indexamajig: Simplify Felix options

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;
 };