.format(value) for value in align.getRotation()))
self._ui.alignScale_lineEdit.setText(
realFormat.format(align.getScale()))
self._ui.alignTranslation_lineEdit.setText(", ".join(
realFormat.format(value) for value in align.getTranslation()))
def _alignMarkersClicked(self):
state = self._ui.alignMarkers_checkBox.checkState()
self._getAlign().setAlignMarkers(state == QtCore.Qt.Checked)
def _alignRotationEntered(self):
values = QLineEdit_parseVector3(self._ui.alignRotation_lineEdit)
if values:
self._getAlign().setRotation(values)
else:
print("Invalid model rotation Euler angles entered")
self._updateAlignWidgets()
def _alignScaleEntered(self):
value = QLineEdit_parseRealNonNegative(self._ui.alignScale_lineEdit)
if value > 0.0:
self._getAlign().setScale(value)
else:
print("Invalid model scale entered")
self._updateAlignWidgets()
def _alignTranslationEntered(self):
values = QLineEdit_parseVector3(self._ui.alignTranslation_lineEdit)
if values:
self._getAlign().setTranslation(values)
else:
print("Invalid model translation entered")
self._updateAlignWidgets()
# === fit widgets ===
def _makeConnectionsFit(self):
self._ui.fitMarkerWeight_lineEdit.editingFinished.connect(
self._fitMarkerWeightEntered)
self._ui.fitStrainPenalty_lineEdit.editingFinished.connect(
self._fitStrainPenaltyEntered)
self._ui.fitCurvaturePenalty_lineEdit.editingFinished.connect(
self._fitCurvaturePenaltyEntered)
self._ui.fitEdgeDiscontinuityPenalty_lineEdit.editingFinished.connect(
self._fitEdgeDiscontinuityPenaltyEntered)
self._ui.fitIterations_spinBox.valueChanged.connect(
self._fitIterationsValueChanged)
self._ui.fitUpdateReferenceState_checkBox.clicked.connect(
self._fitUpdateReferenceStateClicked)
def _getFit(self):
assert isinstance(self._currentFitterStep, FitterStepFit)
return self._currentFitterStep
def _updateFitWidgets(self):
"""
Update fit widgets to display parameters from fit step.
"""
fit = self._getFit()
realFormat = "{:.16}"
self._ui.fitMarkerWeight_lineEdit.setText(
realFormat.format(fit.getMarkerWeight()))
self._ui.fitStrainPenalty_lineEdit.setText(
realFormat.format(fit.getStrainPenaltyWeight()))
self._ui.fitCurvaturePenalty_lineEdit.setText(
realFormat.format(fit.getCurvaturePenaltyWeight()))
self._ui.fitEdgeDiscontinuityPenalty_lineEdit.setText(
realFormat.format(fit.getEdgeDiscontinuityPenaltyWeight()))
self._ui.fitIterations_spinBox.setValue(fit.getNumberOfIterations())
self._ui.fitUpdateReferenceState_checkBox.setCheckState(
QtCore.Qt.Checked if fit.isUpdateReferenceState(
) else QtCore.Qt.Unchecked)
def _fitMarkerWeightEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitMarkerWeight_lineEdit)
if value >= 0.0:
self._getFit().setMarkerWeight(value)
else:
print("Invalid marker weight; must be non-negative")
self._updateFitWidgets()
def _fitStrainPenaltyEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitStrainPenalty_lineEdit)
if value >= 0.0:
self._getFit().setStrainPenaltyWeight(value)
else:
print("Invalid penalty weight; must be non-negative")
self._updateFitWidgets()
def _fitCurvaturePenaltyEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitCurvaturePenalty_lineEdit)
if value >= 0.0:
self._getFit().setCurvaturePenaltyWeight(value)
else:
print("Invalid penalty weight; must be non-negative")
self._updateFitWidgets()
def _fitEdgeDiscontinuityPenaltyEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitEdgeDiscontinuityPenalty_lineEdit)
if value >= 0.0:
self._getFit().setEdgeDiscontinuityPenaltyWeight(value)
else:
print("Invalid penalty weight; must be non-negative")
self._updateFitWidgets()
def _fitIterationsValueChanged(self, value):
self._getFit().setNumberOfIterations(value)
def _fitUpdateReferenceStateClicked(self):
state = self._ui.fitUpdateReferenceState_checkBox.checkState()
self._getFit().setUpdateReferenceState(state == QtCore.Qt.Checked)
def _stepsAddFitClicked(self):
"""
Add a new fit step.
"""
self._currentFitterStep = FitterStepFit(self._fitter)
self._buildStepsList()
def _stepsAddAlignClicked(self):
"""
Add a new align step.
"""
self._currentFitterStep = FitterStepAlign(self._fitter)
self._buildStepsList()
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_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 GeometricFitWidget(QtGui.QWidget):
"""
User interface for github.com/ABI-Software/scaffoldfitter
"""
def __init__(self, model, parent=None):
"""
"""
super(GeometricFitWidget, self).__init__(parent)
self._ui = Ui_GeometricFitWidget()
self._ui.setupUi(self)
self._ui.alignmentsceneviewerwidget.setContext(model.getContext())
self._ui.alignmentsceneviewerwidget.setModel(model)
self._model = model
self._fitter = self._model.getFitter()
self._region = self._fitter.getRegion()
self._scene = self._region.getScene()
self._currentFitterStep = self._fitter.getInitialFitterStepConfig(
) # always exists
self._ui.alignmentsceneviewerwidget.graphicsInitialized.connect(
self._graphicsInitialized)
self._callback = None
self._setupConfigWidgets()
self._updateGeneralWidgets()
self._updateDisplayWidgets()
self._makeConnections()
def _graphicsInitialized(self):
"""
Callback for when SceneviewerWidget is initialised
"""
self._sceneChanged()
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
sceneviewer.setTransparencyMode(sceneviewer.TRANSPARENCY_MODE_SLOW)
self._autoPerturbLines()
sceneviewer.viewAll()
def _sceneChanged(self):
"""
Set custom scene from model.
"""
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
self._model.createGraphics()
sceneviewer.setScene(self._model.getScene())
self._refreshGraphics()
def _refreshGraphics(self):
"""
Autorange spectrum and force redraw of graphics.
"""
self._model.autorangeSpectrum()
self._ui.alignmentsceneviewerwidget.paintGL()
def _makeConnections(self):
self._makeConnectionsGeneral()
self._makeConnectionsDisplay()
self._makeConnectionsConfig()
self._makeConnectionsAlign()
self._makeConnectionsFit()
def registerDoneExecution(self, callback):
self._callback = callback
def _autoPerturbLines(self):
"""
Enable scene viewer perturb lines iff solid surfaces are drawn with lines.
Call whenever lines, surfaces or translucency changes
"""
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
sceneviewer.setPerturbLinesFlag(self._model.needPerturbLines())
# === general widgets ===
def _makeConnectionsGeneral(self):
self._ui.stepsAddAlign_pushButton.clicked.connect(
self._stepsAddAlignClicked)
self._ui.stepsAddConfig_pushButton.clicked.connect(
self._stepsAddConfigClicked)
self._ui.stepsAddFit_pushButton.clicked.connect(
self._stepsAddFitClicked)
self._ui.stepsDelete_pushButton.clicked.connect(
self._stepsDeleteClicked)
self._ui.steps_listView.clicked[QtCore.QModelIndex].connect(
self._stepsListItemClicked)
self._ui.done_pushButton.clicked.connect(self._doneButtonClicked)
self._ui.stdViews_pushButton.clicked.connect(
self._stdViewsButtonClicked)
self._ui.viewAll_pushButton.clicked.connect(self._viewAllButtonClicked)
def _updateGeneralWidgets(self):
self._ui.identifier_label.setText("Identifier: " +
self._model.getIdentifier())
self._buildStepsList()
def _stepsAddAlignClicked(self):
"""
Add a new align step.
"""
self._currentFitterStep = FitterStepAlign()
self._fitter.addFitterStep(
self._currentFitterStep) # Future: , lastFitterStep
self._buildStepsList()
def _stepsAddConfigClicked(self):
"""
Add a new config step.
"""
self._currentFitterStep = FitterStepConfig()
self._fitter.addFitterStep(
self._currentFitterStep) # Future: , lastFitterStep
self._buildStepsList()
def _stepsAddFitClicked(self):
"""
Add a new fit step.
"""
self._currentFitterStep = FitterStepFit()
self._fitter.addFitterStep(
self._currentFitterStep) # Future: , lastFitterStep
self._buildStepsList()
def runToStep(self, endStep):
"""
Run fitter steps up to specified end step.
"""
fitterSteps = self._fitter.getFitterSteps()
endIndex = fitterSteps.index(endStep)
sceneChanged = self._fitter.run(
endStep, self._model.getOutputModelFileNameStem())
if sceneChanged:
for index in range(endIndex + 1, len(fitterSteps)):
self._refreshStepItem(fitterSteps[index])
self._sceneChanged()
else:
for index in range(1, endIndex + 1):
self._refreshStepItem(fitterSteps[index])
self._refreshGraphics()
def _stepsDeleteClicked(self):
"""
Delete the currently selected step, except for initial config.
Select next step after, or before if none.
"""
assert self._currentFitterStep is not self._fitter.getInitialFitterStepConfig(
)
if self._currentFitterStep.hasRun():
# reload and run to step before current
fitterSteps = self._fitter.getFitterSteps()
index = fitterSteps.index(self._currentFitterStep)
self._fitter.run(fitterSteps[index - 1])
self._sceneChanged()
self._currentFitterStep = self._fitter.removeFitterStep(
self._currentFitterStep)
self._buildStepsList()
def _stepsListItemClicked(self, modelIndex):
"""
Changes current step and possibly changes checked/run status.
"""
model = modelIndex.model()
item = model.itemFromIndex(modelIndex)
step = item.data()
if step != self._currentFitterStep:
self._currentFitterStep = step
self._updateFitterStepWidgets()
isInitialConfig = step is self._fitter.getInitialFitterStepConfig()
isChecked = True if isInitialConfig else (item.checkState()
== QtCore.Qt.Checked)
if step.hasRun() != isChecked:
if isChecked:
endStep = step
else:
fitterSteps = self._fitter.getFitterSteps()
index = fitterSteps.index(step)
endStep = fitterSteps[index - 1]
self.runToStep(endStep)
def _buildStepsList(self):
"""
Fill the graphics list view with the list of graphics for current region/scene
"""
self._stepsItems = QtGui.QStandardItemModel(self._ui.steps_listView)
selectedIndex = None
firstStep = True
fitterSteps = self._fitter.getFitterSteps()
for step in fitterSteps:
name = None
if isinstance(step, FitterStepAlign):
name = "Align"
elif isinstance(step, FitterStepConfig):
name = "Config"
elif isinstance(step, FitterStepFit):
name = "Fit"
else:
assert False, "GeometricFitWidget. Unknown FitterStep type"
item = QtGui.QStandardItem(name)
item.setData(step)
item.setEditable(False)
if firstStep:
item.setCheckable(False)
firstStep = False
else:
item.setCheckable(True)
item.setCheckState(QtCore.Qt.Checked if step.hasRun(
) else QtCore.Qt.Unchecked)
self._stepsItems.appendRow(item)
if step == self._currentFitterStep:
selectedIndex = self._stepsItems.indexFromItem(item)
self._ui.steps_listView.setModel(self._stepsItems)
self._ui.steps_listView.setCurrentIndex(selectedIndex)
self._ui.steps_listView.show()
self._updateFitterStepWidgets()
def _refreshStepItem(self, step):
"""
Update check state and selection of step in steps list view.
:param stepIndex: Row index of item in step items.
"""
index = self._fitter.getFitterSteps().index(step)
item = self._stepsItems.item(index)
if step is not self._fitter.getInitialFitterStepConfig():
item.setCheckState(
QtCore.Qt.Checked if step.hasRun() else QtCore.Qt.Unchecked)
if step == self._currentFitterStep:
self._ui.steps_listView.setCurrentIndex(
self._stepsItems.indexFromItem(item))
def _updateFitterStepWidgets(self):
"""
Update and display widgets for currentFitterStep
"""
isInitialConfig = self._currentFitterStep == self._fitter.getInitialFitterStepConfig(
)
isAlign = isinstance(self._currentFitterStep, FitterStepAlign)
isConfig = isinstance(self._currentFitterStep, FitterStepConfig)
isFit = isinstance(self._currentFitterStep, FitterStepFit)
if isAlign:
self._updateAlignWidgets()
elif isConfig:
self._ui.configInitial_groupBox.setVisible(isInitialConfig)
self._updateConfigWidgets()
elif isFit:
self._updateFitWidgets()
self._ui.align_groupBox.setVisible(isAlign)
self._ui.config_groupBox.setVisible(isConfig)
self._ui.fit_groupBox.setVisible(isFit)
self._ui.stepsDelete_pushButton.setEnabled(not isInitialConfig)
def _doneButtonClicked(self):
self._model.done()
self._ui.dockWidget.setFloating(False)
self._callback()
def _stdViewsButtonClicked(self):
sceneviewer = self._ui.alignmentsceneviewerwidget.getSceneviewer()
if sceneviewer is not None:
result, eyePosition, lookatPosition, upVector = sceneviewer.getLookatParameters(
)
upVector = normalize(upVector)
viewVector = sub(lookatPosition, eyePosition)
viewDistance = magnitude(viewVector)
viewVector = normalize(viewVector)
viewX = dot(viewVector, [1.0, 0.0, 0.0])
viewY = dot(viewVector, [0.0, 1.0, 0.0])
viewZ = dot(viewVector, [0.0, 0.0, 1.0])
upX = dot(upVector, [1.0, 0.0, 0.0])
upY = dot(upVector, [0.0, 1.0, 0.0])
upZ = dot(upVector, [0.0, 0.0, 1.0])
if (viewZ < -0.999) and (upY > 0.999):
# XY -> XZ
viewVector = [0.0, 1.0, 0.0]
upVector = [0.0, 0.0, 1.0]
elif (viewY > 0.999) and (upZ > 0.999):
# XZ -> YZ
viewVector = [-1.0, 0.0, 0.0]
upVector = [0.0, 0.0, 1.0]
else:
# XY
viewVector = [0.0, 0.0, -1.0]
upVector = [0.0, 1.0, 0.0]
eyePosition = sub(lookatPosition, mult(viewVector, viewDistance))
sceneviewer.setLookatParametersNonSkew(eyePosition, lookatPosition,
upVector)
def _viewAllButtonClicked(self):
self._ui.alignmentsceneviewerwidget.viewAll()
# === display widgets ===
def _makeConnectionsDisplay(self):
self._ui.displayAxes_checkBox.clicked.connect(self._displayAxesClicked)
self._ui.displayMarkerDataPoints_checkBox.clicked.connect(
self._displayMarkerDataPointsClicked)
self._ui.displayMarkerDataNames_checkBox.clicked.connect(
self._displayMarkerDataNamesClicked)
self._ui.displayMarkerDataProjections_checkBox.clicked.connect(
self._displayMarkerDataProjectionsClicked)
self._ui.displayMarkerPoints_checkBox.clicked.connect(
self._displayMarkerPointsClicked)
self._ui.displayMarkerNames_checkBox.clicked.connect(
self._displayMarkerNamesClicked)
self._ui.displayDataPoints_checkBox.clicked.connect(
self._displayDataPointsClicked)
self._ui.displayDataProjections_checkBox.clicked.connect(
self._displayDataProjectionsClicked)
self._ui.displayDataProjectionPoints_checkBox.clicked.connect(
self._displayDataProjectionPointsClicked)
self._ui.displayNodePoints_checkBox.clicked.connect(
self._displayNodePointsClicked)
self._ui.displayNodeNumbers_checkBox.clicked.connect(
self._displayNodeNumbersClicked)
self._ui.displayNodeDerivativeLabelsD1_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD1Clicked)
self._ui.displayNodeDerivativeLabelsD2_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD2Clicked)
self._ui.displayNodeDerivativeLabelsD3_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD3Clicked)
self._ui.displayNodeDerivativeLabelsD12_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD12Clicked)
self._ui.displayNodeDerivativeLabelsD13_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD13Clicked)
self._ui.displayNodeDerivativeLabelsD23_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD23Clicked)
self._ui.displayNodeDerivativeLabelsD123_checkBox.clicked.connect(
self._displayNodeDerivativeLabelsD123Clicked)
self._ui.displayNodeDerivatives_checkBox.clicked.connect(
self._displayNodeDerivativesClicked)
self._ui.displayElementAxes_checkBox.clicked.connect(
self._displayElementAxesClicked)
self._ui.displayElementNumbers_checkBox.clicked.connect(
self._displayElementNumbersClicked)
self._ui.displayLines_checkBox.clicked.connect(
self._displayLinesClicked)
self._ui.displayLinesExterior_checkBox.clicked.connect(
self._displayLinesExteriorClicked)
self._ui.displaySurfaces_checkBox.clicked.connect(
self._displaySurfacesClicked)
self._ui.displaySurfacesExterior_checkBox.clicked.connect(
self._displaySurfacesExteriorClicked)
self._ui.displaySurfacesTranslucent_checkBox.clicked.connect(
self._displaySurfacesTranslucentClicked)
self._ui.displaySurfacesWireframe_checkBox.clicked.connect(
self._displaySurfacesWireframeClicked)
def _updateDisplayWidgets(self):
"""
Update display widgets to display settings for model graphics display.
"""
self._ui.displayAxes_checkBox.setChecked(self._model.isDisplayAxes())
self._ui.displayMarkerDataPoints_checkBox.setChecked(
self._model.isDisplayMarkerDataPoints())
self._ui.displayMarkerDataNames_checkBox.setChecked(
self._model.isDisplayMarkerDataNames())
self._ui.displayMarkerDataProjections_checkBox.setChecked(
self._model.isDisplayMarkerDataProjections())
self._ui.displayMarkerPoints_checkBox.setChecked(
self._model.isDisplayMarkerPoints())
self._ui.displayMarkerNames_checkBox.setChecked(
self._model.isDisplayMarkerNames())
self._ui.displayDataPoints_checkBox.setChecked(
self._model.isDisplayDataPoints())
self._ui.displayDataProjections_checkBox.setChecked(
self._model.isDisplayDataProjections())
self._ui.displayDataProjectionPoints_checkBox.setChecked(
self._model.isDisplayDataProjectionPoints())
self._ui.displayNodePoints_checkBox.setChecked(
self._model.isDisplayNodePoints())
self._ui.displayNodeNumbers_checkBox.setChecked(
self._model.isDisplayNodeNumbers())
self._ui.displayNodeDerivativeLabelsD1_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D1"))
self._ui.displayNodeDerivativeLabelsD2_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D2"))
self._ui.displayNodeDerivativeLabelsD3_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D3"))
self._ui.displayNodeDerivativeLabelsD12_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D12"))
self._ui.displayNodeDerivativeLabelsD13_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D13"))
self._ui.displayNodeDerivativeLabelsD23_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D23"))
self._ui.displayNodeDerivativeLabelsD123_checkBox.setChecked(
self._model.isDisplayNodeDerivativeLabels("D123"))
self._ui.displayNodeDerivatives_checkBox.setChecked(
self._model.isDisplayNodeDerivatives())
self._ui.displayElementNumbers_checkBox.setChecked(
self._model.isDisplayElementNumbers())
self._ui.displayElementAxes_checkBox.setChecked(
self._model.isDisplayElementAxes())
self._ui.displayLines_checkBox.setChecked(self._model.isDisplayLines())
self._ui.displayLinesExterior_checkBox.setChecked(
self._model.isDisplayLinesExterior())
self._ui.displaySurfaces_checkBox.setChecked(
self._model.isDisplaySurfaces())
self._ui.displaySurfacesExterior_checkBox.setChecked(
self._model.isDisplaySurfacesExterior())
self._ui.displaySurfacesTranslucent_checkBox.setChecked(
self._model.isDisplaySurfacesTranslucent())
self._ui.displaySurfacesWireframe_checkBox.setChecked(
self._model.isDisplaySurfacesWireframe())
def _displayAxesClicked(self):
self._model.setDisplayAxes(self._ui.displayAxes_checkBox.isChecked())
def _displayMarkerDataPointsClicked(self):
self._model.setDisplayMarkerDataPoints(
self._ui.displayMarkerDataPoints_checkBox.isChecked())
def _displayMarkerDataNamesClicked(self):
self._model.setDisplayMarkerDataNames(
self._ui.displayMarkerDataNames_checkBox.isChecked())
def _displayMarkerDataProjectionsClicked(self):
self._model.setDisplayMarkerDataProjections(
self._ui.displayMarkerDataProjections_checkBox.isChecked())
def _displayMarkerPointsClicked(self):
self._model.setDisplayMarkerPoints(
self._ui.displayMarkerPoints_checkBox.isChecked())
def _displayMarkerNamesClicked(self):
self._model.setDisplayMarkerNames(
self._ui.displayMarkerNames_checkBox.isChecked())
def _displayDataPointsClicked(self):
self._model.setDisplayDataPoints(
self._ui.displayDataPoints_checkBox.isChecked())
def _displayDataProjectionsClicked(self):
self._model.setDisplayDataProjections(
self._ui.displayDataProjections_checkBox.isChecked())
def _displayDataProjectionPointsClicked(self):
self._model.setDisplayDataProjectionPoints(
self._ui.displayDataProjectionPoints_checkBox.isChecked())
def _displayNodePointsClicked(self):
self._model.setDisplayNodePoints(
self._ui.displayNodePoints_checkBox.isChecked())
def _displayNodeNumbersClicked(self):
self._model.setDisplayNodeNumbers(
self._ui.displayNodeNumbers_checkBox.isChecked())
def _displayNodeDerivativesClicked(self):
self._model.setDisplayNodeDerivatives(
self._ui.displayNodeDerivatives_checkBox.isChecked())
def _displayNodeDerivativeLabelsD1Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D1", self._ui.displayNodeDerivativeLabelsD1_checkBox.isChecked())
def _displayNodeDerivativeLabelsD2Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D2", self._ui.displayNodeDerivativeLabelsD2_checkBox.isChecked())
def _displayNodeDerivativeLabelsD3Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D3", self._ui.displayNodeDerivativeLabelsD3_checkBox.isChecked())
def _displayNodeDerivativeLabelsD12Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D12",
self._ui.displayNodeDerivativeLabelsD12_checkBox.isChecked())
def _displayNodeDerivativeLabelsD13Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D13",
self._ui.displayNodeDerivativeLabelsD13_checkBox.isChecked())
def _displayNodeDerivativeLabelsD23Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D23",
self._ui.displayNodeDerivativeLabelsD23_checkBox.isChecked())
def _displayNodeDerivativeLabelsD123Clicked(self):
self._model.setDisplayNodeDerivativeLabels(
"D123",
self._ui.displayNodeDerivativeLabelsD123_checkBox.isChecked())
def _displayElementAxesClicked(self):
self._model.setDisplayElementAxes(
self._ui.displayElementAxes_checkBox.isChecked())
def _displayElementNumbersClicked(self):
self._model.setDisplayElementNumbers(
self._ui.displayElementNumbers_checkBox.isChecked())
def _displayLinesClicked(self):
self._model.setDisplayLines(self._ui.displayLines_checkBox.isChecked())
self._autoPerturbLines()
def _displayLinesExteriorClicked(self):
self._model.setDisplayLinesExterior(
self._ui.displayLinesExterior_checkBox.isChecked())
def _displaySurfacesClicked(self):
self._model.setDisplaySurfaces(
self._ui.displaySurfaces_checkBox.isChecked())
self._autoPerturbLines()
def _displaySurfacesExteriorClicked(self):
self._model.setDisplaySurfacesExterior(
self._ui.displaySurfacesExterior_checkBox.isChecked())
def _displaySurfacesTranslucentClicked(self):
self._model.setDisplaySurfacesTranslucent(
self._ui.displaySurfacesTranslucent_checkBox.isChecked())
self._autoPerturbLines()
def _displaySurfacesWireframeClicked(self):
self._model.setDisplaySurfacesWireframe(
self._ui.displaySurfacesWireframe_checkBox.isChecked())
# === config widgets ===
def _setupConfigWidgets(self):
"""
Set up config widgets and display values from fitter object.
"""
self._ui.configModelCoordinates_fieldChooser.setRegion(self._region)
self._ui.configModelCoordinates_fieldChooser.setNullObjectName("-")
self._ui.configModelCoordinates_fieldChooser.setConditional(
fieldIsManagedCoordinates)
self._ui.configModelCoordinates_fieldChooser.setField(
self._fitter.getModelCoordinatesField())
self._ui.configDataCoordinates_fieldChooser.setRegion(self._region)
self._ui.configDataCoordinates_fieldChooser.setNullObjectName("-")
self._ui.configDataCoordinates_fieldChooser.setConditional(
fieldIsManagedCoordinates)
self._ui.configDataCoordinates_fieldChooser.setField(
self._fitter.getDataCoordinatesField())
self._ui.configMarkerGroup_fieldChooser.setRegion(self._region)
self._ui.configMarkerGroup_fieldChooser.setNullObjectName("-")
self._ui.configMarkerGroup_fieldChooser.setConditional(
fieldIsManagedGroup)
self._ui.configMarkerGroup_fieldChooser.setField(
self._fitter.getMarkerGroup())
def _makeConnectionsConfig(self):
self._ui.configModelCoordinates_fieldChooser.currentIndexChanged.connect(
self._configModelCoordinatesFieldChanged)
self._ui.configDataCoordinates_fieldChooser.currentIndexChanged.connect(
self._configDataCoordinatesFieldChanged)
self._ui.configMarkerGroup_fieldChooser.currentIndexChanged.connect(
self._configMarkerGroupChanged)
self._ui.configProjectionCentreGroups_checkBox.clicked.connect(
self._configProjectionCentreGroupsClicked)
def _getConfig(self):
config = self._currentFitterStep
assert isinstance(config, FitterStepConfig)
return config
def _updateConfigWidgets(self):
"""
Update config widgets to display settings for Fitter.
"""
config = self._getConfig()
self._ui.configProjectionCentreGroups_checkBox.setCheckState(
QtCore.Qt.Checked if config.isProjectionCentreGroups(
) else QtCore.Qt.Unchecked)
def _configModelCoordinatesFieldChanged(self, index):
"""
Callback for change in model coordinates field chooser widget.
"""
field = self._ui.configModelCoordinates_fieldChooser.getField()
if field:
self._fitter.setModelCoordinatesField(field)
def _configDataCoordinatesFieldChanged(self, index):
"""
Callback for change in data coordinates field chooser widget.
"""
field = self._ui.configDataCoordinates_fieldChooser.getField()
if field:
self._fitter.setDataCoordinatesField(field)
def _configMarkerGroupChanged(self, index):
"""
Callback for change in marker group field chooser widget.
"""
group = self._ui.configMarkerGroup_fieldChooser.getField()
if group:
self._fitter.setMarkerGroup(group)
def _configProjectionCentreGroupsClicked(self):
state = self._ui.configProjectionCentreGroups_checkBox.checkState()
config = self._getConfig()
if config.setProjectionCentreGroups(state == QtCore.Qt.Checked):
fitterSteps = self._fitter.getFitterSteps()
index = fitterSteps.index(config)
if config.hasRun() and (((index + 1) == len(fitterSteps)) or
(not fitterSteps[index + 1].hasRun())):
config.run()
self._refreshStepItem(config)
self._refreshGraphics()
# === align widgets ===
def _makeConnectionsAlign(self):
self._ui.alignGroups_checkBox.clicked.connect(self._alignGroupsClicked)
self._ui.alignMarkers_checkBox.clicked.connect(
self._alignMarkersClicked)
self._ui.alignRotation_lineEdit.editingFinished.connect(
self._alignRotationEntered)
self._ui.alignScale_lineEdit.editingFinished.connect(
self._alignScaleEntered)
self._ui.alignTranslation_lineEdit.editingFinished.connect(
self._alignTranslationEntered)
def _getAlign(self):
align = self._currentFitterStep
assert isinstance(align, FitterStepAlign)
return align
def _updateAlignWidgets(self):
"""
Update align widgets to display parameters from current align step.
"""
align = self._getAlign()
realFormat = "{:.4g}"
self._ui.alignGroups_checkBox.setCheckState(
QtCore.Qt.Checked if align.isAlignGroups(
) else QtCore.Qt.Unchecked)
self._ui.alignMarkers_checkBox.setCheckState(
QtCore.Qt.Checked if align.isAlignMarkers(
) else QtCore.Qt.Unchecked)
self._ui.alignRotation_lineEdit.setText(", ".join(
realFormat.format(value) for value in align.getRotation()))
self._ui.alignScale_lineEdit.setText(
realFormat.format(align.getScale()))
self._ui.alignTranslation_lineEdit.setText(", ".join(
realFormat.format(value) for value in align.getTranslation()))
def _alignGroupsClicked(self):
state = self._ui.alignGroups_checkBox.checkState()
self._getAlign().setAlignGroups(state == QtCore.Qt.Checked)
def _alignMarkersClicked(self):
state = self._ui.alignMarkers_checkBox.checkState()
self._getAlign().setAlignMarkers(state == QtCore.Qt.Checked)
def _alignRotationEntered(self):
values = QLineEdit_parseVector3(self._ui.alignRotation_lineEdit)
if values:
self._getAlign().setRotation(values)
else:
print("Invalid model rotation Euler angles entered")
self._updateAlignWidgets()
def _alignScaleEntered(self):
value = QLineEdit_parseRealNonNegative(self._ui.alignScale_lineEdit)
if value > 0.0:
self._getAlign().setScale(value)
else:
print("Invalid model scale entered")
self._updateAlignWidgets()
def _alignTranslationEntered(self):
values = QLineEdit_parseVector3(self._ui.alignTranslation_lineEdit)
if values:
self._getAlign().setTranslation(values)
else:
print("Invalid model translation entered")
self._updateAlignWidgets()
# === fit widgets ===
def _makeConnectionsFit(self):
self._ui.fitLineWeight_lineEdit.editingFinished.connect(
self._fitLineWeightEntered)
self._ui.fitMarkerWeight_lineEdit.editingFinished.connect(
self._fitMarkerWeightEntered)
self._ui.fitStrainPenalty_lineEdit.editingFinished.connect(
self._fitStrainPenaltyEntered)
self._ui.fitCurvaturePenalty_lineEdit.editingFinished.connect(
self._fitCurvaturePenaltyEntered)
self._ui.fitEdgeDiscontinuityPenalty_lineEdit.editingFinished.connect(
self._fitEdgeDiscontinuityPenaltyEntered)
self._ui.fitIterations_spinBox.valueChanged.connect(
self._fitIterationsValueChanged)
self._ui.fitMaximumSubIterations_spinBox.valueChanged.connect(
self._fitMaximumSubIterationsValueChanged)
self._ui.fitUpdateReferenceState_checkBox.clicked.connect(
self._fitUpdateReferenceStateClicked)
def _getFit(self):
assert isinstance(self._currentFitterStep, FitterStepFit)
return self._currentFitterStep
def _updateFitWidgets(self):
"""
Update fit widgets to display parameters from fit step.
"""
fit = self._getFit()
realFormat = "{:.16}"
self._ui.fitLineWeight_lineEdit.setText(
realFormat.format(fit.getLineWeight()))
self._ui.fitMarkerWeight_lineEdit.setText(
realFormat.format(fit.getMarkerWeight()))
self._ui.fitStrainPenalty_lineEdit.setText(
realFormat.format(fit.getStrainPenaltyWeight()))
self._ui.fitCurvaturePenalty_lineEdit.setText(
realFormat.format(fit.getCurvaturePenaltyWeight()))
self._ui.fitEdgeDiscontinuityPenalty_lineEdit.setText(
realFormat.format(fit.getEdgeDiscontinuityPenaltyWeight()))
self._ui.fitIterations_spinBox.setValue(fit.getNumberOfIterations())
self._ui.fitMaximumSubIterations_spinBox.setValue(
fit.getMaximumSubIterations())
self._ui.fitUpdateReferenceState_checkBox.setCheckState(
QtCore.Qt.Checked if fit.isUpdateReferenceState(
) else QtCore.Qt.Unchecked)
def _fitLineWeightEntered(self):
value = QLineEdit_parseRealNonNegative(self._ui.fitLineWeight_lineEdit)
if value >= 0.0:
self._getFit().setLineWeight(value)
else:
print("Invalid line weight; must be non-negative")
self._updateFitWidgets()
def _fitMarkerWeightEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitMarkerWeight_lineEdit)
if value >= 0.0:
self._getFit().setMarkerWeight(value)
else:
print("Invalid marker weight; must be non-negative")
self._updateFitWidgets()
def _fitStrainPenaltyEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitStrainPenalty_lineEdit)
if value >= 0.0:
self._getFit().setStrainPenaltyWeight(value)
else:
print("Invalid penalty weight; must be non-negative")
self._updateFitWidgets()
def _fitCurvaturePenaltyEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitCurvaturePenalty_lineEdit)
if value >= 0.0:
self._getFit().setCurvaturePenaltyWeight(value)
else:
print("Invalid penalty weight; must be non-negative")
self._updateFitWidgets()
def _fitEdgeDiscontinuityPenaltyEntered(self):
value = QLineEdit_parseRealNonNegative(
self._ui.fitEdgeDiscontinuityPenalty_lineEdit)
if value >= 0.0:
self._getFit().setEdgeDiscontinuityPenaltyWeight(value)
else:
print("Invalid penalty weight; must be non-negative")
self._updateFitWidgets()
def _fitIterationsValueChanged(self, value):
self._getFit().setNumberOfIterations(value)
def _fitMaximumSubIterationsValueChanged(self, value):
self._getFit().setMaximumSubIterations(value)
def _fitUpdateReferenceStateClicked(self):
state = self._ui.fitUpdateReferenceState_checkBox.checkState()
self._getFit().setUpdateReferenceState(state == QtCore.Qt.Checked)
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)