1 # calibcant - tools for thermally calibrating AFM cantilevers
3 # Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
5 # This file is part of calibcant.
7 # calibcant is free software: you can redistribute it and/or
8 # modify it under the terms of the GNU Lesser General Public
9 # License as published by the Free Software Foundation, either
10 # version 3 of the License, or (at your option) any later version.
12 # calibcant is distributed in the hope that it will be useful,
13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 # GNU Lesser General Public License for more details.
17 # You should have received a copy of the GNU Lesser General Public
18 # License along with calibcant. If not, see
19 # <http://www.gnu.org/licenses/>.
21 """Acquire, save, and load cantilever calibration bump data.
23 For measuring photodiode sensitivity.
25 The relevent physical quantities are:
26 Vzp_out Output z-piezo voltage (what we generate)
27 Vzp Applied z-piezo voltage (after external ZPGAIN)
28 Zp The z-piezo position
29 Zcant The cantilever vertical deflection
30 Vphoto The photodiode vertical deflection voltage (what we measure)
32 Which are related by the parameters:
34 zp_sensitivity Zp / Vzp
35 photo_sensitivity Vphoto / Zcant
37 Cantilever calibration assumes a pre-calibrated z-piezo
38 (zp_sensitivity) and amplifier (zp_gain). In our lab, the z-piezo is
39 calibrated by imaging a calibration sample, which has features with
40 well defined sizes, and the gain is set with a knob on our modified
43 Photo-sensitivity is measured by bumping the cantilever against the
44 surface, where `Zp = Zcant` (see the `bump_*()` family of functions).
45 The measured slope Vphoto/Vout is converted to photo-sensitivity via
47 Vphoto/Vzp_out * Vzp_out/Vzp * Vzp/Zp * Zp/Zcant = Vphoto/Zcant
48 (measured) (1/zp_gain) (1/zp_sensitivity) (1) (photo_sensitivity)
50 We do all these measurements a few times to estimate statistical
53 The functions are layed out in the families:
55 For each family, * can be any of:
56 acquire get real-world data
57 save store real-world data to disk
58 load get real-world data from disk
59 analyze interperate the real-world data.
60 plot show a nice graphic to convince people we're working :p
62 A family name without any _* extension (e.g. `bump()`), runs `*_acquire()`,
63 `*_save()`, `*_analyze()`.
65 If `base_config['matplotlib']` is `True`, `*_analyze()` will call
66 `*_plot()` internally.
69 import numpy as _numpy
71 from pypiezo.base import convert_meters_to_bits as _convert_meters_to_bits
72 from pypiezo.base import convert_bits_to_meters as _convert_bits_to_meters
74 from . import LOG as _LOG
75 from .bump_analyze import bump_analyze as _bump_analyze
76 from .bump_analyze import bump_save as _bump_save
79 def bump_acquire(afm, bump_config):
80 """Ramps `push_depth` closer and returns to the original position.
83 afm a pyafm.AFM instance
84 bump_config a .config._BumpConfig instance
86 Returns the acquired ramp data dictionary, with data in DAC/ADC bits.
88 afm.move_just_onto_surface(
89 depth=bump_config['initial-position'], far=bump_config['far-steps'])
91 _LOG.info('bump the surface to a depth of %g m'
92 % bump_config['push-depth'])
94 axis = afm.piezo.axis_by_name(afm.axis_name)
96 start_pos = afm.piezo.last_output[afm.axis_name]
97 start_pos_m = _convert_bits_to_meters(
98 axis.axis_channel_config, axis.axis_config, start_pos)
99 close_pos_m = start_pos_m + bump_config['push-depth']
100 close_pos = _convert_meters_to_bits(
101 axis.axis_channel_config, axis.axis_config, close_pos_m)
103 dtype = afm.piezo.channel_dtype(afm.axis_name, direction='output')
104 appr = _numpy.linspace(
105 start_pos, close_pos, bump_config['samples']).astype(dtype)
106 # switch numpy.append to numpy.concatenate with version 2.0+
107 out = _numpy.append(appr, appr[::-1])
108 out = out.reshape((len(out), 1))
110 # (samples) / (meters) * (meters/second) = (samples/second)
111 freq = (bump_config['samples'] / bump_config['push-depth']
112 * bump_config['push-speed'])
114 data = afm.piezo.ramp(out, freq, output_names=[afm.axis_name],
115 input_names=['deflection'])
117 out = out.reshape((len(out),))
118 data = data.reshape((data.size,))
119 return {afm.axis_name: out, 'deflection': data}
121 def bump(afm, bump_config, filename, group='/'):
122 """Wrapper around bump_acquire(), bump_analyze(), bump_save().
126 >>> from pycomedi.device import Device
127 >>> from pycomedi.subdevice import StreamingSubdevice
128 >>> from pycomedi.channel import AnalogChannel, DigitalChannel
129 >>> from pycomedi.constant import AREF, IO_DIRECTION, SUBDEVICE_TYPE, UNIT
130 >>> from pypiezo.afm import AFMPiezo
131 >>> from pypiezo.base import PiezoAxis, InputChannel
132 >>> from pypiezo.config import (HDF5_ChannelConfig, HDF5_AxisConfig,
134 >>> from stepper import Stepper
135 >>> from pyafm import AFM
136 >>> from .config import HDF5_BumpConfig
138 >>> fd,filename = tempfile.mkstemp(suffix='.h5', prefix='calibcant-')
141 >>> d = Device('/dev/comedi0')
144 Setup an `AFMPiezo` instance.
146 >>> s_in = d.find_subdevice_by_type(SUBDEVICE_TYPE.ai,
147 ... factory=StreamingSubdevice)
148 >>> s_out = d.find_subdevice_by_type(SUBDEVICE_TYPE.ao,
149 ... factory=StreamingSubdevice)
151 >>> axis_channel = s_out.channel(
152 ... 0, factory=AnalogChannel, aref=AREF.ground)
153 >>> input_channel = s_in.channel(0, factory=AnalogChannel, aref=AREF.diff)
154 >>> for chan in [axis_channel, input_channel]:
155 ... chan.range = chan.find_range(unit=UNIT.volt, min=-10, max=10)
157 We set the minimum voltage for the `z` axis to -9 (a volt above
158 the minimum possible voltage) to help with testing
159 `.get_surface_position`. Without this minimum voltage, small
160 calibration errors could lead to a railed -10 V input for the
161 first few surface approaching steps, which could lead to an
162 `EdgeKink` error instead of a `FlatFit` error.
164 >>> axis_config = HDF5_AxisConfig(filename, '/bump/config/z/axis')
165 >>> axis_config.update(
166 ... {'gain':20, 'sensitivity':8e-9, 'minimum':-9})
167 >>> axis_channel_config = HDF5_ChannelConfig(
168 ... filename, '/bump/config/z/channel')
169 >>> input_channel_config = HDF5_ChannelConfig(
170 ... filename, '/bump/config/deflection/channel')
172 >>> a = PiezoAxis(axis_config=axis_config,
173 ... axis_channel_config=axis_channel_config,
174 ... axis_channel=axis_channel, name='z')
177 >>> c = InputChannel(
178 ... channel_config=input_channel_config, channel=input_channel,
179 ... name='deflection')
182 >>> piezo = AFMPiezo(axes=[a], input_channels=[c])
184 Setup a `stepper` instance.
186 >>> s_d = d.find_subdevice_by_type(SUBDEVICE_TYPE.dio)
187 >>> d_channels = [s_d.channel(i, factory=DigitalChannel)
188 ... for i in (0, 1, 2, 3)]
189 >>> for chan in d_channels:
190 ... chan.dio_config(IO_DIRECTION.output)
192 >>> def write(value):
193 ... s_d.dio_bitfield(bits=value, write_mask=2**4-1)
195 >>> stepper = Stepper(write=write)
197 Setup an `AFM` instance.
199 >>> afm = AFM(piezo, stepper)
203 >>> bump_config = HDF5_BumpConfig(
204 ... filename=filename, group='/bump/config/bump')
205 >>> bump(afm, bump_config, filename, group='/bump')
206 TODO: replace skipped example data with real-world values
207 >>> pprint_HDF5(filename) # doctest: +ELLIPSIS, +REPORT_UDIFF
209 Close the Comedi device.
213 Cleanup our temporary config file.
215 >>> os.remove(filename)
217 deflection_channel = afm.piezo.input_channel_by_name('deflection')
218 axis = afm.piezo.axis_by_name(afm.axis_name)
220 data = bump_acquire(afm, bump_config)
221 photo_sensitivity = _bump_analyze(
222 data, bump_config, z_channel_config=axis.axis_channel_config,
223 z_axis_config=axis.axis_config,
224 deflection_channel_config=deflection_channel.channel_config)
226 filename, group, data, bump_config,
227 z_channel_config=axis.axis_channel_config,
228 z_axis_config=axis.axis_config,
229 deflection_channel_config=deflection_channel.channel_config,
230 processed_bump=photo_sensitivity)
231 return photo_sensitivity