IMP: EMReaderWriter.h Source File

00001 /**
00002  *  \file EMReaderWriter.h
00003  *  \brief Classes to read or write density files in EM format.
00004  *
00005  *  Copyright 2007-2010 IMP Inventors. All rights reserved.
00006  *
00007  */
00008 
00009 #ifndef IMPEM_EM_READER_WRITER_H
00010 #define IMPEM_EM_READER_WRITER_H
00011 
00012 #include "em_config.h"
00013 #include "MapReaderWriter.h"
00014 #include "DensityHeader.h"
00015 #include "def.h"
00016 
00017 IMPEM_BEGIN_NAMESPACE
00018 
00019 class IMPEMEXPORT EMHeader
00020 {
00021 public:
00022 #ifndef SWIG
00023   class EMHeaderParse
00024   {
00025   public:
00026     static const int COMMENT_SIZE               = 80;
00027     static const int VOLTAGE_OFFSET             = 0;
00028     static const int CS_OFFSET                  = 1;
00029     static const int APERTURE_OFFSET            = 2;
00030     static const int MAGNIFICATION_OFFSET       = 3;
00031     static const int POSTMAGNIFICATION_OFFSET   = 4;
00032     static const int EXPOSURETIME_OFFSET        = 5;
00033     static const int OBJECTPIXELSIZE_OFFSET     = 6;
00034     static const int MICROSCOPE_OFFSET          = 7;
00035     static const int PIXELSIZE_OFFSET           = 8;
00036     static const int CCDAREA_OFFSET             = 9;
00037     static const int DEFOCUS_OFFSET             = 10;
00038     static const int ASTIGAMATISM_OFFSET        = 11;
00039     static const int ASTIGAMATISMANGLE_OFFSET   = 12;
00040     static const int FOCUSINCREMENT_OFFSET      = 13;
00041     static const int COUNTSPERELECTRON_OFFSET   = 14;
00042     static const int INTENSITY_OFFSET           = 15;
00043     static const int ENERGYSLITWIDTH_OFFSET     = 16;
00044     static const int ENERGYOFFSET_OFFSET        = 17;
00045     static const int TILTANGLE_OFFSET           = 18;
00046     static const int TILTAXIS_OFFSET            = 19;
00047     static const int MARKERX_OFFSET             = 20;
00048     static const int MARKERY_OFFSET             = 21;
00049     static const int LSWAP_OFFSET               = 22;
00050 
00051     void InitEMHeader(EMHeader &header) {
00052       float scale = 1000.0;
00053       header.magic                  = (int)magic;
00054       header.type                   = (int)type;
00055       header.nx                     = nx;
00056       header.ny                     = ny;
00057       header.nz                     = nz;
00058       strncpy(header.comment, comment,COMMENT_SIZE);
00059       header.comment[COMMENT_SIZE]  = '\0';
00060       header.voltage                = (float)emdata[VOLTAGE_OFFSET];
00061       header.Cs                     = (float)emdata[CS_OFFSET]/scale;
00062       header.Aperture               = (float)emdata[APERTURE_OFFSET];
00063       header.Magnification          = (float)emdata[MAGNIFICATION_OFFSET];
00064       header.Postmagnification      = (float)emdata[POSTMAGNIFICATION_OFFSET]
00065                                       /scale;
00066       header.Exposuretime           = (float)emdata[EXPOSURETIME_OFFSET];
00067       header.Objectpixelsize        = (float)emdata[OBJECTPIXELSIZE_OFFSET]
00068                                       /scale;
00069       header.Microscope             = (float)emdata[MICROSCOPE_OFFSET];
00070       header.Pixelsize              = (float)emdata[PIXELSIZE_OFFSET]/scale;
00071       header.CCDArea                = (float)emdata[CCDAREA_OFFSET]/scale;
00072       header.Defocus                = (float)emdata[DEFOCUS_OFFSET];
00073       header.Astigmatism            = (float)emdata[ASTIGAMATISM_OFFSET]/scale;
00074       header.AstigmatismAngle       = (float)emdata[ASTIGAMATISMANGLE_OFFSET];
00075       header.FocusIncrement         = (float)emdata[FOCUSINCREMENT_OFFSET]
00076                                       /scale;
00077       header.CountsPerElectron      = (float)emdata[COUNTSPERELECTRON_OFFSET]
00078                                       /scale;
00079       header.Intensity              = (float)emdata[INTENSITY_OFFSET]/scale;
00080       header.EnergySlitwidth        = (float)emdata[ENERGYSLITWIDTH_OFFSET];
00081       header.EnergyOffset           = (float)emdata[ENERGYOFFSET_OFFSET];
00082       header.Tiltangle              = (float)emdata[TILTANGLE_OFFSET]/scale;
00083       header.Tiltaxis               = (float)emdata[TILTAXIS_OFFSET]/scale;
00084       header.MarkerX                = (float)emdata[MARKERX_OFFSET];
00085       header.MarkerY                = (float)emdata[MARKERY_OFFSET];
00086       header.lswap                  = emdata[LSWAP_OFFSET];
00087 
00088     }
00089     void Init(const EMHeader &header) {
00090       magic    = (unsigned char)header.magic;
00091       type     = (unsigned char)header.type;
00092       nx       = header.nx;
00093       ny       = header.ny;
00094       nz       = header.nz;
00095       strncpy(comment,header.comment, COMMENT_SIZE);
00096       float scale=1000.0;
00097       emdata[VOLTAGE_OFFSET]              = (int)header.voltage;
00098       emdata[CS_OFFSET]                   = (int)(header.Cs*scale);
00099       emdata[APERTURE_OFFSET]             = (int)header.Aperture;
00100       emdata[MAGNIFICATION_OFFSET]        = (int)header.Magnification;
00101       emdata[POSTMAGNIFICATION_OFFSET]    = (int)(header.Postmagnification
00102                                                   * scale);
00103       emdata[EXPOSURETIME_OFFSET]         = (int)header.Exposuretime ;
00104       emdata[OBJECTPIXELSIZE_OFFSET]      = (int)(header.Objectpixelsize
00105                                                   * scale);
00106       emdata[MICROSCOPE_OFFSET]           = (int)header.Microscope;
00107       emdata[PIXELSIZE_OFFSET]            = (int)(header.Pixelsize * scale);
00108       emdata[CCDAREA_OFFSET]              = (int)(header.CCDArea * scale);
00109       emdata[DEFOCUS_OFFSET]              = (int)header.Defocus;
00110       emdata[ASTIGAMATISM_OFFSET]         = (int)(header.Astigmatism   * scale);
00111       emdata[ASTIGAMATISMANGLE_OFFSET]    = (int)header.AstigmatismAngle;
00112       emdata[FOCUSINCREMENT_OFFSET]       = (int)(header.FocusIncrement
00113                                                   * scale);
00114       emdata[COUNTSPERELECTRON_OFFSET]    = (int)(header.FocusIncrement
00115                                                   * scale);
00116       emdata[INTENSITY_OFFSET]            = (int)(header.Intensity * scale);
00117       emdata[ENERGYSLITWIDTH_OFFSET]      = (int)header.EnergySlitwidth;
00118       emdata[ENERGYOFFSET_OFFSET]         = (int)header.EnergyOffset ;
00119       emdata[TILTANGLE_OFFSET]            = (int)(header.Tiltangle *scale);
00120       emdata[TILTAXIS_OFFSET]             = (int)(header.Tiltaxis * scale);
00121       emdata[MARKERX_OFFSET]              = (int)header.MarkerX;
00122       emdata[MARKERY_OFFSET]              = (int)header.MarkerY;
00123       emdata[LSWAP_OFFSET]                = header.lswap;
00124 
00125     }
00126     //actual information in the EM header
00127     unsigned char magic;
00128     unsigned char dummy[2];
00129     unsigned char type;
00130     int nx,ny,nz;
00131     char comment[80];
00132     int emdata[40];
00133     char dummy_long[256];
00134 
00135   };
00136 #endif // SWIG
00137 
00138 
00139 
00140   EMHeader(){}
00141   EMHeader(const DensityHeader &header);
00142   void generate_common_header(DensityHeader &header);
00143 
00144 
00145   //// Outputs coordinates delimited by single space.
00146   friend std::ostream& operator<<(std::ostream& s, const EMHeader &h) {
00147     return s <<"size : " << h.nx << "  " << h.ny << "  " << h.nz
00148       << std::endl << "magic: " << h.magic << std::endl <<
00149       "type:  " << h.type <<  std::endl <<
00150       " comment : " << h.comment <<  std::endl <<
00151       " voltage : " << h.voltage <<  std::endl <<
00152       "cs: " << h.Cs << std::endl <<
00153       "aperture: " << h.Aperture<< std::endl <<
00154       "Magnification " << h.Magnification<< std::endl <<
00155       " Postmagnification "<< h.Postmagnification << std::endl <<
00156       " Exposuretime  " << h.Exposuretime << std::endl <<
00157       "Objectpixelsize  " << h.Objectpixelsize << std::endl <<
00158       "Microscope  " << h.Microscope << std::endl <<
00159       "pixel-size:  " << h.Pixelsize << std::endl;
00160   }
00161 
00162 
00163   //attributes
00164   int magic;
00165   int type;
00166   int nx,ny,nz;
00167   char comment[81];
00168   float voltage;
00169   float Cs;
00170   float Aperture;
00171   float Magnification;
00172   float Postmagnification;
00173   float Exposuretime;
00174   float Objectpixelsize;
00175   float Microscope;
00176   float Pixelsize;
00177   float CCDArea;
00178   float Defocus;
00179   float Astigmatism;
00180   float AstigmatismAngle;
00181   float FocusIncrement;
00182   float CountsPerElectron;
00183   float Intensity;
00184   float EnergySlitwidth;
00185   float EnergyOffset;
00186   float Tiltangle;
00187   float Tiltaxis;
00188   float MarkerX;
00189   float MarkerY;
00190   int lswap;
00191 };
00192 
00193 
00194 class IMPEMEXPORT EMReaderWriter : public MapReaderWriter
00195 {
00196 public:
00197  //! Reads a density file in EM format and stores the information
00198  /**
00199   \param[in] filename name of the file to read
00200   \param[in] data pointer to the data
00201   \param[in] header DensityHeader() to store the header information
00202   \exception IOException in case that the filename was not found
00203   */
00204   void Read(const char *filename, float **data, DensityHeader &header);
00205   //! Writes a density file in EM format with the header information
00206   /**
00207      \param[in] filename name of the file to read
00208      \param[in] data pointer to the data
00209      \param[in] header DensityHeader() with the header information
00210   */
00211   void Write(const char* filename, const float *data,
00212              const DensityHeader &header);
00213 protected:
00214   //! Reads the header
00215   //! Reads the data
00216   /**
00217   \param file ifstream of the file to read
00218   \param header EMHeader to store the header information
00219   */
00220   void ReadHeader(std::ifstream &file, EMHeader &header);
00221   //! Reads the data
00222   /**
00223   \param file ifstream of the file to read
00224   \param data pointer to store the data
00225   \param header EMHeader() to store the header information
00226   \exception IOException if the data allocation had failed
00227   \exception  IOException is the requested data type is not implemented
00228   */
00229   void ReadData(std::ifstream &file, float **data, const EMHeader &header);
00230   //! Writes the header
00231   /**
00232   \param[in] file ofstream of the file to write
00233   \param[in] header EMHeader() with the header information
00234   \exception IOException if the writing operation had failed.
00235   */
00236   void WriteHeader(std::ostream& s, const EMHeader &header);
00237 };
00238 
00239 IMPEM_END_NAMESPACE
00240 
00241 #endif  /* IMPEM_EM_READER_WRITER_H */