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-rw-r--r--libcrystfel/src/index.c196
-rw-r--r--libcrystfel/src/index.h57
2 files changed, 107 insertions, 146 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 7d912902..fd4384d7 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -3,12 +3,12 @@
*
* Perform indexing (somehow)
*
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2010-2012 Thomas White <taw@physics.org>
+ * 2010-2013 Thomas White <taw@physics.org>
* 2010-2011 Richard Kirian <rkirian@asu.edu>
* 2012 Lorenzo Galli
*
@@ -52,16 +52,6 @@
#include "cell-utils.h"
-/* Base class constructor for unspecialised indexing private data */
-IndexingPrivate *indexing_private(IndexingMethod indm)
-{
- struct _indexingprivate *priv;
- priv = calloc(1, sizeof(struct _indexingprivate));
- priv->indm = indm;
- return priv;
-}
-
-
static const char *maybes(int n)
{
if ( n == 1 ) return "";
@@ -71,7 +61,7 @@ static const char *maybes(int n)
IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
const char *filename, struct detector *det,
- double nominal_photon_energy)
+ double nominal_photon_energy, float *ltl)
{
int n;
int nm = 0;
@@ -83,22 +73,23 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
for ( n=0; n<nm; n++ ) {
- switch ( indm[n] ) {
-
- case INDEXING_NONE :
- ERROR("Tried to prepare INDEXING_NONE!\n");
- break;
+ switch ( indm[n] & INDEXING_METHOD_MASK ) {
case INDEXING_DIRAX :
- iprivs[n] = indexing_private(indm[n]);
+ iprivs[n] = NULL;
break;
case INDEXING_MOSFLM :
- iprivs[n] = indexing_private(indm[n]);
+ iprivs[n] = NULL;
break;
case INDEXING_REAX :
- iprivs[n] = reax_prepare();
+ iprivs[n] = reax_prepare(cell, filename, det);
+ break;
+
+ default :
+ ERROR("Don't know how to prepare indexing method %i\n",
+ indm[n]);
break;
}
@@ -118,7 +109,7 @@ void cleanup_indexing(IndexingPrivate **priv)
while ( priv[n] != NULL ) {
- switch ( priv[n]->indm ) {
+ switch ( priv[n]->indm & INDEXING_METHOD_MASK ) {
case INDEXING_NONE :
free(priv[n]);
@@ -136,6 +127,11 @@ void cleanup_indexing(IndexingPrivate **priv)
reax_cleanup(priv[n]);
break;
+ default :
+ ERROR("Don't know how to clean up indexing method %i\n",
+ priv[n]->indm);
+ break;
+
}
n++;
@@ -166,9 +162,14 @@ void map_all_peaks(struct image *image)
}
-void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
- int cellr, int verbose, IndexingPrivate **ipriv,
- int config_insane, const float *ltl)
+static void try_indexer(struct image *image, IndexingMethod indm,
+ IndexingPrivate *ipriv)
+{
+}
+
+
+void index_pattern(struct image *image,
+ IndexingMethod *indms, IndexingPrivate **iprivs)
{
int i;
int n = 0;
@@ -176,102 +177,46 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
if ( indm == NULL ) return;
map_all_peaks(image);
- image->indexed_cell = NULL;
+ image->crystals = NULL;
+ image->n_crystals = 0;
- while ( indm[n] != INDEXING_NONE ) {
+ while ( indms[n] != INDEXING_NONE ) {
- image->ncells = 0;
-
- /* Index as appropriate */
- switch ( indm[n] ) {
-
- case INDEXING_NONE :
- return;
-
- case INDEXING_DIRAX :
- run_dirax(image);
- break;
-
- case INDEXING_MOSFLM :
- run_mosflm(image, cell);
- break;
-
- case INDEXING_REAX :
- reax_index(ipriv[n], image, cell);
- break;
-
- }
- if ( image->ncells == 0 ) {
- n++;
- continue;
- }
-
- for ( i=0; i<image->ncells; i++ ) {
-
- UnitCell *new_cell = NULL;
- UnitCell *cand = image->candidate_cells[i];
-
- 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 :
- new_cell = cell_new_from_cell(cand);
- break;
-
- case CELLR_REDUCE :
- new_cell = match_cell(cand, cell, verbose,
- ltl, 1);
- break;
-
- case CELLR_COMPARE :
- new_cell = match_cell(cand, cell, verbose,
- ltl, 0);
- break;
-
- case CELLR_COMPARE_AB :
- new_cell = match_cell_ab(cand, cell);
- break;
+ if ( try_indexer(image, indms[n], iprivs[i]) ) break;
+ n++;
- }
+ }
+}
- /* No cell? Move on to the next candidate */
- if ( new_cell == NULL ) continue;
- /* Sanity check */
- image->indexed_cell = new_cell;
- if ( !config_insane && !peak_sanity_check(image) ) {
- cell_free(new_cell);
- image->indexed_cell = NULL;
- continue;
- }
+/* Set the default indexer flags. May need tweaking depending on the method */
+static IndexingMethod defaults(IndexingMethod a)
+{
+ return a | INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_PEAKS;
+}
- goto done; /* Success */
- }
+/* Set the indexer flags for "raw mode" ("--cell-reduction=none") */
+static IndexingMethod set_raw(IndexingMethod a)
+{
+ /* Disable all unit cell checks */
+ a &= ~(INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_CELL_AXES);
+ return a;
+}
- for ( i=0; i<image->ncells; i++ ) {
- cell_free(image->candidate_cells[i]);
- image->candidate_cells[i] = NULL;
- }
- /* Move on to the next indexing method */
- n++;
+/* Set the indexer flags for "bad mode" ("--insane) */
+static IndexingMethod set_bad(IndexingMethod a)
+{
+ /* Disable the peak check */
+ return a & ~INDEXING_CHECK_PEAKS;
+}
- }
-done:
- for ( i=0; i<image->ncells; i++ ) {
- /* May free(NULL) if all algorithms were tried and no success */
- cell_free(image->candidate_cells[i]);
- }
+/* Set the indexer flags for "axes mode" ("--cell-reduction=compare") */
+static IndexingMethod set_axes(IndexingMethod a)
+{
+ return (a & ~INDEXING_CHECK_COMBINATIONS) | INDEXING_CHECK_CELL_AXES;
}
@@ -281,25 +226,38 @@ IndexingMethod *build_indexer_list(const char *str, int *need_cell)
char **methods;
IndexingMethod *list;
int tmp;
+ int nmeth = 0;
if ( need_cell == NULL ) need_cell = &tmp;
*need_cell = 0;
- n = assplode(str, ",", &methods, ASSPLODE_NONE);
+ n = assplode(str, ",-", &methods, ASSPLODE_NONE);
list = malloc((n+1)*sizeof(IndexingMethod));
+ *nmeth = -1; /* So that the first method is #0 */
for ( i=0; i<n; i++ ) {
if ( strcmp(methods[i], "dirax") == 0) {
- list[i] = INDEXING_DIRAX;
+ list[++nmeth] = defaults(INDEXING_DIRAX);
+
} else if ( strcmp(methods[i], "mosflm") == 0) {
- list[i] = INDEXING_MOSFLM;
+ list[++nmeth] = defaults(INDEXING_MOSFLM);
+
} else if ( strcmp(methods[i], "reax") == 0) {
- list[i] = INDEXING_REAX;
- *need_cell = 1;
+ /* ReAx doesn't need any cell check */
+ list[++nmeth] = set_raw(defaults(INDEXING_REAX));
+
+ } else if ( strcmp(methods[i], "raw") == 0) {
+ list[nmeth] = set_raw(list[nmeth]);
+
+ } else if ( strcmp(methods[i], "bad") == 0) {
+ list[nmeth] = set_bad(list[nmeth]);
+
+ } else if ( strcmp(methods[i], "axes") == 0) {
+ list[nmeth] = set_axes(list[nmeth]);
+
} else {
- ERROR("Unrecognised indexing method '%s'\n",
- methods[i]);
+ ERROR("Bad list of indexing methods: '%s'\n", str);
return NULL;
}
@@ -307,7 +265,7 @@ IndexingMethod *build_indexer_list(const char *str, int *need_cell)
}
free(methods);
- list[i] = INDEXING_NONE;
+ list[++nmeth] = INDEXING_NONE;
return list;
}
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 4a724645..d5b01b43 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -3,13 +3,13 @@
*
* Perform indexing (somehow)
*
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2010-2012 Thomas White <taw@physics.org>
+ * 2010-2013 Thomas White <taw@physics.org>
* 2010 Richard Kirian
* 2012 Lorenzo Galli
*
@@ -53,20 +53,25 @@
* An enumeration of all the available indexing methods.
**/
typedef enum {
- INDEXING_NONE,
- INDEXING_DIRAX,
- INDEXING_MOSFLM,
- INDEXING_REAX,
-} IndexingMethod;
+ INDEXING_NONE = 0,
+
+ /* The core indexing methods themselves */
+ INDEXING_DIRAX = 1,
+ INDEXING_MOSFLM = 2,
+ INDEXING_REAX = 3,
+
+ /* Bits at the top of the IndexingMethod are flags which modify the
+ * behaviour of the indexer, at the moment just by adding checks. */
+ INDEXING_CHECK_CELL_COMBINATIONS = 256,
+ INDEXING_CHECK_CELL_AXES = 512,
+ INDEXING_CHECK_PEAKS = 1024,
+
+} IndexingMethod;
-/* Cell reduction methods */
-enum {
- CELLR_NONE,
- CELLR_REDUCE,
- CELLR_COMPARE,
- CELLR_COMPARE_AB,
-};
+/* This defines the bits in "IndexingMethod" which are used to represent the
+ * core of the indexing method */
+#define INDEXING_METHOD_MASK (0xff)
/**
@@ -75,24 +80,22 @@ enum {
* This is an opaque data structure containing information needed by the
* indexing method.
**/
-typedef struct _indexingprivate IndexingPrivate;
+typedef void *IndexingPrivate;
-extern IndexingPrivate *indexing_private(IndexingMethod indm);
+extern IndexingMethod *build_indexer_list(const char *str, int *need_cell);
extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
- const char *filename,
- struct detector *det,
- double nominal_photon_energy);
-
-extern void map_all_peaks(struct image *image);
+ const char *filename,
+ struct detector *det,
+ double nominal_photon_energy,
+ float *ltl);
-extern void index_pattern(struct image *image, UnitCell *cell,
- IndexingMethod *indm, int cellr, int verbose,
- IndexingPrivate **priv, int config_insane,
- const float *ltl);
+extern void index_pattern(struct image *image,
+ IndexingMethod *indms, IndexingPrivate **iprivs);
extern void cleanup_indexing(IndexingPrivate **priv);
-extern IndexingMethod *build_indexer_list(const char *str, int *need_cell);
+/* For indexing methods to call */
+extern IndexingPrivate *indexing_private(IndexingMethod indm);
#endif /* INDEX_H */
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