in progress newimage conversion: DO NOT TAG STABLE

ftoz.cc

@@ -138,11 +138,10 @@ int main(int argc,char *argv[])
     ColumnVector zs(numTS);
     F2z::ComputeFStats(fs, dof1, dof2, 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) 

glim.cc

@@ -9,24 +9,24 @@
 #include <sstream>
 
 #include "glim.h"
-#include "miscmaths/miscmaths.h"
 #include "utils/log.h"
-#include "miscmaths/volume.h"
+#include "newimage/newimageall.h"
 
 #ifndef NO_NAMESPACE
 using namespace MISCMATHS;
 using namespace Utilities;
+using namespace NEWIMAGE;
 
 namespace FILM {
 #endif
 
-  Glim::Glim(VolumeSeries& p_y, const Matrix& p_x):
+  Glim::Glim(Matrix& p_y, const Matrix& p_x):
     y(p_y),
     x(p_x),
     numTS(p_y.Ncols()),
     sizeTS(p_y.Nrows()),
     numParams(p_x.Ncols()),
-    r(sizeTS, numTS, p_y.getInfo(), p_y.getPreThresholdPositions()),
+    r(sizeTS, numTS),
     pinv_x(p_x.Ncols(), sizeTS),
     V(sizeTS,sizeTS),
     RV(sizeTS,sizeTS),
@@ -39,32 +39,26 @@ namespace FILM {
     { 
     }
 
-  void Glim::Save()
+  void Glim::Save(const volume<float>& mask,volumeinfo vinfo)
     {
       // Need to save b, sigmaSquareds, corrections and dof 
       Log& logger = LogSingleton::getInstance();
-     
-      // b:
-      Volume peVol;
+   
+      volume4D<float> output;
+
       for(int i = 1; i <= numParams; i++)
 	{
-	  peVol = b.Row(i).AsColumn();
-	  peVol.setInfo(y.getInfo());
-	  peVol.setPreThresholdPositions(y.getPreThresholdPositions());
-	  peVol.unthreshold();	
-	  
-	  // Add param number to "pe" to create filename:
 	  ostringstream osc;
 	  osc << i;
-	  
-	  peVol.writeAsFloat(logger.getDir() + "/pe" + osc.str().c_str());
+	  output.setmatrix(b.Row(i),mask);
+	  FslSetCalMinMax(&vinfo,output.min(),output.max());
+	  save_volume4D(output,logger.getDir() + "/pe" + osc.str().c_str(),vinfo);
 	}
 
-      // sigmaSquareds:
-      sigmaSquareds.setInfo(y.getInfo());
-      sigmaSquareds.setPreThresholdPositions(y.getPreThresholdPositions());
-      sigmaSquareds.unthreshold();	
-      sigmaSquareds.writeAsFloat(logger.getDir() + "/sigmasquareds");
+      output.setmatrix(sigmaSquareds.AsRow(),mask);
+      FslSetCalMinMax(&vinfo,output.min(),output.max());
+      save_volume4D(output,logger.getDir() + "/sigmasquareds",vinfo);
+
 
       // dof:
       ColumnVector dofVec(1);
@@ -76,7 +70,7 @@ namespace FILM {
     }
 
   // Called on entire data set:
-  VolumeSeries& Glim::ComputeResids()
+  Matrix& Glim::ComputeResids()
     {
       Tracer ts("ComputeResids");
 

glim.h

@@ -11,13 +11,12 @@
 #define WANT_STREAM
 #define WANT_MATH
 
-#include "newmatap.h"
-#include "newmatio.h"
-#include "miscmaths/volumeseries.h"
-#include "miscmaths/volume.h"
+#include "miscmaths/miscmaths.h"
+#include "newimage/newimageall.h"
 
 using namespace NEWMAT;
 using namespace MISCMATHS;
+using namespace NEWIMAGE;
 namespace FILM{
 
 #if !defined(__glim_h)
@@ -28,11 +27,11 @@ namespace FILM{
   class Glim
     {
     public:
-      Glim(VolumeSeries& p_y, const Matrix& p_x); 
+      Glim(Matrix& p_y, const Matrix& p_x); 
 
-      void Save();
+      void Save(const volume<float>& mask,volumeinfo vinfo);
 
-      VolumeSeries& ComputeResids();      
+      Matrix& ComputeResids();      
       void ComputePes();
       void SetVrow(const ColumnVector& p_vrow, const int ind);
       void SetGlobalVrow(const ColumnVector& p_vrow);
@@ -46,17 +45,17 @@ namespace FILM{
       
       void SetCorrection(const Matrix& corr, const int ind);
       void ConstructV(const ColumnVector& p_vrow);
-      void setData(VolumeSeries& p_y) { y = p_y; }
+      void setData(Matrix& p_y) { y = p_y; }
 
       // y = bx + r
-      VolumeSeries& y;
+      Matrix& y;
       const Matrix& x;
 
       int numTS;
       int sizeTS;
       int numParams;
 
-      VolumeSeries r;
+      Matrix r;
       Matrix pinv_x;
       Matrix V;
       Matrix RV;
@@ -67,7 +66,7 @@ namespace FILM{
       // Data to be saved:
       Matrix corrections;
       Matrix b;
-      Volume sigmaSquareds;
+      ColumnVector sigmaSquareds;
       float dof;
     };