diff options
| -rw-r--r-- | Makefile.am | 2 | ||||
| -rw-r--r-- | Makefile.in | 2 | ||||
| -rw-r--r-- | src/Makefile.am | 2 | ||||
| -rw-r--r-- | src/Makefile.in | 9 | ||||
| -rw-r--r-- | src/index-priv.h | 29 | ||||
| -rw-r--r-- | src/index.c | 41 | ||||
| -rw-r--r-- | src/index.h | 12 | ||||
| -rw-r--r-- | src/indexamajig.c | 27 | ||||
| -rw-r--r-- | src/templates.c | 41 | ||||
| -rw-r--r-- | src/templates.h | 30 |
10 files changed, 180 insertions, 15 deletions
diff --git a/Makefile.am b/Makefile.am index b3905371..e8cc6ffd 100644 --- a/Makefile.am +++ b/Makefile.am @@ -6,5 +6,5 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \ src/filters.h src/diffraction-gpu.h src/cl-utils.h \ data/defs.h src/parameters-lcls.tmp \ data/diffraction.cl data/sfac src/likelihood.h src/symmetry.h \ - src/povray.h + src/povray.h src/index-priv.h SUBDIRS = src data diff --git a/Makefile.in b/Makefile.in index 6d42920d..55a85578 100644 --- a/Makefile.in +++ b/Makefile.in @@ -203,7 +203,7 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \ src/filters.h src/diffraction-gpu.h src/cl-utils.h \ data/defs.h src/parameters-lcls.tmp \ data/diffraction.cl data/sfac src/likelihood.h src/symmetry.h \ - src/povray.h + src/povray.h src/index-priv.h SUBDIRS = src data all: config.h diff --git a/src/Makefile.am b/src/Makefile.am index 34f8a9a0..81089265 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -22,7 +22,7 @@ process_hkl_LDADD = @LIBS@ indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \ peaks.c index.c filters.c diffraction.c detector.c \ - sfac.c dirax.c reflections.c + sfac.c dirax.c reflections.c templates.c indexamajig_LDADD = @LIBS@ if HAVE_OPENCL indexamajig_SOURCES += diffraction-gpu.c cl-utils.c diff --git a/src/Makefile.in b/src/Makefile.in index 4716d60e..23079835 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -88,15 +88,15 @@ hdfsee_OBJECTS = $(am_hdfsee_OBJECTS) hdfsee_DEPENDENCIES = am__indexamajig_SOURCES_DIST = indexamajig.c hdf5-file.c utils.c \ cell.c image.c peaks.c index.c filters.c diffraction.c \ - detector.c sfac.c dirax.c reflections.c diffraction-gpu.c \ - cl-utils.c + detector.c sfac.c dirax.c reflections.c templates.c \ + diffraction-gpu.c cl-utils.c @HAVE_OPENCL_TRUE@am__objects_1 = diffraction-gpu.$(OBJEXT) \ @HAVE_OPENCL_TRUE@ cl-utils.$(OBJEXT) am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \ utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) peaks.$(OBJEXT) \ index.$(OBJEXT) filters.$(OBJEXT) diffraction.$(OBJEXT) \ detector.$(OBJEXT) sfac.$(OBJEXT) dirax.$(OBJEXT) \ - reflections.$(OBJEXT) $(am__objects_1) + reflections.$(OBJEXT) templates.$(OBJEXT) $(am__objects_1) indexamajig_OBJECTS = $(am_indexamajig_OBJECTS) indexamajig_DEPENDENCIES = am__pattern_sim_SOURCES_DIST = pattern_sim.c diffraction.c utils.c \ @@ -259,7 +259,7 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \ process_hkl_LDADD = @LIBS@ indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \ peaks.c index.c filters.c diffraction.c detector.c sfac.c \ - dirax.c reflections.c $(am__append_3) + dirax.c reflections.c templates.c $(am__append_3) indexamajig_LDADD = @LIBS@ @HAVE_GTK_TRUE@hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c \ @HAVE_GTK_TRUE@ filters.c @@ -432,6 +432,7 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sfac.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/statistics.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/symmetry.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/templates.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@ .c.o: diff --git a/src/index-priv.h b/src/index-priv.h new file mode 100644 index 00000000..3d8c8a22 --- /dev/null +++ b/src/index-priv.h @@ -0,0 +1,29 @@ +/* + * index-priv.h + * + * Indexing private data + * + * (c) 2006-2010 Thomas White <taw@physics.org> + * + * Part of CrystFEL - crystallography with a FEL + * + */ + + +#ifndef INDEXPRIV_H +#define INDEXPRIV_H + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + + +#include "index.h" + +struct _indexingprivate +{ + IndexingMethod indm; +}; + + +#endif /* INDEXPRIV_H */ diff --git a/src/index.c b/src/index.c index 70b23640..7273d64b 100644 --- a/src/index.c +++ b/src/index.c @@ -27,6 +27,33 @@ #include "sfac.h" #include "detector.h" #include "index.h" +#include "index-priv.h" +#include "templates.h" + + +/* Base class constructor for unspecialised indexing private data */ +static IndexingPrivate *indexing_private(IndexingMethod indm) +{ + struct _indexingprivate *priv; + priv = calloc(1, sizeof(struct _indexingprivate)); + priv->indm = indm; + return priv; +} + + +IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell, + const char *filename) +{ + switch ( indm ) { + case INDEXING_NONE : + return indexing_private(indm); + case INDEXING_DIRAX : + return indexing_private(indm); + case INDEXING_TEMPLATE : + return generate_templates(cell, filename); + } + return 0; +} static void write_drx(struct image *image) @@ -60,7 +87,7 @@ static void write_drx(struct image *image) void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm, - int no_match, int verbose) + int no_match, int verbose, IndexingPrivate *ipriv) { int i; int nc = 0; @@ -87,8 +114,16 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm, image->ncells = 0; /* Index (or not) as appropriate */ - if ( indm == INDEXING_NONE ) return; - if ( indm == INDEXING_DIRAX ) run_dirax(image); + switch ( indm ) { + case INDEXING_NONE : + return; + case INDEXING_DIRAX : + run_dirax(image); + break; + case INDEXING_TEMPLATE : + match_templates(image, ipriv); + break; + } if ( image->ncells == 0 ) { STATUS("No candidate cells found.\n"); diff --git a/src/index.h b/src/index.h index b30db837..1c637f47 100644 --- a/src/index.h +++ b/src/index.h @@ -19,16 +19,22 @@ #include "cell.h" - +#include "image.h" typedef enum { INDEXING_NONE, INDEXING_DIRAX, - INDEXING_MATCH + INDEXING_TEMPLATE } IndexingMethod; +typedef struct _indexingprivate IndexingPrivate; + +extern IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell, + const char *filename); + extern void index_pattern(struct image *image, UnitCell *cell, - IndexingMethod indm, int no_match, int verbose); + IndexingMethod indm, int no_match, int verbose, + IndexingPrivate *priv); #endif /* INDEX_H */ diff --git a/src/indexamajig.c b/src/indexamajig.c index f7eef166..ec4e18c4 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -64,6 +64,7 @@ struct process_args int config_sa; struct detector *det; IndexingMethod indm; + IndexingPrivate *ipriv; const double *intensities; struct gpu_context *gctx; @@ -98,6 +99,7 @@ static void show_help(const char *s) " --indexing=<method> Use 'method' for indexing. Choose from:\n" " none : no indexing\n" " dirax : invoke DirAx\n" +" template : index by template matching\n" " -g. --geometry=<file> Get detector geometry from file.\n" "\n\nWith just the above options, this program does not do much of practical " "use.\nYou should also enable some of the following:\n\n" @@ -339,7 +341,7 @@ static struct process_result process_image(struct process_args *pargs) /* Calculate orientation matrix (by magic) */ if ( config_writedrx || (indm != INDEXING_NONE) ) { index_pattern(&image, cell, indm, config_nomatch, - config_verbose); + config_verbose, pargs->ipriv); } /* No cell at this point? Then we're done. */ @@ -478,6 +480,9 @@ int main(int argc, char *argv[]) int i; pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER; pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER; + char prepare_line[1024]; + char prepare_filename[1024]; + IndexingPrivate *ipriv; /* Long options */ const struct option longopts[] = { @@ -597,6 +602,8 @@ int main(int argc, char *argv[]) indm = INDEXING_NONE; } else if ( strcmp(indm_str, "dirax") == 0) { indm = INDEXING_DIRAX; + } else if ( strcmp(indm_str, "template") == 0) { + indm = INDEXING_TEMPLATE; } else { ERROR("Unrecognised indexing method '%s'\n", indm_str); return 1; @@ -615,7 +622,7 @@ int main(int argc, char *argv[]) } free(geometry); - if ( !config_nomatch ) { + if ( (!config_nomatch) || (indm == INDEXING_TEMPLATE) ) { cell = load_cell_from_pdb(pdb); if ( cell == NULL ) { ERROR("Couldn't read unit cell (from %s)\n", pdb); @@ -627,6 +634,21 @@ int main(int argc, char *argv[]) } free(pdb); + /* Get first filename and use it to set up the indexing */ + rval = fgets(prepare_line, 1023, fh); + if ( rval == NULL ) { + ERROR("Failed to get filename to prepare indexing.\n"); + return 1; + } + chomp(prepare_line); + snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line); + ipriv = prepare_indexing(indm, cell, prepare_filename); + if ( ipriv == NULL ) { + ERROR("Failed to prepare indexing.\n"); + return 1; + } + rewind(fh); + gsl_set_error_handler_off(); n_images = 0; n_hits = 0; @@ -673,6 +695,7 @@ int main(int argc, char *argv[]) pargs->config_sa = config_sa; pargs->cell = cell; pargs->det = det; + pargs->ipriv = ipriv; pargs->indm = indm; pargs->intensities = intensities; pargs->gctx = gctx; diff --git a/src/templates.c b/src/templates.c new file mode 100644 index 00000000..db28b9b9 --- /dev/null +++ b/src/templates.c @@ -0,0 +1,41 @@ +/* + * templates.c + * + * Indexing by template matching + * + * (c) 2006-2010 Thomas White <taw@physics.org> + * + * Part of CrystFEL - crystallography with a FEL + * + */ + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + + +#include "index.h" +#include "index-priv.h" + + +/* Private data for template indexing */ +struct _indexingprivate_template +{ + struct _indexingprivate base; +}; + + +IndexingPrivate *generate_templates(UnitCell *cell, const char *filename) +{ + struct _indexingprivate_template *priv; + + priv = calloc(1, sizeof(struct _indexingprivate_template)); + priv->base.indm = INDEXING_TEMPLATE; + + return (struct _indexingprivate *)priv; +} + + +void match_templates(struct image *image, IndexingPrivate *ipriv) +{ +} diff --git a/src/templates.h b/src/templates.h new file mode 100644 index 00000000..dad46843 --- /dev/null +++ b/src/templates.h @@ -0,0 +1,30 @@ +/* + * templates.h + * + * Indexing by template matching + * + * (c) 2006-2010 Thomas White <taw@physics.org> + * + * Part of CrystFEL - crystallography with a FEL + * + */ + +#ifndef TEMPLATES_H +#define TEMPLATES_H + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + + +#include "index.h" +#include "image.h" +#include "cell.h" + +extern IndexingPrivate *generate_templates(UnitCell *cell, + const char *filename); + + +extern void match_templates(struct image *image, IndexingPrivate *ipriv); + +#endif /* TEMPLATES_H */ |