diff options
| -rw-r--r-- | Makefile | 10 | ||||
| -rw-r--r-- | nnls.c | 417 | ||||
| -rw-r--r-- | nnls.h | 1 | ||||
| -rw-r--r-- | nnls_solver.c | 169 |
4 files changed, 597 insertions, 0 deletions
diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..47c2fcf --- /dev/null +++ b/Makefile @@ -0,0 +1,10 @@ +VERSION=\"v0.0.1\" +CC = gcc +NNLS_CFLAGS = -O3 -s -mtune=native -Wall -lm -lz -DVERSION=$(VERSION) + +all: nnls_solver + +nnls_solver: + $(CC) nnls_solver.c nnls.c -o nnls_solver $(NNLS_CFLAGS) +clean: + rm -vf nnls_solver @@ -0,0 +1,417 @@ +/* + * nnls.c (c) 2003-2009 Turku PET Centre + * This file contains the routine NNLS (nonnegative least squares) + * and the subroutines required by it, except h12, which is in + * file 'lss_h12.c'. + * + * This routine is based on the text and fortran code in + * C.L. Lawson and R.J. Hanson, Solving Least Squares Problems, + * Prentice-Hall, Englewood Cliffs, New Jersey, 1974. + * Version: + * 2002-08-19 Vesa Oikonen + * 2003-05-08 Kaisa Sederholm & VO + * Included function nnlsWght(). + * 2003-05-12 KS + * Variable a_dim1 excluded + * + * Usage of the coefficient matrix altered so that it is + * given in a[][] instead of a[]. + * 2003-11-06 VO + * If n<2, then itmax is set to n*n instead of previous n*3. + * 2004-09-17 VO + * Doxygen style comments. + * 2006-24-04 Pauli Sundberg + * Added some debuging output, and made some comments more precise. + * 2007-05-17 VO + * 2009-04-16 VO + * Corrected a bug in nnls() which may have caused an infinite loop. + * 009-04-27 VO + * Added function nnlsWghtSquared() for faster pixel-by-pixel calculations. + * Checking for exceeding iteration count is corrected in nnls(). + */ +#include <stdio.h> +#include <stdint.h> +#include <assert.h> +#include <stdlib.h> +#include <math.h> +#define MAX(a,b) ((a) >= (b) ? (a) : (b)) +#define ABS(x) ((x) >= 0 ? (x) : -(x)) + +int64_t h12( int64_t mode, int64_t lpivot, int64_t l1, int64_t m, double *u, int64_t u_dim1, double *up, double *cm, int64_t ice, int64_t icv, int64_t ncv) { + double d1, b, clinv, cl, sm; + int64_t k, j; + + /* Check parameters */ + if (mode!=1 && mode!=2) + return(1); + if (m<1 || u==NULL || u_dim1<1 || cm==NULL) + assert(0); + // return(1); + if (lpivot<0 || lpivot>=l1 || l1>m) + // assert(0); + return(1); + + /* Function Body */ + cl = ABS( u[lpivot*u_dim1] ); + // cl= (d1 = u[lpivot*u_dim1], fabs(d1)); + + if (mode==2) + { /* Apply transformation I+U*(U**T)/B to cm[] */ + if(cl<=0.) + // assert(0); + return(0); + } + else + { /* Construct the transformation */ + + + /* This is the way provided in the original pseudocode + sm = 0; + for (j = l1; j < m; j++) + { + d1 = u[j * u_dim1]; + sm += d1*d1; + } + d1 = u[lpivot * u_dim1]; + sm += d1*d1; + sm = sqrt(sm); + + if (u[lpivot*u_dim1] > 0) + sm=-sm; + + up[0] = u[lpivot*u_dim1] - sm; + u[lpivot*u_dim1]=sm; + printf("Got sum: %f\n",sm); + */ + + /* and this trying to compensate overflow */ + for (j=l1; j<m; j++) + { // Computing MAX + cl = MAX( ABS( u[j*u_dim1] ), cl ); + } + // zero vector? + + if (cl<=0.) + return(0); + + clinv=1.0/cl; + + // Computing 2nd power + d1=u[lpivot*u_dim1]*clinv; + sm=d1*d1; + + for (j=l1; j<m; j++) + { + d1=u[j*u_dim1]*clinv; + sm+=d1*d1; + } + cl *= sqrt(sm); + + if (u[lpivot*u_dim1] > 0.) + cl=-cl; + up[0] = u[lpivot*u_dim1] - cl; + u[lpivot*u_dim1]=cl; + } + + // no vectors where to apply? only change pivot vector! + b=up[0] * u[lpivot*u_dim1]; + + /* b must be nonpositive here; if b>=0., then return */ + if (b == 0) + return(0); + + // ok, for all vectors we want to apply + for (j =0; j < ncv; j++) { + sm = cm[ lpivot * ice + j * icv ] * (up[0]); + + for (k=l1; k<m; k++) + sm += cm[ k * ice + j*icv ] * u[ k*u_dim1 ]; + + if (sm != 0.0) { + sm *= (1/b); + // cm[lpivot, j] = .. + cm[ lpivot * ice + j*icv] += sm * (up[0]); + for (k= l1; k<m; k++) + { + cm[ k*ice + j*icv] += u[k * u_dim1]*sm; + } + } + } + + return(0); +} + + +void g1(double a, double b, double *cterm, double *sterm, double *sig) +{ + double d1, xr, yr; + + if( fabs(a) > fabs(b) ) { + xr = b / a; + d1 = xr; + yr = sqrt(d1*d1 + 1.); + d1 = 1./yr; + *cterm=(a>=0.0 ? fabs(d1) : -fabs(d1)); + *sterm=(*cterm)*xr; + *sig=fabs(a)*yr; + } else if( b != 0.) { + xr = a / b; + d1 = xr; + yr = sqrt(d1 * d1 + 1.); + d1 = 1. / yr; + *sterm=(b>=0.0 ? fabs(d1) : -fabs(d1)); + *cterm=(*sterm)*xr; *sig=fabs(b)*yr; + } else { + *sig=0.; *cterm=0.; *sterm=1.; + } +} + + +int64_t nnls_algorithm(double *a, int64_t m,int64_t n, double *b, double *x, double *rnorm) { + int64_t pfeas; + int ret=0; + int64_t iz; + int64_t jz; + int64_t k, j=0, l, itmax, izmax=0, ii, jj=0, ip; + double d1, d2, sm, up, ss; + double temp, wmax, t, alpha, asave, dummy, unorm, ztest, cc; + + + /* Check the parameters and data */ + if(m <= 0 || n <= 0 || a == NULL || b == NULL || x == NULL) + return(2); + + /* Allocate memory for working space, if required */ + double *w = (double*)calloc(n, sizeof(double)); + double *zz = (double*)calloc(m, sizeof(double)); + int64_t *index = (int64_t*)calloc(n, sizeof(int64_t)); + if(w == NULL || zz == NULL || index == NULL) + return(2); + + /* Initialize the arrays INDEX[] and X[] */ + for(k=0; k<n; k++) { + x[k]=0.; + index[k]=k; + } + + int64_t iz2 = n - 1; + int64_t iz1 = 0; + int64_t iter=0; + int64_t nsetp=0; + int64_t npp1=0; + + /* Main loop; quit if all coeffs are already in the solution or */ + /* if M cols of A have been triangularized */ + if(n < 3) + itmax=n*3; + else + itmax=n*n; + + + while(iz1 <= iz2 && nsetp < m) { + /* Compute components of the dual (negative gradient) vector W[] */ + for(iz=iz1; iz<=iz2; iz++) { + j=index[iz]; + sm=0.; + for(l=npp1; l<m; l++) + sm+=a[j*m + l]*b[l]; + w[j]=sm; + } + + while(1) { + /* Find largest positive W[j] */ + for(wmax=0., iz=iz1; iz<=iz2; iz++) { + j=index[iz]; if(w[j]>wmax) {wmax=w[j]; izmax=iz;}} + + /* Terminate if wmax<=0.; */ + /* it indicates satisfaction of the Kuhn-Tucker conditions */ + if(wmax<=0.0) + break; + + iz=izmax; + j=index[iz]; + + /* The sign of W[j] is ok for j to be moved to set P. */ + /* Begin the transformation and check new diagonal element to avoid */ + /* near linear dependence. */ + asave=a[j*m + npp1]; + h12(1, npp1, npp1+1, m, &a[j*m +0], 1, &up, &dummy, 1, 1, 0); + unorm=0.; + if(nsetp!=0){ + for(l=0; l<nsetp; l++) { + d1=a[j*m + l]; + unorm+=d1*d1; + } + } + + unorm=sqrt(unorm); + d2=unorm+(d1=a[j*m + npp1], fabs(d1)) * 0.01; + if((d2-unorm)>0.) { + /* Col j is sufficiently independent. Copy B into ZZ, update ZZ */ + /* and solve for ztest ( = proposed new value for X[j] ) */ + for(l=0; l<m; l++) zz[l]=b[l]; + h12(2, npp1, npp1+1, m, &a[j*m + 0], 1, &up, zz, 1, 1, 1); + ztest=zz[npp1]/a[j*m +npp1]; + /* See if ztest is positive */ + if(ztest>0.) break; + } + + /* Reject j as a candidate to be moved from set Z to set P. Restore */ + /* A[npp1,j], set W[j]=0., and loop back to test dual coeffs again */ + a[j*m+ npp1]=asave; w[j]=0.; + } /* while(1) */ + + if(wmax<=0.0) + break; + + /* Index j=INDEX[iz] has been selected to be moved from set Z to set P. */ + /* Update B and indices, apply householder transformations to cols in */ + /* new set Z, zero subdiagonal elts in col j, set W[j]=0. */ + for(l=0; l<m; ++l) + b[l]=zz[l]; + + index[iz]=index[iz1]; + index[iz1]=j; + iz1++; + npp1++; + nsetp=npp1; + + if(iz1<=iz2) { + for(jz=iz1; jz<=iz2; jz++) { + jj=index[jz]; + h12(2, nsetp-1, npp1, m, &a[j*m +0], 1, &up, &a[jj*m +0], 1, m, 1); + } + } + + if(nsetp!=m) { + for(l=npp1; l<m; l++) + a[j*m +l]=0.; + } + + w[j]=0.; + + /* Solve the triangular system; store the solution temporarily in Z[] */ + for(l=0; l<nsetp; l++) { + ip=nsetp-(l+1); + if(l!=0) for(ii=0; ii<=ip; ii++) zz[ii]-=a[jj*m + ii]*zz[ip+1]; + jj=index[ip]; zz[ip]/=a[jj*m +ip]; + } + + /* Secondary loop begins here */ + while(++iter < itmax) { + /* See if all new constrained coeffs are feasible; if not, compute alpha */ + for(alpha = 2.0, ip = 0; ip < nsetp; ip++) { + l=index[ip]; + if(zz[ip]<=0.) { + t = -x[l]/(zz[ip]-x[l]); + if(alpha > t) { + alpha = t; + jj = ip - 1; + } + } + } + + /* If all new constrained coeffs are feasible then still alpha==2. */ + /* If so, then exit from the secondary loop to main loop */ + if(alpha==2.0) + break; + + /* Use alpha (0.<alpha<1.) to interpolate between old X and new ZZ */ + for(ip=0; ip<nsetp; ip++) { + l = index[ip]; + x[l] += alpha*(zz[ip]-x[l]); + } + + /* Modify A and B and the INDEX arrays to move coefficient i */ + /* from set P to set Z. */ + k=index[jj+1]; pfeas=1; + do { + x[k]=0.; + if(jj!=(nsetp-1)) { + jj++; + for(j=jj+1; j<nsetp; j++) { + ii=index[j]; index[j-1]=ii; + g1(a[ii*m + (j-1)], a[ii*m + j], &cc, &ss, &a[ii*m + j-1]); + for(a[ii*m + j]=0., l=0; l<n; l++) if(l!=ii) { + /* Apply procedure G2 (CC,SS,A(J-1,L),A(J,L)) */ + temp=a[l*m + j-1]; + a[l*m + j-1]=cc*temp+ss*a[l*m + j]; + a[l*m + j]=-ss*temp+cc*a[l*m + j]; + } + /* Apply procedure G2 (CC,SS,B(J-1),B(J)) */ + temp=b[j-1]; b[j-1]=cc*temp+ss*b[j]; b[j]=-ss*temp+cc*b[j]; + } + } + npp1=nsetp-1; nsetp--; iz1--; index[iz1]=k; + + /* See if the remaining coeffs in set P are feasible; they should */ + /* be because of the way alpha was determined. If any are */ + /* infeasible it is due to round-off error. Any that are */ + /* nonpositive will be set to zero and moved from set P to set Z */ + for(jj=0, pfeas=1; jj<nsetp; jj++) { + k=index[jj]; if(x[k]<=0.) {pfeas=0; break;} + } + } while(pfeas==0); + + /* Copy B[] into zz[], then solve again and loop back */ + for(k=0; k<m; k++) + zz[k]=b[k]; + for(l=0; l<nsetp; l++) { + ip=nsetp-(l+1); + if(l!=0) for(ii=0; ii<=ip; ii++) zz[ii]-=a[jj*m + ii]*zz[ip+1]; + jj=index[ip]; zz[ip]/=a[jj*m + ip]; + } + } /* end of secondary loop */ + + if(iter>=itmax) { + ret = 1; + break; + } + + for(ip=0; ip<nsetp; ip++) { + k=index[ip]; + x[k]=zz[ip]; + } + } /* end of main loop */ + + /* Compute the norm of the final residual vector */ + sm=0.; + + if (rnorm != NULL) { + if (npp1<m) + for (k=npp1; k<m; k++) + sm+=(b[k] * b[k]); + else + for (j=0; j<n; j++) + w[j]=0.; + *rnorm=sqrt(sm); + } + + /* Free working space, if it was allocated here */ + free(w); + free(zz); + free(index); + return(ret); +} +/* nnls_ */ + + +double *nnls(double *a_matrix, double *b_matrix, int64_t height, int64_t width) { + + double *solution = (double*)calloc(height, sizeof(double)); + + if(solution == NULL) { + fprintf(stderr, "could not allocate enough memory for nnls\n"); + exit(EXIT_FAILURE); + } + + int ret = nnls_algorithm(a_matrix, width, height, b_matrix, solution, NULL); + if(ret == 1) { + printf("NNLS has reached the maximum iterations\n"); + } else if(ret == 2) { + fprintf(stderr, "NNLS could not allocate enough memory\n"); + exit(EXIT_FAILURE); + } + + return solution; +} @@ -0,0 +1 @@ +double *nnls(double *a_matrix, double *b_matrix, int height, int width); diff --git a/nnls_solver.c b/nnls_solver.c new file mode 100644 index 0000000..a8e6798 --- /dev/null +++ b/nnls_solver.c @@ -0,0 +1,169 @@ +#include <ctype.h> +#include <errno.h> +#include <getopt.h> +#include <math.h> +#include <stdio.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <unistd.h> + +#include "nnls.h" + +#define USAGE "." + +int load_a_matrix(char *filename) { + + long x = 0; + long y = 0; + char *line = NULL; + size_t len = 0; + + fh = fopen(filename, "r"); + if(fh == NULL) { + fprintf(stderr, "Could not open %s\n", filename); + exit(EXIT_FAILURE); + } + + if(getline(&line, &len, fp) != -1) { + + } + + while ((read = getline(&line, &len, fp)) != -1) { + + } + + +} +int main(int argc, char **argv) { + + + int c; + + char *a_matrix_filename = NULL; + char *b_matrix_filename = NULL; + char *output_filename = NULL; + char *format = NULL; + + long x = 0; + long y = 0; + + int verbose = 0; + + long width = 0; + long height = 0; + + while (1) { + static struct option long_options[] = { + {"a", required_argument, 0, 'a'}, + {"b", required_argument, 0, 'b'}, + {"output", required_argument, 0, 'o'}, + {"verbose", no_argument, 0, 'v'}, + {"format", required_argument, 0, 'f'}, + {"version", no_argument, 0, 'V'}, + {0, 0, 0, 0} + }; + + int option_index = 0; + + c = getopt_long (argc, argv, "i:o:hdvV", long_options, &option_index); + + if (c == -1) + break; + + switch (c) { + case 0: + case 'a': + a_matrix_filename = optarg; + break; + case 'b': + b_matrix_filename = optarg; + break; + case 'o': + output_filename = optarg; + break; + case 'f': + format = optarg; + break; + case 'v': + verbose = 1; + break; + case 'V': + printf("%s\n", VERSION); + exit(EXIT_SUCCESS); + break; + case 'h': + printf("%s\n", USAGE); + exit(EXIT_SUCCESS); + break; + default: + break; + } + } + + + if(a_matrix_filename == NULL) { + fprintf(stderr, "Error: a matrix file (-a) must be specified\n\n"); + fprintf(stderr, "%s\n", USAGE); + exit(EXIT_FAILURE); + } + + if(b_matrix_filename == NULL) { + fprintf(stderr, "Error: b matrix file (-b) must be specified\n\n"); + fprintf(stderr, "%s\n", USAGE); + exit(EXIT_FAILURE); + } + + if(output_filename == NULL) { + fprintf(stderr, "Error: output filename (-o) must be specified\n\n"); + fprintf(stderr, "%s\n", USAGE); + exit(EXIT_FAILURE); + } + + if(format == NULL) { + format = "%10lf"; + } + + if(verbose) { + printf("a matrix: %s\n", a_matrix_filename); + printf("b matrix: %s\n", a_matrix_filename); + printf("output file: %s\n", output_filename); + } + + if(access (a_matrix_filename, F_OK) == -1) { + fprintf(stderr, "Error: could not open %s\n", a_matrix_filename); + exit(EXIT_FAILURE); + } + + if(access (b_matrix_filename, F_OK) == -1) { + fprintf(stderr, "Error: could not open %s\n", b_matrix_filename); + exit(EXIT_FAILURE); + } + + // load our matricies + double *a_matrix = load_a_matrix(a_matrix_filename); + double *b_matrix = load_b_matrix(b_matrix_filename); + + // run NNLS + double *solution = nnls(a_matrix, b_matrix, height, width); + + // print to stdout if the user supplies "-" as the output argument + FILE *output_fh = NULL; + if(strcmp(output_filename, "-") == 0) { + output_fh = stdout; + } + else { + output_fh = fopen(output_filename, "w"); + } + + if(output_fh == NULL) { + fprintf(stderr, "Could not open %s for writing\n", output_filename); + exit(EXIT_FAILURE); + } + for(x = 0; x < height; x++) { + fprintf(output_fh, format, solution[x]); + } + fclose(output_fh); + + return EXIT_SUCCESS; +} |