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-rw-r--r--libcrystfel/src/hdf5-file.c89
-rw-r--r--src/partial_sim.c71
2 files changed, 114 insertions, 46 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index ad9495b5..ed3b1e29 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -384,57 +384,60 @@ int hdf5_write_image(const char *filename, struct image *image)
H5Dclose(dh);
- arr = malloc(image->spectrum_size*sizeof(double));
- if ( arr == NULL ) {
- H5Fclose(fh);
- return 1;
- }
- for ( i=0; i<image->spectrum_size; i++ ) {
- arr[i] = 1.0e10/image->spectrum[i].k;
- }
+ if ( image->spectrum_size > 0 ) {
- size[0] = image->spectrum_size;
- sh = H5Screate_simple(1, size, NULL);
+ arr = malloc(image->spectrum_size*sizeof(double));
+ if ( arr == NULL ) {
+ H5Fclose(fh);
+ return 1;
+ }
+ for ( i=0; i<image->spectrum_size; i++ ) {
+ arr[i] = 1.0e10/image->spectrum[i].k;
+ }
- dh = H5Dcreate2(gh, "spectrum_wavelengths_A", H5T_NATIVE_DOUBLE, sh,
- H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
- if ( dh < 0 ) {
- H5Fclose(fh);
- return 1;
- }
- r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
- H5S_ALL, H5P_DEFAULT, arr);
- H5Dclose(dh);
+ size[0] = image->spectrum_size;
+ sh = H5Screate_simple(1, size, NULL);
- for ( i=0; i<image->spectrum_size; i++ ) {
- arr[i] = image->spectrum[i].weight;
- }
- dh = H5Dcreate2(gh, "spectrum_weights", H5T_NATIVE_DOUBLE, sh,
- H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
- if ( dh < 0 ) {
- H5Fclose(fh);
- return 1;
- }
- r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
- H5S_ALL, H5P_DEFAULT, arr);
+ dh = H5Dcreate2(gh, "spectrum_wavelengths_A", H5T_NATIVE_DOUBLE,
+ sh, H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ H5Fclose(fh);
+ return 1;
+ }
+ r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+ H5S_ALL, H5P_DEFAULT, arr);
+ H5Dclose(dh);
- H5Dclose(dh);
- free(arr);
+ for ( i=0; i<image->spectrum_size; i++ ) {
+ arr[i] = image->spectrum[i].weight;
+ }
+ dh = H5Dcreate2(gh, "spectrum_weights", H5T_NATIVE_DOUBLE, sh,
+ H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ H5Fclose(fh);
+ return 1;
+ }
+ r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+ H5S_ALL, H5P_DEFAULT, arr);
- size[0] = 1;
- sh = H5Screate_simple(1, size, NULL);
+ H5Dclose(dh);
+ free(arr);
- dh = H5Dcreate2(gh, "number_of_samples", H5T_NATIVE_INT, sh,
- H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
- if ( dh < 0 ) {
- H5Fclose(fh);
- return 1;
- }
+ size[0] = 1;
+ sh = H5Screate_simple(1, size, NULL);
+
+ dh = H5Dcreate2(gh, "number_of_samples", H5T_NATIVE_INT, sh,
+ H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ H5Fclose(fh);
+ return 1;
+ }
- r = H5Dwrite(dh, H5T_NATIVE_INT, H5S_ALL,
- H5S_ALL, H5P_DEFAULT, &image->nsamples);
+ r = H5Dwrite(dh, H5T_NATIVE_INT, H5S_ALL,
+ H5S_ALL, H5P_DEFAULT, &image->nsamples);
- H5Dclose(dh);
+ H5Dclose(dh);
+ }
H5Gclose(gh);
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 97e2d14d..5b05218f 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -169,6 +169,46 @@ static void calculate_partials(Crystal *cr,
}
+static void draw_and_write_image(struct image *image, RefList *reflections,
+ gsl_rng *rng)
+{
+ Reflection *refl;
+ RefListIterator *iter;
+ const int background = 3000;
+ int i;
+
+ image->data = calloc(image->width*image->height, sizeof(float));
+
+ for ( refl = first_refl(reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ double Ip;
+ double dfs, dss;
+ int fs, ss;
+
+ Ip = get_intensity(refl);
+
+ get_detector_pos(refl, &dfs, &dss);
+ fs = nearbyint(dfs);
+ ss = nearbyint(dss);
+ assert(fs >= 0);
+ assert(ss >= 0);
+ assert(fs < image->width);
+ assert(ss < image->height);
+ image->data[fs + image->width*ss] += Ip;
+
+ }
+
+ for ( i=0; i<image->width*image->height; i++ ) {
+ image->data[i] += poisson_noise(rng, background);
+ }
+
+ hdf5_write_image(image->filename, image);
+ free(image->data);
+}
+
+
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
@@ -181,6 +221,7 @@ static void show_help(const char *s)
" -i, --input=<file> Read reflections from <file>.\n"
" Default: generate random ones instead (see -r).\n"
" -o, --output=<file> Write partials in stream format to <file>.\n"
+" --images=<prefix> Write images to <prefix>NNN.h5.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -b, --beam=<file> Get beam parameters from file\n"
" -p, --pdb=<file> PDB file from which to get the unit cell.\n"
@@ -221,6 +262,8 @@ struct queue_args
struct image *template_image;
double max_q;
+ char *image_prefix;
+
/* The overall histogram */
double p_hist[NBINS];
unsigned long int n_ref[NBINS];
@@ -241,6 +284,8 @@ struct worker_args
double p_hist[NBINS];
unsigned long int n_ref[NBINS];
double p_max[NBINS];
+
+ int n;
};
@@ -258,6 +303,7 @@ static void *create_job(void *vqargs)
wargs->image = *qargs->template_image;
qargs->n_started++;
+ wargs->n = qargs->n_started;
return wargs;
}
@@ -293,7 +339,13 @@ static void run_job(void *vwargs, int cookie)
orientation = random_quaternion(qargs->rngs[cookie]);
crystal_set_cell(cr, cell_rotate(qargs->cell, orientation));
- snprintf(wargs->image.filename, 255, "dummy.h5");
+ if ( qargs->image_prefix != NULL ) {
+ snprintf(wargs->image.filename, 255, "%s%i.h5",
+ qargs->image_prefix, wargs->n);
+ } else {
+ snprintf(wargs->image.filename, 255, "dummy.h5");
+ }
+
reflections = find_intersections(&wargs->image, cr);
crystal_set_reflections(cr, reflections);
@@ -310,6 +362,11 @@ static void run_job(void *vwargs, int cookie)
qargs->max_q, qargs->full_stddev,
qargs->noise_stddev, qargs->rngs[cookie]);
+ if ( qargs->image_prefix != NULL ) {
+ draw_and_write_image(&wargs->image, reflections,
+ qargs->rngs[cookie]);
+ }
+
/* Give a slightly incorrect cell in the stream */
mess_up_cell(cr, qargs->cnoise, qargs->rngs[cookie]);
@@ -372,6 +429,7 @@ int main(int argc, char *argv[])
double noise_stddev = 20.0;
gsl_rng *rng_for_seeds;
int config_random = 0;
+ char *image_prefix = NULL;
/* Long options */
const struct option longopts[] = {
@@ -389,6 +447,7 @@ int main(int argc, char *argv[])
{"osf-stddev", 1, NULL, 3},
{"full-stddev", 1, NULL, 4},
{"noise-stddev", 1, NULL, 5},
+ {"images", 1, NULL, 6},
{"really-random", 0, &config_random, 1},
@@ -492,6 +551,10 @@ int main(int argc, char *argv[])
}
break;
+ case 6 :
+ image_prefix = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -595,8 +658,8 @@ int main(int argc, char *argv[])
free(output_file);
image.det = det;
- image.width = det->max_fs;
- image.height = det->max_ss;
+ image.width = det->max_fs + 1;
+ image.height = det->max_ss + 1;
image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy));
image.div = beam->divergence;
@@ -609,6 +672,7 @@ int main(int argc, char *argv[])
image.indexed_by = INDEXING_SIMULATION;
image.num_peaks = 0;
image.num_saturated_peaks = 0;
+ image.spectrum_size = 0;
if ( random_intensities ) {
full = reflist_new();
@@ -629,6 +693,7 @@ int main(int argc, char *argv[])
qargs.full_stddev = full_stddev;
qargs.noise_stddev = noise_stddev;
qargs.max_q = largest_q(&image);
+ qargs.image_prefix = image_prefix;
qargs.rngs = malloc(n_threads * sizeof(gsl_rng *));
if ( qargs.rngs == NULL ) {
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 18:18:09 +0000