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-rw-r--r--libcrystfel/src/index.c9
-rw-r--r--libcrystfel/src/index.h5
-rw-r--r--libcrystfel/src/taketwo.c2
-rw-r--r--libcrystfel/src/taketwo.h22
-rw-r--r--src/indexamajig.c51
-rw-r--r--src/process_image.h2
6 files changed, 79 insertions, 12 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index bdabb062..b00f13aa 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -64,6 +64,8 @@ struct _indexingprivate
UnitCell *target_cell;
float tolerance[4];
+ struct taketwo_options *ttopts;
+
int n_methods;
IndexingMethod *methods;
void **engine_private;
@@ -157,7 +159,8 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
struct detector *det, float *ltl,
- int no_refine, const char *options)
+ int no_refine, const char *options,
+ struct taketwo_options *ttopts)
{
int i, n;
char **method_strings;
@@ -216,6 +219,8 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
}
for ( i=0; i<4; i++ ) ipriv->tolerance[i] = ltl[i];
+ ipriv->ttopts = ttopts;
+
return ipriv;
}
@@ -339,7 +344,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
break;
case INDEXING_TAKETWO :
- r = taketwo_index(image, mpriv);
+ r = taketwo_index(image, ipriv->ttopts, mpriv);
break;
default :
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 2107ed80..8b3aadeb 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -157,10 +157,13 @@ extern IndexingMethod get_indm_from_string(const char *method);
#include "detector.h"
#include "cell.h"
#include "image.h"
+#include "taketwo.h"
+
extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
struct detector *det, float *ltl,
- int no_refine, const char *options);
+ int no_refine, const char *options,
+ struct taketwo_options *ttopts);
extern void index_pattern(struct image *image, IndexingPrivate *ipriv);
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index 7ae77f4a..307c6737 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -1511,7 +1511,7 @@ static UnitCell *run_taketwo(UnitCell *cell, struct rvec *rlps, int rlp_count)
/* CrystFEL interface hooks */
-int taketwo_index(struct image *image, void *priv)
+int taketwo_index(struct image *image, struct taketwo_options *opts, void *priv)
{
Crystal *cr;
UnitCell *cell;
diff --git a/libcrystfel/src/taketwo.h b/libcrystfel/src/taketwo.h
index 4c06e334..a03292a8 100644
--- a/libcrystfel/src/taketwo.h
+++ b/libcrystfel/src/taketwo.h
@@ -3,13 +3,13 @@
*
* Rewrite of TakeTwo algorithm (Acta D72 (8) 956-965) for CrystFEL
*
- * Copyright © 2016 Helen Ginn
- * Copyright © 2016 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2016-2017 Helen Ginn
+ * Copyright © 2016-2017 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2016 Helen Ginn <helen@strubi.ox.ac.uk>
- * 2016 Thomas White <taw@physics.org>
+ * 2016 Helen Ginn <helen@strubi.ox.ac.uk>
+ * 2016-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -32,10 +32,20 @@
#define TAKETWO_H
#include "cell.h"
+#include "index.h"
+
+struct taketwo_options
+{
+ int member_thresh;
+ double len_tol;
+ double angle_tol;
+ double trace_tol;
+};
+
extern void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell,
struct detector *det, float *ltl);
-extern int taketwo_index(struct image *image, void *priv);
+extern int taketwo_index(struct image *image, struct taketwo_options *opts, void *priv);
extern void taketwo_cleanup(IndexingPrivate *pp);
#endif /* TAKETWO_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index ce87fde6..33eed81f 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -62,7 +62,7 @@
#include "reflist-utils.h"
#include "cell-utils.h"
#include "integration.h"
-
+#include "taketwo.h"
#include "im-sandbox.h"
@@ -171,6 +171,11 @@ static void show_help(const char *s)
" Given as a list of comma separated list of \n"
" indexer specific, key word arguments.\n"
" Example: \"arg1=10,arg2=500\" \n"
+"\nLow-level options for the TakeTwo indexer:\n\n"
+" --taketwo-member-threshold Minimum number of members in network\n"
+" --taketwo-len-tolerance Reciprocal space length tolerance (1/A)\n"
+" --taketwo-angle-tolerance Reciprocal space angle tolerance (in degrees)\n"
+" --taketwo-trace-tolerance Rotation matrix trace tolerance\n"
);
}
@@ -276,6 +281,10 @@ int main(int argc, char *argv[])
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;
/* Long options */
const struct option longopts[] = {
@@ -344,6 +353,10 @@ int main(int argc, char *argv[])
{"min-res", 1, NULL, 29},
{"max-res", 1, NULL, 30},
{"min-peaks", 1, NULL, 31},
+ {"taketwo-member-thresh", 1, NULL, 32},
+ {"taketwo-len-tol", 1, NULL, 33},
+ {"taketwo-angle-tol", 1, NULL, 34},
+ {"taketwo-trace-tol", 1, NULL, 35},
{0, 0, NULL, 0}
};
@@ -551,6 +564,39 @@ int main(int argc, char *argv[])
iargs.min_peaks = atoi(optarg);
break;
+ case 32:
+ if ( sscanf(optarg, "%i", &iargs.taketwo_opts.member_thresh) != 1 )
+ {
+ ERROR("Invalid value for --taketwo-member-threshold\n");
+ return 1;
+ }
+ break;
+
+ case 33:
+ if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.len_tol) != 1 )
+ {
+ ERROR("Invalid value for --taketwo-len-tolerance\n");
+ return 1;
+ }
+ break;
+
+ case 34:
+ if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.angle_tol) != 1 )
+ {
+ ERROR("Invalid value for --taketwo-angle-tolerance\n");
+ return 1;
+ }
+ break;
+
+
+ case 35:
+ if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.trace_tol) != 1 )
+ {
+ ERROR("Invalid value for --taketwo-trace-tolerance\n");
+ return 1;
+ }
+ break;
+
case 0 :
break;
@@ -803,7 +849,8 @@ int main(int argc, char *argv[])
iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
iargs.tols, no_refine,
- iargs.felix_options);
+ iargs.felix_options,
+ &iargs.taketwo_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 ec51c188..3e87b922 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -39,6 +39,7 @@ struct index_args;
#include "integration.h"
#include "im-sandbox.h"
#include "time-accounts.h"
+#include "taketwo.h"
enum {
@@ -100,6 +101,7 @@ struct index_args
float fix_divergence;
char *felix_options;
int profile; /* Whether or not to do wall clock profiling */
+ struct taketwo_options taketwo_opts;
};
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-25 01:23:53 +0000