map.cpp 15 KB
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#include <fstream>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <cstring>
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#include <math.h>
#include <fftw3.h>
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#include "map.h"
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#include "param.h"

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using namespace std;

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int bioem_RefMap::readRefMaps(bioem_param& param)
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{
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  //**************************************************************************************
  //***********************Reading reference Particle Maps************************
  //**************************************************************************************
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  if (loadMap)
    {
      FILE* fp = fopen("maps.dump", "rb");
      if (fp == NULL)
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	{
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	  cout << "Error opening dump file\n";
	  exit(1);
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	}
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      fread(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
      if (ntotRefMap > BIOEM_MAX_MAPS)
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	{
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	  cout << "BIOEM_MAX_MAPS too small, some maps dropped\n";
	  ntotRefMap = BIOEM_MAX_MAPS;
	}
      fread(&Ref[0], sizeof(Ref[0]), ntotRefMap, fp);
      fclose(fp);
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      cout << "Particle Maps read from Map Dump \nTotal Number of particles: " << ntotRefMap ;
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      cout << "\n+++++++++++++++++++++++++++++++++++++++ \n";
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    }
  else
    {

      if(readMRC){
	
             ntotRefMap=0;
	     
	      if(readMultMRC)
	      {
		
	      ifstream input(filemap);
	      
	      if (!input.good())
	      {
		cout << "Failed to open file contaning MRC names: " << filemap << "\n";
		exit(0);
	      }
	      
	      char line[512] = {0};
	      char mapname[100];
	      char tmpm[10] = {0};
              const char* indifile;
	      
	      while (!input.eof())
	      {
		input.getline(line,512);
		char tmpVals[100]  = {' '};

		strncpy (tmpVals,line,100);
		sscanf (tmpVals,"%99c",mapname);
		
		// Check for last line
		strncpy (tmpm,mapname,3);		
	        if(strcmp(tmpm,"XXX")!=0){
		indifile = mapname;  
		//Reading Multiple MRC
		read_MRC(indifile,param);
		
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		}
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		for(int i=0;i<3;i++)mapname[i] = 'X';	
		for(int i=3;i<100;i++)mapname[i] = {0};	
		
	      }
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	      cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
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	      cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
	      
	      } else {
	      
		read_MRC(filemap,param);
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		cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
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		cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
		
	      }
      
      }
      else {

	int nummap=-1;
	int lasti=0;
	int lastj=0;
	ifstream input(filemap);
	if (!input.good())
	  {
	    cout << "Particle Maps Failed to open file" << endl ;
	    exit(1);
	  }

	char line[512] = {' '};
	char tmpLine[512] = {' '};

	while (!input.eof())
	  {
	    input.getline(line,512);

	    strncpy(tmpLine,line,strlen(line));
	    char *token = strtok(tmpLine," ");

	    if (strcmp(token,"PARTICLE")==0) // to count the number of maps
	      {
		nummap++;
		if (nummap % 128 == 0)
		  {
		    cout << "..." << nummap << "\n";
		  }
		if (nummap == BIOEM_MAX_MAPS)
		  {
		    cout << "BIOEM_MAX_MAPS too small\n";
		    exit(1);
		  }
		if(lasti!=param.param_device.NumberPixels && lastj!=param.param_device.NumberPixels && nummap>0)
		  {
		    cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << lasti << ", j " << lastj << ")" << "\n";
		    exit(1);
		  }
	      }
	    else
	      {
		int i,j;
		float z;

		char tmpVals[36]  = {' '};

		strncpy (tmpVals,line,8);
		sscanf (tmpVals,"%d",&i);

		strncpy (tmpVals,line+8,8);
		sscanf (tmpVals,"%d",&j);

		strncpy (tmpVals,line+16,12);
		sscanf (tmpVals,"%f",&z);
		//checking for Map limits
		if(i>0 && i-1 <BIOEM_MAP_SIZE_X&& j>0 && j-1<BIOEM_MAP_SIZE_Y && nummap < BIOEM_MAX_MAPS)
		  {
		    Ref[nummap].points[i-1][j-1] = (myfloat_t) z;
		    lasti=i;
		    lastj=j;
		  }
		else
		  {
		    cout << "PROBLEM READING MAP (Map number " << nummap << ", i " << i << ", j " << j << ")" << "\n";
		    exit(1);
		  }
	      }
	  }
	cout << ".";
	ntotRefMap=nummap+1;
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	cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
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	cout << "Particle Maps read from Standard File\n" ;	
      }
        cout << "Total Number of particles: " << ntotRefMap ;
	cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
	
      if (dumpMap)
	{
	  FILE* fp = fopen("maps.dump", "w+b");
	  if (fp == NULL)
	    {
	      cout << "Error opening dump file\n";
	      exit(1);
	    }
	  fwrite(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
	  fwrite(&Ref[0], sizeof(Ref[0]), ntotRefMap, fp);
	  fclose(fp);
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	}
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    }
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  return(0);
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}

int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
{
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  //**************************************************************************************
  //********** Routine that pre-calculates Kernels for Convolution ***********************
  //**************************************************************************************
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  myfloat_t* localMap;
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  localMap= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
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  RefMapsFFT = new mycomplex_t[ntotRefMap * param.RefMapSize];
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  mycomplex_t* localout;
  localout= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
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  for (int iRefMap = 0; iRefMap < ntotRefMap ; iRefMap++)
    {
      //Assigning localMap values to padded Map
      for(int i=0; i< param.param_device.NumberPixels; i++)
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	{
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	  for(int j=0; j< param.param_device.NumberPixels; j++)
	    {
	      localMap[i*param.param_device.NumberPixels+j]=Ref[iRefMap].points[i][j];
	    }
	}
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      //Calling FFT_Forward
      myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localMap,localout);
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      // Normalizing and saving the Reference CTFs
      mycomplex_t* RefMap = &RefMapsFFT[iRefMap * param.RefMapSize];
      for(int i=0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D ; i++ )
	{
	  RefMap[i][0]=localout[i][0];
	  RefMap[i][1]=localout[i][1];
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	}
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    }
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  myfftw_free(localMap);
  myfftw_free(localout);

  return(0);
}

int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
  {
        myfloat_t st,st2; 
	unsigned long count;
	FILE *fin;
	float currfloat;
	int nc, nr, ns, swap, header_ok = 1;
	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;
	float dmin, dmax, dmean;
        int n_range_viol0, n_range_viol1;

	fin = fopen(filename, "rb");
	if( fin == NULL ) {
	  cout << "ERROR opening MRC: " << filename;
	  exit(1);
	}
	n_range_viol0 = test_mrc(filename,0);
	 n_range_viol1 = test_mrc(filename,1);
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  if (n_range_viol0 < n_range_viol1) { //* guess endianism 
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    swap = 0;
    if (n_range_viol0 > 0) {
      printf(" Warning: %i header field range violations detected in file %s \n", n_range_viol0,filename);
    }
  } else {
    swap = 1;
    if (n_range_viol1 > 0) {
      printf("Warning: %i header field range violations detected in file %s \n", n_range_viol1,filename);
    }
  }
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       printf("\n+++++++++++++++++++++++++++++++++++++++++++\n");
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	printf("Reading Information from MRC: %s \n", filename);
	header_ok *= read_int(&nc,fin,swap);
	header_ok *= read_int(&nr,fin,swap);
	header_ok *= read_int(&ns,fin,swap);
	header_ok *= read_int(&mode,fin,swap);
	header_ok *= read_int(&ncstart,fin,swap);
	header_ok *= read_int(&nrstart,fin,swap);
	header_ok *= read_int(&nsstart,fin,swap);
	header_ok *= read_int(&mx,fin,swap);
	header_ok *= read_int(&my,fin,swap);
	header_ok *= read_int(&mz,fin,swap);
	header_ok *= read_float(&xlen,fin,swap);
	header_ok *= read_float(&ylen,fin,swap);
	header_ok *= read_float(&zlen,fin,swap);
	header_ok *= read_float(&a_tmp,fin,swap);
	header_ok *= read_float(&b_tmp,fin,swap);
	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_float(&dmin,fin,swap);
	header_ok *= read_float(&dmax,fin,swap);
	header_ok *= read_float(&dmean,fin,swap);
	header_ok *= read_int(&ispg,fin,swap);
	header_ok *= read_int(&nsymbt,fin,swap);
	header_ok *= read_int(&lskflg,fin,swap);

	printf("Number Columns  = %8d \n",nc);
	printf("Number Rows     = %8d \n",nr);
	printf("Number Sections = %8d \n",ns);
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	printf("MODE = %4d (only data type mode 2: 32-bit)\n",mode);
       printf("NSYMBT = %4d (# bytes symmetry operators)\n",nsymbt);
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	/* printf("  NCSTART = %8d  (index of first column, counting from 0)\n",ncstart);
	   printf(">  NRSTART = %8d  (index of first row, counting from 0)\n",nrstart);
	   printf("  NSSTART = %8d  (index of first section, counting from 0)\n",nsstart);
	   printf("       MX = %8d  (# of X intervals in unit cell)\n",mx);
	   printf("       MY = %8d  (# of Y intervals in unit cell)\n",my);
	   printf("       MZ = %8d  (# of Z intervals in unit cell)\n",mz);
	   printf(" X length = %8.3f  (unit cell dimension)\n",xlen);
	   printf(" Y length = %8.3f  (unit cell dimension)\n",ylen);
	   printf(" Z length = %8.3f  (unit cell dimension)\n",zlen);
	   printf("    Alpha = %8.3f  (unit cell angle)\n",a_tmp);
	   printf("     Beta = %8.3f  (unit cell angle)\n",b_tmp);
	   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("     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);
	   printf("     ISPG = %8d  (space group number - ignored)\n",ispg);
	   printf("   NSYMBT = %8d  (# bytes storing symmetry operators)\n",nsymbt);
	   printf("   LSKFLG = %8d  (skew matrix flag: 0:none, 1:follows)\n",lskflg);*/

	if (header_ok == 0) {
	  cout << "ERROR reading MRC header: " << filename;
	  exit(1);
	}

	if(nr!=param.param_device.NumberPixels || nc!=param.param_device.NumberPixels )
	  {
	    cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
	    exit(1);
	  }


	if(mode!=2)
	  {
	    cout << "ERROR with MRC mode " << mode << "\n";
	    cout << "Currently mode 2 is the only one allowed" << "\n";
	    exit(1);

	  } else
	  {  
               rewind (fin);
	    for (count=0; count<256; ++count) if (read_float_empty(fin)==0) {
		cout << "ERROR Converting Data: " <<  filename;
		exit(1);
	      }

	    for (count=0; count<(unsigned long)nsymbt; ++count) if (read_char_float(&currfloat,fin)==0) {
		cout << "ERROR Converting Data: " <<  filename;
		exit(1);    
	      }
      
	    for ( int nmap = 0 ; nmap < ns ; nmap ++ )
              {
        
               st=0.0;
               st2=0.0;
	      for ( int j = 0 ; j < nr ; j ++ )
		for ( int i = 0 ; i < nc ; i ++ )
		  {
		    if (read_float(&currfloat,fin,swap)==0) {
		      cout << "ERROR Converting Data: " <<  filename;
		      exit(1);
		    } else {
                      Ref[nmap+ntotRefMap].points[i][j] = currfloat;
                      st += currfloat;
                      st2 += currfloat*currfloat;
	
		    }
		  }	

            //Normaling maps to zero mean and unit standard deviation
                    st /= float(nr*nc);
                    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";                          
                          }
              }
           ntotRefMap += ns ;
	 //  cout << ntotRefMap << "\n";
	  }
	fclose (fin);
	
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	return(0);
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  }
  
int bioem_RefMap::read_float(float *currfloat, FILE *fin, int swap) {
  unsigned char *cptr, tmp;

  if (fread(currfloat,4,1,fin)!=1) return 0;
  if (swap == 1) {
    cptr = (unsigned char *)currfloat;
    tmp = cptr[0];
    cptr[0]=cptr[3];
    cptr[3]=tmp;
    tmp = cptr[1];
    cptr[1]=cptr[2];
    cptr[2]=tmp;
  }
  return 1;
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}
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int  bioem_RefMap::read_int(int *currlong, FILE *fin, int swap) {
  unsigned char *cptr, tmp;

  if (fread(currlong,4,1,fin)!=1) return 0;
  if (swap == 1) {
    cptr = (unsigned char *)currlong;
    tmp = cptr[0];
    cptr[0]=cptr[3];
    cptr[3]=tmp;
    tmp = cptr[1];
    cptr[1]=cptr[2];
    cptr[2]=tmp;
  }
  return 1;
}
int  bioem_RefMap::read_float_empty (FILE *fin) {
  float currfloat;

  if (fread(&currfloat,4,1,fin)!=1) return 0;
  return 1;
}

int  bioem_RefMap::read_char_float (float *currfloat, FILE *fin) {
  char currchar;

  if (fread(&currchar,1,1,fin)!=1) return 0;
  *currfloat=(float)currchar;
  return 1;
}

int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
  FILE *fin;
  int nc, nr, ns, mx, my, mz;
  int mode, ncstart, nrstart, nsstart;
  float xlen, ylen, zlen;
  int i, header_ok = 1, n_range_viols = 0;
  int mapc, mapr, maps;
  float alpha, beta, gamma;
  float dmin, dmax, dmean, dummy, xorigin, yorigin, zorigin;

  fin = fopen(vol_file, "rb");
  if( fin == NULL ) {
  	 cout << "ERROR opening MRC: " << vol_file;
          exit(1);
  }

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 //* read header info 
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  header_ok *= read_int(&nc,fin,swap);
  header_ok *= read_int(&nr,fin,swap);
  header_ok *= read_int(&ns,fin,swap);
  header_ok *= read_int(&mode,fin,swap);
  header_ok *= read_int(&ncstart,fin,swap);
  header_ok *= read_int(&nrstart,fin,swap);
  header_ok *= read_int(&nsstart,fin,swap);
  header_ok *= read_int(&mx,fin,swap);
  header_ok *= read_int(&my,fin,swap);
  header_ok *= read_int(&mz,fin,swap);
  header_ok *= read_float(&xlen,fin,swap);
  header_ok *= read_float(&ylen,fin,swap);
  header_ok *= read_float(&zlen,fin,swap);
  header_ok *= read_float(&alpha,fin,swap);
  header_ok *= read_float(&beta,fin,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_float(&dmin,fin,swap);
  header_ok *= read_float(&dmax,fin,swap);
  header_ok *= read_float(&dmean,fin,swap);
  for (i=23; i<50; ++i) header_ok *= read_float(&dummy,fin,swap);
  header_ok *= read_float(&xorigin,fin,swap);
  header_ok *= read_float(&yorigin,fin,swap);
  header_ok *= read_float(&zorigin,fin,swap);
  fclose (fin);
  if (header_ok == 0) {
 	cout << "ERROR reading MRC header: " << vol_file;
          exit(1);
  }

  n_range_viols += (nc>5000); n_range_viols += (nc<0);
  n_range_viols += (nr>5000); n_range_viols += (nr<0);
  n_range_viols += (ns>5000); n_range_viols += (ns<0);
  n_range_viols += (ncstart>5000); n_range_viols += (ncstart<-5000);
  n_range_viols += (nrstart>5000); n_range_viols += (nrstart<-5000);
  n_range_viols += (nsstart>5000); n_range_viols += (nsstart<-5000);
  n_range_viols += (mx>5000); n_range_viols += (mx<0);
  n_range_viols += (my>5000); n_range_viols += (my<0);
  n_range_viols += (mz>5000); n_range_viols += (mz<0);
  n_range_viols += (alpha>360.0f); n_range_viols += (alpha<-360.0f);
  n_range_viols += (beta>360.0f); n_range_viols += (beta<-360.0f);
  n_range_viols += (gamma>360.0f); n_range_viols += (gamma<-360.0f);

  return n_range_viols;
}