*** empty log message ***

ContrastMgr.cc

@@ -16,6 +16,7 @@
 #include "t2z.h"
 #include "f2z.h"
 #include "paradigm.h"
+#include "tracer_plus.h"
 
 using namespace Utilities;
 
@@ -62,14 +63,13 @@ namespace FILM {
 
   void ContrastMgr::run()
   {
-    Tracer ts("ContrastMgr::run");
+    Tracer_Plus ts("ContrastMgr::run");
 
     Load();
 
     // Loop through tcontrasts:
     for(int c = 1; c <= parad.getTContrasts().Nrows(); c++)
       {
-
 	if(ContrastMgrOptions::getInstance().verbose)
 	  {
 	    cerr << "T contrast no. " << c << endl;
@@ -88,7 +88,6 @@ namespace FILM {
     // Loop through fcontrasts:
     for(int c = 1; c <= parad.getFContrasts().Nrows(); c++)
       {
-	
 	SetFContrast(c, c+ContrastMgrOptions::getInstance().copenumber-1);
 
 	if(ContrastMgrOptions::getInstance().verbose)
@@ -108,25 +107,26 @@ namespace FILM {
 
   void ContrastMgr::Load()
   {
-    Tracer ts("ContrastMgr::Load");
+    Tracer_Plus ts("ContrastMgr::Load");
     // Need to read in b, sigmaSquareds, corrections and dof 
     Log& logger = Log::getInstance();
-     
+
     // Load contrasts:     
     parad.load("", ContrastMgrOptions::getInstance().contrastfname, ContrastMgrOptions::getInstance().fcontrastfname, false, 0);
        
     numParams = parad.getTContrasts().Ncols(); 
+
     if(ContrastMgrOptions::getInstance().verbose)
       {
-	logger.str() << "T Contrasts:" << endl << parad.getTContrasts();
-	logger.str() << "F Contrasts:" << endl << parad.getFContrasts();
+	cerr << "T Contrasts:" << endl << parad.getTContrasts();
+	cerr << "F Contrasts:" << endl << parad.getFContrasts();
       }
 
     // sigmaSquareds:
     sigmaSquareds.read(logger.getDir() + "/sigmasquareds");
     sigmaSquareds.threshold(0.0);
-    numTS = sigmaSquareds.getVolumeSize();
-     
+    numTS = sigmaSquareds.getVolumeSize();    
+ 
     // b:
     Volume peVol;
     b.ReSize(numTS, numParams);
@@ -148,7 +148,7 @@ namespace FILM {
 
     // dof:
     ColumnVector dofVec = MISCMATHS::read_ascii_matrix(logger.getDir() + "/dof");
-    dof = dofVec(1);
+    dof = dofVec(1);   
 
     // corrections - maybe ASCII (old version) or avw file:
     ifstream in;
@@ -158,6 +158,12 @@ namespace FILM {
 	// avw format
 	is_avw_corrections = true;
 	corrections.read(logger.getDir() + "/corrections");
+	if(corrections.getDims().x == sigmaSquareds.getDims().x)
+	  {
+	    // unthresholded avw
+	    corrections.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
+	    corrections.thresholdSeries();
+	  }
       }
     else
       {
@@ -172,7 +178,7 @@ namespace FILM {
 
   void ContrastMgr::SaveFContrast(const string& suffix)
   {
-    Tracer ts("ContrastMgr::SaveFContrast");
+    Tracer_Plus ts("ContrastMgr::SaveFContrast");
     Log& logger = Log::getInstance();
 
     // prepare contrast number:
@@ -195,7 +201,7 @@ namespace FILM {
 
   void ContrastMgr::SaveTContrast(const string& suffix)
   {
-    Tracer ts("ContrastMgr::SaveTContrast");
+    Tracer_Plus ts("ContrastMgr::SaveTContrast");
     Log& logger = Log::getInstance();
     
     // prepare contrast number:
@@ -237,7 +243,7 @@ namespace FILM {
 
   void ContrastMgr::GetCorrection(Matrix& corr, const int ind)
   {
-    Tracer ts("ContrastMgr::GetCorrection");
+    Tracer_Plus ts("ContrastMgr::GetCorrection");
 
     // puts ColumnVector of length p*p from correction
     // into Matrix corr which is p*p:
@@ -254,7 +260,7 @@ namespace FILM {
 
   void ContrastMgr::ComputeZStat()
   {
-    Tracer ts("ContrastMgr::ComputeZStat");
+    Tracer_Plus ts("ContrastMgr::ComputeZStat");
 
     Log& logger = Log::getInstance();
 
@@ -297,7 +303,7 @@ namespace FILM {
 
   void ContrastMgr::ComputeCope()
   { 
-    Tracer ts("ContrastMgr::ComputeCope");
+    Tracer_Plus ts("ContrastMgr::ComputeCope");
     cb.ReSize(numTS);
 
     for(int i = 1; i <= numTS; i++)
@@ -308,7 +314,7 @@ namespace FILM {
 
   void ContrastMgr::ComputeNeff()
   {
-    Tracer ts("ContrastMgr::ComputeNeff");
+    Tracer_Plus ts("ContrastMgr::ComputeNeff");
    
     Log& logger = Log::getInstance();
     Matrix corr;
@@ -344,7 +350,7 @@ namespace FILM {
 
   void ContrastMgr::ComputeFStat()
   {
-    Tracer ts("ContrastMgr::ComputeFStat");
+    Tracer_Plus ts("ContrastMgr::ComputeFStat");
     
     //Log& logger = Log::getInstance();
     Matrix corr;
@@ -377,7 +383,7 @@ namespace FILM {
 
   void ContrastMgr::ComputeVarCope()
   { 
-    Tracer ts("ContrastMgr::ComputeVarCope");
+    Tracer_Plus ts("ContrastMgr::ComputeVarCope");
     varcb.ReSize(numTS);
 
     for(int i = 1; i <= numTS; i++)