LandmarkRegistration.py

import os
import unittest
from __main__ import vtk, qt, ctk, slicer

import RegistrationLib

#
# LandmarkRegistration
#

class LandmarkRegistration:
  def __init__(self, parent):
    parent.title = "Landmark Registration"
    parent.categories = ["Registration"]
    parent.dependencies = []
    parent.contributors = ["Steve Pieper (Isomics)"] # replace with "Firstname Lastname (Org)"
    parent.helpText = """
    This module organizes a fixed and moving volume along with a set of corresponding
    landmarks (paired fiducials) to assist in manual registration.
    """
    parent.acknowledgementText = """
    This file was developed by Steve Pieper, Isomics, Inc.
    It was partially funded by NIH grant 3P41RR013218-12S1
    and this work is part of the National Alliance for Medical Image
    Computing (NAMIC), funded by the National Institutes of Health
    through the NIH Roadmap for Medical Research, Grant U54 EB005149.
    Information on the National Centers for Biomedical Computing
    can be obtained from http://nihroadmap.nih.gov/bioinformatics.
    """ # replace with organization, grant and thanks.
    self.parent = parent

    # Add this test to the SelfTest module's list for discovery when the module
    # is created.  Since this module may be discovered before SelfTests itself,
    # create the list if it doesn't already exist.
    try:
      slicer.selfTests
    except AttributeError:
      slicer.selfTests = {}
    slicer.selfTests['LandmarkRegistration'] = self.runTest

  def runTest(self):
    tester = LandmarkRegistrationTest()
    tester.runTest()

#
# qLandmarkRegistrationWidget
#

class LandmarkRegistrationWidget:
  """The module GUI widget"""
  def __init__(self, parent = None):
    self.logic = LandmarkRegistrationLogic()
    self.sliceNodesByViewName = {}
    self.sliceNodesByVolumeID = {}
    self.observerTags = []
    self.viewNames = ("Fixed", "Moving", "Transformed")
    self.volumeSelectDialog = None
    self.currentRegistrationInterface = None

    if not parent:
      self.parent = slicer.qMRMLWidget()
      self.parent.setLayout(qt.QVBoxLayout())
      self.parent.setMRMLScene(slicer.mrmlScene)
    else:
      self.parent = parent
    self.layout = self.parent.layout()
    if not parent:
      self.setup()
      self.parent.show()

  def setup(self):
    """Instantiate and connect widgets ..."""

    #
    # Reload and Test area
    #
    if True:
      """Developer interface"""
      reloadCollapsibleButton = ctk.ctkCollapsibleButton()
      reloadCollapsibleButton.text = "Advanced - Reload && Test"
      reloadCollapsibleButton.collapsed = False
      self.layout.addWidget(reloadCollapsibleButton)
      reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)

      # reload button
      # (use this during development, but remove it when delivering
      #  your module to users)
      self.reloadButton = qt.QPushButton("Reload")
      self.reloadButton.toolTip = "Reload this module."
      self.reloadButton.name = "LandmarkRegistration Reload"
      reloadFormLayout.addWidget(self.reloadButton)
      self.reloadButton.connect('clicked()', self.onReload)

      # reload and test button
      # (use this during development, but remove it when delivering
      #  your module to users)
      self.reloadAndTestButton = qt.QPushButton("Reload and Test")
      self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
      reloadFormLayout.addWidget(self.reloadAndTestButton)
      self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)

      # reload and run specific tests
      scenarios = ("Basic", "Affine", "ThinPlate")
      for scenario in scenarios:
        button = qt.QPushButton("Reload and Test %s" % scenario)
        self.reloadAndTestButton.toolTip = "Reload this module and then run the %s self test." % scenario
        reloadFormLayout.addWidget(button)
        button.connect('clicked()', lambda s=scenario: self.onReloadAndTest(scenario=s))

    self.selectVolumesButton = qt.QPushButton("Select Volumes To Register")
    self.selectVolumesButton.connect('clicked(bool)', self.enter)
    self.layout.addWidget(self.selectVolumesButton)

    self.interfaceFrame = qt.QWidget(self.parent)
    self.interfaceFrame.setLayout(qt.QVBoxLayout())
    self.layout.addWidget(self.interfaceFrame)

    #
    # Parameters Area
    #
    parametersCollapsibleButton = ctk.ctkCollapsibleButton()
    parametersCollapsibleButton.text = "Parameters"
    self.interfaceFrame.layout().addWidget(parametersCollapsibleButton)
    parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)

    self.volumeSelectors = {}
    for viewName in self.viewNames:
      self.volumeSelectors[viewName] = slicer.qMRMLNodeComboBox()
      self.volumeSelectors[viewName].nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
      self.volumeSelectors[viewName].selectNodeUponCreation = False
      self.volumeSelectors[viewName].addEnabled = False
      self.volumeSelectors[viewName].removeEnabled = True
      self.volumeSelectors[viewName].noneEnabled = True
      self.volumeSelectors[viewName].showHidden = False
      self.volumeSelectors[viewName].showChildNodeTypes = True
      self.volumeSelectors[viewName].setMRMLScene( slicer.mrmlScene )
      self.volumeSelectors[viewName].setToolTip( "Pick the %s volume." % viewName.lower() )
      self.volumeSelectors[viewName].enabled = False
      parametersFormLayout.addRow("%s Volume " % viewName, self.volumeSelectors[viewName])

    self.volumeSelectors["Transformed"].addEnabled = True
    self.volumeSelectors["Transformed"].selectNodeUponCreation = True
    self.volumeSelectors["Transformed"].setToolTip( "Pick the transformed volume, which is the target for the registration." )

    self.linearTransformSelector = slicer.qMRMLNodeComboBox()
    self.linearTransformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
    self.linearTransformSelector.selectNodeUponCreation = True
    self.linearTransformSelector.addEnabled = True
    self.linearTransformSelector.removeEnabled = True
    self.linearTransformSelector.noneEnabled = True
    self.linearTransformSelector.showHidden = False
    self.linearTransformSelector.showChildNodeTypes = False
    self.linearTransformSelector.setMRMLScene( slicer.mrmlScene )
    self.linearTransformSelector.setToolTip( "The transform for linear registration" )
    self.linearTransformSelector.enabled = False
    parametersFormLayout.addRow("Target Linear Transform ", self.linearTransformSelector)

    #
    # Visualization Widget
    # - handy options for controlling the view
    #
    self.visualizationWidget = RegistrationLib.VisualizationWidget(self.logic)
    self.visualizationWidget.connect("layoutRequested(mode,volumesToShow)", self.onLayout)
    parametersFormLayout.addRow(self.visualizationWidget.widget)

    #
    # Landmarks Widget
    # - manages landmarks
    #
    self.landmarksWidget = RegistrationLib.LandmarksWidget(self.logic)
    self.landmarksWidget.connect("landmarkPicked(landmarkName)", self.onLandmarkPicked)
    self.landmarksWidget.connect("landmarkMoved(landmarkName)", self.onLandmarkMoved)
    parametersFormLayout.addRow(self.landmarksWidget.widget)

    #
    # Registration Options
    #
    self.registrationCollapsibleButton = ctk.ctkCollapsibleButton()
    self.registrationCollapsibleButton.text = "Registration"
    self.interfaceFrame.layout().addWidget(self.registrationCollapsibleButton)
    registrationFormLayout = qt.QFormLayout(self.registrationCollapsibleButton)

    #
    # registration type selection
    # - allows selection of the active registration type to display
    #
    try:
      slicer.modules.registrationPlugins
    except AttributeError:
      slicer.modules.registrationPlugins = {}

    self.registrationTypeBox = qt.QGroupBox("Registration Type")
    self.registrationTypeBox.setLayout(qt.QFormLayout())
    self.registrationTypeButtons = {}
    self.registrationTypes = slicer.modules.registrationPlugins.keys()
    self.registrationTypes.sort()
    for registrationType in self.registrationTypes:
      plugin = slicer.modules.registrationPlugins[registrationType]
      self.registrationTypeButtons[registrationType] = qt.QRadioButton()
      self.registrationTypeButtons[registrationType].text = plugin.name
      self.registrationTypeButtons[registrationType].setToolTip(plugin.tooltip)
      self.registrationTypeButtons[registrationType].connect("clicked()",
                                lambda t=registrationType: self.onRegistrationType(t))
      self.registrationTypeBox.layout().addWidget(
                                self.registrationTypeButtons[registrationType])
    registrationFormLayout.addWidget(self.registrationTypeBox)

    # connections
    for selector in self.volumeSelectors.values():
      selector.connect("currentNodeChanged(vtkMRMLNode*)", self.onVolumeNodeSelect)

    # listen to the scene
    self.addObservers()

    # Add vertical spacer
    self.layout.addStretch(1)

  def enter(self):
    self.interfaceFrame.enabled = False
    self.setupDialog()

  def setupDialog(self):
    """setup dialog"""

    if not self.volumeSelectDialog:
      self.volumeSelectDialog = qt.QDialog(slicer.util.mainWindow())
      self.volumeSelectDialog.objectName = 'LandmarkRegistrationVolumeSelect'
      self.volumeSelectDialog.setLayout( qt.QVBoxLayout() )

      self.volumeSelectLabel = qt.QLabel()
      self.volumeSelectDialog.layout().addWidget( self.volumeSelectLabel )

      self.volumeSelectorFrame = qt.QFrame()
      self.volumeSelectorFrame.objectName = 'VolumeSelectorFrame'
      self.volumeSelectorFrame.setLayout( qt.QFormLayout() )
      self.volumeSelectDialog.layout().addWidget( self.volumeSelectorFrame )

      self.volumeDialogSelectors = {}
      for viewName in ('Fixed', 'Moving',):
        self.volumeDialogSelectors[viewName] = slicer.qMRMLNodeComboBox()
        self.volumeDialogSelectors[viewName].nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
        self.volumeDialogSelectors[viewName].selectNodeUponCreation = False
        self.volumeDialogSelectors[viewName].addEnabled = False
        self.volumeDialogSelectors[viewName].removeEnabled = True
        self.volumeDialogSelectors[viewName].noneEnabled = True
        self.volumeDialogSelectors[viewName].showHidden = False
        self.volumeDialogSelectors[viewName].showChildNodeTypes = True
        self.volumeDialogSelectors[viewName].setMRMLScene( slicer.mrmlScene )
        self.volumeDialogSelectors[viewName].setToolTip( "Pick the %s volume." % viewName.lower() )
        self.volumeSelectorFrame.layout().addRow("%s Volume " % viewName, self.volumeDialogSelectors[viewName])

      self.volumeButtonFrame = qt.QFrame()
      self.volumeButtonFrame.objectName = 'VolumeButtonFrame'
      self.volumeButtonFrame.setLayout( qt.QHBoxLayout() )
      self.volumeSelectDialog.layout().addWidget( self.volumeButtonFrame )

      self.volumeDialogApply = qt.QPushButton("Apply", self.volumeButtonFrame)
      self.volumeDialogApply.objectName = 'VolumeDialogApply'
      self.volumeDialogApply.setToolTip( "Use currently selected volume nodes." )
      self.volumeButtonFrame.layout().addWidget(self.volumeDialogApply)

      self.volumeDialogCancel = qt.QPushButton("Cancel", self.volumeButtonFrame)
      self.volumeDialogCancel.objectName = 'VolumeDialogCancel'
      self.volumeDialogCancel.setToolTip( "Cancel current operation." )
      self.volumeButtonFrame.layout().addWidget(self.volumeDialogCancel)

      self.volumeDialogApply.connect("clicked()", self.onVolumeDialogApply)
      self.volumeDialogCancel.connect("clicked()", self.volumeSelectDialog.hide)

    self.volumeSelectLabel.setText( "Pick the volumes to use for landmark-based linear registration" )
    self.volumeSelectDialog.show()

  # volumeSelectDialog callback (slot)
  def onVolumeDialogApply(self):
    self.volumeSelectDialog.hide()
    fixedID = self.volumeDialogSelectors['Fixed'].currentNodeID
    movingID = self.volumeDialogSelectors['Moving'].currentNodeID
    if fixedID and movingID:
      self.volumeSelectors['Fixed'].setCurrentNodeID(fixedID)
      self.volumeSelectors['Moving'].setCurrentNodeID(movingID)
      # create transform and transformed if needed
      transform = self.linearTransformSelector.currentNode()
      if not transform:
        self.linearTransformSelector.addNode()
        transform = self.linearTransformSelector.currentNode()
      transformed = self.volumeSelectors['Transformed'].currentNode()
      if not transformed:
        volumesLogic = slicer.modules.volumes.logic()
        moving = self.volumeSelectors['Moving'].currentNode()
        transformedName = "%s-transformed" % moving.GetName()
        transformed = slicer.util.getNode(transformedName)
        if not transformed:
          transformed = volumesLogic.CloneVolume(slicer.mrmlScene, moving, transformedName)
      self.volumeSelectors['Transformed'].setCurrentNode(transformed)
      self.onLayout()
      self.interfaceFrame.enabled = True

  def cleanup(self):
    self.removeObservers()
    self.landmarksWidget.removeLandmarkObservers()

  def addObservers(self):
    """Observe the mrml scene for changes that we wish to respond to.
    scene observer:
     - whenever a new node is added, check if it was a new fiducial.
       if so, transform it into a landmark by creating a matching
       fiducial for other volumes
    fiducial obserers:
     - when fiducials are manipulated, perform (or schedule) an update
       to the currently active registration method.
    """
    tag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAddedEvent, self.landmarksWidget.requestNodeAddedUpdate)
    tag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeRemovedEvent, self.landmarksWidget.requestNodeAddedUpdate)
    self.observerTags.append( (slicer.mrmlScene, tag) )

  def removeObservers(self):
    """Remove observers and any other cleanup needed to
    disconnect from the scene"""
    for obj,tag in self.observerTags:
      obj.RemoveObserver(tag)
    self.observerTags = []

  def registationState(self):
    """Return an instance of RegistrationState populated
    with current gui parameters"""
    state = RegistrationLib.RegistrationState()
    state.logic = self.logic
    state.fixed = self.volumeSelectors["Fixed"].currentNode()
    state.moving = self.volumeSelectors["Moving"].currentNode()
    state.transformed = self.volumeSelectors["Transformed"].currentNode()
    state.fixedFiducials = self.logic.volumeFiducialList(state.fixed)
    state.movingFiducials = self.logic.volumeFiducialList(state.moving)
    state.transformedFiducials = self.logic.volumeFiducialList(state.transformed)
    state.linearTransform = self.linearTransformSelector.currentNode()
    return(state)

  def currentVolumeNodes(self):
    """List of currently selected volume nodes"""
    volumeNodes = []
    for selector in self.volumeSelectors.values():
      volumeNode = selector.currentNode()
      if volumeNode:
        volumeNodes.append(volumeNode)
    return(volumeNodes)

  def onVolumeNodeSelect(self):
    """When one of the volume selectors is changed"""
    volumeNodes = self.currentVolumeNodes()
    self.landmarksWidget.setVolumeNodes(volumeNodes)
    fixed = self.volumeSelectors['Fixed'].currentNode()
    moving = self.volumeSelectors['Moving'].currentNode()
    transformed = self.volumeSelectors['Transformed'].currentNode()
    self.registrationCollapsibleButton.enabled = bool(fixed and moving)
    self.logic.hiddenFiducialVolumes = (transformed,)

  def onLayout(self, layoutMode="Axi/Sag/Cor",volumesToShow=None):
    """When the layout is changed by the VisualizationWidget
    volumesToShow: list of the volumes to include, None means include all
    """
    volumeNodes = []
    activeViewNames = []
    for viewName in self.viewNames:
      volumeNode = self.volumeSelectors[viewName].currentNode()
      if volumeNode and not (volumesToShow and viewName not in volumesToShow):
        volumeNodes.append(volumeNode)
        activeViewNames.append(viewName)
    import CompareVolumes
    compareLogic = CompareVolumes.CompareVolumesLogic()
    oneViewModes = ('Axial', 'Sagittal', 'Coronal',)
    if layoutMode in oneViewModes:
      self.sliceNodesByViewName = compareLogic.viewerPerVolume(volumeNodes,viewNames=activeViewNames,orientation=layoutMode)
    elif layoutMode == 'Axi/Sag/Cor':
      self.sliceNodesByViewName = compareLogic.viewersPerVolume(volumeNodes)
    self.overlayFixedOnTransformed()
    self.updateSliceNodesByVolumeID()
    self.onLandmarkPicked(self.landmarksWidget.selectedLandmark)

  def overlayFixedOnTransformed(self):
    """If there are viewers showing the tranfsformed volume
    in the background, make the foreground volume be the fixed volume
    and set opacity to 0.5"""
    fixedNode = self.volumeSelectors['Fixed'].currentNode()
    transformedNode = self.volumeSelectors['Transformed'].currentNode()
    if transformedNode:
      compositeNodes = slicer.util.getNodes('vtkMRMLSliceCompositeNode*')
      for compositeNode in compositeNodes.values():
        if compositeNode.GetBackgroundVolumeID() == transformedNode.GetID():
          compositeNode.SetForegroundVolumeID(fixedNode.GetID())
          compositeNode.SetForegroundOpacity(0.5)

  def onRegistrationType(self,pickedRegistrationType):
    """Pick which registration type to display"""
    if self.currentRegistrationInterface:
      self.currentRegistrationInterface.destroy()
    interfaceClass = slicer.modules.registrationPlugins[pickedRegistrationType]
    self.currentRegistrationInterface = interfaceClass(self.registrationCollapsibleButton)
    self.currentRegistrationInterface.create(self.registationState)

  def updateSliceNodesByVolumeID(self):
    """Build a mapping to a list of slice nodes
    node that are currently displaying a given volumeID"""
    compositeNodes = slicer.util.getNodes('vtkMRMLSliceCompositeNode*')
    self.sliceNodesByVolumeID = {}
    if self.sliceNodesByViewName:
      for sliceNode in self.sliceNodesByViewName.values():
        for compositeNode in compositeNodes.values():
          if compositeNode.GetLayoutName() == sliceNode.GetLayoutName():
            volumeID = compositeNode.GetBackgroundVolumeID()
            if self.sliceNodesByVolumeID.has_key(volumeID):
              self.sliceNodesByVolumeID[volumeID].append(sliceNode)
            else:
              self.sliceNodesByVolumeID[volumeID] = [sliceNode,]

  def restrictLandmarksToViews(self):
    """Set fiducials so they only show up in the view
    for the volume on which they were defined"""
    volumeNodes = self.currentVolumeNodes()
    if self.sliceNodesByViewName:
      landmarks = self.logic.landmarksForVolumes(volumeNodes)
      for landmarkName in landmarks:
        for fiducialList,index in landmarks[landmarkName]:
          displayNode = fiducialList.GetDisplayNode()
          displayNode.RemoveAllViewNodeIDs()
          volumeNodeID = fiducialList.GetAttribute("AssociatedNodeID")
          if volumeNodeID:
            if self.sliceNodesByVolumeID.has_key(volumeNodeID):
              for sliceNode in self.sliceNodesByVolumeID[volumeNodeID]:
                displayNode.AddViewNodeID(sliceNode.GetID())
                for hiddenVolume in self.logic.hiddenFiducialVolumes:
                  if hiddenVolume and volumeNodeID == hiddenVolume.GetID():
                    displayNode.SetVisibility(False)

  def onLandmarkPicked(self,landmarkName):
    """Jump all slice views such that the selected landmark
    is visible"""
    if not self.landmarksWidget.movingView:
      # only change the fiducials if they are not being manipulated
      self.restrictLandmarksToViews()
    self.updateSliceNodesByVolumeID()
    volumeNodes = self.currentVolumeNodes()
    landmarksByName = self.logic.landmarksForVolumes(volumeNodes)
    if landmarksByName.has_key(landmarkName):
      for fiducialList,index in landmarksByName[landmarkName]:
        volumeNodeID = fiducialList.GetAttribute("AssociatedNodeID")
        if self.sliceNodesByVolumeID.has_key(volumeNodeID):
          point = [0,]*3
          fiducialList.GetNthFiducialPosition(index,point)
          for sliceNode in self.sliceNodesByVolumeID[volumeNodeID]:
            if sliceNode.GetLayoutName() != self.landmarksWidget.movingView:
              sliceNode.JumpSliceByCentering(*point)

  def onLandmarkMoved(self,landmarkName):
    """Called when a landmark is moved (probably through
    manipulation of the widget in the slice view).
    This updates the active registration"""
    if self.currentRegistrationInterface:
      state = self.registationState()
      self.currentRegistrationInterface.onLandmarkMoved(state)

  def onReload(self,moduleName="LandmarkRegistration"):
    """Generic reload method for any scripted module.
    ModuleWizard will subsitute correct default moduleName.
    Note: customized for use in LandmarkRegistration
    """
    import imp, sys, os, slicer

    # first, destroy the current plugin, since it will
    # contain subclasses of the RegistrationLib modules
    if self.currentRegistrationInterface:
      self.currentRegistrationInterface.destroy()

    # now reload the RegistrationLib 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)
    for subModuleName in ("pqWidget", "Visualization", "Landmarks", ):
      fp = open(filePath, "r")
      globals()[subModuleName] = imp.load_module(
          subModuleName, fp, filePath, ('.py', 'r', imp.PY_SOURCE))
      fp.close()

    # now reload all the support code and have the plugins
    # re-register themselves with slicer
    oldPlugins = slicer.modules.registrationPlugins
    slicer.modules.registrationPlugins = {}
    for plugin in oldPlugins.values():
      pluginModuleName = plugin.__module__.lower()
      if hasattr(slicer.modules,pluginModuleName):
        # for a plugin from an extension, need to get the source path
        # from the module
        module = getattr(slicer.modules,pluginModuleName)
        sourceFile = module.path
      else:
        # for a plugin built with slicer itself, the file path comes
        # from the pyc path noted as __file__ at startup time
        sourceFile = plugin.sourceFile.replace('.pyc', '.py')
      imp.load_source(plugin.__module__, sourceFile)
    oldPlugins = None

    widgetName = moduleName + "Widget"

    # now reload the widget module 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().parent()
    for child in parent.children():
      try:
        child.hide()
      except AttributeError:
        pass
    # Remove spacer items
    item = parent.layout().itemAt(0)
    while item:
      parent.layout().removeItem(item)
      item = parent.layout().itemAt(0)

    # delete the old widget instance
    if hasattr(globals()['slicer'].modules, widgetName):
      getattr(globals()['slicer'].modules, widgetName).cleanup()

    # create new widget inside existing parent
    globals()[widgetName.lower()] = eval(
        'globals()["%s"].%s(parent)' % (moduleName, widgetName))
    globals()[widgetName.lower()].setup()
    setattr(globals()['slicer'].modules, widgetName, globals()[widgetName.lower()])

  def onReloadAndTest(self,moduleName="LandmarkRegistration",scenario=None):
    try:
      self.onReload()
      evalString = 'globals()["%s"].%sTest()' % (moduleName, moduleName)
      tester = eval(evalString)
      tester.runTest(scenario=scenario)
    except Exception, e:
      import traceback
      traceback.print_exc()
      qt.QMessageBox.warning(slicer.util.mainWindow(),
          "Reload and Test", 'Exception!\n\n' + str(e) + "\n\nSee Python Console for Stack Trace")


#
# LandmarkRegistrationLogic
#

class LandmarkRegistrationLogic:
  """This class should implement all the actual
  computation done by your module.  The interface
  should be such that other python code can import
  this class and make use of the functionality without
  requiring an instance of the Widget

  The representation of Landmarks is in terms of matching FiducialLists
  with one list per VolumeNode.

  volume1 <-- associated node -- FiducialList1
                                 - anatomy 1
                                 - anatomy 2
                                 ...
  volume2 <-- associated node -- FiducialList2
                                 - anatomy 1
                                 - anatomy 2
                                 ...

  The Fiducial List is only made visible in the viewer that
  has the associated node in the bg.

  Set of identically named fiducials in lists associated with the
  current moving and fixed volumes define a 'landmark'.

  Note that it is the name, not the index, of the anatomy that defines
  membership in a landmark.  Use a pair (fiducialListNodes,index) to
  identify a fiducial.
  """
  def __init__(self):
    self.linearMode = 'Rigid'
    self.hiddenFiducialVolumes = ()

  def addFiducial(self,name,position=(0,0,0),associatedNode=None):
    """Add an instance of a fiducial to the scene for a given
    volume node.  Creates a new list if needed.
    If list already has a fiducial with the given name, then
    set the position to the passed value.
    """

    markupsLogic = slicer.modules.markups.logic()
    originalActiveListID = markupsLogic.GetActiveListID() # TODO: naming convention?
    slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)

    # make the fiducial list if required
    listName = associatedNode.GetName() + "-landmarks"
    fiducialList = slicer.util.getNode(listName)
    if not fiducialList:
      fiducialListNodeID = markupsLogic.AddNewFiducialNode(listName,slicer.mrmlScene)
      fiducialList = slicer.util.getNode(fiducialListNodeID)
      if associatedNode:
        fiducialList.SetAttribute("AssociatedNodeID", associatedNode.GetID())
      displayNode = fiducialList.GetDisplayNode()
      # TODO: pick appropriate defaults
      # 135,135,84
      displayNode.SetTextScale(6.)
      displayNode.SetGlyphScale(6.)
      displayNode.SetGlyphTypeFromString('StarBurst2D')
      displayNode.SetColor((1,1,0))
      #displayNode.GetAnnotationTextDisplayNode().SetColor((1,1,0))
      displayNode.SetVisibility(True)

    # make this active so that the fids will be added to it
    markupsLogic.SetActiveListID(fiducialList)

    foundLandmarkFiducial = False
    fiducialSize = fiducialList.GetNumberOfFiducials()
    for fiducialIndex in range(fiducialSize):
      if fiducialList.GetNthFiducialLabel(fiducialIndex) == name:
        fiducialList.SetNthFiducialPosition(fiducialIndex, *position)
        foundLandmarkFiducial = True
        break

    if not foundLandmarkFiducial:
      fiducialList.AddFiducial(*position)
      fiducialIndex = fiducialList.GetNumberOfFiducials()-1

    fiducialList.SetNthFiducialLabel(fiducialIndex, name)
    fiducialList.SetNthFiducialSelected(fiducialIndex, False)
    fiducialList.SetNthMarkupLocked(fiducialIndex, False)

    originalActiveList = slicer.util.getNode(originalActiveListID)
    if originalActiveList:
      markupsLogic.SetActiveListID(originalActiveList)
    slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)

  def addLandmark(self,volumeNodes=[], position=(0,0,0)):
    """Add a new landmark by adding correspondingly named
    fiducials to all the current volume nodes.
    Find a unique name for the landmark and place it at the origin.
    """
    landmarks = self.landmarksForVolumes(volumeNodes)
    index = 0
    while True:
      landmarkName = 'L-%d' % index
      if not landmarkName in landmarks.keys():
        break
      index += 1
    for volumeNode in volumeNodes:
      fiducial = self.addFiducial(landmarkName, position=position,associatedNode=volumeNode)
    return landmarkName

  def removeLandmarkForVolumes(self,landmark,volumeNodes):
    """Remove the fiducial nodes from all the volumes.
    """
    slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)
    landmarks = self.landmarksForVolumes(volumeNodes)
    if landmarks.has_key(landmark):
      for fiducialList,fiducialIndex in landmarks[landmark]:
        fiducialList.RemoveMarkup(fiducialIndex)
    slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)

  def volumeFiducialList(self,volumeNode):
    """return fiducial list node that is
    list associated with the given volume node"""
    listName = volumeNode.GetName() + "-landmarks"
    return slicer.util.getNode(listName)

  def landmarksForVolumes(self,volumeNodes):
    """Return a dictionary of keyed by
    landmark name containing pairs (fiducialListNodes,index)
    Only fiducials that exist for all volumes are returned."""
    landmarksByName = {}
    for volumeNode in volumeNodes:
      listForVolume = self.volumeFiducialList(volumeNode)
      if listForVolume:
        fiducialSize = listForVolume.GetNumberOfMarkups()
        for fiducialIndex in range(fiducialSize):
          fiducialName = listForVolume.GetNthFiducialLabel(fiducialIndex)
          if landmarksByName.has_key(fiducialName):
            landmarksByName[fiducialName].append((listForVolume,fiducialIndex))
          else:
            landmarksByName[fiducialName] = [(listForVolume,fiducialIndex),]
    for fiducialName in landmarksByName.keys():
      if len(landmarksByName[fiducialName]) != len(volumeNodes):
        landmarksByName.__delitem__(fiducialName)
    return landmarksByName

  def ensureFiducialInListForVolume(self,volumeNode,landmarkName,landmarkPosition):
    """Make sure the fiducial list associated with the given
    volume node contains a fiducial named landmarkName and that it
    is associated with volumeNode.  If it does not have one, add one
    and put it at landmarkPosition."""
    fiducialList = self.volumeFiducialList(volumeNode)
    fiducialSize = fiducialList.GetNumberOfMarkups()
    for fiducialIndex in range(fiducialSize):
      if fiducialList.GetNthFiducialLabel(fiducialIndex) == landmarkName:
        fiducialList.SetNthMarkupAssociatedNodeID(fiducialIndex, volumeNode.GetID())
        return None
    # if we got here, then there is no fiducial with this name so add one
    fiducialList.AddFiducial(*landmarkPosition)
    fiducialIndex = fiducialList.GetNumberOfFiducials()-1
    fiducialList.SetNthFiducialLabel(fiducialIndex, landmarkName)
    fiducialList.SetNthFiducialSelected(fiducialIndex, False)
    fiducialList.SetNthMarkupLocked(fiducialIndex, False)
    return landmarkName

  def collectAssociatedFiducials(self,volumeNodes):
    """Look at each fiducial list in scene and find any fiducials associated
    with one of our volumes but not in in one of our lists.
    Add the fiducial as a landmark and delete it from the other list.
    Return the name of the last added landmark if it exists.
    """
    addedLandmark = None
    volumeNodeIDs = []
    for volumeNode in volumeNodes:
      volumeNodeIDs.append(volumeNode.GetID())
    landmarksByName = self.landmarksForVolumes(volumeNodes)
    fiducialListsInScene = slicer.util.getNodes('vtkMRMLMarkupsFiducialNode*')
    landmarkFiducialLists = []
    for landmarkName in landmarksByName.keys():
      for fiducialList,index in landmarksByName[landmarkName]:
        if fiducialList not in landmarkFiducialLists:
          landmarkFiducialLists.append(fiducialList)
    listIndexToRemove = [] # remove back to front after identifying them
    for fiducialList in fiducialListsInScene.values():
      if fiducialList not in landmarkFiducialLists:
        # this is not one of our fiducial lists, so look for fiducials
        # associated with one of our volumes
        fiducialSize = fiducialList.GetNumberOfMarkups()
        for fiducialIndex in range(fiducialSize):
          associated = fiducialList.GetNthMarkupAssociatedNodeID(fiducialIndex)
          if fiducialList.GetNthMarkupAssociatedNodeID(fiducialIndex) in volumeNodeIDs:
            # found one, so add it as a landmark
            landmarkPosition = fiducialList.GetMarkupPointVector(fiducialIndex,0)
            addedLandmark = self.addLandmark(volumeNodes,landmarkPosition)
            listIndexToRemove.insert(0,(fiducialList,fiducialIndex))
    for fiducialList,fiducialIndex in listIndexToRemove:
      fiducialList.RemoveMarkup(fiducialIndex)
    return addedLandmark

  def landmarksFromFiducials(self,volumeNodes):
    """Look through all fiducials in the scene and make sure they
    are in a fiducial list that is associated with the same
    volume node.  If they are in the wrong list fix the node id, and make a new
    duplicate fiducial in the correct list.
    This can be used when responding to new fiducials added to the scene.
    Returns the most recently added landmark (or None).
    """
    addedLandmark = None
    for volumeNode in volumeNodes:
      fiducialList = self.volumeFiducialList(volumeNode)
      if not fiducialList:
        print("no fiducialList for volume %s" % volumeNode.GetName())
        continue
      fiducialSize = fiducialList.GetNumberOfMarkups()
      for fiducialIndex in range(fiducialSize):
        fiducialAssociatedVolumeID = fiducialList.GetNthMarkupAssociatedNodeID(fiducialIndex)
        landmarkName = fiducialList.GetNthFiducialLabel(fiducialIndex)
        landmarkPosition = fiducialList.GetMarkupPointVector(fiducialIndex,0)
        if fiducialAssociatedVolumeID != volumeNode.GetID():
          # fiducial was placed on a viewer associated with the non-active list, so change it
          fiducialList.SetNthMarkupAssociatedNodeID(fiducialIndex,volumeNode.GetID())
        # now make sure all other lists have a corresponding fiducial (same name)
        for otherVolumeNode in volumeNodes:
          if otherVolumeNode != volumeNode:
            addedFiducial = self.ensureFiducialInListForVolume(otherVolumeNode,landmarkName,landmarkPosition)
            if addedFiducial:
              addedLandmark = addedFiducial
    return addedLandmark

  def vtkPointsForVolumes(self, volumeNodes, fiducialNodes):
    """Return dictionary of vtkPoints instances containing the fiducial points
    associated with current landmarks, indexed by volume"""
    points = {}
    for volumeNode in volumeNodes:
      points[volumeNode] = vtk.vtkPoints()
    sameNumberOfNodes = len(volumeNodes) == len(fiducialNodes) 
    noNoneNodes = None not in volumeNodes and None not in fiducialNodes
    if sameNumberOfNodes and noNoneNodes:
      fiducialCount = fiducialNodes[0].GetNumberOfFiducials()
      for fiducialNode in fiducialNodes:
        if fiducialCount != fiducialNode.GetNumberOfFiducials():
          raise Exception("Fiducial counts don't match {0}".format(fiducialCount))
      point = [0,]*3
      indices = range(fiducialCount)
      for fiducials,volumeNode in zip(fiducialNodes,volumeNodes):
        for index in indices:
          fiducials.GetNthFiducialPosition(index,point)
          points[volumeNode].InsertNextPoint(point)
    return points

  def resliceThroughTransform(self, sourceNode, transform, referenceNode, targetNode):
    """
    Fills the targetNode's vtkImageData with the source after
    applying the transform.  Uses spacing from referenceNode. Ignores any vtkMRMLTransforms.
    sourceNode, referenceNode, targetNode: vtkMRMLScalarVolumeNodes
    transform: vtkAbstractTransform
    """

    # get the transform from RAS back to source pixel space
    sourceRASToIJK = vtk.vtkMatrix4x4()
    sourceNode.GetRASToIJKMatrix(sourceRASToIJK)

    # get the transform from target image space to RAS
    referenceIJKToRAS = vtk.vtkMatrix4x4()
    targetNode.GetIJKToRASMatrix(referenceIJKToRAS)

    # this is the ijkToRAS concatenated with the passed in (abstract)transform
    self.resliceTransform = vtk.vtkGeneralTransform()
    self.resliceTransform.Concatenate(sourceRASToIJK)
    self.resliceTransform.Concatenate(transform)
    self.resliceTransform.Concatenate(referenceIJKToRAS)

    # use the matrix to extract the volume and convert it to an array
    self.reslice = vtk.vtkImageReslice()
    self.reslice.SetInterpolationModeToLinear()
    self.reslice.InterpolateOn()
    self.reslice.SetResliceTransform(self.resliceTransform)
    self.reslice.SetInput( sourceNode.GetImageData() )

    dimensions = referenceNode.GetImageData().GetDimensions()
    self.reslice.SetOutputExtent(0, dimensions[0]-1, 0, dimensions[1]-1, 0, dimensions[2]-1)
    self.reslice.SetOutputOrigin((0,0,0))
    self.reslice.SetOutputSpacing((1,1,1))

    self.reslice.UpdateWholeExtent()
    targetNode.SetAndObserveImageData(self.reslice.GetOutput())


  def run(self,inputVolume,outputVolume):
    """
    Run the actual algorithm
    """
    return True


class LandmarkRegistrationTest(unittest.TestCase):
  """
  This is the test case for your scripted module.
  """

  def delayDisplay(self,message,msec=1000):
    """This utility method displays a small dialog and waits.
    This does two things: 1) it lets the event loop catch up
    to the state of the test so that rendering and widget updates
    have all taken place before the test continues and 2) it
    shows the user/developer/tester the state of the test
    so that we'll know when it breaks.
    """
    print(message)
    self.info = qt.QDialog()
    self.infoLayout = qt.QVBoxLayout()
    self.info.setLayout(self.infoLayout)
    self.label = qt.QLabel(message,self.info)
    self.infoLayout.addWidget(self.label)
    qt.QTimer.singleShot(msec, self.info.close)
    self.info.exec_()

  def setUp(self):
    """ Do whatever is needed to reset the state - typically a scene clear will be enough.
    """
    slicer.mrmlScene.Clear(0)

  def runTest(self,scenario=None):
    """Run as few or as many tests as needed here.
    """
    self.setUp()
    if scenario == "Basic":
      self.test_LandmarkRegistrationBasic()
    elif scenario == "Affine":
      self.test_LandmarkRegistrationAffine()
    elif scenario == "ThinPlate":
      self.test_LandmarkRegistrationThinPlate()
    else:
      self.test_LandmarkRegistrationBasic()
      self.test_LandmarkRegistrationAffine()
      self.test_LandmarkRegistrationThinPlate()

  def test_LandmarkRegistrationBasic(self):
    """
    This tests basic landmarking with two volumes
    """

    self.delayDisplay("Starting test_LandmarkRegistrationBasic")
    #
    # first, get some data
    #
    import SampleData
    sampleDataLogic = SampleData.SampleDataLogic()
    mrHead = sampleDataLogic.downloadMRHead()
    dtiBrain = sampleDataLogic.downloadDTIBrain()
    self.delayDisplay('Two data sets loaded')

    mainWindow = slicer.util.mainWindow()
    mainWindow.moduleSelector().selectModule('LandmarkRegistration')

    w = slicer.modules.LandmarkRegistrationWidget
    w.volumeSelectors["Fixed"].setCurrentNode(dtiBrain)
    w.volumeSelectors["Moving"].setCurrentNode(mrHead)

    logic = LandmarkRegistrationLogic()

    for name,point in (
      ('middle-of-right-eye', [35.115070343017578, 74.803565979003906, -21.032917022705078]),
      ('tip-of-nose', [0.50825262069702148, 128.85432434082031, -48.434154510498047]),
      ('right-ear', [80.0, -26.329217910766602, -15.292181015014648]),
      ):
      logic.addFiducial(name, position=point,associatedNode=mrHead)

    for name,point in (
      ('middle-of-right-eye', [28.432207107543945, 71.112533569335938, -41.938472747802734]),
      ('tip-of-nose', [0.9863210916519165, 94.6998291015625, -49.877540588378906]),
      ('right-ear', [79.28509521484375, -12.95069694519043, 5.3944296836853027]),
      ):
      logic.addFiducial(name, position=point,associatedNode=dtiBrain)

    w.onVolumeNodeSelect()
    w.onLayout()
    w.onLandmarkPicked('tip-of-nose')

    self.delayDisplay('test_LandmarkRegistrationBasic passed!')

  def test_LandmarkRegistrationAffine(self):
    """
    This tests basic linear registration with two
    volumes (pre- post-surgery)
    """

    self.delayDisplay("Starting test_LandmarkRegistrationAffine")
    #
    # first, get some data
    #
    import SampleData
    sampleDataLogic = SampleData.SampleDataLogic()
    pre,post = sampleDataLogic.downloadDentalSurgery()
    self.delayDisplay('Two data sets loaded')

    mainWindow = slicer.util.mainWindow()
    mainWindow.moduleSelector().selectModule('LandmarkRegistration')

    w = slicer.modules.LandmarkRegistrationWidget
    w.setupDialog()
    w.volumeDialogSelectors["Fixed"].setCurrentNode(post)
    w.volumeDialogSelectors["Moving"].setCurrentNode(pre)
    w.onVolumeDialogApply()

    # initiate linear registration
    w.registrationTypeButtons["Affine"].checked = True
    w.registrationTypeButtons["Affine"].clicked()

    w.onLayout(layoutMode="Axi/Sag/Cor")

    self.delayDisplay('test_LandmarkRegistrationAffine passed!')

  def test_LandmarkRegistrationThinPlate(self):
    """Test the thin plate spline transform"""
    self.test_LandmarkRegistrationAffine()

    self.delayDisplay('starting test_LandmarkRegistrationThinPlate')

    mainWindow = slicer.util.mainWindow()
    mainWindow.moduleSelector().selectModule('LandmarkRegistration')

    w = slicer.modules.LandmarkRegistrationWidget
    pre = w.volumeSelectors["Fixed"].currentNode()
    post = w.volumeSelectors["Moving"].currentNode()

    for name,point in (
      ('L-0', [-91.81303405761719, -36.81013488769531, 76.78043365478516]),
      ('L-1', [-91.81303405761719, -41.065155029296875, 19.57413101196289]),
      ('L-2', [-89.75, -121.12535858154297, 33.5537223815918]),
      ('L-3', [-91.29727935791016, -148.6207275390625, 54.980953216552734]),
      ('L-4', [-89.75, -40.17485046386719, 153.87451171875]),
      ('L-5', [-144.15321350097656, -128.45083618164062, 69.85309600830078]),
      ('L-6', [-40.16628646850586, -128.70603942871094, 71.85968017578125]),):
        w.logic.addFiducial(name, position=point,associatedNode=post)

    for name,point in (
      ('L-0', [-89.75, -48.97413635253906, 70.87068939208984]),
      ('L-1', [-91.81303405761719, -47.7024040222168, 14.120864868164062]),
      ('L-2', [-89.75, -130.1315155029297, 31.712587356567383]),
      ('L-3', [-90.78448486328125, -160.6336212158203, 52.85344696044922]),
      ('L-4', [-85.08663940429688, -47.26158905029297, 143.84193420410156]),
      ('L-5', [-144.1186065673828, -138.91270446777344, 68.24700927734375]),
      ('L-6', [-40.27879333496094, -141.29898071289062, 67.36009216308594]),):
        w.logic.addFiducial(name, position=point,associatedNode=pre)


    # initiate linear registration
    w.registrationTypeButtons["ThinPlate"].checked = True
    w.registrationTypeButtons["ThinPlate"].clicked()

    w.landmarksWidget.pickLandmark('L-4')
    w.onRegistrationType("ThinPlate")

    w.currentRegistrationInterface.onThinPlateApply()

    self.delayDisplay('test_LandmarkRegistrationThinPlate passed!')