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-rw-r--r--libcrystfel/src/grainspotter.c501
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diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
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+/*
+ * 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);
+}
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