# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2012 W. Trevor King <wking@drexel.edu>
#
# This file is part of calibcant.
#
-# calibcant is free software: you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public
-# License as published by the Free Software Foundation, either
-# version 3 of the License, or (at your option) any later version.
+# calibcant is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
#
-# calibcant is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Lesser General Public License for more details.
+# calibcant is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
-# You should have received a copy of the GNU Lesser General Public
-# License along with calibcant. If not, see
-# <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU General Public License along with
+# calibcant. If not, see <http://www.gnu.org/licenses/>.
"""Calculate `k` from arrays of bumps, temperatures, and vibrations.
>>> import os
>>> import tempfile
>>> import numpy
->>> from pypiezo.config import pprint_HDF5
->>> from .config import HDF5_CalibrationConfig
+>>> from h5config.storage.hdf5 import HDF5_Storage, pprint_HDF5
+>>> from .config import CalibrationConfig
>>> fd,filename = tempfile.mkstemp(suffix='.h5', prefix='calibcant-')
>>> os.close(fd)
->>> calibration_config = HDF5_CalibrationConfig(filename, '/calib/config/')
+>>> calibration_config = CalibrationConfig(storage=HDF5_Storage(
+... filename=filename, group='/calib/config/'))
>>> bumps = numpy.array((15.9e6, 16.9e6, 16.3e6))
>>> temperatures = numpy.array((295, 295.2, 294.8))
>>> vibrations = numpy.array((2.20e-5, 2.22e-5, 2.21e-5))
/
/calib
/calib/config
- <HDF5 dataset "num-bumps": shape (), type "|S2">
+ <HDF5 dataset "bump": shape (), type "|S1">
+<BLANKLINE>
+ <HDF5 dataset "num-bumps": shape (), type "<i4">
10
- <HDF5 dataset "num-temperatures": shape (), type "|S2">
+ <HDF5 dataset "num-temperatures": shape (), type "<i4">
10
- <HDF5 dataset "num-vibrations": shape (), type "|S2">
+ <HDF5 dataset "num-vibrations": shape (), type "<i4">
20
- <HDF5 dataset "temperature-sleep": shape (), type "|S1">
+ <HDF5 dataset "temperature": shape (), type "|S1">
+<BLANKLINE>
+ <HDF5 dataset "temperature-sleep": shape (), type "<i4">
1
- <HDF5 dataset "vibration-spacing": shape (), type "|S5">
+ <HDF5 dataset "vibration": shape (), type "|S1">
+<BLANKLINE>
+ <HDF5 dataset "vibration-spacing": shape (), type "<f8">
5e-05
/calib/processed
/calib/processed/spring-constant
_matplotlib = None
_matplotlib_import_error = e
-from pypiezo.config import h5_create_group as _h5_create_group
+from h5config.storage.hdf5 import HDF5_Storage as _HDF5_Storage
+from h5config.storage.hdf5 import h5_create_group as _h5_create_group
from . import LOG as _LOG
-from . import base_config as _base_config
+from . import package_config as _package_config
from .bump_analyze import bump_analyze as _bump_analyze
from .bump_analyze import bump_load as _bump_load
from .bump_analyze import bump_save as _bump_save
-from .config import HDF5_CalibrationConfig as _HDF5_CalibrationConfig
+from .config import CalibrationConfig as _CalibrationConfig
from .T_analyze import T_analyze as _temperature_analyze
from .T_analyze import T_load as _temperature_load
from .T_analyze import T_save as _temperature_save
_LOG.info('vibration variance (V^2) : %g +/- %g (%g)'
% (v2_m, v2_s, v2_s/v2_m))
- if _base_config['matplotlib']:
+ if _package_config['matplotlib']:
calib_plot(bumps, temperatures, vibrations)
return (k, k_s)
cwg = _h5_create_group(f, group)
if calibration_config is not None:
config_cwg = _h5_create_group(cwg, 'config')
- calibration_config.save(group=config_cwg)
+ storage = _HDF5_Storage()
+ storage.save(config=calibration_config, group=config_cwg)
if bumps is not None:
try:
del cwg['raw/photodiode-sensitivity/data']
except KeyError:
pass
try:
- k = f[group+'processed/spring-constant/data'][...]
+ k = float(f[group+'processed/spring-constant/data'][...])
except KeyError:
pass
try:
- k_s = f[group+'processed/spring-constant/standard-deviation'][...]
+ k_s = float(
+ f[group+'processed/spring-constant/standard-deviation'][...])
except KeyError:
pass
- calibration_config = _HDF5_CalibrationConfig(
- filename=filename, group=group+'config/')
+ calibration_config = _CalibrationConfig(storage=_HDF5_Storage(
+ filename=filename, group=group+'config/'))
calibration_config.load()
return (bumps, temperatures, vibrations, calibration_config, k, k_s)
vib_axes.plot(vibrations, 'b.-')
vib_axes.set_ylabel('thermal deflection variance (V^2)')
- figure.show()
+ if hasattr(figure, 'show'):
+ figure.show()
def calib_load_all(filename, group='/'):
filename, group+'calibration/')
bump_details = []
for i in range(calibration_config['num-bumps']):
- (raw_bump,bump_config,z_channel_config,z_axis_config,
- deflection_channel_config,processed_bump) = _bump_load(
+ (raw_bump,bump_config,z_axis_config,deflection_channel_config,
+ processed_bump) = _bump_load(
filename=filename, group='%sbump/%d/' % (group, i))
bump_details.append({
'raw_bump': raw_bump,
'bump_config': bump_config,
- 'z_channel_config': z_channel_config,
'z_axis_config': z_axis_config,
'deflection_channel_config': deflection_channel_config,
'processed_bump': processed_bump,
assert group.endswith('/'), group
bumps,temperatures,vibrations,calibration_config,k,k_s = calib_load(
filename, group+'calibration/')
+ if bumps is None:
+ bumps = _numpy.zeros(
+ (calibration_config['num-bumps'],), dtype=float)
+ if temperatures is None:
+ temperatures = _numpy.zeros(
+ (calibration_config['num-temperatures'],), dtype=float)
+ if vibrations is None:
+ vibrations = _numpy.zeros(
+ (calibration_config['num-vibrations'],), dtype=float)
changed_bump = changed_temperature = changed_vibration = False
for i in range(calibration_config['num-bumps']):
+ _changed_bump = False
bump_group = '%sbump/%d/' % (group, i)
- (raw_bump,bump_config,z_channel_config,z_axis_config,
+ (raw_bump,bump_config,z_axis_config,
deflection_channel_config,processed_bump) = _bump_load(
filename=filename, group=bump_group)
sensitivity = _bump_analyze(
data=raw_bump, bump_config=bump_config,
- z_channel_config=z_channel_config,
z_axis_config=z_axis_config,
deflection_channel_config=deflection_channel_config)
bumps[i] = sensitivity
- rel_error = abs(sensitivity - processed_bump)/processed_bump
- if rel_error > maximum_relative_error:
- _LOG.warn(("new analysis doesn't match for bump %d: %g -> %g "
- "(difference: %g, relative error: %g)")
- % (i, processed_bump, sensitivity,
- sensitivity-processed_bump, rel_error))
+ if processed_bump is None:
+ _changed_bump = True
+ _LOG.warn('new analysis for bump %d: %g' % (i, sensitivity))
+ else:
+ rel_error = abs(sensitivity - processed_bump)/processed_bump
+ if rel_error > maximum_relative_error:
+ _changed_bump = True
+ _LOG.warn(("new analysis doesn't match for bump %d: %g -> %g "
+ "(difference: %g, relative error: %g)")
+ % (i, processed_bump, sensitivity,
+ sensitivity-processed_bump, rel_error))
+ if _changed_bump and not dry_run:
changed_bump = True
- if not dry_run:
- _bump_save(filename, bump_group, processed_bump=sensitivity)
+ _bump_save(filename, bump_group, processed_bump=sensitivity)
for i in range(calibration_config['num-temperatures']):
+ _changed_temperature = False
temperature_group = '%stemperature/%d/' % (group, i)
(raw_temperature,temperature_config,processed_temperature
) = _temperature_load(
temperature = _temperature_analyze(
raw_temperature, temperature_config)
temperatures[i] = temperature
- rel_error = abs(temperature - processed_temperature
- )/processed_temperature
- if rel_error > maximum_relative_error:
- _LOG.warn(("new analysis doesn't match for temperature %d: "
- "%g -> %g (difference: %g, relative error: %g)")
- % (i, processed_temperature, temperature,
- temperature-processed_temperature, rel_error))
+ if processed_temperature is None:
+ _changed_temperature = True
+ _LOG.warn('new analysis for temperature %d: %g' % (i, temperature))
+ else:
+ rel_error = abs(temperature - processed_temperature
+ )/processed_temperature
+ if rel_error > maximum_relative_error:
+ _changed_temperature = True
+ _LOG.warn(("new analysis doesn't match for temperature %d: "
+ "%g -> %g (difference: %g, relative error: %g)")
+ % (i, processed_temperature, temperature,
+ temperature-processed_temperature, rel_error))
+ if _changed_temperature and not dry_run:
changed_temperature = True
- if not dry_run:
- _temperature_save(
- filename, temperature_group,
- processed_T=temperature)
+ _temperature_save(
+ filename, temperature_group,
+ processed_T=temperature)
for i in range(calibration_config['num-vibrations']):
+ _changed_vibration = False
vibration_group = '%svibration/%d/' % (group, i)
(raw_vibration,vibration_config,deflection_channel_config,
processed_vibration) = _vibration_load(
deflection=raw_vibration, vibration_config=vibration_config,
deflection_channel_config=deflection_channel_config)
vibrations[i] = variance
- rel_error = abs(variance - processed_vibration)/processed_vibration
- if rel_error > maximum_relative_error:
- _LOG.warn(("new analysis doesn't match for vibration %d: %g -> %g "
- "(difference: %g, relative error: %g)")
- % (i, processed_vibration, variance,
- variance-processed_vibration, rel_error))
+ if processed_vibration is None:
+ _changed_vibration = True
+ _LOG.warn('new analysis for vibration %d: %g' % (i, variance))
+ else:
+ rel_error = abs(variance - processed_vibration)/processed_vibration
+ if rel_error > maximum_relative_error:
+ _changed_vibration = True
+ _LOG.warn(("new analysis doesn't match for vibration %d: "
+ "%g -> %g (difference: %g, relative error: %g)")
+ % (i, processed_vibration, variance,
+ variance-processed_vibration, rel_error))
+ if _changed_vibration and not dry_run:
changed_vibration = True
- if not dry_run:
- _vibration_save(
- filename, vibration_group, processed_vibration=variance)
+ _vibration_save(
+ filename, vibration_group, processed_vibration=variance)
calib_group = '%scalibration/' % group
new_k,new_k_s = calib_analyze(
bumps=bumps, temperatures=temperatures, vibrations=vibrations)
- rel_error = abs(new_k-k)/k
- if rel_error > maximum_relative_error:
- _LOG.warn(("new analysis doesn't match for k: %g -> %g "
- "(difference: %g, relative error: %g)")
- % (k, new_k, new_k-k, rel_error))
- if not dry_run:
- calib_save(filename, calib_group, k=new_k)
- rel_error = abs(new_k_s-k_s)/k_s
- if rel_error > maximum_relative_error:
- _LOG.warn(("new analysis doesn't match for k_s: %g -> %g "
- "(difference: %g, relative error: %g)")
- % (k_s, new_k_s, new_k_s-k_s, rel_error))
- if not dry_run:
- calib_save(filename, calib_group, k_s=new_k_s)
+ new_calib_k = False
+ if k is None:
+ new_calib_k = True
+ _LOG.warn('new analysis for k: %g' % new_k)
+ else:
+ rel_error = abs(new_k-k)/k
+ if rel_error > maximum_relative_error:
+ new_calib_k = True
+ _LOG.warn(("new analysis doesn't match for k: %g -> %g "
+ "(difference: %g, relative error: %g)")
+ % (k, new_k, new_k-k, rel_error))
+ if new_calib_k and not dry_run:
+ calib_save(filename, calib_group, k=new_k)
+ new_calib_k_s = False
+ if k_s is None:
+ new_calib_k_s = True
+ _LOG.warn('new analysis for k_s: %g' % new_k_s)
+ else:
+ rel_error = abs(new_k_s-k_s)/k_s
+ if rel_error > maximum_relative_error:
+ new_calib_k_s = True
+ _LOG.warn(("new analysis doesn't match for k_s: %g -> %g "
+ "(difference: %g, relative error: %g)")
+ % (k_s, new_k_s, new_k_s-k_s, rel_error))
+ if new_calib_k_s and not dry_run:
+ calib_save(filename, calib_group, k_s=new_k_s)
return (new_k, new_k_s)
def calib_plot_all(bumps, bump_details, temperatures, temperature_details,
for i,bump in enumerate(bump_details):
sensitivity = _bump_analyze(
data=bump['raw_bump'], bump_config=bump['bump_config'],
- z_channel_config=bump['z_channel_config'],
z_axis_config=bump['z_axis_config'],
deflection_channel_config=bump['deflection_channel_config'],
plot=True)
projects / calibcant.git / blobdiff