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Image.h

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/**
 *  \file Image.h
 *  \brief Management of IMP images for Electron Microscopy
 *  \author Javier Velazquez-Muriel
 *  Copyright 2007-2010 IMP Inventors. All rights reserved.
*/

#ifndef IMPEM_IMAGE_H
#define IMPEM_IMAGE_H

// #define DEBUG

#include "em_config.h"
#include "ImageHeader.h"
#include "ImageReaderWriter.h"
#include "IMP/algebra/Matrix2D.h"
#include "IMP/algebra/Rotation2D.h"
#include <complex>
#include <limits>
#include <typeinfo>

IMPEM_BEGIN_NAMESPACE


//! Template class for managing 2D Electron Microscopy images in IMP
template<typename T>
class Image
{
public:

typedef Image<T> This;

  //! Empty constructor
  Image() {
    name_ = "";
    if (typeid(T) == typeid(double)) {
      header_.set_image_type(ImageHeader::IMG_IMPEM);
    }
  }

  //! Constructor with size
  Image(Int Ydim, Int Xdim) {
    data_.resize(Ydim, Xdim);
    header_.set_header();
    if (typeid(T) == typeid(double)) {
      header_.set_image_type(ImageHeader::IMG_IMPEM);
    }
  }

  //! Access to the matrix of data
  algebra::Matrix2D<T>& get_data() {
    return data_;
  }

  //! Set the matrix of data
  void set_data(algebra::Matrix2D<T> &v) {
  data_.resize(v);
    for(unsigned long i=0;i<v.num_elements();i++) {
      data_.data()[i] = v.data()[i];
    }
    this->adjust_header();
  }

  //! Access to the header
  ImageHeader& get_header() {
    return header_;
  }

  //! Adjusts the information of the imager header taking into account the
  //! dimensions of the data and setting the time, date, type, etc ...
  void adjust_header() {
    if (typeid(T) == typeid(std::complex< double >)) {
      header_.set_image_type(ImageHeader::IMG_FOURIER);
    } else if (typeid(T) == typeid(double) ||
               typeid(T) == typeid(double)) {
      header_.set_image_type(ImageHeader::IMG_IMPEM);
    }
    header_.set_number_of_slices(1.0);
    header_.set_number_of_rows(data_.get_number_of_rows());
    header_.set_number_of_columns(data_.get_number_of_columns());
    header_.set_time();
    header_.set_date();
    header_.set_title(name_);
    header_.set_header(); // Initialize header
  }

  //! Reads the image from the file
  void read(String filename,ImageReaderWriter<T>& reader) {
    IMP_LOG(VERBOSE, "reading EM image " << std::endl);
    reader.read(filename,header_,data_);
  }

  //! Writes the image to a file
  void write(String filename, ImageReaderWriter<T>& writer) {
    adjust_header(); // First adjust the header to guarantee consistence
    writer.write(filename,header_,data_);
  }

protected:
  //! Name of the image. Frequently it will be the name of the file
  String name_;
  //! Matrix with the data for the image
  algebra::Matrix2D<T> data_;
  //! Header for the image with all the pertinent information
  ImageHeader header_;

}; // Image

// #undef DEBUG

IMPEM_END_NAMESPACE
#endif  /* IMPEM_IMAGE_H */

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