bioem.cpp

bioem_algorithm.h

@@ -154,15 +154,17 @@ __device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient,
        
 		                bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
 
-        /*      		  if(pProbAngle.ConstAngle < logpro)
-                	{
-                        	pProbAngle.forAngles = pProbAngle.forAngles * exp(-logpro + pProbAngle.ConstAngle);
-	                        pProbAngle.ConstAngle = logpro;
-        		 }*/
                         myfloat_t ttmp;
-                        ttmp=lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels);
-                        if(ttmp>0)pProbCC.forCC += exp( - ttmp);
-//                        pProbCC.forCC  =ttmp;
+                        ttmp= (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels);
+                        if(not param.flipped){
+                        // Storing the lowest cross correlations
+                        if(pProbCC.forCC > ttmp) pProbCC.forCC = ttmp;
+                        }
+                        else{
+                        //Storing the highest cross correlations
+                         if(pProbCC.forCC < ttmp) pProbCC.forCC = ttmp;
+			}
+//                        pProbCC.forCC  = ttmp;
                       cc++;  
                 	}
              	}

include/param.h

@@ -22,7 +22,8 @@ public:
 // If to write Probabilities of Angles from Model
 	bool writeAngles;
         bool writeCC;
-	 int CCdisplace;
+        bool flipped;
+	int CCdisplace;
 
 };
 

map.cpp

@@ -180,6 +180,11 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 				}
 			}
 		}
+                if(lasti != param.param_device.NumberPixels && lastj != param.param_device.NumberPixels )
+                                {
+                                        cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << lasti << ", j " << lastj << ")" << "\n";
+                                        exit(1);
+                }
 		cout << ".";
 		ntotRefMap = nummap + 1;
 		maps = (myfloat_t*) reallocchk(maps, refMapSize * sizeof(myfloat_t) * ntotRefMap);

param.cpp

@@ -74,6 +74,9 @@ int bioem_param::readParameters(const char* fileinput)
 	bool yesMDC = false ;
 	bool yesGCen = false ;
 
+        //Default not flipped micrographs
+        param_device.flipped=false;
+
 	ifstream input(fileinput);
 	if (!input.good())
 	{
@@ -229,6 +232,11 @@ int bioem_param::readParameters(const char* fileinput)
                         param_device.CCdisplace=int(atoi(token));
                         if (param_device.CCdisplace < 0 ) { cout << "*** Error: Negative CROSSCOR_DISPLACE "; exit(1);}
                         cout << "Writing Cross Correlation Displacement " <<  param_device.CCdisplace << "  \n";
+                }
+                 else if (strcmp(token, "FLIPPED") == 0)               
+		{
+                        param_device.flipped = true;
+                        cout << "Micrograph Flipped Intensities \n";
                 }
                 else if (strcmp(token, "DO_AA_RADIUS") == 0)
                 {