def onExit(self, goingTo, transitionType):
if goingTo.id() != 'Landmarks' and goingTo.id(
) != 'LoadData': # Change to next step
return
pNode = self.parameterNode()
# TODO: add storeWidgetStateToParameterNode() -- move all pNode-related stuff
# there?
if self.__roi != None:
self.__roi.RemoveObserver(self.__roiObserverTag)
self.__roi.SetDisplayVisibility(0)
if self.__roiSelector.currentNode() != None:
pNode.SetNodeReferenceID('roiNode',
self.__roiSelector.currentNode().GetID())
if self.__vrDisplayNode != None:
#self.__vrDisplayNode.VisibilityOff()
pNode.SetNodeReferenceID('vrDisplayNode',
self.__vrDisplayNode.GetID())
if goingTo.id() == 'Landmarks': # Change to next step
#create progress bar dialog
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(0)
self.progress.setCancelButton(0)
self.progress.setMinimumWidth(500)
self.progress.setWindowModality(2)
self.progress.setLabelText('Cropping and resampling volume...')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
self.doStepProcessing()
#close progress bar
self.progress.setValue(2)
self.progress.repaint()
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.close()
self.progress = None
super(DefineROIStep, self).onExit(goingTo, transitionType)
def onOk(self):
address = self.dicomEntries['Destination Address'].text
port = self.dicomEntries['Destination Port'].text
settings = qt.QSettings()
settings.setValue('DICOM.sendAddress', address)
settings.setValue('DICOM.sendPort', port)
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.setMaximum(len(self.files))
self.progressValue = 0
try:
DICOMLib.DICOMSender(self.files, address, port, progressCallback = self.onProgress)
except Exception as result:
qt.QMessageBox.warning(self.dialog, 'DICOM Send', 'Could not send data: %s' % result)
self.progress.close()
self.dialog.close()
def loadCheckedLoadables(self):
"""Invoke the load method on each plugin for the DICOMLoadable
instances that are selected"""
if self.advancedViewButton.checkState() == 0:
self.examineForLoading()
self.loadableTable.updateSelectedFromCheckstate()
loadableCount = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if loadable.selected:
loadableCount += 1
self.progress = qt.QProgressDialog(self.window)
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(loadableCount)
step = 0
loadingResult = ''
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if self.progress.wasCanceled:
break
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
if loadable.selected:
self.progress.labelText = '\nLoading %s' % loadable.name
slicer.app.processEvents()
if not plugin.load(loadable):
loadingResult = '%s\nCould not load: %s as a %s' % (
loadingResult, loadable.name, plugin.loadType)
step += 1
self.progress.setValue(step)
slicer.app.processEvents()
self.progress.close()
self.progress = None
if loadingResult:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'DICOM loading',
loadingResult)
if not self.setBrowserPersistence:
self.close()
def onLoadButton(self):
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(100)
uid = self.selection.data(self.dicomModelUIDRole)
role = self.dicomModelTypes[self.selection.data(
self.dicomModelTypeRole)]
toLoad = {}
if role == "Patient":
self.progress.show()
self.loadPatient(uid)
elif role == "Study":
self.progress.show()
self.loadStudy(uid)
elif role == "Series":
self.loadSeries(uid)
elif role == "Image":
pass
self.progress.close()
self.progress = None
def loadCheckedLoadables(self):
"""Invoke the load method on each plugin for the DICOMLoadable
instances that are selected"""
self.loadableTable.updateCheckstate()
loadableCount = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if loadable.selected:
loadableCount += 1
self.progress = qt.QProgressDialog(self.window)
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(loadableCount)
step = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if self.progress.wasCanceled:
break
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
if loadable.selected:
self.progress.labelText = '\nLoading %s' % loadable.name
slicer.app.processEvents()
if not plugin.load(loadable):
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Load',
'Could not load: %s as a %s' %
(loadable.name, plugin.loadType))
step += 1
self.progress.setValue(step)
slicer.app.processEvents()
self.progress.close()
self.progress = None
self.close()
def onEntry(self, comingFrom, transitionType):
super(DefineROIStep, self).onEntry(comingFrom, transitionType)
# setup the interface
lm = slicer.app.layoutManager()
lm.setLayout(3)
#create progress bar dialog
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(0)
self.progress.setCancelButton(0)
self.progress.setMinimumWidth(500)
self.progress.setWindowModality(2)
self.progress.setLabelText('Generating Volume Rendering...')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
#read scalar volume node ID from previous step
pNode = self.parameterNode()
self.__baselineVolume = pNode.GetNodeReference('baselineVolume')
#if ROI was created previously, get its transformation matrix and update current ROI
roiTransformNode = pNode.GetNodeReference('roiTransform')
if not roiTransformNode:
roiTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(roiTransformNode)
pNode.SetNodeReferenceID('roiTransform', roiTransformNode.GetID())
dm = vtk.vtkMatrix4x4()
self.__baselineVolume.GetIJKToRASDirectionMatrix(dm)
dm.SetElement(0, 3, 0)
dm.SetElement(1, 3, 0)
dm.SetElement(2, 3, 0)
dm.SetElement(0, 0, abs(dm.GetElement(0, 0)))
dm.SetElement(1, 1, abs(dm.GetElement(1, 1)))
dm.SetElement(2, 2, abs(dm.GetElement(2, 2)))
roiTransformNode.SetMatrixTransformToParent(dm)
Helper.SetBgFgVolumes(self.__baselineVolume.GetID())
Helper.SetLabelVolume(None)
# use this transform node to align ROI with the axes of the baseline
# volume
self.__roiTransformNode = pNode.GetNodeReference('roiTransform')
if not self.__roiTransformNode:
Helper.Error(
'Internal error! Error code CT-S2-NRT, please report!')
# get the roiNode from parameters node, if it exists, and initialize the
# GUI
self.updateWidgetFromParameterNode(pNode)
# start VR
if self.__roi != None:
self.__roi.SetDisplayVisibility(1)
# Make sure the GUI is fully initilized because user will see it for a few seconds, while VR is being set up
slicer.app.processEvents()
self.InitVRDisplayNode()
#close progress bar
self.progress.setValue(2)
self.progress.repaint()
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.close()
self.progress = None
#pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def onEntry(self,comingFrom,transitionType):
super(ApproachStep, self).onEntry(comingFrom, transitionType)
# setup the interface
lm = slicer.app.layoutManager()
if lm == None:
return
#lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutSideBySideView)
customLayout = ("<layout type=\"horizontal\" split=\"true\" >"
" <item>"
" <view class=\"vtkMRMLSliceNode\" singletontag=\"Red\">"
" <property name=\"orientation\" action=\"default\">Axial</property>"
" <property name=\"viewlabel\" action=\"default\">R</property>"
" <property name=\"viewcolor\" action=\"default\">#F34A33</property>"
" </view>"
" </item>"
" <item>"
" <view class=\"vtkMRMLSliceNode\" singletontag=\"Yellow\">"
" <property name=\"orientation\" action=\"default\">Axial</property>"
" <property name=\"viewlabel\" action=\"default\">Y</property>"
" <property name=\"viewcolor\" action=\"default\">#EDD54C</property>"
" </view>"
" </item>"
" <item>"
" <view class=\"vtkMRMLSliceNode\" singletontag=\"Green\">"
" <property name=\"orientation\" action=\"default\">Axial</property>"
" <property name=\"viewlabel\" action=\"default\">G</property>"
" <property name=\"viewcolor\" action=\"default\">#6EB04B</property>"
" </view>"
" </item>"
"</layout>")
customLayoutId=502
#layoutManager = slicer.app.layoutManager()
lm.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
lm.setLayout(customLayoutId)
markup = slicer.modules.markups.logic()
markup.AddNewFiducialNode('Vertebrae Labels')
landmarks = slicer.mrmlScene.GetNodesByName('Vertebrae Labels')
self.fidNode = landmarks.GetItemAsObject(0)
slicer.app.applicationLogic().PropagateVolumeSelection(1)
#create progress bar dialog
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(0)
self.progress.setCancelButton(0)
self.progress.setMinimumWidth(500)
self.progress.setWindowModality(2)
self.progress.setLabelText('Generating Volume Rendering...')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
#read scalar volume node ID from previous step
pNode = self.__parameterNode
baselineVolume = Helper.getNodeByID(pNode.GetParameter('baselineVolumeID'))
self.__baselineVolume = baselineVolume
roiTransformID = pNode.GetParameter('roiTransformID')
roiTransformNode = None
if roiTransformID != '':
roiTransformNode = Helper.getNodeByID(roiTransformID)
else:
roiTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(roiTransformNode)
pNode.SetParameter('roiTransformID', roiTransformNode.GetID())
dm = vtk.vtkMatrix4x4()
baselineVolume.GetIJKToRASDirectionMatrix(dm)
dm.SetElement(0,3,0)
dm.SetElement(1,3,0)
dm.SetElement(2,3,0)
dm.SetElement(0,0,abs(dm.GetElement(0,0)))
dm.SetElement(1,1,abs(dm.GetElement(1,1)))
dm.SetElement(2,2,abs(dm.GetElement(2,2)))
roiTransformNode.SetAndObserveMatrixTransformToParent(dm)
Helper.SetBgFgVolumes(pNode.GetParameter('baselineVolumeID'))
Helper.SetLabelVolume(None)
# use this transform node to align ROI with the axes of the baseline
# volume
roiTfmNodeID = pNode.GetParameter('roiTransformID')
if roiTfmNodeID != '':
self.__roiTransformNode = Helper.getNodeByID(roiTfmNodeID)
else:
Helper.Error('Internal error! Error code CT-S2-NRT, please report!')
# get the roiNode from parameters node, if it exists, and initialize the
# GUI
self.updateWidgetFromParameterNode(pNode)
if self.__roi != None:
self.__roi.SetDisplayVisibility(0)
self.InitVRDisplayNode()
#close progress bar
self.progress.setValue(2)
self.progress.repaint()
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.close()
self.progress = None
#turn off rendering to save memory
slicer.mrmlScene.GetNodesByName('GPURayCastVolumeRendering').GetItemAsObject(0).SetVisibility(0)
#pNode.SetParameter('currentStep', self.stepid)
# Enable Slice Intersections
viewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode')
viewNodes.UnRegister(slicer.mrmlScene)
viewNodes.InitTraversal()
viewNode = viewNodes.GetNextItemAsObject()
while viewNode:
viewNode.SetSliceIntersectionVisibility(1)
viewNode = viewNodes.GetNextItemAsObject()
self.redTransform = vtk.vtkTransform()
viewSlice = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
self.redTransform.SetMatrix(viewSlice.GetSliceToRAS())
#print "Red Transform"
#print self.redTransform
self.yellowTransform = vtk.vtkTransform()
viewSlice = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow')
self.yellowTransform.SetMatrix(viewSlice.GetSliceToRAS())
#print "Yellow Transform"
#print self.yellowTransform
self.greenTransform = vtk.vtkTransform()
viewSlice = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeGreen')
self.greenTransform.SetMatrix(viewSlice.GetSliceToRAS())
#print "Green Transform"
#print self.greenTransform
n = self.__baselineVolume
for color in ['Red', 'Yellow', 'Green']:
a = slicer.app.layoutManager().sliceWidget(color).sliceLogic().GetSliceNode().GetFieldOfView()
slicer.app.layoutManager().sliceWidget(color).sliceLogic().GetSliceCompositeNode().SetBackgroundVolumeID(n.GetID())
lm.sliceWidget("Yellow").sliceController().fitSliceToBackground()
lm.sliceWidget("Red").sliceController().fitSliceToBackground()
lm.sliceWidget("Green").sliceController().fitSliceToBackground()
qt.QTimer.singleShot(0, self.killButton)
self.showThreshold()
self.loadLandmarks()
def offerLoadables(self, uid, role):
"""Get all the loadable options at the currently selected level
and present them in the loadable table"""
fileLists = []
if role == "Series":
fileLists.append(slicer.dicomDatabase.filesForSeries(uid))
if role == "Study":
series = slicer.dicomDatabase.seriesForStudy(uid)
for serie in series:
fileLists.append(slicer.dicomDatabase.filesForSeries(serie))
if role == "Patient":
studies = slicer.dicomDatabase.studiesForPatient(uid)
for study in studies:
series = slicer.dicomDatabase.seriesForStudy(study)
for serie in series:
fileList = slicer.dicomDatabase.filesForSeries(serie)
fileLists.append(fileList)
allFileCount = missingFileCount = 0
for fileList in fileLists:
for filePath in fileList:
allFileCount += 1
if not os.path.exists(filePath):
missingFileCount += 1
if missingFileCount > 0:
qt.QMessageBox.warning(
self.window, "DICOM",
"Warning: %d of %d files listed in the database for this %s cannot be found on disk."
% (missingFileCount, allFileCount, role))
if missingFileCount == allFileCount:
return
self.progress = qt.QProgressDialog(self.window)
self.progress.modal = True
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(len(slicer.modules.dicomPlugins))
step = 0
loadEnabled = False
self.loadablesByPlugin = {}
for pluginClass in slicer.modules.dicomPlugins:
if not self.pluginInstances.has_key(pluginClass):
self.pluginInstances[
pluginClass] = slicer.modules.dicomPlugins[pluginClass]()
plugin = self.pluginInstances[pluginClass]
if self.progress.wasCanceled:
break
self.progress.labelText = '\nChecking %s' % pluginClass
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
try:
self.loadablesByPlugin[plugin] = plugin.examine(fileLists)
loadEnabled = loadEnabled or self.loadablesByPlugin[
plugin] != []
except Exception, e:
import traceback
traceback.print_exc()
qt.QMessageBox.warning(
self.window, "DICOM",
"Warning: Plugin failed: %s\n\nSee python console for error message."
% pluginClass)
print("DICOM Plugin failed: %s", str(e))
step += 1
def setup(self):
"""Init the widget """
# ScriptedLoadableModuleWidget.setup(self)
settings = qt.QSettings()
if (SlicerUtil.IsDevelopment):
# reload button
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onBtnReloadClicked)
self.logic = PicasaSnapLogic()
self.__addObservers__()
######## Credentials
self.credentialsCollapsibleButton = ctk.ctkCollapsibleButton()
self.credentialsCollapsibleButton.text = "Credentials"
self.layout.addWidget(self.credentialsCollapsibleButton)
self.credentialsLayout = qt.QFormLayout(
self.credentialsCollapsibleButton)
self.isUserLogged = False
self.loginLineEdit = qt.QLineEdit()
self.credentialsLayout.addRow("Login: "******"Password: "******"Remember my credentials")
self.rememberCredentialsCheckBox.toolTip = "Check for an automatic login when the application starts"
self.loginButton = qt.QPushButton("Login")
self.loginButton.toolTip = "Login in Picassa service (Google credentials)"
self.logoutButton = qt.QPushButton("Logout")
self.logoutButton.toolTip = "Logout to connect with another user's credentials"
# Add all the items, they will be shown/hidden in refreshCredentialsUI function
self.credentialsLayout.addRow(self.rememberCredentialsCheckBox,
self.loginButton)
self.credentialsLayout.addRow(None, self.logoutButton)
######## Snapshots (main frame)
self.mainCollapsibleButton = ctk.ctkCollapsibleButton()
self.mainCollapsibleButton.text = "Snapshots"
self.layout.addWidget(self.mainCollapsibleButton)
self.mainLayout = qt.QVBoxLayout(self.mainCollapsibleButton)
############### Current snapshots
self.currentSnapshotsFrame = qt.QFrame()
self.currentSnapshotsLayout = qt.QVBoxLayout()
self.currentSnapshotsFrame.setLayout(self.currentSnapshotsLayout)
self.currentSnapshotsFrame.setFrameShape(qt.QFrame.StyledPanel)
self.mainLayout.addWidget(self.currentSnapshotsFrame)
self.snapshotsLabel = qt.QLabel("Snapshots to upload:")
self.snapshotsLabel.setStyleSheet(
"font-weight:bold; font-size:14px; margin-bottom:10px")
self.currentSnapshotsLayout.addWidget(self.snapshotsLabel)
# Subframe that contains the checkbox list
self.currentSnapshotsInnerFrame = qt.QFrame()
self.currentSnapshotsInnerLayout = qt.QVBoxLayout()
self.currentSnapshotsInnerFrame.setLayout(
self.currentSnapshotsInnerLayout)
self.currentSnapshotsLayout.addWidget(self.currentSnapshotsInnerFrame)
self.noItemsLabel = qt.QLabel(
"(There are not any snapshots at the moment)")
# Add the label by default. It will be hidden if there is any snapshot
self.currentSnapshotsInnerLayout.addWidget(self.noItemsLabel)
self.loadExistingSnapshotsFirstLoad()
############### Albums
# Try to login before getting the albums
self.login()
msgBox = None
if self.isUserLogged:
# Show message box while loading the data
msgBox = qt.QMessageBox(qt.QMessageBox.Information, 'Login',
'Connecting with Picasa. Please wait...',
qt.QMessageBox.Cancel)
msgBox.show()
try:
self.albumNameFrame = qt.QFrame()
self.albumNameLayout = qt.QHBoxLayout()
self.albumNameFrame.setLayout(self.albumNameLayout)
self.albumNameFrame.setFrameShape(qt.QFrame.StyledPanel)
self.albumNameLabel = qt.QLabel("Album name:")
self.albumNameLabel.setStyleSheet("font-weight:bold;")
self.albumNamesComboBox = qt.QComboBox()
self.loadAlbums()
self.albumNameLayout.addWidget(self.albumNameLabel)
self.albumNameLayout.addWidget(self.albumNamesComboBox)
self.mainLayout.addWidget(self.albumNameFrame)
############### Tags
self.tagsFrame = qt.QFrame()
self.tagsLayout = qt.QGridLayout()
self.tagsFrame.setLayout(self.tagsLayout)
self.tagsFrame.setFrameShape(qt.QFrame.StyledPanel)
self.tagsLabel = qt.QLabel(
"Tags (select all that apply, you can filter o create new tags):"
)
self.tagsLabel.setStyleSheet(
"font-weight: bold; margin-bottom: 10px; margin-top: 5px")
self.tagsLayout.addWidget(self.tagsLabel, 0, 0, 1, 3)
# Add input to filter tags and button to add a new one
self.tagsFilterLineEdit = qt.QLineEdit()
self.tagsFilterLineEdit.toolTip = "Type here to filter your tags. If you press the return key all the visible tags will be checked"
#self.tagsFilterLineEdit.setStyleSheet(style)
self.tagsLayout.addWidget(self.tagsFilterLineEdit, 1, 0, 1, 2)
self.newTagButton = qt.QPushButton("New tag")
#self.newTagButton.setStyleSheet("background-color: #5D74C6; color:white")
self.newTagButton.setIconSize(qt.QSize(20, 20))
self.newTagButton.setIcon(
qt.QIcon(self.CIP_ICON_DIR + "/Plus - 48.png"))
self.newTagButton.setFixedWidth(75)
self.newTagButton.toolTip = "Add a new tag (the tag will not be created until you upload any picture with it)"
self.tagsLayout.addWidget(self.newTagButton, 1, 2)
self.loadTags()
############### Upload snapshots controls
self.uploadSnapsButtonFrame = qt.QFrame()
self.uploadSnapsLayout = qt.QHBoxLayout()
self.uploadSnapsButtonFrame.setLayout(self.uploadSnapsLayout)
#self(qt.QFrame.HLine)
self.mainLayout.addWidget(self.uploadSnapsButtonFrame)
self.uploadSnapshotsButton = qt.QPushButton()
self.uploadSnapshotsButton.text = "Upload to Picasa!"
self.uploadSnapshotsButton.toolTip = "Upload selected screenshots to Picassa"
self.uploadSnapshotsButton.setStyleSheet(
"background-color: #5D74C6; color: white; font-weight: bold; font-size:14px"
)
self.uploadSnapshotsButton.setIcon(
qt.QIcon(self.CIP_ICON_DIR + "/Upload - 64.png"))
self.uploadSnapshotsButton.setIconSize(qt.QSize(24, 24))
self.uploadSnapshotsButton.setFixedSize(170, 35)
self.uploadSnapsLayout.addWidget(self.uploadSnapshotsButton)
############### Progress bar
self.progressBar = qt.QProgressDialog()
self.progressBar.setMinimum(0)
self.progressBar.setMinimumDuration(0)
self.progressBar.setWindowModality(True)
# Check for updates in CIP
#autoUpdate = SlicerUtil.settingGetOrSetDefault("PicasaSnap", "AutoUpdate", 1)
#uw = AutoUpdateWidget(parent=self.parent, autoUpdate=autoUpdate)
#uw.addAutoUpdateCheckObserver(self.onAutoUpdateStateChanged)
# self.uploadProgressFrame = qt.QFrame()
# self.uploadProgressLayout = qt.QVBoxLayout()
# self.uploadProgressFrame.setLayout(self.uploadProgressLayout)
#
# # Gif image
# self.imUploading = qt.QMovie("%s/loading.gif" % self.CIP_ICON_DIR, qt.QByteArray())
# # Label to contain the gif
# self.lblImLoading = qt.QLabel()
# # Fix the dimensions of the image (by fixing the dimensions of the label that contains it)
# self.lblImLoading.setFixedWidth(40)
# # Other image parameters
# self.imUploading.setCacheMode(qt.QMovie.CacheAll)
# self.imUploading.setSpeed(100)
# # Assign the label to the image (don't start it yet, it will be started when we are uploading)
# self.lblImLoading.setMovie(self.imUploading)
# #self.imUploading.start()
# self.uploadProgressLayout.addWidget(self.lblImLoading)
#
# # Label that will show the progress
# self.lblUploading = qt.QLabel("Uploading %i/%i images...")
# self.uploadProgressLayout.addWidget(self.lblUploading)
#
# Cancel uploading button
# self.btnCancelUpload = qt.QPushButton("Cancel")
# self.btnCancelUpload.toolTip = "Cancel the process"
# self.btnCancelUpload.setFixedWidth(100)
# self.uploadProgressLayout.addWidget(self.btnCancelUpload)
# self.mainLayout.addWidget(self.uploadProgressFrame)
#
# # Hide the progress frame
# self.uploadProgressFrame.hide()
######## Connections
self.uploadSnapshotsButton.connect(
'clicked (bool)', self.onUploadSnapshotsButtonClicked)
self.loginButton.connect('clicked (bool)',
self.onLoginButtonClicked)
self.logoutButton.connect('clicked (bool)',
self.onLogoutButtonClicked)
self.loginLineEdit.returnPressed.connect(
self.onLoginPasswordReturnKeyPressed)
self.passwordLineEdit.returnPressed.connect(
self.onLoginPasswordReturnKeyPressed)
self.albumNamesComboBox.connect("currentIndexChanged (int)",
self.onAlbumsCurrentIndexChanged)
self.newTagButton.connect('clicked (bool)',
self.onNewTagButtonClicked)
self.tagsFilterLineEdit.connect('textEdited (QString)',
self.onFilterTagsEdited)
self.tagsFilterLineEdit.returnPressed.connect(
self.onFilterTagsReturnKeyPressed)
# Add vertical spacer
self.layout.addStretch(1)
finally:
# Hide MesageBox if it was visible
if msgBox:
msgBox.close()
def doStepProcessing(self):
print 'Step processing'
'''
timer = qt.QTimer()
timer.setInterval(1000)
timer.setSingleShot(0)
timer.connect('timeout()', self.updateProgress)
'''
# pop up progress dialog to prevent user from messing around
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(0)
self.progress.setCancelButton(0)
self.progress.setWindowModality(2)
self.progress.setLabelText('Registering followup image to baseline')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
# qt.QTimer.singleShot(0, self.updateProgress)
'''
Step logic:
1) register followup to baseline
2) resample followup to baseline ROI
3) given baselineROI, followupROI and baseline segmentation, run each of
the change detection metrics
'''
pNode = self.parameterNode()
# (1) register followup to baseline
# If the followup transform is initialized, do not register!
if pNode.GetParameter('followupTransformID') == '':
baselineVolumeID = pNode.GetParameter('baselineVolumeID')
followupVolumeID = pNode.GetParameter('followupVolumeID')
self.__followupTransform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(self.__followupTransform)
parameters = {}
parameters["fixedVolume"] = baselineVolumeID
parameters["movingVolume"] = followupVolumeID
parameters["initializeTransformMode"] = "useMomentsAlign"
parameters["useRigid"] = True
parameters["useScaleVersor3D"] = False
parameters["useScaleSkewVersor3D"] = False
parameters["useAffine"] = True
parameters["linearTransform"] = self.__followupTransform.GetID()
# apparently this is needed even if not b-spline (see bug report 1542)
parameters["forceMINumberOfThreads"] = -1
# FIXME: make sure brainsfit is available first?
cliNode = None
cliNode = slicer.cli.run(slicer.modules.brainsfit, cliNode, parameters, wait_for_completion = True)
status = cliNode.GetStatusString()
'''
while status != 'Completed':
# while status == 'Running' or status == 'Scheduled' or status == 'Idle':
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
status = cliNode.GetStatusString()
print 'Registration completed: status = ', status
'''
if status == 'Completed':
Helper.Info('registration completed OK')
else:
Helper.ErrorPopup('Registration step failed. Unable to proceed. Please quit Slicer and report this issue including the output from the error log.')
return
pNode.SetParameter('followupTransformID', self.__followupTransform.GetID())
print 'AnalyzeROIStep: registration completed!'
else:
print 'AnalyzeROIStep: registration not required!'
self.progress.setLabelText('Estimating changes')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
# self.__cliObserverTag = self.__cliNode.AddObserver('ModifiedEvent', self.processRegistrationCompletion)
# self.__registrationStatus.setText('Wait ...')
# self.__registrationButton.setEnabled(0)
# (2) resample followup to baselineROI
baselineVolumeROI = slicer.mrmlScene.GetNodeByID(pNode.GetParameter('croppedBaselineVolumeID'))
followupVolume = slicer.mrmlScene.GetNodeByID(pNode.GetParameter('followupVolumeID'))
followupVolumeROI = slicer.modules.volumes.logic().CloneVolume(slicer.mrmlScene, followupVolume, 'followupROI')
parameters = {}
parameters["inputVolume"] = pNode.GetParameter('followupVolumeID')
parameters["referenceVolume"] = pNode.GetParameter('croppedBaselineVolumeID')
parameters["outputVolume"] = followupVolumeROI.GetID()
parameters["transformationFile"] = pNode.GetParameter('followupTransformID')
parameters["interpolationType"] = "bs"
cliNode = None
cliNode = slicer.cli.run(slicer.modules.resamplescalarvectordwivolume, cliNode, parameters, 1)
status = cliNode.GetStatusString()
if status == 'Completed':
Helper.Info('ResampleScalarVectorDWIVolume completed OK')
pNode.SetParameter('croppedFollowupVolumeID', followupVolumeROI.GetID())
else:
Helper.Error('Failed to resample!')
# (3) calculate each of the metrics
# most of the parameters will be the same for all metrics
parameters = {}
parameters['baselineVolume'] = pNode.GetParameter('croppedBaselineVolumeID')
parameters['followupVolume'] = pNode.GetParameter('croppedFollowupVolumeID')
parameters['baselineSegmentationVolume'] = pNode.GetParameter('croppedBaselineVolumeSegmentationID')
baselineVolume = slicer.mrmlScene.GetNodeByID(pNode.GetParameter('croppedBaselineVolumeID'))
metricsList = pNode.GetParameter('metrics')
if metricsList == '':
Helper.Error('doStepProcessing(): metrics list is empty!')
resultVolumesList = ''
moduleManager = slicer.app.moduleManager()
for m in string.split(metricsList,','):
# TODO: processing should be separated from the workflow! need to move
# this into a different place
pluginName = m
# pluginName = pluginName.lower()
vl = slicer.modules.volumes.logic()
outputVolume = vl.CreateLabelVolume(slicer.mrmlScene, baselineVolume, 'changesVolume_'+m)
outputReport = slicer.app.temporaryPath+os.sep+pluginName+'_report.txt'
parameters["tmpDirectory"] = slicer.app.temporaryPath
parameters['outputVolume'] = outputVolume.GetID()
parameters['reportFileName'] = outputReport
plugin = moduleManager.module(pluginName)
if plugin != None:
cliNode = None
Helper.Info('About to run '+m+' metric!')
cliNode = slicer.cli.run(plugin, cliNode, parameters, 1)
'''
TODO: error checking for CLI!
'''
labelsColorNode = slicer.modules.colors.logic().GetColorTableNodeID(10)
outputVolume.GetDisplayNode().SetAndObserveColorNodeID(labelsColorNode)
if resultVolumesList != '':
resultVolumesList = resultVolumesList + ','
resultVolumesList = resultVolumesList + outputVolume.GetID()
outputVolume.SetDescription(Helper.readFileAsString(outputReport))
pNode.SetParameter('resultVolumes', resultVolumesList)
Helper.Info('Selected metrics: '+pNode.GetParameter('metrics'))
Helper.Info('Metrics processing results:'+pNode.GetParameter('resultVolumes'))
# close the progress window
'''
timer.stop()
'''
self.progress.setValue(2)
self.progress.repaint()
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.close()
self.progress = None
def __init__(self, dataNode, labelNode, featureParameterDict,
featureClassParametersDict, keys):
self.dataNode = dataNode
self.labelNode = labelNode
self.featureParameterDict = featureParameterDict # ( keys=featureNames,values=dict(keys=parameterNames,values=parameterValues) )
self.featureClassParametersDict = featureClassParametersDict # ( keys=featureClassNames,values=dict(keys=parameterNames,values=parameterValues) )
self.keys = keys
# initialize Progress Bar
self.progressBar = qt.QProgressDialog(slicer.util.mainWindow())
self.progressBar.minimumDuration = 0
self.progressBar.show()
self.progressBar.setValue(0)
self.progressBar.setMaximum(len(self.keys))
self.progressBar.labelText = 'Calculating for %s: ' % self.dataNode.GetName(
)
# create Numpy Arrays
self.nodeArrayVolume = self.createNumpyArray(self.dataNode)
self.nodeArrayLabelMapROI = self.createNumpyArray(self.labelNode)
# extract voxel coordinates (ijk) and values from self.dataNode within the ROI defined by self.labelNode
self.targetVoxels, self.targetVoxelsCoordinates = self.tumorVoxelsAndCoordinates(
self.nodeArrayLabelMapROI, self.nodeArrayVolume)
# create a padded, rectangular matrix with shape equal to the shape of the tumor
self.matrix, self.matrixCoordinates = self.paddedTumorMatrixAndCoordinates(
self.targetVoxels, self.targetVoxelsCoordinates)
# get Histogram data
self.bins, self.grayLevels, self.numGrayLevels = self.getHistogramData(
self.targetVoxels)
########
# Manage feature classes for Heterogeneity feature calculations and consolidate into self.FeatureVector
# TODO: create a parent class for all feature classes
self.FeatureVector = collections.OrderedDict()
# Node Information
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"Node Information", len(self.FeatureVector))
self.nodeInformation = FeatureExtractionLib.NodeInformation(
self.dataNode, self.labelNode, self.keys)
self.FeatureVector.update(self.nodeInformation.EvaluateFeatures())
# First Order Statistics
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"First Order Statistics",
len(self.FeatureVector))
self.firstOrderStatistics = FeatureExtractionLib.FirstOrderStatistics(
self.targetVoxels, self.bins, self.numGrayLevels, self.keys)
self.FeatureVector.update(self.firstOrderStatistics.EvaluateFeatures())
# Shape/Size and Morphological Features)
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"Morphology Statistics",
len(self.FeatureVector))
# extend padding by one row/column for all 6 directions
maxDimsSA = tuple(map(operator.add, self.matrix.shape, ([2, 2, 2])))
matrixSA, matrixSACoordinates = self.padMatrix(self.matrix,
self.matrixCoordinates,
maxDimsSA,
self.targetVoxels)
self.morphologyStatistics = FeatureExtractionLib.MorphologyStatistics(
self.labelNode, matrixSA, matrixSACoordinates, self.targetVoxels,
self.keys)
self.FeatureVector.update(self.morphologyStatistics.EvaluateFeatures())
# Texture Features(GLCM)
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"GLCM Texture Features",
len(self.FeatureVector))
self.textureFeaturesGLCM = FeatureExtractionLib.TextureGLCM(
self.grayLevels, self.numGrayLevels, self.matrix,
self.matrixCoordinates, self.targetVoxels, self.keys)
self.FeatureVector.update(self.textureFeaturesGLCM.EvaluateFeatures())
# Texture Features(GLRL)
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"GLRL Texture Features",
len(self.FeatureVector))
self.textureFeaturesGLRL = FeatureExtractionLib.TextureGLRL(
self.grayLevels, self.numGrayLevels, self.matrix,
self.matrixCoordinates, self.targetVoxels, self.keys)
self.FeatureVector.update(self.textureFeaturesGLRL.EvaluateFeatures())
# Geometrical Measures
# TODO: progress bar does not update to Geometrical Measures while calculating (create separate thread?)
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"Geometrical Measures", len(self.FeatureVector))
self.geometricalMeasures = FeatureExtractionLib.GeometricalMeasures(
self.labelNode, self.matrix, self.matrixCoordinates,
self.targetVoxels, self.keys)
self.FeatureVector.update(self.geometricalMeasures.EvaluateFeatures())
# Renyi Dimensions
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"Renyi Dimensions", len(self.FeatureVector))
# extend padding to dimension lengths equal to next power of 2
maxDims = tuple(
[int(pow(2, math.ceil(numpy.log2(numpy.max(self.matrix.shape)))))
] * 3)
matrixPadded, matrixPaddedCoordinates = self.padMatrix(
self.matrix, self.matrixCoordinates, maxDims, self.targetVoxels)
self.renyiDimensions = FeatureExtractionLib.RenyiDimensions(
matrixPadded, matrixPaddedCoordinates, self.keys)
self.FeatureVector.update(self.renyiDimensions.EvaluateFeatures())
# close progress bar
self.updateProgressBar(self.progressBar, self.dataNode.GetName(),
"Populating Summary Table",
len(self.FeatureVector))
self.progressBar.close()
self.progressBar = None
# filter for user-queried features only
self.FeatureVector = collections.OrderedDict(
(k, self.FeatureVector[k]) for k in self.keys)
