From 303a4c9e6cdf72dc0164b015a833a2d34cbbba02 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 30 Jan 2013 11:09:57 +0100 Subject: Stream changes --- libcrystfel/src/crystal.c | 11 +- libcrystfel/src/crystal.h | 9 + libcrystfel/src/image.h | 2 +- libcrystfel/src/stream.c | 451 +++++++++++++++++++++++++++------------------- libcrystfel/src/stream.h | 32 ++-- 5 files changed, 294 insertions(+), 211 deletions(-) (limited to 'libcrystfel') diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c index 85430b6f..3c0649cc 100644 --- a/libcrystfel/src/crystal.c +++ b/libcrystfel/src/crystal.c @@ -50,10 +50,8 @@ struct _crystal { /* Information about the crystal */ - UnitCell *indexed_cell; - UnitCell *candidate_cells[MAX_CELL_CANDIDATES]; - int ncells; - double m; /* Mosaicity in radians */ + UnitCell *cell; + double m; /* Mosaicity in radians */ double osf; double profile_radius; int pr_dud; @@ -83,6 +81,11 @@ Crystal *crystal_new() cryst = malloc(sizeof(Crystal)); if ( cryst == NULL ) return NULL; + cryst->cell = NULL; + cryst->reflections = NULL; + cryst->diffracting_resolution = 0.0; + cryst->n_saturated = 0; + return cryst; } diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h index 466116a4..e5e40589 100644 --- a/libcrystfel/src/crystal.h +++ b/libcrystfel/src/crystal.h @@ -53,5 +53,14 @@ extern void crystal_free(Crystal *cryst); extern UnitCell *crystal_get_cell(Crystal *cryst); extern double crystal_get_profile_radius(Crystal *cryst); extern RefList *crystal_get_reflections(Crystal *cryst); +extern double crystal_get_resolution_limit(Crystal *cryst); +extern long long int crystal_get_num_saturated_reflections(Crystal *cryst); + +extern void crystal_set_cell(Crystal *cryst, UnitCell *cell); +extern void crystal_set_profile_radius(Crystal *cryst, double r); +extern void crystal_set_reflections(Crystal *cryst, RefList *reflist); +extern void crystal_set_resolution_limit(Crystal *cryst, double res); +extern void crystal_set_num_saturated_reflections(Crystal *cryst, int n); + #endif /* CRYSTAL_H */ diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index bd90a920..d54cf43f 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -132,7 +132,7 @@ struct image { uint16_t *flags; double *twotheta; - struct crystal **crystals; + Crystal **crystals; int n_crystals; struct detector *det; diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index b8ff9238..943ee656 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -3,12 +3,12 @@ * * Stream tools * - * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * * Authors: - * 2010-2012 Thomas White + * 2010-2013 Thomas White * 2011 Richard Kirian * 2011 Andrew Aquila * @@ -37,6 +37,7 @@ #include #include #include +#include #include "cell.h" #include "utils.h" @@ -45,83 +46,27 @@ #include "reflist.h" #include "reflist-utils.h" +#define LATEST_MAJOR_VERSION (2) +#define LATEST_MINOR_VERSION (1) #define CHUNK_START_MARKER "----- Begin chunk -----" #define CHUNK_END_MARKER "----- End chunk -----" #define PEAK_LIST_START_MARKER "Peaks from peak search" #define PEAK_LIST_END_MARKER "End of peak list" +#define CRYSTAL_START_MARKER "--- Begin crystal" +#define CRYSTAL_END_MARKER "--- End crystal" #define REFLECTION_START_MARKER "Reflections measured after indexing" /* REFLECTION_END_MARKER is over in reflist-utils.h because it is also * used to terminate a standalone list of reflections */ -static void exclusive(const char *a, const char *b) -{ - ERROR("The stream options '%s' and '%s' are mutually exclusive.\n", - a, b); -} - -int parse_stream_flags(const char *a) +struct _stream { - int n, i; - int ret = STREAM_NONE; - char **flags; - - n = assplode(a, ",", &flags, ASSPLODE_NONE); - - for ( i=0; ifh, CRYSTAL_START_MARKER"\n"); - fprintf(ofh, "Image filename: %s\n", i->filename); + cell = crystal_get_cell(cr); + assert(cell != NULL); - if ( i->indexed_cell != NULL ) { + cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga); + fprintf(st->fh, "Cell parameters %7.5f %7.5f %7.5f nm," + " %7.5f %7.5f %7.5f deg\n", + a*1.0e9, b*1.0e9, c*1.0e9, + rad2deg(al), rad2deg(be), rad2deg(ga)); - cell_get_parameters(i->indexed_cell, &a, &b, &c, - &al, &be, &ga); - fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm," - " %7.5f %7.5f %7.5f deg\n", - a*1.0e9, b*1.0e9, c*1.0e9, - rad2deg(al), rad2deg(be), rad2deg(ga)); + cell_get_reciprocal(cell, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + fprintf(st->fh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n", + asx/1e9, asy/1e9, asz/1e9); + fprintf(st->fh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n", + bsx/1e9, bsy/1e9, bsz/1e9); + fprintf(st->fh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n", + csx/1e9, csy/1e9, csz/1e9); - cell_get_reciprocal(i->indexed_cell, &asx, &asy, &asz, - &bsx, &bsy, &bsz, - &csx, &csy, &csz); - fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n", - asx/1e9, asy/1e9, asz/1e9); - fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n", - bsx/1e9, bsy/1e9, bsz/1e9); - fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n", - csx/1e9, csy/1e9, csz/1e9); + reflist = crystal_get_reflections(cr); + if ( reflist != NULL ) { - } else { + fprintf(st->fh, "diffraction_resolution_limit" + " = %.2f nm^-1 or %.2f A\n", + crystal_get_resolution_limit(cr)/1e9, + 1e9 / crystal_get_resolution_limit(cr)); - fprintf(ofh, "No unit cell from indexing.\n"); + fprintf(st->fh, "num_saturated_reflections = %lli\n", + crystal_get_num_saturated_reflections(cr)); } - fprintf(ofh, "photon_energy_eV = %f\n", - J_to_eV(ph_lambda_to_en(i->lambda))); + if ( include_reflections ) { + + fprintf(st->fh, "\n"); - if ( i->reflections != NULL ) { + if ( reflist != NULL ) { - fprintf(ofh, "diffraction_resolution_limit" - " = %.2f nm^-1 or %.2f A\n", - i->diffracting_resolution/1e9, - 1e9 / i->diffracting_resolution); + fprintf(st->fh, REFLECTION_START_MARKER"\n"); + write_reflections_to_file(st->fh, reflist); + fprintf(st->fh, REFLECTION_END_MARKER"\n"); + + } else { - fprintf(ofh, "num_saturated_reflections" - " = %lli\n", i->n_saturated); + fprintf(st->fh, "No integrated reflections.\n"); + } } + fprintf(st->fh, CRYSTAL_START_MARKER"\n\n"); +} + + +void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile, + int include_peaks, int include_reflections) +{ + int j; + + fprintf(st->fh, CHUNK_START_MARKER"\n"); + + fprintf(st->fh, "Image filename: %s\n", i->filename); + if ( i->det != NULL ) { int j; for ( j=0; jdet->n_panels; j++ ) { - fprintf(ofh, "camera_length_%s = %f\n", + fprintf(st->fh, "camera_length_%s = %f\n", i->det->panels[j].name, i->det->panels[j].clen); } } - copy_hdf5_fields(hdfile, i->copyme, ofh); + copy_hdf5_fields(hdfile, i->copyme, st->fh); - if ( (f & STREAM_PEAKS) - || ((f & STREAM_PEAKS_IF_INDEXED) && (i->indexed_cell != NULL)) - || ((f & STREAM_PEAKS_IF_NOT_INDEXED) && (i->indexed_cell == NULL)) ) - { - fprintf(ofh, "\n"); - write_peaks(i, ofh); + if ( include_peaks ) { + fprintf(st->fh, "\n"); + write_peaks(i, st->fh); } - if ( f & STREAM_INTEGRATED ) { - - fprintf(ofh, "\n"); - - if ( i->reflections != NULL ) { - - fprintf(ofh, REFLECTION_START_MARKER"\n"); - write_reflections_to_file(ofh, i->reflections); - fprintf(ofh, REFLECTION_END_MARKER"\n"); - - } else { - - fprintf(ofh, "No integrated reflections.\n"); + fprintf(st->fh, "photon_energy_eV = %f\n", + J_to_eV(ph_lambda_to_en(i->lambda))); - } + fprintf(st->fh, "\n"); + for ( j=0; jn_crystals; j++ ) { + write_crystal(st, i->crystals[j], include_reflections); } - fprintf(ofh, CHUNK_END_MARKER"\n\n"); + fprintf(st->fh, CHUNK_END_MARKER"\n\n"); } @@ -328,8 +283,7 @@ static int find_start_of_chunk(FILE *fh) } -/* Read the next chunk from a stream and fill in 'image' */ -int read_chunk(FILE *fh, struct image *image) +void read_crystal(Stream *st, struct image *image) { char line[1024]; char *rval = NULL; @@ -337,22 +291,116 @@ int read_chunk(FILE *fh, struct image *image) int have_as = 0; int have_bs = 0; int have_cs = 0; + Crystal *cr; + int n; + Crystal **crystals_new; + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal!\n"); + return; + } + + do { + + float u, v, w; + + rval = fgets(line, 1023, st->fh); + + /* Trouble? */ + if ( rval == NULL ) break; + + chomp(line); + if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3 ) { + as.u = u*1e9; as.v = v*1e9; as.w = w*1e9; + have_as = 1; + } + + if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3 ) { + bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9; + have_bs = 1; + } + + if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3 ) { + cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9; + have_cs = 1; + } + + if ( have_as && have_bs && have_cs ) { + + UnitCell *cell; + + cell = crystal_get_cell(cr); + + if ( cell != NULL ) { + ERROR("Duplicate cell found in stream!\n"); + ERROR("I'll use the most recent one.\n"); + cell_free(cell); + } + + cell = cell_new_from_reciprocal_axes(as, bs, cs); + crystal_set_cell(cr, cell); + + have_as = 0; have_bs = 0; have_cs = 0; + + } + + if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) { + int n = atoi(line+28); + crystal_set_num_saturated_reflections(cr, n); + } + + if ( strcmp(line, REFLECTION_START_MARKER) == 0 ) { + + RefList *reflections; + + reflections = read_reflections_from_file(st->fh); + + if ( reflections == NULL ) { + ERROR("Failed while reading reflections\n"); + break; + } + + crystal_set_reflections(cr, reflections); + + } + + if ( strcmp(line, CRYSTAL_END_MARKER) == 0 ) break; + + } while ( 1 ); + + /* Add crystal to the list for this image */ + n = image->n_crystals+1; + crystals_new = realloc(image->crystals, n*sizeof(Crystal *)); + + if ( crystals_new == NULL ) { + ERROR("Failed to expand crystal list!\n"); + } else { + image->crystals = crystals_new; + image->crystals[image->n_crystals++] = cr; + } + +} + + +/* Read the next chunk from a stream and fill in 'image' */ +int read_chunk(Stream *st, struct image *image) +{ + char line[1024]; + char *rval = NULL; int have_filename = 0; int have_ev = 0; - if ( find_start_of_chunk(fh) ) return 1; + if ( find_start_of_chunk(st->fh) ) return 1; image->lambda = -1.0; image->features = NULL; - image->reflections = NULL; - image->indexed_cell = NULL; - image->n_saturated = 0; + image->crystals = NULL; + image->n_crystals = 0; do { - float u, v, w; - - rval = fgets(line, 1023, fh); + rval = fgets(line, 1023, st->fh); /* Trouble? */ if ( rval == NULL ) break; @@ -364,6 +412,11 @@ int read_chunk(FILE *fh, struct image *image) have_filename = 1; } + if ( strncmp(line, "photon_energy_eV = ", 19) == 0 ) { + image->lambda = ph_en_to_lambda(eV_to_J(atof(line+19))); + have_ev = 1; + } + if ( strncmp(line, "camera_length_", 14) == 0 ) { if ( image->det != NULL ) { @@ -390,56 +443,19 @@ int read_chunk(FILE *fh, struct image *image) } } - if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3 ) { - as.u = u*1e9; as.v = v*1e9; as.w = w*1e9; - have_as = 1; - } - - if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3 ) { - bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9; - have_bs = 1; - } - - if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3 ) { - cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9; - have_cs = 1; - } - - if ( have_as && have_bs && have_cs ) { - if ( image->indexed_cell != NULL ) { - ERROR("Duplicate cell found in stream!\n"); - cell_free(image->indexed_cell); - } - image->indexed_cell = cell_new_from_reciprocal_axes(as, - bs, - cs); - have_as = 0; have_bs = 0; have_cs = 0; - } - - if ( strncmp(line, "photon_energy_eV = ", 19) == 0 ) { - image->lambda = ph_en_to_lambda(eV_to_J(atof(line+19))); - have_ev = 1; - } - - if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) { - image->n_saturated = atoi(line+28); - } - if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) { - if ( read_peaks(fh, image) ) { + if ( read_peaks(st->fh, image) ) { ERROR("Failed while reading peaks\n"); return 1; } } - if ( strcmp(line, REFLECTION_START_MARKER) == 0 ) { - image->reflections = read_reflections_from_file(fh); - if ( image->reflections == NULL ) { - ERROR("Failed while reading reflections\n"); - return 1; - } + if ( strcmp(line, CRYSTAL_START_MARKER) == 0 ) { + read_crystal(st, image); } + /* A chunk must have at least a filename and a wavelength, + * otherwise it's incomplete */ if ( strcmp(line, CHUNK_END_MARKER) == 0 ) { if ( have_filename && have_ev ) return 0; ERROR("Incomplete chunk found in input file.\n"); @@ -457,7 +473,6 @@ void write_stream_header(FILE *ofh, int argc, char *argv[]) { int i; - fprintf(ofh, "CrystFEL stream format 2.0\n"); fprintf(ofh, "Command line:"); for ( i=0; ifh = fopen(filename, "r"); + if ( st->fh == NULL ) { + free(st); + return NULL; } - rval = fgets(line, 1023, fh); - fclose(fh); + + char line[1024]; + char *rval; + + rval = fgets(line, 1023, st->fh); if ( rval == NULL ) { - return -1; + ERROR("Failed to read stream version.\n"); + close_stream(st); + return NULL; } + if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) { - return 1; + st->major_version = 2; + st->minor_version = 0; + } else if ( strncmp(line, "CrystFEL stream format 2.1", 26) == 0 ) { + st->major_version = 2; + st->minor_version = 1; + } else { + ERROR("Invalid stream, or stream format is too new.\n"); + close_stream(st); + return NULL; } - else { - return 0; + + return st; +} + + +Stream *open_stream_for_write(const char *filename) +{ + Stream *st; + + st = malloc(sizeof(struct _stream)); + if ( st == NULL ) return NULL; + + st->fh = fopen(filename, "w"); + if ( st->fh == NULL ) { + free(st); + return NULL; } + + st->major_version = LATEST_MAJOR_VERSION; + st->minor_version = LATEST_MINOR_VERSION; + + fprintf(st->fh, "CrystFEL stream format %i.%i\n", + st->major_version, st->minor_version); + + return st; +} + + +void close_stream(Stream *st) +{ + fclose(st->fh); + free(st); +} + + +int is_stream(const char *filename) +{ + FILE *fh; + char line[1024]; + char *rval; + + fh = fopen(filename, "r"); + if ( fh == NULL ) return 0; + + rval = fgets(line, 1023, fh); + fclose(fh); + if ( rval == NULL ) return 0; + + if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) return 1; + if ( strncmp(line, "CrystFEL stream format 2.1", 26) == 0 ) return 1; + + return 0; } diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h index a544798f..db74583d 100644 --- a/libcrystfel/src/stream.h +++ b/libcrystfel/src/stream.h @@ -3,11 +3,11 @@ * * Stream tools * - * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2010-2012 Thomas White + * 2010-2013 Thomas White * 2011 Andrew Aquila * * This file is part of CrystFEL. @@ -38,30 +38,20 @@ struct image; struct hdfile; -/* Possible options dictating what goes into the output stream */ -enum -{ - STREAM_NONE = 0, - STREAM_INTEGRATED = 1<<0, - STREAM_PEAKS = 1<<2, - STREAM_PEAKS_IF_INDEXED = 1<<3, - STREAM_PEAKS_IF_NOT_INDEXED = 1<<4, -}; +typedef struct _stream Stream; +extern Stream *open_stream_for_read(const char *filename); +extern Stream *open_stream_for_write(const char *filename); +extern void close_stream(Stream *st); -extern int count_patterns(FILE *fh); - -extern void write_stream_header(FILE *ofh, int argc, char *argv[]); - -extern void write_chunk(FILE *ofh, struct image *image, struct hdfile *hdfile, - int flags); +extern void write_chunk(Stream *st, struct image *image, struct hdfile *hdfile, + int include_peaks, int include_reflections); -extern int parse_stream_flags(const char *a); - -extern int read_chunk(FILE *fh, struct image *image); +extern int read_chunk(Stream *st, struct image *image); +/* Nasty functions that should be avoided */ +extern int count_patterns(FILE *fh); extern int skip_some_files(FILE *fh, int n); - extern int is_stream(const char *filename); #endif /* STREAM_H */ -- cgit v1.2.3