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Diffstat (limited to 'libcrystfel/src/utils.h')
| -rw-r--r-- | libcrystfel/src/utils.h | 236 |
1 files changed, 236 insertions, 0 deletions
diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h new file mode 100644 index 00000000..1179a57f --- /dev/null +++ b/libcrystfel/src/utils.h @@ -0,0 +1,236 @@ +/* + * utils.h + * + * Utility stuff + * + * (c) 2006-2010 Thomas White <taw@physics.org> + * + * Part of CrystFEL - crystallography with a FEL + * + */ + +#ifndef UTILS_H +#define UTILS_H + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +#include <math.h> +#include <complex.h> +#include <string.h> +#include <stdlib.h> +#include <pthread.h> +#include <gsl/gsl_matrix.h> +#include <gsl/gsl_vector.h> + + +#include "thread-pool.h" + + +/* -------------------------- Fundamental constants ------------------------ */ + +/* Electron charge in C */ +#define ELECTRON_CHARGE (1.6021773e-19) + +/* Planck's constant (Js) */ +#define PLANCK (6.62606896e-34) + +/* Speed of light in vacuo (m/s) */ +#define C_VACUO (299792458) + +/* Thomson scattering length (m) */ +#define THOMSON_LENGTH (2.81794e-15) + + +/* ------------------------------ Quaternions ------------------------------- */ + +/** + * quaternion: + * + * <programlisting> + * struct quaternion + * { + * double w + * double x + * double y + * double z + * }; + * </programlisting> + * + * A structure representing a quaternion. + * + **/ +struct quaternion; + +struct quaternion { + double w; + double x; + double y; + double z; +}; + +extern struct quaternion normalise_quaternion(struct quaternion q); +extern double quaternion_modulus(struct quaternion q); +extern struct quaternion random_quaternion(void); +extern int quaternion_valid(struct quaternion q); +extern struct rvec quat_rot(struct rvec q, struct quaternion z); + + +/* --------------------------- Useful functions ----------------------------- */ + +extern void show_matrix_eqn(gsl_matrix *M, gsl_vector *v, int r); +extern size_t notrail(char *s); +extern void chomp(char *s); + +typedef enum { + ASSPLODE_NONE = 0, + ASSPLODE_DUPS = 1<<0 +} AssplodeFlag; +extern int assplode(const char *a, const char *delims, char ***pbits, + AssplodeFlag flags); + +extern void progress_bar(int val, int total, const char *text); +extern double random_flat(double max); +extern double flat_noise(double expected, double width); +extern double gaussian_noise(double expected, double stddev); +extern int poisson_noise(double expected); + +/* Keep these ones inline, to avoid function call overhead */ +static inline struct quaternion invalid_quaternion(void) +{ + struct quaternion quat; + quat.w = 0.0; + quat.x = 0.0; + quat.y = 0.0; + quat.z = 0.0; + return quat; +} + +static inline double distance(double x1, double y1, double x2, double y2) +{ + return sqrt((x2-x1)*(x2-x1) + (y2-y1)*(y2-y1)); +} + +static inline double modulus(double x, double y, double z) +{ + return sqrt(x*x + y*y + z*z); +} + +static inline double modulus_squared(double x, double y, double z) { + return x*x + y*y + z*z; +} + +static inline double distance3d(double x1, double y1, double z1, + double x2, double y2, double z2) +{ + return modulus(x1-x2, y1-y2, z1-z2); +} + +/* Answer in radians */ +static inline double angle_between(double x1, double y1, double z1, + double x2, double y2, double z2) +{ + double mod1 = modulus(x1, y1, z1); + double mod2 = modulus(x2, y2, z2); + double cosine = (x1*x2 + y1*y2 + z1*z2) / (mod1*mod2); + + /* Fix domain if outside due to rounding */ + if ( cosine > 1.0 ) cosine = 1.0; + if ( cosine < -1.0 ) cosine = -1.0; + + return acos(cosine); +} + +static inline int within_tolerance(double a, double b, double percent) +{ + double tol = fabs(a) * (percent/100.0); + if ( fabs(b-a) < tol ) return 1; + return 0; +} + + +/* ----------------------------- Useful macros ------------------------------ */ + +#define rad2deg(a) ((a)*180/M_PI) +#define deg2rad(a) ((a)*M_PI/180) + +#define is_odd(a) ((a)%2==1) + +#define biggest(a,b) ((a>b) ? (a) : (b)) +#define smallest(a,b) ((a<b) ? (a) : (b)) + + +/* Photon energy (J) to wavelength (m) */ +#define ph_en_to_lambda(a) ((PLANCK*C_VACUO)/(a)) + +/* Photon wavelength (m) to energy (J) */ +#define ph_lambda_to_en(a) ((PLANCK*C_VACUO)/(a)) + +/* eV to Joules */ +#define eV_to_J(a) ((a)*ELECTRON_CHARGE) + +/* Joules to eV */ +#define J_to_eV(a) ((a)/ELECTRON_CHARGE) + +#define UNUSED __attribute__((unused)) + +/* -------------------- Indexed lists for specified types ------------------- */ + +#include "defs.h" + +#define LIST_SIZE (IDIM*IDIM*IDIM) + +/* Create functions for storing reflection intensities indexed as h,k,l */ +#define LABEL(x) x##_intensity +#define TYPE double +#include "list_tmp.h" + +/* CAs above, but for phase values */ +#define LABEL(x) x##_phase +#define TYPE double +#include "list_tmp.h" + +/* As above, but for (unsigned) integer counts */ +#define LABEL(x) x##_count +#define TYPE unsigned int +#include "list_tmp.h" + +/* As above, but for simple flags */ +#define LABEL(x) x##_flag +#define TYPE unsigned char +#include "list_tmp.h" + + +/* ------------------------------ Message macros ---------------------------- */ + +extern pthread_mutex_t stderr_lock; + +#define ERROR(...) { \ + int error_print_val = get_status_label(); \ + pthread_mutex_lock(&stderr_lock); \ + if ( error_print_val >= 0 ) { \ + fprintf(stderr, "%3i: ", error_print_val); \ + } \ + fprintf(stderr, __VA_ARGS__); \ + pthread_mutex_unlock(&stderr_lock); \ + } + +#define STATUS(...) { \ + int status_print_val = get_status_label(); \ + pthread_mutex_lock(&stderr_lock); \ + if ( status_print_val >= 0 ) { \ + fprintf(stderr, "%3i: ", status_print_val); \ + } \ + fprintf(stderr, __VA_ARGS__); \ + pthread_mutex_unlock(&stderr_lock); \ + } + + +/* ------------------------------ File handling ----------------------------- */ + +extern char *check_prefix(char *prefix); +extern char *safe_basename(const char *in); + + +#endif /* UTILS_H */ |