Changeset 172 for trunk/examples/retina/benchmark_noise.py

Timestamp:

05/12/08 18:49:09 (4 years ago)

Author:

LaurentPerrinet

Message:

more polishing to allow easier copy/paste of code

Files:

• trunk/examples/retina/benchmark_noise.py (modified) (5 diffs)

trunk/examples/retina/benchmark_noise.py

@@ -5 +5 @@
 ==================
 
-Just studying how different background noise current is integrated by the neurons on one fiber.
+Just studying how different background noise current are integrated by the
+neurons on the retinal fibers.
+
+Illustrates how one many use parameters to explore one set of parameters and
+compute a CRF function. See benchmark_linear to store time varrying values.
 
 Laurent Perrinet, INCM, CNRS
@@ -13 +17 @@
 """
 
-import os, datetime, numpy, shelve
+import os, sys, numpy, shelve
 
 from NeuroTools.parameters import *
@@ -25 +29 @@
 p.noise_std = ParameterRange(list(10.**(numpy.linspace(-.50,1.,N_exp_noise))))
 
-results = shelve.open('results/benchmark_noise')
+import retina as model
+
+
+retina = model.Retina(N) 
+retina.params['snr'] = 0 # no input
+
+
+name = sys.argv[0].split('.')[0] # name of the current script withpout the '.py' part
+results = shelve.open('results/mat-' + name)
 try:
     CRF = results['CRF']
-    params = results['params']
+except:
     
-except:
-    import retina as model
-
-
-    retina = model.Retina(N)
-    retina.params['snr'] = 0
     # calculates the dimension of the parameter space
     results_dim, results_label = p.parameter_space_dimension_labels()
 
     # creates results array with size of parameter space dimension
-
     CRF = numpy.empty(results_dim)
 
-    pbar=progressbar.ProgressBar(widgets=["calculating", " ", progressbar.Percentage(), ' ',
+    pbar=progressbar.ProgressBar(widgets=[name, " ", progressbar.Percentage(), ' ',
             progressbar.Bar(), ' ', progressbar.ETA()], maxval=numpy.prod(results_dim))
     for i_exp,experiment in enumerate(p.iter_inner()):
@@ -56 +61 @@
         pbar.update(i_exp)
 
+    results['CRF'] = CRF
 
-
-
-    results['params'] = params
-    results['CRF'] = CRF
     pbar.finish()
 
@@ -75 +77 @@
 """
 
-
-#params = retina.params
-N, simtime = params['N'], params['simtime']
+N, simtime = retina.params['N'], retina.params['simtime']
 
 import pylab
 
-#pylab.rcParams.update(pylab_params(fig_width_pt =497.9/5, ratio = 1/1.2))
-pylab.figure(num = 1)#, dpi=200, facecolor='w', edgecolor='k')
-
-#Lmargin, Rmargin, dmargin, umargin = 0.15, 0.05, 0.15,  0.05
-#pylab.axes([Lmargin, dmargin , 1.0 - Rmargin- Lmargin,1.0-umargin-dmargin]) # [left, bottom, width, height]
+pylab.figure(num = 1)
 
 pylab.plot(p.noise_std._values,CRF,'go-', label='line 1', linewidth=2)
 pylab.ylabel('Firing Frequency (Hz)')
 pylab.xlabel('Noise amplitude')
-#pylab.axis('tight')
-pylab.savefig('results/benchmark_noise.pdf')#, dpi=300) #
-#command = 'epstopdf  "%s" "%s"'% (pdffile, psfile)
-#os.system(command)
 
-#TODO: make a plot showing it's the right point process with a histogram
+pylab.savefig('results/fig-' + name + '.pdf')
+pylab.savefig('results/fig-' + name + '.png', dpi = 300)
+