MOD: Allow selecting baud rate for serial port communication

Other changes: - Disallow not selecting COM port in COM port selection dialog by defaulting to the first COM port in the list. Previously, it was possible to pass an empty string as the COM port by not making the selection. - When the "Serial port" checkbox is pressed and the user presses "Cancel" in the dialog that is opened, uncheck the "Serial port" checkbox instead of keeping it checked. - Be explicit about if the serial port is in use or not, instead of inferring it from the COM port variable being set or not. - Pass the serial port parameters (COM port, baud rate) directly to the Navigation class, instead of passing them through NeuronavigationPanel. - Minor improvements to style and naming of the variables.

MOD: Allow selecting baud rate for serial port communication
Other changes: - Disallow not selecting COM port in COM port selection dialog by defaulting to the first COM port in the list. Previously, it was possible to pass an empty string as the COM port by not making the selection. - When the "Serial port" checkbox is pressed and the user presses "Cancel" in the dialog that is opened, uncheck the "Serial port" checkbox instead of keeping it checked. - Be explicit about if the serial port is in use or not, instead of inferring it from the COM port variable being set or not. - Pass the serial port parameters (COM port, baud rate) directly to the Navigation class, instead of passing them through NeuronavigationPanel. - Minor improvements to style and naming of the variables.
Olli-Pekka Kahilakoski
1 parent 9460b9cd
Showing 6 changed files with 84 additions and 44 deletions Show diff stats
invesalius/constants.py
invesalius/data/serial_port_connection.py
invesalius/data/trackers.py
invesalius/gui/dialogs.py
invesalius/gui/task_navigator.py
invesalius/navigation/navigation.py
@@ -830,3 +830,7 @@ TREKKER_CONFIG = {&#39;seed_max&#39;: 1, &#39;step_size&#39;: 0.1, &#39;min_fod&#39;: 0.1, &#39;probe_qualit
 MARKER_FILE_MAGICK_STRING = "INVESALIUS3_MARKER_FILE_"
 CURRENT_MARKER_FILE_VERSION = 0
 WILDCARD_MARKER_FILES = _("Marker scanner coord files (*.mkss)|*.mkss") 
+
+# Serial port
+BAUD_RATES = [300, 1200, 2400, 4800, 9600, 19200, 38400, 57600, 115200]
+BAUD_RATE_DEFAULT_SELECTION = 4
@@ -28,7 +28,7 @@ from invesalius.pubsub import pub as Publisher
 class SerialPortConnection(threading.Thread):
     BINARY_PULSE = b'\x01'
  
-    def __init__(self, port, serial_port_queue, event, sleep_nav):
+    def __init__(self, com_port, baud_rate, serial_port_queue, event, sleep_nav):
         """
         Thread created to communicate using the serial port to interact with software during neuronavigation.
         """
@@ -37,28 +37,29 @@ class SerialPortConnection(threading.Thread):
         self.connection = None
         self.stylusplh = False
  
-        self.port = port
+        self.com_port = com_port
+        self.baud_rate = baud_rate
         self.serial_port_queue = serial_port_queue
         self.event = event
         self.sleep_nav = sleep_nav
  
     def Connect(self):
-        if self.port is None:
+        if self.com_port is None:
             print("Serial port init error: COM port is unset.")
             return
         try:
             import serial
-            self.connection = serial.Serial(self.port, baudrate=115200, timeout=0)
-            print("Connection to port {} opened.".format(self.port))
+            self.connection = serial.Serial(self.com_port, baudrate=self.baud_rate, timeout=0)
+            print("Connection to port {} opened.".format(self.com_port))
  
             Publisher.sendMessage('Serial port connection', state=True)
         except:
-            print("Serial port init error: Connecting to port {} failed.".format(self.port))
+            print("Serial port init error: Connecting to port {} failed.".format(self.com_port))
  
     def Disconnect(self):
         if self.connection:
             self.connection.close()
-            print("Connection to port {} closed.".format(self.port))
+            print("Connection to port {} closed.".format(self.com_port))
  
             Publisher.sendMessage('Serial port connection', state=False)
  
@@ -74,12 +75,11 @@ class SerialPortConnection(threading.Thread):
             trigger_on = False
             try:
                 lines = self.connection.readlines()
+                if lines:
+                    trigger_on = True
             except:
                 print("Error: Serial port could not be read.")
  
-            if lines:
-                trigger_on = True
-
             if self.stylusplh:
                 trigger_on = True
                 self.stylusplh = False
@@ -266,7 +266,7 @@ def PlhSerialConnection(tracker_id):
     import serial
     from wx import ID_OK
     trck_init = None
-    dlg_port = dlg.SetCOMport()
+    dlg_port = dlg.SetCOMPort(select_baud_rate=False)
     if dlg_port.ShowModal() == ID_OK:
         com_port = dlg_port.GetValue()
         try:
@@ -4322,7 +4322,8 @@ class SetNDIconfigs(wx.Dialog):
         self._init_gui()
  
     def serial_ports(self):
-        """ Lists serial port names and pre-select the description containing NDI
+        """
+        Lists serial port names and pre-select the description containing NDI
         """
         import serial.tools.list_ports
  
@@ -4430,13 +4431,16 @@ class SetNDIconfigs(wx.Dialog):
         return self.com_ports.GetString(self.com_ports.GetSelection()).encode(const.FS_ENCODE), fn_probe, fn_ref, fn_obj
  
  
-class SetCOMport(wx.Dialog):
-    def __init__(self, title=_("Select COM port")):
-        wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, title, style=wx.DEFAULT_DIALOG_STYLE|wx.FRAME_FLOAT_ON_PARENT|wx.STAY_ON_TOP)
+class SetCOMPort(wx.Dialog):
+    def __init__(self, select_baud_rate, title=_("Select COM port")):
+        wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, title, style=wx.DEFAULT_DIALOG_STYLE | wx.FRAME_FLOAT_ON_PARENT | wx.STAY_ON_TOP)
+
+        self.select_baud_rate = select_baud_rate
         self._init_gui()
  
     def serial_ports(self):
-        """ Lists serial port names
+        """
+        Lists serial port names
         """
         import serial.tools.list_ports
         if sys.platform.startswith('win'):
@@ -4446,12 +4450,26 @@ class SetCOMport(wx.Dialog):
         return ports
  
     def _init_gui(self):
-        self.com_ports = wx.ComboBox(self, -1, style=wx.CB_DROPDOWN|wx.CB_READONLY)
+        # COM port selection
         ports = self.serial_ports()
-        self.com_ports.Append(ports)
+        self.com_port_dropdown = wx.ComboBox(self, -1, choices=ports, style=wx.CB_DROPDOWN | wx.CB_READONLY)
+        self.com_port_dropdown.SetSelection(0)
+
+        com_port_text_and_dropdown = wx.BoxSizer(wx.VERTICAL)
+        com_port_text_and_dropdown.Add(wx.StaticText(self, wx.ID_ANY, "COM port"), 0, wx.TOP | wx.RIGHT,5)
+        com_port_text_and_dropdown.Add(self.com_port_dropdown, 0, wx.EXPAND)
  
-       # self.goto_orientation.SetSelection(cb_init)
+        # Baud rate selection
+        if self.select_baud_rate:
+            baud_rates_as_strings = [str(baud_rate) for baud_rate in const.BAUD_RATES]
+            self.baud_rate_dropdown = wx.ComboBox(self, -1, choices=baud_rates_as_strings, style=wx.CB_DROPDOWN | wx.CB_READONLY)
+            self.baud_rate_dropdown.SetSelection(const.BAUD_RATE_DEFAULT_SELECTION)
  
+            baud_rate_text_and_dropdown = wx.BoxSizer(wx.VERTICAL)
+            baud_rate_text_and_dropdown.Add(wx.StaticText(self, wx.ID_ANY, "Baud rate"), 0, wx.TOP | wx.RIGHT,5)
+            baud_rate_text_and_dropdown.Add(self.baud_rate_dropdown, 0, wx.EXPAND)
+
+        # OK and Cancel buttons
         btn_ok = wx.Button(self, wx.ID_OK)
         btn_ok.SetHelpText("")
         btn_ok.SetDefault()
@@ -4464,10 +4482,16 @@ class SetCOMport(wx.Dialog):
         btnsizer.AddButton(btn_cancel)
         btnsizer.Realize()
  
+        # Set up the main sizer
         main_sizer = wx.BoxSizer(wx.VERTICAL)
  
         main_sizer.Add((5, 5))
-        main_sizer.Add(self.com_ports, 1, wx.EXPAND|wx.LEFT|wx.RIGHT, 5)
+        main_sizer.Add(com_port_text_and_dropdown, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+
+        if self.select_baud_rate:
+            main_sizer.Add((5, 5))
+            main_sizer.Add(baud_rate_text_and_dropdown, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+
         main_sizer.Add((5, 5))
         main_sizer.Add(btnsizer, 0, wx.EXPAND)
         main_sizer.Add((5, 5))
@@ -4478,7 +4502,14 @@ class SetCOMport(wx.Dialog):
         self.CenterOnParent()
  
     def GetValue(self):
-        return self.com_ports.GetString(self.com_ports.GetSelection())
+        com_port = self.com_port_dropdown.GetString(self.com_port_dropdown.GetSelection())
+
+        if self.select_baud_rate:
+            baud_rate = self.baud_rate_dropdown.GetString(self.baud_rate_dropdown.GetSelection())
+        else:
+            baud_rate = None
+
+        return com_port, baud_rate
  
  
 class ManualWWWLDialog(wx.Dialog):
@@ -222,8 +222,8 @@ class InnerFoldPanel(wx.Panel):
         checkcamera.Bind(wx.EVT_CHECKBOX, self.OnVolumeCamera)
         self.checkcamera = checkcamera
  
-        # Check box to create markers from serial port
-        tooltip = wx.ToolTip(_("Enable serial port communication for creating markers"))
+        # Check box to use serial port to trigger pulse signal and create markers
+        tooltip = wx.ToolTip(_("Enable serial port communication to trigger pulse and create markers"))
         checkbox_serial_port = wx.CheckBox(self, -1, _('Serial port'))
         checkbox_serial_port.SetToolTip(tooltip)
         checkbox_serial_port.SetValue(False)
@@ -285,14 +285,17 @@ class InnerFoldPanel(wx.Panel):
                 self.checkobj.Enable(True)
  
     def OnEnableSerialPort(self, evt, ctrl):
-        com_port = None
         if ctrl.GetValue():
             from wx import ID_OK
-            dlg_port = dlg.SetCOMport()
-            if dlg_port.ShowModal() == ID_OK:
-                com_port = dlg_port.GetValue()
+            dlg_port = dlg.SetCOMPort(select_baud_rate=True)
+            if dlg_port.ShowModal() != ID_OK:
+                ctrl.SetValue(False)
+                return
  
-        Publisher.sendMessage('Update serial port', serial_port=com_port)
+            com_port, baud_rate = dlg_port.GetValue()
+            Publisher.sendMessage('Update serial port', serial_port_in_use=True, com_port=com_port, baud_rate=baud_rate)
+        else:
+            Publisher.sendMessage('Update serial port', serial_port_in_use=False)
  
     def OnShowObject(self, evt=None, flag=None, obj_name=None, polydata=None, use_default_object=True):
         if not evt:
@@ -490,7 +493,6 @@ class NeuronavigationPanel(wx.Panel):
         Publisher.subscribe(self.LoadImageFiducials, 'Load image fiducials')
         Publisher.subscribe(self.SetImageFiducial, 'Set image fiducial')
         Publisher.subscribe(self.SetTrackerFiducial, 'Set tracker fiducial')
-        Publisher.subscribe(self.UpdateSerialPort, 'Update serial port')
         Publisher.subscribe(self.UpdateTrackObjectState, 'Update track object state')
         Publisher.subscribe(self.UpdateImageCoordinates, 'Set cross focal point')
         Publisher.subscribe(self.OnDisconnectTracker, 'Disconnect tracker')
@@ -614,9 +616,6 @@ class NeuronavigationPanel(wx.Panel):
     def UpdateTrackObjectState(self, evt=None, flag=None, obj_name=None, polydata=None, use_default_object=True):
         self.navigation.track_obj = flag
  
-    def UpdateSerialPort(self, serial_port):
-        self.navigation.serial_port = serial_port
-
     def ResetICP(self):
         self.icp.ResetICP()
         self.checkbox_icp.Enable(False)
@@ -168,7 +168,9 @@ class Navigation():
         self.sleep_nav = const.SLEEP_NAVIGATION
  
         # Serial port
-        self.serial_port = None
+        self.serial_port_in_use = False
+        self.com_port = None
+        self.baud_rate = None
         self.serial_port_connection = None
  
         # During navigation
@@ -178,6 +180,7 @@ class Navigation():
  
     def __bind_events(self):
         Publisher.subscribe(self.CoilAtTarget, 'Coil at target')
+        Publisher.subscribe(self.UpdateSerialPort, 'Update serial port')
  
     def CoilAtTarget(self, state):
         self.coil_at_target = state
@@ -186,8 +189,10 @@ class Navigation():
         self.sleep_nav = sleep
         self.serial_port_connection.sleep_nav = sleep
  
-    def SerialPortEnabled(self):
-        return self.serial_port is not None
+    def UpdateSerialPort(self, serial_port_in_use, com_port=None, baud_rate=None):
+        self.serial_port_in_use = serial_port_in_use
+        self.com_port = com_port
+        self.baud_rate = baud_rate
  
     def SetReferenceMode(self, value):
         self.ref_mode_id = value
@@ -215,7 +220,7 @@ class Navigation():
         return fre, fre <= const.FIDUCIAL_REGISTRATION_ERROR_THRESHOLD
  
     def PedalStateChanged(self, state):
-        if state is True and self.coil_at_target and self.SerialPortEnabled():
+        if state is True and self.coil_at_target and self.serial_port_in_use:
             self.serial_port_connection.SendPulse()
  
     def StartNavigation(self, tracker):
@@ -227,7 +232,7 @@ class Navigation():
         if self.event.is_set():
             self.event.clear()
  
-        vis_components = [self.SerialPortEnabled(), self.view_tracts, self.peel_loaded]
+        vis_components = [self.serial_port_in_use, self.view_tracts, self.peel_loaded]
         vis_queues = [self.coord_queue, self.serial_port_queue, self.tracts_queue, self.icp_queue]
  
         Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components)
@@ -276,12 +281,13 @@ class Navigation():
  
         if not errors:
             #TODO: Test the serial port thread
-            if self.SerialPortEnabled():
+            if self.serial_port_in_use:
                 self.serial_port_connection = spc.SerialPortConnection(
-                    self.serial_port,
-                    self.serial_port_queue,
-                    self.event,
-                    self.sleep_nav,
+                    com_port=self.com_port,
+                    baud_rate=self.baud_rate,
+                    serial_port_queue=self.serial_port_queue,
+                    event=self.event,
+                    sleep_nav=self.sleep_nav,
                 )
                 self.serial_port_connection.Connect()
                 jobs_list.append(self.serial_port_connection)
@@ -327,7 +333,7 @@ class Navigation():
         if self.serial_port_connection is not None:
             self.serial_port_connection.join()
  
-        if self.SerialPortEnabled():
+        if self.serial_port_in_use:
             self.serial_port_queue.clear()
             self.serial_port_queue.join()
  
@@ -338,5 +344,5 @@ class Navigation():
             self.tracts_queue.clear()
             self.tracts_queue.join()
  
-        vis_components = [self.SerialPortEnabled(), self.view_tracts,  self.peel_loaded]
+        vis_components = [self.serial_port_in_use, self.view_tracts,  self.peel_loaded]
         Publisher.sendMessage("Navigation status", nav_status=False, vis_status=vis_components)
...	...	@@ -830,3 +830,7 @@ TREKKER_CONFIG = {'seed_max': 1, 'step_size': 0.1, 'min_fod': 0.1, 'probe_qualit
830	830	MARKER_FILE_MAGICK_STRING = "INVESALIUS3_MARKER_FILE_"
831	831	CURRENT_MARKER_FILE_VERSION = 0
832	832	WILDCARD_MARKER_FILES = _("Marker scanner coord files (.mkss)\|.mkss")
	833	+
	834	+# Serial port
	835	+BAUD_RATES = [300, 1200, 2400, 4800, 9600, 19200, 38400, 57600, 115200]
	836	+BAUD_RATE_DEFAULT_SELECTION = 4
...	...
...	...	@@ -28,7 +28,7 @@ from invesalius.pubsub import pub as Publisher
28	28	class SerialPortConnection(threading.Thread):
29	29	BINARY_PULSE = b'\x01'
30	30
31		- def __init__(self, port, serial_port_queue, event, sleep_nav):
	31	+ def __init__(self, com_port, baud_rate, serial_port_queue, event, sleep_nav):
32	32	"""
33	33	Thread created to communicate using the serial port to interact with software during neuronavigation.
34	34	"""
...	...	@@ -37,28 +37,29 @@ class SerialPortConnection(threading.Thread):
37	37	self.connection = None
38	38	self.stylusplh = False
39	39
40		- self.port = port
	40	+ self.com_port = com_port
	41	+ self.baud_rate = baud_rate
41	42	self.serial_port_queue = serial_port_queue
42	43	self.event = event
43	44	self.sleep_nav = sleep_nav
44	45
45	46	def Connect(self):
46		- if self.port is None:
	47	+ if self.com_port is None:
47	48	print("Serial port init error: COM port is unset.")
48	49	return
49	50	try:
50	51	import serial
51		- self.connection = serial.Serial(self.port, baudrate=115200, timeout=0)
52		- print("Connection to port {} opened.".format(self.port))
	52	+ self.connection = serial.Serial(self.com_port, baudrate=self.baud_rate, timeout=0)
	53	+ print("Connection to port {} opened.".format(self.com_port))
53	54
54	55	Publisher.sendMessage('Serial port connection', state=True)
55	56	except:
56		- print("Serial port init error: Connecting to port {} failed.".format(self.port))
	57	+ print("Serial port init error: Connecting to port {} failed.".format(self.com_port))
57	58
58	59	def Disconnect(self):
59	60	if self.connection:
60	61	self.connection.close()
61		- print("Connection to port {} closed.".format(self.port))
	62	+ print("Connection to port {} closed.".format(self.com_port))
62	63
63	64	Publisher.sendMessage('Serial port connection', state=False)
64	65
...	...	@@ -74,12 +75,11 @@ class SerialPortConnection(threading.Thread):
74	75	trigger_on = False
75	76	try:
76	77	lines = self.connection.readlines()
	78	+ if lines:
	79	+ trigger_on = True
77	80	except:
78	81	print("Error: Serial port could not be read.")
79	82
80		- if lines:
81		- trigger_on = True
82		-
83	83	if self.stylusplh:
84	84	trigger_on = True
85	85	self.stylusplh = False
...	...
...	...	@@ -266,7 +266,7 @@ def PlhSerialConnection(tracker_id):
266	266	import serial
267	267	from wx import ID_OK
268	268	trck_init = None
269		- dlg_port = dlg.SetCOMport()
	269	+ dlg_port = dlg.SetCOMPort(select_baud_rate=False)
270	270	if dlg_port.ShowModal() == ID_OK:
271	271	com_port = dlg_port.GetValue()
272	272	try:
...	...
...	...	@@ -4322,7 +4322,8 @@ class SetNDIconfigs(wx.Dialog):
4322	4322	self._init_gui()
4323	4323
4324	4324	def serial_ports(self):
4325		- """ Lists serial port names and pre-select the description containing NDI
	4325	+ """
	4326	+ Lists serial port names and pre-select the description containing NDI
4326	4327	"""
4327	4328	import serial.tools.list_ports
4328	4329
...	...	@@ -4430,13 +4431,16 @@ class SetNDIconfigs(wx.Dialog):
4430	4431	return self.com_ports.GetString(self.com_ports.GetSelection()).encode(const.FS_ENCODE), fn_probe, fn_ref, fn_obj
4431	4432
4432	4433
4433		-class SetCOMport(wx.Dialog):
4434		- def __init__(self, title=_("Select COM port")):
4435		- wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, title, style=wx.DEFAULT_DIALOG_STYLE\|wx.FRAME_FLOAT_ON_PARENT\|wx.STAY_ON_TOP)
	4434	+class SetCOMPort(wx.Dialog):
	4435	+ def __init__(self, select_baud_rate, title=_("Select COM port")):
	4436	+ wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, title, style=wx.DEFAULT_DIALOG_STYLE \| wx.FRAME_FLOAT_ON_PARENT \| wx.STAY_ON_TOP)
	4437	+
	4438	+ self.select_baud_rate = select_baud_rate
4436	4439	self._init_gui()
4437	4440
4438	4441	def serial_ports(self):
4439		- """ Lists serial port names
	4442	+ """
	4443	+ Lists serial port names
4440	4444	"""
4441	4445	import serial.tools.list_ports
4442	4446	if sys.platform.startswith('win'):
...	...	@@ -4446,12 +4450,26 @@ class SetCOMport(wx.Dialog):
4446	4450	return ports
4447	4451
4448	4452	def _init_gui(self):
4449		- self.com_ports = wx.ComboBox(self, -1, style=wx.CB_DROPDOWN\|wx.CB_READONLY)
	4453	+ # COM port selection
4450	4454	ports = self.serial_ports()
4451		- self.com_ports.Append(ports)
	4455	+ self.com_port_dropdown = wx.ComboBox(self, -1, choices=ports, style=wx.CB_DROPDOWN \| wx.CB_READONLY)
	4456	+ self.com_port_dropdown.SetSelection(0)
	4457	+
	4458	+ com_port_text_and_dropdown = wx.BoxSizer(wx.VERTICAL)
	4459	+ com_port_text_and_dropdown.Add(wx.StaticText(self, wx.ID_ANY, "COM port"), 0, wx.TOP \| wx.RIGHT,5)
	4460	+ com_port_text_and_dropdown.Add(self.com_port_dropdown, 0, wx.EXPAND)
4452	4461
4453		- # self.goto_orientation.SetSelection(cb_init)
	4462	+ # Baud rate selection
	4463	+ if self.select_baud_rate:
	4464	+ baud_rates_as_strings = [str(baud_rate) for baud_rate in const.BAUD_RATES]
	4465	+ self.baud_rate_dropdown = wx.ComboBox(self, -1, choices=baud_rates_as_strings, style=wx.CB_DROPDOWN \| wx.CB_READONLY)
	4466	+ self.baud_rate_dropdown.SetSelection(const.BAUD_RATE_DEFAULT_SELECTION)
4454	4467
	4468	+ baud_rate_text_and_dropdown = wx.BoxSizer(wx.VERTICAL)
	4469	+ baud_rate_text_and_dropdown.Add(wx.StaticText(self, wx.ID_ANY, "Baud rate"), 0, wx.TOP \| wx.RIGHT,5)
	4470	+ baud_rate_text_and_dropdown.Add(self.baud_rate_dropdown, 0, wx.EXPAND)
	4471	+
	4472	+ # OK and Cancel buttons
4455	4473	btn_ok = wx.Button(self, wx.ID_OK)
4456	4474	btn_ok.SetHelpText("")
4457	4475	btn_ok.SetDefault()
...	...	@@ -4464,10 +4482,16 @@ class SetCOMport(wx.Dialog):
4464	4482	btnsizer.AddButton(btn_cancel)
4465	4483	btnsizer.Realize()
4466	4484
	4485	+ # Set up the main sizer
4467	4486	main_sizer = wx.BoxSizer(wx.VERTICAL)
4468	4487
4469	4488	main_sizer.Add((5, 5))
4470		- main_sizer.Add(self.com_ports, 1, wx.EXPAND\|wx.LEFT\|wx.RIGHT, 5)
	4489	+ main_sizer.Add(com_port_text_and_dropdown, 1, wx.EXPAND \| wx.LEFT \| wx.RIGHT, 5)
	4490	+
	4491	+ if self.select_baud_rate:
	4492	+ main_sizer.Add((5, 5))
	4493	+ main_sizer.Add(baud_rate_text_and_dropdown, 1, wx.EXPAND \| wx.LEFT \| wx.RIGHT, 5)
	4494	+
4471	4495	main_sizer.Add((5, 5))
4472	4496	main_sizer.Add(btnsizer, 0, wx.EXPAND)
4473	4497	main_sizer.Add((5, 5))
...	...	@@ -4478,7 +4502,14 @@ class SetCOMport(wx.Dialog):
4478	4502	self.CenterOnParent()
4479	4503
4480	4504	def GetValue(self):
4481		- return self.com_ports.GetString(self.com_ports.GetSelection())
	4505	+ com_port = self.com_port_dropdown.GetString(self.com_port_dropdown.GetSelection())
	4506	+
	4507	+ if self.select_baud_rate:
	4508	+ baud_rate = self.baud_rate_dropdown.GetString(self.baud_rate_dropdown.GetSelection())
	4509	+ else:
	4510	+ baud_rate = None
	4511	+
	4512	+ return com_port, baud_rate
4482	4513
4483	4514
4484	4515	class ManualWWWLDialog(wx.Dialog):
...	...
...	...	@@ -222,8 +222,8 @@ class InnerFoldPanel(wx.Panel):
222	222	checkcamera.Bind(wx.EVT_CHECKBOX, self.OnVolumeCamera)
223	223	self.checkcamera = checkcamera
224	224
225		- # Check box to create markers from serial port
226		- tooltip = wx.ToolTip(_("Enable serial port communication for creating markers"))
	225	+ # Check box to use serial port to trigger pulse signal and create markers
	226	+ tooltip = wx.ToolTip(_("Enable serial port communication to trigger pulse and create markers"))
227	227	checkbox_serial_port = wx.CheckBox(self, -1, _('Serial port'))
228	228	checkbox_serial_port.SetToolTip(tooltip)
229	229	checkbox_serial_port.SetValue(False)
...	...	@@ -285,14 +285,17 @@ class InnerFoldPanel(wx.Panel):
285	285	self.checkobj.Enable(True)
286	286
287	287	def OnEnableSerialPort(self, evt, ctrl):
288		- com_port = None
289	288	if ctrl.GetValue():
290	289	from wx import ID_OK
291		- dlg_port = dlg.SetCOMport()
292		- if dlg_port.ShowModal() == ID_OK:
293		- com_port = dlg_port.GetValue()
	290	+ dlg_port = dlg.SetCOMPort(select_baud_rate=True)
	291	+ if dlg_port.ShowModal() != ID_OK:
	292	+ ctrl.SetValue(False)
	293	+ return
294	294
295		- Publisher.sendMessage('Update serial port', serial_port=com_port)
	295	+ com_port, baud_rate = dlg_port.GetValue()
	296	+ Publisher.sendMessage('Update serial port', serial_port_in_use=True, com_port=com_port, baud_rate=baud_rate)
	297	+ else:
	298	+ Publisher.sendMessage('Update serial port', serial_port_in_use=False)
296	299
297	300	def OnShowObject(self, evt=None, flag=None, obj_name=None, polydata=None, use_default_object=True):
298	301	if not evt:
...	...	@@ -490,7 +493,6 @@ class NeuronavigationPanel(wx.Panel):
490	493	Publisher.subscribe(self.LoadImageFiducials, 'Load image fiducials')
491	494	Publisher.subscribe(self.SetImageFiducial, 'Set image fiducial')
492	495	Publisher.subscribe(self.SetTrackerFiducial, 'Set tracker fiducial')
493		- Publisher.subscribe(self.UpdateSerialPort, 'Update serial port')
494	496	Publisher.subscribe(self.UpdateTrackObjectState, 'Update track object state')
495	497	Publisher.subscribe(self.UpdateImageCoordinates, 'Set cross focal point')
496	498	Publisher.subscribe(self.OnDisconnectTracker, 'Disconnect tracker')
...	...	@@ -614,9 +616,6 @@ class NeuronavigationPanel(wx.Panel):
614	616	def UpdateTrackObjectState(self, evt=None, flag=None, obj_name=None, polydata=None, use_default_object=True):
615	617	self.navigation.track_obj = flag
616	618
617		- def UpdateSerialPort(self, serial_port):
618		- self.navigation.serial_port = serial_port
619		-
620	619	def ResetICP(self):
621	620	self.icp.ResetICP()
622	621	self.checkbox_icp.Enable(False)
...	...
...	...	@@ -168,7 +168,9 @@ class Navigation():
168	168	self.sleep_nav = const.SLEEP_NAVIGATION
169	169
170	170	# Serial port
171		- self.serial_port = None
	171	+ self.serial_port_in_use = False
	172	+ self.com_port = None
	173	+ self.baud_rate = None
172	174	self.serial_port_connection = None
173	175
174	176	# During navigation
...	...	@@ -178,6 +180,7 @@ class Navigation():
178	180
179	181	def __bind_events(self):
180	182	Publisher.subscribe(self.CoilAtTarget, 'Coil at target')
	183	+ Publisher.subscribe(self.UpdateSerialPort, 'Update serial port')
181	184
182	185	def CoilAtTarget(self, state):
183	186	self.coil_at_target = state
...	...	@@ -186,8 +189,10 @@ class Navigation():
186	189	self.sleep_nav = sleep
187	190	self.serial_port_connection.sleep_nav = sleep
188	191
189		- def SerialPortEnabled(self):
190		- return self.serial_port is not None
	192	+ def UpdateSerialPort(self, serial_port_in_use, com_port=None, baud_rate=None):
	193	+ self.serial_port_in_use = serial_port_in_use
	194	+ self.com_port = com_port
	195	+ self.baud_rate = baud_rate
191	196
192	197	def SetReferenceMode(self, value):
193	198	self.ref_mode_id = value
...	...	@@ -215,7 +220,7 @@ class Navigation():
215	220	return fre, fre <= const.FIDUCIAL_REGISTRATION_ERROR_THRESHOLD
216	221
217	222	def PedalStateChanged(self, state):
218		- if state is True and self.coil_at_target and self.SerialPortEnabled():
	223	+ if state is True and self.coil_at_target and self.serial_port_in_use:
219	224	self.serial_port_connection.SendPulse()
220	225
221	226	def StartNavigation(self, tracker):
...	...	@@ -227,7 +232,7 @@ class Navigation():
227	232	if self.event.is_set():
228	233	self.event.clear()
229	234
230		- vis_components = [self.SerialPortEnabled(), self.view_tracts, self.peel_loaded]
	235	+ vis_components = [self.serial_port_in_use, self.view_tracts, self.peel_loaded]
231	236	vis_queues = [self.coord_queue, self.serial_port_queue, self.tracts_queue, self.icp_queue]
232	237
233	238	Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components)
...	...	@@ -276,12 +281,13 @@ class Navigation():
276	281
277	282	if not errors:
278	283	#TODO: Test the serial port thread
279		- if self.SerialPortEnabled():
	284	+ if self.serial_port_in_use:
280	285	self.serial_port_connection = spc.SerialPortConnection(
281		- self.serial_port,
282		- self.serial_port_queue,
283		- self.event,
284		- self.sleep_nav,
	286	+ com_port=self.com_port,
	287	+ baud_rate=self.baud_rate,
	288	+ serial_port_queue=self.serial_port_queue,
	289	+ event=self.event,
	290	+ sleep_nav=self.sleep_nav,
285	291	)
286	292	self.serial_port_connection.Connect()
287	293	jobs_list.append(self.serial_port_connection)
...	...	@@ -327,7 +333,7 @@ class Navigation():
327	333	if self.serial_port_connection is not None:
328	334	self.serial_port_connection.join()
329	335
330		- if self.SerialPortEnabled():
	336	+ if self.serial_port_in_use:
331	337	self.serial_port_queue.clear()
332	338	self.serial_port_queue.join()
333	339
...	...	@@ -338,5 +344,5 @@ class Navigation():
338	344	self.tracts_queue.clear()
339	345	self.tracts_queue.join()
340	346
341		- vis_components = [self.SerialPortEnabled(), self.view_tracts, self.peel_loaded]
	347	+ vis_components = [self.serial_port_in_use, self.view_tracts, self.peel_loaded]
342	348	Publisher.sendMessage("Navigation status", nav_status=False, vis_status=vis_components)
...	...