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-rw-r--r--libcrystfel/src/felix.c724
1 files changed, 724 insertions, 0 deletions
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
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+++ b/libcrystfel/src/felix.c
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+/*
+ * felix.c
+ *
+ * Invoke Felix for multi-crystal autoindexing.
+ *
+ * Copyright © 2015 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2015 Thomas White <taw@physics.org>
+ * 2015 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
+ *
+ * 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 <pty.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/wait.h>
+#include <unistd.h>
+#include <assert.h>
+#include <fcntl.h>
+#include <errno.h>
+
+#ifdef HAVE_CLOCK_GETTIME
+#include <time.h>
+#else
+#include <sys/time.h>
+#endif
+
+
+#include "image.h"
+#include "utils.h"
+#include "peaks.h"
+#include "cell.h"
+#include "cell-utils.h"
+#include "felix.h"
+
+
+#define FELIX_VERBOSE 0
+#define MAX_MEAN_IA 0.25
+#define MIN_NGV 15
+#define MIN_NGV_UNIQUE 10
+
+
+/* Global private data, prepared once */
+struct felix_private
+{
+ IndexingMethod indm;
+ UnitCell *cell;
+
+ /* Options specific to Felix */
+ int spacegroup;
+ float tthrange_min;
+ float tthrange_max;
+ float etarange_min;
+ float etarange_max;
+ float domega;
+ float omegarange_min;
+ float omegarange_max;
+ int min_measurements; /* related to "cuts" */
+ float min_completeness; /* related to "cuts" */
+ float min_uniqueness; /* related to "cuts" */
+ int n_voxels; /* related to "frustsumsize" */
+ float test_fraction; /* related to "frustsumsize" */
+ float sigma_tth; /* related to "uncertainties" */
+ float sigma_eta; /* related to "uncertainties" */
+ float sigma_omega; /* related to "uncertainties" */
+ int n_sigmas;
+ int force4frustums;
+
+ /*Felix v0.3 options*/
+ int orispace_frustum;
+ int orispace_octa;
+ char *readhkl_file;
+ float maxtime;
+
+};
+
+
+/* Data needed to call Felix */
+struct felix_data {
+
+ struct felix_private *gp;
+
+ /* Low-level stuff */
+ int pty;
+ pid_t pid;
+ char *rbuffer;
+ int rbufpos;
+ int rbuflen;
+
+};
+
+
+static int read_felix(struct felix_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;
+ float mean_ia;
+ /* int ngv_unique; /* Used in Felix 0.1 */
+ int ngv;
+ 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 *.felix file.\n");
+ return 1;
+ }
+
+ do {
+
+ Crystal *cr;
+ UnitCell *cell;
+
+ /* One line per grain */
+ if ( fgets( line, 1024, fh ) == NULL ) {
+ break;
+ }
+ /* File format of the .felix files
+ * version 0.1 - 0.2
+ *
+ * r = sscanf(line, "%i %f %i %i %f %f %f %f %f %f %f %f %f"
+ * "%f %f %f %f %f %f %f %f %f %f %f %f",
+ * &d1, &mean_ia, &ngv, &ngv_unique, &d2, &d2, &d2,
+ * &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2,
+ * &ubi11, &ubi12, &ubi13,
+ * &ubi21, &ubi22, &ubi23,
+ * &ubi31, &ubi32, &ubi33);
+ *
+ * if ( r != 25 ) {
+ * ERROR("Only %i parameters in .felix file\n", r);
+ * return 1;
+ * }
+ */
+
+ /* version 0.3 - present */
+ r = sscanf(line, "%i %f %i %f %f %f %f %f %f"
+ "%f %f %f %f %f %f %f %f %f %f %f %f",
+ &d1, &mean_ia, &ngv, &d2, &d2,
+ &d2, &d2, &d2, &d2, &d2, &d2, &d2,
+ &ubi11, &ubi12, &ubi13,
+ &ubi21, &ubi22, &ubi23,
+ &ubi31, &ubi32, &ubi33);
+
+ if ( r != 21 ) {
+ ERROR("Only %i parameters in .felix file, check version and format.\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);
+
+ /* Poor indexing criterion for Felix v0.1
+ *
+ * if (mean_ia > MAX_MEAN_IA || ngv < MIN_NGV ||
+ * ngv_unique < MIN_NGV_UNIQUE ){
+ * crystal_set_user_flag(cr, 1);
+ */
+
+ /* Poor indexing criterion for Felix v0.3 */
+
+ if ( mean_ia > MAX_MEAN_IA || ngv < MIN_NGV ){
+ crystal_set_user_flag(cr, 1);
+ }
+
+ /* All crystals are saved to the image,
+ * but only good ones will be later written to the stream file.
+ */
+
+ 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 felix_data *gs)
+{
+ #if FELIX_VERBOSE
+ STATUS("%s\n", line);
+ #endif
+}
+
+
+static int felix_readable(struct image *image, struct felix_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 felix_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 */
+ rad2deg(atan2(f->ry, f->rx)), 0.0); /* eta, omega */
+
+ }
+ fclose(fh);
+}
+
+
+static char *write_ini(struct image *image, struct felix_private *gp)
+{
+ FILE *fh;
+ char *filename;
+ char gveFilename[1024];
+ char logFilename[1024];
+ double tt;
+
+ filename = malloc(1024);
+ if ( filename == NULL ) return NULL;
+
+ snprintf(filename, 1023, "xfel-%i.ini", image->id);
+ snprintf(gveFilename, 1023, "xfel-%i.gve", image->id);
+ snprintf(logFilename, 1023, "xfel-%i.log", 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 %i\n", gp->spacegroup);
+ fprintf(fh, "tthrange %f %f\n", gp->tthrange_min, gp->tthrange_max);
+ fprintf(fh, "etarange %f %f\n", gp->etarange_min, gp->etarange_max);
+ fprintf(fh, "domega %f\n", gp->domega);
+ fprintf(fh, "omegarange %f %f\n", gp->omegarange_min, gp->omegarange_max);
+ fprintf(fh, "filespecs %s %s\n", gveFilename, logFilename);
+ fprintf(fh, "cuts %i %f %f\n", gp->min_measurements, gp->min_completeness,
+ gp->min_uniqueness);
+ fprintf(fh, "frustumsize %i %f\n", gp->n_voxels,
+ gp->test_fraction);
+ fprintf(fh, "uncertainties %f %f %f\n", gp->sigma_tth,
+ gp->sigma_eta, gp->sigma_omega);
+ fprintf(fh, "nsigmas %i\n", gp->n_sigmas);
+
+ if ( gp->force4frustums == 1 ){
+ fprintf(fh, "force4frustums\n");
+ }
+
+ if ( gp->orispace_frustum == 1 ){
+ fprintf(fh, "orispace frustum\n");
+ } else if ( gp->orispace_octa ==1 ){
+ fprintf(fh, "orispace octa\n");
+ } else{
+ ERROR("No felix supported orispace specified.\n");
+ free(filename);
+ filename = NULL;
+ }
+
+ /* If an hkl file is not specified, generate the peak list. */
+ if ( gp->readhkl_file != NULL ){
+ fprintf(fh, "readhkl %s\n", gp->readhkl_file);
+ } else{
+ fprintf(fh, "genhkl\n");
+ }
+
+ fprintf(fh, "maxtime %f\n", gp->maxtime);
+
+ fclose(fh);
+
+ return filename;
+}
+
+
+int felix_index(struct image *image, IndexingPrivate *ipriv)
+{
+ unsigned int opts;
+ int status;
+ int rval;
+ struct felix_data *felix;
+ struct felix_private *gp = (struct felix_private *) ipriv;
+ char *ini_filename;
+ char gff_filename[1024];
+
+ write_gve (image, gp);
+ ini_filename = write_ini (image, gp);
+
+ if ( ini_filename == NULL ) {
+ ERROR("Failed to write ini file for Felix.\n");
+ return 0;
+ }
+
+ felix = malloc(sizeof(struct felix_data));
+ if ( felix == NULL ) {
+ ERROR("Couldn't allocate memory for Felix data.\n");
+ return 0;
+ }
+
+ felix->gp = gp;
+
+ snprintf(gff_filename, 1023, "xfel-%i.felix", image->id);
+ remove(gff_filename);
+
+ felix->pid = forkpty(&felix->pty, NULL, NULL, NULL);
+ if ( felix->pid == -1 ) {
+ ERROR("Failed to fork for Felix: %s\n", strerror(errno));
+ return 0;
+ }
+ if ( felix->pid == 0 ) {
+
+ /* Child process: invoke Felix */
+ struct termios t;
+
+ /* Turn echo off */
+ tcgetattr(STDIN_FILENO, &t);
+ t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
+ tcsetattr(STDIN_FILENO, TCSANOW, &t);
+
+ STATUS("Running Felix '%s'\n", ini_filename);
+ execlp("Felix", "", ini_filename, (char *)NULL);
+ ERROR("Failed to invoke Felix.\n");
+ _exit(0);
+
+ }
+
+ free(ini_filename);
+
+ felix->rbuffer = malloc(256);
+ felix->rbuflen = 256;
+ felix->rbufpos = 0;
+
+ /* Set non-blocking */
+ opts = fcntl(felix->pty, F_GETFL);
+ fcntl(felix->pty, F_SETFL, opts | O_NONBLOCK);
+
+ do {
+
+ fd_set fds;
+ struct timeval tv;
+ int sval;
+
+ FD_ZERO(&fds);
+ FD_SET(felix->pty, &fds);
+
+ tv.tv_sec = gp->maxtime + 1.0;
+ tv.tv_usec = 0;
+
+ sval = select(felix->pty+1, &fds, NULL, NULL, &tv);
+
+ if ( sval == -1 ) {
+
+ const int err = errno;
+
+ switch ( err ) {
+
+ case EINTR:
+ STATUS("Restarting select()\n");
+ rval = 0;
+ break;
+
+ default:
+ ERROR("select() failed: %s\n", strerror(err));
+ rval = 1;
+
+ }
+
+ } else if ( sval != 0 ) {
+ rval = felix_readable(image, felix);
+ } else {
+ ERROR("No response from Felix..\n");
+ rval = 1;
+ }
+
+ } while ( !rval );
+
+ close(felix->pty);
+ free(felix->rbuffer);
+ waitpid(felix->pid, &status, 0);
+
+ if ( status != 0 ) {
+ ERROR("Felix either timed out, or is not working properly.\n");
+ free(felix);
+ return 0;
+ }
+
+ if ( read_felix(gp, image, gff_filename) != 0 ) {
+ free(felix);
+ return 0;
+ }
+
+ /* Success! */
+ free(felix);
+ return 1;
+
+}
+
+IndexingPrivate *felix_prepare(IndexingMethod *indm, UnitCell *cell,
+ struct detector *det, float *ltl,
+ const char *options)
+{
+ struct felix_private *gp;
+ char *temp_options=NULL;
+ char *option=NULL;
+
+ if ( cell == NULL ) {
+ ERROR("Felix needs a unit cell.\n");
+ return NULL;
+ }
+
+ if ( options != NULL ){
+ temp_options = strdup(options);
+ }
+
+ gp = calloc(1, sizeof(*gp));
+ if ( gp == NULL ) return NULL;
+
+ /* Flags that Felix knows about */
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
+ | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
+
+ gp->cell = cell;
+ gp->indm = *indm;
+
+ /* Default values of felix options */
+ gp->spacegroup = 0;
+ gp->tthrange_min = 0;
+ gp->tthrange_max = 30.0;
+ gp->etarange_min = 0;
+ gp->etarange_max = 360;
+ gp->domega = 2;
+ gp->omegarange_min = -1.0;
+ gp->omegarange_max = 1.0;
+ gp->min_measurements = 15;
+ gp->min_completeness = 0.001;
+ gp->min_uniqueness = 0.5;
+ gp->n_voxels = 100;
+ gp->test_fraction = 0.75;
+ gp->sigma_tth = 0.15;
+ gp->sigma_eta = 0.2;
+ gp->sigma_omega = 0.2;
+ gp->n_sigmas = 2;
+ gp->force4frustums = 0;
+ gp->orispace_frustum = 1;
+ gp->orispace_octa = 0;
+ gp->readhkl_file = NULL;
+ gp->maxtime = 30.0;
+
+ /*Parse the options string and fill in the necessary private variables. */
+ if (temp_options != NULL){
+ while((option=strsep(&temp_options, ","))!=NULL) {
+
+ if ( strncmp(option, "spacegroup=", 11) == 0 ){
+ gp->spacegroup = atoi(option+11);
+ }
+
+ if ( strncmp(option, "tthrange_min=", 13) == 0 ){
+ gp->tthrange_min = atof(option+13);
+ }
+
+ if ( strncmp(option, "tthrange_max=", 13 ) == 0 ){
+ gp->tthrange_max = atof(option+13);
+ }
+
+ if ( strncmp(option, "etarange_min=", 13 ) == 0 ){
+ gp->etarange_min = atof(option+13);
+ }
+
+ if ( strncmp(option, "etarange_max=", 13 ) == 0 ){
+ gp->etarange_max = atof(option+13);
+ }
+
+ if ( strncmp(option, "domega=", 7) == 0 ){
+ gp->domega = atof(option+7);
+ }
+
+ if ( strncmp(option, "omegarange_min=", 15) == 0 ){
+ gp->omegarange_min = atof(option+15);
+ }
+
+ if ( strncmp(option, "omegarange_max=", 15) == 0 ){
+ gp->omegarange_max = atof(option+15);
+ }
+
+ if ( strncmp(option, "min_measurements=", 17) == 0 ){
+ gp->min_measurements = atoi(option+17);
+ }
+
+ if ( strncmp(option, "min_completeness=", 17) == 0 ){
+ gp->min_completeness = atof(option+17);
+ }
+
+ if ( strncmp(option, "min_uniqueness=", 15) == 0 ){
+ gp->min_uniqueness = atof(option+15);
+ }
+
+ if ( strncmp(option, "n_voxels=", 9) == 0 ){
+ gp->n_voxels = atoi(option+9);
+ }
+
+ if ( strncmp(option, "test_fraction=", 14) == 0 ){
+ gp->test_fraction = atof(option+14);
+ }
+
+ if ( strncmp(option, "sigma_tth=", 10) == 0 ){
+ gp->sigma_tth = atof(option+10);
+ }
+
+ if ( strncmp(option, "sigma_eta=", 10) == 0 ){
+ gp->sigma_eta = atof(option+10);
+ }
+
+ if ( strncmp(option, "sigma_omega=", 12) == 0 ){
+ gp->sigma_omega = atof(option+12);
+ }
+
+ if ( strncmp(option, "n_sigmas=", 9) == 0 ){
+ gp->n_sigmas = atoi(option+9);
+ }
+
+ if ( strncmp(option, "force4frustums", 14) == 0 ){
+ gp->force4frustums = 1;
+ }
+
+ /* Only allow one orispace command.
+ * orispace frustum is the default, so have to turn off to use octa.
+ */
+ if ( strncmp(option, "orispace_octa", 13) == 0 ){
+ gp->orispace_octa = 1;
+ gp->orispace_frustum = 0;
+ }
+
+ if ( strncmp(option, "readhkl=", 8) == 0 ){
+ gp->readhkl_file = strdup(option+8);
+ }
+
+ if ( strncmp(option, "maxtime=", 8) == 0 ){
+ gp->maxtime = atof(option+8);
+ }
+
+ }
+ }
+
+ /* Make sure that they at least specified the spacegroup number.*/
+
+ if ( gp->spacegroup == 0 ){
+ ERROR("Felix requires that you specify the spacegroup number.\n");
+ ERROR("You should use the argument --felix-options=spacegroup=xx\n");
+ return NULL;
+ }
+
+ free(temp_options);
+ free(option);
+
+ return (IndexingPrivate *) gp;
+}
+
+
+void felix_cleanup(IndexingPrivate *pp)
+{
+ struct felix_private *p;
+
+ p = (struct felix_private *) pp;
+ free(p->readhkl_file);
+ free(p);
+}
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