diff options
Diffstat (limited to 'src/stream.c')
| -rw-r--r-- | src/stream.c | 128 |
1 files changed, 68 insertions, 60 deletions
diff --git a/src/stream.c b/src/stream.c index 2a75216d..4b2bea9f 100644 --- a/src/stream.c +++ b/src/stream.c @@ -23,6 +23,7 @@ #include "image.h" #include "stream.h" #include "reflist.h" +#include "reflist-utils.h" #define CHUNK_START_MARKER "----- Begin chunk -----" @@ -32,7 +33,6 @@ #define REFLECTION_START_MARKER "Reflections measured after indexing" #define REFLECTION_END_MARKER "End of reflections" - static void exclusive(const char *a, const char *b) { ERROR("The stream options '%s' and '%s' are mutually exclusive.\n", @@ -103,10 +103,9 @@ int count_patterns(FILE *fh) rval = fgets(line, 1023, fh); if ( rval == NULL ) continue; - if ( (strncmp(line, "Reflections from indexing", 25) == 0) - || (strncmp(line, "New pattern", 11) == 0) ) { - n_total_patterns++; - } + chomp(line); + if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_total_patterns++; + } while ( rval != NULL ); return n_total_patterns; @@ -147,6 +146,7 @@ static UnitCell *read_orientation_matrix(FILE *fh) static int read_reflections(FILE *fh, struct image *image) { char *rval = NULL; + int first = 1; image->reflections = reflist_new(); @@ -164,17 +164,20 @@ static int read_reflections(FILE *fh, struct image *image) if ( rval == NULL ) continue; chomp(line); - if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0; + if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return 0; r = sscanf(line, "%i %i %i %f %s %f %f %i %f %f", &h, &k, &l, &intensity, phs, &sigma, &res, &cts, &fs, &ss); - if ( r != 10 ) return 1; - - refl = add_refl(image->reflections, h, k, l); - set_int(refl, intensity); - set_detector_pos(refl, fs, ss, 0.0); - /* FIXME: Set ESD */ + if ( (r != 10) && (!first) ) return 1; + + first = 0; + if ( r == 10 ) { + refl = add_refl(image->reflections, h, k, l); + set_int(refl, intensity); + set_detector_pos(refl, fs, ss, 0.0); + set_esd_intensity(refl, sigma); + } } while ( rval != NULL ); @@ -184,45 +187,10 @@ static int read_reflections(FILE *fh, struct image *image) } -static void write_reflections(struct image *image, FILE *ofh) -{ - Reflection *refl; - RefListIterator *iter; - - fprintf(ofh, REFLECTION_START_MARKER"\n"); - /* FIXME: Unify this with write_reflections() over in reflections.c */ - fprintf(ofh, " h k l I phase sigma(I) " - " 1/d(nm^-1) counts fs/px ss/px\n"); - - for ( refl = first_refl(image->reflections, &iter); - refl != NULL; - refl = next_refl(refl, iter) ) { - - signed int h, k, l; - double intensity, esd_i, s; - double fs, ss; - - get_indices(refl, &h, &k, &l); - get_detector_pos(refl, &fs, &ss); - intensity = get_intensity(refl); - esd_i = 0.0; /* FIXME! */ - s = 0.0; /* FIXME! */ - - /* h, k, l, I, sigma(I), s */ - fprintf(ofh, - "%3i %3i %3i %10.2f %s %10.2f %10.2f %7i %6.1f %6.1f\n", - h, k, l, intensity, " -", esd_i, s/1.0e9, 1, - fs, ss); - - } - - fprintf(ofh, REFLECTION_END_MARKER"\n"); -} - - static int read_peaks(FILE *fh, struct image *image) { char *rval = NULL; + int first = 1; image->features = image_feature_list_new(); @@ -239,9 +207,17 @@ static int read_peaks(FILE *fh, struct image *image) if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0; r = sscanf(line, "%f %f %f %f", &x, &y, &d, &intensity); - if ( r != 4 ) return 1; + if ( (r != 4) && (!first) ) { + ERROR("Failed to parse peak list line.\n"); + ERROR("The failed line was: '%s'\n", line); + return 1; + } - image_add_feature(image->features, x, y, image, 1.0, NULL); + first = 0; + if ( r == 4 ) { + image_add_feature(image->features, x, y, + image, 1.0, NULL); + } } while ( rval != NULL ); @@ -255,7 +231,7 @@ static void write_peaks(struct image *image, FILE *ofh) int i; fprintf(ofh, PEAK_LIST_START_MARKER"\n"); - fprintf(ofh, " fs/px ss/px (1/d)/nm^-1 Intensity\n"); + fprintf(ofh, " fs/px ss/px (1/d)/nm^-1 Intensity\n"); for ( i=0; i<image_feature_count(image->features); i++ ) { @@ -269,7 +245,7 @@ static void write_peaks(struct image *image, FILE *ofh) r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); q = modulus(r.u, r.v, r.w); - fprintf(ofh, "%8.3f %8.3f %8.3f %12.3f\n", + fprintf(ofh, "%6.1f %6.1f %10.2f %10.2f\n", f->fs, f->ss, q/1.0e9, f->intensity); } @@ -330,8 +306,12 @@ void write_chunk(FILE *ofh, struct image *i, int f) } if ( (f & STREAM_PIXELS) || (f & STREAM_INTEGRATED) ) { + fprintf(ofh, "\n"); - write_reflections(i, ofh); + fprintf(ofh, REFLECTION_START_MARKER"\n"); + write_reflections_to_file(ofh, i->reflections, i->indexed_cell); + fprintf(ofh, REFLECTION_END_MARKER"\n"); + } fprintf(ofh, CHUNK_END_MARKER"\n\n"); @@ -374,10 +354,11 @@ int read_chunk(FILE *fh, struct image *image) if ( find_start_of_chunk(fh) ) return 1; image->i0_available = 0; - if ( image->features != NULL ) { - image_feature_list_free(image->features); - image->features = NULL; - } + image->i0 = 1.0; + image->lambda = -1.0; + image->features = NULL; + image->reflections = NULL; + image->indexed_cell = NULL; do { @@ -426,16 +407,22 @@ int read_chunk(FILE *fh, struct image *image) } if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) { - if ( read_peaks(fh, image) ) return 1; + if ( read_peaks(fh, image) ) { + ERROR("Failed while reading peaks\n"); + return 1; + } } if ( strcmp(line, REFLECTION_START_MARKER) == 0 ) { - if ( read_reflections(fh, image) ) return 1; + if ( read_reflections(fh, image) ) { + ERROR("Failed while reading reflections\n"); + return 1; + } } } while ( strcmp(line, CHUNK_END_MARKER) != 0 ); - if ( have_filename && have_cell && have_ev ) return 0; + if ( have_filename && have_ev ) return 0; ERROR("Incomplete chunk found in input file.\n"); return 1; @@ -496,3 +483,24 @@ int find_chunk(FILE *fh, UnitCell **cell, char **filename, double *ev) return 1; } + + +int skip_some_files(FILE *fh, int n) +{ + char *rval = NULL; + int n_patterns = 0; + + do { + + char line[1024]; + + if ( n_patterns == n ) return 0; + + rval = fgets(line, 1023, fh); + if ( rval == NULL ) continue; + if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_patterns++; + + } while ( rval != NULL ); + + return 1; +} |