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FIX: ruff format
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@rmatsuda
rmatsuda committed Jul 25, 2024
1 parent 3a79ea7 commit 79a7775
Showing 1 changed file with 91 additions and 64 deletions.
155 changes: 91 additions & 64 deletions invesalius/net/neuronavigation_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,22 +69,39 @@ def assert_valid(self, connection):
assert self._hasmethod(connection, "set_callback__set_vector_field")

def __bind_events(self):
Publisher.subscribe(self.start_navigation, 'Start navigation')
Publisher.subscribe(self.stop_navigation, 'Stop navigation')
Publisher.subscribe(self.update_target_mode, 'Set target mode')
Publisher.subscribe(self.update_coil_at_target, 'Coil at target')
Publisher.subscribe(self.update_tracker_poses, 'From Neuronavigation: Update tracker poses')
Publisher.subscribe(self.update_target_orientation, 'Update target orientation')
Publisher.subscribe(self.connect_to_robot, 'Neuronavigation to Robot: Connect to robot')
Publisher.subscribe(self.set_target, 'Neuronavigation to Robot: Set target')
Publisher.subscribe(self.unset_target, 'Neuronavigation to Robot: Unset target')
Publisher.subscribe(self.set_tracker_fiducials, 'Neuronavigation to Robot: Set tracker fiducials')
Publisher.subscribe(self.collect_robot_pose, 'Neuronavigation to Robot: Collect coordinates for the robot transformation matrix')
Publisher.subscribe(self.reset_robot_transformation_matrix, 'Neuronavigation to Robot: Reset coordinates collection for the robot transformation matrix')
Publisher.subscribe(self.estimate_robot_transformation_matrix, 'Neuronavigation to Robot: Estimate robot transformation matrix')
Publisher.subscribe(self.set_robot_transformation_matrix, 'Neuronavigation to Robot: Set robot transformation matrix')
Publisher.subscribe(self.update_displacement_to_target, 'Neuronavigation to Robot: Update displacement to target')
Publisher.subscribe(self.set_objective, 'Neuronavigation to Robot: Set objective')
Publisher.subscribe(self.start_navigation, "Start navigation")
Publisher.subscribe(self.stop_navigation, "Stop navigation")
Publisher.subscribe(self.update_target_mode, "Set target mode")
Publisher.subscribe(self.update_coil_at_target, "Coil at target")
Publisher.subscribe(self.update_tracker_poses, "From Neuronavigation: Update tracker poses")
Publisher.subscribe(self.update_target_orientation, "Update target orientation")
Publisher.subscribe(self.connect_to_robot, "Neuronavigation to Robot: Connect to robot")
Publisher.subscribe(self.set_target, "Neuronavigation to Robot: Set target")
Publisher.subscribe(self.unset_target, "Neuronavigation to Robot: Unset target")
Publisher.subscribe(
self.set_tracker_fiducials, "Neuronavigation to Robot: Set tracker fiducials"
)
Publisher.subscribe(
self.collect_robot_pose,
"Neuronavigation to Robot: Collect coordinates for the robot transformation matrix",
)
Publisher.subscribe(
self.reset_robot_transformation_matrix,
"Neuronavigation to Robot: Reset coordinates collection for the robot transformation matrix",
)
Publisher.subscribe(
self.estimate_robot_transformation_matrix,
"Neuronavigation to Robot: Estimate robot transformation matrix",
)
Publisher.subscribe(
self.set_robot_transformation_matrix,
"Neuronavigation to Robot: Set robot transformation matrix",
)
Publisher.subscribe(
self.update_displacement_to_target,
"Neuronavigation to Robot: Update displacement to target",
)
Publisher.subscribe(self.set_objective, "Neuronavigation to Robot: Set objective")

# Functions for InVesalius to send updates.

Expand All @@ -108,10 +125,7 @@ def update_target_mode(self, enabled):

def update_target_orientation(self, target_id, orientation):
if self.connection is not None:
self.connection.update_target_orientation(
target_id=target_id,
orientation=orientation
)
self.connection.update_target_orientation(target_id=target_id, orientation=orientation)

# Functions for InVesalius to send updates.

Expand Down Expand Up @@ -143,11 +157,9 @@ def unset_target(self):
if self.connection is not None:
self.connection.unset_target()

def set_tracker_fiducials(self, tracker_fiducials):
def set_tracker_fiducials(self, tracker_fiducials):
if self.connection is not None:
self.connection.update_set_tracker_fiducials(
tracker_fiducials=tracker_fiducials
)
self.connection.update_set_tracker_fiducials(tracker_fiducials=tracker_fiducials)

def collect_robot_pose(self, data):
if self.connection is not None:
Expand All @@ -163,9 +175,8 @@ def estimate_robot_transformation_matrix(self, data):

def set_robot_transformation_matrix(self, data):
if self.connection is not None:
self.connection.set_robot_transformation_matrix(
matrix_tracker_to_robot=data
)
self.connection.set_robot_transformation_matrix(matrix_tracker_to_robot=data)

def update_displacement_to_target(self, displacement):
if self.connection is not None:
self.connection.update_displacement_to_target(
Expand Down Expand Up @@ -209,7 +220,9 @@ def update_coil_mesh(self, polydata):
#
# Assert that all polygons have an equal number of vertices, reshape the array, and drop n_i's.
#
assert np.all(polygons_raw[0::self.N_VERTICES_IN_POLYGON + 1] == self.N_VERTICES_IN_POLYGON)
assert np.all(
polygons_raw[0 :: self.N_VERTICES_IN_POLYGON + 1] == self.N_VERTICES_IN_POLYGON
)

polygons = polygons_raw.reshape(-1, self.N_VERTICES_IN_POLYGON + 1)[:, 1:]

Expand All @@ -220,36 +233,38 @@ def update_coil_mesh(self, polydata):

def update_coil_at_target(self, state):
if self.connection is not None:
self.connection.update_coil_at_target(
state=state
)

def initialize_efield(self, cortex_model_path, mesh_models_paths, coil_model_path, coil_set, conductivities_inside, conductivities_outside, dI_per_dt):
self.connection.update_coil_at_target(state=state)

def initialize_efield(
self,
cortex_model_path,
mesh_models_paths,
coil_model_path,
coil_set,
conductivities_inside,
conductivities_outside,
dI_per_dt,
):
if self.connection is not None:
return self.connection.initialize_efield(
cortex_model_path=cortex_model_path,
mesh_models_paths= mesh_models_paths,
coil_model_path =coil_model_path,
coil_set = coil_set,
conductivities_inside= conductivities_inside,
conductivities_outside = conductivities_outside,
dI_per_dt= dI_per_dt,
mesh_models_paths=mesh_models_paths,
coil_model_path=coil_model_path,
coil_set=coil_set,
conductivities_inside=conductivities_inside,
conductivities_outside=conductivities_outside,
dI_per_dt=dI_per_dt,
)
return None

def init_efield_config_file(self, config_file):
if self.connection is not None:
return self.connection.init_efield_json(
config_file=config_file
)
return self.connection.init_efield_json(config_file=config_file)
return None

def efield_coil(self, coil_model_path, coil_set):
if self.connection is not None:
return self.connection.set_coil(
coil_model_path=coil_model_path,
coil_set=coil_set
)
return self.connection.set_coil(coil_model_path=coil_model_path, coil_set=coil_set)

def set_dIperdt(self, dIperdt):
if self.connection is not None:
Expand Down Expand Up @@ -278,22 +293,17 @@ def update_efield_vector(self, position, orientation, T_rot):
def update_efield_vectorROI(self, position, orientation, T_rot, id_list):
if self.connection is not None:
return self.connection.update_efield_vectorROI(
position=position,
orientation=orientation,
T_rot=T_rot,
id_list=id_list
position=position, orientation=orientation, T_rot=T_rot, id_list=id_list
)
return None

def update_efield_vectorROIMax(self, position, orientation, T_rot, id_list):
if self.connection is not None:
return self.connection.update_efield_vectorROIMax(
position=position,
orientation=orientation,
T_rot=T_rot,
id_list=id_list
position=position, orientation=orientation, T_rot=T_rot, id_list=id_list
)
return None

# Functions for InVesalius to receive updates via callbacks.

def __set_callbacks(self, connection):
Expand All @@ -304,7 +314,9 @@ def __set_callbacks(self, connection):
connection.set_callback__robot_pose_collected(self.robot_pose_collected)
connection.set_callback__set_objective(self.set_objective_to_neuronavigation)
connection.set_callback__close_robot_dialog(self.close_robot_dialog)
connection.set_callback__update_robot_transformation_matrix(self.update_robot_transformation_matrix)
connection.set_callback__update_robot_transformation_matrix(
self.update_robot_transformation_matrix
)
connection.set_callback__set_vector_field(self.set_vector_field)

def add_pedal_callback(self, name, callback, remove_when_released=False):
Expand All @@ -320,29 +332,44 @@ def remove_pedal_callback(self, name):
self.connection.remove_pedal_callback(name=name)

def open_orientation_dialog(self, target_id):
wx.CallAfter(Publisher.sendMessage, 'Open marker orientation dialog', marker_id=target_id)
wx.CallAfter(Publisher.sendMessage, "Open marker orientation dialog", marker_id=target_id)

def stimulation_pulse_received(self):
# TODO: If marker should not be created always when receiving a stimulation pulse, add the logic here.
wx.CallAfter(Publisher.sendMessage, 'Create marker', marker_type=MarkerType.COIL_POSE)
wx.CallAfter(Publisher.sendMessage, "Create marker", marker_type=MarkerType.COIL_POSE)

def set_vector_field(self, vector_field):
wx.CallAfter(Publisher.sendMessage, 'Set vector field', vector_field=vector_field)
wx.CallAfter(Publisher.sendMessage, "Set vector field", vector_field=vector_field)

def update_robot_status(self, status):
wx.CallAfter(Publisher.sendMessage, 'Robot to Neuronavigation: Update robot status', robot_status=status)
wx.CallAfter(
Publisher.sendMessage,
"Robot to Neuronavigation: Update robot status",
robot_status=status,
)

def robot_connection_status(self, status):
wx.CallAfter(Publisher.sendMessage, 'Robot to Neuronavigation: Robot connection status', data=status)
wx.CallAfter(
Publisher.sendMessage, "Robot to Neuronavigation: Robot connection status", data=status
)

def robot_pose_collected(self, status):
wx.CallAfter(Publisher.sendMessage, 'Robot to Neuronavigation: Coordinates for the robot transformation matrix collected')
wx.CallAfter(
Publisher.sendMessage,
"Robot to Neuronavigation: Coordinates for the robot transformation matrix collected",
)

def set_objective_to_neuronavigation(self, objective):
wx.CallAfter(Publisher.sendMessage, 'Robot to Neuronavigation: Set objective', objective=objective)
wx.CallAfter(
Publisher.sendMessage, "Robot to Neuronavigation: Set objective", objective=objective
)

def close_robot_dialog(self, status):
wx.CallAfter(Publisher.sendMessage, 'Robot to Neuronavigation: Close robot dialog')
wx.CallAfter(Publisher.sendMessage, "Robot to Neuronavigation: Close robot dialog")

def update_robot_transformation_matrix(self, matrix):
wx.CallAfter(Publisher.sendMessage, 'Robot to Neuronavigation: Update robot transformation matrix', data=matrix)
wx.CallAfter(
Publisher.sendMessage,
"Robot to Neuronavigation: Update robot transformation matrix",
data=matrix,
)

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