aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src
diff options
context:
space:
mode:
Diffstat (limited to 'libcrystfel/src')
-rw-r--r--libcrystfel/src/asdf.c3
-rw-r--r--libcrystfel/src/dirax.c3
-rw-r--r--libcrystfel/src/felix.c3
-rw-r--r--libcrystfel/src/index.c80
-rw-r--r--libcrystfel/src/index.h30
-rw-r--r--libcrystfel/src/mosflm.c3
-rw-r--r--libcrystfel/src/xds.c3
7 files changed, 98 insertions, 27 deletions
diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c
index e5d3466f..87f00716 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/asdf.c
@@ -1178,7 +1178,8 @@ IndexingPrivate *asdf_prepare(IndexingMethod *indm, UnitCell *cell,
/* Flags that asdf knows about */
*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
- | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS;
+ | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
+ | INDEXING_RETRY | INDEXING_MULTI;
dp = malloc(sizeof(struct asdf_private));
if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index fb69cece..014a4790 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -654,7 +654,8 @@ IndexingPrivate *dirax_prepare(IndexingMethod *indm, UnitCell *cell,
/* Flags that DirAx knows about */
*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
- | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS;
+ | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
+ | INDEXING_RETRY | INDEXING_MULTI;
dp = malloc(sizeof(struct dirax_private));
if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
index f5bae88a..2a6a0e44 100644
--- a/libcrystfel/src/felix.c
+++ b/libcrystfel/src/felix.c
@@ -676,7 +676,8 @@ IndexingPrivate *felix_prepare(IndexingMethod *indm, UnitCell *cell,
/* Flags that Felix knows about */
*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
- | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
+ | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS
+ | INDEXING_RETRY | INDEXING_MULTI;
gp->cell = cell;
gp->indm = *indm;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 2e54859d..af5b81c7 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -346,6 +346,46 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
}
+/* indm = the current indexing method
+ * r = the result from try_indexer() on this method just now
+ * image = the image structure
+ *
+ * Returns false for "try again", true for "no, stop now"
+ */
+static int finished_retry(IndexingMethod indm, int r, struct image *image)
+{
+ if ( r == 0 ) {
+
+ /* Indexing failed on the previous attempt. Maybe try again
+ * after poking the peak list a bit */
+
+ if ( indm & INDEXING_RETRY ) {
+ /* Retry with fewer peaks */
+ return delete_weakest_peaks(image->features);
+ } else {
+ /* Indexing failed, opted not to try again */
+ return 1;
+ }
+
+ } else {
+
+ /* Indexing succeeded on previous attempt. Maybe try again
+ * after deleting the explained peaks */
+
+ if ( indm & INDEXING_MULTI ) {
+ /* Remove "used" spots and try for
+ * another lattice */
+ Crystal *cr;
+ cr = image->crystals[image->n_crystals-1];
+ return delete_explained_peaks(image, cr);
+ } else {
+ return 1;
+ }
+
+ }
+}
+
+
void index_pattern(struct image *image,
IndexingMethod *indms, IndexingPrivate **iprivs)
{
@@ -373,18 +413,7 @@ void index_pattern(struct image *image,
r = try_indexer(image, indms[n], iprivs[n]);
ntry++;
-
- if ( r == 0 ) {
- /* Retry with fewer peaks */
- done = delete_weakest_peaks(image->features);
- } else {
- /* Remove "used" spots and try for
- * another lattice */
- Crystal *cr;
- cr = image->crystals[image->n_crystals-1];
- done = delete_explained_peaks(image, cr);
- }
-
+ done = finished_retry(indms[n], r, image);
if ( ntry > 5 ) done = 1;
} while ( !done );
@@ -459,11 +488,12 @@ static IndexingMethod set_cellparams(IndexingMethod a)
return a | INDEXING_USE_CELL_PARAMETERS;
}
+
char *indexer_str(IndexingMethod indm)
{
char *str;
- str = malloc(32);
+ str = malloc(256);
if ( str == NULL ) {
ERROR("Failed to allocate string.\n");
return NULL;
@@ -538,6 +568,18 @@ char *indexer_str(IndexingMethod indm)
strcat(str, "-nocell");
}
+ if ( indm & INDEXING_RETRY ) {
+ strcat(str, "-retry");
+ } else {
+ strcat(str, "-noretry");
+ }
+
+ if ( indm & INDEXING_MULTI ) {
+ strcat(str, "-multi");
+ } else {
+ strcat(str, "-nomulti");
+ }
+
return str;
}
@@ -605,6 +647,18 @@ IndexingMethod *build_indexer_list(const char *str)
} else if ( strcmp(methods[i], "nocell") == 0) {
list[nmeth] = set_nocellparams(list[nmeth]);
+ } else if ( strcmp(methods[i], "retry") == 0) {
+ list[nmeth] |= INDEXING_RETRY;
+
+ } else if ( strcmp(methods[i], "noretry") == 0) {
+ list[nmeth] &= ~INDEXING_RETRY;
+
+ } else if ( strcmp(methods[i], "multi") == 0) {
+ list[nmeth] |= INDEXING_MULTI;
+
+ } else if ( strcmp(methods[i], "nomulti") == 0) {
+ list[nmeth] &= ~INDEXING_MULTI;
+
} else {
ERROR("Bad list of indexing methods: '%s'\n", str);
return NULL;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 0ce74e37..855af70d 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -3,13 +3,13 @@
*
* Perform indexing (somehow)
*
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2010-2015 Thomas White <taw@physics.org>
+ * 2010-2016 Thomas White <taw@physics.org>
* 2010 Richard Kirian
* 2012 Lorenzo Galli
* 2015 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
@@ -40,25 +40,31 @@
#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \
- | INDEXING_CHECK_CELL_COMBINATIONS)
+ | INDEXING_CHECK_CELL_COMBINATIONS \
+ | INDEXING_RETRY | INDEXING_MULTI)
-#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS \
- | INDEXING_CHECK_CELL_COMBINATIONS)
+#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS \
+ | INDEXING_CHECK_CELL_COMBINATIONS \
+ | INDEXING_RETRY | INDEXING_MULTI)
#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_USE_LATTICE_TYPE \
- | INDEXING_USE_CELL_PARAMETERS)
+ | INDEXING_USE_CELL_PARAMETERS \
+ | INDEXING_RETRY | INDEXING_MULTI)
-#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX \
+/* Note: no INDEXING_MULTI because Felix is already multi-crystal */
+#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX \
| INDEXING_USE_LATTICE_TYPE \
- | INDEXING_USE_CELL_PARAMETERS)
+ | INDEXING_USE_CELL_PARAMETERS \
+ | INDEXING_RETRY)
/* Axis check is needed for XDS, because it likes to permute the axes */
#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_CHECK_CELL_AXES \
- | INDEXING_CHECK_PEAKS)
+ | INDEXING_CHECK_PEAKS \
+ | INDEXING_RETRY | INDEXING_MULTI)
/**
* IndexingMethod:
@@ -80,6 +86,10 @@
* guide the indexing process.
* @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
* indexingprocess.
+ * @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
+ * lattice and try again in the hope of finding another crystal.
*
* An enumeration of all the available indexing methods. The dummy value
* @INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was
@@ -105,6 +115,8 @@ typedef enum {
INDEXING_CHECK_PEAKS = 1024,
INDEXING_USE_LATTICE_TYPE = 2048,
INDEXING_USE_CELL_PARAMETERS = 4096,
+ INDEXING_RETRY = 8192,
+ INDEXING_MULTI = 16384
} IndexingMethod;
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index fe917d27..5b4b623f 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -871,7 +871,8 @@ IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
/* Flags that MOSFLM knows about */
*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
| INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
- | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS;
+ | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS
+ | INDEXING_RETRY | INDEXING_MULTI;
if ( (*indm & INDEXING_USE_LATTICE_TYPE)
&& !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 36898949..ea0fc836 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -676,7 +676,8 @@ IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
/* Flags that XDS knows about */
*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
| INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE
- | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS;
+ | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS
+ | INDEXING_RETRY | INDEXING_MULTI;
xp->ltl = ltl;
xp->cell = cell;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-08 04:39:05 +0000