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-rw-r--r--libcrystfel/src/xds.c321
1 files changed, 321 insertions, 0 deletions
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
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+++ b/libcrystfel/src/xds.c
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+/*
+ * xds.c
+ *
+ * Invoke xds crystal autoindexing
+ *
+ * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2010-2013 Thomas White <taw@physics.org>
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <unistd.h>
+#include <sys/wait.h>
+#include <fcntl.h>
+#include <assert.h>
+#include <sys/ioctl.h>
+#include <errno.h>
+
+#if HAVE_FORKPTY_LINUX
+#include <pty.h>
+#elif HAVE_FORKPTY_BSD
+#include <util.h>
+#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; i<n; i++ ) {
+
+ struct imagefeature *f;
+ struct panel *p;
+ double xs, ys, rx, ry, x, y;
+
+ f = image_get_feature(image->features, 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);
+}
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