def setupOutputSection(self):
self.outputCollapsibleButton = ctk.ctkCollapsibleButton()
self.outputCollapsibleButton.objectName = "Output"
self.outputCollapsibleButton.text = "Output"
self.layout.addWidget(self.outputCollapsibleButton)
self.outputCollapsibleButton.connect(
'toggled(bool)', lambda toggle: self.onWorkflowStepChanged(
self.outputCollapsibleButton, toggle))
outputFormLayout = qt.QFormLayout(self.outputCollapsibleButton)
self.computeStatusTextEdit = qt.QPlainTextEdit()
self.computeStatusTextEdit.setTextInteractionFlags(
qt.Qt.TextSelectableByMouse)
self.computeStatusTextEdit.maximumHeight = 75
outputFormLayout.addRow(self.computeStatusTextEdit)
self.measurementTree = slicer.qMRMLSubjectHierarchyTreeView()
self.measurementTree.setMRMLScene(slicer.mrmlScene)
qSize = qt.QSizePolicy()
qSize.setHorizontalPolicy(qt.QSizePolicy.MinimumExpanding)
qSize.setVerticalPolicy(qt.QSizePolicy.MinimumExpanding)
qSize.setVerticalStretch(1)
self.measurementTree.setSizePolicy(qSize)
self.measurementTree.setColumnHidden(
self.measurementTree.model().idColumn, True)
self.measurementTree.setColumnHidden(
self.measurementTree.model().transformColumn, True)
outputFormLayout.addRow(self.measurementTree)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# 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)
self.inputDirSelector = ctk.ctkPathLineEdit()
self.inputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.inputDirSelector.settingKey = 'Philips4dUsDicomPatcherInputDir'
parametersFormLayout.addRow("Input DICOM directory:",
self.inputDirSelector)
self.outputDirSelector = ctk.ctkPathLineEdit()
self.outputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirSelector.settingKey = 'Philips4dUsDicomPatcherOutputDir'
parametersFormLayout.addRow("Output DICOM directory:",
self.outputDirSelector)
self.enableDicomOutputCheckBox = qt.QCheckBox()
self.enableDicomOutputCheckBox.checked = True
self.enableDicomOutputCheckBox.setToolTip(
"If checked, patched 4D US DICOM files will be saved as DICOM files"
)
parametersFormLayout.addRow("Export to DICOM files",
self.enableDicomOutputCheckBox)
self.anonymizeDicomCheckBox = qt.QCheckBox()
self.anonymizeDicomCheckBox.checked = False
self.anonymizeDicomCheckBox.setToolTip(
"If checked, then patient identifiable information will be removed from the patched DICOM files"
)
parametersFormLayout.addRow(" Anonymize DICOM files",
self.anonymizeDicomCheckBox)
self.enableNrrdOutputCheckBox = qt.QCheckBox()
self.enableNrrdOutputCheckBox.checked = False
self.enableNrrdOutputCheckBox.setToolTip(
"If checked, 4D US DICOM files will be saved as NRRD files")
parametersFormLayout.addRow("Export to NRRD files",
self.enableNrrdOutputCheckBox)
#
# Patch Button
#
self.patchButton = qt.QPushButton("Patch")
self.patchButton.toolTip = "Fix and optionally anonymize DICOM files"
parametersFormLayout.addRow(self.patchButton)
# connections
self.patchButton.connect('clicked(bool)', self.onPatchButton)
self.statusLabel = qt.QPlainTextEdit()
self.statusLabel.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
parametersFormLayout.addRow(self.statusLabel)
# Add vertical spacer
self.layout.addStretch(1)
self.logic = Philips4dUsDicomPatcherLogic()
self.logic.logCallback = self.addLog
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 = "PlusRemote 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)
# Module requires openigtlinkremote
try:
slicer.modules.openigtlinkremote
except:
self.errorLabel = qt.QLabel(
"Could not find OpenIGTLink Remote module")
self.layout.addWidget(self.errorLabel)
return
# IGTLink Connector
connectorCollapsibleButton = ctk.ctkCollapsibleButton()
connectorCollapsibleButton.text = "OpenIGTLink Connector"
self.layout.addWidget(connectorCollapsibleButton)
connectorLayout = qt.QFormLayout(connectorCollapsibleButton)
self.linkInputSelector = slicer.qMRMLNodeComboBox()
self.linkInputSelector.nodeTypes = (("vtkMRMLIGTLConnectorNode"), "")
self.linkInputSelector.selectNodeUponCreation = True
self.linkInputSelector.addEnabled = False
self.linkInputSelector.removeEnabled = True
self.linkInputSelector.noneEnabled = False
self.linkInputSelector.showHidden = False
self.linkInputSelector.showChildNodeTypes = False
self.linkInputSelector.setMRMLScene(slicer.mrmlScene)
self.linkInputSelector.setToolTip("Pick connector node")
connectorLayout.addRow("OpenIGTLinkConnector: ",
self.linkInputSelector)
# Recording
recordingCollapsibleButton = ctk.ctkCollapsibleButton()
recordingCollapsibleButton.text = "Recording"
self.layout.addWidget(recordingCollapsibleButton)
recordingLayout = qt.QFormLayout(recordingCollapsibleButton)
self.captureIDBox = qt.QLineEdit()
recordingLayout.addRow("Capture Device ID: ", self.captureIDBox)
self.fileNameBox = qt.QLineEdit()
recordingLayout.addRow("Filename: ", self.fileNameBox)
# Move to the same row, use grid layout
recordingControlsLayout = qt.QGridLayout()
self.startRecordingButton = qt.QPushButton("Start Recording")
recordingControlsLayout.addWidget(self.startRecordingButton, 0, 0)
self.stopRecordingButton = qt.QPushButton("Stop Recording")
recordingControlsLayout.addWidget(self.stopRecordingButton, 0, 1)
recordingLayout.addRow(recordingControlsLayout)
# Reconstruction
reconstructionCollapsibleButton = ctk.ctkCollapsibleButton()
reconstructionCollapsibleButton.text = "Reconstruction"
self.layout.addWidget(reconstructionCollapsibleButton)
reconstructionLayout = qt.QFormLayout(reconstructionCollapsibleButton)
liveReconstructionLayout = qt.QGridLayout()
self.startReconstuctionButton = qt.QPushButton(
"Start Live Reconstruction")
liveReconstructionLayout.addWidget(self.startReconstuctionButton, 0, 0)
self.stopReconstructionButton = qt.QPushButton(
"Stop Live Reconstruction")
liveReconstructionLayout.addWidget(self.stopReconstructionButton, 0, 1)
reconstructionLayout.addRow(liveReconstructionLayout)
self.reconstructVolumeButton = qt.QPushButton(
"Reconstruct Recorded Volume")
reconstructionLayout.addRow(self.reconstructVolumeButton)
# Transform Update
transformUpdateCollapsibleButton = ctk.ctkCollapsibleButton()
transformUpdateCollapsibleButton.text = "Transform Update"
self.layout.addWidget(transformUpdateCollapsibleButton)
transformUpdateLayout = qt.QFormLayout(
transformUpdateCollapsibleButton)
self.transformUpdateInputSelector = slicer.qMRMLNodeComboBox()
self.transformUpdateInputSelector.nodeTypes = ((
"vtkMRMLLinearTransformNode"), "")
self.transformUpdateInputSelector.selectNodeUponCreation = True
self.transformUpdateInputSelector.addEnabled = False
self.transformUpdateInputSelector.removeEnabled = True
self.transformUpdateInputSelector.renameEnabled = True
self.transformUpdateInputSelector.noneEnabled = False
self.transformUpdateInputSelector.showHidden = False
self.transformUpdateInputSelector.showChildNodeTypes = False
self.transformUpdateInputSelector.setMRMLScene(slicer.mrmlScene)
self.transformUpdateInputSelector.setToolTip("Pick transform node")
transformUpdateLayout.addRow("Transform node: ",
self.transformUpdateInputSelector)
self.updateTransformButton = qt.QPushButton("Update")
transformUpdateLayout.addRow(self.updateTransformButton)
self.configFileNameBox = qt.QLineEdit()
transformUpdateLayout.addRow("Filename: ", self.configFileNameBox)
self.saveTransformButton = qt.QPushButton("Save Config")
transformUpdateLayout.addRow(self.saveTransformButton)
replyUpdateCollapsibleButton = ctk.ctkCollapsibleButton()
replyUpdateCollapsibleButton.text = "Reply"
self.layout.addWidget(replyUpdateCollapsibleButton)
replyLayout = qt.QFormLayout(replyUpdateCollapsibleButton)
self.replyBox = qt.QPlainTextEdit()
self.replyBox.setReadOnly(True)
replyLayout.addRow(self.replyBox)
# connections
self.startRecordingButton.connect('clicked(bool)',
self.onStartRecording)
self.stopRecordingButton.connect('clicked(bool)', self.onStopRecording)
self.startReconstuctionButton.connect('clicked(bool)',
self.onStartReconstruction)
self.stopReconstructionButton.connect('clicked(bool)',
self.onStopReconstruction)
self.reconstructVolumeButton.connect('clicked(bool)',
self.onReconstVolume)
self.updateTransformButton.connect('clicked(bool)',
self.onUpdateTransform)
self.saveTransformButton.connect('clicked(bool)', self.onSaveTransform)
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# 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)
self.inputDirSelector = ctk.ctkPathLineEdit()
self.inputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.inputDirSelector.settingKey = 'DICOMPatcherInputDir'
parametersFormLayout.addRow("Input DICOM directory:", self.inputDirSelector)
self.outputDirSelector = ctk.ctkPathLineEdit()
self.outputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirSelector.settingKey = 'DICOMPatcherOutputDir'
parametersFormLayout.addRow("Output DICOM directory:", self.outputDirSelector)
self.normalizeFileNamesCheckBox = qt.QCheckBox()
self.normalizeFileNamesCheckBox.checked = True
self.normalizeFileNamesCheckBox.setToolTip("Replace file and folder names with automatically generated names."
" Fixes errors caused by file path containins special characters or being too long.")
parametersFormLayout.addRow("Normalize file names", self.normalizeFileNamesCheckBox)
self.forceSamePatientNameIdInEachDirectoryCheckBox = qt.QCheckBox()
self.forceSamePatientNameIdInEachDirectoryCheckBox.checked = False
self.forceSamePatientNameIdInEachDirectoryCheckBox.setToolTip("Generate patient name and ID from the first file in a directory"
" and force all other files in the same directory to have the same patient name and ID."
" Enable this option if a separate patient directory is created for each patched file.")
parametersFormLayout.addRow("Force same patient name and ID in each directory", self.forceSamePatientNameIdInEachDirectoryCheckBox)
self.generateMissingIdsCheckBox = qt.QCheckBox()
self.generateMissingIdsCheckBox.checked = True
self.generateMissingIdsCheckBox.setToolTip("Generate missing patient, study, series IDs. It is assumed that"
" all files in a directory belong to the same series. Fixes error caused by too aggressive anonymization"
" or incorrect DICOM image converters.")
parametersFormLayout.addRow("Generate missing patient/study/series IDs", self.generateMissingIdsCheckBox)
self.generateImagePositionFromSliceThicknessCheckBox = qt.QCheckBox()
self.generateImagePositionFromSliceThicknessCheckBox.checked = True
self.generateImagePositionFromSliceThicknessCheckBox.setToolTip("Generate 'image position sequence' for"
" multi-frame files that only have 'SliceThickness' field. Fixes error in Dolphin 3D CBCT scanners.")
parametersFormLayout.addRow("Generate slice position for multi-frame volumes", self.generateImagePositionFromSliceThicknessCheckBox)
self.anonymizeDicomCheckBox = qt.QCheckBox()
self.anonymizeDicomCheckBox.checked = False
self.anonymizeDicomCheckBox.setToolTip("If checked, then some patient identifiable information will be removed"
" from the patched DICOM files. There are many fields that can identify a patient, this function does not remove all of them.")
parametersFormLayout.addRow("Partially anonymize", self.anonymizeDicomCheckBox)
#
# Patch Button
#
self.patchButton = qt.QPushButton("Patch")
self.patchButton.toolTip = "Fix DICOM files in input directory and write them to output directory"
parametersFormLayout.addRow(self.patchButton)
#
# Import Button
#
self.importButton = qt.QPushButton("Import")
self.importButton.toolTip = "Import DICOM files in output directory into Slicer DICOM database"
parametersFormLayout.addRow(self.importButton)
#
# Switch to DICOM module Button
#
self.switchToDICOMModuleButton = qt.QPushButton("Go to DICOM module")
self.switchToDICOMModuleButton.toolTip = "Open DICOM module where imported data can be loaded into the scene"
parametersFormLayout.addRow(self.switchToDICOMModuleButton)
# connections
self.patchButton.connect('clicked(bool)', self.onPatchButton)
self.importButton.connect('clicked(bool)', self.onImportButton)
self.switchToDICOMModuleButton.connect('clicked(bool)', self.onSwitchToDICOMModuleButton)
self.statusLabel = qt.QPlainTextEdit()
self.statusLabel.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
parametersFormLayout.addRow(self.statusLabel)
# Add vertical spacer
self.layout.addStretch(1)
self.logic = DICOMPatcherLogic()
self.logic.logCallback = self.addLog
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# 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)
self.inputDirSelector = ctk.ctkPathLineEdit()
self.inputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.inputDirSelector.settingKey = 'DicomPatcherInputDir'
parametersFormLayout.addRow("Input DICOM directory:",
self.inputDirSelector)
self.outputDirSelector = ctk.ctkPathLineEdit()
self.outputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirSelector.settingKey = 'DicomPatcherOutputDir'
parametersFormLayout.addRow("Output DICOM directory:",
self.outputDirSelector)
self.generateMissingIdsCheckBox = qt.QCheckBox()
self.generateMissingIdsCheckBox.checked = True
self.generateMissingIdsCheckBox.setToolTip(
"If checked, then missing patient, study, series IDs are generated. It is assumed that all files in a directory belong to the same series. Fixes error caused by too aggressive anonymization or incorrect DICOM image converters."
)
parametersFormLayout.addRow("Generate missing IDs",
self.generateMissingIdsCheckBox)
self.generateImagePositionFromSliceThicknessCheckBox = qt.QCheckBox()
self.generateImagePositionFromSliceThicknessCheckBox.checked = True
self.generateImagePositionFromSliceThicknessCheckBox.setToolTip(
"If checked, then image position sequence is generated for multi-frame files that only have SliceThickness field. Fixes error in Dolphin 3D CBCT scanners."
)
parametersFormLayout.addRow(
"Generate slice position for multi-frame volumes",
self.generateImagePositionFromSliceThicknessCheckBox)
self.anonymizeDicomCheckBox = qt.QCheckBox()
self.anonymizeDicomCheckBox.checked = False
self.anonymizeDicomCheckBox.setToolTip(
"If checked, then some patient identifiable information will be removed from the patched DICOM files. There are many fields that can identify a patient, this function does not remove all of them."
)
parametersFormLayout.addRow("Anonymize DICOM files",
self.anonymizeDicomCheckBox)
#
# Patch Button
#
self.patchButton = qt.QPushButton("Patch")
self.patchButton.toolTip = "Fix and optionally anonymize DICOM files"
parametersFormLayout.addRow(self.patchButton)
# connections
self.patchButton.connect('clicked(bool)', self.onPatchButton)
self.statusLabel = qt.QPlainTextEdit()
self.statusLabel.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
parametersFormLayout.addRow(self.statusLabel)
# Add vertical spacer
self.layout.addStretch(1)
self.logic = DicomPatcherLogic()
self.logic.logCallback = self.addLog
