TIFFImageReaderWriter.h

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/**
 *  \file IMP/em2d/TIFFImageReaderWriter.h
 *  \brief Management of reading/writing TIFF images
 *
 *  Copyright 2007-2021 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPEM2D_TIFF_IMAGE_READER_WRITER_H
#define IMPEM2D_TIFF_IMAGE_READER_WRITER_H

#include "IMP/em2d/ImageReaderWriter.h"
#include <boost/filesystem.hpp>
#include <IMP/log_macros.h>

IMPEM2D_BEGIN_NAMESPACE

//! Management of reading/writing TIFF images
class TIFFImageReaderWriter : public ImageReaderWriter {

 public:
  TIFFImageReaderWriter() {}

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

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

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

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

  //! Reads an image file in TIFF 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_OVERRIDE {
    IMP_LOG_VERBOSE("reading with TIFFImageReaderWriter" << std::endl);
    // read
    cv::Mat temp = cv::imread(filename, 0);
    if (temp.empty()) {
      IMP_THROW("Error reading from TIFF Image " << filename, IOException);
    }
    temp.assignTo(data, CV_64FC1);
    // fill the header with default values
    header.clear();
  }

  //! Writes an EM image in TIFF 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 16-bit image.
              You might be discarding float information.
   */
  void write_to_ints(const String &filename, em::ImageHeader &header,
                     const cv::Mat &data) const IMP_OVERRIDE {
    IMP_UNUSED(header);
    // discard header
    IMP_LOG(IMP::WARNING,
            "Writing with TIFFImageReaderWriter "
            "discards image header "
                << std::endl);
    // check extension
    String ext = boost::filesystem::extension(filename);
    IMP_LOG_VERBOSE("TIFFImageReaderWriter writing to " << filename
                                                         << std::endl);
    if (ext != ".tiff" && ext != ".tif") {
      IMP_THROW(
          "TIFFImageReaderWriter: The filename extension is not .tiff "
          "or .tif",
          IOException);
    }

    // Convert the data value to 16-bit so it can be written as TIFF
    cv::Mat TIFF_data;
    double max, min;
    cv::minMaxLoc(data, &min, &max);
    double TIFF_max = 255;
    double TIFF_min = 0;
    double alpha = (TIFF_max - TIFF_min) / (max - min);
    double beta = TIFF_min - alpha * min;
    data.convertTo(TIFF_data, CV_8UC1, alpha, beta);
    // write image
    cv::minMaxLoc(TIFF_data, &min, &max);

    cv::imwrite(filename, TIFF_data);
  }

  IMP_OBJECT_METHODS(TIFFImageReaderWriter);
};

IMPEM2D_END_NAMESPACE

#endif /* IMPEM2D_TIFF_IMAGE_READER_WRITER_H */