diff options
| -rw-r--r-- | doc/reference/libcrystfel/CrystFEL-sections.txt | 61 | ||||
| -rw-r--r-- | libcrystfel/src/utils.c | 276 | ||||
| -rw-r--r-- | libcrystfel/src/utils.h | 86 |
3 files changed, 221 insertions, 202 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index d58c5725..3968dd5d 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -8,6 +8,8 @@ reflist_new reflist_free reflection_new reflection_free +reflist_add_notes +reflist_get_notes <SUBSECTION> add_refl add_refl_to_list @@ -18,7 +20,6 @@ next_refl find_refl next_found_refl <SUBSECTION> -get_excitation_error get_detector_pos get_panel get_partiality @@ -77,6 +78,7 @@ copy_reflist find_equiv_in_list resolution_limits max_intensity +reflist_add_command_and_version </SECTION> <SECTION> @@ -151,32 +153,32 @@ solve_svd AssplodeFlag C_VACUO ELECTRON_CHARGE -ERROR -J_to_eV PLANCK -STATUS THOMSON_LENGTH assplode -biggest -check_prefix chomp -deg2rad -eV_to_J gaussian_noise -safe_basename progress_bar -rad2deg -is_odd poisson_noise notrail +random_flat +flat_noise +show_matrix +STATUS +ERROR +J_to_eV +eV_to_J +biggest smallest +check_prefix +safe_basename +deg2rad +rad2deg +is_odd ph_en_to_lambda ph_lambda_to_en ph_eV_to_lambda ph_lambda_to_eV -random_flat -flat_noise -show_matrix likely unlikely UNUSED @@ -218,6 +220,20 @@ ImageFeatureList SpectrumType sample <SUBSECTION> +imagefile +imagefile_close +imagefile_copy_fields +imagefile_field_list +imagefile_get_hdfile +imagefile_get_type +imagefile_open +imagefile_read +imagefile_read_simple +<SUBSECTION> +new_imagefile_field_list +add_imagefile_field +free_imagefile_field_list +<SUBSECTION> image_add_feature image_feature_closest image_reflection_closest @@ -268,10 +284,11 @@ INDEXING_DEFAULTS_ASDF INDEXING_DEFAULTS_FELIX INDEXING_METHOD_MASK INDEXING_CONTROL_FLAGS -build_indexer_list +setup_indexing cleanup_indexing -prepare_indexing +get_indm_from_string index_pattern +index_pattern_2 indexer_str dirax_prepare run_dirax @@ -314,6 +331,7 @@ describe_symmetry symmetry_name set_symmetry_name get_matrix_name +pointgroup_warning is_centrosymmetric is_centric </SECTION> @@ -351,15 +369,14 @@ rigid_group rg_collection <SUBSECTION> copy_geom -fill_in_values +fill_in_adu free_detector_geometry get_detector_geometry get_detector_geometry_2 write_detector_geometry write_detector_geometry_2 -find_panel +panel_number find_panel_by_name -find_panel_number simple_geometry record_image get_pixel_extents @@ -378,6 +395,7 @@ rigid_group_is_in_collection single_panel_data_source find_rigid_group_collection_by_name detector_has_clen_references +adjust_centering_for_rail </SECTION> <SECTION> @@ -466,6 +484,7 @@ crystal_get_resolution_limit crystal_get_user_flag crystal_get_num_implausible_reflections crystal_get_notes +crystal_get_det_shift crystal_set_cell crystal_set_image crystal_set_mosaicity @@ -479,6 +498,7 @@ crystal_set_user_flag crystal_set_num_implausible_reflections crystal_set_notes crystal_add_notes +crystal_set_det_shift </SECTION> <SECTION> @@ -500,7 +520,9 @@ y_gradient <FILE>peaks</FILE> peak_sanity_check search_peaks +search_peaks_peakfinder8 make_BgMask +peakfinder8 validate_peaks sort_peaks </SECTION> @@ -557,6 +579,7 @@ close_stream read_chunk read_chunk_2 write_chunk +write_chunk_2 rewind_stream is_stream write_command diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c index 461da0cd..90d81a71 100644 --- a/libcrystfel/src/utils.c +++ b/libcrystfel/src/utils.c @@ -387,144 +387,6 @@ int poisson_noise(gsl_rng *rng, double expected) } -/** - * SECTION:quaternion - * @short_description: Simple quaternion handling - * @title: Quaternion - * @section_id: - * @see_also: - * @include: "utils.h" - * @Image: - * - * There is a simple quaternion structure in CrystFEL. At the moment, it is - * only used when simulating patterns, as an argument to cell_rotate() to - * orient the unit cell. - */ - -/** - * quaternion_modulus: - * @q: A %quaternion - * - * If a quaternion represents a pure rotation, its modulus should be unity. - * - * Returns: the modulus of the given quaternion. - **/ -double quaternion_modulus(struct quaternion q) -{ - return sqrt(q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z); -} - - -/** - * normalise_quaternion: - * @q: A %quaternion - * - * Rescales the quaternion such that its modulus is unity. - * - * Returns: the normalised version of @q - **/ -struct quaternion normalise_quaternion(struct quaternion q) -{ - double mod; - struct quaternion r; - - mod = quaternion_modulus(q); - - r.w = q.w / mod; - r.x = q.x / mod; - r.y = q.y / mod; - r.z = q.z / mod; - - return r; -} - - -/** - * random_quaternion: - * @rng: A GSL random number generator to use - * - * Returns: a randomly generated, normalised, quaternion. - **/ -struct quaternion random_quaternion(gsl_rng *rng) -{ - struct quaternion q; - - q.w = 2.0*gsl_rng_uniform(rng) - 1.0; - q.x = 2.0*gsl_rng_uniform(rng) - 1.0; - q.y = 2.0*gsl_rng_uniform(rng) - 1.0; - q.z = 2.0*gsl_rng_uniform(rng) - 1.0; - q = normalise_quaternion(q); - - return q; -} - - -/** - * quaternion_valid: - * @q: A %quaternion - * - * Checks if the given quaternion is normalised. - * - * This function performs a nasty floating point comparison of the form - * <code>(modulus > 0.999) && (modulus < 1.001)</code>, and so should not be - * relied upon to spot anything other than the most obvious input error. - * - * Returns: 1 if the quaternion is normalised, 0 if not. - **/ -int quaternion_valid(struct quaternion q) -{ - double qmod; - - qmod = quaternion_modulus(q); - - /* Modulus = 1 to within some tolerance? - * Nasty allowance for floating-point accuracy follows... */ - if ( (qmod > 0.999) && (qmod < 1.001) ) return 1; - - return 0; -} - - -/** - * quat_rot - * @q: A vector (in the form of a "struct rvec") - * @z: A %quaternion - * - * Rotates a vector according to a quaternion. - * - * Returns: A rotated version of @p. - **/ -struct rvec quat_rot(struct rvec q, struct quaternion z) -{ - struct rvec res; - double t01, t02, t03, t11, t12, t13, t22, t23, t33; - - t01 = z.w*z.x; - t02 = z.w*z.y; - t03 = z.w*z.z; - t11 = z.x*z.x; - t12 = z.x*z.y; - t13 = z.x*z.z; - t22 = z.y*z.y; - t23 = z.y*z.z; - t33 = z.z*z.z; - - res.u = (1.0 - 2.0 * (t22 + t33)) * q.u - + (2.0 * (t12 + t03)) * q.v - + (2.0 * (t13 - t02)) * q.w; - - res.v = (2.0 * (t12 - t03)) * q.u - + (1.0 - 2.0 * (t11 + t33)) * q.v - + (2.0 * (t01 + t23)) * q.w; - - res.w = (2.0 * (t02 + t13)) * q.u - + (2.0 * (t23 - t01)) * q.v - + (1.0 - 2.0 * (t11 + t22)) * q.w; - - return res; -} - - /* Return non-zero if c is in delims */ static int assplode_isdelim(const char c, const char *delims) { @@ -691,3 +553,141 @@ void utils_fudge_gslcblas() { STATUS("%p\n", cblas_sgemm); } + + +/** + * SECTION:quaternion + * @short_description: Simple quaternion handling + * @title: Quaternion + * @section_id: + * @see_also: + * @include: "utils.h" + * @Image: + * + * There is a simple quaternion structure in CrystFEL. At the moment, it is + * only used when simulating patterns, as an argument to cell_rotate() to + * orient the unit cell. + */ + +/** + * quaternion_modulus: + * @q: A %quaternion + * + * If a quaternion represents a pure rotation, its modulus should be unity. + * + * Returns: the modulus of the given quaternion. + **/ +double quaternion_modulus(struct quaternion q) +{ + return sqrt(q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z); +} + + +/** + * normalise_quaternion: + * @q: A %quaternion + * + * Rescales the quaternion such that its modulus is unity. + * + * Returns: the normalised version of @q + **/ +struct quaternion normalise_quaternion(struct quaternion q) +{ + double mod; + struct quaternion r; + + mod = quaternion_modulus(q); + + r.w = q.w / mod; + r.x = q.x / mod; + r.y = q.y / mod; + r.z = q.z / mod; + + return r; +} + + +/** + * random_quaternion: + * @rng: A GSL random number generator to use + * + * Returns: a randomly generated, normalised, quaternion. + **/ +struct quaternion random_quaternion(gsl_rng *rng) +{ + struct quaternion q; + + q.w = 2.0*gsl_rng_uniform(rng) - 1.0; + q.x = 2.0*gsl_rng_uniform(rng) - 1.0; + q.y = 2.0*gsl_rng_uniform(rng) - 1.0; + q.z = 2.0*gsl_rng_uniform(rng) - 1.0; + q = normalise_quaternion(q); + + return q; +} + + +/** + * quaternion_valid: + * @q: A %quaternion + * + * Checks if the given quaternion is normalised. + * + * This function performs a nasty floating point comparison of the form + * <code>(modulus > 0.999) && (modulus < 1.001)</code>, and so should not be + * relied upon to spot anything other than the most obvious input error. + * + * Returns: 1 if the quaternion is normalised, 0 if not. + **/ +int quaternion_valid(struct quaternion q) +{ + double qmod; + + qmod = quaternion_modulus(q); + + /* Modulus = 1 to within some tolerance? + * Nasty allowance for floating-point accuracy follows... */ + if ( (qmod > 0.999) && (qmod < 1.001) ) return 1; + + return 0; +} + + +/** + * quat_rot + * @q: A vector (in the form of a "struct rvec") + * @z: A %quaternion + * + * Rotates a vector according to a quaternion. + * + * Returns: A rotated version of @p. + **/ +struct rvec quat_rot(struct rvec q, struct quaternion z) +{ + struct rvec res; + double t01, t02, t03, t11, t12, t13, t22, t23, t33; + + t01 = z.w*z.x; + t02 = z.w*z.y; + t03 = z.w*z.z; + t11 = z.x*z.x; + t12 = z.x*z.y; + t13 = z.x*z.z; + t22 = z.y*z.y; + t23 = z.y*z.z; + t33 = z.z*z.z; + + res.u = (1.0 - 2.0 * (t22 + t33)) * q.u + + (2.0 * (t12 + t03)) * q.v + + (2.0 * (t13 - t02)) * q.w; + + res.v = (2.0 * (t12 - t03)) * q.u + + (1.0 - 2.0 * (t11 + t33)) * q.v + + (2.0 * (t01 + t23)) * q.w; + + res.w = (2.0 * (t02 + t13)) * q.u + + (2.0 * (t23 - t01)) * q.v + + (1.0 - 2.0 * (t11 + t22)) * q.w; + + return res; +} diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h index 4955f875..a759ff15 100644 --- a/libcrystfel/src/utils.h +++ b/libcrystfel/src/utils.h @@ -61,44 +61,10 @@ #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; -}; - #ifdef __cplusplus extern "C" { #endif -extern struct quaternion normalise_quaternion(struct quaternion q); -extern double quaternion_modulus(struct quaternion q); -extern struct quaternion random_quaternion(gsl_rng *rng); -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); @@ -126,17 +92,6 @@ extern double flat_noise(gsl_rng *rng, double expected, double width); extern double gaussian_noise(gsl_rng *rng, double expected, double stddev); extern int poisson_noise(gsl_rng *rng, 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)); @@ -275,6 +230,47 @@ extern char *safe_basename(const char *in); #define unlikely(x) (x) #endif + +/* ------------------------------ Quaternions ------------------------------- */ + +/** + * quaternion: + * @w: component + * @x: component + * @y: component + * @z: component + * + * 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(gsl_rng *rng); +extern int quaternion_valid(struct quaternion q); +extern struct rvec quat_rot(struct rvec q, struct quaternion z); + +/* 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; +} + + + #ifdef __cplusplus } #endif |