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authorValerio Mariani <valerio.mariani@desy.de>2014-04-01 17:42:52 +0200
committerThomas White <taw@physics.org>2014-09-05 18:04:14 +0200
commitb25636f0d9810432f46bdf528b597a2f56689630 (patch)
treeeb39a1b07b05559672bc4fd11a6f2a209cd8b4d8
parent4a36677bacc10e5fbd5905ea9751f1a6603250f7 (diff)
Versioning of reflection and peak I/O
-rw-r--r--libcrystfel/src/stream.c278
1 files changed, 224 insertions, 54 deletions
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 11eb8dbf..5d30b796 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -54,7 +54,7 @@
#include "reflist-utils.h"
#define LATEST_MAJOR_VERSION (2)
-#define LATEST_MINOR_VERSION (2)
+#define LATEST_MINOR_VERSION (3)
#define AT_LEAST_VERSION(st, a, b) ((st->major_version>=(a)) \
&& (st->minor_version>=(b)))
@@ -68,7 +68,6 @@ struct _stream
int minor_version;
};
-
static int read_peaks(FILE *fh, struct image *image)
{
char *rval = NULL;
@@ -79,6 +78,45 @@ static int read_peaks(FILE *fh, struct image *image)
do {
char line[1024];
+ float x, y, d, intensity;
+ int r;
+
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) continue;
+ chomp(line);
+
+ 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) ) {
+ 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,
+ image, intensity, NULL);
+ }
+
+ } while ( rval != NULL );
+
+ /* Got read error of some kind before finding PEAK_LIST_END_MARKER */
+ return 1;
+}
+
+
+static int read_peaks_2_3(FILE *fh, struct image *image)
+{
+ char *rval = NULL;
+ int first = 1;
+
+ image->features = image_feature_list_new();
+
+ do {
+
+ char line[1024];
char pn[32];
float x, y, d, intensity;
int r;
@@ -91,7 +129,7 @@ static int read_peaks(FILE *fh, struct image *image)
if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0;
- r = sscanf(line, "%f %f %s %f %f", &x, &y, pn, &d, &intensity);
+ r = sscanf(line, "%f %f %f %f %s", &x, &y, &d, &intensity, pn);
if ( (r != 5) && (!first) ) {
ERROR("Failed to parse peak list line.\n");
ERROR("The failed line was: '%s'\n", line);
@@ -122,7 +160,35 @@ static void write_peaks(struct image *image, FILE *ofh)
int i;
fprintf(ofh, PEAK_LIST_START_MARKER"\n");
- fprintf(ofh, " fs/px ss/px panel (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++ ) {
+
+ struct imagefeature *f;
+ struct rvec r;
+ double q;
+
+ f = image_get_feature(image->features, i);
+ if ( f == NULL ) continue;
+
+ 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);
+
+ }
+
+ fprintf(ofh, PEAK_LIST_END_MARKER"\n");
+}
+
+
+static void write_peaks_2_3(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 Panel\n");
for ( i=0; i<image_feature_count(image->features); i++ ) {
@@ -132,7 +198,6 @@ static void write_peaks(struct image *image, FILE *ofh)
struct panel *p;
double write_fs, write_ss;
-
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
@@ -143,8 +208,8 @@ static void write_peaks(struct image *image, FILE *ofh)
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);
+ fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f %s\n",
+ write_fs, write_ss, q/1.0e9, f->intensity, p->name);
}
@@ -152,7 +217,7 @@ static void write_peaks(struct image *image, FILE *ofh)
}
-static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
+static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
{
char *rval = NULL;
int first = 1;
@@ -212,7 +277,62 @@ static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
}
-static RefList *read_stream_reflections(FILE *fh, struct detector *det)
+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_2_2(FILE *fh)
{
char *rval = NULL;
int first = 1;
@@ -226,10 +346,7 @@ static RefList *read_stream_reflections(FILE *fh, struct detector *det)
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;
@@ -237,22 +354,19 @@ static RefList *read_stream_reflections(FILE *fh, struct detector *det)
if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
- 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) ) {
+ 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) ) {
reflist_free(out);
return NULL;
}
first = 0;
- if ( r == 10 ) {
+ if ( r == 9 ) {
- p = find_panel_by_name(det,pn);
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
- 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_detector_pos(refl, 0.0, fs, ss);
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
set_peak(refl, pk);
@@ -267,13 +381,13 @@ static RefList *read_stream_reflections(FILE *fh, struct detector *det)
}
-static void write_stream_reflections(FILE *fh, RefList *list, struct image *image)
+static void write_stream_reflections_2_2(FILE *fh, RefList *list)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I sigma(I) peak background"
- " fs/px ss/px panel\n");
+ " fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
@@ -283,8 +397,6 @@ static void write_stream_reflections(FILE *fh, RefList *list, struct image *imag
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);
@@ -296,25 +408,66 @@ static void write_stream_reflections(FILE *fh, RefList *list, struct image *imag
/* 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);
+
+ }
+}
+
+
+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,
- "%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);
+ "%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f\n",
+ h, k, l, intensity, phs, esd_i, red, fs, ss);
}
}
-static void write_stream_reflections_2_1(FILE *fh, RefList *list, struct image *image)
+static void write_stream_reflections_2_3(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 panel\n");
+ " counts fs/px ss/px panel\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
@@ -351,8 +504,9 @@ static void write_stream_reflections_2_1(FILE *fh, RefList *list, struct image *
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);
+ "%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f %s\n",
+ h, k, l, intensity, phs, esd_i, red, write_fs, write_ss,
+ p->name);
}
}
@@ -392,22 +546,22 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
fprintf(st->fh, "Cell parameters %7.5f %7.5f %7.5f nm,"
- " %7.5f %7.5f %7.5f deg\n",
- a*1.0e9, b*1.0e9, c*1.0e9,
- rad2deg(al), rad2deg(be), rad2deg(ga));
+ " %7.5f %7.5f %7.5f deg\n",
+ a*1.0e9, b*1.0e9, c*1.0e9,
+ rad2deg(al), rad2deg(be), rad2deg(ga));
cell_get_reciprocal(cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
+ &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
fprintf(st->fh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
asx/1e9, asy/1e9, asz/1e9);
fprintf(st->fh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
bsx/1e9, bsy/1e9, bsz/1e9);
fprintf(st->fh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
- csx/1e9, csy/1e9, csz/1e9);
+ csx/1e9, csy/1e9, csz/1e9);
fprintf(st->fh, "lattice_type = %s\n",
- str_lattice(cell_get_lattice_type(cell)));
+ str_lattice(cell_get_lattice_type(cell)));
fprintf(st->fh, "centering = %c\n", cell_get_centering(cell));
fprintf(st->fh, "unique_axis = %c\n", cell_get_unique_axis(cell));
@@ -418,14 +572,14 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
if ( reflist != NULL ) {
fprintf(st->fh, "diffraction_resolution_limit"
- " = %.2f nm^-1 or %.2f A\n",
- crystal_get_resolution_limit(cr)/1e9,
- 1e10 / crystal_get_resolution_limit(cr));
+ " = %.2f nm^-1 or %.2f A\n",
+ crystal_get_resolution_limit(cr)/1e9,
+ 1e9 / crystal_get_resolution_limit(cr));
fprintf(st->fh, "num_reflections = %i\n",
num_integrated_reflections(reflist));
fprintf(st->fh, "num_saturated_reflections = %lli\n",
- crystal_get_num_saturated_reflections(cr));
+ crystal_get_num_saturated_reflections(cr));
}
@@ -434,12 +588,15 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
if ( reflist != NULL ) {
fprintf(st->fh, REFLECTION_START_MARKER"\n");
- if ( AT_LEAST_VERSION(st, 2, 2) ) {
- write_stream_reflections(st->fh, reflist, crystal_get_image(cr));
+ if ( AT_LEAST_VERSION(st, 2, 3) ) {
+ write_stream_reflections_2_3(st->fh, reflist,
+ crystal_get_image(cr));
+ } else if ( AT_LEAST_VERSION(st, 2, 2) ) {
+ write_stream_reflections_2_2(st->fh, reflist);
} else {
/* This function writes like a normal reflection
* list was written in stream 2.1 */
- write_stream_reflections_2_1(st->fh, reflist, crystal_get_image(cr));
+ write_stream_reflections_2_1(st->fh, reflist);
}
fprintf(st->fh, REFLECTION_END_MARKER"\n");
@@ -514,7 +671,11 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
fprintf(st->fh, "num_peaks = %lli\n", i->num_peaks);
fprintf(st->fh, "num_saturated_peaks = %lli\n", i->num_saturated_peaks);
if ( include_peaks ) {
- write_peaks(i, st->fh);
+ if ( AT_LEAST_VERSION(st, 2, 3) ) {
+ write_peaks_2_3(i, st->fh);
+ } else {
+ write_peaks(i, st->fh);
+ }
}
for ( j=0; j<i->n_crystals; j++ ) {
@@ -658,10 +819,12 @@ 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, image->det);
+ if ( AT_LEAST_VERSION(st, 2, 3) ) {
+ reflist = read_stream_reflections_2_3(st->fh, image->det);
+ } else if ( AT_LEAST_VERSION(st, 2, 2) ) {
+ reflist = read_stream_reflections_2_2(st->fh);
} else {
- reflist = read_stream_reflections_2_1(st->fh, image->det);
+ reflist = read_stream_reflections_2_1(st->fh);
}
if ( reflist == NULL ) {
ERROR("Failed while reading reflections\n");
@@ -806,9 +969,16 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
}
}
- if ( (srf & STREAM_READ_PEAKS)
- && (strcmp(line, PEAK_LIST_START_MARKER) == 0) ) {
- if ( read_peaks(st->fh, image) ) {
+ if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) {
+
+ int fail;
+
+ if ( AT_LEAST_VERSION(st, 2, 3) ) {
+ fail = read_peaks_2_3(st->fh, image);
+ } else {
+ fail = read_peaks(st->fh, image);
+ }
+ if ( fail ) {
ERROR("Failed while reading peaks\n");
return 1;
}