Mask 3d preview (#252)

* Added methods to preview mask * Added a button in viewer volume to activate mask 3d view * Some cleaning and style modifications * Showing mask preview and updating after edition * Created a method to mark mask as modified * Added update 3D preview in region growing tools * Added update 3D preview in brain segmentation * Added update 3D preview in swap and flip mask * Added update 3D preview in threshold * Improved rendering of mask * Better showing mask in volume viewer * Flip * Removed the new button in volume viewer * Increased the size of 3d preview in datanotebook * Fixed problem with VTK7 * Fixed problem with VTK7 * Avoiding deepcopy * Using IsoSurface when in VTK > 8 and with GPU support * Created the class VolumeMask to keep all stuf about mask volume raycasting * Changing volume mask colour when changing mask colour * Changing mask axes also change volume mask rendering * When remove mask removing volume mask visualization * Changing mask threshold was not updating mask preview * Added callbacks for when modifying mask * Added method to remove modified callbacks * Created menu to mask 3d preview * Enable mask preview is working * Rendering volume viewer after activating mask preview * Loading and removing mask preview via menu * Autoreload working * Update working * Removed mask preview from data notebook and task slice * Auto reload mask preview shortcut

Mask 3d preview (#252)
* Added methods to preview mask * Added a button in viewer volume to activate mask 3d view * Some cleaning and style modifications * Showing mask preview and updating after edition * Created a method to mark mask as modified * Added update 3D preview in region growing tools * Added update 3D preview in brain segmentation * Added update 3D preview in swap and flip mask * Added update 3D preview in threshold * Improved rendering of mask * Better showing mask in volume viewer * Flip * Removed the new button in volume viewer * Increased the size of 3d preview in datanotebook * Fixed problem with VTK7 * Fixed problem with VTK7 * Avoiding deepcopy * Using IsoSurface when in VTK > 8 and with GPU support * Created the class VolumeMask to keep all stuf about mask volume raycasting * Changing volume mask colour when changing mask colour * Changing mask axes also change volume mask rendering * When remove mask removing volume mask visualization * Changing mask threshold was not updating mask preview * Added callbacks for when modifying mask * Added method to remove modified callbacks * Created menu to mask 3d preview * Enable mask preview is working * Rendering volume viewer after activating mask preview * Loading and removing mask preview via menu * Autoreload working * Update working * Removed mask preview from data notebook and task slice * Auto reload mask preview shortcut
Thiago Franco de Moraes · GitHub
1 parent 3349921d
Showing 15 changed files with 385 additions and 83 deletions Show diff stats
invesalius/constants.py
invesalius/control.py
invesalius/data/converters.py
invesalius/data/mask.py
invesalius/data/slice_.py
invesalius/data/styles.py
invesalius/data/viewer_volume.py
invesalius/data/volume.py
invesalius/gui/data_notebook.py
invesalius/gui/default_viewers.py
invesalius/gui/frame.py
invesalius/project.py
invesalius/segmentation/brain/segment.py
invesalius/session.py
invesalius/utils.py
@@ -516,6 +516,9 @@ ID_DENSITY_MEASURE = wx.NewId()
 ID_MASK_DENSITY_MEASURE = wx.NewId()
 ID_CREATE_SURFACE = wx.NewId()
 ID_CREATE_MASK = wx.NewId()
+ID_MASK_3D_PREVIEW = wx.NewId()
+ID_MASK_3D_RELOAD = wx.NewId()
+ID_MASK_3D_AUTO_RELOAD = wx.NewId()
  
 ID_GOTO_SLICE = wx.NewId()
 ID_GOTO_COORD = wx.NewId()
@@ -126,6 +126,12 @@ class Controller():
  
         Publisher.subscribe(self.create_project_from_matrix, 'Create project from matrix')
  
+        Publisher.subscribe(self.show_mask_preview, 'Show mask preview')
+
+        Publisher.subscribe(self.enable_mask_preview, 'Enable mask 3D preview')
+        Publisher.subscribe(self.disable_mask_preview, 'Disable mask 3D preview')
+        Publisher.subscribe(self.update_mask_preview, 'Update mask 3D preview')
+
     def SetBitmapSpacing(self, spacing):
         proj = prj.Project()
         proj.spacing = spacing
@@ -1108,3 +1114,30 @@ class Controller():
  
         if err_msg:
             dialog.MessageBox(None, "It was not possible to launch new instance of InVesalius3 dsfa dfdsfa sdfas fdsaf asdfasf dsaa", err_msg)
+
+    def show_mask_preview(self, index, flag=True):
+        proj = prj.Project()
+        mask = proj.mask_dict[index]
+        slc = self.Slice.do_threshold_to_all_slices(mask)
+        mask.create_3d_preview()
+        Publisher.sendMessage("Load mask preview", mask_3d_actor=mask.volume._actor, flag=flag)
+        Publisher.sendMessage("Reload actual slice")
+
+    def enable_mask_preview(self):
+        mask = self.Slice.current_mask
+        if mask is not None:
+            self.Slice.do_threshold_to_all_slices(mask)
+            mask.create_3d_preview()
+            Publisher.sendMessage("Load mask preview", mask_3d_actor=mask.volume._actor, flag=True)
+            Publisher.sendMessage("Render volume viewer")
+
+    def disable_mask_preview(self):
+        mask = self.Slice.current_mask
+        if mask is not None:
+            Publisher.sendMessage("Remove mask preview", mask_3d_actor=mask.volume._actor)
+            Publisher.sendMessage("Render volume viewer")
+
+    def update_mask_preview(self):
+        mask = self.Slice.current_mask
+        if mask is not None:
+            mask._update_imagedata()
@@ -24,8 +24,7 @@ import vtk
 from vtk.util import numpy_support
  
  
-def to_vtk(n_array, spacing, slice_number, orientation, origin=(0, 0, 0), padding=(0, 0, 0)):
-
+def to_vtk(n_array, spacing=(1.0, 1.0, 1.0), slice_number=0, orientation='AXIAL', origin=(0, 0, 0), padding=(0, 0, 0)):
     if orientation == "SAGITTAL":
         orientation = "SAGITAL"
  
@@ -67,6 +66,37 @@ def to_vtk(n_array, spacing, slice_number, orientation, origin=(0, 0, 0), paddin
     return image_copy
  
  
+def to_vtk_mask(n_array, spacing=(1.0, 1.0, 1.0), origin=(0.0, 0.0, 0.0)):
+    dz, dy, dx = n_array.shape
+    ox, oy, oz = origin
+    sx, sy, sz = spacing
+
+    ox -= sx
+    oy -= sy
+    oz -= sz
+
+    v_image = numpy_support.numpy_to_vtk(n_array.flat)
+    extent = (0, dx - 1, 0, dy - 1,  0, dz - 1)
+
+    # Generating the vtkImageData
+    image = vtk.vtkImageData()
+    image.SetOrigin(ox, oy, oz)
+    image.SetSpacing(sx, sy, sz)
+    image.SetDimensions(dx - 1, dy - 1, dz - 1)
+    # SetNumberOfScalarComponents and SetScalrType were replaced by
+    # AllocateScalars
+    #  image.SetNumberOfScalarComponents(1)
+    #  image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
+    image.AllocateScalars(numpy_support.get_vtk_array_type(n_array.dtype), 1)
+    image.SetExtent(extent)
+    image.GetPointData().SetScalars(v_image)
+
+    #  image_copy = vtk.vtkImageData()
+    #  image_copy.DeepCopy(image)
+
+    return image
+
+
 def np_rgba_to_vtk(n_array, spacing=(1.0, 1.0, 1.0)):
     dy, dx, dc = n_array.shape
     v_image = numpy_support.numpy_to_vtk(n_array.reshape(dy*dx, dc))
@@ -22,18 +22,21 @@ import plistlib
 import random
 import shutil
 import tempfile
-
-import numpy as np
-import vtk
+import time
+import weakref
  
 import invesalius.constants as const
+import invesalius.data.converters as converters
 import invesalius.data.imagedata_utils as iu
 import invesalius.session as ses
-
+from invesalius.data.volume import VolumeMask
+import numpy as np
+import vtk
 from invesalius_cy import floodfill
-
 from pubsub import pub as Publisher
 from scipy import ndimage
+from vtk.util import numpy_support
+
  
 class EditionHistoryNode(object):
     def __init__(self, index, orientation, array, clean=False):
@@ -189,7 +192,9 @@ class Mask():
     def __init__(self):
         Mask.general_index += 1
         self.index = Mask.general_index
-        self.imagedata = ''
+        self.matrix = None
+        self.spacing = (1.0, 1.0, 1.0)
+        self.imagedata = None
         self.colour = random.choice(const.MASK_COLOUR)
         self.opacity = const.MASK_OPACITY
         self.threshold_range = const.THRESHOLD_RANGE
@@ -198,7 +203,11 @@ class Mask():
         self.is_shown = 1
         self.edited_points = {}
         self.was_edited = False
+        self.volume = None
+        self.auto_update_mask = True
+        self.modified_time = 0
         self.__bind_events()
+        self._modified_callbacks = []
  
         self.history = EditionHistory()
  
@@ -206,11 +215,24 @@ class Mask():
         Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
         Publisher.subscribe(self.OnSwapVolumeAxes, 'Swap volume axes')
  
+    def as_vtkimagedata(self):
+        print("Converting to VTK")
+        vimg = converters.to_vtk_mask(self.matrix, self.spacing)
+        print("Converted")
+        return vimg
+
+    def set_colour(self, colour):
+        self.colour = colour
+        if self.volume is not None:
+            self.volume.set_colour(colour)
+            Publisher.sendMessage("Render volume viewer")
+
     def save_history(self, index, orientation, array, p_array, clean=False):
         self.history.new_node(index, orientation, array, p_array, clean)
  
     def undo_history(self, actual_slices):
         self.history.undo(self.matrix, actual_slices)
+        self.modified()
  
         # Marking the project as changed
         session = ses.Session()
@@ -218,6 +240,7 @@ class Mask():
  
     def redo_history(self, actual_slices):
         self.history.redo(self.matrix, actual_slices)
+        self.modified()
  
         # Marking the project as changed
         session = ses.Session()
@@ -226,6 +249,27 @@ class Mask():
     def on_show(self):
         self.history._config_undo_redo(self.is_shown)
  
+    def create_3d_preview(self):
+        if self.volume is None:
+            if self.imagedata is None:
+                self.imagedata = self.as_vtkimagedata()
+            self.volume = VolumeMask(self)
+            self.volume.create_volume()
+
+    def _update_imagedata(self, update_volume_viewer=True):
+        if self.imagedata is not None:
+            dz, dy, dx = self.matrix.shape
+            #  np_image = numpy_support.vtk_to_numpy(self.imagedata.GetPointData().GetScalars())
+            #  np_image[:] = self.matrix.reshape(-1)
+            self.imagedata.SetDimensions(dx - 1, dy - 1, dz - 1)
+            self.imagedata.SetSpacing(self.spacing)
+            self.imagedata.SetExtent(0, dx - 1, 0, dy - 1,  0, dz - 1)
+            self.imagedata.Modified()
+            self.volume._actor.Update()
+
+            if update_volume_viewer:
+                Publisher.sendMessage("Render volume viewer")
+
     def SavePlist(self, dir_temp, filelist):
         mask = {}
         filename = u'mask_%d' % self.index
@@ -284,10 +328,15 @@ class Mask():
         elif axis == 2:
             submatrix[:] = submatrix[:, :, ::-1]
             self.matrix[0, 0, 1::] = self.matrix[0, 0, :0:-1]
+        self.modified()
  
     def OnSwapVolumeAxes(self, axes):
         axis0, axis1 = axes
         self.matrix = self.matrix.swapaxes(axis0, axis1)
+        if self.volume:
+            self.imagedata = self.as_vtkimagedata()
+            self.volume.change_imagedata()
+        self.modified()
  
     def _save_mask(self, filename):
         shutil.copyfile(self.temp_file, filename)
@@ -300,6 +349,22 @@ class Mask():
     def _set_class_index(self, index):
         Mask.general_index = index
  
+    def add_modified_callback(self, callback):
+        ref = weakref.WeakMethod(callback)
+        self._modified_callbacks.append(ref)
+
+    def remove_modified_callback(self, callback):
+        callbacks = []
+        removed = False
+        for cb in self._modified_callbacks:
+            if cb() is not None:
+                if cb() != callback:
+                    callbacks.append(cb)
+                else:
+                    removed = True
+        self._modified_callbacks = callbacks
+        return removed
+
     def create_mask(self, shape):
         """
         Creates a new mask object. This method do not append this new mask into the project.
@@ -311,11 +376,35 @@ class Mask():
         shape = shape[0] + 1, shape[1] + 1, shape[2] + 1
         self.matrix = np.memmap(self.temp_file, mode='w+', dtype='uint8', shape=shape)
  
+    def modified(self, all_volume=False):
+        if all_volume:
+            self.matrix[0] = 1
+            self.matrix[:, 0, :] = 1
+            self.matrix[:, :, 0] = 1
+        if ses.Session().auto_reload_preview:
+            self._update_imagedata()
+        self.modified_time = time.monotonic()
+        callbacks = []
+        print(self._modified_callbacks)
+        for callback in self._modified_callbacks:
+            if callback() is not None:
+                callback()()
+                callbacks.append(callback)
+        self._modified_callbacks = callbacks
+
     def clean(self):
         self.matrix[1:, 1:, 1:] = 0
-        self.matrix[0, :, :] = 1
-        self.matrix[:, 0, :] = 1
-        self.matrix[:, :, 0] = 1
+        self.modified(all_volume=True)
+
+    def cleanup(self):
+        if self.is_shown:
+            self.history._config_undo_redo(False)
+        if self.volume:
+            Publisher.sendMessage("Unload volume", volume=self.volume._actor)
+            Publisher.sendMessage("Render volume viewer")
+            self.imagedata = None
+            self.volume = None
+        del self.matrix
  
     def copy(self, copy_name):
         """
@@ -334,6 +423,7 @@ class Mask():
  
         new_mask.create_mask(shape=[i-1 for i in self.matrix.shape])
         new_mask.matrix[:] = self.matrix[:]
+        new_mask.spacing = self.spacing
  
         return new_mask
  
@@ -384,7 +474,4 @@ class Mask():
                 self.save_history(index, orientation, matrix.copy(), cp_mask)
  
     def __del__(self):
-        if self.is_shown:
-            self.history._config_undo_redo(False)
-        del self.matrix
         os.remove(self.temp_file)
@@ -384,9 +384,21 @@ class Slice(metaclass=utils.Singleton):
         self.current_mask.matrix[:] = 0
         self.current_mask.clear_history()
  
+        if self.current_mask.auto_update_mask and self.current_mask.volume is not None:
+            to_reload = True
+            self.SetMaskThreshold(
+                index,
+                threshold_range,
+                slice_number = None,
+                orientation = None
+            )
+            self.discard_all_buffers()
+            Publisher.sendMessage("Reload actual slice")
+            self.current_mask.modified(all_volume=True)
+            return
+
         to_reload = False
         if threshold_range != self.current_mask.threshold_range:
-            to_reload = True
             for orientation in self.buffer_slices:
                 self.buffer_slices[orientation].discard_vtk_mask()
                 self.SetMaskThreshold(
@@ -417,6 +429,7 @@ class Slice(metaclass=utils.Singleton):
  
         if to_reload:
             Publisher.sendMessage("Reload actual slice")
+        self.current_mask.modified(all_volume=False)
  
     def __set_current_mask_threshold_actual_slice(self, threshold_range):
         if self.current_mask is None:
@@ -1061,7 +1074,7 @@ class Slice(metaclass=utils.Singleton):
     def SetMaskColour(self, index, colour, update=True):
         "Set a mask colour given its index and colour (RGB 0-1 values)"
         proj = Project()
-        proj.mask_dict[index].colour = colour
+        proj.mask_dict[index].set_colour(colour)
  
         (r, g, b) = colour[:3]
         colour_wx = [r * 255, g * 255, b * 255]
@@ -1108,6 +1121,7 @@ class Slice(metaclass=utils.Singleton):
             # TODO: find out a better way to do threshold
             if slice_number is None:
                 for n, slice_ in enumerate(self.matrix):
+                    print(n)
                     m = np.ones(slice_.shape, self.current_mask.matrix.dtype)
                     m[slice_ < thresh_min] = 0
                     m[slice_ > thresh_max] = 0
@@ -1346,6 +1360,7 @@ class Slice(metaclass=utils.Singleton):
         """
         future_mask = Mask()
         future_mask.create_mask(self.matrix.shape)
+        future_mask.spacing = self.spacing
  
         if name:
             future_mask.name = name
@@ -1605,6 +1620,7 @@ class Slice(metaclass=utils.Singleton):
  
         future_mask = Mask()
         future_mask.create_mask(self.matrix.shape)
+        future_mask.spacing = spacing
         future_mask.name = new_name
  
         future_mask.matrix[:] = 1
@@ -1805,6 +1821,7 @@ class Slice(metaclass=utils.Singleton):
         self.buffer_slices["CORONAL"].discard_vtk_mask()
         self.buffer_slices["SAGITAL"].discard_vtk_mask()
  
+        self.current_mask.modified(target == '3D')
         Publisher.sendMessage("Reload actual slice")
  
     def calc_image_density(self, mask=None):
@@ -1445,6 +1445,7 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         self.viewer._flush_buffer = True
         self.viewer.slice_.apply_slice_buffer_to_mask(self.orientation)
         self.viewer._flush_buffer = False
+        self.viewer.slice_.current_mask.modified()
  
     def EOnScrollForward(self, evt, obj):
         iren = self.viewer.interactor
@@ -1822,7 +1823,6 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
             self.viewer.slice_.current_mask.matrix[0 , 0, n+1]
             markers = self.matrix[:, :, n]
  
-
         ww = self.viewer.slice_.window_width
         wl = self.viewer.slice_.window_level
  
@@ -1866,6 +1866,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
  
  
             self.viewer.slice_.current_mask.was_edited = True
+            self.viewer.slice_.current_mask.modified()
             self.viewer.slice_.current_mask.clear_history()
  
             # Marking the project as changed
@@ -2017,10 +2018,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
                 mask[(tmp_mask==2) & ((mask == 0) | (mask == 2) | (mask == 253))] = 2
                 mask[(tmp_mask==1) & ((mask == 0) | (mask == 2) | (mask == 253))] = 253
  
-            #mask[:] = tmp_mask
-            self.viewer.slice_.current_mask.matrix[0] = 1
-            self.viewer.slice_.current_mask.matrix[:, 0, :] = 1
-            self.viewer.slice_.current_mask.matrix[:, :, 0] = 1
+            self.viewer.slice_.current_mask.modified(True)
  
             self.viewer.slice_.discard_all_buffers()
             self.viewer.slice_.current_mask.clear_history()
@@ -2403,6 +2401,7 @@ class FloodFillMaskInteractorStyle(DefaultInteractorStyle):
         self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
  
         self.viewer.slice_.current_mask.was_edited = True
+        self.viewer.slice_.current_mask.modified(True)
         Publisher.sendMessage('Reload actual slice')
  
  
@@ -2522,6 +2521,7 @@ class CropMaskInteractorStyle(DefaultInteractorStyle):
             self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
  
             self.viewer.slice_.current_mask.was_edited = True
+            self.viewer.slice_.current_mask.modified(True)
             Publisher.sendMessage('Reload actual slice')
  
  
@@ -2713,6 +2713,7 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
         self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
  
         self.viewer.slice_.current_mask.was_edited = True
+        self.viewer.slice_.current_mask.modified(self.config.target == '3D')
         Publisher.sendMessage('Reload actual slice')
  
     def do_2d_seg(self):
@@ -320,6 +320,9 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.UpdateMarkerOffsetPosition, 'Update marker offset')
         Publisher.subscribe(self.AddPeeledSurface, 'Update peel')
  
+        Publisher.subscribe(self.load_mask_preview, 'Load mask preview')
+        Publisher.subscribe(self.remove_mask_preview, 'Remove mask preview')
+
     def SetStereoMode(self, mode):
         ren_win = self.interactor.GetRenderWindow()
  
@@ -1663,6 +1666,19 @@ class Viewer(wx.Panel):
         # self._to_show_ball -= 1
         # self._check_and_set_ball_visibility()
  
+    def load_mask_preview(self, mask_3d_actor, flag=True):
+        if flag:
+            self.ren.AddVolume(mask_3d_actor)
+        else:
+            self.ren.RemoveVolume(mask_3d_actor)
+
+        if self.ren.GetActors().GetNumberOfItems() == 0 and self.ren.GetVolumes().GetNumberOfItems() == 1:
+            self.ren.ResetCamera()
+            self.ren.ResetCameraClippingRange()
+
+    def remove_mask_preview(self, mask_3d_actor):
+        self.ren.RemoveVolume(mask_3d_actor)
+
     def OnSetViewAngle(self, view):
         self.SetViewAngle(view)
  
@@ -1893,11 +1909,9 @@ class SlicePlane:
         Publisher.sendMessage('Update slice 3D',
                               widget=self.plane_z,
                               orientation="AXIAL")
-               
  
     def DeletePlanes(self):
         del self.plane_x
         del self.plane_y
-        del self.plane_z 
-    
+        del self.plane_z
  
@@ -19,6 +19,7 @@
 import plistlib
 import os
 import weakref
+from distutils.version import LooseVersion
  
 import numpy
 import vtk
@@ -707,9 +708,93 @@ class Volume():
         #else:
         #    valor = value 
         return value - scale[0]
-   
-        
-class CutPlane: 
+
+class VolumeMask:
+    def __init__(self, mask):
+        self.mask = mask
+        self.colour = mask.colour
+        self._volume_mapper = None
+        self._flip = None
+        self._color_transfer = None
+        self._piecewise_function = None
+        self._actor = None
+
+    def create_volume(self):
+        if self._actor is None:
+            if int(ses.Session().rendering) == 0:
+                self._volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
+                #volume_mapper.AutoAdjustSampleDistancesOff()
+                self._volume_mapper.IntermixIntersectingGeometryOn()
+                pix_diag = 2.0
+                self._volume_mapper.SetImageSampleDistance(0.25)
+                self._volume_mapper.SetSampleDistance(pix_diag / 5.0)
+            else:
+                self._volume_mapper = vtk.vtkGPUVolumeRayCastMapper()
+                self._volume_mapper.UseJitteringOn()
+
+                if LooseVersion(vtk.vtkVersion().GetVTKVersion()) > LooseVersion('8.0'):
+                    self._volume_mapper.SetBlendModeToIsoSurface()
+
+            #  else:
+                #  isosurfaceFunc = vtk.vtkVolumeRayCastIsosurfaceFunction()
+                #  isosurfaceFunc.SetIsoValue(127)
+
+                #  self._volume_mapper = vtk.vtkVolumeRayCastMapper()
+                #  self._volume_mapper.SetVolumeRayCastFunction(isosurfaceFunc)
+
+            self._flip = vtk.vtkImageFlip()
+            self._flip.SetInputData(self.mask.imagedata)
+            self._flip.SetFilteredAxis(1)
+            self._flip.FlipAboutOriginOn()
+
+            self._volume_mapper.SetInputConnection(self._flip.GetOutputPort())
+            self._volume_mapper.Update()
+
+            r, g, b = self.colour
+
+            self._color_transfer = vtk.vtkColorTransferFunction()
+            self._color_transfer.RemoveAllPoints()
+            self._color_transfer.AddRGBPoint(0.0, 0, 0, 0)
+            self._color_transfer.AddRGBPoint(254.0, r, g, b)
+            self._color_transfer.AddRGBPoint(255.0, r, g, b)
+
+            self._piecewise_function = vtk.vtkPiecewiseFunction()
+            self._piecewise_function.RemoveAllPoints()
+            self._piecewise_function.AddPoint(0.0, 0.0)
+            self._piecewise_function.AddPoint(127, 1.0)
+
+            self._volume_property = vtk.vtkVolumeProperty()
+            self._volume_property.SetColor(self._color_transfer)
+            self._volume_property.SetScalarOpacity(self._piecewise_function)
+            self._volume_property.ShadeOn()
+            self._volume_property.SetInterpolationTypeToLinear()
+            #vp.SetSpecular(1.75)
+            #vp.SetSpecularPower(8)
+
+            if not self._volume_mapper.IsA("vtkGPUVolumeRayCastMapper"):
+                self._volume_property.SetScalarOpacityUnitDistance(pix_diag)
+            else:
+                if LooseVersion(vtk.vtkVersion().GetVTKVersion()) > LooseVersion('8.0'):
+                    self._volume_property.GetIsoSurfaceValues().SetValue(0, 127)
+
+            self._actor = vtk.vtkVolume()
+            self._actor.SetMapper(self._volume_mapper)
+            self._actor.SetProperty(self._volume_property)
+            self._actor.Update()
+
+    def change_imagedata(self):
+        self._flip.SetInputData(self.mask.imagedata)
+
+    def set_colour(self, colour):
+        self.colour = colour
+        r, g, b = self.colour
+        self._color_transfer.RemoveAllPoints()
+        self._color_transfer.AddRGBPoint(0.0, 0, 0, 0)
+        self._color_transfer.AddRGBPoint(254.0, r, g, b)
+        self._color_transfer.AddRGBPoint(255.0, r, g, b)
+
+
+class CutPlane:
     def __init__(self, img, volume_mapper):
         self.img = img
         self.volume_mapper = volume_mapper
@@ -576,12 +576,9 @@ class MasksListCtrlPanel(InvListCtrl):
         Publisher.sendMessage('Show mask', index=index, value=flag)
  
  
-
-    def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)",
-                      colour=None):
+    def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)", colour=None):
         self.InsertItem(index, "")
-        self.SetItem(index, 1, label,
-                           imageId=self.mask_list_index[index])
+        self.SetItem(index, 1, label, imageId=self.mask_list_index[index])
         self.SetItem(index, 2, threshold)
         #  self.SetItemImage(index, 1)
         #  for key in self.mask_list_index.keys():
@@ -319,7 +319,6 @@ import wx.lib.buttons as btn
 from pubsub import pub as Publisher
 import wx.lib.colourselect as csel
  
-[BUTTON_RAYCASTING, BUTTON_VIEW, BUTTON_SLICE_PLANE, BUTTON_3D_STEREO, BUTTON_TARGET] = [wx.NewId() for num in range(5)]
 RAYCASTING_TOOLS = wx.NewId()
  
 ID_TO_NAME = {}
@@ -330,6 +329,8 @@ ID_TO_ITEMSLICEMENU = {}
 ID_TO_ITEM_3DSTEREO = {}
 ID_TO_STEREO_NAME = {}
  
+ICON_SIZE = (32, 32)
+
  
 class VolumeViewerCover(wx.Panel):
     def __init__(self, parent):
@@ -349,47 +350,22 @@ class VolumeToolPanel(wx.Panel):
         wx.Panel.__init__(self, parent)
  
         # VOLUME RAYCASTING BUTTON
-        BMP_RAYCASTING = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "volume_raycasting.png"),
-                                    wx.BITMAP_TYPE_PNG)
-
-        BMP_SLICE_PLANE = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "slice_plane.png"),
-                                    wx.BITMAP_TYPE_PNG)
-
-
-        BMP_3D_STEREO = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "3D_glasses.png"),
-                                    wx.BITMAP_TYPE_PNG)
-
-        BMP_TARGET = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "target.png"),
-                                    wx.BITMAP_TYPE_PNG)
-
-
-        button_raycasting = pbtn.PlateButton(self, BUTTON_RAYCASTING,"",
-                BMP_RAYCASTING, style=pbtn.PB_STYLE_SQUARE,
-                size=(32,32))
-
-        button_stereo = pbtn.PlateButton(self, BUTTON_3D_STEREO,"",
-                BMP_3D_STEREO, style=pbtn.PB_STYLE_SQUARE,
-                    size=(32,32))
-
-        button_slice_plane = self.button_slice_plane = pbtn.PlateButton(self, BUTTON_SLICE_PLANE,"",
-        BMP_SLICE_PLANE, style=pbtn.PB_STYLE_SQUARE,
-        size=(32,32))
-
-        button_target = self.button_target = pbtn.PlateButton(self, BUTTON_TARGET,"",
-        BMP_TARGET, style=pbtn.PB_STYLE_SQUARE|pbtn.PB_STYLE_TOGGLE,
-        size=(32,32))
+        BMP_RAYCASTING = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("volume_raycasting.png")), wx.BITMAP_TYPE_PNG)
+        BMP_SLICE_PLANE = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("slice_plane.png")), wx.BITMAP_TYPE_PNG)
+        BMP_3D_STEREO = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("3D_glasses.png")), wx.BITMAP_TYPE_PNG)
+        BMP_TARGET = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("target.png")), wx.BITMAP_TYPE_PNG)
+        BMP_3D_MASK = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("file_from_internet.png")), wx.BITMAP_TYPE_PNG)
+
+        self.button_raycasting = pbtn.PlateButton(self, -1,"", BMP_RAYCASTING, style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
+        self.button_stereo = pbtn.PlateButton(self, -1,"", BMP_3D_STEREO, style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
+        self.button_slice_plane = pbtn.PlateButton(self, -1, "", BMP_SLICE_PLANE, style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
+        self.button_target = pbtn.PlateButton(self, -1,"", BMP_TARGET, style=pbtn.PB_STYLE_SQUARE|pbtn.PB_STYLE_TOGGLE, size=ICON_SIZE)
         self.button_target.Enable(0)
-
-        self.button_raycasting = button_raycasting
-        self.button_stereo = button_stereo
+        #  self.button_3d_mask = pbtn.PlateButton(self, -1, "", BMP_3D_MASK, style=pbtn.PB_STYLE_SQUARE|pbtn.PB_STYLE_TOGGLE, size=ICON_SIZE)
  
         # VOLUME VIEW ANGLE BUTTON
-        BMP_FRONT = wx.Bitmap(ID_TO_BMP[const.VOL_FRONT][1],
-                              wx.BITMAP_TYPE_PNG)
-        button_view = pbtn.PlateButton(self, BUTTON_VIEW, "",
-                                        BMP_FRONT, size=(32,32),
-                                        style=pbtn.PB_STYLE_SQUARE)
-        self.button_view = button_view
+        BMP_FRONT = wx.Bitmap(ID_TO_BMP[const.VOL_FRONT][1], wx.BITMAP_TYPE_PNG)
+        self.button_view = pbtn.PlateButton(self, -1, "", BMP_FRONT, size=(32,32), style=pbtn.PB_STYLE_SQUARE)
  
         # VOLUME COLOUR BUTTON
         if sys.platform.startswith('linux'):
@@ -399,18 +375,17 @@ class VolumeToolPanel(wx.Panel):
             size = (24,24)
             sp = 5
  
-        button_colour= csel.ColourSelect(self, 111,colour=(0,0,0),
-                                        size=size)
-        self.button_colour = button_colour
+        self.button_colour= csel.ColourSelect(self, -1, colour=(0,0,0), size=size)
  
         # SIZER TO ORGANIZE ALL
         sizer = wx.BoxSizer(wx.VERTICAL)
-        sizer.Add(button_colour, 0, wx.ALL, sp)
-        sizer.Add(button_raycasting, 0, wx.TOP|wx.BOTTOM, 1)
-        sizer.Add(button_view, 0, wx.TOP|wx.BOTTOM, 1)
-        sizer.Add(button_slice_plane, 0, wx.TOP|wx.BOTTOM, 1)
-        sizer.Add(button_stereo, 0, wx.TOP|wx.BOTTOM, 1)
-        sizer.Add(button_target, 0, wx.TOP | wx.BOTTOM, 1)
+        sizer.Add(self.button_colour, 0, wx.ALL, sp)
+        sizer.Add(self.button_raycasting, 0, wx.TOP|wx.BOTTOM, 1)
+        sizer.Add(self.button_view, 0, wx.TOP|wx.BOTTOM, 1)
+        sizer.Add(self.button_slice_plane, 0, wx.TOP|wx.BOTTOM, 1)
+        sizer.Add(self.button_stereo, 0, wx.TOP|wx.BOTTOM, 1)
+        sizer.Add(self.button_target, 0, wx.TOP | wx.BOTTOM, 1)
+        #  sizer.Add(self.button_3d_mask, 0, wx.TOP | wx.BOTTOM, 1)
  
         self.navigation_status = False
         self.status_target_select = False
@@ -118,6 +118,7 @@ class Frame(wx.Frame):
         self.actived_interpolated_slices = main_menu.view_menu
         self.actived_navigation_mode = main_menu.mode_menu
         self.actived_dbs_mode = main_menu.mode_dbs
+        self.tools_menu = main_menu.tools_menu
  
         # Set menus, status and task bar
         self.SetMenuBar(main_menu)
@@ -538,6 +539,15 @@ class Frame(wx.Frame):
         elif id == const.ID_CROP_MASK:
             self.OnCropMask()
  
+        elif id == const.ID_MASK_3D_PREVIEW:
+            self.OnEnableMask3DPreview(value=self.tools_menu.IsChecked(const.ID_MASK_3D_PREVIEW))
+
+        elif id == const.ID_MASK_3D_AUTO_RELOAD:
+            ses.Session().auto_reload_preview = self.tools_menu.IsChecked(const.ID_MASK_3D_AUTO_RELOAD)
+
+        elif id == const.ID_MASK_3D_RELOAD:
+            self.OnUpdateMaskPreview()
+
         elif id == const.ID_CREATE_SURFACE:
             Publisher.sendMessage('Open create surface dialog')
  
@@ -769,6 +779,15 @@ class Frame(wx.Frame):
     def OnCropMask(self):
         Publisher.sendMessage('Enable style', style=const.SLICE_STATE_CROP_MASK)
  
+    def OnEnableMask3DPreview(self, value):
+        if value:
+            Publisher.sendMessage('Enable mask 3D preview')
+        else:
+            Publisher.sendMessage('Disable mask 3D preview')
+
+    def OnUpdateMaskPreview(self):
+        Publisher.sendMessage('Update mask 3D preview')
+
     def ShowPluginsFolder(self):
         """
         Show getting started window.
@@ -954,6 +973,22 @@ class MenuBar(wx.MenuBar):
         self.crop_mask_menu = mask_menu.Append(const.ID_CROP_MASK, _("Crop"))
         self.crop_mask_menu.Enable(False)
  
+        mask_menu.AppendSeparator()
+
+        mask_preview_menu = wx.Menu()
+
+        self.mask_preview = mask_preview_menu.Append(const.ID_MASK_3D_PREVIEW, _("Enable") + "\tCtrl+Shift+M", "", wx.ITEM_CHECK)
+        self.mask_preview.Enable(False)
+
+        self.mask_auto_reload = mask_preview_menu.Append(const.ID_MASK_3D_AUTO_RELOAD, _("Auto reload") + "\tCtrl+Shift+U", "", wx.ITEM_CHECK)
+        self.mask_auto_reload.Check(ses.Session().auto_reload_preview)
+        self.mask_auto_reload.Enable(False)
+
+        self.mask_preview_reload = mask_preview_menu.Append(const.ID_MASK_3D_RELOAD, _("Reload") + "\tCtrl+Shift+R")
+        self.mask_preview_reload.Enable(False)
+
+        mask_menu.Append(-1, _('Mask 3D Preview'), mask_preview_menu)
+
         # Segmentation Menu
         segmentation_menu = wx.Menu()
         self.threshold_segmentation = segmentation_menu.Append(const.ID_THRESHOLD_SEGMENTATION, _(u"Threshold\tCtrl+Shift+T"))
@@ -995,6 +1030,7 @@ class MenuBar(wx.MenuBar):
         tools_menu.Append(-1,  _(u"Mask"), mask_menu)
         tools_menu.Append(-1, _(u"Segmentation"), segmentation_menu)
         tools_menu.Append(-1, _(u"Surface"), surface_menu)
+        self.tools_menu = tools_menu
  
         #View
         self.view_menu = view_menu = wx.Menu()
@@ -1200,6 +1236,9 @@ class MenuBar(wx.MenuBar):
     def OnAddMask(self, mask):
         self.num_masks += 1
         self.bool_op_menu.Enable(self.num_masks >= 2)
+        self.mask_preview.Enable(True)
+        self.mask_auto_reload.Enable(True)
+        self.mask_preview_reload.Enable(True)
  
     def OnRemoveMasks(self, mask_indexes):
         self.num_masks -= len(mask_indexes)
@@ -1208,6 +1247,9 @@ class MenuBar(wx.MenuBar):
     def OnShowMask(self, index, value):
         self.clean_mask_menu.Enable(value)
         self.crop_mask_menu.Enable(value)
+        self.mask_preview.Enable(value)
+        self.mask_auto_reload.Enable(value)
+        self.mask_preview_reload.Enable(value)
  
  
 # ------------------------------------------------------------------
@@ -120,6 +120,8 @@ class Project(metaclass=Singleton):
     def RemoveMask(self, index):
         new_dict = {}
         for i in self.mask_dict:
+            mask = self.mask_dict[i]
+            mask.cleanup()
             if i < index:
                 new_dict[i] = self.mask_dict[i]
             if i > index:
@@ -331,6 +333,7 @@ class Project(metaclass=Singleton):
             filename = project["masks"][index]
             filepath = os.path.join(dirpath, filename)
             m = msk.Mask()
+            m.spacing = self.spacing
             m.OpenPList(filepath)
             self.mask_dict[m.index] = m
  
@@ -175,8 +175,8 @@ class SegmentProcess(ctx.Process):
                 self.mask = slc.Slice().create_new_mask(name=name)
  
         self.mask.was_edited = True
-        self.mask.matrix[:] = 1
         self.mask.matrix[1:, 1:, 1:] = (self._probability_array >= threshold) * 255
+        self.mask.modified(True)
  
     def get_completion(self):
         return self._comm_array[0]
@@ -34,7 +34,7 @@ import json
 from pubsub import pub as Publisher
 import wx
  
-from invesalius.utils import Singleton, debug, decode
+from invesalius.utils import Singleton, debug, decode, deep_merge_dict
 from random import randint
  
 from invesalius import inv_paths
@@ -59,6 +59,7 @@ class Session(metaclass=Singleton):
             'session': {
                 'status': 3,
                 'language': '',
+                'auto_reload_preview': False,
             },
             'project': {
             },
@@ -76,6 +77,7 @@ class Session(metaclass=Singleton):
             'surface_interpolation': ('session', 'surface_interpolation'),
             'rendering': ('session', 'rendering'),
             'slice_interpolation': ('session', 'slice_interpolation'),
+            'auto_reload_preview': ('session', 'auto_reload_preview'),
             'recent_projects': ('project', 'recent_projects'),
             'homedir': ('paths', 'homedir'),
             'tempdir': ('paths', 'homedir'),
@@ -95,6 +97,7 @@ class Session(metaclass=Singleton):
                 'surface_interpolation': 1,
                 'rendering': 0,
                 'slice_interpolation': 0,
+                'auto_reload_preview': False,
             },
  
             'project': {
@@ -268,7 +271,8 @@ class Session(metaclass=Singleton):
     def _read_cfg_from_json(self, json_filename):
         with open(json_filename, 'r') as cfg_file:
             cfg_dict = json.load(cfg_file)
-            self._values.update(cfg_dict)
+            self._value = deep_merge_dict(self._values, cfg_dict)
+            print(self._values)
  
         # Do not reading project status from the config file, since there
         # isn't a recover session tool in InVesalius yet.
@@ -23,6 +23,7 @@ import re
 import locale
 import math
 import traceback
+import collections.abc
  
 from distutils.version import LooseVersion
 from functools import wraps
@@ -487,3 +488,13 @@ def log_traceback(ex):
     tb_lines = [line.rstrip('\n') for line in
         traceback.format_exception(ex.__class__, ex, ex_traceback)]
     return ''.join(tb_lines)
+
+
+
+def deep_merge_dict(d, u):
+    for k, v in u.items():
+        if isinstance(v, collections.abc.Mapping):
+            d[k] = deep_merge_dict(d.get(k, {}), v)
+        else:
+            d[k] = v
+    return d
...	...	@@ -516,6 +516,9 @@ ID_DENSITY_MEASURE = wx.NewId()
516	516	ID_MASK_DENSITY_MEASURE = wx.NewId()
517	517	ID_CREATE_SURFACE = wx.NewId()
518	518	ID_CREATE_MASK = wx.NewId()
	519	+ID_MASK_3D_PREVIEW = wx.NewId()
	520	+ID_MASK_3D_RELOAD = wx.NewId()
	521	+ID_MASK_3D_AUTO_RELOAD = wx.NewId()
519	522
520	523	ID_GOTO_SLICE = wx.NewId()
521	524	ID_GOTO_COORD = wx.NewId()
...	...
...	...	@@ -126,6 +126,12 @@ class Controller():
126	126
127	127	Publisher.subscribe(self.create_project_from_matrix, 'Create project from matrix')
128	128
	129	+ Publisher.subscribe(self.show_mask_preview, 'Show mask preview')
	130	+
	131	+ Publisher.subscribe(self.enable_mask_preview, 'Enable mask 3D preview')
	132	+ Publisher.subscribe(self.disable_mask_preview, 'Disable mask 3D preview')
	133	+ Publisher.subscribe(self.update_mask_preview, 'Update mask 3D preview')
	134	+
129	135	def SetBitmapSpacing(self, spacing):
130	136	proj = prj.Project()
131	137	proj.spacing = spacing
...	...	@@ -1108,3 +1114,30 @@ class Controller():
1108	1114
1109	1115	if err_msg:
1110	1116	dialog.MessageBox(None, "It was not possible to launch new instance of InVesalius3 dsfa dfdsfa sdfas fdsaf asdfasf dsaa", err_msg)
	1117	+
	1118	+ def show_mask_preview(self, index, flag=True):
	1119	+ proj = prj.Project()
	1120	+ mask = proj.mask_dict[index]
	1121	+ slc = self.Slice.do_threshold_to_all_slices(mask)
	1122	+ mask.create_3d_preview()
	1123	+ Publisher.sendMessage("Load mask preview", mask_3d_actor=mask.volume._actor, flag=flag)
	1124	+ Publisher.sendMessage("Reload actual slice")
	1125	+
	1126	+ def enable_mask_preview(self):
	1127	+ mask = self.Slice.current_mask
	1128	+ if mask is not None:
	1129	+ self.Slice.do_threshold_to_all_slices(mask)
	1130	+ mask.create_3d_preview()
	1131	+ Publisher.sendMessage("Load mask preview", mask_3d_actor=mask.volume._actor, flag=True)
	1132	+ Publisher.sendMessage("Render volume viewer")
	1133	+
	1134	+ def disable_mask_preview(self):
	1135	+ mask = self.Slice.current_mask
	1136	+ if mask is not None:
	1137	+ Publisher.sendMessage("Remove mask preview", mask_3d_actor=mask.volume._actor)
	1138	+ Publisher.sendMessage("Render volume viewer")
	1139	+
	1140	+ def update_mask_preview(self):
	1141	+ mask = self.Slice.current_mask
	1142	+ if mask is not None:
	1143	+ mask._update_imagedata()
...	...
...	...	@@ -24,8 +24,7 @@ import vtk
24	24	from vtk.util import numpy_support
25	25
26	26
27		-def to_vtk(n_array, spacing, slice_number, orientation, origin=(0, 0, 0), padding=(0, 0, 0)):
28		-
	27	+def to_vtk(n_array, spacing=(1.0, 1.0, 1.0), slice_number=0, orientation='AXIAL', origin=(0, 0, 0), padding=(0, 0, 0)):
29	28	if orientation == "SAGITTAL":
30	29	orientation = "SAGITAL"
31	30
...	...	@@ -67,6 +66,37 @@ def to_vtk(n_array, spacing, slice_number, orientation, origin=(0, 0, 0), paddin
67	66	return image_copy
68	67
69	68
	69	+def to_vtk_mask(n_array, spacing=(1.0, 1.0, 1.0), origin=(0.0, 0.0, 0.0)):
	70	+ dz, dy, dx = n_array.shape
	71	+ ox, oy, oz = origin
	72	+ sx, sy, sz = spacing
	73	+
	74	+ ox -= sx
	75	+ oy -= sy
	76	+ oz -= sz
	77	+
	78	+ v_image = numpy_support.numpy_to_vtk(n_array.flat)
	79	+ extent = (0, dx - 1, 0, dy - 1, 0, dz - 1)
	80	+
	81	+ # Generating the vtkImageData
	82	+ image = vtk.vtkImageData()
	83	+ image.SetOrigin(ox, oy, oz)
	84	+ image.SetSpacing(sx, sy, sz)
	85	+ image.SetDimensions(dx - 1, dy - 1, dz - 1)
	86	+ # SetNumberOfScalarComponents and SetScalrType were replaced by
	87	+ # AllocateScalars
	88	+ # image.SetNumberOfScalarComponents(1)
	89	+ # image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
	90	+ image.AllocateScalars(numpy_support.get_vtk_array_type(n_array.dtype), 1)
	91	+ image.SetExtent(extent)
	92	+ image.GetPointData().SetScalars(v_image)
	93	+
	94	+ # image_copy = vtk.vtkImageData()
	95	+ # image_copy.DeepCopy(image)
	96	+
	97	+ return image
	98	+
	99	+
70	100	def np_rgba_to_vtk(n_array, spacing=(1.0, 1.0, 1.0)):
71	101	dy, dx, dc = n_array.shape
72	102	v_image = numpy_support.numpy_to_vtk(n_array.reshape(dy*dx, dc))
...	...
...	...	@@ -22,18 +22,21 @@ import plistlib
22	22	import random
23	23	import shutil
24	24	import tempfile
25		-
26		-import numpy as np
27		-import vtk
	25	+import time
	26	+import weakref
28	27
29	28	import invesalius.constants as const
	29	+import invesalius.data.converters as converters
30	30	import invesalius.data.imagedata_utils as iu
31	31	import invesalius.session as ses
32		-
	32	+from invesalius.data.volume import VolumeMask
	33	+import numpy as np
	34	+import vtk
33	35	from invesalius_cy import floodfill
34		-
35	36	from pubsub import pub as Publisher
36	37	from scipy import ndimage
	38	+from vtk.util import numpy_support
	39	+
37	40
38	41	class EditionHistoryNode(object):
39	42	def __init__(self, index, orientation, array, clean=False):
...	...	@@ -189,7 +192,9 @@ class Mask():
189	192	def __init__(self):
190	193	Mask.general_index += 1
191	194	self.index = Mask.general_index
192		- self.imagedata = ''
	195	+ self.matrix = None
	196	+ self.spacing = (1.0, 1.0, 1.0)
	197	+ self.imagedata = None
193	198	self.colour = random.choice(const.MASK_COLOUR)
194	199	self.opacity = const.MASK_OPACITY
195	200	self.threshold_range = const.THRESHOLD_RANGE
...	...	@@ -198,7 +203,11 @@ class Mask():
198	203	self.is_shown = 1
199	204	self.edited_points = {}
200	205	self.was_edited = False
	206	+ self.volume = None
	207	+ self.auto_update_mask = True
	208	+ self.modified_time = 0
201	209	self.__bind_events()
	210	+ self._modified_callbacks = []
202	211
203	212	self.history = EditionHistory()
204	213
...	...	@@ -206,11 +215,24 @@ class Mask():
206	215	Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
207	216	Publisher.subscribe(self.OnSwapVolumeAxes, 'Swap volume axes')
208	217
	218	+ def as_vtkimagedata(self):
	219	+ print("Converting to VTK")
	220	+ vimg = converters.to_vtk_mask(self.matrix, self.spacing)
	221	+ print("Converted")
	222	+ return vimg
	223	+
	224	+ def set_colour(self, colour):
	225	+ self.colour = colour
	226	+ if self.volume is not None:
	227	+ self.volume.set_colour(colour)
	228	+ Publisher.sendMessage("Render volume viewer")
	229	+
209	230	def save_history(self, index, orientation, array, p_array, clean=False):
210	231	self.history.new_node(index, orientation, array, p_array, clean)
211	232
212	233	def undo_history(self, actual_slices):
213	234	self.history.undo(self.matrix, actual_slices)
	235	+ self.modified()
214	236
215	237	# Marking the project as changed
216	238	session = ses.Session()
...	...	@@ -218,6 +240,7 @@ class Mask():
218	240
219	241	def redo_history(self, actual_slices):
220	242	self.history.redo(self.matrix, actual_slices)
	243	+ self.modified()
221	244
222	245	# Marking the project as changed
223	246	session = ses.Session()
...	...	@@ -226,6 +249,27 @@ class Mask():
226	249	def on_show(self):
227	250	self.history._config_undo_redo(self.is_shown)
228	251
	252	+ def create_3d_preview(self):
	253	+ if self.volume is None:
	254	+ if self.imagedata is None:
	255	+ self.imagedata = self.as_vtkimagedata()
	256	+ self.volume = VolumeMask(self)
	257	+ self.volume.create_volume()
	258	+
	259	+ def _update_imagedata(self, update_volume_viewer=True):
	260	+ if self.imagedata is not None:
	261	+ dz, dy, dx = self.matrix.shape
	262	+ # np_image = numpy_support.vtk_to_numpy(self.imagedata.GetPointData().GetScalars())
	263	+ # np_image[:] = self.matrix.reshape(-1)
	264	+ self.imagedata.SetDimensions(dx - 1, dy - 1, dz - 1)
	265	+ self.imagedata.SetSpacing(self.spacing)
	266	+ self.imagedata.SetExtent(0, dx - 1, 0, dy - 1, 0, dz - 1)
	267	+ self.imagedata.Modified()
	268	+ self.volume._actor.Update()
	269	+
	270	+ if update_volume_viewer:
	271	+ Publisher.sendMessage("Render volume viewer")
	272	+
229	273	def SavePlist(self, dir_temp, filelist):
230	274	mask = {}
231	275	filename = u'mask_%d' % self.index
...	...	@@ -284,10 +328,15 @@ class Mask():
284	328	elif axis == 2:
285	329	submatrix[:] = submatrix[:, :, ::-1]
286	330	self.matrix[0, 0, 1::] = self.matrix[0, 0, :0:-1]
	331	+ self.modified()
287	332
288	333	def OnSwapVolumeAxes(self, axes):
289	334	axis0, axis1 = axes
290	335	self.matrix = self.matrix.swapaxes(axis0, axis1)
	336	+ if self.volume:
	337	+ self.imagedata = self.as_vtkimagedata()
	338	+ self.volume.change_imagedata()
	339	+ self.modified()
291	340
292	341	def _save_mask(self, filename):
293	342	shutil.copyfile(self.temp_file, filename)
...	...	@@ -300,6 +349,22 @@ class Mask():
300	349	def _set_class_index(self, index):
301	350	Mask.general_index = index
302	351
	352	+ def add_modified_callback(self, callback):
	353	+ ref = weakref.WeakMethod(callback)
	354	+ self._modified_callbacks.append(ref)
	355	+
	356	+ def remove_modified_callback(self, callback):
	357	+ callbacks = []
	358	+ removed = False
	359	+ for cb in self._modified_callbacks:
	360	+ if cb() is not None:
	361	+ if cb() != callback:
	362	+ callbacks.append(cb)
	363	+ else:
	364	+ removed = True
	365	+ self._modified_callbacks = callbacks
	366	+ return removed
	367	+
303	368	def create_mask(self, shape):
304	369	"""
305	370	Creates a new mask object. This method do not append this new mask into the project.
...	...	@@ -311,11 +376,35 @@ class Mask():
311	376	shape = shape[0] + 1, shape[1] + 1, shape[2] + 1
312	377	self.matrix = np.memmap(self.temp_file, mode='w+', dtype='uint8', shape=shape)
313	378
	379	+ def modified(self, all_volume=False):
	380	+ if all_volume:
	381	+ self.matrix[0] = 1
	382	+ self.matrix[:, 0, :] = 1
	383	+ self.matrix[:, :, 0] = 1
	384	+ if ses.Session().auto_reload_preview:
	385	+ self._update_imagedata()
	386	+ self.modified_time = time.monotonic()
	387	+ callbacks = []
	388	+ print(self._modified_callbacks)
	389	+ for callback in self._modified_callbacks:
	390	+ if callback() is not None:
	391	+ callback()()
	392	+ callbacks.append(callback)
	393	+ self._modified_callbacks = callbacks
	394	+
314	395	def clean(self):
315	396	self.matrix[1:, 1:, 1:] = 0
316		- self.matrix[0, :, :] = 1
317		- self.matrix[:, 0, :] = 1
318		- self.matrix[:, :, 0] = 1
	397	+ self.modified(all_volume=True)
	398	+
	399	+ def cleanup(self):
	400	+ if self.is_shown:
	401	+ self.history._config_undo_redo(False)
	402	+ if self.volume:
	403	+ Publisher.sendMessage("Unload volume", volume=self.volume._actor)
	404	+ Publisher.sendMessage("Render volume viewer")
	405	+ self.imagedata = None
	406	+ self.volume = None
	407	+ del self.matrix
319	408
320	409	def copy(self, copy_name):
321	410	"""
...	...	@@ -334,6 +423,7 @@ class Mask():
334	423
335	424	new_mask.create_mask(shape=[i-1 for i in self.matrix.shape])
336	425	new_mask.matrix[:] = self.matrix[:]
	426	+ new_mask.spacing = self.spacing
337	427
338	428	return new_mask
339	429
...	...	@@ -384,7 +474,4 @@ class Mask():
384	474	self.save_history(index, orientation, matrix.copy(), cp_mask)
385	475
386	476	def __del__(self):
387		- if self.is_shown:
388		- self.history._config_undo_redo(False)
389		- del self.matrix
390	477	os.remove(self.temp_file)
...	...
...	...	@@ -384,9 +384,21 @@ class Slice(metaclass=utils.Singleton):
384	384	self.current_mask.matrix[:] = 0
385	385	self.current_mask.clear_history()
386	386
	387	+ if self.current_mask.auto_update_mask and self.current_mask.volume is not None:
	388	+ to_reload = True
	389	+ self.SetMaskThreshold(
	390	+ index,
	391	+ threshold_range,
	392	+ slice_number = None,
	393	+ orientation = None
	394	+ )
	395	+ self.discard_all_buffers()
	396	+ Publisher.sendMessage("Reload actual slice")
	397	+ self.current_mask.modified(all_volume=True)
	398	+ return
	399	+
387	400	to_reload = False
388	401	if threshold_range != self.current_mask.threshold_range:
389		- to_reload = True
390	402	for orientation in self.buffer_slices:
391	403	self.buffer_slices[orientation].discard_vtk_mask()
392	404	self.SetMaskThreshold(
...	...	@@ -417,6 +429,7 @@ class Slice(metaclass=utils.Singleton):
417	429
418	430	if to_reload:
419	431	Publisher.sendMessage("Reload actual slice")
	432	+ self.current_mask.modified(all_volume=False)
420	433
421	434	def __set_current_mask_threshold_actual_slice(self, threshold_range):
422	435	if self.current_mask is None:
...	...	@@ -1061,7 +1074,7 @@ class Slice(metaclass=utils.Singleton):
1061	1074	def SetMaskColour(self, index, colour, update=True):
1062	1075	"Set a mask colour given its index and colour (RGB 0-1 values)"
1063	1076	proj = Project()
1064		- proj.mask_dict[index].colour = colour
	1077	+ proj.mask_dict[index].set_colour(colour)
1065	1078
1066	1079	(r, g, b) = colour[:3]
1067	1080	colour_wx = [r * 255, g * 255, b * 255]
...	...	@@ -1108,6 +1121,7 @@ class Slice(metaclass=utils.Singleton):
1108	1121	# TODO: find out a better way to do threshold
1109	1122	if slice_number is None:
1110	1123	for n, slice_ in enumerate(self.matrix):
	1124	+ print(n)
1111	1125	m = np.ones(slice_.shape, self.current_mask.matrix.dtype)
1112	1126	m[slice_ < thresh_min] = 0
1113	1127	m[slice_ > thresh_max] = 0
...	...	@@ -1346,6 +1360,7 @@ class Slice(metaclass=utils.Singleton):
1346	1360	"""
1347	1361	future_mask = Mask()
1348	1362	future_mask.create_mask(self.matrix.shape)
	1363	+ future_mask.spacing = self.spacing
1349	1364
1350	1365	if name:
1351	1366	future_mask.name = name
...	...	@@ -1605,6 +1620,7 @@ class Slice(metaclass=utils.Singleton):
1605	1620
1606	1621	future_mask = Mask()
1607	1622	future_mask.create_mask(self.matrix.shape)
	1623	+ future_mask.spacing = spacing
1608	1624	future_mask.name = new_name
1609	1625
1610	1626	future_mask.matrix[:] = 1
...	...	@@ -1805,6 +1821,7 @@ class Slice(metaclass=utils.Singleton):
1805	1821	self.buffer_slices["CORONAL"].discard_vtk_mask()
1806	1822	self.buffer_slices["SAGITAL"].discard_vtk_mask()
1807	1823
	1824	+ self.current_mask.modified(target == '3D')
1808	1825	Publisher.sendMessage("Reload actual slice")
1809	1826
1810	1827	def calc_image_density(self, mask=None):
...	...
...	...	@@ -1445,6 +1445,7 @@ class EditorInteractorStyle(DefaultInteractorStyle):
1445	1445	self.viewer._flush_buffer = True
1446	1446	self.viewer.slice_.apply_slice_buffer_to_mask(self.orientation)
1447	1447	self.viewer._flush_buffer = False
	1448	+ self.viewer.slice_.current_mask.modified()
1448	1449
1449	1450	def EOnScrollForward(self, evt, obj):
1450	1451	iren = self.viewer.interactor
...	...	@@ -1822,7 +1823,6 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
1822	1823	self.viewer.slice_.current_mask.matrix[0 , 0, n+1]
1823	1824	markers = self.matrix[:, :, n]
1824	1825
1825		-
1826	1826	ww = self.viewer.slice_.window_width
1827	1827	wl = self.viewer.slice_.window_level
1828	1828
...	...	@@ -1866,6 +1866,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
1866	1866
1867	1867
1868	1868	self.viewer.slice_.current_mask.was_edited = True
	1869	+ self.viewer.slice_.current_mask.modified()
1869	1870	self.viewer.slice_.current_mask.clear_history()
1870	1871
1871	1872	# Marking the project as changed
...	...	@@ -2017,10 +2018,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
2017	2018	mask[(tmp_mask==2) & ((mask == 0) \| (mask == 2) \| (mask == 253))] = 2
2018	2019	mask[(tmp_mask==1) & ((mask == 0) \| (mask == 2) \| (mask == 253))] = 253
2019	2020
2020		- #mask[:] = tmp_mask
2021		- self.viewer.slice_.current_mask.matrix[0] = 1
2022		- self.viewer.slice_.current_mask.matrix[:, 0, :] = 1
2023		- self.viewer.slice_.current_mask.matrix[:, :, 0] = 1
	2021	+ self.viewer.slice_.current_mask.modified(True)
2024	2022
2025	2023	self.viewer.slice_.discard_all_buffers()
2026	2024	self.viewer.slice_.current_mask.clear_history()
...	...	@@ -2403,6 +2401,7 @@ class FloodFillMaskInteractorStyle(DefaultInteractorStyle):
2403	2401	self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
2404	2402
2405	2403	self.viewer.slice_.current_mask.was_edited = True
	2404	+ self.viewer.slice_.current_mask.modified(True)
2406	2405	Publisher.sendMessage('Reload actual slice')
2407	2406
2408	2407
...	...	@@ -2522,6 +2521,7 @@ class CropMaskInteractorStyle(DefaultInteractorStyle):
2522	2521	self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
2523	2522
2524	2523	self.viewer.slice_.current_mask.was_edited = True
	2524	+ self.viewer.slice_.current_mask.modified(True)
2525	2525	Publisher.sendMessage('Reload actual slice')
2526	2526
2527	2527
...	...	@@ -2713,6 +2713,7 @@ class FloodFillSegmentInteractorStyle(DefaultInteractorStyle):
2713	2713	self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
2714	2714
2715	2715	self.viewer.slice_.current_mask.was_edited = True
	2716	+ self.viewer.slice_.current_mask.modified(self.config.target == '3D')
2716	2717	Publisher.sendMessage('Reload actual slice')
2717	2718
2718	2719	def do_2d_seg(self):
...	...
...	...	@@ -320,6 +320,9 @@ class Viewer(wx.Panel):
320	320	Publisher.subscribe(self.UpdateMarkerOffsetPosition, 'Update marker offset')
321	321	Publisher.subscribe(self.AddPeeledSurface, 'Update peel')
322	322
	323	+ Publisher.subscribe(self.load_mask_preview, 'Load mask preview')
	324	+ Publisher.subscribe(self.remove_mask_preview, 'Remove mask preview')
	325	+
323	326	def SetStereoMode(self, mode):
324	327	ren_win = self.interactor.GetRenderWindow()
325	328
...	...	@@ -1663,6 +1666,19 @@ class Viewer(wx.Panel):
1663	1666	# self._to_show_ball -= 1
1664	1667	# self._check_and_set_ball_visibility()
1665	1668
	1669	+ def load_mask_preview(self, mask_3d_actor, flag=True):
	1670	+ if flag:
	1671	+ self.ren.AddVolume(mask_3d_actor)
	1672	+ else:
	1673	+ self.ren.RemoveVolume(mask_3d_actor)
	1674	+
	1675	+ if self.ren.GetActors().GetNumberOfItems() == 0 and self.ren.GetVolumes().GetNumberOfItems() == 1:
	1676	+ self.ren.ResetCamera()
	1677	+ self.ren.ResetCameraClippingRange()
	1678	+
	1679	+ def remove_mask_preview(self, mask_3d_actor):
	1680	+ self.ren.RemoveVolume(mask_3d_actor)
	1681	+
1666	1682	def OnSetViewAngle(self, view):
1667	1683	self.SetViewAngle(view)
1668	1684
...	...	@@ -1893,11 +1909,9 @@ class SlicePlane:
1893	1909	Publisher.sendMessage('Update slice 3D',
1894	1910	widget=self.plane_z,
1895	1911	orientation="AXIAL")
1896		-
1897	1912
1898	1913	def DeletePlanes(self):
1899	1914	del self.plane_x
1900	1915	del self.plane_y
1901		- del self.plane_z
1902		-
	1916	+ del self.plane_z
1903	1917
...	...
...	...	@@ -19,6 +19,7 @@
19	19	import plistlib
20	20	import os
21	21	import weakref
	22	+from distutils.version import LooseVersion
22	23
23	24	import numpy
24	25	import vtk
...	...	@@ -707,9 +708,93 @@ class Volume():
707	708	#else:
708	709	# valor = value
709	710	return value - scale[0]
710		-
711		-
712		-class CutPlane:
	711	+
	712	+class VolumeMask:
	713	+ def __init__(self, mask):
	714	+ self.mask = mask
	715	+ self.colour = mask.colour
	716	+ self._volume_mapper = None
	717	+ self._flip = None
	718	+ self._color_transfer = None
	719	+ self._piecewise_function = None
	720	+ self._actor = None
	721	+
	722	+ def create_volume(self):
	723	+ if self._actor is None:
	724	+ if int(ses.Session().rendering) == 0:
	725	+ self._volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
	726	+ #volume_mapper.AutoAdjustSampleDistancesOff()
	727	+ self._volume_mapper.IntermixIntersectingGeometryOn()
	728	+ pix_diag = 2.0
	729	+ self._volume_mapper.SetImageSampleDistance(0.25)
	730	+ self._volume_mapper.SetSampleDistance(pix_diag / 5.0)
	731	+ else:
	732	+ self._volume_mapper = vtk.vtkGPUVolumeRayCastMapper()
	733	+ self._volume_mapper.UseJitteringOn()
	734	+
	735	+ if LooseVersion(vtk.vtkVersion().GetVTKVersion()) > LooseVersion('8.0'):
	736	+ self._volume_mapper.SetBlendModeToIsoSurface()
	737	+
	738	+ # else:
	739	+ # isosurfaceFunc = vtk.vtkVolumeRayCastIsosurfaceFunction()
	740	+ # isosurfaceFunc.SetIsoValue(127)
	741	+
	742	+ # self._volume_mapper = vtk.vtkVolumeRayCastMapper()
	743	+ # self._volume_mapper.SetVolumeRayCastFunction(isosurfaceFunc)
	744	+
	745	+ self._flip = vtk.vtkImageFlip()
	746	+ self._flip.SetInputData(self.mask.imagedata)
	747	+ self._flip.SetFilteredAxis(1)
	748	+ self._flip.FlipAboutOriginOn()
	749	+
	750	+ self._volume_mapper.SetInputConnection(self._flip.GetOutputPort())
	751	+ self._volume_mapper.Update()
	752	+
	753	+ r, g, b = self.colour
	754	+
	755	+ self._color_transfer = vtk.vtkColorTransferFunction()
	756	+ self._color_transfer.RemoveAllPoints()
	757	+ self._color_transfer.AddRGBPoint(0.0, 0, 0, 0)
	758	+ self._color_transfer.AddRGBPoint(254.0, r, g, b)
	759	+ self._color_transfer.AddRGBPoint(255.0, r, g, b)
	760	+
	761	+ self._piecewise_function = vtk.vtkPiecewiseFunction()
	762	+ self._piecewise_function.RemoveAllPoints()
	763	+ self._piecewise_function.AddPoint(0.0, 0.0)
	764	+ self._piecewise_function.AddPoint(127, 1.0)
	765	+
	766	+ self._volume_property = vtk.vtkVolumeProperty()
	767	+ self._volume_property.SetColor(self._color_transfer)
	768	+ self._volume_property.SetScalarOpacity(self._piecewise_function)
	769	+ self._volume_property.ShadeOn()
	770	+ self._volume_property.SetInterpolationTypeToLinear()
	771	+ #vp.SetSpecular(1.75)
	772	+ #vp.SetSpecularPower(8)
	773	+
	774	+ if not self._volume_mapper.IsA("vtkGPUVolumeRayCastMapper"):
	775	+ self._volume_property.SetScalarOpacityUnitDistance(pix_diag)
	776	+ else:
	777	+ if LooseVersion(vtk.vtkVersion().GetVTKVersion()) > LooseVersion('8.0'):
	778	+ self._volume_property.GetIsoSurfaceValues().SetValue(0, 127)
	779	+
	780	+ self._actor = vtk.vtkVolume()
	781	+ self._actor.SetMapper(self._volume_mapper)
	782	+ self._actor.SetProperty(self._volume_property)
	783	+ self._actor.Update()
	784	+
	785	+ def change_imagedata(self):
	786	+ self._flip.SetInputData(self.mask.imagedata)
	787	+
	788	+ def set_colour(self, colour):
	789	+ self.colour = colour
	790	+ r, g, b = self.colour
	791	+ self._color_transfer.RemoveAllPoints()
	792	+ self._color_transfer.AddRGBPoint(0.0, 0, 0, 0)
	793	+ self._color_transfer.AddRGBPoint(254.0, r, g, b)
	794	+ self._color_transfer.AddRGBPoint(255.0, r, g, b)
	795	+
	796	+
	797	+class CutPlane:
713	798	def __init__(self, img, volume_mapper):
714	799	self.img = img
715	800	self.volume_mapper = volume_mapper
...	...
...	...	@@ -576,12 +576,9 @@ class MasksListCtrlPanel(InvListCtrl):
576	576	Publisher.sendMessage('Show mask', index=index, value=flag)
577	577
578	578
579		-
580		- def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)",
581		- colour=None):
	579	+ def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)", colour=None):
582	580	self.InsertItem(index, "")
583		- self.SetItem(index, 1, label,
584		- imageId=self.mask_list_index[index])
	581	+ self.SetItem(index, 1, label, imageId=self.mask_list_index[index])
585	582	self.SetItem(index, 2, threshold)
586	583	# self.SetItemImage(index, 1)
587	584	# for key in self.mask_list_index.keys():
...	...
...	...	@@ -319,7 +319,6 @@ import wx.lib.buttons as btn
319	319	from pubsub import pub as Publisher
320	320	import wx.lib.colourselect as csel
321	321
322		-[BUTTON_RAYCASTING, BUTTON_VIEW, BUTTON_SLICE_PLANE, BUTTON_3D_STEREO, BUTTON_TARGET] = [wx.NewId() for num in range(5)]
323	322	RAYCASTING_TOOLS = wx.NewId()
324	323
325	324	ID_TO_NAME = {}
...	...	@@ -330,6 +329,8 @@ ID_TO_ITEMSLICEMENU = {}
330	329	ID_TO_ITEM_3DSTEREO = {}
331	330	ID_TO_STEREO_NAME = {}
332	331
	332	+ICON_SIZE = (32, 32)
	333	+
333	334
334	335	class VolumeViewerCover(wx.Panel):
335	336	def __init__(self, parent):
...	...	@@ -349,47 +350,22 @@ class VolumeToolPanel(wx.Panel):
349	350	wx.Panel.__init__(self, parent)
350	351
351	352	# VOLUME RAYCASTING BUTTON
352		- BMP_RAYCASTING = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "volume_raycasting.png"),
353		- wx.BITMAP_TYPE_PNG)
354		-
355		- BMP_SLICE_PLANE = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "slice_plane.png"),
356		- wx.BITMAP_TYPE_PNG)
357		-
358		-
359		- BMP_3D_STEREO = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "3D_glasses.png"),
360		- wx.BITMAP_TYPE_PNG)
361		-
362		- BMP_TARGET = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "target.png"),
363		- wx.BITMAP_TYPE_PNG)
364		-
365		-
366		- button_raycasting = pbtn.PlateButton(self, BUTTON_RAYCASTING,"",
367		- BMP_RAYCASTING, style=pbtn.PB_STYLE_SQUARE,
368		- size=(32,32))
369		-
370		- button_stereo = pbtn.PlateButton(self, BUTTON_3D_STEREO,"",
371		- BMP_3D_STEREO, style=pbtn.PB_STYLE_SQUARE,
372		- size=(32,32))
373		-
374		- button_slice_plane = self.button_slice_plane = pbtn.PlateButton(self, BUTTON_SLICE_PLANE,"",
375		- BMP_SLICE_PLANE, style=pbtn.PB_STYLE_SQUARE,
376		- size=(32,32))
377		-
378		- button_target = self.button_target = pbtn.PlateButton(self, BUTTON_TARGET,"",
379		- BMP_TARGET, style=pbtn.PB_STYLE_SQUARE\|pbtn.PB_STYLE_TOGGLE,
380		- size=(32,32))
	353	+ BMP_RAYCASTING = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("volume_raycasting.png")), wx.BITMAP_TYPE_PNG)
	354	+ BMP_SLICE_PLANE = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("slice_plane.png")), wx.BITMAP_TYPE_PNG)
	355	+ BMP_3D_STEREO = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("3D_glasses.png")), wx.BITMAP_TYPE_PNG)
	356	+ BMP_TARGET = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("target.png")), wx.BITMAP_TYPE_PNG)
	357	+ BMP_3D_MASK = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("file_from_internet.png")), wx.BITMAP_TYPE_PNG)
	358	+
	359	+ self.button_raycasting = pbtn.PlateButton(self, -1,"", BMP_RAYCASTING, style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
	360	+ self.button_stereo = pbtn.PlateButton(self, -1,"", BMP_3D_STEREO, style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
	361	+ self.button_slice_plane = pbtn.PlateButton(self, -1, "", BMP_SLICE_PLANE, style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
	362	+ self.button_target = pbtn.PlateButton(self, -1,"", BMP_TARGET, style=pbtn.PB_STYLE_SQUARE\|pbtn.PB_STYLE_TOGGLE, size=ICON_SIZE)
381	363	self.button_target.Enable(0)
382		-
383		- self.button_raycasting = button_raycasting
384		- self.button_stereo = button_stereo
	364	+ # self.button_3d_mask = pbtn.PlateButton(self, -1, "", BMP_3D_MASK, style=pbtn.PB_STYLE_SQUARE\|pbtn.PB_STYLE_TOGGLE, size=ICON_SIZE)
385	365
386	366	# VOLUME VIEW ANGLE BUTTON
387		- BMP_FRONT = wx.Bitmap(ID_TO_BMP[const.VOL_FRONT][1],
388		- wx.BITMAP_TYPE_PNG)
389		- button_view = pbtn.PlateButton(self, BUTTON_VIEW, "",
390		- BMP_FRONT, size=(32,32),
391		- style=pbtn.PB_STYLE_SQUARE)
392		- self.button_view = button_view
	367	+ BMP_FRONT = wx.Bitmap(ID_TO_BMP[const.VOL_FRONT][1], wx.BITMAP_TYPE_PNG)
	368	+ self.button_view = pbtn.PlateButton(self, -1, "", BMP_FRONT, size=(32,32), style=pbtn.PB_STYLE_SQUARE)
393	369
394	370	# VOLUME COLOUR BUTTON
395	371	if sys.platform.startswith('linux'):
...	...	@@ -399,18 +375,17 @@ class VolumeToolPanel(wx.Panel):
399	375	size = (24,24)
400	376	sp = 5
401	377
402		- button_colour= csel.ColourSelect(self, 111,colour=(0,0,0),
403		- size=size)
404		- self.button_colour = button_colour
	378	+ self.button_colour= csel.ColourSelect(self, -1, colour=(0,0,0), size=size)
405	379
406	380	# SIZER TO ORGANIZE ALL
407	381	sizer = wx.BoxSizer(wx.VERTICAL)
408		- sizer.Add(button_colour, 0, wx.ALL, sp)
409		- sizer.Add(button_raycasting, 0, wx.TOP\|wx.BOTTOM, 1)
410		- sizer.Add(button_view, 0, wx.TOP\|wx.BOTTOM, 1)
411		- sizer.Add(button_slice_plane, 0, wx.TOP\|wx.BOTTOM, 1)
412		- sizer.Add(button_stereo, 0, wx.TOP\|wx.BOTTOM, 1)
413		- sizer.Add(button_target, 0, wx.TOP \| wx.BOTTOM, 1)
	382	+ sizer.Add(self.button_colour, 0, wx.ALL, sp)
	383	+ sizer.Add(self.button_raycasting, 0, wx.TOP\|wx.BOTTOM, 1)
	384	+ sizer.Add(self.button_view, 0, wx.TOP\|wx.BOTTOM, 1)
	385	+ sizer.Add(self.button_slice_plane, 0, wx.TOP\|wx.BOTTOM, 1)
	386	+ sizer.Add(self.button_stereo, 0, wx.TOP\|wx.BOTTOM, 1)
	387	+ sizer.Add(self.button_target, 0, wx.TOP \| wx.BOTTOM, 1)
	388	+ # sizer.Add(self.button_3d_mask, 0, wx.TOP \| wx.BOTTOM, 1)
414	389
415	390	self.navigation_status = False
416	391	self.status_target_select = False
...	...