fix file endings

bioem.cpp

@@ -57,8 +57,8 @@ int bioem::configure(int ac, char* av[])
 	param.writeAngles = false;
 	param.dumpMap = false;
 	param.loadMap = false;
-	RefMap.readMRC = false;
-	RefMap.readMultMRC = false;
+	RefMap.readMRC = false;
+	RefMap.readMultMRC = false;
 
 	// *************************************************************************************
 	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
@@ -68,17 +68,17 @@ int bioem::configure(int ac, char* av[])
 
 	try {
 		po::options_description desc("Command line inputs");
-		desc.add_options()
-		("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
-		("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
-		("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
-		("ReadPDB", "(Optional) If reading model file in PDB format")
-		("ReadMRC", "(Optional) If reading particle file in MRC format")
-		("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
-		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
-		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
-		("help", "(Optional) Produce help message")
-		;
+		desc.add_options()
+		("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
+		("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
+		("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
+		("ReadPDB", "(Optional) If reading model file in PDB format")
+		("ReadMRC", "(Optional) If reading particle file in MRC format")
+		("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
+		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
+		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
+		("help", "(Optional) Produce help message")
+		;
 
 
 		po::positional_options_description p;
@@ -86,8 +86,8 @@ int bioem::configure(int ac, char* av[])
 		p.add("Modelfile", -1);
 		p.add("Particlesfile", -1);
 		p.add("ReadPDB", -1);
-		p.add("ReadMRC", -1);
-		p.add("ReadMultipleMRC", -1);
+		p.add("ReadMRC", -1);
+		p.add("ReadMultipleMRC", -1);
 		p.add("DumpMaps", -1);
 		p.add("LoadMapDump", -1);
 
@@ -125,17 +125,17 @@ int bioem::configure(int ac, char* av[])
 			Model.readPDB = true;
 		}
 
-		if (vm.count("ReadMRC"))
-		{
-			cout << "Reading particle file in MRC format.\n";
-			RefMap.readMRC=true;
-		}
-
-		if (vm.count("ReadMultipleMRC"))
-		{
-			cout << "Reading Multiple MRCs.\n";
-			RefMap.readMultMRC=true;
-		}
+		if (vm.count("ReadMRC"))
+		{
+			cout << "Reading particle file in MRC format.\n";
+			RefMap.readMRC=true;
+		}
+
+		if (vm.count("ReadMultipleMRC"))
+		{
+			cout << "Reading Multiple MRCs.\n";
+			RefMap.readMultMRC=true;
+		}
 
 		if (vm.count("DumpMaps"))
 		{
@@ -379,8 +379,8 @@ int bioem::run()
 
 int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
 {
-	//***************************************************************************************
-	//***** BioEM routine for comparing reference maps to convoluted maps *****
+	//***************************************************************************************
+	//***** BioEM routine for comparing reference maps to convoluted maps *****
 	if (FFTAlgo)
 	{
 		//With FFT Algorithm
@@ -405,8 +405,8 @@ int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, myc
 
 inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC)
 {
-	//***************************************************************************************
-	//***** Calculating cross correlation in FFTALGOrithm *****
+	//***************************************************************************************
+	//***** Calculating cross correlation in FFTALGOrithm *****
 
 	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
 	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)

include/map.h

@@ -34,16 +34,16 @@ public:
 	int precalculate(bioem_param& param, bioem& bio);
 	int PreCalculateMapsFFT(bioem_param& param);
 
-	int  read_int(int *currlong, FILE *fin, int swap);
-	int  read_float(float *currfloat, FILE *fin, int swap);
-	int  read_float_empty (FILE *fin);
-	int  read_char_float (float *currfloat, FILE *fin) ;
-	int  test_mrc (const char *vol_file, int swap);
-	int  read_MRC(const char* filename,bioem_param& param);
+	int  read_int(int *currlong, FILE *fin, int swap);
+	int  read_float(float *currfloat, FILE *fin, int swap);
+	int  read_float_empty (FILE *fin);
+	int  read_char_float (float *currfloat, FILE *fin) ;
+	int  test_mrc (const char *vol_file, int swap);
+	int  read_MRC(const char* filename,bioem_param& param);
 
 	mycomplex_t* RefMapsFFT;
 
-	bool readMRC,readMultMRC;
+	bool readMRC,readMultMRC;
 
 	int ntotRefMap;
 	int numPixels;

param.cpp

@@ -42,22 +42,22 @@ int bioem_param::readParameters()
 	// ***************************** Reading Input Parameters ******************************
 	// **************************************************************************************
 
-	// Control for Parameters
-	bool yesPixSi = false;
-	bool yesNumPix = false;
-	bool yesGPal = false;
-	bool yesGPbe = false;
-	bool yesGPEnv = false;
-	bool yesGPamp = false;
-	bool yesGPpha = false;
-	bool yesSTEnv = false;
-	bool yesSTamp = false;
-	bool yesSTpha = false;
-	bool yesGSPamp = false ;
-	bool yesGSPEnv = false ;
-	bool yesGSPpha = false ;
-	bool yesMDC = false ;
-	bool yesGCen = false ;	
+	// Control for Parameters
+	bool yesPixSi = false;
+	bool yesNumPix = false;
+	bool yesGPal = false;
+	bool yesGPbe = false;
+	bool yesGPEnv = false;
+	bool yesGPamp = false;
+	bool yesGPpha = false;
+	bool yesSTEnv = false;
+	bool yesSTamp = false;
+	bool yesSTpha = false;
+	bool yesGSPamp = false ;
+	bool yesGSPEnv = false ;
+	bool yesGSPpha = false ;
+	bool yesMDC = false ;
+	bool yesGCen = false ;	
 
 	ifstream input(fileinput);
 	if (!input.good())
@@ -87,116 +87,116 @@ int bioem_param::readParameters()
 		{
 			token = strtok(NULL, " ");
 			pixelSize = atof(token);
-			if (pixelSize < 0 ) { cout << "*** Error: Negative pixelSize "; exit(1);}
-			cout << "Pixel Sixe " << pixelSize << "\n";
-			yesPixSi= true;
+			if (pixelSize < 0 ) { cout << "*** Error: Negative pixelSize "; exit(1);}
+			cout << "Pixel Sixe " << pixelSize << "\n";
+			yesPixSi= true;
 		}
 		else if (strcmp(token, "NUMBER_PIXELS") == 0)
 		{
 			token = strtok(NULL, " ");
 			param_device.NumberPixels = int(atoi(token));
-			if (param_device.NumberPixels < 0 ) { cout << "*** Error: Negative Number of Pixels "; exit(1);}
-			cout << "Number of Pixels " << param_device.NumberPixels << "\n";			
-			yesNumPix= true ;
+			if (param_device.NumberPixels < 0 ) { cout << "*** Error: Negative Number of Pixels "; exit(1);}
+			cout << "Number of Pixels " << param_device.NumberPixels << "\n";			
+			yesNumPix= true ;
 		}
 		else if (strcmp(token, "GRIDPOINTS_ALPHA") == 0)
 		{
 			token = strtok(NULL, " ");
 			angleGridPointsAlpha = int(atoi(token));
-			if (angleGridPointsAlpha < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ALPHA "; exit(1);}
-			cout << "Grid points alpha " << angleGridPointsAlpha << "\n";
-			yesGPal= true;
+			if (angleGridPointsAlpha < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ALPHA "; exit(1);}
+			cout << "Grid points alpha " << angleGridPointsAlpha << "\n";
+			yesGPal= true;
 		}
 		else if (strcmp(token, "GRIDPOINTS_BETA") == 0)
 		{
 			token = strtok(NULL, " ");
 			angleGridPointsBeta = int(atoi(token));
-			if (angleGridPointsBeta < 0 ) { cout << "*** Error: Negative GRIDPOINTS_BETA "; exit(1);}
-			cout << "Grid points beta " << angleGridPointsBeta << "\n";
-			yesGPbe= true;
+			if (angleGridPointsBeta < 0 ) { cout << "*** Error: Negative GRIDPOINTS_BETA "; exit(1);}
+			cout << "Grid points beta " << angleGridPointsBeta << "\n";
+			yesGPbe= true;
 		}
 
 		else if (strcmp(token, "GRIDPOINTS_ENVELOPE") == 0)
 		{
 			token = strtok(NULL, " ");
 			numberGridPointsEnvelop = int(atoi(token));
-			if (numberGridPointsDisplaceCenter < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ENVELOPE "; exit(1);}
-			cout << "Grid points envelope " << numberGridPointsEnvelop << "\n";
-			yesGPEnv = true;
+			if (numberGridPointsDisplaceCenter < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ENVELOPE "; exit(1);}
+			cout << "Grid points envelope " << numberGridPointsEnvelop << "\n";
+			yesGPEnv = true;
 		}
 		else if (strcmp(token, "START_ENVELOPE") == 0)
 		{
 			token = strtok(NULL, " ");
 			startGridEnvelop = atof(token);
-			if (startGridEnvelop < 0 ) { cout << "*** Error: Negative START_ENVELOPE "; exit(1);}
-			cout << "Start Envelope " << startGridEnvelop << "\n";
-			yesSTEnv = true ;
+			if (startGridEnvelop < 0 ) { cout << "*** Error: Negative START_ENVELOPE "; exit(1);}
+			cout << "Start Envelope " << startGridEnvelop << "\n";
+			yesSTEnv = true ;
 		}
 		else if (strcmp(token, "GRIDSPACE_ENVELOPE") == 0)
 		{
 			token = strtok(NULL, " ");
 			gridEnvelop = atof(token);
-			if (gridEnvelop < 0 ) { cout << "*** Error: Negative GRIDSPACE_ENVELOPE "; exit(1);}
-			cout << "Grid spacing Envelope " << gridEnvelop << "\n";
-			yesGSPEnv = true ;
+			if (gridEnvelop < 0 ) { cout << "*** Error: Negative GRIDSPACE_ENVELOPE "; exit(1);}
+			cout << "Grid spacing Envelope " << gridEnvelop << "\n";
+			yesGSPEnv = true ;
+		}
+		else if (strcmp(token,"GRIDPOINTS_PSF_PHASE")==0)
+		{
+			token = strtok(NULL," ");
+			numberGridPointsCTF_phase=int(atoi(token));
+			cout << "Grid points PSF " << numberGridPointsCTF_phase << "\n";
+			yesGPpha = true;
+		}
+		else if (strcmp(token,"START_PSF_PHASE")==0)
+		{
+			token = strtok(NULL," ");
+			startGridCTF_phase=atof(token);
+			cout << "Start PSF " << startGridCTF_phase << "\n";
+			yesSTpha = true ;
+		}
+		else if (strcmp(token,"GRIDSPACE_PSF_PHASE")==0)
+		{
+			token = strtok(NULL," ");
+			gridCTF_phase=atof(token);
+			cout << "Grid Space PSF " << gridCTF_phase << "\n";
+			yesGSPpha = true ;
+		}
+		else if (strcmp(token,"GRIDPOINTS_PSF_AMP")==0)
+		{
+			token = strtok(NULL," ");
+			numberGridPointsCTF_amp=int(atoi(token));
+			cout << "Grid points PSF " << numberGridPointsCTF_amp << "\n";
+			yesGPamp = true ;
+		}
+		else if (strcmp(token,"START_PSF_AMP")==0)
+		{
+			token = strtok(NULL," ");
+			startGridCTF_amp=atof(token);
+			cout << "Start PSF " << startGridCTF_amp << "\n";
+			yesSTamp = true ;
+		}
+		else if (strcmp(token,"GRIDSPACE_PSF_AMP")==0)
+		{
+			token = strtok(NULL," ");
+			gridCTF_amp=atof(token);
+			cout << "Grid Space PSF " << gridCTF_amp << "\n";
+			yesGSPamp = true ;
 		}
-		else if (strcmp(token,"GRIDPOINTS_PSF_PHASE")==0)
-		{
-			token = strtok(NULL," ");
-			numberGridPointsCTF_phase=int(atoi(token));
-			cout << "Grid points PSF " << numberGridPointsCTF_phase << "\n";
-			yesGPpha = true;
-		}
-		else if (strcmp(token,"START_PSF_PHASE")==0)
-		{
-			token = strtok(NULL," ");
-			startGridCTF_phase=atof(token);
-			cout << "Start PSF " << startGridCTF_phase << "\n";
-			yesSTpha = true ;
-		}
-		else if (strcmp(token,"GRIDSPACE_PSF_PHASE")==0)
-		{
-			token = strtok(NULL," ");
-			gridCTF_phase=atof(token);
-			cout << "Grid Space PSF " << gridCTF_phase << "\n";
-			yesGSPpha = true ;
-		}
-		else if (strcmp(token,"GRIDPOINTS_PSF_AMP")==0)
-		{
-			token = strtok(NULL," ");
-			numberGridPointsCTF_amp=int(atoi(token));
-			cout << "Grid points PSF " << numberGridPointsCTF_amp << "\n";
-			yesGPamp = true ;
-		}
-		else if (strcmp(token,"START_PSF_AMP")==0)
-		{
-			token = strtok(NULL," ");
-			startGridCTF_amp=atof(token);
-			cout << "Start PSF " << startGridCTF_amp << "\n";
-			yesSTamp = true ;
-		}
-		else if (strcmp(token,"GRIDSPACE_PSF_AMP")==0)
-		{
-			token = strtok(NULL," ");
-			gridCTF_amp=atof(token);
-			cout << "Grid Space PSF " << gridCTF_amp << "\n";
-			yesGSPamp = true ;
-		}
 		else if (strcmp(token, "MAX_D_CENTER") == 0)
 		{
 			token = strtok(NULL, " ");
 			param_device.maxDisplaceCenter = int(atoi(token));
-			if (param_device.maxDisplaceCenter < 0 ) { cout << "*** Error: Negative MAX_D_CENTER "; exit(1);}
-			cout << "Maximum displacement Center " <<  param_device.maxDisplaceCenter << "\n";
-			yesMDC = true;
+			if (param_device.maxDisplaceCenter < 0 ) { cout << "*** Error: Negative MAX_D_CENTER "; exit(1);}
+			cout << "Maximum displacement Center " <<  param_device.maxDisplaceCenter << "\n";
+			yesMDC = true;
 		}
 		else if (strcmp(token, "PIXEL_GRID_CENTER") == 0)
 		{
 			token = strtok(NULL, " ");
 			param_device.GridSpaceCenter = int(atoi(token));
-			if (param_device.GridSpaceCenter < 0 ) { cout << "*** Error: Negative PIXEL_GRID_CENTER "; exit(1);}
-			cout << "Grid space displacement center " <<   param_device.GridSpaceCenter << "\n";
-			yesGCen = true;
+			if (param_device.GridSpaceCenter < 0 ) { cout << "*** Error: Negative PIXEL_GRID_CENTER "; exit(1);}
+			cout << "Grid space displacement center " <<   param_device.GridSpaceCenter << "\n";
+			yesGCen = true;
 		}
 		else if (strcmp(token, "WRITE_PROB_ANGLES") == 0)
 		{
@@ -206,41 +206,41 @@ int bioem_param::readParameters()
 	}
 	input.close();
 
-	// Checks for ALL INPUT 
-	if( not ( yesPixSi ) ){ cout << "**** INPUT MISSING: Please provide PIXEL_SIZE\n" ; exit (1);};
-	if( not ( yesNumPix ) ){ cout << "**** INPUT MISSING: Please provide NUMBER_PIXELS \n" ; exit (1);};
-	if( not ( yesGPal ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA \n" ; exit (1);};
-	if( not ( yesGPbe ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_BETA \n" ; exit (1);};
-	if( not (  yesGPEnv ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ENVELOPE \n" ; exit (1);};
-	if( not (  yesGPamp ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_AMP \n" ; exit (1);};
-	if( not (  yesGPpha ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_PHASE \n" ; exit (1);};
-	if( not (  yesSTEnv  ) ) { cout << "**** INPUT MISSING: Please provide START_ENVELOPE \n" ; exit (1);};
-	if( not (  yesSTamp  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_AMP \n" ; exit (1);};
-	if( not (  yesSTpha  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_PHASE \n" ; exit (1);};
-	if( not (  yesGSPamp  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_AMP \n" ; exit (1);};
-	if( not ( yesGSPEnv  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_ENVELOPE \n" ; exit (1);};
-	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);};
-
-	//More checks with input parameters
-
-	// Envelope should not have a standard deviation greater than Npix/2 
-	if(sqrt(1./( (myfloat_t) numberGridPointsDisplaceCenter  * gridEnvelop + startGridEnvelop))> float(param_device.NumberPixels)/2.0) {
-		cout << "MAX Standar deviation of envelope is larger than Allowed KERNEL Length " ;
-		exit(1);
-	}
-	// Envelop param should be positive
-	if( startGridCTF_amp < 0 || startGridCTF_amp > 1){
-		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
-		exit(1);
-	}
-
-	if( (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp < 0 || (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp > 1){
-		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
-		exit(1);
-	}
-
+	// Checks for ALL INPUT 
+	if( not ( yesPixSi ) ){ cout << "**** INPUT MISSING: Please provide PIXEL_SIZE\n" ; exit (1);};
+	if( not ( yesNumPix ) ){ cout << "**** INPUT MISSING: Please provide NUMBER_PIXELS \n" ; exit (1);};
+	if( not ( yesGPal ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA \n" ; exit (1);};
+	if( not ( yesGPbe ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_BETA \n" ; exit (1);};
+	if( not (  yesGPEnv ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ENVELOPE \n" ; exit (1);};
+	if( not (  yesGPamp ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_AMP \n" ; exit (1);};
+	if( not (  yesGPpha ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_PHASE \n" ; exit (1);};
+	if( not (  yesSTEnv  ) ) { cout << "**** INPUT MISSING: Please provide START_ENVELOPE \n" ; exit (1);};
+	if( not (  yesSTamp  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_AMP \n" ; exit (1);};
+	if( not (  yesSTpha  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_PHASE \n" ; exit (1);};
+	if( not (  yesGSPamp  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_AMP \n" ; exit (1);};
+	if( not ( yesGSPEnv  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_ENVELOPE \n" ; exit (1);};
+	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);};
+
+	//More checks with input parameters
+
+	// Envelope should not have a standard deviation greater than Npix/2 
+	if(sqrt(1./( (myfloat_t) numberGridPointsDisplaceCenter  * gridEnvelop + startGridEnvelop))> float(param_device.NumberPixels)/2.0) {
+		cout << "MAX Standar deviation of envelope is larger than Allowed KERNEL Length " ;
+		exit(1);
+	}
+	// Envelop param should be positive
+	if( startGridCTF_amp < 0 || startGridCTF_amp > 1){
+		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
+		exit(1);
+	}
+
+	if( (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp < 0 || (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp > 1){
+		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
+		exit(1);
+	}
+
 
 
 	cout << " +++++++++++++++++++++++++++++++++++++++++ \n";