Compressed Sparse Row Format (CSR)

Compressed Sparse Row Format (CSR)

• • three NumPy arrays: indices, indptr, data

    • indices is array of column indices
    • data is array of corresponding nonzero values
    • indptr points to row starts in indices and data
    • length is n_row + 1, last item = number of values = length of both indices and data
    • nonzero values of the i-th row are data[indptr[i]:indptr[i+1]] with column indices indices[indptr[i]:indptr[i+1]]
    • item (i, j) can be accessed as data[indptr[i]+k], where k is position of j in indices[indptr[i]:indptr[i+1]]

  • subclass of _cs_matrix (common CSR/CSC functionality)

    • subclass of _data_matrix (sparse matrix classes with .data attribute)

• fast matrix vector products and other arithmetics (sparsetools)

• constructor accepts:

  • dense matrix (array)
  • sparse matrix
  • shape tuple (create empty matrix)
  • (data, ij) tuple
  • (data, indices, indptr) tuple

• efficient row slicing, row-oriented operations
• slow column slicing, expensive changes to the sparsity structure

• use:

  • actual computations (most linear solvers support this format)

Examples¶

• create empty CSR matrix:

  >>> mtx = sparse.csr_matrix((3, 4), dtype=np.int8)
  
         
         
  >>> mtx.todense()
  
         
         
  matrix([[0, 0, 0, 0],
  
         
         
          [0, 0, 0, 0],
  
         
         
          [0, 0, 0, 0]], dtype=int8)
  
         
         
  

• create using (data, ij) tuple:

  >>> row = np.array([0, 0, 1, 2, 2, 2])
  
         
         
  >>> col = np.array([0, 2, 2, 0, 1, 2])
  
         
         
  >>> data = np.array([1, 2, 3, 4, 5, 6])
  
         
         
  >>> mtx = sparse.csr_matrix((data, (row, col)), shape=(3, 3))
  
         
         
  >>> mtx     
  
         
         
  <3x3 sparse matrix of type '<... 'numpy.int64'>'
  
         
         
          with 6 stored elements in Compressed Sparse Row format>
  
         
         
  >>> mtx.todense()   
  
         
         
  matrix([[1, 0, 2],
  
         
         
          [0, 0, 3],
  
         
         
          [4, 5, 6]]...)
  
         
         
  >>> mtx.data        
  
         
         
  array([1, 2, 3, 4, 5, 6]...)
  
         
         
  >>> mtx.indices
  
         
         
  array([0, 2, 2, 0, 1, 2], dtype=int32)
  
         
         
  >>> mtx.indptr
  
         
         
  array([0, 2, 3, 6], dtype=int32)
  
         
         
  

• create using (data, indices, indptr) tuple:

  >>> data = np.array([1, 2, 3, 4, 5, 6])
  
         
         
  >>> indices = np.array([0, 2, 2, 0, 1, 2])
  
         
         
  >>> indptr = np.array([0, 2, 3, 6])
  
         
         
  >>> mtx = sparse.csr_matrix((data, indices, indptr), shape=(3, 3))
  
         
         
  >>> mtx.todense()
  
         
         
  matrix([[1, 0, 2],
  
         
         
          [0, 0, 3],
  
         
         
          [4, 5, 6]])
  
         
         
  

See https://scipy-lectures.org/advanced/scipy_sparse/csr_matrix.html

https://docs.scipy.org/doc/scipy-0.15.1/reference/generated/scipy.sparse.csr_matrix.html