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-rw-r--r--libcrystfel/src/stream.c208
-rw-r--r--libcrystfel/src/stream.h10
-rw-r--r--src/partial_sim.c6
-rw-r--r--src/process_image.c11
4 files changed, 195 insertions, 40 deletions
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 2d4d6260..77d65531 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -80,6 +80,8 @@ static int read_peaks(FILE *fh, struct image *image)
char line[1024];
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;
@@ -96,8 +98,26 @@ static int read_peaks(FILE *fh, struct image *image)
first = 0;
if ( r == 4 ) {
- image_add_feature(image->features, x, y,
- image, intensity, NULL);
+
+ if ( image->det != NULL ) {
+
+ p = find_orig_panel(image->det, x, y);
+ if ( p == NULL ) {
+ ERROR("Panel not found\n");
+ return 1;
+ }
+
+ add_x = x-p->orig_min_fs+p->min_fs;
+ add_y = y-p->orig_min_ss+p->min_ss;
+
+ image_add_feature(image->features, add_x, add_y,
+ image, intensity, NULL);
+
+ } else {
+
+ image_add_feature(image->features, x, y,
+ image, intensity, NULL);
+ }
}
} while ( rval != NULL );
@@ -161,7 +181,7 @@ static int read_peaks_2_3(FILE *fh, struct image *image)
}
-static void write_peaks(struct image *image, FILE *ofh)
+static int write_peaks(struct image *image, FILE *ofh)
{
int i;
@@ -180,16 +200,40 @@ 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);
+ if ( image->det != NULL ) {
+
+ struct panel *p;
+ double write_fs, write_ss;
+
+ p = find_orig_panel(image->det, f->fs, f->ss);
+ if ( p == NULL ) {
+ ERROR("Panel not found\n");
+ return 1;
+ }
+
+ /* Convert coordinates to match arrangement of panels in HDF5
+ * file */
+ 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 %10.2f %10.2f\n",
+ write_fs, write_ss, q/1.0e9, f->intensity);
+
+ } else {
+
+ fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f\n",
+ f->fs, f->ss, q/1.0e9, f->intensity);
+
+ }
}
fprintf(ofh, PEAK_LIST_END_MARKER"\n");
+ return 0;
}
-static void write_peaks_2_3(struct image *image, FILE *ofh)
+static int write_peaks_2_3(struct image *image, FILE *ofh)
{
int i;
@@ -211,6 +255,10 @@ static void write_peaks_2_3(struct image *image, FILE *ofh)
q = modulus(r.u, r.v, r.w);
p = find_panel(image->det, f->fs, f->ss);
+ if ( p == NULL ) {
+ ERROR("Panel not found\n");
+ return 1;
+ }
/* Convert coordinates to match arrangement of panels in HDF5
* file */
@@ -223,6 +271,7 @@ static void write_peaks_2_3(struct image *image, FILE *ofh)
}
fprintf(ofh, PEAK_LIST_END_MARKER"\n");
+ return 0;
}
@@ -285,7 +334,7 @@ static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
}
-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;
@@ -325,7 +374,22 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
- set_detector_pos(refl, 0.0, fs, ss);
+
+ if ( det != NULL ) {
+
+ double write_fs, write_ss;
+ struct panel *p;
+
+ p = find_orig_panel(det, fs, ss);
+ write_fs = fs - p->orig_min_fs + p->min_fs;
+ write_ss = ss - p->orig_min_ss + p->min_ss;
+ set_detector_pos(refl, 0.0, write_fs, write_ss);
+
+ } else {
+
+ set_detector_pos(refl, 0.0, fs, ss);
+
+ }
set_esd_intensity(refl, sigma);
set_redundancy(refl, cts);
@@ -341,7 +405,7 @@ static RefList *read_stream_reflections_2_1(FILE *fh)
}
-static RefList *read_stream_reflections_2_2(FILE *fh)
+static RefList *read_stream_reflections_2_2(FILE *fh, struct detector *det)
{
char *rval = NULL;
int first = 1;
@@ -375,7 +439,23 @@ static RefList *read_stream_reflections_2_2(FILE *fh)
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
- set_detector_pos(refl, 0.0, fs, ss);
+
+ if ( det != NULL ) {
+
+ double write_fs, write_ss;
+ struct panel *p;
+
+ p = find_orig_panel(det, fs, ss);
+ write_fs = fs - p->orig_min_fs + p->min_fs;
+ write_ss = ss - p->orig_min_ss + p->min_ss;
+ set_detector_pos(refl, 0.0, write_fs, write_ss);
+
+ } else {
+
+ set_detector_pos(refl, 0.0, fs, ss);
+
+ }
+
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
set_peak(refl, pk);
@@ -390,7 +470,8 @@ static RefList *read_stream_reflections_2_2(FILE *fh)
}
-static void write_stream_reflections_2_1(FILE *fh, RefList *list)
+static int write_stream_reflections_2_1(FILE *fh, RefList *list,
+ struct image *image)
{
Reflection *refl;
RefListIterator *iter;
@@ -426,14 +507,38 @@ static void write_stream_reflections_2_1(FILE *fh, RefList *list)
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);
+ if ( image->det != NULL ) {
+
+ struct panel *p;
+ double write_fs, write_ss;
+
+ p = find_orig_panel(image->det, fs, ss);
+ if ( p == NULL ) {
+ ERROR("Panel not found\n");
+ return 1;
+ }
+
+ /* Convert coordinates to match arrangement of panels in HDF5
+ * file */
+ 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, write_fs, write_ss);
+
+ } else {
+
+ 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);
+ }
}
+ return 0;
}
-static void write_stream_reflections_2_2(FILE *fh, RefList *list)
+static int write_stream_reflections_2_2(FILE *fh, RefList *list,
+ struct image *image)
{
Reflection *refl;
RefListIterator *iter;
@@ -460,16 +565,39 @@ static void write_stream_reflections_2_2(FILE *fh, RefList *list)
/* Reflections with redundancy = 0 are not written */
if ( get_redundancy(refl) == 0 ) continue;
- 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);
+ if ( image->det != NULL ) {
+
+ struct panel *p;
+ double write_fs, write_ss;
+
+ p = find_orig_panel(image->det, fs, ss);
+ if ( p == NULL ) {
+ ERROR("Panel not found\n");
+ return 1;
+ }
+ /* Convert coordinates to match arrangement of panels in HDF5
+ * file */
+ 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, write_fs, write_ss);
+
+ } else {
+
+ 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);
+ }
}
+ return 0;
}
-static void write_stream_reflections_2_3(FILE *fh, RefList *list,
- struct image *image)
+static int write_stream_reflections_2_3(FILE *fh, RefList *list,
+ struct image *image)
{
Reflection *refl;
RefListIterator *iter;
@@ -499,6 +627,11 @@ static void write_stream_reflections_2_3(FILE *fh, RefList *list,
if ( get_redundancy(refl) == 0 ) continue;
p = find_panel(image->det,fs,ss);
+ if ( p == NULL ) {
+ ERROR("Panel not found\n");
+ return 1;
+ }
+
write_fs = fs-p->min_fs+p->orig_min_fs;
write_ss = ss-p->min_ss+p->orig_min_ss;
@@ -509,6 +642,7 @@ static void write_stream_reflections_2_3(FILE *fh, RefList *list,
write_fs, write_ss, p->name);
}
+ return 0;
}
@@ -529,7 +663,7 @@ static int num_integrated_reflections(RefList *list)
}
-static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
+static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
{
UnitCell *cell;
RefList *reflist;
@@ -538,6 +672,7 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
double csx, csy, csz;
double a, b, c, al, be, ga;
double rad;
+ int ret = 0;
fprintf(st->fh, CRYSTAL_START_MARKER"\n");
@@ -589,16 +724,20 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
if ( reflist != NULL ) {
+ struct image *image;
+
+ image = crystal_get_image(cr);
+
fprintf(st->fh, REFLECTION_START_MARKER"\n");
if ( AT_LEAST_VERSION(st, 2, 3) ) {
- write_stream_reflections_2_3(st->fh, reflist,
- crystal_get_image(cr));
+ ret = write_stream_reflections_2_3(st->fh, reflist,
+ image);
} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
- write_stream_reflections_2_2(st->fh, reflist);
+ ret = write_stream_reflections_2_2(st->fh, reflist, image);
} else {
/* This function writes like a normal reflection
* list was written in stream 2.1 */
- write_stream_reflections_2_1(st->fh, reflist);
+ ret = write_stream_reflections_2_1(st->fh, reflist, image);
}
fprintf(st->fh, REFLECTION_END_MARKER"\n");
@@ -610,14 +749,17 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
}
fprintf(st->fh, CRYSTAL_END_MARKER"\n");
+
+ return ret;
}
-void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
- int include_peaks, int include_reflections, struct event* ev)
+int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
+ int include_peaks, int include_reflections, struct event* ev)
{
int j;
char *indexer;
+ int ret = 0;
fprintf(st->fh, CHUNK_START_MARKER"\n");
@@ -679,19 +821,21 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
fprintf(st->fh, "num_saturated_peaks = %lli\n", i->num_saturated_peaks);
if ( include_peaks ) {
if ( AT_LEAST_VERSION(st, 2, 3) ) {
- write_peaks_2_3(i, st->fh);
+ ret = write_peaks_2_3(i, st->fh);
} else {
- write_peaks(i, st->fh);
+ ret = write_peaks(i, st->fh);
}
}
for ( j=0; j<i->n_crystals; j++ ) {
- write_crystal(st, i->crystals[j], include_reflections);
+ ret = write_crystal(st, i->crystals[j], include_reflections);
}
fprintf(st->fh, CHUNK_END_MARKER"\n");
fflush(st->fh);
+
+ return ret;
}
@@ -832,11 +976,11 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
* after 2.2 */
if ( AT_LEAST_VERSION(st, 2, 3) ) {
reflist = read_stream_reflections_2_3(st->fh,
- image->det);
+ image->det);
} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
- reflist = read_stream_reflections_2_2(st->fh);
+ reflist = read_stream_reflections_2_2(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");
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index e98ee02d..43e45923 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -91,10 +91,12 @@ extern int get_stream_fd(Stream *st);
extern void close_stream(Stream *st);
extern int read_chunk(Stream *st, struct image *image);
-extern int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf);
-extern void write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
- int include_peaks, int include_reflections,
- struct event *ev);
+extern int read_chunk_2(Stream *st, struct image *image,
+ StreamReadFlags srf);
+
+extern int write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
+ int include_peaks, int include_reflections,
+ struct event *ev);
extern void write_command(Stream *st, int argc, char *argv[]);
extern void write_geometry_file(Stream *st, const char *geom_filename);
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 1252cd86..6e5f1ced 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -390,8 +390,12 @@ static void finalise_job(void *vqargs, void *vwargs)
struct worker_args *wargs = vwargs;
struct queue_args *qargs = vqargs;
int i;
+ int ret;
- write_chunk(qargs->stream, &wargs->image, NULL, 0, 1, NULL);
+ ret = write_chunk(qargs->stream, &wargs->image, NULL, 0, 1, NULL);
+ if ( ret != 0) {
+ ERROR("Warning: error writing stream file.\n");
+ }
for ( i=0; i<NBINS; i++ ) {
qargs->n_ref[i] += wargs->n_ref[i];
diff --git a/src/process_image.c b/src/process_image.c
index 807facd9..f09d06b4 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -122,6 +122,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
struct image image;
int i;
int r;
+ int ret;
char *rn;
image.features = NULL;
@@ -252,9 +253,13 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
iargs->int_diag_k, iargs->int_diag_l,
results_pipe);
- write_chunk(st, &image, hdfile,
- iargs->stream_peaks, iargs->stream_refls,
- pargs->filename_p_e->ev);
+ ret = write_chunk(st, &image, hdfile,
+ iargs->stream_peaks, iargs->stream_refls,
+ pargs->filename_p_e->ev);
+ if ( ret != 0 ) {
+ ERROR("Error writing stream file.\n");
+ }
+
for ( i=0; i<image.n_crystals; i++ ) {
cell_free(crystal_get_cell(image.crystals[i]));
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 22:02:16 +0000