temporary update to new susan

AutoCorrEstimator.cc

@@ -388,21 +388,15 @@ namespace FILM {
 	    // Establish epi thresh to use:
 	    usanthresh = 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);
 	
-	// Setup external call to susan program:
-	ostringstream osc3;
-	string preSmoothVol = "preSmoothVol";
-	string postSmoothVol = "postSmoothVol";
-	
-	osc3 << susanpath << " "
-	     << logger.getDir() << "/" << preSmoothVol << " 1 " 
-	     << logger.getDir() << "/" << postSmoothVol << " " 
-	     << masksize << " 3D 0 1 " << usanfname << " " << usanthresh << " " 
-	     << logger.getDir() << "/" << "usanSize";
-	
-	// Loop through first third of volumes
-	// assume the rest are zero
-	int factor = 10000;
+
 	
 	// Setup volume for reading and writing volumes:
 	Volume vol(acEst.getNumSeries(), xdata.getInfo(), xdata.getPreThresholdPositions());
@@ -410,39 +404,26 @@ namespace FILM {
 	int i = 2;
 	
 	cerr << "Spatially smoothing auto corr estimates" << endl;
-	
-	cerr << osc3.str() << endl;
-	
+		
 	for(; i <= lag; i++)
 	  {
 	    // output unsmoothed estimates:
-	    vol = acEst.getVolume(i).AsColumn()*factor;
-	    vol.unthreshold();
-	    vol.writeAsInt(logger.getDir() + "/" + preSmoothVol);
-	    
-	    // call susan:
-	    system(osc3.str().c_str());
+	    //vol = acEst.getVolume(i).AsColumn()*factor;
+	    //vol.unthreshold();
+	    //vol.writeAsInt(logger.getDir() + "/" + preSmoothVol);
 	    
+            //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);
+	    //vol.read(logger.getDir() + "/" + postSmoothVol);
+	    //vol.threshold();
+	    //acEst.setVolume(static_cast<RowVector>((vol/factor).AsRow()), i);
 	    cerr << ".";
 	  }
-	cerr << endl;
-	
-	// Clear unwanted written files
-	ostringstream osc;
-	osc << "rm -rf " 
-	    << logger.getDir() + "/" + postSmoothVol + "* "
-	    << logger.getDir() + "/" + preSmoothVol + "* "
-	    << logger.getDir() + "/usanSize*";
-	
-	cerr << osc.str() << endl;
-	
-	system(osc.str().c_str());
 	
-	cerr << "Completed" << endl;
+	cerr << endl << "Completed" << endl;
       }
   }