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-rw-r--r--src/cell.c22
-rw-r--r--src/cell.h1
-rw-r--r--src/index.c21
-rw-r--r--src/index.h12
-rw-r--r--src/indexamajig.c34
5 files changed, 79 insertions, 11 deletions
diff --git a/src/cell.c b/src/cell.c
index b6accd58..7002f9fa 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -759,6 +759,28 @@ UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose)
}
+int cells_similar(UnitCell *cell1, UnitCell *cell2)
+{
+ double a1, b1, c1, al1, be1, ga1;
+ double a2, b2, c2, al2, be2, ga2;
+ double ltl = 5.0; /* percent */
+ double angtol = deg2rad(1.5);
+
+ cell_get_parameters(cell1, &a1, &b1, &c1, &al1, &be1, &ga1);
+ cell_get_parameters(cell2, &a2, &b2, &c2, &al2, &be2, &ga2);
+
+ if ( !within_tolerance(a1, a2, ltl) ) return 0;
+ if ( !within_tolerance(b1, b2, ltl) ) return 0;
+ if ( !within_tolerance(c1, c2, ltl) ) return 0;
+
+ if ( fabs(al1-al2) > angtol ) return 0;
+ if ( fabs(be1-be2) > angtol ) return 0;
+ if ( fabs(ga1-ga2) > angtol ) return 0;
+
+ return 1;
+}
+
+
/* Return sin(theta)/lambda = 1/2d. Multiply by two if you want 1/d */
double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
{
diff --git a/src/cell.h b/src/cell.h
index a4d32bf8..d3edb503 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -76,6 +76,7 @@ extern double resolution(UnitCell *cell,
extern void cell_print(UnitCell *cell);
extern UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose);
+extern int cells_similar(UnitCell *c1, UnitCell *c2);
extern UnitCell *load_cell_from_pdb(const char *filename);
diff --git a/src/index.c b/src/index.c
index 0c656042..f285cccb 100644
--- a/src/index.c
+++ b/src/index.c
@@ -124,7 +124,7 @@ void map_all_peaks(struct image *image)
void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
- int no_match, int verbose, IndexingPrivate *ipriv)
+ int cellr, int verbose, IndexingPrivate *ipriv)
{
int i;
@@ -150,7 +150,7 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
return;
}
- if ( no_match || (indm == INDEXING_TEMPLATE) ) {
+ if ( (cellr == CELLR_NONE) || (indm == INDEXING_TEMPLATE) ) {
image->indexed_cell = image->candidate_cells[0];
if ( verbose ) {
STATUS("--------------------\n");
@@ -172,7 +172,22 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
STATUS("--------------------\n");
}
- new_cell = match_cell(image->candidate_cells[i], cell, verbose);
+ /* Match or reduce the cell as appropriate */
+ switch ( cellr ) {
+ case CELLR_NONE :
+ /* Never happens */
+ break;
+ case CELLR_REDUCE :
+ new_cell = match_cell(image->candidate_cells[i],
+ cell, verbose);
+ break;
+ case CELLR_COMPARE :
+ if ( cells_similar(image->candidate_cells[i], cell) ) {
+ new_cell = image->candidate_cells[i];
+ }
+ break;
+ }
+
image->indexed_cell = new_cell;
if ( new_cell != NULL ) {
STATUS("Matched on attempt %i.\n", i);
diff --git a/src/index.h b/src/index.h
index 0b740995..81549e00 100644
--- a/src/index.h
+++ b/src/index.h
@@ -22,6 +22,8 @@
#include "image.h"
#include "detector.h"
+
+/* Indexing methods */
typedef enum {
INDEXING_NONE,
INDEXING_DIRAX,
@@ -29,6 +31,14 @@ typedef enum {
} IndexingMethod;
+/* Cell reduction methods */
+enum {
+ CELLR_NONE,
+ CELLR_REDUCE,
+ CELLR_COMPARE
+};
+
+
typedef struct _indexingprivate IndexingPrivate;
extern IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
@@ -39,7 +49,7 @@ extern IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
extern void map_all_peaks(struct image *image);
extern void index_pattern(struct image *image, UnitCell *cell,
- IndexingMethod indm, int no_match, int verbose,
+ IndexingMethod indm, int cellr, int verbose,
IndexingPrivate *priv);
extern void cleanup_indexing(IndexingPrivate *priv);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 324e090f..2b733f04 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -59,7 +59,6 @@ struct static_index_args
int config_nearbragg;
int config_gpu;
int config_simulate;
- int config_nomatch;
int config_polar;
int config_sanity;
int config_satcorr;
@@ -72,6 +71,7 @@ struct static_index_args
const double *intensities;
struct gpu_context *gctx;
int peaks;
+ int cellr;
double nominal_photon_energy;
/* Output stream */
@@ -313,7 +313,6 @@ static void process_image(void *pp, int cookie)
int config_nearbragg = pargs->static_args.config_nearbragg;
int config_gpu = pargs->static_args.config_gpu;
int config_simulate = pargs->static_args.config_simulate;
- int config_nomatch = pargs->static_args.config_nomatch;
int config_polar = pargs->static_args.config_polar;
IndexingMethod indm = pargs->static_args.indm;
const double *intensities = pargs->static_args.intensities;
@@ -397,7 +396,7 @@ static void process_image(void *pp, int cookie)
/* Calculate orientation matrix (by magic) */
if ( config_writedrx || (indm != INDEXING_NONE) ) {
- index_pattern(&image, cell, indm, config_nomatch,
+ index_pattern(&image, cell, indm, pargs->static_args.cellr,
config_verbose, pargs->static_args.ipriv);
}
@@ -522,7 +521,6 @@ int main(int argc, char *argv[])
int config_simulate = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
- int config_nomatch = 0;
int config_gpu = 0;
int config_verbose = 0;
int config_alternate = 0;
@@ -543,6 +541,8 @@ int main(int argc, char *argv[])
char *pdb = NULL;
char *prefix = NULL;
char *speaks = NULL;
+ char *scellr = NULL;
+ int cellr;
int peaks;
int nthreads = 1;
int i;
@@ -564,6 +564,7 @@ int main(int argc, char *argv[])
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
{"peaks", 1, NULL, 2},
+ {"cell-reduction", 1, NULL, 3},
{"near-bragg", 0, &config_nearbragg, 1},
{"write-drx", 0, &config_writedrx, 1},
{"indexing", 1, NULL, 'z'},
@@ -572,7 +573,6 @@ int main(int argc, char *argv[])
{"simulate", 0, &config_simulate, 1},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
- {"no-match", 0, &config_nomatch, 1},
{"verbose", 0, &config_verbose, 1},
{"alternate", 0, &config_alternate, 1},
{"intensities", 1, NULL, 'q'},
@@ -647,6 +647,10 @@ int main(int argc, char *argv[])
speaks = strdup(optarg);
break;
+ case 3 :
+ scellr = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -743,6 +747,22 @@ int main(int argc, char *argv[])
}
free(indm_str);
+ if ( scellr == NULL ) {
+ STATUS("You didn't specify a cell reduction method, so I'm"
+ " going to use 'reduce'.\n");
+ cellr = CELLR_REDUCE;
+ } else if ( strcmp(scellr, "none") == 0 ) {
+ cellr = CELLR_NONE;
+ } else if ( strcmp(scellr, "reduce") == 0) {
+ cellr = CELLR_REDUCE;
+ } else if ( strcmp(scellr, "compare") == 0) {
+ cellr = CELLR_COMPARE;
+ } else {
+ ERROR("Unrecognised cell reduction method '%s'\n", scellr);
+ return 1;
+ }
+ free(scellr); /* free(NULL) is OK. */
+
if ( geometry == NULL ) {
ERROR("You need to specify a geometry file with --geometry\n");
return 1;
@@ -755,7 +775,7 @@ int main(int argc, char *argv[])
}
free(geometry);
- if ( (!config_nomatch) || (indm == INDEXING_TEMPLATE) ) {
+ if ( (cellr != CELLR_NONE) || (indm == INDEXING_TEMPLATE) ) {
cell = load_cell_from_pdb(pdb);
if ( cell == NULL ) {
ERROR("Couldn't read unit cell (from %s)\n", pdb);
@@ -814,12 +834,12 @@ int main(int argc, char *argv[])
qargs.static_args.config_nearbragg = config_nearbragg;
qargs.static_args.config_gpu = config_gpu;
qargs.static_args.config_simulate = config_simulate;
- qargs.static_args.config_nomatch = config_nomatch;
qargs.static_args.config_polar = config_polar;
qargs.static_args.config_sanity = config_sanity;
qargs.static_args.config_satcorr = config_satcorr;
qargs.static_args.config_sa = config_sa;
qargs.static_args.config_closer = config_closer;
+ qargs.static_args.cellr = cellr;
qargs.static_args.threshold = threshold;
qargs.static_args.det = det;
qargs.static_args.indm = indm;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 14:15:23 +0000