SHOGUN
4.1.0
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Classes | |
struct | IndexSorter |
Public Member Functions | |
virtual const char * | get_name () const |
template<> | |
float64_t * | linspace (complex128_t start, complex128_t end, int32_t n) |
linspace not implemented for complex128_t, returns null instead More... | |
virtual CSGObject * | shallow_copy () const |
virtual CSGObject * | deep_copy () const |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
void | unset_generic () |
virtual void | print_serializable (const char *prefix="") |
virtual bool | save_serializable (CSerializableFile *file, const char *prefix="") |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="") |
void | set_global_io (SGIO *io) |
SGIO * | get_global_io () |
void | set_global_parallel (Parallel *parallel) |
Parallel * | get_global_parallel () |
void | set_global_version (Version *version) |
Version * | get_global_version () |
SGStringList< char > | get_modelsel_names () |
void | print_modsel_params () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
void | build_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict) |
virtual void | update_parameter_hash () |
virtual bool | parameter_hash_changed () |
virtual bool | equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) |
virtual CSGObject * | clone () |
Constructor/Destructor. | |
CMath () | |
Constructor - initializes log-table. More... | |
virtual | ~CMath () |
Destructor - frees logtable. More... | |
Static Public Member Functions | |
template<class T > | |
static T | min (T *vec, int32_t len) |
template<class T > | |
static T | max (T *vec, int32_t len) |
template<class T > | |
static T | clamp (T value, T lb, T ub) |
template<class T > | |
static int32_t | arg_max (T *vec, int32_t inc, int32_t len, T *maxv_ptr=NULL) |
template<class T > | |
static int32_t | arg_min (T *vec, int32_t inc, int32_t len, T *minv_ptr=NULL) |
static float64_t | exp (float64_t x) |
static float64_t | dot (const bool *v1, const bool *v2, int32_t n) |
Compute dot product between v1 and v2 (blas optimized) More... | |
static floatmax_t | dot (const floatmax_t *v1, const floatmax_t *v2, int32_t n) |
Compute dot product between v1 and v2 (blas optimized) More... | |
static float64_t | dot (const float64_t *v1, const float64_t *v2, int32_t n) |
Compute dot product between v1 and v2 (blas optimized) More... | |
static float32_t | dot (const float32_t *v1, const float32_t *v2, int32_t n) |
Compute dot product between v1 and v2 (blas optimized) More... | |
static float64_t | dot (const uint64_t *v1, const uint64_t *v2, int32_t n) |
compute dot product between v1 and v2 (for 64bit unsigned ints) More... | |
static float64_t | dot (const int64_t *v1, const int64_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 64bit ints) More... | |
static float64_t | dot (const int32_t *v1, const int32_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 32bit ints) More... | |
static float64_t | dot (const uint32_t *v1, const uint32_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 32bit unsigned ints) More... | |
static float64_t | dot (const uint16_t *v1, const uint16_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 16bit unsigned ints) More... | |
static float64_t | dot (const int16_t *v1, const int16_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 16bit unsigned ints) More... | |
static float64_t | dot (const char *v1, const char *v2, int32_t n) |
Compute dot product between v1 and v2 (for 8bit (un)signed ints) More... | |
static float64_t | dot (const uint8_t *v1, const uint8_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 8bit (un)signed ints) More... | |
static float64_t | dot (const int8_t *v1, const int8_t *v2, int32_t n) |
Compute dot product between v1 and v2 (for 8bit (un)signed ints) More... | |
static float64_t | dot (const float64_t *v1, const char *v2, int32_t n) |
Compute dot product between v1 and v2. More... | |
static float64_t | area_under_curve (float64_t *xy, int32_t len, bool reversed) |
static bool | strtof (const char *str, float32_t *float_result) |
static bool | strtod (const char *str, float64_t *double_result) |
static bool | strtold (const char *str, floatmax_t *long_double_result) |
static int64_t | factorial (int32_t n) |
template<class T > | |
static void | permute (SGVector< T > v, CRandom *rand=NULL) |
template<class T > | |
static int32_t | get_num_nonzero (T *vec, int32_t len) |
static int32_t | get_num_nonzero (complex128_t *vec, int32_t len) |
static int64_t | nchoosek (int32_t n, int32_t k) |
static void | linspace (float64_t *output, float64_t start, float64_t end, int32_t n=100) |
template<class T > | |
static float64_t * | linspace (T start, T end, int32_t n) |
template<class T > | |
static SGVector< float64_t > | linspace_vec (T start, T end, int32_t n) |
template<class T > | |
static T | log_sum_exp (SGVector< T > values) |
template<class T > | |
static T | log_mean_exp (SGVector< T > values) |
static void | sort (int32_t *a, int32_t cols, int32_t sort_col=0) |
static void | sort (float64_t *a, int32_t *idx, int32_t N) |
template<class T > | |
static void | qsort (T *output, int32_t size) |
template<class T > | |
static void | insertion_sort (T *output, int32_t size) |
template<class T > | |
static void | radix_sort (T *array, int32_t size) |
template<class T > | |
static uint8_t | byte (T word, uint16_t p) |
static uint8_t | byte (complex128_t word, uint16_t p) |
byte not implemented for complex128_t More... | |
template<class T > | |
static void | radix_sort_helper (T *array, int32_t size, uint16_t i) |
static void | radix_sort_helper (complex128_t *array, int32_t size, uint16_t i) |
radix_sort_helper not implemented for complex128_t More... | |
template<class T > | |
static void | qsort (T **vector, index_t length) |
static void | qsort (complex128_t **vector, index_t length) |
qsort not implemented for complex128_t More... | |
template<class T > | |
static void | qsort (SGVector< T > vector) |
template<class T > | |
static SGVector< index_t > | argsort (SGVector< T > vector) |
template<class T > | |
static bool | is_sorted (SGVector< T > vector) |
template<class T > | |
static void | display_bits (T word, int32_t width=8 *sizeof(T)) |
static void | display_bits (complex128_t word, int32_t width=8 *sizeof(complex128_t)) |
disply_bits not implemented for complex128_t More... | |
template<class T1 , class T2 > | |
static void | qsort_index (T1 *output, T2 *index, uint32_t size) |
template<class T > | |
static void | qsort_index (complex128_t *output, T *index, uint32_t size) |
qsort_index not implemented for complex128_t More... | |
template<class T1 , class T2 > | |
static void | qsort_backward_index (T1 *output, T2 *index, int32_t size) |
template<class T > | |
static void | qsort_backword_index (complex128_t *output, T *index, uint32_t size) |
qsort_backword_index not implemented for complex128_t More... | |
template<class T1 , class T2 > | |
static void | parallel_qsort_index (T1 *output, T2 *index, uint32_t size, int32_t n_threads, int32_t limit=262144) |
template<class T > | |
static void | parallel_qsort_index (complex128_t *output, T *index, uint32_t size, int32_t n_threads, int32_t limit=0) |
parallel_qsort_index not implemented for complex128_t More... | |
template<class T1 , class T2 > | |
static void * | parallel_qsort_index (void *p) |
helper function for parallel_qsort_index. More... | |
template<class T > | |
static void | min (float64_t *output, T *index, int32_t size) |
static void | min (float64_t *output, complex128_t *index, int32_t size) |
complex128_t cannot be used as index More... | |
template<class T > | |
static void | nmin (float64_t *output, T *index, int32_t size, int32_t n) |
static void | nmin (float64_t *output, complex128_t *index, int32_t size, int32_t n) |
complex128_t cannot be used as index More... | |
template<class T > | |
static int32_t | binary_search_helper (T *output, int32_t size, T elem) |
static int32_t | binary_search_helper (complex128_t *output, int32_t size, complex128_t elem) |
binary_search_helper not implemented for complex128_t More... | |
template<class T > | |
static int32_t | binary_search (T *output, int32_t size, T elem) |
static int32_t | binary_search (complex128_t *output, int32_t size, complex128_t elem) |
binary_search not implemented for complex128_t More... | |
template<class T > | |
static int32_t | binary_search (T **vector, index_t length, T *elem) |
static int32_t | binary_search (complex128_t **vector, index_t length, complex128_t *elem) |
binary_search not implemented for complex128_t More... | |
template<class T > | |
static int32_t | binary_search_max_lower_equal (T *output, int32_t size, T elem) |
static int32_t | binary_search_max_lower_equal (complex128_t *output, int32_t size, complex128_t elem) |
binary_search_max_lower_equal not implemented for complex128_t More... | |
static float64_t | Align (char *seq1, char *seq2, int32_t l1, int32_t l2, float64_t gapCost) |
static float64_t | real (complex128_t c) |
static float64_t | imag (complex128_t c) |
static uint32_t | get_seed () |
returns number generator seed More... | |
static uint32_t | get_log_range () |
returns range of logtable More... | |
static int | is_finite (double f) |
checks whether a float is finite More... | |
static int | is_infinity (double f) |
checks whether a float is infinity More... | |
static int | is_nan (double f) |
checks whether a float is nan More... | |
min/max/abs functions. | |
template<class T > | |
static T | min (T a, T b) |
template<class T > | |
static T | max (T a, T b) |
template<class T > | |
static T | abs (T a) |
static float64_t | abs (complex128_t a) |
misc functions | |
template<class T > | |
static bool | fequals_abs (const T &a, const T &b, const float64_t eps) |
template<class T > | |
static bool | fequals (const T &a, const T &b, const float64_t eps, bool tolerant=false) |
static float64_t | get_abs_tolerance (float64_t true_value, float64_t rel_tolerance) |
static float64_t | round (float64_t d) |
static float64_t | floor (float64_t d) |
static float64_t | ceil (float64_t d) |
template<class T > | |
static T | sign (T a) |
template<class T > | |
static void | swap (T &a, T &b) |
template<class T > | |
static T | sq (T x) |
static float32_t | sqrt (float32_t x) |
static float64_t | sqrt (float64_t x) |
static floatmax_t | sqrt (floatmax_t x) |
static float32_t | invsqrt (float32_t x) |
x^0.5, x being a complex128_t More... | |
Exponential methods (x^n) | |
static floatmax_t | powl (floatmax_t x, floatmax_t n) |
static int32_t | pow (bool x, int32_t n) |
static int32_t | pow (int32_t x, int32_t n) |
static float64_t | pow (float64_t x, int32_t n) |
static float64_t | pow (float64_t x, float64_t n) |
static complex128_t | pow (complex128_t x, int32_t n) |
static complex128_t | pow (complex128_t x, complex128_t n) |
static complex128_t | pow (complex128_t x, float64_t n) |
static complex128_t | pow (float64_t x, complex128_t n) |
Trignometric and Hyperbolic Functions | |
exp(x), x being a complex128_t | |
static float64_t | tan (float64_t x) |
static float64_t | atan (float64_t x) |
tan(x), x being a complex128_t More... | |
static float64_t | atan2 (float64_t y, float64_t x) |
atan(x), x being a complex128_t not implemented More... | |
static float64_t | tanh (float64_t x) |
atan2(x), x being a complex128_t not implemented More... | |
static float64_t | sin (float64_t x) |
tanh(x), x being a complex128_t More... | |
static float64_t | asin (float64_t x) |
sin(x), x being a complex128_t More... | |
static float64_t | sinh (float64_t x) |
asin(x), x being a complex128_t not implemented More... | |
static float64_t | cos (float64_t x) |
sinh(x), x being a complex128_t More... | |
static float64_t | acos (float64_t x) |
cos(x), x being a complex128_t More... | |
static float64_t | cosh (float64_t x) |
acos(x), x being a complex128_t not implemented More... | |
Logarithmic functions | |
cosh(x), x being a complex128_t | |
static float64_t | log10 (float64_t v) |
static float64_t | log2 (float64_t v) |
log10(x), x being a complex128_t More... | |
static float64_t | log (float64_t v) |
static index_t | floor_log (index_t n) |
log(x), x being a complex128_t More... | |
Random Functions | |
static void | init_random (uint32_t initseed=0) |
static uint64_t | random () |
static uint64_t | random (uint64_t min_value, uint64_t max_value) |
static int64_t | random (int64_t min_value, int64_t max_value) |
static uint32_t | random (uint32_t min_value, uint32_t max_value) |
static int32_t | random (int32_t min_value, int32_t max_value) |
static float32_t | random (float32_t min_value, float32_t max_value) |
static float64_t | random (float64_t min_value, float64_t max_value) |
static floatmax_t | random (floatmax_t min_value, floatmax_t max_value) |
static float32_t | normal_random (float32_t mean, float32_t std_dev) |
static float64_t | normal_random (float64_t mean, float64_t std_dev) |
static float32_t | randn_float () |
static float64_t | randn_double () |
summing functions | |
static float64_t | logarithmic_sum (float64_t p, float64_t q) |
Public Attributes | |
SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
Parameter * | m_gradient_parameters |
uint32_t | m_hash |
Protected Member Functions | |
virtual void | load_serializable_pre () throw (ShogunException) |
virtual void | load_serializable_post () throw (ShogunException) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
constants | |
static const float64_t | NOT_A_NUMBER = NAN |
not a number More... | |
static const float64_t | INFTY = INFINITY |
infinity More... | |
static const float64_t | ALMOST_INFTY = +1e+300 |
static const float64_t | ALMOST_NEG_INFTY = -1e+300 |
almost neg (log) infinity More... | |
static const float64_t | PI =M_PI |
static const float64_t | MACHINE_EPSILON =DBL_EPSILON |
static const float64_t | MAX_REAL_NUMBER =DBL_MAX |
static const float64_t | MIN_REAL_NUMBER =DBL_MIN |
static const float32_t | F_MAX_VAL32 =FLT_MAX |
static const float32_t | F_MIN_NORM_VAL32 =FLT_MIN |
static const float64_t | F_MAX_VAL64 =DBL_MAX |
static const float64_t | F_MIN_NORM_VAL64 =DBL_MIN |
static const float32_t | F_MIN_VAL32 =(FLT_MIN * FLT_EPSILON) |
static const float64_t | F_MIN_VAL64 =(DBL_MIN * DBL_EPSILON) |
static int32_t | LOGRANGE = 0 |
range for logtable: log(1+exp(x)) -LOGRANGE <= x <= 0 More... | |
static uint32_t | seed = 0 |
random generator seed More... | |
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Finds an element in a sorted array of pointers via binary search Every element is dereferenced once before being compared
vector | array of pointers to search in (assumed being sorted) |
length | length of array |
elem | pointer to element to search for |
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Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.
dict | dictionary of parameters to be built. |
Definition at line 597 of file SGObject.cpp.
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Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.
Definition at line 714 of file SGObject.cpp.
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A deep copy. All the instance variables will also be copied.
Definition at line 198 of file SGObject.cpp.
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Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!
May be overwritten but please do with care! Should not be necessary in most cases.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
Definition at line 618 of file SGObject.cpp.
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Compares the value of two floats (handles special cases, such as NaN, Inf etc.) Note: returns true if a == b == NAN Implementation inspired by http://floating-point-gui.de/errors/comparison/
a | first value to compare |
b | second value to compare |
eps | threshold for values to be equal/different |
tolerant | allows linient check on float equality (within accuracy) |
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Definition at line 498 of file SGObject.cpp.
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Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
Definition at line 522 of file SGObject.cpp.
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Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 535 of file SGObject.cpp.
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If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
Definition at line 296 of file SGObject.cpp.
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Builds an array with n linearly spaced elements between start and end.
output | array with linearly spaced elements within the interval |
start | beginning of the interval to divide |
end | upper bound of the interval to divide |
n | number of elements used to divide the interval |
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Returns an array with n linearly spaced elements between start and end.
start | beginning of the interval to divide |
end | upper bound of the interval to divide |
n | number of elements used to divide the interval |
float64_t* linspace | ( | complex128_t | start, |
complex128_t | end, | ||
int32_t | n | ||
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Returns a vector with n linearly spaced elements between start and end.
start | beginning of the interval to divide |
end | upper bound of the interval to divide |
n | number of elements used to divide the interval |
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Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
file | where to load from |
prefix | prefix for members |
Definition at line 369 of file SGObject.cpp.
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Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.
ShogunException | will be thrown if an error occurs. |
Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 426 of file SGObject.cpp.
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Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.
ShogunException | will be thrown if an error occurs. |
Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.
Definition at line 421 of file SGObject.cpp.
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Sum logarithmic probabilities. Probability measures are summed up but are now given in logspace where direct summation of exp(operand) is not possible due to numerical problems, i.e. eg. exp(-1000)=0. Therefore we do log( exp(a) + exp(b)) = a + log (1 + exp (b-a)) where a = max(p,q) and b min(p,q).
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Returns a Gaussian or Normal random number. Using the polar form of the Box-Muller transform. http://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform#Polar_form
Returns a Gaussian or Normal random number. Using the polar form of the Box-Muller transform. http://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform#Polar_form
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Performs a quicksort on an array output of length size it is sorted in ascending order (for type T1) and returns the index (type T2) matlab alike [sorted,index]=sort(output) parallel version
output | input array |
index | index array |
size | size of the array |
n_threads | number of threads |
limit | sort limit |
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Definition at line 262 of file SGObject.cpp.
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prints all parameter registered for model selection and their type
Definition at line 474 of file SGObject.cpp.
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prints registered parameters out
prefix | prefix for members |
Definition at line 308 of file SGObject.cpp.
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Save this object to file.
file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
Definition at line 314 of file SGObject.cpp.
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protectedvirtualinherited |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.
ShogunException | will be thrown if an error occurs. |
Reimplemented in CKernel.
Definition at line 436 of file SGObject.cpp.
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protectedvirtualinherited |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.
ShogunException | will be thrown if an error occurs. |
Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.
Definition at line 431 of file SGObject.cpp.
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inherited |
Definition at line 41 of file SGObject.cpp.
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inherited |
Definition at line 46 of file SGObject.cpp.
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inherited |
Definition at line 51 of file SGObject.cpp.
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inherited |
Definition at line 56 of file SGObject.cpp.
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inherited |
Definition at line 61 of file SGObject.cpp.
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inherited |
Definition at line 66 of file SGObject.cpp.
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inherited |
Definition at line 71 of file SGObject.cpp.
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inherited |
Definition at line 76 of file SGObject.cpp.
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inherited |
Definition at line 81 of file SGObject.cpp.
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inherited |
Definition at line 86 of file SGObject.cpp.
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inherited |
Definition at line 91 of file SGObject.cpp.
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inherited |
Definition at line 96 of file SGObject.cpp.
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inherited |
Definition at line 101 of file SGObject.cpp.
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inherited |
Definition at line 106 of file SGObject.cpp.
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inherited |
Definition at line 111 of file SGObject.cpp.
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inherited |
set generic type to T
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inherited |
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inherited |
set the parallel object
parallel | parallel object to use |
Definition at line 241 of file SGObject.cpp.
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inherited |
set the version object
version | version object to use |
Definition at line 283 of file SGObject.cpp.
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virtualinherited |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 192 of file SGObject.cpp.
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static |
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static |
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static |
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static |
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static |
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static |
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static |
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static |
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static |
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inherited |
unset generic type
this has to be called in classes specializing a template class
Definition at line 303 of file SGObject.cpp.
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virtualinherited |
Updates the hash of current parameter combination
Definition at line 248 of file SGObject.cpp.
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static |
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inherited |
io
Definition at line 369 of file SGObject.h.
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staticprotected |
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inherited |
parameters wrt which we can compute gradients
Definition at line 384 of file SGObject.h.
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inherited |
Hash of parameter values
Definition at line 387 of file SGObject.h.
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inherited |
model selection parameters
Definition at line 381 of file SGObject.h.
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inherited |
parameters
Definition at line 378 of file SGObject.h.
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static |
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inherited |
parallel
Definition at line 372 of file SGObject.h.
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inherited |
version
Definition at line 375 of file SGObject.h.