ADD: NeuronavigationApi to send coil pose via connection object (#413)

Olli-Pekka Kahilakoski · GitHub
1 parent a6843134
Showing 4 changed files with 100 additions and 7 deletions Show diff stats
app.py
invesalius/gui/task_navigator.py
invesalius/navigation/navigation.py
invesalius/net/neuronavigation_api.py
@@ -490,9 +490,20 @@ def print_events(topic=Publisher.AUTO_TOPIC, **msg_data):
     utils.debug("%s\n\tParameters: %s" % (topic, msg_data))
-def main():
+def main(connection=None):
     """
     Initialize InVesalius GUI
+
+    Parameters:
+        connection: An object to communicate with the outside world.
+          In theory, can be any object supports certain function calls.
+          See invesalius.net.neuronavigation_api for a comprehensive
+          description of how the object is used.
+
+          Note that if InVesalius is started in the usual way by running
+          app.py, the connection object defaults to None. To enable this
+          functionality, InVesalius needs to be started by calling the main
+          function directly with a proper connection object.
     """
     options, args = parse_command_line()
@@ -513,6 +524,10 @@ def main():
         PedalConnection().start()
+    from invesalius.net.neuronavigation_api import NeuronavigationApi
+
+    NeuronavigationApi(connection)
+
     if options.no_gui:
         non_gui_startup(options, args)
     else:
@@ -73,6 +73,8 @@ from invesalius.navigation.navigation import Navigation
 from invesalius.navigation.tracker import Tracker
 from invesalius.navigation.robot import Robot
+from invesalius.net.neuronavigation_api import NeuronavigationApi
+
 HAS_PEDAL_CONNECTION = True
 try:
     from invesalius.net.pedal_connection import PedalConnection
@@ -172,6 +174,8 @@ class InnerFoldPanel(wx.Panel):
         tracker = Tracker()
         pedal_connection = PedalConnection() if HAS_PEDAL_CONNECTION else None
+        neuronavigation_api = NeuronavigationApi()
+
         # Fold panel style
         style = fpb.CaptionBarStyle()
         style.SetCaptionStyle(fpb.CAPTIONBAR_GRADIENT_V)
@@ -180,7 +184,12 @@ class InnerFoldPanel(wx.Panel):
         # Fold 1 - Navigation panel
         item = fold_panel.AddFoldPanel(_("Neuronavigation"), collapsed=True)
-        ntw = NeuronavigationPanel(item, tracker, pedal_connection)
+        ntw = NeuronavigationPanel(
+            parent=item,
+            tracker=tracker,
+            pedal_connection=pedal_connection,
+            neuronavigation_api=neuronavigation_api,
+        )
         fold_panel.ApplyCaptionStyle(item, style)
         fold_panel.AddFoldPanelWindow(item, ntw, spacing=0,
@@ -336,7 +345,7 @@ class InnerFoldPanel(wx.Panel):
 class NeuronavigationPanel(wx.Panel):
-    def __init__(self, parent, tracker, pedal_connection):
+    def __init__(self, parent, tracker, pedal_connection, neuronavigation_api):
         wx.Panel.__init__(self, parent)
         try:
             default_colour = wx.SystemSettings.GetColour(wx.SYS_COLOUR_MENUBAR)
@@ -350,8 +359,10 @@ class NeuronavigationPanel(wx.Panel):
         # Initialize global variables
         self.pedal_connection = pedal_connection
+
         self.navigation = Navigation(
             pedal_connection=pedal_connection,
+            neuronavigation_api=neuronavigation_api,
         )
         self.icp = ICP()
         self.tracker = tracker
@@ -64,7 +64,7 @@ class QueueCustom(queue.Queue):
 class UpdateNavigationScene(threading.Thread):
-    def __init__(self, vis_queues, vis_components, event, sle):
+    def __init__(self, vis_queues, vis_components, event, sle, neuronavigation_api):
         """Class (threading) to update the navigation scene with all graphical elements.
         Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
@@ -77,6 +77,8 @@ class UpdateNavigationScene(threading.Thread):
         :type event: threading.Event
         :param sle: Sleep pause in seconds
         :type sle: float
+        :param neuronavigation_api: An API object for communicating the coil position.
+        :type neuronavigation_api: invesalius.net.neuronavigation_api.NeuronavigationAPI
         """
         threading.Thread.__init__(self, name='UpdateScene')
@@ -84,6 +86,7 @@ class UpdateNavigationScene(threading.Thread):
         self.coord_queue, self.serial_port_queue, self.tracts_queue, self.icp_queue, self.robot_target_queue = vis_queues
         self.sle = sle
         self.event = event
+        self.neuronavigation_api = neuronavigation_api
     def run(self):
         # count = 0
@@ -121,6 +124,12 @@ class UpdateNavigationScene(threading.Thread):
                 if view_obj:
                     wx.CallAfter(Publisher.sendMessage, 'Update object matrix', m_img=m_img, coord=coord)
                     wx.CallAfter(Publisher.sendMessage, 'Update object arrow matrix', m_img=m_img, coord=coord, flag= self.peel_loaded)
+
+                self.neuronavigation_api.update_coil_pose(
+                    position=coord[:3],
+                    orientation=coord[3:],
+                )
+
                 self.coord_queue.task_done()
                 # print('UpdateScene: done {}'.format(count))
                 # count += 1
@@ -132,8 +141,9 @@ class UpdateNavigationScene(threading.Thread):
 class Navigation():
-    def __init__(self, pedal_connection):
+    def __init__(self, pedal_connection, neuronavigation_api):
         self.pedal_connection = pedal_connection
+        self.neuronavigation_api = neuronavigation_api
         self.image_fiducials = np.full([3, 3], np.nan)
         self.correg = None
@@ -329,8 +339,15 @@ class Navigation():
                 else:
                     jobs_list.append(dti.ComputeTractsThread(self.trk_inp, queues, self.event, self.sleep_nav))
-            jobs_list.append(UpdateNavigationScene(vis_queues, vis_components,
-                                                    self.event, self.sleep_nav))
+            jobs_list.append(
+                UpdateNavigationScene(
+                    vis_queues=vis_queues,
+                    vis_components=vis_components,
+                    event=self.event,
+                    sle=self.sleep_nav,
+                    neuronavigation_api=self.neuronavigation_api,
+                )
+            )
             for jobs in jobs_list:
                 # jobs.daemon = True
@@ -0,0 +1,50 @@
+#--------------------------------------------------------------------------
+# Software:     InVesalius - Software de Reconstrucao 3D de Imagens Medicas
+# Copyright:    (C) 2001  Centro de Pesquisas Renato Archer
+# Homepage:     http://www.softwarepublico.gov.br
+# Contact:      invesalius@cti.gov.br
+# License:      GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
+#--------------------------------------------------------------------------
+#    Este programa e software livre; voce pode redistribui-lo e/ou
+#    modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
+#    publicada pela Free Software Foundation; de acordo com a versao 2
+#    da Licenca.
+#
+#    Este programa eh distribuido na expectativa de ser util, mas SEM
+#    QUALQUER GARANTIA; sem mesmo a garantia implicita de
+#    COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
+#    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
+#    detalhes.
+#--------------------------------------------------------------------------
+
+from invesalius.utils import Singleton
+
+class NeuronavigationApi(metaclass=Singleton):
+    """
+    An API used internally in InVesalius to communicate with the
+    outside world.
+
+    When something noteworthy happens when running InVesalius, e.g.,
+    the coil is moved during neuronavigation, an object created from
+    this class can be used to update that information.
+
+    When created for the first time, takes a connection object obtained
+    from outside InVesalius (see the main entrypoint in app.py).
+
+    If connection object is not given or it is None, skip doing the updates.
+    """
+    def __init__(self, connection=None):
+        if connection is not None:
+            assert self._hasmethod(connection, 'update_coil_pose')
+
+        self.connection = connection
+
+    def _hasmethod(self, obj, name):
+        return hasattr(obj, name) and callable(getattr(obj, name))
+
+    def update_coil_pose(self, position, orientation):
+        if self.connection is not None:
+            self.connection.update_coil_pose(
+                position=position,
+                orientation=orientation,
+            )
	@@ -490,9 +490,20 @@ def print_events(topic=Publisher.AUTO_TOPIC, **msg_data):		@@ -490,9 +490,20 @@ def print_events(topic=Publisher.AUTO_TOPIC, **msg_data):
490	utils.debug("%s\n\tParameters: %s" % (topic, msg_data))	490	utils.debug("%s\n\tParameters: %s" % (topic, msg_data))
491		491
492		492
493	-def main():	493	+def main(connection=None):
494	"""	494	"""
495	Initialize InVesalius GUI	495	Initialize InVesalius GUI
		496	+
		497	+ Parameters:
		498	+ connection: An object to communicate with the outside world.
		499	+ In theory, can be any object supports certain function calls.
		500	+ See invesalius.net.neuronavigation_api for a comprehensive
		501	+ description of how the object is used.
		502	+
		503	+ Note that if InVesalius is started in the usual way by running
		504	+ app.py, the connection object defaults to None. To enable this
		505	+ functionality, InVesalius needs to be started by calling the main
		506	+ function directly with a proper connection object.
496	"""	507	"""
497	options, args = parse_command_line()	508	options, args = parse_command_line()
498		509
	@@ -513,6 +524,10 @@ def main():		@@ -513,6 +524,10 @@ def main():
513		524
514	PedalConnection().start()	525	PedalConnection().start()
515		526
		527	+ from invesalius.net.neuronavigation_api import NeuronavigationApi
		528	+
		529	+ NeuronavigationApi(connection)
		530	+
516	if options.no_gui:	531	if options.no_gui:
517	non_gui_startup(options, args)	532	non_gui_startup(options, args)
518	else:	533	else:
@@ -0,0 +1,50 @@		@@ -0,0 +1,50 @@
	1	+#--------------------------------------------------------------------------
	2	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
	3	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
	4	+# Homepage: http://www.softwarepublico.gov.br
	5	+# Contact: invesalius@cti.gov.br
	6	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
	7	+#--------------------------------------------------------------------------
	8	+# Este programa e software livre; voce pode redistribui-lo e/ou
	9	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
	10	+# publicada pela Free Software Foundation; de acordo com a versao 2
	11	+# da Licenca.
	12	+#
	13	+# Este programa eh distribuido na expectativa de ser util, mas SEM
	14	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
	15	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
	16	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
	17	+# detalhes.
	18	+#--------------------------------------------------------------------------
	19	+
	20	+from invesalius.utils import Singleton
	21	+
	22	+class NeuronavigationApi(metaclass=Singleton):
	23	+ """
	24	+ An API used internally in InVesalius to communicate with the
	25	+ outside world.
	26	+
	27	+ When something noteworthy happens when running InVesalius, e.g.,
	28	+ the coil is moved during neuronavigation, an object created from
	29	+ this class can be used to update that information.
	30	+
	31	+ When created for the first time, takes a connection object obtained
	32	+ from outside InVesalius (see the main entrypoint in app.py).
	33	+
	34	+ If connection object is not given or it is None, skip doing the updates.
	35	+ """
	36	+ def __init__(self, connection=None):
	37	+ if connection is not None:
	38	+ assert self._hasmethod(connection, 'update_coil_pose')
	39	+
	40	+ self.connection = connection
	41	+
	42	+ def _hasmethod(self, obj, name):
	43	+ return hasattr(obj, name) and callable(getattr(obj, name))
	44	+
	45	+ def update_coil_pose(self, position, orientation):
	46	+ if self.connection is not None:
	47	+ self.connection.update_coil_pose(
	48	+ position=position,
	49	+ orientation=orientation,
	50	+ )