Merge pull request #31 from tfmoraes/fixes_pre_beta5

Fixes some little issues before new version Fixes: Only accepts boolean operations when there 2 or more masks Watershed and Editor new shortcuts Better watershed progress dialog Added a tool menu Icons to MacOSX Combobox problems with the surface indexes Added an Ok and a Cancel button to the Watershed config dialog Only showing editor and watershed brush when enter in the renderviewer

Merge pull request #31 from tfmoraes/fixes_pre_beta5
Fixes some little issues before new version Fixes: Only accepts boolean operations when there 2 or more masks Watershed and Editor new shortcuts Better watershed progress dialog Added a tool menu Icons to MacOSX Combobox problems with the surface indexes Added an Ok and a Cancel button to the Watershed config dialog Only showing editor and watershed brush when enter in the renderviewer
Thiago Franco de Moraes
2 parents f68939cd b07a0770
Showing 111 changed files with 371 additions and 251 deletions Show diff stats
icons/3D_glasses.png
icons/3D_glasses_original.png
icons/Floppy.png
icons/annotation.png
icons/bool_difference.png
icons/bool_disjunction.png
icons/bool_intersection.png
icons/bool_union.png
icons/configuration.png
icons/connectivity_largest.png
icons/connectivity_manual.png
icons/connectivity_split_all.png
icons/cross.png
icons/cross_original.png
icons/data_duplicate.png
icons/data_new.png
icons/data_remove.png
icons/file_export.png
icons/file_from_internet.png
icons/file_from_internet_original.png
@@ -451,8 +451,10 @@ VTK_WARNING = 0
 [ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,
 ID_PROJECT_CLOSE, ID_PROJECT_INFO, ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET,
-ID_PRINT_SCREENSHOT, ID_EXIT, ID_IMPORT_OTHERS_FILES, ID_ANALYZE_IMPORT, ID_PREFERENCES, 
-ID_DICOM_NETWORK] = [wx.NewId() for number in range(14)]
+ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_ANALYZE_IMPORT, ID_PREFERENCES,
+ID_DICOM_NETWORK] = [wx.NewId() for number in range(13)]
+ID_EXIT = wx.ID_EXIT
+ID_ABOUT = wx.ID_ABOUT
 [ID_EDIT_UNDO, ID_EDIT_REDO, ID_EDIT_LIST] =\
@@ -464,7 +466,6 @@ ID_DICOM_NETWORK] = [wx.NewId() for number in range(14)]
 [ID_VIEW_FULL, ID_VIEW_TEXT, ID_VIEW_3D_BACKGROUND] =\
     [wx.NewId() for number in range(3)]
-ID_ABOUT = wx.NewId()
 ID_START = wx.NewId()
 ID_FLIP_X = wx.NewId()
@@ -476,6 +477,7 @@ ID_SWAP_XZ = wx.NewId()
 ID_SWAP_YZ = wx.NewId()
 ID_BOOLEAN_MASK = wx.NewId()
+ID_CLEAN_MASK = wx.NewId()
 #---------------------------------------------------------
 STATE_DEFAULT = 1000
@@ -285,6 +285,12 @@ class Mask():
         shape = shape[0] + 1, shape[1] + 1, shape[2] + 1
         self.matrix = numpy.memmap(self.temp_file, mode='w+', dtype='uint8', shape=shape)
+    def clean(self):
+        self.matrix[1:, 1:, 1:] = 0
+        self.matrix[0, :, :] = 1
+        self.matrix[:, 0, :] = 1
+        self.matrix[:, :, 0] = 1
+
     def copy(self, copy_name):
         """
         creates and return a copy from the mask instance.
@@ -142,6 +142,7 @@ class Slice(object):
         Publisher.subscribe(self.__set_mask_name, 'Change mask name')
         Publisher.subscribe(self.__show_mask, 'Show mask')
         Publisher.subscribe(self.__hide_current_mask, 'Hide current mask')
+        Publisher.subscribe(self.__clean_current_mask, 'Clean current mask')
         Publisher.subscribe(self.__set_current_mask_threshold_limits,
                                         'Update threshold limits')
@@ -211,6 +212,7 @@ class Slice(object):
                     buffer_.discard_vtk_mask()
                     buffer_.discard_mask()
+                Publisher.sendMessage('Show mask', (item, 0))
                 Publisher.sendMessage('Reload actual slice')
     def OnDuplicateMasks(self, pubsub_evt):
@@ -385,6 +387,15 @@ class Slice(object):
             value = False
             Publisher.sendMessage('Show mask', (index, value))
+    def __clean_current_mask(self, pubsub_evt):
+        if self.current_mask:
+            self.current_mask.clean()
+            for buffer_ in self.buffer_slices.values():
+                buffer_.discard_vtk_mask()
+                buffer_.discard_mask()
+            self.current_mask.clear_history()
+            self.current_mask.was_edited = True
+
     def create_temp_mask(self):
         temp_file = tempfile.mktemp()
         shape = self.matrix.shape
@@ -1012,6 +1023,7 @@ class Slice(object):
         if show:
             self.current_mask = mask
+            Publisher.sendMessage('Show mask', (mask.index, 1))
             Publisher.sendMessage('Change mask selected', mask.index)
             Publisher.sendMessage('Update slice viewer')
@@ -57,7 +57,7 @@ WATERSHED_OPERATIONS = {_(&quot;Erase&quot;): BRUSH_ERASE,
                         _("Background"): BRUSH_BACKGROUND,}
 def get_LUT_value(data, window, level):
-    return np.piecewise(data, 
+    return np.piecewise(data,
                         [data <= (level - 0.5 - (window-1)/2),
                          data > (level - 0.5 + (window-1)/2)],
                         [0, 255, lambda data: ((data - (level - 0.5))/(window-1) + 0.5)*(255-0)])
@@ -100,8 +100,8 @@ class BaseImageInteractorStyle(vtk.vtkInteractorStyleImage):
 class DefaultInteractorStyle(BaseImageInteractorStyle):
     """
-    Interactor style responsible for Default functionalities: 
-    * Zoom moving mouse with right button pressed; 
+    Interactor style responsible for Default functionalities:
+    * Zoom moving mouse with right button pressed;
     * Change the slices with the scroll.
     """
     def __init__(self, viewer):
@@ -129,10 +129,33 @@ class DefaultInteractorStyle(BaseImageInteractorStyle):
         evt.StartDolly()
     def OnScrollForward(self, evt, obj):
-        self.viewer.OnScrollForward()
+        iren = self.viewer.interactor
+        viewer = self.viewer
+        if  iren.GetShiftKey():
+            opacity = viewer.slice_.opacity + 0.1
+            if opacity <= 1:
+                viewer.slice_.opacity = opacity
+                self.viewer.slice_.buffer_slices['AXIAL'].discard_vtk_mask()
+                self.viewer.slice_.buffer_slices['CORONAL'].discard_vtk_mask()
+                self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
+                Publisher.sendMessage('Reload actual slice')
+        else:
+            self.viewer.OnScrollForward()
     def OnScrollBackward(self, evt, obj):
-        self.viewer.OnScrollBackward()
+        iren = self.viewer.interactor
+        viewer = self.viewer
+
+        if iren.GetShiftKey():
+            opacity = viewer.slice_.opacity - 0.1
+            if opacity >= 0.1:
+                viewer.slice_.opacity = opacity
+                self.viewer.slice_.buffer_slices['AXIAL'].discard_vtk_mask()
+                self.viewer.slice_.buffer_slices['CORONAL'].discard_vtk_mask()
+                self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
+                Publisher.sendMessage('Reload actual slice')
+        else:
+            self.viewer.OnScrollBackward()
 class CrossInteractorStyle(DefaultInteractorStyle):
@@ -182,7 +205,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
         # Forcing focal point to be setted in the center of the pixel.
         coord_cross = self.slice_actor.GetInput().GetPoint(position)
-        coord = self.calcultate_scroll_position(position)   
+        coord = self.calcultate_scroll_position(position)
         self.ScrollSlice(coord)
         Publisher.sendMessage('Update cross position', coord_cross)
@@ -190,7 +213,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
                                    coord_cross)
         Publisher.sendMessage('Set camera in volume', coord_cross)
         Publisher.sendMessage('Render volume viewer')
-        
+
         iren.Render()
@@ -292,7 +315,7 @@ class WWWLInteractorStyle(DefaultInteractorStyle):
             const.WINDOW_LEVEL['Manual'] = (self.acum_achange_window,\
                                            self.acum_achange_level)
             Publisher.sendMessage('Check window and level other')
-            Publisher.sendMessage('Update window level value',(self.acum_achange_window, 
+            Publisher.sendMessage('Update window level value',(self.acum_achange_window,
                                                                 self.acum_achange_level))
             #Necessary update the slice plane in the volume case exists
             Publisher.sendMessage('Update slice viewer')
@@ -339,7 +362,7 @@ class LinearMeasureInteractorStyle(DefaultInteractorStyle):
         slice_number = self.slice_data.number
         self.picker.Pick(x, y, 0, render)
         x, y, z = self.picker.GetPickPosition()
-        if self.picker.GetViewProp(): 
+        if self.picker.GetViewProp():
             Publisher.sendMessage("Add measurement point",
                                   ((x, y,z), const.LINEAR,
                                    ORIENTATIONS[self.orientation],
@@ -383,7 +406,7 @@ class AngularMeasureInteractorStyle(DefaultInteractorStyle):
         slice_number = self.slice_data.number
         self.picker.Pick(x, y, 0, render)
         x, y, z = self.picker.GetPickPosition()
-        if self.picker.GetViewProp(): 
+        if self.picker.GetViewProp():
             Publisher.sendMessage("Add measurement point",
                                   ((x, y,z), const.ANGULAR,
                                    ORIENTATIONS[self.orientation],
@@ -434,7 +457,7 @@ class SpinInteractorStyle(DefaultInteractorStyle):
         ren = iren.FindPokedRenderer(mouse_x, mouse_y)
         cam = ren.GetActiveCamera()
         if (self.left_pressed):
-            self.viewer.UpdateTextDirection(cam)    
+            self.viewer.UpdateTextDirection(cam)
             obj.Spin()
             obj.OnRightButtonDown()
@@ -456,7 +479,7 @@ class ZoomInteractorStyle(DefaultInteractorStyle):
     """
     def __init__(self, viewer):
         DefaultInteractorStyle.__init__(self, viewer)
-        
+
         self.viewer = viewer
         self.AddObserver("MouseMoveEvent", self.OnZoomMoveLeft)
@@ -532,6 +555,14 @@ class ChangeSliceInteractorStyle(DefaultInteractorStyle):
         self.last_position = position[1]
+class EditorConfig(object):
+    __metaclass__= utils.Singleton
+    def __init__(self):
+        self.operation = const.BRUSH_THRESH
+        self.cursor_type = const.BRUSH_CIRCLE
+        self.cursor_size = const.BRUSH_SIZE
+
+
 class EditorInteractorStyle(DefaultInteractorStyle):
     def __init__(self, viewer):
         DefaultInteractorStyle.__init__(self, viewer)
@@ -539,6 +570,8 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         self.viewer = viewer
         self.orientation = self.viewer.orientation
+        self.config = EditorConfig()
+
         self.picker = vtk.vtkWorldPointPicker()
         self.AddObserver("EnterEvent", self.OnEnterInteractor)
@@ -553,13 +586,55 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         self.AddObserver("MouseWheelForwardEvent",self.EOnScrollForward)
         self.AddObserver("MouseWheelBackwardEvent", self.EOnScrollBackward)
+        Publisher.subscribe(self.set_bsize, 'Set edition brush size')
+        Publisher.subscribe(self.set_bformat, 'Set brush format')
+        Publisher.subscribe(self.set_boperation, 'Set edition operation')
+
+        self._set_cursor()
+        self.viewer.slice_data.cursor.Show(0)
+
+    def CleanUp(self):
+        Publisher.unsubscribe(self.set_bsize, 'Set edition brush size')
+        Publisher.unsubscribe(self.set_bformat, 'Set brush format')
+        Publisher.unsubscribe(self.set_boperation, 'Set edition operation')
+
+    def set_bsize(self, pubsub_evt):
+        size = pubsub_evt.data
+        self.config.cursor_size = size
+        self.viewer.slice_data.cursor.SetSize(size)
+
+    def set_bformat(self, pubsub_evt):
+        self.config.cursor_type = pubsub_evt.data
+        self._set_cursor()
+
+    def set_boperation(self, pubsub_evt):
+        self.config.operation = pubsub_evt.data
+
+    def _set_cursor(self):
+        if self.config.cursor_type == const.BRUSH_SQUARE:
+            cursor = ca.CursorRectangle()
+        elif self.config.cursor_type == const.BRUSH_CIRCLE:
+            cursor = ca.CursorCircle()
+
+        cursor.SetOrientation(self.orientation)
+        n = self.viewer.slice_data.number
+        coordinates = {"SAGITAL": [n, 0, 0],
+                       "CORONAL": [0, n, 0],
+                       "AXIAL": [0, 0, n]}
+        cursor.SetPosition(coordinates[self.orientation])
+        spacing = self.viewer.slice_.spacing
+        cursor.SetSpacing(spacing)
+        cursor.SetColour(self.viewer._brush_cursor_colour)
+        cursor.SetSize(self.config.cursor_size)
+        self.viewer.slice_data.SetCursor(cursor)
+
     def OnEnterInteractor(self, obj, evt):
         if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
             return
         self.viewer.slice_data.cursor.Show()
         self.viewer.interactor.SetCursor(wx.StockCursor(wx.CURSOR_BLANK))
         self.viewer.interactor.Render()
-        
+
     def OnLeaveInteractor(self, obj, evt):
         self.viewer.slice_data.cursor.Show(0)
         self.viewer.interactor.SetCursor(wx.StockCursor(wx.CURSOR_DEFAULT))
@@ -569,11 +644,10 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
             return
-
         viewer = self.viewer
         iren = viewer.interactor
-        operation = viewer._brush_cursor_op 
+        operation = self.config.operation
         if operation == const.BRUSH_THRESH:
             if iren.GetControlKey():
                 if iren.GetShiftKey():
@@ -590,7 +664,7 @@ class EditorInteractorStyle(DefaultInteractorStyle):
             operation = const.BRUSH_ERASE
         viewer._set_editor_cursor_visibility(1)
- 
+
         mouse_x, mouse_y = iren.GetEventPosition()
         render = iren.FindPokedRenderer(mouse_x, mouse_y)
         slice_data = viewer.get_slice_data(render)
@@ -601,10 +675,10 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         slice_data.cursor.Show()
         self.picker.Pick(mouse_x, mouse_y, 0, render)
-        
+
         coord = self.get_coordinate_cursor()
         position = slice_data.actor.GetInput().FindPoint(coord)
-        
+
         if position != -1:
             coord = slice_data.actor.GetInput().GetPoint(position)
@@ -630,12 +704,12 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         iren = viewer.interactor
         viewer._set_editor_cursor_visibility(1)
- 
+
         mouse_x, mouse_y = iren.GetEventPosition()
         render = iren.FindPokedRenderer(mouse_x, mouse_y)
         slice_data = viewer.get_slice_data(render)
-        operation = viewer._brush_cursor_op 
+        operation = self.config.operation
         if operation == const.BRUSH_THRESH:
             if iren.GetControlKey():
                 if iren.GetShiftKey():
@@ -656,12 +730,12 @@ class EditorInteractorStyle(DefaultInteractorStyle):
             #i.cursor.Show(0)
         self.picker.Pick(mouse_x, mouse_y, 0, render)
-        
+
         #if (self.pick.GetViewProp()):
             #self.interactor.SetCursor(wx.StockCursor(wx.CURSOR_BLANK))
         #else:
             #self.interactor.SetCursor(wx.StockCursor(wx.CURSOR_DEFAULT))
-            
+
         coord = self.get_coordinate_cursor()
         position = viewer.slice_data.actor.GetInput().FindPoint(coord)
@@ -672,7 +746,7 @@ class EditorInteractorStyle(DefaultInteractorStyle):
             coord = slice_data.actor.GetInput().GetPoint(position)
         slice_data.cursor.SetPosition(coord)
         #self.__update_cursor_position(slice_data, coord)
-        
+
         if (self.left_pressed):
             cursor = slice_data.cursor
             position = slice_data.actor.GetInput().FindPoint(coord)
@@ -680,7 +754,7 @@ class EditorInteractorStyle(DefaultInteractorStyle):
             if position < 0:
                 position = viewer.calculate_matrix_position(coord)
-                
+
             viewer.slice_.edit_mask_pixel(operation, cursor.GetPixels(),
                                         position, radius, self.orientation)
             # TODO: To create a new function to reload images to viewer.
@@ -698,32 +772,35 @@ class EditorInteractorStyle(DefaultInteractorStyle):
     def EOnScrollForward(self, evt, obj):
         iren = self.viewer.interactor
+        viewer = self.viewer
         if iren.GetControlKey():
             mouse_x, mouse_y = iren.GetEventPosition()
             render = iren.FindPokedRenderer(mouse_x, mouse_y)
             slice_data = self.viewer.get_slice_data(render)
             cursor = slice_data.cursor
             size = cursor.radius * 2
+            size += 1
-            if size < 100:
-                Publisher.sendMessage('Set edition brush size', size + 1)
+            if size <= 100:
+                Publisher.sendMessage('Set edition brush size', size)
                 cursor.SetPosition(cursor.position)
                 self.viewer.interactor.Render()
-            
         else:
             self.OnScrollForward(obj, evt)
     def EOnScrollBackward(self, evt, obj):
         iren = self.viewer.interactor
+        viewer = self.viewer
         if iren.GetControlKey():
             mouse_x, mouse_y = iren.GetEventPosition()
             render = iren.FindPokedRenderer(mouse_x, mouse_y)
             slice_data = self.viewer.get_slice_data(render)
             cursor = slice_data.cursor
             size = cursor.radius * 2
+            size -= 1
             if size > 0:
-                Publisher.sendMessage('Set edition brush size', size - 1)
+                Publisher.sendMessage('Set edition brush size', size)
                 cursor.SetPosition(cursor.position)
                 self.viewer.interactor.Render()
         else:
@@ -742,41 +819,29 @@ class EditorInteractorStyle(DefaultInteractorStyle):
         return x, y, z
-class WatershedProgressWindow(wx.Frame):
-    def __init__(self, process, parent=None):
-        wx.Frame.__init__(self, parent, -1)
+class WatershedProgressWindow(object):
+    def __init__(self, process):
         self.process = process
-        self._build_gui()
-        self._bind_wx_events()
-        self.timer = wx.Timer(self)
-        self.timer.Start(1000)
-
-    def _build_gui(self):
-        self.gauge = wx.Gauge(self, -1, 100)
-        self.btn_cancel = wx.Button(self, wx.ID_CANCEL)
-        
-        sizer = wx.BoxSizer(wx.VERTICAL)
-        sizer.Add(wx.StaticText(self, -1, _("Applying watershed")))
-        sizer.Add(self.gauge, 0, wx.EXPAND)
-        sizer.Add(self.btn_cancel, 0, wx.ALIGN_LEFT)
-
-        self.SetSizer(sizer)
-        sizer.Fit(self)
-        self.Layout()
-
-    def __del__(self):
-        self.timer.Stop()
-
-    def _bind_wx_events(self):
-        self.Bind(wx.EVT_TIMER, self.TimeHandler)
-        self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_cancel)
-
-    def on_cancel(self, evt):
-        self.timer.Stop()    
+        self.title = "InVesalius 3"
+        self.msg = _("Applying watershed ...")
+        self.style = wx.PD_APP_MODAL | wx.PD_APP_MODAL | wx.PD_CAN_ABORT
+
+        self.dlg = wx.ProgressDialog(self.title,
+                                     self.msg,
+                                     parent = None,
+                                     style  = self.style)
+
+        self.dlg.Bind(wx.EVT_BUTTON, self.Cancel)
+        self.dlg.Show()
+
+    def Cancel(self, evt):
         self.process.terminate()
-    def TimeHandler(self, evt):
-        self.gauge.Pulse()
+    def Update(self):
+        self.dlg.Pulse()
+
+    def Close(self):
+        self.dlg.Destroy()
 class WatershedConfig(object):
@@ -851,6 +916,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         Publisher.subscribe(self.set_bformat, 'Set watershed brush format')
         self._set_cursor()
+        self.viewer.slice_data.cursor.Show(0)
     def SetUp(self):
         mask = self.viewer.slice_.current_mask.matrix
@@ -898,7 +964,6 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         cursor.SetColour(self.viewer._brush_cursor_colour)
         cursor.SetSize(self.config.cursor_size)
         self.viewer.slice_data.SetCursor(cursor)
-        self.viewer.interactor.Render()
     def set_bsize(self, pubsub_evt):
         size = pubsub_evt.data
@@ -913,42 +978,50 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
             return
         self.viewer.slice_data.cursor.Show()
-        #self.viewer.interactor.SetCursor(wx.StockCursor(wx.CURSOR_BLANK))
+        self.viewer.interactor.SetCursor(wx.StockCursor(wx.CURSOR_BLANK))
         self.viewer.interactor.Render()
-        
+
     def OnLeaveInteractor(self, obj, evt):
         self.viewer.slice_data.cursor.Show(0)
-        #self.viewer.interactor.SetCursor(wx.StockCursor(wx.CURSOR_DEFAULT))
+        self.viewer.interactor.SetCursor(wx.StockCursor(wx.CURSOR_DEFAULT))
         self.viewer.interactor.Render()
     def WOnScrollBackward(self, obj, evt):
+        iren = self.viewer.interactor
         viewer = self.viewer
-        iren = viewer.interactor
         if iren.GetControlKey():
-            if viewer.slice_.opacity > 0:
-                viewer.slice_.opacity -= 0.1
-                self.viewer.slice_.buffer_slices['AXIAL'].discard_vtk_mask()
-                self.viewer.slice_.buffer_slices['CORONAL'].discard_vtk_mask()
-                self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
-                viewer.OnScrollBar()
+            mouse_x, mouse_y = iren.GetEventPosition()
+            render = iren.FindPokedRenderer(mouse_x, mouse_y)
+            slice_data = self.viewer.get_slice_data(render)
+            cursor = slice_data.cursor
+            size = cursor.radius * 2
+            size -= 1
+
+            if size > 0:
+                Publisher.sendMessage('Set watershed brush size', size)
+                cursor.SetPosition(cursor.position)
+                self.viewer.interactor.Render()
         else:
             self.OnScrollBackward(obj, evt)
-
     def WOnScrollForward(self, obj, evt):
+        iren = self.viewer.interactor
         viewer = self.viewer
-        iren = viewer.interactor
         if iren.GetControlKey():
-            if viewer.slice_.opacity < 1:
-                viewer.slice_.opacity += 0.1
-                self.viewer.slice_.buffer_slices['AXIAL'].discard_vtk_mask()
-                self.viewer.slice_.buffer_slices['CORONAL'].discard_vtk_mask()
-                self.viewer.slice_.buffer_slices['SAGITAL'].discard_vtk_mask()
-                viewer.OnScrollBar()
+            mouse_x, mouse_y = iren.GetEventPosition()
+            render = iren.FindPokedRenderer(mouse_x, mouse_y)
+            slice_data = self.viewer.get_slice_data(render)
+            cursor = slice_data.cursor
+            size = cursor.radius * 2
+            size += 1
+
+            if size <= 100:
+                Publisher.sendMessage('Set watershed brush size', size)
+                cursor.SetPosition(cursor.position)
+                self.viewer.interactor.Render()
         else:
             self.OnScrollForward(obj, evt)
-
     def OnBrushClick(self, obj, evt):
         if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
             return
@@ -957,7 +1030,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         iren = viewer.interactor
         viewer._set_editor_cursor_visibility(1)
- 
+
         mouse_x, mouse_y = iren.GetEventPosition()
         render = iren.FindPokedRenderer(mouse_x, mouse_y)
         slice_data = viewer.get_slice_data(render)
@@ -968,10 +1041,10 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         slice_data.cursor.Show()
         self.picker.Pick(mouse_x, mouse_y, 0, render)
-        
+
         coord = self.get_coordinate_cursor()
         position = slice_data.actor.GetInput().FindPoint(coord)
-        
+
         if position != -1:
             coord = slice_data.actor.GetInput().GetPoint(position)
@@ -1017,7 +1090,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         iren = viewer.interactor
         viewer._set_editor_cursor_visibility(1)
- 
+
         mouse_x, mouse_y = iren.GetEventPosition()
         render = iren.FindPokedRenderer(mouse_x, mouse_y)
         slice_data = viewer.get_slice_data(render)
@@ -1027,12 +1100,12 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
             #i.cursor.Show(0)
         self.picker.Pick(mouse_x, mouse_y, 0, render)
-        
+
         #if (self.pick.GetViewProp()):
             #self.interactor.SetCursor(wx.StockCursor(wx.CURSOR_BLANK))
         #else:
             #self.interactor.SetCursor(wx.StockCursor(wx.CURSOR_DEFAULT))
-            
+
         coord = self.get_coordinate_cursor()
         position = viewer.slice_data.actor.GetInput().FindPoint(coord)
@@ -1043,7 +1116,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
             coord = slice_data.actor.GetInput().GetPoint(position)
         slice_data.cursor.SetPosition(coord)
         #self.__update_cursor_position(slice_data, coord)
-        
+
         if (self.left_pressed):
             cursor = slice_data.cursor
             position = slice_data.actor.GetInput().FindPoint(coord)
@@ -1104,7 +1177,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
         ww = self.viewer.slice_.window_width
         wl = self.viewer.slice_.window_level
-        
+
         if BRUSH_BACKGROUND in markers and BRUSH_FOREGROUND in markers:
             #w_algorithm = WALGORITHM[self.config.algorithm]
             bstruct = generate_binary_structure(2, CON2D[self.config.con_2d])
@@ -1146,9 +1219,7 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
             self.viewer.slice_.current_mask.was_edited = True
             self.viewer.slice_.current_mask.clear_history()
-            Publisher.sendMessage('Reload actual slice')
-        else:
-            self.viewer.OnScrollBar(update3D=False)
+        Publisher.sendMessage('Reload actual slice')
     def get_coordinate_cursor(self):
         # Find position
@@ -1253,18 +1324,14 @@ class WaterShedInteractorStyle(DefaultInteractorStyle):
                                         self.config.use_ww_wl, wl, ww, q))
             wp = WatershedProgressWindow(p)
-            wp.Center(wx.BOTH)
-            wp.Show()
-            wp.MakeModal()
-
             p.start()
             while q.empty() and p.is_alive():
                 time.sleep(0.5)
+                wp.Update()
                 wx.Yield()
-            wp.MakeModal(False)
-            wp.Destroy()
+            wp.Close()
             del wp
             if q.empty():
@@ -84,7 +84,7 @@ class Surface():
         #plist_filepath = os.path.join(dir_temp, filename + '.plist')
         temp_plist = tempfile.mktemp()
         plistlib.writePlist(surface, temp_plist)
-        
+
         filelist[temp_plist] = plist_filename
         return plist_filename
@@ -145,7 +145,7 @@ class SurfaceManager():
         Publisher.subscribe(self.OnDuplicate, "Duplicate surfaces")
         Publisher.subscribe(self.OnRemove,"Remove surfaces")
         Publisher.subscribe(self.UpdateSurfaceInterpolation, 'Update Surface Interpolation')
-    
+
     def OnDuplicate(self, pubsub_evt):
         selected_items = pubsub_evt.data
         proj = prj.Project()
@@ -155,7 +155,7 @@ class SurfaceManager():
             # compute copy name
             name = original_surface.name
             names_list = [surface_dict[i].name for i in surface_dict.keys()]
-            new_name = utl.next_copy_name(name, names_list) 
+            new_name = utl.next_copy_name(name, names_list)
             # create new mask
             self.CreateSurfaceFromPolydata(polydata = original_surface.polydata,
                                            overwrite = False,
@@ -221,7 +221,7 @@ class SurfaceManager():
             index_list.append(index)
             #self.ShowActor(index, True)
-        Publisher.sendMessage('Show multiple surfaces', (index_list, True)) 
+        Publisher.sendMessage('Show multiple surfaces', (index_list, True))
     def OnLargestSurface(self, pubsub_evt):
         """
@@ -329,7 +329,8 @@ class SurfaceManager():
                                     surface.colour, surface.volume,
                                     surface.transparency))
         self.last_surface_index = index
-        self.ShowActor(index, True)
+        if surface.is_shown:
+            self.ShowActor(index, True)
     def OnLoadSurfaceDict(self, pubsub_evt):
         surface_dict = pubsub_evt.data
@@ -388,10 +389,10 @@ class SurfaceManager():
         matrix = slice_.matrix
         filename_img = slice_.matrix_filename
         spacing = slice_.spacing
-        
+
         algorithm = surface_parameters['method']['algorithm']
         options = surface_parameters['method']['options']
-        
+
         surface_name = surface_parameters['options']['name']
         quality = surface_parameters['options']['quality']
         fill_holes = surface_parameters['options']['fill']
@@ -425,7 +426,7 @@ class SurfaceManager():
             pipeline_size += 1
         if keep_largest:
             pipeline_size += 1
-    
+
         ## Update progress value in GUI
         UpdateProgress = vu.ShowProgress(pipeline_size)
         UpdateProgress(0, _("Creating 3D surface..."))
@@ -438,7 +439,7 @@ class SurfaceManager():
             flip_image = True
         n_processors = multiprocessing.cpu_count()
-            
+
         pipe_in, pipe_out = multiprocessing.Pipe()
         o_piece = 1
         piece_size = 2000
@@ -455,7 +456,7 @@ class SurfaceManager():
                                                 mask.temp_file,
                                                 mask.matrix.shape,
                                                 mask.matrix.dtype,
-                                                spacing, 
+                                                spacing,
                                                 mode, min_value, max_value,
                                                 decimate_reduction,
                                                 smooth_relaxation_factor,
@@ -642,7 +643,7 @@ class SurfaceManager():
             polydata.SetSource(None)
             polydata.DebugOn()
             del filled_polydata
-        
+
         normals = vtk.vtkPolyDataNormals()
         normals.ReleaseDataFlagOn()
         normals_ref = weakref.ref(normals)
@@ -741,19 +742,19 @@ class SurfaceManager():
                                     (surface.index, surface.name,
                                     surface.colour, surface.volume,
                                     surface.transparency))
-        
+
         #When you finalize the progress. The bar is cleaned.
         UpdateProgress = vu.ShowProgress(1)
         UpdateProgress(0, _("Ready"))
         Publisher.sendMessage('Update status text in GUI', _("Ready"))
-        
+
         Publisher.sendMessage('End busy cursor')
         del actor
     def UpdateSurfaceInterpolation(self, pub_evt):
         interpolation = int(ses.Session().surface_interpolation)
         key_actors = self.actors_dict.keys()
-        
+
         for key in self.actors_dict:
             self.actors_dict[key].GetProperty().SetInterpolation(interpolation)
         Publisher.sendMessage('Render volume viewer')
@@ -62,6 +62,7 @@ class ContourMIPConfig(wx.Panel):
         wx.Panel.__init__(self, prnt)
         self.mip_size_spin = wx.SpinCtrl(self, -1, min=1, max=240,
                                          initial=const.PROJECTION_MIP_SIZE)
+        self.mip_size_spin.SetValue(const.PROJECTION_MIP_SIZE)
         self.mip_size_spin.SetToolTip(wx.ToolTip(_("Number of slices used to compound the visualization.")))
         w, h = self.mip_size_spin.GetTextExtent('M')
         self.mip_size_spin.SetMinSize((5 * w + 10, -1))
@@ -525,12 +526,6 @@ class Viewer(wx.Panel):
         ren.GetActiveCamera().Zoom(1.0)
         self.interactor.Render()
-    def ChangeBrushSize(self, pubsub_evt):
-        size = pubsub_evt.data
-        self._brush_cursor_size = size
-        #for slice_data in self.slice_data_list:
-        self.slice_data.cursor.SetSize(size)
-
     def ChangeBrushColour(self, pubsub_evt):
         vtk_colour = pubsub_evt.data[3]
         self._brush_cursor_colour = vtk_colour
@@ -545,27 +540,6 @@ class Viewer(wx.Panel):
         if self.slice_data.cursor:
             self.slice_data.cursor.SetColour(colour_vtk)
-    def ChangeBrushActor(self, pubsub_evt):
-        brush_type = pubsub_evt.data
-        slice_data = self.slice_data
-        self._brush_cursor_type = brush_type
-
-        if brush_type == const.BRUSH_SQUARE:
-            cursor = ca.CursorRectangle()
-        elif brush_type == const.BRUSH_CIRCLE:
-            cursor = ca.CursorCircle()
-
-        cursor.SetOrientation(self.orientation)
-        coordinates = {"SAGITAL": [slice_data.number, 0, 0],
-                       "CORONAL": [0, slice_data.number, 0],
-                       "AXIAL": [0, 0, slice_data.number]}
-        cursor.SetPosition(coordinates[self.orientation])
-        cursor.SetSpacing(self.slice_.spacing)
-        cursor.SetColour(self._brush_cursor_colour)
-        cursor.SetSize(self._brush_cursor_size)
-        slice_data.SetCursor(cursor)
-        self.interactor.Render()
-
     def Navigation(self, pubsub_evt):
         # Get point from base change
         x, y, z = pubsub_evt.data
@@ -700,14 +674,8 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.Navigation,
                                  'Co-registered Points')
         ###
-        Publisher.subscribe(self.ChangeBrushSize,
-                                 'Set edition brush size')
         Publisher.subscribe(self.ChangeBrushColour,
                                  'Add mask')
-        Publisher.subscribe(self.ChangeBrushActor,
-                                 'Set brush format')
-        Publisher.subscribe(self.ChangeBrushOperation,
-                                 'Set edition operation')
         Publisher.subscribe(self.UpdateWindowLevelValue,
                             'Update window level value')
@@ -833,9 +801,6 @@ class Viewer(wx.Panel):
         if (state != const.SLICE_STATE_EDITOR):
             Publisher.sendMessage('Set interactor default cursor')
-    def ChangeBrushOperation(self, pubsub_evt):
-        self._brush_cursor_op = pubsub_evt.data
-
     def __bind_events_wx(self):
         self.scroll.Bind(wx.EVT_SCROLL, self.OnScrollBar)
         self.scroll.Bind(wx.EVT_SCROLL_THUMBTRACK, self.OnScrollBarRelease)
@@ -230,10 +230,6 @@ class UpperTaskPanel(wx.Panel):
                                       wx.DefaultSize,FPB_DEFAULT_STYLE,
                                       fpb.FPB_SINGLE_FOLD)
-        sizer = wx.BoxSizer(wx.VERTICAL)
-        sizer.Add(fold_panel, 1, wx.GROW|wx.EXPAND)
-        self.SetSizer(sizer)
-
         image_list = wx.ImageList(16,16)
         image_list.Add(GetExpandedIconBitmap())
         image_list.Add(GetCollapsedIconBitmap())
@@ -288,6 +284,10 @@ class UpperTaskPanel(wx.Panel):
         fold_panel.Expand(fold_panel.GetFoldPanel(0))
         self.fold_panel = fold_panel
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        sizer.Add(fold_panel, 1, wx.GROW|wx.EXPAND)
+        self.SetSizerAndFit(sizer)
+
         self.SetStateProjectClose()
         self.__bind_events()
@@ -104,7 +104,7 @@ class ResizeImageDialog(wx.Dialog):
                    pos=wx.DefaultPosition,
                    style=wx.DEFAULT_DIALOG_STYLE)
         self.PostCreate(pre)
-        
+
         lbl_message = wx.StaticText(self, -1, _("InVesalius is running on a 32-bit operating system or has insufficient memory. \nIf you want to work with 3D surfaces or volume rendering, \nit is recommended to reduce the medical images resolution."))
         icon = wx.ArtProvider.GetBitmap(wx.ART_WARNING, wx.ART_MESSAGE_BOX, (32,32))
         bmp = wx.StaticBitmap(self, -1, icon)
@@ -143,7 +143,7 @@ class ResizeImageDialog(wx.Dialog):
         sizer_general.Fit(self)
         self.Layout()
         self.Centre()
-    
+
     def SetValue(self, value):
         self.num_ctrl_porcent.SetValue(value)
@@ -611,7 +611,7 @@ class NewMask(wx.Dialog):
         thresh_min, thresh_max = project.threshold_modes[_("Bone")]
         original_colour = random.choice(const.MASK_COLOUR)
         self.colour = original_colour
-        colour = [255*i for i in original_colour] 
+        colour = [255*i for i in original_colour]
         colour.append(100)
         gradient = grad.GradientSlider(self, -1, int(bound_min),
                                         int(bound_max),
@@ -673,7 +673,7 @@ class NewMask(wx.Dialog):
         proj = prj.Project()
         if thresh  in proj.threshold_modes.values():
             preset_name = proj.threshold_modes.get_key(thresh)[0]
-            index = self.thresh_list.index(preset_name) 
+            index = self.thresh_list.index(preset_name)
             self.combo_thresh.SetSelection(index)
         else:
             index = self.thresh_list.index(_("Custom"))
@@ -790,14 +790,14 @@ def ShowAboutDialog(parent):
                         "Dimitris Glezos",
                         "Eugene Liscio",
                         u"Frédéric Lopez",
-                        "Javier de Lima Moreno"
+                        "Javier de Lima Moreno",
                         "Nikos Korkakakis",
                         "Massimo Crisantemo",
                         "Raul Bolliger Neto",
                         "Sebastian Hilbert",
                         "Semarang Pari"]
-    #info.DocWriters = ["Fabio Francisco da Silva (PT)"] 
+    #info.DocWriters = ["Fabio Francisco da Silva (PT)"]
     info.Artists = ["Otavio Henrique Junqueira Amorim"]
@@ -1101,7 +1101,7 @@ class SurfaceCreationOptionsPanel(wx.Panel):
         import constants as const
         import data.surface as surface
         import project as prj
-        
+
         wx.Panel.__init__(self, parent, ID)
         # LINE 1: Surface name
@@ -1151,7 +1151,7 @@ class SurfaceCreationOptionsPanel(wx.Panel):
         flag_link = wx.EXPAND|wx.GROW|wx.ALL
         flag_button = wx.ALL | wx.EXPAND| wx.GROW
-        fixed_sizer = wx.FlexGridSizer(rows=2, cols=2, hgap=10, vgap=5)
+        fixed_sizer = wx.FlexGridSizer(rows=3, cols=2, hgap=10, vgap=5)
         fixed_sizer.AddGrowableCol(0, 1)
         fixed_sizer.AddMany([ (label_surface, 1, flag_link, 0),
                               (text, 1, flag_button, 0),
@@ -1208,7 +1208,7 @@ class CAOptions(wx.Panel):
     def __init__(self, parent):
         wx.Panel.__init__(self, parent, -1)
         self._build_widgets()
-    
+
     def _build_widgets(self):
         sb = wx.StaticBox(self, -1, _('Options'))
         self.angle = floatspin.FloatSpin(self, -1, value=0.7, min_val=0.0,
@@ -1222,7 +1222,7 @@ class CAOptions(wx.Panel):
         self.min_weight = floatspin.FloatSpin(self, -1, value=0.2, min_val=0.0,
                                          max_val=1.0, increment=0.1,
                                          digits=1)
-        
+
         self.steps = wx.SpinCtrl(self, -1, value='10', min=1, max=100)
         layout_sizer = wx.FlexGridSizer(rows=4, cols=2, hgap=5, vgap=5)
@@ -1285,7 +1285,7 @@ class SurfaceMethodPanel(wx.Panel):
         self.SetSizer(self.main_sizer)
         self.Layout()
         self.Fit()
-        
+
         if self.mask_edited:
             self.cb_types.SetValue(_(u'Context aware smoothing'))
             self.ca_options.Enable()
@@ -1324,9 +1324,9 @@ class SurfaceMethodPanel(wx.Panel):
         algorithm = self.GetAlgorithmSelected()
         options = self.GetOptions()
-        return {"algorithm": algorithm, 
+        return {"algorithm": algorithm,
                 "options": options}
-        
+
     def ReloadMethodsOptions(self):
         self.cb_types.Clear()
         self.cb_types.AppendItems([i for i in sorted(self.alg_types)
@@ -1388,32 +1388,37 @@ class ClutImagedataDialog(wx.Dialog):
         if gen_evt:
             self.clut_widget._generate_event()
- 
-class WatershedOptions(wx.Panel):
-    def __init__(self, parent):
+
+class WatershedOptionsPanel(wx.Panel):
+    def __init__(self, parent, config):
         wx.Panel.__init__(self, parent)
-        
+
         self.algorithms = ("Watershed", "Watershed IFT")
         self.con2d_choices = (4, 8)
         self.con3d_choices = (6, 18, 26)
+        self.config = config
+
         self._init_gui()
-        self._bind_events()
     def _init_gui(self):
         self.choice_algorithm = wx.RadioBox(self, -1, "Algorithm",
-                                           choices=("Watershed", "Watershed IFT"),
+                                           choices=self.algorithms,
                                            style=wx.NO_BORDER | wx.HORIZONTAL)
+        self.choice_algorithm.SetSelection(self.algorithms.index(self.config.algorithm))
         self.choice_2dcon = wx.RadioBox(self, -1, "2D",
                                         choices=[str(i) for i in self.con2d_choices],
                                         style=wx.NO_BORDER | wx.HORIZONTAL)
+        self.choice_2dcon.SetSelection(self.con2d_choices.index(self.config.con_2d))
         self.choice_3dcon = wx.RadioBox(self, -1, "3D",
                                         choices=[str(i) for i in self.con3d_choices],
                                         style=wx.NO_BORDER | wx.HORIZONTAL)
+        self.choice_3dcon.SetSelection(self.con3d_choices.index(self.config.con_3d))
         self.gaussian_size = wx.SpinCtrl(self, -1, "", min=1, max=10)
+        self.gaussian_size.SetValue(self.config.mg_size)
         box_sizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Conectivity"), wx.VERTICAL)
         box_sizer.Add(self.choice_2dcon, 0, wx.ALIGN_CENTER_VERTICAL,2)
@@ -1432,47 +1437,52 @@ class WatershedOptions(wx.Panel):
         sizer.Fit(self)
         self.Layout()
-    def _bind_events(self):
-        self.choice_algorithm.Bind(wx.EVT_RADIOBOX, self.OnSetAlgorithm)
-        self.gaussian_size.Bind(wx.EVT_SPINCTRL, self.OnSetGaussianSize)
-        self.choice_2dcon.Bind(wx.EVT_RADIOBOX, self.OnSetCon2D)
-        self.choice_3dcon.Bind(wx.EVT_RADIOBOX, self.OnSetCon3D)
-
-    def OnSetAlgorithm(self, evt):
-        v = self.algorithms[evt.GetInt()]
-        Publisher.sendMessage("Set watershed algorithm", v)
-
-    def OnSetGaussianSize(self, evt):
-        v = self.gaussian_size.GetValue()
-        Publisher.sendMessage("Set watershed gaussian size", v)
-
-    def OnSetCon2D(self, evt):
-        v = self.con2d_choices[evt.GetInt()]
-        Publisher.sendMessage("Set watershed 2d con", v)
-
-    def OnSetCon3D(self, evt):
-        v = self.con3d_choices[evt.GetInt()]
-        Publisher.sendMessage("Set watershed 3d con", v)
+    def apply_options(self):
+        self.config.algorithm = self.algorithms[self.choice_algorithm.GetSelection()]
+        self.config.con_2d = self.con2d_choices[self.choice_2dcon.GetSelection()]
+        self.config.con_3d = self.con3d_choices[self.choice_3dcon.GetSelection()]
+        self.config.mg_size = self.gaussian_size.GetValue()
 class WatershedOptionsDialog(wx.Dialog):
-    def __init__(self):
+    def __init__(self, config):
         pre = wx.PreDialog()
         pre.Create(wx.GetApp().GetTopWindow(), -1, style=wx.DEFAULT_DIALOG_STYLE|wx.FRAME_FLOAT_ON_PARENT)
         self.PostCreate(pre)
+        self.config = config
+
         self._init_gui()
     def _init_gui(self):
-        wop = WatershedOptions(self)
+        wop = WatershedOptionsPanel(self, self.config)
+        self.wop = wop
+
+        sizer = wx.BoxSizer(wx.VERTICAL)
+
+        btn_ok = wx.Button(self, wx.ID_OK)
+        btn_ok.SetDefault()
+
+        btn_cancel = wx.Button(self, wx.ID_CANCEL)
+
+        btnsizer = wx.StdDialogButtonSizer()
+        btnsizer.AddButton(btn_ok)
+        btnsizer.AddButton(btn_cancel)
+        btnsizer.Realize()
-        sizer = wx.BoxSizer(wx.VERTICAL) 
         sizer.Add(wop, 0, wx.EXPAND)
+        sizer.Add(btnsizer, 0, wx.EXPAND)
+        sizer.AddSpacer(5)
         self.SetSizer(sizer)
         sizer.Fit(self)
         self.Layout()
+        btn_ok.Bind(wx.EVT_BUTTON, self.OnOk)
+
+    def OnOk(self, evt):
+        self.wop.apply_options()
+        evt.Skip()
 class MaskBooleanDialog(wx.Dialog):
     def __init__(self, masks):
@@ -1500,7 +1510,7 @@ class MaskBooleanDialog(wx.Dialog):
         icon_folder = '../icons/'
         op_choices = ((_(u"Union"), const.BOOLEAN_UNION, 'bool_union.png'),
-                      (_(u"Difference"), const.BOOLEAN_DIFF, 'bool_difference.png'), 
+                      (_(u"Difference"), const.BOOLEAN_DIFF, 'bool_difference.png'),
                       (_(u"Intersection"), const.BOOLEAN_AND, 'bool_intersection.png'),
                       (_(u"Exclusive disjunction"), const.BOOLEAN_XOR, 'bool_disjunction.png'))
         self.op_boolean = wx.combo.BitmapComboBox(self, -1, op_choices[0][0], choices=[])
@@ -51,7 +51,7 @@ class MessageWatershed(wx.PopupWindow):
     def __init__(self, prnt, msg):
         wx.PopupWindow.__init__(self, prnt, -1)
         self.txt = wx.StaticText(self, -1, msg)
-        
+
         self.sizer = wx.BoxSizer(wx.HORIZONTAL)
         self.sizer.Add(self.txt, 1, wx.EXPAND)
         self.SetSizer(self.sizer)
@@ -81,10 +81,10 @@ class Frame(wx.Frame):
         self.SetIcon(wx.Icon(icon_path, wx.BITMAP_TYPE_ICO))
         self.mw = None
-        
+
         if sys.platform != 'darwin':
             self.Maximize()
-        
+
         self.sizeChanged = True
         #Necessary update AUI (statusBar in special)
         #when maximized in the Win 7 and XP
@@ -381,12 +381,12 @@ class Frame(wx.Frame):
         elif id == const.ID_START:
             self.ShowGettingStarted()
         elif id == const.ID_PREFERENCES:
-            self.ShowPreferences()      
+            self.ShowPreferences()
         elif id == const.ID_DICOM_NETWORK:
-            self.ShowRetrieveDicomPanel() 
+            self.ShowRetrieveDicomPanel()
         elif id in (const.ID_FLIP_X, const.ID_FLIP_Y, const.ID_FLIP_Z):
-            axis = {const.ID_FLIP_X: 2, 
-                    const.ID_FLIP_Y: 1, 
+            axis = {const.ID_FLIP_X: 2,
+                    const.ID_FLIP_Y: 1,
                     const.ID_FLIP_Z: 0}[id]
             self.FlipVolume(axis)
         elif id in (const.ID_SWAP_XY, const.ID_SWAP_XZ, const.ID_SWAP_YZ):
@@ -401,6 +401,8 @@ class Frame(wx.Frame):
         elif id == const.ID_BOOLEAN_MASK:
             self.OnMaskBoolean()
+        elif id == const.ID_CLEAN_MASK:
+            self.OnCleanMask()
     def OnSize(self, evt):
         """
@@ -429,10 +431,10 @@ class Frame(wx.Frame):
         if self.preferences.ShowModal() == wx.ID_OK:
             values = self.preferences.GetPreferences()
             self.preferences.Close()
-            
+
             ses.Session().rendering = values[const.RENDERING]
             ses.Session().surface_interpolation = values[const.SURFACE_INTERPOLATION]
-            ses.Session().language = values[const.LANGUAGE]         
+            ses.Session().language = values[const.LANGUAGE]
             Publisher.sendMessage('Remove Volume')
             Publisher.sendMessage('Reset Reaycasting')
@@ -479,7 +481,7 @@ class Frame(wx.Frame):
         Show save as dialog.
         """
         Publisher.sendMessage('Show save dialog', True)
-        
+
     def ShowAnalyzeImporter(self):
         """
         Show save as dialog.
@@ -488,12 +490,12 @@ class Frame(wx.Frame):
     def FlipVolume(self, axis):
         Publisher.sendMessage('Flip volume', axis)
-        Publisher.sendMessage('Reload actual slice') 
+        Publisher.sendMessage('Reload actual slice')
     def SwapAxes(self, axes):
         Publisher.sendMessage('Swap volume axes', axes)
         Publisher.sendMessage('Update scroll')
-        Publisher.sendMessage('Reload actual slice') 
+        Publisher.sendMessage('Reload actual slice')
     def OnUndo(self):
         print "Undo"
@@ -503,11 +505,13 @@ class Frame(wx.Frame):
         print "Redo"
         Publisher.sendMessage('Redo edition')
-
     def OnMaskBoolean(self):
         print "Mask boolean"
         Publisher.sendMessage('Show boolean dialog')
-      
+
+    def OnCleanMask(self):
+        Publisher.sendMessage('Clean current mask')
+        Publisher.sendMessage('Reload actual slice')
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
@@ -546,12 +550,18 @@ class MenuBar(wx.MenuBar):
         sub(self.OnEnableUndo, "Enable undo")
         sub(self.OnEnableRedo, "Enable redo")
+        sub(self.OnAddMask, "Add mask")
+        sub(self.OnRemoveMasks, "Remove masks")
+        sub(self.OnShowMask, "Show mask")
+
+        self.num_masks = 0
+
     def __init_items(self):
         """
         Create all menu and submenus, and add them to self.
         """
         # TODO: This definetely needs improvements... ;)
-        
+
         #Import Others Files
         others_file_menu = wx.Menu()
         others_file_menu.Append(const.ID_ANALYZE_IMPORT, "Analyze")
@@ -594,7 +604,7 @@ class MenuBar(wx.MenuBar):
         file_edit = wx.Menu()
         #file_edit.AppendMenu(wx.NewId(), _('Flip'), flip_menu)
         #file_edit.AppendMenu(wx.NewId(), _('Swap axes'), swap_axes_menu)
-        
+
         d = const.ICON_DIR
         if not(sys.platform == 'darwin'):
@@ -620,10 +630,18 @@ class MenuBar(wx.MenuBar):
         #app(const.ID_EDIT_LIST, "Show Undo List...")
         #################################################################
+        # Tool menu
+        tools_menu = wx.Menu()
+
         # Mask Menu
         mask_menu = wx.Menu()
-        mask_menu.Append(const.ID_BOOLEAN_MASK, _(u"Boolean operations"))
-        file_edit.AppendMenu(-1,  _(u"Mask"), mask_menu)
+        self.bool_op_menu = mask_menu.Append(const.ID_BOOLEAN_MASK, _(u"Boolean operations"))
+        self.bool_op_menu.Enable(False)
+
+        self.clean_mask_menu = mask_menu.Append(const.ID_CLEAN_MASK, _(u"Clean Mask\tCtrl+Shift+A"))
+        self.clean_mask_menu.Enable(False)
+
+        tools_menu.AppendMenu(-1,  _(u"Mask"), mask_menu)
         # VIEW
@@ -666,13 +684,14 @@ class MenuBar(wx.MenuBar):
         help_menu.Append(const.ID_ABOUT, _("About..."))
         #help_menu.Append(107, "Check For Updates Now...")
-        if platform.system() == 'Darwin':
-           wx.App.SetMacAboutMenuItemId(const.ID_ABOUT)
-           wx.App.SetMacExitMenuItemId(const.ID_EXIT)
+        #if platform.system() == 'Darwin':
+           #wx.App.SetMacAboutMenuItemId(const.ID_ABOUT)
+           #wx.App.SetMacExitMenuItemId(const.ID_EXIT)
         # Add all menus to menubar
         self.Append(file_menu, _("File"))
         self.Append(file_edit, _("Edit"))
+        self.Append(tools_menu, _(u"Tools"))
         #self.Append(view_menu, "View")
         #self.Append(tools_menu, "Tools")
         self.Append(options_menu, _("Options"))
@@ -716,6 +735,20 @@ class MenuBar(wx.MenuBar):
             self.FindItemById(wx.ID_REDO).Enable(True)
         else:
             self.FindItemById(wx.ID_REDO).Enable(False)
+
+    def OnAddMask(self, pubsub_evt):
+        self.num_masks += 1
+        self.bool_op_menu.Enable(self.num_masks >= 2)
+
+    def OnRemoveMasks(self, pubsub_evt):
+        self.num_masks -= len(pubsub_evt.data)
+        self.bool_op_menu.Enable(self.num_masks >= 2)
+
+    def OnShowMask(self, pubsub_evt):
+        index, value = pubsub_evt.data
+        self.clean_mask_menu.Enable(value)
+
+
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
@@ -682,7 +682,7 @@ class EditionTools(wx.Panel):
         spin_brush_size = wx.SpinCtrl(self, -1, "", size=(width + 20, -1))
         spin_brush_size.SetRange(1,100)
         spin_brush_size.SetValue(const.BRUSH_SIZE)
-        spin_brush_size.Bind(wx.EVT_TEXT, self.OnBrushSize)
+        spin_brush_size.Bind(wx.EVT_SPINCTRL, self.OnBrushSize)
         self.spin = spin_brush_size
         combo_brush_op = wx.ComboBox(self, -1, "", size=(15,-1),
@@ -740,6 +740,7 @@ class EditionTools(wx.Panel):
                                         'Update threshold limits')
         Publisher.subscribe(self.ChangeMaskColour, 'Change mask colour')
         Publisher.subscribe(self.SetGradientColour, 'Add mask')
+        Publisher.subscribe(self._set_brush_size, 'Set edition brush size')
     def ChangeMaskColour(self, pubsub_evt):
         colour = pubsub_evt.data
@@ -792,6 +793,10 @@ class EditionTools(wx.Panel):
         # Strangelly this is being called twice
         Publisher.sendMessage('Set edition brush size',self.spin.GetValue())
+    def _set_brush_size(self, pubsub_evt):
+        size = pubsub_evt.data
+        self.spin.SetValue(size)
+
     def OnComboBrushOp(self, evt):
         brush_op_id = evt.GetSelection()
         Publisher.sendMessage('Set edition operation', brush_op_id)
@@ -837,7 +842,7 @@ class WatershedTool(EditionTools):
         spin_brush_size = wx.SpinCtrl(self, -1, "", size=(width + 20, -1))
         spin_brush_size.SetRange(1,100)
         spin_brush_size.SetValue(const.BRUSH_SIZE)
-        spin_brush_size.Bind(wx.EVT_TEXT, self.OnBrushSize)
+        spin_brush_size.Bind(wx.EVT_SPINCTRL, self.OnBrushSize)
         self.spin = spin_brush_size
         combo_brush_op = wx.ComboBox(self, -1, "", size=(15,-1),
@@ -897,6 +902,7 @@ class WatershedTool(EditionTools):
         self.SetAutoLayout(1)
         self.__bind_events_wx()
+        self.__bind_pubsub_evt()
     def __bind_events_wx(self):
@@ -907,6 +913,9 @@ class WatershedTool(EditionTools):
         self.btn_exp_watershed.Bind(wx.EVT_BUTTON, self.OnExpandWatershed)
         self.btn_wconfig.Bind(wx.EVT_BUTTON, self.OnConfig)
+    def __bind_pubsub_evt(self):
+        Publisher.subscribe(self._set_brush_size, 'Set watershed brush size')
+
     def ChangeMaskColour(self, pubsub_evt):
         colour = pubsub_evt.data
         self.gradient_thresh.SetColour(colour)
@@ -951,6 +960,10 @@ class WatershedTool(EditionTools):
         # Strangelly this is being called twice
         Publisher.sendMessage('Set watershed brush size',self.spin.GetValue())
+    def _set_brush_size(self, pubsub_evt):
+        size = pubsub_evt.data
+        self.spin.SetValue(size)
+
     def OnComboBrushOp(self, evt):
         brush_op = self.combo_brush_op.GetValue()
         Publisher.sendMessage('Set watershed operation', brush_op)
@@ -964,7 +977,9 @@ class WatershedTool(EditionTools):
         Publisher.sendMessage('Set use ww wl', value)
     def OnConfig(self, evt):
-        dlg.WatershedOptionsDialog().Show()
+        from data.styles import WatershedConfig
+        config = WatershedConfig()
+        dlg.WatershedOptionsDialog(config).Show()
     def OnExpandWatershed(self, evt):
         Publisher.sendMessage('Expand watershed to 3D AXIAL')
@@ -400,15 +400,14 @@ class SurfaceProperties(wx.Panel):
         default_colour = wx.SystemSettings_GetColour(wx.SYS_COLOUR_MENUBAR)
         self.SetBackgroundColour(default_colour)
-        self.surface_dict = utl.TwoWaysDictionary()
+        self.surface_list = []
         ## LINE 1
         # Combo related to mask naem
-        combo_surface_name = wx.ComboBox(self, -1, "", choices=
-                                         self.surface_dict.keys() or ["", ],
+        combo_surface_name = wx.ComboBox(self, -1,
                                      style=wx.CB_DROPDOWN|wx.CB_READONLY)
-        combo_surface_name.SetSelection(0)
+        #combo_surface_name.SetSelection(0)
         if sys.platform != 'win32':
             combo_surface_name.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
         combo_surface_name.Bind(wx.EVT_COMBOBOX, self.OnComboName)
@@ -476,20 +475,23 @@ class SurfaceProperties(wx.Panel):
     def OnRemoveSurfaces(self, pubsub_evt):
         list_index = pubsub_evt.data
-        old_dict = self.surface_dict
-        new_dict = utl.TwoWaysDictionary()
-        for index in list_index:
-            self.combo_surface_name.Delete(index)
-
-            for name in old_dict:
-                if old_dict[name] < index:
-                    new_dict[name] = old_dict[name]
-                if old_dict[name] > index:
-                    new_dict[name] = old_dict[name] -1
-            old_dict = new_dict
-        self.surface_dict = new_dict
-
-
+        old_dict = self.surface_list
+        new_dict = []
+        i = 0
+        for n, (name, index) in enumerate(old_dict):
+            if n not in list_index:
+                new_dict.append([name, i])
+                i+=1
+        self.surface_list = new_dict
+
+        s = self.combo_surface_name.GetSelection()
+        self.combo_surface_name.SetItems([n[0] for n in self.surface_list])
+
+        if self.surface_list:
+            if s in list_index:
+                self.combo_surface_name.SetSelection(0)
+            else:
+                self.combo_surface_name.SetSelection(s)
     def OnCloseProject(self, pubsub_evt):
         self.CloseProject()
@@ -501,32 +503,39 @@ class SurfaceProperties(wx.Panel):
     def ChangeSurfaceName(self, pubsub_evt):
         index, name = pubsub_evt.data
-        old_name = self.surface_dict.get_key(index)
-        self.surface_dict.remove(old_name)
-        self.surface_dict[name] = index
+        self.surface_list[index][0] = name
         self.combo_surface_name.SetString(index, name)
-        self.combo_surface_name.Refresh()
     def InsertNewSurface(self, pubsub_evt):
         #not_update = len(pubsub_evt.data) == 5
         index = pubsub_evt.data[0]
         name = pubsub_evt.data[1]
         colour = [value*255 for value in pubsub_evt.data[2]]
-        overwrite = name in self.surface_dict.keys()
-        #if index not in self.surface_dict.values():
-        if not overwrite or not self.surface_dict:
-            self.surface_dict[name] = index
-            index = self.combo_surface_name.Append(name)
+        i = 0
+        print name, index, self.surface_list
+        try:
+            i = self.surface_list.index([name, index])
+            overwrite = True
+        except ValueError:
+            overwrite = False
+
+        if overwrite:
+            self.surface_list[i] = [name, index]
+        else:
+            self.surface_list.append([name, index])
+            i = len(self.surface_list) - 1
+
+        self.combo_surface_name.SetItems([n[0] for n in self.surface_list])
+        self.combo_surface_name.SetSelection(i)
         transparency = 100*pubsub_evt.data[4]
         self.button_colour.SetColour(colour)
         self.slider_transparency.SetValue(transparency)
-        self.combo_surface_name.SetSelection(index)
         Publisher.sendMessage('Update surface data', (index))
     def OnComboName(self, evt):
         surface_name = evt.GetString()
         surface_index = evt.GetSelection()
-        Publisher.sendMessage('Change surface selected', surface_index)
+        Publisher.sendMessage('Change surface selected', self.surface_list[surface_index][1])
     def OnSelectColour(self, evt):
         colour = [value/255.0 for value in evt.GetValue()]
	@@ -285,6 +285,12 @@ class Mask():		@@ -285,6 +285,12 @@ class Mask():
285	shape = shape[0] + 1, shape[1] + 1, shape[2] + 1	285	shape = shape[0] + 1, shape[1] + 1, shape[2] + 1
286	self.matrix = numpy.memmap(self.temp_file, mode='w+', dtype='uint8', shape=shape)	286	self.matrix = numpy.memmap(self.temp_file, mode='w+', dtype='uint8', shape=shape)
287		287
		288	+ def clean(self):
		289	+ self.matrix[1:, 1:, 1:] = 0
		290	+ self.matrix[0, :, :] = 1
		291	+ self.matrix[:, 0, :] = 1
		292	+ self.matrix[:, :, 0] = 1
		293	+
288	def copy(self, copy_name):	294	def copy(self, copy_name):
289	"""	295	"""
290	creates and return a copy from the mask instance.	296	creates and return a copy from the mask instance.
	@@ -62,6 +62,7 @@ class ContourMIPConfig(wx.Panel):		@@ -62,6 +62,7 @@ class ContourMIPConfig(wx.Panel):
62	wx.Panel.__init__(self, prnt)	62	wx.Panel.__init__(self, prnt)
63	self.mip_size_spin = wx.SpinCtrl(self, -1, min=1, max=240,	63	self.mip_size_spin = wx.SpinCtrl(self, -1, min=1, max=240,
64	initial=const.PROJECTION_MIP_SIZE)	64	initial=const.PROJECTION_MIP_SIZE)
		65	+ self.mip_size_spin.SetValue(const.PROJECTION_MIP_SIZE)
65	self.mip_size_spin.SetToolTip(wx.ToolTip(_("Number of slices used to compound the visualization.")))	66	self.mip_size_spin.SetToolTip(wx.ToolTip(_("Number of slices used to compound the visualization.")))
66	w, h = self.mip_size_spin.GetTextExtent('M')	67	w, h = self.mip_size_spin.GetTextExtent('M')
67	self.mip_size_spin.SetMinSize((5 * w + 10, -1))	68	self.mip_size_spin.SetMinSize((5 * w + 10, -1))
	@@ -525,12 +526,6 @@ class Viewer(wx.Panel):		@@ -525,12 +526,6 @@ class Viewer(wx.Panel):
525	ren.GetActiveCamera().Zoom(1.0)	526	ren.GetActiveCamera().Zoom(1.0)
526	self.interactor.Render()	527	self.interactor.Render()
527		528
528	- def ChangeBrushSize(self, pubsub_evt):
529	- size = pubsub_evt.data
530	- self._brush_cursor_size = size
531	- #for slice_data in self.slice_data_list:
532	- self.slice_data.cursor.SetSize(size)
533	-
534	def ChangeBrushColour(self, pubsub_evt):	529	def ChangeBrushColour(self, pubsub_evt):
535	vtk_colour = pubsub_evt.data[3]	530	vtk_colour = pubsub_evt.data[3]
536	self._brush_cursor_colour = vtk_colour	531	self._brush_cursor_colour = vtk_colour
	@@ -545,27 +540,6 @@ class Viewer(wx.Panel):		@@ -545,27 +540,6 @@ class Viewer(wx.Panel):
545	if self.slice_data.cursor:	540	if self.slice_data.cursor:
546	self.slice_data.cursor.SetColour(colour_vtk)	541	self.slice_data.cursor.SetColour(colour_vtk)
547		542
548	- def ChangeBrushActor(self, pubsub_evt):
549	- brush_type = pubsub_evt.data
550	- slice_data = self.slice_data
551	- self._brush_cursor_type = brush_type
552	-
553	- if brush_type == const.BRUSH_SQUARE:
554	- cursor = ca.CursorRectangle()
555	- elif brush_type == const.BRUSH_CIRCLE:
556	- cursor = ca.CursorCircle()
557	-
558	- cursor.SetOrientation(self.orientation)
559	- coordinates = {"SAGITAL": [slice_data.number, 0, 0],
560	- "CORONAL": [0, slice_data.number, 0],
561	- "AXIAL": [0, 0, slice_data.number]}
562	- cursor.SetPosition(coordinates[self.orientation])
563	- cursor.SetSpacing(self.slice_.spacing)
564	- cursor.SetColour(self._brush_cursor_colour)
565	- cursor.SetSize(self._brush_cursor_size)
566	- slice_data.SetCursor(cursor)
567	- self.interactor.Render()
568	-
569	def Navigation(self, pubsub_evt):	543	def Navigation(self, pubsub_evt):
570	# Get point from base change	544	# Get point from base change
571	x, y, z = pubsub_evt.data	545	x, y, z = pubsub_evt.data
	@@ -700,14 +674,8 @@ class Viewer(wx.Panel):		@@ -700,14 +674,8 @@ class Viewer(wx.Panel):
700	Publisher.subscribe(self.Navigation,	674	Publisher.subscribe(self.Navigation,
701	'Co-registered Points')	675	'Co-registered Points')
702	###	676	###
703	- Publisher.subscribe(self.ChangeBrushSize,
704	- 'Set edition brush size')
705	Publisher.subscribe(self.ChangeBrushColour,	677	Publisher.subscribe(self.ChangeBrushColour,
706	'Add mask')	678	'Add mask')
707	- Publisher.subscribe(self.ChangeBrushActor,
708	- 'Set brush format')
709	- Publisher.subscribe(self.ChangeBrushOperation,
710	- 'Set edition operation')
711		679
712	Publisher.subscribe(self.UpdateWindowLevelValue,	680	Publisher.subscribe(self.UpdateWindowLevelValue,
713	'Update window level value')	681	'Update window level value')
	@@ -833,9 +801,6 @@ class Viewer(wx.Panel):		@@ -833,9 +801,6 @@ class Viewer(wx.Panel):
833	if (state != const.SLICE_STATE_EDITOR):	801	if (state != const.SLICE_STATE_EDITOR):
834	Publisher.sendMessage('Set interactor default cursor')	802	Publisher.sendMessage('Set interactor default cursor')
835		803
836	- def ChangeBrushOperation(self, pubsub_evt):
837	- self._brush_cursor_op = pubsub_evt.data
838	-
839	def __bind_events_wx(self):	804	def __bind_events_wx(self):
840	self.scroll.Bind(wx.EVT_SCROLL, self.OnScrollBar)	805	self.scroll.Bind(wx.EVT_SCROLL, self.OnScrollBar)
841	self.scroll.Bind(wx.EVT_SCROLL_THUMBTRACK, self.OnScrollBarRelease)	806	self.scroll.Bind(wx.EVT_SCROLL_THUMBTRACK, self.OnScrollBarRelease)