# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2012 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2013 W. Trevor King <wking@tremily.us>
#
# This file is part of calibcant.
#
if not data.get('vibrations', None):
data['vibration'] = _numpy.zeros(
(config['num-vibrations'],), dtype=float)
+ if 'raw' not in data:
+ data['raw'] = {}
+ if 'bump' not in data['raw']:
+ data['raw']['bump'] = _numpy.zeros((config['num-bumps'],), dtype=float)
+ if 'temperature' not in data['raw']:
+ data['raw']['temperature'] = _numpy.zeros(
+ (config['num-temperatures'],), dtype=float)
+ if 'vibration' not in data['raw']:
+ data['raw']['vibration'] = _numpy.zeros(
+ (config['num-vibrations'],), dtype=float)
axis_config = config['afm']['piezo'].select_config(
setting_name='axes',
attribute_value=config['afm']['main-axis'],
get_attribute=_get_axis_name)
input_config = config['afm']['piezo'].select_config(
setting_name='inputs', attribute_value='deflection')
- bumps_changed = temperatures_changed = vibrations_changed = False
calibration_group = None
if not isinstance(group, _h5py.Group) and not dry_run:
f = _h5py.File(filename, mode='a')
else:
f = None
try:
- if len(data.get('raw', {}).get('bump', [])) != len(data['bump']):
- bumps_changed = True
- for i,bump in enumerate(raw_data['bump']):
+ bumps_changed = len(data['raw']['bump']) != len(data['bump'])
+ for i,bump in enumerate(raw_data.get('bump', [])): # compare values
data['bump'][i],changed = check_bump(
- index=i, bump=bump, z_axis_config=axis_config,
+ index=i, bump=bump, config=config, z_axis_config=axis_config,
deflection_channel_config=input_config, plot=plot,
maximum_relative_error=maximum_relative_error)
if changed and not dry_run:
bumps_changed = True
bump_group = _h5_create_group(group, 'bump/{}'.format(i))
_bump_save(group=bump_group, processed=data['bump'][i])
- if len(data.get('raw', {}).get('temperature', [])
- ) != len(data['temperature']):
- temperatures_changed = True
- for i,temperature in enumerate(raw_data['temperature']):
+ temperatures_changed = len(data['raw']['temperature']) != len(
+ data['temperature'])
+ for i,temperature in enumerate(raw_data.get('temperature', [])):
data['temperature'][i],changed = check_temperature(
- index=i, temperature=temperature,
+ index=i, temperature=temperature, config=config,
maximum_relative_error=maximum_relative_error)
if changed and not dry_run:
temperatures_changed = True
temperature_group = _h5_create_group(
group, 'temperature/{}'.format(i))
_temperature_save(
- group=temerature_group, processed=data['temperature'][i])
- if len(data.get('raw', {}).get('vibration', [])
- ) != len(data['vibration']):
- vibrations_changed = True
- for i,vibration in enumerate(raw_data['vibration']):
+ group=temperature_group, processed=data['temperature'][i])
+ vibrations_changed = len(data['raw']['vibration']) != len(
+ data['vibration'])
+ for i,vibration in enumerate(raw_data.get('vibration', [])):
data['vibration'][i],changed = check_vibration(
- index=i, vibration=vibration,
+ index=i, vibration=vibration, config=config,
deflection_channel_config=input_config, plot=plot,
maximum_relative_error=maximum_relative_error)
if changed and not dry_run:
vibration_group = _h5_create_group(
group, 'vibration/{}'.format(i))
_vibration_save(
- group=vibration_group, processed=data['vibration'])
+ group=vibration_group, processed=data['vibration'][i])
if (bumps_changed or temperatures_changed or vibrations_changed
) and not dry_run:
calibration_group = _h5_create_group(group, 'calibration')
if vibrations_changed:
save_results(
group=calibration_group, vibration=data['vibration'])
- if len(raw_data['bump']) != len(data['bump']):
+ if len(raw_data.get('bump', [])) != len(data['bump']):
raise ValueError(
'not enough raw bump data: {} of {}'.format(
- len(raw_data['bump']), len(data['bump'])))
- if len(raw_data['temperature']) != len(data['temperature']):
+ len(raw_data.get('bump', [])), len(data['bump'])))
+ if len(raw_data.get('temperature', [])) != len(data['temperature']):
raise ValueError(
'not enough raw temperature data: {} of {}'.format(
- len(raw_data['temperature']), len(data['temperature'])))
+ len(raw_data.get('temperature', [])),
+ len(data['temperature'])))
if len(raw_data['vibration']) != len(data['vibration']):
raise ValueError(
'not enough raw vibration data: {} of {}'.format(
- len(raw_data['vibration']), len(data['vibration'])))
+ len(raw_data.get('vibration', [])),
+ len(data['vibration'])))
k,k_s,changed = check_calibration(
k=data.get('processed', {}).get('spring_constant', None),
k_s=data.get('processed', {}).get(
if f:
f.close()
if plot:
- _plot(bumps=data['raw']['bump'],
- temperatures=data['raw']['temperature'],
- vibrations=data['raw']['vibration'])
+ _plot(bumps=data['bump'],
+ temperatures=data['temperature'],
+ vibrations=data['vibration'])
return (k, k_s)
-def check_bump(index, bump, maximum_relative_error, **kwargs):
+def check_bump(index, bump, config=None, maximum_relative_error=0, **kwargs):
changed = False
+ try:
+ bump_config = bump['config']['bump']
+ except KeyError:
+ bump_config = config['bump']
sensitivity = _bump_analyze(
- config=bump['config']['bump'], data=bump['raw'], **kwargs)
+ config=bump_config, data=bump['raw'], **kwargs)
if bump.get('processed', None) is None:
changed = True
_LOG.warn('new analysis for bump {}: {}'.format(index, sensitivity))
sensitivity-bump['processed'], rel_error))
return (sensitivity, changed)
-def check_temperature(index, temperature, maximum_relative_error, **kwargs):
+def check_temperature(index, temperature, config=None,
+ maximum_relative_error=0, **kwargs):
changed = False
+ try:
+ temp_config = temperature['config']['temperature']
+ except KeyError:
+ temp_config = config['temperature']
temp = _temperature_analyze(
- config=temperature['config']['temperature'],
+ config=temp_config,
temperature=temperature['raw'], **kwargs)
if temperature.get('processed', None) is None:
changed = True
temp-temperature['processed'], rel_error))
return (temp, changed)
-def check_vibration(index, vibration, maximum_relative_error, **kwargs):
+def check_vibration(index, vibration, config=None, maximum_relative_error=0,
+ **kwargs):
changed = False
+ try:
+ vib_config = vibration['config']['vibration']
+ except KeyError:
+ vib_config = config['vibration']
variance = _vibration_analyze(
- config=vibration['config']['vibration'],
- deflection=vibration['raw'], **kwargs)
+ config=vib_config, deflection=vibration['raw'], **kwargs)
if vibration.get('processed', None) is None:
changed = True
- _LOG.warn('new analysis for temperature {}: {}'.format(
+ _LOG.warn('new analysis for vibration {}: {}'.format(
index, variance))
else:
rel_error = abs(variance-vibration['processed'])/vibration['processed']
if rel_error > maximum_relative_error:
+ changed = True
_LOG.warn(("new analysis doesn't match for vibration {}: {} != {} "
"(difference: {}, relative error: {})").format(
index, variance, vibration['processed'],
projects / calibcant.git / blobdiff