Correction to Normalization

bioem.cpp

@@ -601,7 +601,7 @@ int bioem::run()
 			outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " ";
 			outputProbFile << pProbMap.max.max_prob_cent_x << " ";
 			outputProbFile << pProbMap.max.max_prob_cent_y << " " ;
-	                outputProbFile << pProbMap.max.max_prob_norm  << " " ;
+	                outputProbFile << pProbMap.max.max_prob_norm << " " ; // param.param_device.Ntotpi / param.param_device.Ntotpi << " " ;
         	        outputProbFile << pProbMap.max.max_prob_mu ;
                 	outputProbFile << "\n";
 
@@ -824,7 +824,8 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
 					if( dist < rad2 )
 					{
 						localproj[ii * param.param_device.NumberPixels + jj] += param.pixelSize * 2 * sqrt( rad2 - dist ) * Model.points[n].density
-							/ Model.NormDen * 3 / (4 * M_PI * rad2 *  Model.points[n].radius); 	
+//							/ Model.NormDen * 3 / (4 * M_PI * rad2 *  Model.points[n].radius); 	
+							* 3 / (4 * M_PI * rad2 *  Model.points[n].radius); 
 					}
 				}
 			}
@@ -845,7 +846,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
 				continue;
 			}
 
-			localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density / Model.NormDen;
+			localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density;//Model.NormDen;
 		}
 	}
 
@@ -890,12 +891,14 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
 
 	mycomplex_t* tmp = param.fft_scratch_complex[omp_get_thread_num()];
 
+ 	myfloat_t norm = (myfloat_t) (param.param_device.NumberPixels *  param.param_device.NumberPixels);
+
 	// **** Multiplying FFTmap with corresponding kernel ****
 	const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
 	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
 	{
-		localmultFFT[i][0] = lproj[i][0] * refCTF[i][0] + lproj[i][1] * refCTF[i][1];
-		localmultFFT[i][1] = lproj[i][1] * refCTF[i][0] - lproj[i][0] * refCTF[i][1];
+		localmultFFT[i][0] = ( lproj[i][0] * refCTF[i][0] + lproj[i][1] * refCTF[i][1] ) ;
+		localmultFFT[i][1] = ( lproj[i][1] * refCTF[i][0] - lproj[i][0] * refCTF[i][1] ) ;
 		// cout << "GG " << i << " " << j << " " << refCTF[i][0] << " " << refCTF[i][1] <<" " <<lproj[i][0] <<" " <<lproj[i][1] << "\n";
 	}
 

main.cpp

@@ -31,8 +31,8 @@
 int mpi_rank;
 int mpi_size;
 #else
-const int mpi_rank = 0;
-const int mpi_size = 1;
+int mpi_rank = 0;
+int mpi_size = 1;
 #endif
 
 #include "cmodules/timer.h"