PyScript - NMGRL/pychron GitHub Wiki

PyScript

Procedures

Any pyscript placed in your scripts\procedures directory will be executable from the Procedures menu. Procedures are usefully for learning pyscripts, debugging your valve sequences, and for running convenient valve sequences such as loading an "air" into the mass spectrometer.

Automated Runs

Automated runs are a collections of 4 pyscripts. Automated Runs are constructed and grouped into Experiments using the Experiment Editor. Making experiments is covered in a later section, for now we will focus making the 4 individual pyscripts and understanding each ones role.

1. extraction
2. measurement
3. post_equilibration
4. post_measurement

Note Each pyscript is optional, but at least one pyscript is required. For example, if you want to do a lower temperature degas of your samples in an automated way but without analyzing the gas, set measurement to ---.

The following is a more detailed discussion on how to construct extraction and measurement pyscripts.

Extraction

extraction, post_equilibration and post_measurement are Extraction PyScripts. These scripts have access to valves, extraction devices (furnaces, laser systems, cryogenic traps), and any other device activated in pychron.

You can accomplish almost everything you need for extraction with open, close, sleep and info.

def main():
   info('this is an example extraction script')
   n = 5
   vname = 'V1'
   for i in range(n):
       open(vname)
       sleep(3)
       close(vname)
       sleep(3)

   info(f'cycling valve {vname} {n} times complete')

Keep in mind that pyscripts are python scripts so you can use functions to make your scripts more readable, reusable.

def main():
   # load a triple air shot
   for i in range(3):
       load_air_shot()

def load_air_shot():
    # load air into pipette
    close('outer')
    open('inner')
    sleep(10)
    close('inner')
    # expand
    open('outer')
    sleep(10)

❗A very useful attribute accessible in an extraction pyscript is analysis_type. This can be used to make one extraction script for both blank and sample analyses.

def main():
    if analysis_type=='blank':
        sleep(duration)
    else:
        info('begin interval')
        extract(extract_value, extract_units)
        sleep(duration)
        end_extract()
        disable()

    # do cleanup
    sleep(cleanup)

❗Very useful attributes accessible in an extraction pyscript are position, extract_value, duration and cleanup. All of these values are set for each run in the Experiment Editor

def main():
    for pi in positions:
        move_to_position(pi)
        extract(extract_value, duration)
    sleep(cleanup)

⚠️ position is always a list even if only one value is specified in the experiment.

Measurement