Merge pull request #403 from sotodela/278_add_visualization_for_the_direction_of_the_marker

278 add visualization for the direction of the marker

Merge pull request #403 from sotodela/278_add_visualization_for_the_direction_of_the_marker
278 add visualization for the direction of the marker
Renan · GitHub
2 parents 2d8f59df 6e312c12
Showing 4 changed files with 95 additions and 60 deletions Show diff stats
invesalius/constants.py
invesalius/data/styles.py
invesalius/data/viewer_volume.py
invesalius/gui/task_navigator.py
@@ -671,7 +671,7 @@ Z_COLUMN = 6
 MARKER_COLOUR = (1.0, 1.0, 0.)
 MARKER_SIZE = 2
-
+ARROW_MARKER_SIZE = 10
 CALIBRATION_TRACKER_SAMPLES = 10
 FIDUCIAL_REGISTRATION_ERROR_THRESHOLD = 3.0
@@ -486,7 +486,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
         x, y, z = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)
         self.viewer.UpdateSlicesPosition([x, y, z])
         # This "Set cross" message is needed to update the cross in the other slices
-        Publisher.sendMessage('Set cross focal point', position=[x, y, z, 0., 0., 0.])
+        Publisher.sendMessage('Set cross focal point', position=[x, y, z, None, None, None])
         Publisher.sendMessage('Update slice viewer')
     def OnScrollBar(self, *args, **kwargs):
@@ -494,7 +494,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
         # the actual orientation.
         x, y, z = self.viewer.cross.GetFocalPoint()
         self.viewer.UpdateSlicesPosition([x, y, z])
-        Publisher.sendMessage('Set cross focal point', position=[x, y, z, 0., 0., 0.])
+        Publisher.sendMessage('Set cross focal point', position=[x, y, z, None, None, None])
         Publisher.sendMessage('Update slice viewer')
@@ -70,8 +70,8 @@ class Viewer(wx.Panel):
         self.initial_focus = None
-        self.staticballs = []
-
+        self.static_markers = []
+        self.static_arrows = []
         self.style = None
         interactor = wxVTKRenderWindowInteractor(self, -1, size = self.GetSize())
@@ -278,6 +278,7 @@ class Viewer(wx.Panel):
         # Related to marker creation in navigation tools
         Publisher.subscribe(self.AddMarker, 'Add marker')
+        Publisher.subscribe(self.AddMarkerwithOrientation, 'Add arrow marker')
         Publisher.subscribe(self.HideAllMarkers, 'Hide all markers')
         Publisher.subscribe(self.ShowAllMarkers, 'Show all markers')
         Publisher.subscribe(self.RemoveAllMarkers, 'Remove all markers')
@@ -579,7 +580,7 @@ class Viewer(wx.Panel):
         """
         Set all markers, overwriting the previous markers.
         """
-        self.RemoveAllMarkers(len(self.staticballs))
+        self.RemoveAllMarkers(len(self.static_markers))
         target_selected = False
         for marker in markers:
@@ -607,6 +608,21 @@ class Viewer(wx.Panel):
         self.UpdateRender()
+    def AddMarkerwithOrientation(self, arrow_id, size, color, coord):
+        """
+        Markers arrow with orientation created by navigation tools and rendered in volume viewer.
+        """
+        self.arrow_marker_id = arrow_id
+        coord_flip = list(coord)
+        coord_flip[1] = -coord_flip[1]
+
+        arrow_actor = self.Add_ObjectArrow(coord_flip[:3], coord_flip[3:6], color, size)
+        self.static_markers.append(arrow_actor)
+        self.ren.AddActor(self.static_markers[self.arrow_marker_id])
+        self.arrow_marker_id += 1
+
+        self.Refresh()
+
     def AddMarker(self, ball_id, size, colour, coord):
         """
         Markers created by navigation tools and rendered in volume viewer.
@@ -626,12 +642,12 @@ class Viewer(wx.Panel):
         prop.SetColor(colour)
         # adding a new actor for the present ball
-        self.staticballs.append(vtk.vtkActor())
+        self.static_markers.append(vtk.vtkActor())
-        self.staticballs[self.ball_id].SetMapper(mapper)
-        self.staticballs[self.ball_id].SetProperty(prop)
+        self.static_markers[self.ball_id].SetMapper(mapper)
+        self.static_markers[self.ball_id].SetProperty(prop)
-        self.ren.AddActor(self.staticballs[self.ball_id])
+        self.ren.AddActor(self.static_markers[self.ball_id])
         self.ball_id += 1
         #self.UpdateRender()
@@ -667,33 +683,33 @@ class Viewer(wx.Panel):
     def HideAllMarkers(self, indexes):
         ballid = indexes
         for i in range(0, ballid):
-            self.staticballs[i].SetVisibility(0)
+            self.static_markers[i].SetVisibility(0)
         self.UpdateRender()
     def ShowAllMarkers(self, indexes):
         ballid = indexes
         for i in range(0, ballid):
-            self.staticballs[i].SetVisibility(1)
+            self.static_markers[i].SetVisibility(1)
         self.UpdateRender()
     def RemoveAllMarkers(self, indexes):
         ballid = indexes
         for i in range(0, ballid):
-            self.ren.RemoveActor(self.staticballs[i])
-        self.staticballs = []
+            self.ren.RemoveActor(self.static_markers[i])
+        self.static_markers = []
         self.UpdateRender()
     def RemoveMultipleMarkers(self, index):
         for i in reversed(index):
-            self.ren.RemoveActor(self.staticballs[i])
-            del self.staticballs[i]
+            self.ren.RemoveActor(self.static_markers[i])
+            del self.static_markers[i]
             self.ball_id = self.ball_id - 1
         self.UpdateRender()
     def BlinkMarker(self, index):
         if self.timer:
             self.timer.Stop()
-            self.staticballs[self.index].SetVisibility(1)
+            self.static_markers[self.index].SetVisibility(1)
         self.index = index
         self.timer = wx.Timer(self)
         self.Bind(wx.EVT_TIMER, self.OnBlinkMarker, self.timer)
@@ -701,7 +717,7 @@ class Viewer(wx.Panel):
         self.timer_count = 0
     def OnBlinkMarker(self, evt):
-        self.staticballs[self.index].SetVisibility(int(self.timer_count % 2))
+        self.static_markers[self.index].SetVisibility(int(self.timer_count % 2))
         self.Refresh()
         self.timer_count += 1
@@ -709,20 +725,20 @@ class Viewer(wx.Panel):
         if self.timer:
             self.timer.Stop()
             if index is None:
-                self.staticballs[self.index].SetVisibility(1)
+                self.static_markers[self.index].SetVisibility(1)
                 self.Refresh()
             self.index = False
     def SetNewColor(self, index, color):
-        self.staticballs[index].GetProperty().SetColor([round(s/255.0, 3) for s in color])
+        self.static_markers[index].GetProperty().SetColor([round(s / 255.0, 3) for s in color])
         self.Refresh()
     def OnTargetMarkerTransparency(self, status, index):
         if status:
-            self.staticballs[index].GetProperty().SetOpacity(1)
+            self.static_markers[index].GetProperty().SetOpacity(1)
             # self.staticballs[index].GetProperty().SetOpacity(0.4)
         else:
-            self.staticballs[index].GetProperty().SetOpacity(1)
+            self.static_markers[index].GetProperty().SetOpacity(1)
     def OnUpdateAngleThreshold(self, angle):
         self.anglethreshold = angle
@@ -992,16 +1008,10 @@ class Viewer(wx.Panel):
             self.RemoveTarget()
             self.DisableCoilTracker()
-    def CreateTargetAim(self):
-        if self.aim_actor:
-            self.RemoveTargetAim()
-            self.aim_actor = None
-
-        vtk_colors = vtk.vtkNamedColors()
-
+    def CreateVTKObjectMatrix(self, direction, orientation):
         m_img = dco.coordinates_to_transformation_matrix(
-            position=self.target_coord[:3],
-            orientation=self.target_coord[3:],
+            position=direction,
+            orientation=orientation,
             axes='sxyz',
         )
         m_img = np.asmatrix(m_img)
@@ -1012,7 +1022,16 @@ class Viewer(wx.Panel):
             for col in range(0, 4):
                 m_img_vtk.SetElement(row, col, m_img[row, col])
-        self.m_img_vtk = m_img_vtk
+        return m_img_vtk
+
+    def CreateTargetAim(self):
+        if self.aim_actor:
+            self.RemoveTargetAim()
+            self.aim_actor = None
+
+        vtk_colors = vtk.vtkNamedColors()
+
+        self.m_img_vtk = self.CreateVTKObjectMatrix(self.target_coord[:3], self.target_coord[3:])
         filename = os.path.join(inv_paths.OBJ_DIR, "aim.stl")
@@ -1023,7 +1042,7 @@ class Viewer(wx.Panel):
         # Transform the polydata
         transform = vtk.vtkTransform()
-        transform.SetMatrix(m_img_vtk)
+        transform.SetMatrix(self.m_img_vtk)
         transformPD = vtk.vtkTransformPolyDataFilter()
         transformPD.SetTransform(transform)
         transformPD.SetInputConnection(reader.GetOutputPort())
@@ -1071,7 +1090,7 @@ class Viewer(wx.Panel):
         self.dummy_coil_actor.GetProperty().SetSpecularPower(10)
         self.dummy_coil_actor.GetProperty().SetOpacity(.3)
         self.dummy_coil_actor.SetVisibility(1)
-        self.dummy_coil_actor.SetUserMatrix(m_img_vtk)
+        self.dummy_coil_actor.SetUserMatrix(self.m_img_vtk)
         self.ren.AddActor(self.dummy_coil_actor)
@@ -1424,8 +1443,9 @@ class Viewer(wx.Panel):
         actor.GetProperty().SetLineWidth(5)
         actor.AddPosition(0, 0, 0)
         actor.SetScale(size)
-        actor.SetPosition(direction)
-        actor.SetOrientation(orientation)
+
+        m_img_vtk = self.CreateVTKObjectMatrix(direction, orientation)
+        actor.SetUserMatrix(m_img_vtk)
         return actor
@@ -359,7 +359,7 @@ class NeuronavigationPanel(wx.Panel):
         self.nav_status = False
         self.tracker_fiducial_being_set = None
-        self.current_coord = 0, 0, 0
+        self.current_coord = 0, 0, 0, None, None, None
         # Initialize list of buttons and numctrls for wx objects
         self.btns_set_fiducial = [None, None, None, None, None, None]
@@ -704,7 +704,7 @@ class NeuronavigationPanel(wx.Panel):
         if self.btns_set_fiducial[n].GetValue():
             coord = self.numctrls_fiducial[n][0].GetValue(),\
                     self.numctrls_fiducial[n][1].GetValue(),\
-                    self.numctrls_fiducial[n][2].GetValue(), 0, 0, 0
+                    self.numctrls_fiducial[n][2].GetValue(), None, None, None
             Publisher.sendMessage('Set image fiducial', fiducial_name=fiducial_name, coord=coord[0:3])
@@ -1144,9 +1144,9 @@ class MarkersPanel(wx.Panel):
         x : float = 0
         y : float = 0
         z : float = 0
-        alpha : float = 0
-        beta : float = 0
-        gamma : float = 0
+        alpha : float = dataclasses.field(default = None)
+        beta : float = dataclasses.field(default = None)
+        gamma : float = dataclasses.field(default = None)
         r : float = 0
         g : float = 1
         b : float = 0
@@ -1161,7 +1161,7 @@ class MarkersPanel(wx.Panel):
         # x, y, z, alpha, beta, gamma can be jointly accessed as coord
         @property
         def coord(self):
-            return list((self.x, self.y, self.z, self.alpha, self.beta, self.gamma),)
+            return list((self.x, self.y, self.z, self.alpha, self.beta, self.gamma))
         @coord.setter
         def coord(self, new_coord):
@@ -1201,11 +1201,18 @@ class MarkersPanel(wx.Panel):
                 else:
                     res += ('%s\t' % str(getattr(self, field.name)))
-            # Add world coordinates (in addition to the internal ones).
-            position_world, orientation_world = imagedata_utils.convert_invesalius_to_world(
-                position=[self.x, self.y, self.z],
-                orientation=[self.alpha, self.beta, self.gamma],
-            )
+            if self.alpha is not None and self.beta is not None and self.gamma is not None:
+                # Add world coordinates (in addition to the internal ones).
+                position_world, orientation_world = imagedata_utils.convert_invesalius_to_world(
+                    position=[self.x, self.y, self.z],
+                    orientation=[self.alpha, self.beta, self.gamma],
+                )
+
+            else:
+                position_world, orientation_world = imagedata_utils.convert_invesalius_to_world(
+                      position=[self.x, self.y, self.z],
+                      orientation=[0,0,0],
+                 )
             res += '\t'.join(map(lambda x: 'N/A' if x is None else str(x), (*position_world, *orientation_world)))
             return res
@@ -1215,8 +1222,10 @@ class MarkersPanel(wx.Panel):
             properly formatted, might throw an exception and leave the object
             in an inconsistent state."""
             for field, str_val in zip(dataclasses.fields(self.__class__), inp_str.split('\t')):
-                if field.type is float:
+                if field.type is float and str_val != 'None':
                     setattr(self, field.name, float(str_val))
+                if field.type is float and str_val == 'None':
+                    setattr(self, field.name, None)
                 if field.type is int:
                     setattr(self, field.name, int(str_val))
                 if field.type is str:
@@ -1253,8 +1262,7 @@ class MarkersPanel(wx.Panel):
         self.session = ses.Session()
-        self.current_coord = 0, 0, 0, 0, 0, 0
-        self.current_angle = 0, 0, 0
+        self.current_coord = 0, 0, 0, None, None, None
         self.current_seed = 0, 0, 0
         self.current_robot_target_matrix = [None] * 9
         self.markers = []
@@ -1264,6 +1272,7 @@ class MarkersPanel(wx.Panel):
         self.marker_colour = const.MARKER_COLOUR
         self.marker_size = const.MARKER_SIZE
+        self.arrow_marker_size = const.ARROW_MARKER_SIZE
         self.current_session = 1
         # Change marker size
@@ -1431,13 +1440,11 @@ class MarkersPanel(wx.Panel):
         return list(itertools.chain(*(const.BTNS_IMG_MARKERS[i].values() for i in const.BTNS_IMG_MARKERS)))
     def UpdateCurrentCoord(self, position):
-        self.current_coord = position
-        #self.current_angle = pubsub_evt.data[1][3:]
+        self.current_coord = list(position)
     def UpdateNavigationStatus(self, nav_status, vis_status):
         if not nav_status:
-            sleep(0.5)
-            #self.current_coord[3:] = 0, 0, 0
+            self.current_coord[3:] = None, None, None
             self.nav_status = False
         else:
             self.nav_status = True
@@ -1615,8 +1622,8 @@ class MarkersPanel(wx.Panel):
                     if marker.is_target:
                         self.__set_marker_as_target(len(self.markers) - 1)
-        except:
-            wx.MessageBox(_("Invalid markers file."), _("InVesalius 3"))     
+        except Exception as e:
+            wx.MessageBox(_("Invalid markers file."), _("InVesalius 3"))
     def OnMarkersVisibility(self, evt, ctrl):
         if ctrl.GetValue():
@@ -1681,10 +1688,18 @@ class MarkersPanel(wx.Panel):
         new_robot_marker.robot_target_matrix = self.current_robot_target_matrix
         # Note that ball_id is zero-based, so we assign it len(self.markers) before the new marker is added
-        Publisher.sendMessage('Add marker', ball_id=len(self.markers),
-                                            size=new_marker.size,
-                                            colour=new_marker.colour,
-                                            coord=new_marker.coord[:3])
+        if all([elem is not None for elem in new_marker.coord[3:]]):
+            Publisher.sendMessage('Add arrow marker', arrow_id=len(self.markers),
+                                  size=self.arrow_marker_size,
+                                  color=new_marker.colour,
+                                  coord=new_marker.coord)
+        else:
+            Publisher.sendMessage('Add marker', ball_id=len(self.markers),
+                                  size=new_marker.size,
+                                  colour=new_marker.colour,
+                                  coord=new_marker.coord[:3])
+
+
         self.markers.append(new_marker)
         self.robot_markers.append(new_robot_marker)
	@@ -671,7 +671,7 @@ Z_COLUMN = 6		@@ -671,7 +671,7 @@ Z_COLUMN = 6
671		671
672	MARKER_COLOUR = (1.0, 1.0, 0.)	672	MARKER_COLOUR = (1.0, 1.0, 0.)
673	MARKER_SIZE = 2	673	MARKER_SIZE = 2
674	-	674	+ARROW_MARKER_SIZE = 10
675	CALIBRATION_TRACKER_SAMPLES = 10	675	CALIBRATION_TRACKER_SAMPLES = 10
676	FIDUCIAL_REGISTRATION_ERROR_THRESHOLD = 3.0	676	FIDUCIAL_REGISTRATION_ERROR_THRESHOLD = 3.0
677		677
	@@ -486,7 +486,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):		@@ -486,7 +486,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
486	x, y, z = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)	486	x, y, z = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)
487	self.viewer.UpdateSlicesPosition([x, y, z])	487	self.viewer.UpdateSlicesPosition([x, y, z])
488	# This "Set cross" message is needed to update the cross in the other slices	488	# This "Set cross" message is needed to update the cross in the other slices
489	- Publisher.sendMessage('Set cross focal point', position=[x, y, z, 0., 0., 0.])	489	+ Publisher.sendMessage('Set cross focal point', position=[x, y, z, None, None, None])
490	Publisher.sendMessage('Update slice viewer')	490	Publisher.sendMessage('Update slice viewer')
491		491
492	def OnScrollBar(self, args, *kwargs):	492	def OnScrollBar(self, args, *kwargs):
	@@ -494,7 +494,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):		@@ -494,7 +494,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
494	# the actual orientation.	494	# the actual orientation.
495	x, y, z = self.viewer.cross.GetFocalPoint()	495	x, y, z = self.viewer.cross.GetFocalPoint()
496	self.viewer.UpdateSlicesPosition([x, y, z])	496	self.viewer.UpdateSlicesPosition([x, y, z])
497	- Publisher.sendMessage('Set cross focal point', position=[x, y, z, 0., 0., 0.])	497	+ Publisher.sendMessage('Set cross focal point', position=[x, y, z, None, None, None])
498	Publisher.sendMessage('Update slice viewer')	498	Publisher.sendMessage('Update slice viewer')
499		499
500		500