bin/calibcant-calibrate.py

   1 #!/usr/bin/env python
   2 # calibcant - tools for thermally calibrating AFM cantilevers
   3 #
   4 # Copyright
   5
   6 """Run a cantilever calibration using the default AFM
   7 (``pyafm.storage.load_afm()``).
   8 """
   9
  10 import argparse as _argparse
  11 import time as _time
  12
  13 from calibcant.calibrate import Calibrator as _Calibrator
  14 from pyafm.storage import load_afm as _load_afm
  15 import calibcant.config as _config
  16
  17
  18 _module_doc = __doc__
  19
  20 def main(args):
  21     parser = _argparse.ArgumentParser(description=_module_doc)
  22     parser.add_argument(
  23         '--num-bumps', type=int,
  24         help='Number of surface bumps')
  25     parser.add_argument(
  26         '--num-temperatures', type=int,
  27         help='Number of temperature measurements')
  28     parser.add_argument(
  29         '--num-vibrations', type=int,
  30         help='Number of thermal vibration measurements')
  31
  32     args = parser.parse_args(args)
  33
  34     timestamp = '{0}-{1:02d}-{2:02d}T{3:02d}-{4:02d}-{5:02d}'.format(
  35         *_time.localtime())
  36     filename = '{}-calibcant-data.h5'.format(timestamp)
  37     config = _config.CalibrateConfig()
  38     config['bump'] = _config.BumpConfig()
  39     config['bump'].update(
  40         {'model':_config.Linear, 'initial-position':-150e-9})
  41     config['temperature'] = _config.TemperatureConfig()
  42     config['vibration'] = _config.VibrationConfig()
  43     if args.num_bumps is None:
  44         args.num_bumps = config['num-bumps']
  45     else:
  46         config['num-bumps'] = args.num_bumps
  47     if args.num_temperatures is None:
  48         args.num_temperatures = config['num-temperatures']
  49     else:
  50         config['num-temperatures'] = args.num_temperatures
  51     if args.num_vibrations is None:
  52         args.num_vibrations = config['num-vibrations']
  53     else:
  54         config['num-vibrations'] = args.num_vibrations
  55     insufficient_calibration_data = 0 in [
  56         args.num_bumps, args.num_temperatures, args.num_vibrations]
  57     devices = []
  58     try:
  59         afm = _load_afm()
  60         afm.load_from_config(devices=devices)
  61         calibrator = _Calibrator(config=config, afm=afm)
  62         calibrator.setup_config()
  63         deflection = afm.piezo.read_deflection()
  64         try:
  65             afm.stepper_approach(target_deflection=deflection + 1e3)
  66             if insufficient_calibration_data:
  67                 data = calibrator.acquire(filename=filename)
  68             else:
  69                 k,k_s,data = calibrator.calibrate(filename=filename)
  70         except:
  71             afm.move_away_from_surface()
  72             afm.piezo.zero()
  73             raise
  74     finally:
  75         for device in devices:
  76             device.close()
  77     if insufficient_calibration_data:
  78         for count,field,label in [
  79             (args.num_bumps, 'bump', 'photodiode sensitivity (V/m)'),
  80             (args.num_temperatures, 'temperature', 'temperature (K)'),
  81             (args.num_vibrations, 'vibration', 'variance (V**2)')]:
  82             if count:
  83                 d = data[field]
  84                 print('{}: {:g} +/- {:g}'.format(label, d.mean(), d.std()))
  85     else:
  86         print('k: {:g} +/- {:g}'.format(k, k_s))
  87     return 0
  88
  89 if __name__ == '__main__':
  90     import sys
  91
  92     sys.exit(main(sys.argv[1:]))