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-rw-r--r--src/image.c144
-rw-r--r--src/image.h184
2 files changed, 0 insertions, 328 deletions
diff --git a/src/image.c b/src/image.c
deleted file mode 100644
index 75a8af0a..00000000
--- a/src/image.c
+++ /dev/null
@@ -1,144 +0,0 @@
-/*
- * image.c
- *
- * Handle images and image features
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#include <stdlib.h>
-#include <assert.h>
-#include <math.h>
-#include <stdio.h>
-
-#include "image.h"
-#include "utils.h"
-
-/**
- * SECTION:image
- * @short_description: Data structure representing an image
- * @title: Image
- * @section_id:
- * @see_also:
- * @include: "image.h"
- * @Image:
- *
- * The <structname>image</structname> structure represents an image, usually one
- * frame from a large series of diffraction patterns, which might be from the
- * same or different crystals.
- */
-
-
-struct _imagefeaturelist
-{
- struct imagefeature *features;
- int n_features;
-};
-
-
-void image_add_feature(ImageFeatureList *flist, double fs, double ss,
- struct image *parent, double intensity, const char *name)
-{
- if ( flist->features ) {
- flist->features = realloc(flist->features,
- (flist->n_features+1)
- *sizeof(struct imagefeature));
- } else {
- assert(flist->n_features == 0);
- flist->features = malloc(sizeof(struct imagefeature));
- }
-
- flist->features[flist->n_features].fs = fs;
- flist->features[flist->n_features].ss = ss;
- flist->features[flist->n_features].intensity = intensity;
- flist->features[flist->n_features].parent = parent;
- flist->features[flist->n_features].name = name;
- flist->features[flist->n_features].valid = 1;
-
- flist->n_features++;
-
-}
-
-
-ImageFeatureList *image_feature_list_new()
-{
- ImageFeatureList *flist;
-
- flist = malloc(sizeof(ImageFeatureList));
-
- flist->n_features = 0;
- flist->features = NULL;
-
- return flist;
-}
-
-
-void image_feature_list_free(ImageFeatureList *flist)
-{
- if ( !flist ) return;
-
- if ( flist->features ) free(flist->features);
- free(flist);
-}
-
-
-struct imagefeature *image_feature_closest(ImageFeatureList *flist,
- double fs, double ss,
- double *d, int *idx)
-{
- int i;
- double dmin = +HUGE_VAL;
- int closest = 0;
-
- for ( i=0; i<flist->n_features; i++ ) {
-
- double ds;
-
- ds = distance(flist->features[i].fs, flist->features[i].ss,
- fs, ss);
-
- if ( ds < dmin ) {
- dmin = ds;
- closest = i;
- }
-
- }
-
- if ( dmin < +HUGE_VAL ) {
- *d = dmin;
- *idx = closest;
- return &flist->features[closest];
- }
-
- *d = +INFINITY;
- return NULL;
-}
-
-
-int image_feature_count(ImageFeatureList *flist)
-{
- if ( flist == NULL ) return 0;
- return flist->n_features;
-}
-
-
-struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx)
-{
- /* Sanity check */
- if ( flist == NULL ) return NULL;
- if ( idx > flist->n_features ) return NULL;
-
- if ( flist->features[idx].valid == 0 ) return NULL;
-
- return &flist->features[idx];
-}
-
-
-void image_remove_feature(ImageFeatureList *flist, int idx)
-{
- flist->features[idx].valid = 0;
-}
diff --git a/src/image.h b/src/image.h
deleted file mode 100644
index e21ebe85..00000000
--- a/src/image.h
+++ /dev/null
@@ -1,184 +0,0 @@
-/*
- * 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 */
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