Question

I am new to python and trying to get Kauffman’s NK model work in it…I found the code online and was hoping I could make some changes over time but I am not able to run the code…It is giving error on line 31…’f = open(options.in_filenames)’….I am sure I am missing something really small….any help would be appreciated…

import csv
from numpy import *
import Gnuplot
import time
from optparse import OptionParser
from pylab import *


# set up and read command line options


parser = OptionParser()
parser.add_option("-f", "--file", dest="in_filenames",
                  help="read data from FILE - enclose comma-separated file list in quotes e.g. \"FILE1, FILE2\"", metavar="FILE")


(options, args) = parser.parse_args()



# set up constants

# column titles
columnvar_titles = (["A", "N", "K"])
series_titles = (["Average Fitness", "Maximum Fitness","Minimum Fitness",
        "Average Wait Before Move","Maximum Wait Before Move",
        "Minimum Wait Before Move","Average Number of Fitter Neighbours",
        "Maximum Number of Fitter Neighbours",
        "Minimum Number of Fitter Neighbours"])


f = open(options.in_filenames)
reader = csv.reader(f)
floats = []
options_dict={}


# start from the first line in the file
# read lines until we hit a blank
# lines will be in form "Key: Value"
# so split them and build a dictionary
while (1):
    readstring = reader.next()
    if len(readstring)==0:
        break
    dict_entry = readstring[0].split(': ', 1)
    options_dict[dict_entry[0]] = dict_entry[1]
    #print readstring
    #print reader.line_num

#print options_dict
#print len(options_dict)

#print options_dict['Fitness_method']

# after the model parameters, we have blank line(s) before the data headers
# keep skipping blanks, then grab the first non-blank line
# then read the first line into a list of strings.
while (1):
    readstring = reader.next()
    if len(readstring) > 0:
        column_headers = readstring;
        break

#print column_headers

# need to check if we have a 'run' column
# single run gui output doesn't produce one, so need to add to column headers
# First six cols are "run, tick, A_size_of, RNGseed, [N & K]_size_of"
# "tick is already contained in the data, but is overwritten with K_size_of
# as it needs to be moved
# set add_run_data -  flag to insert corresponding columns into the numeric data
add_run_data = 0
if column_headers[0]!="run":
    column_headers[0] = "K_size_of"
    column_headers = ["run", "tick", "A_size_of", "RngSeed", "N_size_of"] + column_headers
    add_run_data = 1
    print "Processing one run GUI output format..."
else:
    print "Processing batch mode output..."

#print column_headers

# read lines from the data until we hit a blank.
# if data is numeric, put it into out 2d list of floats
countlines=0
while (1):
    try:
        readstring=reader.next()
        countlines = countlines + 1
        if len(readstring)==0:
            print "Stopped reading"
            break
        try:
            floats.append(map(float, readstring))
        except:
            print "Bad data - not adding"
    except StopIteration:
        #print "Read:", countlines
        break

print "Read", countlines, "lines of data from file"     

#print floats       
xdata=array(floats)
#print xdata
# if we needed to add column headers before, we are dealing with single run
# output. If so, we need to add columns at the left of the data. 
# First six cols are "run, tick, A_size_of, RNGseed, [N & K]_size_of"
# We add five (not six) cols, since "tick" is currently in the data already
# Other values are run = 1 (by def), RNGSeed (doesn't matter)
# A, N, K values are taken from the dictionary made from the header data in the file

if add_run_data == 1:
    newcol = ones((xdata.shape[0],5), dtype="float")
    xdata = concatenate((newcol, xdata), axis=1)
    A_val = float(options_dict['A_size_of'])
    N_val = float(options_dict['N_size_of'])
    K_val = float(options_dict['K_size_of'])
    #print A_val, N_val, K_val
    xdata[:,1] = xdata[:,5] # ticks - already there but needs to move
    xdata[:,2] = A_val
    xdata[:,3] = 0 #RNG seed doesn't matter
    xdata[:,4] = N_val
    xdata[:,5] = K_val #overwrites original tick column
    #print column_headers
    #print xdata[1]



A_uniques = unique(xdata[:,2])
N_uniques = unique(xdata[:,4])
K_uniques = unique(xdata[:,5])

series_total = len(A_uniques) * len(N_uniques) * len(K_uniques) 

# set up an array to hold averages (no columns for run number or rng seed)
# needs to move to handle multiple variables
maxticks = xdata[:,1].max()
#print series_total
#print maxticks
#print xdata.shape[1]-2
averages = zeros((series_total, maxticks, xdata.shape[1]-2), float)

# three loop setup for varying A / N / K values

series_counter = 0
Aseries_name=""
Nseries_name=""
Kseries_name=""
series_keys=[]

for A_value in A_uniques:
    if len(A_uniques)>1:
        Aseries_name = "A=" + str(A_value) + ", "
    dataA = compress(xdata[:,2]==A_value, xdata, axis=0)

    for N_value in N_uniques:
        #if len(N_uniques)>1:
        Nseries_name = "N=" + str(N_value) 
        dataAN = compress(dataA[:,4]==N_value, dataA, axis = 0)

        for K_value in K_uniques:
            #if len(K_uniques)>1:
            Kseries_name = ", " + "K=" + str(K_value)

            dataANK = compress(dataAN[:,5]==K_value, dataAN, axis = 0)

            series_keys.append(Aseries_name + Nseries_name + Kseries_name)



            # when multiple variables are used, run values continue to count from the
            # previous variable value (e.g. A=2 (runs 1-100) A=3 (runs 101-200))
            # we need to number the runs in ascending order from 1.
            firstrun=dataANK[:,0].min()
            lastrun=dataANK[:,0].max()
            totalruns = 1 + lastrun - firstrun

            #print firstrun, lastrun, totalruns

            # for each run, find the last actual tick data
            last_tick_array = zeros((totalruns, dataANK.shape[1]), float)
            #print last_tick_array.shape

            for k in arange(totalruns): # for each run get the data for the last tick
                this_run=compress(dataANK[:,0]==k+firstrun, dataANK, axis=0)
                last_tick_array[k]=this_run[-1]

            #print "Last tick array"

            #print last_tick_array[-1]

            print "Processing simulation " + str(series_counter+1) + "/" + str(series_total)
            for i in arange(maxticks):  # for each tick value up to the maximum
                # array to hold one tick from each run for averaging
                # will contain either actual or extrapolated data
                selected_ticks = zeros((totalruns, dataANK.shape[1]), float)
                #print selected_ticks
                # get dataANK for this tick from all runs. May be empty.
                this_tick = compress(dataANK[:,1]==i+1, dataANK, axis=0)
                #print "this tick"
                #print this_tick
                for j in arange(totalruns): # for each run
                    if (i+1) < last_tick_array[j,1]:# do we have actual data?
                        #print "Using real data"
                        # if so, get it
                        selected_ticks[j] = compress(this_tick[:,0]==j+firstrun, this_tick, axis=0)
                        #print selected_ticks
                    else:
                        # if not, use the last tick we do have
                        #print "Using last tick"
                        selected_ticks[j] = last_tick_array[j]
                #print "selected_ticks"
                #print selected_ticks[0]
                averages[series_counter][i][0]=i+1  # tick number
                averages[series_counter][i][1]=selected_ticks[:,2].max() #A_size_of
                averages[series_counter][i][2]=selected_ticks[:,4].min() #N_size_of
                averages[series_counter][i][3]=selected_ticks[:,5].min() #K_size_of
                for m in xrange(6,16):
                    #print m
                    averages[series_counter][i][m-2]=selected_ticks[:,m].mean()


            # increment to fill next index
            series_counter = series_counter + 1

# matplotlib plots

print "Plotting graphs..."

matplotlib.use('Agg')

for graph_num in (4,5,6,7,8,9,10,11,12,13):
    ylabel(column_headers[graph_num+2])



    for ser in range(series_total):
        plot(averages[ser][:,0], averages[ser][:,graph_num], label=series_keys[ser])

    legend(loc='center right').draw_frame(0)
    show()
    savefig('nk' + column_headers[graph_num+2] + '.png')
    clf()


print "Writing CSV files"

f1 = open("nk_allticks.csv","wt")
csv1 = csv.writer(f1)

f2 = open("nk_finaltick.csv","wt")
csv2 = csv.writer(f2)

column_headers.remove('RngSeed')

# replace spaces for underscores in column headers for better file compatability
for i in range(len(column_headers)):
    column_headers[i]=column_headers[i].replace(' ','_')


try:
    csv1.writerow(column_headers[1:])
    csv2.writerow(column_headers[1:])
    for series in range(series_total):
        csv1.writerows(averages[series])
        csv2.writerow(averages[series][-1])
finally:
    f1.close
    f2.close

f3 = open("nk_allticks_crosstab.csv","wt")
csv3 = csv.writer(f3)

out_array = zeros((averages[0].shape[0], 1 +(series_total * 10)), float)
out_array[:,0] = averages[0][:,0]

headers=[1000]#[8 * series_total]
headers[0]="tick"

datacol = 1
for column_num in (3, 4,5,6,7,8,9,10,11,12):
    for ser in range (series_total):
        headers.append((column_headers[column_num+2] + " " + series_keys[ser]).replace(' ','_'))
        out_array[:,datacol] = averages[ser][:,column_num+1]
        #print averages[ser][0]

        datacol  = datacol + 1


#print headers
#print out_array.shape

try:
    csv3.writerow(headers)
    csv3.writerows(out_array)
finally:
    f3.close    

Answer 1

You need to tell it which file to open. When you run the script you’d need to do something like –

python myscript.py -f myfile

Otherwise, you have not given it a file. Use the interpreter, it’s great for catching these things.

>>> from optparse import OptionParser
>>> parser = OptionParser()
>>> parser.add_option("-f", "--file", dest="in_filenames",
...                   help="read data from FILE - enclose comma-separated file list in quotes e.g. \"FILE1, FILE2\"", metavar="FILE")
<Option at 0x29f47c8: -f/--file>
>>> (options, args) = parser.parse_args()
>>> options # Notice that in_filenames is None here
<Values at 0x29f6648: {'in_filenames': None}>
>>> import sys
>>> sys.argv
['']
>>> sys.argv = ['','-f','myfile'] # Let's explicitly set the argument
>>> (options, args) = parser.parse_args()
>>> options # Now it works...
<Values at 0x29fd848: {'in_filenames': 'myfile'}>