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csv_plush_genome_sizes.py
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csv_plush_genome_sizes.py
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#import math
import os
#import sys
# Set these before running:
csv_format = "wide" # Can be wide or long
######## For GPTP Plush Paper
dirs = [("Replace Space With Newline", "Results/bench-prog-synth/replace-space-with-newline/parent-selection/lexicase/"),
("Syllables", "Results/bench-prog-synth/syllables/parent-selection/lexicase/"),
("Negative To Zero", "Results/bench-prog-synth/negative-to-zero/parent-selection/lexicase/"),
("X-Word Lines", "Results/bench-prog-synth/x-word-lines/parent-selection/lexicase/"),
("Count Odds", "Results/bench-prog-synth/count-odds/parent-selection/lexicase/")]
######## For dissertation
#dirs = [("lexicase", "Results/bench-prog-synth/replace-space-with-newline/parent-selection/lexicase/"),
# ("tourney7", "Results/bench-prog-synth/replace-space-with-newline/parent-selection/tourney-7/"),
# ("ifs7", "Results/bench-prog-synth/replace-space-with-newline/parent-selection/ifs-7/")]
# dirs = [("lexicase", "Results/bench-prog-synth/mirror-image/parent-selection/lexicase/"),
# ("tourney7", "Results/bench-prog-synth/mirror-image/parent-selection/tourney-7/"),
# ("ifs7", "Results/bench-prog-synth/mirror-image/parent-selection/ifs-7/")]
######### Old
#dir1 = "Results/GECCO13/bio-normal/"
#dir2 = "Results/GECCO13/bio-45/"
#dir3 = "Results/GECCO13/bio-ultra/"
#dir4 = "Results/equal-size-ULTRA/bio/"
#dir1 = "Results/GECCO13/pagie-no-erc-normal/"
#dir2 = "Results/GECCO13/pagie-hogeweg-no-erc-45/"
#dir3 = "Results/GECCO13/pagie-no-erc-ultra/"
#dir4 = "Results/equal-size-ULTRA/pagie-no-erc/"
#dir1 = "Results/GECCO13/mux6-normal/"
#dir2 = "Results/GECCO13/mux6-ultra/"
#dir4 = "Results/equal-size-ULTRA/mux6/"
#dir1 = "Results/GECCO13/factorial-normal/"
#dir2 = "Results/GECCO13/factorial-ultra/"
#dir3 = "Results/GECCO13/factorial-ultra-large/"
#dir1 = "Results/GECCO13/factorial-normal-500gens/"
#dir2 = "Results/GECCO13/factorial-ultra-500gens/"
#dir4 = "Results/equal-size-ULTRA/factorial/"
# dir1 = "Results/gecco13/DM/mom2-lex-ultra"
# dir2 = "Results/plush-testing/dm2-ultra-lex/"
# dir3 = "Results/plush-testing/dm2-zero-align-dev/"
# dir4 = "Results/plush-testing/dm2-noops/"
# prefix1 = "log"
# prefix2 = "bio-normallog"
#dirs = [("Normal", dir1, prefix1),
# ("Normal_45", dir2, prefix1),
# ("ULTRA", dir3, prefix1),
# ("ULTRA-Equal-Sizes", dir4, prefix1)]
# dirs = [("Push", dir1, prefix1),
# ("Plush", dir2, prefix1),
# ("PlushNoops", dir4, prefix1),
# ("PlushNoAlignDev", dir3, prefix1)]
outputFileSuffix = ".txt"
def my_mean(list_of_nums):
if len(list_of_nums) == 0:
return 0.0
return float(sum(list_of_nums)) / float(len(list_of_nums))
def getProgramSizes(outputDirectory, outputFilePrefix):
global max_gen
i = 0
if outputDirectory[-1] != '/':
outputDirectory += '/'
dirList = os.listdir(outputDirectory)
max_generations = 0
sizes_per_gen = []
while (outputFilePrefix + str(i) + outputFileSuffix) in dirList:
fileName = (outputFilePrefix + str(i) + outputFileSuffix)
f = open(outputDirectory + fileName)
gen = 0
mean_size = 0
for line in f:
if i == 0:
if line.startswith("max-generations"):
max_generations = int(line.split()[-1])
max_gen = max_generations
sizes_per_gen = [[] for x in range(max_generations + 1)]
if line.startswith(";; -*- Report"):
gen = int(line.split()[-1])
if line.startswith("Average genome size in population (length)"):
mean_size = float(line.split()[-1])
sizes_per_gen[gen].append(mean_size)
i += 1
return sizes_per_gen
if csv_format == "long":
print "Condition,Generation,MeanGenomeSize"
# for (condition, directory, prefix) in dirs:
# sizes = getProgramSizes(directory, prefix)
for (condition, directory) in dirs:
sizes = getProgramSizes(directory, "log")
for gen, gen_sizes in enumerate(sizes):
print "%s,%i,%f" % (condition, gen, my_mean(gen_sizes))
elif csv_format == "wide":
print "generation," + str([n for (n,d) in dirs]).replace(" ","").replace("]","").replace("[","").replace("'","")
dir_size_lists = [getProgramSizes(d, "log") for (n,d) in dirs]
# print "dir_size_lists = ", dir_size_lists
for g in range(max_gen+1):
out_str = str(g) + ","
for size_list in dir_size_lists:
try:
size = "%0.3f," % my_mean(size_list[g])
except:
size = ","
out_str += size
print out_str[:-1]
else:
print "Invalid csv_format:", csv_format