Counter

#imports for program to work

#increases functionality with directories
import glob
#manipulate different runtime environments
import sys
#provides expression patterns (something to do with strings)
import re
#working with files and other operating system functions
import os
#binary data to python strings/numbers
import struct
#access to mathematical functions
import math
#html functionality
import cgi
#exception handling (catches and reports back)
import cgitb
#file writing
import itertools

files = ["raw.txt"]

#=================================================================

if __name__ == "__main__":
    # Program starts here

    #test program starts
    print "This works."

    #create output file
    outputFile = open('HitOut.txt', "w")
    #save name
    pathname = "raw.txt"
    print pathname
    #read file and save to 'text'
    f = open(pathname, 'r')
    text = f.read()
    f.close()
    #list hits
    hits = []
    #saves rows
    rows = text.splitlines()

    #properties for hits
    x_list = []
    y_list = []
    used = []

    #i is row ID
    i = 0
    #couner for ID
    count = 0
    #loops through all rows
    for row in rows:
        #print i, row
        vals = row.split(' ')
        #j is column ID
        j = 0
        #loops through all values
        for val in vals:
            #if holds val other than 0
            if val != '0':
                #saves location and val
                hit = '#' + repr(count) + '#' + repr(i) + ':' + repr(j) + ':' + repr(val)
                x_list.append(i)
                y_list.append(j)
                used.append('no')
                hits.append(hit)
                count += 1
        #print i,j, val
        #increase coords
            j += 1
        i += 1

    #count for writing all hits
    n = 0
    m = len(hits)
    m += 1

    #loops through all hits and writes
    while (n < m-1):
        outputFile.write(hits[n])
        n += 1

    #close file
    outputFile.close()

    #=================================================================================
    ##Clusters

    #create output file for clusters
    outputFile = open('Cluster_ID.txt', "w")

    #var for loop
    count2 = 0
    count3 = 0
    x = 0
    y = 0

    #clusters
    cluster = []
    identify = []
    new = 0

    #loops for each hit to identify clusters
    while count2 < count + 1
        #check not already in cluster
        if used[count2] = 'no'
        cluster.append(new)
        identify.append(count2)
            #compares all hits against
            while count3 < count + 1
                #skips current selection
                if count3 != count2


            count3 += 1
        count2 += 1
        count3 = 0