JPGImageReaderWriter.h

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/**
 *  \file IMP/em2d/JPGImageReaderWriter.h
 *  \brief Management of JPG format for EM images
 *  Copyright 2007-2018 IMP Inventors. All rights reserved.
*/

#ifndef IMPEM2D_JPG_IMAGE_READER_WRITER_H
#define IMPEM2D_JPG_IMAGE_READER_WRITER_H

#include "IMP/em2d/em2d_config.h"
#include "IMP/em2d/opencv_interface.h"
#include "IMP/em/ImageHeader.h"
#include <boost/filesystem/convenience.hpp>

IMPEM2D_BEGIN_NAMESPACE

//! Class to read and write EM images in JPG format.
class JPGImageReaderWriter : public ImageReaderWriter {
 public:
  JPGImageReaderWriter() {}

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

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

  //! Reads an image file in JPG format
  /*!
    \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
    \warning:  The header passed is filled with standard values
      If you need full header information you must work with other
      format. Eg, Spider.
  */
  void read_from_ints(const String &filename, em::ImageHeader &header,
                      cv::Mat &data) const {
    IMP_LOG_VERBOSE("reading with JPGImageReaderWriter" << std::endl);
    // read
    cv::Mat temp = cv::imread(filename, 0);
    if (temp.empty()) {
      IMP_THROW("Error reading from JPG Image " << filename, IOException);
    }
    temp.assignTo(data, CV_64FC1);
    // fill the header with default values
    header.clear();
  }

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

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

  //! Writes an EM image in JPG 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
    \warning: Careful: This function writes a 8-bit image.
              You might be discarding float information.
   */
  void write_to_ints(const String &filename, em::ImageHeader &header,
                     const cv::Mat &data) const {
    IMP_UNUSED(header);
    // discard header
    IMP_LOG(IMP::WARNING,
            "Writing with JPGImageReaderWriter "
            "discards image header "
                << std::endl);
    // check extension
    String ext = boost::filesystem::extension(filename);
    IMP_LOG_VERBOSE("JPGImageReaderWriter writing to " << filename
                                                        << std::endl);
    if (ext != ".jpg" && ext != ".jpeg") {
      IMP_THROW(
          "JPGImageReaderWriter: The filename extension is not .jpg "
          "or .jpeg",
          IOException);
    }

    // Convert the data value to 8-bit so it can be written as JPG
    cv::Mat jpg_data;
    double max, min;
    cv::minMaxLoc(data, &min, &max);
    double jpg_max = 255;
    double jpg_min = 0;
    double alpha = (jpg_max - jpg_min) / (max - min);
    double beta = jpg_min - alpha * min;
    data.convertTo(jpg_data, CV_8UC1, alpha, beta);
    // write image
    std::vector<int> flags;
    flags.push_back(CV_IMWRITE_JPEG_QUALITY);
    flags.push_back(100);  // 100% quality image
    cv::imwrite(filename, jpg_data, flags);
  }

  IMP_OBJECT_METHODS(JPGImageReaderWriter);
};

IMPEM2D_END_NAMESPACE

#endif /* IMPEM2D_JPG_IMAGE_READER_WRITER_H */