Merge branch 'master' into icp

rmatsuda
2 parents 78c5f802 d498a62e
Showing 113 changed files with 355 additions and 317 deletions Show diff stats
app.py
icons/3D_glasses_original.png
icons/be.bmp
icons/be.png
icons/brush_circle.jpg
icons/brush_circle.png
icons/brush_square.jpg
icons/brush_square.png
icons/ca.bmp
icons/ca.png
icons/cross_original.png
icons/cs.bmp
icons/cs.png
icons/de_DE.bmp
icons/de_DE.png
icons/el_GR.bmp
icons/el_GR.png
icons/en.bmp
icons/en.png
icons/es.bmp
@@ -40,7 +40,11 @@ if sys.platform == &#39;win32&#39;:
         #  #wxversion.ensureMinimal('2.8-unicode', optionsRequired=True)
         #  #wxversion.select('2.8-unicode', optionsRequired=True)
         #  #  wxversion.ensureMinimal('4.0')
-        
+
+# Forcing to use X11, OpenGL in wxPython doesn't work with Wayland.
+if sys.platform not in ("win32", "darwin"):
+    os.environ["GDK_BACKEND"] = "x11"
+
 import wx
 try:
     from wx.adv import SplashScreen
@@ -98,7 +102,7 @@ class InVesalius(wx.App):
         """
         Initialize splash screen and main frame.
         """
-        
+
         from multiprocessing import freeze_support
         freeze_support()
  
@@ -179,18 +183,18 @@ class Inv3SplashScreen(SplashScreen):
  
         #  session.SaveConfigFileBackup()
  
-           
+
         # Only after language was defined, splash screen will be
         # shown
         if lang:
-            
+
             #import locale
             #try:
             #    locale.setlocale(locale.LC_ALL, '')
             #except locale.Error:
             #    pass
-            
-            
+
+
             # For pt_BR, splash_pt.png should be used
             if (lang.startswith('pt')):
                 icon_file = "splash_pt.png"
@@ -202,13 +206,13 @@ class Inv3SplashScreen(SplashScreen):
                 abs_file_path = os.path.abspath(".." + os.sep)
                 path = abs_file_path
                 path = os.path.join(path, 'icons', icon_file)
-            
+
             else:
  
                 path = os.path.join(".","icons", icon_file)
                 if not os.path.exists(path):
                     path = os.path.join(".", "icons", "splash_en.png")
-				
+
             bmp = wx.Image(path).ConvertToBitmap()
  
             try:
@@ -232,10 +236,10 @@ class Inv3SplashScreen(SplashScreen):
         from invesalius.gui.frame import Frame
         from invesalius.control import Controller
         from invesalius.project import Project
-        
+
         self.main = Frame(None)
         self.control = Controller(self.main)
-        
+
         self.fc = wx.CallLater(200, self.ShowMain)
         options, args = parse_comand_line()
         wx.CallLater(1, use_cmd_optargs, options, args)
@@ -498,7 +502,7 @@ def main():
 if __name__ == '__main__':
     #Is needed because of pyinstaller
     multiprocessing.freeze_support()
-    
+
     #Needed in win 32 exe
     if hasattr(sys,"frozen") and sys.platform.startswith('win'):
  
@@ -523,4 +527,3 @@ if __name__ == &#39;__main__&#39;:
  
     # Init application
     main()
-
@@ -500,34 +500,6 @@ def img2memmap(group):
     return matrix, scalar_range, temp_file
  
  
-def imgnormalize(data, srange=(0, 255)):
-    """
-    Normalize image pixel intensity for int16 gray scale values.
-
-    :param data: image matrix
-    :param srange: range for normalization, default is 0 to 255
-    :return: normalized pixel intensity matrix
-    """
-
-    dataf = numpy.asarray(data)
-    rangef = numpy.asarray(srange)
-    faux = numpy.ravel(dataf).astype(float)
-    minimum = numpy.min(faux)
-    maximum = numpy.max(faux)
-    lower = rangef[0]
-    upper = rangef[1]
-
-    if minimum == maximum:
-        datan = numpy.ones(dataf.shape)*(upper + lower) / 2.
-    else:
-        datan = (faux-minimum)*(upper-lower) / (maximum-minimum) + lower
-
-    datan = numpy.reshape(datan, dataf.shape)
-    datan = datan.astype(numpy.int16)
-
-    return datan
-
-
 def get_LUT_value_255(data, window, level):
     shape = data.shape
     data_ = data.ravel()
@@ -539,6 +511,8 @@ def get_LUT_value_255(data, window, level):
     return data
  
  
-def image_normalize(image, min_=0.0, max_=1.0):
+def image_normalize(image, min_=0.0, max_=1.0, output_dtype=np.int16):
+    output = np.empty(shape=image.shape, dtype=output_dtype)
     imin, imax = image.min(), image.max()
-    return (image - imin) * ((max_ - min_) / (imax - imin)) + min_
+    output[:] = (image - imin) * ((max_ - min_) / (imax - imin)) + min_
+    return output
@@ -301,7 +301,10 @@ class Slice(metaclass=utils.Singleton):
  
         for name in self.aux_matrices:
             m = self.aux_matrices[name]
-            f = m.filename
+            try:
+                f = m.filename
+            except AttributeError:
+                continue
             m._mmap.close()
             m = None
             os.remove(f)
@@ -347,6 +350,8 @@ class Slice(metaclass=utils.Singleton):
             self.SetMaskEditionThreshold(index, threshold_range)
  
     def __set_current_mask_threshold(self, threshold_range):
+        if self.current_mask is None:
+            return
         index = self.current_mask.index
         self.num_gradient += 1
         self.current_mask.matrix[:] = 0
@@ -387,6 +392,8 @@ class Slice(metaclass=utils.Singleton):
             Publisher.sendMessage("Reload actual slice")
  
     def __set_current_mask_threshold_actual_slice(self, threshold_range):
+        if self.current_mask is None:
+            return
         index = self.current_mask.index
         for orientation in self.buffer_slices:
             self.buffer_slices[orientation].discard_vtk_mask()
@@ -624,7 +631,7 @@ class Slice(metaclass=utils.Singleton):
             self.buffer_slices[orientation].vtk_image = image
             self.buffer_slices[orientation].vtk_mask = mask
  
-        if self.to_show_aux == "watershed" and self.current_mask.is_shown:
+        if self.to_show_aux == "watershed" and self.current_mask is not None and self.current_mask.is_shown:
             m = self.get_aux_slice("watershed", orientation, slice_number)
             tmp_vimage = converters.to_vtk(m, self.spacing, slice_number, orientation)
             cimage = self.do_custom_colour(
@@ -102,13 +102,13 @@ class ContourMIPConfig(wx.Panel):
         self.txt_mip_border = wx.StaticText(self, -1, _("Sharpness"))
  
         sizer = wx.BoxSizer(wx.HORIZONTAL)
-        sizer.Add(txt_mip_size, 0, wx.EXPAND | wx.ALL, 2)
+        sizer.Add(txt_mip_size, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 2)
         sizer.Add(self.mip_size_spin, 0)
         try:
             sizer.Add(10, 0)
         except TypeError:
             sizer.Add((10, 0))
-        sizer.Add(self.txt_mip_border, 0, wx.EXPAND | wx.ALL, 2)
+        sizer.Add(self.txt_mip_border, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 2)
         sizer.Add(self.border_spin, 0, wx.EXPAND)
         try:
             sizer.Add(10, 0)
@@ -1438,8 +1438,12 @@ class Viewer(wx.Panel):
             index = max_slice_number - 1
         inverted = self.mip_ctrls.inverted.GetValue()
         border_size = self.mip_ctrls.border_spin.GetValue()
-        image = self.slice_.GetSlices(self.orientation, index,
-                                      self.number_slices, inverted, border_size)
+        try:
+            image = self.slice_.GetSlices(self.orientation, index,
+                                          self.number_slices, inverted,
+                                          border_size)
+        except IndexError:
+            return
         self.slice_data.actor.SetInputData(image)
         for actor in self.actors_by_slice_number[self.slice_data.number]:
             self.slice_data.renderer.RemoveActor(actor)
@@ -81,6 +81,8 @@ class BrainSegmenterDialog(wx.Dialog):
         self.txt_threshold.SetMinClientSize((w, -1))
         self.chk_new_mask = wx.CheckBox(self, wx.ID_ANY, _("Create new mask"))
         self.chk_new_mask.SetValue(True)
+        self.chk_apply_wwwl = wx.CheckBox(self, wx.ID_ANY, _("Apply WW&WL"))
+        self.chk_apply_wwwl.SetValue(False)
         self.progress = wx.Gauge(self, -1)
         self.lbl_progress_caption = wx.StaticText(self, -1, _("Elapsed time:"))
         self.lbl_time = wx.StaticText(self, -1, _("00:00:00"))
@@ -115,11 +117,12 @@ class BrainSegmenterDialog(wx.Dialog):
         sizer_3.Add(
             self.sld_threshold,
             1,
-            wx.ALIGN_CENTER | wx.BOTTOM | wx.EXPAND | wx.LEFT | wx.RIGHT,
+            wx.BOTTOM | wx.EXPAND | wx.LEFT | wx.RIGHT,
             5,
         )
         sizer_3.Add(self.txt_threshold, 0, wx.ALL, 5)
         main_sizer.Add(sizer_3, 0, wx.EXPAND, 0)
+        main_sizer.Add(self.chk_apply_wwwl, 0, wx.EXPAND | wx.ALL, 5)
         main_sizer.Add(self.chk_new_mask, 0, wx.EXPAND | wx.ALL, 5)
         main_sizer.Add(self.progress, 0, wx.EXPAND | wx.ALL, 5)
         time_sizer = wx.BoxSizer(wx.HORIZONTAL)
@@ -128,15 +131,15 @@ class BrainSegmenterDialog(wx.Dialog):
         main_sizer.Add(time_sizer, 0, wx.EXPAND | wx.ALL, 5)
         sizer_buttons = wx.BoxSizer(wx.HORIZONTAL)
         sizer_buttons.Add(
-            self.btn_close, 0, wx.ALIGN_BOTTOM | wx.ALIGN_RIGHT | wx.ALL, 5
+            self.btn_close, 0, wx.ALIGN_BOTTOM | wx.ALL, 5
         )
         sizer_buttons.Add(
-            self.btn_stop, 0, wx.ALIGN_BOTTOM | wx.ALIGN_RIGHT | wx.ALL, 5
+            self.btn_stop, 0, wx.ALIGN_BOTTOM | wx.ALL, 5
         )
         sizer_buttons.Add(
-            self.btn_segment, 0, wx.ALIGN_BOTTOM | wx.ALIGN_RIGHT | wx.ALL, 5
+            self.btn_segment, 0, wx.ALIGN_BOTTOM | wx.ALL, 5
         )
-        main_sizer.Add(sizer_buttons, 0, wx.ALIGN_BOTTOM | wx.ALIGN_RIGHT | wx.ALL, 0)
+        main_sizer.Add(sizer_buttons, 0, wx.ALIGN_RIGHT | wx.ALL, 0)
         self.SetSizer(main_sizer)
         main_sizer.Fit(self)
         main_sizer.SetSizeHints(self)
@@ -216,6 +219,7 @@ class BrainSegmenterDialog(wx.Dialog):
             device_id = self.plaidml_devices[self.cb_devices.GetValue()]
         except (KeyError, AttributeError):
             device_id = "llvm_cpu.0"
+        apply_wwwl = self.chk_apply_wwwl.GetValue()
         create_new_mask = self.chk_new_mask.GetValue()
         use_gpu = self.chk_use_gpu.GetValue()
         prob_threshold = self.sld_threshold.GetValue() / 100.0
@@ -224,8 +228,11 @@ class BrainSegmenterDialog(wx.Dialog):
         self.btn_segment.Disable()
         self.chk_new_mask.Disable()
  
+        window_width = slc.Slice().window_width
+        window_level = slc.Slice().window_level
+
         try:
-            self.ps = segment.SegmentProcess(image, create_new_mask, backend, device_id, use_gpu)
+            self.ps = segment.SegmentProcess(image, create_new_mask, backend, device_id, use_gpu, apply_wwwl, window_width, window_level)
             self.ps.start()
         except (multiprocessing.ProcessError, OSError, ValueError) as err:
             self.OnStop(None)
@@ -351,18 +351,89 @@ class ButtonControlPanel(wx.Panel):
         else:
            dlg.MaskSelectionRequiredForDuplication()
  
-class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
  
+class InvListCtrl(wx.ListCtrl):
     def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
-                 size=wx.DefaultSize, style=wx.LC_REPORT):
+                 size=wx.DefaultSize, style=wx.LC_REPORT | wx.LC_EDIT_LABELS):
+        wx.ListCtrl.__init__(self, parent, ID, pos, size, style=style)
+        self.__bind_events_wx()
  
-        # native look and feel for MacOS
-        #if wx.Platform == "__WXMAC__":
-        #    wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
+    def __bind_events_wx(self):
+        self.Bind(wx.EVT_LEFT_DOWN, self.OnClickItem)
+        self.Bind(wx.EVT_LEFT_DCLICK, self.OnDblClickItem)
+
+    def CreateColourBitmap(self, colour):
+        """
+        Create a wx Image with a mask colour.
+        colour: colour in rgb format(0 - 1)
+        """
+        image = self.image_gray
+        new_image = Image.new("RGB", image.size)
+        for x in range(image.size[0]):
+            for y in range(image.size[1]):
+                pixel_colour = [int(i*image.getpixel((x,y)))
+                                for i in colour]
+                new_image.putpixel((x,y), tuple(pixel_colour))
+
+        wx_image = wx.Image(new_image.size[0],
+                            new_image.size[1])
+        try:
+            wx_image.SetData(new_image.tostring())
+        except Exception:
+            wx_image.SetData(new_image.tobytes())
+        return wx.Bitmap(wx_image.Scale(16, 16))
+
+    def OnClickItem(self, evt):
+        self._click_check = False
+        item_idx, flag = (self.HitTest(evt.GetPosition()))
+        if item_idx > -1:
+            column_clicked = self.get_column_clicked(evt.GetPosition())
+            if column_clicked == 0:
+                self._click_check = True
+                item = self.GetItem(item_idx, 0)
+                flag = not bool(item.GetImage())
+                self.SetItemImage(item_idx, int(flag))
+                self.OnCheckItem(item_idx, flag)
+                return
+        evt.Skip()
  
-        wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
-        listmix.TextEditMixin.__init__(self)
-        listmix.CheckListCtrlMixin.__init__(self)
+    def OnDblClickItem(self, evt):
+        self._click_check = False
+        item_idx, flag = (self.HitTest(evt.GetPosition()))
+        if item_idx > -1:
+            column_clicked = self.get_column_clicked(evt.GetPosition())
+            if column_clicked == 1:
+                item = self.GetItem(item_idx, 1)
+                self.enter_edition(item)
+                return
+        evt.Skip()
+
+    def enter_edition(self, item):
+        ctrl = self.EditLabel(item.GetId())
+        w, h = ctrl.GetClientSize()
+        w = self.GetColumnWidth(1)
+        ctrl.SetClientSize(w, h)
+        ctrl.SetValue(item.GetText())
+        ctrl.SelectAll()
+
+
+    def get_column_clicked(self, position):
+        epx, epy = position
+        wpx, wpy = self.GetPosition()
+        width_sum = 0
+        for i in range(self.GetColumnCount()):
+            width_sum += self.GetColumnWidth(i)
+            if (epx - wpx) <= width_sum:
+                return i
+        return -1
+
+
+
+class MasksListCtrlPanel(InvListCtrl):
+    def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
+                 size=wx.DefaultSize, style=wx.LC_REPORT | wx.LC_EDIT_LABELS):
+        super().__init__(parent, ID, pos, size, style=style)
+        self._click_check = False
         self.mask_list_index = {}
         self.current_index = 0
         self.__init_columns()
@@ -371,12 +442,9 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
         self.__bind_events()
  
     def __bind_events_wx(self):
-        self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)
-        self.Bind(wx.EVT_LIST_BEGIN_LABEL_EDIT, self.OnBeginLabelEdit)
         self.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnEditLabel)
         self.Bind(wx.EVT_KEY_UP, self.OnKeyEvent)
  
-
     def __bind_events(self):
         Publisher.subscribe(self.AddMask, 'Add mask')
         Publisher.subscribe(self.EditMaskThreshold,
@@ -438,7 +506,6 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
                 self.current_index -= 1
                 self.SetItemImage(self.current_index, 1)
  
-
     def OnCloseProject(self):
         self.DeleteAllItems()
         self.mask_list_index = {}
@@ -475,13 +542,13 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
     def __init_image_list(self):
         self.imagelist = wx.ImageList(16, 16)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
         img_null = self.imagelist.Add(bitmap)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
@@ -489,23 +556,16 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
  
         self.SetImageList(self.imagelist,wx.IMAGE_LIST_SMALL)
  
-        self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
-
-    def OnBeginLabelEdit(self, evt):
-        if evt.GetColumn() == 1:
-            evt.Skip()
-        else:
-            evt.Veto()
+        self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
  
     def OnEditLabel(self, evt):
-        Publisher.sendMessage('Change mask name',
-                              index=evt.GetIndex(), name=evt.GetLabel())
+        if not evt.IsEditCancelled():
+            index = evt.GetIndex()
+            self.SetItem(index, 1, evt.GetLabel())
+            Publisher.sendMessage('Change mask name',
+                                  index=evt.GetIndex(), name=evt.GetLabel())
         evt.Skip()
  
-    def OnItemActivated(self, evt):
-        self.ToggleItem(evt.Index)
-        #  pass
-
     def OnCheckItem(self, index, flag):
         if flag:
             for key in self.mask_list_index.keys():
@@ -515,26 +575,7 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
             self.current_index = index
         Publisher.sendMessage('Show mask', index=index, value=flag)
  
-    def CreateColourBitmap(self, colour):
-        """
-        Create a wx Image with a mask colour.
-        colour: colour in rgb format(0 - 1)
-        """
-        image = self.image_gray
-        new_image = Image.new("RGB", image.size)
-        for x in range(image.size[0]):
-            for y in range(image.size[1]):
-                pixel_colour = [int(i*image.getpixel((x,y)))
-                                for i in colour]
-                new_image.putpixel((x,y), tuple(pixel_colour))
  
-        wx_image = wx.Image(new_image.size[0],
-                            new_image.size[1])
-        try:
-            wx_image.SetData(new_image.tostring())
-        except Exception:
-            wx_image.SetData(new_image.tobytes())
-        return wx.Bitmap(wx_image.Scale(16, 16))
  
     def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)",
                       colour=None):
@@ -718,19 +759,11 @@ class SurfaceButtonControlPanel(wx.Panel):
     def AffineStatus(self, affine, status):
         self.affinestatus = status
  
-class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
-
+class SurfacesListCtrlPanel(InvListCtrl):
     def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
-                 size=wx.DefaultSize, style=wx.LC_REPORT):
-
-        # native look and feel for MacOS
-        #if wx.Platform == "__WXMAC__":
-        #    wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
-
-        wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
-        listmix.TextEditMixin.__init__(self)
-        listmix.CheckListCtrlMixin.__init__(self)
-
+                 size=wx.DefaultSize, style=wx.LC_REPORT | wx.LC_EDIT_LABELS):
+        super().__init__(parent, ID, pos, size, style=style)
+        self._click_check = False
         self.__init_columns()
         self.__init_image_list()
         self.__init_evt()
@@ -752,8 +785,6 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
         Publisher.subscribe(self.OnShowMultiple, 'Show multiple surfaces')
  
     def __bind_events_wx(self):
-        self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)
-        self.Bind(wx.EVT_LIST_BEGIN_LABEL_EDIT, self.OnBeginLabelEdit)
         self.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnEditLabel)
         #self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected_)
         self.Bind(wx.EVT_KEY_UP, self.OnKeyEvent)
@@ -841,13 +872,13 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
     def __init_image_list(self):
         self.imagelist = wx.ImageList(16, 16)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
         img_null = self.imagelist.Add(bitmap)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
@@ -855,7 +886,7 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
  
         self.SetImageList(self.imagelist,wx.IMAGE_LIST_SMALL)
  
-        self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
+        self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
  
     def OnBeginLabelEdit(self, evt):
         if evt.GetColumn() == 1:
@@ -864,11 +895,10 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
             evt.Veto()
  
     def OnEditLabel(self, evt):
-        Publisher.sendMessage('Change surface name', index=evt.GetIndex(), name=evt.GetLabel())
-        evt.Skip()
-
-    def OnItemActivated(self, evt):
-        self.ToggleItem(evt.Index)
+        if not evt.IsEditCancelled():
+            index = evt.GetIndex()
+            self.SetItem(index, 1, evt.GetLabel())
+            Publisher.sendMessage('Change surface name', index=evt.GetIndex(), name=evt.GetLabel())
         evt.Skip()
  
     def OnCheckItem(self, index, flag):
@@ -944,28 +974,6 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
         self.SetItem(index, 4, transparency)
         self.SetItemImage(index, 1)
  
-    def CreateColourBitmap(self, colour):
-        """
-        Create a wx Image with a mask colour.
-        colour: colour in rgb format(0 - 1)
-        """
-        image = self.image_gray
-        new_image = Image.new("RGB", image.size)
-        for x in range(image.size[0]):
-            for y in range(image.size[1]):
-                pixel_colour = [int(i*image.getpixel((x,y)))
-                                for i in colour]
-                new_image.putpixel((x,y), tuple(pixel_colour))
-
-        wx_image = wx.Image(new_image.size[0],
-                            new_image.size[1])
-        try:
-            wx_image.SetData(new_image.tostring())
-        except Exception:
-            wx_image.SetData(new_image.tobytes())
-
-        return wx.Bitmap(wx_image.Scale(16, 16))
-
     def EditSurfaceTransparency(self, surface_index, transparency):
         """
         Set actor transparency (oposite to opacity) according to given actor
@@ -985,19 +993,11 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
 #-------------------------------------------------
 #-------------------------------------------------
  
-class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
-
+class MeasuresListCtrlPanel(InvListCtrl):
     def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
-                 size=wx.DefaultSize, style=wx.LC_REPORT):
-
-        # native look and feel for MacOS
-        #if wx.Platform == "__WXMAC__":
-        #    wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
-
-        wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
-        listmix.TextEditMixin.__init__(self)
-        listmix.CheckListCtrlMixin.__init__(self)
-
+                 size=wx.DefaultSize, style=wx.LC_REPORT | wx.LC_EDIT_LABELS):
+        super().__init__(parent, ID, pos, size, style=style)
+        self._click_check = False
         self.__init_columns()
         self.__init_image_list()
         self.__init_evt()
@@ -1017,13 +1017,10 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
         Publisher.subscribe(self.OnRemoveGUIMeasure, 'Remove GUI measurement')
  
     def __bind_events_wx(self):
-        self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)
-        self.Bind(wx.EVT_LIST_BEGIN_LABEL_EDIT, self.OnBeginLabelEdit)
         self.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnEditLabel)
         self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected_)
         self.Bind(wx.EVT_KEY_UP, self.OnKeyEvent)
  
-
     def OnKeyEvent(self, event):
         keycode = event.GetKeyCode()
         # Delete key
@@ -1116,13 +1113,13 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
     def __init_image_list(self):
         self.imagelist = wx.ImageList(16, 16)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
         img_null = self.imagelist.Add(bitmap)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
@@ -1130,7 +1127,7 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
  
         self.SetImageList(self.imagelist,wx.IMAGE_LIST_SMALL)
  
-        self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
+        self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
  
     def OnBeginLabelEdit(self, evt):
         if evt.GetColumn() == 1:
@@ -1139,14 +1136,12 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
             evt.Veto()
  
     def OnEditLabel(self, evt):
-        Publisher.sendMessage('Change measurement name', index=evt.GetIndex(), name=evt.GetLabel())
+        if not evt.IsEditCancelled():
+            index = evt.GetIndex()
+            self.SetItem(index, 1, evt.GetLabel())
+            Publisher.sendMessage('Change measurement name', index=evt.GetIndex(), name=evt.GetLabel())
         evt.Skip()
  
-    def OnItemActivated(self, evt):
-        self.ToggleItem(evt.Index)
-        evt.Skip()
-
-
     def OnCheckItem(self, index, flag):
         Publisher.sendMessage('Show measurement', index=index, visibility=flag)
  
@@ -1238,27 +1233,6 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
         self.SetItemImage(index, 1)
         self.Refresh()
  
-    def CreateColourBitmap(self, colour):
-        """
-        Create a wx Image with a mask colour.
-        colour: colour in rgb format(0 - 1)
-        """
-        image = self.image_gray
-        new_image = Image.new("RGB", image.size)
-        for x in range(image.size[0]):
-            for y in range(image.size[1]):
-                pixel_colour = [int(i*image.getpixel((x,y)))
-                                for i in colour]
-                new_image.putpixel((x,y), tuple(pixel_colour))
-
-        wx_image = wx.Image(new_image.size[0],
-                            new_image.size[1])
-        try:
-            wx_image.SetData(new_image.tostring())
-        except:
-            wx_image.SetData(new_image.tobytes())
-        return wx.Bitmap(wx_image.Scale(16, 16))
-
     def EditItemColour(self, measure_index, colour):
         """
         """
@@ -1273,19 +1247,12 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
 #*******************************************************************
  
  
-class AnnotationsListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
+class AnnotationsListCtrlPanel(wx.ListCtrl):
     # TODO: Remove edimixin, allow only visible and invisible
     def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
-                 size=wx.DefaultSize, style=wx.LC_REPORT):
-
-        # native look and feel for MacOS
-        #if wx.Platform == "__WXMAC__":
-        #    wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
-
-        wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
-        listmix.TextEditMixin.__init__(self)
-        listmix.CheckListCtrlMixin.__init__(self)
-
+                 size=wx.DefaultSize, style=wx.LC_REPORT | wx.LC_EDIT_LABELS):
+        wx.ListCtrl.__init__(self, parent, ID, pos, size, style=style)
+        self._click_check = False
         self.__init_columns()
         self.__init_image_list()
         self.__init_evt()
@@ -1311,19 +1278,19 @@ class AnnotationsListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.Check
     def __init_image_list(self):
         self.imagelist = wx.ImageList(16, 16)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
         img_check = self.imagelist.Add(bitmap)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
         img_null = self.imagelist.Add(bitmap)
  
-        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
+        image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
         bitmap = wx.Bitmap(image.Scale(16, 16))
         bitmap.SetWidth(16)
         bitmap.SetHeight(16)
@@ -123,6 +123,7 @@ class Panel(wx.Panel):
  
         #self.SetSizerAndFit(sizer)
         self.SetSizer(sizer)
+        self.Layout()
  
  
 # Lower fold panel
@@ -111,7 +111,7 @@ class Panel(wx.Panel):
         p3.SetPopupMenu(menu)
  
  
-        if sys.platform == 'win32':
+        if sys.platform == 'win32' or wx.VERSION >= (4, 1):
             self.aui_manager.AddPane(p1, s1)
             self.aui_manager.AddPane(p2, s2)
             self.aui_manager.AddPane(p3, s3)
@@ -604,7 +604,7 @@ class VolumeToolPanel(wx.Panel):
         id = evt.GetId()
         item = ID_TO_ITEMSLICEMENU[id]
         checked = item.IsChecked()
-        label = item.GetLabel()
+        label = item.GetItemLabelText()
  
         if not (checked):
             Publisher.sendMessage('Disable plane', plane_label=label)
@@ -245,9 +245,7 @@ WILDCARD_OPEN = &quot;InVesalius 3 project (*.inv3)|*.inv3|&quot; \
 WILDCARD_ANALYZE = "Analyze 7.5 (*.hdr)|*.hdr|" \
                    "All files (*.*)|*.*"
  
-WILDCARD_NIFTI = "NIfTI 1 (*.nii)|*.nii|" \
-                 "Compressed NIfTI (*.nii.gz)|*.nii.gz|" \
-                 "HDR NIfTI (*.hdr)|*.hdr|" \
+WILDCARD_NIFTI = "NIfTI 1 (*.nii;*.nii.gz;*.hdr)|*.nii;*.nii.gz;*.hdr|" \
                  "All files (*.*)|*.*"
 #".[jJ][pP][gG]"
 WILDCARD_PARREC = "PAR/REC (*.par)|*.par|" \
@@ -1950,17 +1948,17 @@ class WatershedOptionsPanel(wx.Panel):
                                          min_value=1, max_value=10)
  
         box_sizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Conectivity"), wx.VERTICAL)
-        box_sizer.Add(self.choice_2dcon, 0, wx.ALIGN_CENTER_VERTICAL,2)
-        box_sizer.Add(self.choice_3dcon, 0, wx.ALIGN_CENTER_VERTICAL,2)
+        box_sizer.Add(self.choice_2dcon, 0, wx.ALL, 5)
+        box_sizer.Add(self.choice_3dcon, 0, wx.ALL, 5)
  
         g_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        g_sizer.Add(wx.StaticText(self, -1, _("Gaussian sigma")), 0, wx.ALIGN_RIGHT | wx.ALL, 5)
-        g_sizer.Add(self.gaussian_size, 0, wx.ALIGN_LEFT | wx.ALL, 5)
+        g_sizer.Add(wx.StaticText(self, -1, _("Gaussian sigma")), 0, wx.ALIGN_CENTER | wx.ALL, 5)
+        g_sizer.Add(self.gaussian_size, 0, wx.ALL, 5)
  
         sizer = wx.BoxSizer(wx.VERTICAL)
-        sizer.Add(self.choice_algorithm, 0, wx.ALIGN_CENTER_VERTICAL,2)
-        sizer.Add(box_sizer, 1, wx.EXPAND,2)
-        sizer.Add(g_sizer, 0, wx.ALIGN_LEFT, 2)
+        sizer.Add(self.choice_algorithm, 0, wx.ALL, 5)
+        sizer.Add(box_sizer, 1, wx.EXPAND | wx.ALL, 5)
+        sizer.Add(g_sizer, 0, wx.ALL, 5)
  
         self.SetSizer(sizer)
         sizer.Fit(self)
@@ -1998,8 +1996,7 @@ class WatershedOptionsDialog(wx.Dialog):
         btnsizer.Realize()
  
         sizer.Add(wop, 0, wx.EXPAND)
-        sizer.Add(btnsizer, 0, wx.EXPAND)
-        sizer.AddSpacer(5)
+        sizer.Add(btnsizer, 0, wx.ALIGN_RIGHT | wx.BOTTOM, 5)
  
         self.SetSizer(sizer)
         sizer.Fit(self)
@@ -2060,16 +2057,16 @@ class MaskBooleanDialog(wx.Dialog):
  
         gsizer = wx.FlexGridSizer(rows=3, cols=2, hgap=5, vgap=5)
  
-        gsizer.Add(wx.StaticText(self, -1, _(u"Mask 1")))
+        gsizer.Add(wx.StaticText(self, -1, _(u"Mask 1")), 0, wx.ALIGN_CENTER_VERTICAL)
         gsizer.Add(self.mask1, 1, wx.EXPAND)
-        gsizer.Add(wx.StaticText(self, -1, _(u"Operation")))
+        gsizer.Add(wx.StaticText(self, -1, _(u"Operation")), 0, wx.ALIGN_CENTER_VERTICAL)
         gsizer.Add(self.op_boolean, 1, wx.EXPAND)
-        gsizer.Add(wx.StaticText(self, -1, _(u"Mask 2")))
+        gsizer.Add(wx.StaticText(self, -1, _(u"Mask 2")), 0, wx.ALIGN_CENTER_VERTICAL)
         gsizer.Add(self.mask2, 1, wx.EXPAND)
  
         sizer = wx.BoxSizer(wx.VERTICAL)
-        sizer.Add(gsizer, 0, wx.EXPAND | wx.ALIGN_CENTER | wx.ALL, border=5)
-        sizer.Add(btnsizer, 0, wx.EXPAND | wx.ALIGN_CENTER | wx.ALL, border=5)
+        sizer.Add(gsizer, 0, wx.EXPAND | wx.ALL, border=5)
+        sizer.Add(btnsizer, 0, wx.EXPAND | wx.ALL, border=5)
  
         self.SetSizer(sizer)
         sizer.Fit(self)
@@ -2798,8 +2795,8 @@ class SelectPartsOptionsDialog(wx.Dialog):
         sizer.AddSpacer(5)
  
         btn_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        btn_sizer.Add(self.btn_ok, 0, flag=wx.ALIGN_RIGHT, border=5)
-        btn_sizer.Add(self.btn_cancel, 0, flag=wx.LEFT|wx.ALIGN_RIGHT, border=5)
+        btn_sizer.Add(self.btn_ok, 0)# flag=wx.ALIGN_RIGHT, border=5)
+        btn_sizer.Add(self.btn_cancel, 0, flag=wx.LEFT, border=5)
  
         sizer.Add(btn_sizer, 0, flag=wx.ALIGN_RIGHT|wx.LEFT|wx.RIGHT, border=5)
         sizer.AddSpacer(5)
@@ -3202,8 +3199,8 @@ class FillHolesAutoDialog(wx.Dialog):
         sizer.AddSpacer(5)
  
         btn_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        btn_sizer.Add(self.apply_btn, 0, flag=wx.ALIGN_RIGHT, border=5)
-        btn_sizer.Add(self.close_btn, 0, flag=wx.LEFT|wx.ALIGN_RIGHT, border=5)
+        btn_sizer.Add(self.apply_btn, 0)# flag=wx.ALIGN_RIGHT, border=5)
+        btn_sizer.Add(self.close_btn, 0, flag=wx.LEFT, border=5)
  
         sizer.Add(btn_sizer, 0, flag=wx.ALIGN_RIGHT|wx.LEFT|wx.RIGHT, border=5)
  
@@ -789,8 +789,8 @@ class SingleImagePreview(wx.Panel):
         in_sizer.Add(checkbox, 0)
  
         sizer = wx.BoxSizer(wx.VERTICAL)
-        sizer.Add(self.panel, 20, wx.GROW|wx.EXPAND)
-        sizer.Add(in_sizer, 1, wx.GROW|wx.EXPAND)
+        sizer.Add(self.panel, 1, wx.GROW|wx.EXPAND)
+        sizer.Add(in_sizer, 0, wx.GROW|wx.EXPAND)
         sizer.Fit(self)
  
         self.SetSizer(sizer)
@@ -214,7 +214,7 @@ class Frame(wx.Frame):
         # Add toolbars to manager
         # This is pretty tricky -- order on win32 is inverted when
         # compared to linux2 & darwin
-        if sys.platform == 'win32':
+        if sys.platform == 'win32' or wx.VERSION >= (4, 1):
             t1 = ProjectToolBar(self)
             t2 = HistoryToolBar(self)
             t3 = LayoutToolBar(self)
@@ -259,6 +259,8 @@ class Frame(wx.Frame):
         # TODO: Allow saving and restoring perspectives
         self.perspective_all = aui_manager.SavePerspective()
  
+        self.Layout()
+
     def _BeginBusyCursor(self):
         """
         Start busy cursor.
@@ -1941,11 +1943,11 @@ class LayoutToolBar(AuiToolBar):
         d = inv_paths.ICON_DIR
         if sys.platform == 'darwin':
             # Bitmaps for show/hide task panel item
-            p = os.path.join(d, "layout_data_only_original.gif")
-            self.BMP_WITH_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_GIF)
+            p = os.path.join(d, "layout_data_only_original.png")
+            self.BMP_WITH_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_PNG)
  
-            p = os.path.join(d, "layout_full_original.gif")
-            self.BMP_WITHOUT_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_GIF)
+            p = os.path.join(d, "layout_full_original.png")
+            self.BMP_WITHOUT_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_PNG)
  
             # Bitmaps for show/hide task item
             p = os.path.join(d, "text_inverted_original.png")
@@ -1956,11 +1958,11 @@ class LayoutToolBar(AuiToolBar):
  
         else:
             # Bitmaps for show/hide task panel item
-            p = os.path.join(d, "layout_data_only.gif")
-            self.BMP_WITH_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_GIF)
+            p = os.path.join(d, "layout_data_only.png")
+            self.BMP_WITH_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_PNG)
  
-            p = os.path.join(d, "layout_full.gif")
-            self.BMP_WITHOUT_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_GIF)
+            p = os.path.join(d, "layout_full.png")
+            self.BMP_WITHOUT_MENU = wx.Bitmap(str(p), wx.BITMAP_TYPE_PNG)
  
             # Bitmaps for show/hide task item
             p = os.path.join(d, "text_inverted.png")
@@ -104,7 +104,7 @@ class InnerPanel(wx.Panel):
  
         inner_sizer = wx.BoxSizer(wx.HORIZONTAL)
         inner_sizer.Add(btnsizer, 0, wx.LEFT|wx.TOP, 5)
-        inner_sizer.Add(self.combo_interval, 0, wx.LEFT|wx.RIGHT|wx.TOP, 5)
+        inner_sizer.Add(self.combo_interval, 0, wx.ALIGN_CENTER_VERTICAL|wx.LEFT|wx.RIGHT|wx.TOP, 5)
         panel.SetSizer(inner_sizer)
         inner_sizer.Fit(panel)
  
@@ -71,8 +71,8 @@ class ComboBoxLanguage:
         self.bitmapCmb = bitmapCmb = BitmapComboBox(parent, style=wx.CB_READONLY)
         for key in self.locales_key:
             # Based on composed flag filename, get bitmap
-            filepath =  os.path.join(ICON_DIR, "%s.bmp"%(key))
-            bmp = wx.Bitmap(filepath, wx.BITMAP_TYPE_BMP)
+            filepath =  os.path.join(ICON_DIR, "%s.png" % (key))
+            bmp = wx.Bitmap(filepath, wx.BITMAP_TYPE_PNG)
             # Add bitmap and info to Combo
             bitmapCmb.Append(dict_locales[key], bmp, key)
             # Set default combo item if available on the list
@@ -123,8 +123,8 @@ class LanguageDialog(wx.Dialog):
     #    self.bitmapCmb = bitmapCmb = BitmapComboBox(self, style=wx.CB_READONLY)
     #    for key in self.locales_key:
     #        # Based on composed flag filename, get bitmap
-    #        filepath =  os.path.join(ICON_DIR, "%s.bmp"%(key))
-    #        bmp = wx.Bitmap(filepath, wx.BITMAP_TYPE_BMP)
+    #        filepath =  os.path.join(ICON_DIR, "%s.png"%(key))
+    #        bmp = wx.Bitmap(filepath, wx.BITMAP_TYPE_PNG)
     #        # Add bitmap and info to Combo
     #        bitmapCmb.Append(dict_locales[key], bmp, key)
     #        # Set default combo item if available on the list
@@ -49,13 +49,13 @@ class Preferences(wx.Dialog):
         self.book.AddPage(self.pnl_language, _("Language"))
  
         line = wx.StaticLine(self, -1, size=(20, -1), style=wx.LI_HORIZONTAL)
-        sizer.Add(line, 0, wx.GROW | wx.ALIGN_CENTER_VERTICAL | wx.RIGHT | wx.TOP, 5)
+        sizer.Add(line, 0, wx.GROW | wx.RIGHT | wx.TOP, 5)
  
         btnsizer = self.CreateStdDialogButtonSizer(wx.OK | wx.CANCEL)
         sizer.Add(
             btnsizer,
             0,
-            wx.GROW | wx.ALIGN_CENTER_VERTICAL | wx.RIGHT | wx.TOP | wx.BOTTOM,
+            wx.GROW | wx.RIGHT | wx.TOP | wx.BOTTOM,
             5,
         )
  
@@ -211,7 +211,7 @@ class InnerFoldPanel(wx.Panel):
         line_sizer = wx.BoxSizer(wx.HORIZONTAL)
         line_sizer.Add(checkcamera, 0, wx.ALIGN_LEFT | wx.RIGHT | wx.LEFT, 5)
         line_sizer.Add(checktrigger, 0, wx.ALIGN_CENTER)
-        line_sizer.Add(checkobj, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.LEFT, 5)
+        line_sizer.Add(checkobj, 0, wx.RIGHT | wx.LEFT, 5)
         line_sizer.Fit(self)
  
         # Panel sizer to expand fold panel
@@ -410,7 +410,7 @@ class NeuronavigationPanel(wx.Panel):
                              (nav_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL)])
  
         main_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        main_sizer.Add(group_sizer, 1, wx.ALIGN_CENTER_HORIZONTAL, 10)
+        main_sizer.Add(group_sizer, 1)# wx.ALIGN_CENTER_HORIZONTAL, 10)
         self.sizer = main_sizer
         self.SetSizer(main_sizer)
         self.Fit()
@@ -852,7 +852,7 @@ class ObjectRegistrationPanel(wx.Panel):
  
         line_checks = wx.BoxSizer(wx.HORIZONTAL)
         line_checks.Add(checkrecordcoords, 0, wx.ALIGN_LEFT | wx.RIGHT | wx.LEFT, 5)
-        line_checks.Add(checktrack, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.LEFT, 5)
+        line_checks.Add(checktrack, 0, wx.RIGHT | wx.LEFT, 5)
  
         # Add line sizers into main sizer
         main_sizer = wx.BoxSizer(wx.VERTICAL)
@@ -1082,7 +1082,7 @@ class MarkersPanel(wx.Panel):
         group_sizer.Add(sizer_create, 0, wx.TOP | wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
         group_sizer.Add(sizer_btns, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
         group_sizer.Add(sizer_delete, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
-        group_sizer.Add(self.lc, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_HORIZONTAL, 5)
+        group_sizer.Add(self.lc, 0, wx.EXPAND | wx.ALL, 5)
         group_sizer.Fit(self)
  
         self.SetSizer(group_sizer)
@@ -141,7 +141,7 @@ class InnerTaskPanel(wx.Panel):
  
         line_sizer = wx.BoxSizer(wx.HORIZONTAL)
         line_sizer.Add(check_box, 0, wx.ALIGN_LEFT|wx.RIGHT|wx.LEFT, 5)
-        line_sizer.Add(next_btn_sizer, 1, wx.EXPAND|wx.ALIGN_RIGHT|wx.RIGHT|wx.LEFT, 5)
+        line_sizer.Add(next_btn_sizer, 1, wx.EXPAND|wx.RIGHT|wx.LEFT, 5)
         line_sizer.Fit(self)
  
         # Add line sizers into main sizer
@@ -423,6 +423,7 @@ class InnerFoldPanel(wx.Panel):
         try:
             _id = panel_seg_id[panel_id]
             self.fold_panel.Expand(self.fold_panel.GetFoldPanel(_id))
+            self.Layout()
         except KeyError:
             pass
  
@@ -688,11 +689,11 @@ class EditionTools(wx.Panel):
         ## LINE 2
         menu = wx.Menu()
  
-        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.jpg"), wx.BITMAP_TYPE_JPEG)
+        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.png"), wx.BITMAP_TYPE_PNG)
         item = wx.MenuItem(menu, MENU_BRUSH_CIRCLE, _("Circle"))
         item.SetBitmap(CIRCLE_BMP)
  
-        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.jpg"), wx.BITMAP_TYPE_JPEG)
+        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.png"), wx.BITMAP_TYPE_PNG)
         item2 = wx.MenuItem(menu, MENU_BRUSH_SQUARE, _("Square"))
         item2.SetBitmap(SQUARE_BMP)
  
@@ -803,8 +804,8 @@ class EditionTools(wx.Panel):
                                   threshold_range=(thresh_min, thresh_max))
  
     def OnMenu(self, evt):
-        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.jpg"), wx.BITMAP_TYPE_JPEG)
-        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.jpg"), wx.BITMAP_TYPE_JPEG)
+        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.png"), wx.BITMAP_TYPE_PNG)
+        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.png"), wx.BITMAP_TYPE_PNG)
  
         brush = {MENU_BRUSH_CIRCLE: const.BRUSH_CIRCLE,
                  MENU_BRUSH_SQUARE: const.BRUSH_SQUARE}
@@ -852,11 +853,11 @@ class WatershedTool(EditionTools):
         ## LINE 2
         menu = wx.Menu()
  
-        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.jpg"), wx.BITMAP_TYPE_JPEG)
+        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.png"), wx.BITMAP_TYPE_PNG)
         item = wx.MenuItem(menu, MENU_BRUSH_CIRCLE, _("Circle"))
         item.SetBitmap(CIRCLE_BMP)
  
-        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.jpg"), wx.BITMAP_TYPE_JPEG)
+        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.png"), wx.BITMAP_TYPE_PNG)
         item2 = wx.MenuItem(menu, MENU_BRUSH_SQUARE, _("Square"))
         item2.SetBitmap(SQUARE_BMP)
  
@@ -973,8 +974,8 @@ class WatershedTool(EditionTools):
         self.gradient_thresh.SetMaxValue(thresh_max)
  
     def OnMenu(self, evt):
-        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.jpg"), wx.BITMAP_TYPE_JPEG)
-        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.jpg"), wx.BITMAP_TYPE_JPEG)
+        SQUARE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_square.png"), wx.BITMAP_TYPE_PNG)
+        CIRCLE_BMP = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "brush_circle.png"), wx.BITMAP_TYPE_PNG)
  
         brush = {MENU_BRUSH_CIRCLE: const.BRUSH_CIRCLE,
                  MENU_BRUSH_SQUARE: const.BRUSH_SQUARE}
@@ -30,6 +30,7 @@ except ImportError:
  
 from pubsub import pub as Publisher
 import wx.lib.colourselect as csel
+import wx.lib.scrolledpanel as scrolled
  
 import invesalius.constants as const
 import invesalius.data.slice_ as slice_
@@ -74,9 +75,9 @@ class TaskPanel(wx.Panel):
         # Contour - slider
         # enable / disable Fill holes
  
-class InnerTaskPanel(wx.Panel):
+class InnerTaskPanel(scrolled.ScrolledPanel):
     def __init__(self, parent):
-        wx.Panel.__init__(self, parent)
+        scrolled.ScrolledPanel.__init__(self, parent)
         default_colour = self.GetBackgroundColour()
         backgroud_colour = wx.Colour(255,255,255)
         self.SetBackgroundColour(backgroud_colour)
@@ -134,6 +135,13 @@ class InnerTaskPanel(wx.Panel):
  
         self.sizer = main_sizer
  
+        self.SetupScrolling()
+
+        self.Bind(wx.EVT_SIZE, self.OnSize)
+
+    def OnSize(self, evt):
+        self.SetupScrolling()
+
     def OnButton(self, evt):
         id = evt.GetId()
         if id == BTN_NEW:
@@ -437,9 +445,9 @@ class SurfaceTools(wx.Panel):
  
  
  
-class SurfaceProperties(wx.Panel):
+class SurfaceProperties(scrolled.ScrolledPanel):
     def __init__(self, parent):
-        wx.Panel.__init__(self, parent)
+        scrolled.ScrolledPanel.__init__(self, parent)
         try:
             default_colour = wx.SystemSettings.GetColour(wx.SYS_COLOUR_MENUBAR)
         except AttributeError:
@@ -507,8 +515,16 @@ class SurfaceProperties(wx.Panel):
         self.Update()
         #self.SetAutoLayout(1)
  
+        self.SetupScrolling()
+
+        self.Bind(wx.EVT_SIZE, self.OnResize)
+
         self.__bind_events()
  
+    def OnResize(self, evt):
+        print("Resize")
+        self.SetupScrolling()
+
     def __bind_events(self):
         Publisher.subscribe(self.InsertNewSurface,
                                 'Update surface info in GUI')
@@ -79,7 +79,7 @@ class InnerTaskPanel(wx.Panel):
  
         # Image(s) for buttons
         BMP_ANNOTATE = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "annotation.png"), wx.BITMAP_TYPE_PNG)
-        BMP_ANGLE = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "measure_angle.jpg"), wx.BITMAP_TYPE_JPEG)
+        BMP_ANGLE = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "measure_angle.png"), wx.BITMAP_TYPE_PNG)
         BMP_DISTANCE = wx.Bitmap(os.path.join(inv_paths.ICON_DIR, "measure_line.png"), wx.BITMAP_TYPE_PNG)
         BMP_ANNOTATE.SetWidth(25)
         BMP_ANNOTATE.SetHeight(25)
@@ -26,7 +26,15 @@ from wx.lib import intctrl
  
 from invesalius.gui.widgets.inv_spinctrl import InvSpinCtrl
  
-PUSH_WIDTH = 7
+try:
+    dc = wx.MemoryDC()
+    font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
+    dc.SetFont(font)
+    PUSH_WIDTH = dc.GetTextExtent("M")[0] // 2 + 1
+    del dc
+    del font
+except Exception:
+    PUSH_WIDTH = 7
  
 myEVT_SLIDER_CHANGED = wx.NewEventType()
 EVT_SLIDER_CHANGED = wx.PyEventBinder(myEVT_SLIDER_CHANGED, 1)
@@ -70,6 +78,8 @@ class GradientSlider(wx.Panel):
         self.colour = colour
         self.selected = 0
  
+        self._gradient_colours = None
+
         self.CalculateControlPositions()
  
     def _bind_events_wx(self):
@@ -131,27 +141,43 @@ class GradientSlider(wx.Panel):
  
         width_transparency = self.max_position - self.min_position
  
-        # Drawing the left blank area.
-        pen = wx.Pen((0, 0, 0))
-        brush = wx.Brush((0, 0, 0))
-        dc.SetPen(pen)
-        dc.SetBrush(brush)
-        dc.DrawRectangle(0, 0, PUSH_WIDTH, h)
-
-        # Drawing the right blank area.
-        pen = wx.Pen((255, 255, 255))
-        brush = wx.Brush((255, 255, 255))
-        dc.SetPen(pen)
-        dc.SetBrush(brush)
-        dc.DrawRectangle(x_init_gradient + width_gradient, 0, PUSH_WIDTH, h)
-
-        # Drawing the gradient.
-        dc.GradientFillLinear(
-            (x_init_gradient, y_init_gradient, width_gradient, height_gradient),
-            (0, 0, 0),
-            (255, 255, 255),
-        )
-
+        gc = wx.GraphicsContext.Create(dc)
+
+        points = ((0, PUSH_WIDTH, (0, 0, 0), (0, 0, 0)),
+                  (PUSH_WIDTH, w - PUSH_WIDTH, (0, 0, 0), (255, 255, 255)),
+                  (w - PUSH_WIDTH, w, (255, 255, 255), (255, 255, 255)))
+
+        # Drawing the gradient background
+        for p1, p2, c1, c2 in points:
+            brush = gc.CreateLinearGradientBrush(p1, 0, p2, h, c1, c2)
+            gc.SetBrush(brush)
+            path = gc.CreatePath()
+            path.AddRectangle(p1, 0, p2 - p1, h)
+            gc.StrokePath(path)
+            gc.FillPath(path)
+
+        # Drawing the transparent coloured overlay
+        if self._gradient_colours is None:
+            brush = wx.Brush(wx.Colour(*self.colour))
+            pen = wx.Pen(wx.Colour(*self.colour))
+            gc.SetBrush(brush)
+            gc.SetPen(pen)
+            path = gc.CreatePath()
+            path.AddRectangle(self.min_position, 0, width_transparency, h)
+            gc.FillPath(path)
+            gc.StrokePath(path)
+        else:
+            for i, (c1, c2) in enumerate(zip(self._gradient_colours, self._gradient_colours[1:])):
+                p1 = self.min_position + i * width_transparency / len(self._gradient_colours)
+                p2 = self.min_position + (i + 1) * width_transparency / len(self._gradient_colours)
+                brush = gc.CreateLinearGradientBrush(p1, 0, p2, h, c1, c2)
+                gc.SetBrush(brush)
+                path = gc.CreatePath()
+                path.AddRectangle(p1, 0, p2 - p1, h)
+                gc.StrokePath(path)
+                gc.FillPath(path)
+
+        # Drawing the pushes
         try:
             n = wx.RendererNative.Get()
         except AttributeError:
@@ -161,14 +187,14 @@ class GradientSlider(wx.Panel):
         n.DrawPushButton(self, dc, (x_init_push1, 0, PUSH_WIDTH, h))
         n.DrawPushButton(self, dc, (x_init_push2, 0, PUSH_WIDTH, h))
  
-        # Drawing the transparent slider.
-        bytes = numpy.array(self.colour * width_transparency * h, "B")
-        try:
-            slider = wx.Bitmap.FromBufferRGBA(width_transparency, h, bytes)
-        except:
-            pass
-        else:
-            dc.DrawBitmap(slider, self.min_position, 0, True)
+        #  # Drawing the transparent slider.
+        #  bytes = numpy.array(self.colour * width_transparency * h, "B")
+        #  try:
+            #  slider = wx.Bitmap.FromBufferRGBA(width_transparency, h, bytes)
+        #  except:
+            #  pass
+        #  else:
+            #  dc.DrawBitmap(slider, self.min_position, 0, True)
  
     def OnEraseBackGround(self, evt):
         # Only to avoid this widget to flick.
@@ -316,6 +342,9 @@ class GradientSlider(wx.Panel):
     def SetColour(self, colour):
         self.colour = colour
  
+    def SetGradientColours(self, colors):
+        self._gradient_colours = colors
+
     def SetMinRange(self, min_range):
         self.min_range = min_range
         self.CalculateControlPositions()
@@ -485,6 +514,9 @@ class GradientCtrl(wx.Panel):
         self.gradient_slider.SetColour(colour)
         self.gradient_slider.Refresh()
  
+    def SetGradientColours(self, colors):
+        self.gradient_slider.SetGradientColours(colors)
+
     def SetMaxRange(self, value):
         self.spin_min.SetMax(value)
         self.spin_max.SetMax(value)
@@ -205,7 +205,7 @@ class SliceMenu(wx.Menu):
     def OnPopup(self, evt):
         id = evt.GetId()
         item = self.ID_TO_TOOL_ITEM[evt.GetId()]
-        key = item.GetLabel()
+        key = item.GetItemLabelText()
         if(key in const.WINDOW_LEVEL.keys()):
             window, level = const.WINDOW_LEVEL[key]
             Publisher.sendMessage('Bright and contrast adjustment image',
@@ -38,6 +38,8 @@ OLD_USER_LOG_DIR = OLD_USER_INV_DIR.joinpath(&quot;logs&quot;)
  
 INV_TOP_DIR = pathlib.Path(__file__).parent.parent.resolve()
  
+PLUGIN_DIRECTORY = INV_TOP_DIR.joinpath("plugins") 
+
 ICON_DIR = INV_TOP_DIR.joinpath("icons")
 SAMPLE_DIR = INV_TOP_DIR.joinpath("samples")
 DOC_DIR = INV_TOP_DIR.joinpath("docs")
@@ -25,6 +25,7 @@ from pubsub import pub as Publisher
  
 import invesalius.constants as consts
 from invesalius import inv_paths
+from itertools import chain
  
  
 def import_source(module_name, module_file_path):
@@ -44,7 +45,8 @@ class PluginManager:
  
     def find_plugins(self):
         self.plugins = {}
-        for p in sorted(inv_paths.USER_PLUGINS_DIRECTORY.glob("*")):
+        for p in sorted(chain(inv_paths.USER_PLUGINS_DIRECTORY.glob("*"),\
+                inv_paths.PLUGIN_DIRECTORY.glob("*"))):
             if p.is_dir():
                 try:
                     with p.joinpath("plugin.json").open() as f:
@@ -130,23 +130,23 @@ class DicomGroup:
         else:
             filelist = [dicom.image.file for dicom in
                         self.slices_dict.values()]
-       
+
         # Sort slices using GDCM
-        if (self.dicom.image.orientation_label != "CORONAL"):
-            #Organize reversed image
-            sorter = gdcm.IPPSorter()
-            sorter.SetComputeZSpacing(True)
-            sorter.SetZSpacingTolerance(1e-10)
-            try:
-                sorter.Sort([utils.encode(i, const.FS_ENCODE) for i in filelist])
-            except TypeError:
-                sorter.Sort(filelist)
-            filelist = sorter.GetFilenames()
+        #if (self.dicom.image.orientation_label != "CORONAL"):
+        #Organize reversed image
+        sorter = gdcm.IPPSorter()
+        sorter.SetComputeZSpacing(True)
+        sorter.SetZSpacingTolerance(1e-10)
+        try:
+            sorter.Sort([utils.encode(i, const.FS_ENCODE) for i in filelist])
+        except TypeError:
+            sorter.Sort(filelist)
+        filelist = sorter.GetFilenames()
  
         # for breast-CT of koning manufacturing (KBCT)
         if list(self.slices_dict.values())[0].parser.GetManufacturerName() == "Koning":
             filelist.sort()
-        
+
         return filelist
  
     def GetHandSortedList(self):
@@ -82,15 +82,15 @@ def SelectLargerDicomGroup(patient_group):
 def SortFiles(filelist, dicom):
     # Sort slices
     # FIXME: Coronal Crash. necessary verify
-    if (dicom.image.orientation_label != "CORONAL"):
-        ##Organize reversed image
-        sorter = gdcm.IPPSorter()
-        sorter.SetComputeZSpacing(True)
-        sorter.SetZSpacingTolerance(1e-10)
-        sorter.Sort(filelist)
-
-        #Getting organized image
-        filelist = sorter.GetFilenames()
+    # if (dicom.image.orientation_label != "CORONAL"):
+    ##Organize reversed image
+    sorter = gdcm.IPPSorter()
+    sorter.SetComputeZSpacing(True)
+    sorter.SetZSpacingTolerance(1e-10)
+    sorter.Sort(filelist)
+
+    #Getting organized image
+    filelist = sorter.GetFilenames()
  
     return filelist
  
@@ -20,6 +20,17 @@ SIZE = 48
 OVERLAP = SIZE // 2 + 1
  
  
+def get_LUT_value(data, window, level):
+    shape = data.shape
+    data_ = data.ravel()
+    data = np.piecewise(data_,
+                        [data_ <= (level - 0.5 - (window-1)/2),
+                         data_ > (level - 0.5 + (window-1)/2)],
+                        [0, window, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(window)])
+    data.shape = shape
+    return data
+
+
 def gen_patches(image, patch_size, overlap):
     sz, sy, sx = image.shape
     i_cuts = list(
@@ -63,8 +74,10 @@ def brain_segment(image, probability_array, comm_array):
         model = keras.models.model_from_json(json_file.read())
     model.load_weights(str(folder.joinpath("model.h5")))
     model.compile("Adam", "binary_crossentropy")
+    
+    keras.utils.plot_model(model, "model.png", show_shapes=True, show_layer_names=True)
  
-    image = imagedata_utils.image_normalize(image, 0.0, 1.0)
+    image = imagedata_utils.image_normalize(image, 0.0, 1.0, output_dtype=np.float32)
     sums = np.zeros_like(image)
     # segmenting by patches
     for completion, sub_image, patch in gen_patches(image, SIZE, OVERLAP):
@@ -80,7 +93,7 @@ def brain_segment(image, probability_array, comm_array):
  
 ctx = multiprocessing.get_context('spawn')
 class SegmentProcess(ctx.Process):
-    def __init__(self, image, create_new_mask, backend, device_id, use_gpu):
+    def __init__(self, image, create_new_mask, backend, device_id, use_gpu, apply_wwwl=False, window_width=255, window_level=127):
         multiprocessing.Process.__init__(self)
  
         self._image_filename = image.filename
@@ -102,6 +115,10 @@ class SegmentProcess(ctx.Process):
         self.device_id = device_id
         self.use_gpu = use_gpu
  
+        self.apply_wwwl = apply_wwwl
+        self.window_width = window_width
+        self.window_level = window_level
+
         self._pconn, self._cconn = multiprocessing.Pipe()
         self._exception = None
  
@@ -122,6 +139,12 @@ class SegmentProcess(ctx.Process):
             shape=self._image_shape,
             mode="r",
         )
+
+        print(image.min(), image.max())
+        if self.apply_segment_threshold:
+            print("Applying window level")
+            image = get_LUT_value(image, self.window_width, self.window_level)
+
         probability_array = np.memmap(
             self._prob_array_filename,
             dtype=np.float32,
...	...	@@ -40,7 +40,11 @@ if sys.platform == 'win32':
40	40	# #wxversion.ensureMinimal('2.8-unicode', optionsRequired=True)
41	41	# #wxversion.select('2.8-unicode', optionsRequired=True)
42	42	# # wxversion.ensureMinimal('4.0')
43		-
	43	+
	44	+# Forcing to use X11, OpenGL in wxPython doesn't work with Wayland.
	45	+if sys.platform not in ("win32", "darwin"):
	46	+ os.environ["GDK_BACKEND"] = "x11"
	47	+
44	48	import wx
45	49	try:
46	50	from wx.adv import SplashScreen
...	...	@@ -98,7 +102,7 @@ class InVesalius(wx.App):
98	102	"""
99	103	Initialize splash screen and main frame.
100	104	"""
101		-
	105	+
102	106	from multiprocessing import freeze_support
103	107	freeze_support()
104	108
...	...	@@ -179,18 +183,18 @@ class Inv3SplashScreen(SplashScreen):
179	183
180	184	# session.SaveConfigFileBackup()
181	185
182		-
	186	+
183	187	# Only after language was defined, splash screen will be
184	188	# shown
185	189	if lang:
186		-
	190	+
187	191	#import locale
188	192	#try:
189	193	# locale.setlocale(locale.LC_ALL, '')
190	194	#except locale.Error:
191	195	# pass
192		-
193		-
	196	+
	197	+
194	198	# For pt_BR, splash_pt.png should be used
195	199	if (lang.startswith('pt')):
196	200	icon_file = "splash_pt.png"
...	...	@@ -202,13 +206,13 @@ class Inv3SplashScreen(SplashScreen):
202	206	abs_file_path = os.path.abspath(".." + os.sep)
203	207	path = abs_file_path
204	208	path = os.path.join(path, 'icons', icon_file)
205		-
	209	+
206	210	else:
207	211
208	212	path = os.path.join(".","icons", icon_file)
209	213	if not os.path.exists(path):
210	214	path = os.path.join(".", "icons", "splash_en.png")
211		-
	215	+
212	216	bmp = wx.Image(path).ConvertToBitmap()
213	217
214	218	try:
...	...	@@ -232,10 +236,10 @@ class Inv3SplashScreen(SplashScreen):
232	236	from invesalius.gui.frame import Frame
233	237	from invesalius.control import Controller
234	238	from invesalius.project import Project
235		-
	239	+
236	240	self.main = Frame(None)
237	241	self.control = Controller(self.main)
238		-
	242	+
239	243	self.fc = wx.CallLater(200, self.ShowMain)
240	244	options, args = parse_comand_line()
241	245	wx.CallLater(1, use_cmd_optargs, options, args)
...	...	@@ -498,7 +502,7 @@ def main():
498	502	if __name__ == '__main__':
499	503	#Is needed because of pyinstaller
500	504	multiprocessing.freeze_support()
501		-
	505	+
502	506	#Needed in win 32 exe
503	507	if hasattr(sys,"frozen") and sys.platform.startswith('win'):
504	508
...	...	@@ -523,4 +527,3 @@ if __name__ == '__main__':
523	527
524	528	# Init application
525	529	main()
526		-
...	...
...	...	@@ -500,34 +500,6 @@ def img2memmap(group):
500	500	return matrix, scalar_range, temp_file
501	501
502	502
503		-def imgnormalize(data, srange=(0, 255)):
504		- """
505		- Normalize image pixel intensity for int16 gray scale values.
506		-
507		- :param data: image matrix
508		- :param srange: range for normalization, default is 0 to 255
509		- :return: normalized pixel intensity matrix
510		- """
511		-
512		- dataf = numpy.asarray(data)
513		- rangef = numpy.asarray(srange)
514		- faux = numpy.ravel(dataf).astype(float)
515		- minimum = numpy.min(faux)
516		- maximum = numpy.max(faux)
517		- lower = rangef[0]
518		- upper = rangef[1]
519		-
520		- if minimum == maximum:
521		- datan = numpy.ones(dataf.shape)*(upper + lower) / 2.
522		- else:
523		- datan = (faux-minimum)*(upper-lower) / (maximum-minimum) + lower
524		-
525		- datan = numpy.reshape(datan, dataf.shape)
526		- datan = datan.astype(numpy.int16)
527		-
528		- return datan
529		-
530		-
531	503	def get_LUT_value_255(data, window, level):
532	504	shape = data.shape
533	505	data_ = data.ravel()
...	...	@@ -539,6 +511,8 @@ def get_LUT_value_255(data, window, level):
539	511	return data
540	512
541	513
542		-def image_normalize(image, min_=0.0, max_=1.0):
	514	+def image_normalize(image, min_=0.0, max_=1.0, output_dtype=np.int16):
	515	+ output = np.empty(shape=image.shape, dtype=output_dtype)
543	516	imin, imax = image.min(), image.max()
544		- return (image - imin) * ((max_ - min_) / (imax - imin)) + min_
	517	+ output[:] = (image - imin) * ((max_ - min_) / (imax - imin)) + min_
	518	+ return output
...	...
...	...	@@ -301,7 +301,10 @@ class Slice(metaclass=utils.Singleton):
301	301
302	302	for name in self.aux_matrices:
303	303	m = self.aux_matrices[name]
304		- f = m.filename
	304	+ try:
	305	+ f = m.filename
	306	+ except AttributeError:
	307	+ continue
305	308	m._mmap.close()
306	309	m = None
307	310	os.remove(f)
...	...	@@ -347,6 +350,8 @@ class Slice(metaclass=utils.Singleton):
347	350	self.SetMaskEditionThreshold(index, threshold_range)
348	351
349	352	def __set_current_mask_threshold(self, threshold_range):
	353	+ if self.current_mask is None:
	354	+ return
350	355	index = self.current_mask.index
351	356	self.num_gradient += 1
352	357	self.current_mask.matrix[:] = 0
...	...	@@ -387,6 +392,8 @@ class Slice(metaclass=utils.Singleton):
387	392	Publisher.sendMessage("Reload actual slice")
388	393
389	394	def __set_current_mask_threshold_actual_slice(self, threshold_range):
	395	+ if self.current_mask is None:
	396	+ return
390	397	index = self.current_mask.index
391	398	for orientation in self.buffer_slices:
392	399	self.buffer_slices[orientation].discard_vtk_mask()
...	...	@@ -624,7 +631,7 @@ class Slice(metaclass=utils.Singleton):
624	631	self.buffer_slices[orientation].vtk_image = image
625	632	self.buffer_slices[orientation].vtk_mask = mask
626	633
627		- if self.to_show_aux == "watershed" and self.current_mask.is_shown:
	634	+ if self.to_show_aux == "watershed" and self.current_mask is not None and self.current_mask.is_shown:
628	635	m = self.get_aux_slice("watershed", orientation, slice_number)
629	636	tmp_vimage = converters.to_vtk(m, self.spacing, slice_number, orientation)
630	637	cimage = self.do_custom_colour(
...	...
...	...	@@ -102,13 +102,13 @@ class ContourMIPConfig(wx.Panel):
102	102	self.txt_mip_border = wx.StaticText(self, -1, _("Sharpness"))
103	103
104	104	sizer = wx.BoxSizer(wx.HORIZONTAL)
105		- sizer.Add(txt_mip_size, 0, wx.EXPAND \| wx.ALL, 2)
	105	+ sizer.Add(txt_mip_size, 0, wx.ALIGN_CENTER_VERTICAL \| wx.ALL, 2)
106	106	sizer.Add(self.mip_size_spin, 0)
107	107	try:
108	108	sizer.Add(10, 0)
109	109	except TypeError:
110	110	sizer.Add((10, 0))
111		- sizer.Add(self.txt_mip_border, 0, wx.EXPAND \| wx.ALL, 2)
	111	+ sizer.Add(self.txt_mip_border, 0, wx.ALIGN_CENTER_VERTICAL \| wx.ALL, 2)
112	112	sizer.Add(self.border_spin, 0, wx.EXPAND)
113	113	try:
114	114	sizer.Add(10, 0)
...	...	@@ -1438,8 +1438,12 @@ class Viewer(wx.Panel):
1438	1438	index = max_slice_number - 1
1439	1439	inverted = self.mip_ctrls.inverted.GetValue()
1440	1440	border_size = self.mip_ctrls.border_spin.GetValue()
1441		- image = self.slice_.GetSlices(self.orientation, index,
1442		- self.number_slices, inverted, border_size)
	1441	+ try:
	1442	+ image = self.slice_.GetSlices(self.orientation, index,
	1443	+ self.number_slices, inverted,
	1444	+ border_size)
	1445	+ except IndexError:
	1446	+ return
1443	1447	self.slice_data.actor.SetInputData(image)
1444	1448	for actor in self.actors_by_slice_number[self.slice_data.number]:
1445	1449	self.slice_data.renderer.RemoveActor(actor)
...	...
...	...	@@ -81,6 +81,8 @@ class BrainSegmenterDialog(wx.Dialog):
81	81	self.txt_threshold.SetMinClientSize((w, -1))
82	82	self.chk_new_mask = wx.CheckBox(self, wx.ID_ANY, _("Create new mask"))
83	83	self.chk_new_mask.SetValue(True)
	84	+ self.chk_apply_wwwl = wx.CheckBox(self, wx.ID_ANY, _("Apply WW&WL"))
	85	+ self.chk_apply_wwwl.SetValue(False)
84	86	self.progress = wx.Gauge(self, -1)
85	87	self.lbl_progress_caption = wx.StaticText(self, -1, _("Elapsed time:"))
86	88	self.lbl_time = wx.StaticText(self, -1, _("00:00:00"))
...	...	@@ -115,11 +117,12 @@ class BrainSegmenterDialog(wx.Dialog):
115	117	sizer_3.Add(
116	118	self.sld_threshold,
117	119	1,
118		- wx.ALIGN_CENTER \| wx.BOTTOM \| wx.EXPAND \| wx.LEFT \| wx.RIGHT,
	120	+ wx.BOTTOM \| wx.EXPAND \| wx.LEFT \| wx.RIGHT,
119	121	5,
120	122	)
121	123	sizer_3.Add(self.txt_threshold, 0, wx.ALL, 5)
122	124	main_sizer.Add(sizer_3, 0, wx.EXPAND, 0)
	125	+ main_sizer.Add(self.chk_apply_wwwl, 0, wx.EXPAND \| wx.ALL, 5)
123	126	main_sizer.Add(self.chk_new_mask, 0, wx.EXPAND \| wx.ALL, 5)
124	127	main_sizer.Add(self.progress, 0, wx.EXPAND \| wx.ALL, 5)
125	128	time_sizer = wx.BoxSizer(wx.HORIZONTAL)
...	...	@@ -128,15 +131,15 @@ class BrainSegmenterDialog(wx.Dialog):
128	131	main_sizer.Add(time_sizer, 0, wx.EXPAND \| wx.ALL, 5)
129	132	sizer_buttons = wx.BoxSizer(wx.HORIZONTAL)
130	133	sizer_buttons.Add(
131		- self.btn_close, 0, wx.ALIGN_BOTTOM \| wx.ALIGN_RIGHT \| wx.ALL, 5
	134	+ self.btn_close, 0, wx.ALIGN_BOTTOM \| wx.ALL, 5
132	135	)
133	136	sizer_buttons.Add(
134		- self.btn_stop, 0, wx.ALIGN_BOTTOM \| wx.ALIGN_RIGHT \| wx.ALL, 5
	137	+ self.btn_stop, 0, wx.ALIGN_BOTTOM \| wx.ALL, 5
135	138	)
136	139	sizer_buttons.Add(
137		- self.btn_segment, 0, wx.ALIGN_BOTTOM \| wx.ALIGN_RIGHT \| wx.ALL, 5
	140	+ self.btn_segment, 0, wx.ALIGN_BOTTOM \| wx.ALL, 5
138	141	)
139		- main_sizer.Add(sizer_buttons, 0, wx.ALIGN_BOTTOM \| wx.ALIGN_RIGHT \| wx.ALL, 0)
	142	+ main_sizer.Add(sizer_buttons, 0, wx.ALIGN_RIGHT \| wx.ALL, 0)
140	143	self.SetSizer(main_sizer)
141	144	main_sizer.Fit(self)
142	145	main_sizer.SetSizeHints(self)
...	...	@@ -216,6 +219,7 @@ class BrainSegmenterDialog(wx.Dialog):
216	219	device_id = self.plaidml_devices[self.cb_devices.GetValue()]
217	220	except (KeyError, AttributeError):
218	221	device_id = "llvm_cpu.0"
	222	+ apply_wwwl = self.chk_apply_wwwl.GetValue()
219	223	create_new_mask = self.chk_new_mask.GetValue()
220	224	use_gpu = self.chk_use_gpu.GetValue()
221	225	prob_threshold = self.sld_threshold.GetValue() / 100.0
...	...	@@ -224,8 +228,11 @@ class BrainSegmenterDialog(wx.Dialog):
224	228	self.btn_segment.Disable()
225	229	self.chk_new_mask.Disable()
226	230
	231	+ window_width = slc.Slice().window_width
	232	+ window_level = slc.Slice().window_level
	233	+
227	234	try:
228		- self.ps = segment.SegmentProcess(image, create_new_mask, backend, device_id, use_gpu)
	235	+ self.ps = segment.SegmentProcess(image, create_new_mask, backend, device_id, use_gpu, apply_wwwl, window_width, window_level)
229	236	self.ps.start()
230	237	except (multiprocessing.ProcessError, OSError, ValueError) as err:
231	238	self.OnStop(None)
...	...
...	...	@@ -351,18 +351,89 @@ class ButtonControlPanel(wx.Panel):
351	351	else:
352	352	dlg.MaskSelectionRequiredForDuplication()
353	353
354		-class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
355	354
	355	+class InvListCtrl(wx.ListCtrl):
356	356	def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
357		- size=wx.DefaultSize, style=wx.LC_REPORT):
	357	+ size=wx.DefaultSize, style=wx.LC_REPORT \| wx.LC_EDIT_LABELS):
	358	+ wx.ListCtrl.__init__(self, parent, ID, pos, size, style=style)
	359	+ self.__bind_events_wx()
358	360
359		- # native look and feel for MacOS
360		- #if wx.Platform == "__WXMAC__":
361		- # wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
	361	+ def __bind_events_wx(self):
	362	+ self.Bind(wx.EVT_LEFT_DOWN, self.OnClickItem)
	363	+ self.Bind(wx.EVT_LEFT_DCLICK, self.OnDblClickItem)
	364	+
	365	+ def CreateColourBitmap(self, colour):
	366	+ """
	367	+ Create a wx Image with a mask colour.
	368	+ colour: colour in rgb format(0 - 1)
	369	+ """
	370	+ image = self.image_gray
	371	+ new_image = Image.new("RGB", image.size)
	372	+ for x in range(image.size[0]):
	373	+ for y in range(image.size[1]):
	374	+ pixel_colour = [int(i*image.getpixel((x,y)))
	375	+ for i in colour]
	376	+ new_image.putpixel((x,y), tuple(pixel_colour))
	377	+
	378	+ wx_image = wx.Image(new_image.size[0],
	379	+ new_image.size[1])
	380	+ try:
	381	+ wx_image.SetData(new_image.tostring())
	382	+ except Exception:
	383	+ wx_image.SetData(new_image.tobytes())
	384	+ return wx.Bitmap(wx_image.Scale(16, 16))
	385	+
	386	+ def OnClickItem(self, evt):
	387	+ self._click_check = False
	388	+ item_idx, flag = (self.HitTest(evt.GetPosition()))
	389	+ if item_idx > -1:
	390	+ column_clicked = self.get_column_clicked(evt.GetPosition())
	391	+ if column_clicked == 0:
	392	+ self._click_check = True
	393	+ item = self.GetItem(item_idx, 0)
	394	+ flag = not bool(item.GetImage())
	395	+ self.SetItemImage(item_idx, int(flag))
	396	+ self.OnCheckItem(item_idx, flag)
	397	+ return
	398	+ evt.Skip()
362	399
363		- wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
364		- listmix.TextEditMixin.__init__(self)
365		- listmix.CheckListCtrlMixin.__init__(self)
	400	+ def OnDblClickItem(self, evt):
	401	+ self._click_check = False
	402	+ item_idx, flag = (self.HitTest(evt.GetPosition()))
	403	+ if item_idx > -1:
	404	+ column_clicked = self.get_column_clicked(evt.GetPosition())
	405	+ if column_clicked == 1:
	406	+ item = self.GetItem(item_idx, 1)
	407	+ self.enter_edition(item)
	408	+ return
	409	+ evt.Skip()
	410	+
	411	+ def enter_edition(self, item):
	412	+ ctrl = self.EditLabel(item.GetId())
	413	+ w, h = ctrl.GetClientSize()
	414	+ w = self.GetColumnWidth(1)
	415	+ ctrl.SetClientSize(w, h)
	416	+ ctrl.SetValue(item.GetText())
	417	+ ctrl.SelectAll()
	418	+
	419	+
	420	+ def get_column_clicked(self, position):
	421	+ epx, epy = position
	422	+ wpx, wpy = self.GetPosition()
	423	+ width_sum = 0
	424	+ for i in range(self.GetColumnCount()):
	425	+ width_sum += self.GetColumnWidth(i)
	426	+ if (epx - wpx) <= width_sum:
	427	+ return i
	428	+ return -1
	429	+
	430	+
	431	+
	432	+class MasksListCtrlPanel(InvListCtrl):
	433	+ def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
	434	+ size=wx.DefaultSize, style=wx.LC_REPORT \| wx.LC_EDIT_LABELS):
	435	+ super().__init__(parent, ID, pos, size, style=style)
	436	+ self._click_check = False
366	437	self.mask_list_index = {}
367	438	self.current_index = 0
368	439	self.__init_columns()
...	...	@@ -371,12 +442,9 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
371	442	self.__bind_events()
372	443
373	444	def __bind_events_wx(self):
374		- self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)
375		- self.Bind(wx.EVT_LIST_BEGIN_LABEL_EDIT, self.OnBeginLabelEdit)
376	445	self.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnEditLabel)
377	446	self.Bind(wx.EVT_KEY_UP, self.OnKeyEvent)
378	447
379		-
380	448	def __bind_events(self):
381	449	Publisher.subscribe(self.AddMask, 'Add mask')
382	450	Publisher.subscribe(self.EditMaskThreshold,
...	...	@@ -438,7 +506,6 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
438	506	self.current_index -= 1
439	507	self.SetItemImage(self.current_index, 1)
440	508
441		-
442	509	def OnCloseProject(self):
443	510	self.DeleteAllItems()
444	511	self.mask_list_index = {}
...	...	@@ -475,13 +542,13 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
475	542	def __init_image_list(self):
476	543	self.imagelist = wx.ImageList(16, 16)
477	544
478		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
	545	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
479	546	bitmap = wx.Bitmap(image.Scale(16, 16))
480	547	bitmap.SetWidth(16)
481	548	bitmap.SetHeight(16)
482	549	img_null = self.imagelist.Add(bitmap)
483	550
484		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
	551	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
485	552	bitmap = wx.Bitmap(image.Scale(16, 16))
486	553	bitmap.SetWidth(16)
487	554	bitmap.SetHeight(16)
...	...	@@ -489,23 +556,16 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
489	556
490	557	self.SetImageList(self.imagelist,wx.IMAGE_LIST_SMALL)
491	558
492		- self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
493		-
494		- def OnBeginLabelEdit(self, evt):
495		- if evt.GetColumn() == 1:
496		- evt.Skip()
497		- else:
498		- evt.Veto()
	559	+ self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
499	560
500	561	def OnEditLabel(self, evt):
501		- Publisher.sendMessage('Change mask name',
502		- index=evt.GetIndex(), name=evt.GetLabel())
	562	+ if not evt.IsEditCancelled():
	563	+ index = evt.GetIndex()
	564	+ self.SetItem(index, 1, evt.GetLabel())
	565	+ Publisher.sendMessage('Change mask name',
	566	+ index=evt.GetIndex(), name=evt.GetLabel())
503	567	evt.Skip()
504	568
505		- def OnItemActivated(self, evt):
506		- self.ToggleItem(evt.Index)
507		- # pass
508		-
509	569	def OnCheckItem(self, index, flag):
510	570	if flag:
511	571	for key in self.mask_list_index.keys():
...	...	@@ -515,26 +575,7 @@ class MasksListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCt
515	575	self.current_index = index
516	576	Publisher.sendMessage('Show mask', index=index, value=flag)
517	577
518		- def CreateColourBitmap(self, colour):
519		- """
520		- Create a wx Image with a mask colour.
521		- colour: colour in rgb format(0 - 1)
522		- """
523		- image = self.image_gray
524		- new_image = Image.new("RGB", image.size)
525		- for x in range(image.size[0]):
526		- for y in range(image.size[1]):
527		- pixel_colour = [int(i*image.getpixel((x,y)))
528		- for i in colour]
529		- new_image.putpixel((x,y), tuple(pixel_colour))
530	578
531		- wx_image = wx.Image(new_image.size[0],
532		- new_image.size[1])
533		- try:
534		- wx_image.SetData(new_image.tostring())
535		- except Exception:
536		- wx_image.SetData(new_image.tobytes())
537		- return wx.Bitmap(wx_image.Scale(16, 16))
538	579
539	580	def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)",
540	581	colour=None):
...	...	@@ -718,19 +759,11 @@ class SurfaceButtonControlPanel(wx.Panel):
718	759	def AffineStatus(self, affine, status):
719	760	self.affinestatus = status
720	761
721		-class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
722		-
	762	+class SurfacesListCtrlPanel(InvListCtrl):
723	763	def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
724		- size=wx.DefaultSize, style=wx.LC_REPORT):
725		-
726		- # native look and feel for MacOS
727		- #if wx.Platform == "__WXMAC__":
728		- # wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
729		-
730		- wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
731		- listmix.TextEditMixin.__init__(self)
732		- listmix.CheckListCtrlMixin.__init__(self)
733		-
	764	+ size=wx.DefaultSize, style=wx.LC_REPORT \| wx.LC_EDIT_LABELS):
	765	+ super().__init__(parent, ID, pos, size, style=style)
	766	+ self._click_check = False
734	767	self.__init_columns()
735	768	self.__init_image_list()
736	769	self.__init_evt()
...	...	@@ -752,8 +785,6 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
752	785	Publisher.subscribe(self.OnShowMultiple, 'Show multiple surfaces')
753	786
754	787	def __bind_events_wx(self):
755		- self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)
756		- self.Bind(wx.EVT_LIST_BEGIN_LABEL_EDIT, self.OnBeginLabelEdit)
757	788	self.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnEditLabel)
758	789	#self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected_)
759	790	self.Bind(wx.EVT_KEY_UP, self.OnKeyEvent)
...	...	@@ -841,13 +872,13 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
841	872	def __init_image_list(self):
842	873	self.imagelist = wx.ImageList(16, 16)
843	874
844		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
	875	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
845	876	bitmap = wx.Bitmap(image.Scale(16, 16))
846	877	bitmap.SetWidth(16)
847	878	bitmap.SetHeight(16)
848	879	img_null = self.imagelist.Add(bitmap)
849	880
850		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
	881	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
851	882	bitmap = wx.Bitmap(image.Scale(16, 16))
852	883	bitmap.SetWidth(16)
853	884	bitmap.SetHeight(16)
...	...	@@ -855,7 +886,7 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
855	886
856	887	self.SetImageList(self.imagelist,wx.IMAGE_LIST_SMALL)
857	888
858		- self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
	889	+ self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
859	890
860	891	def OnBeginLabelEdit(self, evt):
861	892	if evt.GetColumn() == 1:
...	...	@@ -864,11 +895,10 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
864	895	evt.Veto()
865	896
866	897	def OnEditLabel(self, evt):
867		- Publisher.sendMessage('Change surface name', index=evt.GetIndex(), name=evt.GetLabel())
868		- evt.Skip()
869		-
870		- def OnItemActivated(self, evt):
871		- self.ToggleItem(evt.Index)
	898	+ if not evt.IsEditCancelled():
	899	+ index = evt.GetIndex()
	900	+ self.SetItem(index, 1, evt.GetLabel())
	901	+ Publisher.sendMessage('Change surface name', index=evt.GetIndex(), name=evt.GetLabel())
872	902	evt.Skip()
873	903
874	904	def OnCheckItem(self, index, flag):
...	...	@@ -944,28 +974,6 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
944	974	self.SetItem(index, 4, transparency)
945	975	self.SetItemImage(index, 1)
946	976
947		- def CreateColourBitmap(self, colour):
948		- """
949		- Create a wx Image with a mask colour.
950		- colour: colour in rgb format(0 - 1)
951		- """
952		- image = self.image_gray
953		- new_image = Image.new("RGB", image.size)
954		- for x in range(image.size[0]):
955		- for y in range(image.size[1]):
956		- pixel_colour = [int(i*image.getpixel((x,y)))
957		- for i in colour]
958		- new_image.putpixel((x,y), tuple(pixel_colour))
959		-
960		- wx_image = wx.Image(new_image.size[0],
961		- new_image.size[1])
962		- try:
963		- wx_image.SetData(new_image.tostring())
964		- except Exception:
965		- wx_image.SetData(new_image.tobytes())
966		-
967		- return wx.Bitmap(wx_image.Scale(16, 16))
968		-
969	977	def EditSurfaceTransparency(self, surface_index, transparency):
970	978	"""
971	979	Set actor transparency (oposite to opacity) according to given actor
...	...	@@ -985,19 +993,11 @@ class SurfacesListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
985	993	#-------------------------------------------------
986	994	#-------------------------------------------------
987	995
988		-class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
989		-
	996	+class MeasuresListCtrlPanel(InvListCtrl):
990	997	def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
991		- size=wx.DefaultSize, style=wx.LC_REPORT):
992		-
993		- # native look and feel for MacOS
994		- #if wx.Platform == "__WXMAC__":
995		- # wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
996		-
997		- wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
998		- listmix.TextEditMixin.__init__(self)
999		- listmix.CheckListCtrlMixin.__init__(self)
1000		-
	998	+ size=wx.DefaultSize, style=wx.LC_REPORT \| wx.LC_EDIT_LABELS):
	999	+ super().__init__(parent, ID, pos, size, style=style)
	1000	+ self._click_check = False
1001	1001	self.__init_columns()
1002	1002	self.__init_image_list()
1003	1003	self.__init_evt()
...	...	@@ -1017,13 +1017,10 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
1017	1017	Publisher.subscribe(self.OnRemoveGUIMeasure, 'Remove GUI measurement')
1018	1018
1019	1019	def __bind_events_wx(self):
1020		- self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)
1021		- self.Bind(wx.EVT_LIST_BEGIN_LABEL_EDIT, self.OnBeginLabelEdit)
1022	1020	self.Bind(wx.EVT_LIST_END_LABEL_EDIT, self.OnEditLabel)
1023	1021	self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected_)
1024	1022	self.Bind(wx.EVT_KEY_UP, self.OnKeyEvent)
1025	1023
1026		-
1027	1024	def OnKeyEvent(self, event):
1028	1025	keycode = event.GetKeyCode()
1029	1026	# Delete key
...	...	@@ -1116,13 +1113,13 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
1116	1113	def __init_image_list(self):
1117	1114	self.imagelist = wx.ImageList(16, 16)
1118	1115
1119		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
	1116	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
1120	1117	bitmap = wx.Bitmap(image.Scale(16, 16))
1121	1118	bitmap.SetWidth(16)
1122	1119	bitmap.SetHeight(16)
1123	1120	img_null = self.imagelist.Add(bitmap)
1124	1121
1125		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
	1122	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
1126	1123	bitmap = wx.Bitmap(image.Scale(16, 16))
1127	1124	bitmap.SetWidth(16)
1128	1125	bitmap.SetHeight(16)
...	...	@@ -1130,7 +1127,7 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
1130	1127
1131	1128	self.SetImageList(self.imagelist,wx.IMAGE_LIST_SMALL)
1132	1129
1133		- self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
	1130	+ self.image_gray = Image.open(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
1134	1131
1135	1132	def OnBeginLabelEdit(self, evt):
1136	1133	if evt.GetColumn() == 1:
...	...	@@ -1139,14 +1136,12 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
1139	1136	evt.Veto()
1140	1137
1141	1138	def OnEditLabel(self, evt):
1142		- Publisher.sendMessage('Change measurement name', index=evt.GetIndex(), name=evt.GetLabel())
	1139	+ if not evt.IsEditCancelled():
	1140	+ index = evt.GetIndex()
	1141	+ self.SetItem(index, 1, evt.GetLabel())
	1142	+ Publisher.sendMessage('Change measurement name', index=evt.GetIndex(), name=evt.GetLabel())
1143	1143	evt.Skip()
1144	1144
1145		- def OnItemActivated(self, evt):
1146		- self.ToggleItem(evt.Index)
1147		- evt.Skip()
1148		-
1149		-
1150	1145	def OnCheckItem(self, index, flag):
1151	1146	Publisher.sendMessage('Show measurement', index=index, visibility=flag)
1152	1147
...	...	@@ -1238,27 +1233,6 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
1238	1233	self.SetItemImage(index, 1)
1239	1234	self.Refresh()
1240	1235
1241		- def CreateColourBitmap(self, colour):
1242		- """
1243		- Create a wx Image with a mask colour.
1244		- colour: colour in rgb format(0 - 1)
1245		- """
1246		- image = self.image_gray
1247		- new_image = Image.new("RGB", image.size)
1248		- for x in range(image.size[0]):
1249		- for y in range(image.size[1]):
1250		- pixel_colour = [int(i*image.getpixel((x,y)))
1251		- for i in colour]
1252		- new_image.putpixel((x,y), tuple(pixel_colour))
1253		-
1254		- wx_image = wx.Image(new_image.size[0],
1255		- new_image.size[1])
1256		- try:
1257		- wx_image.SetData(new_image.tostring())
1258		- except:
1259		- wx_image.SetData(new_image.tobytes())
1260		- return wx.Bitmap(wx_image.Scale(16, 16))
1261		-
1262	1236	def EditItemColour(self, measure_index, colour):
1263	1237	"""
1264	1238	"""
...	...	@@ -1273,19 +1247,12 @@ class MeasuresListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckLis
1273	1247	#*******************************************************************
1274	1248
1275	1249
1276		-class AnnotationsListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.CheckListCtrlMixin):
	1250	+class AnnotationsListCtrlPanel(wx.ListCtrl):
1277	1251	# TODO: Remove edimixin, allow only visible and invisible
1278	1252	def __init__(self, parent, ID=-1, pos=wx.DefaultPosition,
1279		- size=wx.DefaultSize, style=wx.LC_REPORT):
1280		-
1281		- # native look and feel for MacOS
1282		- #if wx.Platform == "__WXMAC__":
1283		- # wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
1284		-
1285		- wx.ListCtrl.__init__(self, parent, ID, pos, size, style=wx.LC_REPORT)
1286		- listmix.TextEditMixin.__init__(self)
1287		- listmix.CheckListCtrlMixin.__init__(self)
1288		-
	1253	+ size=wx.DefaultSize, style=wx.LC_REPORT \| wx.LC_EDIT_LABELS):
	1254	+ wx.ListCtrl.__init__(self, parent, ID, pos, size, style=style)
	1255	+ self._click_check = False
1289	1256	self.__init_columns()
1290	1257	self.__init_image_list()
1291	1258	self.__init_evt()
...	...	@@ -1311,19 +1278,19 @@ class AnnotationsListCtrlPanel(wx.ListCtrl, listmix.TextEditMixin, listmix.Check
1311	1278	def __init_image_list(self):
1312	1279	self.imagelist = wx.ImageList(16, 16)
1313	1280
1314		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.jpg"))
	1281	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_visible.png"))
1315	1282	bitmap = wx.Bitmap(image.Scale(16, 16))
1316	1283	bitmap.SetWidth(16)
1317	1284	bitmap.SetHeight(16)
1318	1285	img_check = self.imagelist.Add(bitmap)
1319	1286
1320		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.jpg"))
	1287	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_invisible.png"))
1321	1288	bitmap = wx.Bitmap(image.Scale(16, 16))
1322	1289	bitmap.SetWidth(16)
1323	1290	bitmap.SetHeight(16)
1324	1291	img_null = self.imagelist.Add(bitmap)
1325	1292
1326		- image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_colour.jpg"))
	1293	+ image = wx.Image(os.path.join(inv_paths.ICON_DIR, "object_colour.png"))
1327	1294	bitmap = wx.Bitmap(image.Scale(16, 16))
1328	1295	bitmap.SetWidth(16)
1329	1296	bitmap.SetHeight(16)
...	...
...	...	@@ -123,6 +123,7 @@ class Panel(wx.Panel):
123	123
124	124	#self.SetSizerAndFit(sizer)
125	125	self.SetSizer(sizer)
	126	+ self.Layout()
126	127
127	128
128	129	# Lower fold panel
...	...
...	...	@@ -111,7 +111,7 @@ class Panel(wx.Panel):
111	111	p3.SetPopupMenu(menu)
112	112
113	113
114		- if sys.platform == 'win32':
	114	+ if sys.platform == 'win32' or wx.VERSION >= (4, 1):
115	115	self.aui_manager.AddPane(p1, s1)
116	116	self.aui_manager.AddPane(p2, s2)
117	117	self.aui_manager.AddPane(p3, s3)
...	...	@@ -604,7 +604,7 @@ class VolumeToolPanel(wx.Panel):
604	604	id = evt.GetId()
605	605	item = ID_TO_ITEMSLICEMENU[id]
606	606	checked = item.IsChecked()
607		- label = item.GetLabel()
	607	+ label = item.GetItemLabelText()
608	608
609	609	if not (checked):
610	610	Publisher.sendMessage('Disable plane', plane_label=label)
...	...
...	...	@@ -245,9 +245,7 @@ WILDCARD_OPEN = "InVesalius 3 project (.inv3)\|.inv3\|" \
245	245	WILDCARD_ANALYZE = "Analyze 7.5 (.hdr)\|.hdr\|" \
246	246	"All files (.)\|."
247	247
248		-WILDCARD_NIFTI = "NIfTI 1 (.nii)\|.nii\|" \
249		- "Compressed NIfTI (.nii.gz)\|.nii.gz\|" \
250		- "HDR NIfTI (.hdr)\|.hdr\|" \
	248	+WILDCARD_NIFTI = "NIfTI 1 (.nii;.nii.gz;.hdr)\|.nii;.nii.gz;.hdr\|" \
251	249	"All files (.)\|."
252	250	#".[jJ][pP][gG]"
253	251	WILDCARD_PARREC = "PAR/REC (.par)\|.par\|" \
...	...	@@ -1950,17 +1948,17 @@ class WatershedOptionsPanel(wx.Panel):
1950	1948	min_value=1, max_value=10)
1951	1949
1952	1950	box_sizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Conectivity"), wx.VERTICAL)
1953		- box_sizer.Add(self.choice_2dcon, 0, wx.ALIGN_CENTER_VERTICAL,2)
1954		- box_sizer.Add(self.choice_3dcon, 0, wx.ALIGN_CENTER_VERTICAL,2)
	1951	+ box_sizer.Add(self.choice_2dcon, 0, wx.ALL, 5)
	1952	+ box_sizer.Add(self.choice_3dcon, 0, wx.ALL, 5)
1955	1953
1956	1954	g_sizer = wx.BoxSizer(wx.HORIZONTAL)
1957		- g_sizer.Add(wx.StaticText(self, -1, _("Gaussian sigma")), 0, wx.ALIGN_RIGHT \| wx.ALL, 5)
1958		- g_sizer.Add(self.gaussian_size, 0, wx.ALIGN_LEFT \| wx.ALL, 5)
	1955	+ g_sizer.Add(wx.StaticText(self, -1, _("Gaussian sigma")), 0, wx.ALIGN_CENTER \| wx.ALL, 5)
	1956	+ g_sizer.Add(self.gaussian_size, 0, wx.ALL, 5)
1959	1957
1960	1958	sizer = wx.BoxSizer(wx.VERTICAL)
1961		- sizer.Add(self.choice_algorithm, 0, wx.ALIGN_CENTER_VERTICAL,2)
1962		- sizer.Add(box_sizer, 1, wx.EXPAND,2)
1963		- sizer.Add(g_sizer, 0, wx.ALIGN_LEFT, 2)
	1959	+ sizer.Add(self.choice_algorithm, 0, wx.ALL, 5)
	1960	+ sizer.Add(box_sizer, 1, wx.EXPAND \| wx.ALL, 5)
	1961	+ sizer.Add(g_sizer, 0, wx.ALL, 5)
1964	1962
1965	1963	self.SetSizer(sizer)
1966	1964	sizer.Fit(self)
...	...	@@ -1998,8 +1996,7 @@ class WatershedOptionsDialog(wx.Dialog):
1998	1996	btnsizer.Realize()
1999	1997
2000	1998	sizer.Add(wop, 0, wx.EXPAND)
2001		- sizer.Add(btnsizer, 0, wx.EXPAND)
2002		- sizer.AddSpacer(5)
	1999	+ sizer.Add(btnsizer, 0, wx.ALIGN_RIGHT \| wx.BOTTOM, 5)
2003	2000
2004	2001	self.SetSizer(sizer)
2005	2002	sizer.Fit(self)
...	...	@@ -2060,16 +2057,16 @@ class MaskBooleanDialog(wx.Dialog):
2060	2057
2061	2058	gsizer = wx.FlexGridSizer(rows=3, cols=2, hgap=5, vgap=5)
2062	2059
2063		- gsizer.Add(wx.StaticText(self, -1, _(u"Mask 1")))
	2060	+ gsizer.Add(wx.StaticText(self, -1, _(u"Mask 1")), 0, wx.ALIGN_CENTER_VERTICAL)
2064	2061	gsizer.Add(self.mask1, 1, wx.EXPAND)
2065		- gsizer.Add(wx.StaticText(self, -1, _(u"Operation")))
	2062	+ gsizer.Add(wx.StaticText(self, -1, _(u"Operation")), 0, wx.ALIGN_CENTER_VERTICAL)
2066	2063	gsizer.Add(self.op_boolean, 1, wx.EXPAND)
2067		- gsizer.Add(wx.StaticText(self, -1, _(u"Mask 2")))
	2064	+ gsizer.Add(wx.StaticText(self, -1, _(u"Mask 2")), 0, wx.ALIGN_CENTER_VERTICAL)
2068	2065	gsizer.Add(self.mask2, 1, wx.EXPAND)
2069	2066
2070	2067	sizer = wx.BoxSizer(wx.VERTICAL)
2071		- sizer.Add(gsizer, 0, wx.EXPAND \| wx.ALIGN_CENTER \| wx.ALL, border=5)
2072		- sizer.Add(btnsizer, 0, wx.EXPAND \| wx.ALIGN_CENTER \| wx.ALL, border=5)
	2068	+ sizer.Add(gsizer, 0, wx.EXPAND \| wx.ALL, border=5)
	2069	+ sizer.Add(btnsizer, 0, wx.EXPAND \| wx.ALL, border=5)
2073	2070
2074	2071	self.SetSizer(sizer)
2075	2072	sizer.Fit(self)
...	...	@@ -2798,8 +2795,8 @@ class SelectPartsOptionsDialog(wx.Dialog):
2798	2795	sizer.AddSpacer(5)
2799	2796
2800	2797	btn_sizer = wx.BoxSizer(wx.HORIZONTAL)
2801		- btn_sizer.Add(self.btn_ok, 0, flag=wx.ALIGN_RIGHT, border=5)
2802		- btn_sizer.Add(self.btn_cancel, 0, flag=wx.LEFT\|wx.ALIGN_RIGHT, border=5)
	2798	+ btn_sizer.Add(self.btn_ok, 0)# flag=wx.ALIGN_RIGHT, border=5)
	2799	+ btn_sizer.Add(self.btn_cancel, 0, flag=wx.LEFT, border=5)
2803	2800
2804	2801	sizer.Add(btn_sizer, 0, flag=wx.ALIGN_RIGHT\|wx.LEFT\|wx.RIGHT, border=5)
2805	2802	sizer.AddSpacer(5)
...	...	@@ -3202,8 +3199,8 @@ class FillHolesAutoDialog(wx.Dialog):
3202	3199	sizer.AddSpacer(5)
3203	3200
3204	3201	btn_sizer = wx.BoxSizer(wx.HORIZONTAL)
3205		- btn_sizer.Add(self.apply_btn, 0, flag=wx.ALIGN_RIGHT, border=5)
3206		- btn_sizer.Add(self.close_btn, 0, flag=wx.LEFT\|wx.ALIGN_RIGHT, border=5)
	3202	+ btn_sizer.Add(self.apply_btn, 0)# flag=wx.ALIGN_RIGHT, border=5)
	3203	+ btn_sizer.Add(self.close_btn, 0, flag=wx.LEFT, border=5)
3207	3204
3208	3205	sizer.Add(btn_sizer, 0, flag=wx.ALIGN_RIGHT\|wx.LEFT\|wx.RIGHT, border=5)
3209	3206
...	...
...	...	@@ -789,8 +789,8 @@ class SingleImagePreview(wx.Panel):
789	789	in_sizer.Add(checkbox, 0)
790	790
791	791	sizer = wx.BoxSizer(wx.VERTICAL)
792		- sizer.Add(self.panel, 20, wx.GROW\|wx.EXPAND)
793		- sizer.Add(in_sizer, 1, wx.GROW\|wx.EXPAND)
	792	+ sizer.Add(self.panel, 1, wx.GROW\|wx.EXPAND)
	793	+ sizer.Add(in_sizer, 0, wx.GROW\|wx.EXPAND)
794	794	sizer.Fit(self)
795	795
796	796	self.SetSizer(sizer)
...	...