Merge branch 'devel_drohr' of gitta.rzg.mpg.de:BioEM into devel_drohr

bioem.cpp

@@ -356,6 +356,20 @@ int bioem::run()
 				pProbAngle.ConstAngle = -99999999;
 			}
 		}
+		 if (param.param_device.writeCC)
+        	{      int  cc=0;
+                	 for (int cent_x = 0; cent_x < param.param_device.NumberPixels -param.param_device.CCdisplace ; cent_x = cent_x + param.param_device.CCdisplace)
+                         {
+                                 for (int cent_y = 0; cent_y < param.param_device.NumberPixels - param.param_device.CCdisplace ; cent_y = cent_y + param.param_device.CCdisplace)
+                                 {
+        	                       cout << cc << " " << cent_x << " " << cent_y <<"\n"; 
+                                 bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
+                                 pProbCC.forCC = 0.0;
+ 
+                                 cc++;
+                                 }
+                         }
+		}                 
 	}
 	// **************************************************************************************
 	deviceStartRun();
@@ -606,16 +620,16 @@ int bioem::run()
 			if(param.param_device.writeCC)
 			{
 				int  cc=0;
-				for (int cent_x = 0; cent_x < param.param_device.NumberPixels; cent_x = cent_x + param.param_device.CCdisplace)
-				{
-					for (int cent_y = 0; cent_y < param.param_device.NumberPixels; cent_y = cent_y + param.param_device.CCdisplace)
-					{
+			for (int cent_x = 0; cent_x < param.param_device.NumberPixels -param.param_device.CCdisplace ; cent_x = cent_x + param.param_device.CCdisplace)
+                         {
+                                 for (int cent_y = 0; cent_y < param.param_device.NumberPixels - param.param_device.CCdisplace ; cent_y = cent_y + param.param_device.CCdisplace)
+                                 {
 						bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
-						ccProbfile << " " << iRefMap << " " << cent_x << " " << cent_y << " " << log(pProbCC.forCC) <<"\n";
-					}
+						ccProbfile << " " << iRefMap << " " << cent_x << " " << cent_y << " " << pProbCC.forCC <<"\n";
 				}
 
 			}
+                       }
 		}
 
 		if(param.param_device.writeAngles)

bioem_algorithm.h

@@ -146,12 +146,13 @@ __device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient,
 	if (param.writeCC)
         {
           int  cc=0;
-	   for (int cent_x = 0; cent_x < param.NumberPixels; cent_x = cent_x + param.CCdisplace)
-        	{
-                	for (int cent_y = 0; cent_y < param.NumberPixels; cent_y = cent_y + param.CCdisplace)
-                	{     
+		for (int cent_x = 0; cent_x < param.NumberPixels -param.CCdisplace ; cent_x = cent_x + param.CCdisplace)
+                         {
+                                 for (int cent_y = 0; cent_y < param.NumberPixels - param.CCdisplace ; cent_y = cent_y + param.CCdisplace)
+                                 {
+
        
-	                bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
+		                bioem_Probability_cc& pProbCC = pProb.getProbCC(iRefMap, cc);
 
         /*      		  if(pProbAngle.ConstAngle < logpro)
                 	{
@@ -161,7 +162,8 @@ __device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient,
                         myfloat_t ttmp;
                         ttmp=lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels);
                         if(ttmp>0)pProbCC.forCC += exp( - ttmp);
-                        cc++;  
+//                        pProbCC.forCC  =ttmp;
+                      cc++;  
                 	}
              	}
         }

include/map.h

@@ -140,6 +140,7 @@ public:
 		ptr_map = (bioem_Probability_map*) ptr;
 		ptr_angle = (bioem_Probability_angle*) (&ptr_map[nMaps]);
 		ptr_cc = (bioem_Probability_cc*) (&ptr_angle[nMaps * nAngles]);
+//                ptr_cc = (bioem_Probability_cc*) (&ptr_angle[nMaps * 2000 ]);
 	}
 };
 

param.cpp

@@ -225,7 +225,9 @@ int bioem_param::readParameters(const char* fileinput)
                 }
 		else if (strcmp(token, "CROSSCOR_DISPLACE") == 0)
                 {
+		        token = strtok(NULL, " ");
                         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, "DO_AA_RADIUS") == 0)
@@ -253,7 +255,7 @@ int bioem_param::readParameters(const char* fileinput)
 	if( not ( yesGSPpha  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_PHASE \n" ; exit (1);};
 	if( not (  yesMDC  ) ) { cout << "**** INPUT MISSING: Please provide MAX_D_CENTER \n" ; exit (1);};
 	if( not (  yesGCen  ) ) { cout << "**** INPUT MISSING: Please provide PIXEL_GRID_CENTER \n" ; exit (1);};
-
+	if( param_device.writeCC && param_device.CCdisplace < 1 ){ cout << "**** INPUT MISSING: Please provide CROSSCOR_DISPLACE \n" ; exit (1);};
 
     //if only one grid point for PSF kernel:
     if( (myfloat_t) numberGridPointsCTF_amp == 1 ) gridCTF_amp = startGridCTF_amp;