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/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef IMAGE_H
#define IMAGE_H
#include <stdint.h>
#include <complex.h>
#include <sys/types.h>
#include "utils.h"
#include "cell.h"
#include "detector.h"
#include "reflist.h"
#define MAX_CELL_CANDIDATES (32)
/* Structure describing a feature in an image */
struct imagefeature {
struct image *parent;
double fs;
double ss;
double intensity;
/* Reciprocal space coordinates (m^-1 of course) of this feature */
double rx;
double ry;
double rz;
/* Internal use only */
int valid;
const char *name;
};
/* An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
/**
* image:
*
* <programlisting>
* struct image
* {
* float *data;
* uint16_t *flags;
* double *twotheta;
*
* UnitCell *indexed_cell;
* UnitCell *candidate_cells[MAX_CELL_CANDIDATES];
* int ncells;
* struct detector *det;
* struct beam_params *beam;
* char *filename;
* const struct copy_hdf5_field *copyme;
*
* int id;
*
* double m;
*
* double lambda;
* double div;
* double bw;
* double osf;
* double profile_radius;
* int pr_dud;
* double diffracting_resolution;
*
* int width;
* int height;
*
* RefList *reflections;
*
* ImageFeatureList *features;
* };
* </programlisting>
*
* 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>candidate_cells</structfield> is an array of unit cells directly
* returned by the low-level indexing system. <structfield>ncells</structfield>
* is the number of candidate unit cells which were found. The maximum number
* of cells which may be returned is <function>MAX_CELL_CANDIDATES</function>.
* <structfield>indexed_cell</structfield> contains the "correct" unit cell
* after cell reduction or matching has been performed. The job of the cell
* reduction is to convert the list of candidate cells into a single indexed
* cell, or <function>NULL</function> on failure.
*
* <structfield>copyme</structfield> represents a list of HDF5 fields to copy
* to the output stream.
**/
struct image;
struct image {
float *data;
uint16_t *flags;
double *twotheta;
UnitCell *indexed_cell;
UnitCell *candidate_cells[MAX_CELL_CANDIDATES];
int ncells;
struct detector *det;
struct beam_params *beam; /* The nominal beam parameters */
char *filename;
const struct copy_hdf5_field *copyme;
int id; /* ID number of the thread
* handling this image */
/* Information about the crystal */
double m; /* Mosaicity in radians */
/* Per-shot radiation values */
double lambda; /* Wavelength in m */
double div; /* Divergence in radians */
double bw; /* Bandwidth as a fraction */
double osf; /* Overall scaling factor */
double profile_radius; /* Radius of reflection */
int pr_dud; /* Post refinement failed */
double diffracting_resolution; /* Max 1/d in m^-1 */
int width;
int height;
/* Integrated (or about-to-be-integrated) reflections */
RefList *reflections;
/* Detected peaks */
ImageFeatureList *features;
};
/* 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 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,
double *d, int *idx);
extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
#endif /* IMAGE_H */
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