SHOGUN
3.2.1
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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="", int32_t param_version=Version::get_version_parameter()) |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter()) |
DynArray< TParameter * > * | load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") |
DynArray< TParameter * > * | load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") |
void | map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos) |
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 |
ParameterMap * | m_parameter_map |
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 TParameter * | migrate (DynArray< TParameter * > *param_base, const SGParamInfo *target) |
virtual void | one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) |
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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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 1243 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 1360 of file SGObject.cpp.
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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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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 200 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 1264 of file SGObject.cpp.
get distance matrix
Definition at line 127 of file Distance.h.
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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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get distance type we are
Implements CDenseDistance< float64_t >.
Definition at line 61 of file BrayCurtisDistance.h.
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get feature class the distance can deal with
Implements CDistance.
Definition at line 42 of file DenseDistance.h.
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get feature type the distance can deal with
Implements CDistance.
Reimplemented in CMahalanobisDistance, CEuclideanDistance, CAttenuatedEuclideanDistance, and CRealDistance.
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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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Definition at line 1135 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 1159 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 1172 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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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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FIXME: precompute matrix should be dropped, handling should be via customdistance
Definition at line 261 of file Distance.h.
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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 297 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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load the kernel matrix
loader | File object via which to load data |
Definition at line 107 of file Distance.cpp.
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maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)
file_version | parameter version of the file |
current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
file | file to load from |
prefix | prefix for members |
Definition at line 704 of file SGObject.cpp.
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inherited |
loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned
param_info | information of parameter |
file_version | parameter version of the file, must be <= provided parameter version |
file | file to load from |
prefix | prefix for members |
Definition at line 545 of file SGObject.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 |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
Definition at line 374 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 1062 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 1057 of file SGObject.cpp.
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Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match
param_base | set of TParameter instances that are mapped to the provided target parameter infos |
base_version | version of the parameter base |
target_param_infos | set of SGParamInfo instances that specify the target parameter base |
Definition at line 742 of file SGObject.cpp.
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creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.
If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
Definition at line 949 of file SGObject.cpp.
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This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
replacement | (used as output) here the TParameter instance which is returned by migration is created into |
to_migrate | the only source that is used for migration |
old_name | with this parameter, a name change may be specified |
Definition at line 889 of file SGObject.cpp.
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Definition at line 263 of file SGObject.cpp.
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prints all parameter registered for model selection and their type
Definition at line 1111 of file SGObject.cpp.
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prints registered parameters out
prefix | prefix for members |
Definition at line 309 of file SGObject.cpp.
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takes all necessary steps if the lhs is removed from distance matrix
Definition at line 130 of file Distance.cpp.
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remove lhs and rhs from distance
Definition at line 119 of file Distance.cpp.
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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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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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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 |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
Definition at line 315 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 1072 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 1067 of file SGObject.cpp.
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Definition at line 42 of file SGObject.cpp.
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Definition at line 47 of file SGObject.cpp.
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Definition at line 52 of file SGObject.cpp.
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Definition at line 57 of file SGObject.cpp.
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Definition at line 62 of file SGObject.cpp.
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Definition at line 67 of file SGObject.cpp.
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Definition at line 72 of file SGObject.cpp.
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Definition at line 77 of file SGObject.cpp.
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Definition at line 82 of file SGObject.cpp.
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Definition at line 87 of file SGObject.cpp.
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Definition at line 92 of file SGObject.cpp.
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Definition at line 97 of file SGObject.cpp.
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Definition at line 102 of file SGObject.cpp.
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Definition at line 107 of file SGObject.cpp.
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Definition at line 112 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 243 of file SGObject.cpp.
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set the version object
version | version object to use |
Definition at line 284 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 194 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 304 of file SGObject.cpp.
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Updates the hash of current parameter combination
Definition at line 250 of file SGObject.cpp.
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io
Definition at line 496 of file SGObject.h.
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feature vectors to occur on the left hand side
Definition at line 343 of file Distance.h.
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parameters wrt which we can compute gradients
Definition at line 511 of file SGObject.h.
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Hash of parameter values
Definition at line 517 of file SGObject.h.
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model selection parameters
Definition at line 508 of file SGObject.h.
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map for different parameter versions
Definition at line 514 of file SGObject.h.
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parameters
Definition at line 505 of file SGObject.h.
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number of feature vectors on the left hand side
Definition at line 348 of file Distance.h.
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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 499 of file SGObject.h.
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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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feature vectors to occur on the right hand side
Definition at line 345 of file Distance.h.
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version
Definition at line 502 of file SGObject.h.