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/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2021 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/>.
*
*/
#ifndef IMAGE_H
#define IMAGE_H
#include <stdint.h>
#include <complex.h>
#include <sys/types.h>
struct imagefeature;
struct image;
#include "utils.h"
#include "cell.h"
#include "reflist.h"
#include "crystal.h"
#include "index.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 */
const char *name; /**< Text name, e.g. "5,3,-1" */
};
/** An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
typedef struct _image_data_arrays ImageDataArrays;
#define HEADER_CACHE_SIZE (128)
typedef enum
{
HEADER_FLOAT,
HEADER_INT,
HEADER_STR
} HeaderCacheType;
struct header_cache_entry {
char *header_name;
HeaderCacheType type;
union {
int val_int;
double val_float;
char *val_str;
};
};
typedef enum
{
DATA_SOURCE_TYPE_UNKNOWN,
DATA_SOURCE_TYPE_NONE,
DATA_SOURCE_TYPE_HDF5,
DATA_SOURCE_TYPE_CBF,
DATA_SOURCE_TYPE_CBFGZ,
DATA_SOURCE_TYPE_MSGPACK,
DATA_SOURCE_TYPE_SEEDEE
} DataSourceType;
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;
DataSourceType data_source_type;
/** \name The filename and event ID for the image
* @{ */
char *filename;
char *ev;
/** @} */
/** The data block, e.g. received over ZMQ, for the image.
* filenename/ev OR this should be filled in, but not both */
void *data_block;
size_t data_block_size;
char *meta_data;
/** A list of metadata read from the stream */
struct header_cache_entry *header_cache[HEADER_CACHE_SIZE];
int n_cached_headers;
/** 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;
/** Re-usable data array structure, or NULL if not used */
ImageDataArrays *ida;
};
#ifdef __cplusplus
extern "C" {
#endif
/* File classifiers */
extern int is_hdf5_file(const char *filename, int *err);
extern int is_cbf_file(const char *filename, int *err);
extern int is_cbfgz_file(const char *filename, int *err);
/* 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 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);
extern void mark_resolution_range_as_bad(struct image *image,
double min, double max);
extern struct image *image_new(void);
extern struct image *image_read(const DataTemplate *dtempl,
const char *filename,
const char *event,
int no_image_data,
int no_mask_data,
ImageDataArrays *ida);
extern struct image *image_create_for_simulation(const DataTemplate *dtempl);
extern struct image *image_read_data_block(const DataTemplate *dtempl,
void *data_block,
size_t data_block_size,
char *meta_data,
DataSourceType type,
int serial,
int no_image_data,
int no_mask_data,
ImageDataArrays *ida);
extern void image_free(struct image *image);
extern int image_read_header_float(struct image *image, const char *from,
double *val);
/* NB image_read_header_int and image_read_header_str should exist, but there
* is currently no use for them. Get in touch if you disagree! */
extern void image_cache_header_float(struct image *image,
const char *header_name,
double header_val);
extern void image_cache_header_int(struct image *image,
const char *header_name,
int header_val);
extern void image_cache_header_str(struct image *image,
const char *header_name,
const char *header_val);
extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
const char *filename,
const char *event,
int half_pixel_shift);
extern char **image_expand_frames(const DataTemplate *dtempl,
const char *filename, int *nframes);
extern ImageDataArrays *image_data_arrays_new(void);
extern void image_data_arrays_free(ImageDataArrays *ida);
extern int image_create_dp_bad(struct image *image,
const DataTemplate *dtempl);
extern int image_set_zero_data(struct image *image,
const DataTemplate *dtempl);
#ifdef __cplusplus
}
#endif
#endif /* IMAGE_H */
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