JRC2013Vis.py

import os

import ctk
import qt

import slicer
from DICOMLib import DICOMUtils
from slicer.ScriptedLoadableModule import *
from slicer.util import TESTING_DATA_URL


#
# JRC2013Vis
#


class JRC2013Vis(ScriptedLoadableModule):
    def __init__(self, parent):
        ScriptedLoadableModule.__init__(self, parent)
        parent.title = "JRC2013Vis"  # TODO make this more human readable by adding spaces
        parent.categories = ["Testing.TestCases"]
        parent.dependencies = []
        parent.contributors = ["Nicholas Herlambang (AZE R&D)"]  # replace with "Firstname Lastname (Org)"
        parent.helpText = """
    This module was developed as a self test to perform the operations needed for the JRC 2013 Visualization Tutorial
    """
        parent.acknowledgementText = """
    This file was originally developed by Steve Pieper, Isomics, Inc.  and was partially funded by NIH grant 3P41RR013218-12S1.
"""  # replace with organization, grant and thanks.


#
# qJRC2013VisWidget
#


class JRC2013VisWidget(ScriptedLoadableModuleWidget):
    def setup(self):
        ScriptedLoadableModuleWidget.setup(self)
        # Instantiate and connect widgets ...

        # start/stop DICOM peer
        self.startStopDicomPeerButton = qt.QPushButton("Start/Stop DICOM peer")
        self.startStopDicomPeerButton.setCheckable(True)
        self.layout.addWidget(self.startStopDicomPeerButton)
        self.startStopDicomPeerButton.connect("toggled(bool)", self.onStartStopDicomPeer)

        # Collapsible button
        testsCollapsibleButton = ctk.ctkCollapsibleButton()
        testsCollapsibleButton.text = "A collapsible button"
        self.layout.addWidget(testsCollapsibleButton)

        # Layout within the collapsible button
        formLayout = qt.QFormLayout(testsCollapsibleButton)

        # test buttons
        tests = (("Part 1: DICOM", self.onPart1DICOM), ("Part 2: Head", self.onPart2Head), ("Part 3: Liver", self.onPart3Liver), ("Part 4: Lung", self.onPart4Lung))
        for text, slot in tests:
            testButton = qt.QPushButton(text)
            testButton.toolTip = "Run the test."
            formLayout.addWidget(testButton)
            testButton.connect("clicked(bool)", slot)

        # Add vertical spacer
        self.layout.addStretch(1)

    def onPart1DICOM(self):
        tester = JRC2013VisTest()
        tester.setUp()
        tester.test_Part1DICOM()

    def onPart2Head(self):
        tester = JRC2013VisTest()
        tester.setUp()
        tester.test_Part2Head()

    def onPart3Liver(self):
        tester = JRC2013VisTest()
        tester.setUp()
        tester.test_Part3Liver()

    def onPart4Lung(self):
        tester = JRC2013VisTest()
        tester.setUp()
        tester.test_Part4Lung()

    def onStartStopDicomPeer(self, flag):
        if flag:
            self.startStopDicomPeerButton.setEnabled(False)
            dicomFilesDirectory = slicer.app.temporaryPath
            configFilePath = dicomFilesDirectory + "/Dcmtk-db/dcmqrscp.cfg"
            processCurrentPath = dicomFilesDirectory + "/Dcmtk-db/"

            if slicer.util.confirmYesNoDisplay("Do you want to choose local DCMTK database folder?"):
                print("Yes")
                dicomFilesDirectory = qt.QFileDialog.getExistingDirectory(None, "Select DCMTK database folder")
                configFilePath = dicomFilesDirectory + "/dcmqrscp.cfg"
                processCurrentPath = dicomFilesDirectory
            else:
                import SampleData

                SampleData.downloadFromURL(
                    fileNames="Dcmtk-db.zip",
                    uris=TESTING_DATA_URL + "MD5/6bfb01cf5ffb8e3af9b1c0c9556f0c6b45f0ec40305a9539ed7a9f0dcfe378e3",
                    checksums="SHA256:6bfb01cf5ffb8e3af9b1c0c9556f0c6b45f0ec40305a9539ed7a9f0dcfe378e3")[0]

            import subprocess

            dcmqrscpExeOptions = (
                "/bin",
                "/../CTK-build/CMakeExternals/Install/bin",
                "/../DCMTK-install/bin",
                "/../DCMTK-build/bin",
                "/../DCMTK-build/bin/Release",
                "/../DCMTK-build/bin/Debug",
                "/../DCMTK-build/bin/RelWithDebInfo",
                "/../DCMTK-build/bin/MinSizeRel",
            )

            dcmqrscpExePath = None
            dcmqrscpExeName = "/dcmqrscp"
            if slicer.app.os == "win":
                dcmqrscpExeName = dcmqrscpExeName + ".exe"
            for path in dcmqrscpExeOptions:
                testPath = slicer.app.slicerHome + path + dcmqrscpExeName
                if os.path.exists(testPath):
                    dcmqrscpExePath = testPath
                    break
            if not dcmqrscpExePath:
                raise UserWarning("Could not find dcmqrscp executable")

            args = (dcmqrscpExePath, "-c", configFilePath)
            print("Start DICOM peer")
            self.popen = subprocess.Popen(args, stdout=subprocess.PIPE, cwd=processCurrentPath)
            self.startStopDicomPeerButton.setEnabled(True)
        else:
            print("Stop DICOM peer")
            self.popen.kill()


#
# JRC2013VisLogic
#


class JRC2013VisLogic(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
    """

    pass


class JRC2013VisTest(ScriptedLoadableModuleTest):
    """This is the test case for your scripted module."""

    def setUp(self):
        """Do whatever is needed to reset the state - typically a scene clear will be enough."""
        self.delayDisplay("Closing the scene")
        layoutManager = slicer.app.layoutManager()
        layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
        slicer.mrmlScene.Clear(0)

    def runTest(self):
        """Run as few or as many tests as needed here."""
        self.setUp()
        self.test_Part1DICOM()
        self.setUp()
        self.test_Part2Head()
        self.setUp()
        self.test_Part3Liver()
        self.setUp()
        self.test_Part4Lung()

    def test_Part1DICOM(self):
        """Test the DICOM part of the test using the head atlas"""
        import os

        self.delayDisplay("Starting the DICOM test")
        #
        # first, get the data - a zip file of dicom data
        #
        import SampleData

        dicomFilesDirectory = SampleData.downloadFromURL(
            fileNames="Dcmtk-db.zip",
            uris=TESTING_DATA_URL + "MD5/7a43d121a51a631ab0df02071e5ba6ed",
            checksums="MD5:7a43d121a51a631ab0df02071e5ba6ed")[0]

        try:
            self.delayDisplay("Switching to temp database directory")
            originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase("tempDICOMDatbase")

            self.delayDisplay("Start Local DICOM Q/R SCP")
            import subprocess
            import os

            configFilePath = dicomFilesDirectory + "/Dcmtk-db/dcmqrscp.cfg"
            processCurrentPath = dicomFilesDirectory + "/Dcmtk-db/"
            print("configFilePath: " + os.path.abspath(configFilePath))
            print("processCurrentPath: " + os.path.abspath(processCurrentPath))

            dcmqrscpExeOptions = (
                "/bin",
                "/../CTK-build/CMakeExternals/Install/bin",
                "/../DCMTK-install/bin",
                "/../DCMTK-build/bin",
                "/../DCMTK-build/bin/Release",
                "/../DCMTK-build/bin/Debug",
                "/../DCMTK-build/bin/RelWithDebInfo",
                "/../DCMTK-build/bin/MinSizeRel",
            )

            dcmqrscpExePath = None
            dcmqrscpExeName = "/dcmqrscp"
            if slicer.app.os == "win":
                dcmqrscpExeName = dcmqrscpExeName + ".exe"
            for path in dcmqrscpExeOptions:
                testPath = slicer.app.slicerHome + path + dcmqrscpExeName
                if os.path.exists(testPath):
                    dcmqrscpExePath = testPath
                    break
            if not dcmqrscpExePath:
                raise UserWarning("Could not find dcmqrscp executable")

            args = (dcmqrscpExePath, "-c", configFilePath)
            popen = subprocess.Popen(args, stdout=subprocess.PIPE, cwd=processCurrentPath)

            self.delayDisplay("Retrieve DICOM")
            slicer.util.selectModule("DICOM")
            dicomRetrieve = ctk.ctkDICOMRetrieve()
            dicomRetrieve.setKeepAssociationOpen(True)
            dicomRetrieve.setDatabase(slicer.dicomDatabase)
            dicomRetrieve.setCallingAETitle("SlicerAE")
            dicomRetrieve.setCalledAETitle("DCMTK")
            dicomRetrieve.setPort(12345)
            dicomRetrieve.setHost("localhost")
            dicomRetrieve.getStudy("1.2.124.113932.1.170.223.162.178.20050502.160340.12640015")
            popen.kill()

            # Select first patient
            browserWidget = slicer.modules.DICOMWidget.browserWidget
            browserWidget.dicomBrowser.dicomTableManager().patientsTable().selectFirst()
            browserWidget.examineForLoading()

            self.delayDisplay("Loading Selection")
            browserWidget.loadCheckedLoadables()

            self.delayDisplay("Change Level")
            layoutManager = slicer.app.layoutManager()
            redWidget = layoutManager.sliceWidget("Red")
            slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))

            self.delayDisplay("Change Window")
            slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))

            self.delayDisplay("Change Layout")
            layoutManager = slicer.app.layoutManager()
            layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)

            self.delayDisplay("Zoom")
            slicer.util.clickAndDrag(redWidget, button="Right", start=(10, 10), end=(10, 40))

            self.delayDisplay("Pan")
            slicer.util.clickAndDrag(redWidget, button="Middle", start=(10, 10), end=(40, 40))

            self.delayDisplay("Center")
            redWidget.sliceController().fitSliceToBackground()

            self.delayDisplay("Lightbox")
            redWidget.sliceController().setLightboxTo6x6()

            self.delayDisplay("Conventional Layout")
            layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)

            self.delayDisplay("No Lightbox")
            redWidget.sliceController().setLightboxTo1x1()

            self.delayDisplay("Four Up Layout")
            layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)

            self.delayDisplay("Shift Mouse")
            slicer.util.clickAndDrag(redWidget, button="None", start=(100, 100), end=(140, 140), modifiers=["Shift"])

            self.delayDisplay("Conventional, Link, Slice Model")
            layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
            redWidget.sliceController().setSliceLink(True)
            redWidget.sliceController().setSliceVisible(True)

            self.delayDisplay("Rotate")
            threeDView = layoutManager.threeDWidget(0).threeDView()
            slicer.util.clickAndDrag(threeDView)

            self.delayDisplay("Zoom")
            threeDView = layoutManager.threeDWidget(0).threeDView()
            slicer.util.clickAndDrag(threeDView, button="Right")

            self.delayDisplay("Test passed!")
        except Exception as e:
            import traceback

            traceback.print_exc()
            self.delayDisplay("Test caused exception!\n" + str(e))

        self.delayDisplay("Restoring original database directory")
        DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)

    def test_Part2Head(self):
        """Test using the head atlas - may not be needed - Slicer4Minute is already tested"""
        self.delayDisplay("Starting the test")
        #
        # first, get some data
        # TODO: This is a very old scene with missing scene view screenshots
        #   that is why error is reported while attempting to load it.
        #   It would be better to replace with a new scene.
        #
        import SampleData

        SampleData.downloadFromURL(
            fileNames="3DHeadData.mrb",
            loadFiles=True,
            uris=TESTING_DATA_URL + "SHA256/e2c7944095dd92be7961bed37f3c8f49e6f40c7f31d4fe865753b6efddae7993",
            checksums="SHA256:e2c7944095dd92be7961bed37f3c8f49e6f40c7f31d4fe865753b6efddae7993")
        self.delayDisplay("Finished with download and loading\n")

        try:
            logic = JRC2013VisLogic()
            mainWindow = slicer.util.mainWindow()
            layoutManager = slicer.app.layoutManager()
            threeDView = layoutManager.threeDWidget(0).threeDView()
            redWidget = layoutManager.sliceWidget("vtkMRMLSliceNode1")  # it would be 'Red' in a recent scene
            redController = redWidget.sliceController()
            greenWidget = layoutManager.sliceWidget("vtkMRMLSliceNode2")  # it would be 'Green' in a recent scene
            greenController = greenWidget.sliceController()

            self.delayDisplay("Models and Slice Model")
            mainWindow.moduleSelector().selectModule("Models")
            redWidget.sliceController().setSliceVisible(True)

            self.delayDisplay("Scroll Slices")
            for offset in range(-20, 20, 2):
                redController.setSliceOffsetValue(offset)

            self.delayDisplay("Skin Opacity")
            # turn off skin and skull
            skin = slicer.util.getNode(pattern="Skin.vtk")
            skin.GetDisplayNode().SetOpacity(0.5)

            self.delayDisplay("Skin and Skull Visibility")
            skin.GetDisplayNode().SetVisibility(0)
            skull = slicer.util.getNode(pattern="skull_bone.vtk")
            skull.GetDisplayNode().SetVisibility(0)

            self.delayDisplay("Green slice and Clipping")
            greenWidget.sliceController().setSliceVisible(True)
            hemispheric_white_matter = slicer.util.getNode(pattern="hemispheric_white_matter.vtk")
            hemispheric_white_matter.GetDisplayNode().SetClipping(1)
            clip = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLClipModelsNode")
            clip.SetRedSliceClipState(0)
            clip.SetYellowSliceClipState(0)
            clip.SetGreenSliceClipState(2)

            viewNode = threeDView.mrmlViewNode()
            cameras = slicer.util.getNodes("vtkMRMLCameraNode*")
            for cameraNode in cameras.values():
                if cameraNode.GetActiveTag() == viewNode.GetID():
                    break
            cameraNode.GetCamera().Azimuth(90)
            cameraNode.GetCamera().Elevation(20)

            self.delayDisplay("Rotate")
            slicer.util.clickAndDrag(threeDView)

            self.delayDisplay("Zoom")
            threeDView = layoutManager.threeDWidget(0).threeDView()
            slicer.util.clickAndDrag(threeDView, button="Right")

            self.delayDisplay("Test passed!")
        except Exception as e:
            import traceback

            traceback.print_exc()
            self.delayDisplay("Test caused exception!\n" + str(e))

    def test_Part3Liver(self):
        """Test using the liver example data"""
        self.delayDisplay("Starting the test")
        #
        # first, get some data
        #
        import SampleData

        SampleData.downloadFromURL(
            fileNames="LiverData.mrb",
            loadFiles=True,
            uris=TESTING_DATA_URL + "SHA256/a39075d3e87f80bbf8eba1e0222ee68c60036e57c3db830db08f3022f424e221",
            checksums="SHA256:a39075d3e87f80bbf8eba1e0222ee68c60036e57c3db830db08f3022f424e221")
        self.delayDisplay("Finished with download and loading\n")

        try:
            logic = JRC2013VisLogic()
            mainWindow = slicer.util.mainWindow()
            layoutManager = slicer.app.layoutManager()
            threeDView = layoutManager.threeDWidget(0).threeDView()
            redWidget = layoutManager.sliceWidget("Red")
            redController = redWidget.sliceController()
            viewNode = threeDView.mrmlViewNode()
            cameras = slicer.util.getNodes("vtkMRMLCameraNode*")
            for cameraNode in cameras.values():
                if cameraNode.GetActiveTag() == viewNode.GetID():
                    break

            self.delayDisplay("Segment II invisible")
            mainWindow.moduleSelector().selectModule("Models")
            segmentII = slicer.util.getNode("LiverSegment_II")
            segmentII.GetDisplayNode().SetVisibility(0)
            slicer.util.clickAndDrag(threeDView, start=(10, 200), end=(10, 10))

            self.delayDisplay("Segment II visible")
            segmentII.GetDisplayNode().SetVisibility(1)
            cameraNode.GetCamera().Azimuth(0)
            cameraNode.GetCamera().Elevation(0)

            self.delayDisplay("View Adrenal")
            segmentII.GetDisplayNode().SetVisibility(1)
            cameraNode.GetCamera().Azimuth(180)
            cameraNode.GetCamera().Elevation(-30)

            segmentVII = slicer.util.getNode("LiverSegment_II")
            redWidget.sliceController().setSliceVisible(True)

            self.delayDisplay("Middle Hepatic")
            models = slicer.util.getNodes("vtkMRMLModelNode*")
            for modelNode in models.values():
                modelNode.GetDisplayNode().SetVisibility(0)

            segmentVII = slicer.util.getNode("LiverSegment_II")
            transparentNodes = ("MiddleHepaticVein_and_Branches", "LiverSegment_IVb", "LiverSegmentV")
            for nodeName in transparentNodes:
                modelNode = slicer.util.getNode(nodeName)
                modelNode.GetDisplayNode().SetOpacity(0.5)
                modelNode.GetDisplayNode().SetVisibility(1)
            redWidget.sliceController().setSliceVisible(True)
            cameraNode.GetCamera().Azimuth(30)
            cameraNode.GetCamera().Elevation(-20)

            self.delayDisplay("Test passed!")
        except Exception as e:
            import traceback

            traceback.print_exc()
            self.delayDisplay("Test caused exception!\n" + str(e))

    def test_Part4Lung(self):
        """Test using the lung data"""

        self.delayDisplay("Starting the test")
        #
        # first, get some data
        #
        import SampleData

        SampleData.downloadFromURL(
            fileNames="LungData.mrb",
            loadFiles=True,
            uris=TESTING_DATA_URL + "SHA256/9da091065aa42edbba2d436a2ef21a093792e8a76455c28e5b80590b04f5a73e",
            checksums="SHA256:9da091065aa42edbba2d436a2ef21a093792e8a76455c28e5b80590b04f5a73e")
        self.delayDisplay("Finished with download and loading\n")

        try:
            mainWindow = slicer.util.mainWindow()
            layoutManager = slicer.app.layoutManager()
            threeDView = layoutManager.threeDWidget(0).threeDView()
            redWidget = layoutManager.sliceWidget("Red")
            redController = redWidget.sliceController()
            viewNode = threeDView.mrmlViewNode()
            cameras = slicer.util.getNodes("vtkMRMLCameraNode*")
            for cameraNode in cameras.values():
                if cameraNode.GetActiveTag() == viewNode.GetID():
                    break

            self.delayDisplay("Reset view")
            threeDView.resetFocalPoint()
            mainWindow.moduleSelector().selectModule("Models")

            self.delayDisplay("View Question 1")
            cameraNode.GetCamera().Azimuth(-100)
            cameraNode.GetCamera().Elevation(-40)
            redWidget.sliceController().setSliceVisible(True)
            lungs = slicer.util.getNode("chestCT_lungs")
            lungs.GetDisplayNode().SetVisibility(0)

            self.delayDisplay("View Question 2")
            cameraNode.GetCamera().Azimuth(-65)
            cameraNode.GetCamera().Elevation(-20)
            lungs.GetDisplayNode().SetVisibility(1)
            lungs.GetDisplayNode().SetOpacity(0.24)
            redController.setSliceOffsetValue(-50)

            self.delayDisplay("View Question 3")
            cameraNode.GetCamera().Azimuth(-165)
            cameraNode.GetCamera().Elevation(-10)
            redWidget.sliceController().setSliceVisible(False)

            self.delayDisplay("View Question 4")
            cameraNode.GetCamera().Azimuth(20)
            cameraNode.GetCamera().Elevation(-10)
            lowerLobeNodes = slicer.util.getNodes("*LowerLobe*")
            for showNode in lowerLobeNodes:
                self.delayDisplay("Showing Node %s" % showNode, 300)
                for node in lowerLobeNodes:
                    displayNode = lowerLobeNodes[node].GetDisplayNode()
                    if displayNode:
                        displayNode.SetVisibility(1 if node == showNode else 0)

            self.delayDisplay("Test passed!")
        except Exception as e:
            import traceback

            traceback.print_exc()
            self.delayDisplay("Test caused exception!\n" + str(e))