libmia-2.4-dev 2.4.3-5 / usr / include / mia-2.4 / mia / 2d / image.hh

/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
 *
 * MIA is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with MIA; if not, see <http://www.gnu.org/licenses/>.
 *
 */


#ifndef mia_2d_2dimage_hh
#define mia_2d_2dimage_hh

#include <mia/core/attributes.hh>
#include <mia/core/pixeltype.hh>
#include <mia/core/filter.hh>
#include <mia/core/msgstream.hh>
#include <mia/core/tools.hh>
#include <mia/core/type_traits.hh>
#include <mia/2d/vectorfield.hh>

NS_MIA_BEGIN

#define ATTR_IMAGE_KMEANS_CLASSES "kmeans"


/**
   \ingroup basic
   \brief This is the base class for 2D images that can hold generic pixel data

This class is the abstract base class for 2D images that can be passed around
without the program knowing, what actual pixel type an image holds.
It provides access to the image size and the pixel type, and it also
is a container for generic attributes.
*/
class EXPORT_2D C2DImage: public CAttributedData {
public:
	/** The type description provides information about the data type that is
        used by the plug-in system */
        static const char *data_descr;

        /// a definition of the image dimension type for
	typedef C2DBounds dimsize_type;

	/// 2D Image pointer type 
	typedef std::shared_ptr<C2DImage > Pointer;

        virtual  ~C2DImage();

        /// \returns the pixel type
	EPixelType get_pixel_type() const;

        /// \returns the size of the image
	const C2DBounds& get_size() const;

        /// \returns the size of a pixel in real-world units
	C2DFVector get_pixel_size() const;

        /// \param  pixel set the pixel real world size to the given value
	void set_pixel_size(const C2DFVector& pixel);


        /// \returns the origin in real-world units
	C2DFVector get_origin() const;

        /// \param  origin set the origin in world coordinates 
	void set_origin(const C2DFVector& origin);

        /**
        returns a copy of this image
        Abstract method
        */
	virtual C2DImage* clone() const __attribute__((warn_unused_result))  = 0;

	virtual std::pair<double, double> get_minmax_intensity() const = 0; 

	virtual void make_single_ref() = 0; 
	
 protected:
         /** Constructor initializes the size and the pixel type
         */
         C2DImage(const C2DBounds& size, EPixelType type);

         /** Constructor initializes from the attributes, the size and the pixel type
         */
         C2DImage(const CAttributedData& attributes, const C2DBounds& size, EPixelType type);

         /** standard constructor initializes the size to (0,0), and the pixel type
         to "unknown"
         */
         C2DImage();

 private:
	C2DBounds m_size;
	EPixelType m_pixel_type;
};

/// Shared pointer representation of the 2D Image
typedef C2DImage::Pointer P2DImage;

/// helper type for image series 
typedef std::vector<P2DImage> C2DImageSeries;

typedef std::shared_ptr<C2DImageSeries> P2DImageSeries;

typedef std::vector<C2DImageSeries> C2DImageSeriesGroup; 
typedef std::map<std::string, C2DImageSeriesGroup> C2DImageGroupedSeries; 


/**
   \ingroup basic 
   \brief This is the template version of a 2D image that is used for holding real data.

   The purpouse of this class is to hold actual pixel data and provide access to it.
*/

template <typename T>
class EXPORT_2D T2DImage : public C2DImage {
public:
	/// define the super class of this class for generic processing 
	typedef C2DImage Super;

	/// \cond SELFEXPLAINING 
	typedef typename T2DDatafield<T>::iterator iterator;
	typedef typename T2DDatafield<T>::const_iterator const_iterator;
	typedef typename T2DDatafield<T>::const_reference const_reference;
	typedef typename T2DDatafield<T>::reference reference;
	typedef typename T2DDatafield<T>::const_pointer const_pointer;
	typedef typename T2DDatafield<T>::pointer pointer;
	typedef typename T2DDatafield<T>::value_type value_type;
	typedef typename T2DDatafield<T>::difference_type difference_type;
	typedef typename T2DDatafield<T>::size_type size_type;
	typedef typename T2DDatafield<T>::range_iterator range_iterator; 
	typedef typename T2DDatafield<T>::const_range_iterator const_range_iterator; 
	typedef typename T2DDatafield<T>::range_iterator_with_boundary_flag range_iterator_with_boundary_flag; 
	typedef typename T2DDatafield<T>::const_range_iterator_with_boundary_flag const_range_iterator_with_boundary_flag; 

	typedef	typename T2DDatafield<T>::data_array data_array;

	/// \endcond

	/**
	   Create a 2D image with the given size and initialize it with the given data 
	   \param size 
	   \param init_data must at least be of size (size.x*size.y)
	*/
	T2DImage(const C2DBounds& size, const T* init_data);

	/**
	   Create a 2D image with the given size and initialize it with the given data 
	   \param size 
	   \param init_data must at least be of size (size.x*size.y)
	*/
	T2DImage(const C2DBounds& size, const std::vector<T>& init_data);
	/**
	   Create a 2D image with thegiven size and attach the given meta-data list. 
	   \param size image size 
	   \param attr meta-data to be added 
	 */
	T2DImage(const C2DBounds& size, const CAttributedData& attr);

	/**
	   Create a 2D image with the given size and initialize it with the given data 
	   \param size 
	*/
	T2DImage(const C2DBounds& size);

	/**
	   Copy constructor 
	 */
	T2DImage(const T2DImage& orig);

	/**
	   Constructor to create the image by using a 2D data field 
	   \param orig the input data field 
	*/
	T2DImage(const T2DDatafield<T>& orig);

	/**
	   Constructor to create the image by using a 2D data field and a given meta data set. 
	   \param orig the input data field 
	   \param attr the meta data 
	*/
	T2DImage(const T2DDatafield<T>& orig, const CAttributedData& attr);
	
	T2DImage();

	/**
	   \returns a dynamically created copy of the image
	 */
	virtual C2DImage* clone() const __attribute__((warn_unused_result));
	
	/// forwarding function to access the underlying T2DDatafield
	const_reference operator()(size_t  x, size_t  y) const {
		return m_image(x,y);
	}
	
	/// forwarding function to access the underlying T2DDatafield
	reference operator()(size_t  x, size_t  y){
		return m_image(x,y);
	}
	
	/// forwarding function to access the underlying T2DDatafield
	const_reference operator[](size_t  idx) const {
		return m_image[idx];
	}
	
	/// forwarding function to access the underlying T2DDatafield
	reference operator[](size_t  idx){
		return m_image[idx];
	}
	
	/// forwarding function to access the underlying T2DDatafield
	const_reference operator()(const C2DBounds& l) const{
		return m_image(l.x,l.y);
	}
	
	/// forwarding function to access the underlying T2DDatafield
	reference operator()(const C2DBounds& l){
		return m_image(l.x,l.y);
	}

	/// forwarding function to access the underlying T2DDatafield
	const_iterator begin()const {
		return m_image.begin();
	}

	/// forwarding function to access the underlying T2DDatafield
	const_iterator end()const {
		return m_image.end();
	}

	/// forwarding function to access the underlying T2DDatafield
	iterator begin() {
		return m_image.begin();
	}

	/// forwarding function to access the underlying T2DDatafield
	iterator end() {
		return m_image.end();
	}

	/// forwarding function to access the underlying T2DDatafield
	const_iterator begin_at(size_t x, size_t y)const {
		return m_image.begin_at(x,  y);
	}

	/// forwarding function to access the underlying T2DDatafield
	iterator begin_at(size_t x, size_t y) {
		return m_image.begin_at(x,  y);
	}

	/// forwarding function to access the specified range of the underlying T2DDatafield 
	range_iterator begin_range(const C2DBounds& begin, const C2DBounds& end) {
		return m_image.begin_range(begin, end); 
	}
	
	/// forwarding function to access the specified range of the underlying T2DDatafield 
	range_iterator end_range(const C2DBounds& begin, const C2DBounds& end){
		return m_image.end_range(begin, end); 
	}

	/// forwarding function to access the specified range of the underlying T2DDatafield 
	const_range_iterator begin_range(const C2DBounds& begin, const C2DBounds& end)const {
		return m_image.begin_range(begin, end); 
	}

	/// forwarding function to access the specified range of the underlying T2DDatafield 
	const_range_iterator end_range(const C2DBounds& begin, const C2DBounds& end) const{
		return m_image.end_range(begin, end); 
	}

	/// forwarding function to access the underlying T2DDatafield
	size_t size() const;

	/// get direct access to the data field 
	const T2DDatafield<T>& data() const;

	/// forwarding function to access the underlying T2DDatafield
	void get_data_line_x(size_t y, std::vector<T>& buffer) const;

	/// forwarding function to access the underlying T2DDatafield
	void get_data_line_y(size_t x, std::vector<T>& buffer) const;
	
	/// forwarding function to access the underlying T2DDatafield
	void put_data_line_x(size_t y, const std::vector<T>& buffer);

	/// forwarding function to access the underlying T2DDatafield
	void put_data_line_y(size_t x, const std::vector<T>& buffer);
	
	/** 
	    evaluate the image gradient afthe given grid position by using centered finite differences 
	    \param idx linear index into the image data 
	    \returns the approximated gradient 
	 */
	C2DFVector get_gradient(size_t idx) const;
	
	/**
	   Evaluate the gradient by using linerly interpolated finite differences 
	   \param p continious coordinate into the image domain 
	   \returns gradient at position p 
	 */
	C2DFVector get_gradient(const C2DFVector& p) const;

	/// \returns a pair (minimum, maximum) pixel intensity 
	std::pair<double, double> get_minmax_intensity() const;

	void make_single_ref(); 
private:
	T2DDatafield<T> m_image;
};

/**
   \ingroup test 
   \brief a class to print out the intensity values of two images to compare them 
*/
class CImageComparePrinter: public TFilter<int> {
public:
	template <typename T, typename S>
	int operator () (const T2DImage<T>& src, const T2DImage<S>& ref) const {
		typename T2DImage<T>::const_iterator si = src.begin();
		typename T2DImage<T>::const_iterator se = src.end();
		typename T2DImage<S>::const_iterator ri = ref.begin();

		while (si != se)
			cvdebug() << *si++ << " expect " << *ri++ << "\n";
		return 0;
	}
};

/**
   @cond INTERNAL 
*/
template <typename S> 
struct plugin_data_type<T2DImage<S> > {
	typedef C2DImage type; 
}; 
/// @endcond

/**
   Evaluate if two images are equal in size, pixel type and all its pixels. 
   Meta data is not considered, nor is the pixel size 
   \param a
   \param b
   \returns result of comparison 
   \remark pixel size should probably also compared 
   \remark who calls this function anyway? 
 */
EXPORT_2D bool operator == (const C2DImage& a, const C2DImage& b);

/**
   Evaluate if two images are not equal in size, pixel type or all its pixels. 
   Meta data is not considered, nor is the pixel size. 
*/
inline bool operator != (const C2DImage& a, const C2DImage& b)
{
	return ! (a == b );
}


/**
   Evaluate the gradient of an image using finite differences
   \remark should be changed to use interpolator
 */
EXPORT_2D C2DFVectorfield get_gradient(const C2DImage& image);

/**
   \brief functor to copy an image into paointer representation 

   This functor copies a 2D image into a P2DImage representation 
   that is used in filters and cost functions. 
*/
class CopyC2DImageToP2DImage {
public: 
	template <typename T>
	P2DImage operator () (const T2DImage<T>& image) const {
		return P2DImage(new T2DImage<T>(image)); 
	}
};

/// \brief 2D image with binary values 
typedef T2DImage<bool> C2DBitImage;

/// \brief 2D image with signed 8 bit integer values 
typedef T2DImage<signed char> C2DSBImage;

/// \brief 2D image with unsigned 8 bit integer values 
typedef T2DImage<unsigned char> C2DUBImage;

/// \brief 2D image with signed 16 bit integer values 
typedef T2DImage<signed short> C2DSSImage;

/// \brief 2D image with unsigned 16 bit integer values 
typedef T2DImage<unsigned short> C2DUSImage;

/// \brief 2D image with signed 32 bit integer values 
typedef T2DImage<signed int> C2DSIImage;

/// \brief 2D image with unsigned 32 bit integer values 
typedef T2DImage<unsigned int> C2DUIImage;

#ifdef LONG_64BIT
/// \brief 2D image with signed 64 bit integer values 
typedef T2DImage<signed long> C2DSLImage;

/// \brief 2D image with unsigned 64 bit integer values 
typedef T2DImage<unsigned long> C2DULImage;
#endif

/// \brief 2D image with single precsion floating point values 
typedef T2DImage<float> C2DFImage;

/// \brief 2D image with double  precsion floating point values 
typedef T2DImage<double> C2DDImage;

/**
   @cond INTERNAL 
   @ingroup traits 
   \brief Helper class for 2D filter application 
   
   This class specializes the __bind_all template for 2D images 
   to enable the use of  mia::filter, mia::accumulate, and the likes.  
 */
template <>
struct Binder<C2DImage> {
	/// trait to have a common name for all the derived classes
	typedef __bind_all<T2DImage> Derived;
};

//@endcond INTERNAL 

/**
   \brief functor to convert an image with an abitrary pixel type to single floating point pixels 
   
   This functor provides the often used funcionality to convert a 2D image from 
   any pixel representation to a pixel type O representation.  
   The data is just copied. 
   For conversion with scaling and proepry clamping you should use the convert filter 
   provided through C2DFilterPluginHandler. 
   \tparam O output pixel type
   
 */
template <typename O>
struct FConvert2DImageToPixeltypeO: public TFilter<T2DImage<O> > {

	/**
	   Operator to do the actual conversion. 
	   \param image input image 
	   \returns the image converted floating point pixel values 
	 */
	template <typename T>
	T2DImage<O> operator () (const T2DImage<T> &image) const {
		T2DImage<O> result(image.get_size(), image);
		copy(image.begin(), image.end(), result.begin());
		return result;
	}

	/**
	   Operator to do redirect the base class representation through mia::filter
	   \param image input image 
	   \returns the image converted floating point pixel values 
	 */

	T2DImage<O> operator () (const C2DImage &image) const {
		return filter(*this, image); 
	}

	/**
	   Operator to do redirect the pointer representation through mia::filter
	   \param image input image pointer 
	   \returns the image converted floating point pixel values 
	 */

	T2DImage<O> operator () (P2DImage image) const {
		return filter(*this, *image); 
	}
};


/**
   \brief short name for 2DImage to float pixel repn copy functor

   Since copy-conversion to a floating pixel type image is used often 
   we provide here a typedef for the functor.  
*/
typedef FConvert2DImageToPixeltypeO<float> FCopy2DImageToFloatRepn; 


NS_MIA_END

#endif