aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--src/index.c245
-rw-r--r--src/index.h10
-rw-r--r--src/indexamajig.c54
3 files changed, 196 insertions, 113 deletions
diff --git a/src/index.c b/src/index.c
index edfa33e5..4d2a158f 100644
--- a/src/index.c
+++ b/src/index.c
@@ -43,39 +43,67 @@ static IndexingPrivate *indexing_private(IndexingMethod indm)
}
-IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
+IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
const char *filename, struct detector *det,
double nominal_photon_energy)
{
- switch ( indm ) {
- case INDEXING_NONE :
- return indexing_private(indm);
- case INDEXING_DIRAX :
- return indexing_private(indm);
- case INDEXING_MOSFLM :
- return indexing_private(indm);
- case INDEXING_TEMPLATE :
- return generate_templates(cell, filename, det,
- nominal_photon_energy);
+ int n;
+ int nm = 0;
+ IndexingPrivate **iprivs;
+
+ while ( indm[nm] != INDEXING_NONE ) nm++;
+ STATUS("Preparing %i indexing methods.\n", nm);
+ iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
+
+ for ( n=0; n<nm; n++ ) {
+
+ switch ( indm[n] ) {
+ case INDEXING_NONE :
+ ERROR("Tried to prepare INDEXING_NONE!\n");
+ break;
+ case INDEXING_DIRAX :
+ iprivs[n] = indexing_private(indm[n]);
+ break;
+ case INDEXING_MOSFLM :
+ iprivs[n] = indexing_private(indm[n]);
+ break;
+ case INDEXING_TEMPLATE :
+ iprivs[n] = generate_templates(cell, filename, det,
+ nominal_photon_energy);
+ break;
+ }
+
+ n++;
+
}
- return 0;
+ iprivs[n] = NULL;
+
+ return iprivs;
}
-void cleanup_indexing(IndexingPrivate *priv)
+void cleanup_indexing(IndexingPrivate **priv)
{
- switch ( priv->indm ) {
- case INDEXING_NONE :
- free(priv);
- break;
- case INDEXING_DIRAX :
- free(priv);
- break;
- case INDEXING_MOSFLM :
- free(priv);
- break;
- case INDEXING_TEMPLATE :
- free_templates(priv);
+ int n = 0;
+
+ while ( priv[n] != NULL ) {
+
+ switch ( priv[n]->indm ) {
+ case INDEXING_NONE :
+ free(priv[n]);
+ break;
+ case INDEXING_DIRAX :
+ free(priv[n]);
+ break;
+ case INDEXING_MOSFLM :
+ free(priv[n]);
+ break;
+ case INDEXING_TEMPLATE :
+ free_templates(priv[n]);
+ }
+
+ n++;
+
}
}
@@ -246,81 +274,93 @@ void map_all_peaks(struct image *image)
}
-void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
- int cellr, int verbose, IndexingPrivate *ipriv)
+void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
+ int cellr, int verbose, IndexingPrivate **ipriv)
{
int i;
+ int n = 0;
map_all_peaks(image);
- write_drx(image);
- image->ncells = 0;
+ while ( indm[n] != INDEXING_NONE ) {
- /* Index (or not) as appropriate */
- switch ( indm ) {
- case INDEXING_NONE :
- return;
- case INDEXING_DIRAX :
- run_dirax(image);
- break;
- case INDEXING_MOSFLM :
- write_spt(image);
- write_img(image); /* dummy image. not needed for each frame.*/
- run_mosflm(image,cell);
- break;
- case INDEXING_TEMPLATE :
- match_templates(image, ipriv);
- break;
- }
-
- if ( image->ncells == 0 ) {
- STATUS("No candidate cells found.\n");
- return;
- }
+ image->ncells = 0;
- if ( (cellr == CELLR_NONE) || (indm == INDEXING_TEMPLATE) ) {
- image->indexed_cell = image->candidate_cells[0];
- if ( verbose ) {
- STATUS("--------------------\n");
- STATUS("The indexed cell (matching not performed):\n");
- cell_print(image->indexed_cell);
- STATUS("--------------------\n");
+ /* Index as appropriate */
+ switch ( indm[n] ) {
+ case INDEXING_NONE :
+ return;
+ case INDEXING_DIRAX :
+ STATUS("Running DirAx...\n");
+ write_drx(image);
+ run_dirax(image);
+ break;
+ case INDEXING_MOSFLM :
+ STATUS("Running MOSFLM...\n");
+ write_spt(image);
+ write_img(image); /* dummy image */
+ run_mosflm(image, cell);
+ break;
+ case INDEXING_TEMPLATE :
+ match_templates(image, ipriv[n]);
+ break;
}
- return;
- }
- for ( i=0; i<image->ncells; i++ ) {
-
- UnitCell *new_cell = NULL;
-
- if ( verbose ) {
- STATUS("--------------------\n");
- STATUS("Candidate cell %i (before matching):\n", i);
- cell_print(image->candidate_cells[i]);
- STATUS("--------------------\n");
+ if ( image->ncells == 0 ) {
+ STATUS("No candidate cells found.\n");
+ return;
}
- /* 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, 1);
- break;
- case CELLR_COMPARE :
- new_cell = match_cell(image->candidate_cells[i],
- cell, verbose, 0);
- break;
+ if ( (cellr == CELLR_NONE) || (indm[n] == INDEXING_TEMPLATE) ) {
+ image->indexed_cell = image->candidate_cells[0];
+ if ( verbose ) {
+ STATUS("--------------------\n");
+ STATUS("The indexed cell (matching not"
+ " performed):\n");
+ cell_print(image->indexed_cell);
+ STATUS("--------------------\n");
+ }
+ return;
}
- image->indexed_cell = new_cell;
- if ( new_cell != NULL ) {
- STATUS("Matched on attempt %i.\n", i);
- goto done;
+ for ( i=0; i<image->ncells; i++ ) {
+
+ UnitCell *new_cell = NULL;
+
+ if ( verbose ) {
+ STATUS("--------------------\n");
+ STATUS("Candidate cell %i (before matching):\n",
+ i);
+ cell_print(image->candidate_cells[i]);
+ STATUS("--------------------\n");
+ }
+
+ /* 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, 1);
+ break;
+ case CELLR_COMPARE :
+ new_cell = match_cell(image->candidate_cells[i],
+ cell, verbose, 0);
+ break;
+ }
+
+ image->indexed_cell = new_cell;
+ if ( new_cell != NULL ) {
+ STATUS("Matched on attempt %i.\n", i);
+ goto done;
+ }
+
}
+ /* Move on to the next indexing method */
+ n++;
+
}
done:
@@ -328,3 +368,38 @@ done:
cell_free(image->candidate_cells[i]);
}
}
+
+
+IndexingMethod *build_indexer_list(const char *str, int *need_cell)
+{
+ int n, i;
+ char **methods;
+ IndexingMethod *list;
+ *need_cell = 0;
+
+ n = assplode(str, ",", &methods, ASSPLODE_NONE);
+ list = malloc((n+1)*sizeof(IndexingMethod));
+
+ for ( i=0; i<n; i++ ) {
+
+ if ( strcmp(methods[i], "dirax") == 0) {
+ list[i] = INDEXING_DIRAX;
+ } else if ( strcmp(methods[i], "mosflm") == 0) {
+ list[i] = INDEXING_MOSFLM;
+ } else if ( strcmp(methods[i], "template") == 0) {
+ list[i] = INDEXING_TEMPLATE;
+ *need_cell = 1;
+ } else {
+ ERROR("Unrecognised indexing method '%s'\n",
+ methods[i]);
+ return NULL;
+ }
+
+ free(methods[i]);
+
+ }
+ free(methods);
+ list[i] = INDEXING_NONE;
+
+ return list;
+}
diff --git a/src/index.h b/src/index.h
index 29be9dcc..b58c9b53 100644
--- a/src/index.h
+++ b/src/index.h
@@ -42,7 +42,7 @@ enum {
typedef struct _indexingprivate IndexingPrivate;
-extern IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
+extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
const char *filename,
struct detector *det,
double nominal_photon_energy);
@@ -50,9 +50,11 @@ 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 cellr, int verbose,
- IndexingPrivate *priv);
+ IndexingMethod *indm, int cellr, int verbose,
+ IndexingPrivate **priv);
-extern void cleanup_indexing(IndexingPrivate *priv);
+extern void cleanup_indexing(IndexingPrivate **priv);
+
+extern IndexingMethod *build_indexer_list(const char *str, int *need_cell);
#endif /* INDEX_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 8d762fa4..a2b5e80d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -68,8 +68,8 @@ struct static_index_args
float threshold;
float min_gradient;
struct detector *det;
- IndexingMethod indm;
- IndexingPrivate *ipriv;
+ IndexingMethod *indm;
+ IndexingPrivate **ipriv;
const double *intensities;
const unsigned char *flags;
const char *sym; /* Symmetry of "intensities" and "flags" */
@@ -325,7 +325,7 @@ static void process_image(void *pp, int cookie)
int config_gpu = pargs->static_args.config_gpu;
int config_simulate = pargs->static_args.config_simulate;
int config_polar = pargs->static_args.config_polar;
- IndexingMethod indm = pargs->static_args.indm;
+ IndexingMethod *indm = pargs->static_args.indm;
const double *intensities = pargs->static_args.intensities;
const unsigned char *flags = pargs->static_args.flags;
struct gpu_context *gctx = pargs->static_args.gctx;
@@ -543,7 +543,10 @@ int main(int argc, char *argv[])
float min_gradient = 100000.0;
struct detector *det;
char *geometry = NULL;
- IndexingMethod indm;
+ IndexingMethod *indm;
+ IndexingPrivate **ipriv;
+ int indexer_needs_cell;
+ int reduction_needs_cell;
char *indm_str = NULL;
UnitCell *cell;
double *intensities = NULL;
@@ -561,7 +564,6 @@ int main(int argc, char *argv[])
pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER;
char prepare_line[1024];
char prepare_filename[1024];
- IndexingPrivate *ipriv;
struct queue_args qargs;
struct beam_params *beam = NULL;
double nominal_photon_energy;
@@ -784,31 +786,30 @@ int main(int argc, char *argv[])
" try to index anything.\n"
"If that isn't what you wanted, re-run with"
" --indexing=<method>.\n");
- indm = INDEXING_NONE;
- } else if ( strcmp(indm_str, "none") == 0 ) {
- indm = INDEXING_NONE;
- } else if ( strcmp(indm_str, "dirax") == 0) {
- indm = INDEXING_DIRAX;
- } else if ( strcmp(indm_str, "mosflm") == 0) {
- indm = INDEXING_MOSFLM;
- } else if ( strcmp(indm_str, "template") == 0) {
- indm = INDEXING_TEMPLATE;
+ indm = NULL;
} else {
- ERROR("Unrecognised indexing method '%s'\n", indm_str);
- return 1;
+ indm = build_indexer_list(indm_str, &indexer_needs_cell);
+ if ( indm == NULL ) {
+ ERROR("Invalid indexer list '%s'\n", indm_str);
+ return 1;
+ }
+ free(indm_str);
}
- free(indm_str);
+ reduction_needs_cell = 0;
if ( scellr == NULL ) {
STATUS("You didn't specify a cell reduction method, so I'm"
" going to use 'reduce'.\n");
cellr = CELLR_REDUCE;
+ reduction_needs_cell = 1;
} else if ( strcmp(scellr, "none") == 0 ) {
cellr = CELLR_NONE;
} else if ( strcmp(scellr, "reduce") == 0) {
cellr = CELLR_REDUCE;
+ reduction_needs_cell = 1;
} else if ( strcmp(scellr, "compare") == 0) {
cellr = CELLR_COMPARE;
+ reduction_needs_cell = 1;
} else {
ERROR("Unrecognised cell reduction method '%s'\n", scellr);
return 1;
@@ -827,14 +828,15 @@ int main(int argc, char *argv[])
}
free(geometry);
- if ( (cellr != CELLR_NONE) || (indm == INDEXING_TEMPLATE) ) {
+ if ( reduction_needs_cell || indexer_needs_cell ) {
cell = load_cell_from_pdb(pdb);
if ( cell == NULL ) {
ERROR("Couldn't read unit cell (from %s)\n", pdb);
return 1;
}
} else {
- STATUS("No cell needed because --no-match was used.\n");
+ STATUS("No cell needed for these choices of indexing"
+ " and reduction.\n");
cell = NULL;
}
free(pdb);
@@ -866,11 +868,15 @@ int main(int argc, char *argv[])
qargs.use_this_one_instead = prepare_line;
/* Prepare the indexer */
- ipriv = prepare_indexing(indm, cell, prepare_filename, det,
- nominal_photon_energy);
- if ( ipriv == NULL ) {
- ERROR("Failed to prepare indexing.\n");
- return 1;
+ if ( indm != NULL ) {
+ ipriv = prepare_indexing(indm, cell, prepare_filename, det,
+ nominal_photon_energy);
+ if ( ipriv == NULL ) {
+ ERROR("Failed to prepare indexing.\n");
+ return 1;
+ }
+ } else {
+ ipriv = NULL;
}
gsl_set_error_handler_off();
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-18 09:34:34 +0000