3 # calibcant - tools for thermally calibrating AFM cantilevers
5 # Copyright (C) 2007,2008, William Trevor King
7 # This program is free software; you can redistribute it and/or
8 # modify it under the terms of the GNU General Public License as
9 # published by the Free Software Foundation; either version 3 of the
10 # License, or (at your option) any later version.
12 # This program is distributed in the hope that it will be useful, but
13 # WITHOUT ANY WARRANTY; without even the implied warranty of
14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
15 # See the GNU General Public License for more details.
17 # You should have received a copy of the GNU General Public License
18 # along with this program; if not, write to the Free Software
19 # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
22 # The author may be contacted at <wking@drexel.edu> on the Internet, or
23 # write to Trevor King, Drexel University, Physics Dept., 3141 Chestnut St.,
24 # Philadelphia PA 19104, USA.
27 Separate the more general bump_analyze() from the other bump_*()
28 functions in calibcant. Also provide a command line interface
29 for analyzing data acquired through other workflows.
31 The relevant physical quantities are :
32 Vzp_out Output z-piezo voltage (what we generate)
33 Vzp Applied z-piezo voltage (after external ZPGAIN)
34 Zp The z-piezo position
35 Zcant The cantilever vertical deflection
36 Vphoto The photodiode vertical deflection voltage (what we measure)
38 Which are related by the parameters :
40 zpSensitivity Zp / Vzp
41 photoSensitivity Vphoto / Zcant
43 photoSensitivity is measured by bumping the cantilever against the
44 surface, where Zp = Zcant (see calibrate.bump_aquire()). The measured
45 slope Vphoto/Vout is converted to photoSensitivity with bump_analyze().
50 import common # common module for the calibcant package
51 import config # config module for the calibcant package
53 from splittable_kwargs import splittableKwargsFunction, \
54 make_splittable_kwargs_function
57 @splittableKwargsFunction()
58 def Vzp_bits2nm(data_bits, zpGain=config.zpGain,
59 zpSensitivity=config.zpSensitivity,
60 Vzp_out2V=config.Vzp_out2V):
61 scale_Vzp_bits2V = Vzp_out2V(1) - Vzp_out2V(0)
62 data_V = data_bits / scale_Vzp_bits2V
64 data_nm = data_V * zpGain * zpSensitivity
67 @splittableKwargsFunction()
68 def Vphoto_bits2V(data_bits, Vphoto_in2V=config.Vphoto_in2V):
69 scale_Vphoto_bits2V = Vphoto_in2V(1) - Vphoto_in2V(0)
70 Vphoto_V = data_bits / scale_Vphoto_bits2V
74 @splittableKwargsFunction((Vzp_bits2nm, 'data_bits'),
75 (Vphoto_bits2V, 'data_bits'))
76 def slope_bitspbit2Vpnm(slope_bitspbit, **kwargs):
77 zp_kwargs,photo_kwargs = slope_bitspbit2Vpnm._splitargs(slope_bitspbit2Vpnm, kwargs)
79 Vphoto_bits = slope_bitspbit * Vzp_bits
80 return Vphoto_bits2V(Vphoto_bits, **photo_kwargs)/Vzp_bits2nm(Vzp_bits, **zp_kwargs)
82 #@splittableKwargsFunction((bump_fit, 'zpiezo_output_bits',
83 # 'deflection_input_bits'),
84 # (slope_bitspbit2Vpnm, 'slope_bitspbit'))
85 # Some of the child functions aren't yet defined, so postpone
86 # make-splittable until later in the module.
87 def bump_analyze(data, **kwargs) :
89 Return the slope of the bump ;).
91 data dictionary of data in DAC/ADC bits
92 Vzp_out2V function that converts output DAC bits to Volts
93 Vphoto_in2V function that converts input ADC bits to Volts
94 zpGain zpiezo applied voltage per output Volt
95 zpSensitivity nm zpiezo response per applied Volt
97 photoSensitivity (Vphoto/Zcant) in Volts/nm
98 Checks for strong correlation (r-value) and low randomness chance (p-value)
100 With the current implementation, the data is regressed in DAC/ADC bits
101 and THEN converted, so we're assuming that both conversions are LINEAR.
102 if they aren't, rewrite to convert before the regression.
104 bump_fit_kwargs,slope_bitspbit2Vpnm_kwargs = \
105 bump_analyze._splitargs(bump_analyze, kwargs)
106 Vphoto2Vzp_out_bit = bump_fit(data['Z piezo output'],
107 data['Deflection input'],
109 return slope_bitspbit2Vpnm(Vphoto2Vzp_out_bit, **slope_bitspbit2Vpnm_kwargs)
111 def limited_quadratic(x, params):
114 flat region (off-surface)
115 quadratic region (in-contact)
116 flat region (high-voltage-rail)
118 x_contact (x value for the surface-contact kink)
119 y_contact (y value for the surface-contact kink)
120 slope (dy/dx at the surface-contact kink)
121 quad (d**2 y / dx**2, allow decreasing sensitivity with increased x)
123 high_voltage_rail = 2**16 - 1 # bits
124 x_contact,y_contact,slope,quad = params
125 y = slope*(x-x_contact) + quad*(x-x_contact)**2+ y_contact
126 y = numpy.clip(y, y_contact, high_voltage_rail)
129 def limited_quadratic_param_guess(x, y) :
131 Guess rough parameters for a limited_quadratic model. Assumes the
132 bump approaches (raising the deflection as it does so) first.
133 Retracting after the approach is optional. Approximates the contact
134 position and an on-surface (high) position by finding first crossings
135 of thresholds 0.3 and 0.7 of the y value's total range. Not the
136 most efficient algorithm, but it seems fairly robust.
138 y_contact = float(y.min())
139 y_max = float(y.max())
141 y_low = y_contact + 0.3 * (y_max-y_contact)
142 y_high = y_contact + 0.7 * (y_max-y_contact)
146 while y[i] < y_high :
149 x_contact = float(x[i_low])
150 x_high = float(x[i_high])
151 slope = (y_high - y_contact) / (x_high - x_contact)
153 return (x_contact, y_contact, slope, quad)
155 def limited_quadratic_sensitivity(params):
157 Return the estimated sensitivity to small deflections according to
158 limited_quadratic fit parameters.
163 @splittableKwargsFunction()
164 def bump_fit(zpiezo_output_bits, deflection_input_bits,
165 paramGuesser=limited_quadratic_param_guess,
166 model=limited_quadratic,
167 sensitivity_from_fit_params=limited_quadratic_sensitivity,
169 x = zpiezo_output_bits
170 y = deflection_input_bits
171 def residual(p, y, x) :
172 return model(x, p) - y
173 paramGuess = paramGuesser(x, y)
174 p,cov,info,mesg,ier = \
175 scipy.optimize.leastsq(residual, paramGuess, args=(y, x),
176 full_output=True, maxfev=int(10e3))
177 if config.TEXT_VERBOSE :
178 print "Fitted params:",p
179 print "Covariance mx:",cov
183 print "Solution converged"
185 print "Solution did not converge"
186 if plotVerbose or config.PYLAB_VERBOSE :
187 yguess = model(x, paramGuess)
188 #yguess = None # Don't print the guess, since I'm convinced it's ok ;).
190 bump_plot(data={"Z piezo output":x, "Deflection input":y},
191 yguess=yguess, yfit=yfit, plotVerbose=plotVerbose)
192 return sensitivity_from_fit_params(p)
194 @splittableKwargsFunction()
195 def bump_save(data, log_dir=None) :
196 "Save the dictionary data, using data_logger.data_log()"
198 log = data_logger.data_log(log_dir, noclobber_logsubdir=False,
200 log.write_dict_of_arrays(data)
202 def bump_load(datafile) :
203 "Load the dictionary data, using data_logger.date_load()"
204 dl = data_logger.data_load()
205 data = dl.read_dict_of_arrays(datafile)
208 @splittableKwargsFunction()
209 def bump_plot(data, yguess=None, yfit=None, plotVerbose=False) :
210 "Plot the bump (Vphoto vs Vzp) if plotVerbose or PYLAB_VERBOSE == True"
211 if plotVerbose or config.PYLAB_VERBOSE :
212 common._import_pylab()
213 common._pylab.figure(config.BASE_FIGNUM)
214 if yfit != None: # two subplot figure
215 common._pylab.subplot(211)
216 common._pylab.hold(False)
217 common._pylab.plot(data["Z piezo output"], data["Deflection input"],
219 common._pylab.hold(True)
221 common._pylab.plot(data["Z piezo output"], yguess,
224 common._pylab.plot(data["Z piezo output"], yfit,
226 common._pylab.hold(False)
227 common._pylab.title("bump surface")
228 common._pylab.legend(loc='upper left')
229 common._pylab.xlabel("Z piezo output voltage (bits)")
230 common._pylab.ylabel("Photodiode input voltage (bits)")
232 # second subplot for residual
233 common._pylab.subplot(212)
234 common._pylab.plot(data["Z piezo output"],
235 data["Deflection input"] - yfit,
236 'r-', label='residual')
237 common._pylab.legend(loc='upper right')
238 common._pylab.xlabel("Z piezo output voltage (bits)")
239 common._pylab.ylabel("Photodiode input voltage (bits)")
242 make_splittable_kwargs_function(bump_analyze,
243 (bump_fit, 'zpiezo_output_bits',
244 'deflection_input_bits'),
245 (slope_bitspbit2Vpnm, 'slope_bitspbit'))
247 @splittableKwargsFunction((bump_analyze, 'data'))
248 def bump_load_analyze_tweaked(tweak_file, **kwargs):
249 "Load the output file of tweak_calib_bump.sh, return an array of slopes"
250 bump_analyze_kwargs, = \
251 bump_load_analyze_tweaked._splitargs(bump_load_analyze_tweaked, kwargs)
252 photoSensitivity = []
253 for line in file(tweak_file, 'r') :
254 parsed = line.split()
255 path = parsed[0].strip()
256 if path[0] == '#' : # a comment
258 if config.TEXT_VERBOSE :
259 print "Reading data from %s with ranges %s" % (path, parsed[1:])
261 full_data = bump_load(path)
262 if len(parsed) == 1 :
263 data = full_data # use whole bump
265 # use the listed sections
268 for rng in parsed[1:] :
272 zp.extend(full_data['Z piezo output'][starti:stopi])
273 df.extend(full_data['Deflection input'][starti:stopi])
274 data = {'Z piezo output': numpy.array(zp),
275 'Deflection input': numpy.array(df)}
276 pSi = bump_analyze(data, **bump_analyze_kwargs)
277 photoSensitivity.append(pSi)
278 return numpy.array(photoSensitivity, dtype=numpy.float)
280 # commandline interface functions
283 def read_data(ifile):
284 "ifile can be a filename string or open (seekable) file object"
285 if ifile == None : ifile = sys.stdin
286 unlabeled_data=scipy.io.read_array(ifile)
288 data['Z piezo output'] = unlabeled_data[:,0]
289 data['Deflection input'] = unlabeled_data[:,1]
292 def remove_further_than(data, zp_crit) :
294 ndata['Z piezo output'] = []
295 ndata['Deflection input'] = []
296 for zp,df in zip(data['Z piezo output'],data['Deflection input']) :
298 ndata['Z piezo output'].append(zp)
299 ndata['Deflection input'].append(df)
302 if __name__ == '__main__' :
303 # command line interface
304 from optparse import OptionParser
306 usage_string = ('%prog <input-file>\n'
307 '2008, W. Trevor King.\n'
309 'There are two operation modes, one to analyze a single bump file,\n'
310 'and one to analyze tweak files.\n'
312 'Single file mode (the default) :\n'
313 'Scales raw DAC/ADC bit data and fits a straight line.\n'
314 'Returns photodiode sensitivity Vphotodiode/Zcantilever in V/nm.\n'
315 '<input-file> should be whitespace-delimited, 2 column ASCII\n'
316 'without a header line. e.g: "<zp_DAC>\\t<deflection_ADC>\\n"\n'
319 'Runs the same analysis as in single file mode for each bump in\n'
320 'a tweak file. Each line in the tweak file specifies a single bump.\n'
321 'Blank lines and those beginning with a pound sign (#) are ignored.\n'
322 'The format of a line is a series of whitespace-separated fields--\n'
323 'a base file path followed by optional point index ranges, e.g.:\n'
324 '20080919/20080919132500_bump_surface 10:651 1413:2047\n'
325 'which only discards all points outside the index ranges [10,651)\n'
326 'and [1413,2047) (indexing starts at 0).\n'
328 parser = OptionParser(usage=usage_string, version='%prog '+common.VERSION)
329 parser.add_option('-o', '--output-file', dest='ofilename',
330 help='write output to FILE (default stdout)',
331 type='string', metavar='FILE')
332 parser.add_option('-c', '--comma-out', dest='comma_out', action='store_true',
333 help='Output comma-seperated values (default %default)',
335 parser.add_option('-p', '--pylab', dest='pylab', action='store_true',
336 help='Produce pylab fit checks during execution',
338 parser.add_option('-t', '--tweak-mode', dest='tweakmode', action='store_true',
339 help='Run in tweak-file mode',
341 parser.add_option('-d', '--datalogger-mode', dest='datalogger_mode', action='store_true',
342 help='Run input files with datalogger.read_dict_of_arrays(). This is useful, for example, to test a single line from a tweakfile.',
344 parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
345 help='Print lots of debugging information',
348 options,args = parser.parse_args()
350 assert len(args) >= 1, "Need an input file"
354 if options.ofilename != None :
355 ofile = file(options.ofilename, 'w')
358 config.TEXT_VERBOSE = options.verbose
359 config.PYLAB_INTERACTIVE = False
360 config.PYLAB_VERBOSE = options.pylab
361 config.GNUPLOT_VERBOSE = False
363 if options.tweakmode == False :
364 if options.datalogger_mode:
365 data = bump_load(ifilename)
367 data = read_data(ifilename)
368 photoSensitivity = bump_analyze(data)
370 print >> ofile, photoSensitivity
371 else : # tweak file mode
372 slopes = bump_load_analyze_tweaked(ifilename)
373 if options.comma_out :
377 common.write_array(ofile, slopes, sep)
379 if options.ofilename != None :