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LungCTAnalyzer.py
3384 lines (2803 loc) · 169 KB
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LungCTAnalyzer.py
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import os
import requests
import unittest
import glob
import time
import logging
import vtk, qt, ctk, slicer
import sys, subprocess
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
from SegmentStatisticsPlugins import *
#
# LungCTAnalyzer
#
class LungCTAnalyzer(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "Lung CT Analyzer"
self.parent.categories = ["Chest Imaging Platform"]
self.parent.dependencies = [] # TODO: add here list of module names that this module requires
self.parent.contributors = ["Rudolf Bumm (KSGR Switzerland)"]
self.parent.helpText = """Lung analysis consists of producing five different segmentations of lungs based on Hounsfield unit range:
Bulla / emphysema, inflated lung, infiltrated llung, collapsed lung and thoracic vessels. It allows a volume quantification
as well as a spacial representation of the diseased lung regions. Furthermore, we introduce a new parameter - CovidQ -
for an instant estimation of the severity of infestation. See more information in <a href="https://github.com/rbumm/SlicerLungCTAnalyzer">module documentation</a>.<br>
The extension transmits basic information when you use it (simple usage counter). No IP or any personal data are being sent.
"""
self.parent.acknowledgementText = """
The first version of this file was originally developed by Rudolf Bumm, Kantonsspital Graubünden, Switzerland. Parts of this code were inspired by a code snippet (https://gist.github.com/lassoan/5ad51c89521d3cd9c5faf65767506b37) of Andras Lasso, PerkLab.
"""
# Additional initialization step after application startup is complete
slicer.app.connect("startupCompleted()", registerSampleData)
#
# Register sample data sets in Sample Data module
#
def registerSampleData():
"""
Add data sets to Sample Data module.
"""
# It is always recommended to provide sample data for users to make it easy to try the module,
# but if no sample data is available then this method (and associated startupCompeted signal connection) can be removed.
import SampleData
iconsPath = os.path.join(os.path.dirname(__file__), 'Resources/Icons')
# To ensure that the source code repository remains small (can be downloaded and installed quickly)
# it is recommended to store data sets that are larger than a few MB in a Github release.
# load demo chest CT
SampleData.SampleDataLogic.registerCustomSampleDataSource(
category="Lung",
sampleName='DemoChestCT',
uris='https://github.com/rbumm/SlicerLungCTAnalyzer/releases/download/SampleData/LungCTAnalyzerChestCT.nrrd',
fileNames='DemoChestCT.nrrd',
nodeNames='DemoChestCT',
thumbnailFileName=os.path.join(iconsPath, 'DemoChestCT.png'),
loadFileType='VolumeFile',
checksums='SHA256:9bb74f4383bce0ced80243916e785ce564cc2c8f535e8273da8a04f80dff4287'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
category="Lung",
sampleName='DemoLungMasks',
uris='https://github.com/rbumm/SlicerLungCTAnalyzer/releases/download/SampleData/LungCTAnalyzerMaskSegmentation.seg.nrrd',
fileNames='DemoLungMasks.seg.nrrd',
nodeNames='DemoLungMasks',
thumbnailFileName=os.path.join(iconsPath, 'DemoLungMasks.png'),
loadFileType='SegmentationFile',
checksums='SHA256:79f151b42cf999c1ecf13ee793da6cf649b54fe8634ec07723e4a1f44e53b57c'
)
#
# LungCTAnalyzerWidget
#
class LungCTAnalyzerWidget(ScriptedLoadableModuleWidget, VTKObservationMixin):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent=None):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
self.version = 2.69
ScriptedLoadableModuleWidget.__init__(self, parent)
VTKObservationMixin.__init__(self) # needed for parameter node observation
self.logic = None
self._parameterNode = None
self._updatingGUIFromParameterNode = False
self.inputFilename = None
self.batchProcessingInputDir = ""
self.batchProcessingOutputDir = ""
self.batchProcessingTestMode = False
self.batchProcessingIsCancelled = False
self.csvOnly = False
self.useCalibratedCT = False
self.scanInput = False
self.lobeAnalysis = False
self.areaAnalysis = False
self.batchProcessing = False
self.isNiiGzFormat = False
self.checkForUpdates = True
self.resetmode = False
def setup(self):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer).
# Additional widgets can be instantiated manually and added to self.layout.
uiWidget = slicer.util.loadUI(self.resourcePath('UI/LungCTAnalyzer.ui'))
self.layout.addWidget(uiWidget)
self.layout.objectName = "Lung CT Analyzer layout"
self.ui = slicer.util.childWidgetVariables(uiWidget)
# Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's
# "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's.
# "setMRMLScene(vtkMRMLScene*)" slot.
uiWidget.setMRMLScene(slicer.mrmlScene)
# Create logic class. Logic implements all computations that should be possible to run
# in batch mode, without a graphical user interface.
self.logic = LungCTAnalyzerLogic()
self.volumeRenderingPropertyUpdateTimer = qt.QTimer()
self.volumeRenderingPropertyUpdateTimer.setInterval(1000)
self.volumeRenderingPropertyUpdateTimer.setSingleShot(True)
self.volumeRenderingPropertyUpdateTimer.timeout.connect(self.updateVolumeRenderingProperty)
# Connections
# These connections ensure that we update parameter node when scene is closed
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent, self.onSceneStartClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent, self.onSceneEndClose)
# These connections ensure that we update the GUI when scene is imported
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndImportEvent, self.onSceneEndImport)
# These connections ensure that whenever user changes some settings on the GUI, that is saved in the MRML scene
# (in the selected parameter node).
# Input image and segmentation
self.ui.inputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.inputSegmentationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSegmentationSelected)
self.ui.toggleInputSegmentationVisibility2DPushButton.connect('clicked()', self.onToggleInputSegmentationVisibility2D)
self.ui.toggleInputSegmentationVisibility3DPushButton.connect('clicked()', self.onToggleInputSegmentationVisibility3D)
# Output options
self.ui.generateStatisticsCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.lobeAnalysisCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.areaAnalysisCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.niigzFormatCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.lungMaskedVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.outputSegmentationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.outputResultsTableSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.volumeRenderingPropertyNodeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI)
self.ui.testModeCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.csvOnlyCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.useCalibratedCTCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
self.ui.scanInputCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
# Advanced options
self.ui.checkForUpdatesCheckBox.connect('toggled(bool)', self.updateParameterNodeFromGUI)
# Thresholds
self.ui.BullaRangeWidget.connect('valuesChanged(double,double)', self.onBullaRangeWidgetChanged)
self.ui.InflatedRangeWidget.connect('valuesChanged(double,double)', self.onInflatedRangeWidgetChanged)
self.ui.InfiltratedRangeWidget.connect('valuesChanged(double,double)', self.onInfiltratedRangeWidgetChanged)
self.ui.CollapsedRangeWidget.connect('valuesChanged(double,double)', self.onCollapsedRangeWidgetChanged)
self.ui.VesselsRangeWidget.connect('valuesChanged(double,double)', self.onVesselsRangeWidgetChanged)
self.ui.restoreDefaultsButton.connect('clicked(bool)', self.onRestoreDefaultsButton)
self.ui.saveThresholdsButton.connect('clicked(bool)', self.onSaveThresholdsButton)
self.ui.loadThresholdsButton.connect('clicked(bool)', self.onLoadThresholdsButton)
self.ui.createPDFReportButton.connect('clicked(bool)', self.onCreatePDFReportButton)
# Connect path selectors
self.ui.inputDirectoryPathLineEdit.connect('currentPathChanged(const QString&)', self.onInputDirectoryPathLineEditChanged)
self.ui.outputDirectoryPathLineEdit.connect('currentPathChanged(const QString&)', self.onOutputDirectoryPathLineEditChanged)
self.ui.batchProcessingButton.connect('clicked(bool)', self.onBatchProcessingButton)
self.ui.cancelBatchProcessingButton.connect('clicked(bool)', self.onCancelBatchProcessingButton)
# Report Dir
self.ui.selectReportDirectoryButton.connect('clicked(bool)', self.onSelectReportDirectoryButton)
self.ui.selectReportDirectoryButton.directoryChanged.connect(self.onReportDirectoryChanged)
self.ui.selectReportDirectoryButton.connect('clicked(bool)', self.onSelectReportDirectoryButton)
self.ui.openReportDirectoryButton.connect('clicked(bool)', self.onOpenReportDirectoryButton)
settings=qt.QSettings(slicer.app.launcherSettingsFilePath, qt.QSettings.IniFormat)
self.ui.inputDirectoryPathLineEdit.currentPath = settings.value("LungCtAnalyzer/batchProcessingInputFolder", "")
self.ui.outputDirectoryPathLineEdit.currentPath = settings.value("LungCtAnalyzer/batchProcessingOutputFolder", "")
if settings.value("LungCtAnalyzer/BullaRangeWidgetMinimumValue", "") != "":
self.ui.BullaRangeWidget.minimumValue = float(settings.value("LungCtAnalyzer/BullaRangeWidgetMinimumValue", ""))
if settings.value("LungCtAnalyzer/BullaRangeMaximumValue", "") != "":
self.ui.BullaRangeWidget.maximumValue = float(settings.value("LungCtAnalyzer/BullaRangeWidgetMaximumValue", ""))
if settings.value("LungCtAnalyzer/InflatedRangeWidgetMinimumValue", "") != "":
self.ui.InflatedRangeWidget.minimumValue = float(settings.value("LungCtAnalyzer/InflatedRangeWidgetMinimumValue", ""))
if settings.value("LungCtAnalyzer/InflatedRangeMaximumValue", "") != "":
self.ui.InflatedRangeWidget.maximumValue = float(settings.value("LungCtAnalyzer/InflatedRangeWidgetMaximumValue", ""))
if settings.value("LungCtAnalyzer/InfiltratedRangeWidgetMinimumValue", "") != "":
self.ui.InfiltratedRangeWidget.minimumValue = float(settings.value("LungCtAnalyzer/InfiltratedRangeWidgetMinimumValue", ""))
if settings.value("LungCtAnalyzer/InfiltratedRangeMaximumValue", "") != "":
self.ui.InfiltratedRangeWidget.maximumValue = float(settings.value("LungCtAnalyzer/InfiltratedRangeWidgetMaximumValue", ""))
if settings.value("LungCtAnalyzer/CollapsedRangeWidgetMinimumValue", "") != "":
self.ui.CollapsedRangeWidget.minimumValue = float(settings.value("LungCtAnalyzer/CollapsedRangeWidgetMinimumValue", ""))
if settings.value("LungCtAnalyzer/CollapsedRangeMaximumValue", "") != "":
self.ui.CollapsedRangeWidget.maximumValue = float(settings.value("LungCtAnalyzer/CollapsedRangeWidgetMaximumValue", ""))
if settings.value("LungCtAnalyzer/VesselsRangeWidgetMinimumValue", "") != "":
self.ui.VesselsRangeWidget.minimumValue = float(settings.value("LungCtAnalyzer/VesselsRangeWidgetMinimumValue", ""))
if settings.value("LungCtAnalyzer/VesselsRangeMaximumValue", "") != "":
self.ui.VesselsRangeWidget.maximumValue = float(settings.value("LungCtAnalyzer/VesselsRangeWidgetMaximumValue", ""))
if settings.value("LungCtAnalyzer/testModeCheckBoxChecked", "") != "":
self.batchProcessingTestMode = eval(settings.value("LungCtAnalyzer/testModeCheckBoxChecked", ""))
self.ui.testModeCheckBox.checked = eval(settings.value("LungCtAnalyzer/testModeCheckBoxChecked", ""))
if settings.value("LungCtAnalyzer/csvOnlyCheckBoxChecked", "") != "":
self.csvOnly = eval(settings.value("LungCtAnalyzer/csvOnlyCheckBoxChecked", ""))
self.ui.csvOnlyCheckBox.checked = eval(settings.value("LungCtAnalyzer/csvOnlyCheckBoxChecked", ""))
if settings.value("LungCtAnalyzer/useCalibratedCTCheckBoxChecked", "") != "":
self.useCalibratedCT = eval(settings.value("LungCtAnalyzer/useCalibratedCTCheckBoxChecked", ""))
self.ui.useCalibratedCTCheckBox.checked = eval(settings.value("LungCtAnalyzer/useCalibratedCTCheckBoxChecked", ""))
if settings.value("LungCtAnalyzer/scanInputCheckBoxChecked", "") != "":
self.scanInput = eval(settings.value("LungCtAnalyzer/scanInputCheckBoxChecked", ""))
self.ui.scanInputCheckBox.checked = eval(settings.value("LungCtAnalyzer/scanInputCheckBoxChecked", ""))
if settings.value("LungCtAnalyzer/lobeAnalysisCheckBoxChecked", "") != "":
self.lobeAnalysis = eval(settings.value("LungCtAnalyzer/lobeAnalysisCheckBoxChecked", ""))
self.ui.lobeAnalysisCheckBox.checked = eval(settings.value("LungCtAnalyzer/lobeAnalysisCheckBoxChecked", ""))
if settings.value("LungCtAnalyzer/areaAnalysisCheckBoxChecked", "") != "":
self.areaAnalysis = eval(settings.value("LungCtAnalyzer/areaAnalysisCheckBoxChecked", ""))
self.ui.areaAnalysisCheckBox.checked = eval(settings.value("LungCtAnalyzer/areaAnalysisCheckBoxChecked", ""))
if settings.value("LungCtAnalyzer/niigzFormatCheckBoxChecked", "") != "":
self.isNiiGzFormat = eval(settings.value("LungCtAnalyzer/niigzFormatCheckBoxChecked", ""))
self.ui.niigzFormatCheckBox.checked = eval(settings.value("LungCtAnalyzer/niigzFormatCheckBoxChecked", ""))
# Opacities
self.opacitySliders = {
"Emphysema": self.ui.bullaOpacityWidget,
"Inflated": self.ui.infiltratedOpacityWidget,
"Infiltration": self.ui.infiltratedOpacityWidget,
"Collapsed": self.ui.collapsedOpacityWidget,
"Vessels": self.ui.vesselsOpacityWidget,
}
for segment in self.opacitySliders:
self.opacitySliders[segment].connect('valueChanged(double)', self.updateVolumeRenderingPropertyFromGUI)
# Buttons
self.ui.downloadCovidDataButton.connect('clicked()', self.onDownloadCovidData)
self.ui.applyButton.connect('clicked()', self.onApplyButton)
self.ui.showResultsTablePushButton.connect('clicked()', self.onShowResultsTable)
self.ui.saveResultsCSVButton.connect('clicked()', self.onSaveResultsCSV)
self.ui.showCovidResultsTableButton.connect('clicked()', self.onShowCovidResultsTable)
self.ui.showEmphysemaResultsTableButton.connect('clicked()', self.onShowEmphysemaResultsTable)
self.ui.toggleOutputSegmentationVisibility2DPushButton.connect('clicked()', self.onToggleOutputSegmentationVisibility2D)
self.ui.toggleOutputSegmentationVisibility3DPushButton.connect('clicked()', self.onToggleOutputSegmentationVisibility3D)
self.ui.toggleMaskedVolumeDisplay2DPushButton.connect('clicked()', self.onMaskedVolumeDisplay2D)
self.ui.toggleMaskedVolumeDisplay3DPushButton.connect('clicked()', self.onMaskedVolumeDisplay3D)
self.reportFolder = ""
import configparser
parser = configparser.SafeConfigParser()
parser.read(slicer.app.slicerUserSettingsFilePath + 'LCTA.INI')
if parser.has_option('reportFolder', 'path'):
self.reportFolder = parser.get('reportFolder','path')
else:
self.reportFolder = f"{slicer.app.defaultScenePath}/LungCTAnalyzerReports/"
from pathlib import Path
Path(self.reportFolder).mkdir(parents=True, exist_ok=True)
parser.add_section('reportFolder')
parser.set('reportFolder', 'path', self.reportFolder)
with open(slicer.app.slicerUserSettingsFilePath + 'LCTA.INI', 'w') as configfile: # save
parser.write(configfile)
self.ui.selectReportDirectoryButton.directory = self.reportFolder
if parser.has_option('Updates', 'check'):
self.checkForUpdates = parser.getboolean('Updates','check')
else:
parser.add_section('Updates')
parser.set('Updates', 'check', str(True))
self.checkForUpdates = True
with open(slicer.app.slicerUserSettingsFilePath + 'LCTA.INI', 'w') as configfile: # save
parser.write(configfile)
# Make sure parameter node is initialized (needed for module reload)
self.logic.inputSegmentation = None
self.logic.inputVolume = None
self.initializeParameterNode()
slicer.app.applicationLogic().FitSliceToAll()
# Set initial button texts
if hasattr(self.logic, "inputSegmentation"):
if self.logic.inputSegmentation:
segmentationDisplayNode = self.logic.inputSegmentation.GetDisplayNode()
if segmentationDisplayNode.GetVisibility2D():
self.ui.toggleInputSegmentationVisibility2DPushButton.text = "Hide mask segments in 2D"
else:
self.ui.toggleInputSegmentationVisibility2DPushButton.text = "Show mask segments in 2D"
if self.logic.inputSegmentation.GetDisplayNode().GetVisibility3D() and self.logic.inputSegmentation.GetSegmentation().ContainsRepresentation("Closed surface"):
self.ui.toggleInputSegmentationVisibility3DPushButton.text = "Hide mask segments in 3D"
else:
self.ui.toggleInputSegmentationVisibility3DPushButton.text = "Show mask segments in 3D"
else:
self.ui.toggleInputSegmentationVisibility2DPushButton.text = "Show mask segments in 2D"
self.ui.toggleInputSegmentationVisibility3DPushButton.text = "Show mask segments in 3D"
if hasattr(self.logic, "outputSegmentation"):
if self.logic.outputSegmentation:
segmentationDisplayNode = self.logic.outputSegmentation.GetDisplayNode()
if segmentationDisplayNode.GetVisibility2D():
self.ui.toggleOutputSegmentationVisibility2DPushButton.text = "Hide output segments in 2D"
else:
self.ui.toggleOutputSegmentationVisibility2DPushButton.text = "Show output segments in 2D"
if self.logic.outputSegmentation.GetDisplayNode().GetVisibility3D() and self.logic.outputSegmentation.GetSegmentation().ContainsRepresentation("Closed surface"):
self.ui.toggleOutputSegmentationVisibility3DPushButton.text = "Hide output segments in 3D"
else:
self.ui.toggleOutputSegmentationVisibility3DPushButton.text = "Show output segments in 3D"
else:
self.ui.toggleOutputSegmentationVisibility2DPushButton.text = "Show output segments in 2D"
self.ui.toggleOutputSegmentationVisibility3DPushButton.text = "Show output segments in 3D"
if hasattr(self.logic, "showLungMaskedVolumeIn2D"):
if self.logic.showLungMaskedVolumeIn2D:
self.ui.toggleMaskedVolumeDisplay2DPushButton.text = "Hide preview in 2D"
else:
self.ui.toggleMaskedVolumeDisplay2DPushButton.text = "Show preview in 2D"
else:
self.ui.toggleMaskedVolumeDisplay2DPushButton.text = "Show preview in 2D"
if hasattr(self.logic, "wasVisible3D"):
if self.logic.wasVisible3D:
self.ui.toggleMaskedVolumeDisplay3DPushButton.text = "Show preview in 3D"
else:
self.ui.toggleMaskedVolumeDisplay3DPushButton.text = "Hide preview in 3D"
else:
self.ui.toggleMaskedVolumeDisplay3DPushButton.text = "Show preview in 3D"
self.show3DWarning = True
# show version on GUI
self.versionText = "Lung CT Analyzer V %.2f" % self.version
self.ui.versionLabel.text = self.versionText
# show uses
import os
import requests
def get_users(program):
try:
url = 'http://scientific-networks.de/get_users.php'
api_key = "WVnB2F7Uibt2TC"
params = {'api_key': api_key, 'prog': program, 'year': "2023"}
response = requests.get(url, params=params, timeout=5)
return response.json()
except requests.exceptions.RequestException as e:
print(f"Unable to get users {e}")
return None # or some default values
# use it
uses = get_users("lcta")
if uses:
usage_text = str(uses) + " uses since 9/23"
self.ui.label_uses.text = usage_text
from urllib.request import urlopen
import json
if self.checkForUpdates:
link = "https://github.com/rbumm/SlicerLungCTAnalyzer/blob/master/version.json?raw=true"
try:
f = urlopen(link)
myfile = f.read()
#print(myfile)
dct = json.loads(myfile)
#print(dct["version"])
if self.version < float(dct["version"]):
slicer.util.messageBox("There is a new version of Lung CT Analyzer available. \n Please consider updating via the extension manager.")
else:
print("Lung CT analyzer is up to date.")
except Exception as e:
qt.QApplication.restoreOverrideCursor()
slicer.util.errorDisplay("Failed to check current version: "+str(e))
else :
print("Checking of Lung CT analyzer updates is disabled.")
def cleanup(self):
"""
Called when the application closes and the module widget is destroyed.
"""
self.removeObservers()
import configparser
parser = configparser.SafeConfigParser()
parser.read(slicer.app.slicerUserSettingsFilePath + 'LCTA.INI')
if parser.has_option('Updates', 'check'):
if self.checkForUpdates:
parser.set('Updates','check',str(True))
else:
parser.set('Updates','check',str(False))
else:
parser.add_section('Updates')
if self.checkForUpdates:
parser.set('Updates','check',str(True))
else:
parser.set('Updates','check',str(False))
with open(slicer.app.slicerUserSettingsFilePath + 'LCTA.INI', 'w') as configfile: # save
parser.write(configfile)
def enter(self):
"""
Called each time the user opens this module.
"""
# Make sure parameter node exists and observed
print("Enter")
self.initializeParameterNode()
self.updateParameterNodeFromGUI()
def exit(self):
"""
Called each time the user opens a different module.
"""
# Do not react to parameter node changes (GUI wlil be updated when the user enters into the module)
self.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateGUIFromParameterNode)
def onSceneStartClose(self, caller, event):
"""
Called just before the scene is closed.
"""
# Parameter node will be reset, do not use it anymore
self.setParameterNode(None)
def onSceneEndImport(self, caller, event):
"""
Called just after the scene is imported
"""
return
def onSceneEndClose(self, caller, event):
"""
Called just after the scene is closed.
"""
# If this module is shown while the scene is closed then recreate a new parameter node immediately
if self.parent.isEntered:
self.initializeParameterNode()
def initializeParameterNode(self):
"""
Ensure parameter node exists and observed.
"""
# print("initializeParameterNode")
# Parameter node stores all user choices in parameter values, node selections, etc.
# so that when the scene is saved and reloaded, these settings are restored.
self.setParameterNode(self.logic.getParameterNode())
# Select default input nodes if nothing is selected yet to save a few clicks for the user
if not self.logic.inputVolume:
firstVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
if firstVolumeNode:
self.logic.inputVolume = firstVolumeNode
if not self.logic.inputSegmentation:
segNode = slicer.util.getFirstNodeByClassByName("vtkMRMLSegmentationNode", "Lung segmentation")
if segNode:
self.logic.inputSegmentation = segNode
segmentation = segNode.GetSegmentation()
self.logic.rightLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("right lung")
print("right lung segment exists")
self.logic.leftLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("left lung")
print("left lung segment exists")
#initial masks always on
segmentationDisplayNode = self.logic.inputSegmentation.GetDisplayNode()
segmentationDisplayNode.Visibility2DOn()
self.ui.toggleInputSegmentationVisibility2DPushButton.text = "Hide mask segments in 2D"
segmentationDisplayNode.Visibility3DOff()
self.ui.toggleInputSegmentationVisibility3DPushButton.text = "Show mask segments in 3D"
#initial masks always on
if self.logic.inputSegmentation:
segmentationDisplayNode = self.logic.inputSegmentation.GetDisplayNode()
segmentationDisplayNode.Visibility2DOn()
self.ui.toggleInputSegmentationVisibility2DPushButton.text = "Hide mask segments in 2D"
segmentationDisplayNode.Visibility3DOff()
self.ui.toggleInputSegmentationVisibility3DPushButton.text = "Show mask segments in 3D"
if (self.logic.inputVolume and self.logic.inputSegmentation
and self.logic.rightLungMaskSegmentID and self.logic.leftLungMaskSegmentID):
self.ui.applyButton.toolTip = "Compute results"
self.ui.applyButton.enabled = True
def checkInputVolumeAndSegmentations(self):
"""
"""
self.logic.inputVolume = self.ui.inputVolumeSelector.currentNode()
if not self.logic.inputVolume:
slicer.util.messageBox("No input volume.")
raise ValueError("No input volume.")
else:
print("self.logic.inputVolume found")
self.logic.inputSegmentation = self.ui.inputSegmentationSelector.currentNode()
if self.logic.inputSegmentation:
print("self.logic.inputsegmentation found")
segmentation = self.logic.inputSegmentation.GetSegmentation()
self.logic.rightLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("right lung")
if not self.logic.rightLungMaskSegmentID:
slicer.util.messageBox("right lung input segmentent missing.")
raise ValueError("Right lung input segment missing.")
else:
print("Right lung input segment found.")
self.logic.leftLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("left lung")
if not self.logic.leftLungMaskSegmentID:
slicer.util.messageBox("Left lung input segment missing.")
raise ValueError("Left lung input segment missing.")
else:
print("Left lung input segment found.")
else:
slicer.util.messageBox("Input segmentation missing.")
raise ValueError("No input segmentation.")
if self.lobeAnalysis:
lobeMissing = False
for lobeName in ['right upper lobe', 'right middle lobe', 'right lower lobe', 'left upper lobe', 'left lower lobe' ]:
sourceSegID = self.logic.inputSegmentation.GetSegmentation().GetSegmentIdBySegmentName(lobeName)
if not sourceSegID:
slicer.util.messageBox(lobeName + " input segment missing. Recreate input segmentation with AI and lobe generation.")
lobeMissing = True
else:
print(lobeName + " input segment found.")
if lobeMissing:
raise ValueError("Lobe input segment is missing.")
def setParameterNode(self, inputParameterNode):
"""
Set and observe parameter node.
Observation is needed because when the parameter node is changed then the GUI must be updated immediately.
"""
if inputParameterNode:
self.logic.setDefaultParameters(inputParameterNode)
# Unobserve previously selected parameter node and add an observer to the newly selected.
# Changes of parameter node are observed so that whenever parameters are changed by a script or any other module
# those are reflected immediately in the GUI.
if self._parameterNode is not None:
self.removeObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateGUIFromParameterNode)
self._parameterNode = inputParameterNode
if self._parameterNode is not None:
self.addObserver(self._parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateGUIFromParameterNode)
# Initial GUI update
self.updateGUIFromParameterNode()
def updateGUIFromParameterNode(self, caller=None, event=None):
"""
This method is called whenever parameter node is changed.
The module GUI is updated to show the current state of the parameter node.
"""
# logging.info("updateGUIFromParameterNode")
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
# Make sure GUI changes do not call updateParameterNodeFromGUI (it could cause infinite loop)
self._updatingGUIFromParameterNode = True
if not self.batchProcessing:
thresholds = self.logic.thresholds
self.ui.BullaRangeWidget.minimumValue = thresholds['thresholdBullaLower']
self.ui.BullaRangeWidget.maximumValue = thresholds['thresholdBullaInflated']
self.ui.InflatedRangeWidget.minimumValue = thresholds['thresholdBullaInflated']
self.ui.InflatedRangeWidget.maximumValue = thresholds['thresholdInflatedInfiltrated']
self.ui.InfiltratedRangeWidget.minimumValue = thresholds['thresholdInflatedInfiltrated']
self.ui.InfiltratedRangeWidget.maximumValue = thresholds['thresholdInfiltratedCollapsed']
self.ui.CollapsedRangeWidget.minimumValue = thresholds['thresholdInfiltratedCollapsed']
self.ui.CollapsedRangeWidget.maximumValue = thresholds['thresholdCollapsedVessels']
self.ui.VesselsRangeWidget.minimumValue = thresholds['thresholdCollapsedVessels']
self.ui.VesselsRangeWidget.maximumValue = thresholds['thresholdVesselsUpper']
# Update node selectors and sliders
self.ui.inputVolumeSelector.setCurrentNode(self.logic.inputVolume)
wasBlocked = self.ui.inputSegmentationSelector.blockSignals(True)
self.ui.inputSegmentationSelector.setCurrentNode(self.logic.inputSegmentation)
self.ui.inputSegmentationSelector.blockSignals(wasBlocked)
self.ui.lungMaskedVolumeSelector.setCurrentNode(self.logic.lungMaskedVolume)
self.ui.outputSegmentationSelector.setCurrentNode(self.logic.outputSegmentation)
self.ui.outputResultsTableSelector.setCurrentNode(self.logic.resultsTable)
self.ui.volumeRenderingPropertyNodeSelector.setCurrentNode(self.logic.volumeRenderingPropertyNode)
self.ui.selectReportDirectoryButton.directory = self.reportFolder
self.ui.testModeCheckBox.checked = self.batchProcessingTestMode
self.ui.csvOnlyCheckBox.checked = self.csvOnly
self.ui.useCalibratedCTCheckBox.checked = self.useCalibratedCT
self.ui.scanInputCheckBox.checked = self.scanInput
self.ui.checkForUpdatesCheckBox.checked = self.checkForUpdates
self.ui.generateStatisticsCheckBox.checked = self.logic.generateStatistics
self.ui.lobeAnalysisCheckBox.checked = self.lobeAnalysis
self.ui.areaAnalysisCheckBox.checked = self.areaAnalysis
self.ui.niigzFormatCheckBox.checked = self.isNiiGzFormat
# Update buttons states and tooltips
self.ui.applyButton.toolTip = "Compute results"
self.ui.applyButton.enabled = True
self.ui.createPDFReportButton.enabled = (self.logic.resultsTable is not None)
self.ui.saveResultsCSVButton.enabled = (self.logic.resultsTable is not None)
self.ui.showResultsTablePushButton.enabled = (self.logic.resultsTable is not None)
self.ui.showCovidResultsTableButton.enabled = (self.logic.covidResultsTable is not None)
self.ui.showEmphysemaResultsTableButton.enabled = (self.logic.emphysemaResultsTable is not None)
self.ui.toggleInputSegmentationVisibility2DPushButton.enabled = (self.logic.inputSegmentation is not None)
self.ui.toggleInputSegmentationVisibility3DPushButton.enabled = (self.logic.inputSegmentation is not None)
self.ui.toggleOutputSegmentationVisibility2DPushButton.enabled = (self.logic.outputSegmentation is not None)
self.ui.toggleOutputSegmentationVisibility3DPushButton.enabled = (self.logic.outputSegmentation is not None)
# If thresholds are changed then volume rendering needs an update, too
self.volumeRenderingPropertyUpdateTimer.start()
# All the GUI updates are done
self._updatingGUIFromParameterNode = False
def updateVolumeRenderingPropertyFromGUI(self):
self.volumeRenderingPropertyUpdateTimer.start()
def updateParameterNodeFromGUI(self, caller=None, event=None):
"""
This method is called when the user makes any change in the GUI.
The changes are saved into the parameter node (so that they are restored when the scene is saved and loaded).
"""
if self._parameterNode is None or self._updatingGUIFromParameterNode:
return
wasModified = self._parameterNode.StartModify() # Modify all properties in a single batch
settings=qt.QSettings(slicer.app.launcherSettingsFilePath, qt.QSettings.IniFormat)
self.logic.inputVolume = self.ui.inputVolumeSelector.currentNode()
self.logic.inputSegmentation = self.ui.inputSegmentationSelector.currentNode()
if self.logic.inputSegmentation:
segmentation = self.logic.inputSegmentation.GetSegmentation()
self.logic.rightLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("right lung")
# print(self.logic.rightLungMaskSegmentID)
self.logic.leftLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("left lung")
# print(self.logic.leftLungMaskSegmentID)
thresholds = {}
thresholds['thresholdBullaLower'] = self.ui.BullaRangeWidget.minimumValue
thresholds['thresholdBullaInflated'] = self.ui.BullaRangeWidget.maximumValue
thresholds['thresholdInflatedInfiltrated'] = self.ui.InflatedRangeWidget.maximumValue
thresholds['thresholdInfiltratedCollapsed'] = self.ui.InfiltratedRangeWidget.maximumValue
thresholds['thresholdCollapsedVessels'] = self.ui.CollapsedRangeWidget.maximumValue
thresholds['thresholdVesselsUpper'] = self.ui.VesselsRangeWidget.maximumValue
self.logic.thresholds = thresholds
settings.setValue("LungCtAnalyzer/BullaRangeWidgetMinimumValue", str(self.ui.BullaRangeWidget.minimumValue))
settings.setValue("LungCtAnalyzer/BullaRangeWidgetMaximumValue", str(self.ui.BullaRangeWidget.maximumValue))
settings.setValue("LungCtAnalyzer/InflatedRangeWidgetMinimumValue", str(self.ui.InflatedRangeWidget.minimumValue))
settings.setValue("LungCtAnalyzer/InflatedRangeWidgetMaximumValue", str(self.ui.InflatedRangeWidget.maximumValue))
settings.setValue("LungCtAnalyzer/InfiltratedRangeWidgetMinimumValue", str(self.ui.InfiltratedRangeWidget.minimumValue))
settings.setValue("LungCtAnalyzer/InfiltratedRangeWidgetMaximumValue", str(self.ui.InfiltratedRangeWidget.maximumValue))
settings.setValue("LungCtAnalyzer/CollapsedRangeWidgetMinimumValue", str(self.ui.CollapsedRangeWidget.minimumValue))
settings.setValue("LungCtAnalyzer/CollapsedRangeWidgetMaximumValue", str(self.ui.CollapsedRangeWidget.maximumValue))
settings.setValue("LungCtAnalyzer/VesselsRangeWidgetMinimumValue", str(self.ui.VesselsRangeWidget.minimumValue))
settings.setValue("LungCtAnalyzer/VesselsRangeWidgetMaximumValue", str(self.ui.VesselsRangeWidget.maximumValue))
self.batchProcessingTestMode = self.ui.testModeCheckBox.checked
settings.setValue("LungCtAnalyzer/testModeCheckBoxChecked", str(self.batchProcessingTestMode))
self.csvOnly = self.ui.csvOnlyCheckBox.checked
settings.setValue("LungCtAnalyzer/csvOnlyCheckBoxChecked", str(self.csvOnly))
self.useCalibratedCT = self.ui.useCalibratedCTCheckBox.checked
settings.setValue("LungCtAnalyzer/useCalibratedCTCheckBoxChecked", str(self.useCalibratedCT))
self.scanInput = self.ui.scanInputCheckBox.checked
settings.setValue("LungCtAnalyzer/scanInputCheckBoxChecked", str(self.scanInput))
self.logic.lungMaskedVolume = self.ui.lungMaskedVolumeSelector.currentNode()
self.logic.outputSegmentation = self.ui.outputSegmentationSelector.currentNode()
self.logic.resultsTable = self.ui.outputResultsTableSelector.currentNode()
self.logic.volumeRenderingPropertyNode = self.ui.volumeRenderingPropertyNodeSelector.currentNode()
self.checkForUpdates = self.ui.checkForUpdatesCheckBox.checked
self.logic.generateStatistics = self.ui.generateStatisticsCheckBox.checked
self.lobeAnalysis = self.ui.lobeAnalysisCheckBox.checked
settings.setValue("LungCtAnalyzer/lobeAnalysisCheckBoxChecked", str(self.lobeAnalysis))
self.areaAnalysis = self.ui.areaAnalysisCheckBox.checked
settings.setValue("LungCtAnalyzer/areaAnalysisCheckBoxChecked", str(self.areaAnalysis))
self.isNiiGzFormat = self.ui.niigzFormatCheckBox.checked
settings.setValue("LungCtAnalyzer/niigzFormatCheckBoxChecked", str(self.isNiiGzFormat))
self.logic.countBullae = False
self._parameterNode.EndModify(wasModified)
def updateVolumeRenderingProperty(self):
thresholds = self.logic.thresholds
volumeRenderingPropertyNode = self.logic.volumeRenderingPropertyNode
if volumeRenderingPropertyNode:
scalarOpacity = vtk.vtkPiecewiseFunction()
colorTransferFunction = vtk.vtkColorTransferFunction()
scalarOpacity.AddPoint(-3000.0, 0.0)
colorTransferFunction.AddRGBPoint(-3000.0, 0.0, 0.0, 0.0)
first = True
for segmentProperty in self.logic.segmentProperties:
opacity = self.opacitySliders[segmentProperty["name"]].value * 0.01
lowerThresholdName, upperThresholdName = segmentProperty["thresholds"]
lowerThreshold = thresholds[lowerThresholdName]
upperThreshold = thresholds[upperThresholdName]-0.1
if first:
scalarOpacity.AddPoint(lowerThreshold-0.1, 0.0)
first = False
scalarOpacity.AddPoint(lowerThreshold, opacity)
scalarOpacity.AddPoint(upperThreshold, opacity)
color = segmentProperty["color"]
colorTransferFunction.AddRGBPoint(lowerThreshold, *color)
colorTransferFunction.AddRGBPoint(upperThreshold, *color)
scalarOpacity.AddPoint(upperThreshold+0.1, 0.0)
scalarOpacity.AddPoint(5000, 0.0)
volumeProperty = volumeRenderingPropertyNode.GetVolumeProperty()
volumeProperty.GetScalarOpacity().DeepCopy(scalarOpacity)
volumeProperty.GetRGBTransferFunction().DeepCopy(colorTransferFunction)
def onInputDirectoryPathLineEditChanged(self):
self.batchProcessingInputDir = self.ui.inputDirectoryPathLineEdit.currentPath
settings=qt.QSettings(slicer.app.launcherSettingsFilePath, qt.QSettings.IniFormat)
settings.setValue("LungCtAnalyzer/batchProcessingInputFolder", self.ui.inputDirectoryPathLineEdit.currentPath);
def onOutputDirectoryPathLineEditChanged(self):
self.batchProcessingOutputDir = self.ui.outputDirectoryPathLineEdit.currentPath
settings=qt.QSettings(slicer.app.launcherSettingsFilePath, qt.QSettings.IniFormat)
settings.setValue("LungCtAnalyzer/batchProcessingOutputFolder", self.ui.outputDirectoryPathLineEdit.currentPath);
def showStatusMessage(self, msg, timeoutMsec=500):
slicer.util.showStatusMessage(msg, timeoutMsec)
slicer.app.processEvents()
def onCancelBatchProcessingButton(self):
print("Batch processing is cancelled by user.")
self.batchProcessingIsCancelled = True
def showCriticalError(self, msg):
slicer.util.messageBox(msg)
raise ValueError(msg)
def setThresholdsFromGUI(self):
scriptThresholds = {
'thresholdBullaLower': -1050.,
'thresholdBullaInflated': -950.,
'thresholdInflatedInfiltrated': -750.,
'thresholdInfiltratedCollapsed': -400.,
'thresholdCollapsedVessels': 0.,
'thresholdVesselsUpper': 3000.,
}
scriptThresholds['thresholdBullaLower'] = self.ui.BullaRangeWidget.minimumValue
scriptThresholds['thresholdBullaInflated'] = self.ui.BullaRangeWidget.maximumValue
scriptThresholds['thresholdInflatedInfiltrated'] = self.ui.InflatedRangeWidget.maximumValue
scriptThresholds['thresholdInfiltratedCollapsed'] = self.ui.InfiltratedRangeWidget.maximumValue
scriptThresholds['thresholdCollapsedVessels'] = self.ui.CollapsedRangeWidget.maximumValue
scriptThresholds['thresholdVesselsUpper'] = self.ui.VesselsRangeWidget.maximumValue
self.logic.setThresholds(self.logic.getParameterNode(), scriptThresholds)
def onBatchProcessingButton(self):
self.batchProcessingIsCancelled = False
if self.batchProcessingInputDir == "":
self.showCriticalError("No input directory given.")
if self.batchProcessingOutputDir == "":
self.showCriticalError("No output directory given.")
if self.batchProcessingInputDir == self.batchProcessingOutputDir:
self.showCriticalError("Input and output directotry can not be the same path.")
if not os.path.exists(self.batchProcessingInputDir):
self.showCriticalError("Input folder does not exist.")
counter = 0
pattern = ''
pattern = '/' '**/*.mrb'
if self.isNiiGzFormat:
pattern = '/' '**/*.nii.gz'
else:
pattern = '/' '**/*.mrb'
filesToProcess = 0
for filepath in glob.iglob(self.batchProcessingInputDir + pattern, recursive=True):
pathhead, pathtail = os.path.split(filepath)
if (pathtail.lower() == "ct_seg.mrb" and not self.isNiiGzFormat) or (pathtail.lower() == "ct.nii.gz" and self.isNiiGzFormat):
# input data must be in subdirectories of self.batchProcessingInputDir
if pathhead == self.batchProcessingInputDir:
self.showCriticalError("Unsupported data structure: Data files in input folder detected, they must be placed in subfolders.")
# input data must be in immediate child directory of self.batchProcessingInputDir
parentDir = os.path.dirname(pathhead)
if parentDir != self.batchProcessingInputDir:
self.showCriticalError("Unsupported data structure: There seem to be input data in sub-subfolders of the input folder. Only one subfolder dimension is allowed.")
filesToProcess += 1
if self.batchProcessingTestMode:
print("Input file '" + filepath + "' detected ...")
if filesToProcess == 0:
self.showCriticalError("No files to process. Each input file must be placed in a separate subdirectory of the input folder.")
minutesRequired = (filesToProcess * 180) / 60
if not self.batchProcessingTestMode and not slicer.util.confirmYesNoDisplay("If each analysis takes about 3 minutes, batch segmentation of " + str(filesToProcess) + " input files will last around " + str(minutesRequired) + " minutes. Are you sure you want to continue?"):
logging.info('Batch processing cancelled by user.')
return
if self.batchProcessingTestMode and filesToProcess < 3:
self.showCriticalError("Not enough input files for test mode (3 needed) during recursive reading below input directory path.")
startWatchTime = time.time()
self.batchProcessing = True
counter = 0
if self.scanInput:
_doanalyze = False
_dowrite = False
else:
_doanalyze = True
_dowrite = True
durationProcess = 0
if self.batchProcessingTestMode:
filesToProcess = 3
for filepath in glob.iglob(self.batchProcessingInputDir + pattern, recursive=True):
pathhead, pathtail = os.path.split(filepath)
filename = pathtail.lower()
_doread = False
if filename == "ct_seg.mrb" and not self.isNiiGzFormat:
_doread = True
if filename == "ct.nii.gz" and self.isNiiGzFormat and not self.useCalibratedCT:
_doread = True
if filename == "ct_calibrated.nii.gz" and self.isNiiGzFormat and self.useCalibratedCT:
_doread = True
if pathhead != self.batchProcessingInputDir:
_doread = True
if _doread:
startProcessWatchTime = time.time()
counter += 1
slicer.mrmlScene.Clear(0)
if not self.isNiiGzFormat:
# input is not NRRD format
slicer.util.loadScene(filepath)
if self.useCalibratedCT:
firstVolumeNode = slicer.util.getFirstNodeByClassByName("vtkMRMLScalarVolumeNode","CT_calibrated")
# to prevent crash TODO find out why
ctVolumeNode = slicer.util.getFirstNodeByClassByName("vtkMRMLScalarVolumeNode","CT")
if ctVolumeNode:
slicer.mrmlScene.RemoveNode(ctVolumeNode)
else:
firstVolumeNode = slicer.util.getFirstNodeByClassByName("vtkMRMLScalarVolumeNode","CT")
if firstVolumeNode:
self.logic.inputVolume = firstVolumeNode
else:
raise ValueError("No input volume.")
if not self.logic.inputSegmentation:
segNode = slicer.util.getFirstNodeByClassByName("vtkMRMLSegmentationNode", "Lung segmentation")
if segNode:
self.logic.inputSegmentation = segNode
else:
# input is NIFTI format
# Get color node with random colors
randomColorsNode = slicer.mrmlScene.GetNodeByID('vtkMRMLColorTableNodeRandom')
rgba = [0, 0, 0, 0]
self.inputVolume = slicer.util.loadVolume(filepath)
self.logic.inputSegmentation = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode', 'Lung segmentation')
pattern = '/' '**/*.nii.gz'
print(self.batchProcessingInputDir)
# inpathtail is the first level source folder
inpathhead, inpathtail = os.path.split(pathhead)
for filepath2 in glob.iglob(self.batchProcessingInputDir + '/' + inpathtail + '/lung_segmentations/' + pattern, recursive=True):
pathhead2, pathtail2 = os.path.split(filepath2)
print(f"Importing {filepath2}")
underscore_str = pathtail2.replace(".nii.gz","")
segmentName = underscore_str.replace("_" , " ")
labelmapVolumeNode = slicer.util.loadLabelVolume(filepath2, {"name": segmentName})
segmentId = self.logic.inputSegmentation.GetSegmentation().AddEmptySegment(segmentName, segmentName)
updatedSegmentIds = vtk.vtkStringArray()
updatedSegmentIds.InsertNextValue(segmentId)
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, self.logic.inputSegmentation, updatedSegmentIds)
slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
segmentation = self.logic.inputSegmentation.GetSegmentation()
self.logic.rightLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("right lung")
self.logic.leftLungMaskSegmentID = segmentation.GetSegmentIdBySegmentName("left lung")
print("Analyzing '" + filepath + "' ...", end='\r')
if _doanalyze:
self.onApplyButton()
if _dowrite:
outpathhead, outpathtail = os.path.split(pathhead)
targetdir = self.batchProcessingOutputDir + "/" + outpathtail + "/"
if not os.path.exists(targetdir):
os.makedirs(targetdir)
self.logic.saveExtendedDataToFile(self.batchProcessingOutputDir + "/results.csv", filepath, counter, outpathtail)
self.logic.saveExtendedRegionDataToFile(self.batchProcessingOutputDir + "/regionResults.csv", filepath, counter, outpathtail)
self.logic.saveExtendedLobeDataToFile(self.batchProcessingOutputDir + "/lobeResults.csv", filepath, counter, outpathtail)
if not self.csvOnly:
if self.isNiiGzFormat:
# write NIFTI format
self.showStatusMessage("Writing NIFTI output files for input " + str(counter) + "/" + str(filesToProcess) + " to '" + targetdir + "' ...")
for volumeNode in slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode"):
volumeNode.AddDefaultStorageNode()
slicer.util.saveNode(volumeNode, targetdir + volumeNode.GetName().lower().replace(" ", "_") + ".nii.gz")
numberOfSegments = self.logic.outputSegmentation.GetSegmentation().GetNumberOfSegments()
for i in range(numberOfSegments):
segment = self.logic.outputSegmentation.GetSegmentation().GetNthSegment(i)
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
segID = self.logic.outputSegmentation.GetSegmentation().GetSegmentIdBySegment(segment)
strArr = [str(segID)]
slicer.modules.segmentations.logic().ExportSegmentsToLabelmapNode (self.logic.outputSegmentation, strArr, labelmapVolumeNode, self.logic.inputVolume)
labelmapVolumeNode.AddDefaultStorageNode()
if not os.path.exists(targetdir + "lung_analysis_segmentations/"):
os.makedirs(targetdir + "lung_analysis_segmentations/")
slicer.util.saveNode(labelmapVolumeNode, targetdir + "lung_analysis_segmentations/" + segment.GetName().lower().replace(" ", "_") + ".seg.nii.gz")
slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
else:
# write default format
sceneSaveFilename = targetdir + "ct_seg_analyzed.mrb"
self.showStatusMessage("Writing mrb output file for input " + str(counter) + "/" + str(filesToProcess) + " (last process: {0:.2f} s ".format(durationProcess) + " processing and write time) to '" + sceneSaveFilename + "' ...")
if slicer.util.saveScene(sceneSaveFilename):
logging.info("Scene saved to: {0}".format(sceneSaveFilename))
else:
logging.error("Scene saving failed")
stopProcessWatchTime = time.time()
durationProcess = stopProcessWatchTime - startProcessWatchTime
# let slicer process events and update its display
slicer.app.processEvents()
time.sleep(3)
if self.batchProcessingIsCancelled:
break