import logging
import os
import time
import vtk
import importlib
import slicer
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
#
# MusculoskeletalAnalysis
#
class MusculoskeletalAnalysis(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "Musculoskeletal Analysis"
self.parent.categories = ["Quantification"]
self.parent.dependencies = ["CorticalAnalysis", "CancellousAnalysis", "DensityAnalysis", "IntervertebralAnalysis"] # TODO: add here list of module names that this module requires
self.parent.contributors = ["Joseph Szatkowski (Washington University in St. Louis)"]
# TODO: update with short description of the module and a link to online module documentation
self.parent.helpText = """
1. Select a volume containing the image to analyze.\n
2. Select a segmentation representing the area to analyze. For cortical analysis exclude the medullary cavity. For cancellous analysis exclude the cortical bone.\n
3. Use the threshold slider to select a threshold identifying the bone.\n
4. Select the function to perform. See <a href="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/blob/main/README.md">here</a> for more information.\n
5. Select the directory to send the output files to. If files already exist they will be appended to.\n
6. Click "Apply"\n
ADVANCED\n
7. If the image volume is not the original DICOM, select the original DICOM node to get DICOM tags from.
"""
# TODO: replace with organization, grant and thanks
self.parent.acknowledgementText = """
Developed by the Washington University in St. Louis Musculoskeletal Reseach Center with the assistance of Michael Brodt, Anish Jagannathan, Matthew Silva, and Simon Tang.\n
This file was partially funded by NIH grant P30 AR074992.
"""
# 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.
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='Cortical1',
# Thumbnail should have size of approximately 260x280 pixels and stored in Resources/Icons folder.
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images" set to "Single".
thumbnailFileName=os.path.join(iconsPath, 'Cortical1.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CorticalSample1.nrrd",
fileNames='CorticalSample1.nrrd',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:740fcdbe9c7341ffeb2fb44e68e25098077281e11d541163379bf301db4b65b9',
# This node name will be used when the data set is loaded
nodeNames='Cortical1'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='CorticalMask1',
# Thumbnail should have size of approximately 260x280 pixels and stored in Resources/Icons folder.
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images" set to "Single".
thumbnailFileName=os.path.join(iconsPath, 'CorticalMask1.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CorticalMaskSample1.seg.nrrd",
fileNames='CorticalMaskSample1.seg.nrrd',
loadFileType='SegmentationFile',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:1cdd2ea240d848d3d5241eddffe2467f5bf49f80dab50937c8127eb511fa3b9a',
# This node name will be used when the data set is loaded
nodeNames='CorticalMask1'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='Cortical2',
# Thumbnail should have size of approximately 260x280 pixels and stored in Resources/Icons folder.
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images" set to "Single".
thumbnailFileName=os.path.join(iconsPath, 'Cortical2.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CorticalSample2.nrrd",
fileNames='CorticalSample2.nrrd',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:8e0869839abc008000d32d8ffef923a89ee7fd10fd974d63baa1daecb47154f5',
# This node name will be used when the data set is loaded
nodeNames='Cortical2'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='CorticalMask2',
# Thumbnail should have size of approximately 260x280 pixels and stored in Resources/Icons folder.
# It can be created by Screen Capture module, "Capture all views" option enabled, "Number of images" set to "Single".
thumbnailFileName=os.path.join(iconsPath, 'CorticalMask2.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CorticalMaskSample2.seg.nrrd",
fileNames='CorticalMaskSample2.seg.nrrd',
loadFileType='SegmentationFile',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:509b7e5b16a838bf743ec083677ac7a1a2b1f7f3d2fb8ad93e75b38619150d7e',
# This node name will be used when the data set is loaded
nodeNames='CorticalMask2'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='Cancellous1',
thumbnailFileName=os.path.join(iconsPath, 'Cancellous1.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CancellousSample1.nrrd",
fileNames='CancellousSample1.nrrd',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:cb47e20fd9d4caf210a256db8317f2553f409399834b0bc15b28e57daf46ba89',
# This node name will be used when the data set is loaded
nodeNames='Cancellous1'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='CancellousMask1',
thumbnailFileName=os.path.join(iconsPath, 'CancellousMask1.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CancellousMaskSample1.seg.nrrd",
fileNames='CancellousMaskSample1.seg.nrrd',
loadFileType='SegmentationFile',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:1d632557a415b0d84dfaca4bf743aa9319e5a5e805e7a997d76c6f7bd9e75160',
# This node name will be used when the data set is loaded
nodeNames='CancellousMask1'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='Cancellous2',
thumbnailFileName=os.path.join(iconsPath, 'Cancellous2.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CancellousSample2.nrrd",
fileNames='CancellousSample2.nrrd',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:fd594a087700afcb3a1fc6c0ee4fa087f263eda86f93f0cfc317927876bda813',
# This node name will be used when the data set is loaded
nodeNames='Cancellous2'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='CancellousMask2',
thumbnailFileName=os.path.join(iconsPath, 'CancellousMask2.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/CancellousMaskSample2.seg.nrrd",
fileNames='CancellousMaskSample2.seg.nrrd',
loadFileType='SegmentationFile',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:473cb8d1a2ccc8973eb7f0b69eb297d2d4119155b1a9940cb5e11d2ccd4e1315',
# This node name will be used when the data set is loaded
nodeNames='CancellousMask2'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='Intervertebral1',
thumbnailFileName=os.path.join(iconsPath, 'Intervertebral1.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/IntervertebralSample1.nrrd",
fileNames='Intervertebral1.nrrd',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:26706cec367bded189182e8b3e02c804bdad5267cee25f95202ee240823841a9',
# This node name will be used when the data set is loaded
nodeNames='Intervertebral1'
)
SampleData.SampleDataLogic.registerCustomSampleDataSource(
# Category and sample name displayed in Sample Data module
category='MusculoskeletalAnalysis',
sampleName='IntervertebralMask1',
thumbnailFileName=os.path.join(iconsPath, 'IntervertebralMask1.png'),
# Download URL and target file name
uris="https://github.com/WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis/releases/download/v1.1-assets/IntervertebralMaskSample1.seg.nrrd",
fileNames='IntervertebralMaskSample1.seg.nrrd',
loadFileType='SegmentationFile',
# Checksum to ensure file integrity. Can be computed by this command:
# import hashlib; print(hashlib.sha256(open(filename, "rb").read()).hexdigest())
checksums='SHA256:7c140faa9924dd47d14df1208d5dc130479a8c64bfba6b741e02362465f7183f',
# This node name will be used when the data set is loaded
nodeNames='IntervertebralMask1'
)
#
# MusculoskeletalAnalysisWidget
#
class MusculoskeletalAnalysisWidget(ScriptedLoadableModuleWidget, VTKObservationMixin):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/main/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.
"""
ScriptedLoadableModuleWidget.__init__(self, parent)
VTKObservationMixin.__init__(self) # needed for parameter node observation
self.logic = None
self._parameterNode = None
self._updatingGUIFromParameterNode = 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/MusculoskeletalAnalysis.ui'))
self.layout.addWidget(uiWidget)
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 = MusculoskeletalAnalysisLogic()
# 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 whenever user changes some settings on the GUI, that is saved in the MRML scene
# (in the selected parameter node).
self.ui.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.inputVolumeChanged)
self.ui.segmentSelector.connect("currentNodeChanged(vtkMRMLNode*)",self.segmentNodeChanged)
self.ui.segmentSelector.connect("currentSegmentChanged(QString)",self.segmentChanged)
self.ui.segmentSelector.connect("segmentSelectionChanged(QStringList)", self.segmentChanged)
self.ui.thresholdSelector.connect("thresholdValuesChanged(double, double)", self.updateParameterNodeFromGUI)
self.ui.analysisSelector.connect("currentTextChanged(const QString)", self.updateParameterNodeFromGUI)
self.ui.DICOMOptions.connect("buttonClicked(QAbstractButton*)", self.updateParameterNodeFromGUI)
self.ui.DICOMSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.DICOMSeriesChanged)
self.ui.voxelSizeLineEdit.connect("editingFinished()", self.updateParameterNodeFromGUI)
self.ui.scalingLineEdit.connect("editingFinished()", self.updateParameterNodeFromGUI)
self.ui.densitySlopeLineEdit.connect("editingFinished()", self.updateParameterNodeFromGUI)
self.ui.densityInterceptLineEdit.connect("editingFinished()", self.updateParameterNodeFromGUI)
self.ui.rescaleSlopeLineEdit.connect("editingFinished()", self.updateParameterNodeFromGUI)
self.ui.rescaleInterceptLineEdit.connect("editingFinished()", self.updateParameterNodeFromGUI)
self.ui.outputDirectorySelector.connect("currentPathChanged(const QString)", self.updateParameterNodeFromGUI)
# Buttons
self.ui.applyButton.connect('clicked(bool)', self.onApplyButton)
# Hidden elements
self.ui.AnalysisProgress.hide()
# Make sure parameter node is initialized (needed for module reload)
self.initializeParameterNode()
def cleanup(self):
"""
Called when the application closes and the module widget is destroyed.
"""
self.removeObservers()
def enter(self):
"""
Called each time the user opens this module.
"""
# Make sure parameter node exists and observed
self.initializeParameterNode()
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 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.
"""
# 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._parameterNode.GetNodeReference("InputVolume"):
firstVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
if firstVolumeNode:
self._parameterNode.SetNodeReferenceID("InputVolume", firstVolumeNode.GetID())
if not self._parameterNode.GetNodeReference("SegmentNode"):
firstSegmentNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLSegmentationNode")
if firstSegmentNode:
self._parameterNode.SetNodeReferenceID("SegmentNode", firstSegmentNode.GetID())
self.ui.segmentSelector.setCurrentNode(firstSegmentNode)
if not self._parameterNode.GetParameter("SegmentID"):
if self._parameterNode.GetNodeReference("SegmentNode"):
segmentation = self._parameterNode.GetNodeReference("SegmentNode").GetSegmentation()
self._parameterNode.SetParameter("SegmentID", segmentation.GetNthSegmentID(0))
if not self._parameterNode.GetNodeReference("DICOMNode"):
firstVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
if firstVolumeNode:
self._parameterNode.SetNodeReferenceID("DICOMNode", firstVolumeNode.GetID())
# Set default state for flags
self._parameterNode.SetParameter("Analyzing", "False")
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.
"""
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
# Update node selectors and sliders
self.ui.thresholdSelector.setMRMLVolumeNode(self._parameterNode.GetNodeReference("InputVolume"))
if self._parameterNode.GetParameter("LowerThreshold") and self._parameterNode.GetParameter("UpperThreshold"):
self.ui.thresholdSelector.setLowerThreshold(float(self._parameterNode.GetParameter("LowerThreshold")))
self.ui.thresholdSelector.setUpperThreshold(float(self._parameterNode.GetParameter("UpperThreshold")))
self.ui.analysisSelector.setCurrentText(str(self._parameterNode.GetParameter("Analysis")))
self.ui.AlternateDICOMCheckBox.setChecked(self._parameterNode.GetParameter("UseAlt")=="True")
self.ui.ManualDICOMCheckBox.setChecked(self._parameterNode.GetParameter("UseMan")=="True")
self.ui.DICOMSelector.setCurrentNode(self._parameterNode.GetNodeReference("DICOMNode"))
self.ui.voxelSizeLineEdit.setText(self._parameterNode.GetParameter("0018,0050"))
self.ui.scalingLineEdit.setText(self._parameterNode.GetParameter("0029,1000"))
self.ui.densitySlopeLineEdit.setText(self._parameterNode.GetParameter("0029,1004"))
self.ui.densityInterceptLineEdit.setText(self._parameterNode.GetParameter("0029,1005"))
self.ui.rescaleSlopeLineEdit.setText(self._parameterNode.GetParameter("0028,1053"))
self.ui.rescaleInterceptLineEdit.setText(self._parameterNode.GetParameter("0028,1052"))
self.ui.outputDirectorySelector.setCurrentPath(str(self._parameterNode.GetParameter("OutputDirectory")))
# Update buttons states and tooltips
if self._parameterNode.GetNodeReference("InputVolume"):
self.ui.thresholdSelector.enabled = True
else:
self.ui.thresholdSelector.enabled = False
if self._parameterNode.GetParameter("MultiSelect") == 'True':
self.ui.segmentSelector.multiSelection = True
self.ui.thresholdSelector.enabled = False
self.ui.thresholdSelector.setVisible(False)
else:
self.ui.segmentSelector.multiSelection = False
self.ui.thresholdSelector.enabled = True
self.ui.thresholdSelector.setVisible(True)
# Update advanced options
self.ui.DICOMSelector.enabled = (self._parameterNode.GetParameter("UseAlt")=="True")
manual = (self._parameterNode.GetParameter("UseMan")=="True")
self.ui.voxelSizeLineEdit.enabled=manual
self.ui.scalingLineEdit.enabled=manual
self.ui.densitySlopeLineEdit.enabled=manual
self.ui.densityInterceptLineEdit.enabled=manual
self.ui.rescaleSlopeLineEdit.enabled=manual
self.ui.rescaleInterceptLineEdit.enabled=manual
self.ui.voxelSizeLabel.enabled=manual
self.ui.scalingLabel.enabled=manual
self.ui.densitySlopeLabel.enabled=manual
self.ui.densityInterceptLabel.enabled=manual
self.ui.rescaleSlopeLabel.enabled=manual
self.ui.rescaleInterceptLabel.enabled=manual
# Update Apply Button
if self._parameterNode.GetParameter("Analyzing")=="True":
self.ui.applyButton.toolTip = "Currently running analysis"
self.ui.applyButton.enabled = False
elif self._parameterNode.GetNodeReference("InputVolume") and self._parameterNode.GetParameter("SegmentID") and (self._parameterNode.GetParameter("UseDICOM")=="False" or self._parameterNode.GetNodeReferenceID("DICOMNode")):
self.ui.applyButton.toolTip = "Perform the selected analysis"
self.ui.applyButton.enabled = True
else:
self.ui.applyButton.toolTip = "Select input volume node, input segment, and output directory"
self.ui.applyButton.enabled = False
# All the GUI updates are done
self._updatingGUIFromParameterNode = False
def inputVolumeChanged(self, event):
"""
Called when the input volume is changed in the selector.
Passes the caller information to updateParameterNode
"""
self.updateParameterNodeFromGUI(event, "InputVolume")
def segmentNodeChanged(self, event):
"""
Called when the segment node is changed in the selector.
Passes the caller information to updateParameterNode
"""
self.updateParameterNodeFromGUI(event, "SegmentNode")
def segmentChanged(self, event):
"""
Called when the segment is changed in the selector.
Passes the caller information to updateParameterNode
"""
self.updateParameterNodeFromGUI(event, "Segment")
def DICOMSeriesChanged(self, event):
self.updateParameterNodeFromGUI(event, "DICOM")
def updateParameterNodeFromGUI(self, event=None, caller=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
self._parameterNode.SetNodeReferenceID("InputVolume", self.ui.inputSelector.currentNodeID)
if caller == "InputVolume":
if event is None:
self._parameterNode.SetNodeReferenceID("InputVolume", None)
else:
self._parameterNode.SetNodeReferenceID("InputVolume", event.GetID())
elif caller == 'SegmentNode':
if event is None:
self._parameterNode.SetNodeReferenceID("SegmentNode", None)
else:
self._parameterNode.SetNodeReferenceID("SegmentNode", event.GetID())
elif caller == 'Segment':
self._parameterNode.SetParameter("SegmentID", str(event))
elif caller == 'DICOM' and event is not None:
self._parameterNode.SetNodeReferenceID("DICOMNode", event.GetID())
self._parameterNode.SetParameter("LowerThreshold", str(self.ui.thresholdSelector.lowerThreshold))
self._parameterNode.SetParameter("UpperThreshold", str(self.ui.thresholdSelector.upperThreshold))
self._parameterNode.SetParameter("Analysis", str(self.ui.analysisSelector.currentText))
self._parameterNode.SetParameter("UseAlt", str(self.ui.AlternateDICOMCheckBox.checked))
self._parameterNode.SetParameter("UseMan", str(self.ui.ManualDICOMCheckBox.checked))
self.setNumParameter("0018,0050", str(self.ui.voxelSizeLineEdit.text))
self.setNumParameter("0029,1000", str(self.ui.scalingLineEdit.text))
self.setNumParameter("0029,1004", str(self.ui.densitySlopeLineEdit.text))
self.setNumParameter("0029,1005", str(self.ui.densityInterceptLineEdit.text))
self.setNumParameter("0028,1053", str(self.ui.rescaleSlopeLineEdit.text))
self.setNumParameter("0028,1052", str(self.ui.rescaleInterceptLineEdit.text))
self._parameterNode.SetParameter("OutputDirectory", str(self.ui.outputDirectorySelector.currentPath))
if self._parameterNode.GetParameter("Analysis") == 'Intervertebral Disc':
self._parameterNode.SetParameter("MultiSelect", 'True')
else:
self._parameterNode.SetParameter("MultiSelect", 'False')
self._parameterNode.EndModify(wasModified)
self.updateGUIFromParameterNode()
# Sets a parameter to a value if the value can be converted to a float, otherwises sets it to blank
def setNumParameter(self, parameter, value):
try:
float(value)
self._parameterNode.SetParameter(parameter, value)
except ValueError:
self._parameterNode.SetParameter(parameter, "")
def onApplyButton(self):
"""
Run processing when user clicks "Apply" button.
"""
with slicer.util.tryWithErrorDisplay("Failed to compute results.", waitCursor=True):
# Compute output
self.logic.process(self._parameterNode.GetNodeReference("InputVolume"), self._parameterNode.GetNodeReference("SegmentNode"), self._parameterNode.GetParameter("SegmentID"),
self.ui.thresholdSelector.lowerThreshold, self.ui.thresholdSelector.upperThreshold, self.ui.analysisSelector.currentText, self.ui.outputDirectorySelector.currentPath,
self.ui.AlternateDICOMCheckBox.checked, self._parameterNode.GetNodeReference("DICOMNode"), self.ui.ManualDICOMCheckBox.checked,
{'0018,0050':self.ui.voxelSizeLineEdit.text, '0029,1000':self.ui.scalingLineEdit.text, '0029,1004':self.ui.densitySlopeLineEdit.text, '0029,1005':self.ui.densityInterceptLineEdit.text, '0028,1053':self.ui.rescaleSlopeLineEdit.text, '0028,1052':self.ui.rescaleInterceptLineEdit.text}, self)
self.updateGUIFromParameterNode()
# Updates
def analysisUpdate(self, cliNode, event):
if cliNode.GetStatus() & cliNode.Completed:
self.ui.AnalysisProgress.setValue(100)
self.ui.AnalysisProgress.hide()
if cliNode.GetStatus() & cliNode.ErrorsMask:
# error
errorText = cliNode.GetErrorText()
print("CLI execution failed: " + errorText)
else:
# success
print("CLI execution succeeded.")
startTime=float(self._parameterNode.GetParameter("startTime"))
stopTime = time.time()
logging.info(f'Processing completed in {stopTime-startTime:.2f} seconds')
# Clean up temp nodes
slicer.mrmlScene.RemoveNode(self._parameterNode.GetNodeReference("labelmapNode"))
slicer.mrmlScene.RemoveNode(self._parameterNode.GetNodeReference("labelmapNode2"))
slicer.mrmlScene.RemoveNode(cliNode)
self._parameterNode.SetParameter("Analyzing", "False")
self.updateGUIFromParameterNode()
else:
self.ui.AnalysisProgress.setValue(cliNode.GetProgress())
#
# MusculoskeletalAnalysisLogic
#
class MusculoskeletalAnalysisLogic(ScriptedLoadableModuleLogic):
"""This class should implement all the actual
computation done by your module. The interface
should be such that other python code can import
this class and make use of the functionality without
requiring an instance of the Widget.
Uses ScriptedLoadableModuleLogic base class, available at:
https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self):
"""
Called when the logic class is instantiated. Can be used for initializing member variables.
"""
ScriptedLoadableModuleLogic.__init__(self)
def setDefaultParameters(self, parameterNode):
"""
Initialize parameter node with default settings.
"""
if not parameterNode.GetParameter("Analysis"):
parameterNode.SetParameter("Analysis", "Cortical Bone")
def process(self, inputVolume, mask, maskLabel, lowerThreshold, upperThreshold, analysis, outputDirectory, altDICOM=False, DICOMNode=None, manDICOM=False, DICOMOptions=None, source=None, wait=False):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param InputVolume: volume to be thresholded
:param Analysis: analysis function to perform
:param OutputDirectory: directory to write output files to
"""
# Check inputs
if not inputVolume:
raise ValueError("Input volume is invalid")
if not mask or not maskLabel:
raise ValueError("Segment is invalid")
if altDICOM and not DICOMNode:
raise ValueError("No DICOM source")
if manDICOM and not all(DICOMOptions):
raise ValueError("Not all DICOM options are selected")
if not os.access(outputDirectory, os.W_OK):
if not os.access(outputDirectory, os.F_OK):
# If directory doesn't exist try to create it
try:
os.makedirs(outputDirectory)
if not os.access(outputDirectory, os.W_OK):
raise ValueError("Output Directory is invalid")
except:
raise ValueError("Output Directory is invalid")
else:
# If directory is not writable for other reason
raise ValueError("Output Directory is invalid")
startTime = time.time()
logging.info('Processing started')
# Get mask segments
if analysis == 'Intervertebral Disc':
maskLabel = maskLabel.strip('()')
labels = maskLabel.split(', ')
maskID = mask.GetSegmentation().GetSegmentIdBySegmentName(labels[0].strip('\''))
maskArray = vtk.vtkStringArray()
maskArray.InsertNextValue(maskID)
labelmap = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(mask, maskArray, labelmap, inputVolume)
maskID2 = mask.GetSegmentation().GetSegmentIdBySegmentName(labels[1].strip('\''))
maskArray2 = vtk.vtkStringArray()
maskArray2.InsertNextValue(maskID2)
labelmap2 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(mask, maskArray2, labelmap2, inputVolume)
else:
maskID = mask.GetSegmentation().GetSegmentIdBySegmentName(maskLabel)
maskArray = vtk.vtkStringArray()
maskArray.InsertNextValue(maskID)
labelmap = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(mask, maskArray, labelmap, inputVolume)
# Get DICOM source
if altDICOM:
dSource = DICOMNode
elif manDICOM:
dSource = DICOMOptions
else:
dSource = inputVolume
if analysis != 'Intervertebral Disc':
# Get Density info
slope=float(self.getDICOMTag(dSource, '0029,1004'))/(float(self.getDICOMTag(dSource, '0029,1000'))*float(self.getDICOMTag(dSource, '0028,1053')))
intercept=float(self.getDICOMTag(dSource, '0029,1005'))-(float(self.getDICOMTag(dSource, '0028,1052'))*slope)
voxelSize = self.getDICOMTag(dSource, '0018,0050')
# Prepare parameters for the selected function
if analysis == "Cortical Bone":
parameters = {"image":inputVolume, "mask":labelmap, "lowerThreshold":lowerThreshold, "upperThreshold":upperThreshold, "voxelSize":voxelSize, "slope":slope, "intercept":intercept, "inputName":inputVolume.GetName(), "output":outputDirectory}
module=slicer.modules.corticalanalysis
requirements = [('scipy', 'scipy'), ('skimage', 'scikit-image'), ('nrrd', 'pynrrd')]
elif analysis == "Cancellous Bone":
parameters = {"image":inputVolume, "mask":labelmap, "lowerThreshold":lowerThreshold, "upperThreshold":upperThreshold, "voxelSize":voxelSize, "slope":slope, "intercept":intercept, "inputName":inputVolume.GetName(), "output":outputDirectory}
module=slicer.modules.cancellousanalysis
requirements = [('scipy', 'scipy'), ('skimage', 'scikit-image'), ('nrrd', 'pynrrd'), ('trimesh', 'trimesh')]
elif analysis == "Bone Density":
parameters = {"image":inputVolume, "mask":labelmap, "voxelSize":voxelSize, "slope":slope, "intercept":intercept, "inputName":inputVolume.GetName(), "output":outputDirectory}
module=slicer.modules.densityanalysis
requirements = [('nrrd', 'pynrrd')]
elif analysis == 'Intervertebral Disc':
parameters = {"image":inputVolume, "mask1":labelmap, "mask2":labelmap2, "voxelSize":voxelSize, "inputName":inputVolume.GetName(), "output":outputDirectory}
module = slicer.modules.intervertebralanalysis
requirements = [('scipy', 'scipy'), ('nrrd', 'pynrrd')]
# Install required python modules
self.importRequest(requirements)
node = slicer.cli.createNode(module, parameters=parameters)
# Set up source before running to avoid race conditions
if source:
source.ui.AnalysisProgress.setValue(0)
source.ui.AnalysisProgress.show()
source._parameterNode.SetParameter("Analyzing", "True")
source._parameterNode.SetNodeReferenceID("labelmapNode", labelmap.GetID())
if 'labelmap2' in locals():
source._parameterNode.SetNodeReferenceID("labelmapNode2", labelmap2.GetID())
source._parameterNode.SetParameter("startTime", str(startTime))
node.AddObserver('ModifiedEvent', source.analysisUpdate)
slicer.cli.run(module=module, node=node, wait_for_completion=wait)
# Used to get dicom metadata from the volume
# source: the volume node or DICOM dict
# tag: The DICOM tag number as a string ('####,####')
def getDICOMTag(self, source, tag):
if type(source) is dict:
data=source[tag]
else:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
volumeItemId = shNode.GetItemByDataNode(source)
seriesInstanceUID = shNode.GetItemUID(volumeItemId, 'DICOM')
db = slicer.dicomDatabase
instanceList = db.instancesForSeries(seriesInstanceUID)
data = db.instanceValue(instanceList[0], tag)
return data
# Check a list of modules to see if they are installed, request permission to install any missing.
# requested: A list of tuples in the format (moduleName, pipName)
def importRequest(self, requested):
missing = []
for r in requested:
if not importlib.util.find_spec(r[0]):
missing.append(r)
if len(missing) > 0:
names, pips = zip(*missing)
if slicer.util.confirmOkCancelDisplay("The following python modules are required: " + ", ".join(names) + ". Do you want to install them?"):
for p in pips:
slicer.util.pip_install(p)
#pass
else:
raise ImportError("Required python modules do not have permission to install")
#
# MusculoskeletalAnalysisTest
#
class MusculoskeletalAnalysisTest(ScriptedLoadableModuleTest):
"""
This is the test case for your scripted module.
Uses ScriptedLoadableModuleTest base class, available at:
https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py
"""
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
slicer.mrmlScene.Clear()
def runTest(self):
"""Run as few or as many tests as needed here.
"""
self.setUp()
self.test_MusculoskeletalAnalysis1()
def test_MusculoskeletalAnalysis1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
# Get/create input data
from datetime import date
import SampleData
# Make sure the scene is clear before starting
slicer.mrmlScene.Clear()
registerSampleData()
try:
# Set test parameters
inputVolume = SampleData.downloadSample('Cortical1')
mask = SampleData.downloadSample('CorticalMask1')
maskLabel = "Segment_1"
lowerThreshold = 4000
upperThreshold = 10000
analysis="Cortical Bone"
options = {"0018,0050":0.0073996, "0028,1052":-1000, "0028,1053":0.4943119, "0029,1000":4096,"0029,1004":365.712, "0029,1005":-199.725998, }
outputDirectory = os.path.expanduser("~\\Documents\\MusculoskeletalAnalysisTest")
self.delayDisplay('Loaded test data set')
# Test the module logic
logic = MusculoskeletalAnalysisLogic()
# Test cortical analysis
logic.process(inputVolume, mask, maskLabel, lowerThreshold, upperThreshold, analysis, outputDirectory, manDICOM=True, DICOMOptions=options, wait=True)
self.testFile(os.path.join(outputDirectory, "cortical.txt"), [str(date.today()), "Cortical1", 0.21890675924688482, 0.06119903498019812, 1094.0291917644427, 0.08353005741605146, 1.6847633350543425, 0.9198784024224288, 0.7648849326319137, 0.47030180777724473, 0.0073996])
finally:
# Clean up nodes
slicer.mrmlScene.Clear()
try:
# Set test parameters
inputVolume = SampleData.downloadSample('Cancellous1')
mask = SampleData.downloadSample('CancellousMask1')
maskLabel = "Segment_1"
lowerThreshold = 1500
upperThreshold = 10000
analysis="Cancellous Bone"
self.delayDisplay('Loaded test data set')
# Test cancellous analysis
logic.process(inputVolume, mask, maskLabel, lowerThreshold, upperThreshold, analysis, outputDirectory, manDICOM=True, DICOMOptions=options, wait=True)
self.testFile(os.path.join(outputDirectory, "cancellous.txt"), [str(date.today()), "Cancellous1", 1.333489381819056, 0.27215499848346064, 0.20409236263449296, 0.05182980579223419, 0.01560752819180971, 0.16437754493704732, 0.06443102087549339, 6.083556001417202, 1.6664854524662474, 365.2072574703726, 589.9997317002255, 0.0073996, 1500.0, 10000.0])
# Reuses cancellous parameters
analysis="Bone Density"
self.delayDisplay('Loaded test data set')
# Test density analysis
logic.process(inputVolume, mask, maskLabel, lowerThreshold, upperThreshold, analysis, outputDirectory, manDICOM=True, DICOMOptions=options, wait=True)
self.testFile(os.path.join(outputDirectory, "density.txt"), ["", "", 2.32469398135312, 147.00866960658377, 309.78804391297064, -255.03709872604347, 1198.6849313585226, "", "", "", "", "", "", "", ""])
finally:
# Clean up nodes
slicer.mrmlScene.Clear()
try:
# Set test parameters
inputVolume = SampleData.downloadSample('Intervertebral1')
mask = SampleData.downloadSample('IntervertebralMask1')
maskLabel = "'Segment_1, Segment_2'"
lowerThreshold = 0
upperThreshold = 0
analysis="Intervertebral Disc"
self.delayDisplay('Loaded test data set')
# Test cancellous analysis
logic.process(inputVolume, mask, maskLabel, lowerThreshold, upperThreshold, analysis, outputDirectory, manDICOM=True, DICOMOptions=options, wait=True)
self.testFile(os.path.join(outputDirectory, "intervertebral.txt"), [str(date.today()), "Intervertebral1", 0.28008754758301957, 0.0694562859207484, 0.24798062791478137, 1.4070918728304844, 1.0306450189585161, 0.1775904, 0.12621094857350137, 0.0073996])
finally:
# Clean up nodes
slicer.mrmlScene.Clear()
self.delayDisplay('Test passed')
# testFile
# Tests that the newest line of an output file matches a specified input
# fileName: The path to the output file. Output file should be a tsv file
# data: A list of strings to compare the file to
# Throws an assertion error if the data does not match
def testFile(self, fileName, data):
# Confirm that file exist
assert os.path.exists(fileName), "Filename "+fileName+" does not exist."
# Get the header from the first line of the file and the most recent data as the last line
with open(fileName) as f:
lines = f.read().splitlines()
firstLine = lines[0]
lastLine = lines[-1]
header = firstLine.split("\t")
testData = lastLine.split("\t")
# Check that the number of rows is correct
assert len(data) == len(testData), "Expected "+ str(len(data)) + " lines, got " + str(len(testData)) + " instead."
for i in range(len(data)):
try:
# Checks that numeric data is within 5%
float(testData[i]) # If the data is not convertable to a float, throws a value error and compares data as a string
assert (float(data[i]) > float(testData[i])*.95 and float(data[i]) < float(testData[i])*1.05) or (float(data[i]) < float(testData[i])*.95 and float(data[i]) > float(testData[i])*1.05), "Value for " + header[i] + ", " + testData[i] + " outside of range of expected value " + str(data[i]) + "."
except ValueError:
# Checks that strings match
assert data[i] == testData[i], "Value for " + header[i] + ", " + testData[i] + ", doesn't match expected value " + str(data[i]) + "."
Datasets
Models
