pyfast_adt.main.adaptor.microscope.adaptor_jeol
Attributes
Classes
every angle for moving the satge must be in deg as input and output, velocity for the stage in radian/s and um for the stage xyz movement |
Module Contents
- pyfast_adt.main.adaptor.microscope.adaptor_jeol.prev_path
- class pyfast_adt.main.adaptor.microscope.adaptor_jeol.Tem_jeol(cam_table=None, master=None)
Bases:
pyfast_adt.main.adaptor.microscope.adaptor_tem.Tem_baseevery angle for moving the satge must be in deg as input and output, velocity for the stage in radian/s and um for the stage xyz movement
- tem = None
- result = []
- master = None
- calibrated_speed = None
- FUNCTION_MODES = ('mag1', 'mag2', 'lowmag', 'samag', 'diff')
- move_stage_up(stage_ampl)
stage ampl is in um and need to be converted to m to work in FEI/ThermoFisher (from API FEI works in m). before was set at -90 as fei, but is needed another 90 deg clockwise to be sincronized properly that’s why now is -180 if it doesn’t work try 0 deg
- move_stage_down(stage_ampl)
- move_stage_left(stage_ampl)
- move_stage_right(stage_ampl)
- move_stage_z_up(stage_ampl)
- move_stage_z_down(stage_ampl)
- move_beam_up(beam_ampl)
- move_beam_down(beam_ampl)
- move_beam_left(beam_ampl)
- move_beam_right(beam_ampl)
- move_stem_beam_up(beam_ampl)
- move_stem_beam_down(beam_ampl)
- move_stem_beam_left(beam_ampl)
- move_stem_beam_right(beam_ampl)
- getFunctionMode()
return one of these strings: Mag1, mag2, lowmag, samag, diff.
- setFunctionMode(value)
you can input in value both a string or an integer of the corresponding mode to change Mag1:0, mag2:1, lowmag:2, samag:3, diff:4.
- diffraction(checked_diff_value, kl=None)
“ this function set directly to 350 KL to fix a bug in temscript, this is ok only for the tecnai spirit, we should set in an external file which is the standard KL to set
- get_defocus()
function that return the objective lens defocus value as an integer?? there are 2 functions OLc and OLf, meaning to coarse and fine, to checkout what is useful
- set_defocus(defocus)
function that set the objective lens defocus value from an integer?? there are 2 functions OLc and OLf, meaning to coarse and fine, to checkout what is settlable
- euc_focus()
- wobbler(checked_wobbler_value)
- move_screen(checked_screen_value)
function to move the fluorescent screen if checked_screen_value is True will move up, otherwise move it down.
- get_screen_position()
return if the screen is up or down as ‘UP’ or ‘DOWN’.
- beam_blank(checked_blank_value)
function to enable beam blanking if checked_blank_value is True blank the beam, otherwise unblank it
- apply_rotation(vector, theta=216.4)
input an x,y vector and return a rotated vector of theta degree, usually used for syncronize the movement of the beam shift with the user reference. the rotation is counterclockwise!!
- fake()
- get_stage(standard=False)
return the current stage position of x, y, z in um a and b in deg. from default API from JEOL return nm and deg
- set_stage_position(x=None, y=None, z=None, a=None, b=None)
set the stage position of x, y, z provided in um a and b given in radians. JEOL API works in nm and deg, so we need to convert the values.
- get_beam_shift()
get the beam shift value in ?? units, it’s using CLA1 lens in JEOL i don’t know if it is correct
- set_beam_shift(beam_pos)
set the beam shift value in ?? units
- connect()
microscope remote connection trough JEOL COM interface generated by TemExt.dll
- get_projection_mode()
- set_magnification(mag_value)
tricky function there are 2 ways to get the info using: getMagnification that return a value integer or using getMagnificationIndex that return an integer as index
- get_magnification()
tricky function there are 2 ways to get the info using: getMagnification that return a value integer or using getMagnificationIndex that return an integer as index
- set_KL(kl_value)
- get_KL()
“return the KL value should be in mm??
- get_intensity(slot=0)
from instamatic the brightness control in the 2100f is CL3. for now implemented using CL3
- set_intensity(intensity=0, slot=0)
from instamatic the brightness control in the 2100f is CL3. for now implemented using CL3
- get_spotsize()
return the cl1 index value, in jeol this should be the the spotsize, 0-based indexing for GetSpotSize, add 1 to be consistent with JEOL software.
- set_spotsize(value)
Set the spotsize
- load_calibration_table(cam_table)
jeol have different mode we need to check the indexes such as mag1 mag2 samag lowmag diff
- set_alpha(angle, velocity=1)
stage alpha movement, velocity in jeol cannot be set directly, the function will wait for the goniometer to stop, the angle should be provided in deg
- isStageMoving()
- microscope_thread_setup(tracking_file='tracking.txt', tracking_dict=None, timer=None, event=None, stop_event=None)
“this function read the tracking file and set up the threads necessary for the acqusition. 3 sockets are necessary to work. if tracking_positions == None and experiment_type == “continuous”, the stage is threaded only for continuous rotation (trackless experiment). if tracking positions != None and experiment_type == “continuous”, the stage is threaded for continuous rotation and the beam is threaded for tracking. if experiment_type == “stepwise”, the beam only is threaded for tracking waiting to pass the target angle to apply the tracking beamshift. in the case of cred, results are displayed in the variable self.result
- calc_stage_speed(speed)
“calculate the speed in rad/s for jeol. speed is provided in degrees/s and return it in rad/s.
- angle_tracking(final_angle, result: list, timer=None, event=None, stop_event=None)
- beamshift_tracking(tracking_dict, result=None, timer=None, event=None, stop_event=None)
this thread live in a separate socket and check continuously the position of the stage. when the angle is in the one to apply the tracking, the beamshift is applied to track the crystal. the thread work passivly waiting for the angle to be reached/passed to work
- beamshift_tracking_stem(tracking_dict, result=None, timer=None, event=None, stop_event=None)
this thread live in a separate socket and check continuously the position of the stage. when the angle is in the one to apply the tracking, the beamshift is applied to track the crystal. the thread work passivly waiting for the angle to be reached/passed to work
- get_voltage()
Get the actual accelaration voltage in kV.
- test_tracking(tracking, ub_class=None)
this thread live in a separate socket and check continuously the position of the stage. when the angle is in the one to apply the tracking, the beamshift is applied to track the crystal. the thread work passivly waiting for the angle to be reached/passed to work
- test_tracking_stem(ub_class)
this thread live in a separate socket and check continuously the position of the stage. when the angle is in the one to apply the tracking, the beamshift is applied to track the crystal. the thread work passivly waiting for the angle to be reached/passed to work
- continuous_rotation(a, speed, event=None, stop_event=None)
in jeol the gonio velocity can be changed only using goniotool an external exe from service. self.tem_stage is an object of the class RemoteMicroscope in fei that control the stage rotation, settled up by the function self.microscope_thread_setup()
- get_illumination_mode()
return micro or nanoprobe for the condenser minilens
- set_illumination_mode(mode)
set micro or nanoprobe for the condenser minilens
- get_instrument_mode()
return the current instrument mode i.e. TEM/STEM
- set_instrument_mode(mode)
set the current instrument mode i.e. TEM/STEM
- pyfast_adt.main.adaptor.microscope.adaptor_jeol.tem