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set of commits for valgrind fixes. test may be broken
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@adalisan
adalisan committed Sep 5, 2017
1 parent cf5e12d commit be28a23
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Showing 4 changed files with 68 additions and 42 deletions.
27 changes: 25 additions & 2 deletions src/graphm/algorithm.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,35 @@
algorithm::algorithm(std::string fconfig)
: rpc(fconfig)
{
gm_ldh=NULL;dalpha_ldh=0;bnosymm=false;
gm_ldh=NULL;
dalpha_ldh=0;
bnosymm=false;
df_norm=0;
N=0;
cdesc_matrix='A';
cscore_matrix='A';
bverbose=false;
sverbfile=std::string("");

N=0;
df_norm=0.0;

}
algorithm::algorithm()
: rpc()
{
gm_ldh=NULL;dalpha_ldh=0;bnosymm=false;df_norm=0;N=0;cdesc_matrix='A';cscore_matrix='A';
gm_ldh=NULL;
dalpha_ldh=0;
bnosymm=false;
df_norm=0;
N=0;
cdesc_matrix='A';
cscore_matrix='A';
bverbose=false;
sverbfile=std::string("");

N=0;
df_norm=0.0;
}

//common framework for graph matching algorithm
Expand Down
4 changes: 2 additions & 2 deletions src/graphm/algorithm.h
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ class match_result
match_result() {
gm_P=NULL;
salgo = "";
gm_P_exact=NULL;
gm_P_exact=NULL;
inum_iteration=-1;
dres = 0.0;
dtime = 0.0;
Expand Down Expand Up @@ -75,7 +75,7 @@ class algorithm : public rpc
{
public:
algorithm(std::string );
algorithm();
algorithm() ;
match_result gmatch(graph& g, graph& h,gsl_matrix* gm_P_i=NULL, gsl_matrix* gm_ldh=NULL,double dalpha_ldh=-1);//common stuff,
virtual match_result match(graph& g, graph& h, gsl_matrix* gm_P_i=NULL, gsl_matrix* gm_ldh=NULL,double dalpha_ldh=-1)=0;//particular method implementation
double graph_dist(graph &g,graph &h,gsl_matrix* gm_P,char cscore_matrix);
Expand Down
6 changes: 4 additions & 2 deletions src/graphm/algorithm_path.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,10 @@

match_result algorithm_path::match(graph& g, graph& h,gsl_matrix* gm_P_i, gsl_matrix* _gm_ldh, double dalpha_ldh)
{
bool bblast_match=(get_param_i("blast_match")==1);
bool bblast_match_end=(get_param_i("blast_match_proj")==1);
bool bblast_match=false;
bblast_match=(get_param_i("blast_match")==1);
bool bblast_match_end=false;
bblast_match_end=(get_param_i("blast_match_proj")==1);
bool bbest_path_proj=(get_param_i("best_path_proj_sol")==1);
bool bbest_path_blast_proj=(get_param_i("best_path_blast_proj_sol")==1);
bool bbest_path_greedy=(get_param_i("best_path_greedy_sol")==1);
Expand Down
73 changes: 37 additions & 36 deletions src/graphm/algorithm_qcv.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,8 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
{
if (bverbose)
*gout<<"QCV matching"<<std::endl;
bool bblast_match_end=(get_param_i("blast_match_proj")==1);
bool bblast_match_end=false;
bblast_match_end=(get_param_i("blast_match_proj")==1);
double dfw_xeps=get_param_d("algo_fw_xeps");
double dfw_feps=get_param_d("algo_fw_feps");
double dhung_max=get_param_d("hungarian_max");
Expand All @@ -37,7 +38,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix* gm_P_bp_temp=NULL;
gsl_matrix* gm_P_bp=NULL;
double fbest_path=1e+300;

if (bbest_path)
{
gm_P_bp_temp=gsl_matrix_alloc(N,N);
Expand All @@ -47,7 +48,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
//some duplicate variables
gsl_matrix* gm_Ag_d=g.get_descmatrix(cdesc_matrix);
gsl_matrix* gm_Ah_d=h.get_descmatrix(cdesc_matrix);
if (pdebug.ivalue) gsl_matrix_printout(gm_Ag_d,"Ag",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(gm_Ag_d,"Ag",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(gm_Ah_d,"Ah",pdebug.strvalue);
//Frank-Wolfe algorithm
bool bstop_algo=false;
Expand All @@ -63,14 +64,14 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_vector_set_zero(gv_col_inc);
gsl_permutation* gp_sol=gsl_permutation_alloc(N);
gsl_permutation_init(gp_sol);


gsl_matrix* gm_dP=gsl_matrix_alloc(N,N);
gvv_dP=gsl_vector_view_array(gm_dP->data,N*N);
gsl_matrix* gm_dP_2=gsl_matrix_alloc(N,N);
//gsl_vector_view gvv_dP_2=gsl_vector_view_array(gm_dP_2->data,N*N);
gsl_matrix_set_zero(gm_dP_2);

if (gm_P_i==NULL)
gsl_matrix_set_all(gm_P,1.0/N);
else
Expand All @@ -79,7 +80,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix_memcpy(gm_P_prev,gm_P);
//perm matrix transformation into vector
gvv_P=gsl_vector_view_array(gm_P->data,N*N);

//and in opposite direction for gradient
gmv_C=gsl_matrix_view_vector(gv_C,N,N);
C=&gmv_C.matrix;
Expand All @@ -89,7 +90,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix * gm_ddP_prev=gsl_matrix_alloc(N,N);
gsl_vector_view gvv_ldh;
if (dalpha_ldh>0)
{
{
gvv_ldh=gsl_vector_view_array(gm_ldh->data,N*N);
if (pdebug.ivalue) gsl_matrix_printout(gm_ldh,"gm_ldh",pdebug.strvalue);
};
Expand All @@ -107,19 +108,19 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
dt1=clock();
//double r=(dt1-dt0)/CLOCKS_PER_SEC;
if (pdebug.ivalue) gsl_matrix_printout(gv_C,"gv_C",pdebug.strvalue);

//result save
gsl_matrix_transpose(C);
if (pdebug.ivalue) gsl_matrix_printout(C,"C=gradient",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(C,"C=gradient",pdebug.strvalue);
gsl_matrix_scale(C,2);
update_C_hungarian(C);
double dscale_factor =gsl_matrix_max_abs(C);
dscale_factor=(dscale_factor>EPSILON)?dscale_factor:EPSILON;
dscale_factor=dhung_max/dscale_factor;
gsl_matrix_scale(C,dscale_factor);
//gsl_matrix_transpose(C);
if (pdebug.ivalue) gsl_matrix_printout(C,"scale(C)",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(C,"scale(C)",pdebug.strvalue);

//hungarian, before the true C matrix must be transposed
gsl_matrix_transpose(C);
dt1=clock();
Expand All @@ -130,15 +131,15 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
update_C_hungarian(C,1,true);//return to the original value
gsl_matrix_scale(C,0.5);

if (pdebug.ivalue) gsl_matrix_printout(gm_P,"gm_P",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(gm_P_prev,"gm_P_prev",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(gm_P,"gm_P",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(gm_P_prev,"gm_P_prev",pdebug.strvalue);

//line search
gsl_matrix_memcpy(gm_dP,gm_P);
gsl_matrix_sub(gm_dP,gm_P_prev);
if (pdebug.ivalue) gsl_matrix_printout(gm_dP,"gm_dP",pdebug.strvalue);

if (pdebug.ivalue) gsl_matrix_printout(gm_dP,"gm_dP",pdebug.strvalue);

double a,b1,b2,bldh;
gsl_matrix_transpose(gm_dP);
gsl_matrix_transpose(gm_P_prev);
Expand All @@ -164,7 +165,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix_transpose(gm_P_prev);
gsl_matrix_transpose(C);
if ((alpha<1) and (alpha>0))
{
{
gsl_matrix_scale(gm_dP,(1-alpha));
gsl_matrix_sub(gm_P,gm_dP);
};
Expand All @@ -176,16 +177,16 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
else
{
dfvalue=f_qcv(gm_Ag_d,gm_Ah_d,gm_P,gm_temp,true);
if (dfvalue>dfvalue_prev)
if (dfvalue>dfvalue_prev)
{gsl_matrix_memcpy(gm_P,gm_P_prev);
dfvalue=dfvalue_prev;};
};
if (pdebug.ivalue) gsl_matrix_printout(gm_P,"gm_P_step_finish",pdebug.strvalue); //sparsity
if (pdebug.ivalue) gsl_matrix_printout(gm_P,"gm_P_step_finish",pdebug.strvalue); //sparsity
long lsparse=0;
for (long j=0;j<N*N;j++)
lsparse+=(gm_P->data[j]<1e-7);
if (bverbose) *gout<<"#zeros="<<lsparse<<", #nonzeros="<<N*N-lsparse<<std::endl;

//stop criterion
dP_norm=gsl_matrix_norm(gm_P_prev,1);
gsl_matrix_sub(gm_P_prev,gm_P);
Expand All @@ -194,7 +195,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
bstop_algo = ((ddP_norm<dfw_xeps*N) and ((abs(dfvalue-dfvalue_prev)<dfw_feps*abs(dfvalue_prev)) or (ddP_norm==0)) or (abs(dfvalue-dfvalue_prev)<1e-20));
dt3=clock();
if (bverbose) *gout<<"x="<<dP_norm<<", f="<<dfvalue<<", dx="<<ddP_norm<<", df="<<(dfvalue_prev-dfvalue)<<", "<<"grad="<<(dfvalue_prev-dfvalue)/ddP_norm<<". Timing="<<(dt1-dt0)/CLOCKS_PER_SEC<<" "<<(dt2-dt1)/CLOCKS_PER_SEC<<" "<<(dt3-dt2)/CLOCKS_PER_SEC<<std::endl;

dfvalue_prev=dfvalue;
//now we test different projection to estimate the best permutation
if (bbest_path_proj)
Expand All @@ -210,7 +211,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix_memcpy(gm_P_bp,gm_P_prev);
};
};

if (bbest_path_blast_proj)
{
//permuation projection
Expand All @@ -224,7 +225,7 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix_memcpy(gm_P_bp,gm_P_prev);
};
};

if (bbest_path_greedy)
{
//permuation projection
Expand All @@ -238,13 +239,13 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix_memcpy(gm_P_bp,gm_P_prev);
};
};

if (bbest_path_blast_greedy)
{
};
gsl_matrix_memcpy(gm_P_prev,gm_P);
};//end Frank-Wolfe cycle

//permuation projection
match_result mres;
mres.gm_P_exact=gsl_matrix_alloc(N,N);
Expand All @@ -259,12 +260,12 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
{
*gout<<"Best path solution is used"<<std::endl;
gsl_matrix_memcpy(gm_P,gm_P_bp);
};
};
gsl_matrix_free(gm_P_bp);
gsl_matrix_free(gm_P_bp_temp);
};
if (pdebug.ivalue) gsl_matrix_printout(gm_P,"gm_P_projected",pdebug.strvalue);
if (pdebug.ivalue) gsl_matrix_printout(gm_P,"gm_P_projected",pdebug.strvalue);

//memory deallocation
gsl_matrix_free(gm_temp);
gsl_matrix_free(gm_dP);
Expand All @@ -277,9 +278,9 @@ match_result algorithm_qcv::match(graph& g, graph& h,gsl_matrix* gm_P_i,gsl_matr
gsl_matrix_free(gm_Ah_d);
gsl_vector_free(gv_col_inc);
gsl_permutation_free(gp_sol);

mres.gm_P=gm_P;

//initial score
mres.vd_trace.push_back(graph_dist(g,h,cscore_matrix));
//final score
Expand Down Expand Up @@ -310,7 +311,7 @@ void algorithm_qcv::qcv_gradient_opt(gsl_matrix *gm_Ag_d,gsl_matrix *gm_Ah_d,gsl
gsl_matrix_transpose(gm_1);

gsl_matrix_add(&gmv_grad.matrix,gm_1);

//first term
if (bnosymm) gsl_matrix_transpose(gm_Ah_d);
//gsl_blas_dgemm(CblasNoTrans,CblasNoTrans,1,&gmv_P.matrix,gm_Ah_d,0,gm_temp);
Expand All @@ -323,16 +324,16 @@ void algorithm_qcv::qcv_gradient_opt(gsl_matrix *gm_Ag_d,gsl_matrix *gm_Ah_d,gsl
gsl_blas_dgemm(CblasNoTrans,CblasNoTrans,1,gm_Ah_d,&gmv_P.matrix,0,gm_temp);
gsl_matrix_transpose(gm_temp);
gsl_blas_dgemm(CblasNoTrans,CblasNoTrans,-1,gm_Ag_d,gm_temp,1,&gmv_grad.matrix);

gsl_matrix_transpose(&gmv_P.matrix);
if (bnosymm) gsl_matrix_transpose(gm_Ah_d);
if (bnosymm) gsl_matrix_transpose(gm_Ah_d);
//III gsl_blas_dgemm_sym(CblasLeft,CblasUpper,CblasNoTrans,CblasNoTrans,-2,gm_Ag_d,gm_temp,1,&gmv_grad.matrix);
gsl_matrix_free(gm_1);

gsl_matrix_transpose(&gmv_grad.matrix);
gsl_matrix_scale(&gmv_grad.matrix,1-dalpha_ldh);//label cost function scaling
gsl_vector_scale(gv_grad,1/df_norm);//normalization

}

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