code cleanup, move fft plan creation to function, remove file name strings from param class

bioem.cpp

@@ -205,20 +205,13 @@ int bioem::configure(int ac, char* av[])
 			 exit(1);
 			}
 		// ********************* Reading Parameter Input ***************************
-		// copying inputfile to param class
-		param.fileinput = infile.c_str();
-		param.readParameters();
+		param.readParameters(infile.c_str());
 
 		// ********************* Reading Model Input ******************************
-		// copying modelfile to model class
-		Model.filemodel = modelfile.c_str();
-		Model.readModel();
+		Model.readModel(modelfile.c_str());
 
 		// ********************* Reading Particle Maps Input **********************
-		// ********* HERE: PROBLEM if maps dont fit on the memory!! ***************
-		// copying mapfile to ref map class
-		param.filemap = mapfile.c_str();
-		RefMap.readRefMaps(param);
+		RefMap.readRefMaps(param, mapfile.c_str());
 	}
 
 #ifdef WITH_MPI
@@ -227,6 +220,7 @@ int bioem::configure(int ac, char* av[])
 	if (mpi_rank != 0) return(1);
 
 	// ****************** Precalculating Necessary Stuff *********************
+	param.PrepareFFTs();
 	precalculate();
 
 	if (getenv("BIOEM_DEBUG_BREAK"))
@@ -382,10 +376,11 @@ int bioem::run()
 
 	// *** Angular Probability ***
 
-	// if(param.writeAngles){
 	ofstream angProbfile;
-	angProbfile.open ("ANG_PROB_iRefMap");
-	// }
+	if(param.writeAngles)
+	{
+		angProbfile.open ("ANG_PROB");
+	}
 
 	ofstream outputProbFile;
 	outputProbFile.open ("Output_Probabilities");
@@ -423,7 +418,10 @@ int bioem::run()
 		}
 	}
 
-	angProbfile.close();
+	if(param.writeAngles)
+	{
+		angProbfile.close();
+	}
 	outputProbFile.close();
 
 	return(0);

bioem_cuda.cu

@@ -343,7 +343,7 @@ int bioem_cuda::deviceInit()
 {
 	deviceExit();
 	
-
+	selectCudaDevice();
 
 	if (FFTAlgo) GPUAlgo = 2;
 

include/map.h

@@ -30,7 +30,7 @@ public:
 		sumsquare_RefMap = NULL;
 		RefMapsFFT = NULL;
 	}
-	int readRefMaps(bioem_param& param);
+	int readRefMaps(bioem_param& param, const char* filemap);
 	int precalculate(bioem_param& param, bioem& bio);
 	int PreCalculateMapsFFT(bioem_param& param);
 

include/model.h

@@ -9,7 +9,7 @@ public:
 	//bioem_model();
 	//~bioem_model();
 
-	int readModel();
+	int readModel(const char* filemodel);
 
 	bool readPDB;
 
@@ -17,8 +17,6 @@ public:
 	myfloat_t getAminoAcidDensity(char *name);
 	myfloat_t NormDen;
 
-	const char* filemodel;
-
 	int nPointsModel;
 	myfloat3_t PointsModel[BIOEM_MODEL_SIZE];
 	myfloat_t radiusPointsModel[BIOEM_MODEL_SIZE];

include/param.h

@@ -10,6 +10,7 @@
 class bioem_param_device
 {
 public:
+// Grids in center assuming equidistance from 0,0
 	int maxDisplaceCenter;
 	int GridSpaceCenter;
 	int NumberPixels;
@@ -25,10 +26,10 @@ public:
 	bioem_param();
 	~bioem_param();
 
-	int readParameters();
+	int readParameters(const char* fileinput);
 	int CalculateGridsParam();
 	int CalculateRefCTF();
-	int InitializeArrays();
+	void PrepareFFTs();
 
 	bioem_param_device param_device;
 
@@ -37,20 +38,14 @@ public:
 	mycomplex_t* refCTF;
 	myfloat3_t* CtfParam;
 
-// File names
-	const char* fileinput;
-	char logFile;
 // If to write Probabilities of Angles from Model
 	bool writeAngles;
-	//int NumberPixels; //in device class
 	myfloat_t pixelSize;
 // Grid Points in Euler angles, assuming uniform sampling d_alpha=d_gamma (in 2pi) & cos(beta)=-1,1
 	int angleGridPointsAlpha;
 	int angleGridPointsBeta;
-// Grids in center assuming equidistance from 0,0
-	//int maxDisplaceCenter; //in device class
+
 	int numberGridPointsDisplaceCenter;
-	//int GridSpaceCenter; //in device class
 // Grid sampling for the convolution kernel
 	//ENVELOPE
 	myfloat_t startGridEnvelop;
@@ -64,16 +59,13 @@ public:
 	int numberGridPointsCTF_amp;
 	myfloat_t gridCTF_amp;
 	// Others
-	//myfloat_t volu;//in device class
 	myfloat3_t* angles;
 	int nTotGridAngles;
 	int nTotCTFs;
-	//myfloat_t Ntotpi;//in device class
 
 	int fft_plans_created;
 	myfftw_plan fft_plan_c2c_forward, fft_plan_c2c_backward, fft_plan_r2c_forward, fft_plan_c2r_backward;
 
-	const char* filemap;
 	bool dumpMap, loadMap;
 
 private:

map.cpp

@@ -21,7 +21,7 @@
 
 using namespace std;
 
-int bioem_RefMap::readRefMaps(bioem_param& param)
+int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
 {
 	numPixels = param.param_device.NumberPixels;
 	refMapSize = param.param_device.NumberPixels * param.param_device.NumberPixels;
@@ -50,11 +50,11 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 
 		if(readMultMRC)
 		{
-			ifstream input(param.filemap);
+			ifstream input(filemap);
 
 			if (!input.good())
 			{
-				cout << "Failed to open file contaning MRC names: " << param.filemap << "\n";
+				cout << "Failed to open file contaning MRC names: " << filemap << "\n";
 				exit(0);
 			}
 
@@ -84,13 +84,13 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 
 			}
 			cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
-			cout << "Particle Maps read from MULTIPLE MRC Files in: " << param.filemap << "\n" ;
+			cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
 		}
 		else
 		{
-			read_MRC(param.filemap,param);
+			read_MRC(filemap,param);
 			cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
-			cout << "Particle Maps read from ONE MRC File: " << param.filemap << "\n" ;
+			cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
 		}
 	}
 	else
@@ -98,7 +98,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 		int nummap = -1;
 		int lasti = 0;
 		int lastj = 0;
-		ifstream input(param.filemap);
+		ifstream input(filemap);
 		if (!input.good())
 		{
 			cout << "Particle Maps Failed to open file" << endl ;

model.cpp

@@ -18,7 +18,7 @@
 using namespace std;
 
 
-int bioem_model::readModel()
+int bioem_model::readModel(const char* filemodel)
 {
 	// **************************************************************************************
 	// ***************Reading reference Models either PDB or x,y,z,r,d format****************

param.cpp

@@ -45,7 +45,7 @@ bioem_param::bioem_param()
 	angles = NULL;
 }
 
-int bioem_param::readParameters()
+int bioem_param::readParameters(const char* fileinput)
 {
 	// **************************************************************************************
 	// ***************************** Reading Input Parameters ******************************
@@ -256,8 +256,23 @@ int bioem_param::readParameters()
 	}
 
 
+	param_device.NumberFFTPixels1D = param_device.NumberPixels / 2 + 1;
+	FFTMapSize = param_device.NumberPixels * param_device.NumberFFTPixels1D;
+
+	//Does currently not work with custom alignment on GPU
+	/*if (FFTMapSize % Alignment)
+	{
+		FFTMapSize += Alignment - FFTMapSize % Alignment;
+	}
+	cout << "Using MAP Size " << FFTMapSize << " (Alignment " << Alignment << ", Unaligned Size " << param_device.NumberPixels * param_device.NumberFFTPixels1D << ")\n";*/
+
 	cout << " +++++++++++++++++++++++++++++++++++++++++ \n";
 
+	return(0);
+}
+
+void bioem_param::PrepareFFTs()
+{
 	cout << "Preparing FFTs\n";
 	releaseFFTPlans();
 	mycomplex_t *tmp_map, *tmp_map2;
@@ -278,21 +293,7 @@ int bioem_param::readParameters()
 
 	myfftw_free(tmp_map);
 	myfftw_free(tmp_map2);
-	fft_plans_created = 1;
-
-	param_device.NumberFFTPixels1D = param_device.NumberPixels / 2 + 1;
-	FFTMapSize = param_device.NumberPixels * param_device.NumberFFTPixels1D;
-
-	//Does currently not work with custom alignment on GPU
-	/*if (FFTMapSize % Alignment)
-	{
-		FFTMapSize += Alignment - FFTMapSize % Alignment;
-	}
-	cout << "Using MAP Size " << FFTMapSize << " (Alignment " << Alignment << ", Unaligned Size " << param_device.NumberPixels * param_device.NumberFFTPixels1D << ")\n";*/
-
-	cout << " +++++++++++++++++++++++++++++++++++++++++ \n";
-
-	return(0);
+	fft_plans_created = 1;	
 }
 
 void bioem_param::releaseFFTPlans()