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Diffstat (limited to 'libcrystfel/src/image.h')
| -rw-r--r-- | libcrystfel/src/image.h | 184 |
1 files changed, 184 insertions, 0 deletions
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h new file mode 100644 index 00000000..4d4ac2d7 --- /dev/null +++ b/libcrystfel/src/image.h @@ -0,0 +1,184 @@ +/* + * image.h + * + * Handle images and image features + * + * (c) 2006-2011 Thomas White <taw@physics.org> + * + * Part of CrystFEL - crystallography with a FEL + * + */ + + +#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 i0; + * int i0_available; + * double osf; + * double profile_radius; + * int pr_dud; + * + * 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 i0; /* Incident intensity */ + int i0_available; /* 0 if f0 wasn't available + * from the input. */ + double osf; /* Overall scaling factor */ + double profile_radius; /* Radius of reflection */ + int pr_dud; /* Post refinement failed */ + + 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 */ |