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-rw-r--r--doc/man/indexamajig.1115
-rw-r--r--libcrystfel/src/felix.c195
-rw-r--r--libcrystfel/src/felix.h14
-rw-r--r--libcrystfel/src/index.c11
-rw-r--r--libcrystfel/src/index.h6
-rw-r--r--src/indexamajig.c133
-rw-r--r--src/process_image.h3
7 files changed, 232 insertions, 245 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 38654294..e1e1e19f 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -362,114 +362,17 @@ These set low-level parameters for the TakeTwo indexing algorithm. Respectively
The defaults are: \fB--taketwo-member-threshold=20\fR, \fB--taketwo-len-tolernace=0.001\fR, \fB--taketwo-angle-tolerance=0.6\fR and \fB--taketwo-trace-tolerance=3\fR.
.PD 0
-.IP \fB--felix-options\fR
-.PD
-Specify a comma-separated list of keyword arguments to change the default parameters passed to the felix indexer. For asthetics, this list can also be preceeded and followed by quotations - as in: \fB--felix-options="arg1=10,arg2=600"\fR. A list of parameters which can be modified through this option is detailed below.
-
-.PD 0
-.IP "\fBspacegroup=\fIn\fR"
-.PD
-Specify the spacegroup number of the crystal structure. For example: spacegroup=96 is P43212.
-
-.PD 0
-.IP "\fBn_voxels=\fIn\fR"
-.PD
-Specify the number of voxels used in the Rodrigues space search.
-(Default: 100)
-
-.PD 0
-.IP "\fBtest_fraction=\fIfract\fR"
-.PD
-Specify the fraction of space to test.
-(Default: 0.75)
-
-.PD 0
-.IP "\fBsigma_tth=\fIsig\fR"
-.PD
-Specify the sigma of the two-theta angle.
-(Default: 0.15)
-
+.IP \fB--felix-tthrange-min=\fIn\fR
+.IP \fB--felix-tthrange-max=\fIn\fR
+.IP \fB--felix-min-measurements=\fIn\fR
+.IP \fB--felix-min-completeness=\fIn\fR
+.IP \fB--felix-min-uniqueness=\fIn\fR
+.IP \fB--felix-num-voxels=\fIn\fR
+.IP \fB--felix-test-fraction=\fIn\fR
+.IP \fB--felix-sigma=\fIn\fR
.PD 0
-.IP "\fBsigma_eta=\fIsig\fR"
-.PD
-Specify the sigma of the eta angle.
-(Default: 0.2)
-
-.PD 0
-.IP "\fBsigma_omega=\fIsig\fR"
-.PD
-Specify the sigma of the omega angle.
-(Default: 0.2)
-
-.PD 0
-.IP "\fBn_sigmas=\fIn\fR"
-.PD
-Specify the number of sigmas to use.
-(Default: 2)
-
-.PD 0
-.IP "\fBtthrange_min=\fImin\fR"
-.PD
-Specify the lower bound of the 2theta angle to consider when indexing (degrees).
-(Default: 0.0)
-
-.PD 0
-.IP "\fBtthrange_max=\fImax\fR"
-.PD
-Specify the upper bound of the 2theta angle to consider when indexing (degrees).
-(Default: 30.0)
+These set low-level parameters for the Felix indexing algorithm.
-.PD 0
-.IP "\fBetarange_min=\fImin\fR"
-.PD
-Specify the lower bound of the eta angle to consider when indexing (degrees).
-(Default: 0.0)
-
-.PD 0
-.IP "\fBetarange_max=\fImax\fR"
-.PD
-Specify the upper bound of the eta angle to consider when indexing (degrees).
-(Default: 360.0)
-
-.PD 0
-.IP "\fBmin_measurements=\fIn\fR"
-.PD
-Specify a cutoff for how many Rodrigues lines cross in the first search.
-(Default: 15)
-
-.PD 0
-.IP "\fBmin_completeness=\fIfract\fR"
-.PD
-Specify a cutoff for the fraction of projected spots which are found in the pattern.
-(Default: 0.001)
-
-.PD 0
-.IP "\fBmin_uniqueness=\fIn\fR"
-.PD
-Specify a cutoff for the fraction of found spots which can belong to other crystallites.
-(Default: 0.5)
-
-.PD 0
-.IP "\fBforce4frustums\fR"
-.PD
-Tell Felix to use four frustums.
-
-.PD 0
-.IP "\fBorispace_octa\fR"
-.PD
-Tell Felix to use octahedral orispace as opposed to frustum.
-(Only possible with Felix.0.31)
-
-.PD 0
-.IP "\fBreadhkl=\fIfile\fR"
-.PD
-Specify a file from which to read in the ideal gvectors for the crystal.
-
-.PD 0
-.IP "\fBmaxtime=\fIn\fR"
-.PD
-Specify a maximum time which Felix is allowed to attempt to index the pattern (seconds)
-(Default: 30 s)
.SH INTEGRATION OPTIONS
.PD 0
.IP \fB--integration=\fR\fImethod\fR
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
index 973b0513..fc1b9e4d 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);
@@ -544,116 +547,70 @@ 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);
+ 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, "min_uniqueness=", 15) == 0 ){
- gp->min_uniqueness = atof(option+15);
+ 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_voxels=", 9) == 0 ){
- gp->n_voxels = atoi(option+9);
+ case L_TETRAGONAL:
+ switch ( cen ) {
+ case 'P' : return 89; /* P422 */
+ case 'I' : return 97; /* I422 */
+ default : return 0;
}
- 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);
- }
+ case L_RHOMBOHEDRAL:
+ return 155; /* R32 */
- if ( strncmp(option, "n_sigmas=", 9) == 0 ){
- gp->n_sigmas = atoi(option+9);
+ case L_HEXAGONAL:
+ switch ( cen ) {
+ case 'P' : return 177; /* P622 */
+ case 'H' : return 143; /* P3 */
+ 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;
- }
-
- if ( strncmp(option, "readhkl=", 8) == 0 ){
- gp->readhkl_file = strdup(option+8);
- }
-
- 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;
- if ( cell == NULL ) {
+ if ( !cell_has_parameters(cell) ) {
ERROR("Felix needs a unit cell.\n");
return NULL;
}
@@ -669,9 +626,15 @@ 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;
@@ -680,9 +643,8 @@ 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;
@@ -691,17 +653,34 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell, const char *options)
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 40568d37..ab9ba744 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 void felix_cleanup(IndexingPrivate *pp);
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 8ac04368..03bd6ae3 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;
@@ -359,7 +360,7 @@ 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 ac386390..15843b2a 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -135,12 +135,14 @@ extern IndexingMethod get_indm_from_string(const char *method);
#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 void index_pattern(struct image *image, IndexingPrivate *ipriv);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 691d6e11..88b61563 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -129,6 +129,7 @@ static void show_help(const char *s)
" --no-refine Skip the prediction refinement step\n"
" --check-peaks Check that most of the peaks can be accounted for\n"
" by the indexing solution\n"
+"\n"
" --taketwo-member-threshold\n"
" Minimum number of members in network\n"
" --taketwo-len-tolerance\n"
@@ -137,8 +138,25 @@ static void show_help(const char *s)
" Reciprocal space angle tolerance (in degrees)\n"
" --taketwo-trace-tolerance\n"
" Rotation matrix equivalence tolerance (in degrees)\n"
-" --felix-options Change the default arguments passed to the indexer\n"
-" Comma-separated list of options, key=val\n"
+"\n"
+" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n"
+" Default: 0\n"
+" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n"
+" Default: 30\n"
+" --felix-min-measurements\n"
+" How many Rodrigue lines cross in the first search\n"
+" Default: 15\n"
+" --felix-min-completeness\n"
+" Fraction of projected spots found in the pattern\n"
+" Default: 0.001\n"
+" --felix-min-uniqueness\n"
+" Fraction of found spots which can belong to other\n"
+" crystallites. Default: 0.5\n"
+" --felix-num-voxels Number of voxels for Rodrigues space search\n"
+" Default: 100\n"
+" --felix-test-fraction Fraction of space to test. Default: 0.75\n"
+" --felix-sigma The sigma of the 2theta, eta and omega angles.\n"
+" Default: 0.2\n"
"\nIntegration options:\n\n"
" --integration=<meth> Integration method (rings,prof2d)-(cen,nocen)\n"
" Default: rings-nocen\n"
@@ -208,7 +226,6 @@ int main(int argc, char *argv[])
char *geom_filename = NULL;
struct beam_params beam;
int have_push_res = 0;
- int len;
char *command_line_peak_path = NULL;
int if_refine = 1;
int if_nocomb = 0;
@@ -266,12 +283,19 @@ int main(int argc, char *argv[])
iargs.fix_profile_r = -1.0;
iargs.fix_bandwidth = -1.0;
iargs.fix_divergence = -1.0;
- iargs.felix_options = NULL;
iargs.profile = 0;
iargs.taketwo_opts.member_thresh = -1;
iargs.taketwo_opts.len_tol = -1.0;
iargs.taketwo_opts.angle_tol = -1.0;
iargs.taketwo_opts.trace_tol = -1.0;
+ iargs.felix_opts.ttmin = -1.0;
+ iargs.felix_opts.ttmax = -1.0;
+ iargs.felix_opts.min_measurements = 0;
+ iargs.felix_opts.min_completeness = -1.0;
+ iargs.felix_opts.min_uniqueness = -1.0;
+ iargs.felix_opts.n_voxels = 0;
+ iargs.felix_opts.test_fraction = -1.0;
+ iargs.felix_opts.sigma = -1.0;
/* Long options */
const struct option longopts[] = {
@@ -347,13 +371,21 @@ int main(int argc, char *argv[])
{"max-res", 1, NULL, 30},
{"min-peaks", 1, NULL, 31},
{"taketwo-member-threshold", 1, NULL, 32},
- {"taketwo-member-thresh", 1, NULL, 32},
+ {"taketwo-member-thresh", 1, NULL, 32}, /* compat */
{"taketwo-len-tolerance", 1, NULL, 33},
- {"taketwo-len-tol", 1, NULL, 33},
+ {"taketwo-len-tol", 1, NULL, 33}, /* compat */
{"taketwo-angle-tolerance", 1, NULL, 34},
- {"taketwo-angle-tol", 1, NULL, 34},
+ {"taketwo-angle-tol", 1, NULL, 34}, /* compat */
{"taketwo-trace-tolerance", 1, NULL, 35},
- {"taketwo-trace-tol", 1, NULL, 35},
+ {"taketwo-trace-tol", 1, NULL, 35}, /* compat */
+ {"felix-ttrange-min", 1, NULL, 36},
+ {"felix-ttrange-max", 1, NULL, 37},
+ {"felix-min-measurements", 1, NULL, 38},
+ {"felix-min-completeness", 1, NULL, 39},
+ {"felix-min-uniqueness", 1, NULL, 40},
+ {"felix-num-voxels", 1, NULL, 41},
+ {"felix-test-fraction", 1, NULL, 42},
+ {"felix-sigma", 1, NULL, 43},
{0, 0, NULL, 0}
};
@@ -524,18 +556,9 @@ int main(int argc, char *argv[])
break;
case 25 :
- /* Remove leading and trailing quotes */
- len = strlen(optarg);
- if ( optarg[len-1] == '\'' || optarg[len-1] == '\"' ){
- optarg[len-1] = 0;
- }
- if ( optarg[0] == '\'' || optarg[0] == '\"' ){
- iargs.felix_options = strdup( optarg+1 );
- }
- else {
- iargs.felix_options = strdup( optarg );
- }
- break;
+ ERROR("--felix-options is no longer used.\n");
+ ERROR("See --help for the new Felix options.\n");
+ return 1;
case 26:
iargs.min_pix_count = atoi(optarg);
@@ -599,6 +622,72 @@ int main(int argc, char *argv[])
iargs.taketwo_opts.trace_tol = deg2rad(iargs.taketwo_opts.trace_tol);
break;
+ case 36:
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.ttmin) != 1 )
+ {
+ ERROR("Invalid value for --felix-tthrange-min\n");
+ return 1;
+ }
+ iargs.felix_opts.ttmin = deg2rad(iargs.felix_opts.ttmin);
+ break;
+
+ case 37:
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.ttmax) != 1 )
+ {
+ ERROR("Invalid value for --felix-tthrange-max\n");
+ return 1;
+ }
+ iargs.felix_opts.ttmax = deg2rad(iargs.felix_opts.ttmax);
+ break;
+
+ case 38:
+ if ( sscanf(optarg, "%i", &iargs.felix_opts.min_measurements) != 1 )
+ {
+ ERROR("Invalid value for --felix-min-measurements\n");
+ return 1;
+ }
+ break;
+
+ case 39:
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.min_completeness) != 1 )
+ {
+ ERROR("Invalid value for --felix-min-completeness\n");
+ return 1;
+ }
+ break;
+
+ case 40:
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.min_uniqueness) != 1 )
+ {
+ ERROR("Invalid value for --felix-min-uniqueness\n");
+ return 1;
+ }
+ break;
+
+ case 41:
+ if ( sscanf(optarg, "%i", &iargs.felix_opts.n_voxels) != 1 )
+ {
+ ERROR("Invalid value for --felix-num-voxels\n");
+ return 1;
+ }
+ break;
+
+ case 42:
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.test_fraction) != 1 )
+ {
+ ERROR("Invalid value for --felix-test-fraction\n");
+ return 1;
+ }
+ break;
+
+ case 43:
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.sigma) != 1 )
+ {
+ ERROR("Invalid value for --felix-sigma\n");
+ return 1;
+ }
+ break;
+
case 0 :
break;
@@ -892,8 +981,8 @@ int main(int argc, char *argv[])
iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
iargs.tols, flags,
- iargs.felix_options,
- &iargs.taketwo_opts);
+ &iargs.taketwo_opts,
+ &iargs.felix_opts);
if ( iargs.ipriv == NULL ) {
ERROR("Failed to set up indexing system\n");
return 1;
diff --git a/src/process_image.h b/src/process_image.h
index 3e87b922..861ee203 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -40,6 +40,7 @@ struct index_args;
#include "im-sandbox.h"
#include "time-accounts.h"
#include "taketwo.h"
+#include "felix.h"
enum {
@@ -99,9 +100,9 @@ struct index_args
float fix_profile_r;
float fix_bandwidth;
float fix_divergence;
- char *felix_options;
int profile; /* Whether or not to do wall clock profiling */
struct taketwo_options taketwo_opts;
+ struct felix_options felix_opts;
};
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 06:37:36 +0000