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()
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)
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.assertTrue(align.isAlignMarkers())
align.setAlignMarkers(False)
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)
class GeometryFitterModel(object):
"""
Geometric fit model adding visualisations to github.com/ABI-Software/scaffoldfitter
"""
def __init__(self, inputZincModelFile, inputZincDataFile, location,
identifier):
"""
:param location: Path to folder for mapclient step name.
"""
self._fitter = Fitter(inputZincModelFile, inputZincDataFile)
# self._fitter.setDiagnosticLevel(1)
self._location = os.path.join(location, identifier)
self._identifier = identifier
self._initGraphicsModules()
self._settings = {
"displayAxes": True,
"displayMarkerDataPoints": True,
"displayMarkerDataNames": False,
"displayMarkerDataProjections": True,
"displayMarkerPoints": True,
"displayMarkerNames": False,
"displayDataPoints": True,
"displayDataProjections": True,
"displayDataProjectionPoints": True,
"displayNodePoints": False,
"displayNodeNumbers": False,
"displayNodeDerivatives": False,
"displayNodeDerivativeLabels": nodeDerivativeLabels[0:3],
"displayElementNumbers": False,
"displayElementAxes": False,
"displayLines": True,
"displayLinesExterior": False,
"displaySurfaces": True,
"displaySurfacesExterior": True,
"displaySurfacesTranslucent": True,
"displaySurfacesWireframe": False
}
self._loadSettings()
self._fitter.load()
def _initGraphicsModules(self):
context = self._fitter.getContext()
self._materialmodule = context.getMaterialmodule()
with ChangeManager(self._materialmodule):
self._materialmodule.defineStandardMaterials()
solid_blue = self._materialmodule.createMaterial()
solid_blue.setName("solid_blue")
solid_blue.setManaged(True)
solid_blue.setAttributeReal3(Material.ATTRIBUTE_AMBIENT,
[0.0, 0.2, 0.6])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE,
[0.0, 0.7, 1.0])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
solid_blue.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.1, 0.1, 0.1])
solid_blue.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
trans_blue = self._materialmodule.createMaterial()
trans_blue.setName("trans_blue")
trans_blue.setManaged(True)
trans_blue.setAttributeReal3(Material.ATTRIBUTE_AMBIENT,
[0.0, 0.2, 0.6])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_DIFFUSE,
[0.0, 0.7, 1.0])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_EMISSION,
[0.0, 0.0, 0.0])
trans_blue.setAttributeReal3(Material.ATTRIBUTE_SPECULAR,
[0.1, 0.1, 0.1])
trans_blue.setAttributeReal(Material.ATTRIBUTE_ALPHA, 0.3)
trans_blue.setAttributeReal(Material.ATTRIBUTE_SHININESS, 0.2)
glyphmodule = context.getGlyphmodule()
glyphmodule.defineStandardGlyphs()
tessellationmodule = context.getTessellationmodule()
defaultTessellation = tessellationmodule.getDefaultTessellation()
defaultTessellation.setRefinementFactors([12])
def _getFitSettingsFileName(self):
return self._location + "-settings.json"
def _getDisplaySettingsFileName(self):
return self._location + "-display-settings.json"
def _loadSettings(self):
# try:
fitSettingsFileName = self._getFitSettingsFileName()
if os.path.isfile(fitSettingsFileName):
with open(fitSettingsFileName, "r") as f:
self._fitter.decodeSettingsJSON(f.read(),
decodeJSONFitterSteps)
# except:
# print('_loadSettings FitSettings EXCEPTION')
# raise()
# try:
displaySettingsFileName = self._getDisplaySettingsFileName()
if os.path.isfile(displaySettingsFileName):
with open(displaySettingsFileName, "r") as f:
savedSettings = json.loads(f.read())
self._settings.update(savedSettings)
# except:
# print('_loadSettings DisplaySettings EXCEPTION')
# pass
def _saveSettings(self):
with open(self._getFitSettingsFileName(), "w") as f:
f.write(self._fitter.encodeSettingsJSON())
with open(self._getDisplaySettingsFileName(), "w") as f:
f.write(json.dumps(self._settings, sort_keys=False, indent=4))
def getOutputModelFileNameStem(self):
return self._location
def getOutputModelFileName(self):
return self._location + ".exf"
def done(self):
self._saveSettings()
self._fitter.run(endStep=None,
modelFileNameStem=self.getOutputModelFileNameStem())
self._fitter.writeModel(self.getOutputModelFileName())
def getIdentifier(self):
return self._identifier
def getContext(self):
return self._fitter.getContext()
def getFitter(self):
return self._fitter
def getRegion(self):
return self._fitter.getRegion()
def getFieldmodule(self):
return self._fitter.getFieldmodule()
def getScene(self):
return self._fitter.getRegion().getScene()
def _getVisibility(self, graphicsName):
return self._settings[graphicsName]
def _setVisibility(self, graphicsName, show):
self._settings[graphicsName] = show
graphics = self.getScene().findGraphicsByName(graphicsName)
graphics.setVisibilityFlag(show)
def _setMultipleGraphicsVisibility(self, graphicsName, show):
'''
Ensure visibility of all graphics with graphicsName is set to boolean show.
'''
self._settings[graphicsName] = show
scene = self.getScene()
graphics = scene.findGraphicsByName(graphicsName)
while graphics.isValid():
graphics.setVisibilityFlag(show)
while True:
graphics = scene.getNextGraphics(graphics)
if (not graphics.isValid()) or (graphics.getName()
== graphicsName):
break
def isDisplayAxes(self):
return self._getVisibility("displayAxes")
def setDisplayAxes(self, show):
self._setVisibility("displayAxes", show)
def isDisplayElementNumbers(self):
return self._getVisibility("displayElementNumbers")
def setDisplayElementNumbers(self, show):
self._setVisibility("displayElementNumbers", show)
def isDisplayLines(self):
return self._getVisibility("displayLines")
def setDisplayLines(self, show):
self._setVisibility("displayLines", show)
def isDisplayLinesExterior(self):
return self._settings["displayLinesExterior"]
def setDisplayLinesExterior(self, isExterior):
self._settings["displayLinesExterior"] = isExterior
lines = self.getScene().findGraphicsByName("displayLines")
lines.setExterior(self.isDisplayLinesExterior())
def isDisplayNodeDerivatives(self):
return self._getVisibility("displayNodeDerivatives")
def setDisplayNodeDerivatives(self, show):
self._settings["displayNodeDerivatives"] = show
scene = self.getScene()
for nodeDerivativeLabel in nodeDerivativeLabels:
graphics = scene.findGraphicsByName("displayNodeDerivatives" +
nodeDerivativeLabel)
graphics.setVisibilityFlag(
show
and self.isDisplayNodeDerivativeLabels(nodeDerivativeLabel))
def isDisplayNodeDerivativeLabels(self, nodeDerivativeLabel):
"""
:param nodeDerivativeLabel: Label from nodeDerivativeLabels ("D1", "D2" ...)
"""
return nodeDerivativeLabel in self._settings[
"displayNodeDerivativeLabels"]
def setDisplayNodeDerivativeLabels(self, nodeDerivativeLabel, show):
"""
:param nodeDerivativeLabel: Label from nodeDerivativeLabels ("D1", "D2" ...)
"""
shown = nodeDerivativeLabel in self._settings[
"displayNodeDerivativeLabels"]
if show:
if not shown:
# keep in same order as nodeDerivativeLabels
nodeDerivativeLabels = []
for label in nodeDerivativeLabels:
if (label == nodeDerivativeLabel
) or self.isDisplayNodeDerivativeLabels(label):
nodeDerivativeLabels.append(label)
self._settings[
"displayNodeDerivativeLabels"] = nodeDerivativeLabels
else:
if shown:
self._settings["displayNodeDerivativeLabels"].remove(
nodeDerivativeLabel)
graphics = self.getScene().findGraphicsByName(
"displayNodeDerivatives" + nodeDerivativeLabel)
graphics.setVisibilityFlag(show and self.isDisplayNodeDerivatives())
def isDisplayMarkerDataPoints(self):
return self._getVisibility("displayMarkerDataPoints")
def setDisplayMarkerDataPoints(self, show):
self._setVisibility("displayMarkerDataPoints", show)
def isDisplayMarkerDataNames(self):
return self._getVisibility("displayMarkerDataNames")
def setDisplayMarkerDataNames(self, show):
self._setVisibility("displayMarkerDataNames", show)
def isDisplayMarkerDataProjections(self):
return self._getVisibility("displayMarkerDataProjections")
def setDisplayMarkerDataProjections(self, show):
self._setVisibility("displayMarkerDataProjections", show)
def isDisplayMarkerPoints(self):
return self._getVisibility("displayMarkerPoints")
def setDisplayMarkerPoints(self, show):
self._setVisibility("displayMarkerPoints", show)
def isDisplayMarkerNames(self):
return self._getVisibility("displayMarkerNames")
def setDisplayMarkerNames(self, show):
self._setVisibility("displayMarkerNames", show)
def isDisplayDataPoints(self):
return self._getVisibility("displayDataPoints")
def setDisplayDataPoints(self, show):
self._setVisibility("displayDataPoints", show)
def isDisplayDataProjections(self):
return self._getVisibility("displayDataProjections")
def setDisplayDataProjections(self, show):
self._setMultipleGraphicsVisibility("displayDataProjections", show)
def isDisplayDataProjectionPoints(self):
return self._getVisibility("displayDataProjectionPoints")
def setDisplayDataProjectionPoints(self, show):
self._setMultipleGraphicsVisibility("displayDataProjectionPoints",
show)
def isDisplayNodeNumbers(self):
return self._getVisibility("displayNodeNumbers")
def setDisplayNodeNumbers(self, show):
self._setVisibility("displayNodeNumbers", show)
def isDisplayNodePoints(self):
return self._getVisibility("displayNodePoints")
def setDisplayNodePoints(self, show):
self._setVisibility("displayNodePoints", show)
def isDisplaySurfaces(self):
return self._getVisibility("displaySurfaces")
def setDisplaySurfaces(self, show):
self._setVisibility("displaySurfaces", show)
def isDisplaySurfacesExterior(self):
return self._settings["displaySurfacesExterior"]
def setDisplaySurfacesExterior(self, isExterior):
self._settings["displaySurfacesExterior"] = isExterior
surfaces = self.getScene().findGraphicsByName("displaySurfaces")
surfaces.setExterior(self.isDisplaySurfacesExterior() if (
self._fitter.getHighestDimensionMesh().getDimension() == 3
) else False)
def isDisplaySurfacesTranslucent(self):
return self._settings["displaySurfacesTranslucent"]
def setDisplaySurfacesTranslucent(self, isTranslucent):
self._settings["displaySurfacesTranslucent"] = isTranslucent
surfaces = self.getScene().findGraphicsByName("displaySurfaces")
surfacesMaterial = self._materialmodule.findMaterialByName(
"trans_blue" if isTranslucent else "solid_blue")
surfaces.setMaterial(surfacesMaterial)
def isDisplaySurfacesWireframe(self):
return self._settings["displaySurfacesWireframe"]
def setDisplaySurfacesWireframe(self, isWireframe):
self._settings["displaySurfacesWireframe"] = isWireframe
surfaces = self.getScene().findGraphicsByName("displaySurfaces")
surfaces.setRenderPolygonMode(
Graphics.RENDER_POLYGON_MODE_WIREFRAME
if isWireframe else Graphics.RENDER_POLYGON_MODE_SHADED)
def isDisplayElementAxes(self):
return self._getVisibility("displayElementAxes")
def setDisplayElementAxes(self, show):
self._setVisibility("displayElementAxes", show)
def needPerturbLines(self):
"""
Return if solid surfaces are drawn with lines, requiring perturb lines to be activated.
"""
region = self.getRegion()
if region is None:
return False
mesh2d = region.getFieldmodule().findMeshByDimension(2)
if mesh2d.getSize() == 0:
return False
return self.isDisplayLines() and self.isDisplaySurfaces(
) and not self.isDisplaySurfacesTranslucent()
def setSelectHighlightGroup(self, group: FieldGroup):
"""
Select and highlight objects in the group.
:param group: FieldGroup to select, or None to clear selection.
"""
fieldmodule = self.getFieldmodule()
with ChangeManager(fieldmodule):
scene = self.getScene()
# can't use SUBELEMENT_HANDLING_MODE_FULL as some groups have been tweaked to omit some faces
selectionGroup = get_scene_selection_group(
scene,
subelementHandlingMode=FieldGroup.SUBELEMENT_HANDLING_MODE_NONE
)
if group:
if selectionGroup:
selectionGroup.clear()
else:
selectionGroup = create_scene_selection_group(
scene,
subelementHandlingMode=FieldGroup.
SUBELEMENT_HANDLING_MODE_NONE)
group_add_group_elements(selectionGroup,
group,
highest_dimension_only=False)
for fieldDomainType in (Field.DOMAIN_TYPE_NODES,
Field.DOMAIN_TYPE_DATAPOINTS):
group_add_group_nodes(
selectionGroup, group,
fieldmodule.findNodesetByFieldDomainType(
fieldDomainType))
else:
if selectionGroup:
selectionGroup.clear()
scene.setSelectionField(Field())
def setSelectHighlightGroupByName(self, groupName):
"""
Select and highlight objects in the group by name.
:param groupName: Name of group to select, or None to clear selection.
"""
fieldmodule = self.getFieldmodule()
group = None
if groupName:
group = fieldmodule.findFieldByName(groupName).castGroup()
if not group.isValid():
group = None
self.setSelectHighlightGroup(group)
def createGraphics(self):
fieldmodule = self.getFieldmodule()
mesh = self._fitter.getHighestDimensionMesh()
meshDimension = mesh.getDimension()
modelCoordinates = self._fitter.getModelCoordinatesField()
componentsCount = modelCoordinates.getNumberOfComponents()
# prepare fields and calculate axis and glyph scaling
with ChangeManager(fieldmodule):
# fields in same order as nodeDerivativeLabels
nodeDerivativeFields = [
fieldmodule.createFieldNodeValue(modelCoordinates, derivative,
1)
for derivative in [
Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D2_DS1DS3, Node.VALUE_LABEL_D2_DS2DS3,
Node.VALUE_LABEL_D3_DS1DS2DS3
]
]
elementDerivativesField = fieldmodule.createFieldConcatenate([
fieldmodule.createFieldDerivative(modelCoordinates, d + 1)
for d in range(meshDimension)
])
cmiss_number = fieldmodule.findFieldByName("cmiss_number")
markerNodeGroup, markerLocation, markerCoordinates, markerName = self._fitter.getMarkerModelFields(
)
# get sizing for axes
axesScale = 1.0
nodes = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
minX, maxX = evaluateFieldNodesetRange(modelCoordinates, nodes)
if componentsCount == 1:
maxRange = maxX - minX
else:
maxRange = maxX[0] - minX[0]
for c in range(1, componentsCount):
maxRange = max(maxRange, maxX[c] - minX[c])
if maxRange > 0.0:
while axesScale * 10.0 < maxRange:
axesScale *= 10.0
while axesScale * 0.1 > maxRange:
axesScale *= 0.1
# fixed width glyph size is based on average element size in all dimensions
mesh1d = fieldmodule.findMeshByDimension(1)
meanLineLength = 0.0
lineCount = mesh1d.getSize()
if lineCount > 0:
one = fieldmodule.createFieldConstant(1.0)
sumLineLength = fieldmodule.createFieldMeshIntegral(
one, modelCoordinates, mesh1d)
cache = fieldmodule.createFieldcache()
result, totalLineLength = sumLineLength.evaluateReal(cache, 1)
glyphWidth = 0.1 * totalLineLength / lineCount
del cache
del sumLineLength
del one
if (lineCount == 0) or (glyphWidth == 0.0):
# use function of coordinate range if no elements
if componentsCount == 1:
maxScale = maxX - minX
else:
first = True
for c in range(componentsCount):
scale = maxX[c] - minX[c]
if first or (scale > maxScale):
maxScale = scale
first = False
if maxScale == 0.0:
maxScale = 1.0
glyphWidth = 0.01 * maxScale
glyphWidthSmall = 0.25 * glyphWidth
# make graphics
scene = self._fitter.getRegion().getScene()
with ChangeManager(scene):
scene.removeAllGraphics()
axes = scene.createGraphicsPoints()
pointattr = axes.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_AXES_XYZ)
pointattr.setBaseSize([axesScale, axesScale, axesScale])
pointattr.setLabelText(1, " " + str(axesScale))
axes.setMaterial(self._materialmodule.findMaterialByName("grey50"))
axes.setName("displayAxes")
axes.setVisibilityFlag(self.isDisplayAxes())
# marker points, projections
markerGroup = self._fitter.getMarkerGroup()
markerDataGroup, markerDataCoordinates, markerDataName = self._fitter.getMarkerDataFields(
)
markerDataLocation, markerDataLocationCoordinates, markerDataDelta = self._fitter.getMarkerDataLocationFields(
)
markerNodeGroup, markerLocation, markerCoordinates, markerName = self._fitter.getMarkerModelFields(
)
markerDataLocationGroupField = self._fitter.getMarkerDataLocationGroupField(
)
markerDataPoints = scene.createGraphicsPoints()
markerDataPoints.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if markerDataLocationGroupField:
markerDataPoints.setSubgroupField(markerDataLocationGroupField)
elif markerGroup:
markerDataPoints.setSubgroupField(markerGroup)
if markerDataCoordinates:
markerDataPoints.setCoordinateField(markerDataCoordinates)
pointattr = markerDataPoints.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_CROSS)
markerDataPoints.setMaterial(
self._materialmodule.findMaterialByName("yellow"))
markerDataPoints.setName("displayMarkerDataPoints")
markerDataPoints.setVisibilityFlag(
self.isDisplayMarkerDataPoints())
markerDataNames = scene.createGraphicsPoints()
markerDataNames.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if markerDataLocationGroupField:
markerDataNames.setSubgroupField(markerDataLocationGroupField)
elif markerGroup:
markerDataNames.setSubgroupField(markerGroup)
if markerDataCoordinates:
markerDataNames.setCoordinateField(markerDataCoordinates)
pointattr = markerDataNames.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
if markerDataName:
pointattr.setLabelField(markerDataName)
markerDataNames.setMaterial(
self._materialmodule.findMaterialByName("yellow"))
markerDataNames.setName("displayMarkerDataNames")
markerDataNames.setVisibilityFlag(self.isDisplayMarkerDataNames())
markerDataProjections = scene.createGraphicsPoints()
markerDataProjections.setFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
if markerDataLocationGroupField:
markerDataProjections.setSubgroupField(
markerDataLocationGroupField)
elif markerGroup:
markerDataProjections.setSubgroupField(markerGroup)
if markerDataCoordinates:
markerDataProjections.setCoordinateField(markerDataCoordinates)
pointAttr = markerDataProjections.getGraphicspointattributes()
pointAttr.setGlyphShapeType(Glyph.SHAPE_TYPE_LINE)
pointAttr.setBaseSize([0.0, 1.0, 1.0])
pointAttr.setScaleFactors([1.0, 0.0, 0.0])
if markerDataDelta:
pointAttr.setOrientationScaleField(markerDataDelta)
markerDataProjections.setMaterial(
self._materialmodule.findMaterialByName("magenta"))
markerDataProjections.setName("displayMarkerDataProjections")
markerDataProjections.setVisibilityFlag(
self.isDisplayMarkerDataProjections())
markerPoints = scene.createGraphicsPoints()
markerPoints.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
if markerGroup:
markerPoints.setSubgroupField(markerGroup)
if markerCoordinates:
markerPoints.setCoordinateField(markerCoordinates)
pointattr = markerPoints.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_CROSS)
markerPoints.setMaterial(
self._materialmodule.findMaterialByName("white"))
markerPoints.setName("displayMarkerPoints")
markerPoints.setVisibilityFlag(self.isDisplayMarkerPoints())
markerNames = scene.createGraphicsPoints()
markerNames.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
if markerGroup:
markerNames.setSubgroupField(markerGroup)
if markerCoordinates:
markerNames.setCoordinateField(markerCoordinates)
pointattr = markerNames.getGraphicspointattributes()
pointattr.setBaseSize(
[glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
if markerName:
pointattr.setLabelField(markerName)
markerNames.setMaterial(
self._materialmodule.findMaterialByName("white"))
markerNames.setName("displayMarkerNames")
markerNames.setVisibilityFlag(self.isDisplayMarkerNames())
# data points, projections and projection points
dataCoordinates = self._fitter.getDataCoordinatesField()
dataPoints = scene.createGraphicsPoints()
dataPoints.setFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
if dataCoordinates:
dataPoints.setCoordinateField(dataCoordinates)
pointattr = dataPoints.getGraphicspointattributes()
# pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_DIAMOND)
# pointattr.setBaseSize([glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_POINT)
dataPoints.setRenderPointSize(3.0)
dataPoints.setMaterial(
self._materialmodule.findMaterialByName("grey50"))
dataPoints.setName("displayDataPoints")
dataPoints.setVisibilityFlag(self.isDisplayDataPoints())
for projectionMeshDimension in range(1, 3):
dataProjectionNodeGroup = self._fitter.getDataProjectionNodeGroupField(
projectionMeshDimension)
if dataProjectionNodeGroup.getNodesetGroup().getSize() == 0:
continue
dataProjectionCoordinates = self._fitter.getDataProjectionCoordinatesField(
projectionMeshDimension)
dataProjectionDelta = self._fitter.getDataProjectionDeltaField(
projectionMeshDimension)
dataProjectionError = self._fitter.getDataProjectionErrorField(
projectionMeshDimension)
dataProjections = scene.createGraphicsPoints()
dataProjections.setFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
dataProjections.setSubgroupField(dataProjectionNodeGroup)
if dataCoordinates:
dataProjections.setCoordinateField(dataCoordinates)
pointAttr = dataProjections.getGraphicspointattributes()
pointAttr.setGlyphShapeType(Glyph.SHAPE_TYPE_LINE)
pointAttr.setBaseSize([0.0, 1.0, 1.0])
pointAttr.setScaleFactors([1.0, 0.0, 0.0])
dataProjections.setRenderLineWidth(2.0 if (
projectionMeshDimension == 1) else 1.0)
if dataProjectionDelta:
pointAttr.setOrientationScaleField(dataProjectionDelta)
if dataProjectionError:
dataProjections.setDataField(dataProjectionError)
spectrummodule = scene.getSpectrummodule()
spectrum = spectrummodule.getDefaultSpectrum()
dataProjections.setSpectrum(spectrum)
dataProjections.setName("displayDataProjections")
dataProjections.setVisibilityFlag(
self.isDisplayDataProjections())
dataProjectionPoints = scene.createGraphicsPoints()
dataProjectionPoints.setFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
dataProjectionPoints.setSubgroupField(dataProjectionNodeGroup)
if dataProjectionCoordinates:
dataProjectionPoints.setCoordinateField(
dataProjectionCoordinates)
pointattr = dataProjectionPoints.getGraphicspointattributes()
# pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_DIAMOND)
# pointattr.setBaseSize([glyphWidthSmall, glyphWidthSmall, glyphWidthSmall])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_POINT)
dataProjectionPoints.setRenderPointSize(3.0)
dataProjectionPoints.setMaterial(
self._materialmodule.findMaterialByName("grey50"))
dataProjectionPoints.setName("displayDataProjectionPoints")
dataProjectionPoints.setVisibilityFlag(
self.isDisplayDataProjectionPoints())
nodePoints = scene.createGraphicsPoints()
nodePoints.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodePoints.setCoordinateField(modelCoordinates)
pointattr = nodePoints.getGraphicspointattributes()
pointattr.setBaseSize([glyphWidth, glyphWidth, glyphWidth])
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_SPHERE)
nodePoints.setMaterial(
self._materialmodule.findMaterialByName("white"))
nodePoints.setName("displayNodePoints")
nodePoints.setVisibilityFlag(self.isDisplayNodePoints())
nodeNumbers = scene.createGraphicsPoints()
nodeNumbers.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodeNumbers.setCoordinateField(modelCoordinates)
pointattr = nodeNumbers.getGraphicspointattributes()
pointattr.setLabelField(cmiss_number)
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
nodeNumbers.setMaterial(
self._materialmodule.findMaterialByName("green"))
nodeNumbers.setName("displayNodeNumbers")
nodeNumbers.setVisibilityFlag(self.isDisplayNodeNumbers())
# names in same order as nodeDerivativeLabels "D1", "D2", "D3", "D12", "D13", "D23", "D123" and nodeDerivativeFields
nodeDerivativeMaterialNames = [
"gold", "silver", "green", "cyan", "magenta", "yellow", "blue"
]
derivativeScales = [1.0, 1.0, 1.0, 0.5, 0.5, 0.5, 0.25]
for i in range(len(nodeDerivativeLabels)):
nodeDerivativeLabel = nodeDerivativeLabels[i]
nodeDerivatives = scene.createGraphicsPoints()
nodeDerivatives.setFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodeDerivatives.setCoordinateField(modelCoordinates)
pointattr = nodeDerivatives.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_ARROW_SOLID)
pointattr.setOrientationScaleField(nodeDerivativeFields[i])
pointattr.setBaseSize([0.0, glyphWidth, glyphWidth])
pointattr.setScaleFactors([derivativeScales[i], 0.0, 0.0])
material = self._materialmodule.findMaterialByName(
nodeDerivativeMaterialNames[i])
nodeDerivatives.setMaterial(material)
nodeDerivatives.setSelectedMaterial(material)
nodeDerivatives.setName("displayNodeDerivatives" +
nodeDerivativeLabel)
nodeDerivatives.setVisibilityFlag(
self.isDisplayNodeDerivatives() and
self.isDisplayNodeDerivativeLabels(nodeDerivativeLabel))
elementNumbers = scene.createGraphicsPoints()
elementNumbers.setFieldDomainType(
Field.DOMAIN_TYPE_MESH_HIGHEST_DIMENSION)
elementNumbers.setCoordinateField(modelCoordinates)
pointattr = elementNumbers.getGraphicspointattributes()
pointattr.setLabelField(cmiss_number)
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_NONE)
elementNumbers.setMaterial(
self._materialmodule.findMaterialByName("cyan"))
elementNumbers.setName("displayElementNumbers")
elementNumbers.setVisibilityFlag(self.isDisplayElementNumbers())
elementAxes = scene.createGraphicsPoints()
elementAxes.setFieldDomainType(
Field.DOMAIN_TYPE_MESH_HIGHEST_DIMENSION)
elementAxes.setCoordinateField(modelCoordinates)
pointattr = elementAxes.getGraphicspointattributes()
pointattr.setGlyphShapeType(Glyph.SHAPE_TYPE_AXES_123)
pointattr.setOrientationScaleField(elementDerivativesField)
if meshDimension == 1:
pointattr.setBaseSize([0.0, 2 * glyphWidth, 2 * glyphWidth])
pointattr.setScaleFactors([0.25, 0.0, 0.0])
elif meshDimension == 2:
pointattr.setBaseSize([0.0, 0.0, 2 * glyphWidth])
pointattr.setScaleFactors([0.25, 0.25, 0.0])
else:
pointattr.setBaseSize([0.0, 0.0, 0.0])
pointattr.setScaleFactors([0.25, 0.25, 0.25])
elementAxes.setMaterial(
self._materialmodule.findMaterialByName("yellow"))
elementAxes.setName("displayElementAxes")
elementAxes.setVisibilityFlag(self.isDisplayElementAxes())
lines = scene.createGraphicsLines()
lines.setCoordinateField(modelCoordinates)
lines.setExterior(self.isDisplayLinesExterior())
lines.setName("displayLines")
lines.setVisibilityFlag(self.isDisplayLines())
surfaces = scene.createGraphicsSurfaces()
surfaces.setCoordinateField(modelCoordinates)
surfaces.setRenderPolygonMode(
Graphics.RENDER_POLYGON_MODE_WIREFRAME if self.
isDisplaySurfacesWireframe(
) else Graphics.RENDER_POLYGON_MODE_SHADED)
surfaces.setExterior(self.isDisplaySurfacesExterior() if (
meshDimension == 3) else False)
surfacesMaterial = self._materialmodule.findMaterialByName(
"trans_blue" if self.isDisplaySurfacesTranslucent(
) else "solid_blue")
surfaces.setMaterial(surfacesMaterial)
surfaces.setName("displaySurfaces")
surfaces.setVisibilityFlag(self.isDisplaySurfaces())
def autorangeSpectrum(self):
scene = self._fitter.getRegion().getScene()
spectrummodule = scene.getSpectrummodule()
spectrum = spectrummodule.getDefaultSpectrum()
spectrum.autorange(scene, Scenefilter())
# === Align Utilities ===
def isStateAlign(self):
return False # disabled as not implemented
def rotateModel(self, axis, angle):
mat1 = axis_angle_to_rotation_matrix(axis, angle)
mat2 = euler_to_rotation_matrix(self._alignSettings["euler_angles"])
newmat = matrix_mult(mat1, mat2)
self._alignSettings["euler_angles"] = rotation_matrix_to_euler(newmat)
self._applyAlignSettings()
def scaleModel(self, factor):
self._alignSettings["scale"] *= factor
self._applyAlignSettings()
def translateModel(self, relativeOffset):
self._alignSettings["offset"] = add(self._alignSettings["offset"],
relativeOffset)
self._applyAlignSettings()
def _autorangeSpectrum(self):
scene = self.getScene()
spectrummodule = scene.getSpectrummodule()
spectrum = spectrummodule.getDefaultSpectrum()
scenefiltermodule = scene.getScenefiltermodule()
scenefilter = scenefiltermodule.getDefaultScenefilter()
spectrum.autorange(scene, scenefilter)
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_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)