diff options
author | Thomas White <taw@physics.org> | 2017-10-27 16:13:49 +0200 |
---|---|---|
committer | Thomas White <taw@physics.org> | 2017-10-27 16:13:49 +0200 |
commit | 29d60af9d37a9d2cf67d7e0b77354d4fd518679a (patch) | |
tree | 506e4e8ef6d3e881db2790d5904813d8b9657d5e /libcrystfel | |
parent | 45038c42847476ce1aee5b09c47fb330a0108cd6 (diff) | |
parent | 3caab16fad2ebd2fcc2f245a6cb4a62fad46f806 (diff) |
Merge branch 'tom/simpler_felix'
Diffstat (limited to 'libcrystfel')
-rw-r--r-- | libcrystfel/src/felix.c | 197 | ||||
-rw-r--r-- | libcrystfel/src/felix.h | 14 | ||||
-rw-r--r-- | libcrystfel/src/index.c | 11 | ||||
-rw-r--r-- | libcrystfel/src/index.h | 6 |
4 files changed, 111 insertions, 117 deletions
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c index 79252b2b..bbd82b0e 100644 --- a/libcrystfel/src/felix.c +++ b/libcrystfel/src/felix.c @@ -188,7 +188,9 @@ static int read_felix(struct felix_private *gp, struct image *image, 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 ) { @@ -383,7 +385,8 @@ static char *write_ini(struct image *image, struct felix_private *gp) &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, "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); @@ -544,112 +547,66 @@ int felix_index(struct image *image, IndexingPrivate *ipriv) } -static void parse_options(const char *options, struct felix_private *gp) +static int sg_number_for_cell(UnitCell *cell) { - char *temp_options; - char *option; - char *freeme; - - temp_options = strdup(options); - freeme = temp_options; - - 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); + 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; } - if ( strncmp(option, "sigma_omega=", 12) == 0 ){ - gp->sigma_omega = atof(option+12); + 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; } - if ( strncmp(option, "n_sigmas=", 9) == 0 ){ - gp->n_sigmas = atoi(option+9); + case L_TETRAGONAL: + switch ( cen ) { + case 'P' : return 89; /* P422 */ + case 'I' : return 97; /* I422 */ + default : return 0; } - 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; - } + case L_RHOMBOHEDRAL: + return 155; /* R32 */ - if ( strncmp(option, "readhkl=", 8) == 0 ){ - gp->readhkl_file = strdup(option+8); + case L_HEXAGONAL: + switch ( cen ) { + case 'P' : return 177; /* P622 */ + case 'H' : return 143; /* P3 */ + default : return 0; } - if ( strncmp(option, "maxtime=", 8) == 0 ){ - gp->maxtime = atof(option+8); + 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; } - - free(freeme); - free(option); } -void *felix_prepare(IndexingMethod *indm, UnitCell *cell, const char *options) + +void *felix_prepare(IndexingMethod *indm, UnitCell *cell, + struct felix_options *opts) { struct felix_private *gp; @@ -659,7 +616,7 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, const char *options) return NULL; } - if ( cell == NULL ) { + if ( !cell_has_parameters(cell) ) { ERROR("Felix needs a unit cell.\n"); return NULL; } @@ -675,9 +632,15 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, const char *options) gp->indm = *indm; /* Default values of felix options */ - gp->spacegroup = 0; - gp->tthrange_min = 0; - gp->tthrange_max = 30.0; + 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; @@ -686,28 +649,44 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, const char *options) 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_tth = 0.2; gp->sigma_eta = 0.2; gp->sigma_omega = 0.2; - gp->n_sigmas = 2; + gp->n_sigmas = 1; gp->force4frustums = 0; gp->orispace_frustum = 1; gp->orispace_octa = 0; gp->readhkl_file = NULL; gp->maxtime = 30.0; + gp->tthrange_min = deg2rad(0.0); + gp->tthrange_max = deg2rad(30.0); - /* Parse the options string and fill in the necessary - * private variables. */ - if ( options != NULL ) parse_options(options, gp); - - /* 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; + if ( opts->ttmin > 0.0 ) { + gp->tthrange_min = opts->ttmin; + } + if ( opts->ttmax > 0.0 ) { + gp->tthrange_max = opts->ttmax; + } + if ( opts->min_measurements > 0 ) { + gp->min_measurements = opts->min_measurements; + } + if ( opts->min_completeness > 0.0 ) { + gp->min_completeness = opts->min_completeness; + } + if ( opts->min_uniqueness > 0.0 ) { + gp->min_uniqueness = opts->min_uniqueness; + } + if ( opts->n_voxels > 0 ) { + gp->n_voxels = opts->n_voxels; + } + if ( opts->test_fraction > 0.0 ) { + gp->test_fraction = opts->test_fraction; + } + if ( opts->sigma > 0.0 ) { + gp->sigma_tth = opts->sigma; + gp->sigma_eta = opts->sigma; + gp->sigma_omega = opts->sigma; } return (IndexingPrivate *)gp; diff --git a/libcrystfel/src/felix.h b/libcrystfel/src/felix.h index 61b1d352..48ffbe9c 100644 --- a/libcrystfel/src/felix.h +++ b/libcrystfel/src/felix.h @@ -36,8 +36,20 @@ #include "cell.h" +struct felix_options +{ + double ttmin; /* radians */ + double ttmax; /* radians */ + int min_measurements; + double min_completeness; + double min_uniqueness; + int n_voxels; + double test_fraction; + double sigma; +}; + extern void *felix_prepare(IndexingMethod *indm, UnitCell *cell, - const char *options); + struct felix_options *opts); extern const char *felix_probe(UnitCell *cell); diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index cdc0e305..62f22c13 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -197,7 +197,7 @@ static char *friendly_indexer_name(IndexingMethod m) static void *prepare_method(IndexingMethod *m, UnitCell *cell, - const char *options) + struct felix_options *felix_opts) { char *str; IndexingMethod in = *m; @@ -230,7 +230,7 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell, break; case INDEXING_FELIX : - priv = felix_prepare(m, cell, options); + priv = felix_prepare(m, cell, felix_opts); break; case INDEXING_TAKETWO : @@ -266,8 +266,9 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell, IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, struct detector *det, float *ltl, - IndexingFlags flags, const char *options, - struct taketwo_options *ttopts) + IndexingFlags flags, + struct taketwo_options *ttopts, + struct felix_options *felix_opts) { int i, n; char **method_strings; @@ -363,7 +364,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, int j; ipriv->engine_private[i] = prepare_method(&methods[i], cell, - options); + felix_opts); if ( ipriv->engine_private[i] == NULL ) return NULL; diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index 4e1f1519..8ece9227 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -136,12 +136,14 @@ extern IndexingMethod get_indm_from_string_2(const char *method, int *err); #include "cell.h" #include "image.h" #include "taketwo.h" +#include "felix.h" extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell, struct detector *det, float *ltl, - IndexingFlags flags, const char *options, - struct taketwo_options *ttopts); + IndexingFlags flags, + struct taketwo_options *ttopts, + struct felix_options *felix_opts); extern char *detect_indexing_methods(UnitCell *cell); |