Data Visualization from a Data File

Analyzing Data from Multiple Files

Overview
Teaching: 20 min Exercises: 0 min	Questions How can I do the same operations on many different files? Objectives Use a library function to get a list of filenames that match a wildcard pattern. Write a for loop to process multiple files. Write a for loop to process multiple files.

import glob

The glob library contains a function, also called glob , that finds files and directories whose names match a pattern. We provide those patterns as strings: the character * matches zero or more characters, while ? matches any one character. We can use this to get the names of all the CSV files in the current directory:

print(glob.glob('inflammation*.csv'))

['inflammation-05.csv', 'inflammation-11.csv', 'inflammation-12.csv', 'inflammation-08.csv', 'inflammation-03.csv', 'inflammation-06.csv', 'inflammation-09.csv', 'inflammation-07.csv', 'inflammation-10.csv', 'inflammation-02.csv', 'inflammation-04.csv', 'inflammation-01.csv']

As these examples show, glob.glob's result is a list of file and directory paths in arbitrary order. This means we can loop over it to do something with each filename in turn. In our case, the "something" we want to do is generate a set of plots for each file in our inflammation dataset. If we want to start by analyzing just the first three files in alphabetical order, we can use the sorted built-in function to generate a new sorted list from the glob.glob output:

import numpy
import matplotlib.pyplot

filenames = sorted(glob.glob('inflammation*.csv'))
filenames = filenames[0:3]
for f in filenames:
    print(f)

    data = numpy.loadtxt(fname=f, delimiter=',')

    fig = matplotlib.pyplot.figure(figsize=(10.0, 3.0))

    axes1 = fig.add_subplot(1, 3, 1)
    axes2 = fig.add_subplot(1, 3, 2)
    axes3 = fig.add_subplot(1, 3, 3)

    axes1.set_ylabel('average')
    axes1.plot(numpy.mean(data, axis=0))

    axes2.set_ylabel('max')
    axes2.plot(numpy.max(data, axis=0))

    axes3.set_ylabel('min')
    axes3.plot(numpy.min(data, axis=0))

    fig.tight_layout()
    matplotlib.pyplot.show()

inflammation-01.csv

inflammation-02.csv

inflammation-03.csv

Sure enough, the maxima of the first two data sets show exactly the same ramp as the first, and their minima show the same staircase structure; a different situation has been revealed in the third dataset, where the maxima are a bit less regular, but the minima are consistently zero.

import glob
import numpy
import matplotlib.pyplot

filenames = glob.glob('inflammation*.csv')

data0 = numpy.loadtxt(fname=filenames[0], delimiter=',')
data1 = numpy.loadtxt(fname=filenames[1], delimiter=',')

fig = matplotlib.pyplot.figure(figsize=(10.0, 3.0))

matplotlib.pyplot.ylabel('Difference in average')
matplotlib.pyplot.plot(data0.mean(axis=0) - data1.mean(axis=0))

fig.tight_layout()
matplotlib.pyplot.show()

filenames = glob.glob('inflammation*.csv')
composite_data = numpy.zeros((60,40))
for f in filenames:
    # sum each new file's data into as it's read
    #
# and then divide the composite_data by number of samples
composite_data /= len(filenames)

import glob
import numpy
import matplotlib.pyplot

filenames = glob.glob('data/inflammation*.csv')
composite_data = numpy.zeros((60,40))

for f in filenames:
    data = numpy.loadtxt(fname = f, delimiter=',')
    composite_data += data

composite_data/=len(filenames)

fig = matplotlib.pyplot.figure(figsize=(10.0, 3.0))

axes1 = fig.add_subplot(1, 3, 1)
axes2 = fig.add_subplot(1, 3, 2)
axes3 = fig.add_subplot(1, 3, 3)

axes1.set_ylabel('average')
axes1.plot(numpy.mean(composite_data, axis=0))

axes2.set_ylabel('max')
axes2.plot(numpy.max(composite_data, axis=0))

axes3.set_ylabel('min')
axes3.plot(numpy.min(composite_data, axis=0))

fig.tight_layout()

matplotlib.pyplot.show()

Source: Software Carpentry Foundation, http://swcarpentry.github.io/swc-releases/2017.08/python-novice-inflammation/04-files/
This work is licensed under a Creative Commons Attribution 4.0 License.