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"))
	@@ -29,6 +29,8 @@ import vtk		@@ -29,6 +29,8 @@ import vtk
29	import constants as const	29	import constants as const
30	import imagedata_utils as iu	30	import imagedata_utils as iu
31		31
		32	+from wx.lib.pubsub import pub as Publisher
		33	+
32	class Mask():	34	class Mask():
33	general_index = -1	35	general_index = -1
34	def __init__(self):	36	def __init__(self):
	@@ -43,6 +45,10 @@ class Mask():		@@ -43,6 +45,10 @@ class Mask():
43	self.is_shown = 1	45	self.is_shown = 1
44	self.edited_points = {}	46	self.edited_points = {}
45	self.was_edited = False	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	def SavePlist(self, filename):	53	def SavePlist(self, filename):
48	mask = {}	54	mask = {}
	@@ -79,6 +85,19 @@ class Mask():		@@ -79,6 +85,19 @@ class Mask():
79	path = os.path.join(dirpath, mask_file)	85	path = os.path.join(dirpath, mask_file)
80	self._open_mask(path, tuple(shape))	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	def _save_mask(self, filename):	101	def _save_mask(self, filename):
83	shutil.copyfile(self.temp_file, filename)	102	shutil.copyfile(self.temp_file, filename)
84		103
	@@ -1311,7 +1311,7 @@ class Viewer(wx.Panel):		@@ -1311,7 +1311,7 @@ class Viewer(wx.Panel):
1311	def __update_camera(self):	1311	def __update_camera(self):
1312	orientation = self.orientation	1312	orientation = self.orientation
1313	proj = project.Project()	1313	proj = project.Project()
1314	- orig_orien = 1 #proj.original_orientation	1314	+ orig_orien = proj.original_orientation
1315		1315
1316	self.cam.SetFocalPoint(0, 0, 0)	1316	self.cam.SetFocalPoint(0, 0, 0)
1317	self.cam.SetViewUp(const.SLICE_POSITION[orig_orien][0][self.orientation])	1317	self.cam.SetViewUp(const.SLICE_POSITION[orig_orien][0][self.orientation])