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Commit 10ee10300e4b7e698ab4e892bc519f1cbec35b53

Authored by okahilak
Committed by GitHub
1 parent 9c40a251
Exists in master

MOD: Compute median over multiple tracker samples in object calibration (#342) 

- This patch does not change the logic of what is done with the tracker
  samples in OnGetObjectFiducials function. However, maybe the logic
  indeed should be changed at some point; add a few comments to the
  code for the future reader of the code to perhaps grasp more easily
  what is done there.
Showing 3 changed files with 33 additions and 16 deletions   Show diff stats
invesalius/constants.py
  Diff comments   View file @10ee103
@@ -660,7 +660,7 @@ BOOLEAN_XOR = 4 @@ -660,7 +660,7 @@ BOOLEAN_XOR = 4
660 MARKER_COLOUR = (1.0, 1.0, 0.) 660 MARKER_COLOUR = (1.0, 1.0, 0.)
661 MARKER_SIZE = 2 661 MARKER_SIZE = 2
662 662
663 -FIDUCIAL_REGISTRATION_TRACKER_SAMPLES = 10 663 +CALIBRATION_TRACKER_SAMPLES = 10
664 FIDUCIAL_REGISTRATION_ERROR_THRESHOLD = 3.0 664 FIDUCIAL_REGISTRATION_ERROR_THRESHOLD = 3.0
665 665
666 SELECT = 0 666 SELECT = 0
invesalius/gui/dialogs.py
  Diff comments   View file @10ee103
@@ -3296,7 +3296,7 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3296,7 +3296,7 @@ class ObjectCalibrationDialog(wx.Dialog):
3296 choice_ref = wx.ComboBox(self, -1, "", size=wx.Size(90, 23), 3296 choice_ref = wx.ComboBox(self, -1, "", size=wx.Size(90, 23),
3297 choices=const.REF_MODE, style=wx.CB_DROPDOWN | wx.CB_READONLY) 3297 choices=const.REF_MODE, style=wx.CB_DROPDOWN | wx.CB_READONLY)
3298 choice_ref.SetToolTip(tooltip) 3298 choice_ref.SetToolTip(tooltip)
3299 - choice_ref.Bind(wx.EVT_COMBOBOX, self.OnChoiceRefMode) 3299 + choice_ref.Bind(wx.EVT_COMBOBOX, self.OnChooseReferenceMode)
3300 choice_ref.SetSelection(1) 3300 choice_ref.SetSelection(1)
3301 choice_ref.Enable(1) 3301 choice_ref.Enable(1)
3302 if self.tracker_id == const.PATRIOT or self.tracker_id == const.ISOTRAKII: 3302 if self.tracker_id == const.PATRIOT or self.tracker_id == const.ISOTRAKII:
@@ -3396,7 +3396,7 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3396,7 +3396,7 @@ class ObjectCalibrationDialog(wx.Dialog):
3396 elif filename.lower().endswith('.vtp'): 3396 elif filename.lower().endswith('.vtp'):
3397 reader = vtk.vtkXMLPolyDataReader() 3397 reader = vtk.vtkXMLPolyDataReader()
3398 else: 3398 else:
3399 - wx.MessageBox(_("File format not reconized by InVesalius"), _("Import surface error")) 3399 + wx.MessageBox(_("File format not recognized by InVesalius"), _("Import surface error"))
3400 return 3400 return
3401 else: 3401 else:
3402 filename = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl") 3402 filename = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
@@ -3482,18 +3482,34 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3482,18 +3482,34 @@ class ObjectCalibrationDialog(wx.Dialog):
3482 return ball_actor, tactor 3482 return ball_actor, tactor
3483 3483
3484 def OnGetObjectFiducials(self, evt): 3484 def OnGetObjectFiducials(self, evt):
  3485 + if not self.tracker.IsTrackerInitialized():
  3486 + ShowNavigationTrackerWarning(0, 'choose')
  3487 + return
  3488 +
3485 btn_id = list(const.BTNS_OBJ[evt.GetId()].keys())[0] 3489 btn_id = list(const.BTNS_OBJ[evt.GetId()].keys())[0]
3486 3490
3487 - if self.trk_init and self.tracker_id:  
3488 - coord_raw = dco.GetCoordinates(self.trk_init, self.tracker_id, self.obj_ref_id)  
3489 - if self.obj_ref_id and btn_id == 4:  
3490 - coord = coord_raw[self.obj_ref_id, :]  
3491 - else:  
3492 - coord = coord_raw[0, :]  
3493 - else:  
3494 - ShowNavigationTrackerWarning(0, 'choose') 3491 + coord, coord_raw = self.tracker.GetTrackerCoordinates(
  3492 + # XXX: Always use static reference mode when getting the coordinates. This is what the
  3493 + # code did previously, as well. At some point, it should probably be thought through
  3494 + # if this is actually what we want or if it should be changed somehow.
  3495 + #
  3496 + ref_mode_id=const.STATIC_REF,
  3497 + n_samples=const.CALIBRATION_TRACKER_SAMPLES,
  3498 + )
3495 3499
3496 - if btn_id == 3: 3500 + # XXX: The condition below happens when setting the "fixed" coordinate in the object calibration.
  3501 + # The case is not handled by GetTrackerCoordinates function, therefore redo some computation
  3502 + # that is already done once by GetTrackerCoordinates, namely, invert the y-coordinate.
  3503 + #
  3504 + # (What is done here does not seem to be completely consistent with "always use static reference
  3505 + # mode" principle above, but it's hard to come up with a simple change to increase the consistency
  3506 + # and not change the function to the point of potentially breaking it.)
  3507 + #
  3508 + if self.obj_ref_id and btn_id == 4:
  3509 + coord = coord_raw[self.obj_ref_id, :]
  3510 + coord[2] = -coord[2]
  3511 +
  3512 + if btn_id == 3:
3497 coord = np.zeros([6,]) 3513 coord = np.zeros([6,])
3498 3514
3499 # Update text controls with tracker coordinates 3515 # Update text controls with tracker coordinates
@@ -3509,7 +3525,7 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3509,7 +3525,7 @@ class ObjectCalibrationDialog(wx.Dialog):
3509 else: 3525 else:
3510 ShowNavigationTrackerWarning(0, 'choose') 3526 ShowNavigationTrackerWarning(0, 'choose')
3511 3527
3512 - def OnChoiceRefMode(self, evt): 3528 + def OnChooseReferenceMode(self, evt):
3513 # When ref mode is changed the tracker coordinates are set to nan 3529 # When ref mode is changed the tracker coordinates are set to nan
3514 # This is for Polhemus FASTRAK wrapper, where the sensor attached to the object can be the stylus (Static 3530 # This is for Polhemus FASTRAK wrapper, where the sensor attached to the object can be the stylus (Static
3515 # reference - Selection 0 - index 0 for coordinates) or can be a 3rd sensor (Dynamic reference - Selection 1 - 3531 # reference - Selection 0 - index 0 for coordinates) or can be a 3rd sensor (Dynamic reference - Selection 1 -
@@ -3517,13 +3533,14 @@ class ObjectCalibrationDialog(wx.Dialog): @@ -3517,13 +3533,14 @@ class ObjectCalibrationDialog(wx.Dialog):
3517 # I use the index 2 directly here to send to the coregistration module where it is possible to access without 3533 # I use the index 2 directly here to send to the coregistration module where it is possible to access without
3518 # any conditional statement the correct index of coordinates. 3534 # any conditional statement the correct index of coordinates.
3519 3535
3520 - if evt.GetSelection(): 3536 + if evt.GetSelection() == 1:
3521 self.obj_ref_id = 2 3537 self.obj_ref_id = 2
3522 if self.tracker_id in [const.FASTRAK, const.DEBUGTRACKRANDOM, const.DEBUGTRACKAPPROACH]: 3538 if self.tracker_id in [const.FASTRAK, const.DEBUGTRACKRANDOM, const.DEBUGTRACKAPPROACH]:
3523 self.choice_sensor.Show(self.obj_ref_id) 3539 self.choice_sensor.Show(self.obj_ref_id)
3524 else: 3540 else:
3525 self.obj_ref_id = 0 3541 self.obj_ref_id = 0
3526 self.choice_sensor.Show(self.obj_ref_id) 3542 self.choice_sensor.Show(self.obj_ref_id)
  3543 +
3527 for m in range(0, 5): 3544 for m in range(0, 5):
3528 self.obj_fiducials[m, :] = np.full([1, 3], np.nan) 3545 self.obj_fiducials[m, :] = np.full([1, 3], np.nan)
3529 self.obj_orients[m, :] = np.full([1, 3], np.nan) 3546 self.obj_orients[m, :] = np.full([1, 3], np.nan)
invesalius/gui/task_navigator.py
  Diff comments   View file @10ee103
@@ -582,7 +582,7 @@ class Tracker(): @@ -582,7 +582,7 @@ class Tracker():
582 for i in range(n_samples): 582 for i in range(n_samples):
583 coord_raw = dco.GetCoordinates(self.trk_init, self.tracker_id, ref_mode_id) 583 coord_raw = dco.GetCoordinates(self.trk_init, self.tracker_id, ref_mode_id)
584 584
585 - if ref_mode_id: 585 + if ref_mode_id == const.DYNAMIC_REF:
586 coord = dco.dynamic_reference_m(coord_raw[0, :], coord_raw[1, :]) 586 coord = dco.dynamic_reference_m(coord_raw[0, :], coord_raw[1, :])
587 else: 587 else:
588 coord = coord_raw[0, :] 588 coord = coord_raw[0, :]
@@ -599,7 +599,7 @@ class Tracker(): @@ -599,7 +599,7 @@ class Tracker():
599 def SetTrackerFiducial(self, ref_mode_id, fiducial_index): 599 def SetTrackerFiducial(self, ref_mode_id, fiducial_index):
600 coord, coord_raw = self.GetTrackerCoordinates( 600 coord, coord_raw = self.GetTrackerCoordinates(
601 ref_mode_id=ref_mode_id, 601 ref_mode_id=ref_mode_id,
602 - n_samples=const.FIDUCIAL_REGISTRATION_TRACKER_SAMPLES, 602 + n_samples=const.CALIBRATION_TRACKER_SAMPLES,
603 ) 603 )
604 604
605 # Update tracker fiducial with tracker coordinates 605 # Update tracker fiducial with tracker coordinates