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Commit e5539630 authored by Matthew Webster's avatar Matthew Webster
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Candidate for Newimage film stable

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ContrastMgr.cc
+ 20
− 33
View file @ e5539630
......@@ -70,7 +70,6 @@ namespace FILM {
void ContrastMgr::run()
{
Tracer_Plus ts("ContrastMgr::run");
Load();
// Loop through tcontrasts:
......@@ -116,31 +115,22 @@ namespace FILM {
Tracer_Plus ts("ContrastMgr::Load");
// Need to read in b, sigmaSquareds, corrections and dof
Log& logger = LogSingleton::getInstance();
// Load contrasts:
parad.load("", ContrastMgrOptions::getInstance().contrastfname, ContrastMgrOptions::getInstance().fcontrastfname, false, 0);
numParams = parad.getTContrasts().Ncols();
if(ContrastMgrOptions::getInstance().verbose)
{
cerr << "T Contrasts:" << endl << parad.getTContrasts();
cerr << "F Contrasts:" << endl << parad.getFContrasts();
}
volume4D<float> input_data;
read_volume4D(input_data,logger.getDir() + "/sigmasquareds",vinfo);
mask=input_data[0];
mask.binarise(0.0,exclusive);
//input_data*=mask;
sigmaSquareds=input_data.matrix(mask);
numTS = sigmaSquareds.Ncols();
mask.binarise(0.0,mask.max()+1,exclusive);
sigmaSquareds=input_data.matrix(mask).AsColumn();
numTS = sigmaSquareds.Nrows();
// b:
ColumnVector peVol;
b.ReSize(numTS, numParams);
......@@ -150,7 +140,7 @@ namespace FILM {
ostringstream osc;
osc << i;
read_volume4D(input_data,logger.getDir() + "/pe" + osc.str().c_str());
peVol=input_data.matrix(mask);
peVol=input_data.matrix(mask).AsColumn();
b.Column(i) = peVol;
}
......@@ -160,7 +150,7 @@ namespace FILM {
if(!in) //avw format
{
read_volume4D(input_data,logger.getDir() + "/dof");
dof=input_data.matrix(mask);
dof=input_data.matrix(mask).AsColumn();
}
else
{
......@@ -201,14 +191,13 @@ namespace FILM {
ostringstream osc;
osc << suffix << c_counter;
volume4D<float> output;
output.set_intent(NIFTI_INTENT_FTEST,0,0,0);
output.setmatrix(fstat);
output.setmatrix(fstat.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
output.set_intent(NIFTI_INTENT_FTEST,0,0,0);
save_volume4D(output,logger.getDir() + "/fstat" + osc.str().c_str(),vinfo);
output.set_intent(NIFTI_INTENT_ZSCORE,0,0,0);
output.setmatrix(zstat);
output.setmatrix(zstat.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
output.set_intent(NIFTI_INTENT_ZSCORE,0,0,0);
save_volume4D(output,logger.getDir() + "/zfstat" + osc.str().c_str(),vinfo);
}
......@@ -216,32 +205,31 @@ namespace FILM {
{
Tracer_Plus ts("ContrastMgr::SaveTContrast");
Log& logger = LogSingleton::getInstance();
// prepare contrast number:
ostringstream osc;
osc << suffix << c_counter;
volume4D<float> output;
output.set_intent(NIFTI_INTENT_NONE,0,0,0);
output.setmatrix(neff);
output.setmatrix(neff.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
output.set_intent(NIFTI_INTENT_NONE,0,0,0);
save_volume4D(output,logger.getDir() + "/neff" + osc.str().c_str(),vinfo);
output.set_intent(NIFTI_INTENT_ESTIMATE,0,0,0);
output.setmatrix(cb);
output.setmatrix(cb.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
save_volume4D(output,logger.getDir() + "/cope" + osc.str().c_str(),vinfo);
output.set_intent(NIFTI_INTENT_ESTIMATE,0,0,0);
output.setmatrix(varcb);
save_volume4D(output,logger.getDir() + "/cope" + osc.str().c_str(),vinfo);
output.setmatrix(varcb.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
output.set_intent(NIFTI_INTENT_ESTIMATE,0,0,0);
save_volume4D(output,logger.getDir() + "/varcope" + osc.str().c_str(),vinfo);
output.set_intent(NIFTI_INTENT_TTEST,0,0,0);
output.setmatrix(tstat);
output.setmatrix(tstat.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
output.set_intent(NIFTI_INTENT_TTEST,0,0,0);
cerr << output.intent_code() << endl;
save_volume4D(output,logger.getDir() + "/tstat" + osc.str().c_str(),vinfo);
output.set_intent(NIFTI_INTENT_ZSCORE,0,0,0);
output.setmatrix(zstat);
output.setmatrix(zstat.AsRow(),mask);
FslSetCalMinMax(&vinfo,output.min(),output.max());
output.set_intent(NIFTI_INTENT_ZSCORE,0,0,0);
save_volume4D(output,logger.getDir() + "/zstat" + osc.str().c_str(),vinfo);
}
......@@ -252,7 +240,6 @@ namespace FILM {
// puts ColumnVector of length p*p from correction
// into Matrix corr which is p*p:
corr.ReSize(numParams, numParams);
for (int i = 1; i <= numParams; i++)
{
for (int j = 1; j <= numParams; j++)
......
Makefile
+ 1
− 1
View file @ e5539630
......@@ -9,7 +9,7 @@ LIBS = -lnewimage -lmiscmaths -lutils -lm -lnewmat -lfslio -lniftiio -lznz -lpro
XFILES = film_gls contrast_mgr ttoz ftoz ttologp
OBJS = ContrastMgrOptions.o ContrastMgr.o BandPassOptions.o gaussComparer.o AutoCorrEstimator.o glm.o paradigm.o glim.o FilmOlsOptions.o FilmGlsOptionsRes.o FilmGlsOptions.o glimGls.o
OBJS = ContrastMgrOptions.o ContrastMgr.o BandPassOptions.o gaussComparer.o AutoCorrEstimator.o glm.o paradigm.o FilmOlsOptions.o FilmGlsOptionsRes.o FilmGlsOptions.o glimGls.o
#OPTFLAGS =
......
film_gls.cc
+ 0
− 2
View file @ e5539630
......@@ -61,7 +61,6 @@ int main(int argc, char *argv[])
int numTS = datam.Ncols();
ColumnVector epivol = reference.matrix(mask).t();
//epivol = datam.Row(int(sizeTS/2)).AsColumn();
// Load paradigm:
Paradigm parad;
......@@ -240,7 +239,6 @@ int main(int argc, char *argv[])
Matrix& threshacm = acEst.getEstimates();
int cutoff = sizeTS/2;
if(globalopts.tukey) cutoff = globalopts.tukeysize;
//cutoff = MISCMATHS::Max(1,cutoff);
threshacm = threshacm.Rows(1,MISCMATHS::Max(1,cutoff));
input_data.setmatrix(threshacm,mask);
......
ftoz.cc
+ 0
− 1
View file @ e5539630
......@@ -26,7 +26,6 @@ public:
string fsfname;
string doffile1;
string doffile2;
string zscoresfname;
public:
globaloptions();
......
glimGls.cc
+ 2
− 46
View file @ e5539630
......@@ -11,11 +11,10 @@
#include "glimGls.h"
#include "miscmaths/miscmaths.h"
#include "utils/log.h"
#include "miscmaths/volume.h"
#include "miscmaths/volumeseries.h"
using namespace MISCMATHS;
using namespace Utilities;
using namespace NEWIMAGE;
namespace FILM {
......@@ -61,50 +60,7 @@ namespace FILM {
SetCorrection(inv_xx, ind);
}
void GlimGls::Save(const VolumeInfo& pvolinfo, const ColumnVector& prethreshpos)
{
// Need to save b, sigmaSquareds, corrections and dof
Log& logger = LogSingleton::getInstance();
VolumeInfo volinfo = pvolinfo;
// b:
Volume peVol;
for(int i = 1; i <= numParams; i++)
{
peVol = b.Row(i).AsColumn();
volinfo.intent_code = NIFTI_INTENT_ESTIMATE;
peVol.setInfo(volinfo);
peVol.setPreThresholdPositions(prethreshpos);
peVol.unthreshold();
// Add param number to "pe" to create filename:
ostringstream osc;
osc << i;
peVol.writeAsFloat(logger.getDir() + "/pe" + osc.str().c_str());
}
// sigmaSquareds:
volinfo.intent_code = NIFTI_INTENT_ESTIMATE;
/*sigmaSquareds.setInfo(volinfo);
sigmaSquareds.setPreThresholdPositions(prethreshpos);
sigmaSquareds.unthreshold();
sigmaSquareds.writeAsFloat(logger.getDir() + "/sigmasquareds");
// dof:
ColumnVector dofVec(1);
dofVec = dof;
write_ascii_matrix(logger.appendDir("dof"), dofVec);
// corrections (are the pes correlation matrix (x.t()*x).i() reshapen to a vector):
VolumeInfo newvolinfo = volinfo;
newvolinfo.v = numParams*numParams;
newvolinfo.intent_code = NIFTI_INTENT_NONE;
corrections.writeThresholdedSeriesAsFloat(newvolinfo,prethreshpos,logger.getDir() + "/corrections");*/
}
void GlimGls::Save(volumeinfo& vinfo, const volume<float>& mask, const float reftdim=1.0)
void GlimGls::Save(volumeinfo vinfo, const volume<float>& mask, const float reftdim=1.0)
{
// Need to save b, sigmaSquareds, corrections and dof
Log& logger = LogSingleton::getInstance();
......
glimGls.h
+ 1
− 6
View file @ e5539630
......@@ -14,13 +14,9 @@
#define WANT_STREAM
#define WANT_MATH
#include "miscmaths/volume.h"
#include "miscmaths/volumeseries.h"
#include "newimage/newimageall.h"
using namespace NEWMAT;
using namespace MISCMATHS;
using namespace NEWIMAGE;
namespace FILM {
......@@ -32,8 +28,7 @@ namespace FILM {
GlimGls(const int pnumTS, const int psizeTS, const int pnumParams);
void setData(const ColumnVector& p_y, const Matrix& p_x, const int ind);
void Save(const VolumeInfo& volinfo, const ColumnVector& prethreshpos);
void Save(volumeinfo& vinfo, const volume<float>& mask,const float reftdim);
void Save(NEWIMAGE::volumeinfo vinfo, const NEWIMAGE::volume<float>& mask,const float reftdim);
ColumnVector& getResiduals() { return r; }
void CleanUp();
......
ttologp.cc
+ 1
− 1
View file @ e5539630
......@@ -133,9 +133,9 @@ int main(int argc,char *argv[])
ColumnVector ps(numTS);
T2z::ComputeZStats(vars, cbs, globalopts.dof, ps);
input.set_intent(NIFTI_INTENT_LOGPVAL,0,0,0);
input.setmatrix(ps.AsRow());
FslSetCalMinMax(&vinfo,input.min(),input.max());
input.set_intent(NIFTI_INTENT_LOGPVAL,0,0,0);
save_volume4D(input,globalopts.logpfname.c_str(),vinfo);
}
......
ttoz.cc
+ 1
− 1
View file @ e5539630
......@@ -137,9 +137,9 @@ int main(int argc,char *argv[])
ColumnVector zs(numTS);
T2z::ComputeZStats(varsm, cbsm, dofsm, zs);
input.set_intent(NIFTI_INTENT_ZSCORE,0,0,0);
input.setmatrix(zs.AsRow());
FslSetCalMinMax(&vinfo,input.min(),input.max());
input.set_intent(NIFTI_INTENT_ZSCORE,0,0,0);
save_volume4D(input,globalopts.zscoresfname,vinfo);
}
catch(Exception p_excp)
......
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