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 import h5py as _h5py
  14 from pyafm.storage import load_afm as _load_afm
  15
  16 from calibcant.calibrate import Calibrator as _Calibrator
  17 import calibcant.config as _config
  18
  19
  20 _module_doc = __doc__
  21
  22 def main(args):
  23     parser = _argparse.ArgumentParser(description=_module_doc)
  24     parser.add_argument(
  25         '--num-bumps', type=int,
  26         help='Number of surface bumps')
  27     parser.add_argument(
  28         '--num-temperatures', type=int,
  29         help='Number of temperature measurements')
  30     parser.add_argument(
  31         '--num-vibrations', type=int,
  32         help='Number of thermal vibration measurements')
  33
  34     args = parser.parse_args(args)
  35
  36     timestamp = '{0}-{1:02d}-{2:02d}T{3:02d}-{4:02d}-{5:02d}'.format(
  37         *_time.localtime())
  38     filename = '{}-calibcant-data.h5'.format(timestamp)
  39     config = _config.CalibrateConfig()
  40     config['bump'] = _config.BumpConfig()
  41     config['bump'].update(
  42         {'model':_config.Linear, 'initial-position':-150e-9})
  43     config['temperature'] = _config.TemperatureConfig()
  44     config['vibration'] = _config.VibrationConfig()
  45     if args.num_bumps is None:
  46         args.num_bumps = config['num-bumps']
  47     else:
  48         config['num-bumps'] = args.num_bumps
  49     if args.num_temperatures is None:
  50         args.num_temperatures = config['num-temperatures']
  51     else:
  52         config['num-temperatures'] = args.num_temperatures
  53     if args.num_vibrations is None:
  54         args.num_vibrations = config['num-vibrations']
  55     else:
  56         config['num-vibrations'] = args.num_vibrations
  57     insufficient_calibration_data = 0 in [
  58         args.num_bumps, args.num_temperatures, args.num_vibrations]
  59     devices = []
  60     try:
  61         afm = _load_afm()
  62         afm.load_from_config(devices=devices)
  63         calibrator = _Calibrator(config=config, afm=afm)
  64         calibrator.setup_config()
  65         deflection = afm.piezo.read_deflection()
  66         try:
  67             position,deflection = afm.stepper_approach(
  68                 target_deflection=deflection + 1e3, record_data=True)
  69             with _h5py.File(filename) as f:
  70                 f['/approach/position'] = position
  71                 f['/approach/deflection'] = deflection
  72             if insufficient_calibration_data:
  73                 data = calibrator.acquire(filename=filename)
  74             else:
  75                 k,k_s,data = calibrator.calibrate(filename=filename)
  76         except:
  77             afm.move_away_from_surface()
  78             afm.piezo.zero()
  79             raise
  80     finally:
  81         for device in devices:
  82             device.close()
  83     if insufficient_calibration_data:
  84         for count,field,label in [
  85             (args.num_bumps, 'bump', 'photodiode sensitivity (V/m)'),
  86             (args.num_temperatures, 'temperature', 'temperature (K)'),
  87             (args.num_vibrations, 'vibration', 'variance (V**2)')]:
  88             if count:
  89                 d = data[field]
  90                 print('{}: {:g} +/- {:g}'.format(label, d.mean(), d.std()))
  91     else:
  92         print('k: {:g} +/- {:g}'.format(k, k_s))
  93     return 0
  94
  95 if __name__ == '__main__':
  96     import sys
  97
  98     sys.exit(main(sys.argv[1:]))