Merge branch 'tom/multicrystal'

Conflicts:
	libcrystfel/src/mosflm.c

1 files changed, 501 insertions, 0 deletions

diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
new file mode 100644
index 00000000..8def8091
--- /dev/null
+++ b/libcrystfel/src/grainspotter.c
@@ -0,0 +1,501 @@
+/*
+ * 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"
+#include "grainspotter.h"
+
+
+#define GRAINSPOTTER_VERBOSE 0
+
+
+/* Global private data, prepared once */
+struct grainspotter_private
+{
+	IndexingMethod indm;
+	UnitCell *cell;
+};
+
+
+/* Data needed during the run of Grainspotter */
+struct grainspotter_data {
+
+	struct grainspotter_private *gp;
+
+	/* Low-level stuff */
+	int                     pty;
+	pid_t                   pid;
+	char                    *rbuffer;
+	int                     rbufpos;
+	int                     rbuflen;
+
+};
+
+
+static int read_matrix(struct grainspotter_private *gp, 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;
+	}
+
+	do {
+
+		Crystal *cr;
+		UnitCell *cell;
+
+		/* 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;
+		}
+
+		cell = cell_new();
+
+		cell_set_cartesian(cell, ubi12/1e10, ubi13/1e10, ubi11/1e10,
+			                 ubi22/1e10, ubi23/1e10, ubi21/1e10,
+			                 ubi32/1e10, ubi33/1e10, ubi31/1e10);
+
+		cr = crystal_new();
+		if ( cr == NULL ) {
+			ERROR("Failed to allocate crystal.\n");
+			return 0;
+		}
+
+		crystal_set_cell(cr, cell);
+		image_add_crystal(image, cr);
+
+	} while ( !feof(fh) );
+
+	fclose(fh);
+
+	if ( gp->indm & INDEXING_CHECK_PEAKS ) {
+		if ( !peak_sanity_check(image, image->crystals,
+		                        image->n_crystals) )
+		{
+			free_all_crystals(image);
+			return 0;
+		}
+	}
+
+        return 0;
+}
+
+
+static void gs_parseline(char *line, struct image *image,
+                         struct grainspotter_data *gs)
+{
+	#if GRAINSPOTTER_VERBOSE
+	STATUS("%s\n", line);
+	#endif
+}
+
+
+static int grainspotter_readable(struct image *image,
+                                 struct grainspotter_data *gs)
+{
+	int rval;
+	int no_string = 0;
+
+	rval = read(gs->pty, gs->rbuffer+gs->rbufpos, gs->rbuflen-gs->rbufpos);
+
+	if ( (rval == -1) || (rval == 0) ) return 1;
+
+	gs->rbufpos += rval;
+	assert(gs->rbufpos <= gs->rbuflen);
+
+	while ( (!no_string) && (gs->rbufpos > 0) ) {
+
+		int i;
+		int block_ready = 0;
+
+		/* See if there's a full line in the buffer yet */
+		for ( i=0; i<gs->rbufpos-1; i++ ) {
+			/* Means the last value looked at is rbufpos-2 */
+
+			if ( (gs->rbuffer[i] == '\r')
+			  && (gs->rbuffer[i+1] == '\n') ) {
+				block_ready = 1;
+				break;
+			}
+
+		}
+
+		if ( block_ready ) {
+
+			unsigned int new_rbuflen;
+			unsigned int endbit_length;
+			char *block_buffer = NULL;
+
+			block_buffer = malloc(i+1);
+			memcpy(block_buffer, gs->rbuffer, i);
+			block_buffer[i] = '\0';
+
+			if ( block_buffer[0] == '\r' ) {
+				memmove(block_buffer, block_buffer+1, i);
+			}
+
+			gs_parseline(block_buffer, image, gs);
+			free(block_buffer);
+			endbit_length = i+2;
+
+			/* Now the block's been parsed, it should be
+			 * forgotten about */
+			memmove(gs->rbuffer,
+			        gs->rbuffer + endbit_length,
+			        gs->rbuflen - endbit_length);
+
+			/* Subtract the number of bytes removed */
+			gs->rbufpos = gs->rbufpos  - endbit_length;
+			new_rbuflen = gs->rbuflen - endbit_length;
+			if ( new_rbuflen == 0 ) new_rbuflen = 256;
+			gs->rbuffer = realloc(gs->rbuffer, new_rbuflen);
+			gs->rbuflen = new_rbuflen;
+
+		} else {
+
+			if ( gs->rbufpos==gs->rbuflen ) {
+
+				/* More buffer space is needed */
+				gs->rbuffer = realloc(gs->rbuffer,
+				                      gs->rbuflen + 256);
+				gs->rbuflen = gs->rbuflen + 256;
+				/* The new space gets used at the next
+				 * read, shortly... */
+
+			}
+			no_string = 1;
+
+		}
+
+	}
+
+	return 0;
+}
+
+
+static void write_gve(struct image *image, struct grainspotter_private *gp)
+{
+	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(gp->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");
+	fprintf(fh, "xfelmode\n");
+
+	fclose(fh);
+
+	return filename;
+}
+
+
+int grainspotter_index(struct image *image, IndexingPrivate *ipriv)
+{
+	unsigned int opts;
+	int status;
+	int rval;
+	struct grainspotter_data *grainspotter;
+	struct grainspotter_private *gp = (struct grainspotter_private *)ipriv;
+	char *ini_filename;
+	char gff_filename[1024];
+
+	write_gve(image, gp);
+	ini_filename = write_ini(image);
+
+	if ( ini_filename == NULL ) {
+		ERROR("Failed to write ini file for GrainSpotter.\n");
+		return 0;
+	}
+
+	grainspotter = malloc(sizeof(struct grainspotter_data));
+	if ( grainspotter == NULL ) {
+		ERROR("Couldn't allocate memory for GrainSpotter data.\n");
+		return 0;
+	}
+
+	grainspotter->gp = gp;
+
+	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 0;
+	}
+	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.0.93 '%s'\n", ini_filename);
+		execlp("GrainSpotter.0.93", "", 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");
+		free(grainspotter);
+		return 0;
+	}
+
+	if ( read_matrix(gp, image, gff_filename) != 0 ) {
+		free(grainspotter);
+		return 0;
+	}
+
+	/* Success! */
+	free(grainspotter);
+	return 1;
+}
+
+
+
+IndexingPrivate *grainspotter_prepare(IndexingMethod *indm, UnitCell *cell,
+                                      const char *filename,
+                                      struct detector *det,
+                                      struct beam_params *beam, float *ltl)
+{
+	struct grainspotter_private *gp;
+
+	if ( cell == NULL ) {
+		ERROR("GrainSpotter needs a unit cell.\n");
+		return NULL;
+	}
+
+	gp = calloc(1, sizeof(*gp));
+	if ( gp == NULL ) return NULL;
+
+	/* Flags that GrainSpotter knows about */
+	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
+	       | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
+
+	gp->cell = cell;
+	gp->indm = *indm;
+
+	return (IndexingPrivate *)gp;
+}
+
+
+void grainspotter_cleanup(IndexingPrivate *pp)
+{
+	struct grainspotter_private *p;
+
+	p = (struct grainspotter_private *)pp;
+	free(p);
+}