diff --git a/wfs_read/LICENSE b/wfs_read/LICENSE new file mode 100644 index 0000000..9cecc1d --- /dev/null +++ b/wfs_read/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/wfs_read/Makefile b/wfs_read/Makefile index 45637de..3545bbd 100644 --- a/wfs_read/Makefile +++ b/wfs_read/Makefile @@ -1,5 +1,5 @@ PROGRAM = readwfs -LDFLAGS = +LDFLAGS = -lm SRCS = $(wildcard *.c) CC = gcc DEFINES = -D_XOPEN_SOURCE=1111 diff --git a/wfs_read/Readme.md b/wfs_read/Readme.md new file mode 100644 index 0000000..71c87f9 --- /dev/null +++ b/wfs_read/Readme.md @@ -0,0 +1,7 @@ +WFS and DAT files analyzer (for BTA Shack-Hartmann reduction utility by ILIT - www.laser.ru) +============================================== + + +DAT analyzer allows to reconstruct wavefront by Zernike coefficients + +WFS analyzer still in progress now. diff --git a/wfs_read/cmdlnopts.c b/wfs_read/cmdlnopts.c index 689ab04..23011af 100644 --- a/wfs_read/cmdlnopts.c +++ b/wfs_read/cmdlnopts.c @@ -52,7 +52,7 @@ myoption cmdlnopts[] = { {"dat", NEED_ARG, NULL, 'd', arg_string, APTR(&G.indat), _("input DAT file name")}, {"output", NEED_ARG, NULL, 'o', arg_string, APTR(&G.outname), _("output file name")}, {"step", NEED_ARG, NULL, 's', arg_double, APTR(&G.step), _("coordinate step in wavefront map (R=1)")}, - {"wfunits", NEED_ARG, NULL, 'u', arg_string, APTR(&G.wfunits), _("units for wavefront measurement in WF map")}, + {"wfunits", NEED_ARG, NULL, 'u', arg_string, APTR(&G.wfunits), _("units for wavefront measurement in output WF map")}, {"wavelength", NEED_ARG, NULL, 'l', arg_double, APTR(&G.wavelength),_("default wavelength (in meters, microns or nanometers), 101..9999nm")}, end_option }; diff --git a/wfs_read/main.c b/wfs_read/main.c index 9591a38..7d578f7 100644 --- a/wfs_read/main.c +++ b/wfs_read/main.c @@ -76,6 +76,21 @@ void proc_DAT(){ } printf("Read coefficients:\n"); for(i = 0; i < Zn; ++i) printf("%4d\t%g\n", i, zerncoeffs[i]); + + int L; + polar *crds = gen_coords(&L); + if(!crds){ + WARNX("malloc()"); + return; + } + printf("%d points\n", L); + double *surf = Zcompose(Zn, zerncoeffs, L, crds); + if(z_save_wavefront(L, crds, surf, GP->outname)) + WARN(_("Can't open file %s"), GP->outname); + else + green(_("Saved to %s\n"), GP->outname); + FREE(crds); + FREE(surf); } /** diff --git a/wfs_read/zernike.c b/wfs_read/zernike.c index f19f53c..68016d1 100644 --- a/wfs_read/zernike.c +++ b/wfs_read/zernike.c @@ -19,16 +19,27 @@ * MA 02110-1301, USA. */ + +#define _GNU_SOURCE (1) // for math.h +#include #include #include "zernike.h" #include "usefull_macros.h" +#ifndef iabs +#define iabs(a) (((a)<(0)) ? (-a) : (a)) +#endif + // coordinate step on a grid static double coord_step = DEFAULT_CRD_STEP; // default wavelength for wavefront (650nm) in meters static double wavelength = DEFAULT_WAVELENGTH; // default coefficient to transform vawefront from wavelengths into user value static double wf_coeff = 1.; +// array of factorials 1..100 +static double *FK = NULL; +// unit for WF measurement +static char *outpunit = DEFAULT_WF_UNIT; /** * Set default coordinate grid step on an unity circle @@ -36,6 +47,7 @@ static double wf_coeff = 1.; * @return 0 if all OK, -1 or 1 if `step` bad */ int z_set_step(double step){ + printf("set to %g\n", step); if(step < DBL_EPSILON) return -1; if(step > 1.) return 1; coord_step = step; @@ -66,17 +78,17 @@ double z_get_wavelength(){ return wavelength; } -// thanks to http://stackoverflow.com/a/3875555/1965803 +// for `const char * const *units` thanks to http://stackoverflow.com/a/3875555/1965803 typedef struct{ - double wf_coeff; - const char * const *units; + double wf_coeff; // multiplier for wavefront units (in .dat files coefficients are in meters) + const char * const *units; // symbol units' names } wf_units; wf_units wfunits[] = { { 1. , (const char * const []){"meter", "m", NULL}}, - {1e-3 , (const char * const []){"millimeter", "mm", NULL}}, - {1e-6 , (const char * const []){"micrometer", "um", "u", NULL}}, - {1e-9 , (const char * const []){"nanometer", "nm", "n", NULL}}, + {1e3 , (const char * const []){"millimeter", "mm", NULL}}, + {1e6 , (const char * const []){"micrometer", "um", "u", NULL}}, + {1e9 , (const char * const []){"nanometer", "nm", "n", NULL}}, {-1. , (const char * const []){"wavelength", "wave", "lambda", "w", "l", NULL}}, {0. , (const char * const []){NULL}} }; @@ -87,15 +99,14 @@ wf_units wfunits[] = { int z_set_wfunit(char *U){ wf_units *u = wfunits; while(u->units[0]){ - const char * const*unit = u->units; + const char * const * unit = u->units; while(*unit){ if(strcasecmp(*unit, U) == 0){ wf_coeff = u->wf_coeff; if(wf_coeff < 0.){ // wavelengths - wf_coeff = 1.; // in wavelengths - }else{ // meters etc - wf_coeff = wavelength / wf_coeff; + wf_coeff = 1./wavelength; // in wavelengths } + outpunit = (char*)u->units[0]; printf("wf_coeff = %g\n", wf_coeff); return 0; } @@ -118,7 +129,7 @@ void z_print_wfunits(){ printf(_("Unit (meters)\tAvailable values\n")); do{ const char * const*unit = u->units; - double val = u->wf_coeff; + double val = 1./u->wf_coeff; if(val > 0.) printf("%-8g\t", val); else @@ -130,3 +141,208 @@ void z_print_wfunits(){ }while((++u)->units[0]); printf("\n"); } + +/** + * Convert polynomial order in Noll notation into n/m + * @param p (i) - order of Zernike polynomial in Noll notation + * @param N (o) - order of polynomial + * @param M (o) - angular parameter + */ +void convert_Zidx(int p, int *N, int *M){ + int n = (int) floor((-1.+sqrt(1.+8.*p)) / 2.); + if(M) *M = (int)(2.0*(p - n*(n+1.)/2. - 0.5*(double)n)); + if(N) *N = n; +} + +/** + * Generate polar coordinates for grid [-1..1] by both coordinates + * with default step + * @param len (o) - size of array + * @return array of coordinates + */ +polar *gen_coords(int *len){ + int WH = 1 + (int)(2. / coord_step), max_sz = WH * WH, L = 0; + polar *coordinates = malloc(max_sz * sizeof(polar)), *cptr = coordinates; + if(!cptr) return NULL; + double x, y; + for(y = -1.; y < 1.; y += coord_step){ + for(x = -1.; x < 1.; x += coord_step){ + double R = sqrt(x*x + y*y); + if(R > 1.) continue; + cptr->r = R; + cptr->theta = atan2(y, x); + ++cptr; + ++L; + } + } + printf("%d points outside circle (ratio = %g, ideal = %g)\n", max_sz - L, ((double)L)/max_sz, M_PI/4.); + if(len) *len = L; + return coordinates; +} + +/** + * Build pre-computed array of factorials from 1 to 100 + */ +void build_factorial(){ + double F = 1.; + int i; + if(FK) return; + FK = MALLOC(double, ZERNIKE_MAX_POWER); + FK[0] = 1.; + for(i = 1; i < ZERNIKE_MAX_POWER; i++) + FK[i] = (F *= (double)i); +} + +/** + * Validation check of zernfun parameters + * return 1 in case of error + */ +int check_parameters(int n, int m, int Sz, polar *P){ + if(Sz < 3 || !P){ + WARNX(_("Size of matrix must be > 2!")); + return 1; + } + if(n > ZERNIKE_MAX_POWER){ + WARNX(_("Order of Zernike polynomial must be <= 100!")); + return 1; + } + int erparm = 0; + if(n < 0) erparm = 1; + if(n < iabs(m)) erparm = 1; // |m| must be <= n + if((n - m) % 2) erparm = 1; // n-m must differ by a prod of 2 + if(erparm) + WARNX(_("Wrong parameters of Zernike polynomial (%d, %d)"), n, m); + else + if(!FK) build_factorial(); + return erparm; +} + +/** + * Build array with R powers (from 0 to n inclusive) + * @param n - power of Zernike polinomial (array size = n+1) + * @param Sz - size of P array + * @param P (i) - polar coordinates of points + */ +double **build_rpow(int n, int Sz, polar *P){ + int i, j, N = n + 1; + double **Rpow = MALLOC(double*, N); + Rpow[0] = MALLOC(double, Sz); + for(i = 0; i < Sz; i++) Rpow[0][i] = 1.; // zero's power + for(i = 1; i < N; i++){ // Rpow - is quater I of cartesian coordinates ('cause other are fully simmetrical) + Rpow[i] = MALLOC(double, Sz); + double *rp = Rpow[i], *rpo = Rpow[i-1]; + polar *p = P; + for(j = 0; j < Sz; j++, rp++, rpo++, p++){ + *rp = (*rpo) * p->r; + } + } + return Rpow; +} + +/** + * Free array of R powers with power n + * @param Rpow (i) - array to free + * @param n - power of Zernike polinomial for that array (array size = n+1) + */ +void free_rpow(double ***Rpow, int n){ + int i, N = n+1; + for(i = 0; i < N; i++) FREE((*Rpow)[i]); + FREE(*Rpow); +} + +/** + * Zernike function for scattering data + * @param n,m - orders of polynomial + * @param Sz - number of points + * @param P(i) - array with points coordinates (polar, r<=1) + * @param norm(o) - (optional) norm coefficient + * @return dynamically allocated array with Z(n,m) for given array P + */ +double *zernfun(int n, int m, int Sz, polar *P, double *norm){ + if(check_parameters(n, m, Sz, P)) return NULL; + int j, k, m_abs = iabs(m), iup = (n-m_abs)/2; + double **Rpow = build_rpow(n, Sz, P); + double ZSum = 0.; + // now fill output matrix + double *Zarr = MALLOC(double, Sz); // output matrix + double *Zptr = Zarr; + polar *p = P; + for(j = 0; j < Sz; j++, p++, Zptr++){ + double Z = 0.; + if(p->r > 1.) continue; // throw out points with R>1 + // calculate R_n^m + for(k = 0; k <= iup; k++){ // Sum + double z = (1. - 2. * (k % 2)) * FK[n - k] // (-1)^k * (n-k)! + /(//----------------------------------- ----- ------------------------------- + FK[k]*FK[(n+m_abs)/2-k]*FK[(n-m_abs)/2-k] // k!((n+|m|)/2-k)!((n-|m|)/2-k)! + ); + Z += z * Rpow[n-2*k][j]; // *R^{n-2k} + } + // normalize + double eps_m = (m) ? 1. : 2.; + Z *= sqrt(2.*(n+1.) / M_PI / eps_m ); + double m_theta = (double)m_abs * p->theta; + // multiply to angular function: + if(m){ + if(m > 0) + Z *= cos(m_theta); + else + Z *= sin(m_theta); + } + *Zptr = Z; + ZSum += Z*Z; + } + if(norm) *norm = ZSum; + // free unneeded memory + free_rpow(&Rpow, n); + return Zarr; +} + +/** + * Restoration of image in points P by Zernike polynomials' coefficients + * @param Zsz (i) - number of actual elements in coefficients array + * @param Zidxs(i) - array with Zernike coefficients + * @param Sz, P(i) - number (Sz) of points (P) + * @return restored image + */ +double *Zcompose(int Zsz, double *Zidxs, int Sz, polar *P){ + int i; + double *image = MALLOC(double, Sz); + for(i = 0; i < Zsz; i++){ // now we fill array + double K = Zidxs[i]; + if(fabs(K) < DBL_EPSILON) continue; // 0.0 + int n, m; + convert_Zidx(i, &n, &m); + double *Zcoeff = zernfun(n, m, Sz, P, NULL); + int j; + double *iptr = image, *zptr = Zcoeff; + for(j = 0; j < Sz; j++, iptr++, zptr++) + *iptr += K * (*zptr); // add next Zernike polynomial + FREE(Zcoeff); + } + return image; +} + +/** + * Save restored wavefront into file `filename` + * @param Sz - size of `P` + * @param P (i) - points coordinates + * @param Z (i) - wavefront shift (in lambdas) + * @param filename (i) - name of output file + * @return 1 if failed + */ +int z_save_wavefront(int Sz, polar *P, double *Z, char *filename){ + if(!P || !Z || Sz < 0 || !filename) return 1; + FILE *f = fopen(filename, "w"); + if(!f) return 1; + fprintf(f, "# X (-1..1)\tY (-1..1)\tZ (%ss)\n", outpunit); + int i; + for(i = 0; i < Sz; ++i, ++P, ++Z){ + double x, y, s, c, r = P->r; + sincos(P->theta, &s, &c); + x = r * c, y = r * s; + fprintf(f, "%g\t%g\t%g\n", x, y, (*Z) * wf_coeff); + } + fclose(f); + return 0; +} diff --git a/wfs_read/zernike.h b/wfs_read/zernike.h index 1e5cc25..5c924b8 100644 --- a/wfs_read/zernike.h +++ b/wfs_read/zernike.h @@ -25,9 +25,16 @@ // default step in coordinate grid #define DEFAULT_CRD_STEP (0.05) // default wavefront unit: lambda -#define DEFAULT_WF_UNIT "lambda" +#define DEFAULT_WF_UNIT "meter" // default wavelength #define DEFAULT_WAVELENGTH (0.65e-6) +// max power of Zernike polynomial +#define ZERNIKE_MAX_POWER (100) + + +typedef struct{ + double r,theta; +} polar; int z_set_step(double step); double z_get_step(); @@ -39,5 +46,11 @@ int z_set_wfunit(char *u); double z_get_wfcoeff(); void z_print_wfunits(); +void convert_Zidx(int p, int *N, int *M); +polar *gen_coords(int *len); + +double *Zcompose(int Zsz, double *Zidxs, int Sz, polar *P); + +int z_save_wavefront(int Sz, polar *P, double *Z, char *filename); #endif // __ZERNIKE_H__