diff options
Diffstat (limited to 'libcrystfel/src/image.h')
| -rw-r--r-- | libcrystfel/src/image.h | 63 |
1 files changed, 22 insertions, 41 deletions
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index afa9e4a7..0d131451 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -3,11 +3,11 @@ * * Handle images and image features * - * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, - * a research centre of the Helmholtz Association. + * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. * * Authors: - * 2009-2012 Thomas White <taw@physics.org> + * 2009-2013 Thomas White <taw@physics.org> * * This file is part of CrystFEL. * @@ -41,9 +41,8 @@ #include "cell.h" #include "detector.h" #include "reflist.h" - - -#define MAX_CELL_CANDIDATES (32) +#include "crystal.h" +#include "index.h" /* Structure describing a feature in an image */ @@ -79,10 +78,10 @@ typedef struct _imagefeaturelist ImageFeatureList; * uint16_t *flags; * double *twotheta; * - * UnitCell *indexed_cell; - * UnitCell *candidate_cells[MAX_CELL_CANDIDATES]; - * int ncells; - + * Crystal **crystals; + * int n_crystals; + * IndexingMethod indexed_by; + * * struct detector *det; * struct beam_params *beam; * char *filename; @@ -90,22 +89,15 @@ typedef struct _imagefeaturelist ImageFeatureList; * * 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; - * long long unsigned int n_saturated; - * + * long long int num_peaks; + * long long int num_saturated_peaks; * ImageFeatureList *features; * }; * </programlisting> @@ -121,14 +113,9 @@ typedef struct _imagefeaturelist ImageFeatureList; * 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>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 HDF5 fields to copy * to the output stream. @@ -141,9 +128,9 @@ struct image { uint16_t *flags; double *twotheta; - UnitCell *indexed_cell; - UnitCell *candidate_cells[MAX_CELL_CANDIDATES]; - int ncells; + Crystal **crystals; + int n_crystals; + IndexingMethod indexed_by; struct detector *det; struct beam_params *beam; /* The nominal beam parameters */ @@ -153,26 +140,17 @@ struct image { 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; - long long int n_saturated; /* Number of overloads */ - /* Detected peaks */ + long long int num_peaks; + long long int num_saturated_peaks; ImageFeatureList *features; }; @@ -196,4 +174,7 @@ extern struct imagefeature *image_feature_closest(ImageFeatureList *flist, extern int image_feature_count(ImageFeatureList *flist); extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx); +extern void image_add_crystal(struct image *image, Crystal *cryst); +extern void free_all_crystals(struct image *image); + #endif /* IMAGE_H */ |