Merge branch 'master' into multimodal_tracking

# Conflicts: # invesalius/constants.py

Merge branch 'master' into multimodal_tracking
# Conflicts: # invesalius/constants.py
Renan
2 parents e35fada3 e1b52082
Showing 7 changed files with 72 additions and 33 deletions Show diff stats
invesalius/constants.py
invesalius/data/serial_port_connection.py
invesalius/data/trackers.py
invesalius/data/viewer_volume.py
invesalius/gui/dialogs.py
invesalius/gui/task_navigator.py
invesalius/navigation/navigation.py
@@ -830,11 +830,12 @@ 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")
+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
+PULSE_DURATION_IN_MILLISECONDS = 0.2
 #Robot
 ROBOT_ElFIN_IP = ['143.107.220.251', '169.254.153.251', '127.0.0.1']
@@ -843,4 +844,3 @@ ROBOT_MOTIONS = {&quot;normal&quot;: 0, &quot;linear out&quot;: 1, &quot;arc&quot;: 2}
 ROBOT_HEAD_VELOCITY_THRESHOLD = 10
 ROBOT_ARC_THRESHOLD_DISTANCE = 100
 ROBOT_VERSOR_SCALE_FACTOR = 70
-
@@ -22,12 +22,12 @@ import threading
 import time
 import wx
+
+from invesalius import constants
 from invesalius.pubsub import pub as Publisher
 class SerialPortConnection(threading.Thread):
-    BINARY_PULSE = b'\x01'
-
     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.
@@ -65,7 +65,7 @@ class SerialPortConnection(threading.Thread):
     def SendPulse(self):
         try:
-            self.connection.write(self.BINARY_PULSE)
+            self.connection.send_break(constants.PULSE_DURATION_IN_MILLISECONDS / 1000)
             Publisher.sendMessage('Serial port pulse triggered')
         except:
             print("Error: Serial port could not be written into.")
@@ -301,9 +301,11 @@ def PlhSerialConnection(tracker_id):
     trck_init = None
     dlg_port = dlg.SetCOMPort(select_baud_rate=False)
     if dlg_port.ShowModal() == ID_OK:
-        com_port = dlg_port.GetValue()
+        com_port = dlg_port.GetCOMPort()
+        baud_rate = 115200
+
         try:
-            trck_init = serial.Serial(com_port, baudrate=115200, timeout=0.03)
+            trck_init = serial.Serial(com_port, baudrate=baud_rate, timeout=0.03)
             if tracker_id == 2:
                 # Polhemus FASTRAK needs configurations first
@@ -726,9 +726,13 @@ class Viewer(wx.Panel):
         self.distthreshold = dist_threshold
     def ActivateTargetMode(self, evt=None, target_mode=None):
+
         vtk_colors = vtk.vtkNamedColors()
         self.target_mode = target_mode
         if self.target_coord and self.target_mode:
+            if self.actor_peel:
+                self.object_orientation_torus_actor.SetVisibility(0)
+                self.obj_projection_arrow_actor.SetVisibility(0)
             self.CreateTargetAim()
             # Create a line
@@ -831,6 +835,9 @@ class Viewer(wx.Panel):
         else:
             self.DisableCoilTracker()
+            if self.actor_peel:
+                self.object_orientation_torus_actor.SetVisibility(1)
+                self.obj_projection_arrow_actor.SetVisibility(1)
     def OnUpdateObjectTargetGuide(self, m_img, coord):
@@ -4809,15 +4809,16 @@ class SetCOMPort(wx.Dialog):
         self.CenterOnParent()
-    def GetValue(self):
+    def GetCOMPort(self):
         com_port = self.com_port_dropdown.GetString(self.com_port_dropdown.GetSelection())
+        return com_port
-        if self.select_baud_rate:
-            baud_rate = self.baud_rate_dropdown.GetString(self.baud_rate_dropdown.GetSelection())
-        else:
-            baud_rate = None
+    def GetBaudRate(self):
+        if not self.select_baud_rate:
+            return None
-        return com_port, baud_rate
+        baud_rate = self.baud_rate_dropdown.GetString(self.baud_rate_dropdown.GetSelection())
+        return baud_rate
 class ManualWWWLDialog(wx.Dialog):
@@ -305,7 +305,7 @@ class InnerFoldPanel(wx.Panel):
                 ctrl.SetValue(False)
                 return
-            com_port = dlg_port.GetValue()
+            com_port = dlg_port.GetCOMPort()
             baud_rate = 115200
             Publisher.sendMessage('Update serial port', serial_port_in_use=True, com_port=com_port, baud_rate=baud_rate)
@@ -410,16 +410,10 @@ class NeuronavigationPanel(wx.Panel):
             self.btns_set_fiducial[n + 3] = ctrl
-        # TODO: Find a better allignment between FRE, text and navigate button
-        txt_fre = wx.StaticText(self, -1, _('FRE:'))
-        txt_icp = wx.StaticText(self, -1, _('Refine:'))
+        # TODO: Find a better alignment between FRE, text and navigate button
-        if pedal_connection is not None and pedal_connection.in_use:
-            txt_pedal_pressed = wx.StaticText(self, -1, _('Pedal pressed:'))
-        else:
-            txt_pedal_pressed = None
-
-        # Fiducial registration error text box
+        # Fiducial registration error text and checkbox
+        txt_fre = wx.StaticText(self, -1, _('FRE:'))
         tooltip = wx.ToolTip(_("Fiducial registration error"))
         txtctrl_fre = wx.TextCtrl(self, value="", size=wx.Size(60, -1), style=wx.TE_CENTRE)
         txtctrl_fre.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
@@ -434,6 +428,8 @@ class NeuronavigationPanel(wx.Panel):
         btn_nav.SetToolTip(tooltip)
         btn_nav.Bind(wx.EVT_TOGGLEBUTTON, partial(self.OnNavigate, btn_nav=btn_nav))
+        # "Refine" text and checkbox
+        txt_icp = wx.StaticText(self, -1, _('Refine:'))
         tooltip = wx.ToolTip(_(u"Refine the coregistration"))
         checkbox_icp = wx.CheckBox(self, -1, _(' '))
         checkbox_icp.SetValue(False)
@@ -442,8 +438,9 @@ class NeuronavigationPanel(wx.Panel):
         checkbox_icp.SetToolTip(tooltip)
         self.checkbox_icp = checkbox_icp
-        # An indicator for pedal trigger
+        # "Pedal pressed" text and an indicator (checkbox) for pedal press
         if pedal_connection is not None and pedal_connection.in_use:
+            txt_pedal_pressed = wx.StaticText(self, -1, _('Pedal pressed:'))
             tooltip = wx.ToolTip(_(u"Is the pedal pressed"))
             checkbox_pedal_pressed = wx.CheckBox(self, -1, _(' '))
             checkbox_pedal_pressed.SetValue(False)
@@ -454,15 +451,27 @@ class NeuronavigationPanel(wx.Panel):
             self.checkbox_pedal_pressed = checkbox_pedal_pressed
         else:
+            txt_pedal_pressed = None
             self.checkbox_pedal_pressed = None
+        # "Lock to target" text and checkbox
+        tooltip = wx.ToolTip(_(u"Allow triggering stimulation pulse only if the coil is at the target"))
+        lock_to_target_text = wx.StaticText(self, -1, _('Lock to target:'))
+        lock_to_target_checkbox = wx.CheckBox(self, -1, _(' '))
+        lock_to_target_checkbox.SetValue(False)
+        lock_to_target_checkbox.Enable(False)
+        lock_to_target_checkbox.Bind(wx.EVT_CHECKBOX, partial(self.OnLockToTargetCheckbox, ctrl=lock_to_target_checkbox))
+        lock_to_target_checkbox.SetToolTip(tooltip)
+
+        self.lock_to_target_checkbox = lock_to_target_checkbox
+
         # Image and tracker coordinates number controls
         for m in range(len(self.btns_set_fiducial)):
             for n in range(3):
                 self.numctrls_fiducial[m].append(
                     wx.lib.masked.numctrl.NumCtrl(parent=self, integerWidth=4, fractionWidth=1))
-        # Sizer to group all GUI objects
+        # Sizers to group all GUI objects
         choice_sizer = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
         choice_sizer.AddMany([(select_tracker_elem, wx.LEFT),
                               (choice_ref, wx.RIGHT)])
@@ -483,10 +492,13 @@ class NeuronavigationPanel(wx.Panel):
                            (txt_icp, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
                            (checkbox_icp, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)])
-        pedal_sizer = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
-        if HAS_PEDAL_CONNECTION and pedal_connection.in_use:
-            pedal_sizer.AddMany([(txt_pedal_pressed, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
-                                (checkbox_pedal_pressed, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)])
+        checkboxes_sizer = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
+        checkboxes_sizer.AddMany([(lock_to_target_text, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
+                                  (lock_to_target_checkbox, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)])
+
+        if pedal_connection is not None and pedal_connection.in_use:
+            checkboxes_sizer.AddMany([(txt_pedal_pressed, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
+                                      (checkbox_pedal_pressed, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)])
         group_sizer = wx.FlexGridSizer(rows=10, cols=1, hgap=5, vgap=5)
         group_sizer.AddGrowableCol(0, 1)
@@ -497,7 +509,7 @@ class NeuronavigationPanel(wx.Panel):
         group_sizer.AddMany([(choice_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL),
                              (coord_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL),
                              (nav_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                             (pedal_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL)])
+                             (checkboxes_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL)])
         main_sizer = wx.BoxSizer(wx.HORIZONTAL)
         main_sizer.Add(group_sizer, 1)# wx.ALIGN_CENTER_HORIZONTAL, 10)
@@ -575,7 +587,6 @@ class NeuronavigationPanel(wx.Panel):
         self.ResetICP()
         self.tracker.UpdateUI(self.select_tracker_elem, self.numctrls_fiducial[3:6], self.txtctrl_fre)
-
     def UpdatePeelVisualization(self, data):
         self.navigation.peel_loaded = data
@@ -614,6 +625,10 @@ class NeuronavigationPanel(wx.Panel):
     def UpdateTarget(self, coord):
         self.navigation.target = coord
+        self.lock_to_target_checkbox.Enable(True)
+        self.lock_to_target_checkbox.SetValue(True)
+        self.navigation.SetLockToTarget(True)
+
     def EnableACT(self, data):
         self.navigation.enable_act = data
@@ -644,6 +659,10 @@ class NeuronavigationPanel(wx.Panel):
         self.ResetICP()
         self.tracker.UpdateUI(self.select_tracker_elem, self.numctrls_fiducial[3:6], self.txtctrl_fre)
+    def OnLockToTargetCheckbox(self, evt, ctrl):
+        value = ctrl.GetValue()
+        self.navigation.SetLockToTarget(value)
+
     def OnChooseTracker(self, evt, ctrl):
         Publisher.sendMessage('Update status text in GUI',
                               label=_("Configuring tracker ..."))
@@ -1394,7 +1413,7 @@ class MarkersPanel(wx.Panel):
     @staticmethod
     def __list_fiducial_labels():
-        """Return the list of marker labels denoting fucials."""
+        """Return the list of marker labels denoting fiducials."""
         return list(itertools.chain(*(const.BTNS_IMG_MARKERS[i].values() for i in const.BTNS_IMG_MARKERS)))
     def UpdateCurrentCoord(self, position):
@@ -177,6 +177,7 @@ class Navigation():
         self.serial_port_connection = None
         # During navigation
+        self.lock_to_target = False
         self.coil_at_target = False
         self.__bind_events()
@@ -197,6 +198,9 @@ class Navigation():
         self.com_port = com_port
         self.baud_rate = baud_rate
+    def SetLockToTarget(self, value):
+        self.lock_to_target = value
+
     def SetReferenceMode(self, value):
         self.ref_mode_id = value
@@ -223,7 +227,13 @@ 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.serial_port_in_use:
+        if not self.serial_port_in_use:
+            return
+
+        permission_to_stimulate = (self.lock_to_target and self.coil_at_target) or \
+                                  not self.lock_to_target
+
+        if state and permission_to_stimulate:
             self.serial_port_connection.SendPulse()
     def StartNavigation(self, tracker):