Stylus visualization is working with Aalto Polaris
TODO: add a stylus calibration tab to GUI

…! Use __ instead

…both Windows and Ubuntu 22

… a warning in this case, but allow navigation to work as normal

…e stylus in vtk)

…e functions were identical, except for r_img in corregistrate_probe... This rotation does not change ICP behavior since ICP only affects the translation

…hether to follow the coil or probe with marker. Join the two Corregistrate threads into one. Edit CoilVisualizer and GUI to work with this change.

Please excuse some stray comments and var-definitions (eg. n_coils)... I will clean these up in future multicoil PR.

… object and remove bogus 'navigation-stylus' object

…tion is started/stopped. Automatically show coil/probe when Track coil is pressed/unpressed

…s as opposed to y-axis. Also, removed unnecessary disabling of 'Track coil' button before navigation.

…nit dialogs. Polaris init dialog now asks for n_coils Coil ROM files.

Rename/repurpose obj_ref_mode to obj_id (this is the index of an object in coord_raw).

Use dicts throughout code so that coils can be controlled by name. Simplify CoilVisualizer and coregistration.

Add coil selection buttons to Preferences ObjectTab.

Improve ObjectTab init by using LoadConfig. Remove self.track_obj state var from GUI, it is a property of Navigation class.

Addition: load/save coil from/to OBR file.

…r fixes

…ad) since the ICP data is constant once created. The ICP data is passed to coregistration when the navigation is started, so it is up to date with the ICP data defined in Refine tab.

…ions

…aris ROM init dialog. Update handling of marker_visibilities to support multiple coils.

…d form.

…or Polaris to load ROM new files.

…w-coil button is right-clicked

…coil_name is specified and in navigation.coil_registrations before robot can be used

…. Add CoilSelectionDone function to simplify preferences code

…d the following:

  Messy multicoil instructions (there will be separate documentation for that)
  Unnecessary feature of changing the index (obj_id) of a registration

…iables.

…UFF format

… Now it is correctly oriented with NIFTI heads. TODO: unify the orientation of MRI and NIFTI heads in vtk?

… Remove obj_id=0 choice in multicoil mode. Automatically select a coil for navigation when it's created. Other fixes related to edge cases in coil creation/selection in multicoil mode

…hen loading state file. Update environment.yml. Minor refactors ie. naming changes.