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/*
* prof2d_check.c
*
* Check 2D profile fitting
*
* Copyright © 2013-2020 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2013-2020 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <stdlib.h>
#include <stdio.h>
#include <image.h>
#include <utils.h>
#include <cell.h>
#include <cell-utils.h>
#include <geometry.h>
#include <integration.h>
#include "histogram.h"
void integrate_prof2d(IntegrationMethod meth,
Crystal *cr, RefList *list,
struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
pthread_mutex_t *term_lock, int **masks);
#define ADD_PX(fs, ss, val) \
if ( ((fs)>0) && ((ss)>0) && ((fs)<w) && ((ss)<h) ) { \
image.dp[0][(fs)+w*(ss)] += (val); \
}
int main(int argc, char *argv[])
{
struct image image;
int fs, ss;
FILE *fh;
unsigned long int seed;
int fail = 0;
const int w = 1024;
const int h = 1024;
RefList *list;
RefListIterator *iter;
Reflection *refl;
UnitCell *cell;
Crystal *cr;
const int ir_inn = 2;
const int ir_mid = 4;
const int ir_out = 6;
Histogram *hi;
double esd_sum = 0.0;
int n = 0;
int n_strong = 0;
int n_weak = 0;
gsl_rng *rng;
rng = gsl_rng_alloc(gsl_rng_mt19937);
fh = fopen("/dev/urandom", "r");
if ( fread(&seed, sizeof(seed), 1, fh) == 1 ) {
gsl_rng_set(rng, seed);
} else {
ERROR("Failed to seed RNG\n");
}
fclose(fh);
image.lambda = ph_eV_to_lambda(9000.0);
image.bw = 0.000001;
image.div = 0.0;
image.spectrum = spectrum_generate_gaussian(image.lambda, image.bw);
image.detgeom = calloc(1, sizeof(struct detgeom));
image.detgeom->n_panels = 1;
image.detgeom->panels = calloc(1, sizeof(struct detgeom_panel));
image.dp = calloc(1, sizeof(float *));
image.bad = calloc(1, sizeof(int *));
image.detgeom->panels[0].w = w;
image.detgeom->panels[0].h = h;
image.detgeom->panels[0].fsx = 1.0;
image.detgeom->panels[0].fsy = 0.0;
image.detgeom->panels[0].ssx = 0.0;
image.detgeom->panels[0].ssy = 1.0;
image.detgeom->panels[0].cnx = -w/2;
image.detgeom->panels[0].cny = -h/2;
image.detgeom->panels[0].cnz = 60.0e-3 / 100e-6;
image.detgeom->panels[0].pixel_pitch = 100e-6; /* 10 px per mm */
image.detgeom->panels[0].adu_per_photon = 10.0;
image.detgeom->panels[0].max_adu = +INFINITY; /* No cutoff */
image.dp[0] = malloc(w*h*sizeof(float));
memset(image.dp[0], 0, w*h*sizeof(float));
image.bad[0] = malloc(w*h*sizeof(int));
memset(image.bad[0], 0, w*h*sizeof(int));
image.sat = NULL;
cell = cell_new();
cell_set_lattice_type(cell, L_CUBIC);
cell_set_centering(cell, 'P');
cell_set_parameters(cell, 200.0e-10, 200.0e-10, 200.0e-10,
deg2rad(90.0), deg2rad(90.0), deg2rad(90.0));
cell = cell_rotate(cell, random_quaternion(rng));
cr = crystal_new();
crystal_set_profile_radius(cr, 0.001e9);
crystal_set_mosaicity(cr, 0.0); /* radians */
crystal_set_cell(cr, cell);
image.crystals = NULL;
image.n_crystals = 0;
list = predict_to_res(cr, &image, detgeom_max_resolution(image.detgeom,
image.lambda));
image_add_crystal_refls(&image, cr, list);
for ( fs=0; fs<w; fs++ ) {
for ( ss=0; ss<h; ss++ ) {
image.dp[0][fs+w*ss] = 10.0*poisson_noise(rng, 40);
}
}
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
double pfs, pss;
int fs, ss;
signed int hj, kj, lj;
get_detector_pos(refl, &pfs, &pss);
fs = pfs; ss = pss;
get_indices(refl, &hj, &kj, &lj);
if ( lj % 2 ) {
const int pk_ph = 1000;
ADD_PX(fs, ss, 10.0*poisson_noise(rng, pk_ph));
ADD_PX(fs-1, ss, 10.0*poisson_noise(rng, pk_ph));
ADD_PX(fs+1, ss, 10.0*poisson_noise(rng, pk_ph));
ADD_PX(fs, ss-1, 10.0*poisson_noise(rng, pk_ph));
ADD_PX(fs, ss+1, 10.0*poisson_noise(rng, pk_ph));
n_strong++;
} else {
/* Absent peak */
n_weak++;
}
}
STATUS("%i strong, %i weak\n", n_strong, n_weak);
integrate_prof2d(INTEGRATION_PROF2D, cr, list, &image,
INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out, 0,
NULL);
printf("Weak reflections:\n");
hi = histogram_init();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
get_indices(refl, &h, &k, &l);
if ( get_redundancy(refl) == 0 ) continue;
if ( l % 2 ) continue; /* Ignore strong reflections */
histogram_add_value(hi, get_intensity(refl));
esd_sum += get_esd_intensity(refl);
n++;
}
printf("Mean calculated sigma(I) = %.2f (%i measurements)\n",
esd_sum / n, n);
histogram_show(hi);
histogram_free(hi);
printf("Strong reflections:\n");
hi = histogram_init();
esd_sum = 0.0;
n = 0;
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
get_indices(refl, &h, &k, &l);
if ( get_redundancy(refl) == 0 ) continue;
if ( l % 2 == 0 ) continue; /* Ignore weak reflections */
histogram_add_value(hi, get_intensity(refl));
esd_sum += get_esd_intensity(refl);
n++;
}
printf("Mean calculated sigma(I) = %.2f (%i measurements)\n",
esd_sum / n, n);
histogram_show(hi);
histogram_free(hi);
detgeom_free(image.detgeom);
free(image.dp[0]);
free(image.dp);
gsl_rng_free(rng);
if ( fail ) return 1;
return 0;
}
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