GRASS GIS 7 Programmer's Manual
7.7.svn(2019)r74109

Authors: probably CERL, David D. Gray, Brad Douglas, Soeren Gebbert and many others
The gmath library provides many common mathematical functions to be used in GRASS modules:
The GRASS numerical math interface also makes use of 3d party libraries to implement linear algebra and fast Fourier transformation functions, like fftwlibrary, BLAS/LAPACK, ccmath and ATLAS. Parts of the ccmath library are integrated in GRASS in lib/external.
There are several tests and benchmarks available for blas level 1, 2 and 3 as well as for ccmath and linear equation solver in the lib/gmath/test directory. These tests and benchmarks are not compiled by default. In case GRASS has been compiled, just change in the test directory and type make. A binary named test.gmath.lib will be available after starting GRASS.
To run all tests just type:
test.gmath.lib a
To run a benchmark to solve a matrix size of 2000x2000 using the KrylovSubspace iterative solver type:
test.gmath.lib solverbench=krylov rows=2000
Several GRASS modules implement there own numerical functions. The goal is to collect all these functions in the GRASS numerical math interface, to standardize them and to modify all modules to make use of the gmath interface.
GMATH provides several functions for vector and matrix memory allocation of different types. These functions should be used to allocate vectors and matrices which are used by gmath linear algebra functions.
Matrix and vector allocation for real types
double *G_alloc_vector(size_t)
double **G_alloc_matrix(int, int)
float *G_alloc_fvector(size_t)
float **G_alloc_fmatrix(int, int)
void G_free_vector(double *)
void G_free_matrix(double **)
void G_free_fvector(float *)
void G_free_fmatrix(float **)
Matrix and vector allocation for integer types
int *G_alloc_ivector(size_t)
int **G_alloc_imatrix(int, int)
void G_free_ivector(int *)
void G_free_imatrix(int **)
Fast Fourier Transformation
int fft(int, double *[2], int, int, int)
int fft2(int, double (*)[2], int, int, int)
Several mathematical functions mostly used by Imagery modules
double G_math_rand_gauss(int, double)
long G_math_max_pow2 (long n)
long G_math_min_pow2 (long n)
float G_math_rand(int)
int del2g(double *[2], int, double)
int getg(double, double *[2], int)
int G_math_egvorder(double *, double **, long)
int G_math_complex_mult (double *v1[2], int size1, double *v2[2], int size2, double *v3[2], int size3)
int G_math_findzc(double conv[], int size, double zc[], double thresh, int num_orients);
Obsolete LU decomposition lend from numerical recipes
int G_ludcmp(double **, int, int *, double *); void G_lubksb(double **a, int n, int *indx, double b[]);
Author: Soeren Gebbert
The gmath library provides its own implementation of blas level 1, 2 and 3 functions for vector  vector, vector  matrix and matrix  matrix operations. OpenMP is internally used to parallelize the vector and matrix operations. Most of the function can be called from inside a OpenMP parallel region. Additionally a wrapper for the ATLAS blas level 1 functions is available. The wrapping functions can also be used, when the ATLAS library is not available. In this case the GRASS blas level 1 implementation is called automatically instead.
Double precision blas level 1 functions
void G_math_d_x_dot_y(double *, double *, double *, int )
void G_math_d_asum_norm(double *, double *, int )
void G_math_d_euclid_norm(double *, double *, int )
void G_math_d_max_norm(double *, double *, int )
void G_math_d_ax_by(double *, double *, double *, double , double , int )
void G_math_d_copy(double *, double *, int )
Single precision blas level 1 functions
void G_math_f_x_dot_y(float *, float *, float *, int )
void G_math_f_asum_norm(float *, float *, int )
void G_math_f_euclid_norm(float *, float *, int )
void G_math_f_max_norm(float *, float *, int )
void G_math_f_ax_by(float *, float *, float *, float , float , int )
void G_math_f_copy(float *, float *, int )
Integer blas level 1 functions
void G_math_i_x_dot_y(int *, int *, double *, int )
void G_math_i_asum_norm(int *, double *, int )
void G_math_i_euclid_norm(int *, double *,int )
void G_math_i_max_norm(int *, int *, int )
void G_math_i_ax_by(int *, int *, int *, int , int , int )
void G_math_i_copy(int *, int *, int )
ATLAS blas level 1 wrapper
double G_math_ddot(double *, double *, int )
float G_math_sdot(float *, float *, int )
float G_math_sdsdot(float *, float *, float , int )
double G_math_dnrm2(double *, int )
double G_math_dasum(double *, int )
double G_math_idamax(double *, int )
float G_math_snrm2(float *, int )
float G_math_sasum(float *, int )
float G_math_isamax(float *, int )
void G_math_dscal(double *, double , int )
void G_math_sscal(float *, float , int )
void G_math_dcopy(double *, double *, int )
void G_math_scopy(float *, float *, int )
void G_math_daxpy(double *, double *, double , int )
void G_math_saxpy(float *, float *, float , int )
void G_math_d_Ax(double **, double *, double *, int , int )
void G_math_f_Ax(float **, float *, float *, int , int )
void G_math_d_x_dyad_y(double *, double *, double **, int, int )
void G_math_f_x_dyad_y(float *, float *, float **, int, int )
void G_math_d_aAx_by(double **, double *, double *, double , double , double *, int , int )
void G_math_f_aAx_by(float **, float *, float *, float , float , float *, int , int )
int G_math_d_A_T(double **A, int rows)
int G_math_f_A_T(float **A, int rows)
void G_math_d_aA_B(double **, double **, double , double **, int , int )
void G_math_f_aA_B(float **, float **, float , float **, int , int )
void G_math_d_AB(double **, double **, double **, int , int , int )
void G_math_f_AB(float **, float **, float **, int , int , int )
Author: Daniel A. Atkinson: ccmath library and documentation
Wrapper Soeren Gebbert
GRASS make use of several functions from the ccmath library. The ccmath library is located in the lib/external directory. The library was designed and developed by Daniel A. Atkinson and is licensed under the terms of the LGPL. Ccmath provides many common mathematical functions. Currently GRASS uses only the linear algebra part of the library. These functions are available via wrapping functions.
The wrapper integrates the ccmath library functions into the gmath structure. Hence only gmath memory allocation function should be used to create vector and matrix structures used by ccmath.
This is the documentation of the linear algebra part of the the ccmath library used by GRASS. It was written by Daniel A. Atkinson and provides a detailed description of the available linear algebra functions.
LINEAR ALGEBRA Summary The matrix algebra library contains functions that perform the standard computations of linear algebra. General areas covered are: o Solution of Linear Systems o Matrix Inversion o Eigensystem Analysis o Matrix Utility Operations o Singular Value Decomposition The operations covered here are fundamental to many areas of mathematics and statistics. Thus, functions in this library segment are called by other library functions. Both real and complex valued matrices are covered by functions in the first four of these categories. Notes on Contents Functions in this library segment provide the basic operations of numerical linear algebra and some useful utility functions for operations on vectors and matrices. The following list describes the functions available for operations with realvalued matrices. o Solving and Inverting Linear Systems: solv  solve a general system of real linear equations. solvps  solve a real symmetric linear system. solvru  solve a real right upper triangular linear system. solvtd  solve a tridiagonal real linear system. minv  invert a general real square matrix. psinv  invert a real symmetric matrix. ruinv  invert a right upper triangular matrix. The solution of a general linear system and efficient algorithms for solving special systems with symmetric and tridiagonal matrices are provided by these functions. The general solution function employs a LU factorization with partial pivoting and it is very robust. It will work efficiently on any problem that is not illconditioned. The symmetric matrix solution is based on a modified Cholesky factorization. It is best used on positive definite matrices that do not require pivoting for numeric stability. Tridiagonal solvers require orderN operations (N = dimension). Thus, they are highly recommended for this important class of sparse systems. Two matrix inversion routines are provided. The general inversion function is again LU based. It is suitable for use on any stable (ie. wellconditioned) problem. The Cholesky based symmetric matrix inversion is efficient and safe for use on matrices known to be positive definite, such as the variance matrices encountered in statistical computations. Both the solver and the inverse functions are designed to enhance data locality. They are very effective on modern microprocessors. o Eigensystem Analysis: eigen  extract all eigen values and vectors of a real symmetric matrix. eigval  extract the eigen values of a real symmetric matrix. evmax  compute the eigen value of maximum absolute magnitude and its corresponding vector for a symmetric matrix. Eigensystem functions operate on real symmetric matrices. Two forms of the general eigen routine are provided because the computation of eigen values only is much faster when vectors are not required. The basic algorithms use a Householder reduction to tridiagonal form followed by QR iterations with shifts to enhance convergence. This has become the accepted standard for symmetric eigensystem computation. The evmax function uses an efficient iterative power method algorithm to extract the eigen value of maximum absolute size and the corresponding eigenvector. o Singular Value Decomposition: svdval  compute the singular values of a m by n real matrix. sv2val  compute the singular values of a real matrix efficiently for m >> n. svduv  compute the singular values and the transformation matrices u and v for a real m by n matrix. sv2uv  compute the singular values and transformation matrices efficiently for m >> n. svdu1v  compute the singular values and transformation matrices u1 and v, where u1 overloads the input with the first n column vectors of u. sv2u1v  compute the singular values and the transformation matrices u1 and v efficiently for m >> n. Singular value decomposition is extremely useful when dealing with linear systems that may be singular. Singular values with values near zero are flags of a potential rank deficiency in the system matrix. They can be used to identify the presence of an illconditioned problem and, in some cases, to deal with the potential instability. They are applied to the linear least squares problem in this library. Singular values also define some important matrix norm parameters such as the 2norm and the condition value. A complete decomposition provides both singular values and an orthogonal decomposition of vector spaces related to the matrix identifying the range and nullspace. Fortunately, a highly stable algorithm based on Householder reduction to bidiagonal form and QR rotations can be used to implement the decomposition. The library provides two forms with one more efficient when the dimensions satisfy m > (3/2)n. General Technical Comments Efficient computation with matrices on modern processors must be adapted to the storage scheme employed for matrix elements. The functions of this library segment do not employ the multidimensional array intrinsic of the C language. Access to elements employs the simple rowmajor scheme described here. Matrices are modeled by the library functions as arrays with elements stored in row order. Thus, the element in the jth row and kth column of the n by n matrix M, stored in the array mat[], is addressed by M[j,k] = mat[n*j+k] , with 0 =< j,k <= n1 . (Remember that C employs zero as the starting index.) The storage order has important implications for data locality. The algorithms employed here all have excellent numerical stability, and the default double precision arithmetic of C enhances this. Thus, any problems encountered in using the matrix algebra functions will almost certainly be due to an illconditioned matrix. (The Hilbert matrices, H[i,j] = 1/(1+i+j) for i,j < n form a good example of such illconditioned systems.) We remind the reader that the appropriate response to such illconditioning is to seek an alternative approach to the problem. The option of increasing precision has already been exploited. Modification of the linear algebra algorithm code is not normally effective in an illconditioned problem.
Ccmath functions available via wrapping:
int G_math_solv(double **,double *,int)
int G_math_solvps(double **,double *,int)
void G_math_solvtd(double *,double *,double *,double *,int)
int G_math_solvru(double **,double *,int)
int G_math_minv(double **,int)
int G_math_psinv(double **,int)
int G_math_ruinv(double **,int)
void G_math_eigval(double **,double *,int)
void G_math_eigen(double **,double *,int)
double G_math_evmax(double **,double *,int)
int G_math_svdval(double *,double **,int,int)
int G_math_sv2val(double *,double **,int,int)
int G_math_svduv(double *,double **,double **, int,double **,int)
int G_math_sv2uv(double *,double **,double **,int,double **,int)
int G_math_svdu1v(double *,double **,int,double **,int)
Author: Soeren Gebbert and other
Besides the ccmath linear equation solver GRASS provides a set of additional direct and iterative linear equation solver for sparse, band and dense matrices. A special sparse matrix structure was implemented to allow the solution of huge sparse linear equation systems.
As iterative linear equation solver are classic (GaussSeidel/SOR, Jacobi) and KrylovSubspace (CG and BiCGStab) solver available. All iterative solver support sparse and dense matrices. The KrylovSubspace solver are parallelized with OpenMP.
As direct solver are LUdecomposition and Gausselimination without pivoting and a bandwidth optimized Cholesky decomposition available. Direct solver only support dense and band(Cholesky only) matrices.
The row vector of the sparse matrix
typedef struct { double *values; //The non null values of the row unsigned int cols; //Number of entries unsigned int *index;//the index number } G_math_spvector;
Sparse matrix and sparse vector functions
G_math_spvector *G_math_alloc_spvector(int )
G_math_spvector **G_math_alloc_spmatrix(int )
void G_math_free_spmatrix(G_math_spvector ** , int )
void G_math_free_spvector(G_math_spvector * )
int G_math_add_spvector(G_math_spvector **, G_math_spvector * , int )
G_math_spvector **G_math_A_to_Asp(double **, int, double)
double **G_math_Asp_to_A(G_math_spvector **, int)
double **G_math_Asp_to_sband_matrix(G_math_spvector **, int, int)
G_math_spvector **G_math_sband_matrix_to_Asp(double **A, int rows, int bandwidth, double epsilon)
void G_math_print_spmatrix(G_math_spvector ** Asp, int rows)
void G_math_Ax_sparse(G_math_spvector **, double *, double *, int )
Conversion of band matrices
double **G_math_matrix_to_sband_matrix(double **, int, int)
double **G_math_sband_matrix_to_matrix(double **A, int rows, int bandwidth)
void G_math_Ax_sband(double ** A, double *x, double *y, int rows, int bandwidth)
Direct linear equation solver
int G_math_solver_gauss(double **, double *, double *, int )
int G_math_solver_lu(double **, double *, double *, int )
int G_math_solver_cholesky(double **, double *, double *, int , int )
void G_math_solver_cholesky_sband(double **A, double *x, double *b, int rows, int bandwidth)
void G_math_solver_cholesky_sband(double **A, double *x, double *b, int rows, int bandwidth)
Classic iterative linear equation solver for dense and sparsematrices
int G_math_solver_jacobi(double **, double *, double *, int , int , double , double )
int G_math_solver_gs(double **, double *, double *, int , int , double , double )
int G_math_solver_sparse_jacobi(G_math_spvector **, double *, double *, int , int , double , double )
int G_math_solver_sparse_gs(G_math_spvector **, double *, double *, int , int , double , double )
KrylovSubspace iterative linear equation solver for dense, band and sparsematrices
int G_math_solver_pcg(double **, double *, double *, int , int , double , int )
int G_math_solver_cg(double **, double *, double *, int , int , double )
int G_math_solver_cg_sband(double **, double *, double *, int, int, int, double)
int G_math_solver_bicgstab(double **, double *, double *, int , int , double )
int G_math_solver_sparse_pcg(G_math_spvector **, double *, double *, int , int , double , int )
int G_math_solver_sparse_cg(G_math_spvector **, double *, double *, int , int , double )
int G_math_solver_sparse_bicgstab(G_math_spvector **, double *, double *, int , int , double )
LU, Gauss and Cholesky decomposition and substitution functions
void G_math_gauss_elimination(double **, double *, int )
void G_math_lu_decomposition(double **, double *, int )
int G_math_cholesky_decomposition(double **, int , int )
void G_math_cholesky_band_decomposition(double **A, double **T, int rows, int bandwidth)
void G_math_backward_substitution(double **, double *, double *, int )
void G_math_forward_substitution(double **, double *, double *, int )
void G_math_cholesky_band_substitution(double **T, double *x, double *b, int rows, int bandwidth)
Author: David D. Gray
Additions: Brad Douglas
(under development)
This chapter provides an explanation of how numerical algebra routines from LAPACK/BLAS can be accessed through the GRASS GIS library "gmath". Most of the functions are wrapper modules for linear algebra problems, a few are locally implemented.
Getting BLAS/LAPACK (one package) if not already provided by the system:
http://www.netlib.org/lapack/
http://netlib.belllabs.com/netlib/master/readme.html
Precompiled binaries of LAPACK/BLAS are provided on many Linux distributions.
The function name convention is as follows:
mat_struct *G_matrix_init (int rows, int cols, int ldim)
Initialise a matrix structure Initialise a matrix structure. Set the number of rows with the first parameter and columns with the second. The third parameter, lead dimension (>= no. of rows) needs attention by the programmer as it is related to the Fortran workspace:
A 3x3 matrix would be stored as
[ x x x _ ][ x x x _ ][ x x x _ ]
This work space corresponds to the sequence:
(1,1) (2,1) (3,1) and unused are (1,2) (2,2) ... and so on, ie. it is column major. So although the programmer uses the normal parameter sequence of (row, col) the entries traverse the data column by column instead of row by row. Each block in the workspace must be large enough (here 4) to hold a whole column (3) , and trailing spaces are unused. The number of rows (ie. size of a column) is therefore not necessarily the same size as the block size allocated to hold them (called the "lead dimension") . Some operations may produce matrices a different size from the inputs, but still write to the same workspace. This may seem awkward, but it does make for efficient code. Unfortunately, this creates a responsibility on the programmer to specify the lead dimension (>= no. of rows). In most cases the programmer can just use the rows. So for 3 rows/2 cols it would be called:
G_matrix_init (3, 2, 3);
mat_struct *G_matrix_set (mat_struct *A, int rows, int cols, int ldim)
Set parameters for a matrix structureSet parameters for a matrix structure that is allocated but not yet initialised fully.
Note:
G_matrix_set() is an alternative to G_matrix_init() . G_matrix_init() initialises and returns a pointer to a dynamically allocated matrix structure (ie. in the process heap) . G_matrix_set() sets the parameters for an already created matrix structure. In both cases the data workspace still has to be allocated dynamically.
Example 1:
mat_struct *A; G_matrix_set (A, 4, 3, 4);
Example 2:
mat_struct A; /* Allocated on the local stack */ G_matrix_set (&A, 4, 3, 4) ;
mat_struct *G_matrix_add (mat_struct *mt1, mat_struct *mt2)
Add two matrices. Add two matrices and return the result. The receiving structure should not be initialised, as the matrix is created by the routine.
mat_struct *G_matrix_product (mat_struct *mt1, mat_struct *mt2)
Multiply two matricesMultiply two matrices and return the result. The receiving structure should not be initialised, as the matrix is created by the routine.
mat_struct *G_matrix_scale (mat_struct *mt1, const double c)
Scale matrix Scale the matrix by a given scalar value and return the result. The receiving structure should not be initialised, as the matrix is created by the routine.
mat_struct *G_matrix_subtract (mat_struct *mt1, mat_struct *mt2)
Subtract two matrices. Subtract two matrices and return the result. The receiving structure should not be initialised, as the matrix is created by the routine.
mat_struct *G_matrix_copy (const mat_struct *A)
Copy a matrix. Copy a matrix by exactly duplicating its structure.
mat_struct *G_matrix_transpose (mat_struct *mt)
Transpose a matrix. Transpose a matrix by creating a new one and populating with transposed element s.
void G_matrix_print (mat_struct *mt)
Print out a matrix. Print out a representation of the matrix to standard output.
int G_matrix_LU_solve (const mat_struct *mt1, mat_struct **xmat0, const mat_struct *bmat, mat_type mtype)
Solve a general system A.X=B. Solve a general system A.X=B, where A is a NxN matrix, X and B are NxC matrices, and we are to solve for C arrays in X given B. Uses LU decomposition.
Links to LAPACK function dgesv_() and similar to perform the core routine. (By default solves for a general nonsymmetric matrix .)
mtype is a flag to indicate what kind of matrix (real/complex, Hermitian, symmetric, general etc.) is used (NONSYM, SYM, HERMITIAN) .
Warning: NOT YET COMPLETE: only some solutions' options available. Now, only general real matrix is supported.
mat_struct *G_matrix_inverse (mat_struct *mt)
Matrix inversion using LU decomposition Calls G_matrix_LU_solve() to obtain matrix inverse using LU decomposition. Returns NULL on failure.
void G_matrix_free (mat_struct *mt)
Free up allocated matrix Free up allocated matrix.
int G_matrix_set_element (mat_struct *mt, int rowval, int colval, double val)
Set the value of the (i,j) th element Set the value of the (i,j) th element to a double value. Index values are Clike ie. zerobased. The row number is given first as is conventional. Returns 1 if the accessed cell is outside the bounds.
double G_matrix_get_element (mat_struct *mt, int rowval, int colval)
Retrieve value of the (i,j) th element Retrieve the value of the (i,j) th element to a double value. Index values are Clike ie. zerobased.
Note: Does currently not set an error flag for bounds checking.
vec_struct *G_matvect_get_column (mat_struct *mt, int col) Retrieve a column of matrix Retrieve a column of the matrix to a vector structure. The receiving structure should not be initialised, as the vector is created by the routine. Col 0 is the first column.
vec_struct *G_matvect_get_row (mat_struct *mt, int row) Retrieve a row of matrix Retrieve a row of the matrix to a vector structure. The receiving structure should not be initialised, as the vector is created by the routine. Row 0 is the first number.
int G_matvect_extract_vector (mat_struct *mt, vtype vt, int indx) Convert matrix to vectorConvert the current matrix structure to a vector structure. The vtype is RVEC or CVEC which specifies a row vector or column vector. The indx indicates the row/column number (zero based) .
int G_matvect_retrieve_matrix (vec_struct *vc) Revert a vector to matrix Revert a vector structure to a matrix .
vec_struct *G_vector_init (int cells, int ldim, vtype vt) Initialise a vector structure Initialise a vector structure. The vtype is RVEC or CVEC which specifies a row vector or column vector.
int G_vector_set (vec_struct *A, int cells, int ldim, vtype vt, int vindx) Set parameters for vector structureSet parameters for a vector structure that is allocated but not yet initialised fully. The vtype is RVEC or CVEC which specifies a row vector or column vector.
vec_struct *G_vector_copy (const vec_struct *vc1, int comp_flag) Copy a vectorCopy a vector to a new vector structure. This preserves the underlying structure unless you specify DO_COMPACT comp_flag:
0 Eliminate unnecessary rows (cols) in matrix
1 ... or not
double G_vector_norm_euclid (vec_struct *vc) Calculates euclidean norm Calculates the euclidean norm of a row or column vector, using BLAS routine dnrm2_()
double G_vector_norm_maxval (vec_struct *vc, int vflag) Calculates maximum value Calculates the maximum value of a row or column vector. The vflag setting defines which value to be calculated:
vflag:
1 Indicates maximum value
1 Indicates minimum value
0 Indicates absolute value [???]
Note: More functions and wrappers will be implemented soon (11/2000) .
The numbers of rows and columns is stored in the matrix structure:
G_message (" M1 rows: %d, M1 cols: %d", m1>rows, m1>cols);
Draft Notes:
G_vector_free() can be done by G_matrix_free() .
#define G_vector_free(x) G_matrix_free( (x) )
Ax calculations can be done with G_matrix_multiply()
Vector print can be done by G_matrix_print() .
#define G_vector_print(x) G_matrix_print( (x) )
The Makefile needs a reference to in LIBES line.
Example module:
#include <grass/config.h> #include <grass/gis.h> #include <grass/gmath.h> int main (int argc, char *argv[]) { mat_struct *matrix; double val; /* init a 3x2 matrix */ matrix = G_matrix_init (3, 2, 3); /* set cell element 0,0 in matrix to 2.2: */ G_matrix_set_element (matrix, 0, 0, 2.2); /* retrieve this value */ val = G_matrix_get_element (matrix, 0, 0); /* print it */ G_message ( "Value: %g", val); /* Free the memory */ G_matrix_free (matrix); return 0; }
See Compiling and Installing GRASS Modules for a complete discussion of Makefiles.