def begin_evolution(self):
# Begin actual evolution
start_time = time.time()
pop = self.pop
pred_pop = self.pred_pop
for g in xrange(self.gen_start_number,
self.gen_start_number + Darwin.NGEN):
creatures, predators = self.simulate(pop, pred_pop)
pop = self.evolve_population(creatures, g)
if len(pred_pop) > 0:
pred_pop = self.evolve_population(predators, g)
if g % 20 == 0:
self.printTimeStats(start_time, g)
self.pop = pop
self.pred_pop = pred_pop
self.gen_start_number = g
f = open(Darwin.save_file, 'w')
self.save_population(f)
stats.save_stats(open('stats_' + Darwin.save_file, 'w'))
stats.plot_all()
def begin_evolution(self):
# Begin actual evolution
start_time = time.time()
pop = self.pop
pred_pop = self.pred_pop
for g in xrange(self.gen_start_number,self.gen_start_number+Darwin.NGEN):
creatures, predators = self.simulate(pop, pred_pop)
pop = self.evolve_population(creatures, g)
if len(pred_pop) > 0:
pred_pop = self.evolve_population(predators, g)
if g % 20 == 0:
self.printTimeStats(start_time, g)
self.pop = pop
self.pred_pop = pred_pop
self.gen_start_number = g
f = open(Darwin.save_file,'w')
self.save_population(f)
stats.save_stats(open('stats_' + Darwin.save_file,'w'))
stats.plot_all()
"""
else: #just copy the files
print "Copying data files to ", data_dir
for csvf in glob.iglob(join(args.indir[0],"*.csv")):
shutil.copyfile(csvf, join(data_dir, os.path.basename(csvf)))
"""
print "Instantiating Slicer and loading series"
slicer = Slicer(taskfile=join(data_dir, 'task.xls'))
filelist=[join(data_dir,f) for f in os.listdir(data_dir) if \
re.compile(".*\.csv").match(f)]
num_subjects = len(filelist)
slicer.load_series_from_csv('raw', filelist)
if args.stats:
pp = PdfPages(join(report_dir, 'stats.pdf'))
stats.plot_all(slicer, pp)
fig, ax = plt.subplots()
ax.plot(range(1, num_subjects + 1))
plt.title("Number of subjects")
pp.savefig(fig)
pp.close()
if args.kernelsvm:
kernel_svm.do_kernelsvm_slicer(slicer)
if args.chartsforpaper:
pp = PdfPages(join(report_dir, 'rolling_median.pdf'))
charts_for_paper.do_charts(slicer, pp)
pp.close()
"""
else: #just copy the files
print "Copying data files to ", data_dir
for csvf in glob.iglob(join(args.indir[0],"*.csv")):
shutil.copyfile(csvf, join(data_dir, os.path.basename(csvf)))
"""
print "Instantiating Slicer and loading series"
slicer = Slicer(taskfile=join(data_dir,'task.xls'))
filelist=[join(data_dir,f) for f in os.listdir(data_dir) if \
re.compile(".*\.csv").match(f)]
num_subjects = len(filelist)
slicer.load_series_from_csv('raw', filelist)
if args.stats:
pp = PdfPages(join(report_dir, 'stats.pdf'))
stats.plot_all(slicer, pp)
fig, ax = plt.subplots()
ax.plot(range(1,num_subjects+1))
plt.title("Number of subjects")
pp.savefig(fig)
pp.close()
if args.kernelsvm:
kernel_svm.do_kernelsvm_slicer(slicer)
if args.chartsforpaper:
pp = PdfPages(join(report_dir, 'rolling_median.pdf'))
charts_for_paper.do_charts(slicer, pp)
pp.close()
