pysawsim/parameter_scan.py

   1 # Copyright (C) 2009-2010  W. Trevor King <wking@drexel.edu>
   2 #
   3 # This program is free software: you can redistribute it and/or modify
   4 # it under the terms of the GNU General Public License as published by
   5 # the Free Software Foundation, either version 3 of the License, or
   6 # (at your option) any later version.
   7 #
   8 # This program is distributed in the hope that it will be useful,
   9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  11 # GNU General Public License for more details.
  12 #
  13 # You should have received a copy of the GNU General Public License
  14 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
  15 #
  16 # The author may be contacted at <wking@drexel.edu> on the Internet, or
  17 # write to Trevor King, Drexel University, Physics Dept., 3141 Chestnut St.,
  18 # Philadelphia PA 19104, USA.
  19
  20 """Experiment vs. simulation comparison and scanning.
  21 """
  22
  23 from os import getpid  # for rss()
  24 import os.path
  25 import pickle
  26 from StringIO import StringIO
  27
  28 import numpy
  29
  30 from . import log
  31 from . import PYSAWSIM_LOG_LEVEL_MSG as _PYSAWSIM_LOG_LEVEL_MSG
  32 from .histogram import Histogram as _Histogram
  33 from .histogram import FIGURE as _FIGURE
  34 from .sawsim_histogram import sawsim_histogram
  35 from .sawsim import SawsimRunner
  36
  37 # import after .histogram, which selects an appropriate backend
  38 import pylab
  39
  40 _multiprocess_can_split_ = True
  41 """Allow nosetests to split tests between processes.
  42 """
  43
  44 EXAMPLE_HISTOGRAM_FILE_CONTENTS = """# Velocity histograms
  45 # Other general comments...
  46
  47 #HISTOGRAM: -v 6e-7
  48 #Force (N)\tUnfolding events
  49 1.4e-10\t1
  50 1.5e-10\t0
  51 1.6e-10\t4
  52 1.7e-10\t6
  53 1.8e-10\t8
  54 1.9e-10\t20
  55 2e-10\t28
  56 2.1e-10\t38
  57 2.2e-10\t72
  58 2.3e-10\t110
  59 2.4e-10\t155
  60 2.5e-10\t247
  61 2.6e-10\t395
  62 2.7e-10\t451
  63 2.8e-10\t430
  64 2.9e-10\t300
  65 3e-10\t116
  66 3.1e-10\t18
  67 3.2e-10\t1
  68
  69 #HISTOGRAM: -v 8e-7
  70 #Force (N)\tUnfolding events
  71 8e-11\t1
  72 9e-11\t0
  73 1e-10\t0
  74 1.1e-10\t1
  75 1.2e-10\t0
  76 1.3e-10\t0
  77 1.4e-10\t0
  78 1.5e-10\t3
  79 1.6e-10\t3
  80 1.7e-10\t4
  81 1.8e-10\t4
  82 1.9e-10\t13
  83 2e-10\t29
  84 2.1e-10\t39
  85 2.2e-10\t60
  86 2.3e-10\t102
  87 2.4e-10\t154
  88 2.5e-10\t262
  89 2.6e-10\t402
  90 2.7e-10\t497
  91 2.8e-10\t541
  92 2.9e-10\t555
  93 3e-10\t325
  94 3.1e-10\t142
  95 3.2e-10\t50
  96 3.3e-10\t13
  97
  98 #HISTOGRAM: -v 1e-6
  99 #Force (N)\tUnfolding events
 100 1.5e-10\t2
 101 1.6e-10\t3
 102 1.7e-10\t7
 103 1.8e-10\t8
 104 1.9e-10\t7
 105 2e-10\t25
 106 2.1e-10\t30
 107 2.2e-10\t58
 108 2.3e-10\t76
 109 2.4e-10\t159
 110 2.5e-10\t216
 111 2.6e-10\t313
 112 2.7e-10\t451
 113 2.8e-10\t568
 114 2.9e-10\t533
 115 3e-10\t416
 116 3.1e-10\t222
 117 3.2e-10\t80
 118 3.3e-10\t24
 119 3.4e-10\t2
 120 """
 121
 122
 123 MEM_DEBUG = False
 124
 125
 126
 127 def rss():
 128     """
 129     For debugging memory usage.
 130
 131     resident set size, the non-swapped physical memory that a task has
 132     used (in kilo-bytes).
 133     """
 134     call = "ps -o rss= -p %d" % getpid()
 135     status,stdout,stderr = invoke(call)
 136     return int(stdout)
 137
 138
 139 class HistogramMatcher (object):
 140     """Compare experimental histograms to simulated data.
 141
 142     The main entry points are `fit()` and `plot()`.
 143
 144     The input `histogram_stream` should contain a series of
 145     experimental histograms with '#HISTOGRAM: <params>` lines starting
 146     each histogram.  `<params>` lists the `sawsim` parameters that are
 147     unique to that experiment.
 148
 149     >>> from .manager.thread import ThreadManager
 150     >>> histogram_stream = StringIO(EXAMPLE_HISTOGRAM_FILE_CONTENTS)
 151     >>> param_format_string = (
 152     ...     '-s cantilever,hooke,0.05 -N1 '
 153     ...     '-s folded,null -N8 '
 154     ...     '-s "unfolded,wlc,{0.39e-9,28e-9}" '
 155     ...     '-k "folded,unfolded,bell,{%g,%g}" -q folded')
 156     >>> m = ThreadManager()
 157     >>> sr = SawsimRunner(manager=m)
 158     >>> hm = HistogramMatcher(histogram_stream, param_format_string, sr, N=3)
 159     >>> hm.plot([[1e-5,1e-3,3],[0.1e-9,1e-9,3]], logx=True, logy=False)
 160     >>> m.teardown()
 161     """
 162     def __init__(self, histogram_stream, param_format_string,
 163                  sawsim_runner, N=400, residual_type='jensen-shannon',
 164                  plot=False):
 165         self.experiment_histograms = self._read_force_histograms(
 166             histogram_stream)
 167         self.param_format_string = param_format_string
 168         self.sawsim_runner = sawsim_runner
 169         self.N = N
 170         self.residual_type = residual_type
 171         self._plot = plot
 172
 173     @staticmethod
 174     def _read_force_histograms(stream):
 175         """
 176         File format:
 177
 178           # comment and blank lines ignored
 179           #HISTOGRAM: <histogram-specific params>
 180           <pysawsim.histogram.Histogram-compatible histogram>
 181           #HISTOGRAM: <other histogram-specific params>
 182           <another pysawsim.histogram.Histogram-compatible histogram>
 183           ...
 184
 185         >>> import sys
 186         >>> stream = StringIO(EXAMPLE_HISTOGRAM_FILE_CONTENTS)
 187         >>> hm = HistogramMatcher(StringIO(), None, None, None)
 188         >>> histograms = hm._read_force_histograms(stream)
 189         >>> sorted(histograms.iterkeys())
 190         ['-v 1e-6', '-v 6e-7', '-v 8e-7']
 191         >>> histograms['-v 1e-6'].to_stream(sys.stdout)
 192         ... # doctest: +NORMALIZE_WHITESPACE, +REPORT_UDIFF
 193         #Force (N)\tUnfolding events
 194         1.5e-10\t2
 195         1.6e-10\t3
 196         1.7e-10\t7
 197         1.8e-10\t8
 198         1.9e-10\t7
 199         2e-10\t25
 200         2.1e-10\t30
 201         2.2e-10\t58
 202         2.3e-10\t76
 203         2.4e-10\t159
 204         2.5e-10\t216
 205         2.6e-10\t313
 206         2.7e-10\t451
 207         2.8e-10\t568
 208         2.9e-10\t533
 209         3e-10\t416
 210         3.1e-10\t222
 211         3.2e-10\t80
 212         3.3e-10\t24
 213         3.4e-10\t2
 214         """
 215         token = '#HISTOGRAM:'
 216         hist_blocks = {None: []}
 217         params = None
 218         for line in stream.readlines():
 219             line = line.strip()
 220             if line.startswith(token):
 221                 params = line[len(token):].strip()
 222                 assert params not in hist_blocks, params
 223                 hist_blocks[params] = []
 224             else:
 225                 hist_blocks[params].append(line)
 226
 227         histograms = {}
 228         for params,block in hist_blocks.iteritems():
 229             if params == None:
 230                 continue
 231             h = _Histogram()
 232             h.from_stream(StringIO('\n'.join(block)))
 233             histograms[params] = h
 234         return histograms
 235
 236     def param_string(self, params, hist_params):
 237         """Generate a string of options to pass to `sawsim`.
 238         """
 239         return '%s %s' % (
 240             self.param_format_string % tuple(params), hist_params)
 241
 242     def residual(self, params):
 243         residual = 0
 244         for hist_params,experiment_hist in self.experiment_histograms.iteritems():
 245             sawsim_hist = sawsim_histogram(
 246                 sawsim_runner=self.sawsim_runner,
 247                 param_string=self.param_string(params, hist_params),
 248                 N=self.N, bin_edges=experiment_hist.bin_edges)
 249             r = experiment_hist.residual(sawsim_hist, type=self.residual_type)
 250             residual += r
 251             if self._plot == True:
 252                 title = ", ".join(["%g" % p for p in params]+[hist_params])
 253                 filename = "residual-%s-%g.png" % (
 254                     title.replace(', ', '_').replace(' ', '_'), r)
 255                 self._plot_residual_comparison(
 256                     experiment_hist, sawsim_hist, residual=r,
 257                     title=title, filename=filename)
 258         log().debug('residual %s: %g' % (params, residual))
 259         return residual
 260
 261     def plot(self, param_ranges, logx=False, logy=False, contour=False,
 262              csv=None):
 263         if csv:
 264             csv.write(','.join(('param 1', 'param 2', 'fit quality')) + '\n')
 265         xranges = param_ranges[0]
 266         yranges = param_ranges[1]
 267         if logx == False:
 268             x = numpy.linspace(*xranges)
 269         else:
 270             m,M,n = xranges
 271             x = numpy.exp(numpy.linspace(numpy.log(m), numpy.log(M), n))
 272         if logy == False:
 273             y = numpy.linspace(*yranges)
 274         else:
 275             m,M,n = yranges
 276             y = numpy.exp(numpy.linspace(numpy.log(m), numpy.log(M), n))
 277         X, Y = pylab.meshgrid(x,y)
 278         C = numpy.zeros((len(y)-1, len(x)-1))
 279         for i,xi in enumerate(x[:-1]):
 280             for j,yj in enumerate(y[:-1]):
 281                 log().info('point %d %d (%d of %d)'
 282                            % (i, j, i*(len(y)-1) + j, (len(x)-1)*(len(y)-1)))
 283                 params = (xi,yj)
 284                 r = self.residual(params)
 285                 if csv:
 286                     csv.write(','.join([str(v) for v in (xi,yj,r)]) + '\n')
 287                 C[j,i] = numpy.log(r) # better resolution in valleys
 288                 if MEM_DEBUG == True:
 289                     log().debug('RSS: %d KB' % rss())
 290         C = numpy.nan_to_num(C) # NaN -> 0
 291         fid = file("histogram_matcher-XYC.pkl", "wb")
 292         pickle.dump([X,Y,C], fid)
 293         fid.close()
 294         # read in with
 295         # import pickle
 296         # [X,Y,C] = pickle.load(file("histogram_matcher-XYC.pkl", "rb"))
 297         # ...
 298         _FIGURE.clear()
 299         axes = _FIGURE.add_subplot(1, 1, 1)
 300         if logx == True:
 301             axes.set_xscale('log')
 302         if logy == True:
 303             axes.set_yscale('log')
 304         if contour == True:
 305             p = axes.contour(X[:-1,:-1], Y[:-1,:-1], C)
 306             # [:-1,:-1] to strip dummy last row & column from X&Y.
 307         else: # pseudocolor plot
 308             p = axes.pcolor(X, Y, C)
 309             axes.autoscale_view(tight=True)
 310         _FIGURE.colorbar(p)
 311         _FIGURE.savefig("figure.png")
 312
 313     def _plot_residual_comparison(self, experiment_hist, theory_hist,
 314                                   residual, title, filename):
 315         _FIGURE.clear()
 316         axes = _FIGURE.add_subplot(1, 1, 1)
 317         axes.hold(True)
 318         axes.hist(x=experiment_hist.bin_edges[:-1],  # one fake entry for each bin
 319                   weights=experiment_hist.counts,    # weigh the fake entries by count
 320                   bins=experiment_hist.bin_edges,
 321                   align='mid', histtype='stepfilled',
 322                   color='r')
 323         axes.hist(x=theory_hist.bin_edges[:-1],  # one fake entry for each bin
 324                   weights=theory_hist.counts,    # weigh the fake entries by count
 325                   bins=theory_hist.bin_edges,
 326                   align='mid', histtype='stepfilled',
 327                   color='b', alpha=0.5)
 328         axes.set_title(title)
 329         _FIGURE.savefig(filename)
 330
 331
 332 def parse_param_ranges_string(string):
 333     """Parse parameter range stings.
 334
 335     '[Amin,Amax,Asteps],[Bmin,Bmax,Bsteps],...'
 336       ->
 337     [[Amin,Amax,Asteps],[Bmin,Bmax,Bsteps],...]
 338
 339     >>> parse_param_ranges_string('[1,2,3],[4,5,6]')
 340     [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]
 341     >>> parse_param_ranges_string('[1,2,3]')
 342     [[1.0, 2.0, 3.0]]
 343     """
 344     ranges = []
 345     for range_string in string.split("],["):
 346         range_number_strings = range_string.strip("[]").split(",")
 347         ranges.append([float(x) for x in range_number_strings])
 348     return ranges
 349
 350
 351 def main(argv=None):
 352     """
 353     >>> import tempfile
 354     >>> f = tempfile.NamedTemporaryFile()
 355     >>> f.write(EXAMPLE_HISTOGRAM_FILE_CONTENTS)
 356     >>> f.flush()
 357     >>> main(['-r', '[1e-5,1e-3,3],[0.1e-9,1e-9,3]',
 358     ...       '-N', '2',
 359     ...       f.name])
 360     >>> f.close()
 361     """
 362     from optparse import OptionParser
 363     import sys
 364
 365     if argv == None:
 366         argv = sys.argv[1:]
 367
 368     sr = SawsimRunner()
 369
 370     usage = '%prog [options] histogram_file'
 371     epilog = '\n'.join([
 372             'Compare simulated results against experimental values over a',
 373             'range of parameters.  Generates a plot of fit quality over',
 374             'the parameter space.  The histogram file should look something',
 375             'like:',
 376             '',
 377             EXAMPLE_HISTOGRAM_FILE_CONTENTS,
 378             ''
 379             '`#HISTOGRAM: <params>` lines start each histogram.  `params`',
 380             'lists the `sawsim` parameters that are unique to that',
 381             'experiment.',
 382             '',
 383             'Each histogram line is of the format:',
 384             '',
 385             '<bin_edge><whitespace><count>',
 386             '',
 387             '`<bin_edge>` should mark the left-hand side of the bin, and',
 388             'all bins should be of equal width (so we know where the last',
 389             'one ends).',
 390             _PYSAWSIM_LOG_LEVEL_MSG,
 391             ])
 392     parser = OptionParser(usage, epilog=epilog)
 393     parser.format_epilog = lambda formatter: epilog+'\n'
 394     for option in sr.optparse_options:
 395         if option.dest == 'param_string':
 396             continue
 397         parser.add_option(option)
 398     parser.add_option('-f','--param-format', dest='param_format',
 399                       metavar='FORMAT',
 400                       help='Convert params to sawsim options (%default).',
 401                       default=('-s cantilever,hooke,0.05 -N1 -s folded,null -N8 -s "unfolded,wlc,{0.39e-9,28e-9}" -k "folded,unfolded,bell,{%g,%g}" -q folded'))
 402     parser.add_option('-p','--initial-params', dest='initial_params',
 403                       metavar='PARAMS',
 404                       help='Initial params for fitting (%default).',
 405                       default='3.3e-4,0.25e-9')
 406     parser.add_option('-r','--param-range', dest='param_range',
 407                       metavar='PARAMS',
 408                       help='Param range for plotting (%default).',
 409                       default='[1e-5,1e-3,20],[0.1e-9,1e-9,20]')
 410     parser.add_option('--logx', dest='logx',
 411                       help='Use a log scale for the x range.',
 412                       default=False, action='store_true')
 413     parser.add_option('--logy', dest='logy',
 414                       help='Use a log scale for the y range.',
 415                       default=False, action='store_true')
 416     parser.add_option('-R','--residual', dest='residual',
 417                       metavar='STRING',
 418                       help='Residual type (from %s; default: %%default).'
 419                       % ', '.join(_Histogram().types()),
 420                       default='jensen-shannon')
 421     parser.add_option('-P','--plot-residuals', dest='plot_residuals',
 422                       help='Generate residual difference plots for each point in the plot range.',
 423                       default=False, action='store_true')
 424     parser.add_option('-c','--contour-plot', dest='contour_plot',
 425                       help='Select contour plot (vs. the default pseudocolor plot).',
 426                       default=False, action='store_true')
 427     parser.add_option('--csv', dest='csv', metavar='FILE',
 428                       help='Save fit qualities to a comma-separated value file FILE.'),
 429
 430     options,args = parser.parse_args(argv)
 431
 432     initial_params = [float(p) for p in options.initial_params.split(",")]
 433     param_ranges = parse_param_ranges_string(options.param_range)
 434     histogram_file = args[0]
 435     csv = None
 436     sr_call_params = sr.initialize_from_options(options)
 437
 438     try:
 439         hm = HistogramMatcher(
 440             file(histogram_file, 'r'),
 441             param_format_string=options.param_format,
 442             sawsim_runner=sr, residual_type=options.residual,
 443             plot=options.plot_residuals, **sr_call_params)
 444         #hm.fit(initial_params)
 445         if options.csv:
 446             csv = open(options.csv, 'w')
 447         hm.plot(param_ranges, logx=options.logx, logy=options.logy,
 448                 contour=options.contour_plot, csv=csv)
 449     finally:
 450         sr.teardown()
 451         if csv:
 452             csv.close()