aboutsummaryrefslogtreecommitdiff
path: root/src/image.h
blob: 781944331c881c7641029b60c589d4b176b2ce85 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
/*
 * image.h
 *
 * Handle images and image features
 *
 * (c) 2006-2010 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 <glib.h>

#include "utils.h"
#include "cell.h"
#include "detector.h"


/* How is the scaling of the image described? */
typedef enum {
	FORMULATION_CLEN,
	FORMULATION_PIXELSIZE
} FormulationMode;


/* Structure describing a feature in an image */
struct imagefeature {

	struct image			*parent;
	double				x;
	double				y;
	double				intensity;

	/* Partner for this feature (in another feature list) or NULL */
	struct imagefeature_struct	*partner;

	/* Distance between this feature and its partner, if any. */
	double				partner_d;

	/* Reciprocal space coordinates (m^-1 of course) of this feature */
	double				rx;
	double				ry;
	double				rz;

	/* Internal use only */
	int				valid;

};

/* An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;


/* A 3D vector in reciprocal space */
struct rvec
{
	double   u;
	double   v;
	double   w;
};


/* Structure describing an image */
struct image {

	int			*hdr;      /* Actual counts */
	int16_t			*data;     /* Integer counts after bloom */
	double complex		*sfacs;
	double			*twotheta;
	struct molecule		*molecule;
	UnitCell		*indexed_cell;
	struct detector		det;

	struct quaternion	orientation;

	/* Image parameters can be given as camera length or pixel size.
	 * If FORMULATION_CLEN, then camera_len and resolution must be given.
	 * If FORMULATION_PIXELSIZE, then pixel_size only is needed.*/
	FormulationMode		fmode;
	double			pixel_size;
	float			camera_len;
	float			resolution;	/* pixels per metre */

	/* Wavelength must always be given */
	double			lambda;		/* Wavelength in m */

	int			width;
	int			height;
	double			x_centre;
	double			y_centre;

	ImageFeatureList	*features;	/* "Experimental" features */
	ImageFeatureList	*rflist;	/* "Predicted" features */

	/* DirAx auto-indexing low-level stuff */
	GIOChannel		*dirax;
	int			dirax_pty;
	pid_t			dirax_pid;
	char			*dirax_rbuffer;
	int			dirax_rbufpos;
	int			dirax_rbuflen;
	GMainLoop		*dirax_ml;

	/* DirAx auto-indexing high-level stuff */
	int			dirax_step;
	int			dirax_read_cell;
};

/* An opaque type representing a list of images */
typedef struct _imagelist ImageList;


/* Image lists */
extern ImageList *image_list_new(void);

extern int image_add(ImageList *list, struct image *image);


/* 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);

extern void image_remove_feature(ImageFeatureList *flist, int idx);

extern struct imagefeature *image_feature_closest(ImageFeatureList *flist,
                                                  double x, double y, double *d,
                                                  int *idx);

extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);

#endif	/* IMAGE_H */