pinfo_table.py

import csv
import sys
import os

import collections

filtered_csv = ""
filter_set_file = ""

all_files = []
file_set = None
counter = None

# bunch of misspelled versions of "personal"
personal_string = ["personal",
                   "prsonal",
                   "pwrsonal",
                   "persanal",
                   "personl",
                   "pursanal",
                   "pesonal",
                   "PI",
                   "p.i."]

personal_clans = []

personal_dictionary = []


def init_personalinfo_dictionary():
    for i in range(47):
        personal_dictionary.append(["npi"]*13)


def fill_list_of_personal_clans():

    with open(filtered_csv, "rU") as personal_comms:
        reader = csv.reader(personal_comms)
        reader.next()
        for row in reader:
            personal_clans.append(row[0])

def generate_nopersonalinfo_files():
    for file in set(personal_clans):
        prefix = file[0:5].split("_")
        #print "original: {}".format(prefix)
        prefix = [int(prefix[0]), prefix_to_array(prefix[1])]
        #print "new: {}".format(prefix)

        personal_dictionary[prefix[0]][prefix[1]] = "pi"
    with open(output_file, "wb") as table:
        writer = csv.writer(table)
        writer.writerow(["subject-visit", "06", "07", "08", "09", "10",
                         "11", "12", "13", "14", "15", "16", "17", "18"])
        for index, subject in enumerate(personal_dictionary[1:]):
            writer.writerow([index+1] + subject)


def fill_pidictionary_with_nofile():
    subj_prefix = ""
    visit_prefix = ""

    nofile_count = 0
    all_files = list_of_all_files()
    for i, subject in enumerate(personal_dictionary[1:]):
        #print "i: {}".format(i)
        for j, visit in enumerate(subject):
            if i <9:
                subj_prefix = '0'+str(i+1)
            else:
                subj_prefix = str(i+1)

            visit_prefix = str(array_to_prefix(j))

            prefix = subj_prefix+"_"+visit_prefix


            if not any(prefix in x for x in all_files):
                #print "prefix: {}".format(subj_prefix+"_"+visit_prefix)
                #print "no file"
                personal_dictionary[i+1][j] = "nf"
                nofile_count += 1

    #print "\n\nnofile_count: {}".format(nofile_count)


def prefix_to_array(prefix):
    if prefix == '06':
        return 0
    elif prefix == '07':
        return 1
    elif prefix == '08':
        return 2
    elif prefix == '09':
        return 3
    elif prefix == '10':
        return 4
    elif prefix == '11':
        return 5
    elif prefix == '12':
        return 6
    elif prefix == '13':
        return 7
    elif prefix == '14':
        return 8
    elif prefix == '15':
        return 9
    elif prefix == '16':
        return 10
    elif prefix == '17':
        return 11
    elif prefix == '18':
        return 12

def array_to_prefix(array):
    if array == 0:
        return '06'
    elif array == 1:
        return '07'
    elif array == 2:
        return '08'
    elif array == 3:
        return '09'
    elif array == 4:
        return '10'
    elif array == 5:
        return '11'
    elif array == 6:
        return '12'
    elif array == 7:
        return '13'
    elif array == 8:
        return '14'
    elif array == 9:
        return '15'
    elif array == 10:
        return '16'
    elif array == 11:
        return '17'
    elif array == 12:
        return '18'

def list_of_all_files():
    files = []
    with open(unfiltered_csv, "rU") as file:
        reader = csv.reader(file)
        reader.next()
        for row in reader:
            files.append(row[0])

    return list(set(files))


if __name__ == "__main__":

    unfiltered_csv = sys.argv[1]
    filtered_csv = sys.argv[2]
    output_file = sys.argv[3]
    all_files = list_of_all_files()


    fill_list_of_personal_clans()
    init_personalinfo_dictionary()

    fill_pidictionary_with_nofile()
    generate_nopersonalinfo_files()