unfold_protein/scan.py

   1 # Copyright (C) 2011 W. Trevor King <wking@drexel.edu>
   2 #
   3 # This file is part of unfold_protein.
   4 #
   5 # Unfold_protein is free software: you can redistribute it and/or
   6 # modify it under the terms of the GNU Lesser General Public
   7 # License as published by the Free Software Foundation, either
   8 # version 3 of the License, or (at your option) any later version.
   9 #
  10 # Unfold_protein is distributed in the hope that it will be useful,
  11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13 # GNU Lesser General Public License for more details.
  14 #
  15 # You should have received a copy of the GNU Lesser General Public
  16 # License along with unfold_protein.  If not, see
  17 # <http://www.gnu.org/licenses/>.
  18
  19 """Define `UnfoldScanner` for sequential unfolding experiments."""
  20
  21 import signal as _signal
  22
  23 from calibcant.calibrate import move_far_from_surface as _move_far_from_surface
  24 import pypiezo.base as _pypiezo_base
  25
  26 from . import LOG as _LOG
  27 from .unfolder import ExceptionTooFar as _ExceptionTooFar
  28 from .unfolder import ExceptionTooClose as _ExceptionTooClose
  29
  30 class UnfoldScanner (object):
  31     def __init__(self, config, unfolder):
  32         self.config = config
  33         self.unfolder = unfolder
  34         self._state = {'x direction': 1}
  35
  36     def run(self):
  37         self._stop = False
  38         _signal.signal(_signal.SIGTERM, self._handle_stop_signal)
  39         for i in range(self.config['velocity']['num loops']):
  40             for velocity in self.config['velocity']['unfolding velocities']:
  41                 if self._stop:
  42                     return
  43                 self.unfolder.config['unfold']['velocity'] = velocity
  44                 try:
  45                     self.unfolder.run()
  46                 except _ExceptionTooFar:
  47                     self.stepper_approach()
  48                 except _ExceptionTooClose:
  49                     self.move_far_from_surface()
  50                     self.stepper_approach()
  51                 else:
  52                     self.position_scan_step()
  53
  54     def _handle_stop_signal(self, signal, frame):
  55         self._stop = True
  56
  57     def move_far_from_surface(self):
  58         _LOG.info('retract with the stepper motor by {} m'.format(
  59                 self.unfolder.config['approach']['far']))
  60         _move_far_from_surface(
  61             stepper=self.unfolder.afm.stepper,
  62             distance=self.unfolder.config['approach']['far'])
  63
  64     def stepper_approach(self):
  65         config = self.unfolder.config['approach']
  66         deflection = self.unfolder.read_deflection()
  67         setpoint = deflection + config['relative setpoint']
  68         def_config = self.unfolder.afm.piezo.config.select_config(
  69             'inputs', 'deflection')
  70         setpoint_bits = _pypiezo_base.convert_volts_to_bits(
  71             def_config, setpoint)
  72         self.unfolder.afm.stepper_approach(target_deflection=setpoint_bits)
  73
  74     def position_scan_step(self):
  75         axis_name = 'x'
  76         config = self.config['position']
  77         axis_config = self.unfolder.afm.piezo.config.select_config(
  78                 'axes', self.unfolder.afm.axis_name,
  79                 get_attribute=_pypiezo_base.get_axis_name
  80                 )
  81         pos = self.unfolder.afm.piezo.last_output[axis_name]
  82         pos_m = _pypiezo_base.convert_bits_to_meters(axis_config, pos)
  83         next_pos_m = pos_m + self._state['x direction']*config['x step']
  84         if next_pos_m > config['x max']:
  85             self._state['x direction'] = -1
  86             next_pos_m = pos_m + self._state['x direction']*config['x step']
  87         elif next_pos_m < config['x min']:
  88             self._state['x direction'] = 1
  89             next_pos_m = pos_m + self._state['x direction']*config['x step']
  90         next_pos = _pypiezo_base.convert_meters_to_bits(
  91             axis_config, next_pos_m)
  92         _LOG.info('move {} from {:g} to {:g} bits'.format(
  93                 axis_name, pos, next_pos))
  94         self.unfolder.afm.piezo.jump(axis_name, next_pos)