diff options
Diffstat (limited to 'libcrystfel/src/image.h')
| -rw-r--r-- | libcrystfel/src/image.h | 134 |
1 files changed, 93 insertions, 41 deletions
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 9fd9b495..9719bb59 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -3,11 +3,11 @@ * * Handle images and image features * - * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2009-2016 Thomas White <taw@physics.org> + * 2009-2017 Thomas White <taw@physics.org> * 2014 Valerio Mariani * * @@ -44,6 +44,8 @@ struct detector; struct imagefeature; struct sample; struct image; +struct imagefile; +struct imagefile_field_list; #include "utils.h" #include "cell.h" @@ -51,6 +53,7 @@ struct image; #include "reflist.h" #include "crystal.h" #include "index.h" +#include "events.h" /** * SpectrumType: @@ -67,7 +70,26 @@ typedef enum { SPECTRUM_TWOCOLOUR } SpectrumType; -/* Structure describing a feature in an image */ + +/** + * imagefeature: + * @parent: Image this feature belongs to + * @fs: Fast scan coordinate + * @ss: Slow scan coordinate + * @p: Pointer to panel + * @intensity: Intensity of peak + * @rx: Reciprocal x coordinate in m^-1 + * @ry: Reciprocal y coordinate in m^-1 + * @rz: Reciprocal z coordinate in m^-1 + * @name: Text name for feature + * + * Represents a peak in an image. + * + * Note carefully that the @fs and @ss coordinates are the distances, measured + * in pixels, from the corner of the panel. They are NOT pixel indices. + * If the peak is in the middle of the first pixel, its coordinates would be + * 0.5,0.5. + */ struct imagefeature { struct image *parent; @@ -81,12 +103,21 @@ struct imagefeature { double ry; double rz; - /* Internal use only */ + const char *name; + + /*< private >*/ int valid; +}; - const char *name; + +/* An enum representing the image file formats we can handle */ +enum imagefile_type +{ + IMAGEFILE_HDF5, + IMAGEFILE_CBF }; + /* An opaque type representing a list of image features */ typedef struct _imagefeaturelist ImageFeatureList; @@ -98,44 +129,46 @@ struct sample }; +/** + * beam_params: + * @photon_energy: eV per photon + * @photon_energy_from: HDF5 dataset name + * @photon_energy_scale: Scale factor for photon energy, if it comes from HDF5 + */ struct beam_params { - double photon_energy; /* eV per photon */ - char *photon_energy_from; /* HDF5 dataset name */ - double photon_energy_scale; /* Scale factor for photon energy, if the - * energy is to be from the HDF5 file */ + double photon_energy; + char *photon_energy_from; + double photon_energy_scale; }; /** * image: - * - * <programlisting> - * struct image - * { - * Crystal **crystals; - * int n_crystals; - * IndexingMethod indexed_by; - * - * struct detector *det; - * struct beam_params *beam; - * char *filename; - * const struct copy_hdf5_field *copyme; - * - * int id; - * - * double lambda; - * double div; - * double bw; - * - * int width; - * int height; - * - * long long int num_peaks; - * long long int num_saturated_peaks; - * ImageFeatureList *features; - * }; - * </programlisting> + * @crystals: Array of crystals in the image + * @n_crystals: The number of crystals in the image + * @indexed_by: Indexing method which indexed this pattern + * @det: Detector structure + * @beam: Beam parameters structure + * @filename: Filename for the image file + * @copyme: Fields to copy from the image file to the stream + * @id: ID number of the thread handling this image + * @serial: Serial number for this image + * @lambda: Wavelength + * @div: Divergence + * @bw: Bandwidth + * @num_peaks: The number of peaks + * @num_saturated_peaks: The number of saturated peaks + * @features: The peaks found in the image + * @dp: The image data, by panel + * @bad: The bad pixel mask, array by panel + * @sat: The per-pixel saturation mask, array by panel + * @event: Event ID for the image + * @stuff_from_stream: Items read back from the stream + * @avg_clen: Mean of camera length values for all panels + * @spectrum: Spectrum information + * @nsamples: Number of spectrum samples + * @spectrum_size: SIze of spectrum array * * The field <structfield>data</structfield> contains the raw image data, if it * is currently available. The data might be available throughout the @@ -152,8 +185,8 @@ struct beam_params * 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. + * <structfield>copyme</structfield> represents a list of fields in the image + * file (e.g. HDF5 fields or CBF headers) to copy to the output stream. **/ struct image; @@ -171,7 +204,7 @@ struct image { struct beam_params *beam; /* The nominal beam parameters */ char *filename; struct event *event; - const struct copy_hdf5_field *copyme; + const struct imagefile_field_list *copyme; struct stuff_from_stream *stuff_from_stream; double avg_clen; /* Average camera length extracted @@ -192,8 +225,8 @@ struct image { double bw; /* Bandwidth as a fraction */ /* Detected peaks */ - long long int num_peaks; - long long int num_saturated_peaks; + long long num_peaks; + long long num_saturated_peaks; ImageFeatureList *features; }; @@ -233,6 +266,25 @@ extern void image_add_crystal(struct image *image, Crystal *cryst); extern void remove_flagged_crystals(struct image *image); extern void free_all_crystals(struct image *image); +/* Image files */ +extern struct imagefile *imagefile_open(const char *filename); +extern int imagefile_read(struct imagefile *f, struct image *image, + struct event *event); +extern int imagefile_read_simple(struct imagefile *f, struct image *image); +extern struct hdfile *imagefile_get_hdfile(struct imagefile *f); +extern enum imagefile_type imagefile_get_type(struct imagefile *f); +extern void imagefile_copy_fields(struct imagefile *f, + const struct imagefile_field_list *copyme, + FILE *fh, struct event *ev); +extern void imagefile_close(struct imagefile *f); + +/* Field lists */ +extern struct imagefile_field_list *new_imagefile_field_list(void); +extern void free_imagefile_field_list(struct imagefile_field_list *f); + +extern void add_imagefile_field(struct imagefile_field_list *copyme, + const char *name); + #ifdef __cplusplus } #endif |