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[refactor] Refactor vertical movement calculation #339

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[refactor] Refactor vertical movement calculation #339

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47ead8c
[refactor] manually calculate correction factor and support SEM movement
Oct 22, 2024
62ff9ac
Merge remote-tracking branch 'origin/main' into refactor-vertical-mov…
Nov 12, 2024
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48 changes: 28 additions & 20 deletions fibsem/microscope.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,7 @@ def stable_move(self,dx: float, dy: float, beam_type: BeamType) -> FibsemStagePo
pass

@abstractmethod
def vertical_move(self, dy: float, dx: float = 0, static_wd: bool = True) -> None:
def vertical_move(self, dy: float, dx: float = 0, static_wd: bool = True, use_perspective: bool = True) -> None:
pass

def move_flat_to_beam(self, beam_type: BeamType, _safe:bool = True) -> None:
Expand Down Expand Up @@ -1194,6 +1194,7 @@ def vertical_move(
dy: float,
dx: float = 0.0,
static_wd: bool = True,
use_perspective: bool = True,
) -> None:
""" Move the stage vertically to correct coincidence point

Expand Down Expand Up @@ -1223,28 +1224,31 @@ def vertical_move(

# TODO: implement perspective correction
PERSPECTIVE_CORRECTION = 0.9
z_move = dy / np.cos(np.deg2rad(90 - self.system.ion.column_tilt)) * PERSPECTIVE_CORRECTION # TODO: MAGIC NUMBER, 90 - fib tilt
z_move = dy
if use_perspective:
z_move = dy / np.cos(np.deg2rad(90 - self.system.ion.column_tilt)) * PERSPECTIVE_CORRECTION # TODO: MAGIC NUMBER, 90 - fib tilt

# TODO: do this manually without autoscript in raw coordinates
# TODO: test if this results in the same movement
# manually calculate the dx, dy, dz
# theta = self.get_stage_position().t # rad
# dy = z_move * np.sin(theta)
# dz = z_move / np.cos(theta)
# logging.debug(f"dx: {dx}, dy: {dy}, dz: {dz}")
# stage_position = FibsemStagePosition(x=dx, y=dy, z=z_move, coordinate_system="RAW")

stage_position = FibsemStagePosition(
x=dx,
z=z_move,
coordinate_system="Specimen"
)
theta = self.get_stage_position().t # rad
dy = z_move * np.sin(theta)
dz = z_move / np.cos(theta)
stage_position = FibsemStagePosition(x=dx, y=dy, z=dz, coordinate_system="RAW")
logging.info(f"Vertical movement: {stage_position}")
self.move_stage_relative(stage_position) # NOTE: this seems to be a bit less than previous... -> perspective correction?

# stage_position = FibsemStagePosition(
# x=dx,
# z=z_move,
# coordinate_system="Specimen"
# )

# move stage
move_settings = MoveSettings(link_z_y=True)
autoscript_position = stage_position.to_autoscript_position(self.stage_is_compustage)
autoscript_position.coordinate_system = CoordinateSystem.SPECIMEN
self.stage.relative_move(autoscript_position, move_settings)
# # move stage
# move_settings = MoveSettings(link_z_y=True)
# autoscript_position = stage_position.to_autoscript_position(self.stage_is_compustage)
# autoscript_position.coordinate_system = CoordinateSystem.SPECIMEN
# self.stage.relative_move(autoscript_position, move_settings)

# restore working distance to adjust for microscope compenstation
if static_wd and not self.stage_is_compustage:
Expand Down Expand Up @@ -3796,6 +3800,7 @@ def vertical_move(
dy: float,
dx: float = 0.0,
static_wd: bool = True,
use_perspective: bool = True
) -> None:
"""
Move the stage vertically to correct eucentric point
Expand Down Expand Up @@ -5591,7 +5596,7 @@ def stable_move(self, dx: float, dy:float, beam_type: BeamType, static_wd: bool=
return stage_position


def vertical_move(self, dy: float, dx:float = 0.0, static_wd: bool=True) -> FibsemStagePosition:
def vertical_move(self, dy: float, dx:float = 0.0, static_wd: bool=True, use_perspective: bool = True) -> FibsemStagePosition:
"""Move the stage vertically by the specified amount."""
# confirm stage is enabled
_check_stage(self.system)
Expand All @@ -5607,7 +5612,10 @@ def vertical_move(self, dy: float, dx:float = 0.0, static_wd: bool=True) -> Fibs

# TODO: implement perspective correction
PERSPECTIVE_CORRECTION = 0.9
z_move = dy / np.cos(np.deg2rad(90 - self.system.ion.column_tilt)) * PERSPECTIVE_CORRECTION # TODO: MAGIC NUMBER, 90 - fib tilt
z_move = dy
if use_perspective:
z_move = dy / np.cos(np.deg2rad(90 - self.system.ion.column_tilt)) * PERSPECTIVE_CORRECTION # TODO: MAGIC NUMBER, 90 - fib tilt


# TODO: do this manually without autoscript in raw coordinates
stage_position = FibsemStagePosition(
Expand Down
17 changes: 13 additions & 4 deletions fibsem/ui/FibsemMovementWidget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -252,11 +252,20 @@ def _double_click_worker(self, layer, event):

log_status_message(f"MOVING_{self.movement_mode.name}_BY_{point.x:.2e}, {point.y:.2e} | {beam_type}")
self.movement_notification_signal.emit("Moving stage ")
# eucentric is only supported for ION beam
if beam_type is BeamType.ION and self.movement_mode is MovementMode.Vertical:
self.microscope.vertical_move(dx=point.x, dy=-point.y
)

# vertical movements correct beam coincidence, stable movements maintain it
if self.movement_mode is MovementMode.Vertical:
if beam_type is BeamType.ION:
self.microscope.vertical_move(dx=point.x, dy=point.y) # only vertical movement
if beam_type is BeamType.ELECTRON:
# stable move -> vertical move
self.microscope.stable_move(
dx=point.x,
dy=point.y,
beam_type=beam_type,
)
# invert vertical movement to maintain coincidence
self.microscope.vertical_move(dx=0, dy=-point.y, use_perspective=False)
else:
# corrected stage movement
self.microscope.stable_move(
Expand Down