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]) + "."