def setup(self):
### DEVELOPER ###
self.reloadButton = qt.QPushButton('Reload')
self.reloadButton.toolTip = 'Developer reload button'
self.reloadButton.name = 'FastFiducial Reload'
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
### END ###
self.slicerVersion = int(slicer.app.majorVersion)
self.fixed = ImageDataContainer(self.slicerVersion)
self.fixed.addToScene(slicer.mrmlScene)
self.moving = ImageDataContainer(self.slicerVersion)
self.interactor = slicer.mrmlScene.AddNode(
slicer.vtkMRMLInteractionNode())
self.selector = slicer.mrmlScene.AddNode(slicer.vtkMRMLSelectionNode())
# self._threeByThreeCompareView()
self._inputLayoutSection()
self._fiducialLayoutSection()
self._registrationLayoutSection()
### DEVELOPER ###
import os
if os.environ['USER'] == 'dmwelch':
self.logic.testingData()
self.fixedVolumeSelector.setCurrentNode(
slicer.util.getNode('fixed*'))
self.movingVolumeSelector.setCurrentNode(
slicer.util.getNode('moving*'))
### ***END*** ###
self.layout.addStretch(1)
def setup(self):
### DEVELOPER ###
self.reloadButton = qt.QPushButton('Reload')
self.reloadButton.toolTip = 'Developer reload button'
self.reloadButton.name = 'FastFiducial Reload'
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
### END ###
self.slicerVersion = int(slicer.app.majorVersion)
self.fixed = ImageDataContainer(self.slicerVersion)
self.fixed.addToScene(slicer.mrmlScene)
self.moving = ImageDataContainer(self.slicerVersion)
self.interactor = slicer.mrmlScene.AddNode(slicer.vtkMRMLInteractionNode())
self.selector = slicer.mrmlScene.AddNode(slicer.vtkMRMLSelectionNode())
# self._threeByThreeCompareView()
self._inputLayoutSection()
self._fiducialLayoutSection()
self._registrationLayoutSection()
### DEVELOPER ###
import os
if os.environ['USER'] == 'dmwelch':
self.logic.testingData()
self.fixedVolumeSelector.setCurrentNode(slicer.util.getNode('fixed*'))
self.movingVolumeSelector.setCurrentNode(slicer.util.getNode('moving*'))
### ***END*** ###
self.layout.addStretch(1)
class FastFiducialWidget:
"""
Slicer module that creates a Qt GUI for fast registration of two data sets
with fiducial markers
"""
def __init__(self, parent=None):
if parent is None:
self.fixed = None
self.moving = None
self.fixedVolumeSelector = None
self.movingVolumeSelector = None
self.interactor = None
self.selector = None
self.slicerVersion = None
# Boilerplate code
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.setup()
self.parent.show()
else:
self.parent = parent
self.layout = self.parent.layout()
self.logic = FastFiducialLogic()
def setup(self):
### DEVELOPER ###
self.reloadButton = qt.QPushButton('Reload')
self.reloadButton.toolTip = 'Developer reload button'
self.reloadButton.name = 'FastFiducial Reload'
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
### END ###
self.slicerVersion = int(slicer.app.majorVersion)
self.fixed = ImageDataContainer(self.slicerVersion)
self.fixed.addToScene(slicer.mrmlScene)
self.moving = ImageDataContainer(self.slicerVersion)
self.interactor = slicer.mrmlScene.AddNode(
slicer.vtkMRMLInteractionNode())
self.selector = slicer.mrmlScene.AddNode(slicer.vtkMRMLSelectionNode())
# self._threeByThreeCompareView()
self._inputLayoutSection()
self._fiducialLayoutSection()
self._registrationLayoutSection()
### DEVELOPER ###
import os
if os.environ['USER'] == 'dmwelch':
self.logic.testingData()
self.fixedVolumeSelector.setCurrentNode(
slicer.util.getNode('fixed*'))
self.movingVolumeSelector.setCurrentNode(
slicer.util.getNode('moving*'))
### ***END*** ###
self.layout.addStretch(1)
def onReload(self, moduleName="FastFiducial"):
""" Generic reload method for any scripted module.
ModuleWizard will subsitute correct default moduleName.
"""
import imp, sys, os, slicer
widgetName = moduleName + "Widget"
# reload the source code
# - set source file path
# - load the module to the global space
filePath = eval('slicer.modules.%s.path' % moduleName.lower())
p = os.path.dirname(filePath)
if not sys.path.__contains__(p):
sys.path.insert(0, p)
fp = open(filePath, "r")
globals()[moduleName] = imp.load_module(moduleName, fp, filePath,
('.py', 'r', imp.PY_SOURCE))
fp.close()
# rebuild the widget
# - find and hide the existing widget
# - create a new widget in the existing parent
parent = slicer.util.findChildren(name='%s Reload' %
moduleName)[0].parent()
print parent
for child in parent.children():
try:
child.hide()
except AttributeError:
pass
globals()[widgetName.lower()] = eval('globals()["%s"].%s(parent)' %
(moduleName, widgetName))
globals()[widgetName.lower()].setup()
def _threeByThreeCompareView(self):
"""
Create scene view with three slice views on top and three beneath
(colors R,G,Y for top and bottom)
"""
layoutManager = slicer.app.layoutManager()
if layoutManager is None:
return
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutThreeOverThreeView)
sliceViewCollection = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLSliceNode')
for ii in range(3):
sliceViewTop = sliceViewCollection.GetItemAsObject(ii)
sliceViewBottom = sliceViewCollection.GetItemAsObject(ii + 3)
color = sliceViewTop.GetLayoutColor()
print "The color of slice %d is %d, %d, %d" % (ii, color[0],
color[1], color[2])
sliceViewBottom.SetLayoutColor(color[0], color[1], color[2])
# Get scene to update!!!
sliceViewBottom.Modified()
slicer.mrmlScene.Modified()
layoutManager.layoutChanged(True)
def displayVolumeInSliceViews(self):
# 1) Determine if top or bottom is empty
# Top = Fixed image
# Bottom = Moving image
sliceViews = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceNode')
# 2) Get volume node
volumes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLScalarVolumeDisplayNode')
if volumes.GetNumberOfItems() == 0:
print 'No volumes found!'
volOne = volumes.GetItemAsObject(0)
volTwo = volumes.GetItemAsObject(1)
# 3) Display volume in correct windows
return true
def _inputLayoutSection(self):
inputCollapsibleButton = FFCollapsibleButton('Input volumes')
self.layout.addWidget(inputCollapsibleButton)
# Layout within the input collapsible button
inputFormLayout = qt.QFormLayout(inputCollapsibleButton)
### Fixed Volume Selector ###
# The fixed volume frame
fixedVolumeFrame = qt.QFrame(inputCollapsibleButton)
fixedVolumeFrame.setLayout(qt.QHBoxLayout())
inputFormLayout.addWidget(fixedVolumeFrame)
# The volume selector button label
fixedVolumeLabel = qt.QLabel('Fixed Volume: ', fixedVolumeFrame)
fixedVolumeFrame.layout().addWidget(fixedVolumeLabel)
# The volume selector buttom
self.fixedVolumeSelector = qMRMLNodeAddVolumeComboBox(
objectName='fixedVolumeSelector', toolTip='Select a fixed volume')
self.fixedVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.setFixedVolumeNode)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.setFixedSliceViews)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.fixedVolumeSelector,
'setMRMLScene(vtkMRMLScene*)')
fixedVolumeFrame.layout().addWidget(self.fixedVolumeSelector)
### The Moving Volume Selector ###
# The moving volume frame
movingVolumeFrame = qt.QFrame(inputCollapsibleButton)
movingVolumeFrame.setLayout(qt.QHBoxLayout())
inputFormLayout.addWidget(movingVolumeFrame)
# The volume selector button label
movingVolumeLabel = qt.QLabel('Moving Volume: ', movingVolumeFrame)
movingVolumeFrame.layout().addWidget(movingVolumeLabel)
# The volume selector buttom
self.movingVolumeSelector = qMRMLNodeAddVolumeComboBox(
objectName='movingVolumeSelector',
toolTip='Select a moving volume')
self.movingVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.setMovingVolumeNode)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.setMovingSliceViews)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.movingVolumeSelector,
'setMRMLScene(vtkMRMLScene*)')
movingVolumeFrame.layout().addWidget(self.movingVolumeSelector)
# Moved from __init__()
self.fixedVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.movingVolumeSelector.setMRMLScene(slicer.mrmlScene)
def setFixedVolumeNode(self, newVolumeNode):
self._setVolumeNode(newVolumeNode, 'fixed')
# self._setFixedSliceViews()
def setMovingVolumeNode(self, newVolumeNode):
self._setVolumeNode(newVolumeNode, 'moving')
# self._setMovingSliceViews()
def _setVolumeNode(self, newVolumeNode, flag):
# print "Attempting to set %s" % flag
newDisplayNode = None
if not newVolumeNode is None:
newDisplayNode = newVolumeNode.GetScalarVolumeDisplayNode()
if flag == 'fixed':
self.fixed.volume = newVolumeNode
self.fixed.display = newDisplayNode
elif flag == 'moving':
self.moving.volume = newVolumeNode
self.moving.display = newDisplayNode
else:
raise Exception('I have no idea why this would ever happen...')
def setFixedSliceViews(self):
pass
def setMovingSliceViews(self):
pass
def _fiducialLayoutSection(self):
fiducialCollapsibleButton = FFCollapsibleButton('Pick fiducials')
self.layout.addWidget(fiducialCollapsibleButton)
# Create first row widgets
fiducialFormLayout = qt.QFormLayout(fiducialCollapsibleButton)
# Create button frame
fiducialPickFrame = qt.QFrame(fiducialCollapsibleButton)
fiducialPickFrame.setLayout(qt.QHBoxLayout())
fiducialFormLayout.addWidget(fiducialPickFrame)
fiducialPickLabel = qt.QLabel('New fiducial: ', fiducialPickFrame)
fiducialPickButton = qt.QPushButton('Create')
fiducialPickLabel.setBuddy(fiducialPickButton)
fiducialPickButton.connect('clicked()', self.createNewFiducial)
fiducialPickButton.connect('clicked()',
self.fixed.fiducialList.Modified)
fiducialPickFrame.layout().addWidget(fiducialPickLabel)
fiducialPickFrame.layout().addWidget(fiducialPickButton)
# self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.setNewFiducial)
# # Create spin box frame
# fiducialEditFrame = qt.QFrame(fiducialCollapsibleButton)
# fiducialEditFrame.setLayout(qt.QHBoxLayout())
# fiducialFormLayout.addWidget(fiducialEditFrame)
# fiducialEditLabel = qt.QLabel('Edit fiducial: ', fiducialEditFrame)
# fiducialEditSpinBox = qt.QSpinBox()
# fiducialEditSpinBox.minimum = 1
# fiducialEditSpinBox.maximum = 5
# fiducialEditSpinBox.prefix = 'Fiducial '
# fiducialEditLabel.setBuddy(fiducialEditSpinBox)
# fiducialEditSpinBox.connect('valueChanged(int)', self.editSelectedFiducial)
# fiducialEditFrame.layout().addWidget(fiducialEditLabel)
# fiducialEditFrame.layout().addWidget(fiducialEditSpinBox)
def createNewFiducial(self):
# TODO: Write this function
# If the lists are not already added to the scene, add them
if not slicer.mrmlScene.IsNodePresent(self.fixed.fiducialList):
slicer.mrmlScene.AddNode(self.fixed.fiducialList)
if not slicer.mrmlScene.IsNodePresent(self.moving.fiducialList):
slicer.mrmlScene.AddNode(self.moving.fiducialList)
# Get the singleton interactor from the scene
self.interactor.SwitchToSinglePlaceMode()
# Get the singleton selector from the scene
self.selector.SetActiveFiducialListID(self.fixed.fiducialList.GetID())
self.selector.SetActiveAnnotationID(self.fixed.newFiducial.GetID())
self.setNewFiducial(slicer.mrmlScene)
def setNewFiducial(self, newSceneNode):
# Allow click to set the new fiducial to the list
if self.fixed.fiducialList:
self.fixed.fiducialList.RemoveObserver(
vtk.vtkCommand.ModifiedEvent)
self.fixed.fiducialList.AddObserver(vtk.vtkCommand.ModifiedEvent,
self.onMRMLNodeAdded)
self.fixed.fiducialList.UpdateScene(newSceneNode)
collection = vtk.vtkCollection()
self.fixed.fiducialList.GetDirectChildren(collection)
print collection.GetNumberOfItems()
######
# create fiducial in volume labeled with fiducial list index
# add fiducial to appropriate list
# else:
# self.createNewFiducial() (i.e. ignore)
# if volume is not marked done:
# mark volume as done
# else:
# give warning
# if both are marked done:
# reset done flag
# quit
# else:
# self.createNewFiducial()
# elif right-click:
# ignore
# elif ESC:
# remove latest fiducial if lengths not equal (assumes ordered list!!!)
# reset done flags
# elif RET:
# ignore (both fiducials need to be set (i.e. both flags need to == 'done'))
# self.selector.AddNewAnnotationIDToList(self.fixed.newFiducial.GetID())
print "Created a new fiducial node"
def onMRMLNodeAdded(self, observer, eventid):
if eventid == slicer.mrmlScene.NodeAddedEvent: #slicer.vtkMRMLAnnotationFiducialNode.FiducialNodeAddedEvent???
# Get the node added
print "Getting the new node ID..."
newNodeID = self.selector.GetActiveAnnotationID()
newNode = slicer.mrmlScene.GetNodeByID(newNodeID)
if newNode.GetClassName() == 'vtkMRMLAnnotationFiducialNode':
print "Adding the new fiducial to the fixed list..."
newHeirarchyNode = newNode.GetParentNode()
newHeirarchyNode.SetParentNodeID(
self.fixed.fiducialList.GetID())
else:
print "Not an annotation node OR not implemented for Slicer3"
def editSelectedFiducial(self, fiducialIndex):
print "The value is %d" % fiducialIndex
# TODO: Write this function
# 1) Get next mouse click or keyboard
# a) If ESC, escape without saving changes
# b) If left-click:
# i) Unlock (modify) ONLY the fiducial with matching index
# (need to get version for Slicer3 to determine list numbering)
# ii) Get fiducial under mouse and modify WITHOUT saving
# iii) call editSelectedFiducial
# c) If right-click:
# i) modify slice views (i.e. ignore)
# d) if RET, save new fiducial location
def _registrationLayoutSection(self):
registrationCollapsibleButton = FFCollapsibleButton('Register Images')
self.layout.addWidget(registrationCollapsibleButton)
registrationFormLayout = qt.QFormLayout(registrationCollapsibleButton)
registrationFrame = qt.QFrame(registrationCollapsibleButton)
registrationFrame.setLayout(qt.QHBoxLayout())
registrationFormLayout.addWidget(registrationFrame)
self.registerButton = qt.QPushButton('Run')
self.registerButton.toolTip = "Run fast registration method"
self.registerButton.connect('clicked()', self.onRegisterButtonClicked)
registrationFrame.layout().addWidget(self.registerButton)
def onRegisterButtonClicked(self):
qt.QMessageBox.information(slicer.util.mainWindow(), 'Register',
'Completed!')
print "Running registration..."
# 1) Run fiducial registration
initialTransformNode = FastFiducialRegistration(
self.fixedFiducialList, self.movingFiducialList)
# 2) Apply resulant transform to moving image
self.movingVolume.SetParentNodeID(initialTransformNode.GetID())
# 3) Run affine registration
finalTransformNode = BRAINSFitEZRegistration(self.fixedVolume,
self.movingVolume,
initialTransformNode)
# 4) Apply transform to moving image
finalTransformNode.SetParentID(initialTransformNode.GetID())
self.movingVolume.SetParentID(finalTransformNode.GetID())
# 5) TODO: Display MMI difference image?
return True
class FastFiducialWidget:
"""
Slicer module that creates a Qt GUI for fast registration of two data sets
with fiducial markers
"""
def __init__(self, parent=None):
if parent is None:
self.fixed = None
self.moving = None
self.fixedVolumeSelector = None
self.movingVolumeSelector = None
self.interactor = None
self.selector = None
self.slicerVersion = None
# Boilerplate code
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.setup()
self.parent.show()
else:
self.parent = parent
self.layout = self.parent.layout()
self.logic = FastFiducialLogic()
def setup(self):
### DEVELOPER ###
self.reloadButton = qt.QPushButton('Reload')
self.reloadButton.toolTip = 'Developer reload button'
self.reloadButton.name = 'FastFiducial Reload'
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
### END ###
self.slicerVersion = int(slicer.app.majorVersion)
self.fixed = ImageDataContainer(self.slicerVersion)
self.fixed.addToScene(slicer.mrmlScene)
self.moving = ImageDataContainer(self.slicerVersion)
self.interactor = slicer.mrmlScene.AddNode(slicer.vtkMRMLInteractionNode())
self.selector = slicer.mrmlScene.AddNode(slicer.vtkMRMLSelectionNode())
# self._threeByThreeCompareView()
self._inputLayoutSection()
self._fiducialLayoutSection()
self._registrationLayoutSection()
### DEVELOPER ###
import os
if os.environ['USER'] == 'dmwelch':
self.logic.testingData()
self.fixedVolumeSelector.setCurrentNode(slicer.util.getNode('fixed*'))
self.movingVolumeSelector.setCurrentNode(slicer.util.getNode('moving*'))
### ***END*** ###
self.layout.addStretch(1)
def onReload(self, moduleName="FastFiducial"):
""" Generic reload method for any scripted module.
ModuleWizard will subsitute correct default moduleName.
"""
import imp, sys, os, slicer
widgetName = moduleName + "Widget"
# reload the source code
# - set source file path
# - load the module to the global space
filePath = eval('slicer.modules.%s.path' % moduleName.lower())
p = os.path.dirname(filePath)
if not sys.path.__contains__(p):
sys.path.insert(0,p)
fp = open(filePath, "r")
globals()[moduleName] = imp.load_module(moduleName, fp, filePath, ('.py', 'r', imp.PY_SOURCE))
fp.close()
# rebuild the widget
# - find and hide the existing widget
# - create a new widget in the existing parent
parent = slicer.util.findChildren(name='%s Reload' % moduleName)[0].parent()
print parent
for child in parent.children():
try:
child.hide()
except AttributeError:
pass
globals()[widgetName.lower()] = eval('globals()["%s"].%s(parent)' % (moduleName, widgetName))
globals()[widgetName.lower()].setup()
def _threeByThreeCompareView(self):
"""
Create scene view with three slice views on top and three beneath
(colors R,G,Y for top and bottom)
"""
layoutManager = slicer.app.layoutManager()
if layoutManager is None:
return
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutThreeOverThreeView)
sliceViewCollection = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceNode')
for ii in range(3):
sliceViewTop = sliceViewCollection.GetItemAsObject(ii)
sliceViewBottom = sliceViewCollection.GetItemAsObject(ii+3)
color = sliceViewTop.GetLayoutColor()
print "The color of slice %d is %d, %d, %d" % (ii, color[0], color[1], color[2])
sliceViewBottom.SetLayoutColor(color[0], color[1], color[2])
# Get scene to update!!!
sliceViewBottom.Modified()
slicer.mrmlScene.Modified()
layoutManager.layoutChanged(True)
def displayVolumeInSliceViews(self):
# 1) Determine if top or bottom is empty
# Top = Fixed image
# Bottom = Moving image
sliceViews = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceNode')
# 2) Get volume node
volumes = slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeDisplayNode')
if volumes.GetNumberOfItems() == 0:
print 'No volumes found!'
volOne = volumes.GetItemAsObject(0)
volTwo = volumes.GetItemAsObject(1)
# 3) Display volume in correct windows
return true
def _inputLayoutSection(self):
inputCollapsibleButton = FFCollapsibleButton('Input volumes')
self.layout.addWidget(inputCollapsibleButton)
# Layout within the input collapsible button
inputFormLayout = qt.QFormLayout(inputCollapsibleButton)
### Fixed Volume Selector ###
# The fixed volume frame
fixedVolumeFrame = qt.QFrame(inputCollapsibleButton)
fixedVolumeFrame.setLayout(qt.QHBoxLayout())
inputFormLayout.addWidget(fixedVolumeFrame)
# The volume selector button label
fixedVolumeLabel = qt.QLabel('Fixed Volume: ', fixedVolumeFrame)
fixedVolumeFrame.layout().addWidget(fixedVolumeLabel)
# The volume selector buttom
self.fixedVolumeSelector = qMRMLNodeAddVolumeComboBox(objectName='fixedVolumeSelector',
toolTip='Select a fixed volume')
self.fixedVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.setFixedVolumeNode)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.setFixedSliceViews)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.fixedVolumeSelector,
'setMRMLScene(vtkMRMLScene*)')
fixedVolumeFrame.layout().addWidget(self.fixedVolumeSelector)
### The Moving Volume Selector ###
# The moving volume frame
movingVolumeFrame = qt.QFrame(inputCollapsibleButton)
movingVolumeFrame.setLayout(qt.QHBoxLayout())
inputFormLayout.addWidget(movingVolumeFrame)
# The volume selector button label
movingVolumeLabel = qt.QLabel('Moving Volume: ', movingVolumeFrame)
movingVolumeFrame.layout().addWidget(movingVolumeLabel)
# The volume selector buttom
self.movingVolumeSelector = qMRMLNodeAddVolumeComboBox(objectName='movingVolumeSelector',
toolTip='Select a moving volume')
self.movingVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.setMovingVolumeNode)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.setMovingSliceViews)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.movingVolumeSelector,
'setMRMLScene(vtkMRMLScene*)')
movingVolumeFrame.layout().addWidget(self.movingVolumeSelector)
# Moved from __init__()
self.fixedVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.movingVolumeSelector.setMRMLScene(slicer.mrmlScene)
def setFixedVolumeNode(self, newVolumeNode):
self._setVolumeNode(newVolumeNode, 'fixed')
# self._setFixedSliceViews()
def setMovingVolumeNode(self, newVolumeNode):
self._setVolumeNode(newVolumeNode, 'moving')
# self._setMovingSliceViews()
def _setVolumeNode(self, newVolumeNode, flag):
# print "Attempting to set %s" % flag
newDisplayNode = None
if not newVolumeNode is None:
newDisplayNode = newVolumeNode.GetScalarVolumeDisplayNode()
if flag == 'fixed':
self.fixed.volume = newVolumeNode
self.fixed.display = newDisplayNode
elif flag == 'moving':
self.moving.volume = newVolumeNode
self.moving.display = newDisplayNode
else:
raise Exception('I have no idea why this would ever happen...')
def setFixedSliceViews(self):
pass
def setMovingSliceViews(self):
pass
def _fiducialLayoutSection(self):
fiducialCollapsibleButton = FFCollapsibleButton('Pick fiducials')
self.layout.addWidget(fiducialCollapsibleButton)
# Create first row widgets
fiducialFormLayout = qt.QFormLayout(fiducialCollapsibleButton)
# Create button frame
fiducialPickFrame = qt.QFrame(fiducialCollapsibleButton)
fiducialPickFrame.setLayout(qt.QHBoxLayout())
fiducialFormLayout.addWidget(fiducialPickFrame)
fiducialPickLabel = qt.QLabel('New fiducial: ', fiducialPickFrame)
fiducialPickButton = qt.QPushButton('Create')
fiducialPickLabel.setBuddy(fiducialPickButton)
fiducialPickButton.connect('clicked()', self.createNewFiducial)
fiducialPickButton.connect('clicked()', self.fixed.fiducialList.Modified)
fiducialPickFrame.layout().addWidget(fiducialPickLabel)
fiducialPickFrame.layout().addWidget(fiducialPickButton)
# self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.setNewFiducial)
# # Create spin box frame
# fiducialEditFrame = qt.QFrame(fiducialCollapsibleButton)
# fiducialEditFrame.setLayout(qt.QHBoxLayout())
# fiducialFormLayout.addWidget(fiducialEditFrame)
# fiducialEditLabel = qt.QLabel('Edit fiducial: ', fiducialEditFrame)
# fiducialEditSpinBox = qt.QSpinBox()
# fiducialEditSpinBox.minimum = 1
# fiducialEditSpinBox.maximum = 5
# fiducialEditSpinBox.prefix = 'Fiducial '
# fiducialEditLabel.setBuddy(fiducialEditSpinBox)
# fiducialEditSpinBox.connect('valueChanged(int)', self.editSelectedFiducial)
# fiducialEditFrame.layout().addWidget(fiducialEditLabel)
# fiducialEditFrame.layout().addWidget(fiducialEditSpinBox)
def createNewFiducial(self):
# TODO: Write this function
# If the lists are not already added to the scene, add them
if not slicer.mrmlScene.IsNodePresent(self.fixed.fiducialList):
slicer.mrmlScene.AddNode(self.fixed.fiducialList)
if not slicer.mrmlScene.IsNodePresent(self.moving.fiducialList):
slicer.mrmlScene.AddNode(self.moving.fiducialList)
# Get the singleton interactor from the scene
self.interactor.SwitchToSinglePlaceMode()
# Get the singleton selector from the scene
self.selector.SetActiveFiducialListID(self.fixed.fiducialList.GetID())
self.selector.SetActiveAnnotationID(self.fixed.newFiducial.GetID())
self.setNewFiducial(slicer.mrmlScene)
def setNewFiducial(self, newSceneNode):
# Allow click to set the new fiducial to the list
if self.fixed.fiducialList:
self.fixed.fiducialList.RemoveObserver(vtk.vtkCommand.ModifiedEvent)
self.fixed.fiducialList.AddObserver(vtk.vtkCommand.ModifiedEvent, self.onMRMLNodeAdded)
self.fixed.fiducialList.UpdateScene(newSceneNode)
collection = vtk.vtkCollection()
self.fixed.fiducialList.GetDirectChildren(collection)
print collection.GetNumberOfItems()
######
# create fiducial in volume labeled with fiducial list index
# add fiducial to appropriate list
# else:
# self.createNewFiducial() (i.e. ignore)
# if volume is not marked done:
# mark volume as done
# else:
# give warning
# if both are marked done:
# reset done flag
# quit
# else:
# self.createNewFiducial()
# elif right-click:
# ignore
# elif ESC:
# remove latest fiducial if lengths not equal (assumes ordered list!!!)
# reset done flags
# elif RET:
# ignore (both fiducials need to be set (i.e. both flags need to == 'done'))
# self.selector.AddNewAnnotationIDToList(self.fixed.newFiducial.GetID())
print "Created a new fiducial node"
def onMRMLNodeAdded(self, observer, eventid):
if eventid == slicer.mrmlScene.NodeAddedEvent: #slicer.vtkMRMLAnnotationFiducialNode.FiducialNodeAddedEvent???
# Get the node added
print "Getting the new node ID..."
newNodeID = self.selector.GetActiveAnnotationID()
newNode = slicer.mrmlScene.GetNodeByID(newNodeID)
if newNode.GetClassName() == 'vtkMRMLAnnotationFiducialNode':
print "Adding the new fiducial to the fixed list..."
newHeirarchyNode = newNode.GetParentNode()
newHeirarchyNode.SetParentNodeID(self.fixed.fiducialList.GetID())
else:
print "Not an annotation node OR not implemented for Slicer3"
def editSelectedFiducial(self, fiducialIndex):
print "The value is %d" % fiducialIndex
# TODO: Write this function
# 1) Get next mouse click or keyboard
# a) If ESC, escape without saving changes
# b) If left-click:
# i) Unlock (modify) ONLY the fiducial with matching index
# (need to get version for Slicer3 to determine list numbering)
# ii) Get fiducial under mouse and modify WITHOUT saving
# iii) call editSelectedFiducial
# c) If right-click:
# i) modify slice views (i.e. ignore)
# d) if RET, save new fiducial location
def _registrationLayoutSection(self):
registrationCollapsibleButton = FFCollapsibleButton('Register Images')
self.layout.addWidget(registrationCollapsibleButton)
registrationFormLayout = qt.QFormLayout(registrationCollapsibleButton)
registrationFrame = qt.QFrame(registrationCollapsibleButton)
registrationFrame.setLayout(qt.QHBoxLayout())
registrationFormLayout.addWidget(registrationFrame)
self.registerButton = qt.QPushButton('Run')
self.registerButton.toolTip = "Run fast registration method"
self.registerButton.connect('clicked()', self.onRegisterButtonClicked)
registrationFrame.layout().addWidget(self.registerButton)
def onRegisterButtonClicked(self):
qt.QMessageBox.information(slicer.util.mainWindow(), 'Register', 'Completed!')
print "Running registration..."
# 1) Run fiducial registration
initialTransformNode = FastFiducialRegistration(self.fixedFiducialList, self.movingFiducialList)
# 2) Apply resulant transform to moving image
self.movingVolume.SetParentNodeID(initialTransformNode.GetID())
# 3) Run affine registration
finalTransformNode = BRAINSFitEZRegistration(self.fixedVolume, self.movingVolume, initialTransformNode)
# 4) Apply transform to moving image
finalTransformNode.SetParentID(initialTransformNode.GetID())
self.movingVolume.SetParentID(finalTransformNode.GetID())
# 5) TODO: Display MMI difference image?
return True