aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/stream.c
diff options
context:
space:
mode:
Diffstat (limited to 'libcrystfel/src/stream.c')
-rw-r--r--libcrystfel/src/stream.c101
1 files changed, 70 insertions, 31 deletions
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 9aaa53df..e1a67714 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -78,8 +78,11 @@ static int read_peaks(FILE *fh, struct image *image)
do {
char line[1024];
+ char pn[32];
float x, y, d, intensity;
int r;
+ struct panel *p = NULL;
+ int add_x, add_y;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
@@ -87,16 +90,22 @@ 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) && (!first) ) {
+ r = sscanf(line, "%f %f %s %f %f", &x, &y, pn, &d, &intensity);
+ if ( (r != 5) && (!first) ) {
ERROR("Failed to parse peak list line.\n");
ERROR("The failed line was: '%s'\n", line);
return 1;
}
first = 0;
- if ( r == 4 ) {
- image_add_feature(image->features, x, y,
+
+ p = find_panel_by_name(image->det, pn);
+
+ add_x = x-p->orig_min_fs+p->min_fs;
+ add_y = x-p->orig_min_ss+p->min_ss;
+
+ if ( r == 5 ) {
+ image_add_feature(image->features, add_x, add_y,
image, intensity, NULL);
}
@@ -112,13 +121,16 @@ 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 panel (1/d)/nm^-1 Intensity\n");
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
struct rvec r;
double q;
+ struct panel *p;
+ double write_fs, write_ss;
+
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
@@ -126,8 +138,12 @@ 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, "%7.2f %7.2f %10.2f %10.2f\n",
- f->fs, f->ss, q/1.0e9, f->intensity);
+ p = find_panel(image->det,f->fs,f->ss);
+ write_fs = f->fs-p->min_fs+p->orig_min_fs;
+ write_ss = f->ss-p->min_ss+p->orig_min_ss;
+
+ fprintf(ofh, "%7.2f %7.2f %s %10.2f %10.2f\n",
+ write_fs, write_ss, p->name, q/1.0e9, f->intensity);
}
@@ -135,7 +151,7 @@ static void write_peaks(struct image *image, FILE *ofh)
}
-static RefList *read_stream_reflections_2_1(FILE *fh)
+static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
{
char *rval = NULL;
int first = 1;
@@ -149,6 +165,7 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
signed int h, k, l;
float intensity, sigma, fs, ss;
char phs[1024];
+ char pn[32];
int cts;
int r;
Reflection *refl;
@@ -159,25 +176,29 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
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) ) {
+ r = sscanf(line, "%i %i %i %f %s %f %i %f %f %s",
+ &h, &k, &l, &intensity, phs, &sigma, &cts, &fs, &ss, pn);
+ if ( (r != 10) && (!first) ) {
reflist_free(out);
return NULL;
}
first = 0;
- if ( r == 9 ) {
+ if ( r == 10 ) {
double ph;
char *v;
+ struct panel *p;
+ float write_fs, write_ss;
+ p = find_panel_by_name(det,pn);
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
- set_detector_pos(refl, 0.0, fs, ss);
+ write_ss = ss-p->orig_min_ss+p->min_ss;
+ write_fs = fs-p->orig_min_fs+p->min_fs;
+ set_detector_pos(refl, 0.0, write_fs, write_ss);
set_esd_intensity(refl, sigma);
set_redundancy(refl, cts);
-
ph = strtod(phs, &v);
if ( v != phs ) set_phase(refl, deg2rad(ph));
@@ -190,7 +211,7 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
}
-static RefList *read_stream_reflections(FILE *fh)
+static RefList *read_stream_reflections(FILE *fh, struct detector *det)
{
char *rval = NULL;
int first = 1;
@@ -204,7 +225,10 @@ static RefList *read_stream_reflections(FILE *fh)
signed int h, k, l;
float intensity, sigma, fs, ss, pk, bg;
int r;
+ char pn[32];
Reflection *refl;
+ struct panel *p;
+ float write_fs, write_ss;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
@@ -212,19 +236,22 @@ static RefList *read_stream_reflections(FILE *fh)
if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
- r = sscanf(line, "%i %i %i %f %f %f %f %f %f",
- &h, &k, &l, &intensity, &sigma, &pk, &bg, &fs, &ss);
- if ( (r != 9) && (!first) ) {
+ r = sscanf(line, "%i %i %i %f %f %f %f %f %f %s",
+ &h, &k, &l, &intensity, &sigma, &pk, &bg, &fs, &ss, pn);
+ if ( (r != 10) && (!first) ) {
reflist_free(out);
return NULL;
}
first = 0;
- if ( r == 9 ) {
+ if ( r == 10 ) {
+ p = find_panel_by_name(det,pn);
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
- set_detector_pos(refl, 0.0, fs, ss);
+ write_ss = ss-p->orig_min_ss+p->min_ss;
+ write_fs = fs-p->orig_min_fs+p->min_fs;
+ set_detector_pos(refl, 0.0, write_fs, write_ss);
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
set_peak(refl, pk);
@@ -239,13 +266,13 @@ static RefList *read_stream_reflections(FILE *fh)
}
-static void write_stream_reflections(FILE *fh, RefList *list)
+static void write_stream_reflections(FILE *fh, RefList *list, struct image *image)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I sigma(I) peak background"
- " fs/px ss/px\n");
+ " fs/px ss/px panel\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
@@ -255,6 +282,8 @@ static void write_stream_reflections(FILE *fh, RefList *list)
signed int h, k, l;
double intensity, esd_i, bg, pk;
double fs, ss;
+ double write_fs, write_ss;
+ struct panel *p = NULL;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
@@ -266,21 +295,25 @@ static void write_stream_reflections(FILE *fh, RefList *list)
/* Reflections with redundancy = 0 are not written */
if ( get_redundancy(refl) == 0 ) continue;
+ p = find_panel(image->det,fs,ss);
+ write_fs = fs-p->min_fs+p->orig_min_fs;
+ write_ss = ss-p->min_ss+p->orig_min_ss;
+
fprintf(fh,
- "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f %6.1f %6.1f\n",
- h, k, l, intensity, esd_i, pk, bg, fs, ss);
+ "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f %6.1f %6.1f %s\n",
+ h, k, l, intensity, esd_i, pk, bg, write_fs, write_ss, p->name);
}
}
-static void write_stream_reflections_2_1(FILE *fh, RefList *list)
+static void write_stream_reflections_2_1(FILE *fh, RefList *list, struct image *image)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I phase sigma(I) "
- " counts fs/px ss/px\n");
+ " counts fs/px ss/px panel\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
@@ -291,8 +324,10 @@ static void write_stream_reflections_2_1(FILE *fh, RefList *list)
double intensity, esd_i, ph;
int red;
double fs, ss;
+ double write_fs, write_ss;
char phs[16];
int have_phase;
+ struct panel *p = NULL;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
@@ -310,9 +345,13 @@ static void write_stream_reflections_2_1(FILE *fh, RefList *list)
strncpy(phs, " -", 15);
}
+ p = find_panel(image->det,fs,ss);
+ write_fs = fs-p->min_fs+p->orig_min_fs;
+ write_ss = ss-p->min_ss+p->orig_min_ss;
+
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);
+ h, k, l, intensity, phs, esd_i, red, write_fs, write_ss);
}
}
@@ -395,11 +434,11 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
fprintf(st->fh, REFLECTION_START_MARKER"\n");
if ( AT_LEAST_VERSION(st, 2, 2) ) {
- write_stream_reflections(st->fh, reflist);
+ write_stream_reflections(st->fh, reflist, crystal_get_image(cr));
} else {
/* This function writes like a normal reflection
* list was written in stream 2.1 */
- write_stream_reflections_2_1(st->fh, reflist);
+ write_stream_reflections_2_1(st->fh, reflist, crystal_get_image(cr));
}
fprintf(st->fh, REFLECTION_END_MARKER"\n");
@@ -619,9 +658,9 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
/* The reflection list format in the stream diverges
* after 2.2 */
if ( AT_LEAST_VERSION(st, 2, 2) ) {
- reflist = read_stream_reflections(st->fh);
+ reflist = read_stream_reflections(st->fh, image->det);
} else {
- reflist = read_stream_reflections_2_1(st->fh);
+ reflist = read_stream_reflections_2_1(st->fh, image->det);
}
if ( reflist == NULL ) {
ERROR("Failed while reading reflections\n");
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 20:20:55 +0000