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/*
* 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)
/* Density of water in kg/m^3 */
#define WATER_DENSITY (1.0e6)
/* Molar mass of water, in kg/mol */
#define WATER_MOLAR_MASS (18.01528e3)
/* Avogadro's number */
#define AVOGADRO (6.022e23)
/* ------------------------------ Quaternions ------------------------------- */
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 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);
}
/* ----------------------------- 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)
/* -------------------- 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 complex structure factors */
#define LABEL(x) x##_sfac
#define TYPE double complex
#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 sigmas */
#define LABEL(x) x##_sigma
#define TYPE double
#include "list_tmp.h"
/* As above, but for simple flags */
#define LABEL(x) x##_flag
#define TYPE unsigned char
#include "list_tmp.h"
/* ----------- Reflection lists indexed by sequence (not indices) ----------- */
typedef struct _reflitemlist ReflItemList; /* Opaque */
struct refl_item {
signed int h;
signed int k;
signed int l;
int op;
};
extern void clear_items(ReflItemList *items);
extern ReflItemList *new_items(void);
extern void delete_items(ReflItemList *items);
extern void add_item(ReflItemList *items,
signed int h, signed int k, signed int l);
extern void add_item_with_op(ReflItemList *items,
signed int h, signed int k, signed int l, int op);
extern int find_item(ReflItemList *items,
signed int h, signed int k, signed int l);
extern struct refl_item *get_item(ReflItemList *items, int i);
extern int num_items(const ReflItemList *items);
extern unsigned int *items_to_counts(ReflItemList *items);
extern void union_op_items(ReflItemList *items, ReflItemList *newi);
extern void union_items(ReflItemList *items, ReflItemList *newi);
extern ReflItemList *intersection_items(ReflItemList *i1, ReflItemList *i2);
/* ------------------------------ 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 */
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