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-rw-r--r--libcrystfel/src/index.c358
-rw-r--r--libcrystfel/src/index.h26
-rw-r--r--libcrystfel/src/stream.c8
3 files changed, 232 insertions, 160 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index a2fdb861..89a98920 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -58,6 +58,17 @@
#include "predict-refine.h"
+struct _indexingprivate
+{
+ UnitCell *target_cell;
+ float tolerance[4];
+
+ int n_methods;
+ IndexingMethod *methods;
+ void **engine_private;
+};
+
+
static int debug_index(struct image *image)
{
Crystal *cr = crystal_new();
@@ -71,74 +82,105 @@ static int debug_index(struct image *image)
}
-IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
- struct detector *det, float *ltl,
- const char *options)
+static void *prepare_method(IndexingMethod *m, UnitCell *cell,
+ struct detector *det, float *ltl,
+ const char *options)
{
- int n;
- int nm = 0;
- IndexingPrivate **iprivs;
+ char *str;
+ IndexingMethod in = *m;
+ void *priv = NULL;
- while ( indm[nm] != INDEXING_NONE ) nm++;
- iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
+ switch ( *m & INDEXING_METHOD_MASK ) {
- for ( n=0; n<nm; n++ ) {
+ case INDEXING_DIRAX :
+ priv = dirax_prepare(m, cell, det, ltl);
+ break;
- int i;
- IndexingMethod in;
- char *str;
+ case INDEXING_ASDF :
+ priv = asdf_prepare(m, cell, det, ltl);
+ break;
- in = indm[n];
+ case INDEXING_MOSFLM :
+ priv = mosflm_prepare(m, cell, det, ltl);
+ break;
- switch ( indm[n] & INDEXING_METHOD_MASK ) {
+ case INDEXING_XDS :
+ priv = xds_prepare(m, cell, det, ltl);
+ break;
- case INDEXING_DIRAX :
- iprivs[n] = dirax_prepare(&indm[n], cell, det, ltl);
- break;
+ case INDEXING_DEBUG :
+ priv = (IndexingPrivate *)strdup("Hello!");
+ break;
- case INDEXING_ASDF :
- iprivs[n] = asdf_prepare(&indm[n], cell, det, ltl);
- break;
+ case INDEXING_FELIX :
+ priv = felix_prepare(m, cell, det, ltl, options);
+ break;
- case INDEXING_MOSFLM :
- iprivs[n] = mosflm_prepare(&indm[n], cell, det, ltl);
- break;
+ default :
+ ERROR("Don't know how to prepare indexing method %i\n", *m);
+ break;
- case INDEXING_XDS :
- iprivs[n] = xds_prepare(&indm[n], cell, det, ltl);
- break;
+ }
- case INDEXING_DEBUG :
- iprivs[n] = (IndexingPrivate *)strdup("Hello!");
- break;
+ str = indexer_str(*m);
- case INDEXING_FELIX :
- iprivs[n] = felix_prepare(&indm[n], cell, det, ltl,
- options);
- break;
+ if ( priv == NULL ) {
+ ERROR("Failed to prepare indexing method %s\n", str);
+ free(str);
+ return NULL;
+ }
- default :
- ERROR("Don't know how to prepare indexing method %i\n",
- indm[n]);
- break;
+ STATUS("Prepared indexing method %s\n", str);
+ free(str);
- }
+ if ( in != *m ) {
+ ERROR("Note: flags were altered to take into account "
+ "the information provided and/or the limitations "
+ "of the indexing method.\nPlease check the "
+ "methods listed above carefully.\n");
+ }
- if ( iprivs[n] == NULL ) return NULL;
+ return priv;
+}
- str = indexer_str(indm[n]);
- STATUS("Prepared indexing method %i: %s\n", n, str);
- free(str);
- if ( in != indm[n] ) {
- ERROR("Note: flags were altered to take into account "
- "the information provided and/or the limitations "
- "of the indexing method.\nPlease check the "
- "methods listed above carefully.\n");
- }
+IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
+ struct detector *det, float *ltl,
+ int no_refine, const char *options)
+{
+ int i, n;
+ char **method_strings;
+ IndexingPrivate *ipriv;
+
+ /* Parse indexing methods */
+ n = assplode(method_list, ",", &method_strings, ASSPLODE_NONE);
+
+ IndexingMethod *methods = malloc(n * sizeof(IndexingMethod));
+ if ( methods == NULL ) {
+ ERROR("Failed to allocate indexing method list\n");
+ return NULL;
+ }
+
+ for ( i=0; i<n; i++ ) {
+ methods[i] = get_indm_from_string(method_strings[i]);
+ }
+
+ ipriv = malloc(sizeof(struct _indexingprivate));
+ if ( ipriv == NULL ) {
+ ERROR("Failed to allocate indexing data\n");
+ return NULL;
+ }
+
+ ipriv->engine_private = malloc((n+1) * sizeof(void *));
+
+ for ( i=0; i<n; i++ ) {
+
+ int j;
- for ( i=0; i<n; i++ ) {
- if ( indm[i] == indm[n] ) {
+ ipriv->engine_private[i] = prepare_method(&methods[i], cell,
+ det, ltl, options);
+ for ( j=0; j<i; j++ ) {
+ if ( methods[i] == methods[j] ) {
ERROR("Duplicate indexing method.\n");
ERROR("Have you specified some flags which "
"aren't accepted by one of your "
@@ -147,55 +189,62 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
}
}
+ }
+
+ ipriv->methods = methods;
+ ipriv->n_methods = n;
+ if ( cell != NULL ) {
+ ipriv->target_cell = cell_new_from_cell(cell);
+ } else {
+ ipriv->target_cell = NULL;
}
- iprivs[n] = NULL;
+ for ( i=0; i<4; i++ ) ipriv->tolerance[i] = ltl[i];
- return iprivs;
+ return ipriv;
}
-void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
+void cleanup_indexing(IndexingPrivate *ipriv)
{
- int n = 0;
+ int n;
- if ( indms == NULL ) return; /* Nothing to do */
- if ( privs == NULL ) return; /* Nothing to do */
+ if ( ipriv == NULL ) return; /* Nothing to do */
- while ( indms[n] != INDEXING_NONE ) {
+ for ( n=0; n<ipriv->n_methods; n++ ) {
- switch ( indms[n] & INDEXING_METHOD_MASK ) {
+ switch ( ipriv->methods[n] & INDEXING_METHOD_MASK ) {
case INDEXING_NONE :
break;
case INDEXING_DIRAX :
- dirax_cleanup(privs[n]);
+ dirax_cleanup(ipriv->engine_private[n]);
break;
case INDEXING_ASDF :
- asdf_cleanup(privs[n]);
+ asdf_cleanup(ipriv->engine_private[n]);
break;
case INDEXING_MOSFLM :
- mosflm_cleanup(privs[n]);
+ mosflm_cleanup(ipriv->engine_private[n]);
break;
case INDEXING_XDS :
- xds_cleanup(privs[n]);
+ xds_cleanup(ipriv->engine_private[n]);
break;
case INDEXING_FELIX :
- felix_cleanup(privs[n]);
+ felix_cleanup(ipriv->engine_private[n]);
break;
case INDEXING_DEBUG :
- free(privs[n]);
+ free(ipriv->engine_private[n]);
break;
default :
ERROR("Don't know how to clean up indexing method %i\n",
- indms[n]);
+ ipriv->methods[n]);
break;
}
@@ -204,8 +253,10 @@ void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
}
- free(indms);
- free(privs);
+ free(ipriv->methods);
+ free(ipriv->engine_private);
+ cell_free(ipriv->target_cell);
+ free(ipriv);
}
@@ -234,7 +285,7 @@ void map_all_peaks(struct image *image)
/* Return non-zero for "success" */
static int try_indexer(struct image *image, IndexingMethod indm,
- IndexingPrivate *ipriv)
+ IndexingPrivate *ipriv, void *mpriv)
{
int i, r;
int n_bad = 0;
@@ -245,19 +296,19 @@ static int try_indexer(struct image *image, IndexingMethod indm,
return 0;
case INDEXING_DIRAX :
- r = run_dirax(image, ipriv);
+ r = run_dirax(image, mpriv);
break;
case INDEXING_ASDF :
- r = run_asdf(image, ipriv);
+ r = run_asdf(image, mpriv);
break;
case INDEXING_MOSFLM :
- r = run_mosflm(image, ipriv);
+ r = run_mosflm(image, mpriv);
break;
case INDEXING_XDS :
- r = run_xds(image, ipriv);
+ r = run_xds(image, mpriv);
break;
case INDEXING_DEBUG :
@@ -265,7 +316,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
break;
case INDEXING_FELIX :
- r = felix_index(image, ipriv);
+ r = felix_index(image, mpriv);
break;
default :
@@ -421,20 +472,18 @@ static int finished_retry(IndexingMethod indm, int r, struct image *image)
}
}
-void index_pattern(struct image *image,
- IndexingMethod *indms, IndexingPrivate **iprivs)
+void index_pattern(struct image *image, IndexingPrivate *ipriv)
{
- index_pattern_2(image, indms, iprivs, NULL);
+ index_pattern_2(image, ipriv, NULL);
}
-void index_pattern_2(struct image *image, IndexingMethod *indms,
- IndexingPrivate **iprivs, int *ping)
+void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
{
int n = 0;
ImageFeatureList *orig;
- if ( indms == NULL ) return;
+ if ( ipriv == NULL ) return;
map_all_peaks(image);
image->crystals = NULL;
@@ -442,7 +491,7 @@ void index_pattern_2(struct image *image, IndexingMethod *indms,
orig = image->features;
- while ( indms[n] != INDEXING_NONE ) {
+ for ( n=0; n<ipriv->n_methods; n++ ) {
int done = 0;
int r;
@@ -453,10 +502,11 @@ void index_pattern_2(struct image *image, IndexingMethod *indms,
do {
- r = try_indexer(image, indms[n], iprivs[n]);
+ r = try_indexer(image, ipriv->methods[n],
+ ipriv, ipriv->engine_private[n]);
success += r;
ntry++;
- done = finished_retry(indms[n], r, image);
+ done = finished_retry(ipriv->methods[n], r, image);
if ( ntry > 5 ) done = 1;
if ( ping != NULL ) (*ping)++;
@@ -468,11 +518,14 @@ void index_pattern_2(struct image *image, IndexingMethod *indms,
* crystals with a different indexing method) */
if ( success ) break;
- n++;
+ }
+ if ( n < ipriv->n_methods ) {
+ image->indexed_by = ipriv->methods[n];
+ } else {
+ image->indexed_by = INDEXING_NONE;
}
- image->indexed_by = indms[n];
image->features = orig;
}
@@ -639,97 +692,118 @@ char *indexer_str(IndexingMethod indm)
}
-IndexingMethod *build_indexer_list(const char *str)
+static IndexingMethod warn_method(const char *str)
+{
+ ERROR("Indexing method must contain exactly one engine name: '%s'\n",
+ str);
+ return INDEXING_ERROR;
+}
+
+
+IndexingMethod get_indm_from_string(const char *str)
{
int n, i;
- char **methods;
- IndexingMethod *list;
- int nmeth = 0;
+ char **bits;
+ IndexingMethod method = INDEXING_NONE;
+ int have_method = 0;
- n = assplode(str, ",-", &methods, ASSPLODE_NONE);
- list = malloc((n+1)*sizeof(IndexingMethod));
+ n = assplode(str, "-", &bits, ASSPLODE_NONE);
- nmeth = -1; /* So that the first method is #0 */
for ( i=0; i<n; i++ ) {
- if ( strcmp(methods[i], "dirax") == 0) {
- list[++nmeth] = INDEXING_DEFAULTS_DIRAX;
+ if ( strcmp(bits[i], "dirax") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEFAULTS_DIRAX;
+ have_method = 1;
- } else if ( strcmp(methods[i], "asdf") == 0) {
- list[++nmeth] = INDEXING_DEFAULTS_ASDF;
+ } else if ( strcmp(bits[i], "asdf") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEFAULTS_ASDF;
+ have_method = 1;
- } else if ( strcmp(methods[i], "mosflm") == 0) {
- list[++nmeth] = INDEXING_DEFAULTS_MOSFLM;
+ } else if ( strcmp(bits[i], "mosflm") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEFAULTS_MOSFLM;
+ have_method = 1;
- } else if ( strcmp(methods[i], "xds") == 0) {
- list[++nmeth] = INDEXING_DEFAULTS_XDS;
+ } else if ( strcmp(bits[i], "xds") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEFAULTS_XDS;
+ have_method = 1;
- } else if ( strcmp(methods[i], "felix") == 0) {
- list[++nmeth] = INDEXING_DEFAULTS_FELIX;
+ } else if ( strcmp(bits[i], "felix") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEFAULTS_FELIX;
+ have_method = 1;
- } else if ( strcmp(methods[i], "none") == 0) {
- list[++nmeth] = INDEXING_NONE;
+ } else if ( strcmp(bits[i], "none") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_NONE;
+ have_method = 1;
- } else if ( strcmp(methods[i], "simulation") == 0) {
- list[++nmeth] = INDEXING_SIMULATION;
- return list;
+ } else if ( strcmp(bits[i], "simulation") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_SIMULATION;
+ return method;
- } else if ( strcmp(methods[i], "debug") == 0) {
- list[++nmeth] = INDEXING_DEBUG;
- return list;
+ } else if ( strcmp(bits[i], "debug") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEBUG;
+ return method;
- } else if ( strcmp(methods[i], "raw") == 0) {
- list[nmeth] = set_raw(list[nmeth]);
+ } else if ( strcmp(bits[i], "raw") == 0) {
+ method = set_raw(method);
- } else if ( strcmp(methods[i], "bad") == 0) {
- list[nmeth] = set_bad(list[nmeth]);
+ } else if ( strcmp(bits[i], "bad") == 0) {
+ method = set_bad(method);
- } else if ( strcmp(methods[i], "comb") == 0) {
- list[nmeth] = set_comb(list[nmeth]); /* Default */
+ } else if ( strcmp(bits[i], "comb") == 0) {
+ method = set_comb(method); /* Default */
- } else if ( strcmp(methods[i], "axes") == 0) {
- list[nmeth] = set_axes(list[nmeth]);
+ } else if ( strcmp(bits[i], "axes") == 0) {
+ method = set_axes(method);
- } else if ( strcmp(methods[i], "latt") == 0) {
- list[nmeth] = set_lattice(list[nmeth]);
+ } else if ( strcmp(bits[i], "latt") == 0) {
+ method = set_lattice(method);
- } else if ( strcmp(methods[i], "nolatt") == 0) {
- list[nmeth] = set_nolattice(list[nmeth]);
+ } else if ( strcmp(bits[i], "nolatt") == 0) {
+ method = set_nolattice(method);
- } else if ( strcmp(methods[i], "cell") == 0) {
- list[nmeth] = set_cellparams(list[nmeth]);
+ } else if ( strcmp(bits[i], "cell") == 0) {
+ method = set_cellparams(method);
- } else if ( strcmp(methods[i], "nocell") == 0) {
- list[nmeth] = set_nocellparams(list[nmeth]);
+ } else if ( strcmp(bits[i], "nocell") == 0) {
+ method = set_nocellparams(method);
- } else if ( strcmp(methods[i], "retry") == 0) {
- list[nmeth] |= INDEXING_RETRY;
+ } else if ( strcmp(bits[i], "retry") == 0) {
+ method |= INDEXING_RETRY;
- } else if ( strcmp(methods[i], "noretry") == 0) {
- list[nmeth] &= ~INDEXING_RETRY;
+ } else if ( strcmp(bits[i], "noretry") == 0) {
+ method &= ~INDEXING_RETRY;
- } else if ( strcmp(methods[i], "multi") == 0) {
- list[nmeth] |= INDEXING_MULTI;
+ } else if ( strcmp(bits[i], "multi") == 0) {
+ method |= INDEXING_MULTI;
- } else if ( strcmp(methods[i], "nomulti") == 0) {
- list[nmeth] &= ~INDEXING_MULTI;
+ } else if ( strcmp(bits[i], "nomulti") == 0) {
+ method &= ~INDEXING_MULTI;
- } else if ( strcmp(methods[i], "refine") == 0) {
- list[nmeth] |= INDEXING_REFINE;
+ } else if ( strcmp(bits[i], "refine") == 0) {
+ method |= INDEXING_REFINE;
- } else if ( strcmp(methods[i], "norefine") == 0) {
- list[nmeth] &= ~INDEXING_REFINE;
+ } else if ( strcmp(bits[i], "norefine") == 0) {
+ method &= ~INDEXING_REFINE;
} else {
ERROR("Bad list of indexing methods: '%s'\n", str);
- return NULL;
+ return INDEXING_ERROR;
}
- free(methods[i]);
+ free(bits[i]);
}
- free(methods);
- list[++nmeth] = INDEXING_NONE;
+ free(bits);
+
+ if ( !have_method ) return warn_method(str);
- return list;
+ return method;
}
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index e5f7764a..8ce553ae 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -84,7 +84,7 @@
* @INDEXING_USE_LATTICE_TYPE: Use lattice type and centering information to
* guide the indexing process.
* @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
- * indexingprocess.
+ * indexing process.
* @INDEXING_RETRY: If the indexer doesn't succeed, delete the weakest peaks
* and try again.
* @INDEXING_MULTI: If the indexer succeeds, delete the peaks explained by the
@@ -108,6 +108,8 @@ typedef enum {
INDEXING_DEBUG = 7,
INDEXING_ASDF = 8,
+ INDEXING_ERROR = 255, /* Unrecognised indexing engine */
+
/* Bits at the top of the IndexingMethod are flags which modify the
* behaviour of the indexer. */
INDEXING_CHECK_CELL_COMBINATIONS = 256,
@@ -136,28 +138,28 @@ extern "C" {
* IndexingPrivate:
*
* This is an opaque data structure containing information needed by the
- * indexing method.
+ * indexing system.
**/
-typedef void *IndexingPrivate;
+typedef struct _indexingprivate IndexingPrivate;
-extern IndexingMethod *build_indexer_list(const char *str);
+/* Convert indexing methods to/from text */
extern char *indexer_str(IndexingMethod indm);
+extern IndexingMethod get_indm_from_string(const char *method);
#include "detector.h"
#include "cell.h"
#include "image.h"
-extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
- struct detector *det, float *ltl,
- const char *options);
+extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
+ struct detector *det, float *ltl,
+ int no_refine, const char *options);
-extern void index_pattern(struct image *image,
- IndexingMethod *indms, IndexingPrivate **iprivs);
+extern void index_pattern(struct image *image, IndexingPrivate *ipriv);
-extern void index_pattern_2(struct image *image, IndexingMethod *indms,
- IndexingPrivate **iprivs, int *ping);
+extern void index_pattern_2(struct image *image, IndexingPrivate *ipriv,
+ int *ping);
-extern void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs);
+extern void cleanup_indexing(IndexingPrivate *ipriv);
#ifdef __cplusplus
}
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index e858172e..17da74b2 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1196,13 +1196,9 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
}
if ( strncmp(line, "indexed_by = ", 13) == 0 ) {
- IndexingMethod *list;
- list = build_indexer_list(line+13);
- if ( list == NULL ) {
+ image->indexed_by = get_indm_from_string(line+13);
+ if ( image->indexed_by == INDEXING_ERROR ) {
ERROR("Failed to read indexer list\n");
- } else {
- image->indexed_by = list[0];
- free(list);
}
}
generated by cgit v1.2.3 (git 2.25.1) at 2025-01-19 12:59:01 +0000