Introduce "libcrystfel"

1 files changed, 236 insertions, 0 deletions

diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
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+++ b/libcrystfel/src/utils.h
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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)
+
+
+/* ------------------------------ 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 */