Pyscript API

Commands

Below are all the available functions that may be used within a PyScript. Python builtins are also available and additional modules may be imported similar to any normal python script.

`classmethod` `abort`

abort()

Abort the current script. :return:

`method` `acquire`

acquire(name=None, clear=False)

`method` `acquire_grain_polygon_blob`

acquire_grain_polygon_blob()

`method` `autofocus`

autofocus(set_zoom=True)

`method` `begin_heating_interval`

begin_heating_interval(
    duration,
    min_rise_rate=None,
    check_time=60,
    check_delay=60,
    check_period=1,
    temperature=None,
    timeout=300,
    tol=10,
    name=None,
    calc_time=False
)

`method` `begin_interval`

begin_interval(duration, name=None, calc_time=False)

Args:

duration (float, int): Duration of interval in seconds
name (str, optional): Optional name of this interval. Useful for logging

Returns: None

`classmethod` `cancel`

cancel(**kw)

Cancel the current script

:return:

`method` `check_reached_setpoint`

check_reached_setpoint()

`method` `close`

close(name=None, description='', cancel_on_failed_actuation=True, ntries=100)

`classmethod` `complete_interval`

complete_interval()

`method` `delay`

delay(duration=0, message=None, calc_time=False)

`method` `disable`

disable()

`method` `drop_sample`

drop_sample(position='')

`method` `dump_sample`

dump_sample()

`method` `enable`

enable()

`method` `end_extract`

end_extract()

`method` `execute_pattern`

execute_pattern(pattern='', block=True, duration=None)

`method` `exit`

exit()

`method` `extract`

extract(power='', units='', block=None)

`method` `extract_pipette`

extract_pipette(identifier='', timeout=300)

this is an atomic command. use the apis_controller config file to define the isolation procedures.

`method` `fire_laser`

fire_laser()

`method` `get_cryo_temp`

get_cryo_temp(value=1)

`method` `get_device`

get_device(name)

`method` `get_manometer_pressure`

get_manometer_pressure(idx=0)

`method` `get_pressure`

get_pressure(controller, gauge)

`method` `get_resource_value`

get_resource_value(name=None)

`method` `get_value`

get_value(name)

`classmethod` `grain_polygon`

grain_polygon()

`method` `_m_info`

_m_info(message=None)

`classmethod` `interval`

interval(dur)

:type dur: float, int

`method` `is_closed`

is_closed(name=None, description='')

`method` `is_open`

is_open(name=None, description='')

`classmethod` `lighting`

lighting(value=75)

`method` `load_and_execute_lascon_script`

load_and_execute_lascon_script(scriptnumber, block=True)

`method` `load_pipette`

load_pipette(identifier, timeout=300)

this is a non blocking command. it simply sends a command to apis to start one of its runscripts.

it is the ExtractionPyScripts responsiblity to handle the waiting. use the waitfor command to wait for signals from apis.

`method` `lock`

lock(name=None, description='')

`method` `move_to_position`

move_to_position(position='', autocenter=True, block=True)

`method` `_m_open`

_m_open(name=None, description='', cancel_on_failed_actuation=True, ntries=100)

`method` `pause`

pause(delay=2)

`method` `power_map`

power_map(cx, cy, padding, bd, power)

`method` `prepare`

prepare()

`method` `ramp`

ramp(start=0, setpoint=0, duration=0, rate=0, period=1)

`method` `release`

release(name=None)

`classmethod` `safe_while`

safe_while(func, timeout=60, period=1, calc_time=False)

`method` `set_cryo`

set_cryo(value, device_name=None, block=False, delay=1)

Set the cryotrap to setpoint value in degrees K.

Args:

value (float,int): Setpoint in degrees K
block (bool,float,int, optional): If True command is blocking, i.e. the command will not return until setpoint reached. If block is a number than block until block>abs(current_temp-setpoint)
delay (float,int): Delay in seconds between each check to determine if blocking is complete.

`method` `set_intensity_scalar`

set_intensity_scalar(v)

`method` `set_light`

set_light(value='')

`method` `set_motor`

set_motor(name='', value='')

`method` `set_motor_lock`

set_motor_lock(name='', value='')

`method` `set_pid_parameters`

set_pid_parameters(v)

`method` `set_resource`

set_resource(name=None, value=1)

`method` `set_response_recorder_period`

set_response_recorder_period(p)

`method` `set_tray`

set_tray(tray='')

`method` `set_x`

set_x(value, velocity='')

`method` `set_xy`

set_xy(value, velocity='')

`method` `set_y`

set_y(value, velocity='')

`method` `set_z`

set_z(value, velocity='')

`method` `sleep`

sleep(duration=0, message=None, calc_time=False)

`method` `snapshot`

snapshot(name='', prefix='', view_snapshot=False, pic_format='.jpg')

if name not specified use RID_Position e.g 12345-01A_3

`method` `start_cryo_recorder`

start_cryo_recorder()

`method` `start_grain_polygon`

start_grain_polygon()

`method` `start_response_recorder`

start_response_recorder()

`method` `start_video_recording`

start_video_recording(name='video')

`method` `stop_cryo_recorder`

stop_cryo_recorder()

`method` `stop_grain_polygon`

stop_grain_polygon()

`method` `stop_response_recorder`

stop_response_recorder()

`method` `stop_video_recording`

stop_video_recording(save_db=True)

`method` `store_manometer_pressure`

store_manometer_pressure(idx=0)

`method` `unlock`

unlock(name=None, description='')

`classmethod` `video_recording`

video_recording(name='video')

`method` `wait`

wait(name=None, criterion=0)

`method` `waitfor`

waitfor(
    func_or_tuple,
    start_message='',
    end_message='',
    check_period=1,
    timeout=0,
    func_kw=None
)

tuple format: (device_name, function_name, comparison, ...) addition tuple elements are passed to function_name

comparison :


   x<10    10<x<20

callable can of form func() or func(ti) or func(ti, i) where ti is the current relative time (relative to start of waitfor) and i is a counter

:param func_or_tuple: wait for function to return True :type func_or_tuple: callable, tuple :param start_message: Message to display at start :type start_message: str :param end_message: Message to display at end :type end_message: str :param check_period: Delay between checks in seconds :type check_period: int, float :param timeout: Cancel waiting after timeout seconds :type timeout: int, float

`method` `wake`

wake()

`method` `warmup`

warmup(block=False)

Context

Below are all the "contextual" values availiable to a PyScript. These contextual values are typically set by the Experiment Editor and used when running an Automated Analysis

analysis_type

Type: str

beam_diameter

Type: NoneType

cleanup

Type: int

cryo_temperature

Type: int

delay_after

Type: int

duration

Type: int

extract_device

Type: str

extract_units

Type: str

extract_value

Type: int

light_value

Type: int

load_identifier

Type: str

next_position

Type: str

pattern

Type: str

position

Type: str

post_cleanup

Type: int

pre_cleanup

Type: int

ramp_duration

Type: int

ramp_rate

Type: int

run_identifier

Type: str

tray

Type: str

Pyscript API

Pyscript API

Commands

classmethod abort

method acquire

method acquire_grain_polygon_blob

method autofocus

method begin_heating_interval

method begin_interval

classmethod cancel

method check_reached_setpoint

method close

classmethod complete_interval

method delay

method disable

method drop_sample

method dump_sample

method enable

method end_extract

method execute_pattern

method exit

method extract

method extract_pipette

method fire_laser

method get_cryo_temp

method get_device

method get_manometer_pressure

method get_pressure

method get_resource_value

method get_value

classmethod grain_polygon

method _m_info

classmethod interval

method is_closed

method is_open

classmethod lighting

method load_and_execute_lascon_script

method load_pipette

method lock

method move_to_position

method _m_open

method pause

method power_map

method prepare

method ramp

method release

classmethod safe_while

method set_cryo

method set_intensity_scalar

method set_light

method set_motor

method set_motor_lock

method set_pid_parameters

method set_resource

method set_response_recorder_period

method set_tray

method set_x

method set_xy

method set_y

method set_z

method sleep

method snapshot

method start_cryo_recorder

method start_grain_polygon

method start_response_recorder

method start_video_recording

method stop_cryo_recorder

method stop_grain_polygon

method stop_response_recorder

method stop_video_recording

method store_manometer_pressure

method unlock

classmethod video_recording

method wait

method waitfor

method wake

method warmup

Context

analysis_type

beam_diameter

`classmethod` `abort`

`method` `acquire`

`method` `acquire_grain_polygon_blob`

`method` `autofocus`

`method` `begin_heating_interval`

`method` `begin_interval`

`classmethod` `cancel`

`method` `check_reached_setpoint`

`method` `close`

`classmethod` `complete_interval`

`method` `delay`

`method` `disable`

`method` `drop_sample`

`method` `dump_sample`

`method` `enable`

`method` `end_extract`

`method` `execute_pattern`

`method` `exit`

`method` `extract`

`method` `extract_pipette`

`method` `fire_laser`

`method` `get_cryo_temp`

`method` `get_device`

`method` `get_manometer_pressure`

`method` `get_pressure`

`method` `get_resource_value`

`method` `get_value`

`classmethod` `grain_polygon`

`method` `_m_info`

`classmethod` `interval`

`method` `is_closed`

`method` `is_open`

`classmethod` `lighting`

`method` `load_and_execute_lascon_script`

`method` `load_pipette`

`method` `lock`

`method` `move_to_position`

`method` `_m_open`

`method` `pause`

`method` `power_map`

`method` `prepare`

`method` `ramp`

`method` `release`

`classmethod` `safe_while`

`method` `set_cryo`

`method` `set_intensity_scalar`

`method` `set_light`

`method` `set_motor`

`method` `set_motor_lock`

`method` `set_pid_parameters`

`method` `set_resource`

`method` `set_response_recorder_period`

`method` `set_tray`

`method` `set_x`

`method` `set_xy`

`method` `set_y`

`method` `set_z`

`method` `sleep`

`method` `snapshot`

`method` `start_cryo_recorder`

`method` `start_grain_polygon`

`method` `start_response_recorder`

`method` `start_video_recording`

`method` `stop_cryo_recorder`

`method` `stop_grain_polygon`

`method` `stop_response_recorder`

`method` `stop_video_recording`

`method` `store_manometer_pressure`

`method` `unlock`

`classmethod` `video_recording`

`method` `wait`

`method` `waitfor`

`method` `wake`

`method` `warmup`