GUIFeatures.cpp

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/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 1999-2008 Soeren Sonnenburg
 * Written (W) 1999-2008 Gunnar Raetsch
 * Copyright (C) 1999-2008 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#include <shogun/ui/GUIFeatures.h>
#include <shogun/ui/SGInterface.h>

#include <shogun/lib/config.h>
#include <shogun/io/SGIO.h>
#include <shogun/io/AsciiFile.h>

using namespace shogun;

CGUIFeatures::CGUIFeatures(CSGInterface* ui_)
: CSGObject(), ui(ui_), train_features(NULL), test_features(NULL),
    ref_features(NULL)
{
}

CGUIFeatures::~CGUIFeatures()
{
    SG_UNREF(train_features);
    SG_UNREF(test_features);
    SG_UNREF(ref_features);
}

void CGUIFeatures::invalidate_train()
{
    CKernel *k = ui->ui_kernel->get_kernel();
    if (k)
        k->remove_lhs();
}

void CGUIFeatures::invalidate_test()
{
    CKernel *k = ui->ui_kernel->get_kernel();
    if (k)
        k->remove_rhs();
}

bool CGUIFeatures::load(
    char* filename, char* fclass, char* type, char* target, int32_t size,
    int32_t comp_features)
{
    bool result=false;
    CFeatures** f_ptr=NULL;

    if (strncmp(target, "TRAIN", 5)==0)
    {
        f_ptr=&train_features;
        invalidate_train();
    }
    else if (strncmp(target, "TEST", 4)==0)
    {
        f_ptr=&test_features;
        invalidate_test();
    }
    else
        SG_ERROR("Unknown target %s, neither TRAIN nor TEST.\n", target);

    SG_UNREF(*f_ptr);
    *f_ptr=NULL;

    CAsciiFile* file=new CAsciiFile(filename);
    if (strncmp(fclass, "SIMPLE", 6)==0)
    {
        if (strncmp(type, "REAL", 4)==0)
        {
            *f_ptr=new CDenseFeatures<float64_t>(file);
        }
        else if (strncmp(type, "BYTE", 4)==0)
        {
            *f_ptr=new CDenseFeatures<uint8_t>(file);
        }
        else if (strncmp(type, "CHAR", 4)==0)
        {
            *f_ptr=new CDenseFeatures<char>(file);
        }
        else if (strncmp(type, "SHORT", 5)==0)
        {
            *f_ptr=new CDenseFeatures<int16_t>(file);
        }
        else
        {
            SG_ERROR("Unknown type.\n");
            return false;
        }
    }
    else if (strncmp(fclass, "SPARSE", 6)==0)
    {
        SG_NOTIMPLEMENTED;
    }
    else if (strncmp(fclass, "STRING", 6)==0)
    {
        if (strncmp(type, "REAL", 4)==0)
        {
            *f_ptr=new CStringFeatures<float64_t>(file);
        }
        else if (strncmp(type, "BYTE", 4)==0)
        {
            *f_ptr=new CStringFeatures<uint8_t>(file, DNA);
        }
        else if (strncmp(type, "CHAR", 4)==0)
        {
            *f_ptr=new CStringFeatures<char>(file, DNA);
        }
        else if (strncmp(type, "SHORT", 5)==0)
        {
            *f_ptr=new CStringFeatures<int16_t>(file);
        }
        else if (strncmp(type, "WORD", 4)==0)
        {
            *f_ptr=new CStringFeatures<uint16_t>(file);
        }
        else if (strncmp(type, "ULONG", 5)==0)
        {
            *f_ptr=new CStringFeatures<uint64_t>(file);
        }
        else
        {
            SG_ERROR("Unknown type.\n");
            return false;
        }
    }
    SG_UNREF(file);

    return result;
}

bool CGUIFeatures::save(char* filename, char* type, char* target)
{
    bool result=false;

    CFeatures** f_ptr=NULL;

    if (strncmp(target, "TRAIN", 5)==0)
    {
        f_ptr=&train_features;
    }
    else if (strncmp(target, "TEST", 4)==0)
    {
        f_ptr=&test_features;
    }
    else
        SG_ERROR("Unknown target %s, neither TRAIN nor TEST.\n", target);

    if (*f_ptr)
    {
        try
        {
            CAsciiFile* file=new CAsciiFile(filename, 'w');
            if (strncmp(type, "REAL", 4)==0)
            {
                ((CDenseFeatures<float64_t>*) (*f_ptr))->save(file);
            }
            else if (strncmp(type, "BYTE", 4)==0)
            {
                ((CDenseFeatures<uint8_t>*) (*f_ptr))->save(file);
            }
            else if (strncmp(type, "CHAR", 4)==0)
            {
                ((CDenseFeatures<char>*) (*f_ptr))->save(file);
            }
            else if (strncmp(type, "SHORT", 5)==0)
            {
                ((CDenseFeatures<int16_t>*) (*f_ptr))->save(file);
            }
            else if (strncmp(type, "WORD", 4)==0)
            {
                ((CDenseFeatures<uint16_t>*) (*f_ptr))->save(file);
            }
            else
            {
                SG_ERROR("Unknown type.\n");
                return false;
            }
            SG_UNREF(file);
        }
        catch (...)
        {
            SG_ERROR("Writing to file %s failed!\n", filename);
        }

        SG_INFO( "Successfully written features into \"%s\" !\n", filename);
        result=true;

    } else
        SG_ERROR("Set features first.\n");

    return result;
}

bool CGUIFeatures::clean(char* target)
{
    if (strncmp(target, "TRAIN", 5)==0)
        set_train_features(NULL);
    else if (strncmp(target, "TEST", 4)==0)
        set_test_features(NULL);
    else
        SG_ERROR("Unknown target %s, neither TRAIN nor TEST.\n", target);

    return true;
}

bool CGUIFeatures::reshape(char* target, int32_t num_feat, int32_t num_vec)
{
    CFeatures** f_ptr=NULL;

    if (strncmp(target, "TRAIN", 5)==0)
    {
        f_ptr=&train_features;
        invalidate_train();
    }
    else if (strncmp(target, "TEST", 4)==0)
    {
        f_ptr=&test_features;
        invalidate_test();
    }
    else
    {
        SG_ERROR("Invalid target %s\n", target);
        return false;
    }

    bool result=false;
    if (f_ptr)
    {
        SG_INFO( "reshape data to %d x %d\n", num_feat, num_vec);
        result=(*f_ptr)->reshape(num_feat, num_vec);

        if (!result)
            SG_ERROR("Reshaping failed.\n");
    }

    return result;
}

CFeatures* CGUIFeatures::get_convert_features(char* target)
{
    CFeatures* features;

    if (strncmp(target, "TEST", 4)==0)
        features=get_test_features();
    else if (strncmp(target, "TRAIN", 5)==0)
        features=get_train_features();
    else
        return NULL;

    if (features->get_feature_class()==C_COMBINED)
        features=((CCombinedFeatures*) features)->get_last_feature_obj();

    return features;
}

bool CGUIFeatures::set_convert_features(CFeatures* features, char* target)
{
    CFeatures* features_prev;

    if (strncmp(target, "TEST", 4)==0)
        features_prev=get_test_features();
    else if (strncmp(target, "TRAIN", 5)==0)
        features_prev=get_train_features();
    else
        return false;

    // in case of combined features delete current (==last) feature obj
    // pointer from list (feature object got deleted already above)
    // and append *f_ptr which holds the newly created feature object
    if (features_prev->get_feature_class()==C_COMBINED)
    {
        CCombinedFeatures* combined=(CCombinedFeatures*) features_prev;
        combined->delete_feature_obj();
        combined->append_feature_obj(features);
        combined->list_feature_objs();
    }
    else // set features to new test/train features
    {
        if (strncmp(target, "TEST", 4)==0)
            set_test_features(features);
        else
            set_train_features(features);
    }

    return true;
}

CSparseFeatures<float64_t>* CGUIFeatures::convert_simple_real_to_sparse_real(
    CDenseFeatures<float64_t>* src)
{
    if (src &&
        src->get_feature_class()==C_DENSE &&
        src->get_feature_type()==F_DREAL)
    {
        //create sparse features with 0 cache
        SG_INFO("Attempting to convert dense feature matrix to a sparse one.\n");
        CSparseFeatures<float64_t>* target=new CSparseFeatures<float64_t>(0);
        int32_t num_f=0;
        int32_t num_v=0;
        float64_t* feats=src->get_feature_matrix(num_f, num_v);
        if (target->set_full_feature_matrix(SGMatrix<float64_t>(feats, num_f, num_v)))
            return target;

        SG_UNREF(target);
    }
    else
        SG_ERROR("No SIMPLE DREAL features available.\n");

    return NULL;
}

CStringFeatures<char>* CGUIFeatures::convert_simple_char_to_string_char(
    CDenseFeatures<char>* src)
{
    if (src && src->get_feature_class()==C_DENSE)
    {
        int32_t num_vec=src->get_num_vectors();
        SGString<char>* strings=SG_MALLOC(SGString<char>, num_vec);
        int32_t max_len=-1;

        for (int32_t i=0; i<num_vec; i++)
        {
            bool to_free=false;
            int32_t len=0;
            char* str=src->get_feature_vector(i, len, to_free);
            strings[i].slen=len ;
            for (int32_t j=0; j<len; j++)
                if (str[j]==0)
                {
                    strings[i].slen=j ;
                    break ;
                } ;
            strings[i].string=SG_MALLOC(char, strings[i].slen);

            for (int32_t j=0; j<strings[i].slen; j++)
                strings[i].string[j]=str[j];

            if (strings[i].slen> max_len)
                max_len=strings[i].slen;

            src->free_feature_vector(str, i, to_free);
        }

        CStringFeatures<char>* target=new CStringFeatures<char>(new CAlphabet(DNA));
        target->set_features(strings, num_vec, max_len);
        return target;
    }
    else
        SG_ERROR("No features of class/type SIMPLE/CHAR available.\n");

    return NULL;
}

CDenseFeatures<float64_t>* CGUIFeatures::convert_simple_word_to_simple_salzberg(
    CDenseFeatures<uint16_t>* src)
{
    CPluginEstimate* pie=ui->ui_pluginestimate->get_estimator();

    if (src &&
        src->get_feature_type()==F_WORD &&
        src->get_feature_class()==C_DENSE &&
        pie)
    {
        CDenseFeatures<float64_t>* target=new CDenseFeatures<float64_t>(0);
        int32_t num_feat=src->get_num_features();
        int32_t num_vec=src->get_num_vectors();
        float64_t* fm=SG_MALLOC(float64_t, num_vec*num_feat);

        if (fm)
        {
            for (int32_t i=0; i<num_vec; i++)
            {
                int32_t len=0;
                bool to_free=false;
                uint16_t* vec = src->get_feature_vector(i, len, to_free);
                ASSERT(num_feat==len);

                for (int32_t j=0; j<num_feat; j++)
                    fm[i*num_feat+j]=
                        pie->get_parameterwise_log_odds(vec[j], j);

                src->free_feature_vector(vec, i, to_free);
            }
            target->set_feature_matrix(SGMatrix<float64_t>(fm, num_feat, num_vec));

        }
        return target;
    }
    else
        SG_ERROR("No SIMPLE WORD features or PluginEstimator available.\n");

    return NULL;
}


CTOPFeatures* CGUIFeatures::convert_string_word_to_simple_top(
    CStringFeatures<uint16_t>* src)
{
    CTOPFeatures* tf=NULL;

    if (src &&
        src->get_feature_class()==C_DENSE &&
        src->get_feature_type()==F_WORD)
    {
        SG_INFO("Converting to TOP features.\n");

        if (ui->ui_hmm->get_pos() && ui->ui_hmm->get_neg())
        {
            ui->ui_hmm->get_pos()->set_observations(src);
            ui->ui_hmm->get_neg()->set_observations(src);

            bool neglinear=false;
            bool poslinear=false;

            tf=new CTOPFeatures(
                0, ui->ui_hmm->get_pos(), ui->ui_hmm->get_neg(),
                neglinear, poslinear);
            ASSERT(tf->set_feature_matrix());
        }
        else
            SG_ERROR("HMMs not correctly assigned!\n");
    }
    else
        SG_ERROR("No SIMPLE WORD features available.\n");

    return tf;
}

CFKFeatures* CGUIFeatures::convert_string_word_to_simple_fk(
    CStringFeatures<uint16_t>* src)
{
    CFKFeatures* fkf=NULL;

    SG_INFO("Converting to FK features.\n");

    if (ui->ui_hmm->get_pos() && ui->ui_hmm->get_neg())
    {
        CStringFeatures<uint16_t>* old_obs_pos=
            ui->ui_hmm->get_pos()->get_observations();
        CStringFeatures<uint16_t>* old_obs_neg=
            ui->ui_hmm->get_neg()->get_observations();

        CStringFeatures<uint16_t>* string_feat=src;
        ui->ui_hmm->get_pos()->set_observations(string_feat);
        ui->ui_hmm->get_neg()->set_observations(string_feat);

        fkf=new CFKFeatures(
            0, ui->ui_hmm->get_pos(), ui->ui_hmm->get_neg());
            //, neglinear, poslinear);
        if (train_features)
            fkf->set_opt_a(((CFKFeatures*) train_features)->get_weight_a());
        else
            SG_ERROR("Need train features to set optimal a.\n");

        ASSERT(fkf->set_feature_matrix());

        ui->ui_hmm->get_pos()->set_observations(old_obs_pos);
        ui->ui_hmm->get_neg()->set_observations(old_obs_neg);
    }
    else
        SG_ERROR("HMMs not correctly assigned!\n");

    return fkf;
}


CDenseFeatures<float64_t>* CGUIFeatures::convert_sparse_real_to_simple_real(
    CSparseFeatures<float64_t>* src)
{
    if (src &&
        src->get_feature_class()==C_SPARSE &&
        src->get_feature_type() == F_DREAL)
    {
        //create dense features with 0 cache
        SG_INFO("Attempting to convert sparse feature matrix to a dense one.\n");
        CDenseFeatures<float64_t>* rf=new CDenseFeatures<float64_t>(0);
        if (rf)
        {
            SGMatrix<float64_t> feats=src->get_full_feature_matrix();
            rf->set_feature_matrix(feats);
            return rf;
        }
    }
    else
        SG_ERROR("No SPARSE REAL features available.\n");

    return NULL;
}

CExplicitSpecFeatures* CGUIFeatures::convert_string_byte_to_spec_word(
        CStringFeatures<uint16_t>* src, bool use_norm)
{
    return new CExplicitSpecFeatures(src, use_norm);
}

CDenseFeatures<float64_t>* CGUIFeatures::convert_simple_char_to_simple_align(
    CDenseFeatures<char>* src, float64_t gap_cost)
{
    if (src &&
        src->get_feature_class()==C_DENSE &&
        src->get_feature_type()==F_CHAR)
    {
        //create dense features with 0 cache
        SG_INFO("Converting CHAR features to REAL ones.\n");

        CDenseFeatures<float64_t>* rf=new CDenseFeatures<float64_t>(0);
        if (rf)
        {
            SG_INFO("Start aligment with gapCost=%1.2f.\n", gap_cost);
            /*rf->Align_char_features(
                src, (CDenseFeatures<char>*) ref_features, gap_cost);*/
            SG_INFO("Conversion was successful.\n");
            return rf;
        }
    }
    else
        SG_ERROR("No SIMPLE CHAR features available.\n");

    SG_ERROR("Conversion failed.\n");
    return NULL;
}

bool CGUIFeatures::set_reference_features(char* target)
{
    if (strncmp(target, "TRAIN", 5)==0)
    {
        SG_UNREF(ref_features);
        ref_features=train_features;
        train_features=NULL;
        invalidate_train();
        return true;
    }
    else if (strncmp(target, "TEST", 4)==0)
    {
        SG_UNREF(ref_features);
        ref_features=test_features;
        test_features=NULL;
        invalidate_test();
        return true;
    }

    return false;
}

void CGUIFeatures::add_train_features(CFeatures* f)
{
    ASSERT(f);
    invalidate_train();

    if (!train_features)
    {
        train_features=new CCombinedFeatures();
        SG_REF(train_features);
    }

    if (train_features->get_feature_class()!=C_COMBINED)
    {
        CFeatures* first_elem=train_features;
        train_features=new CCombinedFeatures();
        SG_REF(train_features);
        ((CCombinedFeatures*) train_features)->append_feature_obj(first_elem);
        ((CCombinedFeatures*) train_features)->list_feature_objs();
        SG_UNREF(first_elem);
    }

    bool result=((CCombinedFeatures*) train_features)->append_feature_obj(f);
    if (result)
        ((CCombinedFeatures*) train_features)->list_feature_objs();
    else
        SG_ERROR("appending feature object failed\n");
}

void CGUIFeatures::add_train_dotfeatures(CDotFeatures* f)
{
    ASSERT(f);
    SG_PRINT("DOTFVEC %d\n", f->get_num_vectors());
    invalidate_train();

    if (!train_features)
    {
        train_features=new CCombinedDotFeatures();
        SG_REF(train_features);
    }

    if (train_features->get_feature_class()!=C_COMBINED_DOT)
    {
        if (!train_features->has_property(FP_DOT))
            SG_ERROR("Trainfeatures not based on DotFeatures.\n");

        CDotFeatures* first_elem=(CDotFeatures*) train_features;
        train_features=new CCombinedDotFeatures();
        SG_REF(train_features);
        ((CCombinedDotFeatures*) train_features)->append_feature_obj(first_elem);
        ((CCombinedDotFeatures*) train_features)->list_feature_objs();
        SG_UNREF(first_elem);
    }

    bool result=((CCombinedDotFeatures*) train_features)->append_feature_obj(f);
    if (result)
        ((CCombinedDotFeatures*) train_features)->list_feature_objs();
    else
        SG_ERROR("appending dot feature object failed\n");
}

void CGUIFeatures::add_test_dotfeatures(CDotFeatures* f)
{
    ASSERT(f);
    invalidate_test();

    if (!test_features)
    {
        test_features=new CCombinedDotFeatures();
        SG_REF(test_features);
    }

    if (test_features->get_feature_class()!=C_COMBINED_DOT)
    {
        if (!test_features->has_property(FP_DOT))
            SG_ERROR("Trainfeatures not based on DotFeatures.\n");

        CDotFeatures* first_elem=(CDotFeatures*) test_features;
        test_features=new CCombinedDotFeatures();
        SG_REF(test_features);
        ((CCombinedDotFeatures*) test_features)->append_feature_obj(first_elem);
        ((CCombinedDotFeatures*) test_features)->list_feature_objs();
        SG_UNREF(first_elem);
    }

    bool result=((CCombinedDotFeatures*) test_features)->append_feature_obj(f);
    if (result)
        ((CCombinedDotFeatures*) test_features)->list_feature_objs();
    else
        SG_ERROR("Appending feature object failed.\n");
}

void CGUIFeatures::add_test_features(CFeatures* f)
{
    ASSERT(f);
    invalidate_test();

    if (!test_features)
    {
        test_features=new CCombinedFeatures();
        SG_REF(test_features);
    }

    if (test_features->get_feature_class()!=C_COMBINED)
    {
        CFeatures* first_elem=test_features;
        test_features=new CCombinedFeatures();
        SG_REF(test_features);
        ((CCombinedFeatures*) test_features)->append_feature_obj(first_elem);
        ((CCombinedFeatures*) test_features)->list_feature_objs();
        SG_UNREF(first_elem);
    }

    bool result=((CCombinedFeatures*) test_features)->append_feature_obj(f);
    if (result)
        ((CCombinedFeatures*) test_features)->list_feature_objs();
    else
        SG_ERROR("Appending feature object failed.\n");
}

bool CGUIFeatures::del_last_feature_obj(char* target)
{
    CCombinedFeatures* cf=NULL;
    if (strncmp(target, "TRAIN", 5)==0)
    {
        if (!train_features)
            SG_ERROR("No train features available.\n");
        if (train_features->get_feature_class()!=C_COMBINED)
            SG_ERROR("Train features are not combined features.\n");

        cf=(CCombinedFeatures*) train_features;
    }
    else if (strncmp(target, "TEST", 4)==0)
    {
        if (!test_features)
            SG_ERROR("No test features available.\n");
        if (test_features->get_feature_class()!=C_COMBINED)
            SG_ERROR("Test features are not combined features.\n");

        cf=(CCombinedFeatures*) test_features;
    }
    else
        SG_ERROR("Unknown target %s, neither TRAIN nor TEST.\n", target);

    if (!cf->delete_feature_obj())
        SG_ERROR("No features available to delete.\n");

    return false;
}