From 6c970262e0d41252b0ada1a80a6c6293ddcdfec9 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 9 Jan 2013 16:00:59 +0100 Subject: GrainSpotter interface (works) --- libcrystfel/src/grainspotter.c | 165 +++++++++++++++++++++++++++++++++++++---- 1 file changed, 152 insertions(+), 13 deletions(-) (limited to 'libcrystfel') diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c index 06f65f08..b7e5ce0a 100644 --- a/libcrystfel/src/grainspotter.c +++ b/libcrystfel/src/grainspotter.c @@ -50,9 +50,10 @@ #include "image.h" -#include "grainspotter.h" #include "utils.h" #include "peaks.h" +#include "cell.h" +#include "cell-utils.h" #define GRAINSPOTTER_VERBOSE 0 @@ -70,30 +71,99 @@ struct grainspotter_data { }; +static int read_matrix(struct image *image) +{ + FILE *fh; + int d1; + float d2; + float ubi11, ubi12, ubi13; + float ubi21, ubi22, ubi23; + float ubi31, ubi32, ubi33; + char filename[1024]; + char line[1024]; + int r; + + snprintf(filename, 1023, "xfel-%i.gff", image->id); + + fh = fopen(filename, "r"); + if ( fh == NULL ) { + ERROR("Can't open '%s'\n", filename); + return 1; + } + + /* Read and discard first line */ + if ( fgets(line, 1024, fh) == NULL ) { + ERROR("Failed to read GFF file.\n"); + return 1; + } + + /* One line per grain */ + if ( fgets(line, 1024, fh) == NULL ) { + ERROR("Failed to read GFF file.\n"); + return 1; + } + + STATUS("'%s'\n", line); + + r = sscanf(line, + "%i %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f", + &d1, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, + &ubi11, &ubi12, &ubi13, &ubi21, &ubi22, &ubi23, &ubi31, &ubi32, &ubi33); + + if ( r != 24 ) { + ERROR("Only %i parameters in GFF file\n", r); + return 1; + } + + fclose(fh); + + image->candidate_cells[0] = cell_new(); + +// cell_set_cartesian(image->candidate_cells[0], +// ubi11/1e10, ubi12/1e10, ubi13/1e10, +// ubi21/1e10, ubi22/1e10, ubi23/1e10, +// ubi31/1e10, ubi32/1e10, ubi33/1e10); + + cell_set_cartesian(image->candidate_cells[0], + ubi12/1e10, ubi13/1e10, ubi11/1e10, + ubi22/1e10, ubi23/1e10, ubi21/1e10, + ubi32/1e10, ubi33/1e10, ubi31/1e10); + + + image->ncells = 1; + cell_print(image->candidate_cells[0]); + + return 0; +} + + static int grainspotter_readable(struct image *image, struct grainspotter_data *grainspotter) { int rval; rval = read(grainspotter->pty, - grainspotter->rbuffer+grainspotter->rbufpos, - grainspotter->rbuflen-grainspotter->rbufpos); + grainspotter->rbuffer, grainspotter->rbuflen); - if ( (rval == -1) || (rval == 0) ) return 1; + if ( rval == -1 ) { + ERROR("Read failed: %s\n", strerror(errno)); + return 1; + } + + grainspotter->rbuffer[rval] = '\0'; - /* FIXME! (if needed) */ - //grainspotter->rbufpos += rval; - //assert(grainspotter->rbufpos <= grainspotter->rbuflen); + printf("GrainSpotter: '%s'\n", grainspotter->rbuffer); return 0; } -static void write_gve(struct image *image) +static void write_gve(struct image *image, UnitCell *cell) { FILE *fh; int i; char filename[1024]; + double a, b, c, al, be, ga; snprintf(filename, 1023, "xfel-%i.gve", image->id); @@ -102,7 +172,14 @@ static void write_gve(struct image *image) ERROR("Couldn't open temporary file '%s'\n", filename); return; } - fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */ + + cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga); + fprintf(fh, "%.6f %.6f %.6f %.6f %.6f %.6f P\n", a*1e10, b*1e10, c*1e10, + rad2deg(al), rad2deg(be), rad2deg(ga)); + fprintf(fh, "# wavelength = %.6f\n", image->lambda*1e10); + fprintf(fh, "# wedge = 0.000000\n"); + fprintf(fh, "# ds h k l\n"); + fprintf(fh, "# xr yr zr xc yc ds eta omega\n"); for ( i=0; ifeatures); i++ ) { @@ -111,11 +188,60 @@ static void write_gve(struct image *image) f = image_get_feature(image->features, i); if ( f == NULL ) continue; - fprintf(fh, "%10f %10f %10f %8f\n", - f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0); + fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n", + f->rz/1e10, f->rx/1e10, f->ry/1e10, + modulus(f->rx, f->ry, f->rz)/1e10, /* dstar */ + atan2(f->ry, f->rx), 0.0); /* eta, omega */ + + } + fclose(fh); +} + + +static char *write_ini(struct image *image) +{ + FILE *fh; + char *filename; + double tt; + + filename = malloc(1024); + if ( filename == NULL ) return NULL; + snprintf(filename, 1023, "xfel-%i.ini", image->id); + + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + free(filename); + return NULL; } + + get_q_for_panel(image->det->furthest_out_panel, + image->det->furthest_out_fs, + image->det->furthest_out_ss, + &tt, 1.0/image->lambda); + + fprintf(fh, "spacegroup 96\n"); + fprintf(fh, "!dsrange 0 1.3\n"); + fprintf(fh, "tthrange 0 %.2f\n", 20.0); + fprintf(fh, "etarange 0 360\n"); + fprintf(fh, "domega 1\n"); + fprintf(fh, "omegarange -0.5 0.5\n"); + fprintf(fh, "filespecs xfel-%i.gve xfel-%i.log\n", + image->id, image->id); + fprintf(fh, "cuts 3 0.1 0.5\n"); + fprintf(fh, "eulerstep 8\n"); + fprintf(fh, "uncertainties 0.1 0.2 .5\n"); + fprintf(fh, "nsigmas 2\n"); + fprintf(fh, "minfracg 0.95\n"); + fprintf(fh, "Nhkls_in_indexing 500\n"); + fprintf(fh, "random 10000\n"); + fprintf(fh, "!positionfit\n"); + fprintf(fh, "genhkl\n"); + fclose(fh); + + return filename; } @@ -125,8 +251,15 @@ void run_grainspotter(struct image *image, UnitCell *cell) int status; int rval; struct grainspotter_data *grainspotter; + char *ini_filename; + + write_gve(image, cell); + ini_filename = write_ini(image); - write_gve(image); + if ( ini_filename == NULL ) { + ERROR("Failed to write ini file for GrainSpotter.\n"); + return; + } grainspotter = malloc(sizeof(struct grainspotter_data)); if ( grainspotter == NULL ) { @@ -149,11 +282,13 @@ void run_grainspotter(struct image *image, UnitCell *cell) t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); tcsetattr(STDIN_FILENO, TCSANOW, &t); - execlp("GrainSpotter.0.90", "", (char *)NULL); + STATUS("Running GrainSpotter.0.90 '%s'\n", ini_filename); + execlp("GrainSpotter.0.90", "", ini_filename, (char *)NULL); ERROR("Failed to invoke GrainSpotter.\n"); _exit(0); } + free(ini_filename); grainspotter->rbuffer = malloc(256); grainspotter->rbuflen = 256; @@ -210,5 +345,9 @@ void run_grainspotter(struct image *image, UnitCell *cell) ERROR("GrainSpotter doesn't seem to be working properly.\n"); } + if ( read_matrix(image) != 0 ) { + ERROR("Failed to read matrix\n"); + } + free(grainspotter); } -- cgit v1.2.3