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Commit d133ced30f965e07402c3c96120888cdd616b02c

Authored by okahilak
Committed by GitHub
1 parent db47444c
Exists in master

MOD: Allow selecting COM port when enabling serial port communication (#325) 

* CLP: Clean up naming in task_navigator.py

Namely, be more specific about the type of trigger input (in this
case, the serial port), as nowadays the MIDI input can be used for
triggering, as well.

* CLP: Remove unused variable 'trigger' from Navigation class

* CLP: More clean-up related to serial port communication

- Change invesalius.data.trigger to invesalius.data.serial_port_connection

- Rename the class TriggerNew to SerialPortConnection

- Remove the old, unused Trigger class

- Rename a couple of variables in SerialPortConnection class

- Replace the incorrect docstring for SerialPortConnection class with a
  brief but more accurate docstring.

* CLP: More clean-up in SerialPortConnection

- Remove commented out code

- Remove some blank lines from function definitions

- Do not import sleep from time library, but instead use time.sleep

* MOD: Allow selecting COM port when enabling serial port communication
Showing 3 changed files with 140 additions and 204 deletions   Show diff stats
invesalius/data/serial_port_connection.py 0 → 100644
  Diff comments   View file @d133ced
@@ -0,0 +1,79 @@ @@ -0,0 +1,79 @@
  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 +import threading
  21 +import time
  22 +
  23 +import wx
  24 +from invesalius.pubsub import pub as Publisher
  25 +
  26 +
  27 +class SerialPortConnection(threading.Thread):
  28 +
  29 + def __init__(self, port, serial_port_queue, event, sleep_nav):
  30 + """
  31 + Thread created to communicate using the serial port to interact with software during neuronavigation.
  32 + """
  33 + threading.Thread.__init__(self, name='Serial port')
  34 +
  35 + self.connection = None
  36 + self.stylusplh = False
  37 +
  38 + self.port = port
  39 + self.serial_port_queue = serial_port_queue
  40 + self.event = event
  41 + self.sleep_nav = sleep_nav
  42 +
  43 + def Enabled(self):
  44 + return self.port is not None
  45 +
  46 + def Connect(self):
  47 + if self.port is None:
  48 + print("Serial port init error: COM port is unset.")
  49 + return
  50 + try:
  51 + import serial
  52 + self.connection = serial.Serial(self.port, baudrate=115200, timeout=0)
  53 + print("Connection to port {} opened.".format(self.port))
  54 + except:
  55 + print("Serial port init error: Connecting to port {} failed.".format(self.port))
  56 +
  57 + def run(self):
  58 + while not self.event.is_set():
  59 + trigger_on = False
  60 + try:
  61 + self.connection.write(b'0')
  62 + time.sleep(0.3)
  63 +
  64 + lines = self.connection.readlines()
  65 + if lines:
  66 + trigger_on = True
  67 +
  68 + if self.stylusplh:
  69 + trigger_on = True
  70 + self.stylusplh = False
  71 +
  72 + self.serial_port_queue.put_nowait(trigger_on)
  73 + time.sleep(self.sleep_nav)
  74 + except:
  75 + print("Trigger not read, error")
  76 + else:
  77 + if self.connection:
  78 + self.connection.close()
  79 + print("Connection to port {} closed.".format(self.port))
invesalius/data/trigger.py
View file @db47444
@@ -1,168 +0,0 @@ @@ -1,168 +0,0 @@
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 -import threading  
21 -from time import sleep  
22 -  
23 -import wx  
24 -from invesalius.pubsub import pub as Publisher  
25 -  
26 -  
27 -class Trigger(threading.Thread):  
28 - """  
29 - Thread created to use external trigger to interact with software during neuronavigation  
30 - """  
31 -  
32 - def __init__(self, nav_id):  
33 - threading.Thread.__init__(self)  
34 - self.trigger_init = None  
35 - self.stylusplh = False  
36 - self.COM = False  
37 - self.nav_id = nav_id  
38 - self.__bind_events()  
39 - try:  
40 - import serial  
41 -  
42 - self.trigger_init = serial.Serial('COM5', baudrate=115200, timeout=0)  
43 - self.COM = True  
44 -  
45 - except:  
46 - #wx.MessageBox(_('Connection with port COM1 failed'), _('Communication error'), wx.OK | wx.ICON_ERROR)  
47 - print("Trigger init error: Connection with port COM1 failed")  
48 - self.COM = False  
49 -  
50 - self._pause_ = False  
51 - self.start()  
52 -  
53 - def __bind_events(self):  
54 - Publisher.subscribe(self.OnStylusPLH, 'PLH Stylus Button On')  
55 -  
56 - def OnStylusPLH(self):  
57 - self.stylusplh = True  
58 -  
59 - def stop(self):  
60 - self._pause_ = True  
61 -  
62 - def run(self):  
63 - while self.nav_id:  
64 - if self.COM:  
65 - self.trigger_init.write(b'0')  
66 - sleep(0.3)  
67 - lines = self.trigger_init.readlines()  
68 - # Following lines can simulate a trigger in 3 sec repetitions  
69 - # sleep(3)  
70 - # lines = True  
71 - if lines:  
72 - wx.CallAfter(Publisher.sendMessage, 'Create marker')  
73 - sleep(0.5)  
74 -  
75 - if self.stylusplh:  
76 - wx.CallAfter(Publisher.sendMessage, 'Create marker')  
77 - sleep(0.5)  
78 - self.stylusplh = False  
79 -  
80 - sleep(0.175)  
81 - if self._pause_:  
82 - if self.trigger_init:  
83 - self.trigger_init.close()  
84 - return  
85 -  
86 -  
87 -class TriggerNew(threading.Thread):  
88 -  
89 - def __init__(self, trigger_queue, event, sle):  
90 - """Class (threading) to compute real time tractography data for visualization in a single loop.  
91 -  
92 - Different than ComputeTractsThread because it does not keep adding tracts to the bundle until maximum,  
93 - is reached. It actually compute all requested tracts at once. (Might be deleted in the future)!  
94 - Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)  
95 - For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one  
96 - vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as  
97 - bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.  
98 - Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.  
99 -  
100 - Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation  
101 -  
102 - :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads  
103 - :type inp: list  
104 - :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene  
105 - :type affine_vtk: vtkMatrix4x4  
106 - :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered  
107 - :type coord_queue: queue.Queue  
108 - :param visualization_queue: Queue instance that manage coordinates to be visualized  
109 - :type visualization_queue: queue.Queue  
110 - :param event: Threading event to coordinate when tasks as done and allow UI release  
111 - :type event: threading.Event  
112 - :param sle: Sleep pause in seconds  
113 - :type sle: float  
114 - """  
115 -  
116 - threading.Thread.__init__(self, name='Trigger')  
117 -  
118 - self.trigger_init = None  
119 - self.stylusplh = False  
120 - # self.COM = False  
121 - # self.__bind_events()  
122 - try:  
123 - import serial  
124 -  
125 - self.trigger_init = serial.Serial('COM5', baudrate=115200, timeout=0)  
126 - # self.COM = True  
127 -  
128 - except:  
129 - #wx.MessageBox(_('Connection with port COM1 failed'), _('Communication error'), wx.OK | wx.ICON_ERROR)  
130 - print("Trigger init error: Connection with port COM failed")  
131 - # self.COM = False  
132 - pass  
133 -  
134 - # self.coord_queue = coord_queue  
135 - self.trigger_queue = trigger_queue  
136 - self.event = event  
137 - self.sle = sle  
138 -  
139 - def run(self):  
140 -  
141 - while not self.event.is_set():  
142 - trigger_on = False  
143 - try:  
144 - self.trigger_init.write(b'0')  
145 - sleep(0.3)  
146 - lines = self.trigger_init.readlines()  
147 - # Following lines can simulate a trigger in 3 sec repetitions  
148 - # sleep(3)  
149 - # lines = True  
150 - if lines:  
151 - trigger_on = True  
152 - # wx.CallAfter(Publisher.sendMessage, 'Create marker')  
153 -  
154 - if self.stylusplh:  
155 - trigger_on = True  
156 - # wx.CallAfter(Publisher.sendMessage, 'Create marker')  
157 - self.stylusplh = False  
158 -  
159 - self.trigger_queue.put_nowait(trigger_on)  
160 - sleep(self.sle)  
161 -  
162 - except:  
163 - print("Trigger not read, error")  
164 - pass  
165 -  
166 - else:  
167 - if self.trigger_init:  
168 - self.trigger_init.close()  
invesalius/gui/task_navigator.py
  Diff comments   View file @d133ced
@@ -54,11 +54,11 @@ if has_trekker: @@ -54,11 +54,11 @@ if has_trekker:
54 54
55 import invesalius.data.coordinates as dco 55 import invesalius.data.coordinates as dco
56 import invesalius.data.coregistration as dcr 56 import invesalius.data.coregistration as dcr
  57 +import invesalius.data.serial_port_connection as spc
57 import invesalius.data.slice_ as sl 58 import invesalius.data.slice_ as sl
58 import invesalius.data.trackers as dt 59 import invesalius.data.trackers as dt
59 import invesalius.data.tractography as dti 60 import invesalius.data.tractography as dti
60 import invesalius.data.transformations as tr 61 import invesalius.data.transformations as tr
61 -import invesalius.data.trigger as trig  
62 import invesalius.data.record_coords as rec 62 import invesalius.data.record_coords as rec
63 import invesalius.data.vtk_utils as vtk_utils 63 import invesalius.data.vtk_utils as vtk_utils
64 import invesalius.gui.dialogs as dlg 64 import invesalius.gui.dialogs as dlg
@@ -215,13 +215,13 @@ class InnerFoldPanel(wx.Panel): @@ -215,13 +215,13 @@ class InnerFoldPanel(wx.Panel):
215 checkcamera.Bind(wx.EVT_CHECKBOX, self.OnVolumeCamera) 215 checkcamera.Bind(wx.EVT_CHECKBOX, self.OnVolumeCamera)
216 self.checkcamera = checkcamera 216 self.checkcamera = checkcamera
217 217
218 - # Check box for trigger monitoring to create markers from serial port  
219 - tooltip = wx.ToolTip(_("Enable external trigger for creating markers"))  
220 - checktrigger = wx.CheckBox(self, -1, _('Ext. trigger'))  
221 - checktrigger.SetToolTip(tooltip)  
222 - checktrigger.SetValue(False)  
223 - checktrigger.Bind(wx.EVT_CHECKBOX, partial(self.OnExternalTrigger, ctrl=checktrigger))  
224 - self.checktrigger = checktrigger 218 + # Check box to create markers from serial port
  219 + tooltip = wx.ToolTip(_("Enable serial port communication for creating markers"))
  220 + checkbox_serial_port = wx.CheckBox(self, -1, _('Serial port'))
  221 + checkbox_serial_port.SetToolTip(tooltip)
  222 + checkbox_serial_port.SetValue(False)
  223 + checkbox_serial_port.Bind(wx.EVT_CHECKBOX, partial(self.OnEnableSerialPort, ctrl=checkbox_serial_port))
  224 + self.checkbox_serial_port = checkbox_serial_port
225 225
226 # Check box for object position and orientation update in volume rendering during navigation 226 # Check box for object position and orientation update in volume rendering during navigation
227 tooltip = wx.ToolTip(_("Show and track TMS coil")) 227 tooltip = wx.ToolTip(_("Show and track TMS coil"))
@@ -234,12 +234,12 @@ class InnerFoldPanel(wx.Panel): @@ -234,12 +234,12 @@ class InnerFoldPanel(wx.Panel):
234 234
235 # if sys.platform != 'win32': 235 # if sys.platform != 'win32':
236 self.checkcamera.SetWindowVariant(wx.WINDOW_VARIANT_SMALL) 236 self.checkcamera.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
237 - checktrigger.SetWindowVariant(wx.WINDOW_VARIANT_SMALL) 237 + checkbox_serial_port.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
238 checkobj.SetWindowVariant(wx.WINDOW_VARIANT_SMALL) 238 checkobj.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
239 239
240 line_sizer = wx.BoxSizer(wx.HORIZONTAL) 240 line_sizer = wx.BoxSizer(wx.HORIZONTAL)
241 line_sizer.Add(checkcamera, 0, wx.ALIGN_LEFT | wx.RIGHT | wx.LEFT, 5) 241 line_sizer.Add(checkcamera, 0, wx.ALIGN_LEFT | wx.RIGHT | wx.LEFT, 5)
242 - line_sizer.Add(checktrigger, 0, wx.ALIGN_CENTER) 242 + line_sizer.Add(checkbox_serial_port, 0, wx.ALIGN_CENTER)
243 line_sizer.Add(checkobj, 0, wx.RIGHT | wx.LEFT, 5) 243 line_sizer.Add(checkobj, 0, wx.RIGHT | wx.LEFT, 5)
244 line_sizer.Fit(self) 244 line_sizer.Fit(self)
245 245
@@ -270,15 +270,22 @@ class InnerFoldPanel(wx.Panel): @@ -270,15 +270,22 @@ class InnerFoldPanel(wx.Panel):
270 270
271 def OnCheckStatus(self, nav_status, vis_status): 271 def OnCheckStatus(self, nav_status, vis_status):
272 if nav_status: 272 if nav_status:
273 - self.checktrigger.Enable(False) 273 + self.checkbox_serial_port.Enable(False)
274 self.checkobj.Enable(False) 274 self.checkobj.Enable(False)
275 else: 275 else:
276 - self.checktrigger.Enable(True) 276 + self.checkbox_serial_port.Enable(True)
277 if self.track_obj: 277 if self.track_obj:
278 self.checkobj.Enable(True) 278 self.checkobj.Enable(True)
279 279
280 - def OnExternalTrigger(self, evt, ctrl):  
281 - Publisher.sendMessage('Update trigger state', trigger_state=ctrl.GetValue()) 280 + def OnEnableSerialPort(self, evt, ctrl):
  281 + com_port = None
  282 + if ctrl.GetValue():
  283 + from wx import ID_OK
  284 + dlg_port = dlg.SetCOMport()
  285 + if dlg_port.ShowModal() == ID_OK:
  286 + com_port = dlg_port.GetValue()
  287 +
  288 + Publisher.sendMessage('Update serial port', serial_port=com_port)
282 289
283 def OnShowObject(self, evt=None, flag=None, obj_name=None, polydata=None): 290 def OnShowObject(self, evt=None, flag=None, obj_name=None, polydata=None):
284 if not evt: 291 if not evt:
@@ -307,8 +314,6 @@ class Navigation(): @@ -307,8 +314,6 @@ class Navigation():
307 self.correg = None 314 self.correg = None
308 self.current_coord = 0, 0, 0 315 self.current_coord = 0, 0, 0
309 self.target = None 316 self.target = None
310 - self.trigger = None  
311 - self.trigger_state = False  
312 self.obj_reg = None 317 self.obj_reg = None
313 self.track_obj = False 318 self.track_obj = False
314 self.m_change = None 319 self.m_change = None
@@ -318,7 +323,7 @@ class Navigation(): @@ -318,7 +323,7 @@ class Navigation():
318 self.coord_queue = QueueCustom(maxsize=1) 323 self.coord_queue = QueueCustom(maxsize=1)
319 self.icp_queue = QueueCustom(maxsize=1) 324 self.icp_queue = QueueCustom(maxsize=1)
320 # self.visualization_queue = QueueCustom(maxsize=1) 325 # self.visualization_queue = QueueCustom(maxsize=1)
321 - self.trigger_queue = QueueCustom(maxsize=1) 326 + self.serial_port_queue = QueueCustom(maxsize=1)
322 self.coord_tracts_queue = QueueCustom(maxsize=1) 327 self.coord_tracts_queue = QueueCustom(maxsize=1)
323 self.tracts_queue = QueueCustom(maxsize=1) 328 self.tracts_queue = QueueCustom(maxsize=1)
324 329
@@ -335,6 +340,17 @@ class Navigation(): @@ -335,6 +340,17 @@ class Navigation():
335 self.seed_radius = const.SEED_RADIUS 340 self.seed_radius = const.SEED_RADIUS
336 self.sleep_nav = const.SLEEP_NAVIGATION 341 self.sleep_nav = const.SLEEP_NAVIGATION
337 342
  343 + # Serial port
  344 + self.serial_port = None
  345 + self.serial_port_connection = None
  346 +
  347 + def UpdateSleep(self, sleep):
  348 + self.sleep_nav = sleep
  349 + self.serial_port_connection.sleep_nav = sleep
  350 +
  351 + def SerialPortEnabled(self):
  352 + return self.serial_port is not None
  353 +
338 def SetImageFiducial(self, fiducial_index, coord): 354 def SetImageFiducial(self, fiducial_index, coord):
339 self.image_fiducials[fiducial_index, :] = coord 355 self.image_fiducials[fiducial_index, :] = coord
340 356
@@ -365,8 +381,8 @@ class Navigation(): @@ -365,8 +381,8 @@ class Navigation():
365 if self.event.is_set(): 381 if self.event.is_set():
366 self.event.clear() 382 self.event.clear()
367 383
368 - vis_components = [self.trigger_state, self.view_tracts, self.peel_loaded]  
369 - vis_queues = [self.coord_queue, self.trigger_queue, self.tracts_queue, self.icp_queue] 384 + vis_components = [self.SerialPortEnabled(), self.view_tracts, self.peel_loaded]
  385 + vis_queues = [self.coord_queue, self.serial_port_queue, self.tracts_queue, self.icp_queue]
370 386
371 Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components) 387 Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components)
372 388
@@ -413,10 +429,16 @@ class Navigation(): @@ -413,10 +429,16 @@ class Navigation():
413 self.event, self.sleep_nav)) 429 self.event, self.sleep_nav))
414 430
415 if not errors: 431 if not errors:
416 - #TODO: Test the trigger thread  
417 - if self.trigger_state:  
418 - # self.trigger = trig.Trigger(nav_id)  
419 - jobs_list.append(trig.TriggerNew(self.trigger_queue, self.event, self.sleep_nav)) 432 + #TODO: Test the serial port thread
  433 + if self.SerialPortEnabled():
  434 + self.serial_port_connection = spc.SerialPortConnection(
  435 + self.serial_port,
  436 + self.serial_port_queue,
  437 + self.event,
  438 + self.sleep_nav,
  439 + )
  440 + self.serial_port_connection.Connect()
  441 + jobs_list.append(self.serial_port_connection)
420 442
421 if self.view_tracts: 443 if self.view_tracts:
422 # initialize Trekker parameters 444 # initialize Trekker parameters
@@ -450,9 +472,12 @@ class Navigation(): @@ -450,9 +472,12 @@ class Navigation():
450 self.coord_queue.clear() 472 self.coord_queue.clear()
451 self.coord_queue.join() 473 self.coord_queue.join()
452 474
453 - if self.trigger_state:  
454 - self.trigger_queue.clear()  
455 - self.trigger_queue.join() 475 + if self.SerialPortEnabled():
  476 + self.serial_port_connection.join()
  477 +
  478 + self.serial_port_queue.clear()
  479 + self.serial_port_queue.join()
  480 +
456 if self.view_tracts: 481 if self.view_tracts:
457 self.coord_tracts_queue.clear() 482 self.coord_tracts_queue.clear()
458 self.coord_tracts_queue.join() 483 self.coord_tracts_queue.join()
@@ -460,7 +485,7 @@ class Navigation(): @@ -460,7 +485,7 @@ class Navigation():
460 self.tracts_queue.clear() 485 self.tracts_queue.clear()
461 self.tracts_queue.join() 486 self.tracts_queue.join()
462 487
463 - vis_components = [self.trigger_state, self.view_tracts, self.peel_loaded] 488 + vis_components = [self.serial_port_connection.Enabled(), self.view_tracts, self.peel_loaded]
464 Publisher.sendMessage("Navigation status", nav_status=False, vis_status=vis_components) 489 Publisher.sendMessage("Navigation status", nav_status=False, vis_status=vis_components)
465 490
466 491
@@ -800,7 +825,7 @@ class NeuronavigationPanel(wx.Panel): @@ -800,7 +825,7 @@ class NeuronavigationPanel(wx.Panel):
800 Publisher.subscribe(self.LoadImageFiducials, 'Load image fiducials') 825 Publisher.subscribe(self.LoadImageFiducials, 'Load image fiducials')
801 Publisher.subscribe(self.SetImageFiducial, 'Set image fiducial') 826 Publisher.subscribe(self.SetImageFiducial, 'Set image fiducial')
802 Publisher.subscribe(self.SetTrackerFiducial, 'Set tracker fiducial') 827 Publisher.subscribe(self.SetTrackerFiducial, 'Set tracker fiducial')
803 - Publisher.subscribe(self.UpdateTriggerState, 'Update trigger state') 828 + Publisher.subscribe(self.UpdateSerialPort, 'Update serial port')
804 Publisher.subscribe(self.UpdateTrackObjectState, 'Update track object state') 829 Publisher.subscribe(self.UpdateTrackObjectState, 'Update track object state')
805 Publisher.subscribe(self.UpdateImageCoordinates, 'Set cross focal point') 830 Publisher.subscribe(self.UpdateImageCoordinates, 'Set cross focal point')
806 Publisher.subscribe(self.OnDisconnectTracker, 'Disconnect tracker') 831 Publisher.subscribe(self.OnDisconnectTracker, 'Disconnect tracker')
@@ -887,7 +912,7 @@ class NeuronavigationPanel(wx.Panel): @@ -887,7 +912,7 @@ class NeuronavigationPanel(wx.Panel):
887 self.navigation.seed_radius = data 912 self.navigation.seed_radius = data
888 913
889 def UpdateSleep(self, data): 914 def UpdateSleep(self, data):
890 - self.navigation.sleep_nav = data 915 + self.navigation.UpdateSleep(data)
891 916
892 def UpdateNumberThreads(self, data): 917 def UpdateNumberThreads(self, data):
893 self.navigation.n_threads = data 918 self.navigation.n_threads = data
@@ -919,8 +944,8 @@ class NeuronavigationPanel(wx.Panel): @@ -919,8 +944,8 @@ class NeuronavigationPanel(wx.Panel):
919 def UpdateTrackObjectState(self, evt=None, flag=None, obj_name=None, polydata=None): 944 def UpdateTrackObjectState(self, evt=None, flag=None, obj_name=None, polydata=None):
920 self.navigation.track_obj = flag 945 self.navigation.track_obj = flag
921 946
922 - def UpdateTriggerState(self, trigger_state):  
923 - self.navigation.trigger_state = trigger_state 947 + def UpdateSerialPort(self, serial_port):
  948 + self.navigation.serial_port = serial_port
924 949
925 def ResetICP(self): 950 def ResetICP(self):
926 self.icp.ResetICP() 951 self.icp.ResetICP()
@@ -2281,8 +2306,8 @@ class UpdateNavigationScene(threading.Thread): @@ -2281,8 +2306,8 @@ class UpdateNavigationScene(threading.Thread):
2281 """ 2306 """
2282 2307
2283 threading.Thread.__init__(self, name='UpdateScene') 2308 threading.Thread.__init__(self, name='UpdateScene')
2284 - self.trigger_state, self.view_tracts, self.peel_loaded = vis_components  
2285 - self.coord_queue, self.trigger_queue, self.tracts_queue, self.icp_queue = vis_queues 2309 + self.serial_port_enabled, self.view_tracts, self.peel_loaded = vis_components
  2310 + self.coord_queue, self.serial_port_queue, self.tracts_queue, self.icp_queue = vis_queues
2286 self.sle = sle 2311 self.sle = sle
2287 self.event = event 2312 self.event = event
2288 2313
@@ -2306,11 +2331,11 @@ class UpdateNavigationScene(threading.Thread): @@ -2306,11 +2331,11 @@ class UpdateNavigationScene(threading.Thread):
2306 # wx.CallAfter(Publisher.sendMessage, 'Update marker offset', coord_offset=coord_offset) 2331 # wx.CallAfter(Publisher.sendMessage, 'Update marker offset', coord_offset=coord_offset)
2307 self.tracts_queue.task_done() 2332 self.tracts_queue.task_done()
2308 2333
2309 - if self.trigger_state:  
2310 - trigger_on = self.trigger_queue.get_nowait() 2334 + if self.serial_port_enabled:
  2335 + trigger_on = self.serial_port_queue.get_nowait()
2311 if trigger_on: 2336 if trigger_on:
2312 wx.CallAfter(Publisher.sendMessage, 'Create marker') 2337 wx.CallAfter(Publisher.sendMessage, 'Create marker')
2313 - self.trigger_queue.task_done() 2338 + self.serial_port_queue.task_done()
2314 2339
2315 #TODO: If using the view_tracts substitute the raw coord from the offset coordinate, so the user 2340 #TODO: If using the view_tracts substitute the raw coord from the offset coordinate, so the user
2316 # see the red cross in the position of the offset marker 2341 # see the red cross in the position of the offset marker