Adapted camera positions to coronal and sagital cases, and added the option to flip image

tfmoraes
1 parent 295c16a0
Showing 11 changed files with 130 additions and 59 deletions Show diff stats
invesalius/constants.py
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/data/mask.py
invesalius/data/slice_.py
invesalius/data/surface_process.py
invesalius/data/viewer_slice.py
invesalius/data/viewer_volume.py
invesalius/data/volume.py
invesalius/gui/dicom_preview_panel.py
invesalius/gui/frame.py
@@ -109,11 +109,11 @@ IMPORT_INTERVAL = [_(&quot;Keep all slices&quot;), _(&quot;Skip 1 for each 2 slices&quot;),
 AXIAL_SLICE_CAM_POSITION = {"AXIAL":(0, 0, 1), "CORONAL":(0, -1, 0), "SAGITAL":(1, 0, 0)}
 AXIAL_SLICE_CAM_VIEW_UP =  {"AXIAL":(0, 1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(0, 0, 1)}
  
-SAGITAL_SLICE_CAM_POSITION = {"AXIAL":(0, 1, 0), "CORONAL":(1, 0, 0), "SAGITAL":(0, 0, -1)}
-SAGITAL_SLICE_CAM_VIEW_UP =  {"AXIAL":(-1, 0, 0), "CORONAL":(0, 1, 0), "SAGITAL":(0, 1, 0)}
+SAGITAL_SLICE_CAM_POSITION = {"AXIAL":(0, 0, 1), "CORONAL":(0, 1, 0), "SAGITAL":(-1, 0, 0)}
+SAGITAL_SLICE_CAM_VIEW_UP =  {"AXIAL":(0, -1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(0, 0, 1)}
  
-CORONAL_SLICE_CAM_POSITION = {"AXIAL":(0, 1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(1, 0, 0)}
-CORONAL_SLICE_CAM_VIEW_UP =  {"AXIAL":(0, 0, -1), "CORONAL":(0, 1, 0), "SAGITAL":(0, 1, 0)}
+CORONAL_SLICE_CAM_POSITION = {"AXIAL":(0, 0, 1), "CORONAL":(0, 1, 0), "SAGITAL":(-1, 0, 0)}
+CORONAL_SLICE_CAM_VIEW_UP =  {"AXIAL":(0, -1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(0, 0, 1)}
  
 SLICE_POSITION = {AXIAL:[AXIAL_SLICE_CAM_VIEW_UP, AXIAL_SLICE_CAM_POSITION],
                   SAGITAL:[SAGITAL_SLICE_CAM_VIEW_UP, SAGITAL_SLICE_CAM_POSITION],
@@ -457,6 +457,9 @@ ID_DICOM_NETWORK] = [wx.NewId() for number in range(14)]
 ID_ABOUT = wx.NewId()
 ID_START = wx.NewId()
  
+ID_FLIP_X = wx.NewId()
+ID_FLIP_Y = wx.NewId()
+ID_FLIP_Z = wx.NewId()
 #---------------------------------------------------------
 STATE_DEFAULT = 1000
 STATE_WL = 1001
@@ -432,6 +432,7 @@ class Controller():
                                 header['glmax'])
         proj.window = proj.threshold_range[1] - proj.threshold_range[0]
         proj.level =  (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
+        proj.spacing = header['pixdim'][1:4]
  
         self.Slice = sl.Slice()
         self.Slice.matrix = matrix
@@ -495,8 +496,11 @@ class Controller():
         if file_range != None and file_range[1] > file_range[0]:
             filelist = filelist[file_range[0]:file_range[1] + 1]
  
-        print ">>>>>>>>>>>>>>>>>>",filelist 
         zspacing = dicom_group.zspacing * interval
+
+        print "\n======================================="
+        print ">>>>>>>>>>>>>>>>>> zspacing", zspacing, interval
+        print "\n======================================="
         size = dicom.image.size
         bits = dicom.image.bits_allocad
         sop_class_uid = dicom.acquisition.sop_class_uid
@@ -457,6 +457,9 @@ def dcm2memmap(files, slice_size, orientation):
             matrix[:, n, :] = array
         elif orientation == 'SAGITTAL':
             array.shape = matrix.shape[0], matrix.shape[1]
+            # TODO: Verify if it's necessary to add the slices swapped only in
+            # sagittal rmi or only in # Rasiane's case or is necessary in all
+            # sagittal cases.
             matrix[:, :, n] = array
         else:
             print array.shape, matrix.shape
@@ -29,6 +29,8 @@ import vtk
 import constants as const
 import imagedata_utils as iu
  
+from wx.lib.pubsub import pub as Publisher
+
 class Mask():
     general_index = -1
     def __init__(self):
@@ -43,6 +45,10 @@ class Mask():
         self.is_shown = 1
         self.edited_points = {}
         self.was_edited = False
+        self.__bind_events()
+
+    def __bind_events(self):
+        Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
  
     def SavePlist(self, filename):
         mask = {}
@@ -79,6 +85,19 @@ class Mask():
         path = os.path.join(dirpath, mask_file)
         self._open_mask(path, tuple(shape))
  
+    def OnFlipVolume(self, pubsub_evt):
+        axis = pubsub_evt.data
+        submatrix = self.matrix[1:, 1:, 1:]
+        if axis == 0:
+            submatrix[:] = submatrix[::-1]
+            self.matrix[1::, 0, 0] = self.matrix[:0:-1, 0, 0]
+        elif axis == 1:
+            submatrix[:] = submatrix[:, ::-1]
+            self.matrix[0, 1::, 0] = self.matrix[0, :0:-1, 0]
+        elif axis == 2:
+            submatrix[:] = submatrix[:, :, ::-1]
+            self.matrix[0, 0, 1::] = self.matrix[0, 0, :0:-1]
+
     def _save_mask(self, filename):
         shutil.copyfile(self.temp_file, filename)
  
@@ -132,6 +132,8 @@ class Slice(object):
         Publisher.subscribe(self.OnRemoveMasks, 'Remove masks')
         Publisher.subscribe(self.OnDuplicateMasks, 'Duplicate masks')
         Publisher.subscribe(self.UpdateSlice3D,'Update slice 3D')
+
+        Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
  
     def GetMaxSliceNumber(self, orientation):
         shape = self.matrix.shape
@@ -703,15 +705,15 @@ class Slice(object):
         cast.ClampOverflowOn()
         cast.Update()
  
-        if (original_orientation == const.AXIAL):
-            flip = vtk.vtkImageFlip()
-            flip.SetInput(cast.GetOutput())
-            flip.SetFilteredAxis(1)
-            flip.FlipAboutOriginOn()
-            flip.Update()
-            widget.SetInput(flip.GetOutput())
-        else:
-            widget.SetInput(cast.GetOutput())
+        #if (original_orientation == const.AXIAL):
+        flip = vtk.vtkImageFlip()
+        flip.SetInput(cast.GetOutput())
+        flip.SetFilteredAxis(1)
+        flip.FlipAboutOriginOn()
+        flip.Update()
+        widget.SetInput(flip.GetOutput())
+        #else:
+            #widget.SetInput(cast.GetOutput())
  
     def UpdateSlice3D(self, pubsub_evt):
         widget, orientation = pubsub_evt.data
@@ -723,15 +725,15 @@ class Slice(object):
         cast.ClampOverflowOn()
         cast.Update()
  
-        if (original_orientation == const.AXIAL):
-            flip = vtk.vtkImageFlip()
-            flip.SetInput(cast.GetOutput())
-            flip.SetFilteredAxis(1)
-            flip.FlipAboutOriginOn()
-            flip.Update()
-            widget.SetInput(flip.GetOutput())
-        else:
-            widget.SetInput(cast.GetOutput())
+        #if (original_orientation == const.AXIAL):
+        flip = vtk.vtkImageFlip()
+        flip.SetInput(cast.GetOutput())
+        flip.SetFilteredAxis(1)
+        flip.FlipAboutOriginOn()
+        flip.Update()
+        widget.SetInput(flip.GetOutput())
+        #else:
+            #widget.SetInput(cast.GetOutput())
  
  
  
@@ -966,6 +968,18 @@ class Slice(object):
         self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype,
                                    mode='r+')
  
+    def OnFlipVolume(self, pubsub_evt):
+        axis = pubsub_evt.data
+        if axis == 0:
+            self.matrix[:] = self.matrix[::-1]
+        elif axis == 1:
+            self.matrix[:] = self.matrix[:, ::-1]
+        elif axis == 2:
+            self.matrix[:] = self.matrix[:, :, ::-1]
+
+        for buffer_ in self.buffer_slices.values():
+            buffer_.discard_buffer()
+
     def OnExportMask(self, pubsub_evt):
         #imagedata = self.current_mask.imagedata
         imagedata = self.imagedata
@@ -97,6 +97,8 @@ class SurfaceProcess(multiprocessing.Process):
         flip.FlipAboutOriginOn()
         flip.Update()
  
+        image = flip.GetOutput()
+
         #filename = tempfile.mktemp(suffix='_%s.vti' % (self.pid))
         #writer = vtk.vtkXMLImageDataWriter()
         #writer.SetInput(mask_vtk)
@@ -110,7 +112,8 @@ class SurfaceProcess(multiprocessing.Process):
         #if self.mode == "CONTOUR":
         #print "Contour"
         contour = vtk.vtkContourFilter()
-        contour.SetInput(flip.GetOutput())
+        contour.SetInput(image)
+        #contour.SetInput(flip.GetOutput())
         if self.from_binary:
             contour.SetValue(0, 127) # initial threshold
         else:
@@ -1311,7 +1311,7 @@ class Viewer(wx.Panel):
     def __update_camera(self):
         orientation = self.orientation
         proj = project.Project()
-        orig_orien = 1 #proj.original_orientation
+        orig_orien = proj.original_orientation
  
         self.cam.SetFocalPoint(0, 0, 0)
         self.cam.SetViewUp(const.SLICE_POSITION[orig_orien][0][self.orientation])
@@ -180,8 +180,6 @@ class Viewer(wx.Panel):
  
         Publisher.subscribe(self.RemoveVolume, 'Remove Volume')
  
-
-
     def SetStereoMode(self, pubsub_evt):
         mode = pubsub_evt.data
         ren_win = self.interactor.GetRenderWindow()
@@ -210,7 +208,6 @@ class Viewer(wx.Panel):
  
         self.interactor.Render()
  
-
     def CreateBallReference(self):
         self.ball_reference = vtk.vtkSphereSource()
         self.ball_reference.SetRadius(5)
@@ -271,7 +268,6 @@ class Viewer(wx.Panel):
  
                 image = image.GetOutput()
  
-
                 # write image file
                 if (filetype == const.FILETYPE_BMP):
                     writer = vtk.vtkBMPWriter()
@@ -289,8 +285,6 @@ class Viewer(wx.Panel):
                 writer.SetFileName(filename)
                 writer.Write()
         Publisher.sendMessage('End busy cursor')
-
-
  
     def OnCloseProject(self, pubsub_evt):
         if self.raycasting_volume:
@@ -844,8 +838,8 @@ class SlicePlane:
     def Create(self):
         plane_x = self.plane_x = vtk.vtkImagePlaneWidget()
         plane_x.InteractionOff()
-        Publisher.sendMessage('Input Image in the widget', 
-                                                (plane_x, 'SAGITAL'))
+        #Publisher.sendMessage('Input Image in the widget', 
+                                                #(plane_x, 'SAGITAL'))
         plane_x.SetPlaneOrientationToXAxes()
         plane_x.TextureVisibilityOn()
         plane_x.SetLeftButtonAction(0)
@@ -856,8 +850,8 @@ class SlicePlane:
  
         plane_y = self.plane_y = vtk.vtkImagePlaneWidget()
         plane_y.DisplayTextOff()
-        Publisher.sendMessage('Input Image in the widget', 
-                                                (plane_y, 'CORONAL'))
+        #Publisher.sendMessage('Input Image in the widget', 
+                                                #(plane_y, 'CORONAL'))
         plane_y.SetPlaneOrientationToYAxes()
         plane_y.TextureVisibilityOn()
         plane_y.SetLeftButtonAction(0)
@@ -869,8 +863,8 @@ class SlicePlane:
  
         plane_z = self.plane_z = vtk.vtkImagePlaneWidget()
         plane_z.InteractionOff()
-        Publisher.sendMessage('Input Image in the widget', 
-                                                (plane_z, 'AXIAL'))
+        #Publisher.sendMessage('Input Image in the widget', 
+                                                #(plane_z, 'AXIAL'))
         plane_z.SetPlaneOrientationToZAxes()
         plane_z.TextureVisibilityOn()
         plane_z.SetLeftButtonAction(0)
@@ -85,6 +85,7 @@ class Volume():
         self.plane = None
         self.plane_on = False
         self.volume = None
+        self.image = None
         self.loaded_image = 0
         self.__bind_events()
  
@@ -109,6 +110,8 @@ class Volume():
  
         Publisher.subscribe(self.ResetRayCasting, 'Reset Reaycasting')
  
+        Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
+
     def ResetRayCasting(self, pub_evt):
         if self.exist:
             self.exist = None
@@ -171,6 +174,13 @@ class Volume():
             colour = self.GetBackgroundColour()
             Publisher.sendMessage('Change volume viewer background colour', colour)
             Publisher.sendMessage('Change volume viewer gui colour', colour)
+
+    def OnFlipVolume(self, pubsub_evt):
+        print "Flipping Volume"
+        self.loaded_image = False
+        del self.image
+        self.image = None
+        self.exist = None
  
     def __load_preset_config(self):
         self.config = prj.Project().raycasting_preset
@@ -461,19 +471,15 @@ class Volume():
         return imagedata
  
     def LoadImage(self):
-        
-
         slice_data = slice_.Slice()
         n_array = slice_data.matrix
         spacing = slice_data.spacing
         slice_number = 0
         orientation = 'AXIAL'
  
-
         image = converters.to_vtk(n_array, spacing, slice_number, orientation) 
         self.image = image
  
-
     def LoadVolume(self):
         proj = prj.Project()
         #image = imagedata_utils.to_vtk(n_array, spacing, slice_number, orientation) 
@@ -491,19 +497,19 @@ class Volume():
         else:
             flip_image = False
  
-        if (flip_image):    
-            update_progress= vtk_utils.ShowProgress(2 + number_filters) 
-            # Flip original vtkImageData
-            flip = vtk.vtkImageFlip()
-            flip.SetInput(image)
-            flip.SetFilteredAxis(1)
-            flip.FlipAboutOriginOn()
-            flip.AddObserver("ProgressEvent", lambda obj,evt:
-                                update_progress(flip, "Rendering..."))
-            flip.Update()
-            image = flip.GetOutput()
-        else:
-            update_progress= vtk_utils.ShowProgress(1 + number_filters)
+        #if (flip_image):    
+        update_progress= vtk_utils.ShowProgress(2 + number_filters) 
+        # Flip original vtkImageData
+        flip = vtk.vtkImageFlip()
+        flip.SetInput(image)
+        flip.SetFilteredAxis(1)
+        flip.FlipAboutOriginOn()
+        flip.AddObserver("ProgressEvent", lambda obj,evt:
+                            update_progress(flip, "Rendering..."))
+        flip.Update()
+        image = flip.GetOutput()
+        #else:
+            #update_progress= vtk_utils.ShowProgress(1 + number_filters)
  
         scale = image.GetScalarRange()
         self.scale = scale
@@ -813,7 +813,12 @@ class SingleImagePreview(wx.Panel):
  
         ## Text related to slice position
         value1 = STR_SPC %(dicom.image.spacing[2])
-        value2 = STR_LOCAL %(dicom.image.position[2])
+        if dicom.image.orientation_label == 'AXIAL':
+            value2 = STR_LOCAL %(dicom.image.position[2])
+        elif dicom.image.orientation_label == 'CORONAL':
+            value2 = STR_LOCAL %(dicom.image.position[1])
+        elif dicom.image.orientation_label == 'SAGITTAL':
+            value2 = STR_LOCAL %(dicom.image.position[0])
         value = "%s\n%s" %(value1, value2)
         self.text_image_location.SetValue(value)
  
@@ -339,6 +339,11 @@ class Frame(wx.Frame):
             self.ShowPreferences()      
         elif id == const.ID_DICOM_NETWORK:
             self.ShowRetrieveDicomPanel() 
+        elif id in (const.ID_FLIP_X, const.ID_FLIP_Y, const.ID_FLIP_Z):
+            axis = {const.ID_FLIP_X: 2, 
+                    const.ID_FLIP_Y: 1, 
+                    const.ID_FLIP_Z: 0}[id]
+            self.FlipVolume(axis)
  
     def OnSize(self, evt):
         """
@@ -409,6 +414,10 @@ class Frame(wx.Frame):
         """
         Publisher.sendMessage('Show analyze dialog', True)
  
+    def FlipVolume(self, axis):
+        Publisher.sendMessage('Flip volume', axis)
+        Publisher.sendMessage('Reload actual slice') 
+
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
@@ -474,12 +483,23 @@ class MenuBar(wx.MenuBar):
         #file_menu.AppendSeparator()
         app(const.ID_EXIT, _("Exit"))
  
-        # EDIT
-        #file_edit = wx.Menu()
-        #app = file_edit.Append
+
+        ############################### EDIT###############################
+        # Flip
+        flip_menu = wx.Menu()
+        app = flip_menu.Append
+        app(const.ID_FLIP_X, _("R <-> L"))
+        app(const.ID_FLIP_Y, _("A <-> P"))
+        app(const.ID_FLIP_Z, _("T <-> B"))
+
+        file_edit = wx.Menu()
+        app = file_edit.Append
+        file_edit.AppendMenu(wx.NewId(), _('Flip'), flip_menu)
         #app(wx.ID_UNDO, "Undo\tCtrl+Z")
         #app(wx.ID_REDO, "Redo\tCtrl+Y")
         #app(const.ID_EDIT_LIST, "Show Undo List...")
+        #################################################################
+
  
         # VIEW
         #view_tool_menu = wx.Menu()
@@ -527,7 +547,7 @@ class MenuBar(wx.MenuBar):
  
         # Add all menus to menubar
         self.Append(file_menu, _("File"))
-        #self.Append(file_edit, "Edit")
+        self.Append(file_edit, "Edit")
         #self.Append(view_menu, "View")
         #self.Append(tools_menu, "Tools")
         self.Append(options_menu, _("Options"))
...	...	@@ -109,11 +109,11 @@ IMPORT_INTERVAL = [_("Keep all slices"), _("Skip 1 for each 2 slices"),
109	109	AXIAL_SLICE_CAM_POSITION = {"AXIAL":(0, 0, 1), "CORONAL":(0, -1, 0), "SAGITAL":(1, 0, 0)}
110	110	AXIAL_SLICE_CAM_VIEW_UP = {"AXIAL":(0, 1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(0, 0, 1)}
111	111
112		-SAGITAL_SLICE_CAM_POSITION = {"AXIAL":(0, 1, 0), "CORONAL":(1, 0, 0), "SAGITAL":(0, 0, -1)}
113		-SAGITAL_SLICE_CAM_VIEW_UP = {"AXIAL":(-1, 0, 0), "CORONAL":(0, 1, 0), "SAGITAL":(0, 1, 0)}
	112	+SAGITAL_SLICE_CAM_POSITION = {"AXIAL":(0, 0, 1), "CORONAL":(0, 1, 0), "SAGITAL":(-1, 0, 0)}
	113	+SAGITAL_SLICE_CAM_VIEW_UP = {"AXIAL":(0, -1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(0, 0, 1)}
114	114
115		-CORONAL_SLICE_CAM_POSITION = {"AXIAL":(0, 1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(1, 0, 0)}
116		-CORONAL_SLICE_CAM_VIEW_UP = {"AXIAL":(0, 0, -1), "CORONAL":(0, 1, 0), "SAGITAL":(0, 1, 0)}
	115	+CORONAL_SLICE_CAM_POSITION = {"AXIAL":(0, 0, 1), "CORONAL":(0, 1, 0), "SAGITAL":(-1, 0, 0)}
	116	+CORONAL_SLICE_CAM_VIEW_UP = {"AXIAL":(0, -1, 0), "CORONAL":(0, 0, 1), "SAGITAL":(0, 0, 1)}
117	117
118	118	SLICE_POSITION = {AXIAL:[AXIAL_SLICE_CAM_VIEW_UP, AXIAL_SLICE_CAM_POSITION],
119	119	SAGITAL:[SAGITAL_SLICE_CAM_VIEW_UP, SAGITAL_SLICE_CAM_POSITION],
...	...	@@ -457,6 +457,9 @@ ID_DICOM_NETWORK] = [wx.NewId() for number in range(14)]
457	457	ID_ABOUT = wx.NewId()
458	458	ID_START = wx.NewId()
459	459
	460	+ID_FLIP_X = wx.NewId()
	461	+ID_FLIP_Y = wx.NewId()
	462	+ID_FLIP_Z = wx.NewId()
460	463	#---------------------------------------------------------
461	464	STATE_DEFAULT = 1000
462	465	STATE_WL = 1001
...	...
...	...	@@ -432,6 +432,7 @@ class Controller():
432	432	header['glmax'])
433	433	proj.window = proj.threshold_range[1] - proj.threshold_range[0]
434	434	proj.level = (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
	435	+ proj.spacing = header['pixdim'][1:4]
435	436
436	437	self.Slice = sl.Slice()
437	438	self.Slice.matrix = matrix
...	...	@@ -495,8 +496,11 @@ class Controller():
495	496	if file_range != None and file_range[1] > file_range[0]:
496	497	filelist = filelist[file_range[0]:file_range[1] + 1]
497	498
498		- print ">>>>>>>>>>>>>>>>>>",filelist
499	499	zspacing = dicom_group.zspacing * interval
	500	+
	501	+ print "\n======================================="
	502	+ print ">>>>>>>>>>>>>>>>>> zspacing", zspacing, interval
	503	+ print "\n======================================="
500	504	size = dicom.image.size
501	505	bits = dicom.image.bits_allocad
502	506	sop_class_uid = dicom.acquisition.sop_class_uid
...	...
...	...	@@ -457,6 +457,9 @@ def dcm2memmap(files, slice_size, orientation):
457	457	matrix[:, n, :] = array
458	458	elif orientation == 'SAGITTAL':
459	459	array.shape = matrix.shape[0], matrix.shape[1]
	460	+ # TODO: Verify if it's necessary to add the slices swapped only in
	461	+ # sagittal rmi or only in # Rasiane's case or is necessary in all
	462	+ # sagittal cases.
460	463	matrix[:, :, n] = array
461	464	else:
462	465	print array.shape, matrix.shape
...	...
...	...	@@ -29,6 +29,8 @@ import vtk
29	29	import constants as const
30	30	import imagedata_utils as iu
31	31
	32	+from wx.lib.pubsub import pub as Publisher
	33	+
32	34	class Mask():
33	35	general_index = -1
34	36	def __init__(self):
...	...	@@ -43,6 +45,10 @@ class Mask():
43	45	self.is_shown = 1
44	46	self.edited_points = {}
45	47	self.was_edited = False
	48	+ self.__bind_events()
	49	+
	50	+ def __bind_events(self):
	51	+ Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
46	52
47	53	def SavePlist(self, filename):
48	54	mask = {}
...	...	@@ -79,6 +85,19 @@ class Mask():
79	85	path = os.path.join(dirpath, mask_file)
80	86	self._open_mask(path, tuple(shape))
81	87
	88	+ def OnFlipVolume(self, pubsub_evt):
	89	+ axis = pubsub_evt.data
	90	+ submatrix = self.matrix[1:, 1:, 1:]
	91	+ if axis == 0:
	92	+ submatrix[:] = submatrix[::-1]
	93	+ self.matrix[1::, 0, 0] = self.matrix[:0:-1, 0, 0]
	94	+ elif axis == 1:
	95	+ submatrix[:] = submatrix[:, ::-1]
	96	+ self.matrix[0, 1::, 0] = self.matrix[0, :0:-1, 0]
	97	+ elif axis == 2:
	98	+ submatrix[:] = submatrix[:, :, ::-1]
	99	+ self.matrix[0, 0, 1::] = self.matrix[0, 0, :0:-1]
	100	+
82	101	def _save_mask(self, filename):
83	102	shutil.copyfile(self.temp_file, filename)
84	103
...	...
...	...	@@ -132,6 +132,8 @@ class Slice(object):
132	132	Publisher.subscribe(self.OnRemoveMasks, 'Remove masks')
133	133	Publisher.subscribe(self.OnDuplicateMasks, 'Duplicate masks')
134	134	Publisher.subscribe(self.UpdateSlice3D,'Update slice 3D')
	135	+
	136	+ Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
135	137
136	138	def GetMaxSliceNumber(self, orientation):
137	139	shape = self.matrix.shape
...	...	@@ -703,15 +705,15 @@ class Slice(object):
703	705	cast.ClampOverflowOn()
704	706	cast.Update()
705	707
706		- if (original_orientation == const.AXIAL):
707		- flip = vtk.vtkImageFlip()
708		- flip.SetInput(cast.GetOutput())
709		- flip.SetFilteredAxis(1)
710		- flip.FlipAboutOriginOn()
711		- flip.Update()
712		- widget.SetInput(flip.GetOutput())
713		- else:
714		- widget.SetInput(cast.GetOutput())
	708	+ #if (original_orientation == const.AXIAL):
	709	+ flip = vtk.vtkImageFlip()
	710	+ flip.SetInput(cast.GetOutput())
	711	+ flip.SetFilteredAxis(1)
	712	+ flip.FlipAboutOriginOn()
	713	+ flip.Update()
	714	+ widget.SetInput(flip.GetOutput())
	715	+ #else:
	716	+ #widget.SetInput(cast.GetOutput())
715	717
716	718	def UpdateSlice3D(self, pubsub_evt):
717	719	widget, orientation = pubsub_evt.data
...	...	@@ -723,15 +725,15 @@ class Slice(object):
723	725	cast.ClampOverflowOn()
724	726	cast.Update()
725	727
726		- if (original_orientation == const.AXIAL):
727		- flip = vtk.vtkImageFlip()
728		- flip.SetInput(cast.GetOutput())
729		- flip.SetFilteredAxis(1)
730		- flip.FlipAboutOriginOn()
731		- flip.Update()
732		- widget.SetInput(flip.GetOutput())
733		- else:
734		- widget.SetInput(cast.GetOutput())
	728	+ #if (original_orientation == const.AXIAL):
	729	+ flip = vtk.vtkImageFlip()
	730	+ flip.SetInput(cast.GetOutput())
	731	+ flip.SetFilteredAxis(1)
	732	+ flip.FlipAboutOriginOn()
	733	+ flip.Update()
	734	+ widget.SetInput(flip.GetOutput())
	735	+ #else:
	736	+ #widget.SetInput(cast.GetOutput())
735	737
736	738
737	739
...	...	@@ -966,6 +968,18 @@ class Slice(object):
966	968	self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype,
967	969	mode='r+')
968	970
	971	+ def OnFlipVolume(self, pubsub_evt):
	972	+ axis = pubsub_evt.data
	973	+ if axis == 0:
	974	+ self.matrix[:] = self.matrix[::-1]
	975	+ elif axis == 1:
	976	+ self.matrix[:] = self.matrix[:, ::-1]
	977	+ elif axis == 2:
	978	+ self.matrix[:] = self.matrix[:, :, ::-1]
	979	+
	980	+ for buffer_ in self.buffer_slices.values():
	981	+ buffer_.discard_buffer()
	982	+
969	983	def OnExportMask(self, pubsub_evt):
970	984	#imagedata = self.current_mask.imagedata
971	985	imagedata = self.imagedata
...	...
...	...	@@ -97,6 +97,8 @@ class SurfaceProcess(multiprocessing.Process):
97	97	flip.FlipAboutOriginOn()
98	98	flip.Update()
99	99
	100	+ image = flip.GetOutput()
	101	+
100	102	#filename = tempfile.mktemp(suffix='_%s.vti' % (self.pid))
101	103	#writer = vtk.vtkXMLImageDataWriter()
102	104	#writer.SetInput(mask_vtk)
...	...	@@ -110,7 +112,8 @@ class SurfaceProcess(multiprocessing.Process):
110	112	#if self.mode == "CONTOUR":
111	113	#print "Contour"
112	114	contour = vtk.vtkContourFilter()
113		- contour.SetInput(flip.GetOutput())
	115	+ contour.SetInput(image)
	116	+ #contour.SetInput(flip.GetOutput())
114	117	if self.from_binary:
115	118	contour.SetValue(0, 127) # initial threshold
116	119	else:
...	...
...	...	@@ -1311,7 +1311,7 @@ class Viewer(wx.Panel):
1311	1311	def __update_camera(self):
1312	1312	orientation = self.orientation
1313	1313	proj = project.Project()
1314		- orig_orien = 1 #proj.original_orientation
	1314	+ orig_orien = proj.original_orientation
1315	1315
1316	1316	self.cam.SetFocalPoint(0, 0, 0)
1317	1317	self.cam.SetViewUp(const.SLICE_POSITION[orig_orien][0][self.orientation])
...	...
...	...	@@ -180,8 +180,6 @@ class Viewer(wx.Panel):
180	180
181	181	Publisher.subscribe(self.RemoveVolume, 'Remove Volume')
182	182
183		-
184		-
185	183	def SetStereoMode(self, pubsub_evt):
186	184	mode = pubsub_evt.data
187	185	ren_win = self.interactor.GetRenderWindow()
...	...	@@ -210,7 +208,6 @@ class Viewer(wx.Panel):
210	208
211	209	self.interactor.Render()
212	210
213		-
214	211	def CreateBallReference(self):
215	212	self.ball_reference = vtk.vtkSphereSource()
216	213	self.ball_reference.SetRadius(5)
...	...	@@ -271,7 +268,6 @@ class Viewer(wx.Panel):
271	268
272	269	image = image.GetOutput()
273	270
274		-
275	271	# write image file
276	272	if (filetype == const.FILETYPE_BMP):
277	273	writer = vtk.vtkBMPWriter()
...	...	@@ -289,8 +285,6 @@ class Viewer(wx.Panel):
289	285	writer.SetFileName(filename)
290	286	writer.Write()
291	287	Publisher.sendMessage('End busy cursor')
292		-
293		-
294	288
295	289	def OnCloseProject(self, pubsub_evt):
296	290	if self.raycasting_volume:
...	...	@@ -844,8 +838,8 @@ class SlicePlane:
844	838	def Create(self):
845	839	plane_x = self.plane_x = vtk.vtkImagePlaneWidget()
846	840	plane_x.InteractionOff()
847		- Publisher.sendMessage('Input Image in the widget',
848		- (plane_x, 'SAGITAL'))
	841	+ #Publisher.sendMessage('Input Image in the widget',
	842	+ #(plane_x, 'SAGITAL'))
849	843	plane_x.SetPlaneOrientationToXAxes()
850	844	plane_x.TextureVisibilityOn()
851	845	plane_x.SetLeftButtonAction(0)
...	...	@@ -856,8 +850,8 @@ class SlicePlane:
856	850
857	851	plane_y = self.plane_y = vtk.vtkImagePlaneWidget()
858	852	plane_y.DisplayTextOff()
859		- Publisher.sendMessage('Input Image in the widget',
860		- (plane_y, 'CORONAL'))
	853	+ #Publisher.sendMessage('Input Image in the widget',
	854	+ #(plane_y, 'CORONAL'))
861	855	plane_y.SetPlaneOrientationToYAxes()
862	856	plane_y.TextureVisibilityOn()
863	857	plane_y.SetLeftButtonAction(0)
...	...	@@ -869,8 +863,8 @@ class SlicePlane:
869	863
870	864	plane_z = self.plane_z = vtk.vtkImagePlaneWidget()
871	865	plane_z.InteractionOff()
872		- Publisher.sendMessage('Input Image in the widget',
873		- (plane_z, 'AXIAL'))
	866	+ #Publisher.sendMessage('Input Image in the widget',
	867	+ #(plane_z, 'AXIAL'))
874	868	plane_z.SetPlaneOrientationToZAxes()
875	869	plane_z.TextureVisibilityOn()
876	870	plane_z.SetLeftButtonAction(0)
...	...
...	...	@@ -85,6 +85,7 @@ class Volume():
85	85	self.plane = None
86	86	self.plane_on = False
87	87	self.volume = None
	88	+ self.image = None
88	89	self.loaded_image = 0
89	90	self.__bind_events()
90	91
...	...	@@ -109,6 +110,8 @@ class Volume():
109	110
110	111	Publisher.subscribe(self.ResetRayCasting, 'Reset Reaycasting')
111	112
	113	+ Publisher.subscribe(self.OnFlipVolume, 'Flip volume')
	114	+
112	115	def ResetRayCasting(self, pub_evt):
113	116	if self.exist:
114	117	self.exist = None
...	...	@@ -171,6 +174,13 @@ class Volume():
171	174	colour = self.GetBackgroundColour()
172	175	Publisher.sendMessage('Change volume viewer background colour', colour)
173	176	Publisher.sendMessage('Change volume viewer gui colour', colour)
	177	+
	178	+ def OnFlipVolume(self, pubsub_evt):
	179	+ print "Flipping Volume"
	180	+ self.loaded_image = False
	181	+ del self.image
	182	+ self.image = None
	183	+ self.exist = None
174	184
175	185	def __load_preset_config(self):
176	186	self.config = prj.Project().raycasting_preset
...	...	@@ -461,19 +471,15 @@ class Volume():
461	471	return imagedata
462	472
463	473	def LoadImage(self):
464		-
465		-
466	474	slice_data = slice_.Slice()
467	475	n_array = slice_data.matrix
468	476	spacing = slice_data.spacing
469	477	slice_number = 0
470	478	orientation = 'AXIAL'
471	479
472		-
473	480	image = converters.to_vtk(n_array, spacing, slice_number, orientation)
474	481	self.image = image
475	482
476		-
477	483	def LoadVolume(self):
478	484	proj = prj.Project()
479	485	#image = imagedata_utils.to_vtk(n_array, spacing, slice_number, orientation)
...	...	@@ -491,19 +497,19 @@ class Volume():
491	497	else:
492	498	flip_image = False
493	499
494		- if (flip_image):
495		- update_progress= vtk_utils.ShowProgress(2 + number_filters)
496		- # Flip original vtkImageData
497		- flip = vtk.vtkImageFlip()
498		- flip.SetInput(image)
499		- flip.SetFilteredAxis(1)
500		- flip.FlipAboutOriginOn()
501		- flip.AddObserver("ProgressEvent", lambda obj,evt:
502		- update_progress(flip, "Rendering..."))
503		- flip.Update()
504		- image = flip.GetOutput()
505		- else:
506		- update_progress= vtk_utils.ShowProgress(1 + number_filters)
	500	+ #if (flip_image):
	501	+ update_progress= vtk_utils.ShowProgress(2 + number_filters)
	502	+ # Flip original vtkImageData
	503	+ flip = vtk.vtkImageFlip()
	504	+ flip.SetInput(image)
	505	+ flip.SetFilteredAxis(1)
	506	+ flip.FlipAboutOriginOn()
	507	+ flip.AddObserver("ProgressEvent", lambda obj,evt:
	508	+ update_progress(flip, "Rendering..."))
	509	+ flip.Update()
	510	+ image = flip.GetOutput()
	511	+ #else:
	512	+ #update_progress= vtk_utils.ShowProgress(1 + number_filters)
507	513
508	514	scale = image.GetScalarRange()
509	515	self.scale = scale
...	...
...	...	@@ -813,7 +813,12 @@ class SingleImagePreview(wx.Panel):
813	813
814	814	## Text related to slice position
815	815	value1 = STR_SPC %(dicom.image.spacing[2])
816		- value2 = STR_LOCAL %(dicom.image.position[2])
	816	+ if dicom.image.orientation_label == 'AXIAL':
	817	+ value2 = STR_LOCAL %(dicom.image.position[2])
	818	+ elif dicom.image.orientation_label == 'CORONAL':
	819	+ value2 = STR_LOCAL %(dicom.image.position[1])
	820	+ elif dicom.image.orientation_label == 'SAGITTAL':
	821	+ value2 = STR_LOCAL %(dicom.image.position[0])
817	822	value = "%s\n%s" %(value1, value2)
818	823	self.text_image_location.SetValue(value)
819	824
...	...