mesh-rb 0.0.1 → 0.0.2

data/ext/mesh/mesh/theory/meshingBenchmark.py

@@ -1,96 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Feb 03 09:45:30 2017
-
-@author: devd
-"""
-
-from __future__ import division
-from createRandomString import *
-from makeGraph import *
-from meshers import *
-import networkx as nx
-import numpy as np
-import os
-
-
-def dumpStrings(strings, length, occupancy, numStrings, meshingMethod, result):
-    """Dumps the generated string set in a text file in a subdirectory."""
-    if length == 0:
-        file_name = 'provided,{}.txt'.format(meshingMethod)
-    else:
-        file_name = '{},{},{},{}.txt'.format(length, occupancy, numStrings, meshingMethod)
-        
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    dest_dir = os.path.join(script_dir, 'dumps')
-    try:
-        os.makedirs(dest_dir)
-    except OSError:
-        pass # already exists
-    path = os.path.join(dest_dir, file_name)
-    output = open(path, 'wb')
-    for s in strings:
-        output.write('{}\n'.format(s))
-    output.write('-{}'.format(result))
-    output.close
-
-
-def experiment(length = 0, occupancy = 0, numStrings = 0, meshingMethod = "dumb", attempts = 0, stringList = None):
-    """Produces a set of random binary strings with specified length and expected
-    occupancy.  Then meshes them using the specified meshing method and returns
-    the percentage of total pages freed.  Also dumps the generated string set
-    to a text file for comparison with other implementations.
-    
-    Meshing methods:
-    dumb = attempt to mesh string 1 w/ string 2 etc. 1 pass only.
-    random = attempt to mesh 2 randomly chosen strings.  specify total number of
-        allowed attempts.
-    maxMatching = converts string set to graph and computes the max matching of
-        graph.  This gives the optimal meshing assuming we only mesh pairs.
-    optimal = converts string set to the graph and computes the minimum clique
-        cover.  This gives the optimal meshing without the "pairs only" constraint.
-    """
-    
-    #note that occupancy is currently the number of ones expected per string, rather than a percentage.
-    if stringList == None:
-        if length == 0 or numStrings == 0:
-            raise Exception('must give a string list or specify length, occupancy, numStrings for generation')
-        strings = createIndependentRandomStrings(length, numStrings, numOnes = occupancy)
-    else:
-        strings = stringList
-    
-    if meshingMethod == "dumb":
-        result = simpleMesher(strings)
-        
-    elif meshingMethod == "random":
-        if attempts == 0:
-            raise Exception('must specify number of attempts for random method')
-        meshed = randomMesher(strings, attempts)
-        result = int(len(meshed)/2)
-        
-    elif meshingMethod == "maxMatching":
-        result = maxMatchingMesher(strings)
-        
-    elif meshingMethod == "optimal":
-        result = optimalMesher(strings)
-    
-    else:
-        print 'hi'
-        
-    dumpStrings(strings, length, occupancy, numStrings, meshingMethod, result)
-    
-
-
-if __name__ == '__main__':
-#    experiment(length = 10, occupancy = 3, numStrings = 10, meshingMethod = "random", attempts = 100)
-#    experiment(stringList = ['0000000000','1111111111','0101010101','1010101010'])
-
-    lengths = [32]
-    occupancies = range(1,10)
-    numsStrings = [80]
-    for i in lengths:
-        for j in occupancies:
-            for k in numsStrings:
-                experiment(length = i, occupancy = j, numStrings = k)
-    
-        

data/ext/mesh/mesh/theory/occupancyComparison.py

@@ -1,133 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Jan 31 19:49:02 2017
-
-@author: devd
-"""
-
-from __future__ import division
-from createRandomString import *
-from makeGraph import *
-#from greedyMesher import *
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
-import networkx as nx
-import numpy as np
-from compute_exp_Y import compute_exp_Y, compute_degree_bound, compute_isolated_edge_bound
-from choose import compute_q
-
-def experiment(length, ones_range_min, ones_range_max, reps, numStrings):
-    constant_strings = []
-    independent_strings = []
-    ones = []
-    constant_occupancy_avg = []
-    constant_occupancy_std_dev = []
-    indep_occupancy_avg = []
-    indep_occupancy_std_dev = []
-    qs = []
-    constant_edges = []
-    independent_edges = []
-    
-    for numOnes in range(ones_range_min, ones_range_max+1):
-        ones.append(numOnes)
-        q = compute_q(length, numOnes)
-        qs.append(q)
-        freed_pages_constant = []
-        freed_pages_independent = []
-        const_edges = []
-        indep_edges = []
-        for iterations in range (reps):
-            for i in range(numStrings):
-               constant_strings.append(createRandomString(length, numOnes))
-               
-            graph = makeGraph(constant_strings)
-            const_edges.append(graph.number_of_edges())
-            frdpgs_constant = len(nx.max_weight_matching(graph))/2
-            perc = (frdpgs_constant/numStrings)*100
-            freed_pages_constant.append(perc)
-            
-#include only q or numOnes by name to choose which version of indep random strings you want            
-#            independent_strings = createIndependentRandomStrings(length, numStrings, q, numOnes)
-            independent_strings = createIndependentRandomStrings(length, numStrings, numOnes = numOnes)
-            graph = makeGraph(independent_strings)
-            indep_edges.append(graph.number_of_edges())
-            frdpgs_indep = len(nx.max_weight_matching(graph))/2
-            perc = (frdpgs_indep/numStrings)*100
-            freed_pages_independent.append(perc)
-        
-            
-            constant_strings = []
-            independent_strings = []
-            
-        
-        m = np.asarray(freed_pages_constant)
-#        raw.append(freed_pages_constant)
-        m_a = np.mean(m)
-        constant_occupancy_avg.append(m_a)
-        m_s = np.std(m)
-        constant_occupancy_std_dev.append(m_s)
-        
-        m = np.asarray(const_edges)
-        constant_edges.append(np.mean(m))
-        
-        m = np.asarray(freed_pages_independent)
-#        raw.append(freed_pages_constant)
-        m_a = np.mean(m)
-        indep_occupancy_avg.append(m_a)
-        m_s = np.std(m)
-        indep_occupancy_std_dev.append(m_s)
-        
-        m = np.asarray(indep_edges)
-        independent_edges.append(np.mean(m))
-        
-    return ones, constant_occupancy_avg, constant_occupancy_std_dev, indep_occupancy_avg, indep_occupancy_std_dev, constant_edges, independent_edges, qs
-
-
-def plot_it(length, ones_range_min, ones_range_max, reps, numStrings):
-    ones, constant_occupancy_avg, constant_occupancy_std_dev, indep_occupancy_avg, indep_occupancy_std_dev, constant_edges, independent_edges, qs = experiment(length, ones_range_min, ones_range_max, reps, numStrings)
-    
-    plt.errorbar(np.asarray(ones), np.asarray(constant_occupancy_avg), np.asarray(constant_occupancy_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.errorbar(np.asarray(ones), np.asarray(indep_occupancy_avg), np.asarray(indep_occupancy_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.ylim([0,60])
-#    plt.xlim([10, 16])
-    plt.ylabel('Percentage of pages freed')
-    plt.xlabel('Number of objects per page')
-    blue_patch = mpatches.Patch(color='blue', label='const occupancy')
-    green_patch = mpatches.Patch(color = 'green', label = 'indep occupancy')
-#    red_patch = mpatches.Patch(color = 'red', label = 'q')
-    plt.legend(handles=[blue_patch, green_patch])
-#    plt.legend(handles=[blue_patch, green_patch, red_patch])
-    plt.title('CONSTANT VS INDEPENDENT OCCUPANCY \n{}-object pages, {} pages. p = n/b'.format(length, numStrings))
-    plt.show()
-#    plt.savefig('constvindep_{},{}'.format(length, numStrings) + '.png', dpi = 1000)
-    plt.close()
-    
-#    plt.errorbar(np.asarray(ones), np.asarray(constant_edges), np.asarray(np.zeros(len(ones))), markersize=3, lw=1, fmt='-o')
-#    plt.errorbar(np.asarray(ones), np.asarray(independent_edges), np.asarray(np.zeros(len(ones))), markersize=3, lw=1, fmt='-o')
-#    plt.show()
-        
-        
-if __name__ == '__main__':        
-    #length = [32,64]
-    length = [64]
-    ones_range_min = 1
-    ones_range_max = 32
-    reps = 10
-    #numStrings = [80,100,150,200]
-    numStrings= [80]
-    
-    
-    for l in length:
-        for n in numStrings:
-            plot_it(l, ones_range_min, int(l/2), reps, n)
-    #        plot_it(l, 10, 13, 10, n)
-            print 'const v indep plot {},{} done'.format(l,n)
-        
-        
-        
-        
-        
-        
-        
-        
-        

data/ext/mesh/mesh/theory/randmatch_vs_greedymatch.py

@@ -1,97 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Apr 15 17:21:40 2016
-
-@author: devd
-"""
-
-from __future__ import division
-from createRandomString import *
-from meshers import *
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
-import networkx as nx
-import numpy as np
-import time
-from math import log, floor, sqrt
-
-def experiment(length, ones_range_min, ones_range_max, reps, numStrings, attempts):
-    strings = []
-    ones = []
-    randmatch_avg = []
-    randmatch_std_dev = []
-    greedymatch_avg = []
-    greedymatch_std_dev = []
-
-    for numOnes in range(ones_range_min, ones_range_max+1):
-        ones.append(numOnes)
-        freed_pages_randmatching = []
-        freed_pages_greedymatching = []
-        for iterations in range (reps):
-            for i in range(numStrings):
-               strings.append(createRandomString(length, numOnes))
-               
-            s = [x for x in strings]
-            frdpgs_randmatching = len(randomMesher(s,attempts))/2
-            perc = (frdpgs_randmatching/numStrings)*100
-            freed_pages_randmatching.append(perc)
-            
-            b, unmatched = greedyMesher(strings)        
-            frdpgs_greedymatching = (numStrings - len(unmatched))/2
-            perc = (frdpgs_greedymatching/numStrings)*100
-            freed_pages_greedymatching.append(perc)
-            
-            strings = []
-        m = np.asarray(freed_pages_randmatching)
-        m_a = np.mean(m)
-        randmatch_avg.append(m_a)
-        m_s = np.std(m)
-        randmatch_std_dev.append(m_s)
-        
-        c = np.asarray(freed_pages_greedymatching)
-        c_a = np.mean(c)
-        greedymatch_avg.append(c_a)
-        c_s = np.std(c)
-        greedymatch_std_dev.append(c_s)
-        
-    return ones, randmatch_avg, randmatch_std_dev, greedymatch_avg, greedymatch_std_dev
-    
-    
-def plot_it(length, ones_range_min, ones_range_max, reps, numStrings, attempts):
-    ones, match_avg, match_std_dev, color_avg, color_std_dev = experiment(length, ones_range_min, ones_range_max, reps, numStrings, attempts)
-    
-    plt.errorbar(np.asarray(ones), np.asarray(match_avg), np.asarray(match_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.errorbar(np.asarray(ones), np.asarray(color_avg), np.asarray(color_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.ylim([0,60])
-    plt.ylabel('Percentage of pages freed')
-    plt.xlabel('Number of objects per page')
-    blue_patch = mpatches.Patch(color='blue', label='random matching')
-    green_patch = mpatches.Patch(color = 'green', label = 'greedy matching')
-    plt.legend(handles=[blue_patch, green_patch])
-    plt.title('RANDOM MATCHING VS GREEDY MATCHING MESHING RESULTS \n{}-object pages, {} pages, n^2 attempts'.format(length, numStrings))
-    plt.show()
-#    plt.savefig('randvgreedy{},{},n^2_attempts'.format(length, numStrings) + '.png', dpi = 1000)
-    plt.close()
-    
-#length = [32,64]
-length = [32]
-ones_range_min = 1
-ones_range_max = 32
-reps = 10
-#numStrings = [80,100,150,200]
-numStrings = [80]
-
-
-start = time.time()
-for l in length:
-    for n in numStrings:
-        #attempts = n
-        #attempts = int(floor(n*log(n,2)))
-        #attempts = int(floor(n*sqrt(n)))
-        #attempts = int(floor(n**1.75))
-        attempts = int(floor(n**2))
-        print 'num attempts: {}'.format(attempts)
-        plot_it(l, ones_range_min, int(l/2), reps, n, attempts)
-        print 'rand match vs greedy match plot {},{} done'.format(l,n)
-end = time.time()
-print('making this took {} seconds'.format(end-start) )

data/ext/mesh/mesh/theory/randmatch_vs_greedymatch_q.py

@@ -1,103 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Apr 15 17:21:40 2016
-
-@author: devd
-"""
-
-from __future__ import division
-from createRandomString import *
-from meshers import *
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
-import networkx as nx
-import numpy as np
-import time
-from math import log, floor, sqrt, factorial
-from choose import compute_q
-
-
-def experiment(length, ones_range_min, ones_range_max, reps, numStrings, attempts):
-    strings = []
-    ones = []
-    randmatch_avg = []
-    randmatch_std_dev = []
-    greedymatch_avg = []
-    greedymatch_std_dev = []
-
-    for numOnes in range(ones_range_min, ones_range_max+1):
-        ones.append(numOnes)
-        freed_pages_randmatching = []
-        freed_pages_greedymatching = []
-        for iterations in range (reps):
-            for i in range(numStrings):
-               strings.append(createRandomString(length, numOnes))
-               
-            s = [x for x in strings]
-            frdpgs_randmatching = len(randomMesher(s,attempts))/2
-            perc = (frdpgs_randmatching/numStrings)*100
-            freed_pages_randmatching.append(perc)
-            
-            b, unmatched = greedyMesher(strings)        
-            frdpgs_greedymatching = (numStrings - len(unmatched))/2
-            perc = (frdpgs_greedymatching/numStrings)*100
-            freed_pages_greedymatching.append(perc)
-            
-            strings = []
-        m = np.asarray(freed_pages_randmatching)
-        m_a = np.mean(m)
-        randmatch_avg.append(m_a)
-        m_s = np.std(m)
-        randmatch_std_dev.append(m_s)
-        
-        c = np.asarray(freed_pages_greedymatching)
-        c_a = np.mean(c)
-        greedymatch_avg.append(c_a)
-        c_s = np.std(c)
-        greedymatch_std_dev.append(c_s)
-        
-    return ones, randmatch_avg, randmatch_std_dev, greedymatch_avg, greedymatch_std_dev
-    
-    
-def plot_it(length, ones_range_min, ones_range_max, reps, numStrings, attempts):
-    ones, match_avg, match_std_dev, color_avg, color_std_dev = experiment(length, ones_range_min, ones_range_max, reps, numStrings, attempts)
-    
-    q = [compute_q(length, x) for x in ones]    
-    
-    
-    plt.errorbar(np.asarray(q), np.asarray(match_avg), np.asarray(match_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.errorbar(np.asarray(q), np.asarray(color_avg), np.asarray(color_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.ylim([0,60])
-#    plt.xlim([0,.2])
-    plt.ylabel('Percentage of pages freed')
-    plt.xlabel('q (probability of 2 pages meshing)')
-    blue_patch = mpatches.Patch(color='blue', label='random matching')
-    green_patch = mpatches.Patch(color = 'green', label = 'greedy matching')
-    plt.legend(handles=[blue_patch, green_patch],bbox_to_anchor=(1, .3))
-    plt.title('RANDOM MATCHING VS GREEDY MATCHING MESHING RESULTS \n{}-object pages, {} pages, n*log(n) attempts'.format(length, numStrings))
-    plt.show()
-#    plt.savefig('randvgreedy{},{},n^1.5_attempts'.format(length, numStrings) + '.png', dpi = 1000)
-    plt.close()
-    
-#length = [32,64]
-length = [32]
-ones_range_min = 1
-ones_range_max = 32
-reps = 10
-#numStrings = [80,100,150,200]
-numStrings = [80]
-
-
-start = time.time()
-for l in length:
-    for n in numStrings:
-        #attempts = n
-#        attempts = int(floor(n*log(n,2)))
-        attempts = int(floor(n*sqrt(n)))
-        #attempts = int(floor(n**1.75))
-        #attempts = int(floor(n**2))
-        print 'num attempts: {}'.format(attempts)
-        plot_it(l, ones_range_min, int(l/2), reps, n, attempts)
-        print 'rand match vs greedy match plot {},{} done'.format(l,n)
-end = time.time()
-print('making this took {} seconds'.format(end-start) )

data/ext/mesh/mesh/theory/randmatch_vs_greedymatch_time.py

@@ -1,117 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Apr 15 17:21:40 2016
-
-@author: devd
-"""
-
-from __future__ import division
-from createRandomString import *
-from meshers import *
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
-import networkx as nx
-import numpy as np
-import time
-from math import log, floor, sqrt
-
-def experiment(length, ones_range_min, ones_range_max, reps, numStrings, attempts):
-    strings = []
-    ones = []
-    randmatch_avg = []
-    randmatch_std_dev = []
-    greedymatch_avg = []
-    greedymatch_std_dev = []
-    rtimeavg = []
-    rtimestd = []
-    gtimeavg = []
-    gtimestd = []
-
-    for numOnes in range(ones_range_min, ones_range_max+1):
-        ones.append(numOnes)
-        freed_pages_randmatching = []
-        freed_pages_greedymatching = []
-        time_rand = []
-        time_greedy = []
-        for iterations in range (reps):
-            for i in range(numStrings):
-               strings.append(createRandomString(length, numOnes))
-            
-            
-            
-            
-            rstart = time.time()
-            
-            s = [x for x in strings]
-#            frdpgs_randmatching = len(randomMesher(s,attempts))/2
-            frdpgs_randmatching = randomMesher(s,attempts)
-            perc = (frdpgs_randmatching/numStrings)*100
-            freed_pages_randmatching.append(perc)
-            
-            rend = time.time()
-            time_rand.append(rend-rstart)
-            
-            gstart = time.time()
-            
-            b, unmatched = greedyMesher(strings)        
-            frdpgs_greedymatching = (numStrings - len(unmatched))/2
-            perc = (frdpgs_greedymatching/numStrings)*100
-            freed_pages_greedymatching.append(perc)
-            
-            gend = time.time()
-            time_greedy.append(gend-gstart)
-            
-            strings = []
-        m = np.asarray(time_rand)
-        m_a = np.mean(m)
-        randmatch_avg.append(m_a)
-        m_s = np.std(m)
-        randmatch_std_dev.append(m_s)
-        
-        c = np.asarray(time_greedy)
-        c_a = np.mean(c)
-        greedymatch_avg.append(c_a)
-        c_s = np.std(c)
-        greedymatch_std_dev.append(c_s)
-        
-    return ones, randmatch_avg, randmatch_std_dev, greedymatch_avg, greedymatch_std_dev
-    
-    
-def plot_it(length, ones_range_min, ones_range_max, reps, numStrings, attempts):
-    ones, match_avg, match_std_dev, color_avg, color_std_dev = experiment(length, ones_range_min, ones_range_max, reps, numStrings, attempts)
-    
-    plt.errorbar(np.asarray(ones), np.asarray(match_avg), np.asarray(match_std_dev), markersize=3, lw=1, fmt='-o')
-    plt.errorbar(np.asarray(ones), np.asarray(color_avg), np.asarray(color_std_dev), markersize=3, lw=1, fmt='-o')
-#    plt.ylim([0,60])
-    plt.ylabel('Time required to compute answer')
-    plt.xlabel('Number of objects per page')
-    blue_patch = mpatches.Patch(color='blue', label='random matching')
-    green_patch = mpatches.Patch(color = 'green', label = 'greedy matching')
-    plt.legend(handles=[blue_patch, green_patch])
-    plt.title('RANDOM MATCHING VS GREEDY MATCHING MESHING TIME REQUIREMENTS \n{}-object pages, {} pages, n^2 attempts'.format(length, numStrings))
-    plt.show()
-#    plt.savefig('randvgreedytime{},{},n^2_attempts'.format(length, numStrings) + '.png', dpi = 1000)
-    plt.close()
-    
-#length = [32,64]
-length = [32]
-ones_range_min = 1
-ones_range_max = 32
-reps = 10
-#numStrings = [80,100,150,200]
-numStrings = [80]
-
-
-start = time.time()
-for l in length:
-    for n in numStrings:
-        #attempts = n
-        #attempts = int(floor(n*log(n,2)))
-#        attempts = int(floor(n*sqrt(n)))
-        #attempts = int(floor(n**1.75))
-        attempts = int(floor(n**2))
-        print 'num attempts: {}'.format(attempts)
-        plot_it(l, ones_range_min, int(l/2), reps, n, attempts)
-        print 'rand match vs greedy match plot {},{} done'.format(l,n)
-end = time.time()
-print('making this took {} seconds'.format(end-start) )