## saving numpy matrix in text file with indices

Question

I am trying to save a 2D matrix A to text file for each non-zero entry. I would like to save it in the below format,

For the (i,j)-th entry, one line as

``````row[i]::column[j]::A[i,j]
``````

where row and column are 1D numpy array corresponding to rows and column indices

I tried,

``````np.savetxt(rel_file,(row,column,A),fmt='%d',delimiter="::",newline="\n");
``````

But, since shape mismatches, i get error. I do not want to iterate over each row and column indices in a loop (I think it is too time consuming, i have 5000*5000 matrix).

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## Answers to saving numpy matrix in text file with indices ( 2 )

1. In my first answer I display all values; with just the nonzeros it's even easier to create the column array. `np.where` does the trick

``````In [1548]: I,J = np.nonzero(A)    # np.where
In [1549]: Acol = np.column_stack((I,J,A[I,J]))
``````

==========

For all values:

Here's a start; it is iterative, but as I commented, so is `np.savetxt`.

``````In [1523]: A=np.arange(25).reshape(5,5)

In [1526]: list(np.ndenumerate(A))
Out[1526]:
[((0, 0), 0),
((0, 1), 1),
((0, 2), 2),
((0, 3), 3),
((0, 4), 4),
((1, 0), 5),

In [1528]: with open('txt','w') as f:
...:     for (i,j),v in np.ndenumerate(A):
...:         f.write('%d::%d::%d\n'%(i,j,v))
...:
In [45]: cat txt
0::0::0
0::1::1
0::2::2
0::3::3
0::4::4
1::0::5
``````

We could make a (n,3) array consisting of the indices and flattened values of `A`. But `savetxt` would still iterate on it, effectively:

``````with open(...) as f:
for row in Acol:
f.write(fmt % tuple(row))
``````

Here's one way of making this 3 column array:

``````In [1535]: I,J = np.meshgrid(np.arange(A.shape[0]),np.arange(A.shape[1]),indexin
...: g='ij')
In [1536]: I
Out[1536]:
array([[0, 0, 0, 0, 0],
[1, 1, 1, 1, 1],
[2, 2, 2, 2, 2],
[3, 3, 3, 3, 3],
[4, 4, 4, 4, 4]])
In [1537]: Acol=np.column_stack((I.ravel(),J.ravel(),A.ravel()))
In [1538]: Acol
Out[1538]:
array([[ 0,  0,  0],
[ 0,  1,  1],
[ 0,  2,  2],
[ 0,  3,  3],
[ 0,  4,  4],
....
``````
2. Heres a simple method that manually reshapes the original array to be a very long array consisting of row, col, value. Just filter the rows for non-zero and it should work. The below example works with this random 50,50 array.

``````a = np.random.randint(0,5, (50, 50))

rows = np.repeat(np.arange(50), 50)
cols = np.tile(np.arange(50), 50)

data = np.column_stack((rows, cols, a.flatten()))

data_filtered = data[data[:, 2] != 0]
np.savetxt('temp.txt',data_filtered,fmt='%d',delimiter="::",newline="\n");
``````