SegmentEditorHollowEffect.py

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import logging
import math
import os

import qt
import vtk

import slicer

from SegmentEditorEffects import *


class SegmentEditorHollowEffect(AbstractScriptedSegmentEditorEffect):
    """This effect makes a segment hollow by replacing it with a shell at the segment boundary"""

    def __init__(self, scriptedEffect):
        scriptedEffect.name = 'Hollow'
        AbstractScriptedSegmentEditorEffect.__init__(self, scriptedEffect)

    def clone(self):
        import qSlicerSegmentationsEditorEffectsPythonQt as effects
        clonedEffect = effects.qSlicerSegmentEditorScriptedEffect(None)
        clonedEffect.setPythonSource(__file__.replace('\\', '/'))
        return clonedEffect

    def icon(self):
        iconPath = os.path.join(os.path.dirname(__file__), 'Resources/Icons/Hollow.png')
        if os.path.exists(iconPath):
            return qt.QIcon(iconPath)
        return qt.QIcon()

    def helpText(self):
        return """Make the selected segment hollow by replacing the segment with a uniform-thickness shell defined by the segment boundary."""

    def setupOptionsFrame(self):

        operationLayout = qt.QVBoxLayout()

        self.insideSurfaceOptionRadioButton = qt.QRadioButton("inside surface")
        self.medialSurfaceOptionRadioButton = qt.QRadioButton("medial surface")
        self.outsideSurfaceOptionRadioButton = qt.QRadioButton("outside surface")
        operationLayout.addWidget(self.insideSurfaceOptionRadioButton)
        operationLayout.addWidget(self.medialSurfaceOptionRadioButton)
        operationLayout.addWidget(self.outsideSurfaceOptionRadioButton)
        self.insideSurfaceOptionRadioButton.setChecked(True)

        self.scriptedEffect.addLabeledOptionsWidget("Use current segment as:", operationLayout)

        self.shellThicknessMMSpinBox = slicer.qMRMLSpinBox()
        self.shellThicknessMMSpinBox.setMRMLScene(slicer.mrmlScene)
        self.shellThicknessMMSpinBox.setToolTip("Thickness of the hollow shell.")
        self.shellThicknessMMSpinBox.quantity = "length"
        self.shellThicknessMMSpinBox.minimum = 0.0
        self.shellThicknessMMSpinBox.value = 3.0
        self.shellThicknessMMSpinBox.singleStep = 1.0

        self.shellThicknessLabel = qt.QLabel()
        self.shellThicknessLabel.setToolTip("Closest achievable thickness. Constrained by the segmentation's binary labelmap representation spacing.")

        shellThicknessFrame = qt.QHBoxLayout()
        shellThicknessFrame.addWidget(self.shellThicknessMMSpinBox)
        self.shellThicknessMMLabel = self.scriptedEffect.addLabeledOptionsWidget("Shell thickness:", shellThicknessFrame)
        self.scriptedEffect.addLabeledOptionsWidget("", self.shellThicknessLabel)

        self.applyToAllVisibleSegmentsCheckBox = qt.QCheckBox()
        self.applyToAllVisibleSegmentsCheckBox.setToolTip("Apply hollow effect to all visible segments in this segmentation node. \
                                                      This operation may take a while.")
        self.applyToAllVisibleSegmentsCheckBox.objectName = self.__class__.__name__ + 'ApplyToAllVisibleSegments'
        self.applyToAllVisibleSegmentsLabel = self.scriptedEffect.addLabeledOptionsWidget("Apply to all segments:", self.applyToAllVisibleSegmentsCheckBox)

        self.applyButton = qt.QPushButton("Apply")
        self.applyButton.objectName = self.__class__.__name__ + 'Apply'
        self.applyButton.setToolTip("Makes the segment hollow by replacing it with a thick shell at the segment boundary.")
        self.scriptedEffect.addOptionsWidget(self.applyButton)

        self.applyButton.connect('clicked()', self.onApply)
        self.shellThicknessMMSpinBox.connect("valueChanged(double)", self.updateMRMLFromGUI)
        self.insideSurfaceOptionRadioButton.connect("toggled(bool)", self.insideSurfaceModeToggled)
        self.medialSurfaceOptionRadioButton.connect("toggled(bool)", self.medialSurfaceModeToggled)
        self.outsideSurfaceOptionRadioButton.connect("toggled(bool)", self.outsideSurfaceModeToggled)
        self.applyToAllVisibleSegmentsCheckBox.connect("stateChanged(int)", self.updateMRMLFromGUI)

    def createCursor(self, widget):
        # Turn off effect-specific cursor for this effect
        return slicer.util.mainWindow().cursor

    def setMRMLDefaults(self):
        self.scriptedEffect.setParameterDefault("ApplyToAllVisibleSegments", 0)
        self.scriptedEffect.setParameterDefault("ShellMode", INSIDE_SURFACE)
        self.scriptedEffect.setParameterDefault("ShellThicknessMm", 3.0)

    def getShellThicknessPixel(self):
        selectedSegmentLabelmapSpacing = [1.0, 1.0, 1.0]
        selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
        if selectedSegmentLabelmap:
            selectedSegmentLabelmapSpacing = selectedSegmentLabelmap.GetSpacing()

        shellThicknessMM = abs(self.scriptedEffect.doubleParameter("ShellThicknessMm"))
        shellThicknessPixel = [int(math.floor(shellThicknessMM / selectedSegmentLabelmapSpacing[componentIndex])) for componentIndex in range(3)]
        return shellThicknessPixel

    def updateGUIFromMRML(self):
        shellThicknessMM = self.scriptedEffect.doubleParameter("ShellThicknessMm")
        wasBlocked = self.shellThicknessMMSpinBox.blockSignals(True)
        self.setWidgetMinMaxStepFromImageSpacing(self.shellThicknessMMSpinBox, self.scriptedEffect.selectedSegmentLabelmap())
        self.shellThicknessMMSpinBox.value = abs(shellThicknessMM)
        self.shellThicknessMMSpinBox.blockSignals(wasBlocked)

        wasBlocked = self.insideSurfaceOptionRadioButton.blockSignals(True)
        self.insideSurfaceOptionRadioButton.setChecked(self.scriptedEffect.parameter("ShellMode") == INSIDE_SURFACE)
        self.insideSurfaceOptionRadioButton.blockSignals(wasBlocked)

        wasBlocked = self.medialSurfaceOptionRadioButton.blockSignals(True)
        self.medialSurfaceOptionRadioButton.setChecked(self.scriptedEffect.parameter("ShellMode") == MEDIAL_SURFACE)
        self.medialSurfaceOptionRadioButton.blockSignals(wasBlocked)

        wasBlocked = self.outsideSurfaceOptionRadioButton.blockSignals(True)
        self.outsideSurfaceOptionRadioButton.setChecked(self.scriptedEffect.parameter("ShellMode") == OUTSIDE_SURFACE)
        self.outsideSurfaceOptionRadioButton.blockSignals(wasBlocked)

        selectedSegmentLabelmapSpacing = [1.0, 1.0, 1.0]
        selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
        if selectedSegmentLabelmap:
            selectedSegmentLabelmapSpacing = selectedSegmentLabelmap.GetSpacing()
            shellThicknessPixel = self.getShellThicknessPixel()
            if shellThicknessPixel[0] < 1 or shellThicknessPixel[1] < 1 or shellThicknessPixel[2] < 1:
                self.shellThicknessLabel.text = "Not feasible at current resolution."
                self.applyButton.setEnabled(False)
            else:
                thicknessMM = self.getShellThicknessMM()
                self.shellThicknessLabel.text = "Actual: {} x {} x {} mm ({}x{}x{} pixel)".format(*thicknessMM, *shellThicknessPixel)
                self.applyButton.setEnabled(True)
        else:
            self.shellThicknessLabel.text = "Empty segment"

        self.setWidgetMinMaxStepFromImageSpacing(self.shellThicknessMMSpinBox, self.scriptedEffect.selectedSegmentLabelmap())

        applyToAllVisibleSegments = qt.Qt.Unchecked if self.scriptedEffect.integerParameter("ApplyToAllVisibleSegments") == 0 else qt.Qt.Checked
        wasBlocked = self.applyToAllVisibleSegmentsCheckBox.blockSignals(True)
        self.applyToAllVisibleSegmentsCheckBox.setCheckState(applyToAllVisibleSegments)
        self.applyToAllVisibleSegmentsCheckBox.blockSignals(wasBlocked)

    def updateMRMLFromGUI(self):
        # Operation is managed separately
        self.scriptedEffect.setParameter("ShellThicknessMm", self.shellThicknessMMSpinBox.value)
        applyToAllVisibleSegments = 1 if self.applyToAllVisibleSegmentsCheckBox.isChecked() else 0
        self.scriptedEffect.setParameter("ApplyToAllVisibleSegments", applyToAllVisibleSegments)

    def insideSurfaceModeToggled(self, toggled):
        if toggled:
            self.scriptedEffect.setParameter("ShellMode", INSIDE_SURFACE)

    def medialSurfaceModeToggled(self, toggled):
        if toggled:
            self.scriptedEffect.setParameter("ShellMode", MEDIAL_SURFACE)

    def outsideSurfaceModeToggled(self, toggled):
        if toggled:
            self.scriptedEffect.setParameter("ShellMode", OUTSIDE_SURFACE)

    def getShellThicknessMM(self):
        selectedSegmentLabelmapSpacing = [1.0, 1.0, 1.0]
        selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
        if selectedSegmentLabelmap:
            selectedSegmentLabelmapSpacing = selectedSegmentLabelmap.GetSpacing()

        shellThicknessPixel = self.getShellThicknessPixel()
        shellThicknessMM = [abs((shellThicknessPixel[i]) * selectedSegmentLabelmapSpacing[i]) for i in range(3)]
        for i in range(3):
            if shellThicknessMM[i] > 0:
                shellThicknessMM[i] = round(shellThicknessMM[i], max(int(-math.floor(math.log10(shellThicknessMM[i]))), 1))
        return shellThicknessMM

    def showStatusMessage(self, msg, timeoutMsec=500):
        slicer.util.showStatusMessage(msg, timeoutMsec)
        slicer.app.processEvents()

    def processHollowing(self):
        # Get modifier labelmap and parameters
        modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
        selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
        # We need to know exactly the value of the segment voxels, apply threshold to make force the selected label value
        labelValue = 1
        backgroundValue = 0
        thresh = vtk.vtkImageThreshold()
        thresh.SetInputData(selectedSegmentLabelmap)
        thresh.ThresholdByLower(0)
        thresh.SetInValue(backgroundValue)
        thresh.SetOutValue(labelValue)
        thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())

        shellMode = self.scriptedEffect.parameter("ShellMode")
        shellThicknessMM = abs(self.scriptedEffect.doubleParameter("ShellThicknessMm"))
        import vtkITK
        margin = vtkITK.vtkITKImageMargin()
        margin.SetInputConnection(thresh.GetOutputPort())
        margin.CalculateMarginInMMOn()

        spacing = selectedSegmentLabelmap.GetSpacing()
        voxelDiameter = min(selectedSegmentLabelmap.GetSpacing())
        if shellMode == MEDIAL_SURFACE:
            margin.SetOuterMarginMM(0.5 * shellThicknessMM)
            margin.SetInnerMarginMM(-0.5 * shellThicknessMM + 0.5 * voxelDiameter)
        elif shellMode == INSIDE_SURFACE:
            margin.SetOuterMarginMM(shellThicknessMM + 0.1 * voxelDiameter)
            margin.SetInnerMarginMM(0.0 + 0.1 * voxelDiameter)  # Don't include the original border (0.0)
        elif shellMode == OUTSIDE_SURFACE:
            margin.SetOuterMarginMM(0.0)
            margin.SetInnerMarginMM(-shellThicknessMM + voxelDiameter)

        modifierLabelmap.DeepCopy(margin.GetOutput())

        margin.Update()
        modifierLabelmap.ShallowCopy(margin.GetOutput())

        # Apply changes
        self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)

    def onApply(self):
        # Make sure the user wants to do the operation, even if the segment is not visible
        if not self.scriptedEffect.confirmCurrentSegmentVisible():
            return

        try:
            # This can be a long operation - indicate it to the user
            qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
            self.scriptedEffect.saveStateForUndo()

            applyToAllVisibleSegments = int(self.scriptedEffect.parameter("ApplyToAllVisibleSegments")) != 0 \
                if self.scriptedEffect.parameter("ApplyToAllVisibleSegments") else False

            if applyToAllVisibleSegments:
                # Process all visible segments
                inputSegmentIDs = vtk.vtkStringArray()
                segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
                segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(inputSegmentIDs)
                segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor
                segmentEditorNode = segmentEditorWidget.mrmlSegmentEditorNode()
                # store which segment was selected before operation
                selectedStartSegmentID = segmentEditorNode.GetSelectedSegmentID()
                if inputSegmentIDs.GetNumberOfValues() == 0:
                    logging.info("Hollow operation skipped: there are no visible segments.")
                    return
                # select input segments one by one, process
                for index in range(inputSegmentIDs.GetNumberOfValues()):
                    segmentID = inputSegmentIDs.GetValue(index)
                    self.showStatusMessage(f'Processing {segmentationNode.GetSegmentation().GetSegment(segmentID).GetName()}...')
                    segmentEditorNode.SetSelectedSegmentID(segmentID)
                    self.processHollowing()
                # restore segment selection
                segmentEditorNode.SetSelectedSegmentID(selectedStartSegmentID)
            else:
                self.processHollowing()

        finally:
            qt.QApplication.restoreOverrideCursor()


INSIDE_SURFACE = 'INSIDE_SURFACE'
MEDIAL_SURFACE = 'MEDIAL_SURFACE'
OUTSIDE_SURFACE = 'OUTSIDE_SURFACE'