fix compilation problem after merging branches

map.cpp

@@ -41,11 +41,11 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 
 		if(readMultMRC)
 		{
-			ifstream input(filemap);
+			ifstream input(param.filemap);
 
 			if (!input.good())
 			{
-				cout << "Failed to open file contaning MRC names: " << filemap << "\n";
+				cout << "Failed to open file contaning MRC names: " << param.filemap << "\n";
 				exit(0);
 			}
 
@@ -69,18 +69,19 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 					indifile = mapname;  
 					//Reading Multiple MRC
 					read_MRC(indifile,param);
-
 				}
 				for(int i=0;i<3;i++)mapname[i] = 'X';	
 				for(int i=3;i<100;i++)mapname[i] = {0};	
 
 			}
 			cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
-			cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
-		} else {
-			read_MRC(filemap,param);
+			cout << "Particle Maps read from MULTIPLE MRC Files in: " << param.filemap << "\n" ;
+		}
+		else
+		{
+			read_MRC(param.filemap,param);
 			cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
-			cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
+			cout << "Particle Maps read from ONE MRC File: " << param.filemap << "\n" ;
 		}
 	}
 	else
@@ -275,7 +276,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 	float xlen, ylen, zlen;
 	int mode, ncstart, nrstart, nsstart, ispg, nsymbt, lskflg;
 	float a_tmp, b_tmp, g_tmp;
-	int  mx, my, mz,mapc, mapr, maps;
+	int  mx, my, mz,mapc, mapr, maps_local;
 	float dmin, dmax, dmean;
 	int n_range_viol0, n_range_viol1;
 
@@ -319,7 +320,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 	header_ok *= read_float(&g_tmp,fin,swap);
 	header_ok *= read_int(&mapc,fin,swap);
 	header_ok *= read_int(&mapr,fin,swap);
-	header_ok *= read_int(&maps,fin,swap);
+	header_ok *= read_int(&maps_local,fin,swap);
 	header_ok *= read_float(&dmin,fin,swap);
 	header_ok *= read_float(&dmax,fin,swap);
 	header_ok *= read_float(&dmean,fin,swap);
@@ -347,7 +348,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 	printf("    Gamma = %8.3f  (unit cell angle)\n",g_tmp);
 	printf("     MAPC = %8d  (columns axis: 1=X,2=Y,3=Z)\n",mapc);
 	printf("     MAPR = %8d  (rows axis: 1=X,2=Y,3=Z)\n",mapr);
-	printf("     MAPS = %8d  (sections axis: 1=X,2=Y,3=Z)\n",maps);
+	printf("     MAPS = %8d  (sections axis: 1=X,2=Y,3=Z)\n",maps_local);
 	printf("     DMIN = %8.3f  (minimum density value - ignored)\n",dmin);
 	printf("     DMAX = %8.3f  (maximum density value - ignored)\n",dmax);
 	printf("    DMEAN = %8.3f  (mean density value - ignored)\n",dmean);
@@ -372,7 +373,8 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 		cout << "Currently mode 2 is the only one allowed" << "\n";
 		exit(1);
 
-	} else
+	}
+	else
 	{  
 		rewind (fin);
 		for (count=0; count<256; ++count) if (read_float_empty(fin)==0) {
@@ -392,11 +394,14 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 			for ( int j = 0 ; j < nr ; j ++ )
 				for ( int i = 0 ; i < nc ; i ++ )
 				{
-					if (read_float(&currfloat,fin,swap)==0) {
+					if (read_float(&currfloat,fin,swap)==0)
+					{
 						cout << "ERROR Converting Data: " <<  filename;
 						exit(1);
-					} else {
-						Ref[nmap+ntotRefMap].points[i][j] = currfloat;
+					}
+					else
+					{
+						maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = (myfloat_t) currfloat;
 						st += currfloat;
 						st2 += currfloat*currfloat;
 					}
@@ -404,10 +409,10 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 
 				//Normaling maps to zero mean and unit standard deviation
 				st /= float(nr*nc);
-				st2 = sqrt(st2/float(nr*nc)-st*st); 
+				st2 = sqrt(st2 / float(nr * nc) - st * st); 
 				for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
-					Ref[nmap+ntotRefMap].points[i][j] =  Ref[nmap+ntotRefMap].points[i][j]/st2 - st/st2;
-					//    if(nmap+ntotRefMap==300)cout << i << " " << j << " " << nmap+ntotRefMap << " " <<  Ref[nmap+ntotRefMap].points[i][j]  << "\n";                          
+					maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] / st2 - st/st2;
+					//if(nmap+ntotRefMap==300) cout << i << " " << j << " " << nmap+ntotRefMap << " " <<  Ref[nmap+ntotRefMap].points[i][j]  << "\n";                          
 				}
 		}
 		ntotRefMap += ns ;
@@ -470,7 +475,7 @@ int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
 	int mode, ncstart, nrstart, nsstart;
 	float xlen, ylen, zlen;
 	int i, header_ok = 1, n_range_viols = 0;
-	int mapc, mapr, maps;
+	int mapc, mapr, maps_local;
 	float alpha, beta, gamma;
 	float dmin, dmax, dmean, dummy, xorigin, yorigin, zorigin;
 
@@ -499,7 +504,7 @@ int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
 	header_ok *= read_float(&gamma,fin,swap);
 	header_ok *= read_int(&mapc,fin,swap);
 	header_ok *= read_int(&mapr,fin,swap);
-	header_ok *= read_int(&maps,fin,swap);
+	header_ok *= read_int(&maps_local,fin,swap);
 	header_ok *= read_float(&dmin,fin,swap);
 	header_ok *= read_float(&dmax,fin,swap);
 	header_ok *= read_float(&dmean,fin,swap);

model.cpp

@@ -119,7 +119,7 @@ int bioem_model::readModel()
 		FILE *file = fopen ( filemodel , "r" );
 		if (file == NULL)
 		{
-			cout << "Error opening file " << filemode, << "\n";
+			cout << "Error opening file " << filemodel << "\n";
 			exit(1);
 		}
 		while ( fgets ( line, sizeof line, file ) != NULL )