From 6594902941cbf9cb1bded9bf11c465766dcf3b6d Mon Sep 17 00:00:00 2001 From: Cornelius Gati Date: Mon, 28 Jan 2013 14:49:41 +0100 Subject: Copied grainspotter.c/.h to xds.c/.h, deleted write_gve and replaced it with write_spt from mosflm.c --- libcrystfel/src/xds.c | 321 ++++++++++++++++++++++++++++++++++++++++++++++++++ libcrystfel/src/xds.h | 42 +++++++ 2 files changed, 363 insertions(+) create mode 100644 libcrystfel/src/xds.c create mode 100644 libcrystfel/src/xds.h (limited to 'libcrystfel/src') diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c new file mode 100644 index 00000000..d7968d6e --- /dev/null +++ b/libcrystfel/src/xds.c @@ -0,0 +1,321 @@ +/* + * xds.c + * + * Invoke xds crystal autoindexing + * + * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2010-2013 Thomas White + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#if HAVE_FORKPTY_LINUX +#include +#elif HAVE_FORKPTY_BSD +#include +#endif + + +#include "image.h" +#include "utils.h" +#include "peaks.h" +#include "cell.h" +#include "cell-utils.h" + + +#define xds_VERBOSE 0 + + +struct xds_data { + + /* Low-level stuff */ + int pty; + pid_t pid; + char *rbuffer; + int rbufpos; + int rbuflen; + +}; + + +static int read_matrix(struct image *image, char *filename) +{ + FILE *fh; + int d1; + float d2; + float ubi11, ubi12, ubi13; + float ubi21, ubi22, ubi23; + float ubi31, ubi32, ubi33; + char line[1024]; + int r; + + 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 xds_readable(struct image *image, + struct xds_data *xds) +{ + int rval; + + rval = read(xds->pty, + xds->rbuffer, xds->rbuflen); + + if ( rval == -1 ) { + ERROR("Read failed: %s\n", strerror(errno)); + return 1; + } + + xds->rbuffer[rval] = '\0'; + + printf("xds: '%s'\n", xds->rbuffer); + + return 0; +} + +static void write_spot(struct image *image, const char *filename) +{ + FILE *fh; + int i; + double fclen = 67.8e-3; /* fake camera length in m */ + int n; + + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + return; + } + + /* Number of pixels in x, number of pixels in y, pixel size (mm), + * YSCALE, OMEGA */ + fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, 0.0, 1.0, 0.0); + + /* INVERTX, ISWUNG */ + fprintf(fh, "%10d %10d\n", 0, 1); + + /* XBEAM, YBEAM */ + fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0); + + n = image_feature_count(image->features); + for ( i=0; ifeatures, i); + if ( f == NULL ) continue; + + p = find_panel(image->det, f->fs, f->ss); + if ( p == NULL ) continue; + + xs = (f->fs-p->min_fs)*p->fsx + (f->ss-p->min_ss)*p->ssx; + ys = (f->fs-p->min_fs)*p->fsy + (f->ss-p->min_ss)*p->ssy; + rx = (xs + p->cnx) / p->res; + ry = (ys + p->cny) / p->res; + + x = -rx*fclen/p->clen; + y = ry*fclen/p->clen; /* Peak positions in m */ + + fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n", + x*1e3, y*1e3, 0.0, 0.0, 1000.0, 10.0); + + } + + fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n", + -999.0,-999.0,-999.0,-999.0,-999.0,-999.0); + fclose(fh); +} + + +//void run_xds(struct image *image, UnitCell *cell) +{ + unsigned int opts; + int status; + int rval; + struct xds_data *xds; + char *ini_filename; + char gff_filename[1024]; + + write_gve(image, cell); + ini_filename = write_ini(image); + + if ( ini_filename == NULL ) { + ERROR("Failed to write ini file for xds.\n"); + return; + } + + xds = malloc(sizeof(struct xds_data)); + if ( xds == NULL ) { + ERROR("Couldn't allocate memory for xds data.\n"); + return; + } + + snprintf(gff_filename, 1023, "xfel-%i.gff", image->id); + remove(gff_filename); + + xds->pid = forkpty(&xds->pty, NULL, NULL, NULL); + if ( xds->pid == -1 ) { + ERROR("Failed to fork for xds: %s\n", strerror(errno)); + return; + } + if ( xds->pid == 0 ) { + + /* Child process: invoke xds */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + STATUS("Running xds.0.90 '%s'\n", ini_filename); + execlp("xds.0.90", "", ini_filename, (char *)NULL); + ERROR("Failed to invoke xds.\n"); + _exit(0); + + } + free(ini_filename); + + xds->rbuffer = malloc(256); + xds->rbuflen = 256; + xds->rbufpos = 0; + + /* Set non-blocking */ + opts = fcntl(xds->pty, F_GETFL); + fcntl(xds->pty, F_SETFL, opts | O_NONBLOCK); + + do { + + fd_set fds; + struct timeval tv; + int sval; + + FD_ZERO(&fds); + FD_SET(xds->pty, &fds); + + tv.tv_sec = 20000; + tv.tv_usec = 0; + + sval = select(xds->pty+1, &fds, NULL, NULL, &tv); + + if ( sval == -1 ) { + + const int err = errno; + + switch ( err ) { + + case EINTR: + STATUS("Restarting select()\n"); + break; + + default: + ERROR("select() failed: %s\n", strerror(err)); + rval = 1; + + } + + } else if ( sval != 0 ) { + rval = xds_readable(image, xds); + } else { + ERROR("No response from xds..\n"); + rval = 1; + } + + } while ( !rval ); + + close(xds->pty); + free(xds->rbuffer); + waitpid(xds->pid, &status, 0); + + if ( status != 0 ) { + ERROR("xds doesn't seem to be working properly.\n"); + } + + if ( read_matrix(image, gff_filename) != 0 ) { + ERROR("Failed to read matrix\n"); + } + + free(xds); +} diff --git a/libcrystfel/src/xds.h b/libcrystfel/src/xds.h new file mode 100644 index 00000000..1aedf57f --- /dev/null +++ b/libcrystfel/src/xds.h @@ -0,0 +1,42 @@ +/* + * grainspotter.h + * + * Invoke GrainSpotter for multi-crystal autoindexing + * + * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2010-2013 Thomas White + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see . + * + */ + +#ifndef GRAINSPOTTER_H +#define GRAINSPOTTER_H + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "cell.h" + + +extern void run_grainspotter(struct image *image, UnitCell *cell); + + +#endif /* GRAINSPOTTER_H */ -- cgit v1.2.3