PyScripts

PyScripts are used to automate various processes, such as extraction of gas and measurement of isotopes.

PyScript

class pychron.pyscripts.pyscript.PyScript(*args: Any, **kwargs: Any)

calculate_estimated_duration(ctx=None, force=False)

maintain a dictionary of previous calculated durations. key=hash(ctx), value=duration

ValvePyScript

class pychron.pyscripts.valve_pyscript.ValvePyScript(*args: Any, **kwargs: Any)

Ramper

class pychron.pyscripts.extraction_line_pyscript.Ramper

ramp(func, start, end, duration, rate=0, period=1)

rate = units/s duration= s

use rate if specified

ExtractionPyScript

class pychron.pyscripts.extraction_line_pyscript.ExtractionPyScript(*args: Any, **kwargs: Any)

The ExtractionPyScript is used to program the extraction and gettering of sample gas.

extract_pipette(identifier='', timeout=300)

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

get_extraction_positions(clear=True)

Returns a list of x,y,z tuples each tuple represents where the extraction occurred

if clear is True (default) self._extraction_positions set to an empty list

Returns

list of x,y,z tuples

Return type

list of tuples

get_output_blob()

Get the extraction device’s output blob

Returns

output blob: binary string representing time v percent output

Return type

str

get_response_blob()

Get the extraction device’s response blob

Returns

response blob. binary string representing time v measured output

Return type

str

get_setpoint_blob()

Get the extraction device’s setpoint blob

Returns

setpoint blob: binary string representing time v requested setpoint

Return type

str

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.

output_achieved()

Return a formated string with the extraction “heating” results:

Requested Output= 100.000
Achieved Output= 99.012

Returns

Formatted string with results

Return type

str

property position

if position is 0 return None

set_default_context(**kw)

provide default values for all the properties exposed in the script

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

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

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

Parameters

• func_or_tuple (callable, tuple) – wait for function to return True

• start_message (str) – Message to display at start

• end_message (str) – Message to display at end

• check_period (int, float) – Delay between checks in seconds

• timeout (int, float) – Cancel waiting after timeout seconds

MeasurementPyScript

class pychron.pyscripts.measurement_pyscript.MeasurementPyScript(*args: Any, **kwargs: Any)

MeasurementPyScripts are used to collect isotopic data

activate_detectors(*dets, **kw)

set the active detectors

Parameters

dets – list

coincidence()

Do a coincidence scan. Peak center all active detectors simulatenously. calculate required deflection corrections to bring all detectors into coincidence

property eqtime

Property. Equilibration time. Get value from AutomatedRun.

Returns

float, int

equilibrate(eqtime=20, inlet=None, outlet=None, do_post_equilibration=True, close_inlet=True, delay=3)

equilibrate the extraction line with the mass spectrometer

inlet or outlet can be a single valve name or a list of valve names.

'A', ('A','B'), ['A','B'], 'A,B'

Parameters

• eqtime – int, equilibration duration in seconds

• inlet – str, tuple or list, inlet valve

• outlet – str, tuple or list, ion pump valve

• do_post_equilibration – bool

• close_inlet – bool

• delay – int, delay in seconds between close of outlet and open of inlet

generate_ic_mftable(detectors, refiso='Ar40', peak_center_config='', n=1, calc_time=False)

Generate an IC MFTable. Use this when doing a Detector Intercalibration. peak centers the refiso on a list of detectors. MFTable saved as ic_mftable

cancel script if generating mftable fails

Parameters

• detectors (list) – list of detectors to peak center

• refiso (str) – isotope to peak center

peak_center(detector='', isotope='', integration_time=1.04, save=True, calc_time=False, directions='Increase', config_name='default')

Calculate the peak center for isotope on detector.

Parameters

• detector – str

• isotope – str

• integration_time – float

• save – bool

position_magnet(pos, detector='AX', use_dac=False, for_collection=True)

Parameters

• pos (str) – location to set magnetic field

• detector – detector to position pos

• use_dac (bool) – is the pos a DAC voltage

examples:

position_magnet(4.54312, use_dac=True) # detector is not relevant
position_magnet(39.962, detector='AX')
position_magnet('Ar40', detector='AX') #Ar40 will be converted to 39.962 use mole weight dict

post_equilibration(block=False)

Run the post equilibration script.

reset(arun)

Reset the script with a new automated run

Parameters

arun (AutomatedRun) – A new AutomatedRun

set_baseline_fits(*fits)

set baseline fits for detectors

Parameters

fits –

set_fits(*fits)

set time vs intensity regression fits for isotopes

Parameters

fits – str, list, or tuple

set_integration_time(v)

Set the integration time

Parameters

v (float) – integration time in seconds

set_time_zero(offset=0)

set the time_zero value. add offset to time_zero

T_o= ion pump closes
offset seconds after T_o. define time_zero

T_eq= inlet closes

property time_zero_offset

Property. Substract time_zero_offset from time value for all data points

Returns

float, int

property truncated

Property. True if run was truncated otherwise False

Returns

bool

property use_cdd_warming

Property. Use CDD Warming. Get value from AutomatedRunSpec

Returns

bool

whiff(ncounts=0, conditionals=None)

Do a whiff measurement.

Whiff’s are quick measurements with conditionals. use them to take action at the beginning of a measurement. For example do a whiff to determine if intensity to great.

Parameters

• ncounts – int

• conditionals – list of dicts