A Python list of Numpy Arrays to CSV?

Question

I have a Python list of Numpy arrays storing X, Y, Z coordinates - like this:

[array([-0.22424938,  0.16117005, -0.39249256])
array([-0.22424938,  0.16050598, -0.39249256])
array([-0.22424938,  0.1598419 , -0.39249256]) ...,
array([ 0.09214371, -0.26184322, -0.39249256])
array([ 0.09214371, -0.26250729, -0.39249256])
array([ 0.09214371, -0.26317136, -0.39249256])]

And I would like to get them into a CSV file so I can plot them in GIS software. I am new to Numpy arrays and I keep getting errors using methods like numpy.ndarray.tofile().

I can iterate the list using

for item in list:
    f.write(str(item))

but it writes the data to the text file as binary data.
I just want to have each XYZ value comma separated with each row storing one XYZ value. Any help is appreciated.

Moses Koledoye · Accepted Answer · 2016-09-08 22:22:37Z

5

Use the csv module with its writerows method:

import csv

with open('my_data.txt', 'w') as f:
    csvwriter = csv.writer(f)
    csvwriter.writerows(list_of_arrays)

answered Sep 8, 2016 at 22:22

Moses Koledoye

78.8k8 gold badges139 silver badges141 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

hpaulj · Accepted Answer · 2016-09-08 22:49:20Z

3

np.savetxt will write the list:

In [553]: data=[array([-0.22424938,  0.16117005, -0.39249256]),
     ...: array([-0.22424938,  0.16050598, -0.39249256]),
     ...: array([-0.22424938,  0.1598419 , -0.39249256]),
     ...: array([ 0.09214371, -0.26184322, -0.39249256]),
     ...: array([ 0.09214371, -0.26250729, -0.39249256]),
     ...: array([ 0.09214371, -0.26317136, -0.39249256]),]
In [554]: np.savetxt('test.txt',data, delimiter=', ', fmt='%12.8f')
In [555]: cat test.txt
 -0.22424938,   0.16117005,  -0.39249256
 -0.22424938,   0.16050598,  -0.39249256
 -0.22424938,   0.15984190,  -0.39249256
  0.09214371,  -0.26184322,  -0.39249256
  0.09214371,  -0.26250729,  -0.39249256
  0.09214371,  -0.26317136,  -0.39249256

np.savetxt really saves an array, but converts the list to array if needed:

In [556]: np.array(data)
Out[556]: 
array([[-0.22424938,  0.16117005, -0.39249256],
       [-0.22424938,  0.16050598, -0.39249256],
       [-0.22424938,  0.1598419 , -0.39249256],
       [ 0.09214371, -0.26184322, -0.39249256],
       [ 0.09214371, -0.26250729, -0.39249256],
       [ 0.09214371, -0.26317136, -0.39249256]])

It then iterates over rows, and writes

f.write(fmt % tuple(row))

where fmt is either the full string you provide or one constructed by replicating the shorter fmt I provided.

Effectively savetxt is doing:

In [558]: fmt='%12.8f, %12.8f, %12.8f'
In [559]: for row in data:
     ...:     print(fmt%tuple(row))
     ...:     
 -0.22424938,   0.16117005,  -0.39249256
 -0.22424938,   0.16050598,  -0.39249256
 -0.22424938,   0.15984190,  -0.39249256
  0.09214371,  -0.26184322,  -0.39249256
  0.09214371,  -0.26250729,  -0.39249256
  0.09214371,  -0.26317136,  -0.39249256

answered Sep 8, 2016 at 22:49

hpaulj

233k14 gold badges260 silver badges392 bronze badges

2 Comments

Apollonia Vitelli Over a year ago

Hey hpaulj, how do you use cat in pyhton?

hpaulj Over a year ago

@ApolloniaVitelli, it's an alias defined for ipython on a linux system. On windows, the defined aliases are different. Try %alias to see what's defined on your system.

Collectives™ on Stack Overflow

A Python list of Numpy Arrays to CSV?

2 Answers 2

Comments

2 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

2 Comments

Your Answer

Sign up or log in

Post as a guest

Related