From 4b2cc069a16bf564404d9f1020733dd2ec0b2275 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Sat, 30 Jan 2016 20:22:56 +0100 Subject: indexamajig: Restore --no-refine Adds yet another indexing option... --- libcrystfel/src/asdf.c | 2 +- libcrystfel/src/dirax.c | 2 +- libcrystfel/src/felix.c | 2 +- libcrystfel/src/index.c | 47 ++++++++++++++++++++++++++++++++--------------- libcrystfel/src/index.h | 17 +++++++++++------ libcrystfel/src/mosflm.c | 2 +- libcrystfel/src/xds.c | 2 +- src/indexamajig.c | 14 ++++++++++++-- src/process_image.h | 1 - 9 files changed, 60 insertions(+), 29 deletions(-) diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c index 39a574ae..c52b04ff 100644 --- a/libcrystfel/src/asdf.c +++ b/libcrystfel/src/asdf.c @@ -1181,7 +1181,7 @@ 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_RETRY | INDEXING_MULTI; + | INDEXING_CONTROL_FLAGS; dp = malloc(sizeof(struct asdf_private)); if ( dp == NULL ) return NULL; diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c index 014a4790..79b6d1ac 100644 --- a/libcrystfel/src/dirax.c +++ b/libcrystfel/src/dirax.c @@ -655,7 +655,7 @@ 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_RETRY | INDEXING_MULTI; + | INDEXING_CONTROL_FLAGS; dp = malloc(sizeof(struct dirax_private)); if ( dp == NULL ) return NULL; diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c index 18f60345..8a978957 100644 --- a/libcrystfel/src/felix.c +++ b/libcrystfel/src/felix.c @@ -679,7 +679,7 @@ 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_RETRY | INDEXING_MULTI; + | INDEXING_CONTROL_FLAGS; gp->cell = cell; gp->indm = *indm; diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index 6a74a958..11931b01 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -235,7 +235,7 @@ void map_all_peaks(struct image *image) static int try_indexer(struct image *image, IndexingMethod indm, IndexingPrivate *ipriv) { - int i, r, n_bad; + int i, r; switch ( indm & INDEXING_METHOD_MASK ) { @@ -272,23 +272,28 @@ static int try_indexer(struct image *image, IndexingMethod indm, } - /* Attempt prediction refinement */ - n_bad = 0; - for ( i=0; icrystals[image->n_crystals-i-1]; - crystal_set_image(cr, image); - crystal_set_user_flag(cr, 0); - crystal_set_profile_radius(cr, 0.02e9); - crystal_set_mosaicity(cr, 0.0); - if ( refine_prediction(image, cr) != 0 ) { - crystal_set_user_flag(cr, 1); - n_bad++; + if ( indm & INDEXING_REFINE ) { + + /* Attempt prediction refinement */ + int n_bad = 0; + for ( i=0; icrystals[image->n_crystals-i-1]; + crystal_set_image(cr, image); + crystal_set_user_flag(cr, 0); + crystal_set_profile_radius(cr, 0.02e9); + crystal_set_mosaicity(cr, 0.0); + if ( refine_prediction(image, cr) != 0 ) { + crystal_set_user_flag(cr, 1); + n_bad++; + } } - } - remove_flagged_crystals(image); + remove_flagged_crystals(image); + + if ( n_bad == r ) return 0; + + } - if ( n_bad == r ) return 0; return r; } @@ -614,6 +619,12 @@ char *indexer_str(IndexingMethod indm) strcat(str, "-nomulti"); } + if ( indm & INDEXING_REFINE ) { + strcat(str, "-refine"); + } else { + strcat(str, "-norefine"); + } + return str; } @@ -693,6 +704,12 @@ IndexingMethod *build_indexer_list(const char *str) } else if ( strcmp(methods[i], "nomulti") == 0) { list[nmeth] &= ~INDEXING_MULTI; + } else if ( strcmp(methods[i], "refine") == 0) { + list[nmeth] |= INDEXING_REFINE; + + } else if ( strcmp(methods[i], "norefine") == 0) { + list[nmeth] &= ~INDEXING_REFINE; + } 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 fc2477da..2fb5a13d 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -41,29 +41,29 @@ #define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \ | INDEXING_CHECK_CELL_COMBINATIONS \ - | INDEXING_RETRY) + | INDEXING_RETRY | INDEXING_REFINE) #define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS \ | INDEXING_CHECK_CELL_COMBINATIONS \ - | INDEXING_RETRY) + | 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_RETRY | INDEXING_REFINE) #define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX \ | INDEXING_USE_LATTICE_TYPE \ | INDEXING_USE_CELL_PARAMETERS \ - | INDEXING_RETRY) + | 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_RETRY | INDEXING_REFINE) /** * IndexingMethod: @@ -89,6 +89,7 @@ * 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 @@ -115,7 +116,8 @@ typedef enum { INDEXING_USE_LATTICE_TYPE = 2048, INDEXING_USE_CELL_PARAMETERS = 4096, INDEXING_RETRY = 8192, - INDEXING_MULTI = 16384 + INDEXING_MULTI = 16384, + INDEXING_REFINE = 32768, } IndexingMethod; @@ -123,6 +125,9 @@ 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) + #ifdef __cplusplus extern "C" { #endif diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c index 5b4b623f..8a546630 100644 --- a/libcrystfel/src/mosflm.c +++ b/libcrystfel/src/mosflm.c @@ -872,7 +872,7 @@ IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell, *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS - | INDEXING_RETRY | INDEXING_MULTI; + | INDEXING_CONTROL_FLAGS; if ( (*indm & INDEXING_USE_LATTICE_TYPE) && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS) diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c index ea0fc836..bda60d89 100644 --- a/libcrystfel/src/xds.c +++ b/libcrystfel/src/xds.c @@ -677,7 +677,7 @@ IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell, *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS - | INDEXING_RETRY | INDEXING_MULTI; + | INDEXING_CONTROL_FLAGS; xp->ltl = ltl; xp->cell = cell; diff --git a/src/indexamajig.c b/src/indexamajig.c index a726c1b2..afc41a17 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -198,6 +198,7 @@ int main(int argc, char *argv[]) struct beam_params beam; int have_push_res = 0; int len; + int no_refine = 0; /* Defaults */ iargs.cell = NULL; @@ -241,7 +242,6 @@ int main(int argc, char *argv[]) iargs.fix_profile_r = -1.0; iargs.fix_bandwidth = -1.0; iargs.fix_divergence = -1.0; - iargs.predict_refine = 1; iargs.felix_options = NULL; /* Long options */ @@ -269,7 +269,7 @@ 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, &iargs.predict_refine, 0}, + {"no-refine", 0, &no_refine, 1}, /* Long-only options which don't actually do anything */ {"no-sat-corr", 0, &iargs.satcorr, 0}, @@ -589,12 +589,22 @@ int main(int argc, char *argv[]) } else { + int i = 0; + indm = build_indexer_list(indm_str); if ( indm == NULL ) { ERROR("Invalid indexer list '%s'\n", indm_str); return 1; } free(indm_str); + + /* If --no-refine, unset the refinement flag on all methods */ + if ( no_refine ) { + while ( indm[i] != INDEXING_NONE ) { + indm[i] &= ~INDEXING_REFINE; + i++; + } + } } /* Parse integration method */ diff --git a/src/process_image.h b/src/process_image.h index 60da7cb8..f474725c 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -88,7 +88,6 @@ struct index_args float fix_profile_r; float fix_bandwidth; float fix_divergence; - int predict_refine; char *felix_options; }; -- cgit v1.2.3