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-rw-r--r--libcrystfel/src/asdf.c42
-rw-r--r--libcrystfel/src/dirax.c31
-rw-r--r--libcrystfel/src/felix.c16
-rw-r--r--libcrystfel/src/index.c198
-rw-r--r--libcrystfel/src/index.h77
-rw-r--r--libcrystfel/src/mosflm.c63
-rw-r--r--libcrystfel/src/taketwo.c19
-rw-r--r--libcrystfel/src/xds.c52
-rw-r--r--src/indexamajig.c38
9 files changed, 168 insertions, 368 deletions
diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c
index 0c43fe7a..bbfd1a56 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/asdf.c
@@ -272,39 +272,14 @@ static int calc_reciprocal(gsl_vector **direct, gsl_vector **reciprocal)
static int check_cell(struct asdf_private *dp, struct image *image,
UnitCell *cell)
{
- UnitCell *out;
Crystal *cr;
- if ( dp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
-
- out = match_cell(cell, dp->template, 0, dp->ltl, 1);
- if ( out == NULL ) return 0;
-
- } else if ( dp->indm & INDEXING_CHECK_CELL_AXES ) {
-
- out = match_cell(cell, dp->template, 0, dp->ltl, 0);
- if ( out == NULL ) return 0;
-
- } else {
- out = cell_new_from_cell(cell);
- }
-
cr = crystal_new();
if ( cr == NULL ) {
ERROR("Failed to allocate crystal.\n");
return 0;
}
-
- crystal_set_cell(cr, out);
-
- if ( dp->indm & INDEXING_CHECK_PEAKS ) {
- if ( !peak_sanity_check(image, &cr, 1) ) {
- crystal_free(cr); /* Frees the cell as well */
- cell_free(out);
- return 0;
- }
- }
-
+ crystal_set_cell(cr, cell);
image_add_crystal(image, cr);
return 1;
@@ -1206,22 +1181,9 @@ void *asdf_prepare(IndexingMethod *indm, UnitCell *cell,
struct detector *det, float *ltl)
{
struct asdf_private *dp;
- int need_cell = 0;
-
- if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
- if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
-
- if ( need_cell && !cell_has_parameters(cell) ) {
- ERROR("Altering your asdf flags because cell parameters were"
- " not provided.\n");
- *indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
- *indm &= ~INDEXING_CHECK_CELL_AXES;
- }
/* Flags that asdf knows about */
- *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
- | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
- | INDEXING_CONTROL_FLAGS;
+ *indm &= INDEXING_METHOD_MASK;
dp = malloc(sizeof(struct asdf_private));
if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index b263eea0..29b735ad 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -108,39 +108,14 @@ struct dirax_data {
static int check_cell(struct dirax_private *dp, struct image *image,
UnitCell *cell)
{
- UnitCell *out;
Crystal *cr;
- if ( dp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
-
- out = match_cell(cell, dp->template, 0, dp->ltl, 1);
- if ( out == NULL ) return 0;
-
- } else if ( dp->indm & INDEXING_CHECK_CELL_AXES ) {
-
- out = match_cell(cell, dp->template, 0, dp->ltl, 0);
- if ( out == NULL ) return 0;
-
- } else {
- out = cell_new_from_cell(cell);
- }
-
cr = crystal_new();
if ( cr == NULL ) {
ERROR("Failed to allocate crystal.\n");
return 0;
}
-
- crystal_set_cell(cr, out);
-
- if ( dp->indm & INDEXING_CHECK_PEAKS ) {
- if ( !peak_sanity_check(image, &cr, 1) ) {
- crystal_free(cr); /* Frees the cell as well */
- cell_free(out);
- return 0;
- }
- }
-
+ crystal_set_cell(cr, cell);
image_add_crystal(image, cr);
return 1;
@@ -655,9 +630,7 @@ void *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_CONTROL_FLAGS;
+ *indm &= INDEXING_METHOD_MASK;
dp = malloc(sizeof(struct dirax_private));
if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
index 6daf4408..4c12778b 100644
--- a/libcrystfel/src/felix.c
+++ b/libcrystfel/src/felix.c
@@ -222,16 +222,7 @@ static int read_felix(struct felix_private *gp, struct image *image,
fclose(fh);
- if ( gp->indm & INDEXING_CHECK_PEAKS ) {
- if ( !peak_sanity_check(image, image->crystals,
- image->n_crystals) )
- {
- free_all_crystals(image);
- return 0;
- }
- }
-
- return n_crystals;
+ return n_crystals;
}
@@ -672,9 +663,8 @@ void *felix_prepare(IndexingMethod *indm, UnitCell *cell,
if ( gp == NULL ) return NULL;
/* Flags that Felix knows about */
- *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
- | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS
- | INDEXING_CONTROL_FLAGS;
+ *indm &= INDEXING_METHOD_MASK
+ | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
gp->cell = cell;
gp->indm = *indm;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 36f99995..e7ae7a37 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -61,6 +61,7 @@
struct _indexingprivate
{
+ IndexingFlags flags;
UnitCell *target_cell;
float tolerance[4];
@@ -72,6 +73,30 @@ struct _indexingprivate
};
+static const char *onoff(int a)
+{
+ if ( a ) return "on";
+ return "off";
+}
+
+
+static void show_indexing_flags(IndexingFlags flags)
+{
+ STATUS(" Check unit cell (combinations): %s\n",
+ onoff(flags & INDEXING_CHECK_CELL_COMBINATIONS));
+ STATUS(" Check unit cell (axis permutations only): %s\n",
+ onoff(flags & INDEXING_CHECK_CELL_AXES));
+ STATUS(" Check peak alignment: %s\n",
+ onoff(flags & INDEXING_CHECK_PEAKS));
+ STATUS(" Refine indexing solutions: %s\n",
+ onoff(flags & INDEXING_REFINE));
+ STATUS(" Multi-lattice indexing (\"delete and retry\"): %s\n",
+ onoff(flags & INDEXING_MULTI));
+ STATUS(" Retry indexing: %s\n",
+ onoff(flags & INDEXING_RETRY));
+}
+
+
static int debug_index(struct image *image)
{
Crystal *cr = crystal_new();
@@ -159,7 +184,7 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
struct detector *det, float *ltl,
- int no_refine, const char *options,
+ IndexingFlags flags, const char *options,
struct taketwo_options *ttopts)
{
int i, n;
@@ -178,10 +203,30 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
for ( i=0; i<n; i++ ) {
methods[i] = get_indm_from_string(method_strings[i]);
if ( methods[i] == INDEXING_ERROR ) {
+ ERROR("----- Notice -----\n");
+ ERROR("The way indexing options are used has changed in this CrystFEL version.\n");
+ ERROR("To disable prediction refinement ('norefine'), use --no-refine.\n");
+ ERROR("To check cell axes only ('axes'), use --no-cell-combinations.\n");
+ ERROR("To disable all unit cell checks ('raw'), use --no-check-cell.\n");
+ ERROR("To disable indexing retry ('noretry'), use --no-retry.\n");
+ ERROR("Multi-lattice indexing ('multi') is now the default: "
+ "use --no-multi to disable it.\n");
+ ERROR("------------------\n");
free(methods);
return NULL;
}
- if ( no_refine ) methods[i] &= ~INDEXING_REFINE;
+ }
+
+ if ( cell == NULL ) {
+ if ( (flags & INDEXING_CHECK_CELL_COMBINATIONS)
+ || (flags & INDEXING_CHECK_CELL_COMBINATIONS) )
+ {
+ ERROR("WARNING: Forcing --no-cell-combinations "
+ "and --no-check-cell because you didn't "
+ "provide a unit cell.\n");
+ flags &= ~INDEXING_CHECK_CELL_COMBINATIONS;
+ flags &= ~INDEXING_CHECK_CELL_AXES;
+ }
}
ipriv = malloc(sizeof(struct _indexingprivate));
@@ -212,6 +257,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
ipriv->methods = methods;
ipriv->n_methods = n;
+ ipriv->flags = flags;
if ( cell != NULL ) {
ipriv->target_cell = cell_new_from_cell(cell);
@@ -222,6 +268,8 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
ipriv->ttopts = ttopts;
+ show_indexing_flags(flags);
+
return ipriv;
}
@@ -369,34 +417,43 @@ static int try_indexer(struct image *image, IndexingMethod indm,
crystal_set_mosaicity(cr, 0.0);
/* Prediction refinement if requested */
- if ( indm & INDEXING_REFINE ) {
-
- UnitCell *out;
-
+ if ( ipriv->flags & INDEXING_REFINE )
+ {
if ( refine_prediction(image, cr) ) {
crystal_set_user_flag(cr, 1);
n_bad++;
continue;
}
+ }
- if ( (indm & INDEXING_CHECK_CELL_COMBINATIONS)
- || (indm & INDEXING_CHECK_CELL_AXES) )
- {
-
- /* Check that the cell parameters are still
- * within the tolerance */
- out = match_cell(crystal_get_cell(cr),
- ipriv->target_cell, 0,
- ipriv->tolerance, 0);
+ /* Unit cell check if requested */
+ assert( !((ipriv->flags & INDEXING_CHECK_CELL_COMBINATIONS)
+ && (ipriv->flags & INDEXING_CHECK_CELL_AXES)) );
+ if ( (ipriv->flags & INDEXING_CHECK_CELL_COMBINATIONS)
+ || (ipriv->flags & INDEXING_CHECK_CELL_AXES) )
+ {
+ UnitCell *out;
+ int reduce;
- if ( out == NULL ) {
- crystal_set_user_flag(cr, 1);
- }
+ if ( ipriv->flags & INDEXING_CHECK_CELL_COMBINATIONS )
+ {
+ reduce = 1;
+ } else {
+ reduce = 0;
+ }
- cell_free(out);
+ out = match_cell(crystal_get_cell(cr),
+ ipriv->target_cell, 0,
+ ipriv->tolerance, reduce);
+ if ( out == NULL ) {
+ crystal_set_user_flag(cr, 1);
+ n_bad++;
+ continue;
}
+ cell_free(crystal_get_cell(cr));
+ crystal_set_cell(cr, out);
}
/* Don't do similarity check if this crystal is bad */
@@ -514,14 +571,15 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
*
* Returns false for "try again", true for "no, stop now"
*/
-static int finished_retry(IndexingMethod indm, int r, struct image *image)
+static int finished_retry(IndexingMethod indm, IndexingFlags flags,
+ 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 ) {
+ if ( flags & INDEXING_RETRY ) {
/* Retry with fewer peaks */
return delete_weakest_peaks(image->features);
} else {
@@ -534,7 +592,7 @@ static int finished_retry(IndexingMethod indm, int r, struct image *image)
/* Indexing succeeded on previous attempt. Maybe try again
* after deleting the explained peaks */
- if ( indm & INDEXING_MULTI ) {
+ if ( flags & INDEXING_MULTI ) {
/* Remove "used" spots and try for another lattice */
Crystal *cr;
cr = image->crystals[image->n_crystals-1];
@@ -581,7 +639,8 @@ void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
ipriv, ipriv->engine_private[n]);
success += r;
ntry++;
- done = finished_retry(ipriv->methods[n], r, image);
+ done = finished_retry(ipriv->methods[n], ipriv->flags,
+ r, image);
if ( ntry > 5 ) done = 1;
if ( ping != NULL ) (*ping)++;
@@ -605,39 +664,6 @@ void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
}
-/* 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;
-}
-
-
-/* Set the indexer flags for "bad mode" ("--insane) */
-static IndexingMethod set_bad(IndexingMethod a)
-{
- /* Disable the peak check */
- return a & ~INDEXING_CHECK_PEAKS;
-}
-
-
-/* Set the indexer flags for "axes mode" ("--cell-reduction=compare") */
-static IndexingMethod set_axes(IndexingMethod a)
-{
- return (a & ~INDEXING_CHECK_CELL_COMBINATIONS)
- | INDEXING_CHECK_CELL_AXES;
-}
-
-
-/* Set the indexer flags for "combination mode" ("--cell-reduction=reduce") */
-static IndexingMethod set_comb(IndexingMethod a)
-{
- return (a & ~INDEXING_CHECK_CELL_AXES)
- | INDEXING_CHECK_CELL_COMBINATIONS;
-}
-
-
/* Set the indexer flags for "use no lattice type information" */
static IndexingMethod set_nolattice(IndexingMethod a)
{
@@ -725,18 +751,6 @@ char *indexer_str(IndexingMethod indm)
if ( (indm & INDEXING_METHOD_MASK) == INDEXING_SIMULATION ) return str;
- if ( indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
- strcat(str, "-comb");
- } else if ( indm & INDEXING_CHECK_CELL_AXES ) {
- strcat(str, "-axes");
- } else {
- strcat(str, "-raw");
- }
-
- if ( !(indm & INDEXING_CHECK_PEAKS) ) {
- strcat(str, "-bad");
- }
-
if ( indm & INDEXING_USE_LATTICE_TYPE ) {
strcat(str, "-latt");
} else {
@@ -749,24 +763,6 @@ 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");
- }
-
- if ( indm & INDEXING_REFINE ) {
- strcat(str, "-refine");
- } else {
- strcat(str, "-norefine");
- }
-
return str;
}
@@ -835,18 +831,6 @@ IndexingMethod get_indm_from_string(const char *str)
method = INDEXING_DEBUG;
return method;
- } else if ( strcmp(bits[i], "raw") == 0) {
- method = set_raw(method);
-
- } else if ( strcmp(bits[i], "bad") == 0) {
- method = set_bad(method);
-
- } else if ( strcmp(bits[i], "comb") == 0) {
- method = set_comb(method); /* Default */
-
- } else if ( strcmp(bits[i], "axes") == 0) {
- method = set_axes(method);
-
} else if ( strcmp(bits[i], "latt") == 0) {
method = set_lattice(method);
@@ -859,24 +843,6 @@ IndexingMethod get_indm_from_string(const char *str)
} else if ( strcmp(bits[i], "nocell") == 0) {
method = set_nocellparams(method);
- } else if ( strcmp(bits[i], "retry") == 0) {
- method |= INDEXING_RETRY;
-
- } else if ( strcmp(bits[i], "noretry") == 0) {
- method &= ~INDEXING_RETRY;
-
- } else if ( strcmp(bits[i], "multi") == 0) {
- method |= INDEXING_MULTI;
-
- } else if ( strcmp(bits[i], "nomulti") == 0) {
- method &= ~INDEXING_MULTI;
-
- } else if ( strcmp(bits[i], "refine") == 0) {
- method |= INDEXING_REFINE;
-
- } else if ( strcmp(bits[i], "norefine") == 0) {
- method &= ~INDEXING_REFINE;
-
} else {
ERROR("Bad list of indexing methods: '%s'\n", str);
return INDEXING_ERROR;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 8b3aadeb..2aad377b 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -39,36 +39,22 @@
#endif
-#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \
- | INDEXING_CHECK_CELL_COMBINATIONS \
- | INDEXING_RETRY | INDEXING_REFINE)
-
-#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS \
- | INDEXING_CHECK_CELL_COMBINATIONS \
- | INDEXING_RETRY | INDEXING_REFINE)
-
-#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS \
- | INDEXING_CHECK_CELL_COMBINATIONS \
- | INDEXING_USE_LATTICE_TYPE \
- | INDEXING_USE_CELL_PARAMETERS \
- | INDEXING_RETRY | INDEXING_REFINE)
-
-#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX \
- | INDEXING_USE_LATTICE_TYPE \
- | INDEXING_USE_CELL_PARAMETERS \
- | INDEXING_RETRY | INDEXING_REFINE)
-
-#define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO | INDEXING_CHECK_PEAKS \
- | INDEXING_USE_CELL_PARAMETERS \
- | INDEXING_USE_LATTICE_TYPE \
- | INDEXING_RETRY | INDEXING_REFINE)
-
-/* 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_RETRY | INDEXING_REFINE)
+#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX)
+
+#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF)
+
+#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_USE_CELL_PARAMETERS)
+
+#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_USE_CELL_PARAMETERS)
+
+#define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO \
+ | INDEXING_USE_CELL_PARAMETERS \
+ | INDEXING_USE_LATTICE_TYPE)
+
+#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_USE_CELL_PARAMETERS)
/**
* IndexingMethod:
@@ -82,21 +68,10 @@
* @INDEXING_ASDF: Use in-built "asdf" indexer
* @INDEXING_TAKETWO: Use in-built "taketwo" indexer
* @INDEXING_ERROR: Special value for unrecognised indexing engine name
- * @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
- * axes for agreement with given cell.
- * @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given
- * cell, and permute them if necessary.
- * @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing
- * result.
* @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
* 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
- * lattice and try again in the hope of finding another crystal.
- * @INDEXING_REFINE: Perform "prediction refinement" after indexing.
*
* An enumeration of all the available indexing methods. The dummy value
* @INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was
@@ -120,14 +95,8 @@ typedef enum {
/* Bits at the top of the IndexingMethod are flags which modify the
* behaviour of the indexer. */
- INDEXING_CHECK_CELL_COMBINATIONS = 256,
- INDEXING_CHECK_CELL_AXES = 512,
- INDEXING_CHECK_PEAKS = 1024,
INDEXING_USE_LATTICE_TYPE = 2048,
INDEXING_USE_CELL_PARAMETERS = 4096,
- INDEXING_RETRY = 8192,
- INDEXING_MULTI = 16384,
- INDEXING_REFINE = 32768,
} IndexingMethod;
@@ -135,8 +104,16 @@ typedef enum {
* core of the indexing method */
#define INDEXING_METHOD_MASK (0xff)
-/* Indexing flags which the indexing method does not need to know about */
-#define INDEXING_CONTROL_FLAGS (INDEXING_RETRY | INDEXING_MULTI | INDEXING_REFINE)
+typedef enum {
+
+ INDEXING_RETRY = 1,
+ INDEXING_MULTI = 2,
+ INDEXING_REFINE = 4,
+ INDEXING_CHECK_CELL_COMBINATIONS = 8,
+ INDEXING_CHECK_CELL_AXES = 16,
+ INDEXING_CHECK_PEAKS = 32,
+
+} IndexingFlags;
#ifdef __cplusplus
extern "C" {
@@ -162,7 +139,7 @@ extern IndexingMethod get_indm_from_string(const char *method);
extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
struct detector *det, float *ltl,
- int no_refine, const char *options,
+ IndexingFlags flags, const char *options,
struct taketwo_options *ttopts);
extern void index_pattern(struct image *image, IndexingPrivate *ipriv);
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index edf8524e..110243cb 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -128,7 +128,6 @@ struct mosflm_data {
static int check_cell(struct mosflm_private *mp, struct image *image,
UnitCell *cell)
{
- UnitCell *out;
Crystal *cr;
/* If we sent lattice information, make sure that we got back what we
@@ -163,35 +162,13 @@ static int check_cell(struct mosflm_private *mp, struct image *image,
}
- if ( mp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
-
- out = match_cell(cell, mp->template, 0, mp->ltl, 1);
- if ( out == NULL ) return 0;
-
- } else if ( mp->indm & INDEXING_CHECK_CELL_AXES ) {
-
- out = match_cell(cell, mp->template, 0, mp->ltl, 0);
- if ( out == NULL ) return 0;
-
- } else {
- out = cell_new_from_cell(cell);
- }
-
cr = crystal_new();
if ( cr == NULL ) {
ERROR("Failed to allocate crystal.\n");
return 0;
}
- crystal_set_cell(cr, out);
-
- if ( mp->indm & INDEXING_CHECK_PEAKS ) {
- if ( !peak_sanity_check(image, &cr, 1) ) {
- cell_free(out);
- crystal_free(cr);
- return 0;
- }
- }
+ crystal_set_cell(cr, cell);
image_add_crystal(image, cr);
@@ -340,8 +317,6 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
mosflm->done = 1;
}
- cell_free(cell);
-
return 0;
}
@@ -850,14 +825,10 @@ void *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
int need_cell = 0;
/* Check if cell parameters are needed/provided */
- if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
- if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
if ( *indm & INDEXING_USE_CELL_PARAMETERS ) need_cell = 1;
if ( need_cell && !cell_has_parameters(cell) ) {
ERROR("Altering your MOSFLM flags because cell parameters were"
" not provided.\n");
- *indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
- *indm &= ~INDEXING_CHECK_CELL_AXES;
*indm &= ~INDEXING_USE_CELL_PARAMETERS;
}
@@ -869,36 +840,8 @@ void *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_CONTROL_FLAGS;
-
- if ( (*indm & INDEXING_USE_LATTICE_TYPE)
- && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
- || (*indm & INDEXING_CHECK_CELL_AXES))
- && (cell_has_parameters(cell)
- || (cell_get_unique_axis(cell) == 'a')
- || (cell_get_unique_axis(cell) == 'b')
- || (cell_get_unique_axis(cell) == 'c')) )
- {
- ERROR("WARNING: The unit cell from %s might have had "
- "its axes permuted from the unit cell you gave.\n"
- "If this is a problem, consider using "
- "mosflm-axes-latt or mosflm-comb-latt instead of "
- "mosflm-raw-latt.\n", indexer_str(*indm));
- /* It'll be OK if INDEXING_CHECK_CELL_PARAMETERS and
- * MOSFLM 7.2.0 or later, but that's getting a bit too
- * complicated to explain to the user. */
- }
-
- if ( (*indm & INDEXING_USE_CELL_PARAMETERS)
- && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
- || (*indm & INDEXING_CHECK_CELL_AXES)) )
- {
- ERROR("WARNING: Using 'mosflm-raw' but providing cell "
- "parameters as prior information to mosflm.\n");
- }
+ *indm &= INDEXING_METHOD_MASK
+ | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
mp = malloc(sizeof(struct mosflm_private));
if ( mp == NULL ) return NULL;
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index 87da44a1..f7a2fda9 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -1460,7 +1460,7 @@ static void cleanup_taketwo_cell(struct TakeTwoCell *ttCell)
* successful.
**/
static UnitCell *run_taketwo(UnitCell *cell, const struct taketwo_options *opts,
- struct rvec *rlps, int rlp_count)
+ struct rvec *rlps, int rlp_count)
{
int cell_vec_count = 0;
int asym_vec_count = 0;
@@ -1581,18 +1581,6 @@ int taketwo_index(struct image *image, const struct taketwo_options *opts,
crystal_set_cell(cr, cell);
- if ( tp->indm & INDEXING_CHECK_PEAKS ) {
- if ( !peak_sanity_check(image, &cr, 1) ) {
- cell_free(cell);
- crystal_free(cr);
- // STATUS("Rubbish!!\n");
-
- return 0;
- } else {
- // STATUS("That's good!\n");
- }
- }
-
image_add_crystal(image, cr);
return 1;
@@ -1605,9 +1593,8 @@ void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell,
struct taketwo_private *tp;
/* Flags that TakeTwo knows about */
- *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
- | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS
- | INDEXING_CONTROL_FLAGS;
+ *indm &= INDEXING_METHOD_MASK | INDEXING_USE_LATTICE_TYPE
+ | INDEXING_USE_CELL_PARAMETERS;
if ( !( (*indm & INDEXING_USE_LATTICE_TYPE)
&& (*indm & INDEXING_USE_CELL_PARAMETERS)) )
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 093b9160..39578c60 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -187,39 +187,14 @@ static int xds_readable(struct image *image, struct xds_data *xds)
static int check_cell(struct xds_private *xp, struct image *image,
UnitCell *cell)
{
- UnitCell *out;
Crystal *cr;
- if ( xp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
-
- out = match_cell(cell, xp->cell, 0, xp->ltl, 1);
- if ( out == NULL ) return 0;
-
- } else if ( xp->indm & INDEXING_CHECK_CELL_AXES ) {
-
- out = match_cell(cell, xp->cell, 0, xp->ltl, 0);
- if ( out == NULL ) return 0;
-
- } else {
- out = cell_new_from_cell(cell);
- }
-
cr = crystal_new();
if ( cr == NULL ) {
ERROR("Failed to allocate crystal.\n");
return 0;
}
-
- crystal_set_cell(cr, out);
-
- if ( xp->indm & INDEXING_CHECK_PEAKS ) {
- if ( !peak_sanity_check(image, &cr, 1) ) {
- cell_free(out);
- crystal_free(cr);
- return 0;
- }
- }
-
+ crystal_set_cell(cr, cell);
image_add_crystal(image, cr);
return 1;
@@ -626,14 +601,10 @@ void *xds_prepare(IndexingMethod *indm, UnitCell *cell,
int need_cell = 0;
/* Check if cell parameters are needed/provided */
- if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
- if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
if ( *indm & INDEXING_USE_CELL_PARAMETERS ) need_cell = 1;
if ( need_cell && !cell_has_parameters(cell) ) {
ERROR("Altering your XDS flags because cell parameters were"
" not provided.\n");
- *indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
- *indm &= ~INDEXING_CHECK_CELL_AXES;
*indm &= ~INDEXING_USE_CELL_PARAMETERS;
}
@@ -652,36 +623,35 @@ void *xds_prepare(IndexingMethod *indm, UnitCell *cell,
}
if ( (*indm & INDEXING_USE_LATTICE_TYPE)
- && !(*indm & INDEXING_USE_CELL_PARAMETERS) ) {
+ && !(*indm & INDEXING_USE_CELL_PARAMETERS) )
+ {
ERROR("Invalid XDS options (-latt-nocell): "
"try xds-nolatt-nocell.\n");
return NULL;
}
if ( (*indm & INDEXING_USE_CELL_PARAMETERS)
- && !(*indm & INDEXING_USE_LATTICE_TYPE) ) {
+ && !(*indm & INDEXING_USE_LATTICE_TYPE) )
+ {
ERROR("Invalid XDS options (-cell-nolatt): "
"try xds-nolatt-nocell.\n");
return NULL;
}
if ( ((*indm & INDEXING_USE_CELL_PARAMETERS)
- || (*indm & INDEXING_USE_LATTICE_TYPE))
- && !(*indm & INDEXING_CHECK_CELL_AXES)
- && !(*indm & INDEXING_CHECK_CELL_COMBINATIONS) ) {
- ERROR("The cell from xds-raw-cell or xds-raw-latt may have had"
+ || (*indm & INDEXING_USE_LATTICE_TYPE)))
+ {
+ ERROR("The cell from xds-cell or xds-latt may have had"
" its axes permuted from the cell you provided. If this"
- " is a problem, consider using xds-axes-cell.\n");
+ " is a problem, consider using xds-cell.\n");
}
xp = calloc(1, sizeof(*xp));
if ( xp == NULL ) return NULL;
/* 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_CONTROL_FLAGS;
+ *indm &= INDEXING_METHOD_MASK | INDEXING_USE_LATTICE_TYPE
+ | INDEXING_USE_CELL_PARAMETERS;
xp->ltl = ltl;
xp->cell = cell;
diff --git a/src/indexamajig.c b/src/indexamajig.c
index a79234d3..44b91338 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -227,8 +227,13 @@ int main(int argc, char *argv[])
struct beam_params beam;
int have_push_res = 0;
int len;
- int no_refine = 0;
char *command_line_peak_path = NULL;
+ int if_refine = 1;
+ int if_comb = 1;
+ int if_axes = 1;
+ int if_peaks = 0;
+ int if_multi = 1;
+ int if_retry = 1;
/* Defaults */
iargs.cell = NULL;
@@ -312,9 +317,14 @@ int main(int argc, char *argv[])
{"no-use-saturated", 0, &iargs.use_saturated, 0},
{"no-revalidate", 0, &iargs.no_revalidate, 1},
{"check-hdf5-snr", 0, &iargs.check_hdf5_snr, 1},
- {"no-refine", 0, &no_refine, 1},
{"profile", 0, &iargs.profile, 1},
{"no-half-pixel-shift",0, &iargs.half_pixel_shift, 0},
+ {"no-refine", 0, &if_refine, 0},
+ {"no-cell-combinations",0,&if_comb, 0},
+ {"no-check-cell", 0, &if_axes, 0},
+ {"check-peaks", 0, &if_peaks, 1},
+ {"no-retry", 0, &if_retry, 0},
+ {"no-multi", 0, &if_multi, 0},
/* Long-only options which don't actually do anything */
{"no-sat-corr", 0, &iargs.satcorr, 0},
@@ -856,8 +866,30 @@ int main(int argc, char *argv[])
} else {
+ IndexingFlags flags = 0;
+
+ if ( if_axes ) {
+ flags |= INDEXING_CHECK_CELL_AXES;
+ }
+ if ( if_comb ) {
+ flags |= INDEXING_CHECK_CELL_COMBINATIONS;
+ flags &= ~INDEXING_CHECK_CELL_AXES; /* Not needed */
+ }
+ if ( if_refine ) {
+ flags |= INDEXING_REFINE;
+ }
+ if ( if_peaks ) {
+ flags |= INDEXING_CHECK_PEAKS;
+ }
+ if ( if_multi ) {
+ flags |= INDEXING_MULTI;
+ }
+ if ( if_retry ) {
+ flags |= INDEXING_RETRY;
+ }
+
iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
- iargs.tols, no_refine,
+ iargs.tols, flags,
iargs.felix_options,
&iargs.taketwo_opts);
if ( iargs.ipriv == NULL ) {
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-04 09:39:05 +0000