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