diff options
| -rw-r--r-- | libcrystfel/src/image.h | 6 | ||||
| -rw-r--r-- | libcrystfel/src/utils.h | 2 | ||||
| -rw-r--r-- | src/diffraction.c | 34 | ||||
| -rw-r--r-- | src/diffraction.h | 3 | ||||
| -rw-r--r-- | src/pattern_sim.c | 17 |
5 files changed, 60 insertions, 2 deletions
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index dffcdb3a..29ce8ae1 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -60,6 +60,7 @@ struct imagefile_field_list; * @SPECTRUM_TOPHAT: A top hat distribution of wavelengths * @SPECTRUM_SASE: A simulated SASE spectrum * @SPECTRUM_TWOCOLOUR: A spectrum containing two peaks + * @SPECTRUM_FROMFILE: An arbitrary spectrum read from input file * * A %SpectrumType represents a type of X-ray energy spectrum to use for * generating simulated data. @@ -67,7 +68,8 @@ struct imagefile_field_list; typedef enum { SPECTRUM_TOPHAT, SPECTRUM_SASE, - SPECTRUM_TWOCOLOUR + SPECTRUM_TWOCOLOUR, + SPECTRUM_FROMFILE } SpectrumType; @@ -124,7 +126,7 @@ typedef struct _imagefeaturelist ImageFeatureList; /* Structure describing a wavelength sample from a spectrum */ struct sample { - double k; + double k; /* 1/m */ double weight; }; diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h index a759ff15..2c756ad7 100644 --- a/libcrystfel/src/utils.h +++ b/libcrystfel/src/utils.h @@ -185,6 +185,8 @@ static inline int within_tolerance(double a, double b, double percent) /* Photon energy (eV) to wavelength (m) */ #define ph_eV_to_lambda(a) ph_en_to_lambda(eV_to_J(a)) +/* Photon energy (eV) to k (1/m) */ +#define ph_eV_to_k(a) ((a)*ELECTRON_CHARGE/PLANCK/C_VACUO) /* ------------------------------ Message macros ---------------------------- */ diff --git a/src/diffraction.c b/src/diffraction.c index 4cceba0e..97750f58 100644 --- a/src/diffraction.c +++ b/src/diffraction.c @@ -608,6 +608,40 @@ struct sample *generate_tophat(struct image *image) } +struct sample *generate_spectrum_fromfile(struct image *image, + char *spectrum_fn) +{ + struct sample *spectrum; + int i; + double k, w; + double w_sum = 0; + + spectrum = malloc(image->nsamples * sizeof(struct sample)); + if ( spectrum == NULL ) return NULL; + + FILE *f; + f = fopen(spectrum_fn, "r"); + + int nsamples = 0; + for ( i=0; i<image->nsamples; i++ ) { + if (fscanf(f, "%lf %lf", &k, &w) != EOF) { + spectrum[i].k = ph_eV_to_k(k); + spectrum[i].weight = w; + w_sum += w; + nsamples += 1; + } else break; + } + + for ( i=0; i<nsamples; i++ ) { + spectrum[i].weight /= w_sum; + } + + image->spectrum_size = nsamples; + + return spectrum; +} + + struct sample *generate_SASE(struct image *image, gsl_rng *rng) { struct sample *spectrum; diff --git a/src/diffraction.h b/src/diffraction.h index ca4e3bde..0f95f83c 100644 --- a/src/diffraction.h +++ b/src/diffraction.h @@ -60,4 +60,7 @@ extern struct sample *generate_SASE(struct image *image, gsl_rng *rng); extern struct sample *generate_twocolour(struct image *image); +extern struct sample *generate_spectrum_fromfile(struct image *image, + char *spectrum_fn); + #endif /* DIFFRACTION_H */ diff --git a/src/pattern_sim.c b/src/pattern_sim.c index 6c9eb880..d47c4b60 100644 --- a/src/pattern_sim.c +++ b/src/pattern_sim.c @@ -368,6 +368,7 @@ int main(int argc, char *argv[]) char *outfile = NULL; char *geometry = NULL; char *spectrum_str = NULL; + char *spectrum_fn = NULL; GradientMethod grad; SpectrumType spectrum_type; int ndone = 0; /* Number of simulations done (images or not) */ @@ -429,6 +430,7 @@ int main(int argc, char *argv[]) {"photon-energy", 1, NULL, 9}, {"nphotons", 1, NULL, 10}, {"beam-radius", 1, NULL, 11}, + {"spectrum-file", 1, NULL, 12}, {0, 0, NULL, 0} }; @@ -590,6 +592,9 @@ int main(int argc, char *argv[]) } break; + case 12 : + spectrum_fn = strdup(optarg); + break; case 0 : break; @@ -695,6 +700,8 @@ int main(int argc, char *argv[]) strcasecmp(spectrum_str, "twocolours") == 0 || strcasecmp(spectrum_str, "twocolors") == 0) { spectrum_type = SPECTRUM_TWOCOLOUR; + } else if ( strcasecmp(spectrum_str, "fromfile") == 0) { + spectrum_type = SPECTRUM_FROMFILE; } else { ERROR("Unrecognised spectrum type '%s'\n", spectrum_str); return 1; @@ -855,6 +862,11 @@ int main(int argc, char *argv[]) STATUS(" X-ray spectrum: two colour, " "separation %.5f %%\n", image.bw*100.0); break; + + case SPECTRUM_FROMFILE: + STATUS(" X-ray spectrum: from %s\n", + spectrum_fn); + break; } if ( random_size ) { STATUS(" Crystal size: random, between " @@ -977,6 +989,11 @@ int main(int argc, char *argv[]) image.spectrum = generate_twocolour(&image); break; + case SPECTRUM_FROMFILE : + image.spectrum = generate_spectrum_fromfile(&image, + spectrum_fn); + break; + } cell_get_parameters(cell, &a, &b, &c, &d, &d, &d); |