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pythonmatrix
Binnie
Binnie

Reputation: 313

rearranging matrix with named column/rows python

I am stuck (and in a bit of a time crunch) and was hoping for some help. This is probably a simple task but I can't seem to solve it..

I have a matrix, say 5 by 5, with an additional starting column of names for the rows and the same names for the columns in a text file like this:

b e a d c
b 0.0 0.1 0.3 0.2 0.5
e 0.1 0.0 0.4 0.9 0.3
a 0.3 0.4 0.0 0.7 0.6
d 0.2 0.9 0.7 0.0 0.1
c 0.5 0.3 0.6 0.1 0.0

I have multiple files that have the same format and size of matrix but the order of the names are different. I need a way to change these around so they are all the same and maintain the 0.0 diagonal. So any swapping I do to the columns I must do to the rows.

I have been searching a bit and it seems like NumPy might do what I want but I have never worked with it or arrays in general. Any help is greatly appreciated!

In short: How do I get a text file into an array which I can then swap around rows and columns to a desired order?

Upvotes: 1

Views: 276

Answers (3)

Jeff Ferland
Jeff Ferland

Reputation: 18292

from copy import copy

f = open('input', 'r')
data = []
for line in f:
    row = line.rstrip().split(' ')
    data.append(row)

#collect labels, strip empty spaces
r = data.pop(0)
c = [row.pop(0) for row in data]
r.pop(0)

origrow, origcol = copy(r), copy(c)

r.sort()
c.sort()

newgrid = []
for row, rowtitle in enumerate(r):
    fromrow = origrow.index(rowtitle)
    newgrid.append(range(len(c)))
    for col, coltitle in enumerate(c):
        #We ask this len(row) times, so memoization
        #might matter on a large matrix
        fromcol = origcol.index(coltitle)
        newgrid[row][col] = data[fromrow][fromcol]

print "\t".join([''] + r)
clabel = c.__iter__()
for line in newgrid:
    print "\t".join([clabel.next()] + line)

Upvotes: 0

YXD
YXD

Reputation: 32521

Here's the start of a horrific Numpy version (use HYRY's answer...)

import numpy as np

with open("myfile", "r") as myfile:
    lines = myfile.read().split("\n")
    floats = [[float(item) for item in line.split()[1:]] for line in lines[1:]]
    floats_transposed = np.array(floats).transpose().tolist()

Upvotes: 0

HYRY
HYRY

Reputation: 97301

I suggest you use pandas:

from StringIO import StringIO
import pandas as pd
data = StringIO("""b e a d c
b 0.0 0.1 0.3 0.2 0.5
e 0.1 0.0 0.4 0.9 0.3
a 0.3 0.4 0.0 0.7 0.6
d 0.2 0.9 0.7 0.0 0.1
c 0.5 0.3 0.6 0.1 0.0
""")
df = pd.read_csv(data, sep=" ")
print df.sort_index().sort_index(axis=1)

output:

     a    b    c    d    e
a  0.0  0.3  0.6  0.7  0.4
b  0.3  0.0  0.5  0.2  0.1
c  0.6  0.5  0.0  0.1  0.3
d  0.7  0.2  0.1  0.0  0.9
e  0.4  0.1  0.3  0.9  0.0

Upvotes: 4

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