[Jboost-cvs] jboost/scripts error.py, 1.3, 1.4 margin.py, 1.7, 1.8 surfing.py, 1.2, 1.3

[Aaron A. <aa...@us...>]

Update of /cvsroot/jboost/jboost/scripts
In directory sc8-pr-cvs6.sourceforge.net:/tmp/cvs-serv6911

Modified Files:
	error.py margin.py surfing.py 
Log Message:
New output format

Index: margin.py
===================================================================
RCS file: /cvsroot/jboost/jboost/scripts/margin.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** margin.py	13 Jun 2007 16:09:14 -0000	1.7
--- margin.py	23 Oct 2007 22:50:42 -0000	1.8
***************
*** 8,20 ****
  import re
  
  def usage():
  	print 'Usage: margin.py    '
! 	print '\t--margins=filename  margins file as output by jboost (-a -2 switch)'
! 	print '\t--scores=filename   scores file as output by jboost (-a -2 switch)'
! 	print '\t--data=filename     train/test filename'
! 	print '\t--spec=filename     spec filename'
! 	print '\t--iteration=NUMBER  the iteration number to inspect'
! 	print '\t--sample            are we interested in a sample of false pos/neg'
! 	print '\t--labels=filename   labels file (if unspecified then created from data file)'
  
  def sortByColumns(list2d, column_indices, in_place=False):
--- 8,21 ----
  import re
  
+ 
+ SEPARATOR = ':'
+ 
  def usage():
  	print 'Usage: margin.py    '
! 	print '\t--boost-info=filename  margins file as output by jboost (-a -2 switch)'
! 	print '\t--data=filename        train/test filename'
! 	print '\t--spec=filename        spec filename'
! 	print '\t--iteration=i,j,k,...  the iterations to inspect, no spaces between commas'
! 	print '\t--sample               are we interested in a sample of false pos/neg'
  
  def sortByColumns(list2d, column_indices, in_place=False):
***************
*** 45,52 ****
  	    '\n'
  	    )
!     f.write('Sensitivity: ' + str(float(len(truepos))/(len(truepos)+len(falseneg))) + '\n');
!     f.write('False Pos Rate: ' + str(float(len(falsepos))/(len(trueneg)+len(falsepos))) + '\n');
  
  
      list= [[margins[w],examples[w]] for w in falseneg.keys()]
      sortByColumns(list, [0], True)
--- 46,58 ----
  	    '\n'
  	    )
!     f.write('Sensitivity: ' +  str(1-float(len(falseneg))/(len(truepos)+len(falseneg))) + '\n')
!     f.write('False Pos Rate: ' + str(float(len(falsepos))/(len(trueneg)+len(falsepos))) + '\n')
  
+     f.write('True pos: ' + str(len(truepos)) + '\n')
+     f.write('False pos: ' + str(len(falsepos)) + '\n')
+     f.write('True neg: ' + str(len(trueneg)) + '\n')
+     f.write('False neg: ' + str(len(falseneg)) + '\n')
  
+     
      list= [[margins[w],examples[w]] for w in falseneg.keys()]
      sortByColumns(list, [0], True)
***************
*** 77,86 ****
  
  
! def write_gnuplot(scores_list, iters, datafile):
  
  	margin_list = []
  	for i in range(len(iters)):
! 		scores = scores_list[i]
! 		margins = scores_list[i] #get_margins(labels, scores);
  		margins.sort()
  		margin_list.append(margins)
--- 83,93 ----
  
  
! def write_gnuplot(m_list, iters, datafile):
  
  	margin_list = []
  	for i in range(len(iters)):
! 		scores = m_list[i]
! 		m = m_list[i]
! 		margins = m[:]
  		margins.sort()
  		margin_list.append(margins)
***************
*** 131,144 ****
  
  	
  
! 	f = open('margin.png.gnuplot', 'w')
  	f.writelines(pngoutlines)
  	f.close()
  
! 	f = open('margin.eps.gnuplot', 'w')
  	f.writelines(epsoutlines)
  	f.close()
  
! 
  
  
--- 138,155 ----
  
  	
+ 	pngfilename = 'margin.png.gnuplot'
+ 	epsfilename = 'margin.eps.gnuplot'
  
! 	f = open(pngfilename, 'w')
  	f.writelines(pngoutlines)
  	f.close()
  
! 	f = open(epsfilename, 'w')
  	f.writelines(epsoutlines)
  	f.close()
  
! 	os.system('gnuplot ' + pngfilename)
! 	os.system('gnuplot ' + epsfilename)
! 	os.system('epstopdf margin.eps')
  
  
***************
*** 164,180 ****
  	
  
! def get_margins(labels, scores):
! 	def computeMargin(score, label):
! 		return score*int(label)
! 
! 	margins= map(computeMargin, scores, labels)
! 	return margins
! 
! 
! 
! def process_data(examples, labels, margins, scores, datafile, sample):
  
  	print 'Examples ' + str(len(examples))
- 	print 'Scores   ' + str(len(scores))
  	print 'Margins  ' + str(len(margins))
  	print 'Generating margins'
--- 175,181 ----
  	
  
! def process_data(examples, labels, margins, datafile, sample):
  
  	print 'Examples ' + str(len(examples))
  	print 'Margins  ' + str(len(margins))
  	print 'Generating margins'
***************
*** 182,187 ****
  	print 'Matching margins with data'
  
- 	#pos_label, neg_label = getLabels(specfile)
- 
  	falsepos = dict([(w,[margins[w],examples[w],labels[w]])
  		    for w in range(len(margins))
--- 183,186 ----
***************
*** 200,203 ****
--- 199,205 ----
  
  
+ #        for i in range(len(margins)):
+ #		print '%d\t %s\t %.2f\t %.2f' % (i, labels[i].strip(), margins[i])
+ 
  	write_files(examples, datafile, sample, margins, falsepos, truepos, falseneg, trueneg)
  	
***************
*** 213,217 ****
  
      try:
!         opts, args= getopt.getopt(sys.argv[1:], '', ['margins=', 'scores=','data=','spec=','labels=', 'iteration=', 'sample'])
      except getopt.GetoptError, inst:
          print 'Received an illegal argument:', inst
--- 215,219 ----
  
      try:
!         opts, args= getopt.getopt(sys.argv[1:], '', ['boost-info=', 'data=', 'spec=', 'iteration=', 'sample'])
      except getopt.GetoptError, inst:
          print 'Received an illegal argument:', inst
***************
*** 219,228 ****
          sys.exit(2)
  
!     marginsfile = scoresfile = datafile = specfile = labelsfile = sample = iteration = None
      for opt,arg in opts:
! 	    if (opt == '--margins'):
! 		    marginsfile = arg
! 	    if (opt == '--scores'):
! 		    scoresfile = arg
  	    if (opt == '--spec'):
  		    specfile = arg
--- 221,228 ----
          sys.exit(2)
  
!     boostfile = datafile = specfile = labelsfile = sample = iteration = None
      for opt,arg in opts:
! 	    if (opt == '--boost-info'):
! 		    boostfile = arg
  	    if (opt == '--spec'):
  		    specfile = arg
***************
*** 237,258 ****
  	
  
!     if(marginsfile == None or scoresfile == None or datafile == None or specfile == None):
  	    print 'Need score, data, and spec file.'
  	    usage()
  	    sys.exit(2)
      
-     if(labelsfile == None):
- 	    labelsfile = datafile + '.labels'
- 	#if os.path.exists(labelsfile):
- 	#    print 'Using label file:', labelsfile
- 	#    # do nothing
- 	#else:
- 	    command = 'cat ' + datafile + ' | sed \'s/.*\(.1\);/\\1/g\' > ' + labelsfile
- 	    print command
- 	    os.system(command)
- 	    command = 'sed -i \'s/ 1/+1/g\' ' + labelsfile
- 	    print command
- 	    os.system(command)
- 
      print 'Reading data'
      f= open(datafile,'r')
--- 237,245 ----
  	
  
!     if(boostfile == None or datafile == None or specfile == None):
  	    print 'Need score, data, and spec file.'
  	    usage()
  	    sys.exit(2)
      
      print 'Reading data'
      f= open(datafile,'r')
***************
*** 260,301 ****
      f.close()
      
!     print 'Reading score values'
!     f= open(scoresfile,'r')
!     data= f.readlines()
!     f.close()
!     score_elements= int((string.split(data[0],'='))[2])
!     
!     print 'Reading margin values'
!     f= open(marginsfile,'r')
      data= f.readlines()
      f.close()
!     margin_elements= int((string.split(data[0],'='))[2])
      
!     print 'Reading labels'
!     f= open(labelsfile,'r')
!     labels= f.readlines()[-score_elements:]
!     f.close()
  
!     scores = []
!     margin_list = []
  
      iters = [1]
      iters[0] = len(data) / (margin_elements+1)
      if (iteration != None):
! 	    iters = map(int, iteration.split(','))
  	    for iter in iters:
! 		    margins = [float(x) for x in data[iter*(margin_elements+1)+1:(iter+1)*(margin_elements+1)]]
! 		    scores = [float(x) for x in data[iter*(score_elements+1)+1:(iter+1)*(score_elements+1)]]
  		    margin_list.append(margins)
      else:
! 	    margins = [float(x) for x in data[-margin_elements:]]
! 	    scores = [float(x) for x in data[-score_elements:]]
  	    margin_list.append(margins)
  
!     write_gnuplot(margin_list, iters, datafile)
! 
!     process_data(examples, labels, margin_list[len(margin_list)-1], scores, datafile, sample)
! 
  
      
  
--- 247,294 ----
      f.close()
      
!     print 'Reading boosting info'
!     f= open(boostfile,'r')
      data= f.readlines()
      f.close()
!     margin_elements= int((string.split(data[0],SEPARATOR))[1].split('=')[1])
      
!     def get_margin(line):
! 	    m = line.split(SEPARATOR)[1]
! 	    m.replace(']','')
! 	    m.replace(';','')
! 	    m.replace(SEPARATOR,'')
! 	    m.replace(' ','')
! 	    m.replace('\t','')
! 	    return float(m)
  
!     def get_label(line):
! 	    m = line.split(SEPARATOR)[-2]
! 	    m.replace(']','')
! 	    m.replace(';','')
! 	    m.replace(SEPARATOR,'')
! 	    m.replace(' ','')
! 	    m.replace('\t','')
! 	    return m
  
+     # if iterations are not specified on command line, we do the last iteration
      iters = [1]
      iters[0] = len(data) / (margin_elements+1)
+ 
+     margin_list = []
      if (iteration != None):
! 	    iters = map(int, [x.strip() for x in iteration.split(',')])
  	    for iter in iters:
! 		    lines = [x for x in data[iter*(margin_elements+1)+1:(iter+1)*(margin_elements+1)]]
! 		    margins = map(get_margin, lines)
  		    margin_list.append(margins)
      else:
! 	    lines = [x for x in data[-margin_elements:]]
! 	    margins = map(get_margin, lines)
  	    margin_list.append(margins)
  
!     labels = map(get_label, [x for x in data[-margin_elements:]])
!     process_data(examples, labels, margin_list[len(margin_list)-1], datafile, sample)
  
+     write_gnuplot(margin_list, iters, datafile)
      
  

Index: surfing.py
===================================================================
RCS file: /cvsroot/jboost/jboost/scripts/surfing.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** surfing.py	12 Jul 2007 16:07:26 -0000	1.2
--- surfing.py	23 Oct 2007 22:50:42 -0000	1.3
***************
*** 9,20 ****
  import math
  
  def usage():
  	print 'Usage: margin.py    '
! 	print '\t--surfing=filename  surfing file as output by jboost (-a -2 switch)'
! 	print '\t--scores=filename   scores file as output by jboost (-a -2 switch)'
! 	print '\t--data=filename     train/test filename'
! 	print '\t--spec=filename     spec filename'
! 	print '\t--booster=type      type={normal, brown}'
! 	print '\t--framerate=num     an integer specifying framerate'
  
  
--- 9,22 ----
  import math
  
+ SEPARATOR=':'
+ 
  def usage():
  	print 'Usage: margin.py    '
! 	print '\t--surfing=filename      surfing file as output by jboost (-a -2 switch)'
! 	print '\t--boost-info=filename   file as output by jboost (-a -2 switch)'
! 	print '\t--data=filename         train/test filename'
! 	print '\t--spec=filename         spec filename'
! 	print '\t--booster=type          type={AdaBoost, LogLossBoost, NormalBoost, BrownBoost}'
! 	print '\t--framerate=num         an integer specifying framerate'
  
  
***************
*** 39,46 ****
  	weights = []
  	s = c= c1 = c2 = theta = 0
! 	if(params[0] == 'brown'):
  		c = float(params[1])
  		s = float(params[2]) #time remaining
! 	elif(params[0] == 'normal'):
  		c = float(params[1])
  		s = c-float(params[2]) #time played
--- 41,49 ----
  	weights = []
  	s = c= c1 = c2 = theta = 0
! 	confidence = False
! 	if(params[0] == 'BrownBoost'):
  		c = float(params[1])
  		s = float(params[2]) #time remaining
! 	elif(params[0] == 'NormalBoost'):
  		c = float(params[1])
  		s = c-float(params[2]) #time played
***************
*** 50,53 ****
--- 53,57 ----
  		c2 = float(params[4])
  		theta = float(params[5])
+ 		confidence = params[6]
  		
  		
***************
*** 57,64 ****
  	for i in range(0,num_steps):
  		mu = var = 0
! 		if params[0] == 'brown': 
  			mu = -s
  			var = c
! 		elif params[0] == 'normal':
  			mu = theta - c1 * (math.exp(-s) - math.exp(-c))
  			var = c2 * (math.exp(-2*s) - math.exp(-2*c)) + 0.05
--- 61,68 ----
  	for i in range(0,num_steps):
  		mu = var = 0
! 		if params[0] == 'BrownBoost': 
  			mu = -s
  			var = c
! 		elif params[0] == 'NormalBoost':
  			mu = theta - c1 * (math.exp(-s) - math.exp(-c))
  			var = c2 * (math.exp(-2*s) - math.exp(-2*c)) + 0.05
***************
*** 67,71 ****
  		y = math.exp(-math.pow(x-mu,2)/(var)) * max_bin 
  		p = (1 - erf((x-mu)/math.sqrt(var)))/2
! 		p = min(2*p, 1)
  		weights.append((x,y,p))
  		x += step
--- 71,76 ----
  		y = math.exp(-math.pow(x-mu,2)/(var)) * max_bin 
  		p = (1 - erf((x-mu)/math.sqrt(var)))/2
! 		if (confidence):
! 			p = min(2*p, 1)
  		weights.append((x,y,p))
  		x += step
***************
*** 115,132 ****
  def paste_gnuplot(num_iterations, framerate): 
  	print 'Starting animated gif creation'
! 	os.system('convert -rotate  90 -delay 5 -loop 0 surfing*.eps surfing.gif')
  	print 'Finished gif creation'
  	print 'See surfing.gif for animation'
  
! line_compare = lambda x,y : cmp(float(string.split(x,'\t')[0]), float(string.split(y,'\t')[0]))
  
  def write_gnuplot(lines, iter, datafile, params):
  
  	lines.sort(line_compare);
! 
! 
! 	margins = [ float(string.split(x,'\t')[0])    for x in lines]
! 	weights = [ float(string.split(x,'\t')[1])    for x in lines]
! 	potentials = [ float(string.split(x,'\t')[2])    for x in lines]
  
  
--- 120,136 ----
  def paste_gnuplot(num_iterations, framerate): 
  	print 'Starting animated gif creation'
! 	os.system('convert -rotate  90 -delay 5 -loop 2 surfing*.eps surfing.gif')
  	print 'Finished gif creation'
  	print 'See surfing.gif for animation'
  
! 
  
  def write_gnuplot(lines, iter, datafile, params):
  
+ 	line_compare = lambda x,y : cmp(float(string.split(x,SEPARATOR)[1]), float(string.split(y,SEPARATOR)[1]))
  	lines.sort(line_compare);
! 	margins = [ float(string.split(x,SEPARATOR)[1])    for x in lines]
! 	weights = [ float(string.split(x,SEPARATOR)[2])    for x in lines]
! 	potentials = [ float(string.split(x,SEPARATOR)[3])    for x in lines]
  
  
***************
*** 155,162 ****
  	epsoutlines.append('set terminal post\n')
  	epsoutlines.append('set output \'surfing%05d.eps\'\n' % (iter))
! 	epsoutlines.append('set title "'+  params[0] +  'boost ' + datafile + ' Surfing: Time Remaining ' + str(params[2]) + '" font "Times,20"\n')
  	epsoutlines.append('set key left top\n')
  	epsoutlines.append('set yzeroaxis lt -1\n')
! 	if params[0]=='normal':
  		epsoutlines.append('set xrange [-1:1]\n')
  		epsoutlines.append('set yrange [0:1]\n')
--- 159,166 ----
  	epsoutlines.append('set terminal post\n')
  	epsoutlines.append('set output \'surfing%05d.eps\'\n' % (iter))
! 	epsoutlines.append('set title "'+  params[0] +  ' ' + datafile + ' Surfing: Time Remaining ' + str(params[2]) + '" font "Times,20"\n')
  	epsoutlines.append('set key left top\n')
  	epsoutlines.append('set yzeroaxis lt -1\n')
! 	if params[0]=='NormalBoost':
  		epsoutlines.append('set xrange [-1:1]\n')
  		epsoutlines.append('set yrange [0:1]\n')
***************
*** 173,177 ****
  				'"surfing_weight.dat" using 1:2 title "Potential" with lines \n')
  #				'delta(t) with lines \n')
! #	if params[0]=='normal':
  #		epsoutlines.append('set parametric\n')
  #		epsoutlines.append('set trange [0:1]\n')
--- 177,181 ----
  				'"surfing_weight.dat" using 1:2 title "Potential" with lines \n')
  #				'delta(t) with lines \n')
! #	if params[0]=='NormalBoost':
  #		epsoutlines.append('set parametric\n')
  #		epsoutlines.append('set trange [0:1]\n')
***************
*** 212,216 ****
  
      try:
!         opts, args= getopt.getopt(sys.argv[1:], '', ['surfing=', 'scores=','data=','spec=','labels=', 'iteration=', 'framerate=', 'booster=', 'sample'])
      except getopt.GetoptError, inst:
          print 'Received an illegal argument:', inst
--- 216,220 ----
  
      try:
!         opts, args= getopt.getopt(sys.argv[1:], '', ['surfing=', 'boost-info=','data=','spec=','labels=', 'iteration=', 'framerate=', 'booster=', 'sample'])
      except getopt.GetoptError, inst:
          print 'Received an illegal argument:', inst
***************
*** 218,231 ****
          sys.exit(2)
  
!     surffile = scoresfile = datafile = framerate = specfile = labelsfile = sample = iteration = booster = None
      for opt,arg in opts:
- 	    if (opt == '--surfing'):
- 		    surffile = arg
  	    if (opt == '--booster'):
  		    booster = arg
  	    if (opt == '--framerate'):
  		    framerate = int(arg)
! 	    if (opt == '--scores'):
! 		    scoresfile = arg
  	    if (opt == '--spec'):
  		    specfile = arg
--- 222,233 ----
          sys.exit(2)
  
!     boostfile = datafile = framerate = specfile = labelsfile = sample = iteration = booster = None
      for opt,arg in opts:
  	    if (opt == '--booster'):
  		    booster = arg
  	    if (opt == '--framerate'):
  		    framerate = int(arg)
! 	    if (opt == '--boost-info'):
! 		    boostfile = arg
  	    if (opt == '--spec'):
  		    specfile = arg
***************
*** 236,241 ****
  	
  
!     if(surffile == None or scoresfile == None or datafile == None or specfile == None):
! 	    print 'Need score, data, and spec file.'
  	    usage()
  	    sys.exit(2)
--- 238,243 ----
  	
  
!     if(boostfile == None or datafile == None or specfile == None):
! 	    print 'Need boosting.info, data, and spec file.'
  	    usage()
  	    sys.exit(2)
***************
*** 244,277 ****
  	    usage()
  	    sys.exit(2)
!     if(booster==None or (booster!='normal' and booster!='brown')):
! 	    print 'Only accepts `normal` and `brown` boost.'
  	    usage()
  	    sys.exit(2)
  	    
!     print 'Reading surfing file'
!     f= open(surffile,'r')
      data= f.readlines()
      f.close()
!     num_elements= int((string.split(data[0],'='))[2])
!     num_iterations = int(string.split(string.split(data[-num_elements-2], ',')[0], '=')[1])
  
!     os.system('rm surfing*.eps surfing*.png')
  
      for iter in range(0, num_iterations+1, framerate):
! 	    if (booster=='brown'):
! 		    total_time = string.split(data[iter*(num_elements+2)+1], ' ')[2]
! 		    time_left  = string.split(data[iter*(num_elements+2)+1], ' ')[3]
! 		    params = ('brown', total_time, time_left)
! 	    if (booster=='normal'):
! 		    total_time = string.split(data[iter*(num_elements+2)+1], ' ')[2]
! 		    time_left  = string.split(data[iter*(num_elements+2)+1], ' ')[3]
! 		    c1 = 1.818
! 		    c2 = 1
! 		    theta = 0.1
! 		    #c1  = string.split(data[iter*(num_elements+2)+1], ' ')[4]
! 		    #c2  = string.split(data[iter*(num_elements+2)+1], ' ')[5]
! 		    #theta  = string.split(data[iter*(num_elements+2)+1], ' ')[6]
! 		    params = ('normal', total_time, time_left, c1, c2, theta)
! 	    lines = [x   for x in data[iter*(num_elements+2)+2:(iter+1)*(num_elements+2)]]
  	    write_gnuplot(lines, iter, datafile, params)
  
--- 246,289 ----
  	    usage()
  	    sys.exit(2)
!     if(booster==None or (booster!='NormalBoost' and booster!='BrownBoost')):
! 	    print 'Only accepts `NormalBoost` and `BrownBoost` boost.'
  	    usage()
  	    sys.exit(2)
  	    
!     print 'Reading boosting.info file'
!     f= open(boostfile,'r')
      data= f.readlines()
      f.close()
!     num_elements= int((string.split(data[0],SEPARATOR)[1].split('=')[1]))
!     num_iterations = int(string.split(string.split(data[-num_elements-1], SEPARATOR)[0], '=')[1])
  
!     #os.system('rm surfing*.eps surfing*.png')
  
      for iter in range(0, num_iterations+1, framerate):
! 	    boost_params_str = string.split(data[iter*(num_elements+1)], SEPARATOR)[2].split('boosting_params=')[1]
! 	    if (booster=='BrownBoost'):
! 		    search_str = 'r='
! 		    total_time = boost_params_str[boost_params_str.index(search_str)+2 :].split(' ')[0]
! 		    search_str = 's='
! 		    time_left = boost_params_str[boost_params_str.index(search_str)+2 :].split(' ')[0]
! 		    params = ('BrownBoost', total_time, time_left)
! 	    if (booster=='NormalBoost'):
! 		    search_str = 'c='
! 		    total_time = boost_params_str[boost_params_str.index(search_str)+2 :].split(' ')[0]
! 		    search_str = 's='
! 		    time_left = boost_params_str[boost_params_str.index(search_str)+2 :].split(' ')[0]
! 		    search_str = 'c1='
! 		    c1 = boost_params_str[boost_params_str.index(search_str)+len(search_str) :].split(' ')[0]
! 		    search_str = 'c2='
! 		    c2 = boost_params_str[boost_params_str.index(search_str)+len(search_str) :].split(' ')[0]
! 		    search_str = 'theta='
! 		    theta = boost_params_str[boost_params_str.index(search_str)+len(search_str) :].split(' ')[0]
! 		    search_str = 'confidence='
! 		    confidence = boost_params_str[boost_params_str.index(search_str)+len(search_str) :].split(' ')[0]
! 		    use_conf = False
! 		    if confidence == 'true' or confidence == 'True' or confidence == '1':
! 			    use_conf = True
! 		    params = ('NormalBoost', total_time, time_left, c1, c2, theta, use_conf)
! 	    lines = [x   for x in data[iter*(num_elements+1)+1:(iter+1)*(num_elements+1)]]
  	    write_gnuplot(lines, iter, datafile, params)
  

Index: error.py
===================================================================
RCS file: /cvsroot/jboost/jboost/scripts/error.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** error.py	19 May 2007 01:57:56 -0000	1.3
--- error.py	23 Oct 2007 22:50:42 -0000	1.4
***************
*** 11,14 ****
--- 11,37 ----
  	print '\t--logaxis           should the axis be log-scaled (default: false)'
  	print '\t--bound             show the bound on training error'
+ 	print '\t--separate          separate the positive and negative examples'
+ 	print '\t--scores=score_file the score file (only needed if --separate used)'
+ 	print '\t--margins=marg_file the margin file (only needed if --separate used)'
+ 
+ def do_separate(score_filename, margin_filename):
+ 	print 'Parsing scores file'
+ 	f = open(score_filename,'r')
+ 	lines = f.readlines()
+ 	f.close()
+ 	
+ 	read_iter = False
+ 	data = []
+ 	for line in lines:
+ 		line = line.strip()
+ 		if (line[:8] =='End time'):
+ 			break
+ 		if (read_iter):
+ 			data.append(get_score(line))
+ 			
+ 
+     
+ 
+ 
  
  def main():
***************
*** 16,29 ****
  
      try:
! 	    opts, args= getopt.getopt(sys.argv[1:], '', ['info=','logaxis','bound'])
      except getopt.GetoptError:
  	    usage()
  	    sys.exit(2)
  	    
!     infofilename = logaxis = showbound = None
      for opt,arg in opts:
  	    if (opt == '--info'):
! 		    infofilename = arg
! 	    elif (opt == '--logaxis'):
  		    logaxis = True
  	    elif (opt == '--bound'):
--- 39,58 ----
  
      try:
! 	    opts, args= getopt.getopt(sys.argv[1:], '', ['info=','logaxis','bound','separate','scores=','margins='])
      except getopt.GetoptError:
  	    usage()
  	    sys.exit(2)
  	    
!     info_filename = logaxis = showbound = show_separate = margin_filename = score_filename = None
      for opt,arg in opts:
  	    if (opt == '--info'):
! 		    info_filename = arg
! 	    if (opt == '--margins'):
! 		    margin_filename = arg
! 	    if (opt == '--info'):
! 		    score_filename = arg
! 	    if (opt == '--separate'):
! 		    show_separate = True
! 	    if (opt == '--logaxis'):
  		    logaxis = True
  	    elif (opt == '--bound'):
***************
*** 31,44 ****
  	
  
!     if(infofilename == None):
! 	usage()
! 	sys.exit(2)
  
!     print 'Reading info file'
!     f = open(infofilename,'r')
      lines = f.readlines()
      f.close()
  
!     def get_data(line):
  	    list = line.split('\t')
  	    ret = {}
--- 60,80 ----
  	
  
!     if (show_separate and (margin_filename==None or score_filename==None)):
! 	    print 'ERROR: Need to specify score and margin file if showing positive and negative elements separately'
! 	    usage()
! 	    sys.exit(2)	    
! 	    
!     if(info_filename == None):
! 	    print 'ERROR: Need to specify info file'
! 	    usage()
! 	    sys.exit(2)
  
!     print 'Parsing info file'
!     f = open(info_filename,'r')
      lines = f.readlines()
      f.close()
  
! 
!     def get_info_data(line):
  	    list = line.split('\t')
  	    ret = {}
***************
*** 49,52 ****
--- 85,89 ----
  	    return ret
  
+ 
      read_iter = False
      data = []
***************
*** 57,61 ****
  		    break
  	    if (read_iter):
! 		    data.append(get_data(line))
  	    if (line=='iter \tbound \ttrain \ttest'):
  		    read_iter = True
--- 94,98 ----
  		    break
  	    if (read_iter):
! 		    data.append(get_info_data(line))
  	    if (line=='iter \tbound \ttrain \ttest'):
  		    read_iter = True
***************
*** 81,85 ****
      outlines.append('set xlabel "Iteration"\n')
      outlines.append('set ylabel "Error"\n')
!     outlines.append('set title "' + infofilename + ' Error"\n')
      if (logaxis):
  	    outlines.append('set logscale x 10\n')
--- 118,122 ----
      outlines.append('set xlabel "Iteration"\n')
      outlines.append('set ylabel "Error"\n')
!     outlines.append('set title "' + info_filename + ' Error"\n')
      if (logaxis):
  	    outlines.append('set logscale x 10\n')
***************
*** 92,100 ****
      outlines.append(out)
  
! 
!     f = open('error.gnuplot', 'w')
      f.writelines(outlines)
      f.close()
  
  if __name__ == "__main__":
      main()
--- 129,149 ----
      outlines.append(out)
  
!     pngfilename = 'error.gnuplot'
!     f = open(pngfilename, 'w')
      f.writelines(outlines)
      f.close()
  
+     os.system('gnuplot ' + pngfilename)
+ 
+ #####################################
+     #    Now do scores file for separate option
+ #####################################
+     
+     if show_separate:
+ 	    do_separate()
+ 
+ 
+ 
+ 
  if __name__ == "__main__":
      main()