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