Merge branch 'tom/grainspotter' into tom/multicrystal

Conflicts:
	libcrystfel/Makefile.am
	libcrystfel/src/index.c
	libcrystfel/src/index.h

5 files changed, 414 insertions, 2 deletions

diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index da7e8f64..ae315594 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -8,7 +8,8 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/symmetry.c src/stream.c src/peaks.c \
                          src/reflist-utils.c src/filters.c \
                          src/render.c src/index.c src/dirax.c src/mosflm.c \
-                         src/cell-utils.c src/integer_matrix.c src/crystal.c
+                         src/cell-utils.c src/integer_matrix.c src/crystal.c \
+                         src/grainspotter.c
 
 if HAVE_FFTW
 libcrystfel_la_SOURCES += src/reax.c
@@ -24,7 +25,8 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
                                  src/render.h src/index.h src/image.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
                                  src/index-priv.h src/reax.h src/cell-utils.h \
-                                 src/integer_matrix.h src/crystal.h
+                                 src/integer_matrix.h src/crystal.h \
+                                 src/grainspotter.h
 
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall
 AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
new file mode 100644
index 00000000..7d0f74ce
--- /dev/null
+++ b/libcrystfel/src/grainspotter.c
@@ -0,0 +1,354 @@
+/*
+ * grainspotter.c
+ *
+ * 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/>.
+ *
+ */
+
+#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 GRAINSPOTTER_VERBOSE 0
+
+
+struct grainspotter_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 grainspotter_readable(struct image *image,
+                                 struct grainspotter_data *grainspotter)
+{
+	int rval;
+
+	rval = read(grainspotter->pty,
+	            grainspotter->rbuffer, grainspotter->rbuflen);
+
+	if ( rval == -1 ) {
+		ERROR("Read failed: %s\n", strerror(errno));
+		return 1;
+	}
+
+	grainspotter->rbuffer[rval] = '\0';
+
+	printf("GrainSpotter: '%s'\n", grainspotter->rbuffer);
+
+	return 0;
+}
+
+
+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);
+
+	fh = fopen(filename, "w");
+	if ( !fh ) {
+		ERROR("Couldn't open temporary file '%s'\n", filename);
+		return;
+	}
+
+	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; i<image_feature_count(image->features); i++ ) {
+
+		struct imagefeature *f;
+
+		f = image_get_feature(image->features, i);
+		if ( f == NULL ) continue;
+
+		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;
+}
+
+
+void run_grainspotter(struct image *image, UnitCell *cell)
+{
+	unsigned int opts;
+	int status;
+	int rval;
+	struct grainspotter_data *grainspotter;
+	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 GrainSpotter.\n");
+		return;
+	}
+
+	grainspotter = malloc(sizeof(struct grainspotter_data));
+	if ( grainspotter == NULL ) {
+		ERROR("Couldn't allocate memory for GrainSpotter data.\n");
+		return;
+	}
+
+	snprintf(gff_filename, 1023, "xfel-%i.gff", image->id);
+	remove(gff_filename);
+
+	grainspotter->pid = forkpty(&grainspotter->pty, NULL, NULL, NULL);
+	if ( grainspotter->pid == -1 ) {
+		ERROR("Failed to fork for GrainSpotter: %s\n", strerror(errno));
+		return;
+	}
+	if ( grainspotter->pid == 0 ) {
+
+		/* Child process: invoke GrainSpotter */
+		struct termios t;
+
+		/* Turn echo off */
+		tcgetattr(STDIN_FILENO, &t);
+		t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
+		tcsetattr(STDIN_FILENO, TCSANOW, &t);
+
+		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;
+	grainspotter->rbufpos = 0;
+
+	/* Set non-blocking */
+	opts = fcntl(grainspotter->pty, F_GETFL);
+	fcntl(grainspotter->pty, F_SETFL, opts | O_NONBLOCK);
+
+	do {
+
+		fd_set fds;
+		struct timeval tv;
+		int sval;
+
+		FD_ZERO(&fds);
+		FD_SET(grainspotter->pty, &fds);
+
+		tv.tv_sec = 30;
+		tv.tv_usec = 0;
+
+		sval = select(grainspotter->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 = grainspotter_readable(image, grainspotter);
+		} else {
+			ERROR("No response from GrainSpotter..\n");
+			rval = 1;
+		}
+
+	} while ( !rval );
+
+	close(grainspotter->pty);
+	free(grainspotter->rbuffer);
+	waitpid(grainspotter->pid, &status, 0);
+
+	if ( status != 0 ) {
+		ERROR("GrainSpotter doesn't seem to be working properly.\n");
+	}
+
+	if ( read_matrix(image, gff_filename) != 0 ) {
+		ERROR("Failed to read matrix\n");
+	}
+
+	free(grainspotter);
+}
diff --git a/libcrystfel/src/grainspotter.h b/libcrystfel/src/grainspotter.h
new file mode 100644
index 00000000..1aedf57f
--- /dev/null
+++ b/libcrystfel/src/grainspotter.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 */
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 275ea4c1..89fdec4f 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -48,6 +48,7 @@
 #include "index.h"
 #include "index-priv.h"
 #include "reax.h"
+#include "grainspotter.h"
 #include "geometry.h"
 #include "cell-utils.h"
 
@@ -82,6 +83,10 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 			                           det, beam, ltl);
 			break;
 
+			case INDEXING_GRAINSPOTTER :
+			iprivs[n] = indexing_private(indm[n]);
+			break;
+
 			case INDEXING_REAX :
 			iprivs[n] = reax_prepare(&indm[n], cell, filename,
 			                         det, beam, ltl);
@@ -144,6 +149,10 @@ void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
 			mosflm_cleanup(privs[n]);
 			break;
 
+			case INDEXING_GRAINSPOTTER :
+			free(priv[n]);
+			break;
+
 			case INDEXING_REAX :
 			reax_cleanup(privs[n]);
 			break;
@@ -360,6 +369,9 @@ IndexingMethod *build_indexer_list(const char *str)
 		} else if ( strcmp(methods[i], "mosflm") == 0) {
 			list[++nmeth] = INDEXING_DEFAULTS_MOSFLM;
 
+		} else if ( strcmp(methods[i], "grainspotter") == 0) {
+			list[++nmeth] = INDEXING_DEFAULTS_GRAINSPOTTER;
+
 		} else if ( strcmp(methods[i], "reax") == 0) {
 			list[++nmeth] = INDEXING_DEFAULTS_REAX;
 
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 7d6656d5..a47ee9a0 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -65,12 +65,14 @@
  **/
 typedef enum {
 
+
 	INDEXING_NONE   = 0,
 
 	/* The core indexing methods themselves */
 	INDEXING_DIRAX  = 1,
 	INDEXING_MOSFLM = 2,
 	INDEXING_REAX   = 3,
+	INDEXING_GRAINSPOTTER = 4,
 
 	/* Bits at the top of the IndexingMethod are flags which modify the
 	 * behaviour of the indexer, at the moment just by adding checks. */