diff options
Diffstat (limited to 'libcrystfel/src')
| -rw-r--r-- | libcrystfel/src/crystal.c | 104 | ||||
| -rw-r--r-- | libcrystfel/src/crystal.h | 48 | ||||
| -rw-r--r-- | libcrystfel/src/image.h | 33 |
3 files changed, 158 insertions, 27 deletions
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c new file mode 100644 index 00000000..85430b6f --- /dev/null +++ b/libcrystfel/src/crystal.c @@ -0,0 +1,104 @@ +/* + * crystal.c + * + * A class representing a single crystal + * + * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2013 Thomas White <taw@physics.org> + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + * + */ + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +#include "crystal.h" +#include "utils.h" + + +/** + * SECTION:crystal + * @short_description: Crystal + * @title: Crystal + * @section_id: + * @see_also: + * @include: "crystal.h" + * @Image: + * + * This structure represents a single crystal. + */ + + +struct _crystal +{ + /* Information about the crystal */ + UnitCell *indexed_cell; + UnitCell *candidate_cells[MAX_CELL_CANDIDATES]; + int ncells; + double m; /* Mosaicity in radians */ + double osf; + double profile_radius; + int pr_dud; + double diffracting_resolution; + + /* Integrated (or about-to-be-integrated) reflections */ + RefList *reflections; + long long int n_saturated; /* Number of overloads */ +}; + + +/************************** Setters and Constructors **************************/ + + +/** + * crystal_new: + * + * Create a new %Crystal. + * + * Returns: the new unit cell, or NULL on failure. + * + */ +Crystal *crystal_new() +{ + Crystal *cryst; + + cryst = malloc(sizeof(Crystal)); + if ( cryst == NULL ) return NULL; + + return cryst; +} + + +/** + * crystal_free: + * @cryst: A %Crystal to free. + * + * Frees a %Crystal, and all internal resources concerning that crystal. + * + */ +void crystal_free(UnitCell *cryst) +{ + if ( cryst == NULL ) return; + free(crysta); +} + + +/********************************** Getters ***********************************/ diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h new file mode 100644 index 00000000..4f53eead --- /dev/null +++ b/libcrystfel/src/crystal.h @@ -0,0 +1,48 @@ +/* + * crystal.h + * + * A class representing a single crystal + * + * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2013 Thomas White <taw@physics.org> + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + * + */ + +#ifndef CRYSTAL_H +#define CRYSTAL_H + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +/** + * Crystal: + * + * This data structure is opaque. You must use the available accessor functions + * to read and write its contents. + **/ +typedef struct _crystal Crystal; + + +extern Crystal *crystal_new(void); +extern void crystal_free(Crystal *cryst); + +#endif /* CRYSTAL_H */ diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index afa9e4a7..bd90a920 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -41,6 +41,7 @@ #include "cell.h" #include "detector.h" #include "reflist.h" +#include "crystal.h" #define MAX_CELL_CANDIDATES (32) @@ -79,10 +80,9 @@ 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; + * * struct detector *det; * struct beam_params *beam; * char *filename; @@ -90,22 +90,13 @@ 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; - * * ImageFeatureList *features; * }; * </programlisting> @@ -141,9 +132,8 @@ struct image { uint16_t *flags; double *twotheta; - UnitCell *indexed_cell; - UnitCell *candidate_cells[MAX_CELL_CANDIDATES]; - int ncells; + struct crystal **crystals; + int n_crystals; struct detector *det; struct beam_params *beam; /* The nominal beam parameters */ @@ -153,25 +143,14 @@ 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 */ ImageFeatureList *features; |