class CIP_ParenchymaSubtypeTrainingWidget(ScriptedLoadableModuleWidget):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
@property
def moduleName(self):
return "CIP_ParenchymaSubtypeTraining"
def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
from functools import partial
def __onNodeAddedObserver__(self, caller, eventId, callData):
"""Node added to the Slicer scene"""
if callData.GetClassName() == 'vtkMRMLScalarVolumeNode' \
and slicer.util.mainWindow().moduleSelector().selectedModule == self.moduleName:
self.__onNewVolumeLoaded__(callData)
# elif callData.GetClassName() == 'vtkMRMLLabelMapVolumeNode':
# self.__onNewLabelmapLoaded__(callData)
self.__onNodeAddedObserver__ = partial(__onNodeAddedObserver__, self)
self.__onNodeAddedObserver__.CallDataType = vtk.VTK_OBJECT
def setup(self):
"""This is called one time when the module GUI is initialized
"""
ScriptedLoadableModuleWidget.setup(self)
# Create objects that can be used anywhere in the module. Example: in most cases there should be just one
# object of the logic class
self.logic = CIP_ParenchymaSubtypeTrainingLogic()
self.currentVolumeLoaded = None
self.blockNodeEvents = False
##########
# Main area
self.mainAreaCollapsibleButton = ctk.ctkCollapsibleButton()
self.mainAreaCollapsibleButton.text = "Main area"
self.layout.addWidget(self.mainAreaCollapsibleButton,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.mainLayout = qt.QGridLayout(self.mainAreaCollapsibleButton)
# Node selector
volumeLabel = qt.QLabel("Active volume: ")
volumeLabel.setStyleSheet("margin-left:5px")
self.mainLayout.addWidget(volumeLabel, 0, 0)
self.volumeSelector = slicer.qMRMLNodeComboBox()
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.volumeSelector.selectNodeUponCreation = True
self.volumeSelector.autoFillBackground = True
self.volumeSelector.addEnabled = False
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setFixedWidth(250)
self.volumeSelector.setStyleSheet("margin: 15px 0")
#self.volumeSelector.selectNodeUponCreation = False
self.mainLayout.addWidget(self.volumeSelector, 0, 1, 1, 3)
labelsStyle = "font-weight: bold; margin: 0 0 5px 5px;"
# Types Radio Buttons
typesLabel = qt.QLabel("Select the type")
typesLabel.setStyleSheet(labelsStyle)
typesLabel.setFixedHeight(15)
self.mainLayout.addWidget(typesLabel, 1, 0)
self.typesFrame = qt.QFrame()
self.typesLayout = qt.QVBoxLayout(self.typesFrame)
self.mainLayout.addWidget(self.typesFrame, 2, 0,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.typesRadioButtonGroup = qt.QButtonGroup()
for key in self.logic.params.mainTypes.iterkeys():
rbitem = qt.QRadioButton(self.logic.params.getMainTypeLabel(key))
self.typesRadioButtonGroup.addButton(rbitem, key)
self.typesLayout.addWidget(rbitem)
self.typesRadioButtonGroup.buttons()[0].setChecked(True)
# Subtypes Radio buttons
subtypesLabel = qt.QLabel("Select the subtype")
subtypesLabel.setStyleSheet(labelsStyle)
subtypesLabel.setFixedHeight(15)
self.mainLayout.addWidget(subtypesLabel, 1, 1)
self.subtypesRadioButtonGroup = qt.QButtonGroup()
self.subtypesFrame = qt.QFrame()
self.subtypesFrame.setMinimumHeight(275)
self.subtypesLayout = qt.QVBoxLayout(self.subtypesFrame)
self.subtypesLayout.setAlignment(SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.subtypesLayout.setStretch(0, 0)
self.mainLayout.addWidget(
self.subtypesFrame, 2, 1,
SlicerUtil.ALIGNMENT_VERTICAL_TOP) # Put the frame in the top
# The content will be loaded dynamically every time the main type is modified
# Artifact radio buttons
self.artifactsLabel = qt.QLabel("Artifact")
self.artifactsLabel.setStyleSheet(labelsStyle)
self.artifactsLabel.setFixedHeight(15)
self.mainLayout.addWidget(self.artifactsLabel, 1, 2)
#self.mainLayout.addWidget(qt.QLabel("Select the artifact"), 1, 1)
self.artifactsRadioButtonGroup = qt.QButtonGroup()
self.artifactsFrame = qt.QFrame()
self.artifactsLayout = qt.QVBoxLayout(self.artifactsFrame)
self.mainLayout.addWidget(self.artifactsFrame, 2, 2,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.artifactsRadioButtonGroup = qt.QButtonGroup()
for artifactId in self.logic.params.artifacts.iterkeys():
rbitem = qt.QRadioButton(
self.logic.params.getArtifactLabel(artifactId))
self.artifactsRadioButtonGroup.addButton(rbitem, artifactId)
self.artifactsLayout.addWidget(rbitem)
self.artifactsRadioButtonGroup.buttons()[0].setChecked(True)
# Load caselist button
self.loadButton = ctk.ctkPushButton()
self.loadButton.text = "Load fiducials file"
self.loadButton.setIcon(
qt.QIcon("{0}/open_file.png".format(SlicerUtil.CIP_ICON_DIR)))
self.loadButton.setIconSize(qt.QSize(20, 20))
self.loadButton.setFixedWidth(135)
self.mainLayout.addWidget(self.loadButton, 3, 0)
# Remove fiducial button
self.removeLastFiducialButton = ctk.ctkPushButton()
self.removeLastFiducialButton.text = "Remove last fiducial"
self.removeLastFiducialButton.toolTip = "Remove the last fiducial added"
self.removeLastFiducialButton.setIcon(
qt.QIcon("{0}/delete.png".format(SlicerUtil.CIP_ICON_DIR)))
self.removeLastFiducialButton.setIconSize(qt.QSize(20, 20))
self.removeLastFiducialButton.setFixedWidth(200)
self.mainLayout.addWidget(self.removeLastFiducialButton, 3, 1)
# Save results button
self.saveResultsButton = ctk.ctkPushButton()
self.saveResultsButton.setText("Save markups")
self.saveResultsButton.toolTip = "Save the markups in the specified directory"
self.saveResultsButton.setIcon(
qt.QIcon("{0}/Save.png".format(SlicerUtil.CIP_ICON_DIR)))
self.saveResultsButton.setIconSize(qt.QSize(20, 20))
self.mainLayout.addWidget(self.saveResultsButton, 4, 0)
# Save results directory button
defaultPath = os.path.join(
SlicerUtil.getSettingsDataFolder(self.moduleName),
"results") # Assign a default path for the results
path = SlicerUtil.settingGetOrSetDefault(self.moduleName,
"SaveResultsDirectory",
defaultPath)
self.saveResultsDirectoryButton = ctk.ctkDirectoryButton()
self.saveResultsDirectoryButton.directory = path
self.saveResultsDirectoryButton.setMaximumWidth(375)
self.mainLayout.addWidget(self.saveResultsDirectoryButton, 4, 1, 1, 2)
#####
# Case navigator
self.caseNavigatorWidget = None
if SlicerUtil.isSlicerACILLoaded():
caseNavigatorAreaCollapsibleButton = ctk.ctkCollapsibleButton()
caseNavigatorAreaCollapsibleButton.text = "Case navigator"
self.layout.addWidget(caseNavigatorAreaCollapsibleButton, 0x0020)
# caseNavigatorLayout = qt.QVBoxLayout(caseNavigatorAreaCollapsibleButton)
# Add a case list navigator
from ACIL.ui import CaseNavigatorWidget
self.caseNavigatorWidget = CaseNavigatorWidget(
self.moduleName, caseNavigatorAreaCollapsibleButton)
self.caseNavigatorWidget.setup()
# Listen for the event of loading a new labelmap
self.caseNavigatorWidget.addObservable(
self.caseNavigatorWidget.EVENT_LABELMAP_LOADED,
self.__onNewILDClassificationLabelmapLoaded__)
self.layout.addStretch()
self.updateState()
# Connections
self.typesRadioButtonGroup.connect("buttonClicked (QAbstractButton*)",
self.__onTypesRadioButtonClicked__)
self.subtypesRadioButtonGroup.connect(
"buttonClicked (QAbstractButton*)",
self.__onSubtypesRadioButtonClicked__)
self.artifactsRadioButtonGroup.connect(
"buttonClicked (QAbstractButton*)",
self.__onSubtypesRadioButtonClicked__)
self.volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.__onCurrentNodeChanged__)
self.loadButton.connect('clicked()', self.openFiducialsFile)
self.removeLastFiducialButton.connect(
'clicked()', self.__onRemoveLastFiducialButtonClicked__)
# self.saveResultsOpenDirectoryDialogButton.connect('clicked()', self.onOpenDirectoryDialogButtonClicked)
self.saveResultsDirectoryButton.connect(
"directoryChanged (QString)",
self.__onSaveResultsDirectoryChanged__)
self.saveResultsButton.connect('clicked()',
self.__onSaveResultsButtonClicked__)
self.observers = []
self.observers.append(
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent,
self.__onNodeAddedObserver__))
self.observers.append(
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent,
self.__onSceneClosed__))
def updateState(self):
""" Refresh the markups state, activate the right fiducials list node (depending on the
current selected type) and creates it when necessary
:return:
"""
# Load the subtypes for this type
subtypesDict = self.logic.getSubtypes(
self.typesRadioButtonGroup.checkedId())
# Remove all the existing buttons
for b in self.subtypesRadioButtonGroup.buttons():
b.hide()
b.delete()
# Add all the subtypes with the full description
for subtype in subtypesDict.iterkeys():
rbitem = qt.QRadioButton(
self.logic.getSubtypeFullDescription(subtype))
self.subtypesRadioButtonGroup.addButton(rbitem, subtype)
self.subtypesLayout.addWidget(rbitem,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
# Check first element by default
self.subtypesRadioButtonGroup.buttons()[0].setChecked(True)
# Set the correct state for fiducials
if self.currentVolumeLoaded is not None:
self.logic.setActiveFiducialsListNode(
self.currentVolumeLoaded,
self.typesRadioButtonGroup.checkedId(),
self.subtypesRadioButtonGroup.checkedId(),
self.artifactsRadioButtonGroup.checkedId())
def saveResultsCurrentNode(self):
""" Get current active node and save the xml fiducials file
"""
try:
d = self.saveResultsDirectoryButton.directory
if not os.path.isdir(d):
# Ask the user if he wants to create the folder
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Create directory?",
"The directory '{0}' does not exist. Do you want to create it?"
.format(d), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
try:
os.makedirs(d)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(d, 0777)
except:
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Directory incorrect',
'The folder "{0}" could not be created. Please select a valid directory'
.format(d))
return
self.logic.saveCurrentFiducials(d,
self.caseNavigatorWidget,
self.uploadFileResult)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
else:
self.logic.saveCurrentFiducials(d, self.caseNavigatorWidget,
self.uploadFileResult)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
except:
Util.print_last_exception()
qt.QMessageBox.critical(
slicer.util.mainWindow(), "Error when saving the results",
"Error when saving the results. Please review the console for additional info"
)
def uploadFileResult(self, result):
if result != Util.OK:
qt.QMessageBox.warning(
slicer.util.mainWindow(), "Error when uploading fiducials",
"There was an error when uploading the fiducials file. This doesn't mean that your file wasn't saved locally!\n"
+ "Please review the console for more information")
def openFiducialsFile(self):
volumeNode = self.volumeSelector.currentNode()
if volumeNode is None:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'Select a volume',
'Please load a volume first')
return
f = qt.QFileDialog.getOpenFileName()
if f:
self.logic.loadFiducialsXml(volumeNode, f)
self.saveResultsDirectoryButton.directory = os.path.dirname(f)
qt.QMessageBox.information(slicer.util.mainWindow(), "File loaded",
"File loaded successfully")
## PRIVATE METHODS
def __checkNewVolume__(self, newVolumeNode):
""" New volume loaded in the scene in some way.
If it's really a new volume, try to save and close the current one
@param newVolumeNode:
"""
if self.blockNodeEvents:
return
self.blockNodeEvents = True
volume = self.currentVolumeLoaded
if volume is not None and newVolumeNode is not None \
and newVolumeNode.GetID() != volume.GetID() \
and not self.logic.isVolumeSaved(volume.GetName()):
# Ask the user if he wants to save the previously loaded volume
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Save results?",
"The fiducials for the volume '{0}' have not been saved. Do you want to save them?"
.format(volume.GetName()), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
self.saveResultsCurrentNode()
# Remove all the previously existing nodes
if self.currentVolumeLoaded is not None and newVolumeNode != self.currentVolumeLoaded:
# Remove previously existing node
self.logic.removeMarkupsAndNode(self.currentVolumeLoaded)
if self.caseNavigatorWidget is not None and newVolumeNode is not None:
# Try to load a previously existing fiducials file downloaded with the ACIL case navigator
fiducialsFileName = newVolumeNode.GetName(
) + Util.file_conventions_extensions[
"ParenchymaTrainingFiducialsXml"]
fiducialsNavigatorFilePath = self.caseNavigatorWidget.logic.getFilePath(
fiducialsFileName)
if os.path.exists(fiducialsNavigatorFilePath):
# The fiducials file was downloaded with the navigator
self.logic.loadFiducialsXml(newVolumeNode,
fiducialsNavigatorFilePath)
if newVolumeNode is not None:
SlicerUtil.setActiveVolumeId(newVolumeNode.GetID())
SlicerUtil.setFiducialsCursorMode(True, True)
self.currentVolumeLoaded = newVolumeNode
self.updateState()
self.blockNodeEvents = False
def __getColorTable__(self):
""" Color table for this module for a better labelmap visualization.
This method is optimized for ILD classification, but it can easily be extended for different visualizations"""
colorTableNode = slicer.util.getNode("CIP_ILDClassification_ColorMap*")
if colorTableNode is None:
# Load the node from disk
p = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"Resources/CIP_ILDClassification_ColorMap.ctbl")
colorTableNode = slicer.modules.colors.logic().LoadColorFile(p)
return colorTableNode
## EVENTS
def enter(self):
"""This is invoked every time that we select this module as the active module in Slicer (not only the first time)"""
self.blockNodeEvents = False
# if len(self.observers) == 0:
# self.observers.append(slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, self.__onNodeAddedObserver__))
# self.observers.append(slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent, self.__onSceneClosed__))
SlicerUtil.setFiducialsCursorMode(True, True)
if self.volumeSelector.currentNodeId != "":
SlicerUtil.setActiveVolumeId(self.volumeSelector.currentNodeId)
self.currentVolumeLoaded = slicer.mrmlScene.GetNodeByID(
self.volumeSelector.currentNodeId)
self.updateState()
def exit(self):
"""This is invoked every time that we switch to another module (not only when Slicer is closed)."""
try:
self.blockNodeEvents = True
SlicerUtil.setFiducialsCursorMode(False)
# for observer in self.observers:
# slicer.mrmlScene.RemoveObserver(observer)
# self.observers.remove(observer)
except:
pass
def cleanup(self):
"""This is invoked as a destructor of the GUI when the module is no longer going to be used"""
try:
for observer in self.observers:
slicer.mrmlScene.RemoveObserver(observer)
self.observers.remove(observer)
except:
pass
def __onNewVolumeLoaded__(self, newVolumeNode):
""" Added a new node in the scene
:param newVolumeNode:
:return:
"""
# Filter the name of the volume to remove possible suffixes added by Slicer
filteredName = SlicerUtil.filterVolumeName(newVolumeNode.GetName())
newVolumeNode.SetName(filteredName)
self.__checkNewVolume__(newVolumeNode)
self.blockNodeEvents = True
self.volumeSelector.setCurrentNode(newVolumeNode)
self.blockNodeEvents = False
def __onNewILDClassificationLabelmapLoaded__(self, labelmapNode, split1,
split2):
""" Load a new ILD classification labelmap volume.
If the labelmap is a known labelmap type, set the right colors and opacity
@param labelmapNode:
"""
if SlicerUtil.isExtensionMatch(labelmapNode,
"ILDClassificationLabelmap"):
colorNode = self.__getColorTable__()
displayNode = labelmapNode.GetDisplayNode()
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
# Change Opacity
SlicerUtil.displayLabelmapVolume(labelmapNode.GetID(), 0.3)
def __onCurrentNodeChanged__(self, volumeNode):
self.__checkNewVolume__(volumeNode)
# if volumeNode:
# #self.logic.reset(volumeNode)
# SlicerUtil.setActiveVolumeId(volumeNode.GetID())
# self.updateState()
def __onTypesRadioButtonClicked__(self, button):
""" One of the radio buttons has been pressed
:param button:
:return:
"""
self.updateState()
def __onSubtypesRadioButtonClicked__(self, button):
""" One of the subtype radio buttons has been pressed
:param button:
:return:
"""
selectedVolume = self.volumeSelector.currentNode()
if selectedVolume is not None:
self.logic.setActiveFiducialsListNode(
selectedVolume, self.typesRadioButtonGroup.checkedId(),
self.subtypesRadioButtonGroup.checkedId(),
self.artifactsRadioButtonGroup.checkedId())
def __onRemoveLastFiducialButtonClicked__(self):
self.logic.removeLastMarkup()
def __onSaveResultsDirectoryChanged__(self, directory):
# f = qt.QFileDialog.getExistingDirectory()
# if f:
# self.saveResultsDirectoryText.setText(f)
SlicerUtil.setSetting(self.moduleName, "SaveResultsDirectory",
directory)
def __onSaveResultsButtonClicked__(self):
self.saveResultsCurrentNode()
def __onSceneClosed__(self, arg1, arg2):
self.currentVolumeLoaded = None
self.logic = CIP_ParenchymaSubtypeTrainingLogic()
class CIP_ParenchymaSubtypeTrainingLabellingWidget(ScriptedLoadableModuleWidget
):
"""GUI object"""
def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
# from functools import partial
# def __onNodeAddedObserver__(self, caller, eventId, callData):
# """Node added to the Slicer scene"""
# # if callData.GetClassName() == 'vtkMRMLScalarVolumeNode' \
# # and slicer.util.mainWindow().moduleSelector().selectedModule == self.moduleName:
# # self.__onNewVolumeLoaded__(callData)
# #if callData.GetClassName() == 'vtkMRMLLabelMapVolumeNode':
# self._onNewLabelmapLoaded_(callData)
#
#
# self.__onNodeAddedObserver__ = partial(__onNodeAddedObserver__, self)
# self.__onNodeAddedObserver__.CallDataType = vtk.VTK_OBJECT
self.firstLoad = True
self.activeEditorTools = None
self.pendingChangesIdsList = []
@property
def labelmapNodeNameExtension(self):
return "parenchymaTrainingLabelMap"
################
# Main methods
################
def setup(self):
"""Init the widget """
# self.firstLoad = True
ScriptedLoadableModuleWidget.setup(self)
# Create objects that can be used anywhere in the module. Example: in most cases there should be just one
# object of the logic class
self._initLogic_()
##########
# Main area
self.mainAreaCollapsibleButton = ctk.ctkCollapsibleButton()
self.mainAreaCollapsibleButton.text = "Main area"
self.layout.addWidget(self.mainAreaCollapsibleButton,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.mainLayout = qt.QGridLayout(self.mainAreaCollapsibleButton)
# Node selector
volumeLabel = qt.QLabel("Active volume: ")
volumeLabel.setStyleSheet("margin-left:5px")
self.mainLayout.addWidget(volumeLabel, 0, 0)
self.volumeSelector = slicer.qMRMLNodeComboBox()
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.volumeSelector.selectNodeUponCreation = True
self.volumeSelector.autoFillBackground = True
self.volumeSelector.addEnabled = False
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setMinimumWidth(150)
self.volumeSelector.setStyleSheet("margin: 15px 0")
# self.volumeSelector.selectNodeUponCreation = False
self.mainLayout.addWidget(self.volumeSelector, 0, 1, 1, 2)
self.volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self._onMainVolumeChanged_)
### Radio buttons frame
self.radioButtonsFrame = qt.QFrame()
self.radioButtonsLayout = qt.QHBoxLayout(self.radioButtonsFrame)
self.typesFrame = qt.QFrame()
self.radioButtonsLayout.addWidget(self.typesFrame)
self.typesLayout = qt.QVBoxLayout(self.typesFrame)
labelsStyle = "font-weight: bold; margin: 0 0 10px 0px;"
# Types Radio Buttons
typesLabel = qt.QLabel("Select type")
typesLabel.setStyleSheet(labelsStyle)
self.typesLayout.addWidget(typesLabel)
self.typesRadioButtonGroup = qt.QButtonGroup()
for key in self.logic.params.mainTypes.keys():
rbitem = qt.QRadioButton(self.logic.params.getMainTypeLabel(key))
self.typesRadioButtonGroup.addButton(rbitem, key)
self.typesLayout.addWidget(rbitem)
self.typesRadioButtonGroup.buttons()[0].setChecked(True)
# Subtypes Radio buttons
# The content will be loaded dynamically every time the main type is modified
self.subtypesFrame = qt.QFrame()
self.radioButtonsLayout.addWidget(self.subtypesFrame)
self.subtypesLayout = qt.QVBoxLayout(self.subtypesFrame)
subtypesLabel = qt.QLabel("Select subtype")
subtypesLabel.setStyleSheet(labelsStyle)
self.subtypesLayout.addWidget(subtypesLabel)
self.subtypesLayout.setAlignment(SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.subtypesRadioButtonGroup = qt.QButtonGroup()
# Add all the subtypes (we will filter later in "updateState" function)
for key in self.logic.params.subtypes.keys():
# Build the description
rbitem = qt.QRadioButton(self.logic.params.getSubtypeLabel(key))
self.subtypesRadioButtonGroup.addButton(rbitem, key)
self.subtypesLayout.addWidget(rbitem,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.subtypesLayout.addStretch()
# Region radio buttons
self.regionsFrame = qt.QFrame()
self.radioButtonsLayout.addWidget(self.regionsFrame)
self.regionsLayout = qt.QVBoxLayout(self.regionsFrame)
regionsLabel = qt.QLabel("Select region")
regionsLabel.setStyleSheet(labelsStyle)
self.regionsLayout.addWidget(regionsLabel)
self.regionsLayout.setAlignment(SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.regionsLayout.setStretch(0, 0)
self.regionsRadioButtonGroup = qt.QButtonGroup()
self.regionsFrame = qt.QFrame()
# Add all the regions
for key in self.logic.params.regions.keys():
# Build the description
rbitem = qt.QRadioButton(self.logic.params.getRegionLabel(key))
self.regionsRadioButtonGroup.addButton(rbitem, key)
self.regionsLayout.addWidget(rbitem,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.regionsLayout.addStretch()
self.regionsRadioButtonGroup.buttons()[0].setChecked(True)
# Artifact radio buttons (Add them to the same layout as the type)
# self.separatorLabel = qt.QLabel("------------")
# labelsStyle = "margin: 5px 0 5px 0;"
# self.separatorLabel.setStyleSheet(labelsStyle)
# self.typesLayout.addWidget(self.separatorLabel)
# self.artifactsLabel = qt.QLabel("Select artifact")
# labelsStyle = "font-weight: bold; margin: 15px 0 10px 0;"
# self.artifactsLabel.setStyleSheet(labelsStyle)
# self.typesLayout.addWidget(self.artifactsLabel)
# self.artifactsRadioButtonGroup = qt.QButtonGroup()
# for artifactId in self.logic.params.artifacts.iterkeys():
# rbitem = qt.QRadioButton(self.logic.params.getArtifactLabel(artifactId))
# self.artifactsRadioButtonGroup.addButton(rbitem, artifactId)
# self.typesLayout.addWidget(rbitem)
# self.artifactsRadioButtonGroup.buttons()[0].setChecked(True)
#
self.typesLayout.setAlignment(SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.typesLayout.addStretch()
# Connections
self.typesRadioButtonGroup.connect("buttonClicked (QAbstractButton*)",
self.__onTypesRadioButtonClicked__)
self.subtypesRadioButtonGroup.connect(
"buttonClicked (QAbstractButton*)",
self.__onSecondaryRadioButtonClicked__)
self.regionsRadioButtonGroup.connect(
"buttonClicked (QAbstractButton*)",
self.__onSecondaryRadioButtonClicked__)
# self.artifactsRadioButtonGroup.connect("buttonClicked (QAbstractButton*)", self.__onTypesRadioButtonClicked__)
self.mainLayout.addWidget(self.radioButtonsFrame, 2, 0, 1, 3,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
# Save results button
self.saveResultsButton = ctk.ctkPushButton()
self.saveResultsButton.setText("Save results")
self.saveResultsButton.toolTip = "Save the results labelmap in the specified directory"
self.saveResultsButton.setIcon(
qt.QIcon("{0}/Save.png".format(SlicerUtil.CIP_ICON_DIR)))
self.saveResultsButton.setIconSize(qt.QSize(20, 20))
self.saveResultsButton.setFixedWidth(135)
self.mainLayout.addWidget(self.saveResultsButton, 4, 0)
self.saveResultsButton.connect('clicked()',
self._onSaveResultsButtonClicked_)
# Save results directory button
defaultPath = os.path.join(
SlicerUtil.getSettingsDataFolder(self.moduleName),
"results") # Assign a default path for the results
path = SlicerUtil.settingGetOrSetDefault(self.moduleName,
"SaveResultsDirectory",
defaultPath)
self.saveResultsDirectoryButton = ctk.ctkDirectoryButton()
self.saveResultsDirectoryButton.directory = path
self.saveResultsDirectoryButton.setMaximumWidth(440)
self.mainLayout.addWidget(self.saveResultsDirectoryButton, 4, 1, 1, 2)
self.saveResultsDirectoryButton.connect(
"directoryChanged (QString)", self._onSaveResultsDirectoryChanged_)
self._createSegmentEditorWidget_()
# MIP viewer (by default it will be hidden)
self.mipCollapsibleButton = ctk.ctkCollapsibleButton()
self.mipCollapsibleButton.text = "MIP viewer"
mipLayout = qt.QVBoxLayout(self.mipCollapsibleButton)
self.mainLayout.addWidget(self.mipCollapsibleButton)
self.mipViewer = CIPUI.MIPViewerWidget(mipLayout)
self.mipCollapsibleButton.setVisible(False)
self.mipViewer.setup()
self.mipViewer.isCrosshairEnabled = False
self.mipCollapsibleButton.collapsed = True
#####
# Case navigator
self.caseNavigatorWidget = None
if SlicerUtil.isSlicerACILLoaded():
caseNavigatorAreaCollapsibleButton = ctk.ctkCollapsibleButton()
caseNavigatorAreaCollapsibleButton.text = "Case navigator"
self.layout.addWidget(caseNavigatorAreaCollapsibleButton, 0x0020)
# caseNavigatorLayout = qt.QVBoxLayout(caseNavigatorAreaCollapsibleButton)
# Add a case list navigator
from ACIL.ui import CaseNavigatorWidget
self.caseNavigatorWidget = CaseNavigatorWidget(
self.moduleName, caseNavigatorAreaCollapsibleButton)
self.caseNavigatorWidget.setup()
# Listen for event in order to save the current labelmap before moving to the next case
self.caseNavigatorWidget.addObservable(
self.caseNavigatorWidget.EVENT_PRE_NEXT,
self._checkSaveChanges_)
self.caseNavigatorWidget.addObservable(
self.caseNavigatorWidget.EVENT_PRE_PREVIOUS,
self._checkSaveChanges_)
self.caseNavigatorWidget.addObservable(
self.caseNavigatorWidget.EVENT_PRE_LABELMAP_LOAD,
self._onPreNavigatorLabelmapLoaded_)
self.caseNavigatorWidget.addObservable(
self.caseNavigatorWidget.EVENT_LABELMAP_LOADED,
self._onNavigatorLabelmapLoaded_)
self.layout.addStretch()
# Extra Connections
self._createSceneObservers_()
self.disableEvents = False
self.setMainTypeGUIProperties()
@property
def currentVolumeLoaded(self):
return self.volumeSelector.currentNode()
def _initLogic_(self):
"""Create a new logic object for the plugin"""
self.logic = CIP_ParenchymaSubtypeTrainingLabellingLogic()
def _createSceneObservers_(self):
"""
Create the observers for the scene in this module
"""
self.observers = []
# self.observers.append(
# slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, self.__onNodeAddedObserver__))
self.observers.append(
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent,
self.__onSceneClosed__))
def saveResultsCurrentNode(self):
""" Get current active node and save the xml fiducials file
"""
try:
d = self.saveResultsDirectoryButton.directory
if not os.path.isdir(d):
# Ask the user if he wants to create the folder
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Create directory?",
"The directory '{0}' does not exist. Do you want to create it?"
.format(d), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
try:
os.makedirs(d)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(d, 0o777)
except:
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Directory incorrect',
'The folder "{0}" could not be created. Please select a valid directory'
.format(d))
return
else:
# Abort process
SlicerUtil.logDevelop("Saving results process aborted",
includePythonConsole=True)
return
# self.logic.saveCurrentFiducials(d, self.caseNavigatorWidget, self.uploadFileResult)
# qt.QMessageBox.information(slicer.util.mainWindow(), 'Results saved',
# "The results have been saved succesfully")
# else:
if SlicerUtil.isSlicerACILLoaded():
question = qt.QMessageBox.question(
slicer.util.mainWindow(), "Save results remotely?",
"Your results will be saved locally. Do you also want to save your results in your remote server? (MAD, etc.)",
qt.QMessageBox.Yes | qt.QMessageBox.No
| qt.QMessageBox.Cancel)
if question == qt.QMessageBox.Cancel:
return
saveInRemoteRepo = question == qt.QMessageBox.Yes
else:
saveInRemoteRepo = False
self.logic.saveCurrentFiducials(
d,
caseNavigatorWidget=self.caseNavigatorWidget,
callbackFunction=self.uploadFileResult,
saveInRemoteRepo=saveInRemoteRepo)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
except:
Util.print_last_exception()
qt.QMessageBox.critical(
slicer.util.mainWindow(), "Error when saving the results",
"Error when saving the results. Please review the console for additional info"
)
def uploadFileResult(self, result):
"""Callback method that will be invoked by the CaseNavigator after uploading a file remotely"""
if result != Util.OK:
qt.QMessageBox.warning(
slicer.util.mainWindow(), "Error when uploading fiducials",
"There was an error when uploading the fiducials file. This doesn't mean that your file wasn't saved locally!\n"
+ "Please review the console for more information")
@property
def colorNode(self):
nodeName = "{}_colorNode".format(self.moduleName)
colorTableNode = SlicerUtil.getNode(nodeName)
if colorTableNode is None:
colorTableNode = self.logic.params.createColormapNode(nodeName)
return colorTableNode
def setMIPViewerVisible(self, show):
self.mipCollapsibleButton.setVisible(show)
def checkMasterAndLabelMapNodes(self):
"""Set an appropiate MasterNode LabelMapNode to the Editor.
The options are:
- There is no masterNode => try to load the one that the user is watching right now, and go on if so.
- There is masterNode and there is no label map => create a default label map node with the name "MasterNodeName_structuresDetection" and set the StructuresDetectionColorMap
- There is masterNode and there is label map => check if the name of the label map is "MasterNodeName_structuresDetection".
- If so: set this one
- Otherwise: create a new labelmap with the name 'MasterNodeName_structureslabelMap' """
if self.disableEvents: return # To avoid infinite loops
if self.editorWidget.masterVolume:
masterNode = self.editorWidget.masterVolume
SlicerUtil.logDevelop(
"Master node in Editor = " + masterNode.GetName(), True)
else:
SlicerUtil.logDevelop(
"No master node in Editor. Retrieving it from the selector...",
False)
masterNode = self.getCurrentGrayscaleNode()
if not masterNode:
# There is no any volume node that the user is watching
SlicerUtil.logDevelop("Still not master node. Exit", False)
return
labelmapNode = self.getOrCreateLabelmap(masterNode)
displayNode = labelmapNode.GetDisplayNode()
if displayNode:
displayNode.SetAndObserveColorNodeID(self.colorNode.GetID())
else:
SlicerUtil.logDevelop(
"There is no DisplayNode for label map " +
labelmapNode.GetName(), True)
slicer.app.applicationLogic().PropagateVolumeSelection(0)
SlicerUtil.changeLabelmapOpacity(0.5)
# Set the right volumes
self.disableEvents = True
#self.editorWidget.masterVolume = masterNode
#self.editorWidget.labelmapVolume = labelmapNode
# trigger editor events
self.editorWidget.helper.setVolumes(masterNode, labelmapNode)
self.disableEvents = False
slicer.app.applicationLogic().FitSliceToAll()
def getOrCreateLabelmap(self, masterNode):
labelmapName = "{0}_{1}".format(masterNode.GetName(),
self.labelmapNodeNameExtension)
labelmapNode = SlicerUtil.getNode(labelmapName)
if labelmapNode is None:
# Create a labelmap for this scalar
labelmapNode = slicer.modules.volumes.logic(
).CreateAndAddLabelVolume(slicer.mrmlScene, masterNode,
labelmapName)
# Make sure that the labelmap has this name (no suffixes)
labelmapNode.SetName(labelmapName)
# Register the labelmap in the case navigator so that it is removed when moving to another case
if SlicerUtil.isSlicerACILLoaded():
self.caseNavigatorWidget.registerVolumeId(labelmapNode.GetID())
SlicerUtil.logDevelop("New label map node created: " +
labelmapName,
includePythonConsole=True)
else:
SlicerUtil.logDevelop("Labelmap loaded", includePythonConsole=True)
return labelmapNode
def getCurrentGrayscaleNode(self):
"""Get the grayscale node that is currently active in the widget"""
#return self.editorWidget.masterVolume
return self.volumeSelector.currentNode()
def getCurrentLabelMapNode(self):
"""Get the labelmap node that is currently active in the widget"""
return self.editorWidget.labelmapVolume
def setCurrentGrayscaleNode(self, node):
"""Get the grayscale node that is currently active in the widget"""
self.editorWidget.masterVolume = node
def setCurrentLabelMapNode(self, node):
"""Get the labelmap node that is currently active in the widget"""
self.editorWidget.labelmapVolume = node
def setMainTypeGUIProperties(self):
"""Show/Hide the right Radio Buttons and set the right color for drawing based on the selected type-subtype"""
# Load the subtypes for this type
subtypesDict = self.logic.getSubtypes(
self.typesRadioButtonGroup.checkedId())
# Hide/Show the subtypes for this type
for b in self.subtypesRadioButtonGroup.buttons():
id = self.subtypesRadioButtonGroup.id(b)
if id in subtypesDict:
b.show()
else:
b.hide()
# if self.artifactsRadioButtonGroup.checkedId() == 0:
# No artifact. Check first element by default
self.subtypesRadioButtonGroup.buttons()[0].setChecked(True)
# Set the right color in the colormap
typeId = self.typesRadioButtonGroup.checkedId()
regionId = self.regionsRadioButtonGroup.checkedId()
colorId = (typeId << 8) + regionId
self.editorWidget.toolsColor.colorSpin.setValue(colorId)
self.editorWidget.setActiveEffect("PaintEffect")
def setSecondaryTypeGUIProperties(self):
subtype = self.subtypesRadioButtonGroup.checkedId()
t = self.typesRadioButtonGroup.checkedId(
) if subtype == 0 else self.subtypesRadioButtonGroup.checkedId()
# if subtype == 0:
# # Subtype "Any". Select main type
# self.editorWidget.toolsColor.colorSpin.setValue(self.typesRadioButtonGroup.checkedId())
# else:
# # Select subtype
# self.editorWidget.toolsColor.colorSpin.setValue(self.subtypesRadioButtonGroup.checkedId())
regionId = self.regionsRadioButtonGroup.checkedId()
colorId = (t << 8) + regionId
self.editorWidget.toolsColor.colorSpin.setValue(colorId)
self.editorWidget.setActiveEffect("PaintEffect")
def saveResults(self):
try:
if SlicerUtil.isSlicerACILLoaded():
saveResultsRemotely = qt.QMessageBox.question(
slicer.util.mainWindow(), "Save volume remotely?",
"Do you want to save the results remotely?",
qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes
else:
saveResultsRemotely = False
# First, save locally to the results directory (as a backup)
labelmap = self.getCurrentLabelMapNode()
localPath = os.path.join(self.saveResultsDirectoryButton.directory,
labelmap.GetName() + ".nrrd")
if saveResultsRemotely:
self.caseNavigatorWidget.uploadVolume(
labelmap,
callbackFunction=self._uploadFileCallback_,
localPath=localPath)
else:
slicer.util.saveNode(labelmap, localPath)
slicer.util.infoDisplay(
"Results saved to '{}'".format(localPath))
except Exception as ex:
Util.print_last_exception()
slicer.util.errorDisplay(ex.message)
##############
# Aux methods
##############
def _onMainVolumeChanged_(self, newVolumeNode):
""" A volume was changed in the main volume selector
:param newVolumeNode:
:return:
"""
if not self.disableEvents:
self.setCurrentGrayscaleNode(newVolumeNode)
self.checkMasterAndLabelMapNodes()
def _onPreNavigatorLabelmapLoaded_(self, volumeNodeName):
self.labelmapToBeRemoved = SlicerUtil.getNode(volumeNodeName)
def _onNavigatorLabelmapLoaded_(self, volumeNode, region, type):
"""When a labelmap is loaded in the CaseNavigator, remove possible preexisting nodes"""
if self.labelmapToBeRemoved:
slicer.mrmlScene.RemoveNode(self.labelmapToBeRemoved)
self.labelmapToBeRemoved = None
self.checkMasterAndLabelMapNodes()
def _createSegmentEditorWidget_(self):
"""Create and initialize a customize Slicer Editor which contains just some the tools that we need for the segmentation"""
import qSlicerSegmentationsModuleWidgetsPythonQt
self.segmentEditorWidget = qSlicerSegmentationsModuleWidgetsPythonQt.qMRMLSegmentEditorWidget(
)
self.segmentEditorWidget.setMaximumNumberOfUndoStates(10)
self.segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
self.segmentEditorWidget.unorderedEffectsVisible = False
self.segmentEditorWidget.setEffectNameOrder([
'Paint', 'Draw', 'Erase', 'Threshold', 'Grow from seeds',
'Scissors'
])
self.layout.addWidget(self.segmentEditorWidget)
# Collapse Volumes selector by default
#self.editorWidget.volumes.collapsed = True
# Remove current listeners for helper box and override them
#self.editorWidget.helper.masterSelector.disconnect("currentNodeChanged(vtkMRMLNode*)")
#self.editorWidget.helper.mergeSelector.disconnect("currentNodeChanged(vtkMRMLNode*)")
# Force to select always a node. It is important to do this at this point, when the events are disconnected,
# because otherwise the editor would display the color selector (just noisy for the user)
#self.editorWidget.helper.masterSelector.noneEnabled = False
# Listen to the event when there is a Master Node selected in the HelperBox
#self.editorWidget.helper.masterSelector.connect("currentNodeChanged(vtkMRMLNode*)", self._onMasterNodeSelect_)
def _collapseEditorWidget_(self, collapsed=True):
"""Collapse/expand the items in EditorWidget"""
self.editorWidget.volumes.collapsed = collapsed
self.editorWidget.editLabelMapsFrame.collapsed = collapsed
def _uploadFileCallback_(self, result):
"""
Callback after uploading a file (xml/labelmap) to the remote server
@param result:
"""
if result == Util.OK:
qt.QMessageBox.information(slicer.util.mainWindow(),
"Results saved successfully",
"Results saved successfully")
else:
qt.QMessageBox.warning(
slicer.util.mainWindow(), "Error when uploading the data",
"There was an error when uploading the results file to the remote server.\n "
"This doesn't mean that your file wasn't saved locally!\n"
"Please review the console for more information")
def _checkSaveChanges_(self):
""" New volume loaded in the scene in some way.
If it's really a new volume, try to save and close the current one
@param newVolumeNode:
"""
if self.currentVolumeLoaded is not None:
# Ask the user if he wants to save the previously loaded volume
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Save results?",
"Do you want to save changes for volume {0}?".format(
self.currentVolumeLoaded.GetName()), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
self.saveResults()
def _onClearLabelmapButtonClicked_(self):
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Clear labelmap?",
"Are you sure you want to clear the current labelmap? (THIS OPERATION CANNOT BE UNDONE)",
qt.QMessageBox.Yes | qt.QMessageBox.No) == qt.QMessageBox.Yes:
SlicerUtil.clearVolume(self.getCurrentLabelMapNode())
#########
# Events
#########
def enter(self):
"""Method that is invoked when we switch to the module in slicer user interface"""
self.disableEvents = False
if self.firstLoad:
self.firstLoad = False
else:
self.checkMasterAndLabelMapNodes()
self.editorWidget.helper.masterSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self._onMasterNodeSelect_)
def _onMasterNodeSelect_(self, node):
if node:
nodeName = node.GetName()
if self.getCurrentGrayscaleNode(
) and self.getCurrentGrayscaleNode().GetName() != nodeName:
SlicerUtil.logDevelop(
"There was a selection of a new master node: {0}. Previous: {1}. We will invoke checkMasterAndLabelMapNodes"
.format(node.GetName(),
self.editorWidget.masterVolume.GetName()),
includePythonConsole=True)
# Update Editor Master node to perform the needed actions.
# We don't use "setVolumes" function because the interface must not be refeshed yet (it will be in checkMasterAndLabelMapNodes)
self.setCurrentGrayscaleNode(node)
# Remove label node to refresh the values properly
self.setCurrentLabelMapNode(None)
self.checkMasterAndLabelMapNodes()
else:
SlicerUtil.logDevelop(
"No master node selected. Trying to remove label map", False)
self.editorWidget.cleanVolumes()
self.setMainTypeGUIProperties()
def __onTypesRadioButtonClicked__(self, button):
""" One of the radio buttons has been pressed
:param button:
:return:
"""
self.setMainTypeGUIProperties()
def __onSecondaryRadioButtonClicked__(self, button):
""" One of the subtype radio buttons has been pressed
:param button:
:return:
"""
self.setSecondaryTypeGUIProperties()
def _onSaveResultsDirectoryChanged_(self, directory):
SlicerUtil.setSetting(self.moduleName, "SaveResultsDirectory",
directory)
def _onSaveResultsButtonClicked_(self):
self.saveResults()
def __onNavigatorCaseChange__(self):
self._checkSaveChanges_()
def __onSceneClosed__(self, arg1, arg2):
self.pendingChangesIdsList = []
self.logic = CIP_ParenchymaSubtypeTrainingLabellingLogic()
def exit(self):
self.editorWidget.helper.masterSelector.disconnect(
"currentNodeChanged(vtkMRMLNode*)")
self.disableEvents = True
def cleanup(self):
pass
class CIP_PointsLabellingWidget(ScriptedLoadableModuleWidget):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
@property
def moduleName(self):
# TODO: get it from file name
return "CIP_PointsLabelling"
def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
from functools import partial
def __onNodeAddedObserver__(self, caller, eventId, callData):
"""Node added to the Slicer scene"""
if callData.GetClassName() == 'vtkMRMLScalarVolumeNode' \
and slicer.util.mainWindow().moduleSelector().selectedModule == self.moduleName:
self.__onNewVolumeLoaded__(callData)
# elif callData.GetClassName() == 'vtkMRMLLabelMapVolumeNode':
# self.__onNewLabelmapLoaded__(callData)
self.__onNodeAddedObserver__ = partial(__onNodeAddedObserver__, self)
self.__onNodeAddedObserver__.CallDataType = vtk.VTK_OBJECT
def _initLogic_(self):
"""Create a new logic object for the plugin"""
self.logic = CIP_PointsLabellingLogic()
def setup(self):
"""This is called one time when the module GUI is initialized
"""
ScriptedLoadableModuleWidget.setup(self)
# Create objects that can be used anywhere in the module. Example: in most cases there should be just one
# object of the logic class
self._initLogic_()
self.currentVolumeLoaded = None
self.blockNodeEvents = False
##########
# Main area
self.mainAreaCollapsibleButton = ctk.ctkCollapsibleButton()
self.mainAreaCollapsibleButton.text = "Main area"
self.layout.addWidget(self.mainAreaCollapsibleButton,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
self.mainLayout = qt.QGridLayout(self.mainAreaCollapsibleButton)
# Node selector
volumeLabel = qt.QLabel("Active volume: ")
volumeLabel.setStyleSheet("margin-left:5px")
self.mainLayout.addWidget(volumeLabel, 0, 0)
self.volumeSelector = slicer.qMRMLNodeComboBox()
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.volumeSelector.selectNodeUponCreation = True
self.volumeSelector.autoFillBackground = True
self.volumeSelector.addEnabled = False
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setFixedWidth(250)
self.volumeSelector.setStyleSheet("margin: 15px 0")
#self.volumeSelector.selectNodeUponCreation = False
self.mainLayout.addWidget(self.volumeSelector, 0, 1, 1, 3)
self.volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.__onCurrentNodeChanged__)
# Radio buttons frame. This will be filled by every child module
self.radioButtonsFrame = qt.QFrame()
self.mainLayout.addWidget(self.radioButtonsFrame, 2, 0, 1, 3,
SlicerUtil.ALIGNMENT_VERTICAL_TOP)
# Load caselist button
self.loadButton = ctk.ctkPushButton()
self.loadButton.text = "Load fiducials file"
self.loadButton.setIcon(
qt.QIcon("{0}/open_file.png".format(SlicerUtil.CIP_ICON_DIR)))
self.loadButton.setIconSize(qt.QSize(20, 20))
self.loadButton.setFixedWidth(135)
self.mainLayout.addWidget(self.loadButton, 3, 0)
self.loadButton.connect('clicked()', self.openFiducialsFile)
# Remove fiducial button
self.removeLastFiducialButton = ctk.ctkPushButton()
self.removeLastFiducialButton.text = "Remove last fiducial"
self.removeLastFiducialButton.toolTip = "Remove the last fiducial added"
self.removeLastFiducialButton.setIcon(
qt.QIcon("{0}/delete.png".format(SlicerUtil.CIP_ICON_DIR)))
self.removeLastFiducialButton.setIconSize(qt.QSize(20, 20))
self.removeLastFiducialButton.setFixedWidth(200)
self.mainLayout.addWidget(self.removeLastFiducialButton, 3, 1)
self.removeLastFiducialButton.connect(
'clicked()', self.__onRemoveLastFiducialButtonClicked__)
# Save results button
self.saveResultsButton = ctk.ctkPushButton()
self.saveResultsButton.setText("Save markups")
self.saveResultsButton.toolTip = "Save the markups in the specified directory"
self.saveResultsButton.setIcon(
qt.QIcon("{0}/Save.png".format(SlicerUtil.CIP_ICON_DIR)))
self.saveResultsButton.setIconSize(qt.QSize(20, 20))
self.saveResultsButton.setFixedWidth(135)
self.mainLayout.addWidget(self.saveResultsButton, 4, 0)
self.saveResultsButton.connect('clicked()',
self.__onSaveResultsButtonClicked__)
# Save results directory button
defaultPath = os.path.join(
SlicerUtil.getSettingsDataFolder(self.moduleName),
"results") # Assign a default path for the results
path = SlicerUtil.settingGetOrSetDefault(self.moduleName,
"SaveResultsDirectory",
defaultPath)
self.saveResultsDirectoryButton = ctk.ctkDirectoryButton()
self.saveResultsDirectoryButton.directory = path
self.saveResultsDirectoryButton.setMaximumWidth(375)
self.mainLayout.addWidget(self.saveResultsDirectoryButton, 4, 1, 1, 2)
self.saveResultsDirectoryButton.connect(
"directoryChanged (QString)",
self.__onSaveResultsDirectoryChanged__)
#####
# Case navigator
self.caseNavigatorWidget = None
if SlicerUtil.isSlicerACILLoaded():
caseNavigatorAreaCollapsibleButton = ctk.ctkCollapsibleButton()
caseNavigatorAreaCollapsibleButton.text = "Case navigator"
self.layout.addWidget(caseNavigatorAreaCollapsibleButton, 0x0020)
# caseNavigatorLayout = qt.QVBoxLayout(caseNavigatorAreaCollapsibleButton)
# Add a case list navigator
from ACIL.ui import CaseNavigatorWidget
self.caseNavigatorWidget = CaseNavigatorWidget(
self.moduleName, caseNavigatorAreaCollapsibleButton)
self.caseNavigatorWidget.setup()
# Listen for the event of loading a new labelmap
# self.caseNavigatorWidget.addObservable(self.caseNavigatorWidget.EVENT_LABELMAP_LOADED, self.__onNewILDClassificationLabelmapLoaded__)
self.caseNavigatorWidget.addObservable(
self.caseNavigatorWidget.EVENT_BUNDLE_CASE_FINISHED,
self.__onFinishCaseBundleLoad__)
self.layout.addStretch()
# Extra Connections
self._createSceneObservers_()
def _createSceneObservers_(self):
"""
Create the observers for the scene in this module
"""
self.observers = []
self.observers.append(
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent,
self.__onNodeAddedObserver__))
self.observers.append(
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent,
self.__onSceneClosed__))
def saveResultsCurrentNode(self):
""" Get current active node and save the xml fiducials file
"""
try:
d = self.saveResultsDirectoryButton.directory
if not os.path.isdir(d):
# Ask the user if he wants to create the folder
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Create directory?",
"The directory '{0}' does not exist. Do you want to create it?"
.format(d), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
try:
os.makedirs(d)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(d, 0777)
except:
qt.QMessageBox.warning(
slicer.util.mainWindow(), 'Directory incorrect',
'The folder "{0}" could not be created. Please select a valid directory'
.format(d))
return
else:
# Abort process
SlicerUtil.logDevelop("Saving results process aborted",
includePythonConsole=True)
return
# self.logic.saveCurrentFiducials(d, self.caseNavigatorWidget, self.uploadFileResult)
# qt.QMessageBox.information(slicer.util.mainWindow(), 'Results saved',
# "The results have been saved succesfully")
# else:
if SlicerUtil.isSlicerACILLoaded():
question = qt.QMessageBox.question(
slicer.util.mainWindow(), "Save results remotely?",
"Your results will be saved locally. Do you also want to save your results in your remote server? (MAD, etc.)",
qt.QMessageBox.Yes | qt.QMessageBox.No
| qt.QMessageBox.Cancel)
if question == qt.QMessageBox.Cancel:
return
saveInRemoteRepo = question == qt.QMessageBox.Yes
else:
saveInRemoteRepo = False
self.logic.saveCurrentFiducials(
d,
caseNavigatorWidget=self.caseNavigatorWidget,
callbackFunction=self.uploadFileResult,
saveInRemoteRepo=saveInRemoteRepo)
qt.QMessageBox.information(
slicer.util.mainWindow(), 'Results saved',
"The results have been saved succesfully")
except:
Util.print_last_exception()
qt.QMessageBox.critical(
slicer.util.mainWindow(), "Error when saving the results",
"Error when saving the results. Please review the console for additional info"
)
def uploadFileResult(self, result):
if result != Util.OK:
qt.QMessageBox.warning(
slicer.util.mainWindow(), "Error when uploading fiducials",
"There was an error when uploading the fiducials file. This doesn't mean that your file wasn't saved locally!\n"
+ "Please review the console for more information")
def openFiducialsFile(self):
volumeNode = self.volumeSelector.currentNode()
if volumeNode is None:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'Select a volume',
'Please load a volume first')
return
f = qt.QFileDialog.getOpenFileName()
if f:
self.logic.loadFiducialsXml(volumeNode, f)
self.saveResultsDirectoryButton.directory = os.path.dirname(f)
qt.QMessageBox.information(slicer.util.mainWindow(), "File loaded",
"File loaded successfully")
## PROTECTED/PRIVATE METHODS
def _checkNewVolume_(self, newVolumeNode):
""" New volume loaded in the scene in some way.
If it's really a new volume, try to save and close the current one
@param newVolumeNode:
"""
if self.blockNodeEvents:
# "Semaphore" to avoid duplicated events
return
self.blockNodeEvents = True
volume = self.currentVolumeLoaded
if volume is not None and newVolumeNode is not None \
and newVolumeNode.GetID() != volume.GetID() \
and not self.logic.isVolumeSaved(volume.GetName()):
# Ask the user if he wants to save the previously loaded volume
if qt.QMessageBox.question(
slicer.util.mainWindow(), "Save results?",
"The fiducials for the volume '{0}' have not been saved. Do you want to save them?"
.format(volume.GetName()), qt.QMessageBox.Yes
| qt.QMessageBox.No) == qt.QMessageBox.Yes:
self.saveResultsCurrentNode()
# Remove all the previously existing nodes
if self.currentVolumeLoaded is not None and newVolumeNode != self.currentVolumeLoaded:
# Remove previously existing node
self.logic.removeMarkupsAndNode(self.currentVolumeLoaded)
if newVolumeNode is not None:
SlicerUtil.setActiveVolumeIds(newVolumeNode.GetID())
SlicerUtil.setFiducialsCursorMode(True, True)
self.currentVolumeLoaded = newVolumeNode
self.updateState()
self.blockNodeEvents = False
def _getColorTable_(self):
""" Color table for this module for a better labelmap visualization.
This must be implemented by child classes"""
raise NotImplementedError(
"This method should be implemented by child classes")
## EVENTS
def enter(self):
"""This is invoked every time that we select this module as the active module in Slicer (not only the first time)"""
self.blockNodeEvents = False
# if len(self.observers) == 0:
# self.observers.append(slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, self.__onNodeAddedObserver__))
# self.observers.append(slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent, self.__onSceneClosed__))
SlicerUtil.setFiducialsCursorMode(True, True)
if self.volumeSelector.currentNodeId != "":
SlicerUtil.setActiveVolumeIds(self.volumeSelector.currentNodeId)
self.currentVolumeLoaded = slicer.mrmlScene.GetNodeByID(
self.volumeSelector.currentNodeId)
self.updateState()
def exit(self):
"""This is invoked every time that we switch to another module (not only when Slicer is closed)."""
try:
self.blockNodeEvents = True
SlicerUtil.setFiducialsCursorMode(False)
except:
pass
def cleanup(self):
"""This is invoked as a destructor of the GUI when the module is no longer going to be used"""
try:
for observer in self.observers:
slicer.mrmlScene.RemoveObserver(observer)
self.observers.remove(observer)
except:
pass
def __onNewVolumeLoaded__(self, newVolumeNode):
""" Added a new node in the scene
:param newVolumeNode:
:return:
"""
# Filter the name of the volume to remove possible suffixes added by Slicer
filteredName = SlicerUtil.filterVolumeName(newVolumeNode.GetName())
newVolumeNode.SetName(filteredName)
self._checkNewVolume_(newVolumeNode)
self.blockNodeEvents = True
self.volumeSelector.setCurrentNode(newVolumeNode)
self.blockNodeEvents = False
def __onCurrentNodeChanged__(self, volumeNode):
self._checkNewVolume_(volumeNode)
def __onFinishCaseBundleLoad__(self, result, id, ids, additionalFilePaths):
"""
Event triggered after a volume and the additional files have been loaded for a case.
In this case, it is important to load a previously existing xml file
@param result:
@param id:
@param ids:
@param additionalFilePaths:
@return:
"""
if result == Util.OK and additionalFilePaths and os.path.exists(
additionalFilePaths[0]):
# Try to load a previously existing fiducials file downloaded with the ACIL case navigator
self.logic.loadFiducialsXml(slicer.util.getNode(id),
additionalFilePaths[0])
def __onRemoveLastFiducialButtonClicked__(self):
self.logic.removeLastFiducial()
def __onSaveResultsDirectoryChanged__(self, directory):
# f = qt.QFileDialog.getExistingDirectory()
# if f:
# self.saveResultsDirectoryText.setText(f)
SlicerUtil.setSetting(self.moduleName, "SaveResultsDirectory",
directory)
def __onSaveResultsButtonClicked__(self):
self.saveResultsCurrentNode()
def __onSceneClosed__(self, arg1, arg2):
self.currentVolumeLoaded = None
self._initLogic_()
