def setQuickieRadius(self,radius):
labelVolume = EditUtil.getLabelVolume()
if labelVolume:
if self.radiusUnitsToggle.text == 'px:':
spacing = labelVolume.GetSpacing()
if self.radiusPixelMode == 'diag':
from math import sqrt
diag = sqrt(reduce(lambda x,y:x+y, map(lambda x: x**2, spacing)))
mmRadius = diag * radius
elif self.radiusPixelMode == 'min':
mmRadius = min(spacing) * radius
else:
print (self,"Unknown pixel mode - using 5mm")
mmRadius = 5
else:
mmRadius = radius
self.disconnectWidgets()
self.radiusSpinBox.setValue(mmRadius)
self.radius.setValue(mmRadius)
self.connectWidgets()
self.updateMRMLFromGUI()
def __init__(self, parent=0):
# get pixel-size-dependent parameters
# calculate this before calling superclass init
# so it can be used to set mrml defaults if needed
labelVolume = EditUtil.getLabelVolume()
if labelVolume and labelVolume.GetImageData():
spacing = labelVolume.GetSpacing()
dimensions = labelVolume.GetImageData().GetDimensions()
self.minimumRadius = 0.5 * min(spacing)
bounds = [a*b for a,b in zip(spacing,dimensions)]
self.maximumRadius = 0.5 * max(bounds)
else:
self.minimumRadius = 0.01
self.maximumRadius = 100
super(PaintEffectOptions,self).__init__(parent)
# option to use 'min' or 'diag'
# - min means pixel radius is min spacing
# - diag means corner to corner length
self.radiusPixelMode = 'min'
def __init__(self, parent=0):
# get pixel-size-dependent parameters
# calculate this before calling superclass init
# so it can be used to set mrml defaults if needed
labelVolume = EditUtil.getLabelVolume()
if labelVolume and labelVolume.GetImageData():
spacing = labelVolume.GetSpacing()
dimensions = labelVolume.GetImageData().GetDimensions()
self.minimumRadius = 0.5 * min(spacing)
bounds = [a * b for a, b in zip(spacing, dimensions)]
self.maximumRadius = 0.5 * max(bounds)
else:
self.minimumRadius = 0.01
self.maximumRadius = 100
super(PaintEffectOptions, self).__init__(parent)
# option to use 'min' or 'diag'
# - min means pixel radius is min spacing
# - diag means corner to corner length
self.radiusPixelMode = 'min'
def setQuickieRadius(self, radius):
labelVolume = EditUtil.getLabelVolume()
if labelVolume:
if self.radiusUnitsToggle.text == 'px:':
spacing = labelVolume.GetSpacing()
if self.radiusPixelMode == 'diag':
from math import sqrt
diag = sqrt(
reduce(lambda x, y: x + y, map(lambda x: x**2,
spacing)))
mmRadius = diag * radius
elif self.radiusPixelMode == 'min':
mmRadius = min(spacing) * radius
else:
print(self, "Unknown pixel mode - using 5mm")
mmRadius = 5
else:
mmRadius = radius
self.disconnectWidgets()
self.radiusSpinBox.setValue(mmRadius)
self.radius.setValue(mmRadius)
self.connectWidgets()
self.updateMRMLFromGUI()
def _onEffectChanged(self, effectName):
if self.currentEffect == effectName:
return
#
# If there is no background volume or label map, do nothing
#
if not EditUtil.getBackgroundVolume():
return
if not EditUtil.getLabelVolume():
return
self.currentEffect = effectName
EditUtil.restoreLabel()
# Update action if possible - if not, we aren't ready to select the effect
if effectName not in self.actions:
return
self.actions[effectName].checked = True
#
# an effect was selected, so build an options GUI
# - check to see if it is an extension effect,
# if not, try to create it, else ignore it
# For extensions, look for 'effect'Options and 'effect'Tool
# in the editorExtensions map and use those to create the
# effect
#
if self.currentOption:
# clean up any existing effect
self.currentOption.__del__()
self.currentOption = None
for tool in self.currentTools:
tool.sliceWidget.unsetCursor()
tool.cleanup()
self.currentTools = []
# look at builtins and extensions
# - TODO: other effect styles are deprecated
effectClass = None
if effectName in slicer.modules.editorExtensions.keys():
effectClass = slicer.modules.editorExtensions[effectName]()
elif effectName in self.editorBuiltins.keys():
effectClass = self.editorBuiltins[effectName]()
if effectClass:
# for effects, create an options gui and an
# instance for every slice view
self.currentOption = effectClass.options(self.optionsFrame)
self.currentOption.setMRMLDefaults()
self.currentOption.undoRedo = self.undoRedo
self.currentOption.defaultEffect = self.defaultEffect
self.currentOption.create()
self.currentOption.updateGUI()
layoutManager = slicer.app.layoutManager()
sliceNodeCount = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLSliceNode')
for nodeIndex in xrange(sliceNodeCount):
# find the widget for each node in scene
sliceNode = slicer.mrmlScene.GetNthNodeByClass(
nodeIndex, 'vtkMRMLSliceNode')
sliceWidget = layoutManager.sliceWidget(
sliceNode.GetLayoutName())
if sliceWidget:
tool = effectClass.tool(sliceWidget)
tool.undoRedo = self.undoRedo
self.currentTools.append(tool)
self.currentOption.tools = self.currentTools
else:
# fallback to internal classes
try:
options = eval("%sOptions" % effectName)
self.currentOption = options(self.optionsFrame)
except NameError, AttributeError:
# No options for this effect, skip it
pass
def create(self):
super(WatershedFromMarkerEffectOptions, self).create()
if not HAVE_SIMPLEITK:
self.warningLabel = qt.QLabel()
self.warningLabel.text = "WatershedFromMarker is not available because\nSimpleITK is not available in this build"
self.widgets.append(self.warningLabel)
self.frame.layout().addWidget(self.warningLabel)
return
labelVolume = EditUtil.getLabelVolume()
if labelVolume and labelVolume.GetImageData():
spacing = labelVolume.GetSpacing()
self.minimumSigma = 0.1 * min(spacing)
self.maximumSigma = 100 * self.minimumSigma
else:
self.minimumSigma = 0.1
self.maximumSigma = 10
self.sigmaFrame = qt.QFrame(self.frame)
self.sigmaFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.sigmaFrame)
self.widgets.append(self.sigmaFrame)
tip = "Increasing this value smooths the segmentation and reduces leaks. This is the sigma used for edge detection."
self.sigmaLabel = qt.QLabel("Object Scale: ", self.frame)
self.sigmaLabel.setToolTip(tip)
self.sigmaFrame.layout().addWidget(self.sigmaLabel)
self.widgets.append(self.sigmaLabel)
self.sigmaSlider = qt.QSlider(qt.Qt.Horizontal, self.frame)
self.sigmaFrame.layout().addWidget(self.sigmaSlider)
self.sigmaFrame.setToolTip(tip)
self.widgets.append(self.sigmaSlider)
self.sigmaSpinBox = qt.QDoubleSpinBox(self.frame)
self.sigmaSpinBox.setToolTip(tip)
self.sigmaSpinBox.suffix = "mm"
self.sigmaFrame.layout().addWidget(self.sigmaSpinBox)
self.widgets.append(self.sigmaSpinBox)
self.sigmaSpinBox.minimum = self.minimumSigma
self.sigmaSlider.minimum = self.minimumSigma
self.sigmaSpinBox.maximum = self.maximumSigma
self.sigmaSlider.maximum = self.maximumSigma
decimals = math.floor(math.log(self.minimumSigma, 10))
if decimals < 0:
self.sigmaSpinBox.decimals = -decimals + 2
self.apply = qt.QPushButton("Apply", self.frame)
self.apply.objectName = self.__class__.__name__ + 'Apply'
self.apply.setToolTip("Apply the extension operation")
self.frame.layout().addWidget(self.apply)
self.widgets.append(self.apply)
helpDoc = \
"""Use this effect to apply the watershed from markers segmentation from multiple initial labels.
The input to this filter is current labelmap image which is expected to contain multiple labels as initial marks. The marks or labels are grown to fill the image and with edges defining the bondaries between. To segment a single object, mark the object, and then it is suggested to surround the object with a negative label on each axis.
The "Object Scale" parameter is use to adjust the smoothness of the output image and prevent leakage. It is used internally for the sigma of the gradient magnitude.
"""
HelpButton(self.frame, helpDoc)
self.sigmaSlider.connect('valueChanged(int)',
self.sigmaSpinBox.setValue)
self.sigmaSpinBox.connect('valueChanged(double)',
self.sigmaSlider.setValue)
# if either widget is changed both should change and this should be triggered
self.connections.append((self.sigmaSpinBox, 'valueChanged(double)',
self.onSigmaValueChanged))
self.connections.append((self.apply, 'clicked()', self.onApply))
# Add vertical spacer
self.frame.layout().addStretch(1)
def makeModel(self,modelName='EditorModel',smooth=True):
#
# create a model using the command line module
# based on the current editor parameters
#
volumeNode = EditUtil.getLabelVolume()
if not volumeNode:
return
#
# set up the model maker node
#
parameters = {}
parameters['Name'] = modelName
parameters["InputVolume"] = volumeNode.GetID()
parameters['FilterType'] = "Sinc"
# build only the currently selected model.
parameters['Labels'] = EditUtil.getLabel()
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters['GenerateAll'] = False
parameters["JointSmoothing"] = False
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
if smooth:
parameters["Decimate"] = 0.25
parameters["Smooth"] = 10
else:
parameters["Decimate"] = 0
parameters["Smooth"] = 0
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelHierarchyNode" )
outHierarchy = None
for n in xrange(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLModelHierarchyNode" )
if node.GetName() == "Editor Models":
outHierarchy = node
break
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene( slicer.mrmlScene )
outHierarchy.SetName( "Editor Models" )
slicer.mrmlScene.AddNode( outHierarchy )
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
slicer.cli.run(modelMaker, None, parameters)
slicer.util.showStatusMessage( "Model Making Started...", 2000 )
def _onEffectChanged(self, effectName):
if self.currentEffect == effectName:
return
#
# If there is no background volume or label map, do nothing
#
if not EditUtil.getBackgroundVolume():
return
if not EditUtil.getLabelVolume():
return
self.currentEffect = effectName
EditUtil.restoreLabel()
# Update action if possible - if not, we aren't ready to select the effect
if effectName not in self.actions:
return
self.actions[effectName].checked = True
#
# an effect was selected, so build an options GUI
# - check to see if it is an extension effect,
# if not, try to create it, else ignore it
# For extensions, look for 'effect'Options and 'effect'Tool
# in the editorExtensions map and use those to create the
# effect
#
if self.currentOption:
# clean up any existing effect
self.currentOption.__del__()
self.currentOption = None
for tool in self.currentTools:
tool.sliceWidget.unsetCursor()
tool.cleanup()
self.currentTools = []
# look at builtins and extensions
# - TODO: other effect styles are deprecated
effectClass = None
if effectName in slicer.modules.editorExtensions.keys():
effectClass = slicer.modules.editorExtensions[effectName]()
elif effectName in self.editorBuiltins.keys():
effectClass = self.editorBuiltins[effectName]()
if effectClass:
# for effects, create an options gui and an
# instance for every slice view
self.currentOption = effectClass.options(self.optionsFrame)
self.currentOption.setMRMLDefaults()
self.currentOption.undoRedo = self.undoRedo
self.currentOption.defaultEffect = self.defaultEffect
self.currentOption.create()
self.currentOption.updateGUI()
layoutManager = slicer.app.layoutManager()
sliceNodeCount = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLSliceNode')
for nodeIndex in xrange(sliceNodeCount):
# find the widget for each node in scene
sliceNode = slicer.mrmlScene.GetNthNodeByClass(nodeIndex, 'vtkMRMLSliceNode')
sliceWidget = layoutManager.sliceWidget(sliceNode.GetLayoutName())
if sliceWidget:
tool = effectClass.tool(sliceWidget)
tool.undoRedo = self.undoRedo
self.currentTools.append(tool)
self.currentOption.tools = self.currentTools
else:
# fallback to internal classes
try:
options = eval("%sOptions" % effectName)
self.currentOption = options(self.optionsFrame)
except NameError, AttributeError:
# No options for this effect, skip it
pass
def create(self):
super(WatershedFromMarkerEffectOptions,self).create()
if not HAVE_SIMPLEITK:
self.warningLabel = qt.QLabel()
self.warningLabel.text = "WatershedFromMarker is not available because\nSimpleITK is not available in this build"
self.widgets.append(self.warningLabel)
self.frame.layout().addWidget(self.warningLabel)
return
labelVolume = EditUtil.getLabelVolume()
if labelVolume and labelVolume.GetImageData():
spacing = labelVolume.GetSpacing()
self.minimumSigma = 0.1 * min(spacing)
self.maximumSigma = 100 * self.minimumSigma
else:
self.minimumSigma = 0.1
self.maximumSigma = 10
self.sigmaFrame = qt.QFrame(self.frame)
self.sigmaFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.sigmaFrame)
self.widgets.append(self.sigmaFrame)
tip = "Increasing this value smooths the segmentation and reduces leaks. This is the sigma used for edge detection."
self.sigmaLabel = qt.QLabel("Object Scale: ", self.frame)
self.sigmaLabel.setToolTip(tip)
self.sigmaFrame.layout().addWidget(self.sigmaLabel)
self.widgets.append(self.sigmaLabel)
self.sigmaSlider = qt.QSlider( qt.Qt.Horizontal, self.frame )
self.sigmaFrame.layout().addWidget(self.sigmaSlider)
self.sigmaFrame.setToolTip(tip)
self.widgets.append(self.sigmaSlider)
self.sigmaSpinBox = qt.QDoubleSpinBox(self.frame)
self.sigmaSpinBox.setToolTip(tip)
self.sigmaSpinBox.suffix = "mm"
self.sigmaFrame.layout().addWidget(self.sigmaSpinBox)
self.widgets.append(self.sigmaSpinBox)
self.sigmaSpinBox.minimum = self.minimumSigma
self.sigmaSlider.minimum = self.minimumSigma
self.sigmaSpinBox.maximum = self.maximumSigma
self.sigmaSlider.maximum = self.maximumSigma
decimals = math.floor(math.log(self.minimumSigma,10))
if decimals < 0:
self.sigmaSpinBox.decimals = -decimals + 2
self.apply = qt.QPushButton("Apply", self.frame)
self.apply.objectName = self.__class__.__name__ + 'Apply'
self.apply.setToolTip("Apply the extension operation")
self.frame.layout().addWidget(self.apply)
self.widgets.append(self.apply)
helpDoc = \
"""Use this effect to apply the watershed from markers segmentation from multiple initial labels.
The input to this filter is current labelmap image which is expected to contain multiple labels as initial marks. The marks or labels are grown to fill the image and with edges defining the bondaries between. To segment a single object, mark the object, and then it is suggested to surround the object with a negative label on each axis.
The "Object Scale" parameter is use to adjust the smoothness of the output image and prevent leakage. It is used internally for the sigma of the gradient magnitude.
"""
HelpButton(self.frame, helpDoc)
self.sigmaSlider.connect( 'valueChanged(int)', self.sigmaSpinBox.setValue )
self.sigmaSpinBox.connect( 'valueChanged(double)', self.sigmaSlider.setValue )
# if either widget is changed both should change and this should be triggered
self.connections.append( ( self.sigmaSpinBox, 'valueChanged(double)', self.onSigmaValueChanged ) )
self.connections.append( (self.apply, 'clicked()', self.onApply) )
# Add vertical spacer
self.frame.layout().addStretch(1)
def makeModel(self, modelName='EditorModel', smooth=True):
#
# create a model using the command line module
# based on the current editor parameters
#
volumeNode = EditUtil.getLabelVolume()
if not volumeNode:
return
#
# set up the model maker node
#
parameters = {}
parameters['Name'] = modelName
parameters["InputVolume"] = volumeNode.GetID()
parameters['FilterType'] = "Sinc"
# build only the currently selected model.
parameters['Labels'] = EditUtil.getLabel()
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters['GenerateAll'] = False
parameters["JointSmoothing"] = False
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
if smooth:
parameters["Decimate"] = 0.25
parameters["Smooth"] = 10
else:
parameters["Decimate"] = 0
parameters["Smooth"] = 0
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
"vtkMRMLModelHierarchyNode")
outHierarchy = None
for n in xrange(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass(
n, "vtkMRMLModelHierarchyNode")
if node.GetName() == "Editor Models":
outHierarchy = node
break
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene(slicer.mrmlScene)
outHierarchy.SetName("Editor Models")
slicer.mrmlScene.AddNode(outHierarchy)
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
slicer.cli.run(modelMaker, None, parameters)
slicer.util.showStatusMessage("Model Making Started...", 2000)
