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Commit a5e09aa7 authored by Christian Beckmann's avatar Christian Beckmann
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Typos

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meldata.cc
+ 5
− 1
View file @ a5e09aa7
......@@ -236,7 +236,7 @@ namespace Melodic{
if(opts.debug.value())
save4D(alldat,"alldat");
//estimate model order
ColumnVector tmpPPCA;
Matrix tmpPPCA;
RowVector AdjEV, PercEV;
Matrix Corr, tmpE;
int order;
......@@ -446,6 +446,10 @@ namespace Melodic{
saveascii(mixFFT,opts.outputfname.value() + "_FTmix");
}
//Output PPCA
if(PPCA.Storage()>0)
saveascii(PPCA, opts.outputfname.value() + "_PPCA");
//Output ICstats
if(ICstats.Storage()>0)
saveascii(ICstats,opts.outputfname.value() + "_ICstats");
......
meldata.h
+ 3
− 3
View file @ a5e09aa7
......@@ -158,8 +158,8 @@ namespace Melodic{
inline void set_EV(Matrix& Arg) {if(EV.Storage()==0)
EV = Arg;}
inline ColumnVector& get_PPCA() {return PPCA;}
inline void set_PPCA(ColumnVector& Arg) {if(PPCA.Storage()==0)
inline Matrix& get_PPCA() {return PPCA;}
inline void set_PPCA(Matrix& Arg) {if(PPCA.Storage()==0)
PPCA = Arg;}
inline Matrix& get_stdNoisei() {return stdNoisei;}
......@@ -225,7 +225,7 @@ namespace Melodic{
volume<float> background;
Matrix Data;
ColumnVector PPCA;
Matrix PPCA;
Matrix jointCC;
bool after_mm;
......
melhlprfns.cc
+ 21
− 19
View file @ a5e09aa7
......@@ -497,7 +497,7 @@ namespace Melodic{
return Res;
} //RowVector cumsum
int ppca_dim(const Matrix& in, const Matrix& weights, ColumnVector& PPCA, RowVector& AdjEV, RowVector& PercEV, Matrix& Corr, Matrix& tmpE, RowVector &tmpD, float resels, string which)
int ppca_dim(const Matrix& in, const Matrix& weights, Matrix& PPCA, RowVector& AdjEV, RowVector& PercEV, Matrix& Corr, Matrix& tmpE, RowVector &tmpD, float resels, string which)
{
std_pca(in,weights,Corr,tmpE,tmpD);
......@@ -506,11 +506,14 @@ namespace Melodic{
adj_eigspec(tmpD.AsRow(),AdjEV,PercEV,NewEV,maxEV,in.Ncols(),resels);
int res;
PPCA = ppca_select(ppca_est(NewEV, in.Ncols(),resels), res, maxEV, which);
PPCA = ppca_est(NewEV, in.Ncols(),resels);
ColumnVector tmp = ppca_select(PPCA, res, maxEV, which);
PPCA = tmp | PPCA;
return res;
} //int ppca_dim
int ppca_dim(const Matrix& in, const Matrix& weights, ColumnVector& PPCA, RowVector& AdjEV, RowVector& PercEV, float resels, string which)
int ppca_dim(const Matrix& in, const Matrix& weights, Matrix& PPCA, RowVector& AdjEV, RowVector& PercEV, float resels, string which)
{
RowVector tmpD;
Matrix tmpE;
......@@ -528,17 +531,16 @@ namespace Melodic{
return res;
} //int ppca_dim
ColumnVector ppca_select(const Matrix& PPCAest, int& dim, int maxEV, string which)
ColumnVector ppca_select(Matrix& PPCAest, int& dim, int maxEV, string which)
{
RowVector estimators(5);
estimators = 1.0;
Matrix PPCA2(PPCAest);
for(int ctr=1; ctr<=PPCA2.Ncols(); ctr++){
PPCA2.Column(ctr) = (PPCA2.Column(ctr) -
min(PPCA2.Column(ctr)).AsScalar()) /
( max(PPCA2.Column(ctr)).AsScalar() -
min(PPCA2.Column(ctr)).AsScalar());
for(int ctr=1; ctr<=PPCAest.Ncols(); ctr++){
PPCAest.Column(ctr) = (PPCAest.Column(ctr) -
min(PPCAest.Column(ctr)).AsScalar()) /
( max(PPCAest.Column(ctr)).AsScalar() -
min(PPCAest.Column(ctr)).AsScalar());
}
int ctr_i = 1;
......@@ -568,30 +570,30 @@ namespace Melodic{
if(which == string("aut"))
if(int(estimators(2)) < int(estimators(1)) && int(estimators(2)) > 15){
res=int(estimators(2));
PPCA << PPCA2.Column(3);
PPCA << PPCAest.Column(3);
}else{
res = int(estimators(1));
PPCA << PPCA2.Column(2);
PPCA << PPCAest.Column(2);
}
if(which == string("lap")){
res = int(estimators(1));
PPCA << PPCA2.Column(2);
PPCA << PPCAest.Column(2);
}
if(which == string("bic")){
res = int(estimators(2));
PPCA << PPCA2.Column(3);
PPCA << PPCAest.Column(3);
}
if(which == string("mdl")){
res = int(estimators(3));
PPCA << PPCA2.Column(4);
PPCA << PPCAest.Column(4);
}
if(which == string("rrn")){
res = int(estimators(4));
PPCA << PPCA2.Column(5);
PPCA << PPCAest.Column(5);
}
if(which == string("aic")){
res = int(estimators(5));
PPCA << PPCA2.Column(6);
PPCA << PPCAest.Column(6);
}
if(which == string("median")){
RowVector unsorted(estimators);
......@@ -600,10 +602,10 @@ namespace Melodic{
res=int(unsorted(3));
while(res != int(estimators(ctr_i)))
ctr_i++;
PPCA << PPCA2.Column(ctr_i);
PPCA << PPCAest.Column(ctr_i);
}
if(res==0 || which == string("mean")){//median estimator
PPCA = mean(PPCA2.Columns(2,6),2);
PPCA = mean(PPCAest.Columns(2,6),2);
res=int(mean(estimators,2).AsScalar());
}
......
melhlprfns.h
+ 3
− 3
View file @ a5e09aa7
......@@ -59,10 +59,10 @@ namespace Melodic{
void adj_eigspec(const RowVector& in, RowVector& out1, RowVector& out2, RowVector& out3, int& out4, int num_vox, float resels);
void adj_eigspec(const RowVector& in, RowVector& out1, RowVector& out2);
int ppca_dim(const Matrix& in, const Matrix& weights, ColumnVector& PPCA, RowVector& AdjEV, RowVector& PercEV, Matrix& Corr, Matrix& tmpE, RowVector &tmpD, float resels, string which);
int ppca_dim(const Matrix& in, const Matrix& weights, ColumnVector& PPCA, RowVector& AdjEV, RowVector& PercEV, float resels, string which);
int ppca_dim(const Matrix& in, const Matrix& weights, Matrix& PPCA, RowVector& AdjEV, RowVector& PercEV, Matrix& Corr, Matrix& tmpE, RowVector &tmpD, float resels, string which);
int ppca_dim(const Matrix& in, const Matrix& weights, Matrix& PPCA, RowVector& AdjEV, RowVector& PercEV, float resels, string which);
int ppca_dim(const Matrix& in, const Matrix& weights, float resels, string which);
ColumnVector ppca_select(const Matrix& PPCAest, int& dim, int maxEV, string which);
ColumnVector ppca_select(Matrix& PPCAest, int& dim, int maxEV, string which);
Matrix ppca_est(const RowVector& eigenvalues, const int N1, const float N2);
Matrix ppca_est(const RowVector& eigenvalues, const int N);
......
meloptions.h
+ 12
− 2
View file @ a5e09aa7
......@@ -83,7 +83,9 @@ class MelodicOptions {
Option<float> tr;
Option<bool> logPower;
Option<bool> addsigchng;
Option<bool> allPPCA;
Option<bool> varplots;
Option<bool> varvals;
Option<string> fn_Tdesign;
Option<string> fn_Tcon;
......@@ -261,9 +263,15 @@ class MelodicOptions {
addsigchng(string("--sigchng"), false,
string("add signal change estimates to report pages\n"),
false, no_argument, false),
varplots(string("--varplots"), false,
string("add std error envelopes to time course plots\n"),
allPPCA(string("--allPPCA"), false,
string("add all PPCA plots\n"),
false, no_argument, false),
varplots(string("--varplots"), false,
string("add std error envelopes to time course plots\n"),
false, no_argument, false),
varvals(string("--varvals"), false,
string("add rank1 values after plots\n"),
false, no_argument, false),
fn_Tdesign(string("--Tdes"), string(""),
string(" design matrix across time-domain"),
false, requires_argument),
......@@ -396,7 +404,9 @@ class MelodicOptions {
options.add(tr);
options.add(logPower);
options.add(addsigchng);
options.add(allPPCA);
options.add(varplots);
options.add(varvals);
options.add(fn_Tdesign);
options.add(fn_Tcon);
options.add(fn_TconF);
......
melreport.cc
+ 15
− 6
View file @ a5e09aa7
......@@ -158,10 +158,10 @@ namespace Melodic{
IChtml << "<img BORDER=0 SRC=\""
+string("t")+num2str(cnum)+".png\"></A><p>" << endl;
// if(melodat.get_numfiles()>1 && melodat.explained_var.Storage()>0
// && melodat.explained_var.Ncols()>=cnum)
// IChtml << "Rank-1 approximation of individual time courses explains "
// << melodat.explained_var(cnum) << "% of variance.<p>" << endl;
if(melodat.get_numfiles()>1 && melodat.explained_var.Storage()>0
&& melodat.explained_var.Ncols()>=cnum && opts.varvals.value())
IChtml << "Rank-1 approximation of individual time courses explains "
<< melodat.explained_var(cnum) << "% of variance.<p>" << endl;
}//time series plot
if(!opts.pspec.value())
......@@ -756,8 +756,17 @@ namespace Melodic{
if(melodat.get_PPCA().Storage()>0){
what = what.Columns(1,melodat.get_PPCA().Nrows());
what &= melodat.get_PPCA().t();
newplot.add_label("dim. estimate");
if(opts.allPPCA.value()&&melodat.get_PPCA().Ncols()==7){
what &= melodat.get_PPCA().Columns(3,7).t();
newplot.add_label("Laplace");
newplot.add_label("BIC");
newplot.add_label("MDL");
newplot.add_label("RRN");
newplot.add_label("AIC");
}else{
what &= melodat.get_PPCA().Column(1).t();
newplot.add_label("dim. estimate");
}
}
newplot.set_Ylabel_fmt("%.2f");
......
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