adding susan function call

AutoCorrEstimator.cc

@@ -16,11 +16,13 @@
 #include "miscmaths/volume.h"
 #include "miscmaths/histogram.h"
 #include "miscmaths/miscmaths.h"
+#include "newimage/newimageall.h"
 #include "glm.h"
 
 using namespace Utilities;
 using namespace NEWMAT;
 using namespace MISCMATHS;
+using namespace NEWIMAGE;
 
 namespace FILM {
 
@@ -369,7 +371,7 @@ namespace FILM {
       return usanthresh;
     } 
 
-  void AutoCorrEstimator::spatiallySmooth(const string& usanfname, const Volume& epivol, int masksize, const string& epifname, const string& susanpath, int usanthresh, int lag) {
+  void AutoCorrEstimator::spatiallySmooth(const string& usanfname, const Volume& epivol, int masksize, const string& epifname, const string& susanpath, int usan_thresh, int lag) {
     Tracer trace("AutoCorrEstimator::spatiallySmooth");
     
     if(xdata.getNumSeries()<=1)
@@ -378,55 +380,52 @@ namespace FILM {
       }
     else
       {
-	Log& logger = LogSingleton::getInstance();
 	
 	if(lag==0)
 	  lag = MISCMATHS::Min(40,int(xdata.getNumVolumes()/4));
 	
-	if(usanthresh == 0)
+	if(usan_thresh == 0)
 	  {
 	    // Establish epi thresh to use:
-	    usanthresh = establishUsanThresh(epivol);
+	    usan_thresh = establishUsanThresh(epivol);
 	  }
 
-  volume<float> susan_vol(xdata.getInfo().x,xdata.getInfo().y,xdata.getInfo().z);
-  volume<float> usan_area(xdata.getInfo().x,xdata.getInfo().y,xdata.getInfo().z);
-  volume<float> usan_vol;
-  read_volume(usan_vol,usanfname);
-  volume<float> kernel;
-  kernel = kernel=gaussian_kernel3D(masksize,xdata.getInfo().vx,xdata.getInfo().vy,xdata.getInfo().vz);
-	
-
+	volume<float> susan_vol(xdata.getInfo().x,xdata.getInfo().y,xdata.getInfo().z);
+	volume<float> usan_area(xdata.getInfo().x,xdata.getInfo().y,xdata.getInfo().z);
+	volume<float> usan_vol;
+	read_volume(usan_vol,usanfname);
+	volume<float> kernel;
+	kernel = kernel=gaussian_kernel3D(masksize,xdata.getInfo().vx,xdata.getInfo().vy,xdata.getInfo().vz);	
 	
 	// Setup volume for reading and writing volumes:
 	Volume vol(acEst.getNumSeries(), xdata.getInfo(), xdata.getPreThresholdPositions());
-	
+
 	int i = 2;
 	
 	cerr << "Spatially smoothing auto corr estimates" << endl;
-		
+	
 	for(; i <= lag; i++)
 	  {
-	    // output unsmoothed estimates:
-	    //vol = acEst.getVolume(i).AsColumn()*factor;
-	    //vol.unthreshold();
-	    //vol.writeAsInt(logger.getDir() + "/" + preSmoothVol);
+	    // setup susan input
+	    vol = acEst.getVolume(i).AsColumn();
+	    vol.unthreshold();
+	    susan_vol.insert_vec(vol);
+
+	    // call susan
+	    susan_vol=susan_convolve(susan_vol,kernel,1,0,1,&usan_area,usan_vol,usan_thresh*usan_thresh);
 	    
-            //TODO copy vol to susan_volume                       
-	      susan_vol=susan_convolve(susan_vol,kernel,1,0,1,&usan_area,usan_vol,usan_thresh*usan_thresh);
-	    //TODO copy susan_volume to vol
-
-	    // read in smoothed volume:
-	    //vol.read(logger.getDir() + "/" + postSmoothVol);
-	    //vol.threshold();
-	    //acEst.setVolume(static_cast<RowVector>((vol/factor).AsRow()), i);
+	    // insert output back into acEst
+	    vol=susan_vol.vec();
+	    vol.threshold();
+	    acEst.setVolume(static_cast<RowVector>((vol).AsRow()), i);
+
 	    cerr << ".";
 	  }
 	
 	cerr << endl << "Completed" << endl;
       }
   }
-
+  
   void AutoCorrEstimator::calcRaw(int lag) { 
     
     cerr << "Calculating raw AutoCorrs...";      

Makefile

@@ -5,7 +5,7 @@ PROJNAME = film
 USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB}
 USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
 
-LIBS = -lmiscmaths -lutils -lm -lnewmat -lfslio -lniftiio -lznz -lprob -lz
+LIBS = -lmiscmaths -lnewimage -lutils -lm -lnewmat -lfslio -lniftiio -lznz -lprob -lz
 
 XFILES = film_gls contrast_mgr ttoz ftoz ttologp