eluka 0.1.0

data/ext/libsvm/tools/grid.py

@@ -0,0 +1,359 @@
+#!/usr/bin/env python
+
+
+
+import os, sys, traceback
+import getpass
+from threading import Thread
+from subprocess import *
+
+if(sys.hexversion < 0x03000000):
+	import Queue
+else:
+	import queue as Queue
+
+
+# svmtrain and gnuplot executable
+
+is_win32 = (sys.platform == 'win32')
+if not is_win32:
+       svmtrain_exe = "../svm-train"
+       gnuplot_exe = "/usr/bin/gnuplot"
+else:
+       # example for windows
+       svmtrain_exe = r"..\windows\svm-train.exe"
+       gnuplot_exe = r"c:\tmp\gnuplot\bin\pgnuplot.exe"
+
+# global parameters and their default values
+
+fold = 5
+c_begin, c_end, c_step = -5,  15, 2
+g_begin, g_end, g_step =  3, -15, -2
+global dataset_pathname, dataset_title, pass_through_string
+global out_filename, png_filename
+
+# experimental
+
+telnet_workers = []
+ssh_workers = []
+nr_local_worker = 1
+
+# process command line options, set global parameters
+def process_options(argv=sys.argv):
+
+    global fold
+    global c_begin, c_end, c_step
+    global g_begin, g_end, g_step
+    global dataset_pathname, dataset_title, pass_through_string
+    global svmtrain_exe, gnuplot_exe, gnuplot, out_filename, png_filename
+    
+    usage = """\
+Usage: grid.py [-log2c begin,end,step] [-log2g begin,end,step] [-v fold] 
+[-svmtrain pathname] [-gnuplot pathname] [-out pathname] [-png pathname]
+[additional parameters for svm-train] dataset"""
+
+    if len(argv) < 2:
+        print(usage)
+        sys.exit(1)
+
+    dataset_pathname = argv[-1]
+    dataset_title = os.path.split(dataset_pathname)[1]
+    out_filename = '%s.out' % dataset_title
+    png_filename = '%s.png' % dataset_title
+    pass_through_options = []
+
+    i = 1
+    while i < len(argv) - 1:
+        if argv[i] == "-log2c":
+            i = i + 1
+            (c_begin,c_end,c_step) = map(float,argv[i].split(","))
+        elif argv[i] == "-log2g":
+            i = i + 1
+            (g_begin,g_end,g_step) = map(float,argv[i].split(","))
+        elif argv[i] == "-v":
+            i = i + 1
+            fold = argv[i]
+        elif argv[i] in ('-c','-g'):
+            print("Option -c and -g are renamed.")
+            print(usage)
+            sys.exit(1)
+        elif argv[i] == '-svmtrain':
+            i = i + 1
+            svmtrain_exe = argv[i]
+        elif argv[i] == '-gnuplot':
+            i = i + 1
+            gnuplot_exe = argv[i]
+        elif argv[i] == '-out':
+            i = i + 1
+            out_filename = argv[i]
+        elif argv[i] == '-png':
+            i = i + 1
+            png_filename = argv[i]
+        else:
+            pass_through_options.append(argv[i])
+        i = i + 1
+
+    pass_through_string = " ".join(pass_through_options)
+    assert os.path.exists(svmtrain_exe),"svm-train executable not found"    
+    assert os.path.exists(gnuplot_exe),"gnuplot executable not found"
+    assert os.path.exists(dataset_pathname),"dataset not found"
+    gnuplot = Popen(gnuplot_exe,stdin = PIPE).stdin
+
+
+def range_f(begin,end,step):
+    # like range, but works on non-integer too
+    seq = []
+    while True:
+        if step > 0 and begin > end: break
+        if step < 0 and begin < end: break
+        seq.append(begin)
+        begin = begin + step
+    return seq
+
+def permute_sequence(seq):
+    n = len(seq)
+    if n <= 1: return seq
+
+    mid = int(n/2)
+    left = permute_sequence(seq[:mid])
+    right = permute_sequence(seq[mid+1:])
+
+    ret = [seq[mid]]
+    while left or right:
+        if left: ret.append(left.pop(0))
+        if right: ret.append(right.pop(0))
+
+    return ret
+
+def redraw(db,best_param,tofile=False):
+    if len(db) == 0: return
+    begin_level = round(max(x[2] for x in db)) - 3
+    step_size = 0.5
+
+    best_log2c,best_log2g,best_rate = best_param
+
+    if tofile:
+        gnuplot.write( "set term png transparent small\n".encode())
+        gnuplot.write( ("set output \"%s\"\n" % png_filename.replace('\\','\\\\')).encode())
+        #gnuplot.write("set term postscript color solid\n".encode())
+        #gnuplot.write(("set output \"%s.ps\"\n" % dataset_title).encode())
+    elif is_win32:
+        gnuplot.write("set term windows\n".encode())
+    else:
+        gnuplot.write( "set term x11\n".encode())
+    gnuplot.write("set xlabel \"log2(C)\"\n".encode())
+    gnuplot.write("set ylabel \"log2(gamma)\"\n".encode())
+    gnuplot.write(("set xrange [%s:%s]\n" % (c_begin,c_end)).encode())
+    gnuplot.write(("set yrange [%s:%s]\n" % (g_begin,g_end)).encode())
+    gnuplot.write("set contour\n".encode())
+    gnuplot.write(("set cntrparam levels incremental %s,%s,100\n" % (begin_level,step_size)).encode())
+    gnuplot.write("unset surface\n".encode())
+    gnuplot.write("unset ztics\n".encode())
+    gnuplot.write("set view 0,0\n".encode())
+    gnuplot.write(("set title \"%s\"\n" % dataset_title).encode())
+    gnuplot.write("unset label\n".encode())
+    gnuplot.write(("set label \"Best log2(C) = %s  log2(gamma) = %s  accuracy = %s%%\" \
+                  at screen 0.5,0.85 center\n" % \
+                  (best_log2c, best_log2g, best_rate)).encode())
+    gnuplot.write(("set label \"C = %s  gamma = %s\""
+                  " at screen 0.5,0.8 center\n" % (2**best_log2c, 2**best_log2g)).encode())
+    gnuplot.write("splot \"-\" with lines\n".encode())
+    
+
+
+    
+    db.sort(key = lambda x:(x[0], -x[1]))
+
+    prevc = db[0][0]
+    for line in db:
+        if prevc != line[0]:
+            gnuplot.write("\n".encode())
+            prevc = line[0]
+        gnuplot.write(("%s %s %s\n" % line).encode())
+    gnuplot.write("e\n".encode())
+    gnuplot.write("\n".encode()) # force gnuplot back to prompt when term set failure
+    gnuplot.flush()
+
+
+def calculate_jobs():
+    c_seq = permute_sequence(range_f(c_begin,c_end,c_step))
+    g_seq = permute_sequence(range_f(g_begin,g_end,g_step))
+    nr_c = float(len(c_seq))
+    nr_g = float(len(g_seq))
+    i = 0
+    j = 0
+    jobs = []
+
+    while i < nr_c or j < nr_g:
+        if i/nr_c < j/nr_g:
+            # increase C resolution
+            line = []
+            for k in range(0,j):
+                line.append((c_seq[i],g_seq[k]))
+            i = i + 1
+            jobs.append(line)
+        else:
+            # increase g resolution
+            line = []
+            for k in range(0,i):
+                line.append((c_seq[k],g_seq[j]))
+            j = j + 1
+            jobs.append(line)
+    return jobs
+
+class WorkerStopToken:  # used to notify the worker to stop
+        pass
+
+class Worker(Thread):
+    def __init__(self,name,job_queue,result_queue):
+        Thread.__init__(self)
+        self.name = name
+        self.job_queue = job_queue
+        self.result_queue = result_queue
+    def run(self):
+        while True:
+            (cexp,gexp) = self.job_queue.get()
+            if cexp is WorkerStopToken:
+                self.job_queue.put((cexp,gexp))
+                # print 'worker %s stop.' % self.name
+                break
+            try:
+                rate = self.run_one(2.0**cexp,2.0**gexp)
+                if rate is None: raise RuntimeError("get no rate")
+            except:
+                # we failed, let others do that and we just quit
+            
+                traceback.print_exception(sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2])
+                
+                self.job_queue.put((cexp,gexp))
+                print('worker %s quit.' % self.name)
+                break
+            else:
+                self.result_queue.put((self.name,cexp,gexp,rate))
+
+class LocalWorker(Worker):
+    def run_one(self,c,g):
+        cmdline = '%s -c %s -g %s -v %s %s %s' % \
+          (svmtrain_exe,c,g,fold,pass_through_string,dataset_pathname)
+        result = Popen(cmdline,shell=True,stdout=PIPE).stdout
+        for line in result.readlines():
+            if str(line).find("Cross") != -1:
+                return float(line.split()[-1][0:-1])
+
+class SSHWorker(Worker):
+    def __init__(self,name,job_queue,result_queue,host):
+        Worker.__init__(self,name,job_queue,result_queue)
+        self.host = host
+        self.cwd = os.getcwd()
+    def run_one(self,c,g):
+        cmdline = 'ssh -x %s "cd %s; %s -c %s -g %s -v %s %s %s"' % \
+          (self.host,self.cwd,
+           svmtrain_exe,c,g,fold,pass_through_string,dataset_pathname)
+        result = Popen(cmdline,shell=True,stdout=PIPE).stdout
+        for line in result.readlines():
+            if str(line).find("Cross") != -1:
+                return float(line.split()[-1][0:-1])
+
+class TelnetWorker(Worker):
+    def __init__(self,name,job_queue,result_queue,host,username,password):
+        Worker.__init__(self,name,job_queue,result_queue)
+        self.host = host
+        self.username = username
+        self.password = password        
+    def run(self):
+        import telnetlib
+        self.tn = tn = telnetlib.Telnet(self.host)
+        tn.read_until("login: ")
+        tn.write(self.username + "\n")
+        tn.read_until("Password: ")
+        tn.write(self.password + "\n")
+
+        # XXX: how to know whether login is successful?
+        tn.read_until(self.username)
+        # 
+        print('login ok', self.host)
+        tn.write("cd "+os.getcwd()+"\n")
+        Worker.run(self)
+        tn.write("exit\n")               
+    def run_one(self,c,g):
+        cmdline = '%s -c %s -g %s -v %s %s %s' % \
+          (svmtrain_exe,c,g,fold,pass_through_string,dataset_pathname)
+        result = self.tn.write(cmdline+'\n')
+        (idx,matchm,output) = self.tn.expect(['Cross.*\n'])
+        for line in output.split('\n'):
+            if str(line).find("Cross") != -1:
+                return float(line.split()[-1][0:-1])
+
+def main():
+
+    # set parameters
+
+    process_options()
+
+    # put jobs in queue
+
+    jobs = calculate_jobs()
+    job_queue = Queue.Queue(0)
+    result_queue = Queue.Queue(0)
+
+    for line in jobs:
+        for (c,g) in line:
+            job_queue.put((c,g))
+
+    job_queue._put = job_queue.queue.appendleft
+
+
+    # fire telnet workers
+
+    if telnet_workers:
+        nr_telnet_worker = len(telnet_workers)
+        username = getpass.getuser()
+        password = getpass.getpass()
+        for host in telnet_workers:
+            TelnetWorker(host,job_queue,result_queue,
+                     host,username,password).start()
+
+    # fire ssh workers
+
+    if ssh_workers:
+        for host in ssh_workers:
+            SSHWorker(host,job_queue,result_queue,host).start()
+
+    # fire local workers
+
+    for i in range(nr_local_worker):
+        LocalWorker('local',job_queue,result_queue).start()
+
+    # gather results
+
+    done_jobs = {}
+
+
+    result_file = open(out_filename, 'w')
+
+
+    db = []
+    best_rate = -1
+    best_c1,best_g1 = None,None
+
+    for line in jobs:
+        for (c,g) in line:
+            while (c, g) not in done_jobs:
+                (worker,c1,g1,rate) = result_queue.get()
+                done_jobs[(c1,g1)] = rate
+                result_file.write('%s %s %s\n' %(c1,g1,rate))
+                result_file.flush()
+                if (rate > best_rate) or (rate==best_rate and g1==best_g1 and c1<best_c1):
+                    best_rate = rate
+                    best_c1,best_g1=c1,g1
+                    best_c = 2.0**c1
+                    best_g = 2.0**g1
+                print("[%s] %s %s %s (best c=%s, g=%s, rate=%s)" % \
+		    (worker,c1,g1,rate, best_c, best_g, best_rate))
+            db.append((c,g,done_jobs[(c,g)]))
+        redraw(db,[best_c1, best_g1, best_rate])
+        redraw(db,[best_c1, best_g1, best_rate],True)
+
+    job_queue.put((WorkerStopToken,None))
+    print("%s %s %s" % (best_c, best_g, best_rate))
+main()

data/ext/libsvm/tools/subset.py

@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+from sys import argv, exit, stdout, stderr
+from random import randint
+
+method = 0
+global n
+global dataset_filename
+subset_filename = ""
+rest_filename = ""
+
+def exit_with_help():
+	print("""\
+Usage: %s [options] dataset number [output1] [output2]
+
+This script selects a subset of the given dataset.
+
+options:
+-s method : method of selection (default 0)
+     0 -- stratified selection (classification only)
+     1 -- random selection
+
+output1 : the subset (optional)
+output2 : rest of the data (optional)
+If output1 is omitted, the subset will be printed on the screen.""" % argv[0])
+	exit(1)
+
+def process_options():
+	global method, n
+	global dataset_filename, subset_filename, rest_filename
+	
+	argc = len(argv)
+	if argc < 3:
+		exit_with_help()
+
+	i = 1
+	while i < len(argv):
+		if argv[i][0] != "-":
+			break
+		if argv[i] == "-s":
+			i = i + 1
+			method = int(argv[i])
+			if method < 0 or method > 1:
+				print("Unknown selection method %d" % (method))
+				exit_with_help()
+		i = i + 1
+
+	dataset_filename = argv[i]
+	n = int(argv[i+1])
+	if i+2 < argc:
+		subset_filename = argv[i+2]
+	if i+3 < argc:
+		rest_filename = argv[i+3]
+
+def main():
+	class Label:
+		def __init__(self, label, index, selected):
+			self.label = label
+			self.index = index
+			self.selected = selected
+
+	process_options()
+	
+	# get labels
+	i = 0
+	labels = []
+	f = open(dataset_filename, 'r')
+	for line in f:
+		labels.append(Label(float((line.split())[0]), i, 0))
+		i = i + 1
+	f.close()
+	l = i
+	
+	# determine where to output
+	if subset_filename != "":
+		file1 = open(subset_filename, 'w')
+	else:
+		file1 = stdout
+	split = 0
+	if rest_filename != "":
+		split = 1	
+		file2 = open(rest_filename, 'w')
+	
+	# select the subset
+	warning = 0
+	if method == 0: # stratified
+		labels.sort(key = lambda x: x.label)
+		
+		label_end = labels[l-1].label + 1
+		labels.append(Label(label_end, l, 0))
+
+		begin = 0
+		label = labels[begin].label
+		for i in range(l+1):
+			new_label = labels[i].label
+			if new_label != label:
+				nr_class = i - begin
+				k = i*n//l - begin*n//l
+				# at least one instance per class
+				if k == 0:
+					k = 1
+					warning = warning + 1
+				for j in range(nr_class):
+					if randint(0, nr_class-j-1) < k:
+						labels[begin+j].selected = 1
+						k = k - 1
+				begin = i
+				label = new_label
+	elif method == 1: # random
+		k = n
+		for i in range(l):
+			if randint(0,l-i-1) < k:
+				labels[i].selected = 1
+				k = k - 1
+			i = i + 1
+
+	# output
+	i = 0
+	if method == 0:
+		labels.sort(key = lambda x: int(x.index))
+	
+	f = open(dataset_filename, 'r')
+	for line in f:
+		if labels[i].selected == 1:
+			file1.write(line)
+		else:
+			if split == 1:
+				file2.write(line)
+		i = i + 1
+
+	if warning > 0:
+		stderr.write("""\
+Warning:
+1. You may have regression data. Please use -s 1.
+2. Classification data unbalanced or too small. We select at least 1 per class.
+   The subset thus contains %d instances.
+""" % (n+warning))
+
+	# cleanup
+	f.close()
+	
+	file1.close()
+	
+	if split == 1:
+		file2.close()
+
+main()