From 7e70aedb6a5c8e757b71e8ce44830a72cf544117 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 20 Oct 2010 06:08:53 -0400 Subject: [PATCH] Add pysawsim.sawsim.main() and bin/sawsim_hist.py calling it. Also fix a number of bugs turned up by trial calls to the new sawsim_hist.py. --- bin/sawsim_hist.py | 6 +++ pysawsim/sawsim_histogram.py | 84 ++++++++++++++++++++++++++++++++---- 2 files changed, 81 insertions(+), 9 deletions(-) create mode 100755 bin/sawsim_hist.py diff --git a/bin/sawsim_hist.py b/bin/sawsim_hist.py new file mode 100755 index 0000000..da573dc --- /dev/null +++ b/bin/sawsim_hist.py @@ -0,0 +1,6 @@ +#!/usr/bin/env python + +from pysawsim import sawsim_histogram as sh + + +sh.main() diff --git a/pysawsim/sawsim_histogram.py b/pysawsim/sawsim_histogram.py index 848ca90..d5eb306 100644 --- a/pysawsim/sawsim_histogram.py +++ b/pysawsim/sawsim_histogram.py @@ -27,7 +27,7 @@ import numpy from . import __version__, log from .histogram import Histogram -from .manager import InvokeJob +from .manager import InvokeJob, MANAGERS, get_manager from .sawsim import parse @@ -56,15 +56,15 @@ class SawsimHistogram (object): CACHE_DIR, hashlib.sha256(param_string).hexdigest()) def _make_cache(self, param_string): - cache_dir = self._cache_dir(params_string) + cache_dir = self._cache_dir(param_string) os.makedirs(cache_dir) - with open(os.path.join(d, 'param_string'), 'w') as f: + with open(os.path.join(cache_dir, 'param_string'), 'w') as f: f.write('# version: %s\n%s\n' % (__version__, param_string)) def _load_cached_data(self, cache_dir, N): data = {} for i in range(N): - simulation_path = os.path.join(d, '%d.dat' % i) + simulation_path = os.path.join(cache_dir, '%d.dat' % i) if os.path.exists(simulation_path): with open(simulation_path, 'r') as f: data[i] = parse(f.read()) @@ -73,7 +73,7 @@ class SawsimHistogram (object): return data def _cache_run(self, cache_dir, i, stdout): - simulation_path = os.path.join(d, '%d.dat' % i) + simulation_path = os.path.join(cache_dir, '%d.dat' % i) with open(simulation_path, 'w') as f: f.write(stdout) @@ -110,9 +110,9 @@ class SawsimHistogram (object): if i in data: continue jobs[i] = manager.async_invoke(InvokeJob( - '%s %s' % (SAWSIM, param_string))) - complete_jobs = manager.wait([job.id for job in jobs]) - for i,job in jobs.iteritems: + target='%s %s' % (SAWSIM, param_string))) + complete_jobs = manager.wait([job.id for job in jobs.itervalues()]) + for i,job in jobs.iteritems(): j = complete_jobs[job.id] assert j.status == 0, j.data if self._use_cache == True: @@ -126,9 +126,75 @@ class SawsimHistogram (object): for d_i in data.values(): events.extend([e.force for e in d_i if e.initial_state == 'folded']) - events = numpy.array(d_i) + events = numpy.array(events) if bin_edges == None: return events h = Histogram() h.from_data(events, bin_edges) return h + + +def main(): + import optparse + import sys + + global SAWSIM, CACHE_DIR + + usage = "%prog [options] velocity_file" + + parser = optparse.OptionParser(usage) + parser.add_option("-s","--sawsim", dest="sawsim", + metavar="PATH", + help="Set sawsim binary (%default).", + default=SAWSIM) + parser.add_option("-p","--params", dest="params", + metavar="PARAMS", + help="Initial params for fitting (%default).", + default=DEFAULT_PARAM_STRING) + parser.add_option("-N", "--number-of-runs", dest="N", + metavar="INT", type='int', + help="Number of sawsim runs at each point in parameter space (%default).", + default=400) + parser.add_option("-w", "--bin-width", dest="bin_width", + metavar="FLOAT", type='float', + help="Histogram bin width in newtons (%default).", + default=None) + parser.add_option("-m", "--manager", dest="manager", + metavar="STRING", + help="Job manager name (one of %s) (%%default)." + % (', '.join(MANAGERS)), + default=MANAGERS[0]) + parser.add_option("-C","--use-cache", dest="use_cache", + help="Use cached simulations if they exist (vs. running new simulations) (%default)", + default=False, action="store_true") + parser.add_option("--clean-cache", dest="clean_cache", + help="Remove previously cached simulations if they exist (%default)", + default=False, action="store_true") + parser.add_option("-d","--cache-dir", dest="cache_dir", + metavar="STRING", + help="Cache directory for sawsim unfolding forces (%default).", + default=CACHE_DIR) + options,args = parser.parse_args() + + SAWSIM = options.sawsim + CACHE_DIR = options.cache_dir + + sh = SawsimHistogram(use_cache=options.use_cache, + clean_cache=options.clean_cache) + + manager = get_manager(options.manager)() + try: + events = sh(param_string=options.params, N=options.N, manager=manager) + finally: + manager.teardown() + + if options.bin_width == None: + sys.stdout.write('# Unfolding force (N)\n') + events.tofile(sys.stdout, sep='\n') + sys.stdout.write('\n') + else: + h = Histogram() + h.from_data(events, bin_edges=h.calculate_bin_edges( + events, options.bin_width)) + h.headings = ['Force (N)', 'Unfolding events'] + h.to_stream(sys.stdout) -- 2.26.2