From 53382f60c7f8955c016725885c04f510f7fe96ee Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 6 Feb 2013 19:15:06 +0100 Subject: Stuff for partial_sim --- src/partial_sim.c | 66 +++++++++++++++++++++++++++++++++---------------------- 1 file changed, 40 insertions(+), 26 deletions(-) diff --git a/src/partial_sim.c b/src/partial_sim.c index facf14ef..4e96fbbc 100644 --- a/src/partial_sim.c +++ b/src/partial_sim.c @@ -54,11 +54,12 @@ #define NBINS 50 -static void mess_up_cell(UnitCell *cell, double cnoise) +static void mess_up_cell(Crystal *cr, double cnoise) { double ax, ay, az; double bx, by, bz; double cx, cy, cz; + UnitCell *cell = crystal_get_cell(cr); //STATUS("Real:\n"); //cell_print(cell); @@ -82,17 +83,18 @@ static void mess_up_cell(UnitCell *cell, double cnoise) /* For each reflection in "partial", fill in what the intensity would be * according to "full" */ -static void calculate_partials(RefList *partial, double osf, +static void calculate_partials(Crystal *cr, RefList *full, const SymOpList *sym, int random_intensities, pthread_mutex_t *full_lock, unsigned long int *n_ref, double *p_hist, - double *p_max, double max_q, UnitCell *cell) + double *p_max, double max_q) { Reflection *refl; RefListIterator *iter; + double res; - for ( refl = first_refl(partial, &iter); + for ( refl = first_refl(crystal_get_reflections(cr), &iter); refl != NULL; refl = next_refl(refl, iter) ) { @@ -137,16 +139,17 @@ static void calculate_partials(RefList *partial, double osf, } } - Ip = osf * p * If; + Ip = crystal_get_osf(cr) * p * If; - bin = NBINS*2.0*resolution(cell, h, k, l) / max_q; + res = resolution(crystal_get_cell(cr), h, k, l); + bin = NBINS*2.0*res/max_q; if ( (bin < NBINS) && (bin>=0) ) { p_hist[bin] += p; n_ref[bin]++; if ( p > p_max[bin] ) p_max[bin] = p; } else { STATUS("Reflection out of histogram range: %e %i %f\n", - resolution(cell, h, k, l), bin, p); + res, bin, p); } Ip = gaussian_noise(Ip, 100.0); @@ -206,13 +209,14 @@ struct queue_args unsigned long int n_ref[NBINS]; double p_max[NBINS]; - FILE *stream; + Stream *stream; }; struct worker_args { struct queue_args *qargs; + Crystal *crystal; struct image image; /* Histogram for this image */ @@ -243,21 +247,34 @@ static void *create_job(void *vqargs) static void run_job(void *vwargs, int cookie) { - double osf; struct quaternion orientation; struct worker_args *wargs = vwargs; struct queue_args *qargs = wargs->qargs; int i; + Crystal *cr; + UnitCell *cell; + RefList *reflections; + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to create crystal.\n"); + return; + } + wargs->crystal = cr; + crystal_set_image(cr, &wargs->image); - osf = gaussian_noise(1.0, 0.3); + crystal_set_osf(cr, gaussian_noise(1.0, 0.3)); + crystal_set_profile_radius(cr, wargs->image.beam->profile_radius); /* Set up a random orientation */ orientation = random_quaternion(); - wargs->image.indexed_cell = cell_rotate(qargs->cell, orientation); + cell = cell_rotate(qargs->cell, orientation); + crystal_set_cell(cr, cell); + cell_free(cell); snprintf(wargs->image.filename, 255, "dummy.h5"); - wargs->image.reflections = find_intersections(&wargs->image, - wargs->image.indexed_cell); + reflections = find_intersections(&wargs->image, cr); + crystal_set_reflections(cr, reflections); for ( i=0; in_ref[i] = 0; @@ -265,14 +282,14 @@ static void run_job(void *vwargs, int cookie) wargs->p_max[i] = 0.0; } - calculate_partials(wargs->image.reflections, osf, qargs->full, + calculate_partials(cr, qargs->full, qargs->sym, qargs->random_intensities, &qargs->full_lock, wargs->n_ref, wargs->p_hist, wargs->p_max, - qargs->max_q, wargs->image.indexed_cell); + qargs->max_q); /* Give a slightly incorrect cell in the stream */ - mess_up_cell(wargs->image.indexed_cell, qargs->cnoise); + mess_up_cell(cr, qargs->cnoise); } @@ -282,7 +299,7 @@ static void finalise_job(void *vqargs, void *vwargs) struct queue_args *qargs = vqargs; int i; - write_chunk(qargs->stream, &wargs->image, NULL, STREAM_INTEGRATED); + write_chunk(qargs->stream, &wargs->image, NULL, 0, 1); for ( i=0; in_ref[i] += wargs->n_ref[i]; @@ -295,8 +312,7 @@ static void finalise_job(void *vqargs, void *vwargs) qargs->n_done++; progress_bar(qargs->n_done, qargs->n_to_do, "Simulating"); - reflist_free(wargs->image.reflections); - cell_free(wargs->image.indexed_cell); + crystal_free(wargs->crystal); free(wargs); } @@ -315,7 +331,7 @@ int main(int argc, char *argv[]) char *sym_str = NULL; SymOpList *sym; UnitCell *cell = NULL; - FILE *ofh; + Stream *stream; int n = 2; int random_intensities = 0; char *save_file = NULL; @@ -496,13 +512,12 @@ int main(int argc, char *argv[]) ERROR("You must give a filename for the output.\n"); return 1; } - ofh = fopen(output_file, "w"); - if ( ofh == NULL ) { + stream = open_stream_for_write(output_file); + if ( stream == NULL ) { ERROR("Couldn't open output file '%s'\n", output_file); return 1; } free(output_file); - write_stream_header(ofh, argc, argv); image.det = det; image.width = det->max_fs; @@ -511,7 +526,6 @@ int main(int argc, char *argv[]) image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy)); image.div = beam->divergence; image.bw = beam->bandwidth; - image.profile_radius = beam->profile_radius; image.filename = malloc(256); image.copyme = NULL; @@ -528,7 +542,7 @@ int main(int argc, char *argv[]) qargs.random_intensities = random_intensities; qargs.cell = cell; qargs.template_image = ℑ - qargs.stream = ofh; + qargs.stream = stream; qargs.cnoise = cnoise; qargs.max_q = largest_q(&image); @@ -574,7 +588,7 @@ int main(int argc, char *argv[]) } - fclose(ofh); + close_stream(stream); cell_free(cell); free_detector_geometry(det); free(beam); -- cgit v1.2.3