From b92c1ffcc6600094cc213f03e31ba30938bbf3ce Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 5 Mar 2014 16:13:23 +0100 Subject: Formatting --- libcrystfel/src/symmetry.c | 2 -- 1 file changed, 2 deletions(-) (limited to 'libcrystfel/src') diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c index 81d87b25..dec8a520 100644 --- a/libcrystfel/src/symmetry.c +++ b/libcrystfel/src/symmetry.c @@ -1110,8 +1110,6 @@ void get_equiv(const SymOpList *ops, const SymOpMask *m, int idx, } - - if ( idx >= n ) { ERROR("Index %i out of range for point group '%s'\n", idx, -- cgit v1.2.3 From 9f768cc81e9b09a153c0ca77ccaeb91c5a0766d3 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 10 Mar 2014 13:47:39 +0100 Subject: Fix reading and writing of reflections in 2.1 stream --- libcrystfel/src/stream.c | 104 ++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 102 insertions(+), 2 deletions(-) (limited to 'libcrystfel/src') diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index db8a4f72..80256829 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -133,6 +133,61 @@ static void write_peaks(struct image *image, FILE *ofh) } +static RefList *read_stream_reflections_2_1(FILE *fh) +{ + char *rval = NULL; + int first = 1; + RefList *out; + + out = reflist_new(); + + do { + + char line[1024]; + signed int h, k, l; + float intensity, sigma, fs, ss; + char phs[1024]; + int cts; + int r; + Reflection *refl; + + rval = fgets(line, 1023, fh); + if ( rval == NULL ) continue; + chomp(line); + + if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out; + + r = sscanf(line, "%i %i %i %f %s %f %i %f %f", + &h, &k, &l, &intensity, phs, &sigma, &cts, &fs, &ss); + if ( (r != 9) && (!first) ) { + reflist_free(out); + return NULL; + } + + first = 0; + if ( r == 9 ) { + + double ph; + char *v; + + refl = add_refl(out, h, k, l); + set_intensity(refl, intensity); + set_detector_pos(refl, 0.0, fs, ss); + set_esd_intensity(refl, sigma); + set_redundancy(refl, cts); + + ph = strtod(phs, &v); + if ( v != phs ) set_phase(refl, deg2rad(ph)); + + } + + } while ( rval != NULL ); + + /* Got read error of some kind before finding PEAK_LIST_END_MARKER */ + return NULL; +} + + static RefList *read_stream_reflections(FILE *fh) { char *rval = NULL; @@ -214,7 +269,50 @@ static void write_stream_reflections(FILE *fh, RefList *list) h, k, l, intensity, esd_i, pk, bg, fs, ss); } +} + + +static void write_stream_reflections_2_1(FILE *fh, RefList *list) +{ + Reflection *refl; + RefListIterator *iter; + + fprintf(fh, " h k l I phase sigma(I) " + " counts fs/px ss/px\n"); + + for ( refl = first_refl(list, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) + { + + signed int h, k, l; + double intensity, esd_i, ph; + int red; + double fs, ss; + char phs[16]; + int have_phase; + + get_indices(refl, &h, &k, &l); + get_detector_pos(refl, &fs, &ss); + intensity = get_intensity(refl); + esd_i = get_esd_intensity(refl); + red = get_redundancy(refl); + ph = get_phase(refl, &have_phase); + + /* Reflections with redundancy = 0 are not written */ + if ( red == 0 ) continue; + if ( have_phase ) { + snprintf(phs, 16, "%8.2f", rad2deg(ph)); + } else { + strncpy(phs, " -", 15); + } + + fprintf(fh, + "%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f\n", + h, k, l, intensity, phs, esd_i, red, fs, ss); + + } } @@ -276,7 +374,9 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections) if ( AT_LEAST_VERSION(st, 2, 2) ) { write_stream_reflections(st->fh, reflist); } else { - write_reflections_to_file(st->fh, reflist); + /* This function writes like a normal reflection + * list was written in stream 2.1 */ + write_stream_reflections_2_1(st->fh, reflist); } fprintf(st->fh, REFLECTION_END_MARKER"\n"); @@ -465,7 +565,7 @@ void read_crystal(Stream *st, struct image *image) if ( AT_LEAST_VERSION(st, 2, 2) ) { reflist = read_stream_reflections(st->fh); } else { - reflist = read_reflections_from_file(st->fh); + reflist = read_stream_reflections_2_1(st->fh); } if ( reflist == NULL ) { ERROR("Failed while reading reflections\n"); -- cgit v1.2.3