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/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2019 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
*
*
* 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef IMAGE_H
#define IMAGE_H
struct detector;
#include <stdint.h>
#include <complex.h>
#include <sys/types.h>
struct imagefeature;
struct sample;
struct image;
struct imagefile;
struct imagefile_field_list;
#include "utils.h"
#include "cell.h"
#include "detector.h"
#include "reflist.h"
#include "crystal.h"
#include "index.h"
#include "events.h"
#include "spectrum.h"
#include "datatemplate.h"
/**
* \file image.h
*
* Information about images
*/
/** Represents a peak in an image. */
struct imagefeature {
/** \name Coordinates on panel (fast scan, slow scan)
* Note carefully that these are the distances, measured in pixels,
* from the corner of the panel. They are NOT pixel indices.
* If the peak is in the middle of the first pixel, its coordinates would be
* 0.5,0.5. */
/**@{*/
double fs;
double ss;
/**@}*/
int pn; /**< Panel number */
double intensity; /**< Intensity */
/** \name Reciprocal space coordinates (m^-1) of this feature */
/** @{ */
double rx;
double ry;
double rz;
/** @} */
const char *name; /**< Text name, e.g. "5,3,-1" */
};
/** An enum representing the image file formats we can handle */
enum imagefile_type
{
IMAGEFILE_HDF5, /**< HDF5 file (single or multiple frames per file) */
IMAGEFILE_CBF, /**< CBF file */
IMAGEFILE_CBFGZ /**< gzipped CBF file, i.e. "file.cbf.gz" */
};
/** An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
struct beam_params
{
double photon_energy; /**< eV per photon */
char *photon_energy_from; /**< HDF5 dataset name */
double photon_energy_scale; /**< Scale factor for photon energy, if it
* comes from an image header */
double bandwidth; /**< FWHM bandwidth as a fraction of
* wavelength */
};
struct image
{
/** The image data, by panel */
float **dp;
/** The bad pixel mask, by panel */
int **bad;
/** The per-pixel saturation values, by panel */
float **sat;
/** Non-zero if the frame was determined to be a "hit" */
int hit;
/**Array of crystals in the image */
Crystal **crystals;
/** The number of crystals in the image (size of \p crystals) */
int n_crystals;
/** Indexing method which indexed this pattern */
IndexingMethod indexed_by;
/** Number of times the indexer was tried before succeeding */
int n_indexing_tries;
/** The detector structure
* @{ */
struct detgeom *detgeom;
struct detector *det; /* FIXME: Deprecated */
/** @} */
/** The nominal beam parameters (or where to get them) */
struct beam_params *beam; /* FIXME: Deprecated */
/** \name The filename and event ID for the image
* @{ */
char *filename;
char *ev;
/** @} */
/** A list of image file headers to copy to the stream */
const struct imagefile_field_list *copyme;
/** A list of metadata read from the stream */
struct stuff_from_stream *stuff_from_stream;
/** Mean of the camera length values for all panels */
double avg_clen;
/** ID number of the worker processing handling this image */
int id;
/** Monotonically increasing serial number for this image */
int serial;
/** Spectrum information */
Spectrum *spectrum;
/** Wavelength of the incident radiation, in metres */
double lambda;
/** Convergence angle of the incident ration, in radians (full angle) */
double div;
/** Full-width half-maximum bandwidth as a fraction, applied to wavelength */
double bw;
/** Resolution estimate based on peaks */
double peak_resolution;
/** List of peaks found in the image */
ImageFeatureList *features;
};
#ifdef __cplusplus
extern "C" {
#endif
/* Feature lists */
extern ImageFeatureList *image_feature_list_new(void);
extern void image_feature_list_free(ImageFeatureList *flist);
extern void image_add_feature(ImageFeatureList *flist, double x, double y,
int pn,
struct image *parent, double intensity,
const char *name);
extern void image_remove_feature(ImageFeatureList *flist, int idx);
extern struct imagefeature *image_feature_closest(ImageFeatureList *flist,
double fs, double ss,
int pn,
double *d, int *idx);
extern Reflection *image_reflection_closest(RefList *rlist,
double fs, double ss,
struct panel *p,
struct detector *det,
double *d);
extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
extern const struct imagefeature *image_get_feature_const(const ImageFeatureList *flist,
int idx);
extern ImageFeatureList *sort_peaks(ImageFeatureList *flist);
extern ImageFeatureList *image_feature_list_copy(const ImageFeatureList *flist);
extern void image_add_crystal(struct image *image, Crystal *cryst);
extern int remove_flagged_crystals(struct image *image);
extern void free_all_crystals(struct image *image);
/* Image files (old API) */
extern struct imagefile *imagefile_open(const char *filename);
extern int imagefile_read(struct imagefile *f, struct image *image,
struct event *event);
extern int imagefile_read_simple(struct imagefile *f, struct image *image);
extern struct hdfile *imagefile_get_hdfile(struct imagefile *f);
extern enum imagefile_type imagefile_get_type(struct imagefile *f);
extern void imagefile_copy_fields(struct imagefile *f,
const struct imagefile_field_list *copyme,
FILE *fh, struct event *ev);
extern void imagefile_close(struct imagefile *f);
extern signed int is_cbf_file(const char *filename);
/* New API */
extern struct image *image_new(void);
extern struct image *image_read(DataTemplate *dtempl, const char *filename,
const char *event);
extern void image_free(struct image *image);
extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
const char *filename,
const char *event,
int half_pixel_shift);
extern struct event_list *image_expand_frames(const DataTemplate *dtempl,
const char *filename);
/* Field lists */
extern struct imagefile_field_list *new_imagefile_field_list(void);
extern void free_imagefile_field_list(struct imagefile_field_list *f);
extern void add_imagefile_field(struct imagefile_field_list *copyme,
const char *name);
#ifdef __cplusplus
}
#endif
#endif /* IMAGE_H */
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