How can I give row and column names to Scipy's csr_matrix?

Question

I don’t know if it’s possible, and it’s possibly a naive question, but how can I set the equivalent of R’s rownames() and colnames() to a scipy.sparse.csr.csr_matrix ?

I saw that my_matrix.dtype.names doesn’t work here, and I can’t find any “index” equivalend for such sparse matrix…

Moreover, pandas.sparse.* is not an option here, because of some open issue…

Thank you so much for your help,

Asked By: Jean Lescut

||

Source

Answer 1

You’ll have to maintain the names separately, as none of scipy’s sparse formats support named indexing. This might look like:

foo = csr_matrix(...)
row_names = np.array(...)
col_names = np.array(...)

# index by name:
row_idx, = np.where(row_names == "my row")
col_idx, = np.where(col_names == "my col")
foo[row_idx, col_idx]

Answered By: perimosocordiae

Answer 2

See the package "SSparseMatrix". (The package uses SciPy’s sparse matrices.)

Here is a creation and row-selection example (in a Python session):

>>> from SSparseMatrix import *
>>> mat = [[1, 0, 0, 3], [4, 0, 0, 5], [0, 3, 0, 5], [0, 0, 1, 0], [0, 0, 0, 5]]
>>> smat = SSparseMatrix(mat)
>>> smat.set_column_names(["a", "b", "c", "d"])
<5x4 SSparseMatrix (sparse matrix with named rows and columns) of type '<class 'numpy.int64'>'
    with 8 stored elements in Compressed Sparse Row format, and fill-in 0.4>
>>> smat.set_row_names(["A", "B", "C", "D", "E"])
<5x4 SSparseMatrix (sparse matrix with named rows and columns) of type '<class 'numpy.int64'>'
    with 8 stored elements in Compressed Sparse Row format, and fill-in 0.4>
>>> smat.print_matrix()
===================================
  |       a       b       c       d
-----------------------------------
A |       1       .       .       3
B |       4       .       .       5
C |       .       3       .       5
D |       .       .       1       .
E |       .       .       .       5
===================================
>>> smat[["A","B"],:].print_matrix()
===================================
  |       a       b       c       d
-----------------------------------
A |       1       .       .       3
B |       4       .       .       5
===================================

Answered By: Anton Antonov

How can I give row and column names to Scipy's csr_matrix?

Question:

Answers: