SpiderImageReaderWriter.h

Go to the documentation of this file.

/**
 *  \file IMP/em2d/SpiderImageReaderWriter.h
 *  \brief Management of Images in Spider format
 *  Copyright 2007-2017 IMP Inventors. All rights reserved.
*/

#ifndef IMPEM2D_SPIDER_IMAGE_READER_WRITER_H
#define IMPEM2D_SPIDER_IMAGE_READER_WRITER_H

#include "IMP/em2d/em2d_config.h"
#include "IMP/em2d/ImageReaderWriter.h"
#include "IMP/em2d/opencv_interface.h"
#include "IMP/em/ImageHeader.h"
#include "IMP/em/header_converters.h"
#include <IMP/algebra/utility.h>
#include <IMP/algebra/endian.h>
#include <IMP/exception.h>
#include <IMP/log_macros.h>
#include <IMP/log.h>
#include <typeinfo>
#include <complex>
#include <string>
#include <cstdio>
#include <iostream>
#include <fstream>
#include <cstring>

IMPEM2D_BEGIN_NAMESPACE

//! Class to read and write EM images in Spider format. They are stored in
//! the header and data passed as arguments
class SpiderImageReaderWriter : public ImageReaderWriter {
 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 writing
   *  \param[in] skip_extra_checkings if true, the most stringent
   * tests for consistency of images are skipped when reading
   */
  SpiderImageReaderWriter(const 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;
  }

  void read(const String &filename, em::ImageHeader &header,
            cv::Mat &data) const {
    this->read_from_floats(filename, header, data);
  }

  void write(const String &filename, em::ImageHeader &header,
             const cv::Mat &data) const {
    this->write_to_floats(filename, header, data);
  }

  void read_from_ints(const String &, em::ImageHeader &, cv::Mat &) const {}

  void write_to_ints(const String &, em::ImageHeader &, const cv::Mat &) const {
  }

  //! Reads an image file in Spider format and stores the content
  //! int the header and data parameters
  /*!
    \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_from_floats(const String &filename, em::ImageHeader &header,
                        cv::Mat &data) const {
    IMP_LOG_VERBOSE("reading with SpiderImageReaderWriter" << std::endl);
    std::ifstream in;
    in.open(filename.c_str(), std::ios::in | std::ios::binary);
    if (in.fail() || in.bad()) {
      IMP_THROW("Error reading from Spider Image " << filename, IOException);
    }
    //! The header format is already in Spider format, just read it
    bool success = header.read(in, skip_type_check_, force_reversed_,
                               skip_extra_checkings_);
    if (!success) {
      IMP_THROW("Error reading header from Spider Image " << filename,
                IOException);
    }
    IMP_LOG_VERBOSE("Header of image " << filename << std::endl << header
                                       << std::endl);
    // Adjust size of the matrix according to the header
    unsigned int rows = (int)header.get_number_of_rows();
    unsigned int cols = (int)header.get_number_of_columns();
    data.create(rows, cols, CV_64FC1);
    // Read with casting
    float aux;
    for (cvDoubleMatIterator it = data.begin<double>();
         it != data.end<double>(); ++it) {
      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);
      }
      (*it) = static_cast<double>(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_to_floats(const String &filename, em::ImageHeader &header,
                       const cv::Mat &data) const {
    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 (cvDoubleConstMatIterator it = data.begin<double>();
         it != data.end<double>(); ++it) {
      aux = (float)(*it);
      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();
  }

  IMP_OBJECT_METHODS(SpiderImageReaderWriter);
};

IMPEM2D_END_NAMESPACE

#endif /* IMPEM2D_SPIDER_IMAGE_READER_WRITER_H */