plotting a histogram for a column in a csv file in python

Question

I am trying to plot a histogram and a scatter plot for a particular column in a given csv file. I am new to programming and I got this code from a friend, and it apparently works but somehow I am getting this error. the code is:

import csv
import numpy as np
import matplotlib.pyplot as plt
f = open('Data for question 13.csv')
data = csv.reader(f)
Area = []; MajorAxisLength = []; MinorAxisLength = []; Perimeter = []
MinIntensity = []; MeanIntensity = []; MaxIntensity = []
header = [Area, MajorAxisLength, MinorAxisLength,Perimeter,MinIntensity,MeanIntensity,MaxIntensity]
for row in data:
    i = 1 
    for name in header:
        name.append(row[i])
        i = i + 1
plt.figure()
plt.hist(Area, bins=50) # error follows after this

Error:

Traceback (most recent call last):
  File "<pyshell#11>", line 1, in <module>
    plt.hist(Area, bins=50, alpha=0.5)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.py", line 2827, in hist
    stacked=stacked, **kwargs)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/axes.py", line 8312, in hist
    xmin = min(xmin, xi.min())
  File "/Library/Python/2.7/site-packages/numpy-1.9.0-py2.7-macosx-10.9-intel.egg/numpy/core/_methods.py", line 29, in _amin
    return umr_minimum(a, axis, None, out, keepdims)
TypeError: cannot perform reduce with flexible type

I am unable to get rid of this error. The answer should be simple but since I am new I have no idea how to deal with it.

Answer 1

You get the error because the input data is interpreted as string by the csv parser while hist requires numeric data. You should explicitly convert each row[i] before appending it.

Answer 2

Assuming you just want to plot some numerical data in your csv file, and that the data is numeric (not text) you could probably use the same method as mentioned here: How to read csv into record array in numpy?

Thus, your code might look like this:

import csv
import numpy as np
import matplotlib.pyplot as plt

data = np.genfromtxt('Data for question 13.csv')  # add more parameter info if neccessary like skipping header lines
plt.figure()
plt.hist(data[:,0], bins=50)  # Area, from OP, is column 0

Info on the genfromtxt function can be found here: http://docs.scipy.org/doc/numpy/reference/generated/numpy.genfromtxt.html

Answer 3

I'm not 100% sure, as I don't have your data file available. But I think row[i] is a string (and not an integer or float). And you can use enumerate to skip the first line. So this should solve the problem:

for n,row in enumerate(data):
    if n > 0:
        i = 1 
        for name in header:
            name.append(float(row[i]))
            i = i + 1