class CIP_ParenchymaAnalysisWidget(ScriptedLoadableModuleWidget):
@property
def moduleName(self):
return os.path.basename(__file__).replace(".py", "")
def __init__(self, parent=None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.chartOptions = ("LAA%-950", "LAA%-925", "LAA%-910", "LAA%-856",
"HAA%-700", "HAA%-600", "HAA%-500", "HAA%-250",
"Perc10", "Perc15", "Mean", "Std", "Kurtosis",
"Skewness", "Ventilation Heterogeneity", "Mass",
"Volume")
# Build the column keys. Here all the columns are declared, but an alternative could be just:
#self.columnsDict = CaseReportsWidget.getColumnKeysNormalizedDictionary(["Volume Name", "Region", "LAA%-950", ...])
self.columnsDict = OrderedDict()
self.columnsDict["VolumeName"] = "Volume Name"
self.columnsDict["Region"] = "Region"
self.columnsDict["LAA950"] = "LAA%-950"
self.columnsDict["LAA925"] = "LAA%-925"
self.columnsDict["LAA910"] = "LAA%-910"
self.columnsDict["LAA856"] = "LAA%-856"
self.columnsDict["HAA700"] = "HAA%-700"
self.columnsDict["HAA600"] = "HAA%-600"
self.columnsDict["HAA500"] = "HAA%-500"
self.columnsDict["HAA250"] = "HAA%-250"
self.columnsDict["Perc10"] = "Perc10"
self.columnsDict["Perc15"] = "Perc15"
self.columnsDict["Mean"] = "Mean"
self.columnsDict["Std"] = "Std"
self.columnsDict["Kurtosis"] = "Kurtosis"
self.columnsDict["Skewness"] = "Skewness"
self.columnsDict[
"VentilationHeterogeneity"] = "Ventilation Heterogeneity"
self.columnsDict["Mass"] = "Mass"
self.columnsDict["Volume"] = "Volume"
self.rTags = ("WholeLung", "RightLung", "LeftLung", "RUL", "RLL",
"RML", "LUL", "LLL", "LUT", "LMT", "LLT", "RUT", "RMT",
"RLT")
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.logic = None
self.CTNode = None
self.labelNode = None
# self.expNode = None
# self.explabelNode = None
self.fileName = None
self.fileDialog = None
if not parent:
self.setup()
self.CTSelector.setMRMLScene(slicer.mrmlScene)
# self.expSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setMRMLScene(slicer.mrmlScene)
# self.explabelSelector.setMRMLScene(slicer.mrmlScene)
self.parent.show()
def enter(self):
if self.labelSelector.currentNode():
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID(
self.labelSelector.currentNode().GetID())
def exit(self):
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID('None')
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# the inps volume selector
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "IO Volumes"
self.parent.layout().addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
parametersFormLayout.setVerticalSpacing(5)
self.CTSelector = slicer.qMRMLNodeComboBox()
self.CTSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.CTSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.CTSelector.selectNodeUponCreation = False
self.CTSelector.addEnabled = False
self.CTSelector.removeEnabled = False
self.CTSelector.noneEnabled = True
self.CTSelector.showHidden = False
self.CTSelector.showChildNodeTypes = False
self.CTSelector.setMRMLScene(slicer.mrmlScene)
self.CTSelector.setToolTip("Pick the CT image to work on.")
parametersFormLayout.addRow("Input CT Volume: ", self.CTSelector)
#
# the label map volume selector
#
self.labelSelector = slicer.qMRMLNodeComboBox()
# self.labelSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
# self.labelSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 1 )
self.labelSelector.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.labelSelector.selectNodeUponCreation = True
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to the algorithm.")
parametersFormLayout.addRow("Label Map Volume: ", self.labelSelector)
# Image filtering section
self.preProcessingWidget = PreProcessingWidget(
self.moduleName, parentWidget=self.parent)
self.preProcessingWidget.setup()
#
# self.splitRadioButton = qt.QRadioButton()
# self.splitRadioButton.setText('Split Label Map')
# self.splitRadioButton.setChecked(0)
# self.parent.layout().addWidget(self.splitRadioButton, 0, 3)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Parenchyma Phenotypes."
self.applyButton.enabled = False
self.applyButton.setFixedSize(300, 30)
self.parent.layout().addWidget(self.applyButton, 0, 4)
# model and view for stats table
self.view = qt.QTableView()
self.view.sortingEnabled = True
self.parent.layout().addWidget(self.view)
# model and view for EXP stats table
"""self.viewexp = qt.QTableView()
self.viewexp.sortingEnabled = True
self.parent.layout().addWidget(self.viewexp)"""
# Histogram Selection
self.HistSection = qt.QFrame()
self.HistSection.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.HistSection)
self.HistSection.setObjectName('HistSection')
self.HistSection.setStyleSheet(
'#HistSection {border: 0.5px solid lightGray; }')
HistSectionTitle = qt.QLabel()
HistSectionTitle.setText('Histogram Section')
# HistSectionTitle.setStyleSheet('border: 1px solid white; color: black')
self.HistSection.layout().addWidget(HistSectionTitle)
self.histogramCheckBoxes = []
self.histFrame = qt.QFrame()
# self.histFrame.setStyleSheet('border: 1px solid white')
self.histFrame.setLayout(qt.QHBoxLayout())
self.GlobalHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.GlobalHistCheckBox)
self.histFrame.layout().addWidget(self.GlobalHistCheckBox)
self.RightHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RightHistCheckBox)
self.histFrame.layout().addWidget(self.RightHistCheckBox)
self.LeftHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LeftHistCheckBox)
self.histFrame.layout().addWidget(self.LeftHistCheckBox)
self.RULHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RULHistCheckBox)
self.histFrame.layout().addWidget(self.RULHistCheckBox)
self.RLLHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RLLHistCheckBox)
self.histFrame.layout().addWidget(self.RLLHistCheckBox)
self.RMLHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RMLHistCheckBox)
self.histFrame.layout().addWidget(self.RMLHistCheckBox)
self.LULHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LULHistCheckBox)
self.histFrame.layout().addWidget(self.LULHistCheckBox)
self.LLLHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LLLHistCheckBox)
self.histFrame.layout().addWidget(self.LLLHistCheckBox)
self.LUTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LUTHistCheckBox)
self.histFrame.layout().addWidget(self.LUTHistCheckBox)
self.LMTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LMTHistCheckBox)
self.histFrame.layout().addWidget(self.LMTHistCheckBox)
self.LLTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LLTHistCheckBox)
self.histFrame.layout().addWidget(self.LLTHistCheckBox)
self.RUTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RUTHistCheckBox)
self.histFrame.layout().addWidget(self.RUTHistCheckBox)
self.RMTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RMTHistCheckBox)
self.histFrame.layout().addWidget(self.RMTHistCheckBox)
self.RLTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RLTHistCheckBox)
self.histFrame.layout().addWidget(self.RLTHistCheckBox)
for i in xrange(len(self.histogramCheckBoxes)):
self.histogramCheckBoxes[i].setText(self.rTags[i])
self.histogramCheckBoxes[i].hide()
self.HistSection.layout().addWidget(self.histFrame)
self.HistSection.enabled = False
# Chart button
self.chartBox = qt.QFrame()
self.chartBox.setObjectName("chartBox")
self.chartBox.setStyleSheet(
'#chartBox {border: 0.5px solid lightGray;}')
self.chartBox.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.chartBox)
chartSectionTitle = qt.QLabel()
chartSectionTitle.setText('Chart Section')
self.chartBox.layout().addWidget(chartSectionTitle)
chartFrame = qt.QFrame()
chartFrame.setLayout(qt.QHBoxLayout())
self.chartBox.layout().addWidget(chartFrame)
self.chartButton = qt.QPushButton("Chart")
self.chartButton.toolTip = "Make a chart from the current statistics."
chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox()
self.chartOption.addItems(self.chartOptions)
chartFrame.layout().addWidget(self.chartOption)
self.chartBox.enabled = False
self.reportsWidget = CaseReportsWidget(self.moduleName,
self.columnsDict,
parentWidget=self.parent)
self.reportsWidget.setup()
self.reportsWidget.showPrintButton(True)
# self.reportsWidget.saveButton.enabled = False
# self.reportsWidget.openButton.enabled = False
# self.reportsWidget.exportButton.enabled = False
# self.reportsWidget.removeButton.enabled = False
# By default, the Print button is hidden
# self.reportsWidget.showPrintButton.enabled = False
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_SAVE_BUTTON_CLICKED, self.onSaveReport)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_PRINT_BUTTON_CLICKED, self.onPrintReport)
self.CTSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onCTSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
self.GlobalHistCheckBox.connect('clicked()', self.onHistogram)
self.RightHistCheckBox.connect('clicked()', self.onHistogram)
self.LeftHistCheckBox.connect('clicked()', self.onHistogram)
self.RULHistCheckBox.connect('clicked()', self.onHistogram)
self.RLLHistCheckBox.connect('clicked()', self.onHistogram)
self.RMLHistCheckBox.connect('clicked()', self.onHistogram)
self.LULHistCheckBox.connect('clicked()', self.onHistogram)
self.LLLHistCheckBox.connect('clicked()', self.onHistogram)
self.LUTHistCheckBox.connect('clicked()', self.onHistogram)
self.LMTHistCheckBox.connect('clicked()', self.onHistogram)
self.LLTHistCheckBox.connect('clicked()', self.onHistogram)
self.RUTHistCheckBox.connect('clicked()', self.onHistogram)
self.RMTHistCheckBox.connect('clicked()', self.onHistogram)
self.RLTHistCheckBox.connect('clicked()', self.onHistogram)
def cleanup(self):
self.reportsWidget.cleanup()
self.reportsWidget = None
def onCTSelect(self, node):
self.CTNode = node
self.applyButton.enabled = bool(
self.CTNode) # and bool(self.labelNode)
self.preProcessingWidget.enableFilteringFrame(bool(self.CTNode))
self.preProcessingWidget.enableLMFrame(bool(not self.labelNode))
if self.CTNode:
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID(
self.CTNode.GetID())
else:
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID('None')
def onLabelSelect(self, node):
self.labelNode = node
self.applyButton.enabled = bool(
self.CTNode) # and bool(self.labelNode)
self.preProcessingWidget.enableFilteringFrame(bool(self.CTNode))
self.preProcessingWidget.enableLMFrame(bool(not self.labelNode))
SlicerUtil.changeLabelmapOpacity(0.5)
if self.labelNode:
self.preProcessingWidget.filterApplication.setChecked(1)
self.preProcessingWidget.filterApplication.setEnabled(0)
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID(
self.labelNode.GetID())
else:
self.preProcessingWidget.filterApplication.setChecked(0)
self.preProcessingWidget.filterApplication.setEnabled(1)
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID('None')
def inputVolumesAreValid(self):
"""Verify that volumes are compatible with label calculation
algorithm assumptions"""
if not self.CTNode: # or not self.labelNode:
qt.QMessageBox.warning(slicer.util.mainWindow(),
"Parenchyma Analysis",
"Please select a CT Input Volume.")
return False
if not self.CTNode.GetImageData(
): # or not self.labelNode.GetImageData():
qt.QMessageBox.warning(slicer.util.mainWindow(),
"Parenchyma Analysis",
"Please select a CT Input Volume.")
return False
if not self.labelNode or not self.labelNode.GetImageData():
warning = self.preProcessingWidget.warningMessageForLM()
if warning == 16384:
self.createLungLabelMap()
else:
qt.QMessageBox.warning(slicer.util.mainWindow(),
"Parenchyma Analysis",
"Please select a Lung Label Map.")
return False
return True
if self.CTNode.GetImageData().GetDimensions(
) != self.labelNode.GetImageData().GetDimensions():
qt.QMessageBox.warning(
slicer.util.mainWindow(), "Parenchyma Analysis",
"Input Volumes do not have the same geometry.")
return False
# if self.preProcessingWidget.filterOnRadioButton.checked:
# self.preProcessingWidget.filterApplication.setChecked(1)
return True
def filterInputCT(self):
self.applyButton.enabled = False
self.applyButton.text = "Filtering..."
# TODO: why doesn't processEvents alone make the label text change?
self.applyButton.repaint()
slicer.app.processEvents()
self.preProcessingWidget.filterInputCT(self.CTNode)
def createLungLabelMap(self):
"""Create the lung label map
"""
self.applyButton.enabled = False
if self.preProcessingWidget.filterOnRadioButton.checked: # and not self.preProcessingWidget.filterApplication.checked:
self.filterInputCT()
inputNode = self.CTNode
self.applyButton.text = "Creating Label Map..."
# TODO: why doesn't processEvents alone make the label text change?
self.applyButton.repaint()
slicer.app.processEvents()
self.labelNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLLabelMapVolumeNode())
name = inputNode.GetName() + '_partialLungLabelMap'
self.labelNode.SetName(slicer.mrmlScene.GenerateUniqueName(name))
self.preProcessingWidget.createPartialLM(inputNode, self.labelNode)
label_image = self.labelNode.GetImageData()
shape = list(label_image.GetDimensions())
input_array = vtk.util.numpy_support.vtk_to_numpy(
label_image.GetPointData().GetScalars())
original_shape = input_array.shape
input_array = input_array.reshape(
shape[2], shape[1],
shape[0]) # input_array.transpose([2, 1, 0]) would not work!
input_image = sitk.GetImageFromArray(input_array)
input_image.SetSpacing(self.labelNode.GetSpacing())
input_image.SetOrigin(self.labelNode.GetOrigin())
my_lung_splitter = lung_splitter(split_thirds=True)
split_lm = my_lung_splitter.execute(input_image)
split = sitk.GetArrayFromImage(split_lm)
input_aa = vtk.util.numpy_support.vtk_to_numpy(
label_image.GetPointData().GetScalars())
input_aa[:] = split.reshape(original_shape)
self.labelNode.StorableModified()
self.labelNode.Modified()
self.labelNode.InvokeEvent(
slicer.vtkMRMLVolumeNode.ImageDataModifiedEvent, self.labelNode)
SlicerUtil.changeLabelmapOpacity(0.5)
def onApply(self):
"""Calculate the parenchyma analysis
"""
if not self.inputVolumesAreValid():
return
self.applyButton.enabled = False
if self.preProcessingWidget.filterOnRadioButton.checked and self.preProcessingWidget.filterApplication.checked:
self.filterInputCT()
self.applyButton.text = "Analysing..."
# TODO: why doesn't processEvents alone make the label text change?
self.applyButton.repaint()
slicer.app.processEvents()
self.logic = CIP_ParenchymaAnalysisLogic(self.CTNode, self.labelNode)
self.populateStats()
self.logic.createHistogram()
for i in xrange(len(self.histogramCheckBoxes)):
self.histogramCheckBoxes[i].setChecked(0)
self.histogramCheckBoxes[i].hide()
for tag in self.rTags:
if tag in self.logic.regionTags:
self.histogramCheckBoxes[self.rTags.index(tag)].show()
self.HistSection.enabled = True
self.chartBox.enabled = True
# self.reportsWidget.saveButton.enabled = True
# self.reportsWidget.openButton.enabled = True
# self.reportsWidget.exportButton.enabled = True
# self.reportsWidget.removeButton.enabled = True
self.applyButton.enabled = True
self.applyButton.text = "Apply"
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID(
self.CTNode.GetID())
self.labelSelector.setCurrentNode(self.labelNode)
def onHistogram(self):
"""Histogram of the selected region
"""
self.histList = []
for i in xrange(len(self.histogramCheckBoxes)):
if self.histogramCheckBoxes[i].checked == True:
self.histList.append(self.rTags[i])
self.logic.AddSelectedHistograms(self.histList)
def onChart(self):
"""chart the parenchyma analysis
"""
valueToPlot = self.chartOptions[self.chartOption.currentIndex]
self.logic.createStatsChart(self.labelNode, valueToPlot)
def onSaveReport(self):
""" Save the current values in a persistent csv file
"""
self.logic.statsAsCSV(self.reportsWidget, self.CTNode)
def onPrintReport(self):
"""
Print a pdf report
"""
emphysema_image_path, ct_slice_path = self.logic.computeEmphysemaOnSlice(
self.CTNode, self.labelNode, op=0.5)
pdfReporter = PdfReporter()
# Get the values that are going to be inserted in the html template
caseName = self.CTNode.GetName()
values = dict()
values["@@PATH_TO_STATIC@@"] = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "Resources/")
values["@@SUBJECT@@"] = "Subject: " + str(caseName)
values["@@GLOBAL_LEVEL@@"] = "{:.2f}%".format(
self.logic.labelStats['LAA%-950', 'WholeLung'])
values["@@SUMMARY@@"] = "Emphysema per region: "
pdfRows = """"""
for tag in self.logic.regionTags:
pdfRows += """<tr>
<td align="center">{} </td>
<td align="center">{:.2f} </td>
</tr>""".format(tag, self.logic.labelStats['LAA%-950', tag])
values["@@TABLE_ROWS@@"] = pdfRows
# Get the path to the html template
htmlTemplatePath = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
"Resources/CIP_ParenchymaAnalysisReport.html")
# Get a list of image absolute paths that may be needed for the report. In this case, we get the ACIL logo
imagesFileList = [SlicerUtil.ACIL_LOGO_PATH]
values["@@EMPHYSEMA_IMAGE@@"] = emphysema_image_path
values["@@CT_IMAGE@@"] = ct_slice_path
# Print the report. Remember that we can optionally specify the absolute path where the report is going to
# be stored
pdfReporter.printPdf(htmlTemplatePath,
values,
self.reportPrinted,
imagesFileList=imagesFileList)
def reportPrinted(self, reportPath):
Util.openFile(reportPath)
def onFileSelected(self, fileName):
self.logic.saveStats(fileName)
def populateStats(self):
if not self.logic:
return
displayNode = self.labelNode.GetDisplayNode()
colorNode = displayNode.GetColorNode()
lut = colorNode.GetLookupTable()
self.items = []
self.model = qt.QStandardItemModel()
self.view.setModel(self.model)
self.view.verticalHeader().visible = False
row = 0
for regionTag, regionValue in zip(self.logic.regionTags,
self.logic.regionValues):
color = qt.QColor()
rgb = lut.GetTableValue(regionValue[0])
color.setRgb(rgb[0] * 255, rgb[1] * 255, rgb[2] * 255)
item = qt.QStandardItem()
item.setData(color, 1)
item.setText(str(regionTag))
item.setData(regionTag, 1)
item.setToolTip(regionTag)
item.setTextAlignment(1)
self.model.setItem(row, 0, item)
self.items.append(item)
col = 1
for k in self.logic.keys:
item = qt.QStandardItem()
item.setText("%.3f" % self.logic.labelStats[k, regionTag])
item.setTextAlignment(4)
self.view.setColumnWidth(col, 15 * len(item.text()))
self.model.setItem(row, col, item)
self.items.append(item)
col += 1
row += 1
self.view.setColumnWidth(0, 15 * len('Region'))
self.model.setHeaderData(0, 1, "Region")
col = 1
for k in self.logic.keys:
# self.view.setColumnWidth(col,15*len(k))
self.model.setHeaderData(col, 1, k)
col += 1
class CIP_InteractiveLobeSegmentationWidget(ScriptedLoadableModuleWidget):
def __init__(self, parent=None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.logic = CIP_InteractiveLobeSegmentationLogic()
self.observerTags = []
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
# def enter(self):
# """Method that is invoked when we switch to the module in slicer user interface"""
# if self.nodeObserver is None:
# self.nodeObserver = slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, self.onNodeAdded)
# self.checkMasterAndLabelMapNodes()
def enter(self):
if self.labelSelector.currentNode():
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID(
self.labelSelector.currentNode().GetID())
def exit(self):
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID('None')
# slicer.mrmlScene.RemoveObserver(self.nodeObserver)
def setup(self):
# Instantiate and connect widgets ...
ScriptedLoadableModuleWidget.setup(self)
if SlicerUtil.IsDevelopment:
self.reloadAndTestButton.visible = False # No valid tests at the moment
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
parametersFormLayout.setVerticalSpacing(5)
#
# Input volume selector
#
self.CTSelector = slicer.qMRMLNodeComboBox()
self.CTSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.CTSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.CTSelector.selectNodeUponCreation = False
self.CTSelector.addEnabled = False
self.CTSelector.removeEnabled = False
self.CTSelector.noneEnabled = True
self.CTSelector.showHidden = False
self.CTSelector.showChildNodeTypes = False
self.CTSelector.setMRMLScene(slicer.mrmlScene)
self.CTSelector.setToolTip("Pick the CT image to work on.")
parametersFormLayout.addRow("Input CT Volume: ", self.CTSelector)
#
# First input volume selector
#
self.labelSelector = slicer.qMRMLNodeComboBox()
# self.labelSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
# self.labelSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 1 )
self.labelSelector.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.labelSelector.selectNodeUponCreation = True
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to the algorithm.")
parametersFormLayout.addRow("Label Map Volume: ", self.labelSelector)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
# self.outputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
# self.outputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 1 )
self.outputSelector.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.addEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.noneEnabled = True
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = True
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip("Pick the output to the algorithm.")
self.outputSelector.baseName = 'Fissures Segmentation Volume'
parametersFormLayout.addRow("Fissures Volume: ", self.outputSelector)
self.preProcessingWidget = PreProcessingWidget(
self.moduleName, parentWidget=self.parent)
self.preProcessingWidget.setup()
self.preProcessingWidget.filterApplication.hide()
self.preProcessingWidget.enableFilteringFrame(True)
self.preProcessingWidget.enableFilterOptions(True)
self.preProcessingWidget.enableLMFrame(True)
self.layoutCollapsibleButton = ctk.ctkCollapsibleButton()
self.layoutCollapsibleButton.text = "Layout Selection"
self.layoutCollapsibleButton.setChecked(False)
self.layoutCollapsibleButton.setFixedSize(600, 40)
self.layout.addWidget(self.layoutCollapsibleButton, 0, 4)
self.layoutFormLayout = qt.QFormLayout(self.layoutCollapsibleButton)
"""spacer = ""
for s in range( 20 ):
spacer += " """
# self.fiducialsFormLayout.setFormAlignment(4)
self.layoutGroupBox = qt.QFrame()
self.layoutGroupBox.setLayout(qt.QVBoxLayout())
self.layoutGroupBox.setFixedHeight(86)
self.layoutFormLayout.addRow(self.layoutGroupBox)
self.buttonGroupBox = qt.QFrame()
self.buttonGroupBox.setLayout(qt.QHBoxLayout())
self.layoutGroupBox.layout().addWidget(self.buttonGroupBox)
# self.layoutFormLayout.addRow(self.buttonGroupBox)
#
# Four-Up Button
#
self.fourUpButton = qt.QPushButton()
self.fourUpButton.toolTip = "Four-up view."
self.fourUpButton.enabled = True
self.fourUpButton.setFixedSize(40, 40)
fourUpIcon = qt.QIcon(":/Icons/LayoutFourUpView.png")
self.fourUpButton.setIcon(fourUpIcon)
self.buttonGroupBox.layout().addWidget(self.fourUpButton)
#
# Red Slice Button
#
self.redViewButton = qt.QPushButton()
self.redViewButton.toolTip = "Red slice only."
self.redViewButton.enabled = True
self.redViewButton.setFixedSize(40, 40)
redIcon = qt.QIcon(":/Icons/LayoutOneUpRedSliceView.png")
self.redViewButton.setIcon(redIcon)
self.buttonGroupBox.layout().addWidget(self.redViewButton)
#
# Yellow Slice Button
#
self.yellowViewButton = qt.QPushButton()
self.yellowViewButton.toolTip = "Yellow slice only."
self.yellowViewButton.enabled = True
self.yellowViewButton.setFixedSize(40, 40)
yellowIcon = qt.QIcon(":/Icons/LayoutOneUpYellowSliceView.png")
self.yellowViewButton.setIcon(yellowIcon)
self.buttonGroupBox.layout().addWidget(self.yellowViewButton)
#
# Green Slice Button
#
self.greenViewButton = qt.QPushButton()
self.greenViewButton.toolTip = "Yellow slice only."
self.greenViewButton.enabled = True
self.greenViewButton.setFixedSize(40, 40)
greenIcon = qt.QIcon(":/Icons/LayoutOneUpGreenSliceView.png")
self.greenViewButton.setIcon(greenIcon)
self.buttonGroupBox.layout().addWidget(self.greenViewButton)
#
# Buttons labels
#
self.labelsGroupBox = qt.QFrame()
hBox = qt.QHBoxLayout()
hBox.setSpacing(10)
self.labelsGroupBox.setLayout(hBox)
self.labelsGroupBox.setFixedSize(450, 26)
self.layoutGroupBox.layout().addWidget(self.labelsGroupBox, 0, 4)
fourUpLabel = qt.QLabel(" Four-up")
# fourUpLabel.setFixedHeight(10)
self.labelsGroupBox.layout().addWidget(fourUpLabel)
redLabel = qt.QLabel(" Axial")
self.labelsGroupBox.layout().addWidget(redLabel)
yellowLabel = qt.QLabel(" Saggital")
self.labelsGroupBox.layout().addWidget(yellowLabel)
greenLabel = qt.QLabel(" Coronal")
self.labelsGroupBox.layout().addWidget(greenLabel)
# Layout connections
self.fourUpButton.connect('clicked()', self.onFourUpButton)
self.redViewButton.connect('clicked()', self.onRedViewButton)
self.yellowViewButton.connect('clicked()', self.onYellowViewButton)
self.greenViewButton.connect('clicked()', self.onGreenViewButton)
#
# Fiducials Area #
self.groupBox = qt.QFrame()
self.groupBox.setLayout(qt.QHBoxLayout())
fiducialsCollapsibleButton = ctk.ctkCollapsibleButton()
fiducialsCollapsibleButton.text = "Fiducials Selection"
self.layout.addWidget(fiducialsCollapsibleButton)
self.fiducialsFormLayout = qt.QFormLayout(fiducialsCollapsibleButton)
self.fiducialsFormLayout.setVerticalSpacing(5)
self.fiducialsFormLayout.addRow(self.groupBox)
# Add fiducial lists button
self.AddLeftListButton = qt.QPushButton("Left oblique fissure")
self.AddLeftListButton.toolTip = "Create a new fiducial list for the left lung oblique fissure."
self.AddLeftListButton.setFixedHeight(40)
self.groupBox.layout().addWidget(self.AddLeftListButton)
# Add fiducial lists button
self.AddRight1ListButton = qt.QPushButton("Right oblique fissure")
self.AddRight1ListButton.toolTip = "Create a new fiducial list for the right lung oblique fissure."
self.AddRight1ListButton.setFixedHeight(40)
self.groupBox.layout().addWidget(self.AddRight1ListButton)
# Add fiducial lists button
self.AddRight2ListButton = qt.QPushButton("Right horizontal fissure")
self.AddRight2ListButton.toolTip = "Create a new fiducial list for the right lung horizontal fissure."
self.AddRight2ListButton.setFixedHeight(40)
self.groupBox.layout().addWidget(self.AddRight2ListButton)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
self.applyButton.setFixedSize(150, 45)
self.layout.addWidget(self.applyButton, 0, 4)
# self.layout.setAlignment(2)
#
# Show Fiducials
#
fiducialButtonsList = []
fiducialButtonsList.append(self.AddLeftListButton)
fiducialButtonsList.append(self.AddRight1ListButton)
fiducialButtonsList.append(self.AddRight2ListButton)
self.visualizationWidget = ILSVisualizationWidget(
self.logic, self.applyButton, fiducialButtonsList)
self.fiducialsFormLayout.addRow(self.visualizationWidget.widget)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.CTSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onCTSelect)
self.labelSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.AddLeftListButton.connect('clicked()', self.onAddLeftListButton)
self.AddRight1ListButton.connect('clicked()',
self.onAddRight1ListButton)
self.AddRight2ListButton.connect('clicked()',
self.onAddRight2ListButton)
self.updateList()
# Add vertical spacer
self.layout.addStretch(1)
def cleanup(self):
pass
def onCTSelect(self, CTNode):
if CTNode:
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID(CTNode.GetID())
else:
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID('None')
def onSelect(self):
self.layoutCollapsibleButton.setChecked(True)
if self.labelSelector.currentNode():
self.preProcessingWidget.enableFilteringFrame(False)
self.preProcessingWidget.enableLMFrame(False)
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID(
self.labelSelector.currentNode().GetID())
SlicerUtil.changeLabelmapOpacity(0.5)
else:
self.preProcessingWidget.enableFilteringFrame(True)
self.preProcessingWidget.enableLMFrame(True)
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetLabelVolumeID('None')
def onFourUpButton(self):
applicationLogic = slicer.app.applicationLogic()
interactionNode = applicationLogic.GetInteractionNode()
interactionNode.Reset(None)
interactionNode.SwitchToPersistentPlaceMode()
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(3)
def onRedViewButton(self):
applicationLogic = slicer.app.applicationLogic()
interactionNode = applicationLogic.GetInteractionNode()
interactionNode.Reset(None)
interactionNode.SwitchToPersistentPlaceMode()
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(6)
def onYellowViewButton(self):
applicationLogic = slicer.app.applicationLogic()
interactionNode = applicationLogic.GetInteractionNode()
interactionNode.Reset(None)
interactionNode.SwitchToPersistentPlaceMode()
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(7)
def onGreenViewButton(self):
applicationLogic = slicer.app.applicationLogic()
interactionNode = applicationLogic.GetInteractionNode()
interactionNode.Reset(None)
interactionNode.SwitchToPersistentPlaceMode()
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(8)
def onAddLeftListButton(self):
# self.applyButton.enabled = self.inputSelector.currentNode() and self.labelSelector.currentNode() and self.outputSelector.currentNode()
self.AddLeftListButton.setStyleSheet(
"background-color: rgb(255,99,71)")
self.AddRight1ListButton.setStyleSheet(
"background-color: rgb(255,255,255)")
self.AddRight2ListButton.setStyleSheet(
"background-color: rgb(255,255,255)")
logic = CIP_InteractiveLobeSegmentationLogic()
self.logic.name = 'LO'
logic.createList('LO')
def onAddRight1ListButton(self):
# self.applyButton.enabled = self.inputSelector.currentNode() and self.labelSelector.currentNode() and self.outputSelector.currentNode()
self.AddRight1ListButton.setStyleSheet(
"background-color: rgb(255,99,71)")
self.AddLeftListButton.setStyleSheet(
"background-color: rgb(255,255,255)")
self.AddRight2ListButton.setStyleSheet(
"background-color: rgb(255,255,255)")
logic = CIP_InteractiveLobeSegmentationLogic()
self.logic.name = 'RO'
logic.createList('RO')
def onAddRight2ListButton(self):
# self.applyButton.enabled = self.inputSelector.currentNode() and self.labelSelector.currentNode() and self.outputSelector.currentNode()
self.AddRight2ListButton.setStyleSheet(
"background-color: rgb(255,99,71)")
self.AddLeftListButton.setStyleSheet(
"background-color: rgb(255,255,255)")
self.AddRight1ListButton.setStyleSheet(
"background-color: rgb(255,255,255)")
logic = CIP_InteractiveLobeSegmentationLogic()
self.logic.name = 'RH'
logic.createList('RH')
def onApplyButton(self):
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
volumeID = red_cn.GetBackgroundVolumeID()
CTNode = SlicerUtil.getNode(volumeID)
if self.labelSelector.currentNode() == None:
warning = self.preProcessingWidget.warningMessageForLM()
if warning == 16384:
labelNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLLabelMapVolumeNode())
labelNode.SetName(CTNode.GetName() + '_partialLungLabelMap')
if not CTNode:
self.applyButton.enabled = True
return False
if self.preProcessingWidget.filterOnRadioButton.checked:
volumesLogic = slicer.modules.volumes.logic()
clonedCTNode = volumesLogic.CloneVolume(
slicer.mrmlScene, CTNode, 'Cloned Volume')
self.filterInputCT(clonedCTNode)
self.createLungLabelMap(clonedCTNode, labelNode)
slicer.mrmlScene.RemoveNode(clonedCTNode)
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(
color).sliceLogic().GetSliceCompositeNode(
).SetBackgroundVolumeID(CTNode.GetID())
else:
self.createLungLabelMap(CTNode, labelNode)
else:
qt.QMessageBox.warning(slicer.util.mainWindow(),
"Parenchyma Analysis",
"Please select a Lung Label Map.")
self.applyButton.enabled = True
return False
self.visualizationWidget.updateScene()
self.applyButton.text = "Segmenting Lobes..."
self.applyButton.repaint()
slicer.app.processEvents()
logic = CIP_InteractiveLobeSegmentationLogic()
self.visualizationWidget.pendingUpdate = True
outputNode = self.outputSelector.currentNode()
if not outputNode:
outputNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(outputNode)
fissureVolume = None
try:
fissureVolume = logic.run(self.labelSelector.currentNode(),
outputNode)
except Exception as e:
import traceback
traceback.print_exc()
qt.QMessageBox.warning(
slicer.util.mainWindow(), "Running", 'Exception!\n\n' +
str(e) + "\n\nSee Python Console for Stack Trace")
# if fissureVolume is not None:
self.outputSelector.setCurrentNode(fissureVolume)
SlicerUtil.changeLabelmapOpacity(0.5)
self.onFourUpButton()
self.applyButton.text = "Apply"
self.applyButton.repaint()
slicer.app.processEvents()
self.applyButton.enabled = True
applicationLogic = slicer.app.applicationLogic()
interactionNode = applicationLogic.GetInteractionNode()
interactionNode.Reset(None)
self.visualizationWidget.pendingUpdate = False
for color in ['Red', 'Yellow', 'Green']:
slicer.app.layoutManager().sliceWidget(color).sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID(CTNode.GetID())
slicer.app.layoutManager().sliceWidget(
color).sliceLogic().GetSliceCompositeNode().SetLabelVolumeID(
self.outputSelector.currentNode().GetID())
def filterInputCT(self, input_node):
# self.applyButton.enabled = False
self.applyButton.text = "Filtering..."
self.applyButton.repaint()
slicer.app.processEvents()
self.preProcessingWidget.filterInputCT(input_node)
def createLungLabelMap(self, input_node, label_node):
"""Create the lung label map
"""
self.applyButton.text = "Creating Label Map..."
self.applyButton.repaint()
slicer.app.processEvents()
self.preProcessingWidget.createPartialLM(input_node, label_node)
SlicerUtil.changeLabelmapOpacity(0.5)
self.labelSelector.setCurrentNode(label_node)
def updateList(self):
"""Observe the mrml scene for changes that we wish to respond to."""
tag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.EndCloseEvent,
self.clearTable)
tag = slicer.mrmlScene.AddObserver(
slicer.mrmlScene.NodeAddedEvent,
self.visualizationWidget.requestNodeAddedUpdate)
self.observerTags.append((slicer.mrmlScene, tag))
def clearTable(self, caller, event):
self.onFourUpButton()
self.visualizationWidget.tableWidget.clearContents()
self.visualizationWidget.tableWidget.setRowCount(0)
self.visualizationWidget.leftRow = 0
self.visualizationWidget.rightObliqueRow = 0
self.visualizationWidget.rightHorizontalRow = 0
self.visualizationWidget.updateScene()
self.visualizationWidget.fiducialsCollapsibleButton.hide()
self.visualizationWidget.removeFiducialObservers()