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authorChun Hong Yoon <chun.hong.yoon@desy.de>2014-01-27 14:02:34 +0100
committerThomas White <taw@physics.org>2014-01-28 15:45:42 +0100
commit6ee21aaa02a5c11bd1269bff0bc7d23b0d402c1e (patch)
treeae9fcc8a362bacedda7d3fbd185ff427836cca1d
parent07f1ba5269db94d44278596d827ac26845914b90 (diff)
Add two colour spectrum
-rw-r--r--libcrystfel/src/image.h3
-rw-r--r--src/diffraction.c65
-rw-r--r--src/diffraction.h2
-rw-r--r--src/pattern_sim.c9
4 files changed, 75 insertions, 4 deletions
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 0c189cad..6b49ad91 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -46,7 +46,8 @@
typedef enum {
SPECTRUM_TOPHAT,
- SPECTRUM_SASE
+ SPECTRUM_SASE,
+ SPECTRUM_TWOCOLOUR
} SpectrumType;
/* Structure describing a feature in an image */
diff --git a/src/diffraction.c b/src/diffraction.c
index 92e18521..82e5c132 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -434,7 +434,7 @@ static int compare_samples(const void *a, const void *b)
static struct sample *get_gaussian_spectrum(double eV_cen, double eV_step,
- double sigma, int spec_size)
+ double sigma, int spec_size, double eV_start)
{
struct sample *spectrum;
int i;
@@ -443,7 +443,12 @@ static struct sample *get_gaussian_spectrum(double eV_cen, double eV_step,
spectrum = malloc(spec_size * sizeof(struct sample));
if ( spectrum == NULL ) return NULL;
- eV = eV_cen - (spec_size/2)*eV_step;
+ if (eV_start == 0) { /* eV starts at 3 sigma below the mean*/
+ eV = eV_cen - (spec_size/2)*eV_step;
+ } else {
+ eV = eV_start;
+ }
+
for ( i=0; i<spec_size; i++ ) {
spectrum[i].k = 1.0/ph_eV_to_lambda(eV);
@@ -568,7 +573,7 @@ struct sample *generate_SASE(struct image *image, gsl_rng *rng)
* points */
double eV_step = 6.0*sigma/(spec_size-1);
- spectrum = get_gaussian_spectrum(eV_cen, eV_step, sigma, spec_size);
+ spectrum = get_gaussian_spectrum(eV_cen, eV_step, sigma, spec_size,0);
/* Add SASE-type noise to Gaussian spectrum */
add_sase_noise(spectrum, spec_size, rng);
@@ -591,6 +596,60 @@ struct sample *generate_SASE(struct image *image, gsl_rng *rng)
return spectrum;
}
+struct sample *generate_twocolour(struct image *image)
+{
+ struct sample *spectrum;
+ struct sample *spectrum1;
+ struct sample *spectrum2;
+ int i;
+
+ double halfwidth = image->bw/2; /* eV */
+
+ const int spec_size = 1024;
+ double eV_cen1; /* Central photon energy for first colour */
+ double eV_cen2; /* Central photon energy for second colour */
+ eV_cen1 = ph_lambda_to_eV(image->lambda) - halfwidth;
+ eV_cen2 = ph_lambda_to_eV(image->lambda) + halfwidth;
+
+ /* Hard-code sigma to be 1/5 of bandwidth */
+ double sigma = image->bw/5; /* eV */
+
+ /* The spectrum will be calculated to a resolution which spreads six
+ * sigmas of the original (no SASE noise) Gaussian pulse over spec_size
+ * points */
+ double eV_start = eV_cen1 - 3*sigma;
+ double eV_end = eV_cen2 + 3*sigma;
+ double eV_step = (eV_end - eV_start)/(spec_size-1);
+
+ spectrum1 = get_gaussian_spectrum(eV_cen1, eV_step, sigma, spec_size, eV_start);
+ spectrum2 = get_gaussian_spectrum(eV_cen2, eV_step, sigma, spec_size, eV_start);
+
+ spectrum = malloc(spec_size * sizeof(struct sample));
+ if ( spectrum == NULL ) return NULL;
+
+ for ( i=0; i<spec_size; i++ ) {
+ spectrum[i].weight = spectrum1[i].weight + spectrum2[i].weight;
+ spectrum[i].k = spectrum1[i].k;
+ }
+
+ /* Normalise intensity (before taking restricted number of samples) */
+ double total_weight = 0.0;
+ for ( i=0; i<spec_size; i++ ) {
+ total_weight += spectrum[i].weight;
+ }
+
+ for ( i=0; i<spec_size; i++ ) {
+ spectrum[i].weight /= total_weight;
+ }
+
+ /* Sort samples in spectrum by weight. Diffraction calculation will
+ * take the requested number, starting from the brightest */
+ qsort(spectrum, spec_size, sizeof(struct sample), compare_samples);
+
+ image->spectrum_size = spec_size;
+
+ return spectrum;
+}
void get_diffraction(struct image *image, int na, int nb, int nc,
const double *intensities, const double *phases,
diff --git a/src/diffraction.h b/src/diffraction.h
index 5b67c198..e397bd3a 100644
--- a/src/diffraction.h
+++ b/src/diffraction.h
@@ -57,4 +57,6 @@ extern struct sample *generate_tophat(struct image *image);
extern struct sample *generate_SASE(struct image *image, gsl_rng *rng);
+extern struct sample *generate_twocolour(struct image *image);
+
#endif /* DIFFRACTION_H */
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 08fc75dd..f23be972 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -451,6 +451,11 @@ int main(int argc, char *argv[])
spectrum_type = SPECTRUM_TOPHAT;
} else if ( strcasecmp(spectrum_str, "sase") == 0) {
spectrum_type = SPECTRUM_SASE;
+ } else if ( strcasecmp(spectrum_str, "twocolour") == 0 ||
+ strcasecmp(spectrum_str, "twocolor") == 0 ||
+ strcasecmp(spectrum_str, "twocolours") == 0 ||
+ strcasecmp(spectrum_str, "twocolors") == 0) {
+ spectrum_type = SPECTRUM_TWOCOLOUR;
} else {
ERROR("Unrecognised spectrum type '%s'\n", spectrum_str);
return 1;
@@ -606,6 +611,10 @@ int main(int argc, char *argv[])
image.spectrum = generate_SASE(&image, rng);
break;
+ case SPECTRUM_TWOCOLOUR :
+ image.spectrum = generate_twocolour(&image);
+ break;
+
}
/* Ensure no residual information */