aver_general.py

#!/usr/bin/python
# Arnfinn Hykkerud Steindal, Tromso Apr 2010; May 2012
# Read a file (-i FILENAME) and make an average of
# values in the first row (if not given as -r ROW).

import sys
import math
from optparse import OptionParser
import re

def aver(mylist):
    tot = 0.0
    for i in mylist:
        tot=tot+i
    return tot/len(mylist)

def f(x,y):
  return min(y-x, y-x+2*math.pi, y-x-2*math.pi, key=abs)

def degaver(mylist):
    sini = 0.0
    cosi = 0.0
    for i in mylist:
        sini = sini + math.sin(math.radians(i))
        cosi = cosi + math.cos(math.radians(i))
    val = math.degrees(math.atan2(sini/len(mylist),cosi/len(mylist)))
    if val<0:
        val = 360+val
    return val

def degstdev(mylist):
    ave=degaver(mylist)
    avecos=math.cos(math.radians(ave))
    avesin=math.sin(math.radians(ave))
    stancos = 0.0
    stansin = 0.0
    stan = 0.0
    for i in mylist:
        degdiff = math.degrees(f(math.radians(i),math.radians(ave)))
        stan = stan + degdiff*degdiff
    return math.sqrt(stan/(len(mylist)-1))

def stdev(mylist):
    ave = aver(mylist)
    stan=0.0
    for i in mylist:
        stan=stan+(i-ave)*(i-ave)
    return math.sqrt(stan/(len(mylist)-1))

def ev2nm(mylist):
    newlist=[]
    for i in mylist:
        newlist.append(1240.0/i)
    return newlist

parser = OptionParser()
parser.add_option("-i", "--input",dest="filename", help="the file to read")
parser.add_option("-r", "--row",type="int", dest="row",  default=1, help="The row where numbers are located")
parser.add_option("-d", "--decimals",type="int", dest="dec", default=4, help="Number of decimals in the printet numbers")
parser.add_option("-p", "--print",action="store_true", default=False, dest="printing", help="Print all the values")
parser.add_option("--ev2nm",action="store_true", default=False, dest="ev2nm", help="Convert from eV to nm before calculating average")
parser.add_option("--av2",action="store_true", default=False, dest="aver2", help="Calculate the average of numbers where two are weighted")
parser.add_option("--deg",action="store_true", default=False, dest="deg", help="Calculate the average of degrees (problem with numbers around zero)")
parser.add_option("--simple",action="store_true", default=False, dest="simple", help="Simple print layout (average stdev)")
parser.add_option("--avnum",type="int", dest="avernum", default=0,help="Calculate the average of the N first values")
(options, args) = parser.parse_args()
file = open(options.filename,'r')
row = options.row-1
dec = str(options.dec)
deg = options.deg

if options.avernum>0:
    lines = file.readlines()[0:options.avernum]
else:
    lines = file.readlines()
tab=[]

for line in lines:
    words = line.split()
    if options.aver2:
        oneex = float(re.sub("\D","",words[0].split(".")[0])+"."+re.sub("\D","",words[0].split(".")[1]))
        onetr = float(re.sub("\D","",words[1].split(".")[0])+"."+re.sub("\D","",words[1].split(".")[1]))
        twoex = float(re.sub("\D","",words[2].split(".")[0])+"."+re.sub("\D","",words[2].split(".")[1]))
        twotr = float(re.sub("\D","",words[3].split(".")[0])+"."+re.sub("\D","",words[3].split(".")[1]))
        ettall=str((oneex*onetr + twoex*twotr)/(onetr + twotr))
#        print "two "+ettall
    else:
        try:
            ettall = words[row]
        except:
            continue
    if "(" in ettall:
        ettall = ettall.replace("(","").replace(")","")
    try:
        test = float(ettall)
    except:
        # skip loop if ettall is not a number
        continue
    if float(ettall) < 0:
        # dirty fix! negative numbers became positive in the re.sub stuff
        ettall = float(ettall)
    else:
#        print "one " +ettall
        try:
            # the script did not eat 1.0e-4 kind of numbers
            ettall = float(ettall)
        except:
            if "." in ettall:
                ettall = float(re.sub("\D","",ettall.split(".")[0])+"."+re.sub("\D","",ettall.split(".")[1]))
#        ettall = float(re.sub("\D","",words[row].split(".")[0])+"."+re.sub("\D","",words[row].split(".")[1]))
            else:
                ettall = float(re.sub("\D","",ettall))
#        ettall = float(re.sub("\D","",words[row]))
    if options.printing:
        print ettall
    tab.append(ettall)


if options.ev2nm:
    tab = ev2nm(tab)

if deg:
    ave=degaver(tab)
    stan = degstdev(tab)
else:
    ave = aver(tab)
    stan = stdev(tab)

if options.simple:
    print str(ave) + "  " + str(stan)
else:
    print "Number of values = "+str(len(tab))
    string = "Average value = %."+dec+"f"
    print string % (ave)
    string = "Standard deviation = %."+dec+"f"
    print string % (stan)