How can I send data from a python script to Matplotlib?

Question

I am fairly new to programing and have a question regarding matplotlib. I wrote a python script that reads in data from the outfile of another program then prints out the data from one column.

f = open( '/home/student/AstroSimulation/out.0001.z0.753.AHF_halos','r')
for line in f:
    if line != ' ':
        line = line.strip()    # Strips end of line character 
        columns = line.split() # Splits into coloumn 
        mass = columns[8]      # Column which contains mass values 
        print(mass)

What I now need to do is have matplotlib take the values printed in 'mass' and plot number versus mean mass. I have read the documents on the matplotlib website, but they are don't really address how to get data from a script(or I just did not see it). If anyone can point me to some documentation that explains how I do this it would be really appreciated. Thank you

Answer 1

You will call matplotlib from within your script, so matplotlib will not "get data from a script" as such. You send it into matplotlib.

You will need to save the masses outside the loop however, but then, it's just a call to the plot() and show() functions in it's most basic form:

import matplotlib.pyplot as plt

masses = []

f = open( '/home/student/AstroSimulation/out.0001.z0.753.AHF_halos','r')
f.readline() # Remove header line
for line in f:
    if line != ' ':
        line = line.strip()    # Strips end of line character 
        columns = line.split() # Splits into coloumn 
        mass = columns[8]      # Column which contains mass values 
        masses.append(mass)
        print(mass)

# If neccessary, process masses in some way

plt.plot(masses)
plt.show()

Answer 2

I was with you right up to "plot the sum over the average". Perhaps you could link to an image that's like the plot you want to make.

In your current script where you print 'mass', you want to append to a list as floating point value:

from matplotlib import pyplot

DATAFILE = '/home/student/AstroSimulation/out.0001.z0.753.AHF_halos'
MASS_COL = 8

masses = []
with open(DATAFILE) as f:
    f_it = iter(f)                   #get an iterator for f
    next(f_it)                       #skip the first line
    for n, line in enumerate(f_it):  #now the for loop uses f_it 
        row = line.strip().split()
        if len(row) > MASS_COL:
            mass = row[MASS_COL]
            try:
                mass = float(mass)
                masses.append(mass)
                print "%0.3f" % mass
            except ValueError:
                print "Error (line %d): %s" % (n, mass)

#crunch mass data 
plot_data = ...

#make a plot
pyplot.plot(plot_data)
pyplot.show()