Stage
Classes
Stage(tem)
Stage control.
Source code in src/instamatic/TEMController/stage.py
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Attributes
a: int
property
writable
Rotation angle.
b: int
property
writable
Secondary rotation angle.
name: str
property
Get name of the class.
x: int
property
writable
X position.
xy: Tuple[int, int]
property
writable
XY position as a tuple.
y: int
property
writable
Y position.
z: int
property
writable
Stage height Z.
Functions
alpha_wobbler(delta=5.0, event=None)
Tilt the stage by plus/minus the value of delta (degrees) If event is not set, press Ctrl-C to interrupt.
Source code in src/instamatic/TEMController/stage.py
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eliminate_backlash_a(target_angle=0.0, step=1.0, n_steps=3, settle_delay=0.2)
Eliminate backlash by relaxing the position. The routine will move
in opposite direction of the targeted angle by n_steps
*step
, and
walk up to the current tilt angle in n_steps
. Based on Suloway et
al., J. Struct. Biol. (2009), doi: 10.1016/j.jsb.2009.03.019.
target_angle: float, target angle for the rotation in degrees step: float, stepsize in degrees n_steps: int > 0, number of steps to walk up to current angle settle_delay: float, delay between movements in seconds to allow the stage to settle
Source code in src/instamatic/TEMController/stage.py
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eliminate_backlash_xy(step=10000, settle_delay=0.2)
Eliminate backlash by in XY by moving the stage away from the
current position, and approaching it from the common direction. Uses
set_xy_with_backlash_correction
internally.
step: float, stepsize in nm settle_delay: float, delay between movements in seconds to allow the stage to settle
Source code in src/instamatic/TEMController/stage.py
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get()
Get stage positions; x, y, z, and status of the rotation axes; a, b.
Source code in src/instamatic/TEMController/stage.py
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is_moving()
Return 'True' if the stage is moving.
Source code in src/instamatic/TEMController/stage.py
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move_along_optical_axis(delta_z)
See Stage.move_in_projection
Source code in src/instamatic/TEMController/stage.py
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move_in_projection(delta_x, delta_y)
Y and z are always perpendicular to the sample stage. To achieve the movement in the projection, x and yshould be broken down into the components z' and y'.
y = y' * cos(a) z = y' * sin(a)
z'| / z | / |/_____ y' \ a \ \ y
Source code in src/instamatic/TEMController/stage.py
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move_xy_with_backlash_correction(shift_x=None, shift_y=None, step=5000, settle_delay=0.2, wait=True)
Move xy by given shifts in stage coordinates with backlash
correction. This is done by moving backwards from the targeted position
by step
, before moving to the targeted position. This function is
meant to be used when precise relative movements are needed, for
example when a shift is calculated from an image. Based on Liu et al.,
Sci. Rep. (2016) DOI: 10.1038/srep29231.
shift_x, shift_y: float, relative movement in x and y (nm) step: float, stepsize in nm settle_delay: float, delay between movements in seconds to allow the stage to settle wait: bool, block until stage movement is complete (JEOL only)
Source code in src/instamatic/TEMController/stage.py
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neutral()
Reset the position of the stage to the 0-position.
Source code in src/instamatic/TEMController/stage.py
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no_wait()
Context manager that prevents blocking stage position calls on properties.
Usage: with ctrl.stage.no_wait(): ctrl.stage.x += 1000 ctrl.stage.y += 1000
Source code in src/instamatic/TEMController/stage.py
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relax_xy(step=100)
Relax the stage by moving it in the opposite direction from the last movement.
Source code in src/instamatic/TEMController/stage.py
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rotating_speed(speed)
Context manager that sets the rotation speed for the duration of the
with
statement (JEOL only).
Usage: with ctrl.stage.rotating_speed(1): ctrl.stage.a = 40.0
Source code in src/instamatic/TEMController/stage.py
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set(x=None, y=None, z=None, a=None, b=None, wait=True)
Wait: bool, block until stage movement is complete (JEOL only)
Source code in src/instamatic/TEMController/stage.py
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set_a_with_speed(a, speed, wait=False)
Rotate to angle a
with speed (JEOL only).
wait: bool, block until stage movement is complete.
Source code in src/instamatic/TEMController/stage.py
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set_rotation_speed(speed=1)
Sets the stage (rotation) movement speed on the TEM.
Source code in src/instamatic/TEMController/stage.py
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set_with_speed(x=None, y=None, z=None, a=None, b=None, wait=True, speed=1.0)
Note that this function only works on FEI machines.
wait: ignored, but necessary for compatibility with JEOL API speed: float, set stage rotation with specified speed (FEI only)
Source code in src/instamatic/TEMController/stage.py
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set_xy_with_backlash_correction(x=None, y=None, step=10000, settle_delay=0.2)
Move to new x/y position with backlash correction. This is done by approaching the target x/y position always from the same direction.
SerialEM uses the same approach (x first, y second, step=10000).
step: float, stepsize in nm settle_delay: float, delay between movements in seconds to allow the stage to settle
Source code in src/instamatic/TEMController/stage.py
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stop()
This will halt the stage preemptively if wait=False
is passed to
Stage.set.
Source code in src/instamatic/TEMController/stage.py
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wait()
Blocking call that waits for stage movement to finish.
Source code in src/instamatic/TEMController/stage.py
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