Introduce "libcrystfel"

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 */