import numpy as _numpy
-from pyafm.storage import load_afm as _load_afm
-from pyafm.config import Kelvin as _Kelvin
from unfold_protein import __version__
-from unfold_protein.unfolder import Unfolder
-from unfold_protein.scan import UnfoldScanner
-import unfold_protein.config as _config
+import unfold_protein.storage as _storage
if __name__ == '__main__':
args = parser.parse_args()
- unfold_config = _config.UnfoldCycleConfig()
- unfold_config['approach'] = _config.ApproachConfig()
- unfold_config['unfold'] = _config.UnfoldConfig()
- unfold_config['save'] = _config.SaveConfig()
- scan_config = _config.ScanConfig()
- scan_config['velocity'] = _config.VelocityScanConfig()
- scan_config['position'] = _config.PositionScanConfig()
-
devices = []
try:
- afm = _load_afm()
- afm.load_from_config(devices=devices)
- afm.piezo.zero()
- unfolder = Unfolder(config=unfold_config, afm=afm)
- scanner = UnfoldScanner(config=scan_config, unfolder=unfolder)
+ scanner = _storage.load_scanner()
+ scanner.load_from_config(devices=devices)
+ scanner.unfolder.afm.piezo.zero()
scanner.run(stepper_tweaks=args.stepper_tweaks)
finally:
- afm.move_away_from_surface()
- afm.piezo.zero()
+ scanner.unfolder.afm.move_away_from_surface()
+ scanner.unfolder.afm.piezo.zero()
for device in devices:
device.close()
if args.song:
import h5config.config as _config
import h5config.tools as _h5config_tools
import numpy as _numpy
+import pyafm.config as _pyafm_config
class PackageConfig (_h5config_tools.PackageConfig):
name='save',
help='Configure saving.',
config_class=SaveConfig),
+ _config.ConfigSetting(
+ name='afm',
+ help='Configure the AFM used for the unfolding experiments.',
+ config_class=_pyafm_config.AFMConfig),
]
class VelocityScanConfig (_config.Config):
]
class ScanConfig (_config.Config):
- "Configure a full `unfold_protein` approach-bind-unfold cycle"
+ "Configure a series of `unfold_protein` unfolding cycles"
settings = [
_config.ConfigSetting(
name='velocity',
name='position',
help='Configure unfolding position scan pattern.',
config_class=PositionScanConfig),
+ _config.ConfigSetting(
+ name='unfold',
+ help='Configure a single approach-bind-unfold cycle.',
+ config_class=UnfoldCycleConfig),
]
import pypiezo.base as _pypiezo_base
from . import LOG as _LOG
+from . import unfolder as _unfolder
from .unfolder import ExceptionTooFar as _ExceptionTooFar
from .unfolder import ExceptionTooClose as _ExceptionTooClose
+
class UnfoldScanner (object):
- def __init__(self, config, unfolder):
+ def __init__(self, config=None, unfolder=None):
self.config = config
self.unfolder = unfolder
self._state = {'x direction': 1}
+ def load_from_config(self, devices):
+ c = self.config # reduce verbosity
+ if self.unfolder is None and c['unfold']:
+ self.unfolder = _unfolder.Unfolder(config=c['unfold'])
+ self.unfolder.load_from_config(devices=devices)
+
+ def setup_config(self):
+ if self.unfolder:
+ self.unfolder.setup_config()
+ self.config['unfolder'] = self.unfolder.config
+ else:
+ self.config['unfolder'] = None
+
def run(self, stepper_tweaks=True):
self._stop = False
_signal.signal(_signal.SIGTERM, self._handle_stop_signal)
self.unfolder.config['unfold']['velocity'] = velocity
try:
self.unfolder.run()
- except _ExceptionTooFar:
+ except _unfolder.ExceptionTooFar:
if stepper_tweaks:
self.stepper_approach()
else:
raise
- except _ExceptionTooClose:
+ except _unfolder.ExceptionTooClose:
if stepper_tweaks:
self.afm.move_away_from_surface()
self.stepper_approach()
--- /dev/null
+# Copyright
+
+import os.path as _os_path
+
+from h5config.storage.hdf5 import HDF5_Storage as _HDF5_Storage
+from h5config.storage.yaml import YAML_Storage as _YAML_Storage
+import pyafm.storage as _pyafm_storage
+
+from . import LOG as _LOG
+from . import config as _config
+from . import scan as _scan
+
+
+DEFAULT_FILENAME = _os_path.expanduser(_os_path.join(
+ '~', '.config', 'unfold-default.yaml'))
+DEFAULT_GROUP = '/'
+
+
+def _get_storage(filename=None, group=None, action=None):
+ if filename is None:
+ filename = DEFAULT_FILENAME
+ if filename.endswith('.h5'):
+ if group is None:
+ group = DEFAULT_GROUP
+ assert group.endswith('/'), group
+ _LOG.info('{} {} {}'.format(action, filename, group))
+ storage = _HDF5_Storage(filename=filename, group=group)
+ elif filename.endswith('.yaml'):
+ assert group is None, group
+ _LOG.info('{} {}'.format(action, filename))
+ storage = _YAML_Storage(filename=filename)
+ else:
+ raise ValueError('unrecognized file extension in {}'.format(filename))
+ return storage
+
+
+def save_scan_config(config, filename=None, group=None):
+ storage = _get_storage(
+ filename=filename, group=group,
+ action='saving unfolding scan config to')
+ storage.save(config=config)
+
+
+def load_scan_config(filename=None, group=None):
+ storage = _get_storage(
+ filename=filename, group=group,
+ action='loading unfolding scan config from')
+ config = _config.ScanConfig(storage=storage)
+ config.load()
+ return config
+
+
+def load_scanner(filename=None, group=None):
+ config = load_scan_config(filename=group, group=group)
+ _LOG.debug(
+ 'constructing UnfoldScanner from configuration:\n{}'.format(
+ config.dump()))
+ scanner = _scan.UnfoldScanner(config=config)
+ return scanner
+
+
+def get_default_config():
+ scan_config = _config.ScanConfig()
+ scan_config['velocity'] = _config.VelocityScanConfig()
+ scan_config['position'] = _config.PositionScanConfig()
+ scan_config['unfold'] = _config.UnfoldCycleConfig()
+ scan_config['unfold']['approach'] = _config.ApproachConfig()
+ scan_config['unfold']['unfold'] = _config.UnfoldConfig()
+ scan_config['unfold']['save'] = _config.SaveConfig()
+ scan_config['unfold']['afm'] = _pyafm_storage.load_config()
+ return scan_config
import os.path as _os_path
import time as _time
-import h5py as _h5py
-import pypiezo.base as _pypiezo_base
from h5config.storage.hdf5 import HDF5_Storage as _HDF5_Storage
from h5config.storage.hdf5 import h5_create_group as _h5_create_group
+import h5py as _h5py
+import pyafm.afm as _pyafm_afm
+import pypiezo.base as _pypiezo_base
from . import LOG as _LOG
from . import package_config as _package_config
class Unfolder (object):
- def __init__(self, config, afm):
+ def __init__(self, config=None, afm=None):
self.config = config
self.afm = afm
- self.zero_piezo()
+ if self.afm:
+ self.zero_piezo()
+
+ def load_from_config(self, devices):
+ c = self.config # reduce verbosity
+ if self.afm is None and c['afm']:
+ self.afm = _pyafm_afm.AFM(config=c['afm'])
+ self.afm.load_from_config(devices=devices)
+
+ def setup_config(self):
+ if self.afm:
+ self.afm.setup_config()
+ self.config['afm'] = self.afm.config
+ else:
+ self.config['afm'] = None
def run(self):
"""Approach-bind-unfold-save[-plot] cycle.
storage = _HDF5_Storage()
config_cwg = _h5_create_group(f, 'config')
storage.save(config=self.config, group=config_cwg)
- afm_piezo_cwg = _h5_create_group(config_cwg, 'afm/piezo')
- storage.save(config=self.afm.piezo.config, group=afm_piezo_cwg)
f['/environment/timestamp'] = timestamp
x_axis_name = 'x'
f['/environment/{}-position/data'.format(x_axis_name)
projects / unfold-protein.git / commitdiff