def memoryCheck(self):
"""Run a periodic memory check in a window"""
if not hasattr(self, 'sysInfo'):
self.sysInfo = slicer.vtkSystemInformation()
self.sysInfoWindow = qt.QTextBrowser()
if self.sysInfoWindow.visible:
return
self.sysInfoWindow.show()
self.memoryCallback()
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
# Data attribtues
self.energy_hwobj = None
self.transmission_hwobj = None
self.resolution_hwobj = None
self.queue_model_hwobj = None
self.session_hwobj = None
# Qt-Slots
self.defineSlot("populate_parameter_widget",({}))
# Properties
self.addProperty("session", "string", "/session")
self.addProperty("queue-model", "string", "/queue-model")
self.addProperty("beamline_setup", "string", "/beamline-setup")
# Layout
self.stack = qt.QWidgetStack(self, 'stack')
self.parameters_widget = DCParametersWidget(self, "parameters_widget")
self.toggle_page_button = qt.QPushButton('View Results',
self, 'toggle_page_button')
self.toggle_page_button.setFixedWidth(100)
self.results_view = qt.QTextBrowser(self, "results_view")
self.stack.addWidget(self.parameters_widget)
self.stack.addWidget(self.results_view)
main_layout = qt.QVBoxLayout(self)
self.layout().addWidget(self.stack)
bottom_layout = qt.QHBoxLayout(main_layout)
bottom_layout.addStretch()
bottom_layout.addWidget(self.toggle_page_button)
# Logic
self.stack.raiseWidget(self.parameters_widget)
self.parameters_widget.collection_type = None
qt.QObject.connect(self.toggle_page_button, qt.SIGNAL('clicked()'),
self.toggle_page)
self.toggle_page_button.setDisabled(True)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
indexPath = self.resourcePath('HTML/SlicerCMF/index.html')
url = qt.QUrl.fromLocalFile(indexPath)
modulesTextBrowser = qt.QTextBrowser()
modulesTextBrowser.setSource(url)
modulesTextBrowser.connect('anchorClicked(QUrl)', self.onAnchorClicked)
sp = qt.QSizePolicy()
sp.setVerticalPolicy(qt.QSizePolicy.Expanding)
sp.setHorizontalPolicy(qt.QSizePolicy.Expanding)
sp.setVerticalStretch(1)
sp.setHorizontalStretch(1)
modulesTextBrowser.setSizePolicy(sp)
self.modulesTextBrowser = modulesTextBrowser
self.layout.addWidget(self.modulesTextBrowser)
def __init__(self, *args):
BaseComponents.BlissWidget.__init__(self, *args)
self.session_hwobj = None
# Framwork-2 properties
self.addProperty("tunable-energy", "boolean", "True")
self.addProperty("session", "string", "/session")
self.addProperty("beamline_setup", "string", "/beamline-setup")
# Qt-Slots
self.defineSlot("populate_edna_parameter_widget", ({}))
# Layout
self.stack = qt.QWidgetStack(self, "stack")
self.parameters_widget = CharParametersWidget(self)
self.toggle_page_button = qt.QPushButton("View Results", self,
"toggle_page_button")
self.toggle_page_button.setFixedWidth(100)
self.results_view = qt.QTextBrowser(self, "results_view")
self.stack.addWidget(self.parameters_widget)
self.stack.addWidget(self.results_view)
main_layout = qt.QVBoxLayout(self)
self.layout().addWidget(self.stack)
bottom_layout = qt.QHBoxLayout(main_layout)
bottom_layout.addStretch()
bottom_layout.addWidget(self.toggle_page_button)
# Logic
self.stack.raiseWidget(self.parameters_widget)
self.parameters_widget.collection_type = None
qt.QObject.connect(self.toggle_page_button, qt.SIGNAL("clicked()"),
self.toggle_page)
self.toggle_page_button.setDisabled(True)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.tutorials = {
"ShapeAnalysisModule":
"https://bit.ly/2Fyn97v", # SPHARM-PDM Generator
"GroupWiseRegistrationModule": "https://bit.ly/2WsFiun",
"RegressionComputation": "https://bit.ly/2uVYche",
"ShapeVariationAnalyzer":
"https://bit.ly/2HYbHVA", # Population Analysis
"SRep": "https://bit.ly/3sTEG3H",
"SRepCreator": "https://bit.ly/3sTEG3H",
"SRepRefinement": "https://bit.ly/3sTEG3H",
}
# The anchor associated with each link corresponds to the name of the module to select.
# For example, after the user click on the link associated with `href="#DataImporter"`,
# the "DataImporter" module is selected.
text = """
<br>
<u>Workflow quick-reference:</u><br>
<br>
The drop-down Modules are ordered to follow the basic workflow for choosing and using data. As a quick reference, the basic steps involve:<br>
<br>
1. Use the <a href="#DataImporter"><b>Data importer</b></a> module to load your segmentations from FreeSurf, FSL, Autoseg, or a bunch of vtp's<br><br>
2. Use <a href="#ShapePopulationViewer"><b>Shape Population Viewer</b></a> to do a quality check on the imported data<br><br>
3. Use <a href="#ShapeAnalysisModule"><b>SPHARM-PDM Generator</b></a> to do spherical harmonics based analysis<br><br>
4. Use the <a href="#GroupWiseRegistrationModule"><b>Study-specific Shape Analysis</b></a> module.<br><br>
5. Use the <a href="#SkeletalRepresentationVisualizer"><b>S-Rep Shape Analysis</b></a> module to do shape analysis via skeletal representations.<br><br>
6. Use the <a href="#ShapeVariationAnalyzer"><b>Shape Evaluator</b></a> module to compute a mean shape and see how the population varies.<br><br>
7. Use <a href="#RegressionComputation"><b>Shape Regressions</b></a> module to do regression based analysis.<br><br>
8. Use the <a href="#MFSDA"><b>Shape Statistics</b></a> module.<br><br>
"""
# TEXTEDIT
self.HomeTextSection = qt.QTextBrowser()
self.HomeTextSection.setHtml(text)
self.HomeTextSection.setMinimumHeight(400)
self.HomeTextSection.connect('anchorClicked(QUrl)',
self.onAnchorClicked)
self.layout.addWidget(self.HomeTextSection)
# SPACER
self.layout.addStretch()
# SAMPLE DATA REGISTRATION
for json_file in [
'DataImporterInputData.json', 'MFSDAInputData.json',
'ShapeRegressionInputData.json', 'SPHARM-PDMTestData.json',
'SPHARM-PDMFiducials.json', 'SRepCreatorData.json',
'SVAInputData.json'
]:
with open(
self.resourcePath('SampleDataDescription/%s' % json_file),
'r') as json_data:
source_data = json.load(json_data)
if 'iconPath' in source_data:
iconPath = self.resourcePath(source_data['iconPath'])
else:
iconPath = None
SampleDataLogic.registerCustomSampleDataSource(
category=source_data['category'],
sampleName=source_data['sampleName'],
uris=source_data['uris'],
checksums=source_data.get('checksums', None),
fileNames=source_data['fileNames'],
nodeNames=None,
thumbnailFileName=iconPath,
loadFileType=None,
customDownloader=self.downloadSampleDataInFolder,
)
# HIDE SAMPLE DATA 'BUILTIN' CATEGORY
slicer.modules.sampledata.widgetRepresentation().self(
).setCategoryVisible('BuiltIn', False)
self.sampleDataModuleTab = None
self.sampleDataTabTextEdit = None
self.moduleNameToSampleDataCategory = {
"DataImporter": "Data Importer",
"MFSDA": "Covariate Significance Testing",
"ShapeAnalysisModule": "SPHARM-PDM",
"RegressionComputation": "Shape Regression",
"ShapeVariationAnalyzer": "Population Analysis",
"SRepCreator": "Skeletal Representation Creator"
}
self.sampleDataModuleTab = self.addSampleDataTab()
self.updateSampleDataTab("Home")
moduleMenu = slicer.util.mainWindow().moduleSelector().modulesMenu()
moduleMenu.connect("currentModuleChanged(QString)",
self.updateSampleDataTab)
def setupWindow(self):
self.setWindowTitle("lapdMouse Data Archive Browser")
self.resize(1000, 600)
if 'lapdMouseDBBrowser' in slicer.util.moduleNames():
self.modulePath = slicer.modules.lapdmousedbbrowser.path.replace(
"lapdMouseDBBrowser.py", "")
else:
self.modulePath = '.'
self.downloadIcon = qt.QIcon(
os.path.join(self.modulePath, 'Resources', 'Icons',
'download.png'))
self.storedIcon = qt.QIcon(
os.path.join(self.modulePath, 'Resources', 'Icons', 'stored.png'))
self.logo = qt.QPixmap(
os.path.join(self.modulePath, 'Resources', 'Icons',
'lapdMouseDBBrowser.png'))
self.banner = qt.QFrame()
self.banner.setLayout(qt.QGridLayout())
logo = qt.QLabel()
logo.setPixmap(self.logo)
self.banner.layout().addWidget(logo, 0, 0)
self.bannerTextBrowser = qt.QTextBrowser()
self.bannerTextBrowser.setOpenExternalLinks(True)
self.bannerTextBrowser.setMaximumHeight(120)
text = "<h1>lapdMouse Data Archive Browser</h1>"
text += "The lapdMouse data archive contains anatomically derived lung models and aerosol deposition measurements of mice for modeling and computational toxicology in mice."
text += " For more details about available datasets, data representation, other software, and support, please visit the <a href=\"https://doi.org/10.25820/9arg-9w56\">lapdMouse archive</a>"
text += "<br />This work was supported in part by NIH project R01ES023863."
self.bannerTextBrowser.html = text
self.banner.layout().addWidget(self.bannerTextBrowser, 0, 1)
self.table = qt.QTableWidget(self)
self.table.setRowCount(0)
self.table.setColumnCount(1)
self.table.setSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Expanding)
self.table.setHorizontalHeaderLabels(["Dataset name"
]) #,"Status","Comment"])
self.table.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
self.table.setSelectionMode(qt.QAbstractItemView.SingleSelection)
self.table.horizontalHeader().setStretchLastSection(True)
self.table.connect("itemSelectionChanged()", self.onDatasetChanged)
self.customForm = qt.QFrame()
self.customForm.setLayout(qt.QFormLayout())
self.customFormName = qt.QLineEdit("", self.customForm)
self.customFormName.readOnly = True
self.customForm.layout().addRow("Name", self.customFormName)
self.customFormDatasetInfo = qt.QLabel('<a href=\"' + self.projectURL +
'\">info</a>')
self.customFormDatasetInfo.setTextFormat(1)
self.customFormDatasetInfo.setOpenExternalLinks(True)
self.customForm.layout().addRow("Info", self.customFormDatasetInfo)
self.customFormAction = qt.QFrame(self.customForm)
self.customFormAction.setLayout(qt.QHBoxLayout())
self.customFormAction.layout().setSpacing(0)
self.customFormAction.layout().setMargin(0)
self.customFormDownloadButton = qt.QPushButton(
"download standard file selection", self.customFormAction)
self.customFormAction.layout().addWidget(self.customFormDownloadButton)
self.customFormDownloadButton.connect("clicked()",
self.onDownloadDataset)
self.customFormLoadButton = qt.QPushButton(
"load standard file selection in Slicer", self.customFormAction)
self.customFormAction.layout().addWidget(self.customFormLoadButton)
self.customFormLoadButton.connect("clicked()", self.onLoadDataset)
self.customForm.layout().addRow("Quick actions", self.customFormAction)
self.customFormFiles = qt.QTableWidget(self.customForm)
self.customFormFiles.setRowCount(0)
self.customFormFiles.setColumnCount(3)
self.customFormFiles.setHorizontalHeaderLabels(
["Status", "Filename", "Size"])
self.customFormFiles.horizontalHeader().setSectionResizeMode(
1, qt.QHeaderView.Stretch)
self.customFormFiles.setSelectionBehavior(
qt.QAbstractItemView.SelectRows)
self.customFormFiles.setMinimumHeight(400)
self.customForm.layout().addRow("Files", self.customFormFiles)
self.customFormAction2 = qt.QFrame(self.customForm)
self.customFormAction2.setLayout(qt.QHBoxLayout())
self.customFormAction2.layout().setSpacing(0)
self.customFormAction2.layout().setMargin(0)
self.customFormDownloadButton2 = qt.QPushButton(
"download selected files", self.customFormAction2)
self.customFormAction2.layout().addWidget(
self.customFormDownloadButton2)
self.customFormDownloadButton2.connect("clicked()",
self.onDownloadSelectedDataset)
self.customFormDeleteButton2 = qt.QPushButton("delete selected files",
self.customFormAction2)
self.customFormAction2.layout().addWidget(self.customFormDeleteButton2)
self.customFormDeleteButton2.connect("clicked()",
self.onDeleteSelectedDataset)
self.customFormLoadButton2 = qt.QPushButton(
"load selected files in Slicer", self.customFormAction2)
self.customFormAction2.layout().addWidget(self.customFormLoadButton2)
self.customFormLoadButton2.connect("clicked()",
self.onLoadSelectedDataset)
self.customForm.layout().addRow("", self.customFormAction2)
splitView = qt.QSplitter(self)
splitView.addWidget(self.table)
splitView.addWidget(self.customForm)
splitView.setSizes([200, 800])
self.updateTable()
self.onDatasetChanged()
self.setMenuWidget(self.banner)
self.setCentralWidget(splitView)
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
