'''
Author: Yotam Gingold <yotam (strudel) yotamgingold.com>
License: Public Domain [CC0](http://creativecommons.org/publicdomain/zero/1.0/)
Description: Wrapper for SuiteSparse qr() and solve() functions. Matlab and Julia have it, Python should have it, too.
'''

from __future__ import print_function, division, absolute_import

# The compilation here works only if the files have been copied locally into the project,
# as the compile requires write access into the directory the files reside in.
#
# In an installed copy of PySPQR, the compile step has already been run by setup.py at packaging time.
#
try:
    from ._sparseqr import ffi, lib
except ImportError:
    print( "=== Wrapper module not compiled; compiling..." )
    from .sparseqr_gen import main
    main()
    print( "=== ...compiled." )

    from ._sparseqr import ffi, lib

# Packaging note:
#
# http://cffi.readthedocs.io/en/latest/cdef.html says that:
#
# Note that some bundler tools that try to find all modules used by a project, like PyInstaller,
# will miss _cffi_backend in the out-of-line mode because your program contains no explicit
# import cffi or import _cffi_backend. You need to add _cffi_backend explicitly (as a "hidden import"
# in PyInstaller, but it can also be done more generally by adding the line import _cffi_backend in your main program).
#
import _cffi_backend

import scipy.sparse
import numpy

from .cffi_asarray import asarray

'''
Helpful links for developers:
    The primary docs:
    http://cffi.readthedocs.io/en/latest/overview.html
    http://cffi.readthedocs.io/en/latest/using.html

    Some helpful examples for #define and NumPy:
    https://kogs-www.informatik.uni-hamburg.de/~seppke/content/teaching/wise1314/20131107_pridoehl-cffi.pdf
'''

## Initialize cholmod
cc = ffi.new("cholmod_common*")
lib.cholmod_l_start( cc )

## Set up cholmod deinit to run when Python exits
def _deinit():
    '''Deinitialize the CHOLMOD library.'''
    lib.cholmod_l_finish( cc )
import atexit
atexit.register(_deinit)


## Data format conversion

def scipy2cholmodsparse( scipy_A ):
    '''Convert a SciPy sparse matrix to a CHOLMOD sparse matrix.

The input is first internally converted to scipy.sparse.coo_matrix format.

When no longer needed, the returned CHOLMOD sparse matrix must be deallocated using cholmod_free_sparse().
'''
    scipy_A = scipy_A.tocoo()

    nnz = scipy_A.nnz

    ## There is a potential performance win if we know A is symmetric and we
    ## can get only the upper or lower triangular elements.
    chol_A = lib.cholmod_l_allocate_triplet( scipy_A.shape[0], scipy_A.shape[1], nnz, 0, lib.CHOLMOD_REAL, cc )

    Ai = ffi.cast( "SuiteSparse_long*", chol_A.i )
    Aj = ffi.cast( "SuiteSparse_long*", chol_A.j )
    Avals = ffi.cast( "double*", chol_A.x )

    Ai[0:nnz] = scipy_A.row
    Aj[0:nnz] = scipy_A.col
    Avals[0:nnz] = scipy_A.data

    chol_A.nnz = nnz

    ## Print what cholmod sees as the matrix.
    # lib.cholmod_l_print_triplet( chol_A, "A".encode('utf-8'), cc )
    assert lib.cholmod_l_check_triplet( chol_A, cc ) == 1

    ## Convert to a cholmod_sparse matrix.
    result = lib.cholmod_l_triplet_to_sparse( chol_A, nnz, cc )
    ## Free the space used by the cholmod triplet matrix.
    _cholmod_free_triplet( chol_A )

    return result

def cholmodsparse2scipy( chol_A ):
    '''Convert a CHOLMOD sparse matrix to a scipy.sparse.coo_matrix.'''
    ## Convert to a cholmod_triplet matrix.
    chol_A = lib.cholmod_l_sparse_to_triplet( chol_A, cc )

    nnz = chol_A.nnz

    Ai = ffi.cast( "SuiteSparse_long*", chol_A.i )
    Aj = ffi.cast( "SuiteSparse_long*", chol_A.j )
    Adata = ffi.cast( "double*", chol_A.x )

    ## Have to pass through list().
    ## https://bitbucket.org/cffi/cffi/issues/292/cant-copy-data-to-a-numpy-array
    ## http://stackoverflow.com/questions/16276268/how-to-pass-a-numpy-array-into-a-cffi-function-and-how-to-get-one-back-out
    '''
    i = numpy.zeros( nnz, dtype = numpy.int64 )
    j = numpy.zeros( nnz, dtype = numpy.int64 )
    data = numpy.zeros( nnz )

    i[0:nnz] = list( Ai[0:nnz] )
    j[0:nnz] = list( Aj[0:nnz] )
    data[0:nnz] = list( Adata[0:nnz] )
    '''
    ## UPDATE: I can do this without going through list() or making two extra copies.
    ## NOTE: Create a copy() of the array data, because the coo_matrix() constructor
    ##       doesn't and the cholmod memory fill get freed.
    i = asarray( ffi, Ai, nnz ).copy()
    j = asarray( ffi, Aj, nnz ).copy()
    data = asarray( ffi, Adata, nnz ).copy()

    scipy_A = scipy.sparse.coo_matrix(
        ( data, ( i, j ) ),
        shape = ( chol_A.nrow, chol_A.ncol )
        )

    ## Free the space used by the cholmod triplet matrix.
    _cholmod_free_triplet( chol_A )

    return scipy_A

def numpy2cholmoddense( numpy_A ):
    '''Convert a NumPy array (rank-1 or rank-2) to a CHOLMOD dense matrix.

Rank-1 arrays are converted to column vectors.

When no longer needed, the returned CHOLMOD dense matrix must be deallocated using cholmod_free_dense().
'''
    numpy_A = numpy.atleast_2d( numpy_A )
    if numpy_A.shape[0] == 1 and numpy_A.shape[1] > 1:  # prefer column vector
        numpy_A = numpy_A.T
    nrow = numpy_A.shape[0]
    ncol = numpy_A.shape[1]
    lda  = nrow  # cholmod_dense is column-oriented
    chol_A = lib.cholmod_l_allocate_dense( nrow, ncol, lda, lib.CHOLMOD_REAL, cc )
    if chol_A == ffi.NULL:
        raise RuntimeError("Failed to allocate chol_A")
    Adata = ffi.cast( "double*", chol_A.x )
    for j in range(ncol):  # FIXME inefficient?
        Adata[(j*lda):((j+1)*lda)] = numpy_A[:,j]
    return chol_A

def cholmoddense2numpy( chol_A ):
    '''Convert a CHOLMOD dense matrix to a NumPy array.'''
    Adata = ffi.cast( "double*", chol_A.x )

    result = asarray( ffi, Adata, chol_A.nrow*chol_A.ncol ).copy()
    result = result.reshape( (chol_A.nrow, chol_A.ncol), order='F' )
    return result

def permutation_vector_to_matrix( E ):
    '''Convert a permutation vector E (list or rank-1 array, length n) to a permutation matrix (n by n).

The result is returned as a scipy.sparse.coo_matrix, where the entries at (E[k], k) are 1.
'''
    n = len( E )
    j = numpy.arange( n )
    return scipy.sparse.coo_matrix( ( numpy.ones(n), ( E, j ) ), shape = ( n, n ) )


## Memory management

# Used only internally by this module (the user sees only sparse and dense formats).
def _cholmod_free_triplet( A ):
    '''Deallocate a CHOLMOD triplet format matrix.'''
    A_ptr = ffi.new("cholmod_triplet**")
    A_ptr[0] = A
    lib.cholmod_l_free_triplet( A_ptr, cc )

def cholmod_free_sparse( A ):
    '''Deallocate a CHOLMOD sparse matrix.'''
    A_ptr = ffi.new("cholmod_sparse**")
    A_ptr[0] = A
    lib.cholmod_l_free_sparse( A_ptr, cc )

def cholmod_free_dense( A ):
    '''Deallocate a CHOLMOD dense matrix.'''
    A_ptr = ffi.new("cholmod_dense**")
    A_ptr[0] = A
    lib.cholmod_l_free_dense( A_ptr, cc )


## Solvers
def rz(A, B, tolerance = None):
    getCTX=int(0)
    chol_A = scipy2cholmodsparse( A )
    chol_b = numpy2cholmoddense(  B )
    chol_Z = ffi.new("cholmod_dense**")
    chol_R = ffi.new("cholmod_sparse**")
    chol_E = ffi.new("SuiteSparse_long**")
    if tolerance is None:
        tolerance=0.
        
    rank = lib.SuiteSparseQR_C(
        ## Input
        lib.SPQR_ORDERING_DEFAULT,
        tolerance,
        A.shape[1],
        getCTX,
        chol_A,
        ffi.NULL,
        chol_b,
        ## Output
        ffi.NULL,
        chol_Z,
        chol_R,
        chol_E,
        ffi.NULL,
        ffi.NULL,
        ffi.NULL,
        cc
        )
    scipy_Z = cholmoddense2numpy( chol_Z[0] )
    scipy_R = cholmodsparse2scipy( chol_R[0] )

    ## If chol_E is null, there was no permutation.
    if chol_E == ffi.NULL:
        E = None
    else:
        E = asarray( ffi, chol_E[0], A.shape[1] ).copy()

    ## Free cholmod stuff
    cholmod_free_dense( chol_Z[0] )
    cholmod_free_sparse( chol_R[0] )

    return scipy_Z, scipy_R, E, rank


def qr( A, tolerance = None ):
    '''
    Given a sparse matrix A,
    returns Q, R, E, rank such that:
        Q*R = A*permutation_vector_to_matrix(E)
    rank is the estimated rank of A.

    If optional `tolerance` parameter is negative, it has the following meanings:
        #define SPQR_DEFAULT_TOL ...       /* if tol <= -2, the default tol is used */
        #define SPQR_NO_TOL ...            /* if -2 < tol < 0, then no tol is used */

    The performance-optimal format for A is scipy.sparse.coo_matrix.

    For solving systems of the form A x = b, see solve().

    qr() can also be used to solve systems, as follows:

        # inputs: scipy.sparse.coo_matrix A, rank-1 numpy.array b (RHS)
        import numpy
        import scipy

        Q, R, E, rank = sparseqr.qr( A )
        r = rank  # r could be min(A.shape) if A is full-rank

        # The system is only solvable if the lower part of Q.T @ B is all zero:
        print( "System is solvable if this is zero:", abs( (( Q.tocsc()[:,r:] ).T ).dot( B ) ).sum() )

        # Use CSC format for fast indexing of columns.
        R  = R.tocsc()[:r,:r]
        Q  = Q.tocsc()[:,:r]
        QB = (Q.T).dot(B).tocsc()  # for best performance, spsolve() wants the RHS to be in CSC format.
        result = scipy.sparse.linalg.spsolve(R, QB)

        # Recover a solution (as a dense array):
        x = numpy.zeros( ( A.shape[1], B.shape[1] ), dtype = result.dtype )
        x[:r] = result.todense()
        x[E] = x.copy()

        # Recover a solution (as a sparse matrix):
        x = scipy.sparse.vstack( ( result.tocoo(), scipy.sparse.coo_matrix( ( A.shape[1] - rank, B.shape[1] ), dtype = result.dtype ) ) )
        x.row = E[ x.row ]

    Be aware that this approach is slow and takes a lot of memory, because qr() explicitly constructs Q.
    Unless you have a large number of systems to solve with the same A, solve() is much faster.
    '''

    chol_A = scipy2cholmodsparse( A )

    chol_Q = ffi.new("cholmod_sparse**")
    chol_R = ffi.new("cholmod_sparse**")
    chol_E = ffi.new("SuiteSparse_long**")

    if tolerance is None: tolerance = lib.SPQR_DEFAULT_TOL

    rank = lib.SuiteSparseQR_C_QR(
        ## Input
        lib.SPQR_ORDERING_DEFAULT,
        tolerance,
        A.shape[0],
        chol_A,
        ## Output
        chol_Q,
        chol_R,
        chol_E,
        cc
        )

    scipy_Q = cholmodsparse2scipy( chol_Q[0] )
    scipy_R = cholmodsparse2scipy( chol_R[0] )

    ## If chol_E is null, there was no permutation.
    if chol_E == ffi.NULL:
        E = None
    else:
        ## Have to pass through list().
        ## https://bitbucket.org/cffi/cffi/issues/292/cant-copy-data-to-a-numpy-array
        ## http://stackoverflow.com/questions/16276268/how-to-pass-a-numpy-array-into-a-cffi-function-and-how-to-get-one-back-out
        # E = numpy.zeros( A.shape[1], dtype = int )
        # E[0:A.shape[1]] = list( chol_E[0][0:A.shape[1]] )
        ## UPDATE: I can do this without going through list() or making two extra copies.
        E = asarray( ffi, chol_E[0], A.shape[1] ).copy()

    ## Free cholmod stuff
    cholmod_free_sparse( chol_Q[0] )
    cholmod_free_sparse( chol_R[0] )
    ## Apparently we don't need to do this. (I get a malloc error.)
    # lib.cholmod_l_free( A.shape[1], ffi.sizeof("SuiteSparse_long"), chol_E, cc )

    return scipy_Q, scipy_R, E, rank


def solve( A, b, tolerance = None ):
    '''
    Given a sparse m-by-n matrix A, and dense or sparse m-by-k matrix (storing k RHS vectors) b,
    solve A x = b in the least-squares sense.

    This is much faster than using qr() to solve the system, since Q is not explicitly constructed.

    Returns x on success, None on failure.

    The format of the returned x (on success) is either dense or sparse, corresponding to
    the format of the b that was supplied.

    The performance-optimal format for A is scipy.sparse.coo_matrix.

    If optional `tolerance` parameter is negative, it has the following meanings:
        #define SPQR_DEFAULT_TOL ...       /* if tol <= -2, the default tol is used */
        #define SPQR_NO_TOL ...            /* if -2 < tol < 0, then no tol is used */
    '''
    if isinstance( b, scipy.sparse.spmatrix ):
        return _solve_with_sparse_rhs( A, b, tolerance )
    else:
        return _solve_with_dense_rhs(  A, b, tolerance )

def _solve_with_dense_rhs( A, b, tolerance = None ):
    '''
    Given a sparse m-by-n matrix A, and dense m-by-k matrix (storing k RHS vectors) b,
    solve A x = b in the least-squares sense.

    This is much faster than using qr() to solve the system, since Q is not explicitly constructed.

    Returns x (dense) on success, None on failure.

    The performance-optimal format for A is scipy.sparse.coo_matrix.

    If optional `tolerance` parameter is negative, it has the following meanings:
        #define SPQR_DEFAULT_TOL ...       /* if tol <= -2, the default tol is used */
        #define SPQR_NO_TOL ...            /* if -2 < tol < 0, then no tol is used */
    '''

    chol_A = scipy2cholmodsparse( A )
    chol_b = numpy2cholmoddense(  b )

    if tolerance is None: tolerance = lib.SPQR_DEFAULT_TOL

    chol_x = lib.SuiteSparseQR_C_backslash(
        ## Input
        lib.SPQR_ORDERING_DEFAULT,
        tolerance,
        chol_A,
        chol_b,
        cc )

    if chol_x == ffi.NULL:
        return None  # failed

    ## Return x with the same shape as b.
    x_shape = list( b.shape )
    x_shape[0] = A.shape[1]
    numpy_x = cholmoddense2numpy( chol_x ).reshape( x_shape )

    ## Free cholmod stuff
    cholmod_free_sparse( chol_A )
    cholmod_free_dense(  chol_b )
    cholmod_free_dense(  chol_x )
    return numpy_x

def _solve_with_sparse_rhs( A, b, tolerance = None ):
    '''
    Given a sparse m-by-n matrix A, and sparse m-by-k matrix (storing k RHS vectors) b,
    solve A x = b in the least-squares sense.

    This is much faster than using qr() to solve the system, since Q is not explicitly constructed.

    Returns x (sparse) on success, None on failure.

    The performance-optimal format for A and b is scipy.sparse.coo_matrix.

    If optional `tolerance` parameter is negative, it has the following meanings:
        #define SPQR_DEFAULT_TOL ...       /* if tol <= -2, the default tol is used */
        #define SPQR_NO_TOL ...            /* if -2 < tol < 0, then no tol is used */
    '''

    chol_A = scipy2cholmodsparse( A )
    chol_b = scipy2cholmodsparse( b )

    if tolerance is None: tolerance = lib.SPQR_DEFAULT_TOL

    chol_x = lib.SuiteSparseQR_C_backslash_sparse(
        ## Input
        lib.SPQR_ORDERING_DEFAULT,
        tolerance,
        chol_A,
        chol_b,
        cc )

    if chol_x == ffi.NULL:
        return None  # failed

    scipy_x = cholmodsparse2scipy( chol_x )

    ## Free cholmod stuff
    cholmod_free_sparse( chol_A )
    cholmod_free_sparse( chol_b )
    cholmod_free_sparse( chol_x )

    return scipy_x


## Usage examples

if __name__ == '__main__':
    # Q, R, E, rank = qr( scipy.sparse.identity(10) )

    print( "Testing qr()" )
    M = scipy.sparse.rand( 10, 8, density = 0.1 )
    Q, R, E, rank = qr( M, tolerance = 0 )
    print( abs( Q*R - M*permutation_vector_to_matrix(E) ).sum() )

    print( "Testing solve(), using dense RHS" )
    b = numpy.random.random(10)  # one RHS, but could also have many (in shape (10,k))
    x = solve( M, b, tolerance = 0 )
    print( x )
    ## This won't be true in general because M is rank deficient.
    # print( abs( M*x - b ).sum() )
    print( b.shape )
    print( x.shape )
    B = numpy.random.random((10,5))  # many RHS
    x = solve( M, B, tolerance = 0 )
    print( x )
    ## This won't be true in general because M is rank deficient.
    # print( abs( M*x - B ).sum() )
    print( B.shape )
    print( x.shape )

    print( "Testing solve(), using sparse RHS" )
    B = scipy.sparse.rand( 10, 5, density = 0.1 )  # many RHS, sparse
    x = solve( M, B, tolerance = 0 )
    print( x )
    ## This won't be true in general because M is rank deficient.
    # print( abs( M*x - B ).sum() )
    print( B.shape )
    print( x.shape )
