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 """Thermal vibration analysis.
23 Separate the more general `vib_analyze()` from the other `vib_*()`
24 functions in calibcant.
26 The relevent physical quantities are :
27 Vphoto The photodiode vertical deflection voltage (what we measure)
30 >>> from pprint import pprint
34 >>> from .config import HDF5_VibrationConfig
35 >>> from pypiezo.config import pprint_HDF5, HDF5_ChannelConfig
36 >>> from pypiezo.base import convert_volts_to_bits
38 >>> fd,filename = tempfile.mkstemp(suffix='.h5', prefix='calibcant-')
41 >>> vibration_config = HDF5_VibrationConfig(
42 ... filename=filename, group='/vibration/config/vibration')
43 >>> vibration_config['frequency'] = 50e3
44 >>> vibration_config.save()
45 >>> deflection_channel_config = HDF5_ChannelConfig(filename=None)
46 >>> deflection_channel_config['maxdata'] = 200
47 >>> deflection_channel_config['conversion-coefficients'] = (0,1)
48 >>> deflection_channel_config['conversion-origin'] = 0
49 >>> deflection_channel_config['inverse-conversion-coefficients'] = (0,1)
50 >>> deflection_channel_config['inverse-conversion-origin'] = 0
52 We'll be generating a test vibration time series with the following
53 parameters. Make sure these are all floats to avoid accidental
54 integer division in later steps.
57 >>> gamma = 1.6e-6 # N*s/m
59 >>> T = 1/vibration_config['frequency']
60 >>> T # doctest: +ELLIPSIS
62 >>> N = int(2**15) # count
65 where `T` is the sampling period, `N` is the number of samples, and
66 `F_sigma` is the standard deviation of the white-noise external force.
67 Note that the resonant frequency is less than the Nyquist frequency so
68 we don't have to worry too much about aliasing.
70 >>> w0 = numpy.sqrt(k/m)
71 >>> f0 = w0/(2*numpy.pi)
72 >>> f0 # doctest: +ELLIPSIS
74 >>> f_nyquist = vibration_config['frequency']/2
75 >>> f_nyquist # doctest: +ELLIPSIS
80 >>> damping = gamma / (2*m*w0)
81 >>> damping # doctest: +ELLIPSIS
87 >>> Q # doctest: +ELLIPSIS
89 >>> (1 / (2*damping)) / Q # doctest: +ELLIPSIS
92 We expect the white-noise power spectral density (PSD) to be a flat
95 >>> F0 = F_sigma**2 * 2 * T
97 because the integral from `0` `1/2T` should be `F_sigma**2`.
99 The expected time series PSD parameters are
102 >>> B = gamma/(m*2*numpy.pi)
103 >>> C = F0/(m**2*(2*numpy.pi)**4)
105 Simulate a time series with the proper PSD using center-differencing.
107 m\ddot{x} + \gamma \dot{x} + kx = F
109 m \frac{x_{i+1} - 2x_i + x_{i-1}}{T**2}
110 + \gamma \frac{x_{i+1}-x_{i-1}}{T}
113 a x_{i+1} + b x_{i} + c x_{i-1} = F_i
115 where `T` is the sampling period, `i=t/T` is the measurement index,
116 `a=m/T**2+gamma/2T`, `b=-2m/T**2+k`, and `c=m/T**2-gamma/2T`.
117 Rearranging and shifting to `j=i-1`
119 x_j = \frac{F_{i-1} - bx_{i-1} - cx_{i-2}}{a}
121 >>> a = m/T**2 + gamma/(2*T)
122 >>> b = -2*m/T**2 + k
123 >>> c = m/T**2 - gamma/(2*T)
124 >>> x = numpy.zeros((N+2,), dtype=numpy.float) # two extra initial points
125 >>> F = numpy.zeros((N,), dtype=numpy.float)
126 >>> for i in range(2, x.size):
127 ... Fp = random.gauss(mu=0, sigma=F_sigma)
131 ... x[i] = (Fp - b*xp - c*xpp)/a
132 >>> x = x[2:] # drop the initial points
134 Convert the simulated data to bits.
137 >>> deflection_bits = convert_volts_to_bits(deflection_channel_config, x)
139 Analyze the simulated data.
141 >>> naive_vibration = vib_analyze_naive(deflection)
142 >>> naive_vibration # doctest: +SKIP
144 >>> abs(naive_vibration / 136.9e6 - 1) < 0.1
147 >>> processed_vibration = vib_analyze(
148 ... deflection_bits, vibration_config, deflection_channel_config)
149 >>> processed_vibration # doctest: +SKIP
152 >>> vib_plot(deflection=deflection_bits, vibration_config=vibration_config)
153 >>> vib_save(filename=filename, group='/vibration/',
154 ... raw_vibration=deflection_bits, vibration_config=vibration_config,
155 ... deflection_channel_config=deflection_channel_config,
156 ... processed_vibration=processed_vibration)
158 >>> pprint_HDF5(filename) # doctest: +ELLIPSIS, +REPORT_UDIFF
162 /vibration/config/deflection
163 <HDF5 dataset "channel": shape (), type "|S1">
165 <HDF5 dataset "conversion-coefficients": shape (), type "|S4">
167 <HDF5 dataset "conversion-origin": shape (), type "|S1">
169 <HDF5 dataset "device": shape (), type "|S12">
171 <HDF5 dataset "inverse-conversion-coefficients": shape (), type "|S4">
173 <HDF5 dataset "inverse-conversion-origin": shape (), type "|S1">
175 <HDF5 dataset "maxdata": shape (), type "|S3">
177 <HDF5 dataset "range": shape (), type "|S1">
179 <HDF5 dataset "subdevice": shape (), type "|S2">
181 /vibration/config/vibration
182 <HDF5 dataset "chunk-size": shape (), type "|S4">
184 <HDF5 dataset "frequency": shape (), type "|S7">
186 <HDF5 dataset "maximum-fit-frequency": shape (), type "|S7">
188 <HDF5 dataset "minimum-fit-frequency": shape (), type "|S5">
190 <HDF5 dataset "model": shape (), type "|S12">
192 <HDF5 dataset "overlap": shape (), type "|S2">
194 <HDF5 dataset "sample-time": shape (), type "|S1">
196 <HDF5 dataset "window": shape (), type "|S4">
198 <HDF5 dataset "processed": shape (), type "<f8">
201 <HDF5 dataset "deflection": shape (32768,), type "<f8">
204 >>> (raw_vibration,vibration_config,deflection_channel_config,
205 ... processed_vibration) = vib_load(
206 ... filename=filename, group='/vibration/')
208 >>> processed_vibration # doctest: +SKIP
210 >>> abs(processed_vibration / 136.5e6 - 1) < 0.1
213 >>> os.remove(filename)
220 import numpy as _numpy
221 from scipy.optimize import leastsq as _leastsq
224 import matplotlib as _matplotlib
225 import matplotlib.pyplot as _matplotlib_pyplot
226 import time as _time # for timestamping lines on plots
227 except (ImportError, RuntimeError), e:
229 _matplotlib_import_error = e
231 import FFT_tools as _FFT_tools
232 from pypiezo.base import convert_bits_to_volts as _convert_bits_to_volts
233 from pypiezo.config import HDF5_ChannelConfig as _HDF5_ChannelConfig
234 from pypiezo.config import h5_create_group as _h5_create_group
236 from . import LOG as _LOG
237 from . import base_config as _base_config
238 from .config import Variance as _Variance
239 from .config import BreitWigner as _BreitWigner
240 from .config import OffsetBreitWigner as _OffsetBreitWigner
241 from .config import HDF5_VibrationConfig as _HDF5_VibrationConfig
244 def vib_analyze_naive(deflection):
245 """Calculate the deflection variance in Volts**2.
247 This method is simple and easy to understand, but it highly
248 succeptible to noise, drift, etc.
251 deflection : numpy array with deflection timeseries in Volts.
253 std = deflection.std()
255 _LOG.debug('naive deflection variance: %g V**2' % var)
258 def vib_analyze(deflection, vibration_config, deflection_channel_config,
260 """Calculate the deflection variance in Volts**2.
262 Improves on `vib_analyze_naive()` by first converting `Vphoto(t)`
263 to frequency space, and fitting a Breit-Wigner in the relevant
264 frequency range (see cantilever_calib.pdf for derivation).
265 However, there may be cases where the fit is thrown off by noise
266 spikes in frequency space. To protect from errors, the fitted
267 variance is compared to the naive variance (where all noise is
268 included), and the minimum variance is returned.
271 deflection Vphoto deflection input in bits.
272 vibration_config `.config._VibrationConfig` instance
273 deflection_channel_config
274 deflection `pypiezo.config._ChannelConfig` instance
275 plot boolean overriding matplotlib config setting.
277 The conversion to frequency space generates an average power
278 spectrum by breaking the data into windowed chunks and averaging
279 the power spectrums for the chunks together. See
280 `FFT_tools.unitary_avg_power_spectrum()` for details.
282 # convert the data from bits to volts
283 deflection_v = _convert_bits_to_volts(
284 deflection_channel_config, deflection)
285 mean = deflection_v.mean()
286 _LOG.debug('average thermal deflection (Volts): %g' % mean)
288 naive_variance = vib_analyze_naive(deflection_v)
289 if vibration_config['model'] == _Variance:
290 return naive_variance
292 # Compute the average power spectral density per unit time (in uV**2/Hz)
293 _LOG.debug('compute the averaged power spectral density in uV**2/Hz')
294 freq_axis,power = _FFT_tools.unitary_avg_power_spectrum(
295 (deflection_v - mean)*1e6, vibration_config['frequency'],
296 vibration_config['chunk-size'], vibration_config['overlap'],
297 vibration_config['window'])
301 min_frequency=vibration_config['minimum-fit-frequency'],
302 max_frequency=vibration_config['maximum-fit-frequency'],
303 offset=vibration_config['model'] == _OffsetBreitWigner)
305 _LOG.debug('fit PSD(f) = C / ((A**2-f**2)**2 + (f*B)**2) with '
306 'A = %g, B = %g, C = %g, D = %g' % (A, B, C, D))
308 if plot or _base_config['matplotlib']:
309 vib_plot(deflection, freq_axis, power, A, B, C, D,
310 vibration_config=vibration_config)
312 # Our A is in uV**2, so convert back to Volts**2
313 fitted_variance = breit_wigner_area(A,B,C) * 1e-12
315 _LOG.debug('fitted deflection variance: %g V**2' % fitted_variance)
317 if _base_config['matplotlib']:
318 vib_plot(deflection, freq_axis, power, A, B, C, D,
319 vibration_config=vibration_config)
321 return min(fitted_variance, naive_variance)
323 def breit_wigner(f, A, B, C, D=0):
324 """Breit-Wigner (sortof).
331 D Optional white-noise offset
333 All parameters must be postive.
335 return abs(C) / ((A**2-f**2)**2 + (B*f)**2) + abs(D)
337 def fit_psd(freq_axis, psd_data, min_frequency=500, max_frequency=25000,
339 """Fit the FFTed vibration data to a Breit-Wigner.
342 freq_axis array of frequencies in Hz
343 psd_data array of PSD amplitudes for the frequencies in freq_axis
344 min_frequency lower bound of Breit-Wigner fitting region
345 max_frequency upper bound of Breit-Wigner fitting region
346 offset add a white-noise offset to the Breit-Wigner model
348 Breit-Wigner model fit parameters `A`, `B`, `C`, and `D`.
350 # cut out the relevent frequency range
351 _LOG.debug('cut the frequency range %g to %g Hz'
352 % (min_frequency, max_frequency))
354 while freq_axis[imin] < min_frequency : imin += 1
356 while freq_axis[imax] < max_frequency : imax += 1
357 assert imax >= imin + 10 , 'less than 10 points in freq range (%g,%g)' % (
358 min_frequency, max_frequency)
360 # generate guesses for Breit-Wigner parameters A, B, C, and D
361 max_psd_index = _numpy.argmax(psd_data[imin:imax]) + imin
362 max_psd = psd_data[max_psd_index]
363 res_freq = freq_axis[max_psd_index]
365 # Breit-Wigner L(x) = C / ((A**2-x**2)**2 + (B*x)**2)
366 # is expected power spectrum for
367 # x'' + B x' + A^2 x'' = F_external(t)/m
369 # C = (2 k_B T B) / (pi m)
371 # A = resonant frequency
372 # peak at x_res = sqrt(A^2 - B^2/2) (by differentiating)
373 # which could be complex if there isn't a peak (overdamped)
374 # peak height = C / (3 x_res^4 + A^4)
378 # Guessing Q = 1 is pretty safe.
382 # so x_res^2 = B^2 Q^2 - B^2/2 = (Q^2-1/2)B^2
383 # B = x_res / sqrt(Q^2-1/2)
384 B_guess = res_freq / _numpy.sqrt(Q_guess**2-0.5)
385 A_guess = Q_guess*B_guess
386 C_guess = max_psd * (-res_freq**4 + A_guess**4)
388 D_guess = psd_data[max_psd_index]
392 _LOG.debug(('guessed params: resonant freq %g, max psd %g, Q %g, A %g, '
393 'B %g, C %g, D %g') % (
394 res_freq, max_psd, Q_guess, A_guess, B_guess, C_guess, D_guess))
395 # Half width w on lower side when L(a-w) = L(a)/2
396 # (a**2 - (a-w)**2)**2 + (b*(a-w))**2 = 2*(b*a)**2
397 # Let W=(a-w)**2, A=a**2, and B=b**2
398 # (A - W)**2 + BW = 2*AB
399 # W**2 - 2AW + A**2 + BW = 2AB
400 # W**2 + (B-2A)W + (A**2-2AB) = 0
401 # W = (2A-B)/2 * [1 +/- sqrt(1 - 4(A**2-2AB)/(B-2A)**2]
402 # = (2A-B)/2 * [1 +/- sqrt(1 - 4A(A-2B)/(B-2A)**2]
403 # (a-w)**2 = (2A-B)/2 * [1 +/- sqrt(1 - 4A(A-2B)/(B-2A)**2]
404 # so w is a disaster ;)
405 # For some values of A and B (non-underdamped), W is imaginary or negative.
407 # The mass m is given by m = k_B T / (pi A)
408 # The spring constant k is given by k = m (omega_0)**2
409 # The quality factor Q is given by Q = omega_0 m / gamma
411 # Fitting the PSD of V = photoSensitivity*x just rescales the parameters
413 # fit Breit-Wigner using scipy.optimize.leastsq
414 def residual(p, y, x):
415 return breit_wigner(x, *p) - y
417 guess = _numpy.array((A_guess, B_guess, C_guess, D_guess))
419 guess = _numpy.array((A_guess, B_guess, C_guess))
421 p,cov,info,mesg,ier = _leastsq(
423 args=(psd_data[imin:imax], freq_axis[imin:imax]),
424 full_output=True, maxfev=10000)
425 _LOG.debug('fitted params: %s' % p)
426 _LOG.debug('covariance matrix: %s' % cov)
427 #_LOG.debug('info: %s' % info)
428 _LOG.debug('message: %s' % mesg)
430 _LOG.debug('solution converged')
432 _LOG.debug('solution did not converge')
438 A=abs(A) # A and B only show up as squares in f(x)
439 B=abs(B) # so ensure we get positive values
442 def breit_wigner_area(A, B, C):
443 # Integrating the the power spectral density per unit time (power) over the
444 # frequency axis [0, fN] returns the total signal power per unit time
445 # int_0^fN power(f)df = 1/T int_0^T |x(t)**2| dt
446 # = <V(t)**2>, the variance for our AC signal.
447 # The variance from our fitted Breit-Wigner is the area under the Breit-Wigner
448 # <V(t)**2> = (pi*C) / (2*B*A**2)
449 return (_numpy.pi * C) / (2 * B * A**2)
451 def vib_save(filename, group='/', raw_vibration=None, vibration_config=None,
452 deflection_channel_config=None, processed_vibration=None):
453 with _h5py.File(filename, 'a') as f:
454 cwg = _h5_create_group(f, group)
455 if raw_vibration is not None:
457 del cwg['raw/deflection']
460 cwg['raw/deflection'] = raw_vibration
461 for config,key in [(vibration_config, 'config/vibration'),
462 (deflection_channel_config,
463 'config/deflection')]:
466 config_cwg = _h5_create_group(cwg, key)
467 config.save(group=config_cwg)
468 if processed_vibration is not None:
473 cwg['processed'] = processed_vibration
475 def vib_load(filename, group='/'):
476 assert group.endswith('/')
477 raw_vibration = processed_vibration = None
479 with _h5py.File(filename, 'a') as f:
481 raw_vibration = f[group+'raw/deflection'][...]
484 for Config,key in [(_HDF5_VibrationConfig, 'config/vibration'),
485 (_HDF5_ChannelConfig, 'config/deflection')]:
486 config = Config(filename=filename, group=group+key)
487 configs.append(config)
489 processed_vibration = f[group+'processed'][...]
492 ret = [raw_vibration]
494 ret.append(processed_vibration)
495 for config in configs:
499 def vib_plot(deflection=None, freq_axis=None, power=None, A=None, B=None,
500 C=None, D=0, vibration_config=None, analyze=False):
501 """Plot 3 subfigures displaying vibration data and analysis.
503 Time series (Vphoto vs sample index) (show any major drift events),
504 A histogram of Vphoto, with a gaussian fit (demonstrate randomness), and
505 FFTed Vphoto data (Vphoto vs Frequency) (show major noise components).
508 raise _matplotlib_import_error
509 figure = _matplotlib_pyplot.figure()
512 assert deflection != None, (
513 'must set at least one of `deflection` or `power`.')
514 time_axes = figure.add_subplot(2, 1, 1)
515 hist_axes = figure.add_subplot(2, 1, 2)
517 elif deflection is None:
518 time_axes = hist_axes = None
519 freq_axes = figure.add_subplot(1, 1, 1)
521 time_axes = figure.add_subplot(3, 1, 1)
522 hist_axes = figure.add_subplot(3, 1, 2)
523 freq_axes = figure.add_subplot(3, 1, 3)
525 timestamp = _time.strftime('%H%M%S')
527 if deflection is not None:
528 time_axes.plot(deflection, 'r.')
529 time_axes.set_title('free oscillation')
531 # plot histogram distribution and gaussian fit
533 n,bins,patches = hist_axes.hist(
534 deflection, bins=30, normed=True, align='mid')
535 gauss = _numpy.zeros((len(bins),), dtype=_numpy.float)
536 mean = deflection.mean()
537 std = deflection.std()
540 gauss = _numpy.sqrt(2*pi)/std * exp(-0.5*((bins-mean)/std)**2)
541 # Matplotlib's normed histogram uses bin heights of n/(len(x)*dbin)
542 dbin = bins[1]-bins[0]
543 hist_axes.plot(bins, gauss/dbin, 'r-')
544 if power is not None:
546 freq_axes.set_yscale('log')
547 freq_axes.plot(freq_axis, power, 'r.-')
548 xmin,xmax = freq_axes.get_xbound()
549 ymin,ymax = freq_axes.get_ybound()
551 # highlight the region we're fitting
553 vibration_config['minimum-fit-frequency'],
554 vibration_config['maximum-fit-frequency'],
555 facecolor='g', alpha=0.1, zorder=-2)
558 fitdata = breit_wigner(freq_axis, A, B, C, D)
559 freq_axes.plot(freq_axis, fitdata, 'b-')
560 noisefloor = D + 0*freq_axis;
561 freq_axes.plot(freq_axis, noisefloor)
564 res_freq = _numpy.sqrt(A**2 - B**2/2)
565 freq_axes.axvline(res_freq, color='b', zorder=-1)
567 freq_axes.set_title('power spectral density %s' % timestamp)
568 freq_axes.axis([xmin,xmax,ymin,ymax])
569 freq_axes.set_xlabel('frequency (Hz)')
570 freq_axes.set_ylabel('PSD')