def __init__(self, widget, parent=None, **kwargs):
super().__init__(parent, **kwargs)
self.widget = widget
widget.setParent(self)
self._scraper = None
self._doc_thread = threading.Thread(target=self._create_scraper)
self._doc_thread.start()
output = qt.QTextEdit(parent=self)
output.setReadOnly(True)
clear_output = qt.QPushButton(parent=self,
text='Clear',
clicked=output.clear)
clear_output.setAutoDefault(False)
doc = qt.QTextEdit(parent=self)
members = qt.QTreeWidget(parent=self)
members.setHeaderHidden(True)
members.itemClicked.connect(partial(self._show_doc, doc))
self._populate_members(members, widget)
HBox(
self,
margin=10,
children=[
# Left side
VBox(children=[50, widget, 50, output, clear_output]),
# Right side
VBox(children=[members, doc])
])
self._connect_widget_signals(output)
def setup(self):
# TEXT
text = """
<br>
<u>Workflow quick-reference:</u><br>
<br>
The drop-down Modules are ordered to follow the basic workflow for choosing and using data. As a quick reference, the basic steps involve:<br>
<br>
1. Use the <a href="#"><b>Data importer</b></a> module to load your segmentations from FreeSurf, FSL, Autoseg, or a bunch of vtp's<br><br>
2. Use <a href="#"><b>Shape Population Viewer</b></a> to do a quality check on the imported data<br><br>
3. Use <a href="#"><b>SPHARM Shape Analysis Module</b></a> to do spherical harmonics based analysis<br><br>
4. Use the <a href="#"><b>Study-specific Shape Analysis</b></a> module.<br><br>
5. Use the <a href="#"><b>S-Rep Shape Analysis</b></a> module to do shape analysis via skeletal representations.<br><br>
6. Use the <a href="#"><b>Shape Evaluator</b></a> module to compute a mean shape and see how the population varies.<br><br>
7. Use <a href="#"><b>Shape Regressions</b></a> module to do regression based analysis.<br><br>
8. Use the <a href="#"><b>Shape Statistics</b></a> module.<br><br>
"""
# TEXTEDIT
self.HomeTextSection = qt.QTextEdit()
self.HomeTextSection.setReadOnly(True)
self.HomeTextSection.setText(text)
self.HomeTextSection.setMinimumHeight(400)
self.HomeTextSection.connect('cursorPositionChanged()', self.slot)
self.layout.addWidget(self.HomeTextSection)
# SPACER
self.layout.addStretch()
def setup(self):
samples = (
('MRHead', self.logic.downloadMRHead),
('CTChest', self.logic.downloadCTChest),
('CTACardio', self.logic.downloadCTACardio),
('DTIBrain', self.logic.downloadDTIBrain),
('MRBrainTumor Time Point 1', self.logic.downloadMRBrainTumor1),
('MRBrainTumor Time Point 2', self.logic.downloadMRBrainTumor2),
('Baseline Volume',
self.logic.downloadWhiteMatterExplorationBaselineVolume),
('DTI Volume', self.logic.downloadWhiteMatterExplorationDTIVolume),
('DWI Volume', self.logic.downloadDiffusionMRIDWIVolume),
('CTAbdomen', self.logic.downloadAbdominalCTVolume),
('CBCTDentalSurgery', self.logic.downloadDentalSurgery),
)
for sample in samples:
b = qt.QPushButton('Download %s' % sample[0])
b.setObjectName('%sPushButton' % sample[0].replace(' ', ''))
self.layout.addWidget(b)
b.connect('clicked()', sample[1])
self.log = qt.QTextEdit()
self.log.readOnly = True
self.layout.addWidget(self.log)
self.logMessage('<p>Status: <i>Idle</i>\n')
# Add spacer to layout
self.layout.addStretch(1)
def __init__(self, parent):
vLayout = qt.QVBoxLayout(parent)
formLayout = qt.QFormLayout()
self.nameEdit = qt.QLineEdit()
formLayout.addRow("Name:", self.nameEdit)
self.categoryEdit = qt.QLineEdit()
formLayout.addRow("Category:", self.categoryEdit)
self.descriptionEdit = qt.QTextEdit()
self.descriptionEdit.acceptRichText = False
formLayout.addRow("Description:", self.descriptionEdit)
self.contributorsList = EditableTreeWidget()
self.contributorsList.rootIsDecorated = False
self.contributorsList.selectionBehavior = qt.QAbstractItemView.SelectRows
self.contributorsList.selectionMode = qt.QAbstractItemView.ExtendedSelection
self.contributorsList.setHeaderLabels(["Name", "Organization"])
formLayout.addRow("Contributors:", self.contributorsList)
vLayout.addLayout(formLayout)
vLayout.addStretch(1)
self.buttonBox = qt.QDialogButtonBox()
self.buttonBox.setStandardButtons(qt.QDialogButtonBox.Ok
| qt.QDialogButtonBox.Cancel)
vLayout.addWidget(self.buttonBox)
def setup(self):
categories = slicer.modules.sampleDataSources.keys()
categories.sort()
if 'BuiltIn' in categories:
categories.remove('BuiltIn')
categories.insert(0, 'BuiltIn')
for category in categories:
frame = ctk.ctkCollapsibleGroupBox(self.parent)
self.layout.addWidget(frame)
frame.title = category
frame.name = '%sCollapsibleGroupBox' % category
layout = qt.QVBoxLayout(frame)
for source in slicer.modules.sampleDataSources[category]:
name = source.sampleName
if not name:
name = source.nodeNames[0]
b = qt.QPushButton('Download %s' % name)
b.name = '%sPushButton' % name
layout.addWidget(b)
if source.customDownloader:
b.connect('clicked()', source.customDownloader)
else:
b.connect(
'clicked()',
lambda s=source: self.logic.downloadFromSource(s))
self.log = qt.QTextEdit()
self.log.readOnly = True
self.layout.addWidget(self.log)
self.logMessage('<p>Status: <i>Idle</i>\n')
# Add spacer to layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
tests = (
('Get Sample Data', self.downloadMRHead),
('Reslicing', self.reslicing),
('Crosshair Jump', self.crosshairJump),
('Web View Test', self.webViewTest),
('Fill Out Web Form Test', self.webViewFormTest),
('Memory Check', self.memoryCheck),
)
for test in tests:
b = qt.QPushButton(test[0])
self.layout.addWidget(b)
b.connect('clicked()', test[1])
self.log = qt.QTextEdit()
self.log.readOnly = True
self.layout.addWidget(self.log)
self.log.insertHtml('<p>Status: <i>Idle</i>\n')
self.log.insertPlainText('\n')
self.log.ensureCursorVisible()
# Add spacer to layout
self.layout.addStretch(1)
def setup(self):
# TEXT
text = """
<br>
<u>Workflow quick-reference:</u><br>
<br>
The drop-down Modules are ordered to follow the basic workflow for processing DICOMS from conventional imaging modalities which are then used in optical image reconstruction. As a quick reference, the basic steps involve:<br>
<br>
1. Use the <a href="#"><b>DICOM</b></a> module to load your MRI/CT/US DICOMS<br><br>
2. Use <a href="#"><b>Volume Rendering</b></a> to view a 3D rendering of your DICOM images<br><br>
3. <a href="#"><b>Crop</b></a> the image volume to the tissue region of interest for which you will reconstruct optical images.<br><br>
4. Use the <a href="#"><b>Segment Editor</b></a> module to segment the tissue into different tissue types which can guide the optical image reconstruction routines<br><br>
5. Use the <a href="#"><b>Markups</b></a> module to place optical source and detector positions.<br><br>
6. Use the <a href="#"><b>Create Mesh</b></a> module to generate a NIRFAST-compatible mesh from the segmented tissue (label maps)<br><br>
7. After creating the mesh, follow tutorials on reconstructing optical images in the NIRFAST Matlab window<br><br>
8. Once optical properties have been reconstructed, open the resulting volumetric mesh in NIRFAST-Slicer and use the <a href="#"><b>Models</b></a> module to visualize the data overlaid on the original DICOM: in the Display menu, check 'Slice Intersections Visible' from the Visibility submenu, and select the parameters to display in the Scalars submenu.<br>
"""
# TEXTEDIT
self.HomeTextSection = qt.QTextEdit()
self.HomeTextSection.setReadOnly(True)
self.HomeTextSection.setText(text)
self.HomeTextSection.setMinimumHeight(400)
self.HomeTextSection.connect('cursorPositionChanged()', self.slot)
self.layout.addWidget(self.HomeTextSection)
# SPACER
self.layout.addStretch()
def __init__(self, parent=None, name=None, fl=0):
qt.QWidget.__init__(self, parent, name, fl)
# AsyncResult to return values
self._async_result = None
# Layout
qt.QVBoxLayout(self)
main_layout = self.layout()
main_layout.setSpacing(10)
main_layout.setMargin(6)
self.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.setCaption("GPhL Workflow parameters")
# Info box
self.info_gbox = qt.QVGroupBox("Info", self, "info_gbox")
main_layout.addWidget(self.info_gbox)
self.info_text = qt.QTextEdit(self.info_gbox, "info_text")
self.info_text.setTextFormat(0) # PlainText
self.info_text.setFont(qt.QFont("Courier"))
self.info_text.setReadOnly(True)
# Special parameter box
self.cplx_gbox = qt.QVGroupBox("Indexing solution", self, "cplx_gbox")
main_layout.addWidget(self.cplx_gbox)
self.cplx_widget = None
# Parameter box
self.parameter_gbox = qt.QVGroupBox("Parameters", self,
"parameter_gbox")
main_layout.addWidget(self.parameter_gbox)
self.params_widget = None
# Button bar
button_layout = qt.QHBoxLayout(None, 0, 6, "button_layout")
hspacer = qt.QSpacerItem(1, 20, qt.QSizePolicy.Expanding,
qt.QSizePolicy.Minimum)
button_layout.addItem(hspacer)
self.continue_button = qt.QPushButton("Continue", self,
"continue_button")
button_layout.addWidget(self.continue_button)
self.cancel_button = qt.QPushButton("Abort", self, "cancel_button")
button_layout.addWidget(self.cancel_button)
main_layout.addLayout(button_layout)
qt.QObject.connect(self.continue_button, qt.SIGNAL("clicked()"),
self.continue_button_click)
qt.QObject.connect(self.cancel_button, qt.SIGNAL("clicked()"),
self.cancel_button_click)
self.resize(qt.QSize(1018, 472).expandedTo(self.minimumSizeHint()))
self.clearWState(qt.Qt.WState_Polished)
def __init__(self, parent=None, name="log_bar_widget", fl=0):
qt.QWidget.__init__(self, parent, name, fl)
self.text_edit = qt.QTextEdit(self, "text_edit")
self.text_edit.setMinimumSize(qt.QSize(0, 55))
self.text_edit.setMaximumSize(qt.QSize(32767, 55))
self.text_edit.setTextFormat(qt.QTextEdit.RichText)
self.text_edit.setReadOnly(True)
main_layout = qt.QHBoxLayout(self)
main_layout.addWidget(self.text_edit)
def __init__(self):
self.ArduinoNode = slicer.mrmlScene.GetFirstNodeByName("arduinoNode")
sceneModifiedObserverTag = self.ArduinoNode.AddObserver(
vtk.vtkCommand.ModifiedEvent, self.addLine)
self.monitor = qt.QTextEdit()
self.monitor.setWindowTitle("Arduino monitor")
self.monitor.setReadOnly(True)
self.monitor.show()
self.messageLenghtLimit = 50
def updateSampleDataTab(self, moduleName):
currentSampleDataLogic = slicer.modules.sampledata.widgetRepresentation(
).self().logic
categoryLayout = self.sampleDataModuleTab.layout()
tutorialTextBrowser = ctk.ctkFittedTextBrowser()
tutorialTextBrowser.frameShape = qt.QFrame.NoFrame
tutorialTextBrowser.openExternalLinks = True
if moduleName == "Home":
# Tutorial link
tutorialHtml = \
"See <a href=\"https://salt.slicer.org/documentation/\">https://salt.slicer.org/documentation/</a> " \
"for overall documentation.<br/>" \
"<br/>" \
"Module specific tutorials and associated data are available in the Tutorials tab specific to each module."
# SampleData
SampleDataWidget.setCategoriesFromSampleDataSources(
categoryLayout, {}, currentSampleDataLogic)
else:
# Tutorial link
if moduleName in self.tutorials:
tutorialHtml = "Click <a href=\"%s\">here</a> to read tutorial. <br/>" % self.tutorials[
moduleName]
else:
tutorialHtml = \
"There is no tutorial for this module. " \
"Consider asking questions on the <a href=\"https://discourse.slicer.org/c/community/slicer-salt\">SlicerSALT forum</a>. <br/>"
# SampleData
if moduleName not in self.moduleNameToSampleDataCategory:
SampleDataWidget.setCategoriesFromSampleDataSources(
categoryLayout, {}, currentSampleDataLogic)
tutorialHtml += \
"<br/>" \
"There is no SampleData available for this module. <br/>"
else:
category = self.moduleNameToSampleDataCategory[moduleName]
sources = {
category: slicer.modules.sampleDataSources[category]
}
SampleDataWidget.setCategoriesFromSampleDataSources(
categoryLayout, sources, currentSampleDataLogic)
tutorialHtml += ""
# Download status
log = qt.QTextEdit()
log.readOnly = True
categoryLayout.addWidget(log)
log.insertHtml('<p>Status: <i>Idle</i></p>')
self.sampleDataTabTextEdit = log
tutorialTextBrowser.setHtml(tutorialHtml)
categoryLayout.insertWidget(0, tutorialTextBrowser)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# This module is often used in developer mode, therefore
# collapse reload & test section by default.
if hasattr(self, "reloadCollapsibleButton"):
self.reloadCollapsibleButton.collapsed = True
self.observerTags = []
self.logic = SampleDataLogic(self.logMessage)
categories = slicer.modules.sampleDataSources.keys()
categories.sort()
if 'BuiltIn' in categories:
categories.remove('BuiltIn')
categories.insert(0, 'BuiltIn')
for category in categories:
frame = ctk.ctkCollapsibleGroupBox(self.parent)
self.layout.addWidget(frame)
frame.title = category
frame.name = '%sCollapsibleGroupBox' % category
layout = qt.QVBoxLayout(frame)
for source in slicer.modules.sampleDataSources[category]:
name = source.sampleName
if not name:
name = source.nodeNames[0]
b = qt.QPushButton('Download %s' % name)
b.name = '%sPushButton' % name
layout.addWidget(b)
if source.customDownloader:
b.connect('clicked()', source.customDownloader)
else:
b.connect(
'clicked()',
lambda s=source: self.logic.downloadFromSource(s))
self.log = qt.QTextEdit()
self.log.readOnly = True
self.layout.addWidget(self.log)
self.logMessage('<p>Status: <i>Idle</i>\n')
# Add spacer to layout
self.layout.addStretch(1)
def setup(self):
samples = (
('MRHead', self.downloadMRHead),
('CTChest', self.downloadCTChest),
('CTACardio', self.downloadCTACardio),
('DTIBrain', self.downloadDTIBrain),
('MRBrainTumor Time Point 1', self.downloadMRBrainTumor1),
('MRBrainTumor Time Point 2', self.downloadMRBrainTumor2),
)
for sample in samples:
b = qt.QPushButton('Download %s' % sample[0])
self.layout.addWidget(b)
b.connect('clicked()', sample[1])
self.log = qt.QTextEdit()
self.log.readOnly = True
self.layout.addWidget(self.log)
self.logMessage('<p>Status: <i>Idle</i>\n')
# Add spacer to layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# start button
self.startServerButton = qt.QPushButton("Start server")
self.startServerButton.name = "StartWebServer"
self.startServerButton.toolTip = "Start web server with the selected options."
self.layout.addWidget(self.startServerButton)
# stop button
self.stopServerButton = qt.QPushButton("Stop server")
self.stopServerButton.name = "StopWebServer"
self.stopServerButton.toolTip = "Start web server with the selected options."
self.layout.addWidget(self.stopServerButton)
# open browser page
self.localConnectionButton = qt.QPushButton(
"Open static pages in external browser")
self.localConnectionButton.toolTip = "Open a connection to the server on the local machine with your system browser."
self.layout.addWidget(self.localConnectionButton)
# open slicer widget
self.localQtConnectionButton = qt.QPushButton(
"Open static pages in internal browser")
self.localQtConnectionButton.toolTip = "Open a connection with Qt to the server on the local machine."
self.layout.addWidget(self.localQtConnectionButton)
# log window
self.log = qt.QTextEdit()
self.log.setSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Expanding)
self.log.readOnly = True
self.layout.addWidget(self.log)
self.logMessage('<p>Status: <i>Idle</i>\n')
# clear log button
self.clearLogButton = qt.QPushButton("Clear Log")
self.clearLogButton.toolTip = "Clear the log window."
self.layout.addWidget(self.clearLogButton)
# TODO: warning dialog on first connect
# TODO: config option for port
# TODO: config option for optional plugins
# TODO: config option for certfile (https)
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.text = "Advanced"
self.layout.addWidget(self.advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(self.advancedCollapsibleButton)
self.advancedCollapsibleButton.collapsed = True
# handlers
self.enableSlicerHandler = qt.QCheckBox()
self.enableSlicerHandler.toolTip = "Enable remote control of Slicer application (stop server to change option)"
advancedFormLayout.addRow('Slicer API: ', self.enableSlicerHandler)
self.enableSlicerHandlerExec = qt.QCheckBox()
self.enableSlicerHandlerExec.toolTip = "Enable execution of arbitrary Python command using Slicer API. It only has effect if Slicer API is enabled, too (stop server to change option)."
advancedFormLayout.addRow('Slicer API exec: ',
self.enableSlicerHandlerExec)
self.enableDICOMHandler = qt.QCheckBox()
self.enableDICOMHandler.toolTip = "Enable serving Slicer DICOM database content via DICOMweb (stop server to change option)"
if hasattr(slicer.modules, "dicom"):
advancedFormLayout.addRow('DICOMweb API: ',
self.enableDICOMHandler)
self.enableStaticPagesHandler = qt.QCheckBox()
self.enableStaticPagesHandler.toolTip = "Enable serving static pages (stop server to change option)"
advancedFormLayout.addRow('Static pages: ',
self.enableStaticPagesHandler)
# log to console
self.logToConsole = qt.QCheckBox()
self.logToConsole.toolTip = "Copy log messages to the python console and parent terminal (disable to improve performance)"
advancedFormLayout.addRow('Log to Console: ', self.logToConsole)
# log to GUI
self.logToGUI = qt.QCheckBox()
self.logToGUI.toolTip = "Copy log messages to the log widget (disable to improve performance)"
advancedFormLayout.addRow('Log to GUI: ', self.logToGUI)
# Initialize GUI
self.updateGUIFromSettings()
self.updateGUIFromLogic()
# Connections
self.startServerButton.connect('clicked(bool)', self.startServer)
self.stopServerButton.connect('clicked(bool)', self.stopServer)
self.enableSlicerHandler.connect('clicked()',
self.updateHandlersFromGUI)
self.enableSlicerHandlerExec.connect('clicked()',
self.updateHandlersFromGUI)
self.enableDICOMHandler.connect('clicked()',
self.updateHandlersFromGUI)
self.enableStaticPagesHandler.connect('clicked()',
self.updateHandlersFromGUI)
self.localConnectionButton.connect('clicked()',
self.openLocalConnection)
self.localQtConnectionButton.connect('clicked()',
self.openQtLocalConnection)
self.clearLogButton.connect('clicked()', self.log.clear)
self.logToConsole.connect('clicked()', self.updateLoggingFromGUI)
self.logToGUI.connect('clicked()', self.updateLoggingFromGUI)
self.updateLoggingFromGUI()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = WebSocketLogic(self)
# Websocket
self.host = "localhost"
self.port = 8180
self.socket = None
# Instantiate and connect widgets ...
#
# Parameters Area
#
websocketCollapsibleButton = ctk.ctkCollapsibleButton()
websocketCollapsibleButton.text = "Websocket"
self.layout.addWidget(websocketCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(websocketCollapsibleButton)
#
# Apply Button
#
self.connectButton = qt.QPushButton("Connect")
self.connectButton.toolTip = "Run the algorithm."
parametersFormLayout.addRow(self.connectButton)
#
# Disconnect Button
#
self.disconnectButton = qt.QPushButton("Disconnect")
parametersFormLayout.addRow(self.disconnectButton)
#
# Python Console
#
self.pythonConsole = qt.QTextEdit()
self.pythonConsole.readOnly = True
parametersFormLayout.addRow(self.pythonConsole)
# connections
self.connectButton.connect('clicked(bool)', self.onConnectButton)
self.disconnectButton.connect('clicked(bool)', self.onDisconnectButton)
# self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
# =-=-=-=-=-=-=-=-=-= QT SOCKET =-=-=-=-=-=-=-=-=-=
# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
# Doc: http://pyqt.sourceforge.net/Docs/PyQt4/qabstractsocket.html
self.socket = qt.QTcpSocket()
self.socket.connect('connected()', self.on_connect)
self.socket.connect('disconnected()', self.on_disconnect)
self.socket.connect('hostFound()', self.on_hostFound)
self.socket.connect('readyRead()', self.handleRead)
# Need to be fixed
self.socket.connect("error( ::QAbstractSocket::SocketError)", self.on_error)
# self.socket.connect('bytesWritten()', self.on_written)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = PFileParserLogic()
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Input Volume: ", self.inputSelector)
# %%%%%%%%%%%%%%% Read PFile button section %%%%%%%%%%%%%%
# Collapsible bar
pCollapsibleBar = ctk.ctkCollapsibleButton()
pCollapsibleBar.text = "fMRSI data"
self.layout.addWidget(pCollapsibleBar)
# Layout within the sample collapsible button
formLayout = qt.QFormLayout(pCollapsibleBar)
# Frame input edit sub-layout
frameLayout = qt.QHBoxLayout(pCollapsibleBar)
pStartAtFrameText = self.createFrameText(
frameLayout, "From frame: ", 100,
"First frame to be read from fMRSI file (1 = first).")
# Add spacer
frameLayout.addStretch(1)
# Text input frame end
pStopAtFrameText = self.createFrameText(
frameLayout, "To frame: ", 100,
"Last frame to be read from fMRSI file.")
# Add horizontal frame to form layout
formLayout.addRow(frameLayout)
# ============== Buttons ==============
# Button widget code
pFileButton = qt.QPushButton("Read PFile...")
pFileButton.toolTip = "Load raw PFile (.7) data"
pFileButton.enabled = False
formLayout.addRow(pFileButton)
# =============== Radio Buttons ========
self.units = ("ppm", "hz", "points")
pUnitsBox = qt.QGroupBox("Units")
pUnitsBox.enabled = False
pUnitsBox.setLayout(qt.QFormLayout())
pUnitsButtons = {}
for units in self.units:
pUnitsButtons[units] = qt.QRadioButton()
pUnitsButtons[units].text = units
pUnitsBox.layout().addRow(pUnitsButtons[units])
self.selectedUnits = self.units[0]
pUnitsButtons[self.selectedUnits].checked = True
formLayout.addRow(pUnitsBox)
# =============== Sliders ==============
# Frame slider
pFrameSlider = ctk.ctkSliderWidget()
pFrameSlider.decimals = 0
pFrameSlider.minimum = 1
pFrameSlider.maximum = 1
pFrameSlider.enabled = False
formLayout.addRow("Frame:", pFrameSlider)
# X axis Slider
pXAxisRange = ctk.ctkRangeWidget()
pXAxisRange.enabled = False
pXAxisRange.minimum = 0.0
pXAxisRange.maximum = 0.0
formLayout.addRow("X axis range:", pXAxisRange)
# Button widget code
pPlotSpectrumButton = qt.QPushButton("Plot Spectrum...")
pPlotSpectrumButton.toolTip = "Plot mean single voxel spectrum from PFile (.7) data"
pPlotSpectrumButton.enabled = False
formLayout.addRow(pPlotSpectrumButton)
# ============== Info Text ==============
# Text Info
pInfoText = qt.QTextEdit()
pInfoText.setReadOnly(True)
pInfoText.setToolTip("Data read from fMRSI file.")
formLayout.addRow(pInfoText)
# connections
pFileButton.connect('clicked(bool)', self.onPFileButtonClicked)
pPlotSpectrumButton.connect('clicked(bool)',
self.onPlotSpectrumButtonClicked)
self.inputSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSelect)
for units in self.units:
pUnitsButtons[units].connect(
'clicked()', lambda u=units: self.onPUnitsButtonsClicked(u))
# Set local var as instance attribute
self.pFileButton = pFileButton
self.pPlotSpectrumButton = pPlotSpectrumButton
self.pInfoText = pInfoText
self.pStartAtFrameText = pStartAtFrameText
self.pStopAtFrameText = pStopAtFrameText
self.pFrameSlider = pFrameSlider
self.pXAxisRange = pXAxisRange
self.pUnitsBox = pUnitsBox
self.pUnitsButtons = pUnitsButtons
# Add spacer
self.layout.addStretch(1)
# Refresh button status
self.onSelect()
def __init__(self, parent, caption=""):
qt.QVBox.__init__(self, parent)
self.setName(caption)
self._text_edit = qt.QTextEdit(self, caption)
self._text_edit.setTextFormat(qt.Qt.LogText)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.caseInfoCollapsibleButton = ctk.ctkCollapsibleButton()
self.caseInfoCollapsibleButton.text = "Case information"
self.caseInfoCollapsibleButton.collapsed = False
self.layout.addWidget(self.caseInfoCollapsibleButton)
self.caseAreaLayout = qt.QGridLayout(self.caseInfoCollapsibleButton)
# Select case
row = 0
self.loadCaseButton = ctk.ctkPushButton()
self.loadCaseButton.text = "Load case"
self.loadCaseButton.toolTip = "Load a case folder"
self.caseAreaLayout.addWidget(self.loadCaseButton, row, 0)
# Reset button
self.resetButton = ctk.ctkPushButton()
self.resetButton.text = "Close case"
self.resetButton.toolTip = "Close the current case"
self.caseAreaLayout.addWidget(self.resetButton, row, 1)
# Case info
row += 1
self.caseInfoFrame = qt.QFrame()
self.caseInfoFrame.setFrameStyle(0x0002 | 0x0010)
self.caseInfoFrame.lineWidth = 2
self.caseInfoFrame.setStyleSheet(
"background-color: #EEEEEE; margin: 10px")
self.caseAreaLayout.addWidget(self.caseInfoFrame, row, 0, 1, 2)
self.caseInfoFrameLayout = qt.QGridLayout()
self.caseInfoFrame.setLayout(self.caseInfoFrameLayout)
self.caseIdLabel = qt.QLabel("Case id: ")
self.caseIdLabel.setStyleSheet("font-weight: bold")
self.caseInfoFrameLayout.addWidget(self.caseIdLabel, 0, 0)
self.showEnhancementCheckboxGroup = qt.QButtonGroup()
self.showJustOriginalButton = qt.QRadioButton("Original only")
self.showJustOriginalButton.setChecked(True)
self.showEnhancementCheckboxGroup.addButton(
self.showJustOriginalButton, 0)
self.caseInfoFrameLayout.addWidget(self.showJustOriginalButton, 1, 0)
self.showOriginalPlusEnhancedButton = qt.QRadioButton(
"Original and enhanced")
self.showEnhancementCheckboxGroup.addButton(
self.showOriginalPlusEnhancedButton, 1)
self.caseInfoFrameLayout.addWidget(self.showOriginalPlusEnhancedButton,
2, 0)
self.showJustEnhancedButton = qt.QRadioButton("Enhanced only")
self.showEnhancementCheckboxGroup.addButton(
self.showJustEnhancedButton, 2)
self.caseInfoFrameLayout.addWidget(self.showJustEnhancedButton, 3, 0)
# Center Volumes button
self.centerVolumesButton = ctk.ctkPushButton()
self.centerVolumesButton.text = "Center image/s"
self.centerVolumesButton.toolTip = "Center all the current visible images"
self.centerVolumesButton.setFixedWidth(200)
# self.centerVolumesButton.toolTip = "Load a case folder"
self.caseInfoFrameLayout.addWidget(self.centerVolumesButton, 4, 0)
# Enhancement fine tuning
self.vascularFactorLabel = qt.QLabel("Vascular factor")
self.vascularFactorLabel.setStyleSheet("font-weight: bold")
self.caseInfoFrameLayout.addWidget(self.vascularFactorLabel, 0, 1)
self.vascularFactorSlider = qt.QSlider()
self.vascularFactorSlider.orientation = 2 # Vertical
self.vascularFactorSlider.value = 5
self.vascularFactorSlider.minimum = 0
self.vascularFactorSlider.maximum = 10
# self.vascularFactorSlider.setStyleSheet("margin-top:10px;padding-top:20px")
# self.vascularFactorSlider.setToolTip("Move the slider for a fine tuning segmentation")
self.caseInfoFrameLayout.addWidget(self.vascularFactorSlider, 1, 1, 4,
1, 0x0004)
self.enhancementFactorLabel = qt.QLabel("Enhancement factor")
self.enhancementFactorLabel.setStyleSheet("font-weight: bold")
self.caseInfoFrameLayout.addWidget(self.enhancementFactorLabel, 0, 2)
self.enhancementFactorSlider = qt.QSlider()
self.enhancementFactorSlider.orientation = 2 # Vertical
self.enhancementFactorSlider.minimum = 0
self.enhancementFactorSlider.maximum = 10
self.enhancementFactorSlider.value = 5
# self.vascularFactorSlider.setStyleSheet("margin-top:10px;padding-top:20px")
# self.vascularFactorSlider.setToolTip("Move the slider for a fine tuning segmentation")
self.caseInfoFrameLayout.addWidget(self.enhancementFactorSlider, 1, 2,
4, 1, 0x0004)
# Editor
row += 1
self.editorWidget = ui.CustomEditorWidget(self.parent)
self.editorWidget.setup()
self.editorCollapsibleButton = self.editorWidget.editLabelMapsFrame
self.editorCollapsibleButton.text = "Edit the current eye image"
self.editorCollapsibleButton.collapsed = False
self.editorWidget.toolsColor.terminologyCollapsibleButton.setVisible(
False)
self.layout.addWidget(self.editorCollapsibleButton)
### DIAGNOSIS
self.diagnosisCollapsibleButton = ctk.ctkCollapsibleButton()
self.diagnosisCollapsibleButton.text = "Diagnosis"
self.diagnosisCollapsibleButton.collapsed = False
self.layout.addWidget(self.diagnosisCollapsibleButton)
self.diagnosisAreaLayout = qt.QVBoxLayout(
self.diagnosisCollapsibleButton)
# Visual Acuity
label = qt.QLabel("Visual acuity (VA): ")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
self.vaFrame = qt.QFrame()
self.vaFrame.setFrameStyle(0x0002 | 0x0010)
self.vaFrame.lineWidth = 2
self.vaFrame.setStyleSheet("background-color: #EEEEEE; margin: 10px")
self.vaFrame.setFixedWidth(240)
self.diagnosisAreaLayout.addWidget(self.vaFrame)
self.vaFrameLayout = qt.QGridLayout(self.vaFrame)
self.vaFrameLayout.addWidget(qt.QLabel("OS"), 0, 0)
self.osLineEdit = qt.QLineEdit()
self.osLineEdit.setFixedWidth(80)
self.osLineEdit.setStyleSheet("background-color: white")
self.vaFrameLayout.addWidget(self.osLineEdit, 0, 1)
self.vaFrameLayout.addWidget(qt.QLabel("OD"), 1, 0)
self.odLineEdit = qt.QLineEdit()
self.odLineEdit.setFixedWidth(80)
self.odLineEdit.setStyleSheet("background-color: white")
self.vaFrameLayout.addWidget(self.odLineEdit, 1, 1)
self.vaModalityButtonGroup = qt.QButtonGroup()
self.scvaRadioButton = qt.QRadioButton()
self.scvaRadioButton.setText("SCVA")
self.vaFrameLayout.addWidget(self.scvaRadioButton, 0, 2)
self.vaModalityButtonGroup.addButton(self.scvaRadioButton)
self.bcvaRadioButton = qt.QRadioButton()
self.bcvaRadioButton.setText("BCVA")
self.vaFrameLayout.addWidget(self.bcvaRadioButton, 1, 2)
self.vaModalityButtonGroup.addButton(self.bcvaRadioButton)
self.ucvaRadioButton = qt.QRadioButton()
self.ucvaRadioButton.setText("UCVA")
self.vaFrameLayout.addWidget(self.ucvaRadioButton, 2, 2)
self.vaModalityButtonGroup.addButton(self.ucvaRadioButton)
# Problems detected
label = qt.QLabel("Problems detected: ")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
self.problemsFrame = qt.QFrame()
self.problemsFrame.setFrameStyle(0x0002 | 0x0010)
self.problemsFrame.lineWidth = 2
self.problemsFrame.setStyleSheet(
"background-color: #EEEEEE; margin: 10px")
self.diagnosisAreaLayout.addWidget(self.problemsFrame)
self.problemsFrameLayout = qt.QGridLayout()
self.problemsFrame.setLayout(self.problemsFrameLayout)
self.problemsButtons = []
self.microaneurysmsCheckbox = qt.QCheckBox()
self.microaneurysmsCheckbox.setText("Microaneurysms")
self.problemsFrameLayout.addWidget(self.microaneurysmsCheckbox, 0, 0)
self.problemsButtons.append(self.microaneurysmsCheckbox)
self.exudatesCheckbox = qt.QCheckBox()
self.exudatesCheckbox.setText("Exudates")
self.problemsFrameLayout.addWidget(self.exudatesCheckbox, 0, 1)
self.problemsButtons.append(self.exudatesCheckbox)
self.haemorrhagesCheckbox = qt.QCheckBox()
self.haemorrhagesCheckbox.setText("Haemorrhages")
self.problemsFrameLayout.addWidget(self.haemorrhagesCheckbox, 0, 2)
self.problemsButtons.append(self.haemorrhagesCheckbox)
self.cottonWoolSpotsCheckbox = qt.QCheckBox()
self.cottonWoolSpotsCheckbox.setText("Cotton wool spots")
self.problemsFrameLayout.addWidget(self.cottonWoolSpotsCheckbox, 1, 0)
self.problemsButtons.append(self.cottonWoolSpotsCheckbox)
self.NeovascularisationCheckbox = qt.QCheckBox()
self.NeovascularisationCheckbox.setText("Neovascularisation")
self.problemsFrameLayout.addWidget(self.NeovascularisationCheckbox, 1,
1)
self.problemsButtons.append(self.NeovascularisationCheckbox)
label = qt.QLabel("Diabetic retinopathy diagnosis: ")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
# Diabetic Retinopathy diagnosis
self.diabeticRetinopathyDiagnosisFrame = qt.QFrame()
self.diabeticRetinopathyDiagnosisFrame.setFrameStyle(0x0002 | 0x0010)
self.diabeticRetinopathyDiagnosisFrame.lineWidth = 2
self.diabeticRetinopathyDiagnosisFrame.setStyleSheet(
"background-color: #EEEEEE; margin: 10px")
self.diagnosisAreaLayout.addWidget(
self.diabeticRetinopathyDiagnosisFrame)
self.diabeticRetinopathyDiagnosisFrameLayout = qt.QHBoxLayout()
self.diabeticRetinopathyDiagnosisFrame.setLayout(
self.diabeticRetinopathyDiagnosisFrameLayout)
self.diagnosisRadioButtonGroup = qt.QButtonGroup()
for i in range(5):
rb = qt.QRadioButton(str(i))
self.diagnosisRadioButtonGroup.addButton(rb, i)
self.diabeticRetinopathyDiagnosisFrameLayout.addWidget(rb)
self.diagnosisRadioButtonGroup.buttons()[0].setChecked(True)
# Additional comments
label = qt.QLabel("Additional comments:")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
row += 1
self.additionalCommentsText = qt.QTextEdit()
self.additionalCommentsText.setStyleSheet("margin: 10px")
self.diagnosisAreaLayout.addWidget(self.additionalCommentsText)
self.saveReportButton = ctk.ctkPushButton()
self.saveReportButton.text = "Save report"
self.saveReportButton.setFixedWidth(300)
self.diagnosisAreaLayout.addWidget(self.saveReportButton)
self.printReportButton = ctk.ctkPushButton()
self.printReportButton.text = "Save and generate PDF"
self.printReportButton.setFixedWidth(300)
self.diagnosisAreaLayout.addWidget(self.printReportButton)
self.expertModeCollapsibleButton = ctk.ctkCollapsibleButton()
self.expertModeCollapsibleButton.text = "Expert mode"
self.expertModeCollapsibleButton.collapsed = True
self.layout.addWidget(self.expertModeCollapsibleButton)
self.expertModeLayout = qt.QVBoxLayout(
self.expertModeCollapsibleButton)
self.expertModeCheckbox = qt.QCheckBox("Activate expert mode")
self.expertModeCheckbox.checked = False
self.expertModeLayout.addWidget(self.expertModeCheckbox)
self.layout.addStretch(1)
# Connections
self.loadCaseButton.connect('clicked()', self.__onLoadCaseClicked__)
# self.loadReportButton.connect('clicked()', self.__onLoadReportClicked__)
self.showEnhancementCheckboxGroup.connect(
"buttonClicked (int)", self.__onEnhancementButtonGroupClicked__)
self.centerVolumesButton.connect('clicked()',
SlicerUtil.centerAllVolumes)
self.vascularFactorSlider.connect('sliderReleased()',
self.__onEnhancementFineTuning__)
self.enhancementFactorSlider.connect('sliderReleased()',
self.__onEnhancementFineTuning__)
self.saveReportButton.connect('clicked()',
self.__onSaveReportClicked__)
self.printReportButton.connect('clicked()',
self.__onPrintReportClicked__)
self.resetButton.connect('clicked()', self.reset)
self.expertModeCheckbox.connect("stateChanged(int)",
self.__onExpertModeStateChanged__)
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent,
self.__onSceneClosed__)
# Set default layout Red
SlicerUtil.changeLayoutRedSingle()
self.refreshUI()
def create(self):
super(TraceAndSelectOptions, self).create()
## Custom threshold box
# Note: This is needed because other tools can disable, hide, or manipulate the default threshold box
# We need one unique to our tool
self.threshLabel = qt.QLabel("Threshold", self.frame)
self.threshLabel.setToolTip(
"In threshold mode, the label will only be set if the background value is within this range."
)
self.frame.layout().addWidget(self.threshLabel)
self.widgets.append(self.threshLabel)
self.thresh = ctk.ctkRangeWidget(self.frame)
self.thresh.spinBoxAlignment = 0xff # put enties on top
self.thresh.singleStep = 0.01
self.setRangeWidgetToBackgroundRange(self.thresh)
self.frame.layout().addWidget(self.thresh)
self.widgets.append(self.thresh)
## End custom threshold box
## Preview checkbox
self.preview = qt.QCheckBox("Preview outlines", self.frame)
self.preview.setToolTip(
"Preview the outline of a selection with right-click.")
self.frame.layout().addWidget(self.preview)
## End preview checkbox
self.modeButtons = qt.QButtonGroup(self.frame)
self.tissueRadioButton = qt.QRadioButton("Tissue Mode", self.frame)
self.boneRadioButton = qt.QRadioButton("Bone/Nerve Mode", self.frame)
self.hbox = qt.QHBoxLayout()
self.hbox.addWidget(self.boneRadioButton)
self.hbox.addWidget(self.tissueRadioButton)
self.frame.layout().addLayout(self.hbox)
self.modeButtons.addButton(self.boneRadioButton)
self.modeButtons.addButton(self.tissueRadioButton)
self.widgets.append(self.tissueRadioButton)
self.widgets.append(self.boneRadioButton)
## ERROR MESSAGE FRAME
self.errorMessageFrame = qt.QTextEdit(self.frame)
self.frame.layout().addWidget(self.errorMessageFrame)
#self.errorMessageFrame.setLayout(qt.QHBoxLayout)
self.errorMessageFrame.setFixedWidth(280)
self.errorMessageFrame.setReadOnly(True)
self.errorMessageFrame.setText('No Error Detected')
self.errorMessageFrame.setStyleSheet("QTextEdit {color:green}")
self.widgets.append(self.errorMessageFrame)
## END ERROR MESSAGE FRAME
## For the offset value selection process
self.offsetvalueFrame = qt.QFrame(self.frame)
self.offsetvalueFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.offsetvalueFrame)
self.widgets.append(self.offsetvalueFrame)
self.offsetvalueLabel = qt.QLabel("Offset Value:",
self.offsetvalueFrame)
self.offsetvalueLabel.setToolTip(
"Set the offset value shift upon an action")
self.offsetvalueFrame.layout().addWidget(self.offsetvalueLabel)
self.widgets.append(self.offsetvalueLabel)
self.offsetvalueSpinBox = qt.QDoubleSpinBox(self.offsetvalueFrame)
self.offsetvalueSpinBox.setToolTip(
"Set the offset value shift upon an action")
self.offsetvalueSpinBox.minimum = -1000
self.offsetvalueSpinBox.maximum = 1000
self.offsetvalueSpinBox.suffix = ""
self.offsetvalueFrame.layout().addWidget(self.offsetvalueSpinBox)
self.widgets.append(self.offsetvalueSpinBox)
## End offset value selection
self.maxPixelsFrame = qt.QFrame(self.frame)
self.maxPixelsFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.maxPixelsFrame)
self.widgets.append(self.maxPixelsFrame)
self.maxPixelsLabel = qt.QLabel("Max Pixels per click:",
self.maxPixelsFrame)
self.maxPixelsLabel.setToolTip("Set the maxPixels for each click")
self.maxPixelsFrame.layout().addWidget(self.maxPixelsLabel)
self.widgets.append(self.maxPixelsLabel)
self.maxPixelsSpinBox = qt.QDoubleSpinBox(self.maxPixelsFrame)
self.maxPixelsSpinBox.setToolTip("Set the maxPixels for each click")
self.maxPixelsSpinBox.minimum = 1
self.maxPixelsSpinBox.maximum = 100000
self.maxPixelsSpinBox.suffix = ""
self.maxPixelsFrame.layout().addWidget(self.maxPixelsSpinBox)
self.widgets.append(self.maxPixelsSpinBox)
# Help Browser
self.helpBrowser = qt.QPushButton("Visit the Webpage")
# End Help Browser
self.frame.layout().addWidget(self.helpBrowser)
HelpButton(
self.frame,
"Use this tool to help you label all voxels enclosed in an area bounded by the the largest path of pixels within the specified threshold."
)
# don't connect the signals and slots directly - instead, add these
# to the list of connections so that gui callbacks can be cleanly
# disabled while the gui is being updated. This allows several gui
# elements to be interlinked with signal/slots but still get updated
# as a unit to the new value of the mrml node.
# self.thresholdPaint.hide()
self.connections.append((self.maxPixelsSpinBox, 'valueChanged(double)',
self.onMaxPixelsSpinBoxChanged))
self.connections.append(
(self.preview, "clicked()", self.onPreviewChanged))
self.connections.append(
(self.tissueRadioButton, "clicked()", self.onTissueButtonChanged))
self.connections.append(
(self.boneRadioButton, "clicked()", self.onBoneButtonChanged))
self.connections.append(
(self.offsetvalueSpinBox, 'valueChanged(double)',
self.onOffsetValueSpinBoxChanged))
self.connections.append((self.thresh, "valuesChanged(double,double)",
self.onThreshValuesChange))
self.connections.append(
(self.helpBrowser, "clicked()", self.onHelpBrowserPressed))
# Add vertical spacer
self.frame.layout().addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
# Set up tabs to split workflow
tabsWidget = qt.QTabWidget()
curvesTab = qt.QWidget()
curvesTabLayout = qt.QFormLayout(curvesTab)
fiducialsTab = qt.QWidget()
fiducialsTabLayout = qt.QFormLayout(fiducialsTab)
batchTab = qt.QWidget()
batchTabLayout = qt.QFormLayout(batchTab)
tabsWidget.addTab(curvesTab, "Merge Curves")
tabsWidget.addTab(fiducialsTab, "Merge Landmark Sets")
tabsWidget.addTab(batchTab, "Batch Merge Landmark Sets")
self.layout.addWidget(tabsWidget)
################## Curves Tab
#
# Parameters Area
#
parametersCurveCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCurveCollapsibleButton.text = "Curve Viewer"
curvesTabLayout.addRow(parametersCurveCollapsibleButton)
# Layout within the dummy collapsible button
parametersCurveFormLayout = qt.QFormLayout(
parametersCurveCollapsibleButton)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.continuousCurvesCheckBox = qt.QCheckBox()
self.continuousCurvesCheckBox.checked = 0
self.continuousCurvesCheckBox.setToolTip(
"If checked, redundant points will be removed on merging.")
parametersCurveFormLayout.addRow("Contiuous curves",
self.continuousCurvesCheckBox)
#
# markups view
#
self.markupsView = slicer.qMRMLSubjectHierarchyTreeView()
self.markupsView.setMRMLScene(slicer.mrmlScene)
self.markupsView.setMultiSelection(True)
self.markupsView.setAlternatingRowColors(True)
self.markupsView.setDragDropMode(qt.QAbstractItemView().DragDrop)
self.markupsView.setColumnHidden(
self.markupsView.model().transformColumn, True)
self.markupsView.sortFilterProxyModel().setNodeTypes(
["vtkMRMLMarkupsCurveNode"])
parametersCurveFormLayout.addRow(self.markupsView)
#
# Merge Button
#
self.mergeButton = qt.QPushButton("Merge highlighted nodes")
self.mergeButton.toolTip = "Generate a single merged markup file from the selected nodes"
self.mergeButton.enabled = False
parametersCurveFormLayout.addRow(self.mergeButton)
# connections
self.mergeButton.connect('clicked(bool)', self.onMergeButton)
self.markupsView.connect('currentItemChanged(vtkIdType)',
self.updateMergeButton)
################ Landmark Set Tab
#
# Parameters Area
#
parametersLMCollapsibleButton = ctk.ctkCollapsibleButton()
parametersLMCollapsibleButton.text = "Landmark Viewer"
fiducialsTabLayout.addRow(parametersLMCollapsibleButton)
# Layout within the dummy collapsible button
parametersLMFormLayout = qt.QGridLayout(parametersLMCollapsibleButton)
#
# markups view
#
self.markupsFiducialView = slicer.qMRMLSubjectHierarchyTreeView()
self.markupsFiducialView.setMRMLScene(slicer.mrmlScene)
self.markupsFiducialView.setMultiSelection(True)
self.markupsFiducialView.setAlternatingRowColors(True)
self.markupsFiducialView.setDragDropMode(
qt.QAbstractItemView().DragDrop)
self.markupsFiducialView.setColumnHidden(
self.markupsView.model().transformColumn, True)
self.markupsFiducialView.sortFilterProxyModel().setNodeTypes(
["vtkMRMLMarkupsFiducialNode"])
parametersLMFormLayout.addWidget(self.markupsFiducialView, 0, 0, 1, 3)
#
# Set landmark type menu
#
boxLabel = qt.QLabel("Select landmark type description to apply: ")
self.LandmarkTypeSelection = qt.QComboBox()
self.LandmarkTypeSelection.addItems(
["Select", "Fixed", "Semi", "No description"])
parametersLMFormLayout.addWidget(boxLabel, 1, 0)
parametersLMFormLayout.addWidget(self.LandmarkTypeSelection, 1, 1)
#
# Apply Landmark Type Button
#
self.ApplyLMButton = qt.QPushButton("Apply to highlighted nodes")
self.ApplyLMButton.toolTip = "Apply the selected landmark type to points in the the selected nodes"
self.ApplyLMButton.enabled = False
parametersLMFormLayout.addWidget(self.ApplyLMButton, 1, 2)
#
# Merge Button
#
self.mergeLMButton = qt.QPushButton("Merge highlighted nodes")
self.mergeLMButton.toolTip = "Generate a single merged markup file from the selected nodes"
self.mergeLMButton.enabled = False
parametersLMFormLayout.addWidget(self.mergeLMButton, 2, 0, 1, 3)
# connections
self.mergeLMButton.connect('clicked(bool)', self.onMergeLMButton)
self.ApplyLMButton.connect('clicked(bool)', self.onApplyLMButton)
self.markupsFiducialView.connect('currentItemChanged(vtkIdType)',
self.updateMergeLMButton)
self.LandmarkTypeSelection.connect('currentIndexChanged(int)',
self.updateApplyLMButton)
################ Batch Run LM Merge Tab
#
# Fixed LM Area
#
fixedBatchCollapsibleButton = ctk.ctkCollapsibleButton()
fixedBatchCollapsibleButton.text = "Fixed LM File Selection"
batchTabLayout.addRow(fixedBatchCollapsibleButton)
# Layout within the dummy collapsible button
fixedBatchLayout = qt.QFormLayout(fixedBatchCollapsibleButton)
#
# Browse Fixed LM Button
#
self.browseFixedLMButton = qt.QPushButton("Select files...")
self.browseFixedLMButton.toolTip = "Select one fixed landmark file for each subject"
self.browseFixedLMButton.enabled = True
fixedBatchLayout.addRow(self.browseFixedLMButton)
#
# File viewer box
#
self.fixedFileTable = qt.QTextEdit()
fixedBatchLayout.addRow(self.fixedFileTable)
#
# Semi LM Area
#
semiBatchCollapsibleButton = ctk.ctkCollapsibleButton()
semiBatchCollapsibleButton.text = "Semi LM File Selection"
batchTabLayout.addRow(semiBatchCollapsibleButton)
# Layout within the dummy collapsible button
semiBatchLayout = qt.QFormLayout(semiBatchCollapsibleButton)
#
# Browse Fixed LM Button
#
self.browseSemiLMButton = qt.QPushButton("Select files...")
self.browseSemiLMButton.toolTip = "Select one semi-landmark file for each subject, in the same order as the fixed landmarks"
self.browseSemiLMButton.enabled = True
semiBatchLayout.addRow(self.browseSemiLMButton)
#
# File viewer box
#
self.semiFileTable = qt.QTextEdit()
semiBatchLayout.addRow(self.semiFileTable)
#
# Merge LM Area
#
batchMergeCollapsibleButton = ctk.ctkCollapsibleButton()
batchMergeCollapsibleButton.text = "Run merge"
batchTabLayout.addRow(batchMergeCollapsibleButton)
# Layout within the dummy collapsible button
batchMergeLayout = qt.QFormLayout(batchMergeCollapsibleButton)
#
# Select output landmark directory
#
self.outputDirectorySelector = ctk.ctkPathLineEdit()
self.outputDirectorySelector.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirectorySelector.toolTip = "Select the output directory where the merged landmark nodes will be saved"
batchMergeLayout.addRow("Select output landmark directory: ",
self.outputDirectorySelector)
#
# Batch Merge Button
#
self.batchMergeButton = qt.QPushButton(
"Merge fixed and semi-landmark nodes")
self.batchMergeButton.toolTip = "Generate a single merged markup file from the selected nodes"
self.batchMergeButton.enabled = False
batchMergeLayout.addRow(self.batchMergeButton)
#
# Clear Button
#
self.clearButton = qt.QPushButton("Clear landmark file selections")
self.clearButton.toolTip = "Clear the landmark files selected in the viewer boxes"
self.clearButton.enabled = False
batchMergeLayout.addRow(self.clearButton)
# connections
self.browseFixedLMButton.connect('clicked(bool)',
self.addFixedByBrowsing)
self.browseSemiLMButton.connect('clicked(bool)',
self.addSemiByBrowsing)
self.outputDirectorySelector.connect('validInputChanged(bool)',
self.onSelectDirectory)
self.batchMergeButton.connect('clicked(bool)', self.onBatchMergeButton)
self.clearButton.connect('clicked(bool)', self.onClearButton)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# This module is often used in developer mode, therefore
# collapse reload & test section by default.
if hasattr(self, "reloadCollapsibleButton"):
self.reloadCollapsibleButton.collapsed = True
self.observerTags = []
self.logic = SampleDataLogic(self.logMessage)
numberOfColumns = 3
iconPath = os.path.join(
os.path.dirname(__file__).replace('\\', '/'), 'Resources', 'Icons')
desktop = qt.QDesktopWidget()
mainScreenSize = desktop.availableGeometry(desktop.primaryScreen)
iconSize = qt.QSize(mainScreenSize.width() / 15,
mainScreenSize.height() / 10)
categories = slicer.modules.sampleDataSources.keys()
categories.sort()
if 'BuiltIn' in categories:
categories.remove('BuiltIn')
categories.insert(0, 'BuiltIn')
for category in categories:
frame = ctk.ctkCollapsibleGroupBox(self.parent)
self.layout.addWidget(frame)
frame.title = category
frame.name = '%sCollapsibleGroupBox' % category
layout = qt.QGridLayout(frame)
columnIndex = 0
rowIndex = 0
for source in slicer.modules.sampleDataSources[category]:
name = source.sampleName
if not name:
name = source.nodeNames[0]
b = qt.QToolButton()
b.setText(name)
# Set thumbnail
if source.thumbnailFileName:
# Thumbnail provided
thumbnailImage = source.thumbnailFileName
else:
# Look for thumbnail image with the name of any node name with .png extension
thumbnailImage = None
for nodeName in source.nodeNames:
if not nodeName:
continue
thumbnailImageAttempt = os.path.join(
iconPath, nodeName + '.png')
if os.path.exists(thumbnailImageAttempt):
thumbnailImage = thumbnailImageAttempt
break
if thumbnailImage and os.path.exists(thumbnailImage):
b.setIcon(qt.QIcon(thumbnailImage))
b.setIconSize(iconSize)
b.setToolButtonStyle(qt.Qt.ToolButtonTextUnderIcon)
qSize = qt.QSizePolicy()
qSize.setHorizontalPolicy(qt.QSizePolicy.Expanding)
b.setSizePolicy(qSize)
b.name = '%sPushButton' % name
layout.addWidget(b, rowIndex, columnIndex)
columnIndex += 1
if columnIndex == numberOfColumns:
rowIndex += 1
columnIndex = 0
if source.customDownloader:
b.connect('clicked()', source.customDownloader)
else:
b.connect(
'clicked()',
lambda s=source: self.logic.downloadFromSource(s))
self.log = qt.QTextEdit()
self.log.readOnly = True
self.layout.addWidget(self.log)
self.logMessage('<p>Status: <i>Idle</i>\n')
# Add spacer to layout
self.layout.addStretch(1)
def _createTextEdit(self, title, **kwargs): textEdit = qt.QTextEdit(title) return self._extendQtGuiElementProperties(textEdit, **kwargs)
