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/*
* peaks.h
*
* Peak search and other image analysis
*
* Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2020 Thomas White <taw@physics.org>
* 2017 Valerio Mariani <valerio.mariani@desy.de>
* 2017-2018 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
*
* 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/>.
*
*/
#ifndef PEAKS_H
#define PEAKS_H
#include <pthread.h>
#include "reflist.h"
#include "crystal.h"
#include "image.h"
#include "detgeom.h"
#ifdef __cplusplus
extern "C" {
#endif
/**
* \file peaks.h
* Peak search functions
*/
enum peak_search_method {
PEAK_PEAKFINDER9,
PEAK_PEAKFINDER8,
PEAK_ZAEF,
PEAK_HDF5,
PEAK_CXI,
PEAK_MSGPACK,
PEAK_NONE,
PEAK_ERROR
};
struct peak_params {
enum peak_search_method method;
float threshold; /* zaef, pf8 */
float min_sq_gradient; /* zaef */
float min_snr; /* zaef, pf8 */
int min_pix_count; /* pf8 */
int max_pix_count; /* pf8 */
int local_bg_radius; /* pf8 */
int min_res; /* pf8 */
int max_res; /* pf8 */
int peakfinder8_fast; /* pf8 */
float min_snr_biggest_pix; /* pf9 */
float min_snr_peak_pix; /* pf9 */
float min_sig; /* pf9 */
float min_peak_over_neighbour; /* pf9 */
float pk_inn;
float pk_mid;
float pk_out;
int half_pixel_shift; /* cxi, hdf5 */
int revalidate;
int noisefilter;
int median_filter;
int check_hdf5_snr;
int use_saturated;
};
extern const char *str_peaksearch(enum peak_search_method meth);
extern enum peak_search_method parse_peaksearch(const char *arg);
extern int *make_BgMask(struct image *image, struct detgeom_panel *p,
int pn, double ir_inn);
extern ImageFeatureList *search_peaks(const struct image *image, float threshold,
float min_gradient, float min_snr, double ir_inn,
double ir_mid, double ir_out, int use_saturated);
extern ImageFeatureList *search_peaks_peakfinder9(const struct image *image,
float min_snr_biggest_pix,
float min_snr_peak_pix,
float min_snr_whole_peak, float min_sig,
float min_peak_over_neighbour,
int window_radius);
extern int indexing_peak_check(const struct image *image, ImageFeatureList *peaks,
Crystal **crystals,
int n_cryst, int multi_mode);
extern ImageFeatureList *validate_peaks(const struct image *image,
ImageFeatureList *peaks,
double min_snr,
int ir_inn, int ir_mid, int ir_out,
int use_saturated, int check_snr);
extern double estimate_peak_resolution(ImageFeatureList *peaks,
double lambda,
struct detgeom *det);
#ifdef __cplusplus
}
#endif
#endif /* PEAKS_H */
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