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authorThomas White <taw@physics.org>2014-03-10 13:47:39 +0100
committerThomas White <taw@physics.org>2014-03-10 13:52:35 +0100
commit9f768cc81e9b09a153c0ca77ccaeb91c5a0766d3 (patch)
tree29751e3ff6b0f2bd09c55a0ba685f9101772c8cb
parent48e14bee0fb56d9a5b4f462105be7dc27cd79347 (diff)
Fix reading and writing of reflections in 2.1 stream
-rw-r--r--libcrystfel/src/stream.c104
1 files changed, 102 insertions, 2 deletions
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");