00001 #ifndef __SGINTERFACE__H_
00002 #define __SGINTERFACE__H_
00003
00004 #include <shogun/lib/memory.h>
00005 #include <shogun/lib/config.h>
00006 #include <shogun/lib/common.h>
00007 #include <shogun/base/SGObject.h>
00008 #include <shogun/features/Features.h>
00009 #include <shogun/features/StringFeatures.h>
00010 #include <shogun/features/SparseFeatures.h>
00011 #include <shogun/features/AttributeFeatures.h>
00012 #include <shogun/kernel/Kernel.h>
00013
00014 #include <shogun/ui/GUIClassifier.h>
00015 #include <shogun/ui/GUIDistance.h>
00016 #include <shogun/ui/GUIFeatures.h>
00017 #include <shogun/ui/GUIHMM.h>
00018 #include <shogun/ui/GUIKernel.h>
00019 #include <shogun/ui/GUILabels.h>
00020 #include <shogun/ui/GUIMath.h>
00021 #include <shogun/ui/GUIPluginEstimate.h>
00022 #include <shogun/ui/GUIPreprocessor.h>
00023 #include <shogun/ui/GUITime.h>
00024 #include <shogun/ui/GUIStructure.h>
00025 #include <shogun/ui/GUISignals.h>
00026
00027 namespace shogun
00028 {
00033 enum IFType
00034 {
00036 UNDEFINED,
00037
00039 SCALAR_INT,
00040 SCALAR_REAL,
00041 SCALAR_BOOL,
00042 STANDARD_STRING,
00043
00045 VECTOR_BOOL,
00046 VECTOR_BYTE,
00047 VECTOR_CHAR,
00048 VECTOR_INT,
00049 VECTOR_REAL,
00050 VECTOR_SHORTREAL,
00051 VECTOR_SHORT,
00052 VECTOR_WORD,
00053
00055 DENSE_INT,
00056 DENSE_REAL,
00057 DENSE_SHORTREAL,
00058 DENSE_SHORT,
00059 DENSE_WORD,
00060
00062 NDARRAY_BYTE,
00063 NDARRAY_CHAR,
00064 NDARRAY_INT,
00065 NDARRAY_REAL,
00066 NDARRAY_SHORTREAL,
00067 NDARRAY_SHORT,
00068 NDARRAY_WORD,
00069
00071 SPARSE_BYTE,
00072 SPARSE_CHAR,
00073 SPARSE_INT,
00074 SPARSE_REAL,
00075 SPARSE_SHORT,
00076 SPARSE_SHORTREAL,
00077 SPARSE_WORD,
00078
00080 STRING_BYTE,
00081 STRING_CHAR,
00082 STRING_INT,
00083 STRING_SHORT,
00084 STRING_WORD,
00085
00087 ATTR_STRUCT
00088 };
00089
00091 enum E_WHICH_OBJ
00092 {
00094 SVM_PRIMAL,
00096 SVM_DUAL,
00098 MKL_PRIMAL,
00100 MKL_DUAL,
00102 MKL_RELATIVE_DUALITY_GAP,
00104 MKL_ABSOLUTE_DUALITY_GAP
00105 };
00106
00108 class CSGInterface : public CSGObject
00109 {
00110 public:
00114 CSGInterface(bool print_copyrights=true);
00115
00117 ~CSGInterface();
00118
00120 virtual void reset();
00121
00123 void translate_arg(CSGInterface* source, CSGInterface* target);
00124
00125
00127 bool cmd_load_features();
00129 bool cmd_save_features();
00131 bool cmd_clean_features();
00133 bool cmd_get_features();
00135 bool cmd_add_features();
00137 bool cmd_add_multiple_features();
00139 bool cmd_add_dotfeatures();
00141 bool cmd_set_features();
00143 bool cmd_set_reference_features();
00145 bool cmd_del_last_features();
00147 bool cmd_convert();
00149 bool cmd_reshape();
00151 bool cmd_load_labels();
00153 bool cmd_set_labels();
00155 bool cmd_get_labels();
00156
00158 bool cmd_set_kernel_normalization();
00160 bool cmd_set_kernel();
00162 bool cmd_add_kernel();
00164 bool cmd_del_last_kernel();
00166 bool cmd_init_kernel();
00168 bool cmd_clean_kernel();
00170 bool cmd_save_kernel();
00172 bool cmd_load_kernel_init();
00174 bool cmd_save_kernel_init();
00176 bool cmd_get_kernel_matrix();
00178 bool cmd_set_WD_position_weights();
00180 bool cmd_get_subkernel_weights();
00182 bool cmd_set_subkernel_weights();
00184 bool cmd_set_subkernel_weights_combined();
00186 bool cmd_get_dotfeature_weights_combined();
00188 bool cmd_set_dotfeature_weights_combined();
00190 bool cmd_set_last_subkernel_weights();
00192 bool cmd_get_WD_position_weights();
00194 bool cmd_get_last_subkernel_weights();
00196 bool cmd_compute_by_subkernels();
00198 bool cmd_init_kernel_optimization();
00200 bool cmd_get_kernel_optimization();
00202 bool cmd_delete_kernel_optimization();
00204 bool cmd_use_diagonal_speedup();
00206 bool cmd_set_kernel_optimization_type();
00208 bool cmd_set_solver();
00210 bool cmd_set_constraint_generator();
00212 bool cmd_set_prior_probs();
00214 bool cmd_set_prior_probs_from_labels();
00215 #ifdef USE_SVMLIGHT
00216
00217 bool cmd_resize_kernel_cache();
00218 #endif //USE_SVMLIGHT
00219
00220
00222 bool cmd_set_distance();
00224 bool cmd_init_distance();
00226 bool cmd_get_distance_matrix();
00227
00229 bool cmd_get_SPEC_consensus();
00231 bool cmd_get_SPEC_scoring();
00233 bool cmd_get_WD_consensus();
00235 bool cmd_compute_POIM_WD();
00237 bool cmd_get_WD_scoring();
00238
00240 bool cmd_new_classifier();
00242 bool cmd_load_classifier();
00244 bool cmd_save_classifier();
00246 bool cmd_get_svm();
00248 bool cmd_get_num_svms();
00250 bool cmd_set_svm();
00252 bool cmd_set_linear_classifier();
00254 bool cmd_classify();
00256 bool cmd_classify_example();
00258 bool cmd_get_classifier();
00260 bool cmd_get_svm_objective();
00262 bool cmd_compute_svm_primal_objective();
00264 bool cmd_compute_svm_dual_objective();
00266 bool cmd_compute_mkl_dual_objective();
00268 bool cmd_compute_relative_mkl_duality_gap();
00270 bool cmd_compute_absolute_mkl_duality_gap();
00272 bool cmd_train_classifier();
00274 bool cmd_do_auc_maximization();
00276 bool cmd_set_perceptron_parameters();
00278 bool cmd_set_svm_qpsize();
00280 bool cmd_set_svm_max_qpsize();
00282 bool cmd_set_svm_bufsize();
00284 bool cmd_set_svm_C();
00286 bool cmd_set_svm_epsilon();
00288 bool cmd_set_svr_tube_epsilon();
00290 bool cmd_set_svm_nu();
00292 bool cmd_set_svm_mkl_parameters();
00294 bool cmd_set_elasticnet_lambda();
00296 bool cmd_set_mkl_block_norm();
00298 bool cmd_set_max_train_time();
00300 bool cmd_set_svm_mkl_enabled();
00302 bool cmd_set_svm_shrinking_enabled();
00304 bool cmd_set_svm_batch_computation_enabled();
00306 bool cmd_set_svm_linadd_enabled();
00308 bool cmd_set_svm_bias_enabled();
00310 bool cmd_set_mkl_interleaved_enabled();
00312 bool cmd_set_krr_tau();
00313
00315 bool cmd_add_preproc();
00317 bool cmd_del_preproc();
00319 bool cmd_attach_preproc();
00321 bool cmd_clean_preproc();
00322
00324 bool cmd_new_hmm();
00326 bool cmd_load_hmm();
00328 bool cmd_save_hmm();
00330 bool cmd_hmm_classify();
00332 bool cmd_hmm_classify_example();
00334 bool cmd_one_class_linear_hmm_classify();
00336 bool cmd_one_class_hmm_classify();
00338 bool cmd_one_class_hmm_classify_example();
00340 bool cmd_output_hmm();
00342 bool cmd_output_hmm_defined();
00344 bool cmd_hmm_likelihood();
00346 bool cmd_likelihood();
00348 bool cmd_save_likelihood();
00350 bool cmd_get_viterbi_path();
00352 bool cmd_viterbi_train_defined();
00354 bool cmd_viterbi_train();
00356 bool cmd_baum_welch_train();
00358 bool cmd_baum_welch_train_defined();
00360 bool cmd_baum_welch_trans_train();
00362 bool cmd_linear_train();
00364 bool cmd_save_path();
00366 bool cmd_append_hmm();
00368 bool cmd_append_model();
00370 bool cmd_set_hmm();
00372 bool cmd_set_hmm_as();
00374 bool cmd_get_hmm();
00376 bool cmd_set_chop();
00378 bool cmd_set_pseudo();
00380 bool cmd_load_definitions();
00382 bool cmd_convergence_criteria();
00384 bool cmd_normalize();
00386 bool cmd_add_states();
00388 bool cmd_permutation_entropy();
00390 bool cmd_relative_entropy();
00392 bool cmd_entropy();
00394 bool cmd_new_plugin_estimator();
00396 bool cmd_train_estimator();
00398 bool cmd_plugin_estimate_classify_example();
00400 bool cmd_plugin_estimate_classify();
00402 bool cmd_set_plugin_estimate();
00404 bool cmd_get_plugin_estimate();
00406 bool cmd_best_path();
00408 bool cmd_best_path_2struct();
00414 bool cmd_set_plif_struct();
00421 bool cmd_get_plif_struct();
00425 bool cmd_precompute_subkernels();
00429 bool cmd_signals_set_model() { return false; };
00433 bool cmd_signals_set_positions();
00437 bool cmd_signals_set_labels();
00441 bool cmd_signals_set_split();
00445 bool cmd_signals_set_train_mask();
00449 bool cmd_signals_add_feature();
00453 bool cmd_signals_add_kernel();
00457 bool cmd_signals_run();
00470 bool cmd_precompute_content_svms();
00474 bool cmd_get_lin_feat();
00478 bool cmd_set_lin_feat();
00479
00483 bool cmd_init_dyn_prog();
00484
00488 bool cmd_clean_up_dyn_prog();
00489
00493 bool cmd_init_intron_list();
00494
00496 bool cmd_long_transition_settings();
00497
00506 bool cmd_precompute_tiling_features();
00518 bool cmd_set_model();
00523 bool cmd_set_feature_matrix_sparse();
00528 bool cmd_set_feature_matrix();
00530 bool cmd_best_path_trans();
00532 bool cmd_best_path_trans_deriv();
00534 bool cmd_best_path_no_b();
00536 bool cmd_best_path_no_b_trans();
00537
00539 bool cmd_crc();
00541 bool cmd_system();
00543 bool cmd_exit();
00545 bool cmd_exec();
00547 bool cmd_set_output();
00549 bool cmd_set_threshold();
00551 bool cmd_init_random();
00553 bool cmd_set_num_threads();
00555 bool cmd_translate_string();
00557 bool cmd_clear();
00559 bool cmd_tic();
00561 bool cmd_toc();
00563 bool cmd_echo();
00565 bool cmd_print();
00567 bool cmd_loglevel();
00569 bool cmd_progress();
00571 bool cmd_syntax_highlight();
00573 bool cmd_get_version();
00575 bool cmd_help();
00577 bool cmd_whos();
00579 bool cmd_send_command();
00581 virtual bool cmd_run_python();
00583 virtual bool cmd_run_octave();
00585 virtual bool cmd_run_r();
00587 virtual bool cmd_pr_loqo();
00588
00591
00592 virtual IFType get_argument_type()=0;
00593
00595 virtual int32_t get_int()=0;
00597 virtual float64_t get_real()=0;
00599 virtual bool get_bool()=0;
00600
00604 virtual char* get_string(int32_t& len)=0;
00605
00610 virtual void get_vector(bool*& vector, int32_t& len);
00615 virtual void get_vector(uint8_t*& vector, int32_t& len)=0;
00620 virtual void get_vector(char*& vector, int32_t& len)=0;
00625 virtual void get_vector(int32_t*& vector, int32_t& len)=0;
00630 virtual void get_vector(float64_t*& vector, int32_t& len)=0;
00635 virtual void get_vector(float32_t*& vector, int32_t& len)=0;
00640 virtual void get_vector(int16_t*& vector, int32_t& len)=0;
00645 virtual void get_vector(uint16_t*& vector, int32_t& len)=0;
00646
00652 virtual void get_matrix(
00653 uint8_t*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00659 virtual void get_matrix(
00660 char*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00666 virtual void get_matrix(
00667 int32_t*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00673 virtual void get_matrix(
00674 float32_t*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00680 virtual void get_matrix(
00681 float64_t*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00687 virtual void get_matrix(
00688 int16_t*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00694 virtual void get_matrix(
00695 uint16_t*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00696
00702 virtual void get_ndarray(
00703 uint8_t*& array, int32_t*& dims, int32_t& num_dims)=0;
00709 virtual void get_ndarray(
00710 char*& array, int32_t*& dims, int32_t& num_dims)=0;
00716 virtual void get_ndarray(
00717 int32_t*& array, int32_t*& dims, int32_t& num_dims)=0;
00723 virtual void get_ndarray(
00724 float32_t*& array, int32_t*& dims, int32_t& num_dims)=0;
00730 virtual void get_ndarray(
00731 float64_t*& array, int32_t*& dims, int32_t& num_dims)=0;
00737 virtual void get_ndarray(
00738 int16_t*& array, int32_t*& dims, int32_t& num_dims)=0;
00744 virtual void get_ndarray(
00745 uint16_t*& array, int32_t*& dims, int32_t& num_dims)=0;
00746
00752 virtual void get_sparse_matrix(
00753 SGSparseVector<float64_t>*& matrix, int32_t& num_feat, int32_t& num_vec)=0;
00754
00755
00756
00757
00758
00759
00760
00761
00762
00763
00769 virtual void get_string_list(
00770 SGString<uint8_t>*& strings, int32_t& num_str,
00771 int32_t& max_string_len)=0;
00777 virtual void get_string_list(
00778 SGString<char>*& strings, int32_t& num_str,
00779 int32_t& max_string_len)=0;
00785 virtual void get_string_list(
00786 SGString<int32_t>*& strings, int32_t& num_str,
00787 int32_t& max_string_len)=0;
00793 virtual void get_string_list(
00794 SGString<int16_t>*& strings, int32_t& num_str,
00795 int32_t& max_string_len)=0;
00801 virtual void get_string_list(
00802 SGString<uint16_t>*& strings, int32_t& num_str,
00803 int32_t& max_string_len)=0;
00804
00808 virtual void get_attribute_struct(
00809 const CDynamicArray<T_ATTRIBUTE>* &attrs)=0;
00810
00811
00815 virtual bool create_return_values(int32_t num_val)=0;
00816
00820 virtual void set_int(int32_t scalar)=0;
00824 virtual void set_real(float64_t scalar)=0;
00828 virtual void set_bool(bool scalar)=0;
00829
00834 virtual void set_vector(const bool* vector, int32_t len);
00839 virtual void set_vector(const uint8_t* vector, int32_t len)=0;
00844 virtual void set_vector(const char* vector, int32_t len)=0;
00849 virtual void set_vector(const int32_t* vector, int32_t len)=0;
00854 virtual void set_vector(const float32_t* vector, int32_t len)=0;
00859 virtual void set_vector(const float64_t* vector, int32_t len)=0;
00864 virtual void set_vector(const int16_t* vector, int32_t len)=0;
00869 virtual void set_vector(const uint16_t* vector, int32_t len)=0;
00870
00876 virtual void set_matrix(
00877 const uint8_t* matrix, int32_t num_feat, int32_t num_vec)=0;
00883 virtual void set_matrix(
00884 const char* matrix, int32_t num_feat, int32_t num_vec)=0;
00890 virtual void set_matrix(
00891 const int32_t* matrix, int32_t num_feat, int32_t num_vec)=0;
00897 virtual void set_matrix(
00898 const float32_t* matrix, int32_t num_feat, int32_t num_vec)=0;
00904 virtual void set_matrix(
00905 const float64_t* matrix, int32_t num_feat, int32_t num_vec)=0;
00911 virtual void set_matrix(
00912 const int16_t* matrix, int32_t num_feat, int32_t num_vec)=0;
00918 virtual void set_matrix(
00919 const uint16_t* matrix, int32_t num_feat, int32_t num_vec)=0;
00920
00927 virtual void set_sparse_matrix(
00928 const SGSparseVector<float64_t>* matrix, int32_t num_feat,
00929 int32_t num_vec, int64_t nnz)=0;
00930
00931
00932
00933
00934
00935
00936
00937
00938
00939
00944 virtual void set_string_list(
00945 const SGString<uint8_t>* strings, int32_t num_str)=0;
00950 virtual void set_string_list(
00951 const SGString<char>* strings, int32_t num_str)=0;
00956 virtual void set_string_list(
00957 const SGString<int32_t>* strings, int32_t num_str)=0;
00962 virtual void set_string_list(
00963 const SGString<int16_t>* strings, int32_t num_str)=0;
00968 virtual void set_string_list(
00969 const SGString<uint16_t>* strings, int32_t num_str)=0;
00970
00974 virtual void set_attribute_struct(
00975 const CDynamicArray<T_ATTRIBUTE>* attrs)=0;
00976
00978 bool handle();
00979
00981 void print_prompt();
00982
00984 int32_t get_nlhs() { return m_nlhs; }
00985
00987 int32_t get_nrhs() { return m_nrhs; }
00988
00989
00990
00992 CGUIClassifier* ui_classifier;
00994 CGUIDistance* ui_distance;
00996 CGUIFeatures* ui_features;
00998 CGUIHMM* ui_hmm;
01000 CGUIKernel* ui_kernel;
01002 CGUILabels* ui_labels;
01004 CGUIMath* ui_math;
01006 CGUIPluginEstimate* ui_pluginestimate;
01008 CGUIPreprocessor* ui_preproc;
01010 CGUITime* ui_time;
01012 CGUIStructure* ui_structure;
01013
01014
01015 protected:
01023 static bool strmatch(const char* str, const char* cmd, int32_t len=-1)
01024 {
01025 if (len==-1)
01026 {
01027 len=strlen(cmd);
01028 if (strlen(str)!=(size_t) len)
01029 return false;
01030 }
01031
01032 return (strncmp(str, cmd, len)==0);
01033 }
01034
01039 static bool strendswith(const char* str, const char* cmd)
01040 {
01041 size_t idx=strlen(str);
01042 size_t len=strlen(cmd);
01043
01044 if (strlen(str) < len)
01045 return false;
01046
01047 str=&str[idx-len];
01048
01049 return (strncmp(str, cmd, len)==0);
01050 }
01052 char* get_command(int32_t &len)
01053 {
01054 ASSERT(m_rhs_counter==0);
01055 if (m_nrhs<=0)
01056 SG_SERROR("No input arguments supplied.\n");
01057
01058 return get_string(len);
01059 }
01060 private:
01062 bool do_compute_objective(E_WHICH_OBJ obj);
01064 bool do_hmm_classify(bool linear=false, bool one_class=false);
01066 bool do_hmm_classify_example(bool one_class=false);
01068 bool do_set_features(bool add=false, bool check_dot=false, int32_t repetitions=1);
01069
01071 void convert_to_bitembedding(CFeatures* &features, bool convert_to_word, bool convert_to_ulong);
01073 void obtain_from_single_string(CFeatures* features);
01075 bool obtain_from_position_list(CFeatures* features);
01077 bool obtain_by_sliding_window(CFeatures* features);
01079 CKernel* create_kernel();
01080
01082 CFeatures* create_custom_string_features(CStringFeatures<uint8_t>* f);
01083
01084 CFeatures* create_custom_real_features(CSimpleFeatures<float64_t>* orig_feat);
01086 char* get_str_from_str_or_direct(int32_t& len);
01087 int32_t get_int_from_int_or_str();
01088 float64_t get_real_from_real_or_str();
01089 bool get_bool_from_bool_or_str();
01090 void get_vector_from_int_vector_or_str(
01091 int32_t*& vector, int32_t& len);
01092 void get_vector_from_real_vector_or_str(
01093 float64_t*& vector, int32_t& len);
01094 int32_t get_vector_len_from_str(int32_t expected_len=0);
01095 char* get_str_from_str(int32_t& len);
01096 int32_t get_num_args_in_str();
01097
01100 char* get_line(FILE* infile=stdin, bool show_prompt=true);
01101
01102 protected:
01104 int32_t m_lhs_counter;
01106 int32_t m_rhs_counter;
01108 int32_t m_nlhs;
01110 int32_t m_nrhs;
01111
01112
01114 FILE* file_out;
01116 char input[10000];
01118 bool echo;
01119
01121 char* m_legacy_strptr;
01122 };
01123
01125 typedef bool (CSGInterface::*CSGInterfacePtr)();
01126
01127 #ifndef DOXYGEN_SHOULD_SKIP_THIS
01128
01129 typedef struct {
01131 const char* command;
01133 CSGInterfacePtr method;
01135 const char* usage_prefix;
01137 const char* usage_suffix;
01138 } CSGInterfaceMethod;
01139 }
01140 #endif
01141
01142 #endif // __SGINTERFACE__H_
