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/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2017 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"
/**
* SpectrumType:
* @SPECTRUM_TOPHAT: A top hat distribution of wavelengths
* @SPECTRUM_SASE: A simulated SASE spectrum
* @SPECTRUM_TWOCOLOUR: A spectrum containing two peaks
*
* A %SpectrumType represents a type of X-ray energy spectrum to use for
* generating simulated data.
**/
typedef enum {
SPECTRUM_TOPHAT,
SPECTRUM_SASE,
SPECTRUM_TWOCOLOUR
} SpectrumType;
/**
* imagefeature:
* @parent: Image this feature belongs to
* @fs: Fast scan coordinate
* @ss: Slow scan coordinate
* @p: Pointer to panel
* @intensity: Intensity of peak
* @rx: Reciprocal x coordinate in m^-1
* @ry: Reciprocal y coordinate in m^-1
* @rz: Reciprocal z coordinate in m^-1
* @name: Text name for feature
*
* Represents a peak in an image.
*
* Note carefully that the @fs and @ss coordinates 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.
*/
struct imagefeature {
struct image *parent;
double fs;
double ss;
struct panel *p;
double intensity;
/* Reciprocal space coordinates (m^-1 of course) of this feature */
double rx;
double ry;
double rz;
const char *name;
/*< private >*/
int valid;
};
/* An enum representing the image file formats we can handle */
enum imagefile_type
{
IMAGEFILE_HDF5,
IMAGEFILE_CBF
};
/* An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
/* Structure describing a wavelength sample from a spectrum */
struct sample
{
double k;
double weight;
};
/**
* beam_params:
* @photon_energy: eV per photon
* @photon_energy_from: HDF5 dataset name
* @photon_energy_scale: Scale factor for photon energy, if it comes from HDF5
*/
struct beam_params
{
double photon_energy;
char *photon_energy_from;
double photon_energy_scale;
};
/**
* image:
* @crystals: Array of crystals in the image
* @n_crystals: The number of crystals in the image
* @indexed_by: Indexing method which indexed this pattern
* @det: Detector structure
* @beam: Beam parameters structure
* @filename: Filename for the image file
* @copyme: Fields to copy from the image file to the stream
* @id: ID number of the thread handling this image
* @serial: Serial number for this image
* @lambda: Wavelength
* @div: Divergence
* @bw: Bandwidth
* @num_peaks: The number of peaks
* @num_saturated_peaks: The number of saturated peaks
* @features: The peaks found in the image
* @dp: The image data, by panel
* @bad: The bad pixel mask, array by panel
* @sat: The per-pixel saturation mask, array by panel
* @event: Event ID for the image
* @stuff_from_stream: Items read back from the stream
* @avg_clen: Mean of camera length values for all panels
* @spectrum: Spectrum information
* @nsamples: Number of spectrum samples
* @spectrum_size: SIze of spectrum array
*
* The field <structfield>data</structfield> contains the raw image data, if it
* is currently available. The data might be available throughout the
* processing of an experimental pattern, but it might not be available when
* simulating, scaling or merging patterns. Similarly,
* <structfield>flags</structfield> contains an array of the same dimensions
* as <structfield>data</structfield> to contain the bad pixel flags.
* <structfield>twotheta</structfield> likewise contains an array of 2*theta
* (scattering angle) values in radians, since these values are generated as a
* by-product of the scattering vector calculation and can be used later for
* calculating intensities from differential scattering cross sections.
*
* <structfield>crystals</structfield> is an array of %Crystal directly
* returned by the low-level indexing system. <structfield>n_crystals</structfield>
* is the number of crystals which were found in the image.
*
* <structfield>copyme</structfield> represents a list of fields in the image
* file (e.g. HDF5 fields or CBF headers) to copy to the output stream.
**/
struct image;
struct image {
float **dp; /* Data in panel */
int **bad; /* Bad pixels by panel */
float **sat; /* Per-pixel saturation values */
Crystal **crystals;
int n_crystals;
IndexingMethod indexed_by;
struct detector *det;
struct beam_params *beam; /* The nominal beam parameters */
char *filename;
struct event *event;
const struct imagefile_field_list *copyme;
struct stuff_from_stream *stuff_from_stream;
double avg_clen; /* Average camera length extracted
* from stuff_from_stream */
int id; /* ID number of the thread
* handling this image */
int serial; /* Monotonically ascending serial
* number for this image */
struct sample *spectrum;
int nsamples; /* Number of wavelengths */
int spectrum_size; /* Size of "spectrum" */
/* Per-shot radiation values */
double lambda; /* Wavelength in m */
double div; /* Divergence in radians */
double bw; /* Bandwidth as a fraction */
/* Detected peaks */
long long num_peaks;
long long num_saturated_peaks;
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,
struct panel *p,
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,
struct panel *p,
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 ImageFeatureList *sort_peaks(ImageFeatureList *flist);
extern void image_add_crystal(struct image *image, Crystal *cryst);
extern void remove_flagged_crystals(struct image *image);
extern void free_all_crystals(struct image *image);
/* Image files */
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);
/* 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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