SHOGUN
4.1.0
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class Bray-Curtis distance
The Bray-Curtis distance (Sorensen distance) is similar to the Manhattan distance with normalization.
\[\displaystyle d(\bf{x},\bf{x}') = \frac{\sum_{i=1}^{n}|x_{i}-x'_{i}|}{\sum_{i=1}^{n}|x_{i} +x'_{i}|} \quad x,x' \in R^{n} \]
Definition at line 32 of file BrayCurtisDistance.h.
Public Member Functions | |
CBrayCurtisDistance () | |
CBrayCurtisDistance (CDenseFeatures< float64_t > *l, CDenseFeatures< float64_t > *r) | |
virtual | ~CBrayCurtisDistance () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual EDistanceType | get_distance_type () |
virtual const char * | get_name () const |
virtual EFeatureClass | get_feature_class () |
virtual EFeatureType | get_feature_type () |
virtual float64_t | distance (int32_t idx_a, int32_t idx_b) |
virtual float64_t | distance_upper_bounded (int32_t idx_a, int32_t idx_b, float64_t upper_bound) |
SGMatrix< float64_t > | get_distance_matrix () |
template<class T > | |
SGMatrix< T > | get_distance_matrix () |
int32_t | compute_row_start (int64_t offs, int32_t n, bool symmetric) |
void | load (CFile *loader) |
void | save (CFile *writer) |
CFeatures * | get_lhs () |
CFeatures * | get_rhs () |
CFeatures * | replace_rhs (CFeatures *rhs) |
CFeatures * | replace_lhs (CFeatures *lhs) |
virtual void | remove_lhs_and_rhs () |
virtual void | remove_lhs () |
takes all necessary steps if the lhs is removed from distance matrix More... | |
virtual void | remove_rhs () |
takes all necessary steps if the rhs is removed from distance matrix More... | |
bool | get_precompute_matrix () |
virtual void | set_precompute_matrix (bool flag) |
virtual int32_t | get_num_vec_lhs () |
virtual int32_t | get_num_vec_rhs () |
virtual bool | has_features () |
bool | lhs_equals_rhs () |
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 () |
Static Public Member Functions | |
template<class T > | |
static void * | get_distance_matrix_helper (void *p) |
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 float64_t | compute (int32_t idx_a, int32_t idx_b) |
void | do_precompute_matrix () |
matrix precomputation More... | |
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) |
Static Protected Member Functions | |
static void * | run_distance_thread (void *p) |
run distance thread More... | |
Protected Attributes | |
float32_t * | precomputed_matrix |
bool | precompute_matrix |
CFeatures * | lhs |
feature vectors to occur on the left hand side More... | |
CFeatures * | rhs |
feature vectors to occur on the right hand side More... | |
int32_t | num_lhs |
int32_t | num_rhs |
default constructor
Definition at line 19 of file BrayCurtisDistance.cpp.
CBrayCurtisDistance | ( | CDenseFeatures< float64_t > * | l, |
CDenseFeatures< float64_t > * | r | ||
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constructor
l | features of left-hand side |
r | features of right-hand side |
Definition at line 24 of file BrayCurtisDistance.cpp.
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virtual |
Definition at line 30 of file BrayCurtisDistance.cpp.
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inherited |
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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virtual |
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virtualinherited |
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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protectedvirtual |
compute distance for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
Implements CDistance.
Definition at line 46 of file BrayCurtisDistance.cpp.
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inherited |
compute row start offset for parallel kernel matrix computation
offs | offset |
n | number of columns |
symmetric | whether matrix is symmetric |
Definition at line 144 of file Distance.h.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
Definition at line 198 of file SGObject.cpp.
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virtualinherited |
get distance function for lhs feature vector a and rhs feature vector b
idx_a | feature vector a at idx_a |
idx_b | feature vector b at idx_b |
Definition at line 189 of file Distance.cpp.
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virtualinherited |
get distance function for lhs feature vector a and rhs feature vector b. The computation of the distance stops if the intermediate result is larger than upper_bound. This is useful to use with John Langford's Cover Tree and it is ONLY implemented for Euclidean distance
idx_a | feature vector a at idx_a |
idx_b | feature vector b at idx_b |
upper_bound | value above which the computation halts |
Reimplemented in CEuclideanDistance.
Definition at line 118 of file Distance.h.
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protectedinherited |
matrix precomputation
Definition at line 227 of file Distance.cpp.
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.
get distance matrix
Definition at line 127 of file Distance.h.
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inherited |
get distance matrix (templated)
Definition at line 317 of file Distance.cpp.
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staticinherited |
helper for computing the kernel matrix in a parallel way
p | thread parameters |
Definition at line 266 of file Distance.cpp.
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virtual |
get distance type we are
Implements CDenseDistance< float64_t >.
Definition at line 61 of file BrayCurtisDistance.h.
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virtualinherited |
get feature class the distance can deal with
Implements CDistance.
Definition at line 42 of file DenseDistance.h.
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virtualinherited |
get feature type the distance can deal with
Implements CDistance.
Reimplemented in CMahalanobisDistance, CEuclideanDistance, CAttenuatedEuclideanDistance, and CRealDistance.
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inherited |
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inherited |
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inherited |
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get left-hand side features used in distance matrix
Definition at line 195 of file Distance.h.
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inherited |
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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get name of the distance
Reimplemented from CDenseDistance< float64_t >.
Definition at line 67 of file BrayCurtisDistance.h.
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virtualinherited |
get number of vectors of lhs features
Reimplemented in CCustomDistance.
Definition at line 283 of file Distance.h.
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virtualinherited |
get number of vectors of rhs features
Reimplemented in CCustomDistance.
Definition at line 292 of file Distance.h.
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inherited |
FIXME: precompute matrix should be dropped, handling should be via customdistance
Definition at line 261 of file Distance.h.
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inherited |
get right-hand side features used in distance matrix
Definition at line 201 of file Distance.h.
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virtualinherited |
test whether features have been assigned to lhs and rhs
Reimplemented in CCustomDistance.
Definition at line 301 of file Distance.h.
init distance
l | features of left-hand side |
r | features of right-hand side |
Reimplemented from CDenseDistance< float64_t >.
Definition at line 35 of file BrayCurtisDistance.cpp.
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virtualinherited |
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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test whether features on lhs and rhs are the same
Definition at line 310 of file Distance.h.
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inherited |
load the kernel matrix
loader | File object via which to load data |
Definition at line 107 of file Distance.cpp.
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virtualinherited |
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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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::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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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::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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virtualinherited |
Definition at line 262 of file SGObject.cpp.
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inherited |
prints all parameter registered for model selection and their type
Definition at line 474 of file SGObject.cpp.
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virtualinherited |
prints registered parameters out
prefix | prefix for members |
Definition at line 308 of file SGObject.cpp.
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virtualinherited |
takes all necessary steps if the lhs is removed from distance matrix
Definition at line 130 of file Distance.cpp.
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virtualinherited |
remove lhs and rhs from distance
Definition at line 119 of file Distance.cpp.
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virtualinherited |
takes all necessary steps if the rhs is removed from distance matrix
takes all necessary steps if the rhs is removed from distance
Definition at line 138 of file Distance.cpp.
replace left-hand side features used in distance matrix
make sure to check that your distance can deal with the supplied features (!)
lhs | features of right-hand side |
Definition at line 167 of file Distance.cpp.
replace right-hand side features used in distance matrix
make sure to check that your distance can deal with the supplied features (!)
rhs | features of right-hand side |
Definition at line 145 of file Distance.cpp.
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staticprotectedinherited |
run distance thread
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inherited |
save kernel matrix
writer | File object via which to save data |
Definition at line 113 of file Distance.cpp.
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virtualinherited |
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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Definition at line 46 of file SGObject.cpp.
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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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Definition at line 61 of file SGObject.cpp.
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Definition at line 66 of file SGObject.cpp.
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Definition at line 71 of file SGObject.cpp.
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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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Definition at line 86 of file SGObject.cpp.
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Definition at line 91 of file SGObject.cpp.
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Definition at line 96 of file SGObject.cpp.
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Definition at line 101 of file SGObject.cpp.
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Definition at line 106 of file SGObject.cpp.
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Definition at line 111 of file SGObject.cpp.
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set generic type to T
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set the parallel object
parallel | parallel object to use |
Definition at line 241 of file SGObject.cpp.
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set the version object
version | version object to use |
Definition at line 283 of file SGObject.cpp.
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virtualinherited |
FIXME: precompute matrix should be dropped, handling should be via customdistance
flag | if precompute_matrix |
Definition at line 268 of file Distance.h.
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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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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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inherited |
io
Definition at line 369 of file SGObject.h.
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protectedinherited |
feature vectors to occur on the left hand side
Definition at line 343 of file Distance.h.
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inherited |
parameters wrt which we can compute gradients
Definition at line 384 of file SGObject.h.
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Hash of parameter values
Definition at line 387 of file SGObject.h.
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model selection parameters
Definition at line 381 of file SGObject.h.
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parameters
Definition at line 378 of file SGObject.h.
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protectedinherited |
number of feature vectors on the left hand side
Definition at line 348 of file Distance.h.
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protectedinherited |
number of feature vectors on the right hand side
Definition at line 350 of file Distance.h.
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parallel
Definition at line 372 of file SGObject.h.
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protectedinherited |
FIXME: precompute matrix should be dropped, handling should be via customdistance
Definition at line 340 of file Distance.h.
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protectedinherited |
FIXME: precompute matrix should be dropped, handling should be via customdistance
Definition at line 335 of file Distance.h.
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protectedinherited |
feature vectors to occur on the right hand side
Definition at line 345 of file Distance.h.
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inherited |
version
Definition at line 375 of file SGObject.h.