def __init__(self, parent):
parent.title = "Editor"
parent.category = ""
parent.contributor = "Steve Pieper"
parent.helpText = """
The Editor allows label maps to be created and edited. The active label map will be modified by the Editor. See <a>http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-4.0</a>.\n\nThe Master Volume refers to the background grayscale volume to be edited (used, for example, when thresholding). The Merge Volume refers to a volume that contains several different label values corresponding to different structures.\n\nBasic usage: selecting the Master and Merge Volume give access to the editor tools. Each tool has a help icon to bring up a dialog with additional information. Hover your mouse pointer over buttons and options to view Balloon Help (tool tips). Use these to define the Label Map.\n\nAdvanced usage: open the Per-Structure Volumes tab to create independent Label Maps for each color you wish to edit. Since many editor tools (such as threshold) will operate on the entire volume, you can use the Per-Structure Volumes feature to isolate these operations on a structure-by-structure basis. Use the Split Merge Volume button to create a set of volumes with independent labels. Use the Add Structure button to add a new volume. Delete Structures will remove all the independent structure volumes. Merge All will assemble the current structures into the Merge Volume. Merge And Build will invoke the Model Maker module on the Merge Volume.
"""
parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>http://www.slicer.org</a> for details. Module implemented by Steve Pieper.
This work is partially supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See <a>http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy</a>).
"""
self.parent = parent
if slicer.mrmlScene.GetTagByClassName( "vtkMRMLScriptedModuleNode" ) != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
if tcl('info exists ::Editor(singleton)') != '':
# TODO: cannot call dialog.exec from pythonqt... This is just a warning anyway
#dialog = qt.QErrorMessage()
#dialog.showMessage("Error: editor singleton already created - Editor initialized twice.")
pass
tcl('set ::Editor(singleton) this')
tcl('set ::Editor(checkPointsEnabled) 1')
iconDir = slicer.app.slicerHome + '/' + os.environ['SLICER_SHARE_DIR'] + '/Tcl/ImageData'
parent.icon = qt.QIcon("%s/ToolbarEditorToolbox.png" % iconDir)
def __init__(self, parent):
parent.title = "Editor"
parent.category = ""
parent.contributor = "Steve Pieper"
parent.helpText = """
The Editor allows label maps to be created and edited. The active label map will be modified by the Editor. See <a>http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-4.0</a>.\n\nThe Master Volume refers to the background grayscale volume to be edited (used, for example, when thresholding). The Merge Volume refers to a volume that contains several different label values corresponding to different structures.\n\nBasic usage: selecting the Master and Merge Volume give access to the editor tools. Each tool has a help icon to bring up a dialog with additional information. Hover your mouse pointer over buttons and options to view Balloon Help (tool tips). Use these to define the Label Map.\n\nAdvanced usage: open the Per-Structure Volumes tab to create independent Label Maps for each color you wish to edit. Since many editor tools (such as threshold) will operate on the entire volume, you can use the Per-Structure Volumes feature to isolate these operations on a structure-by-structure basis. Use the Split Merge Volume button to create a set of volumes with independent labels. Use the Add Structure button to add a new volume. Delete Structures will remove all the independent structure volumes. Merge All will assemble the current structures into the Merge Volume. Merge And Build will invoke the Model Maker module on the Merge Volume.
"""
parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>http://www.slicer.org</a> for details. Module implemented by Steve Pieper.
This work is partially supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See <a>http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy</a>).
"""
self.parent = parent
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
if tcl('info exists ::Editor(singleton)') != '':
# TODO: cannot call dialog.exec from pythonqt... This is just a warning anyway
#dialog = qt.QErrorMessage()
#dialog.showMessage("Error: editor singleton already created - Editor initialized twice.")
pass
tcl('set ::Editor(singleton) this')
tcl('set ::Editor(checkPointsEnabled) 1')
iconDir = slicer.app.slicerHome + '/' + os.environ[
'SLICER_SHARE_DIR'] + '/Tcl/ImageData'
parent.icon = qt.QIcon("%s/ToolbarEditorToolbox.png" % iconDir)
def select(self):
"""select master volume - load merge volume if one with the correct name exists"""
self.master = self.masterSelector.currentNode()
merge = self.mergeVolume()
mergeText = "None"
if merge:
if merge.GetClassName() != "vtkMRMLScalarVolumeNode" or not merge.GetLabelMap():
self.errorDialog( "Error: selected merge label volume is not a label volume" )
else:
# make the source node the active background, and the label node the active label
selectionNode = self.applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( self.master.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID( merge.GetID() )
self.applicationLogic.PropagateVolumeSelection()
mergeText = merge.GetName()
self.merge = merge
else:
# the master exists, but there is no merge volume yet
# bring up dialog to create a merge with a user-selected color node
if self.master:
self.colorSelectDialog()
tcl('EffectSWidget::RotateToVolumePlanes') # make sure slices are aligned to volumes
self.mergeName.setText( mergeText )
self.updateStructures()
# remove all active effects (so that when selected again slice rotation and snap to IJK will happen if needed
tcl('::EffectSWidget::RemoveAll')
# trigger a modified event on the parameter node so that other parts of the GUI
# (such as the EditColor) will know to update and enable themselves
nodeID = tcl('[EditorGetParameterNode] GetID')
pNode = slicer.mrmlScene.GetNodeByID(nodeID)
if pNode:
pNode.Modified()
def onEntry(self, comingFrom, transitionType):
'''
'''
super(EMSegmentQuickStep1, self).onEntry(comingFrom, transitionType)
# Remove everything if needed - did not work properly -however when running it without it then it resets pipeline but leaves nodes in scend !
# self.logic().RemoveTaskAndTempFiles()
# self.reset()
slicer.modules.emsegmentAdvancedDynamicFrame = self.dynamicFrame()
if not self.__initialized:
# use default taskfile
taskFileShort = slicer.modulelogic.vtkMRMLEMSGlobalParametersNode.GetDefaultTaskTclFileName(
)
self.mrmlManager().CreateAndObserveNewParameterSet()
templateNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLEMSTemplateNode')
self.mrmlManager().SetNthParameterName(
templateNodes.GetNumberOfItems() - 1, 'EMEasy')
self.mrmlManager().SetTclTaskFilename(taskFileShort)
self.logic().SourceTaskFiles()
loadResult = self.mrmlManager().SetLoadedParameterSetIndex(
templateNodes.GetItemAsObject(
templateNodes.GetNumberOfItems() - 1))
if int(loadResult) != 0:
Helper.Info(
"EMS node is corrupted - the manager could not be updated with new task: EMQuick"
)
#return False
else:
Helper.Info("Loading completed.")
self.logic().DefineTclTaskFileFromMRML()
# use anatomy label colors
self.mrmlManager().GetGlobalParametersNode().SetColormap(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
# clear the dynamic panel
self.dynamicFrame().setMRMLManager(self.mrmlManager())
self.dynamicFrame().clearElements()
logicTclName = self.logic().GetSlicerCommonInterface(
).GetTclNameFromPointer(self.logic())
tcl('::EMSegmenterPreProcessingTcl::ShowUserInterface ' +
str(logicTclName))
self.__initialized = True
self.loadFromMRML()
def updateCheckPointButtons(self):
previousImagesExist = nextImagesExist = False
if bool(int(tcl('info exists ::Editor(previousCheckPointImages)'))):
previousImagesExist = bool(int(tcl('llength $::Editor(previousCheckPointImages)')))
if bool(int(tcl('info exists ::Editor(nextCheckPointImages)'))):
nextImagesExist = bool(int(tcl('llength $::Editor(nextCheckPointImages)')))
if not self.embedded:
self.effectButtons["PreviousCheckPoint"].setDisabled( not previousImagesExist )
self.effectButtons["NextCheckPoint"].setDisabled( not nextImagesExist )
def RotateToVolumePlanes():
# AF TODO: check with Steve if this has any undesired consequences
# Volumes slicenode has a method for this, no need for tcl
tcl('EffectSWidget::RotateToVolumePlanes')
# snap to IJK to try and avoid rounding errors
sliceLogics = slicer.app.layoutManager().mrmlSliceLogics()
numLogics = sliceLogics.GetNumberOfItems()
for n in range(numLogics):
l = sliceLogics.GetItemAsObject(n)
l.SnapSliceOffsetToIJK()
def RotateToVolumePlanes():
# AF TODO: check with Steve if this has any undesired consequences
# Volumes slicenode has a method for this, no need for tcl
tcl('EffectSWidget::RotateToVolumePlanes')
# snap to IJK to try and avoid rounding errors
sliceLogics = slicer.app.layoutManager().mrmlSliceLogics()
numLogics = sliceLogics.GetNumberOfItems()
for n in range(numLogics):
l = sliceLogics.GetItemAsObject(n)
l.SnapSliceOffsetToIJK()
def updateCheckPointButtons(self):
previousImagesExist = nextImagesExist = False
if bool(int(tcl('info exists ::Editor(previousCheckPointImages)'))):
previousImagesExist = bool(
int(tcl('llength $::Editor(previousCheckPointImages)')))
if bool(int(tcl('info exists ::Editor(nextCheckPointImages)'))):
nextImagesExist = bool(
int(tcl('llength $::Editor(nextCheckPointImages)')))
if not self.embedded:
self.effectButtons["PreviousCheckPoint"].setDisabled(
not previousImagesExist)
self.effectButtons["NextCheckPoint"].setDisabled(
not nextImagesExist)
def onEntry( self, comingFrom, transitionType ):
'''
'''
super( EMSegmentQuickStep1, self ).onEntry( comingFrom, transitionType )
# Remove everything if needed - did not work properly -however when running it without it then it resets pipeline but leaves nodes in scend !
# self.logic().RemoveTaskAndTempFiles()
# self.reset()
slicer.modules.emsegmentAdvancedDynamicFrame = self.dynamicFrame()
if not self.__initialized:
# use default taskfile
taskFileShort = slicer.vtkMRMLEMSGlobalParametersNode.GetDefaultTaskTclFileName()
self.mrmlManager().CreateAndObserveNewParameterSet()
templateNodes = slicer.mrmlScene.GetNodesByClass( 'vtkMRMLEMSTemplateNode' )
self.mrmlManager().SetNthParameterName( templateNodes.GetNumberOfItems() - 1, 'EMEasy' )
self.mrmlManager().SetTclTaskFilename( taskFileShort )
self.logic().SourceTaskFiles()
loadResult = self.mrmlManager().SetLoadedParameterSetIndex( templateNodes.GetItemAsObject( templateNodes.GetNumberOfItems() - 1 ) )
if int( loadResult ) != 0:
Helper.Info( "EMS node is corrupted - the manager could not be updated with new task: EMQuick" )
#return False
else:
Helper.Info( "Loading completed." )
self.logic().DefineTclTaskFileFromMRML()
# use anatomy label colors
self.mrmlManager().GetGlobalParametersNode().SetColormap( 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt' )
# clear the dynamic panel
self.dynamicFrame().setMRMLManager( self.mrmlManager() )
self.dynamicFrame().clearElements()
logicTclName = self.logic().GetSlicerCommonInterface().GetTclNameFromPointer( self.logic() )
tcl( '::EMSegmenterPreProcessingTcl::ShowUserInterface ' + str( logicTclName ) )
self.__initialized = True
self.loadFromMRML()
def onExit(self, goingTo, transitionType):
'''
'''
self.propagateToMRML()
if self.isSimpleMode():
returnValue = tcl("::EMSegmenterSimpleTcl::ValidateCheckList")
if int(returnValue) != 0:
# error
messageBox = qt.QMessageBox.warning(
self, "Error",
"Could not validate the Checklist. Please double check your settings!"
)
return
self.mrmlManager().GetWorkingDataNode(
).SetAlignedTargetNodeIsValid(0)
self.mrmlManager().GetWorkingDataNode().SetAlignedAtlasNodeIsValid(
0)
# disable questions at the pre-processing step
preProcessingStep = slicer.modules.emsegmentPreprocessingStep
if preProcessingStep:
preProcessingStep.disableQuestions()
else:
# disable questions at the pre-processing step
preProcessingStep = slicer.modules.emsegmentPreprocessingStep
if preProcessingStep:
preProcessingStep.enableQuestions()
self.__parent.onExit(goingTo, transitionType)
def create(self):
self.frame = qt.QFrame(self.parent)
self.frame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.frame)
self.label = qt.QLabel(self.frame)
self.label.setText("Label: ")
self.frame.layout().addWidget(self.label)
self.labelName = qt.QLabel(self.frame)
self.labelName.setText("")
self.frame.layout().addWidget(self.labelName)
self.colorSpin = qt.QSpinBox(self.frame)
self.colorSpin.setValue( int(tcl('EditorGetPaintLabel')) )
self.colorSpin.setToolTip( "Click colored patch at right to bring up color selection pop up window. Use the 'c' key to bring up color popup menu." )
self.frame.layout().addWidget(self.colorSpin)
self.colorPatch = qt.QPushButton(self.frame)
self.frame.layout().addWidget(self.colorPatch)
self.updateParameterNode(slicer.mrmlScene, "ModifiedEvent")
self.updateGUIFromMRML(self.parameterNode, "ModifiedEvent")
self.frame.connect( 'destroyed(QObject)', self.cleanup)
self.colorSpin.connect( 'valueChanged(int)', self.updateMRMLFromGUI)
self.colorPatch.connect( 'clicked()', self.showColorBox )
# TODO: change this to look for specfic events (added, removed...)
# but this requires being able to access events by number from wrapped code
tag = slicer.mrmlScene.AddObserver("ModifiedEvent", self.updateParameterNode)
self.observerTags.append( (slicer.mrmlScene, tag) )
def onExit(self, goingTo, transitionType):
"""
"""
self.propagateToMRML()
if self.isSimpleMode():
returnValue = tcl("::EMSegmenterSimpleTcl::ValidateCheckList")
if int(returnValue) != 0:
# error
messageBox = qt.QMessageBox.warning(
self, "Error", "Could not validate the Checklist. Please double check your settings!"
)
return
self.mrmlManager().GetWorkingDataNode().SetAlignedTargetNodeIsValid(0)
self.mrmlManager().GetWorkingDataNode().SetAlignedAtlasNodeIsValid(0)
# disable questions at the pre-processing step
preProcessingStep = slicer.modules.emsegmentPreprocessingStep
if preProcessingStep:
preProcessingStep.disableQuestions()
else:
# disable questions at the pre-processing step
preProcessingStep = slicer.modules.emsegmentPreprocessingStep
if preProcessingStep:
preProcessingStep.enableQuestions()
super(EMSegmentDefineInputChannelsStep, self).onExit(goingTo, transitionType)
def enter(self):
# get the master and merge nodes from the composite node associated
# with the red slice, but only if showing volumes
if self.showVolumesFrame:
# get the slice composite node for the Red slice view (we'll assume it exists
# since we are in the editor) to get the current background and label
compositeNode = self.editUtil.getCompositeNode()
masterNode = slicer.mrmlScene.GetNodeByID( compositeNode.GetBackgroundVolumeID() )
mergeNode = slicer.mrmlScene.GetNodeByID( compositeNode.GetLabelVolumeID() )
self.setMasterNode(masterNode)
self.setMergeNode(mergeNode)
# if not showing volumes, the caller is responsible for setting the master and
# merge nodes, most likely according to a widget within the caller
# Observe the parameter node in order to make changes to
# button states as needed
nodeID = tcl('[EditorGetParameterNode] GetID')
self.parameterNode = slicer.mrmlScene.GetNodeByID(nodeID)
self.parameterNodeTag = self.parameterNode.AddObserver("ModifiedEvent", self.updateGUIFromMRML)
# get access to the magnifier window and turn it off while using
# the Editor to improve performance (TODO: this should probably be
# a setting on the app)
mainWindow = slicer.util.mainWindow()
viewsController = slicer.util.findChildren(mainWindow, 'MRMLThreeDViewsControllerWidget')[0]
viewsController.disableMagnification = True
# resume the current effect, if we left the editor and re-entered
self.resumeEffect()
def create(self):
self.frame = qt.QFrame(self.parent)
self.frame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.frame)
self.label = qt.QLabel(self.frame)
self.label.setText("Label: ")
self.frame.layout().addWidget(self.label)
self.labelName = qt.QLabel(self.frame)
self.labelName.setText("")
self.frame.layout().addWidget(self.labelName)
self.colorSpin = qt.QSpinBox(self.frame)
self.colorSpin.setValue(int(tcl('EditorGetPaintLabel')))
self.colorSpin.setToolTip(
"Click colored patch at right to bring up color selection pop up window. Use the 'c' key to bring up color popup menu."
)
self.frame.layout().addWidget(self.colorSpin)
self.colorPatch = qt.QPushButton(self.frame)
self.frame.layout().addWidget(self.colorPatch)
self.updateParameterNode(slicer.mrmlScene, "ModifiedEvent")
self.updateGUIFromMRML(self.parameterNode, "ModifiedEvent")
self.frame.connect('destroyed(QObject)', self.cleanup)
self.colorSpin.connect('valueChanged(int)', self.updateMRMLFromGUI)
self.colorPatch.connect('clicked()', self.showColorBox)
# TODO: change this to look for specfic events (added, removed...)
# but this requires being able to access events by number from wrapped code
tag = slicer.mrmlScene.AddObserver("ModifiedEvent",
self.updateParameterNode)
self.observerTags.append((slicer.mrmlScene, tag))
def onEntry(self, comingFrom, transitionType):
"""
"""
super(EMSegmentDefineInputChannelsStep, self).onEntry(comingFrom, transitionType)
if self.isSimpleMode():
self.logic().SourceTaskFiles()
# clear the dynamic panel
self.dynamicFrame().setMRMLManager(self.mrmlManager())
self.dynamicFrame().clearElements()
logicTclName = self.logic().GetSlicerCommonInterface().GetTclNameFromPointer(self.logic())
tcl("::EMSegmenterSimpleTcl::ShowCheckList " + str(logicTclName))
self.loadFromMRML()
def onEntry( self, comingFrom, transitionType ):
'''
'''
super( EMSegmentDefineInputChannelsStep, self ).onEntry( comingFrom, transitionType )
if self.isSimpleMode():
self.logic().SourceTaskFiles()
# clear the dynamic panel
self.dynamicFrame().setMRMLManager( self.mrmlManager() )
self.dynamicFrame().clearElements()
logicTclName = self.logic().GetSlicerCommonInterface().GetTclNameFromPointer( self.logic() )
tcl( '::EMSegmenterSimpleTcl::ShowCheckList ' + str( logicTclName ) )
self.loadFromMRML()
def onEntry( self, comingFrom, transitionType ):
'''
'''
self.__parent.onEntry( comingFrom, transitionType )
# we are always in advanced mode, so let's fill the dynamic frame
self.logic().SourceTaskFiles()
self.logic().SourcePreprocessingTclFiles()
# clear the dynamic panel
self.dynamicFrame().setMRMLManager( self.mrmlManager() )
self.dynamicFrame().clearElements()
logicTclName = self.logic().GetSlicerCommonInterface().GetTclNameFromPointer( self.logic() )
tcl( '::EMSegmenterPreProcessingTcl::ShowUserInterface ' + str( logicTclName ) )
self.loadFromMRML()
def edit(self,label):
"""select the picked label for editing"""
merge = self.mergeVolume()
if not merge:
return
colorNode = merge.GetDisplayNode().GetColorNode()
structureName = colorNode.GetColorName( label )
structureVolume = self.structureVolume( structureName )
# make the master node the active background, and the structure label node the active label
selectionNode = self.applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.master.GetID())
if structureVolume:
selectionNode.SetReferenceActiveLabelVolumeID( structureVolume.GetID() )
self.applicationLogic.PropagateVolumeSelection()
tcl('EditorSetPaintLabel %s' % label)
def edit(self, label):
"""select the picked label for editing"""
merge = self.mergeVolume()
if not merge:
return
colorNode = merge.GetDisplayNode().GetColorNode()
structureName = colorNode.GetColorName(label)
structureVolume = self.structureVolume(structureName)
# make the master node the active background, and the structure label node the active label
selectionNode = self.applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.master.GetID())
if structureVolume:
selectionNode.SetReferenceActiveLabelVolumeID(
structureVolume.GetID())
self.applicationLogic.PropagateVolumeSelection(0)
tcl('EditorSetPaintLabel %s' % label)
def updateParameterNode(self, caller, event):
#
# observe the scene to know when to get the parameter node
#
nodeID = tcl('[EditorGetParameterNode] GetID')
node = slicer.mrmlScene.GetNodeByID(nodeID)
if node != self.parameterNode:
if self.parameterNode:
self.parameterNode.RemoveObserver(self.parameterNodeTag)
self.parameterNodeTag = node.AddObserver("ModifiedEvent", self.updateGUIFromMRML)
self.parameterNode = node
def onEntry(self, comingFrom, transitionType):
'''
'''
self.__parent.onEntry(comingFrom, transitionType)
# we are always in advanced mode, so let's fill the dynamic frame
self.logic().SourceTaskFiles()
self.logic().SourcePreprocessingTclFiles()
# clear the dynamic panel
self.dynamicFrame().setMRMLManager(self.mrmlManager())
self.dynamicFrame().clearElements()
logicTclName = self.logic().GetSlicerCommonInterface(
).GetTclNameFromPointer(self.logic())
tcl('::EMSegmenterPreProcessingTcl::ShowUserInterface ' +
str(logicTclName))
self.loadFromMRML()
def select(self):
"""select master volume - load merge volume if one with the correct name exists"""
self.master = self.masterSelector.currentNode()
merge = self.mergeVolume()
mergeText = "None"
if merge:
if merge.GetClassName(
) != "vtkMRMLScalarVolumeNode" or not merge.GetLabelMap():
self.errorDialog(
"Error: selected merge label volume is not a label volume")
else:
# make the source node the active background, and the label node the active label
selectionNode = self.applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.master.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(merge.GetID())
self.applicationLogic.PropagateVolumeSelection(0)
mergeText = merge.GetName()
self.merge = merge
else:
# the master exists, but there is no merge volume yet
# bring up dialog to create a merge with a user-selected color node
if self.master:
self.colorSelectDialog()
tcl('EffectSWidget::RotateToVolumePlanes'
) # make sure slices are aligned to volumes
self.mergeName.setText(mergeText)
self.updateStructures()
# remove all active effects (so that when selected again slice rotation and snap to IJK will happen if needed
tcl('::EffectSWidget::RemoveAll')
# trigger a modified event on the parameter node so that other parts of the GUI
# (such as the EditColor) will know to update and enable themselves
nodeID = tcl('[EditorGetParameterNode] GetID')
pNode = slicer.mrmlScene.GetNodeByID(nodeID)
if pNode:
pNode.Modified()
if self.selectCommand:
self.selectCommand()
def updateParameterNode(self, caller, event):
#
# observe the scene to know when to get the parameter node
#
nodeID = tcl('[EditorGetParameterNode] GetID')
node = slicer.mrmlScene.GetNodeByID(nodeID)
if node != self.parameterNode:
if self.parameterNode:
self.parameterNode.RemoveObserver(self.parameterNodeTag)
self.parameterNodeTag = node.AddObserver("ModifiedEvent",
self.updateGUIFromMRML)
self.parameterNode = node
def runPreProcessing(self):
'''
'''
# notify user
dialog = qt.QMessageBox()
dialog.setWindowTitle("Please wait")
dialog.setText("Please wait while pre-processing runs..")
dialog.setModal(False)
dialog.show()
# message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while pre-processing runs..", qt.QMessageBox.Ignore )
# message.setModal( False )
# message.show()
slicer.app.processEvents()
# run preprocessing
returnValue = tcl("::EMSegmenterPreProcessingTcl::Run")
# message.hide()
dialog.hide()
slicer.app.processEvents()
if not returnValue or int(returnValue) != 0:
# something went wrong!
# error message!
messageBox = qt.QMessageBox.warning(
self, "Error", "Pre-processing did not execute correctly!")
return
workingDataNode = self.mrmlManager().GetWorkingDataNode()
if workingDataNode:
# set flags in the mrml nodes
workingDataNode.SetAlignedTargetNodeIsValid(1)
workingDataNode.SetAlignedAtlasNodeIsValid(1)
# show preprocessing output in sliceViews
volumeCollection = workingDataNode.GetInputTargetNode()
if volumeCollection:
outputNode = volumeCollection.GetNthVolumeNode(0)
# propagate to sliceViews
selectionNode = slicer.app.applicationLogic().GetSelectionNode(
)
selectionNode.SetReferenceActiveVolumeID(outputNode.GetID())
#selectionNode.SetReferenceSecondaryVolumeID( outputNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection()
Helper.Info('=============================================')
Helper.Info('Pre-processing completed successfully')
Helper.Info('=============================================')
def enter(self):
"""
When entering the module, check that the lightbox modes are off
and that we have the volumes loaded
"""
warned = False
sliceLogics = slicer.app.layoutManager().mrmlSliceLogics()
for i in xrange(sliceLogics.GetNumberOfItems()):
sliceLogic = sliceLogics.GetItemAsObject(i)
if sliceLogic:
sliceNode = sliceLogic.GetSliceNode()
if sliceNode.GetLayoutGridRows() != 1 or sliceNode.GetLayoutGridColumns() != 1:
if not warned:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'Editor', 'The Editor Module is not compatible with slice viewers in light box mode.\nViews are being reset.')
warned = True
sliceNode.SetLayoutGrid(1,1)
# get the master and merge nodes from the composite node associated
# with the red slice, but only if showing volumes
if self.showVolumesFrame:
# get the slice composite node for the Red slice view (we'll assume it exists
# since we are in the editor) to get the current background and label
# - set the foreground layer as the active ID
# in the selection node for later calls to PropagateVolumeSelection
compositeNode = self.editUtil.getCompositeNode()
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceSecondaryVolumeID( compositeNode.GetForegroundVolumeID() )
print( 'setting selection node to ', compositeNode.GetForegroundVolumeID() )
bgID = lbID = ""
if compositeNode.GetBackgroundVolumeID():
bgID = compositeNode.GetBackgroundVolumeID()
if compositeNode.GetLabelVolumeID():
lbID = compositeNode.GetLabelVolumeID()
masterNode = slicer.mrmlScene.GetNodeByID( bgID )
mergeNode = slicer.mrmlScene.GetNodeByID( lbID )
self.setMasterNode(masterNode)
self.setMergeNode(mergeNode)
# if not showing volumes, the caller is responsible for setting the master and
# merge nodes, most likely according to a widget within the caller
# Observe the parameter node in order to make changes to
# button states as needed
nodeID = tcl('[EditorGetParameterNode] GetID')
self.parameterNode = slicer.mrmlScene.GetNodeByID(nodeID)
self.parameterNodeTag = self.parameterNode.AddObserver(vtk.vtkCommand.ModifiedEvent, self.updateGUIFromMRML)
# resume the current effect, if we left the editor and re-entered or pick default
# TODO: not fully implemented
#self.activateEffect()
self.helper.onEnter()
def runPreProcessing( self ):
'''
'''
# notify user
dialog = qt.QMessageBox()
dialog.setWindowTitle("Please wait")
dialog.setText("Please wait while pre-processing runs..")
dialog.setModal( False )
dialog.show()
# message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while pre-processing runs..", qt.QMessageBox.Ignore )
# message.setModal( False )
# message.show()
slicer.app.processEvents()
# run preprocessing
returnValue = tcl( "::EMSegmenterPreProcessingTcl::Run" )
# message.hide()
dialog.hide()
slicer.app.processEvents()
if not returnValue or int( returnValue ) != 0:
# something went wrong!
# error message!
messageBox = qt.QMessageBox.warning( self, "Error", "Pre-processing did not execute correctly!" )
return
workingDataNode = self.mrmlManager().GetWorkingDataNode()
if workingDataNode:
# set flags in the mrml nodes
workingDataNode.SetAlignedTargetNodeIsValid( 1 )
workingDataNode.SetAlignedAtlasNodeIsValid( 1 )
# show preprocessing output in sliceViews
volumeCollection = workingDataNode.GetInputTargetNode()
if volumeCollection:
outputNode = volumeCollection.GetNthVolumeNode( 0 )
# propagate to sliceViews
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( outputNode.GetID() )
#selectionNode.SetReferenceSecondaryVolumeID( outputNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection()
Helper.Info( '=============================================' )
Helper.Info( 'Pre-processing completed successfully' )
Helper.Info( '=============================================' )
def editorGetGestureParameterNode(self, id):
node = None
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLScriptedModuleNode')
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(n, 'vtkMRMLScriptedModuleNode')
nodeid = None
if compNode.GetModuleName() == 'Editor':
nodeId = compNode.GetParameter('gestureid')
if nodeId:
val = compNode.SetParameter('gestureid', nodeId)
node = val
break
if node == None:
node = tcl('EditorCreateGestureParameterNode %s' % id)
return node
def enter(self):
"""
When entering the module, check that the lightbox modes are off
and that we have the volumes loaded
"""
warned = False
sliceLogics = slicer.app.layoutManager().mrmlSliceLogics()
for i in xrange(sliceLogics.GetNumberOfItems()):
sliceLogic = sliceLogics.GetItemAsObject(i)
if sliceLogic:
sliceNode = sliceLogic.GetSliceNode()
print("checking %s", sliceNode.GetName())
if sliceNode.GetLayoutGridRows(
) != 1 or sliceNode.GetLayoutGridColumns() != 1:
if not warned:
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Editor',
'The Editor Module is not compatible with slice viewers in light box mode.\nViews are being reset.'
)
warned = True
sliceNode.SetLayoutGrid(1, 1)
# get the master and merge nodes from the composite node associated
# with the red slice, but only if showing volumes
if self.showVolumesFrame:
# get the slice composite node for the Red slice view (we'll assume it exists
# since we are in the editor) to get the current background and label
compositeNode = self.editUtil.getCompositeNode()
bgID = lbID = ""
if compositeNode.GetBackgroundVolumeID():
bgID = compositeNode.GetBackgroundVolumeID()
if compositeNode.GetLabelVolumeID():
lbID = compositeNode.GetLabelVolumeID()
masterNode = slicer.mrmlScene.GetNodeByID(bgID)
mergeNode = slicer.mrmlScene.GetNodeByID(lbID)
self.setMasterNode(masterNode)
self.setMergeNode(mergeNode)
# if not showing volumes, the caller is responsible for setting the master and
# merge nodes, most likely according to a widget within the caller
# Observe the parameter node in order to make changes to
# button states as needed
nodeID = tcl('[EditorGetParameterNode] GetID')
self.parameterNode = slicer.mrmlScene.GetNodeByID(nodeID)
self.parameterNodeTag = self.parameterNode.AddObserver(
"ModifiedEvent", self.updateGUIFromMRML)
def editorGetGestureParameterNode(self, id):
node = None
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLScriptedModuleNode')
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(
n, 'vtkMRMLScriptedModuleNode')
nodeid = None
if compNode.GetModuleName() == 'Editor':
nodeId = compNode.GetParameter('gestureid')
if nodeId:
val = compNode.SetParameter('gestureid', nodeId)
node = val
break
if node == None:
node = tcl('EditorCreateGestureParameterNode %s' % id)
return node
def enter(self):
# get the master and merge nodes from the composite node associated
# with the red slice, but only if showing volumes
if self.showVolumesFrame:
# get the slice composite node for the Red slice view (we'll assume it exists
# since we are in the editor) to get the current background and label
compositeNode = self.editUtil.getCompositeNode()
masterNode = slicer.mrmlScene.GetNodeByID( compositeNode.GetBackgroundVolumeID() )
mergeNode = slicer.mrmlScene.GetNodeByID( compositeNode.GetLabelVolumeID() )
self.setMasterNode(masterNode)
self.setMergeNode(mergeNode)
# if not showing volumes, the caller is responsible for setting the master and
# merge nodes, most likely according to a widget within the caller
# Observe the parameter node in order to make changes to
# button states as needed
nodeID = tcl('[EditorGetParameterNode] GetID')
self.parameterNode = slicer.mrmlScene.GetNodeByID(nodeID)
self.parameterNodeTag = self.parameterNode.AddObserver("ModifiedEvent", self.updateGUIFromMRML)
def enter(self):
"""
When entering the module, check that the lightbox modes are off
and that we have the volumes loaded
"""
warned = False
sliceLogics = slicer.app.layoutManager().mrmlSliceLogics()
for i in xrange(sliceLogics.GetNumberOfItems()):
sliceLogic = sliceLogics.GetItemAsObject(i)
if sliceLogic:
sliceNode = sliceLogic.GetSliceNode()
print("checking %s", sliceNode.GetName())
if sliceNode.GetLayoutGridRows() != 1 or sliceNode.GetLayoutGridColumns() != 1:
if not warned:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'Editor', 'The Editor Module is not compatible with slice viewers in light box mode.\nViews are being reset.')
warned = True
sliceNode.SetLayoutGrid(1,1)
# get the master and merge nodes from the composite node associated
# with the red slice, but only if showing volumes
if self.showVolumesFrame:
# get the slice composite node for the Red slice view (we'll assume it exists
# since we are in the editor) to get the current background and label
compositeNode = self.editUtil.getCompositeNode()
bgID = lbID = ""
if compositeNode.GetBackgroundVolumeID():
bgID = compositeNode.GetBackgroundVolumeID()
if compositeNode.GetLabelVolumeID():
lbID = compositeNode.GetLabelVolumeID()
masterNode = slicer.mrmlScene.GetNodeByID( bgID )
mergeNode = slicer.mrmlScene.GetNodeByID( lbID )
self.setMasterNode(masterNode)
self.setMergeNode(mergeNode)
# if not showing volumes, the caller is responsible for setting the master and
# merge nodes, most likely according to a widget within the caller
# Observe the parameter node in order to make changes to
# button states as needed
nodeID = tcl('[EditorGetParameterNode] GetID')
self.parameterNode = slicer.mrmlScene.GetNodeByID(nodeID)
self.parameterNodeTag = self.parameterNode.AddObserver("ModifiedEvent", self.updateGUIFromMRML)
def validate( self, desiredBranchId ):
'''
'''
super( EMSegmentDefinePreprocessingStep, self ).validate( desiredBranchId )
# check if CMTK should be used,
# then try to find it
# if this fails, ask if we should use BRAINSFit
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager().GetPackageTypeFromString( 'CMTK' ):
# cmtk was selected
cmtkPath = tcl( "::EMSegmenterPreProcessingTcl::Get_CMTK_Installation_Path" )
if cmtkPath == "":
# cmtk was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question( self, "CMTK is not installed", "CMTK is not installed. Do you want to proceed with BRAINSTools instead?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed( desiredBranchId, '', '', False )
return
# same for plastimatch
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager().GetPackageTypeFromString( 'PLASTIMATCH' ):
# plastimatch was selected
plastimatchPath = tcl( "::EMSegmenterPreProcessingTcl::Get_PLASTIMATCH_Installation_Path" )
if plastimatchPath == "":
# plastimatch was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question( self, "PLASTIMATCH is not installed", "PLASTIMATCH is not installed. Do you want to proceed with BRAINSTools instead?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed( desiredBranchId, '', '', False )
return
# same for DEMONS
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager().GetPackageTypeFromString( 'DEMONS' ):
# DEMONS was selected
demonsPath = tcl( "::EMSegmenterPreProcessingTcl::Get_DEMONS_Installation_Path" )
if demonsPath == "":
# demons was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question( self, "DEMONS is not installed", "DEMONS is not installed. Do you want to proceed with BRAINSTools instead?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed( desiredBranchId, '', '', False )
return
# same for DRAMMS
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager().GetPackageTypeFromString( 'DRAMMS' ):
# dramms was selected
drammsPath = tcl( "::EMSegmenterPreProcessingTcl::Get_DRAMMS_Installation_Path" )
if drammsPath == "":
# dramms was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question( self, "DRAMMS is not installed", "DRAMMS is not installed. Do you want to proceed with BRAINSTools instead?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed( desiredBranchId, '', '', False )
return
# same for ANTS
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager().GetPackageTypeFromString( 'ANTS' ):
# ANTS was selected
antsPath = tcl( "::EMSegmenterPreProcessingTcl::Get_ANTS_Installation_Path" )
if antsPath == "":
# ANTS was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question( self, "ANTS is not installed", "ANTS is not installed. Do you want to proceed with BRAINSTools instead?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed( desiredBranchId, '', '', False )
return
#
# check if we should ask questions before running preprocessing and if yes do so!
#
if not self.__askQuestionsBeforeRunningPreprocessing:
# no questions, just run it
self.validationSucceeded( desiredBranchId )
return
# check if preprocessing already ran
# if yes, ask for redo
# if no, ask for start (which takes some time)
workingDataNode = self.mrmlManager().GetWorkingDataNode()
preprocessingAlreadyDone = ( workingDataNode.GetAlignedTargetNodeIsValid() and workingDataNode.GetAlignedAtlasNodeIsValid() )
if preprocessingAlreadyDone:
# ask if we should do it again
answer = qt.QMessageBox.question( self, "Redo Pre-processing of images?", "Do you want to redo pre-processing of input images?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# no calculation
self.__performCalculation = False
else:
# calculation
self.__performCalculation = True
else:
# ask if we should run preprocessing
# if not, stay at this step
answer = qt.QMessageBox.question( self, "Start Pre-processing of images?", "Pre-processing of images might take a while. Do you want to proceed?", qt.QMessageBox.Yes | qt.QMessageBox.No )
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed( desiredBranchId, '', '', False )
return
else:
# perform the calculation!
self.__performCalculation = True
self.validationSucceeded( desiredBranchId )
def findEffects(self, path=""):
# for now, the built in effects are hard-coded to facilitate
# the icons and layout
self.effects = []
# if a list of effects was supplied, then use that list instead of all of the effects
# don't forget to check that the supplied effects are valid: ensure they exist in the lists of available effects
if (self.suppliedEffects):
self.mouseTools = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableMouseTools))
self.operations = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableOperations))
self.nonmodal = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableNonmodal))
self.disabled = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableDisabled))
# if a list of effects is not supplied, then provide all effects
else:
self.mouseTools = EditBox.availableMouseTools
self.operations = EditBox.availableOperations
self.nonmodal = EditBox.availableNonmodal
self.disabled = EditBox.availableDisabled
'''
for key in slicer.modules.editorExtensions.keys():
e = slicer.modules.editorExtensions[key]()
if 'MouseTool' in e.attributes:
self.mouseTools.append(key)
if 'Nonmodal' in e.attributes:
self.operations.append(key)
if 'Disabled' in e.attributes:
self.disabled.append(key)
'''
# combined list of all effects
self.effects = self.mouseTools + self.operations
# add any extensions that have been registered
self.effects = self.effects + tuple(
slicer.modules.editorExtensions.keys())
# for each effect
# - look for implementation class of pattern *Effect
# - get an icon name for the pushbutton
iconDir = os.environ['SLICER_HOME'] + '/' + os.environ[
'SLICER_SHARE_DIR'] + '/Tcl/ImageData/'
self.effectClasses = {}
self.effectIconFiles = {}
self.effectModes = {}
self.icons = {}
for effect in self.effects:
tclclass = tcl('info command %sEffect' % effect)
if tclclass != '':
self.effectClasses[effect] = tclclass
else:
self.effectClasses[effect] = "EffectSWidget"
for iconType in ("", "Selected", "Disabled"):
self.effectIconFiles[
effect, iconType] = iconDir + effect + iconType + '.png'
iconMode = ""
if self.disabled.__contains__(effect):
# - don't use the disabled icon for now - Qt's setEnabled method works fine
#iconMode = "Disabled"
pass
self.effectModes[effect] = iconMode
def RotateToVolumePlanes():
# AF TODO: check with Steve if this has any undesired consequences
tcl('EffectSWidget::RotateToVolumePlanes')
def createUserInterface(self):
'''
'''
slicer.modules.emsegmentinitialdistance = 4
# just call to copy the emsegmenter task to a temp dir
self.logic().GetTasks()
self.__layout = super(EMSegmentQuickStep1, self).createUserInterface()
infoLabel = qt.QLabel(
'This module provides EM segmentation without an atlas.\nIt is possible to segment different structures by manual sampling.\n\n'
)
infoLabel.setFont(self.getBoldFont())
self.__layout.addWidget(infoLabel)
# the input channels
inputChannelGroupBox = qt.QGroupBox()
inputChannelGroupBox.setTitle('Input Datasets')
inputChannelGroupBox.toolTip = 'Please configure the datasets which should be segmented.'
self.__layout.addWidget(inputChannelGroupBox)
inputChannelGroupBoxLayout = qt.QFormLayout(inputChannelGroupBox)
self.__inputChannelList = slicer.modulewidget.qSlicerEMSegmentInputChannelListWidget(
)
self.__inputChannelList.setMRMLManager(self.mrmlManager())
inputChannelGroupBoxLayout.addWidget(self.__inputChannelList)
# add empty row
self.__layout.addRow("", qt.QWidget())
#
# dynamic frame
#
dynamicFrame = qt.QGroupBox()
dynamicFrame.setTitle('Check List')
dynamicFrame.toolTip = 'Please check anything applicable.'
self.__layout.addWidget(dynamicFrame)
dynamicFrameLayout = qt.QVBoxLayout(dynamicFrame)
# .. now pass the layout to the dynamicFrame
self.dynamicFrame().setLayout(dynamicFrameLayout)
#
# end of dynamic frame
#
# check if we have a valid EMEasy MRML Node
templateNodes = slicer.mrmlScene.GetNodesByClassByName(
'vtkMRMLEMSTemplateNode', 'EMEasy')
if templateNodes.GetNumberOfItems() > 0:
# we load the last template node which fits the taskname
templateNode = templateNodes.GetItemAsObject(
templateNodes.GetNumberOfItems() - 1)
loadResult = self.mrmlManager().SetLoadedParameterSetIndex(
templateNode)
if int(loadResult) != 0:
Helper.Info(
"EMS node is corrupted - the manager could not be updated with new task: "
+ taskName)
#return False
else:
Helper.Info("Loading completed.")
self.logic().DefineTclTaskFileFromMRML()
# clear the dynamic panel
self.dynamicFrame().setMRMLManager(self.mrmlManager())
self.dynamicFrame().clearElements()
self.logic().SourceTaskFiles()
slicer.modules.emsegmentAdvancedDynamicFrame = self.dynamicFrame()
logicTclName = self.logic().GetSlicerCommonInterface(
).GetTclNameFromPointer(self.logic())
tcl('::EMSegmenterPreProcessingTcl::ShowUserInterface ' +
str(logicTclName))
slicer.modules.emsegmenteasystep2.disableNumberOfStructures()
self.__initialized = True
class EditBox(object):
def __init__(self,
parent=0,
optionsFrame=None,
embedded=False,
suppliedEffects=[]):
self.effects = []
self.effectButtons = {}
self.effectMapper = qt.QSignalMapper()
self.effectMapper.connect('mapped(const QString&)', self.selectEffect)
self.editUtil = EditUtil.EditUtil()
# check for extensions - if none have been registered, just create the empty dictionary
try:
slicer.modules.editorExtensions
except AttributeError:
slicer.modules.editorExtensions = {}
# embedded boolean specifies whether or not this edit box is to be embedded
# into another moduleWidget
# - if it is, all effect buttons will be displayed in a single row
self.embedded = embedded
# save the list of supplied effects that the caller wants to use
# (should be a subset of EditBox.availableMouseTools + EditBox.availableOperations)
self.suppliedEffects = suppliedEffects
if parent == 0:
self.parent = qt.QFrame()
self.parent.setLayout(qt.QVBoxLayout())
self.create()
self.parent.show()
else:
self.parent = parent
self.create()
# frame that holds widgets specific for each effect
if not optionsFrame:
self.optionsFrame = qt.QFrame(self.parent)
else:
self.optionsFrame = optionsFrame
# state variables for selected effect in the box
# - currentOption is an instance of an option GUI
# - currentTools is a list of EffectTool instances
self.currentOption = None
self.currentTools = []
#
# Public lists of the available effects provided by the editor
#
# effects that change the mouse cursor
availableMouseTools = (
"ChangeIsland",
"ChooseColor",
"ImplicitCube",
"ImplicitEllipse",
"ImplicitRectangle",
"Draw",
"RemoveIslands",
"ConnectedComponents",
"ThresholdBucket",
"ThresholdPaintLabel",
"SaveIsland",
"SlurpColor",
"Paint",
"DefaultTool",
"LevelTracing",
"MakeModel",
"Wand",
"GrowCutSegment",
)
# effects that operate from the menu
availableOperations = (
"ErodeLabel",
"DilateLabel",
"DeleteFiducials",
"LabelOpacity",
"ChangeLabel",
"FiducialVisibilityOff",
"FiducialVisibilityOn",
"GoToEditorModule",
"IdentifyIslands",
"LabelVisibilityOff",
"LabelVisibilityOn",
"NextFiducial",
"SnapToGridOff",
"SnapToGridOn",
"EraseLabel",
"Threshold",
"PinOpen",
"PreviousFiducial",
"InterpolateLabels",
"LabelOpacity",
"ToggleLabelOutline",
"Watershed",
"PreviousCheckPoint",
"NextCheckPoint",
)
# these buttons do not switch you out of the current tool
availableNonmodal = ("FiducialVisibilityOn", "LabelVisibilityOff",
"LabelVisibilityOn", "NextFiducial",
"PreviousFiducial", "DeleteFiducials", "SnapToGridOn",
"SnapToGridOff", "EraseLabel", "PreviousCheckPoint",
"NextCheckPoint", "ToggleLabelOutline",
"SnapToGridOff", "SnapToGridOn", "LabelOpacity")
# these buttons start disabled (check points will re-enable when circumstances are right)
availableDisabled = (
"ChooseColor",
"ImplicitCube",
"ImplicitEllipse",
"ConnectedComponents",
"SlurpColor",
"ThresholdPaintLabel",
"ThresholdBucket",
"DeleteFiducials",
"LabelOpacity",
"FiducialVisibilityOff",
"FiducialVisibilityOn",
"LabelVisibilityOff",
"LabelVisibilityOn",
"SnapToGridOff",
"SnapToGridOn",
"InterpolateLabels",
"LabelOpacity",
"ToggleLabelOutline",
"Watershed",
"Wand",
)
# allow overriding the developers name of the tool for a more user-friendly label name
displayNames = {}
displayNames["PreviousCheckPoint"] = "Undo"
displayNames["NextCheckPoint"] = "Redo"
# calculates the intersection of two flat lists
@classmethod
def listIntersection(cls, inList1, inList2):
outList = [val for val in inList1 if val in inList2]
return outList
# fill the _effects array bases on what you find in the interpreter
# if a list of effects was supplied, then use that list instead of all of the effects
def findEffects(self, path=""):
# for now, the built in effects are hard-coded to facilitate
# the icons and layout
self.effects = []
# if a list of effects was supplied, then use that list instead of all of the effects
# don't forget to check that the supplied effects are valid: ensure they exist in the lists of available effects
if (self.suppliedEffects):
self.mouseTools = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableMouseTools))
self.operations = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableOperations))
self.nonmodal = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableNonmodal))
self.disabled = tuple(
self.listIntersection(self.suppliedEffects,
EditBox.availableDisabled))
# if a list of effects is not supplied, then provide all effects
else:
self.mouseTools = EditBox.availableMouseTools
self.operations = EditBox.availableOperations
self.nonmodal = EditBox.availableNonmodal
self.disabled = EditBox.availableDisabled
'''
for key in slicer.modules.editorExtensions.keys():
e = slicer.modules.editorExtensions[key]()
if 'MouseTool' in e.attributes:
self.mouseTools.append(key)
if 'Nonmodal' in e.attributes:
self.operations.append(key)
if 'Disabled' in e.attributes:
self.disabled.append(key)
'''
# combined list of all effects
self.effects = self.mouseTools + self.operations
# add any extensions that have been registered
self.effects = self.effects + tuple(
slicer.modules.editorExtensions.keys())
# for each effect
# - look for implementation class of pattern *Effect
# - get an icon name for the pushbutton
iconDir = os.environ['SLICER_HOME'] + '/' + os.environ[
'SLICER_SHARE_DIR'] + '/Tcl/ImageData/'
self.effectClasses = {}
self.effectIconFiles = {}
self.effectModes = {}
self.icons = {}
for effect in self.effects:
tclclass = tcl('info command %sEffect' % effect)
if tclclass != '':
self.effectClasses[effect] = tclclass
else:
self.effectClasses[effect] = "EffectSWidget"
for iconType in ("", "Selected", "Disabled"):
self.effectIconFiles[
effect, iconType] = iconDir + effect + iconType + '.png'
iconMode = ""
if self.disabled.__contains__(effect):
# - don't use the disabled icon for now - Qt's setEnabled method works fine
#iconMode = "Disabled"
pass
self.effectModes[effect] = iconMode
#
# create a row of the edit box given a list of
# effect names (items in _effects(list)
#
def createButtonRow(self, effects, rowLabel=""):
f = qt.QFrame(self.parent)
self.parent.layout().addWidget(f)
self.rowFrames.append(f)
hbox = qt.QHBoxLayout()
f.setLayout(hbox)
if rowLabel:
label = qt.QLabel(rowLabel)
hbox.addWidget(label)
for effect in effects:
# check that the effect belongs in our list of effects before including
# (handles non-embedded widgets where the caller has supplied a custom list of effects)
if (effect in self.effects):
i = self.icons[effect] = qt.QIcon(
self.effectIconFiles[effect, self.effectModes[effect]])
a = self.actions[effect] = qt.QAction(i, '', f)
self.effectButtons[effect] = b = self.buttons[
effect] = qt.QToolButton()
b.setDefaultAction(a)
b.setToolTip(effect)
if EditBox.displayNames.has_key(effect):
b.setToolTip(EditBox.displayNames[effect])
hbox.addWidget(b)
if self.disabled.__contains__(effect):
b.setDisabled(1)
# Setup the mapping between button and its associated effect name
self.effectMapper.setMapping(self.buttons[effect], effect)
# Connect button with signal mapper
self.buttons[effect].connect('clicked()', self.effectMapper,
'map()')
hbox.addStretch(1)
# create the edit box
def create(self):
self.findEffects()
#
# the buttons
#
self.rowFrames = []
self.actions = {}
self.buttons = {}
self.icons = {}
self.callbacks = {}
# if not using embedded format: create all of the buttons
# createButtonRow() ensures that only effects in self.effects are exposed,
# so if the user supplied a list of effects only those in that list will be exposed
if (not self.embedded):
self.createButtonRow(
("DefaultTool", "EraseLabel", "Paint", "Draw", "LevelTracing",
"ImplicitRectangle", "IdentifyIslands", "ChangeIsland",
"RemoveIslands", "SaveIsland"))
self.createButtonRow(
("ErodeLabel", "DilateLabel", "Threshold", "ChangeLabel",
"MakeModel", "GrowCutSegment"))
extensions = []
for k in slicer.modules.editorExtensions:
extensions.append(k)
self.createButtonRow(extensions)
# TODO: add back prev/next fiducial
#self.createButtonRow( ("PreviousFiducial", "NextFiducial") )
self.createButtonRow(("PreviousCheckPoint", "NextCheckPoint"),
rowLabel="Undo/Redo: ")
# if using embedded format: create all of the buttons in the effects list in a single row
else:
self.createButtonRow(self.effects)
#
# the labels (not shown in embedded format)
#
self.toolsActiveToolFrame = qt.QFrame(self.parent)
self.toolsActiveToolFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.toolsActiveToolFrame)
self.toolsActiveTool = qt.QLabel(self.toolsActiveToolFrame)
self.toolsActiveTool.setText('Active Tool:')
self.toolsActiveTool.setStyleSheet(
"background-color: rgb(232,230,235)")
self.toolsActiveToolFrame.layout().addWidget(self.toolsActiveTool)
self.toolsActiveToolName = qt.QLabel(self.toolsActiveToolFrame)
self.toolsActiveToolName.setText('')
self.toolsActiveToolName.setStyleSheet(
"background-color: rgb(232,230,235)")
self.toolsActiveToolFrame.layout().addWidget(self.toolsActiveToolName)
self.updateCheckPointButtons()
def setActiveToolLabel(self, name):
if EditBox.displayNames.has_key(name):
name = EditBox.displayNames[name]
self.toolsActiveToolName.setText(name)
# needs to be a valid effect name and state of "", Disabled, or Selected
TODO = """
itcl::body EditBox::setButtonState {effect state} {
$::slicer3::ApplicationGUI SetIconImage \
$_effects($effect,icon) $_effects($effect,imageData$state)
$o($effect,button) SetImageToIcon $_effects($effect,icon)
switch $state {
Selected -
"" {
$o($effect,button) SetState 1
}
"Disabled" {
$o($effect,button) SetState 0
}
}
}
"""
#
# Pause running the current effect, reverting to the default tool
#
def pauseEffect(self):
self.selectEffect("DefaultTool")
#
# Resume running the effect that was being used before a pause (TODO)
#
def resumeEffect(self):
pass
#
# manage the editor effects
#
def selectEffect(self, effect):
from slicer import app
#
# if a modal effect was selected, 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 not self.nonmodal.__contains__(effect):
if self.currentOption:
self.currentOption.__del__()
self.currentOption = None
for tool in self.currentTools:
tool.cleanup()
self.currentTools = []
if effect in slicer.modules.editorExtensions.keys():
extensionEffect = slicer.modules.editorExtensions[effect]()
self.currentOption = extensionEffect.options(self.optionsFrame)
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 = extensionEffect.tool(sliceWidget)
self.currentTools.append(tool)
else:
try:
options = eval("%sOptions" % effect)
self.currentOption = options(self.optionsFrame)
except NameError, AttributeError:
# No options for this effect, skip it
pass
#
# If there is no background volume or label map, do nothing
#
# TODO should do this regardless of whether or not there is an option
if not self.editUtil.getBackgroundVolume():
return
if not self.editUtil.getLabelVolume():
return
app.restoreOverrideCursor()
self.setActiveToolLabel(effect)
if not self.nonmodal.__contains__(effect):
tcl('EffectSWidget::RemoveAll')
tcl('EditorSetActiveToolLabel %s' % effect)
# mouse tool changes cursor, and dismisses popup/menu
mouseTool = False
if self.mouseTools.__contains__(effect):
mouseTool = True
if effect == "DefaultTool":
# do nothing - this will reset cursor mode
tcl('EditorSetActiveToolLabel DefaultTool')
elif effect == "GoToEditorModule":
tcl('EditorSelectModule')
tcl('EditorSetActiveToolLabel DefaultTool')
elif effect == "LabelCheckPoint":
# save a copy of the current label layer into the scene
tcl('EditorLabelCheckPoint')
tcl('EditorSetActiveToolLabel DefaultTool')
elif effect == "PreviousFiducial":
tcl('::FiducialsSWidget::JumpAllToNextFiducial -1')
tcl('EditorSetActiveToolLabel DefaultTool')
elif effect == "NextFiducial":
tcl('::FiducialsSWidget::JumpAllToNextFiducial 1')
tcl('EditorSetActiveToolLabel DefaultTool')
elif effect == "EraseLabel":
tcl('EditorToggleErasePaintLabel')
elif effect == "PreviousCheckPoint":
tcl('EditorPerformPreviousCheckPoint')
elif effect == "NextCheckPoint":
tcl('EditorPerformNextCheckPoint')
else:
if effect == "GrowCutSegment":
self.editorGestureCheckPoint()
#volumesLogic = slicer.modules.volumes.logic()
#print ("VolumesLogic is %s " % volumesLogic)
#tcl('EditorGestureCheckPoint $%s' % volumesLogic)
if mouseTool:
# TODO: make some nice custom cursor shapes
# - for now use the built in override cursor
#pix = qt.QPixmap()
#pix.load(self.effectIconFiles[effect,""])
#cursor = qt.QCursor(pix)
#app.setOverrideCursor(cursor, 0, 0)
cursor = qt.QCursor(1)
app.setOverrideCursor(cursor)
else:
app.restoreOverrideCursor()
#
# create an instance of the effect for each of the active sliceGUIs
# - have the effect reset the tool label when completed
#
ret = tcl('catch "EffectSWidget::Add %s" res' %
self.effectClasses[effect])
if ret != '0':
dialog = qt.QErrorMessage(self.parent)
dialog.showMessage(
"Could not select effect.\n\nError was:\n%s" %
tcl('set res'))
else:
tcl('EffectSWidget::ConfigureAll %s -exitCommand "EditorSetActiveToolLabel DefaultTool"'
% self.effectClasses[effect])
def createUserInterface( self ):
'''
'''
slicer.modules.emsegmentinitialdistance = 4
# just call to copy the emsegmenter task to a temp dir
self.logic().GetTasks()
self.__layout = super( EMSegmentQuickStep1, self ).createUserInterface()
infoLabel = qt.QLabel( 'This module provides EM segmentation without an atlas.\nIt is possible to segment different structures by manual sampling.\n\n' )
infoLabel.setFont( self.getBoldFont() )
self.__layout.addWidget( infoLabel )
# the input channels
inputChannelGroupBox = qt.QGroupBox()
inputChannelGroupBox.setTitle( 'Input Datasets' )
inputChannelGroupBox.toolTip = 'Please configure the datasets which should be segmented.'
self.__layout.addWidget( inputChannelGroupBox )
inputChannelGroupBoxLayout = qt.QFormLayout( inputChannelGroupBox )
self.__inputChannelList = slicer.qSlicerEMSegmentInputChannelListWidget()
self.__inputChannelList.setMRMLManager( self.mrmlManager() )
inputChannelGroupBoxLayout.addWidget( self.__inputChannelList )
# add empty row
self.__layout.addRow( "", qt.QWidget() )
#
# dynamic frame
#
dynamicFrame = qt.QGroupBox()
dynamicFrame.setTitle( 'Check List' )
dynamicFrame.toolTip = 'Please check anything applicable.'
self.__layout.addWidget( dynamicFrame )
dynamicFrameLayout = qt.QVBoxLayout( dynamicFrame )
# .. now pass the layout to the dynamicFrame
self.dynamicFrame().setLayout( dynamicFrameLayout )
#
# end of dynamic frame
#
# check if we have a valid EMEasy MRML Node
templateNodes = slicer.mrmlScene.GetNodesByClassByName( 'vtkMRMLEMSTemplateNode', 'EMEasy' )
if templateNodes.GetNumberOfItems() > 0:
# we load the last template node which fits the taskname
templateNode = templateNodes.GetItemAsObject( templateNodes.GetNumberOfItems() - 1 )
loadResult = self.mrmlManager().SetLoadedParameterSetIndex( templateNode )
if int( loadResult ) != 0:
Helper.Info( "EMS node is corrupted - the manager could not be updated with new task: " + taskName )
#return False
else:
Helper.Info( "Loading completed." )
self.logic().DefineTclTaskFileFromMRML()
# clear the dynamic panel
self.dynamicFrame().setMRMLManager( self.mrmlManager() )
self.dynamicFrame().clearElements()
self.logic().SourceTaskFiles()
slicer.modules.emsegmentAdvancedDynamicFrame = self.dynamicFrame()
logicTclName = self.logic().GetSlicerCommonInterface().GetTclNameFromPointer( self.logic() )
tcl( '::EMSegmenterPreProcessingTcl::ShowUserInterface ' + str( logicTclName ) )
slicer.modules.emsegmenteasystep2.disableNumberOfStructures()
self.__initialized = True
def validate(self, desiredBranchId):
'''
'''
super(EMSegmentDefinePreprocessingStep, self).validate(desiredBranchId)
# check if CMTK should be used,
# then try to find it
# if this fails, ask if we should use BRAINSFit
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager(
).GetPackageTypeFromString('CMTK'):
# cmtk was selected
cmtkPath = tcl(
"::EMSegmenterPreProcessingTcl::Get_CMTK_Installation_Path")
if cmtkPath == "":
# cmtk was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question(
self, "CMTK is not installed",
"CMTK is not installed. Do you want to proceed with BRAINSTools instead?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed(desiredBranchId, '', '', False)
return
# same for plastimatch
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager(
).GetPackageTypeFromString('PLASTIMATCH'):
# plastimatch was selected
plastimatchPath = tcl(
"::EMSegmenterPreProcessingTcl::Get_PLASTIMATCH_Installation_Path"
)
if plastimatchPath == "":
# plastimatch was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question(
self, "PLASTIMATCH is not installed",
"PLASTIMATCH is not installed. Do you want to proceed with BRAINSTools instead?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed(desiredBranchId, '', '', False)
return
# same for DEMONS
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager(
).GetPackageTypeFromString('DEMONS'):
# DEMONS was selected
demonsPath = tcl(
"::EMSegmenterPreProcessingTcl::Get_DEMONS_Installation_Path")
if demonsPath == "":
# demons was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question(
self, "DEMONS is not installed",
"DEMONS is not installed. Do you want to proceed with BRAINSTools instead?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed(desiredBranchId, '', '', False)
return
# same for DRAMMS
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager(
).GetPackageTypeFromString('DRAMMS'):
# dramms was selected
drammsPath = tcl(
"::EMSegmenterPreProcessingTcl::Get_DRAMMS_Installation_Path")
if drammsPath == "":
# dramms was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question(
self, "DRAMMS is not installed",
"DRAMMS is not installed. Do you want to proceed with BRAINSTools instead?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed(desiredBranchId, '', '', False)
return
# same for ANTS
if self.mrmlManager().GetRegistrationPackageType() == self.mrmlManager(
).GetPackageTypeFromString('ANTS'):
# ANTS was selected
antsPath = tcl(
"::EMSegmenterPreProcessingTcl::Get_ANTS_Installation_Path")
if antsPath == "":
# ANTS was not found, ask if we want BRAINSFit instead
answer = qt.QMessageBox.question(
self, "ANTS is not installed",
"ANTS is not installed. Do you want to proceed with BRAINSTools instead?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed(desiredBranchId, '', '', False)
return
#
# check if we should ask questions before running preprocessing and if yes do so!
#
if not self.__askQuestionsBeforeRunningPreprocessing:
# no questions, just run it
self.validationSucceeded(desiredBranchId)
return
# check if preprocessing already ran
# if yes, ask for redo
# if no, ask for start (which takes some time)
workingDataNode = self.mrmlManager().GetWorkingDataNode()
preprocessingAlreadyDone = (
workingDataNode.GetAlignedTargetNodeIsValid()
and workingDataNode.GetAlignedAtlasNodeIsValid())
if preprocessingAlreadyDone:
# ask if we should do it again
answer = qt.QMessageBox.question(
self, "Redo Pre-processing of images?",
"Do you want to redo pre-processing of input images?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# no calculation
self.__performCalculation = False
else:
# calculation
self.__performCalculation = True
else:
# ask if we should run preprocessing
# if not, stay at this step
answer = qt.QMessageBox.question(
self, "Start Pre-processing of images?",
"Pre-processing of images might take a while. Do you want to proceed?",
qt.QMessageBox.Yes | qt.QMessageBox.No)
if answer == qt.QMessageBox.No:
# if no, exit here and stay at this step
self.validationFailed(desiredBranchId, '', '', False)
return
else:
# perform the calculation!
self.__performCalculation = True
self.validationSucceeded(desiredBranchId)
def findEffects(self, path=""):
# for now, the built in effects are hard-coded to facilitate
# the icons and layout
self.effects = []
# if a list of effects was supplied, then use that list instead of all of the effects
# don't forget to check that the supplied effects are valid: ensure they exist in the lists of available effects
if (self.suppliedEffects):
self.mouseTools = tuple(self.listIntersection(self.suppliedEffects, EditBox.availableMouseTools))
self.operations = tuple(self.listIntersection(self.suppliedEffects, EditBox.availableOperations))
self.nonmodal = tuple(self.listIntersection(self.suppliedEffects, EditBox.availableNonmodal))
self.disabled = tuple(self.listIntersection(self.suppliedEffects, EditBox.availableDisabled))
# if a list of effects is not supplied, then provide all effects
else:
self.mouseTools = EditBox.availableMouseTools
self.operations = EditBox.availableOperations
self.nonmodal = EditBox.availableNonmodal
self.disabled = EditBox.availableDisabled
'''
for key in slicer.modules.editorExtensions.keys():
e = slicer.modules.editorExtensions[key]()
if 'MouseTool' in e.attributes:
self.mouseTools.append(key)
if 'Nonmodal' in e.attributes:
self.operations.append(key)
if 'Disabled' in e.attributes:
self.disabled.append(key)
'''
# combined list of all effects
self.effects = self.mouseTools + self.operations
# add any extensions that have been registered
self.effects = self.effects + tuple(slicer.modules.editorExtensions.keys())
# for each effect
# - look for implementation class of pattern *Effect
# - get an icon name for the pushbutton
iconDir = os.environ['SLICER_HOME'] + '/' + os.environ['SLICER_SHARE_DIR'] + '/Tcl/ImageData/'
self.effectClasses = {}
self.effectIconFiles = {}
self.effectModes = {}
self.icons = {}
for effect in self.effects:
tclclass = tcl('info command %sEffect' % effect)
if tclclass != '':
self.effectClasses[effect] = tclclass
else:
self.effectClasses[effect] = "EffectSWidget"
for iconType in ( "", "Selected", "Disabled" ):
self.effectIconFiles[effect,iconType] = iconDir + effect + iconType + '.png'
iconMode = ""
if self.disabled.__contains__(effect):
# - don't use the disabled icon for now - Qt's setEnabled method works fine
#iconMode = "Disabled"
pass
self.effectModes[effect] = iconMode