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SpiderReaderWriter.h

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/**
 *  \file SpiderReaderWriter.h
 *  \brief Management of Spider Headers Electron Microscopy. Compatible with
 *  Spider and Xmipp formats
 *  \author Javier Velazquez-Muriel
 *  Copyright 2007-2010 IMP Inventors. All rights reserved.
*/

#ifndef IMPEM_SPIDER_READER_WRITER_H
#define IMPEM_SPIDER_READER_WRITER_H

#include "IMP/em/em_config.h"
#include "IMP/em/ImageHeader.h"
#include "IMP/em/ImageReaderWriter.h"
#include "IMP/em/header_converters.h"
#include "IMP/em/MapReaderWriter.h"
#include "IMP/em/DensityHeader.h"
#include <IMP/algebra/Matrix2D.h>
#include <IMP/algebra/utility.h>
#include <IMP/algebra/endian.h>
#include <IMP/exception.h>
#include <typeinfo>
#include <complex>
#include <string>
#include <cstdio>
#include <iostream>
#include <fstream>
#include <cstring>

IMPEM_BEGIN_NAMESPACE

//! Class to read EM images in Spider and Xmipp formats. They are stored in
//! the header and data passed as arguments
/**
 * \note Compatible with Xmipp and Spider formats (byte, int, float, complex)
 * \note An ImageHeader class is expected.
 */
template <typename T>
class SpiderImageReaderWriter: public ImageReaderWriter<T>
{
public:
  String filename_;
  bool skip_type_check_;
  bool force_reversed_;
  bool skip_extra_checkings_;

  //! Empty constructor. It does not force reversed header and does not
  //! skip any of the tests
  /**
   *  \note reversed is only used in case that the type_check is skipped
   */
  SpiderImageReaderWriter() {
    skip_type_check_=false;
    force_reversed_=false;
    skip_extra_checkings_=false;
  }

  //! Full constructor.
  /**
   *  \param[in] filename file to read
   *  \param[in] skip_type_check if true, the check for type of image is skipped
   *  \param[in] force_reversed if true, the reverse mode is enforced
   * for reading and writting
   *  \param[in] skip_extra_checkings if true, the most stringent
   * tests for consistency of images are skipped when reading
   */
  SpiderImageReaderWriter(String filename,bool skip_type_check,
                        bool force_reversed,bool skip_extra_checkings) {
    filename_=filename;
    skip_type_check_=skip_type_check;
    force_reversed_=force_reversed;
    skip_extra_checkings_=skip_extra_checkings;
  }

  //! Reads a image file in Spider format and stores the content
  //! the header and data parameters
  /**
    \note: It is assumed that the image is stored as a collection of floats
    \param[in] filename file to read
    \param[in] header header to store the info
    \param[in] data a matrix to store the grid of data of the image
  **/
  void read(String filename, ImageHeader& header,
            algebra::Matrix2D<T>& data) {
#ifdef IMP_DEBUG_SPIDER
    std::cout << "reading with SpiderImageReaderWriter" << std::endl;
#endif
    std::ifstream in;
    in.open(filename.c_str(), std::ios::in | std::ios::binary);
    //! Take advantage that the header format is already in Spider format and
    //! just read it
    header.read(in,skip_type_check_,force_reversed_,skip_extra_checkings_);
#ifdef IMP_DEBUG_SPIDER
    std::cout << header << std::endl;
#endif
    // Adjust size of the matrix according to the header
    data.resize((int)header.get_number_of_rows(),
                (int)header.get_number_of_columns());
    data.read_binary(in,force_reversed_ ^ algebra::get_is_big_endian());
    in.close();
  }

  void read_from_floats(String filename, ImageHeader& header,
            algebra::Matrix2D<T>& data) {
    std::ifstream in;
    in.open(filename.c_str(), std::ios::in | std::ios::binary);
    IMP_USAGE_CHECK(!in.fail(),
        "SpiderReaderWriter::read_from_floats: The file "+
                                        filename+" could be found.");
    //! The header format is already in Spider format, just read it
    header.read(in,skip_type_check_,force_reversed_,skip_extra_checkings_);
#ifdef IMP_DEBUG_SPIDER
    std::cout << header << std::endl;
#endif
    // Adjust size of the matrix according to the header
    data.resize((int)header.get_number_of_rows(),
                (int)header.get_number_of_columns());
    // Read with casting
    float aux;
    for (unsigned long i=0;i<data.num_elements();i++) {
      if (!(force_reversed_ ^ algebra::get_is_big_endian())) {
        in.read(reinterpret_cast< char* >(&aux), sizeof(float));
      } else {
        algebra::reversed_read(reinterpret_cast< char* >(&aux),
                                              sizeof(float),1,in,true);
      }
      data.data()[i] = (T)aux;
    }
    in.close();
  }

  //! Writes an EM image in Spider format
  /**
   *  \param[in] filename file to write
   *  \param[in] header header with the image info
   *  \param[in] data a matrix with the grid of data of the image
   */
  void write(String filename, ImageHeader& header,
            algebra::Matrix2D<T>& data) {
    std::ofstream out;
    out.open(filename.c_str(), std::ios::out | std::ios::binary);
    //! The image header is already in Spider format, just write it
    header.write(out, force_reversed_ ^ algebra::get_is_big_endian());
    data.write_binary(out,force_reversed_ ^ algebra::get_is_big_endian());
    out.close();
  }


  void write_to_floats(String filename, ImageHeader& header,
            algebra::Matrix2D<T>& data) {
    std::ofstream out;
    out.open(filename.c_str(), std::ios::out | std::ios::binary);
    //! The image header is already in Spider format, just write it
    header.write(out, force_reversed_ ^ algebra::get_is_big_endian());

    float aux;
    for (unsigned long i=0;i<data.num_elements();i++) {
      aux = (float)data.data()[i];
      if (!(force_reversed_ ^ algebra::get_is_big_endian())) {
        out.write(reinterpret_cast< char* >(&aux), sizeof(float));
      } else {
        algebra::reversed_write(reinterpret_cast< char* >(&aux),
                       sizeof(float),1,out,true);
      }
    }

    out.close();
  }

};

//! Class to read EM maps (3D) in Spider and Xmipp formats
/**
 * \note: Compatible only with Xmipp 2.2 and Spider floating point maps
 * \note: A DensityHeader class must be provided
 */
class IMPEMEXPORT SpiderMapReaderWriter : public MapReaderWriter {
public:
  String filename_;
  bool skip_type_check_;
  bool force_reversed_;
  bool skip_extra_checkings_;

  //! Empty constructor. It does not force reversed header and does not
  //! skip any of the tests
  SpiderMapReaderWriter() {
    skip_type_check_=false;
    force_reversed_=false;
    skip_extra_checkings_=false;
  }

  //! Full constructor.
  /**
   *  \param[in] filename file to read
   *  \param[in] skip_type_check if true, the check for type of image is skipped
   *  \param[in] force_reversed if true, the reverse mode is enforced
   * for reading and writting
   *  \param[in] skip_extra_checkings if true, the most stringent
   * tests for consistency of images are skipped when reading
   */
  SpiderMapReaderWriter(String filename,bool skip_type_check,
                        bool force_reversed,bool skip_extra_checkings) {
    filename_=filename;
    skip_type_check_=skip_type_check;
    force_reversed_=force_reversed;
    skip_extra_checkings_=skip_extra_checkings;
  }

  //! Reads a map in Spider format and transfers the data and header.
  /**
   *  \param[in] filename file to read
   *  \param[in] data pointer to the structure where to store the data
   *  \param[in] header DensityHeader class where to store the info
   *  from the header.
   */
  void Read(const char *filename, float **data, DensityHeader &header);

  //! Writes a map in Spider format from data and header.
  /**
   *  \param[in] filename file to write
   *  \param[in] data pointer to the structure where data are stored
   *  \param[in] header DensityHeader class where the header info is stored
   *  data from the header.
   */
  void Write(const char *filename,
             const float *data,const DensityHeader &header);
};

IMPEM_END_NAMESPACE

#endif /* IMPEM_SPIDER_READER_WRITER_H */

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