unfold_protein/scan.py

   1 # Copyright (C) 2012 W. Trevor King <wking@tremily.us>
   2 #
   3 # This file is part of unfold_protein.
   4 #
   5 # unfold_protein is free software: you can redistribute it and/or modify it
   6 # under the terms of the GNU General Public License as published by the Free
   7 # Software Foundation, either version 3 of the License, or (at your option) any
   8 # later version.
   9 #
  10 # unfold_protein is distributed in the hope that it will be useful, but WITHOUT
  11 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  12 # FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
  13 # details.
  14 #
  15 # You should have received a copy of the GNU General Public License along with
  16 # unfold_protein.  If not, see <http://www.gnu.org/licenses/>.
  17
  18 """Define `UnfoldScanner` for sequential unfolding experiments."""
  19
  20 import signal as _signal
  21
  22 import pypiezo.base as _pypiezo_base
  23
  24 from . import LOG as _LOG
  25 from .unfolder import ExceptionTooFar as _ExceptionTooFar
  26 from .unfolder import ExceptionTooClose as _ExceptionTooClose
  27
  28 class UnfoldScanner (object):
  29     def __init__(self, config, unfolder):
  30         self.config = config
  31         self.unfolder = unfolder
  32         self._state = {'x direction': 1}
  33
  34     def run(self, stepper_tweaks=True):
  35         self._stop = False
  36         _signal.signal(_signal.SIGTERM, self._handle_stop_signal)
  37         self.unfolder.afm.move_away_from_surface()
  38         self.stepper_approach()
  39         for i in range(self.config['velocity']['num loops']):
  40             _LOG.info('on loop {} of {}'.format(
  41                     i, self.config['velocity']['num loops']))
  42             for velocity in self.config['velocity']['unfolding velocities']:
  43                 if self._stop:
  44                     return
  45                 self.unfolder.config['unfold']['velocity'] = velocity
  46                 try:
  47                     self.unfolder.run()
  48                 except _ExceptionTooFar:
  49                     if stepper_tweaks:
  50                         self.stepper_approach()
  51                     else:
  52                         raise
  53                 except _ExceptionTooClose:
  54                     if stepper_tweaks:
  55                         self.afm.move_away_from_surface()
  56                         self.stepper_approach()
  57                     else:
  58                         raise
  59                 else:
  60                     self.position_scan_step()
  61
  62     def _handle_stop_signal(self, signal, frame):
  63         self._stop = True
  64
  65     def stepper_approach(self):
  66         config = self.unfolder.config['approach']
  67         deflection = self.unfolder.read_deflection()
  68         setpoint = deflection + config['relative setpoint']
  69         def_config = self.unfolder.afm.piezo.config.select_config(
  70             'inputs', 'deflection')
  71         setpoint_bits = _pypiezo_base.convert_volts_to_bits(
  72             def_config, setpoint)
  73         self.unfolder.afm.stepper_approach(target_deflection=setpoint_bits)
  74
  75     def position_scan_step(self):
  76         axis_name = 'x'
  77         config = self.config['position']
  78         axis_config = self.unfolder.afm.piezo.config.select_config(
  79                 'axes', self.unfolder.afm.config['main-axis'],
  80                 get_attribute=_pypiezo_base.get_axis_name
  81                 )
  82         pos = self.unfolder.afm.piezo.last_output[axis_name]
  83         pos_m = _pypiezo_base.convert_bits_to_meters(axis_config, pos)
  84         # HACK
  85         try:
  86             step = float(open('/home/wking/x-step', 'r').read())
  87             _LOG.info('read step from file: {}'.format(step))
  88         except Exception, e:
  89             _LOG.warn('could not read step from file: {}'.format(e))
  90             step = config['x step']
  91         next_pos_m = pos_m + self._state['x direction']*step
  92         if next_pos_m > config['x max']:
  93             self._state['x direction'] = -1
  94             next_pos_m = pos_m + self._state['x direction']*step
  95         elif next_pos_m < config['x min']:
  96             self._state['x direction'] = 1
  97             next_pos_m = pos_m + self._state['x direction']*step
  98         next_pos = _pypiezo_base.convert_meters_to_bits(
  99             axis_config, next_pos_m)
 100         _LOG.info('move {} from {:g} to {:g} bits'.format(
 101                 axis_name, pos, next_pos))
 102         self.unfolder.afm.piezo.jump(axis_name, next_pos)