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 i in self.logic.labelStats["Labels"]:
color = qt.QColor()
rgb = lut.GetTableValue(i)
color.setRgb(rgb[0] * 255, rgb[1] * 255, rgb[2] * 255)
item = qt.QStandardItem()
item.setData(color, qt.Qt.DecorationRole)
item.setToolTip(colorNode.GetColorName(i))
self.model.setItem(row, 0, item)
self.items.append(item)
col = 1
for k in self.logic.keys:
item = qt.QStandardItem()
# set data as float with Qt::DisplayRole
item.setData(float(self.logic.labelStats[i, k]),
qt.Qt.DisplayRole)
item.setToolTip(colorNode.GetColorName(i))
self.model.setItem(row, col, item)
self.items.append(item)
col += 1
row += 1
self.view.setColumnWidth(0, 30)
self.model.setHeaderData(0, 1, " ")
col = 1
for k in self.logic.keys:
self.view.setColumnWidth(col, 15 * len(k))
self.model.setHeaderData(col, 1, k)
col += 1
def populateStats(self):
if not self.logic:
return
#displayNode = self.labelNode.GetNthDataNode(0).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 i in self.logic.labelStats["Labels"]:
color = qt.QColor()
# rgb = lut.GetTableValue(i)
color.setRgb(255, 0, 0)
item = qt.QStandardItem()
item.setData(color, 1)
# item.setToolTip(colorNode.GetColorName(i))
self.model.setItem(row, 0, item)
self.items.append(item)
col = 1
for k in self.logic.keys:
item = qt.QStandardItem()
item.setText(str(self.logic.labelStats[i, k]))
# item.setToolTip(colorNode.GetColorName(i))
self.model.setItem(row, col, item)
self.items.append(item)
col += 1
row += 1
self.view.setColumnWidth(0, 30)
self.model.setHeaderData(0, 1, " ")
col = 1
for k in self.logic.keys:
self.view.setColumnWidth(col, 15 * len(k))
self.model.setHeaderData(col, 1, k)
col += 1
def populateStatistics(self, FeatureVectors):
if not (FeatureVectors):
return
self.items = []
self.model = qt.QStandardItemModel()
self.view.setModel(self.model)
self.view.verticalHeader().visible = False
row = 0
col = 0
wholeNumberKeys = ['Voxel Count', 'Gray Levels', 'Minimum Intensity', 'Maximum Intensity', 'Median Intensity', 'Range']
precisionOnlyKeys = ['Entropy', 'Volume mm^3', 'Volume cc', 'Mean Intensity', 'Mean Deviation', 'Root Mean Square', 'Standard Deviation', 'Surface Area mm^3']
for featureVector in FeatureVectors:
col = 0
for feature in featureVector:
item = qt.QStandardItem()
value = featureVector[feature]
featureFormatted = value
# add formatting here
item.setText(str(featureFormatted))
item.setToolTip(feature)
self.model.setItem(row,col,item)
self.items.append(item)
col += 1
row += 1
self.view.setColumnWidth(0,30)
self.model.setHeaderData(0,1," ")
# set table headers
col = 0
for feature in FeatureVectors[0]:
self.view.setColumnWidth(col,15*len(feature))
self.model.setHeaderData(col,1,feature)
col += 1
def updateTable(self):
self.portsTableModel = qt.QStandardItemModel()
self.portsTable.setModel(self.portsTableModel)
self.transformSliders.reset()
self.removePortButton.enabled = False
self.transformSliders.setMRMLTransformNode(None)
node = self.logic.markupsNode
if node is None:
return
self.itemPortIdxMap = {}
for i in range(node.GetNumberOfFiducials()):
item = qt.QStandardItem()
item.setText(self.logic.getPortName(i))
self.portsTableModel.setItem(i, 0, item)
self.itemPortIdxMap[item] = i
item = qt.QStandardItem()
item.setText('Visible')
item.setCheckable(True)
if self.logic.isToolVisible(i):
checkState = 2 # checked enum
else:
checkState = 0 # unchecked enum
item.setCheckState(checkState)
self.portsTableModel.setItem(i, 1, item)
self.itemPortIdxMap[item] = i
self.portsTableModel.setHeaderData(0, 1, "Port Fiducial Name")
self.portsTableModel.setHeaderData(1, 1, " ")
self.portsTable.setColumnWidth(0, 15 * len("Port Fiducial Name"))
self.portsTableModel.itemChanged.connect(self.onTableItemChanged)
self.portsTable.selectionModel().currentRowChanged.connect(
self.onCurrentToolChanged)
def setup(self):
# Instantiate and connect widgets ...
# #
# # Reload and Test area
# #
# reloadCollapsibleButton = ctk.ctkCollapsibleButton()
# reloadCollapsibleButton.text = "Reload && Test"
# self.layout.addWidget(reloadCollapsibleButton)
# reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# # reload button
# # (use this during development, but remove it when delivering
# # your module to users)
# self.reloadButton = qt.QPushButton("Reload")
# self.reloadButton.toolTip = "Reload this module."
# self.reloadButton.name = "PortPlacement Reload"
# reloadFormLayout.addWidget(self.reloadButton)
# self.reloadButton.connect('clicked()', self.onReload)
# # reload and test button
# # (use this during development, but remove it when delivering
# # your module to users)
# self.reloadAndTestButton = qt.QPushButton("Reload and Test")
# self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
# reloadFormLayout.addWidget(self.reloadAndTestButton)
# self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Ports Area
#
portsCollapsibleButton = ctk.ctkCollapsibleButton()
portsCollapsibleButton.text = "Surgical Ports"
self.layout.addWidget(portsCollapsibleButton)
portsFormLayout = qt.QFormLayout(portsCollapsibleButton)
#
# port fiducial list selector
#
self.portListSelector = slicer.qMRMLNodeComboBox()
self.portListSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.portListSelector.addEnabled = False
self.portListSelector.removeEnabled = False
self.portListSelector.noneEnabled = True
self.portListSelector.setMRMLScene(slicer.mrmlScene)
self.portListSelector.setToolTip("Add surgical ports from a markups node.")
portsFormLayout.addRow("Markups node of surgical ports", self.portListSelector)
#
# Add Port List button
#
self.addPortListButton = qt.QPushButton("Set Port Markups Node")
self.addPortListButton.enabled = False
portsFormLayout.addRow(self.addPortListButton)
#
# Port table
#
self.portsTable = qt.QTableView()
self.portsTableModel = qt.QStandardItemModel()
self.portsTable.setModel(self.portsTableModel)
portsFormLayout.addRow(self.portsTable)
#
# Remove Port button
#
self.removePortButton = qt.QPushButton("Remove Selected Port")
self.removePortButton.enabled = False
portsFormLayout.addRow(self.removePortButton)
#
# Target area
#
targetCollapsibleButton = ctk.ctkCollapsibleButton()
targetCollapsibleButton.text = "Surgical Target"
self.layout.addWidget(targetCollapsibleButton)
targetFormLayout = qt.QFormLayout(targetCollapsibleButton)
#
# target selector
#
self.targetSelector = slicer.qMRMLNodeComboBox()
self.targetSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.targetSelector.addEnabled = False
self.targetSelector.removeEnabled = False
self.targetSelector.noneEnabled = True
self.targetSelector.setMRMLScene(slicer.mrmlScene)
self.targetSelector.setToolTip("Pick the surgical target that the tools should face.")
targetFormLayout.addRow("Surgical Target Fiducial", self.targetSelector)
#
# Retarget button
#
self.retargetButton = qt.QPushButton("Aim Tools at Target")
self.retargetButton.toolTip = "Reset tool orientations to face target fiducial"
self.retargetButton.enabled = False
targetFormLayout.addRow(self.retargetButton)
#
# Port Tool Display Options
#
toolsCollapsibleButton = ctk.ctkCollapsibleButton()
toolsCollapsibleButton.text = "Port Tool Display Options"
self.layout.addWidget(toolsCollapsibleButton)
toolsFormLayout = qt.QFormLayout(toolsCollapsibleButton)
#
# Transform sliders
#
self.transformSliders = slicer.qMRMLTransformSliders()
self.transformSliders.TypeOfTransform = slicer.qMRMLTransformSliders.ROTATION
self.transformSliders.CoordinateReference = slicer.qMRMLTransformSliders.LOCAL
self.transformSliders.Title = 'Tool Orientation'
self.transformSliders.minMaxVisible = False
toolsFormLayout.addRow(self.transformSliders)
#
# radius spin box
#
self.radiusSpinBox = qt.QDoubleSpinBox()
self.radiusSpinBox.setMinimum(0.0)
self.radiusSpinBox.setMaximum(10.0)
self.radiusSpinBox.setValue(2.0)
toolsFormLayout.addRow("Tool radius", self.radiusSpinBox)
#
# length spin box
#
self.lengthSpinBox = qt.QDoubleSpinBox()
self.lengthSpinBox.setMinimum(0.0)
self.lengthSpinBox.setMaximum(250.0)
self.lengthSpinBox.setValue(150.0)
toolsFormLayout.addRow("Tool length", self.lengthSpinBox)
# connections
self.portListSelector.connect('currentNodeChanged(bool)', self.onPortListSelectorChanged)
self.targetSelector.connect('currentNodeChanged(bool)', self.onTargetSelectorChanged)
self.addPortListButton.connect('clicked(bool)', self.onAddPortListButton)
self.removePortButton.connect('clicked(bool)', self.onRemovePortButton)
self.retargetButton.connect('clicked(bool)', self.onRetargetButton)
self.radiusSpinBox.connect('valueChanged(double)', self.onToolShapeChanged)
self.lengthSpinBox.connect('valueChanged(double)', self.onToolShapeChanged)
# Add vertical spacer
self.layout.addStretch(1)
# Add observer to scene for removal of fiducial nodes
self.sceneObserverTag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeRemovedEvent,
self.onNodeRemoved)
# instantiate port placement module logic
self.logic = PortPlacementLogic()
self.currentMarkupsNode = None
self.onMarkupAddedTag = None
def updateStructures(self, caller=None, event=None):
"""re-build the Structures frame
- optional caller and event ignored (for use as vtk observer callback)
"""
if self.setMergeButton.destroyed():
""" TODO: here the python class still exists but the
Qt widgets are gone - need to figure out when to remove observers
and free python code - probably the destroyed() signal.
"""
self.cleanup()
return
self.setMergeButton.setDisabled(not self.master)
# reset to a fresh model
self.brushes = []
self.items = []
self.structures = qt.QStandardItemModel()
self.structuresView.setModel(self.structures)
# if no merge volume exists, disable everything - else enable
merge = self.mergeVolume()
self.addStructureButton.setDisabled(not merge)
self.deleteStructuresButton.setDisabled(not merge)
self.mergeButton.setDisabled(not merge)
self.splitButton.setDisabled(not merge)
self.mergeAndBuildButton.setDisabled(not merge)
self.replaceModels.setDisabled(not merge)
if self.mergeValidCommand:
# will be passed current
self.mergeValidCommand(merge)
if not merge:
return
colorNode = merge.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
masterName = self.master.GetName()
slicer.mrmlScene.InitTraversal()
vNode = slicer.mrmlScene.GetNextNodeByClass("vtkMRMLScalarVolumeNode")
self.row = 0
while vNode:
vName = vNode.GetName()
# match something like "CT-lung-label1"
regexp = "%s-.*-label" % masterName
if re.match(regexp, vName):
# figure out what name it is
# - account for the fact that sometimes a number will be added to the end of the name
start = 1 + len(masterName)
end = vName.rfind("-label")
structureName = vName[start:end]
structureIndex = colorNode.GetColorIndexByName(structureName)
structureColor = lut.GetTableValue(structureIndex)[0:3]
brush = qt.QBrush()
self.brushes.append(brush)
color = qt.QColor()
color.setRgb(structureColor[0] * 255, structureColor[1] * 255,
structureColor[2] * 255)
brush.setColor(color)
# label index
item = qt.QStandardItem()
item.setEditable(False)
item.setText(str(structureIndex))
self.structures.setItem(self.row, 0, item)
self.items.append(item)
# label color
item = qt.QStandardItem()
item.setEditable(False)
item.setData(color, 1)
self.structures.setItem(self.row, 1, item)
self.items.append(item)
# structure name
item = qt.QStandardItem()
item.setEditable(False)
item.setText(structureName)
self.structures.setItem(self.row, 2, item)
self.items.append(item)
# volumeName name
item = qt.QStandardItem()
item.setEditable(False)
item.setText(vName)
self.structures.setItem(self.row, 3, item)
self.items.append(item)
# sort order
item = qt.QStandardItem()
item.setEditable(True)
item.setText("")
self.structures.setItem(self.row, 4, item)
self.items.append(item)
self.row += 1
vNode = slicer.mrmlScene.GetNextNodeByClass(
"vtkMRMLScalarVolumeNode")
self.structuresView.setColumnWidth(0, 70)
self.structuresView.setColumnWidth(1, 50)
self.structuresView.setColumnWidth(2, 60)
self.structuresView.setColumnWidth(3, 100)
self.structuresView.setColumnWidth(4, 10)
self.structures.setHeaderData(0, 1, "Number")
self.structures.setHeaderData(1, 1, "Color")
self.structures.setHeaderData(2, 1, "Name")
self.structures.setHeaderData(3, 1, "Label Volume")
self.structures.setHeaderData(4, 1, "Order")
self.structuresView.setModel(self.structures)
def updateStructures(self,caller=None, event=None):
"""re-build the Structures frame
- optional caller and event ignored (for use as vtk observer callback)
"""
if slicer.mrmlScene.IsBatchProcessing():
return
if self.setMergeButton.destroyed():
""" TODO: here the python class still exists but the
Qt widgets are gone - need to figure out when to remove observers
and free python code - probably the destroyed() signal.
"""
self.cleanup()
return
self.setMergeButton.setDisabled(not self.master)
# reset to a fresh model
self.brushes = []
self.items = []
self.structures = qt.QStandardItemModel()
self.structuresView.setModel(self.structures)
# if no merge volume exists, disable everything - else enable
merge = self.mergeVolume()
self.addStructureButton.setDisabled(not merge)
self.deleteStructuresButton.setDisabled(not merge)
self.mergeButton.setDisabled(not merge)
self.splitButton.setDisabled(not merge)
self.mergeAndBuildButton.setDisabled(not merge)
self.replaceModels.setDisabled(not merge)
if self.mergeValidCommand:
# will be passed current
self.mergeValidCommand(merge)
if not merge:
return
colorNode = merge.GetDisplayNode().GetColorNode()
lut = colorNode.GetLookupTable()
masterName = self.master.GetName()
volumeNodes = self.structureVolumes()
for vNode in volumeNodes:
vName = vNode.GetName()
# figure out what name it is
# - account for the fact that sometimes a number will be added to the end of the name
start = 1+len(masterName)
end = vName.rfind("-label")
structureName = vName[start:end]
structureIndex = colorNode.GetColorIndexByName( structureName )
structureColor = lut.GetTableValue(structureIndex)[0:3]
brush = qt.QBrush()
self.brushes.append(brush)
color = qt.QColor()
color.setRgb(structureColor[0]*255,structureColor[1]*255,structureColor[2]*255)
brush.setColor(color)
# label index
item = qt.QStandardItem()
item.setEditable(False)
item.setText( "%03d"%int(structureIndex) )
self.structures.setItem(self.row,0,item)
self.items.append(item)
# label color
item = qt.QStandardItem()
item.setEditable(False)
item.setData(color,1)
self.structures.setItem(self.row,1,item)
self.items.append(item)
# structure name
item = qt.QStandardItem()
item.setEditable(False)
item.setText(structureName)
self.structures.setItem(self.row,2,item)
self.items.append(item)
# volumeName name
item = qt.QStandardItem()
item.setEditable(False)
item.setText(vName)
self.structures.setItem(self.row,3,item)
self.items.append(item)
# sort order
item = qt.QStandardItem()
item.setEditable(True)
item.setText("")
self.structures.setItem(self.row,4,item)
self.items.append(item)
self.row += 1
for i in range(5):
self.structuresView.resizeColumnToContents(i)
self.structures.setHeaderData(0,1,"Number")
self.structures.setHeaderData(1,1,"Color")
self.structures.setHeaderData(2,1,"Name")
self.structures.setHeaderData(3,1,"Label Volume")
self.structures.setHeaderData(4,1,"Order")
self.structuresView.setModel(self.structures)
self.structuresView.connect("activated(QModelIndex)", self.onStructuresClicked)
self.structuresView.setProperty('SH_ItemView_ActivateItemOnSingleClick', 1)
self.structureLabelNames = []
rows = self.structures.rowCount()
for row in xrange(rows):
self.structureLabelNames.append(self.structures.item(row,2).text())
def populateStats(self):
if not self.logic:
return
displayNode = self.insplabelNode.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
cycle = ['insp']
for i in cycle:
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)
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[i, k, regionTag])
self.model.setItem(row, col, item)
self.items.append(item)
col += 1
row += 1
self.view.setColumnWidth(0, 30)
self.model.setHeaderData(0, 1, "INSP")
col = 1
for k in self.logic.keys:
self.view.setColumnWidth(col, 15 * len(k))
self.model.setHeaderData(col, 1, k)
col += 1
self.itemsexp = []
self.modelexp = qt.QStandardItemModel()
self.viewexp.setModel(self.modelexp)
self.viewexp.verticalHeader().visible = False
row = 0
cycle = ['exp']
for i in cycle:
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)
self.modelexp.setItem(row, 0, item)
self.itemsexp.append(item)
col = 1
for k in self.logic.keys:
item = qt.QStandardItem()
item.setText("%.3f" %
self.logic.labelStats[i, k, regionTag])
self.modelexp.setItem(row, col, item)
self.itemsexp.append(item)
col += 1
row += 1
self.viewexp.setColumnWidth(0, 30)
self.modelexp.setHeaderData(0, 1, "EXP")
col = 1
for k in self.logic.keys:
self.viewexp.setColumnWidth(col, 15 * len(k))
self.modelexp.setHeaderData(col, 1, k)
col += 1
def setup(self):
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Radiomics Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
# self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
reloadCollapsibleButton.collapsed = True
#---------------------------------------------------------
#
# Compute Radiomics area
#
self.computeRadiomicsCollapsibleButton = ctk.ctkCollapsibleButton()
self.computeRadiomicsCollapsibleButton.text = "Slicer Radiomics Platform"
self.layout.addWidget(self.computeRadiomicsCollapsibleButton)
self.computeRadiomicsFormLayout = qt.QFormLayout(
self.computeRadiomicsCollapsibleButton)
#
# Universal Advanced Settings Collapsible Button
#
self.AdvancedSettingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.AdvancedSettingsCollapsibleButton.text = "Advanced Settings"
self.AdvancedSettingsCollapsibleButtonLayout = qt.QHBoxLayout()
self.AdvancedSettingsCollapsibleButton.setLayout(qt.QHBoxLayout())
self.computeRadiomicsFormLayout.addWidget(
self.AdvancedSettingsCollapsibleButton)
self.AdvancedSettingsCollapsibleButton.collapsed = True
self.AdvancedSettingsFrame = qt.QFrame(
self.AdvancedSettingsCollapsibleButton)
self.AdvancedSettingsFrameLayout = qt.QFormLayout()
self.AdvancedSettingsFrame.setLayout(self.AdvancedSettingsFrameLayout)
self.AdvancedSettingsCollapsibleButton.layout().addWidget(
self.AdvancedSettingsFrame)
# Label Values
self.inputLabelValues = qt.QLabel("Label Values:",
self.AdvancedSettingsFrame)
self.inputLabelValuesField = qt.QLineEdit("1",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.inputLabelValues,
self.inputLabelValuesField)
# Interpolation Settings
self.settingsRadioButtonFrame = qt.QFrame(self.AdvancedSettingsFrame)
self.settingsRadioButtonFrame.setLayout(qt.QHBoxLayout())
self.interpolationsGroup = qt.QButtonGroup(
self.settingsRadioButtonFrame)
self.ipRawButton = qt.QRadioButton("Raw")
self.ip1x1x1Button = qt.QRadioButton("(1,1,1)")
self.ip2x2x2Button = qt.QRadioButton("(2,2,2)")
self.ip3x3x3Button = qt.QRadioButton("(3,3,3)")
self.ipRawButton.checked = True
self.interpolationsGroup.addButton(self.ipRawButton)
self.interpolationsGroup.addButton(self.ip1x1x1Button)
self.interpolationsGroup.addButton(self.ip2x2x2Button)
self.interpolationsGroup.addButton(self.ip3x3x3Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ipRawButton)
self.settingsRadioButtonFrame.layout().addWidget(self.ip1x1x1Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ip2x2x2Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ip3x3x3Button)
self.interpHeader = qt.QLabel("Interpolation:")
self.AdvancedSettingsFrameLayout.addRow(self.interpHeader,
self.settingsRadioButtonFrame)
# Bin Width
self.inputBinWidth = qt.QLabel("Bin Width:",
self.AdvancedSettingsFrame)
self.inputBinWidthField = qt.QLineEdit("25",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.inputBinWidth,
self.inputBinWidthField)
# Modality Radio Buttons Frame
self.ModalityRadioButtonFrame = qt.QFrame(self.AdvancedSettingsFrame)
self.ModalityRadioButtonFrame.setLayout(qt.QHBoxLayout())
self.ModalityFileFormatGroup = qt.QButtonGroup(
self.ModalityRadioButtonFrame)
self.CTButton = qt.QRadioButton("CT")
self.CTButton.checked = True
self.MRIButton = qt.QRadioButton("MRI")
self.PETButton = qt.QRadioButton("PET")
self.ModalityFileFormatGroup.addButton(self.CTButton)
self.ModalityFileFormatGroup.addButton(self.MRIButton)
self.ModalityFileFormatGroup.addButton(self.PETButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.CTButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.MRIButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.PETButton)
self.ModalityInputLabel = qt.QLabel("Image Modality:",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.ModalityInputLabel,
self.ModalityRadioButtonFrame)
#
# End Universal Advanced Settings Collapsible Button
#
# Parent Tab Widget
self.computeRadiomicsTabWidget = qt.QTabWidget()
self.computeRadiomicsFormLayout.addWidget(
self.computeRadiomicsTabWidget)
# Radiomics Current Mode
self.tabComputeRadiomicsCurr = qt.QWidget()
self.singleCaseInputFormLayout = qt.QFormLayout()
self.tabComputeRadiomicsCurr.setLayout(self.singleCaseInputFormLayout)
self.tabComputeRadiomicsCurrName = "Single Case Mode"
self.computeRadiomicsTabWidget.addTab(self.tabComputeRadiomicsCurr,
self.tabComputeRadiomicsCurrName)
# Input 1: Input Image
self.input1Frame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.input1Frame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.input1Frame)
self.input1Selector = qt.QLabel("Input Image: ", self.input1Frame)
self.input1Frame.layout().addWidget(self.input1Selector)
self.input1Selector = slicer.qMRMLNodeComboBox(self.input1Frame)
self.input1Selector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.input1Selector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
0)
self.input1Selector.addEnabled = False
self.input1Selector.removeEnabled = False
self.input1Selector.setMRMLScene(slicer.mrmlScene)
self.input1Frame.layout().addWidget(self.input1Selector)
# Input 2: Input Segmentation
self.input2Frame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.input2Frame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.input2Frame)
self.input2Selector = qt.QLabel("Input Label: ", self.input2Frame)
self.input2Frame.layout().addWidget(self.input2Selector)
self.input2Selector = slicer.qMRMLNodeComboBox(self.input2Frame)
self.input2Selector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.input2Selector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
1)
self.input2Selector.addEnabled = False
self.input2Selector.removeEnabled = False
self.input2Selector.setMRMLScene(slicer.mrmlScene)
self.input2Frame.layout().addWidget(self.input2Selector)
# Settings Collapsible Button
self.SettingsCollapsibleButtonCurr = ctk.ctkCollapsibleButton()
self.SettingsCollapsibleButtonCurr.text = "Settings"
self.SettingsCollapsibleButtonCurrLayout = qt.QHBoxLayout()
self.SettingsCollapsibleButtonCurr.setLayout(
self.SettingsCollapsibleButtonCurrLayout)
self.singleCaseInputFormLayout.addWidget(
self.SettingsCollapsibleButtonCurr)
self.SettingsCollapsibleButtonCurr.collapsed = False
self.SettingsFrameCurr = qt.QFrame(self.SettingsCollapsibleButtonCurr)
self.SettingsFrameCurr.setLayout(qt.QFormLayout())
self.SettingsCollapsibleButtonCurrLayout.addWidget(
self.SettingsFrameCurr)
# Settings
self.para2curr = qt.QCheckBox("Use MatlabBridge",
self.tabComputeRadiomicsCurr)
self.para2curr.toolTip = "When checked: Matlab features extracted"
self.para2curr.checked = False
self.SettingsFrameCurr.layout().addRow(self.para2curr)
# Apply Radiomics button
self.RadiomicCurrButtonsFrame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.RadiomicCurrButtonsFrame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.RadiomicCurrButtonsFrame)
self.radiomicsCurrButton = qt.QPushButton(
"Compute Radiomics Features (Single Case)",
self.RadiomicCurrButtonsFrame)
self.radiomicsCurrButton.enabled = True
self.radiomicsCurrButton.toolTip = "Run the feature extraction for a single case."
self.RadiomicCurrButtonsFrame.layout().addWidget(
self.radiomicsCurrButton)
# Chart
self.RadiomicsTableFrame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.RadiomicsTableFrameLayout = qt.QHBoxLayout()
self.RadiomicsTableFrame.setLayout(self.RadiomicsTableFrameLayout)
self.singleCaseInputFormLayout.addWidget(self.RadiomicsTableFrame)
self.RadiomicsTableView = qt.QTableView(self.RadiomicsTableFrame)
self.RadiomicsTableView.sortingEnabled = True
self.RadiomicsTableView.minimumHeight = 175
self.RadiomicsTableView.verticalHeader().visible = False
self.RadiomicsTableView.setColumnWidth(0, 30)
self.RadiomicsTableFrameLayout.addWidget(self.RadiomicsTableView)
self.RadiomicsTableModel = qt.QStandardItemModel()
# Save Table Button
self.saveButton = qt.QPushButton("Save Table to CSV File",
self.RadiomicCurrButtonsFrame)
self.saveButton.toolTip = "Save Radiomics Feature from table to CSV file"
self.saveButton.enabled = False
self.singleCaseInputFormLayout.layout().addWidget(self.saveButton)
"""
#
# The interface we use for batch mode (not part of this module)
#
#---------------------------------------------------------
# Radiomics Batch
self.tabComputeRadiomicsBatch = qt.QWidget()
self.RadiomicsFormLayout = qt.QFormLayout()
self.tabComputeRadiomicsBatch.setLayout(self.RadiomicsFormLayout)
self.tabComputeRadiomicsBatchName = "Batch Mode"
self.computeRadiomicsTabWidget.addTab(self.tabComputeRadiomicsBatch, self.tabComputeRadiomicsBatchName)
# Input 3: Database selection
self.input3Frame = qt.QFrame(self.tabComputeRadiomicsBatch)
self.input3Frame.setLayout(qt.QHBoxLayout())
self.RadiomicsFormLayout.addWidget(self.input3Frame)
self.DatabaseButton = qt.QPushButton("Set Root Patient Directory")
self.DatabaseButton.toolTip = "Set the main Patient Data location"
self.DatabaseButton.enabled = True
self.input3Frame.layout().addWidget(self.DatabaseButton)
self.PatientSelector = qt.QComboBox()
self.PatientSelector.enabled = False
self.input3Frame.layout().addWidget(self.PatientSelector)
# Settings Collapsible Button
self.SettingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.SettingsCollapsibleButton.text = "Settings"
self.SettingsCollapsibleButtonLayout = qt.QHBoxLayout()
self.SettingsCollapsibleButton.setLayout(self.SettingsCollapsibleButtonLayout)
self.RadiomicsFormLayout.addWidget(self.SettingsCollapsibleButton)
self.SettingsCollapsibleButton.collapsed = False
self.SettingsFrame = qt.QFrame(self.SettingsCollapsibleButton)
self.SettingsFrame.setLayout(qt.QFormLayout())
self.SettingsCollapsibleButtonLayout.addWidget(self.SettingsFrame)
# Settings
self.para2 = qt.QCheckBox("Use MatlabBridge", self.SettingsFrame)
self.para2.toolTip = "When checked: Matlab features extracted"
self.para2.checked = True
self.SettingsFrame.layout().addRow(self.para2)
self.para3 = qt.QCheckBox("Clear Database", self.SettingsFrame)
self.para3.toolTip = "When checked: old database is cleared"
self.para3.checked = True
self.SettingsFrame.layout().addRow(self.para3)
# Keywords Collapsible Button
self.KeywordsCollapsibleButton = ctk.ctkCollapsibleButton()
self.KeywordsCollapsibleButton.text = "Keyword Matching"
self.KeywordsCollapsibleButtonLayout = qt.QHBoxLayout()
self.KeywordsCollapsibleButton.setLayout(self.KeywordsCollapsibleButtonLayout)
self.SettingsFrame.layout().addRow(self.KeywordsCollapsibleButton)
self.KeywordsCollapsibleButton.collapsed = True
self.keywordsFrame = qt.QFrame(self.KeywordsCollapsibleButton)
self.keywordsFrame.setLayout(qt.QFormLayout())
self.KeywordsCollapsibleButtonLayout.addWidget(self.keywordsFrame)
self.keywordsHeader = qt.QLabel("Keyword Matching:", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.keywordsHeader)
# File Type Radio Buttons Frame
self.radioButtonFrame = qt.QFrame(self.keywordsFrame)
self.radioButtonFrame.setLayout(qt.QFormLayout())
self.fileFormatGroup = qt.QButtonGroup(self.radioButtonFrame)
self.nrrdButton = qt.QRadioButton("NRRD")
self.nrrdButton.checked = True
self.niftiButton = qt.QRadioButton("NIFTI")
self.fileFormatGroup.addButton(self.nrrdButton)
self.fileFormatGroup.addButton(self.niftiButton)
self.radioButtonFrame.layout().addRow(self.nrrdButton, self.niftiButton)
self.inputMaskHeader = qt.QLabel("Input Image File Type:", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputMaskHeader, self.radioButtonFrame)
# Keywords Frame
self.inputImageKeywords = qt.QLabel("Input Image Keywords:", self.keywordsFrame)
self.inputImageKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageKeywords, self.inputImageKeywordsField )
self.inputImageExclusionKeywords = qt.QLabel("Input Image Exclusion Keywords:", self.keywordsFrame)
self.inputImageExclusionKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageExclusionKeywords, self.inputImageExclusionKeywordsField )
self.inputLabelKeywords = qt.QLabel("Input Label Keywords:", self.keywordsFrame)
self.inputLabelKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelKeywords, self.inputLabelKeywordsField )
self.inputLabelExclusionKeywords = qt.QLabel("Input Label Exclusion Keywords:", self.keywordsFrame)
self.inputLabelExclusionKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelExclusionKeywords, self.inputLabelExclusionKeywordsField )
# Radiomic Mode Buttons
self.RadiomicButtonsFrame = qt.QFrame(self.tabComputeRadiomicsBatch)
self.RadiomicButtonsFrame.setLayout(qt.QHBoxLayout())
self.RadiomicsFormLayout.addWidget(self.RadiomicButtonsFrame)
self.radiomicsBatchButton = qt.QPushButton("Compute Radiomics Features (Batch Mode)")
self.radiomicsBatchButton.toolTip = "Run the feature extraction for database batch."
self.radiomicsBatchButton.enabled = True
self.RadiomicButtonsFrame.layout().addWidget(self.radiomicsBatchButton)
self.RadiomicButtonsFrame.enabled = True
"""
#---------------------------------------------------------
# Connections
#self.DatabaseButton.connect('clicked(bool)', self.onDatabaseButton)
self.radiomicsCurrButton.connect('clicked(bool)', self.onRadiomicsCurr)
#self.radiomicsBatchButton.connect('clicked(bool)', self.onRadiomicsBatch)
self.saveButton.connect('clicked()', self.onSave)
self.layout.addStretch(1) # Add vertical spacer
