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CGUIStructure Class Reference

Detailed Description

UI structure.

Definition at line 28 of file GUIStructure.h.

Inheritance diagram for CGUIStructure:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CGUIStructure ()
 CGUIStructure (CSGInterface *interface)
 ~CGUIStructure ()
bool set_dyn_prog (CDynProg *h)
CDynProgget_dyn_prog ()
float64_tget_feature_matrix (bool copy)
CSparseFeatures< float64_t > * get_feature_matrix_sparse (int32_t index)
bool set_feature_matrix (float64_t *feat, int32_t *dims)
bool set_feature_matrix_sparse (SGSparseVector< float64_t > *f1, SGSparseVector< float64_t > *f2, int32_t *dims)
bool set_feature_dims (int32_t *dims)
int32_t * get_feature_dims ()
bool set_all_pos (int32_t *pos, int32_t Npos)
int32_t * get_all_positions ()
int32_t get_num_positions ()
bool set_content_svm_weights (float64_t *weights, int32_t Nweights, int32_t Mweights)
float64_tget_content_svm_weights ()
int32_t get_num_svm_weights ()
CPlifMatrixget_plif_matrix ()
bool set_orf_info (int32_t *orf_info, int32_t Norf_info, int32_t Morf_info)
int32_t * get_orf_info ()
bool set_use_orf (bool use_orf)
bool get_use_orf ()
bool set_mod_words (int32_t *mod_words, int32_t Nmod_words, int32_t Mmod_words)
int32_t * get_mod_words ()
int32_t get_num_states ()
bool set_num_states (int32_t num)
bool cleanup ()
virtual const char * get_name () const
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_copy () const
virtual bool is_generic (EPrimitiveType *generic) const
template<class T >
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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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 bool update_parameter_hash ()
virtual bool equals (CSGObject *other, float64_t accuracy=0.0)
virtual CSGObjectclone ()

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
Parameterm_gradient_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

virtual TParametermigrate (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)

Protected Attributes

CSGInterface * ui
int32_t m_num_plifs
int32_t m_num_limits
int32_t m_num_states
CDynProgm_dp
float64_tm_feature_matrix
CSparseFeatures< float64_t > * m_feature_matrix_sparse1
CSparseFeatures< float64_t > * m_feature_matrix_sparse2
int32_t * m_feature_dims
int32_t m_num_positions
int32_t * m_all_positions
float64_tm_content_svm_weights
int32_t m_num_svm_weights
int32_t * m_orf_info
bool m_use_orf
int32_t * m_mod_words
CPlifMatrixm_plif_matrix

Constructor & Destructor Documentation

constructor

Definition at line 32 of file GUIStructure.h.

CGUIStructure ( CSGInterface *  interface)

constructor

Parameters:
interface

Definition at line 20 of file GUIStructure.cpp.

destructor

Definition at line 31 of file GUIStructure.cpp.


Member Function Documentation

void build_gradient_parameter_dictionary ( CMap< TParameter *, CSGObject * > *  dict) [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.

Parameters:
dictdictionary of parameters to be built.

Definition at line 1156 of file SGObject.cpp.

bool cleanup ( )

cleanup

Definition at line 234 of file GUIStructure.h.

CSGObject * clone ( ) [virtual, inherited]

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.

Returns:
an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

Definition at line 1273 of file SGObject.cpp.

virtual CSGObject* deep_copy ( ) const [virtual, inherited]

A deep copy. All the instance variables will also be copied.

Definition at line 126 of file SGObject.h.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0 
) [virtual, inherited]

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.

Parameters:
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
Returns:
true if all parameters were equal, false if not

Definition at line 1177 of file SGObject.cpp.

int32_t* get_all_positions ( )

get all positions

Definition at line 144 of file GUIStructure.h.

get content svm weights

Definition at line 166 of file GUIStructure.h.

get dyn prog

Definition at line 51 of file GUIStructure.h.

int32_t* get_feature_dims ( )

get feature dims

Definition at line 127 of file GUIStructure.h.

float64_t* get_feature_matrix ( bool  copy)

get feature matrix

Parameters:
copy

Definition at line 61 of file GUIStructure.h.

get feature matrix sparse

Parameters:
index

Definition at line 77 of file GUIStructure.h.

SGIO * get_global_io ( ) [inherited]

get the io object

Returns:
io object

Definition at line 174 of file SGObject.cpp.

Parallel * get_global_parallel ( ) [inherited]

get the parallel object

Returns:
parallel object

Definition at line 209 of file SGObject.cpp.

Version * get_global_version ( ) [inherited]

get the version object

Returns:
version object

Definition at line 222 of file SGObject.cpp.

int32_t* get_mod_words ( )

get mod words

Definition at line 222 of file GUIStructure.h.

SGStringList< char > get_modelsel_names ( ) [inherited]
Returns:
vector of names of all parameters which are registered for model selection

Definition at line 1060 of file SGObject.cpp.

char * get_modsel_param_descr ( const char *  param_name) [inherited]

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters:
param_namename of the parameter
Returns:
description of the parameter

Definition at line 1084 of file SGObject.cpp.

index_t get_modsel_param_index ( const char *  param_name) [inherited]

Returns index of model selection parameter with provided index

Parameters:
param_namename of model selection parameter
Returns:
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1097 of file SGObject.cpp.

virtual const char* get_name ( ) const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 251 of file GUIStructure.h.

int32_t get_num_positions ( )

get num positions

Definition at line 146 of file GUIStructure.h.

int32_t get_num_states ( )

get num states

Definition at line 224 of file GUIStructure.h.

int32_t get_num_svm_weights ( )

get num svm weights

Definition at line 168 of file GUIStructure.h.

int32_t* get_orf_info ( )

get orf info

Definition at line 190 of file GUIStructure.h.

get plif matrix

Definition at line 171 of file GUIStructure.h.

bool get_use_orf ( )

get use orf

Definition at line 204 of file GUIStructure.h.

bool is_generic ( EPrimitiveType *  generic) const [virtual, inherited]

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters:
genericset to the type of the generic if returning TRUE
Returns:
TRUE if a class template.

Definition at line 228 of file SGObject.cpp.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

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)

Parameters:
file_versionparameter version of the file
current_versionversion from which mapping begins (you want to use Version::get_version_parameter() for this in most cases)
filefile to load from
prefixprefix for members
Returns:
(sorted) array of created TParameter instances with file data

Definition at line 633 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo param_info,
int32_t  file_version,
CSerializableFile file,
const char *  prefix = "" 
) [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

Parameters:
param_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
Returns:
new array with TParameter instances with the attached data

Definition at line 474 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
) [virtual, inherited]

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters:
filewhere to load from
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Definition at line 305 of file SGObject.cpp.

void load_serializable_post ( ) throw (ShogunException) [protected, virtual, inherited]

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.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 989 of file SGObject.cpp.

void load_serializable_pre ( ) throw (ShogunException) [protected, virtual, inherited]

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.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 984 of file SGObject.cpp.

void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
) [inherited]

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

Parameters:
param_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset of SGParamInfo instances that specify the target parameter base

Definition at line 671 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
) [protected, virtual, inherited]

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

Parameters:
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
Returns:
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 878 of file SGObject.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
) [protected, virtual, inherited]

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)

Parameters:
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith this parameter, a name change may be specified

Definition at line 818 of file SGObject.cpp.

void print_modsel_params ( ) [inherited]

prints all parameter registered for model selection and their type

Definition at line 1036 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "") [virtual, inherited]

prints registered parameters out

Parameters:
prefixprefix for members

Definition at line 240 of file SGObject.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
) [virtual, inherited]

Save this object to file.

Parameters:
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Definition at line 246 of file SGObject.cpp.

void save_serializable_post ( ) throw (ShogunException) [protected, virtual, inherited]

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.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 999 of file SGObject.cpp.

void save_serializable_pre ( ) throw (ShogunException) [protected, virtual, inherited]

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.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 994 of file SGObject.cpp.

bool set_all_pos ( int32_t *  pos,
int32_t  Npos 
)

set all pos

Parameters:
pos
Npos

Definition at line 133 of file GUIStructure.h.

bool set_content_svm_weights ( float64_t weights,
int32_t  Nweights,
int32_t  Mweights 
)

set content svm weights

Parameters:
weights
Nweights
Mweights

Definition at line 153 of file GUIStructure.h.

bool set_dyn_prog ( CDynProg h)

set dyn prog

Parameters:
h

Definition at line 43 of file GUIStructure.h.

bool set_feature_dims ( int32_t *  dims)

set feature dims

Parameters:
dims

Definition at line 119 of file GUIStructure.h.

bool set_feature_matrix ( float64_t feat,
int32_t *  dims 
)

set feature matrix

Parameters:
feat
dims

Definition at line 91 of file GUIStructure.h.

bool set_feature_matrix_sparse ( SGSparseVector< float64_t > *  f1,
SGSparseVector< float64_t > *  f2,
int32_t *  dims 
)

set feature matrix sparse

Parameters:
f1
f2
dims

Definition at line 105 of file GUIStructure.h.

void set_generic< complex128_t > ( ) [inherited]

set generic type to T

Definition at line 41 of file SGObject.cpp.

void set_global_io ( SGIO io) [inherited]

set the io object

Parameters:
ioio object to use

Definition at line 167 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel) [inherited]

set the parallel object

Parameters:
parallelparallel object to use

Definition at line 180 of file SGObject.cpp.

void set_global_version ( Version version) [inherited]

set the version object

Parameters:
versionversion object to use

Definition at line 215 of file SGObject.cpp.

bool set_mod_words ( int32_t *  mod_words,
int32_t  Nmod_words,
int32_t  Mmod_words 
)

set mod words

Parameters:
mod_words
Nmod_words
Mmod_words

Definition at line 211 of file GUIStructure.h.

bool set_num_states ( int32_t  num)

set num states

Parameters:
num

Definition at line 228 of file GUIStructure.h.

bool set_orf_info ( int32_t *  orf_info,
int32_t  Norf_info,
int32_t  Morf_info 
)

set orf info

Parameters:
orf_info
Norf_info
Morf_info

Definition at line 178 of file GUIStructure.h.

bool set_use_orf ( bool  use_orf)

set use orf

Parameters:
use_orf

Definition at line 198 of file GUIStructure.h.

virtual CSGObject* shallow_copy ( ) const [virtual, inherited]

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 117 of file SGObject.h.

void unset_generic ( ) [inherited]

unset generic type

this has to be called in classes specializing a template class

Definition at line 235 of file SGObject.cpp.

bool update_parameter_hash ( ) [virtual, inherited]

Updates the hash of current parameter combination.

Returns:
bool if parameter combination has changed since last update.

Definition at line 187 of file SGObject.cpp.


Member Data Documentation

SGIO* io [inherited]

io

Definition at line 473 of file SGObject.h.

int32_t* m_all_positions [protected]

all positions

Definition at line 275 of file GUIStructure.h.

content svm weights

Definition at line 277 of file GUIStructure.h.

CDynProg* m_dp [protected]

dp

Definition at line 263 of file GUIStructure.h.

int32_t* m_feature_dims [protected]

feature dims

Definition at line 271 of file GUIStructure.h.

feature matrix

Definition at line 265 of file GUIStructure.h.

feature matrix sparse 1

Definition at line 267 of file GUIStructure.h.

feature matrix sparse 2

Definition at line 269 of file GUIStructure.h.

parameters wrt which we can compute gradients

Definition at line 488 of file SGObject.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 494 of file SGObject.h.

int32_t* m_mod_words [protected]

mod words

Definition at line 285 of file GUIStructure.h.

model selection parameters

Definition at line 485 of file SGObject.h.

int32_t m_num_limits [protected]

num limits

Definition at line 259 of file GUIStructure.h.

int32_t m_num_plifs [protected]

num plifs

Definition at line 257 of file GUIStructure.h.

int32_t m_num_positions [protected]

num positions

Definition at line 273 of file GUIStructure.h.

int32_t m_num_states [protected]

num states

Definition at line 261 of file GUIStructure.h.

int32_t m_num_svm_weights [protected]

num svm weights

Definition at line 279 of file GUIStructure.h.

int32_t* m_orf_info [protected]

orf info

Definition at line 281 of file GUIStructure.h.

map for different parameter versions

Definition at line 491 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 482 of file SGObject.h.

CPlifMatrix* m_plif_matrix [protected]

plif matrix

Definition at line 287 of file GUIStructure.h.

bool m_use_orf [protected]

use orf

Definition at line 283 of file GUIStructure.h.

Parallel* parallel [inherited]

parallel

Definition at line 476 of file SGObject.h.

CSGInterface* ui [protected]

ui

Definition at line 255 of file GUIStructure.h.

Version* version [inherited]

version

Definition at line 479 of file SGObject.h.


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