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fix various crashers in static interface
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Soeren Sonnenburg committed May 10, 2012
1 parent 1b58787 commit cb41b3b
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Showing 4 changed files with 12 additions and 57 deletions.
2 changes: 1 addition & 1 deletion examples/undocumented/libshogun/Makefile
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Expand Up @@ -2,7 +2,7 @@ LIB_PATH=/usr/lib
INC_PATH=/usr/include
VALGRINDOPTS=--tool=memcheck --error-limit=no --trace-children=yes --leak-check=full --show-reachable=yes

INCLUDES=
INCLUDES=-I/usr/include/atlas
LIBS=
LIBS_ADD=-lshogun

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2 changes: 1 addition & 1 deletion src/shogun/kernel/WeightedDegreePositionStringKernel.cpp
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Expand Up @@ -94,7 +94,7 @@ CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel(
for (int32_t i=0; i<d*(1+max_mismatch); i++)
weights[i]=w[i];

set_shifts(SGVector<int32_t>(s, sl));
set_shifts(SGVector<int32_t>(CMath::clone_vector(s,sl), sl));
}

CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel(
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2 changes: 0 additions & 2 deletions src/shogun/ui/GUIKernel.cpp
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Expand Up @@ -127,7 +127,6 @@ CKernel* CGUIKernel::create_custom(float64_t* kmatrix, int32_t num_feat, int32_t
else
kern->set_full_kernel_matrix_from_full(km);

SG_FREE(kmatrix);
return kern;
}

Expand Down Expand Up @@ -271,7 +270,6 @@ CKernel* CGUIKernel::create_weighteddegreestring(
((CWeightedDegreeStringKernel*) kern)->set_mkl_stepsize(mkl_stepsize);
((CWeightedDegreeStringKernel*) kern)->set_which_degree(single_degree);

SG_FREE(weights);
return kern;
}

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63 changes: 10 additions & 53 deletions src/shogun/ui/SGInterface.cpp
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Expand Up @@ -1824,8 +1824,7 @@ bool CSGInterface::do_set_features(bool add, bool check_dot, int32_t repetitions

feat=new CDenseFeatures<float64_t>(0);
((CDenseFeatures<float64_t>*) feat)->
set_feature_matrix(SGMatrix<float64_t>(fmatrix, num_feat, num_vec).clone());
SG_FREE(fmatrix);
set_feature_matrix(SGMatrix<float64_t>(fmatrix, num_feat, num_vec));

if (m_nrhs==6)
feat = create_custom_real_features((CDenseFeatures<float64_t>*) feat);
Expand All @@ -1840,8 +1839,7 @@ bool CSGInterface::do_set_features(bool add, bool check_dot, int32_t repetitions

feat=new CDenseFeatures<int32_t>(0);
((CDenseFeatures<int32_t>*) feat)->
set_feature_matrix(SGMatrix<int32_t>(fmatrix, num_feat, num_vec).clone());
SG_FREE(fmatrix);
set_feature_matrix(SGMatrix<int32_t>(fmatrix, num_feat, num_vec));
break;
}

Expand All @@ -1852,8 +1850,7 @@ bool CSGInterface::do_set_features(bool add, bool check_dot, int32_t repetitions

feat=new CDenseFeatures<int16_t>(0);
((CDenseFeatures<int16_t>*) feat)->
set_feature_matrix(SGMatrix<int16_t>(fmatrix, num_feat, num_vec).clone());
SG_FREE(fmatrix);
set_feature_matrix(SGMatrix<int16_t>(fmatrix, num_feat, num_vec));
break;
}

Expand All @@ -1864,8 +1861,7 @@ bool CSGInterface::do_set_features(bool add, bool check_dot, int32_t repetitions

feat=new CDenseFeatures<uint16_t>(0);
((CDenseFeatures<uint16_t>*) feat)->
set_feature_matrix(SGMatrix<uint16_t>(fmatrix, num_feat, num_vec).clone());
SG_FREE(fmatrix);
set_feature_matrix(SGMatrix<uint16_t>(fmatrix, num_feat, num_vec));
break;
}

Expand All @@ -1876,8 +1872,7 @@ bool CSGInterface::do_set_features(bool add, bool check_dot, int32_t repetitions

feat=new CDenseFeatures<float32_t>(0);
((CDenseFeatures<float32_t>*) feat)->
set_feature_matrix(SGMatrix<float32_t>(fmatrix, num_feat, num_vec).clone());
SG_FREE(fmatrix);
set_feature_matrix(SGMatrix<float32_t>(fmatrix, num_feat, num_vec));
break;
}

Expand Down Expand Up @@ -2485,16 +2480,9 @@ bool CSGInterface::cmd_set_labels()
int32_t len=0;
get_vector(lab, len);

CLabels* labels=new CLabels(len);
CLabels* labels=new CLabels(SGVector<float64_t>(lab, len));
SG_INFO("num labels: %d\n", labels->get_num_labels());

for (int32_t i=0; i<len; i++)
{
if (!labels->set_label(i, lab[i]))
SG_ERROR("Couldn't set label %d (of %d): %f.\n", i, len, lab[i]);
}
SG_FREE(lab);

if (strmatch(target, "TRAIN"))
ui_labels->set_train_labels(labels);
else if (strmatch(target, "TEST"))
Expand Down Expand Up @@ -2532,15 +2520,9 @@ bool CSGInterface::cmd_get_labels()
if (!labels)
SG_ERROR("No labels.\n");

int32_t num_labels=labels->get_num_labels();
float64_t* lab=SG_MALLOC(float64_t, num_labels);

for (int32_t i=0; i<num_labels ; i++)
lab[i]=labels->get_label(i);

set_vector(lab, num_labels);
SG_FREE(lab);
SGVector<float64_t> lab=labels->get_labels();

set_vector(lab.vector, lab.vlen);
return true;
}

Expand Down Expand Up @@ -4799,9 +4781,6 @@ bool CSGInterface::cmd_set_linear_classifier()

c->set_w(SGVector<float64_t>(w, len));
c->set_bias(bias);

SG_FREE(w);

return true;
}

Expand Down Expand Up @@ -6246,14 +6225,8 @@ bool CSGInterface::cmd_set_plif_struct()
pm->set_plif_names(names, N);
pm->set_plif_transform_type(all_transform, N);

SG_FREE(all_limits);
SG_FREE(all_penalties);
SG_FREE(names);
SG_FREE(all_transform);
SG_FREE(min_values);
SG_FREE(max_values);
SG_FREE(all_use_cache);
SG_FREE(all_use_svm);
SG_FREE(all_do_calc);

return true;
Expand Down Expand Up @@ -6419,7 +6392,6 @@ bool CSGInterface::cmd_set_model()
SG_ERROR("should be equal: Nmod: %i, num_svms: %i\n",Nmod,num_svms);
ASSERT(Mmod == 2)
h->init_mod_words_array(SGMatrix<int32_t>(mod_words, Nmod, Mmod));
SG_FREE(mod_words);

// ARG 4
// links: states -> signal plifs (#states x 2)
Expand All @@ -6429,7 +6401,6 @@ bool CSGInterface::cmd_set_model()
get_matrix(state_signals,num_states,feat_dim3);
ASSERT(num_states==Dim[0]);
pm->compute_signal_plifs(SGMatrix<int32_t>(state_signals, feat_dim3, num_states));
SG_FREE(state_signals);


// ARG 5
Expand All @@ -6443,7 +6414,6 @@ bool CSGInterface::cmd_set_model()

ui_structure->set_orf_info(orf_info, Norf, Morf);
h->set_orf_info(SGMatrix<int32_t>(orf_info, Norf, Morf));
SG_FREE(orf_info);

h->set_num_states(num_states) ;

Expand Down Expand Up @@ -6484,12 +6454,10 @@ bool CSGInterface::cmd_precompute_content_svms()
//int32_t Nweights = ui_structure->get_num_svm_weights();
h->set_pos(SGVector<int32_t>(all_pos, Npos));
h->set_gene_string(SGVector<char>(seq, seq_len));
SG_FREE(seq);
h->create_word_string();
h->precompute_stop_codons();
h->init_content_svm_value_array(num_svms);
h->set_dict_weights(SGMatrix<float64_t>(weights, Nweights, num_svms));
SG_FREE(weights);
h->precompute_content_values();
SG_DEBUG("precompute_content_svms done\n");
return true;
Expand Down Expand Up @@ -6550,8 +6518,6 @@ bool CSGInterface::cmd_set_lin_feat()
h->set_lin_feat(lin_feat, num_svms, seq_len);

SG_FREE(lin_feat);
SG_FREE(seq);
SG_FREE(all_pos);

return true;
}
Expand Down Expand Up @@ -6791,9 +6757,7 @@ bool CSGInterface::cmd_best_path_trans()
ASSERT(PEN);

h->set_p_vector(SGVector<float64_t>(p, num_states));
SG_FREE(p); p=NULL ;
h->set_q_vector(SGVector<float64_t>(q, num_states));
SG_FREE(q); q=NULL ;

if (seg_path!=NULL)
{
Expand All @@ -6803,8 +6767,6 @@ bool CSGInterface::cmd_best_path_trans()
{
h->set_a_trans_matrix(SGMatrix<float64_t>(a_trans, num_a_trans, 3)) ; // segment_id = 0
}
SG_FREE(a_trans);
a_trans=NULL ;

if (!h->check_svm_arrays())
{
Expand All @@ -6819,7 +6781,7 @@ bool CSGInterface::cmd_best_path_trans()

if (seg_path!=NULL)
{
h->best_path_set_segment_loss(SGMatrix<float64_t>(loss, Nloss, Mloss)) ;
h->best_path_set_segment_loss(SGMatrix<float64_t>(loss, Nloss, Mloss, false)) ;
seg_loss_obj->set_segment_loss(loss, Nloss, Mloss);
}
else
Expand All @@ -6829,7 +6791,6 @@ bool CSGInterface::cmd_best_path_trans()
seg_loss_obj->set_segment_loss(zero2, 2, 1);
}
h->set_content_type_array(SGMatrix<float64_t>(seg_path,Nseg_path,Mseg_path));
SG_FREE(seg_path);

bool segment_loss_non_zero=false;
for (int32_t i=0; i<Nloss*Mloss; i++)
Expand Down Expand Up @@ -6880,9 +6841,6 @@ bool CSGInterface::cmd_best_path_trans()
d_my_pos[i*(nbest+nother)+k] = my_pos.matrix[i+k*M] ;
}
}
SG_FREE(states.matrix);
SG_FREE(my_pos.matrix);

set_vector(p_prob.vector,nbest+nother);
set_vector(d_my_path, (nbest+nother)*M);
set_vector(d_my_pos, (nbest+nother)*M);
Expand Down Expand Up @@ -7008,7 +6966,7 @@ bool CSGInterface::cmd_best_path_trans_deriv()
else
{
float64_t zero2[2] = {0.0, 0.0} ;
h->best_path_set_segment_loss(SGMatrix<float64_t>(zero2, 2, 1)) ;
h->best_path_set_segment_loss(SGMatrix<float64_t>(zero2, 2, 1, false)) ;
seg_loss_obj->set_segment_loss(zero2, 2, 1);
}
h->set_content_type_array(SGMatrix<float64_t>(seg_path,Nseg_path,Mseg_path));
Expand Down Expand Up @@ -7068,7 +7026,6 @@ bool CSGInterface::cmd_best_path_trans_deriv()

SG_FREE(p);
SG_FREE(q);
SG_FREE(seg_path);
SG_FREE(a_trans);
SG_FREE(loss);
SG_FREE(mystate_seq);
Expand Down

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