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authorThomas White <taw@physics.org>2020-08-07 17:43:18 +0200
committerThomas White <taw@physics.org>2020-08-07 18:07:07 +0200
commitc0b01532441407dc97eaa9d44b540f1dd0223990 (patch)
treea1526e8bb84d38e8e6dfab05d2d95e1a5b5a3d10 /libcrystfel/src/felix.c
parent08327436744a05e68daf1676f0fa4a82fb74408f (diff)
Move indexers out of API
Diffstat (limited to 'libcrystfel/src/felix.c')
-rw-r--r--libcrystfel/src/felix.c963
1 files changed, 0 insertions, 963 deletions
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
deleted file mode 100644
index 524e68a7..00000000
--- a/libcrystfel/src/felix.c
+++ /dev/null
@@ -1,963 +0,0 @@
-/*
- * felix.c
- *
- * Invoke Felix for multi-crystal autoindexing.
- *
- * Copyright © 2015-2020 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
- *
- * Authors:
- * 2015-2018 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
-
-
-/** \file felix.h */
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <string.h>
-#include <sys/types.h>
-#include <sys/wait.h>
-#include <sys/stat.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
-
-#ifdef HAVE_FORKPTY_PTY_H
-#include <pty.h>
-#endif
-#ifdef HAVE_FORKPTY_UTIL_H
-#include <util.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
-
-
-struct felix_options
-{
- double ttmin; /* radians */
- double ttmax; /* radians */
- int min_visits;
- double min_completeness;
- double max_uniqueness;
- int n_voxels;
- double fraction_max_visits;
- double sigma;
- double domega;
- double max_internal_angle;
-};
-
-
-/* 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_visits; /* related to "cuts" */
- float min_completeness; /* related to "cuts" */
- float max_uniqueness; /* related to "cuts" */
- int n_voxels; /* related to "frustsumsize" */
- float fraction_max_visits; /* 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;
- float max_internal_angle;
-
- /*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;
- char line[1024];
- int r;
- int n_crystals = 0;
-
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("Can't open '%s'\n", filename);
- return 0;
- }
-
- /* Read and discard first line */
- if ( fgets( line, 1024, fh ) == NULL ) {
- ERROR("Failed to read *.felix file.\n");
- return 0;
- }
-
- 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);
- cell_set_lattice_type(cell, cell_get_lattice_type(gp->cell));
- cell_set_centering(cell, cell_get_centering(gp->cell));
- cell_set_unique_axis(cell, cell_get_unique_axis(gp->cell));
-
- 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 > gp->max_internal_angle ){
- 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);
- n_crystals++;
-
- } while ( !feof(fh) );
-
- fclose(fh);
-
- return n_crystals;
-}
-
-
-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.gve");
- 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];
-
- filename = malloc(1024);
- if ( filename == NULL ) return NULL;
-
- snprintf(filename, 1023, "xfel.ini");
- snprintf(gveFilename, 1023, "xfel.gve");
- snprintf(logFilename, 1023, "xfel.log");
-
- fh = fopen(filename, "w");
- if ( !fh ) {
- ERROR("Couldn't open temporary file '%s'\n", filename);
- free(filename);
- return NULL;
- }
-
- fprintf(fh, "spacegroup %i\n", gp->spacegroup);
- fprintf(fh, "tthrange %f %f\n", rad2deg(gp->tthrange_min),
- rad2deg(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_visits, gp->min_completeness,
- gp->max_uniqueness);
- fprintf(fh, "frustumsize %i %f\n", gp->n_voxels,
- gp->fraction_max_visits);
- 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.felix");
- 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", "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;
- }
-
- rval = read_felix(gp, image, gff_filename);
-
- free(felix);
- return rval;
-
-}
-
-
-static int sg_number_for_cell(UnitCell *cell)
-{
- LatticeType lattice = cell_get_lattice_type(cell);
- char cen = cell_get_centering(cell);
-
- switch (lattice)
- {
- case L_TRICLINIC:
- return 1; /* P1 */
-
- case L_MONOCLINIC:
- switch ( cen ) {
- case 'P' : return 3; /* P2 */
- case 'C' : return 5; /* C2 */
- default : return 0;
- }
-
- case L_ORTHORHOMBIC:
- switch ( cen ) {
- case 'P' : return 16; /* P222 */
- case 'C' : return 21; /* C222 */
- case 'F' : return 22; /* F222 */
- case 'I' : return 23; /* I222 */
- case 'A' : return 38; /* Amm2 */
- default : return 0;
- }
-
- case L_TETRAGONAL:
- switch ( cen ) {
- case 'P' : return 89; /* P422 */
- case 'I' : return 97; /* I422 */
- default : return 0;
- }
-
- case L_RHOMBOHEDRAL:
- return 155; /* R32 */
-
- case L_HEXAGONAL:
- switch ( cen ) {
- case 'P' : return 177; /* P622 */
- case 'H' : return 143; /* P3 */
- default : return 0;
- }
-
- case L_CUBIC:
- switch ( cen ) {
- case 'P' : return 207; /* P432 */
- case 'F' : return 209; /* F432 */
- case 'I' : return 211; /* I432 */
- default : return 0;
- }
-
- default:
- return 0;
- }
-}
-
-
-void *felix_prepare(IndexingMethod *indm, UnitCell *cell,
- struct felix_options *opts)
-{
- struct felix_private *gp;
-
- if ( !cell_has_parameters(cell) ) {
- ERROR("Felix needs a unit cell.\n");
- return NULL;
- }
-
- if ( felix_probe(cell) == NULL ) {
- ERROR("Felix does not appear to run properly.\n");
- ERROR("Please check your Felix installation.\n");
- return NULL;
- }
-
- gp = calloc(1, sizeof(*gp));
- if ( gp == NULL ) return NULL;
-
- /* Flags that Felix knows about */
- *indm &= INDEXING_METHOD_MASK
- | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
-
- gp->cell = cell;
- gp->indm = *indm;
-
- /* Default values of felix options */
- gp->spacegroup = sg_number_for_cell(cell);
- if ( gp->spacegroup == 0 ) {
- ERROR("Couldn't determine representative space group for your cell.\n");
- ERROR("Try again with a more conventional cell.\n");
- return NULL;
- }
-
- /* Default parameters */
- gp->n_voxels = 100;
- gp->etarange_min = 0;
- gp->etarange_max = 360;
- gp->domega = 2;
- gp->omegarange_min = -1.0;
- gp->omegarange_max = 1.0;
- gp->min_visits = 15;
- gp->min_completeness = 0.001;
- gp->max_uniqueness = 0.5;
- gp->fraction_max_visits = 0.75;
- gp->sigma_tth = 0.2;
- gp->sigma_eta = 0.2;
- gp->sigma_omega = 0.2;
- gp->n_sigmas = 1;
- gp->force4frustums = 0;
- gp->orispace_frustum = 1;
- gp->orispace_octa = 0;
- gp->readhkl_file = NULL;
- gp->maxtime = 120.0;
- gp->tthrange_min = deg2rad(0.0);
- gp->tthrange_max = deg2rad(30.0);
- gp->max_internal_angle = 0.25;
-
- if ( opts->ttmin > 0.0 ) {
- gp->tthrange_min = opts->ttmin;
- }
- if ( opts->ttmax > 0.0 ) {
- gp->tthrange_max = opts->ttmax;
- }
- if ( opts->min_visits > 0 ) {
- gp->min_visits = opts->min_visits;
- }
- if ( opts->min_completeness > 0.0 ) {
- gp->min_completeness = opts->min_completeness;
- }
- if ( opts->max_uniqueness > 0.0 ) {
- gp->max_uniqueness = opts->max_uniqueness;
- }
- if ( opts->n_voxels > 0 ) {
- gp->n_voxels = opts->n_voxels;
- }
- if ( opts->fraction_max_visits > 0.0 ) {
- gp->fraction_max_visits = opts->fraction_max_visits;
- }
- if ( opts->sigma > 0.0 ) {
- gp->sigma_tth = opts->sigma;
- gp->sigma_eta = opts->sigma;
- gp->sigma_omega = opts->sigma;
- }
- if ( opts->domega > 0.0 ) {
- gp->domega = opts->domega;
- }
- if ( opts->max_internal_angle > 0 ) {
- gp->max_internal_angle = opts->max_internal_angle;
- }
-
- return (IndexingPrivate *)gp;
-}
-
-
-void felix_cleanup(IndexingPrivate *pp)
-{
- struct felix_private *p;
-
- p = (struct felix_private *) pp;
- free(p->readhkl_file);
- free(p);
-}
-
-
-static int file_exists(const char *filename)
-{
- struct stat s;
-
- if ( stat(filename, &s) != 0 ) {
- if ( errno == ENOENT ) return 0;
- ERROR("Failed to check for %s.\n", filename);
- exit(1);
- }
-
- return 1;
-}
-
-
-const char *felix_probe(UnitCell *cell)
-{
- pid_t pid;
- int pty;
- int status;
- FILE *fh;
- char line[1024];
- int ok = 0;
-
- if ( !cell_has_parameters(cell) ) {
- return NULL;
- }
-
- /* Felix will write gmon.out when we test it, which we are
- * are going to delete afterwards. Better check the file doesn't exist
- * first, in case it was important. */
- if ( file_exists("gmon.out") ) {
- ERROR("Please move or delete gmon.out from the working "
- "directory first.\n");
- exit(1);
- }
-
- pid = forkpty(&pty, NULL, NULL, NULL);
- if ( pid == -1 ) {
- return NULL;
- }
- if ( pid == 0 ) {
-
- /* Child process: invoke DirAx */
- struct termios t;
-
- /* Turn echo off */
- tcgetattr(STDIN_FILENO, &t);
- t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
- tcsetattr(STDIN_FILENO, TCSANOW, &t);
-
- execlp("Felix", "Felix", (char *)NULL);
- _exit(1);
-
- }
-
- fh = fdopen(pty, "r");
- if ( fgets(line, 1024, fh) == NULL ) {
- ok = 0;
- } else {
- if ( strncmp(line, "Felix", 5) == 0 ) {
- ok = 1;
- }
- }
-
- fclose(fh);
- close(pty);
- waitpid(pid, &status, 0);
-
- unlink("gmon.out");
-
- if ( ok ) return "felix";
- return NULL;
-}
-
-
-static void felix_show_help()
-{
- printf("Parameters for the Felix indexing algorithm:\n"
-" --felix-domega Degree range of omega (moscaicity) to consider.\n"
-" Default: 2\n"
-" --felix-fraction-max-visits\n"
-" Cutoff for minimum fraction of the max visits.\n"
-" Default: 0.75\n"
-" --felix-max-internal-angle\n"
-" Cutoff for maximum internal angle between observed\n"
-" spots and predicted spots. Default: 0.25\n"
-" --felix-max-uniqueness\n"
-" Cutoff for maximum fraction of found spots which\n"
-" can belong to other crystallites. Default: 0.5\n"
-" --felix-min-completeness\n"
-" Cutoff for minimum fraction of projected spots\n"
-" found in the pattern. Default: 0.001\n"
-" --felix-min-visits\n"
-" Cutoff for minimum number of voxel visits.\n"
-" Default: 15\n"
-" --felix-num-voxels Number of voxels for Rodrigues space search\n"
-" Default: 100\n"
-" --felix-sigma The sigma of the 2theta, eta and omega angles.\n"
-" Default: 0.2\n"
-" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n"
-" Default: 30\n"
-" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n"
-" Default: 0\n"
-);
-}
-
-
-static error_t felix_parse_arg(int key, char *arg,
- struct argp_state *state)
-{
- struct felix_options **opts_ptr = state->input;
- float tmp;
-
- switch ( key ) {
-
- case ARGP_KEY_INIT :
- *opts_ptr = malloc(sizeof(struct felix_options));
- if ( *opts_ptr == NULL ) return ENOMEM;
- (*opts_ptr)->ttmin = -1.0;
- (*opts_ptr)->ttmax = -1.0;
- (*opts_ptr)->min_visits = 0;
- (*opts_ptr)->min_completeness = -1.0;
- (*opts_ptr)->max_uniqueness = -1.0;
- (*opts_ptr)->n_voxels = 0;
- (*opts_ptr)->fraction_max_visits = -1.0;
- (*opts_ptr)->sigma = -1.0;
- (*opts_ptr)->domega = -1.0;
- (*opts_ptr)->max_internal_angle = -1.0;
- break;
-
- case 1 :
- felix_show_help();
- return EINVAL;
-
- case 2 :
- if ( sscanf(arg, "%f", &tmp) != 1 ) {
- ERROR("Invalid value for --felix-tthrange-min\n");
- return EINVAL;
- }
- (*opts_ptr)->ttmin = deg2rad(tmp);
- break;
-
- case 3 :
- if ( sscanf(arg, "%f", &tmp) != 1 ) {
- ERROR("Invalid value for --felix-tthrange-max\n");
- return EINVAL;
- }
- (*opts_ptr)->ttmax = deg2rad(tmp);
- break;
-
- case 4 :
- if ( sscanf(arg, "%d", &(*opts_ptr)->min_visits) != 1 ) {
- ERROR("Invalid value for --felix-min-visits\n");
- return EINVAL;
- }
- break;
-
- case 5 :
- if ( sscanf(arg, "%lf", &(*opts_ptr)->min_completeness) != 1 ) {
- ERROR("Invalid value for --felix-min-completeness\n");
- return EINVAL;
- }
- break;
-
- case 6 :
- if ( sscanf(arg, "%lf", &(*opts_ptr)->max_uniqueness) != 1 ) {
- ERROR("Invalid value for --felix-max-uniqueness\n");
- return EINVAL;
- }
- break;
-
- case 7 :
- if ( sscanf(arg, "%d", &(*opts_ptr)->n_voxels) != 1 ) {
- ERROR("Invalid value for --felix-num-voxels\n");
- return EINVAL;
- }
- break;
-
- case 8 :
- if ( sscanf(arg, "%lf", &(*opts_ptr)->fraction_max_visits) != 1 ) {
- ERROR("Invalid value for --felix-fraction-max-visits\n");
- return EINVAL;
- }
- break;
-
- case 9 :
- if ( sscanf(arg, "%lf", &(*opts_ptr)->sigma) != 1 ) {
- ERROR("Invalid value for --felix-sigma\n");
- return EINVAL;
- }
- break;
-
- case 10 :
- if ( sscanf(arg, "%lf", &(*opts_ptr)->domega) != 1 ) {
- ERROR("Invalid value for --felix-domega\n");
- return EINVAL;
- }
- break;
-
- case 11 :
- if ( sscanf(arg, "%lf", &(*opts_ptr)->max_internal_angle) != 1 ) {
- ERROR("Invalid value for --felix-max-internal-angle\n");
- return EINVAL;
- }
- break;
-
- default :
- return ARGP_ERR_UNKNOWN;
-
- }
-
- return 0;
-}
-
-
-static struct argp_option felix_options[] = {
-
- {"help-felix", 1, NULL, OPTION_NO_USAGE,
- "Show options for Felix indexing algorithm", 99},
- {"felix-tthrange-min", 2, "2theta", OPTION_HIDDEN, NULL},
- {"felix-tthrange-max", 3, "2theta", OPTION_HIDDEN, NULL},
- {"felix-min-visits", 4, "n", OPTION_HIDDEN, NULL},
- {"felix-min-completeness", 5, "frac", OPTION_HIDDEN, NULL},
- {"felix-max-uniqueness", 6, "n", OPTION_HIDDEN, NULL},
- {"felix-num-voxels", 7, "n", OPTION_HIDDEN, NULL},
- {"felix-fraction-max-visits", 8, "n", OPTION_HIDDEN, NULL},
- {"felix-sigma", 9, "n", OPTION_HIDDEN, NULL},
- {"felix-domega", 10, "n", OPTION_HIDDEN, NULL},
- {"felix-max-internal-angle", 11, "ang", OPTION_HIDDEN, NULL},
-
- {0}
-};
-
-
-struct argp felix_argp = { felix_options, felix_parse_arg,
- NULL, NULL, NULL, NULL, NULL };