avwpspec created; transforms 4D files to power spectra

fslpspec.cc

@@ -10,16 +10,11 @@
 #include "newmatap.h"
 #include "newmatio.h"
 #include "newimage/newimageall.h"
-#include "newimage/fmribmain.h"
 
 using namespace NEWIMAGE;
 
 void print_usage(const string& progname) {
   cout << "Usage: " << progname << " <input> [options] [output]" << endl;
-  cout << endl;
-  cout << "  " << endl;
-  cout << "  " << endl;
-  cout << "  e.g.  " << progname << " " << endl;
 }
 
 ReturnMatrix calcFFT(const Matrix& Mat)
@@ -45,26 +40,19 @@ ReturnMatrix calcFFT(const Matrix& Mat)
   return res;
 } //Matrix calcFFT()
 
-int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin, float& lthr, float& uthr) 
+int generate_masks(volume<float> &mask, const volume<float> &vin) 
 {
-  mask = binarise(vin,lthr,uthr,exclusive);
-  masknz = mask * (1.0f - binarise(vin,0.0f, 0.0f));
-  return 0;
-}
 
-int generate_masks(const volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin)
-{
-  masknz = mask * (1.0f - binarise(vin,0.0f, 0.0f));
+  mask = binarise(vin,vin.min(),vin.max());
   return 0;
 }
 
-int fmrib_main_float(int argc, char* argv[]) 
+int fmrib_main(int argc, char* argv[]) 
 {
   string inname=argv[1];
   string maskname="";
   string outname="";
 
-  cout << argc << endl;
   if(argc>2)
     outname=argv[2];
   else
@@ -72,25 +60,23 @@ int fmrib_main_float(int argc, char* argv[])
 
   Matrix iMat, oMat;
   volume4D<float> vout;
-  volume<float> smask, smasknz;
+  volume<float> mask;
   volumeinfo volinfo;
+  float vinTR;
 
   {
-    volume4D<float> vin, mask, masknz;
+    volume4D<float> vin;
     read_volume4D(vin,argv[1],volinfo);
 
-    float lthr=0, uthr=0;
-    generate_masks(mask,masknz,vin,lthr,uthr);
-    
-    smask=mask[0];
-    smasknz=masknz[0];
-
-    iMat = vin.matrix(smasknz);
-  }
+    generate_masks(mask,stddevvol(vin));
+    iMat = vin.matrix(mask);
+    vinTR=vin.TR();
+  } 
 
   oMat = calcFFT(iMat);
-  
-  vout.setmatrix(oMat,smasknz);
+ 
+  vout.setmatrix(oMat,mask);
+  vout.setTR(vinTR);
 
   int retval=0;
   retval = save_volume4D(vout,outname,volinfo);
@@ -103,12 +89,12 @@ int main(int argc,char *argv[])
  Tracer tr("main");
 
   string progname=argv[0];
-  if (argc<3) { 
+  if (argc<2) { 
     print_usage(progname);
     return 1; 
   }
 
-  return fmrib_main_float(argc,argv);
+  return fmrib_main(argc,argv);
 
 }