def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# File area
#
filesCollapsibleButton = ctk.ctkCollapsibleButton()
filesCollapsibleButton.text = "Input files"
filesCollapsibleButton.collapsed = False
self.layout.addWidget(filesCollapsibleButton)
# Layout within the files collapsible button
filesFormLayout = qt.QFormLayout(filesCollapsibleButton)
# select one file
buttonLayout = qt.QHBoxLayout()
self.archetypeText = qt.QLineEdit()
buttonLayout.addWidget(self.archetypeText)
self.addFromArchetype = qt.QPushButton("Browse...")
buttonLayout.addWidget(self.addFromArchetype)
self.archetypeStartNumber = 0
filesFormLayout.addRow("Filename pattern: ", buttonLayout)
# file list group
fileListGroupBox = ctk.ctkCollapsibleGroupBox()
fileListGroupBox.title = "File list"
fileListLayout = qt.QVBoxLayout()
fileListGroupBox.setLayout(fileListLayout)
filesFormLayout.addRow("", fileListGroupBox)
self.addByBrowsingButton = qt.QPushButton("Select files...")
fileListLayout.addWidget(self.addByBrowsingButton)
self.fileTable = qt.QTextBrowser()
fileListLayout.addWidget(self.fileTable)
fileListGroupBox.collapsed = True
# original volume size
self.originalVolumeSizeLabel = qt.QLabel()
filesFormLayout.addRow("Size: ", self.originalVolumeSizeLabel)
# reverse slice order
self.reverseCheckBox = qt.QCheckBox()
self.reverseCheckBox.toolTip = "Read the images in reverse order (flips loaded volume along IS axis)"
filesFormLayout.addRow("Reverse: ", self.reverseCheckBox)
# original spacing
self.spacingWidget = slicer.qMRMLCoordinatesWidget()
self.spacingWidget.setMRMLScene(slicer.mrmlScene)
self.spacingWidget.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByKey | ctk.ctkDoubleSpinBox.DecimalsByShortcuts | ctk.ctkDoubleSpinBox.DecimalsByValue
self.spacingWidget.minimum = 0.0
self.spacingWidget.maximum = 1000000000.0
self.spacingWidget.quantity = "length"
self.spacingWidget.unitAwareProperties = slicer.qMRMLCoordinatesWidget.Precision | slicer.qMRMLCoordinatesWidget.Prefix | slicer.qMRMLCoordinatesWidget.Scaling | slicer.qMRMLCoordinatesWidget.Suffix
self.spacingWidget.coordinates = "1,1,1"
self.spacingWidget.toolTip = "Set the colunm, row, slice spacing; original spacing not including downsample"
filesFormLayout.addRow("Spacing: ", self.spacingWidget)
#
# output area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
outputCollapsibleButton.collapsed = False
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = [
"vtkMRMLScalarVolumeNode", "vtkMRMLVectorVolumeNode"
]
self.outputSelector.showChildNodeTypes = False
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.noneEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.renameEnabled = True
self.outputSelector.addEnabled = True
self.outputSelector.noneDisplay = "(Create new volume)"
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip(
"Pick the output volume to populate or None to autogenerate.")
outputFormLayout.addRow("Output Volume: ", self.outputSelector)
#
# output ROI selector
#
self.outputROISelector = slicer.qMRMLNodeComboBox()
self.outputROISelector.nodeTypes = [
"vtkMRMLAnnotationROINode", "vtkMRMLMarkupsROINode"
]
self.outputROISelector.showChildNodeTypes = False
self.outputROISelector.showHidden = False
self.outputROISelector.showChildNodeTypes = False
self.outputROISelector.noneEnabled = True
self.outputROISelector.removeEnabled = True
self.outputROISelector.renameEnabled = True
self.outputROISelector.addEnabled = False
self.outputROISelector.noneDisplay = "(Full volume)"
self.outputROISelector.setMRMLScene(slicer.mrmlScene)
self.outputROISelector.setToolTip(
"Set the region of the volume that will be loaded")
outputFormLayout.addRow("Region of interest: ", self.outputROISelector)
#
# Quality selector
#
qualityLayout = qt.QVBoxLayout()
self.qualityPreviewRadioButton = qt.QRadioButton("preview")
self.qualityHalfRadioButton = qt.QRadioButton("half resolution")
self.qualityFullRadioButton = qt.QRadioButton("full resolution")
qualityLayout.addWidget(self.qualityPreviewRadioButton)
qualityLayout.addWidget(self.qualityHalfRadioButton)
qualityLayout.addWidget(self.qualityFullRadioButton)
self.qualityPreviewRadioButton.setChecked(True)
outputFormLayout.addRow("Quality: ", qualityLayout)
self.sliceSkipSpinBox = qt.QSpinBox()
self.sliceSkipSpinBox.toolTip = "Skips the selected number of slices between each pair of output volume slices (use, for example, on long thin samples with more slices than in-plane resolution)"
outputFormLayout.addRow("Slice skip: ", self.sliceSkipSpinBox)
# Force grayscale output
self.grayscaleCheckBox = qt.QCheckBox()
self.grayscaleCheckBox.toolTip = "Force reading the image in grayscale. Only makes a difference if the input has color (RGB or RGBA) voxels."
self.grayscaleCheckBox.checked = True
outputFormLayout.addRow("Grayscale: ", self.grayscaleCheckBox)
# output volume size
self.outputVolumeSizeLabel = qt.QLabel()
outputFormLayout.addRow("Output size: ", self.outputVolumeSizeLabel)
# output volume spacing
self.outputSpacingWidget = slicer.qMRMLCoordinatesWidget()
self.outputSpacingWidget.setMRMLScene(slicer.mrmlScene)
self.outputSpacingWidget.readOnly = True
self.outputSpacingWidget.frame = False
self.outputSpacingWidget.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByKey | ctk.ctkDoubleSpinBox.DecimalsByShortcuts | ctk.ctkDoubleSpinBox.DecimalsByValue
self.outputSpacingWidget.minimum = 0.0
self.outputSpacingWidget.maximum = 1000000000.0
self.outputSpacingWidget.quantity = "length"
self.outputSpacingWidget.unitAwareProperties = slicer.qMRMLCoordinatesWidget.Precision | slicer.qMRMLCoordinatesWidget.Prefix | slicer.qMRMLCoordinatesWidget.Scaling | slicer.qMRMLCoordinatesWidget.Suffix
self.outputSpacingWidget.coordinates = "1,1,1"
self.outputSpacingWidget.toolTip = "Slice spacing of the volume that will be loaded"
outputFormLayout.addRow("Output spacing: ", self.outputSpacingWidget)
self.loadButton = qt.QPushButton("Load files")
self.loadButton.toolTip = "Load files as a 3D volume"
self.loadButton.enabled = False
outputFormLayout.addRow(self.loadButton)
# connections
self.reverseCheckBox.connect('toggled(bool)',
self.updateLogicFromWidget)
self.sliceSkipSpinBox.connect("valueChanged(int)",
self.updateLogicFromWidget)
self.spacingWidget.connect("coordinatesChanged(double*)",
self.updateLogicFromWidget)
self.qualityPreviewRadioButton.connect(
"toggled(bool)",
lambda toggled, widget=self.qualityPreviewRadioButton: self.
onQualityToggled(toggled, widget))
self.qualityHalfRadioButton.connect(
"toggled(bool)",
lambda toggled, widget=self.qualityHalfRadioButton: self.
onQualityToggled(toggled, widget))
self.qualityFullRadioButton.connect(
"toggled(bool)",
lambda toggled, widget=self.qualityFullRadioButton: self.
onQualityToggled(toggled, widget))
self.grayscaleCheckBox.connect('toggled(bool)',
self.updateLogicFromWidget)
self.outputROISelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.setOutputROINode)
self.addByBrowsingButton.connect('clicked()', self.addByBrowsing)
self.addFromArchetype.connect('clicked()', self.selectArchetype)
self.archetypeText.connect('textChanged(const QString &)',
self.populateFromArchetype)
self.loadButton.connect('clicked()', self.onLoadButton)
# Add vertical spacer
self.layout.addStretch(1)
self.loadButton.enabled = False
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# File area
#
filesCollapsibleButton = ctk.ctkCollapsibleButton()
filesCollapsibleButton.text = "Files"
filesCollapsibleButton.collapsed = False
self.layout.addWidget(filesCollapsibleButton)
# Layout within the files collapsible button
filesFormLayout = qt.QFormLayout(filesCollapsibleButton)
self.fileModel = qt.QStandardItemModel()
self.fileTable = qt.QTableView()
self.fileTable.horizontalHeader().stretchLastSection = True
self.fileTable.horizontalHeader().visible = False
self.fileTable.setModel(self.fileModel)
filesFormLayout.addRow(self.fileTable)
buttonLayout = qt.QHBoxLayout()
self.addByBrowsingButton = qt.QPushButton("Browse for files")
self.clearButton = qt.QPushButton("Clear")
buttonLayout.addWidget(self.addByBrowsingButton)
buttonLayout.addWidget(self.clearButton)
filesFormLayout.addRow(buttonLayout)
self.propertiesLabel = qt.QLabel()
filesFormLayout.addRow(self.propertiesLabel)
#
# output area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
outputCollapsibleButton.collapsed = False
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode",]
self.outputSelector.showChildNodeTypes = False
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.noneEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.renameEnabled = True
self.outputSelector.addEnabled = True
self.outputSelector.setMRMLScene( slicer.mrmlScene )
self.outputSelector.setToolTip( "Pick the output volume to populate or None to autogenerate." )
outputFormLayout.addRow("Output Volume: ", self.outputSelector)
self.spacing = slicer.qMRMLCoordinatesWidget()
self.spacing.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByKey | ctk.ctkDoubleSpinBox.DecimalsByShortcuts | ctk.ctkDoubleSpinBox.DecimalsByValue
self.spacing.minimum = 0.0
self.spacing.maximum = 1000000000.0
self.spacing.quantity = "length"
self.spacing.unitAwareProperties = slicer.qMRMLCoordinatesWidget.Precision | slicer.qMRMLCoordinatesWidget.Prefix | slicer.qMRMLCoordinatesWidget.Scaling | slicer.qMRMLCoordinatesWidget.Suffix
self.spacing.decimals = 8
self.spacing.coordinates = "1,1,1"
self.spacing.toolTip = "Set the colunm, row, slice spacing in mm; original spacing not including downsample"
outputFormLayout.addRow("Spacing: ", self.spacing)
self.downsample = qt.QCheckBox()
self.downsample.toolTip = "Reduces data size by half in each dimension by skipping every other pixel and slice (uses about 1/8 memory)"
outputFormLayout.addRow("Downsample: ", self.downsample)
self.reverse = qt.QCheckBox()
self.reverse.toolTip = "Read the images in reverse order"
outputFormLayout.addRow("Reverse: ", self.reverse)
self.sliceSkip = ctk.ctkDoubleSpinBox()
self.sliceSkip.decimals = 0
self.sliceSkip.minimum = 0
self.sliceSkip.toolTip = "Skips the selected number of slices (use, for example, on long thin samples with more slices than in-plane resolution)"
outputFormLayout.addRow("Slice skip: ", self.sliceSkip)
self.loadButton = qt.QPushButton("Load files")
outputFormLayout.addRow(self.loadButton)
#
# Add by name area
#
addByNameCollapsibleButton = ctk.ctkCollapsibleButton()
addByNameCollapsibleButton.text = "Add files by name"
addByNameCollapsibleButton.collapsed = True
addByNameFormLayout = qt.QFormLayout(addByNameCollapsibleButton)
# Don't enable Add by name for now - let's see if it's actually needed
# self.layout.addWidget(addByNameCollapsibleButton)
forExample = """
directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'
pathFormat = '%s/1326__rec%04d.png'
start, end = (50, 621)
"""
self.archetypePathEdit = ctk.ctkPathLineEdit()
self.archetypePathEdit.filters = ctk.ctkPathLineEdit().Files
addByNameFormLayout.addRow("Archetype file", self.archetypePathEdit)
self.archetypeFormat = qt.QLineEdit()
addByNameFormLayout.addRow("Name format", self.archetypeFormat)
self.indexRange = ctk.ctkRangeWidget()
self.indexRange.decimals = 0
self.indexRange.maximum = 0
addByNameFormLayout.addRow("Index range", self.indexRange)
self.generateNamesButton = qt.QPushButton("Apply")
self.generateNamesButton.toolTip = "Run the algorithm."
self.generateNamesButton.enabled = False
addByNameFormLayout.addRow(self.generateNamesButton)
# connections
self.addByBrowsingButton.connect('clicked()', self.addByBrowsing)
self.clearButton.connect('clicked()', self.onClear)
self.archetypePathEdit.connect('currentPathChanged(QString)', self.validateInput)
self.archetypePathEdit.connect('currentPathChanged(QString)', self.updateGUIFromArchetype)
self.archetypeFormat.connect('textChanged(QString)', self.validateInput)
self.generateNamesButton.connect('clicked()', self.onGenerateNames)
# self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.validateInput) # TODO - this is missing
self.loadButton.connect('clicked()', self.onLoadButton)
# refill last selection
self.archetypePathEdit.currentPath = slicer.util.settingsValue("ImageStacks/lastArchetypePath", "")
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.validateInput()