"""
afm.move_just_onto_surface(
depth=bump_config['initial-position'], far=bump_config['far-steps'])
+ #afm.piezo.jump('z', 32000)
_LOG.info('bump the surface to a depth of %g m'
% bump_config['push-depth'])
axis = afm.piezo.axis_by_name(afm.axis_name)
start_pos = afm.piezo.last_output[afm.axis_name]
- start_pos_m = _convert_bits_to_meters(
- axis.axis_channel_config, axis.axis_config, start_pos)
+ start_pos_m = _convert_bits_to_meters(axis.config, start_pos)
close_pos_m = start_pos_m + bump_config['push-depth']
- close_pos = _convert_meters_to_bits(
- axis.axis_channel_config, axis.axis_config, close_pos_m)
+ close_pos = _convert_meters_to_bits(axis.config, close_pos_m)
dtype = afm.piezo.channel_dtype(afm.axis_name, direction='output')
appr = _numpy.linspace(
>>> import os
>>> import tempfile
- >>> from h5config.storage.hdf5 import HDF5_Storage, pprint_HDF5
+ >>> from h5config.storage.hdf5 import pprint_HDF5
>>> from pycomedi.device import Device
>>> from pycomedi.subdevice import StreamingSubdevice
>>> from pycomedi.channel import AnalogChannel, DigitalChannel
>>> from pypiezo.base import PiezoAxis, InputChannel
>>> from pypiezo.config import ChannelConfig, AxisConfig
>>> from stepper import Stepper
- >>> from pyafm import AFM
+ >>> from pyafm.afm import AFM
>>> from .config import BumpConfig
>>> fd,filename = tempfile.mkstemp(suffix='.h5', prefix='calibcant-')
first few surface approaching steps, which could lead to an
`EdgeKink` error instead of a `FlatFit` error.
- >>> axis_config = AxisConfig(storage=HDF5_Storage(
- ... filename=filename, group='/bump/config/z/axis'))
+ >>> axis_config = AxisConfig()
>>> axis_config.update(
... {'gain':20, 'sensitivity':8e-9, 'minimum':-9})
- >>> axis_channel_config = ChannelConfig(storage=HDF5_Storage(
- ... filename=filename, group='/bump/config/z/channel'))
- >>> input_channel_config = ChannelConfig(storage=HDF5_Storage(
- ... filename=filename, group='/bump/config/deflection/channel'))
-
- >>> a = PiezoAxis(axis_config=axis_config,
- ... axis_channel_config=axis_channel_config,
- ... axis_channel=axis_channel, name='z')
+ >>> axis_channel_config = ChannelConfig()
+ >>> axis_channel_config['name'] = 'z'
+ >>> axis_config['channel'] = axis_channel_config
+ >>> input_channel_config = ChannelConfig()
+ >>> input_channel_config['name'] = 'deflection'
+
+ >>> a = PiezoAxis(config=axis_config, axis_channel=axis_channel)
>>> a.setup_config()
- >>> c = InputChannel(
- ... channel_config=input_channel_config, channel=input_channel,
- ... name='deflection')
+ >>> c = InputChannel(config=input_channel_config, channel=input_channel)
>>> c.setup_config()
- >>> piezo = AFMPiezo(axes=[a], input_channels=[c])
+ >>> piezo = AFMPiezo(axes=[a], inputs=[c])
Setup a `stepper` instance.
Test a bump:
- >>> bump_config = BumpConfig(storage=HDF5_Storage(
- ... filename=filename, group='/bump/config/bump'))
+ >>> bump_config = BumpConfig()
>>> bump(afm, bump_config, filename, group='/bump')
TODO: replace skipped example data with real-world values
>>> pprint_HDF5(filename) # doctest: +ELLIPSIS, +REPORT_UDIFF
+ /
+ /bump
+ /bump/config
+ /bump/config/bump
+ <HDF5 dataset "far-steps": shape (), type "<i4">
+ 200
+ <HDF5 dataset "initial-position": shape (), type "<f8">
+ -5e-08
+ <HDF5 dataset "model": shape (), type "|S9">
+ quadratic
+ <HDF5 dataset "push-depth": shape (), type "<f8">
+ 2e-07
+ <HDF5 dataset "push-speed": shape (), type "<f8">
+ 1e-06
+ <HDF5 dataset "samples": shape (), type "<i4">
+ 1024
+ <HDF5 dataset "setpoint": shape (), type "<f8">
+ 2.0
+ /bump/config/deflection
+ /bump/config/deflection/channel
+ <HDF5 dataset "channel": shape (), type "<i4">
+ 0
+ <HDF5 dataset "conversion-coefficients": shape (2,), type "<f8">
+ [ -1.00000000e+01 3.05180438e-04]
+ <HDF5 dataset "conversion-origin": shape (), type "<f8">
+ 0.0
+ <HDF5 dataset "device": shape (), type "|S12">
+ /dev/comedi0
+ <HDF5 dataset "inverse-conversion-coefficients": shape (2,), type "<f8">
+ [ 0. 3276.75]
+ <HDF5 dataset "inverse-conversion-origin": shape (), type "<f8">
+ -10.0
+ <HDF5 dataset "maxdata": shape (), type "<i8">
+ 65535
+ <HDF5 dataset "name": shape (), type "|S10">
+ deflection
+ <HDF5 dataset "range": shape (), type "<i4">
+ 0
+ <HDF5 dataset "subdevice": shape (), type "<i4">
+ 0
+ /bump/config/z
+ /bump/config/z/axis
+ /bump/config/z/axis/channel
+ <HDF5 dataset "channel": shape (), type "<i4">
+ 0
+ <HDF5 dataset "conversion-coefficients": shape (2,), type "<f8">
+ [ -1.00000000e+01 3.05180438e-04]
+ <HDF5 dataset "conversion-origin": shape (), type "<f8">
+ 0.0
+ <HDF5 dataset "device": shape (), type "|S12">
+ /dev/comedi0
+ <HDF5 dataset "inverse-conversion-coefficients": shape (2,), type "<f8">
+ [ 0. 3276.75]
+ <HDF5 dataset "inverse-conversion-origin": shape (), type "<f8">
+ -10.0
+ <HDF5 dataset "maxdata": shape (), type "<i8">
+ 65535
+ <HDF5 dataset "name": shape (), type "|S1">
+ z
+ <HDF5 dataset "range": shape (), type "<i4">
+ 0
+ <HDF5 dataset "subdevice": shape (), type "<i4">
+ 1
+ <HDF5 dataset "gain": shape (), type "<i4">
+ 20
+ <HDF5 dataset "maximum": shape (), type "<f8">
+ 10.0
+ <HDF5 dataset "minimum": shape (), type "<i4">
+ -9
+ <HDF5 dataset "monitor": shape (), type "|S1">
+ <BLANKLINE>
+ <HDF5 dataset "sensitivity": shape (), type "<f8">
+ 8e-09
+ <HDF5 dataset "processed": shape (), type "<f8">
+ ...
+ /bump/raw
+ <HDF5 dataset "deflection": shape (2048,), type "<u2">
+ [...]
+ <HDF5 dataset "z": shape (2048,), type "<u2">
+ [...]
Close the Comedi device.
data = bump_acquire(afm, bump_config)
photo_sensitivity = _bump_analyze(
- data, bump_config, z_channel_config=axis.axis_channel_config,
- z_axis_config=axis.axis_config,
- deflection_channel_config=deflection_channel.channel_config)
+ data, bump_config, z_axis_config=axis.config,
+ deflection_channel_config=deflection_channel.config)
_bump_save(
filename, group, data, bump_config,
- z_channel_config=axis.axis_channel_config,
- z_axis_config=axis.axis_config,
- deflection_channel_config=deflection_channel.channel_config,
+ z_axis_config=axis.config,
+ deflection_channel_config=deflection_channel.config,
processed_bump=photo_sensitivity)
return photo_sensitivity
projects / calibcant.git / blobdiff