Copied grainspotter.c/.h to xds.c/.h, deleted write_gve and replaced it with write_spt from mosflm.c

2 files changed, 363 insertions, 0 deletions

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 <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);
+}
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 <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/>.
+ *
+ */
+
+#ifndef GRAINSPOTTER_H
+#define GRAINSPOTTER_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "cell.h"
+
+
+extern void run_grainspotter(struct image *image, UnitCell *cell);
+
+
+#endif	/* GRAINSPOTTER_H */