CILViewer2D.py

# -*- coding: utf-8 -*-
#   Copyright 2017 - 2019 Edoardo Pasca
#   Copyright 2018 Richard Smith
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#
#       http://www.apache.org/licenses/LICENSE-2.0
#
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.

import numpy
import vtk
from ccpi.viewer import (ALT_KEY, CONTROL_KEY, SHIFT_KEY, CROSSHAIR_ACTOR, CURSOR_ACTOR, HELP_ACTOR, HISTOGRAM_ACTOR,
                         LINEPLOT_ACTOR, OVERLAY_ACTOR, SLICE_ACTOR, WIPE_ACTOR, SLICE_ORIENTATION_XY,
                         SLICE_ORIENTATION_XZ, SLICE_ORIENTATION_YZ)
from ccpi.viewer.CILViewerBase import CILViewerBase
from ccpi.viewer.utils import Converter

from ccpi.viewer.widgets import cilviewerBoxWidget, SliceSliderRepresentation, SliderCallback


class CILInteractorStyle(vtk.vtkInteractorStyle):

    def __init__(self, callback):
        self.callback = callback
        self._viewer = callback
        priority = 1.0
        self.debug = False

        self.AddObserver("MouseWheelForwardEvent", self.OnMouseWheelForward, priority)
        self.AddObserver("MouseWheelBackwardEvent", self.OnMouseWheelBackward, priority)
        self.AddObserver('KeyPressEvent', self.OnKeyPress, priority)
        self.AddObserver('KeyReleaseEvent', self.OnKeyRelease, priority)
        self.AddObserver('LeftButtonPressEvent', self.OnLeftButtonPressEvent, priority)
        self.AddObserver('RightButtonPressEvent', self.OnRightButtonPressEvent, priority)
        self.AddObserver('LeftButtonReleaseEvent', self.OnLeftButtonReleaseEvent, priority)
        self.AddObserver('RightButtonReleaseEvent', self.OnRightButtonReleaseEvent, priority)
        self.AddObserver('MouseMoveEvent', self.OnMouseMoveEvent, priority)

        self.InitialEventPosition = (0, 0)

        # Initialise difference from zoom event start point
        self.dy = 0

        self._reslicing_enabled = True

    @property
    def reslicing_enabled(self):
        return self._reslicing_enabled

    @reslicing_enabled.setter
    def reslicing_enabled(self, value):
        if isinstance(value, bool):
            self._reslicing_enabled = value

    def log(self, msg):
        if self.debug:
            print(msg)

    def SetInitialEventPosition(self, xy):
        self.InitialEventPosition = xy

    def GetInitialEventPosition(self):
        return self.InitialEventPosition

    def GetKeyCode(self):
        return self.GetInteractor().GetKeyCode()

    def SetKeyCode(self, keycode):
        self.GetInteractor().SetKeyCode(keycode)

    def GetControlKey(self):
        return self.GetInteractor().GetControlKey()

    def GetShiftKey(self):
        return self.GetInteractor().GetShiftKey()

    def GetAltKey(self):
        return self.GetInteractor().GetAltKey()

    def GetEventPosition(self):
        return self.GetInteractor().GetEventPosition()

    def GetDeltaEventPosition(self):
        x, y = self.GetInteractor().GetEventPosition()
        return (x - self.InitialEventPosition[0], y - self.InitialEventPosition[1])

    def Dolly(self, factor):
        self.callback.camera.Dolly(factor)
        self.callback.ren.ResetCameraClippingRange()

    def GetDimensions(self):
        return self._viewer.img3D.GetDimensions()

    def GetInputData(self):
        return self._viewer.img3D

    def GetSliceOrientation(self):
        return self._viewer.sliceOrientation

    def SetSliceOrientation(self, orientation):
        self._viewer.sliceOrientation = orientation

    def GetActiveSlice(self):
        return self._viewer.getActiveSlice()

    def SetActiveSlice(self, sliceno):
        self._viewer.setActiveSlice(sliceno)

    def UpdatePipeline(self, reset=False):
        self._viewer.updatePipeline(reset)

    def GetActiveCamera(self):
        return self._viewer.ren.GetActiveCamera()

    def SetActiveCamera(self, camera):
        self._viewer.ren.SetActiveCamera(camera)

    def ResetCamera(self):
        self._viewer.ren.ResetCamera()

    def FlipCameraPosition(self, flip=True):
        self._viewer.flipCameraPosition = flip

    def Render(self):
        self._viewer.renWin.Render()

    def UpdateImageSlice(self):
        self._viewer.imageSlice.Update()
        self.AdjustCamera()
        self.Render()

    def AdjustCamera(self):
        self._viewer.AdjustCamera()

    def SaveRender(self, filename):
        self._viewer.saveRender(filename)

    def GetRenderWindow(self):
        return self._viewer.renWin

    def GetRenderer(self):
        return self._viewer.ren

    def GetROIWidget(self):
        return self._viewer.ROIWidget

    def SetEventActive(self, event):
        self._viewer.event.On(event)

    def SetEventInactive(self, event):
        self._viewer.event.Off(event)

    def GetViewerEvent(self, event):
        return self._viewer.event.isActive(event)

    def SetInitialCameraPosition(self, position):
        self._viewer.InitialCameraPosition = position

    def GetInitialCameraPosition(self):
        return self._viewer.InitialCameraPosition

    def SetInitialLevel(self, level):
        self._viewer.InitialLevel = level

    def GetInitialLevel(self):
        return self._viewer.InitialLevel

    def SetInitialWindow(self, window):
        self._viewer.InitialWindow = window

    def GetInitialWindow(self):
        return self._viewer.InitialWindow

    def SetROI(self, roi):
        self._viewer.ROI = roi

    def GetROI(self):
        return self._viewer.ROI

    def GetVisualisationDownsampling(self):
        return self._viewer.visualisation_downsampling

    def SetVisualisationDownsampling(self, value):
        self._viewer.setVisualisationDownsampling(value)

    def CreateAnnotationText(self, display_type, data):
        return self._viewer.createAnnotationText(display_type, data)

    def UpdateCornerAnnotation(self, text, corner):
        self._viewer.updateCornerAnnotation(text, corner)

    def GetPicker(self):
        return self._viewer.picker

    def GetCornerAnnotation(self):
        return self._viewer.cornerAnnotation

    def UpdateROIHistogram(self):
        self._viewer.updateROIHistogram()

    def UpdateLinePlot(self, imagecoordinate, display):
        self._viewer.updateLinePlot(imagecoordinate, display)

    def GetCrosshairs(self):
        actor = self._viewer.crosshairsActor
        vert = self._viewer.vertLine
        horiz = self._viewer.horizLine

        return actor, vert, horiz

    def GetImageWorldExtent(self):
        """
        Compute and return the maximum extent of the image in the rendered world
        """
        return self.image2world(self.GetInputData().GetExtent()[1::2])

    def SetCharEvent(self, char):
        self.GetInteractor().SetKeyCode(char)
        self.OnKeyPress(self.GetInteractor(), "KeyPressEvent")

    def validateValue(self, value, axis):
        return self._viewer.validateValue(value, axis)

    def InitialiseBox(self, clickPosition):
        """
        Set the initial values for the box borders
        :param clickPosition: Display coordinates for the mouse event
        """

        box_pos = cilviewerBoxWidget.GetBoxBoundsFromEventPosition(self._viewer, clickPosition)

        # Set widget placement and make visible
        self._viewer.ROIWidget.PlaceWidget(box_pos)
        self._viewer.ROIWidget.On()
        self.UpdatePipeline()

    ############### Handle events
    def OnMouseWheelForward(self, interactor, event):
        if self.GetInputData() is None:
            return
        maxSlice = self.GetInputData().GetExtent()[self.GetSliceOrientation() * 2 + 1]
        shift = interactor.GetShiftKey()
        advance = 1
        if shift:
            advance = 10

        if (self.GetActiveSlice() + advance <= maxSlice):
            self.SetActiveSlice(self.GetActiveSlice() + advance)

            self.UpdatePipeline()
        else:
            self.log("maxSlice %d request %d" % (maxSlice, self.GetActiveSlice()))

        if self.GetViewerEvent("SHOW_LINE_PROFILE_EVENT"):
            self.DisplayLineProfile(interactor, event, True)

    def OnMouseWheelBackward(self, interactor, event):
        if self.GetInputData() is None:
            return
        minSlice = self.GetInputData().GetExtent()[self.GetSliceOrientation() * 2]
        shift = interactor.GetShiftKey()
        advance = 1
        if shift:
            advance = 10
        if (self.GetActiveSlice() - advance >= minSlice):
            self.SetActiveSlice(self.GetActiveSlice() - advance)
            self.UpdatePipeline()
        else:
            self.log("minSlice %d request %d" % (minSlice, self.GetActiveSlice()))
        if self.GetViewerEvent("SHOW_LINE_PROFILE_EVENT"):
            self.DisplayLineProfile(interactor, event, True)

    def AutoWindowLevelOnVolumeRange(self, update_slice=True):
        '''Auto-adjusts window-level for the slice, based on the 5 and 95th percentiles of the whole image volume.'''
        cmin, cmax = self._viewer.getImageMapRange((5., 95.), method="scalar")
        print("Auto range for volume: ", cmin, cmax)
        window, level = self._viewer.getSliceWindowLevelFromRange(cmin, cmax)

        self._viewer.imageSlice.GetProperty().SetColorLevel(level)
        self._viewer.imageSlice.GetProperty().SetColorWindow(window)

        if update_slice:
            self.UpdateImageSlice()

    def ChangeOrientation(self, new_slice_orientation):
        orientation = self.GetSliceOrientation()
        camera = vtk.vtkCamera()
        camera.ParallelProjectionOn()
        camera.SetFocalPoint(self.GetActiveCamera().GetFocalPoint())
        camera.SetPosition(self.GetActiveCamera().GetPosition())
        self.SetInitialCameraPosition(self.GetActiveCamera().GetPosition())
        camera.SetViewUp(self.GetActiveCamera().GetViewUp())

        if new_slice_orientation == SLICE_ORIENTATION_XY:
            # Equivalent to pressing z
            if orientation == SLICE_ORIENTATION_YZ:
                self.FlipCameraPosition(True)
                camera.Elevation(90)
            elif orientation == SLICE_ORIENTATION_XZ:
                camera.Elevation(-90)
                self.FlipCameraPosition(True)
            camera.SetViewUp(0, -1, 0)
        elif new_slice_orientation == SLICE_ORIENTATION_XZ:
            # Equivalent to pressing y
            if orientation == SLICE_ORIENTATION_XY:
                camera.Elevation(90)
                self.FlipCameraPosition(True)
            elif orientation == SLICE_ORIENTATION_YZ:
                camera.Azimuth(90)
            camera.SetViewUp(0, 0, -1)
        elif new_slice_orientation == SLICE_ORIENTATION_YZ:
            # Equivalent to pressing x
            if orientation == SLICE_ORIENTATION_XY:
                camera.Azimuth(270)
            elif orientation == SLICE_ORIENTATION_XZ:
                self.FlipCameraPosition(True)
                camera.Azimuth(90)
            camera.SetViewUp(0, 0, -1)

        self.SetActiveCamera(camera)
        self.SetSliceOrientation(new_slice_orientation)
        self.UpdatePipeline(True)

    def OnKeyPress(self, interactor, event):
        if self.GetInputData() is None:
            return
        if self.reslicing_enabled and interactor.GetKeyCode() == "x":
            self.ChangeOrientation(SLICE_ORIENTATION_YZ)
        elif self.reslicing_enabled and interactor.GetKeyCode() == "y":
            self.ChangeOrientation(SLICE_ORIENTATION_XZ)
        elif self.reslicing_enabled and interactor.GetKeyCode() == "z":
            self.ChangeOrientation(SLICE_ORIENTATION_XY)
        elif interactor.GetKeyCode() == "a":
            self._viewer.autoWindowLevelOnSliceRange()
        elif interactor.GetKeyCode() == "s":
            filename = "current_render"
            self.SaveRender(filename)

        elif interactor.GetKeyCode() == "q":
            self.log("Render loop terminating by pressing %s" % (interactor.GetKeyCode(), ))
            interactor.SetKeyCode("e")
            self.OnKeyPress(interactor, event)

        elif interactor.GetKeyCode() == "l":
            if self.GetViewerEvent("SHOW_LINE_PROFILE_EVENT"):

                self.SetEventInactive("SHOW_LINE_PROFILE_EVENT")
                self.DisplayLineProfile(interactor, event, False)
            else:
                self.SetEventActive("SHOW_LINE_PROFILE_EVENT")
                self.DisplayLineProfile(interactor, event, True)

        elif interactor.GetKeyCode() == "h":
            self.DisplayHelp()
        elif interactor.GetKeyCode() == "w":
            self.SetEventActive('UPDATE_WINDOW_LEVEL_UNDER_CURSOR')
        elif interactor.GetKeyCode() == "t":
            # tracing event is captured by widget
            if (self._viewer.imageTracer.GetEnabled()):
                self._viewer.imageTracer.Off()
            else:
                self._viewer.imageTracer.On()
        elif interactor.GetKeyCode() == "i":
            # toggle interpolation of slice actor
            is_interpolated = self._viewer.imageSlice.GetProperty().GetInterpolationType()
            if is_interpolated:
                self._viewer.imageSlice.GetProperty().SetInterpolationTypeToNearest()
            else:
                self._viewer.imageSlice.GetProperty().SetInterpolationTypeToLinear()
            self._viewer.updatePipeline()

        elif interactor.GetKeyCode() == '1':
            ev = 'RECTILINEAR_WIPE'
            if self.GetViewerEvent(ev):
                self.SetEventInactive(ev)
            # ImageWithOverlay
            self._viewer.setVisualisationToImageWithOverlay()
            self.AdjustCamera()
            self.Render()

        elif interactor.GetKeyCode() == '2':
            if self._viewer.image2 is not None:
                if self._viewer.vis_mode != CILViewer2D.RECTILINEAR_WIPE:
                    self._viewer.setVisualisationToRectilinearWipe()
                    orient = ['x', 'y', 'z']
                    self.SetCharEvent(orient[self.GetSliceOrientation()])
                    self.SetEventActive('RECTILINEAR_WIPE')

        else:
            self.log("Unhandled event %s" % (interactor.GetKeyCode()))

    def OnKeyRelease(self, interactor, event):
        # remove events on key release
        events = ['UPDATE_WINDOW_LEVEL_UNDER_CURSOR']
        for ev in events:
            if self.GetViewerEvent(ev):
                # print ("remove event {}".format(ev))
                self.SetEventInactive(ev)

    def RemoveROIWidget(self):
        self.SetEventActive("DELETE_ROI_EVENT")
        self.GetROIWidget().Off()
        self._viewer.updateCornerAnnotation("", 1, False)
        self.SetDisplayHistogram(False)
        self.Render()

    def OnLeftButtonPressEvent(self, interactor, event):
        # print ("INTERACTOR", interactor)
        if self.GetInputData() is None:
            return
        alt = interactor.GetAltKey()
        shift = interactor.GetShiftKey()
        ctrl = interactor.GetControlKey()

        self.SetInitialEventPosition(interactor.GetEventPosition())

        if ctrl and not (alt and shift):
            self.SetEventActive("CREATE_ROI_EVENT")
            position = interactor.GetEventPosition()
            self.InitialiseBox(position)
            self.SetDisplayHistogram(True)
            self.Render()
            self.log("Event %s is CREATE_ROI_EVENT" % (event))

        elif alt and not (shift and ctrl):
            self.RemoveROIWidget()
            self.log("Event %s is DELETE_ROI_EVENT" % (event))

        elif not (ctrl and alt and shift):
            self.SetEventActive("PICK_EVENT")
            self.HandlePickEvent(interactor, event)
            self.log("Event %s is PICK_EVENT" % (event))

    def SetDisplayHistogram(self, display):
        if display:
            if (self._viewer.displayHistogram == 0):
                #self.GetRenderer().AddActor(self._viewer.histogramPlotActor)
                self._viewer.AddActor(self._viewer.histogramPlotActor, HISTOGRAM_ACTOR)
                self.firstHistogram = 1
                self.Render()

            self._viewer.histogramPlotActor.VisibilityOn()
            self._viewer.displayHistogram = True
        else:
            self._viewer.histogramPlotActor.VisibilityOff()
            self._viewer.displayHistogram = False

    def OnLeftButtonReleaseEvent(self, interactor, event):
        interactor = self._viewer.getInteractor()

        if self.GetViewerEvent("CREATE_ROI_EVENT"):
            self.OnROIModifiedEvent(interactor, event)

        elif self.GetViewerEvent("PICK_EVENT"):
            self.HandlePickEvent(interactor, event)

        # Turn off CREATE_ROI and PICK_EVENT
        self.SetEventInactive("CREATE_ROI_EVENT")
        self.SetEventInactive("PICK_EVENT")
        self.SetEventInactive("DELETE_ROI_EVENT")

    def OnRightButtonPressEvent(self, interactor, event):
        if self.GetInputData() is None:
            return
        alt = interactor.GetAltKey()
        shift = interactor.GetShiftKey()
        ctrl = interactor.GetControlKey()

        self.SetInitialEventPosition(interactor.GetEventPosition())

        if alt and not (ctrl and shift):
            self.SetEventActive("WINDOW_LEVEL_EVENT")
            if self._viewer.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
                self.log("Event %s is WINDOW_LEVEL_EVENT" % (event))
                self.HandleWindowLevel(interactor, event)
        elif shift and not (ctrl and alt):
            self.SetEventActive("ZOOM_EVENT")
            self.SetInitialCameraPosition(self.GetActiveCamera().GetPosition())
            self.log("Event %s is ZOOM_EVENT" % (event))
        elif ctrl and not (shift and alt):
            self.SetEventActive("PAN_EVENT")
            self.SetInitialCameraPosition(self.GetActiveCamera().GetPosition())
            self.log("Event %s is PAN_EVENT" % (event))

    def OnRightButtonReleaseEvent(self, interactor, event):
        self.log(event)
        if self.GetViewerEvent("WINDOW_LEVEL_EVENT"):
            if self._viewer.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
                self.SetInitialLevel(self._viewer.imageSlice.GetProperty().GetColorLevel())
                self.SetInitialWindow(self._viewer.imageSlice.GetProperty().GetColorWindow())
        elif self.GetViewerEvent("ZOOM_EVENT") or self.GetViewerEvent("PAN_EVENT"):
            self.SetInitialCameraPosition(())

            # Reset difference from start of zoom event
            self.dy = 0

        # self.SetViewerEvent( ViewerEvent.NO_EVENT )
        self.SetEventInactive("WINDOW_LEVEL_EVENT")
        self.SetEventInactive("ZOOM_EVENT")
        self.SetEventInactive("PAN_EVENT")

    def OnROIModifiedEvent(self, interactor, event):
        # Get bounds from 3D ROI
        pd = vtk.vtkPolyData()
        self.GetROIWidget().GetPolyData(pd)
        bounds = pd.GetBounds()

        # Set the values of the ll and ur corners
        ll = (bounds[0], bounds[2], bounds[4])
        ur = (bounds[1], bounds[3], bounds[5])
        vox1 = self.createVox(ll)
        vox2 = self.createVox(ur)

        # Set the ROI using image coordinates
        self.SetROI((vox1, vox2))
        roi = self.GetROI()

        # Debug messages
        self.log("ROI {0}".format(roi))
        self.log("Pixel1 %d,%d,%d Value %f" % vox1)
        self.log("Pixel2 %d,%d,%d Value %f" % vox2)

        # Calculate the size of the ROI
        if self.GetSliceOrientation() == SLICE_ORIENTATION_XY:
            self.log("slice orientation : XY")
            x = abs(roi[1][0] - roi[0][0])
            y = abs(roi[1][1] - roi[0][1])
            z = abs(roi[1][2] - roi[0][2])

        elif self.GetSliceOrientation() == SLICE_ORIENTATION_XZ:
            self.log("slice orientation : XZ")
            x = abs(roi[1][0] - roi[0][0])
            y = abs(roi[1][2] - roi[0][2])
            z = abs(roi[1][1] - roi[0][1])

        elif self.GetSliceOrientation() == SLICE_ORIENTATION_YZ:
            self.log("slice orientation : YZ")
            x = abs(roi[1][1] - roi[0][1])
            y = abs(roi[1][2] - roi[0][2])
            z = abs(roi[1][1] - roi[0][1])

        # Update the text bottom right of the viewer and histogram
        roi_data = (x, y, z, float(x * y) / 1024.)
        text = self.CreateAnnotationText("roi", roi_data)
        self.log(text)
        self.UpdateCornerAnnotation(text, 1)
        self.UpdateROIHistogram()
        # self.SetViewerEvent( ViewerEvent.NO_EVENT )
        self.SetEventInactive("CREATE_ROI_EVENT")

    def OnTracerModifiedEvent(self, interactor, event):
        # Makes sure tracer is visible on current slice:
        self.UpdatePipeline()

###########################  Coordinate conversion methods ############################

    def display2world(self, displayCoords):
        """
        Takes display coordinates and converts them into world coordinates

        :param displayCoords: tuple containing the X,Y coordinates for the point in the display
        :return: The computed world coordinate of the given point as double (x,y,z)
        """
        coord = vtk.vtkCoordinate()
        coord.SetCoordinateSystemToDisplay()
        coord.SetValue(displayCoords[0], displayCoords[1])

        return coord.GetComputedWorldValue(self.GetRenderer())

    def world2display(self, world_coords):
        """
        Takes coordinates in the world system and converts them to 2D display coordinates
        :param world_coords: (x,y,z) coordinate in the world
        :return: (x,y) screen coordinate
        """

        vc = vtk.vtkCoordinate()
        vc.SetCoordinateSystemToWorld()
        vc.SetValue(world_coords)

        return vc.GetComputedDoubleDisplayValue(self.GetRenderer())

    def display2imageCoordinate(self, viewerposition, subvoxel=False):
        """
        Convert display coordinates into image coordinates and add the pixel value

        :param viewerposition: (x,y) position of the selected point in the display window
        :return: (x,y,z,a) x,y,z index of the selected slice + a, the pixel value
        """
        vc = vtk.vtkCoordinate()
        vc.SetCoordinateSystemToViewport()
        vc.SetValue(viewerposition[0:2] + (0.0, ))

        pickPosition = list(vc.GetComputedWorldValue(self.GetRenderer()))
        # print ("PICK POS", pickPosition)

        pickPosition[self.GetSliceOrientation()] = \
            self.GetInputData().GetSpacing()[self.GetSliceOrientation()]  * (self.GetActiveSlice()) # + self.GetInputData().GetOrigin()[self.GetSliceOrientation()])
        self.log("Pick Position " + str(pickPosition))

        if (pickPosition != [0, 0, 0]):

            imagePosition = self.world2imageCoordinate(pickPosition)
            imagePositionF = self.world2imageCoordinateFloat(pickPosition)
            extent = self._viewer.img3D.GetExtent()

            # make sure the pick is on the image
            if imagePosition[0] < extent[0]:
                imagePosition[0] = extent[0]
            if imagePosition[0] > extent[1]:
                imagePosition[0] = extent[1]
            if imagePosition[1] < extent[2]:
                imagePosition[1] = extent[2]
            if imagePosition[1] > extent[3]:
                imagePosition[1] = extent[3]
            if imagePosition[2] < extent[4]:
                imagePosition[2] = extent[4]
            if imagePosition[2] > extent[5]:
                imagePosition[2] = extent[5]

            self.log("imagePosition pre validate {}".format(imagePosition))

            pixelValue = self.GetInputData().GetScalarComponentAsDouble(imagePosition[0], imagePosition[1],
                                                                        imagePosition[2], 0)
            if self._viewer.rescale[0]:
                scale, shift = self._viewer.rescale[1]
                # pix = orig * scale + shift
                # orig = (-shift + pix) / scale
                pixelValue = (-shift + pixelValue) / scale

            if subvoxel:
                for i in range(3):
                    if not i == self.GetSliceOrientation():
                        imagePosition[i] = imagePositionF[i]

            return (self.validateValue(imagePosition[0], 'x'), self.validateValue(imagePosition[1], 'y'),
                    self.validateValue(imagePosition[2], 'z'), pixelValue)
        else:
            return (0, 0, 0, 0)

    def createVox(self, world_coordinates):

        # Translate the world coordinates to an image index
        imagePosition = self.world2imageCoordinate(world_coordinates)

        pixelValue = self.GetInputData().GetScalarComponentAsDouble(imagePosition[0], imagePosition[1],
                                                                    imagePosition[2], 0)
        if self._viewer.rescale[0]:
            scale, shift = self._viewer.rescale[1]
            pixelValue = (-shift + pixelValue) / scale
        return (self.validateValue(imagePosition[0],
                                   'x'), self.validateValue(imagePosition[1],
                                                            'y'), self.validateValue(imagePosition[2], 'z'), pixelValue)

    def world2imageCoordinate(self, world_coordinates):
        """
        Convert from the world or global coordinates to image coordinates
        :param world_coordinates: (x,y,z)
        :return: rounded to next integer (x,y,z) in image coorindates eg. slice index
        """

        dims = self.GetInputData().GetDimensions()
        self.log(dims)
        spac = self.GetInputData().GetSpacing()
        orig = self.GetInputData().GetOrigin()

        return [round((world_coordinates[i]) / spac[i] - orig[i]) for i in range(3)]

    def world2imageCoordinateFloat(self, world_coordinates):
        """
        Convert from the world or global coordinates to image coordinates
        :param world_coordinates: (x,y,z)
        :return: float (x,y,z) in image coorindates eg. slice index
        """
        dims = self.GetInputData().GetDimensions()
        self.log(dims)
        spac = self.GetInputData().GetSpacing()
        orig = self.GetInputData().GetOrigin()

        return [(world_coordinates[i]) / spac[i] - orig[i] for i in range(3)]

    def image2world(self, image_coordinates):
        spac = self.GetInputData().GetSpacing()
        orig = self.GetInputData().GetOrigin()

        return [(image_coordinates[i]) * spac[i] + orig[i] for i in range(3)]

    def imageCoordinate2display(self, imageposition):
        '''
        Convert image coordinates back into viewer coordinates
        :param imageposition: (x,y,z) coordinates in image coordinates
        :return: (x,y,z) coordinates for the window
        '''
        # Truncate to first 3 values x,y,z. Not interested in pixel value.
        ip = imageposition[0:3]

        spac = self.GetInputData().GetSpacing()
        orig = self.GetInputData().GetOrigin()

        # Convert image coordiantes to world coordinates
        world_coord = [spac[i] * (ip[i] - orig[i]) for i in range(3)]

        vc = vtk.vtkCoordinate()
        vc.SetCoordinateSystemToWorld()
        vc.SetValue(world_coord)

        return vc.GetComputedDoubleViewportValue(self.GetRenderer())

    def display2normalisedViewport(self, display_coords):
        wsize = self.GetRenderWindow().GetSize()

        x = display_coords[0] / wsize[0]
        y = display_coords[1] / wsize[1]

        return x, y

    def OnMouseMoveEvent(self, interactor, event):
        if self.GetInputData() is not None:
            if self.GetViewerEvent("WINDOW_LEVEL_EVENT"):
                self.log("Event %s is WINDOW_LEVEL_EVENT" % (event))
                self.HandleWindowLevel(interactor, event)

            elif self.GetViewerEvent("PICK_EVENT"):
                self.HandlePickEvent(interactor, event)

            elif self.GetViewerEvent("ZOOM_EVENT"):
                self.HandleZoomEvent(interactor, event)

            elif self.GetViewerEvent("PAN_EVENT"):
                self.HandlePanEvent(interactor, event)

            elif self.GetViewerEvent("SHOW_LINE_PROFILE_EVENT"):
                self.DisplayLineProfile(interactor, event, True)
            elif self.GetViewerEvent('UPDATE_WINDOW_LEVEL_UNDER_CURSOR'):
                x, y = interactor.GetEventPosition()
                ic = self.display2imageCoordinate((x, y))
                print(x, y, ic, "image coordinate")
                whole_extent = self._viewer.img3D.GetExtent()
                around = numpy.min(numpy.asarray([whole_extent[1], whole_extent[3], whole_extent[5]])) // 10
                print(around, "around")
                extent = [
                    ic[0] - around, ic[0] + around, ic[1] - around, ic[1] + around, ic[2] - around, ic[2] + around
                ]

                orientation = self._viewer.sliceOrientation

                extent[orientation * 2] = self.GetActiveSlice()
                extent[orientation * 2 + 1] = self.GetActiveSlice()

                if extent[0] < whole_extent[0]:
                    extent[0] = whole_extent[0]
                if extent[1] > whole_extent[1]:
                    extent[1] = whole_extent[1]
                if extent[2] < whole_extent[2]:
                    extent[2] = whole_extent[2]
                if extent[3] > whole_extent[3]:
                    extent[3] = whole_extent[3]
                if extent[4] < whole_extent[4]:
                    extent[4] = whole_extent[4]
                if extent[5] > whole_extent[5]:
                    extent[5] = whole_extent[5]
                # get mouse location

                print(*extent, "w extent")
                self._viewer.voicursor.SetInputData(self._viewer.img3D)
                self._viewer.voicursor.SetVOI(*extent)

                self._viewer.voicursor.Update()
                # set window/level for current slices

                self._viewer.iacursor.SetInputConnection(self._viewer.voicursor.GetOutputPort())
                self._viewer.iacursor.SetAutoRangePercentiles(1.0, 99.)
                self._viewer.iacursor.Update()
                # reset color/window
                cmin, cmax = self._viewer.iacursor.GetAutoRange()

                window, level = self._viewer.getSliceWindowLevelFromRange(cmin, cmax)

                self.SetInitialLevel(level)
                self.SetInitialWindow(window)

                self._viewer.imageSlice.GetProperty().SetColorLevel(self.GetInitialLevel())
                self._viewer.imageSlice.GetProperty().SetColorWindow(self.GetInitialWindow())

                self.UpdateImageSlice()

            elif self.GetViewerEvent('RECTILINEAR_WIPE'):
                # get event in image coordinate
                x, y, z, pix = self.display2imageCoordinate(interactor.GetEventPosition())
                # update the wipe depending on the slice orientation
                slice_orientation = self._viewer.getSliceOrientation()
                if slice_orientation == SLICE_ORIENTATION_XY:
                    self._viewer.wipe.SetAxis(0, 1)
                    self._viewer.wipe.SetPosition(x, y)
                elif slice_orientation == SLICE_ORIENTATION_XZ:
                    self._viewer.wipe.SetAxis(0, 2)
                    self._viewer.wipe.SetPosition(x, z)
                elif slice_orientation == SLICE_ORIENTATION_YZ:
                    self._viewer.wipe.SetAxis(2, 1)
                    self._viewer.wipe.SetPosition(z, y)

                self.UpdatePipeline()

    def DisplayHelp(self):
        help_actor = self._viewer.helpActor
        image_slice = self._viewer.imageSlice

        if help_actor.GetVisibility():
            help_actor.VisibilityOff()
            image_slice.VisibilityOn()
            self.Render()
            return

        font_size = 24

        # Create the text mappers and the associated Actor2Ds.

        # The font and text properties (except justification) are the same for
        # each multi line mapper. Let's create a common text property object
        multiLineTextProp = vtk.vtkTextProperty()
        multiLineTextProp.SetFontSize(font_size)
        multiLineTextProp.SetFontFamilyToArial()
        multiLineTextProp.BoldOn()
        multiLineTextProp.ItalicOn()
        multiLineTextProp.ShadowOn()
        multiLineTextProp.SetLineSpacing(1.3)

        # The text is on multiple lines and center-justified (both horizontal and
        # vertical).
        textMapperC = vtk.vtkTextMapper()
        textMapperC.SetInput("Mouse Interactions:\n"
                             "\n"
                             "  - Slice: Mouse Scroll\n"
                             "  - Quick Slice: Shift + Mouse Scroll\n"
                             "  - Pick: Left Click\n"
                             "  - Zoom: Shift + Right Mouse + Move Up/Down\n"
                             "  - Pan: Ctrl + Right Mouse + Move\n"
                             "  - Adjust Window: Alt+ Right Mouse + Move Up/Down\n"
                             "  - Adjust Level: Alt + Right Mouse + Move Left/Right\n"
                             "  Region of Interest (ROI):\n"
                             "      - Create: Ctrl + Left Click\n"
                             "      - Delete: Alt + Left Click\n"
                             "      - Resize: Click + Drag handles\n"
                             "      - Translate: Middle Mouse + Move within ROI\n"
                             "\n"
                             "Keyboard Interactions:\n"
                             "\n"
                             "  - a: Whole image Auto Window/Level\n"
                             "  - w: Region around cursor Auto Window/Level\n"
                             "  - l: Line Profile at cursor\n"
                             "  - s: Save Current Image\n"
                             "  - x: YZ Plane\n"
                             "  - y: XZ Plane\n"
                             "  - z: XY Plane\n"
                             "  - t: Tracing\n"
                             "  - i: toggle interpolation of slice\n"
                             "  - h: this help\n")
        tprop = textMapperC.GetTextProperty()
        tprop.ShallowCopy(multiLineTextProp)
        tprop.SetJustificationToLeft()
        tprop.SetVerticalJustificationToCentered()
        tprop.SetColor(0, 1, 0)

        help_actor.SetMapper(textMapperC)
        help_actor.VisibilityOn()
        image_slice.VisibilityOff()
        self.Render()

    def HandleZoomEvent(self, interactor, event):
        camera = self.GetActiveCamera()

        # Extract change from start of event
        dx, dy = interactor.GetDeltaEventPosition()
        window_y_size = self.GetRenderWindow().GetSize()[1]

        # Determine whether the user is zooming in or out
        change = dy - self.dy

        # Make sure that a change has been registered
        if change != 0:
            # >1 zoom in, <1 zoom out
            camera.Zoom(1 + change / window_y_size)
            self.Render()

        # Set the overall change value
        self.dy = dy

    def HandlePanEvent(self, interactor, event):
        #Camera uses world coordinates, not display coordinates so we have to make a coneversion
        interactor_event_position = interactor.GetEventPosition()
        interactor_initial_event_position = interactor.GetInitialEventPosition()

        event_position = interactor.image2world(interactor.display2imageCoordinate(interactor_event_position)[:-1])
        initial_event_position = interactor.image2world(
            interactor.display2imageCoordinate(interactor_initial_event_position)[:-1])

        #Update initial position to current event position, ready for next panning event:
        interactor.SetInitialEventPosition(interactor_event_position)

        change = []
        for i in range(len(event_position)):
            change.append(event_position[i] - initial_event_position[i])

        camera = self.GetActiveCamera()

        newposition = [i for i in self.GetInitialCameraPosition()]
        newfocalpoint = [i for i in camera.GetFocalPoint()]

        for i in range(len(event_position)):
            newposition[i] -= change[i]
            newfocalpoint[i] -= change[i]

        camera.SetFocalPoint(newfocalpoint)
        camera.SetPosition(newposition)
        self.SetInitialCameraPosition(newposition)

        self.Render()

    def HandleWindowLevel(self, interactor, event):
        dx, dy = interactor.GetDeltaEventPosition()
        self.log("Event delta %d %d" % (dx, dy))
        size = self.GetRenderWindow().GetSize()

        dx = 1 * dx / size[0]
        dy = 1 * dy / size[1]
        window = self.GetInitialWindow()
        level = self.GetInitialLevel()

        if abs(window) > 0.01:
            dx = dx * window
        else:
            dx = dx * (lambda x: -0.01 if x < 0 else 0.01)(window)

        if abs(level) > 0.01:
            dy = dy * level
        else:
            dy = dy * (lambda x: -0.01 if x < 0 else 0.01)(level)

        # Abs so that direction does not flip

        if window < 0.0:
            dx = -1 * dx
        if level < 0.0:
            dy = -1 * dy

        # Compute new window level
        newWindow = window + dx
        newLevel = level + dy

        # Stay away from zero and really small numbers
        if abs(newWindow) < 0.01:
            newWindow = 0.01 * (lambda x: -1 if x < 0 else 1)(newWindow)

        if abs(newLevel) < 0.01:
            newLevel = 0.01 * (lambda x: -1 if x < 0 else 1)(newLevel)

        self._viewer.imageSlice.GetProperty().SetColorLevel(newLevel)
        self._viewer.imageSlice.GetProperty().SetColorWindow(newWindow)
        self.log("new level {0} window {1}".format(newLevel, newWindow))
        self.UpdateImageSlice()

    def HandlePickEvent(self, interactor, event):
        position = interactor.GetEventPosition()
        vox = self.display2imageCoordinate(position)
        self.last_picked_voxel = vox
        # print ("Pixel %d,%d,%d Value %f" % vox )
        self._viewer.cornerAnnotation.VisibilityOn()
        text = self.CreateAnnotationText("pick", vox)
        self.UpdateCornerAnnotation(text, 0)
        self.Render()

    def DisplayLineProfile(self, interactor, event, display):
        x, y = interactor.GetEventPosition()
        ic = self.display2imageCoordinate((x, y))
        self.UpdateLinePlot(ic, display)


###############################################################################


class CILViewer2D(CILViewerBase):
    '''Simple Interactive Viewer based on VTK classes'''
    # visualisation modes
    IMAGE_WITH_OVERLAY = 0
    RECTILINEAR_WIPE = 1

    def __init__(self, dimx=600, dimy=600, ren=None, renWin=None, iren=None, debug=False, enableSliderWidget=True):
        CILViewerBase.__init__(self, dimx=dimx, dimy=dimy, ren=ren, renWin=renWin, iren=iren, debug=debug)

        self.setInteractorStyle(CILInteractorStyle(self))

        self.debug = debug
        self.style.debug = debug

        self.camera = vtk.vtkCamera()
        self.camera.ParallelProjectionOn()
        self.flipCameraPosition = False
        self.ren.SetActiveCamera(self.camera)

        self.axes_initialised = False

        #Actors
        self.iacursor = vtk.vtkImageHistogramStatistics()
        self.voicursor = vtk.vtkExtractVOI()
        #self.sliceActorNo = 0

        # input 2
        self.image2 = None
        self.voi2 = vtk.vtkExtractVOI()
        self.imageSlice2 = vtk.vtkImageSlice()
        self.imageSliceMapper2 = vtk.vtkImageSliceMapper()
        self.imageSlice2.SetMapper(self.imageSliceMapper2)

        # Help text
        self.AddActor(self.helpActor, HELP_ACTOR)

        # ROI Widget
        self.ROIWidget = cilviewerBoxWidget.CreateMoveable(self)

        self.ROIWidget.AddObserver(vtk.vtkWidgetEvent.Select, self.style.OnROIModifiedEvent, 1.0)

        # edge points of the ROI
        self.ROI = ()

        # Edge points of Volumetric ROI
        self.ROIV = None

        #picker
        self.picker = vtk.vtkPropPicker()
        self.picker.PickFromListOn()
        self.picker.AddPickList(self.imageSlice)

        self.iren.SetPicker(self.picker)

        # corner annotation
        self.cornerAnnotation = vtk.vtkCornerAnnotation()
        self.cornerAnnotation.SetMaximumFontSize(12)
        self.cornerAnnotation.PickableOff()
        self.cornerAnnotation.VisibilityOff()
        self.cornerAnnotation.GetTextProperty().ShadowOn()
        self.cornerAnnotation.SetLayerNumber(1)

        #used to scale corner annotation and decide whether to interpolate:
        self.image_is_downsampled = False
        self.visualisation_downsampling = [1, 1, 1]
        self.display_unsampled_coords = False

        # cursor doesn't show up
        self.cursor = vtk.vtkCursor2D()
        self.cursorMapper = vtk.vtkPolyDataMapper2D()
        self.cursorActor = vtk.vtkActor2D()
        self.cursor.SetModelBounds(-10, 10, -10, 10, 0, 0)
        self.cursor.SetFocalPoint(0, 0, 0)
        self.cursor.AllOff()
        self.cursor.AxesOn()
        self.cursorActor.PickableOff()
        self.cursorActor.VisibilityOn()
        self.cursorActor.GetProperty().SetColor(1, 1, 1)
        self.cursorActor.SetLayerNumber(0)
        self.cursorMapper.SetInputData(self.cursor.GetOutput())
        self.cursorActor.SetMapper(self.cursorMapper)
        # self.getRenderer().AddActor(self.cursorActor)
        self.AddActor(self.cursorActor, CURSOR_ACTOR)

        # Zoom
        self.InitialCameraPosition = ()

        # XY Plot actor for histogram
        self.displayHistogram = False
        self.firstHistogram = 0
        self.roiIA = vtk.vtkImageAccumulate()
        self.roiVOI = vtk.vtkExtractVOI()
        self.histogramPlotActor.SetPosition2(0.6, 0.6)
        self.histogramPlotActor.SetPosition(0.4, 0.4)

        # XY Plot for X and Y slices
        self.displayLinePlot = False
        self.linePlot = 0
        self.lineVOIX = vtk.vtkExtractVOI()
        self.lineVOIY = vtk.vtkExtractVOI()
        self.linePlotActor = vtk.vtkXYPlotActor()
        self.linePlotActor.ExchangeAxesOff()
        self.linePlotActor.SetXTitle("")
        self.linePlotActor.SetYTitle("")
        self.linePlotActor.SetXLabelFormat("%.1f")
        self.linePlotActor.SetYLabelFormat("%.1e")
        #self.linePlotActor.SetAdjustXLabels(3)
        #self.linePlotActor.SetXTitle( "Level" )
        #self.linePlotActor.SetYTitle( "N" )
        self.linePlotActor.SetXValuesToValue()
        self.linePlotActor.SetPlotColor(0, (1, 0, 0.5))
        self.linePlotActor.SetPlotColor(1, (1, 1, 0))
        self.linePlotActor.SetPosition(0, 0.1)
        self.linePlotActor.SetPosition2(1, 0.4)

        # Makes sure that x axis only goes as far as the number of pixels in the image
        self.linePlotActor.SetAdjustXLabels(0)

        # Add legend
        self.linePlotActor.SetPlotLabel(0, 'horiz')
        self.linePlotActor.SetPlotLabel(1, 'vert')
        self.linePlotActor.LegendOn()

        # crosshair lines for X Y slices
        self.horizLine = vtk.vtkLine()
        self.vertLine = vtk.vtkLine()
        self.crosshairsActor = vtk.vtkActor()
        # self.getRenderer().AddActor(self.crosshairsActor)
        self.AddActor(self.crosshairsActor, CROSSHAIR_ACTOR)

        # rescale input image
        # contains (scale, shift)
        self.rescale = [False, (1, 0)]

        # ImageTracer
        self.imageTracer = vtk.vtkImageTracerWidget()
        # set Interactor
        self.imageTracer.SetInteractor(self.iren)
        self.imageTracer.SetCaptureRadius(1.5)
        self.imageTracer.GetLineProperty().SetColor(0.8, 0.8, 1.0)
        self.imageTracer.GetLineProperty().SetLineWidth(3.0)
        self.imageTracer.GetHandleProperty().SetColor(0.4, 0.4, 1.0)
        self.imageTracer.GetSelectedHandleProperty().SetColor(1.0, 1.0, 1.0)
        # Set the size of the glyph handle
        self.imageTracer.GetGlyphSource().SetScale(2.0)
        # Set the initial rotation of the glyph if desired.  The default glyph
        # set internally by the widget is a '+' so rotating 45 deg. gives a 'x'
        self.imageTracer.GetGlyphSource().SetRotationAngle(45.0)
        self.imageTracer.GetGlyphSource().Modified()
        self.imageTracer.ProjectToPlaneOn()
        self.imageTracer.SetHandleLeftMouseButton(True)
        # Set autoclose to on
        self.imageTracer.AutoCloseOn()
        self.imageTracer.AddObserver(vtk.vtkWidgetEvent.Select, self.style.OnTracerModifiedEvent, 1.0)

        # Slider widget
        self.sliderWidget = None
        self._sliderWidgetEnabled = enableSliderWidget

        self.__vis_mode = CILViewer2D.IMAGE_WITH_OVERLAY
        self.setVisualisationToImageWithOverlay()

    def log(self, msg):
        if self.debug:
            print(msg)

    def setInput3DData(self, imageData):
        '''alias of setInputData, kept for backward compatibility'''
        return self.setInputData(imageData)

    def setInputData(self, imageData):
        self.log("setInputData")
        self.reset()
        self.img3D = imageData
        self.installPipeline()
        self.axes_initialised = True

    def setInputData2(self, imageData):
        self.image2 = imageData
        # TODO resample on image1
        # print ("setInputData2")
        self.installPipeline2()

    def setInputAsNumpy(self,
                        numpyarray,
                        origin=(0, 0, 0),
                        spacing=(1., 1., 1.),
                        rescale=True,
                        dtype=vtk.VTK_UNSIGNED_SHORT):
        self.rescale[0] = rescale

        img = Converter.numpy2vtkImage(numpyarray, spacing, origin)

        if rescale:
            # rescale to appropriate VTK_UNSIGNED_SHORT
            stats = vtk.vtkImageAccumulate()
            stats.SetInputData(img)
            stats.Update()
            iMin = stats.GetMin()[0]
            iMax = stats.GetMax()[0]
            if (iMax - iMin == 0):
                scale = 1
            else:
                if dtype == vtk.VTK_UNSIGNED_SHORT:
                    scale = vtk.VTK_UNSIGNED_SHORT_MAX / (iMax - iMin)
                elif dtype == vtk.VTK_UNSIGNED_INT:
                    scale = vtk.VTK_UNSIGNED_INT_MAX / (iMax - iMin)

            self.rescale[1] = (scale, -iMin)
            shiftScaler = vtk.vtkImageShiftScale()
            shiftScaler.SetInputData(img)
            shiftScaler.SetScale(scale)
            shiftScaler.SetShift(-iMin)
            shiftScaler.SetOutputScalarType(dtype)
            shiftScaler.Update()
            self.img3D = shiftScaler.GetOutput()
        else:
            self.img3D = img

        self.installPipeline()

    def displaySlice(self, sliceno=[0]):
        self.setActiveSlice(sliceno)
        self.updatePipeline()
        self.renWin.Render()

    def updatePipeline(self, resetcamera=False):
        if self.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
            self.updateImageWithOverlayPipeline(resetcamera=resetcamera)
        elif self.vis_mode == CILViewer2D.RECTILINEAR_WIPE:
            self.updateRectilinearWipePipeline(resetcamera=resetcamera)

        self.AdjustCamera(resetcamera)
        self.renWin.Render()

    def updateRectilinearWipePipeline(self, resetcamera=False):
        extent = self.updateMainVOI()
        self.voi.SetVOI(*extent)
        #TODO what happens if image2 has a different sampling?
        self.voi2.SetVOI(*extent)
        self.wipeSliceMapper.SetOrientation(self.sliceOrientation)

    def updateMainVOI(self):
        # get the current slice
        extent = [i for i in self.img3D.GetExtent()]
        extent[self.sliceOrientation * 2] = self.getActiveSlice()
        extent[self.sliceOrientation * 2 + 1] = self.getActiveSlice()
        self.voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4], extent[5])
        self.log("extent {0}".format(extent))
        self.voi.Update()
        self.log("VOI dimensions {0}".format(self.voi.GetOutput().GetDimensions()))
        return extent

    def updateImageWithOverlayPipeline(self, resetcamera=False):
        self.updateMainVOI()
        self.ia.Update()
        self.imageSliceMapper.SetOrientation(self.sliceOrientation)
        self.imageSlice.Update()

        if self.image2 is not None:
            self.voi2.SetVOI(self.voi.GetVOI())
            self.imageSliceMapper2.SetOrientation(self.sliceOrientation)
            self.imageSlice2.Update()

        text = self.createAnnotationText("slice",
                                         (self.getActiveSlice(), self.img3D.GetDimensions()[self.sliceOrientation] - 1))
        self.updateCornerAnnotation(text, 0)

        if self.displayHistogram:
            self.updateROIHistogram()
        try:
            if not self.img3D is None:
                # print ("self.img3D" , self.img3D)
                # Set the tracer widget's projection normal to the current orientation
                self.imageTracer.SetProjectionNormal(self.sliceOrientation)
                # Set the Tracer widget's position along the current projection normal,
                # we want this on top of the image so it can be seen above all slices.
                # On the X and Z axes, slice 0 is at the top as the axis points into
                # the screen.
                slice_coords = [0, 0, 0]
                # When we are viewing the Y direction, the axis goes into the page
                # so we have to swap which end of the axis the tracer is placed so
                # that it isn't in the shadow of the slice.
                if self.getSliceOrientation() == SLICE_ORIENTATION_XZ:
                    slice_coords[self.getSliceOrientation()] = self.img3D.GetDimensions()[SLICE_ORIENTATION_XZ] - 1
                self.imageTracer.SetProjectionPosition(self.style.image2world(slice_coords)[self.getSliceOrientation()])
            else:
                print("self.img3D None")
        except Exception as ge:
            print(ge)
        self.AdjustCamera(resetcamera)
        self.renWin.Render()

    @property
    def vis_mode(self):
        return self.__vis_mode

    @vis_mode.setter
    def vis_mode(self, value):
        if value in [CILViewer2D.IMAGE_WITH_OVERLAY, CILViewer2D.RECTILINEAR_WIPE]:
            self.__vis_mode = value

    def setVisualisationPipelineMethodTo(self, method):
        if self.img3D is None:
            return
        # get the current visualisation mode
        if self.vis_mode != method:
            # remove current pipeline
            self.uninstallPipeline()
            if self.image2 is not None:
                self.uninstallPipeline2()
            # install the new pipeline
            self.vis_mode = method
            self.installPipeline()

    def setVisualisationToImageWithOverlay(self):
        self.setVisualisationPipelineMethodTo(CILViewer2D.IMAGE_WITH_OVERLAY)

    def setVisualisationToRectilinearWipe(self):
        self.setVisualisationPipelineMethodTo(CILViewer2D.RECTILINEAR_WIPE)

    def installPipeline(self):
        if self.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
            if self.img3D is not None:
                self.installImageWithOverlayPipeline()
            if self.image2 is not None:
                self.installPipeline2()
        elif self.vis_mode == CILViewer2D.RECTILINEAR_WIPE:
            self.installRectilinearWipePipeline()

        if self.getSliderWidgetEnabled():
            self.installSliceSliderWidgetPipeline()

        self.ren.ResetCamera()
        self.ren.Render()

        self.camera.SetViewUp(0, -1, 0)

        if not self.axes_initialised:
            self.camera.Azimuth(180)

        self.AdjustCamera()

        self.ren.AddViewProp(self.cursorActor)
        self.cursorActor.VisibilityOn()

        self.iren.Initialize()
        self.renWin.Render()

    def installPipeline2(self):
        if self.image2 is not None:
            if self.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
                self.installImageWithOverlayPipeline2()
            elif self.vis_mode == CILViewer2D.RECTILINEAR_WIPE:
                pass
        else:
            self.log("installPipeline2 no data")

    def installImageWithOverlayPipeline(self):
        '''Slices a 3D volume and then creates an actor to be rendered'''
        self.log("installPipeline")
        self.ren.AddViewProp(self.cornerAnnotation)

        self.voi.SetInputData(self.img3D)
        #select one slice in Z
        extent = [i for i in self.img3D.GetExtent()]
        for i in range(len(self.slicenos)):
            self.slicenos[i] = round((extent[i * 2 + 1] + extent[i * 2]) / 2)

        extent[self.sliceOrientation * 2] = self.getActiveSlice()
        extent[self.sliceOrientation * 2 + 1] = self.getActiveSlice()

        self.voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4], extent[5])

        self.voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4], extent[5])

        self.voi.Update()

        # set window/level for slice based on values in entire volume:
        self.ia.SetInputData(self.voi.GetOutput())
        self.ia.Update()
        self.style.AutoWindowLevelOnVolumeRange(update_slice=False)
        self.InitialLevel = self.getSliceColorLevel()
        self.InitialWindow = self.getSliceColorWindow()
        self.log("level {0} window {1}".format(self.InitialLevel, self.InitialWindow))

        self.imageSliceMapper.SetInputConnection(self.voi.GetOutputPort())

        if self.image_is_downsampled:
            self.imageSlice.GetProperty().SetInterpolationTypeToLinear()
        else:
            self.imageSlice.GetProperty().SetInterpolationTypeToNearest()

        self.imageSlice.Update()

        self.imageTracer.SetProjectionPosition(self.style.image2world([0, 0, 0])[self.getSliceOrientation()])

        self.AddActor(self.imageSlice, SLICE_ACTOR)

        self.imageTracer.SetViewProp(self.imageSlice)

    def installImageWithOverlayPipeline2(self):
        '''Slices a 3D volume and then creates an actor to be rendered'''
        self.log("installPipeline2")
        if self.image2 is not None:
            # render image2
            self.voi2.SetVOI(self.voi.GetVOI())
            self.voi2.SetInputData(self.image2)
            self.voi2.Update()
            lut = vtk.vtkLookupTable()

            ai = vtk.vtkImageHistogramStatistics()
            ai.SetInputConnection(self.voi2.GetOutputPort())
            ai.Update()

            self.lut2 = lut
            lut.SetNumberOfColors(7)
            lut.SetHueRange(.4, .6)
            lut.SetSaturationRange(1, 1)
            lut.SetValueRange(0.7, 0.7)
            lut.SetAlphaRange(0, 0.5)
            lut.Build()

            cov = vtk.vtkImageMapToColors()
            self.image2map = cov
            cov.SetInputConnection(self.voi2.GetOutputPort())
            cov.SetLookupTable(lut)
            cov.Update()

            self.imageSliceMapper2.SetInputConnection(cov.GetOutputPort())
            self.imageSlice2.Update()
            self.AddActor(self.imageSlice2, OVERLAY_ACTOR)
            self.ren.ResetCamera()
            self.ren.Render()

            self.AdjustCamera()

            self.iren.Initialize()
            self.renWin.Render()
        else:
            print("installPipeline2 no data")

    def installRectilinearWipePipeline(self):
        '''Create the pipeline for the rectilinear wipe'''
        self.log("installRectilinearWipePipeline")
        extent1 = list(self.img3D.GetExtent())
        #extent is slice number N
        for i in range(len(self.slicenos)):
            self.slicenos[i] = round((extent1[i * 2 + 1] + extent1[i * 2]) / 2)
        active_slice_num = self.getActiveSlice()
        orient = self.getSliceOrientation()
        extent1[orient] = active_slice_num
        extent1[orient + 1] = active_slice_num
        extent2 = extent1[:]

        self.voi.SetVOI(*extent1)
        self.voi2.SetVOI(*extent2)

        wipe = vtk.vtkImageRectilinearWipe()
        wipeSliceMapper = vtk.vtkImageSliceMapper()
        wipeSlice = vtk.vtkImageSlice()

        wipe.SetInputConnection(0, self.voi.GetOutputPort())
        wipe.SetInputConnection(1, self.voi2.GetOutputPort())
        # should set the position to center of viewport
        wipe.SetPosition(10, 10)
        wipe.SetWipe(0)

        wipeSliceMapper.SetInputConnection(wipe.GetOutputPort())
        wipeSliceMapper.SetOrientation(orient)

        wipeSlice.SetMapper(wipeSliceMapper)
        wipeSlice.GetProperty().SetInterpolationTypeToNearest()
        wipeSlice.GetProperty().SetColorLevel(self.InitialLevel)
        wipeSlice.GetProperty().SetColorWindow(self.InitialWindow)
        wipeSlice.Update()

        self.wipe = wipe
        self.wipeSliceMapper = wipeSliceMapper
        self.wipeActor = wipeSlice

        self.AddActor(wipeSlice, WIPE_ACTOR)

    def installSliceSliderWidgetPipeline(self):
        '''Create the pipeline for the slice slider widget
        
        The slider widget and representation are created if not already present.
        Currently the slider widget enabled flag is not used.
        '''
        if self.sliderWidget is not None:
            # reset the values to the appropriate ones of the new loaded image
            self.sliderCallback.update_orientation(self.style, 'reset')
            return

        sr = SliceSliderRepresentation()
        sr.SetValue(self.getActiveSlice())
        sr.SetMaximumValue(self.img3D.GetDimensions()[2] - 1)
        sr.SetMinimumValue(0)

        sw = vtk.vtkSliderWidget()
        sw.SetInteractor(self.getInteractor())
        sw.SetRepresentation(sr)
        sw.SetAnimationModeToAnimate()
        sw.EnabledOn()

        cb = SliderCallback(self, sw)

        # Add interaction observers
        # propagate events from the slider to the viewer
        sw.AddObserver(vtk.vtkCommand.InteractionEvent, cb)

        # propagate events from the viewer to the slider
        self.style.AddObserver("MouseWheelForwardEvent", cb.update_from_viewer, 0.9)
        self.style.AddObserver("MouseWheelBackwardEvent", cb.update_from_viewer, 0.9)
        self.style.AddObserver("CharEvent", cb.update_orientation, 0.9)

        # reset the slider
        cb.update_from_viewer(self.style, 'reset')

        # save references
        self.sliderWidget = sw
        self.sliderCallback = cb

    def uninstallSliderWidget(self):
        '''remove the slider widget from the viewer'''
        if self.sliderWidget is not None:
            sr = self.sliderWidget.GetRepresentation()
            if sr is not None:
                sr.RemoveAllObservers()
                coll = vtk.vtkPropCollection()
                sr.GetActors(coll)
                print("coll", coll)
                for actor in coll:
                    print("actor", actor)
                    self.ren.RemoveActor(actor)

    def AdjustCamera(self, resetcamera=False):
        self.ren.ResetCameraClippingRange()

        # adjust camera focal point
        camera = self.getRenderer().GetActiveCamera()
        fp = list(camera.GetFocalPoint())
        pos = list(camera.GetPosition())
        if self.flipCameraPosition:
            fp[self.sliceOrientation] = -self.getActiveSlice()
            pos[self.sliceOrientation] = -pos[self.sliceOrientation]
            self.flipCameraPosition = False
            # have to reset to false so it doesn't flip when we scroll.
        else:
            fp[self.sliceOrientation] = self.getActiveSlice()

        camera.SetFocalPoint(fp)
        camera.SetPosition(pos)

        if resetcamera:
            self.ren.ResetCamera()

    def getROI(self):
        return self.ROI

    def getROIExtent(self):
        p0 = self.ROI[0]
        p1 = self.ROI[1]
        return (p0[0], p1[0], p0[1], p1[1], p0[2], p1[2])

    ############### Handle events are moved to the interactor style

    def setSliceOrientation(self, axis):
        if axis in ['x', 'y', 'z']:
            self.getInteractor().SetKeyCode(axis)
            self.style.OnKeyPress(self.getInteractor(), "KeyPressEvent")

    def setVisualisationDownsampling(self, value):
        super().setVisualisationDownsampling(value)
        if self.image_is_downsampled:
            self.imageSlice.GetProperty().SetInterpolationTypeToLinear()
        else:
            self.imageSlice.GetProperty().SetInterpolationTypeToNearest()

    def setDisplayUnsampledCoordinates(self, value):
        self.display_unsampled_coords = value

    def getDisplayUnsampledCoordinates(self):
        return self.display_unsampled_coords

    def updateCornerAnnotation(self, text, idx=0, visibility=True):
        if visibility:
            self.cornerAnnotation.VisibilityOn()
        else:
            self.cornerAnnotation.VisibilityOff()

        self.cornerAnnotation.SetText(idx, text)
        self.iren.Render()

    def createAnnotationText(self, display_type, data):
        ''' Returns string to be set as the corner annotation, giving
        the coordinates or slice number (may be downsampled or unsampled coordinates)

        Args:
            display_type (str) :    'slice', 'pick', 'roi' - determines the
                                    way in which the data is displayed
            data (tuple):           the data to be displayed.'''

        text = None

        if isinstance(data, tuple):

            if display_type == "slice":
                if self.display_unsampled_coords and self.image_is_downsampled:
                    # Different method for converting to world coords, as we only
                    # have coordinates in one direction
                    data = list(data)
                    slice_coord = [0, 0, 0]
                    axis_length = [0, 0, 0]
                    slice_coord[self.getSliceOrientation()] = data[0]
                    axis_length[self.getSliceOrientation()] = data[1] + 1
                    slice_coord = self.style.image2world(slice_coord)[self.getSliceOrientation()]
                    axis_length = self.style.image2world(axis_length)[self.getSliceOrientation()] - 1
                    data = (round(slice_coord), round(axis_length))
                text = "Slice %d/%d" % data

            else:
                # In all other cases, we have coordinates, and then we have an extra value
                # The extra value shouldn't be converted in the same way
                # TODO: check whether we need some kind of conversion on these 'extra' values
                if self.display_unsampled_coords and self.image_is_downsampled:
                    data = list(data)
                    extra_info = data.pop(-1)
                    data = self.style.image2world(data)
                    data.append(extra_info)
                    # Round the coordinates to integers:
                    # Without rounding the %d formatting
                    # later on just truncates to integer
                    for i, d in enumerate(data):
                        if i < 3:
                            data[i] = round(d)
                    data = tuple(data)

            if display_type == "pick":
                text = "[%d,%d,%d] : %.2g" % data

            elif display_type == "roi":
                text = "ROI: %d x %d x %d, %.2f kp" % data

        return text

    def updateROIHistogram(self):
        self.log("Updating hist")

        extent = [0 for i in range(6)]
        if self.getSliceOrientation() == SLICE_ORIENTATION_XY:
            self.log("slice orientation : XY")
            extent[0] = self.validateValue(min(self.ROI[0][0], self.ROI[1][0]), 'x')
            extent[1] = self.validateValue(max(self.ROI[0][0], self.ROI[1][0]), 'x')
            extent[2] = self.validateValue(min(self.ROI[0][1], self.ROI[1][1]), 'y')
            extent[3] = self.validateValue(max(self.ROI[0][1], self.ROI[1][1]), 'y')
            extent[4] = self.getActiveSlice()
            extent[5] = self.getActiveSlice()
            # y = abs(roi[1][1] - roi[0][1])
        elif self.getSliceOrientation() == SLICE_ORIENTATION_XZ:
            self.log("slice orientation : XZ")
            extent[0] = self.validateValue(min(self.ROI[0][0], self.ROI[1][0]), 'x')
            extent[1] = self.validateValue(max(self.ROI[0][0], self.ROI[1][0]), 'x')
            # x = abs(roi[1][0] - roi[0][0])
            extent[4] = self.validateValue(min(self.ROI[0][2], self.ROI[1][2]), 'z')
            extent[5] = self.validateValue(max(self.ROI[0][2], self.ROI[1][2]), 'z')
            # y = abs(roi[1][2] - roi[0][2])
            extent[2] = self.getActiveSlice()
            extent[3] = self.getActiveSlice()
        elif self.getSliceOrientation() == SLICE_ORIENTATION_YZ:
            self.log("slice orientation : YZ")
            extent[2] = self.validateValue(min(self.ROI[0][1], self.ROI[1][1]), 'y')
            extent[3] = self.validateValue(max(self.ROI[0][1], self.ROI[1][1]), 'y')
            # x = abs(roi[1][1] - roi[0][1])
            extent[4] = self.validateValue(min(self.ROI[0][2], self.ROI[1][2]), 'z')
            extent[5] = self.validateValue(max(self.ROI[0][2], self.ROI[1][2]), 'z')
            # y = abs(roi[1][2] - roi[0][2])
            extent[0] = self.getActiveSlice()
            extent[1] = self.getActiveSlice()

        self.log("updateROIHistogram {0}".format(extent))
        self.roiVOI.SetVOI(extent)
        self.roiVOI.SetInputData(self.img3D)
        self.roiVOI.Update()
        irange = self.roiVOI.GetOutput().GetScalarRange()

        self.roiIA.SetInputData(self.roiVOI.GetOutput())

        self.roiIA.IgnoreZeroOff()
        self.roiIA.SetComponentOrigin(int(irange[0]), 0, 0)
        self.roiIA.SetComponentSpacing(1, 0, 0)
        self.roiIA.Update()

        #use 255 bins
        delta = self.roiIA.GetMax()[0] - self.roiIA.GetMin()[0]
        nbins = 255
        self.roiIA.SetComponentSpacing(delta / nbins, 0, 0)
        self.roiIA.SetComponentExtent(0, nbins, 0, 0, 0, 0)
        self.roiIA.Update()

        self.histogramPlotActor.AddDataSetInputConnection(self.roiIA.GetOutputPort())
        self.histogramPlotActor.SetXRange(irange[0], irange[1])
        self.histogramPlotActor.SetYRange(self.roiIA.GetOutput().GetScalarRange())

    def updateLinePlot(self, imagecoordinate, display):

        self.displayLinePlot = display
        extent_x = list(self.img3D.GetExtent())
        extent_y = list(self.img3D.GetExtent())
        self.log("imagecoordinate {0}".format(imagecoordinate))

        if display:
            #extract profile along X
            if self.getSliceOrientation() == SLICE_ORIENTATION_XY:
                self.log("slice orientation : XY")
                extent_y[0] = imagecoordinate[0]
                extent_y[1] = imagecoordinate[0]

                extent_x[2] = imagecoordinate[1]
                extent_x[3] = imagecoordinate[1]

                extent_y[4] = self.getActiveSlice()
                extent_y[5] = self.getActiveSlice()
                extent_x[4] = self.getActiveSlice()
                extent_x[5] = self.getActiveSlice()

                self.linePlotActor.SetDataObjectXComponent(0, 0)
                self.linePlotActor.SetDataObjectXComponent(1, 1)

                #y = abs(roi[1][1] - roi[0][1])
            elif self.getSliceOrientation() == SLICE_ORIENTATION_XZ:
                self.log("slice orientation : XZ")
                extent_y[0] = imagecoordinate[0]
                extent_y[1] = imagecoordinate[0]
                #x = abs(roi[1][0] - roi[0][0])
                extent_x[4] = imagecoordinate[2]
                extent_x[5] = imagecoordinate[2]
                #y = abs(roi[1][2] - roi[0][2])
                extent_x[2] = self.getActiveSlice()
                extent_x[3] = self.getActiveSlice()
                extent_y[2] = self.getActiveSlice()
                extent_y[3] = self.getActiveSlice()
                self.linePlotActor.SetDataObjectXComponent(0, 0)
                self.linePlotActor.SetDataObjectXComponent(1, 2)

            elif self.getSliceOrientation() == SLICE_ORIENTATION_YZ:
                self.log("slice orientation : YZ")
                extent_y[2] = imagecoordinate[1]
                extent_y[3] = imagecoordinate[1]
                #x = abs(roi[1][1] - roi[0][1])
                extent_x[4] = imagecoordinate[2]
                extent_x[5] = imagecoordinate[2]
                #y = abs(roi[1][2] - roi[0][2])
                extent_x[0] = self.getActiveSlice()
                extent_x[1] = self.getActiveSlice()
                extent_y[0] = self.getActiveSlice()
                extent_y[1] = self.getActiveSlice()

                self.linePlotActor.SetDataObjectXComponent(0, 1)
                self.linePlotActor.SetDataObjectXComponent(1, 2)

            self.log("x {0} extent_x {1}".format(imagecoordinate[0], extent_x))
            self.log("y {0} extent_y {1}".format(imagecoordinate[1], extent_y))
            self.lineVOIX.SetVOI(extent_x)
            self.lineVOIX.SetInputData(self.img3D)
            self.lineVOIX.Update()
            self.lineVOIY.SetVOI(extent_y)
            self.lineVOIY.SetInputData(self.img3D)
            self.lineVOIY.Update()

            # fill
            if self.linePlot == 0:
                self.linePlotActor.AddDataSetInputConnection(self.lineVOIX.GetOutputPort())
                self.linePlotActor.AddDataSetInputConnection(self.lineVOIY.GetOutputPort())
                # self.getRenderer().AddActor(self.linePlotActor)
                self.AddActor(self.linePlotActor, LINEPLOT_ACTOR)
                self.linePlot = 1

            # Set position of line plot

            # Set up character sizes and borders
            width = 8
            border = 12
            height = 12

            # Calculate the world origin in display coordinates
            origin_display = self.style.world2display((0, 0, 0))

            # Calculate the offset due to labels and borders on the graphs y-axis
            max_y = max(int(self.lineVOIY.GetOutput().GetScalarRange()[1]),
                        int(self.lineVOIX.GetOutput().GetScalarRange()[1]))
            y_digits = len(str(max_y))
            x_min_offset = (width * y_digits) + border
            y_min_offset = height + border

            # Offset the origin to account for the labels
            origin_nview = self.style.display2normalisedViewport(
                (origin_display[0] - x_min_offset, origin_display[1] - y_min_offset))

            # Calculate the far right border
            top_right_disp = self.style.world2display(self.style.GetImageWorldExtent())
            top_right_nview = self.style.display2normalisedViewport(
                (top_right_disp[0] + border + height, top_right_disp[1]))

            # Set the position on the image
            self.linePlotActor.SetPosition(origin_nview)
            self.linePlotActor.SetPosition2(top_right_nview[0] - origin_nview[0], 0.4)

            self.log("data length x {0} y {1}".format(self.lineVOIX.GetOutput().GetDimensions(),
                                                      self.lineVOIY.GetOutput().GetDimensions()))
            self.linePlotActor.VisibilityOn()
            self.crosshairsActor.VisibilityOn()

            self.renWin.Render()

        else:
            self.linePlotActor.VisibilityOff()
            self.crosshairsActor.VisibilityOff()

            self.renWin.Render()

    def AddActor(self, actor, name=None):
        '''print("ADDING ACTOR", name)
        self.log("Calling AddActor " + name)
        present_actors = self.ren.GetActors() # Only seems to return some of the actors - possibly only the visible ones?
        present_actors.InitTraversal()
        self.log("Currently present actors {}".format(present_actors))

        print("Current len", present_actors.GetNumberOfItems())
    
        for i in range(present_actors.GetNumberOfItems()):
            nextActor = present_actors.GetNextActor()
            nextActor.SetVisibility(False)
            self.log("{} {} Visibility {}".format(i, nextActor, nextActor.GetVisibility() ))
            self.log("ClassName"+ str( nextActor.GetClassName()))

        
        print("intermediate len", self.ren.GetActors().GetNumberOfItems())        
        if name is None:
            name = 'actor_{}'.format(present_actors.GetNumberOfItems()+1)'''

        self.ren.AddActor(actor)
        self.actors[name] = actor

    def GetActorsDict(self):
        return self.actors

    def GetActor(self, name):
        if name in self.actors:
            actor = self.actors[name]
            return actor
        else:
            return (None)

    def uninstallPipeline(self):
        '''uninstall the current visualisation pipeline'''
        if self.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
            self.removeActor([SLICE_ACTOR, HISTOGRAM_ACTOR])
        elif self.vis_mode == CILViewer2D.RECTILINEAR_WIPE:
            self.removeActor(WIPE_ACTOR)

    def removeActor(self, actor):
        '''remove named actor'''
        if not isinstance(actor, (list, tuple)):
            actor = [actor]
        keys = self.actors.keys()
        for a in actor:
            if a in keys:
                self.ren.RemoveActor(self.actors[a])
                self.actors.pop(a)

    def uninstallPipeline2(self):
        if self.vis_mode == CILViewer2D.IMAGE_WITH_OVERLAY:
            self.removeActor(OVERLAY_ACTOR)
        elif self.vis_mode == CILViewer2D.RECTILINEAR_WIPE:
            # rectilinear wipe visualises 2 images in the same pipeline
            pass

    def reset(self):
        self.uninstallPipeline()
        if self.image2 is not None:
            self.uninstallPipeline2()
        if self.getSliderWidgetEnabled():
            self.uninstallSliderWidget()

    def getSliderWidgetEnabled(self):
        return self._sliderWidgetEnabled

    def setSliderWidgetEnabled(self, enable):
        if enable:
            self._sliderWidgetEnabled = enable