2d/image.hh
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1 /* -*- mia-c++ -*-
2  *
3  * This file is part of MIA - a toolbox for medical image analysis
4  * Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
5  *
6  * MIA is free software; you can redistribute it and/or modify
7  * it under the terms of the GNU General Public License as published by
8  * the Free Software Foundation; either version 3 of the License, or
9  * (at your option) any later version.
10  *
11  * This program is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License for more details.
15  *
16  * You should have received a copy of the GNU General Public License
17  * along with MIA; if not, see <http://www.gnu.org/licenses/>.
18  *
19  */
20 
21 
22 #ifndef mia_2d_2dimage_hh
23 #define mia_2d_2dimage_hh
24 
25 #include <mia/core/attributes.hh>
26 #include <mia/core/pixeltype.hh>
27 #include <mia/core/filter.hh>
28 #include <mia/core/msgstream.hh>
29 #include <mia/core/tools.hh>
30 #include <mia/core/type_traits.hh>
31 #include <mia/2d/vectorfield.hh>
32 
34 
35 #define ATTR_IMAGE_KMEANS_CLASSES "kmeans"
36 
37 
48 public:
51  static const char *data_descr;
52 
55 
57  typedef std::shared_ptr<C2DImage > Pointer;
58 
59  virtual ~C2DImage();
60 
62  EPixelType get_pixel_type() const;
63 
65  const C2DBounds& get_size() const;
66 
68  C2DFVector get_pixel_size() const;
69 
71  void set_pixel_size(const C2DFVector& pixel);
72 
73 
75  C2DFVector get_origin() const;
76 
78  void set_origin(const C2DFVector& origin);
79 
84  virtual C2DImage* clone() const __attribute__((warn_unused_result)) = 0;
85 
86  virtual std::pair<double, double> get_minmax_intensity() const = 0;
87 
88  virtual void make_single_ref() = 0;
89 
90  protected:
93  C2DImage(const C2DBounds& size, EPixelType type);
94 
97  C2DImage(const CAttributedData& attributes, const C2DBounds& size, EPixelType type);
98 
102  C2DImage();
103 
104  private:
105  C2DBounds m_size;
106  EPixelType m_pixel_type;
107 };
108 
110 typedef C2DImage::Pointer P2DImage;
111 
113 typedef std::vector<P2DImage> C2DImageSeries;
114 
115 typedef std::shared_ptr<C2DImageSeries> P2DImageSeries;
116 
117 typedef std::vector<C2DImageSeries> C2DImageSeriesGroup;
118 typedef std::map<std::string, C2DImageSeriesGroup> C2DImageGroupedSeries;
119 
120 
128 template <typename T>
129 class EXPORT_2D T2DImage : public C2DImage {
130 public:
132  typedef C2DImage Super;
133 
135  typedef typename T2DDatafield<T>::iterator iterator;
136  typedef typename T2DDatafield<T>::const_iterator const_iterator;
137  typedef typename T2DDatafield<T>::const_reference const_reference;
138  typedef typename T2DDatafield<T>::reference reference;
139  typedef typename T2DDatafield<T>::const_pointer const_pointer;
140  typedef typename T2DDatafield<T>::pointer pointer;
141  typedef typename T2DDatafield<T>::value_type value_type;
142  typedef typename T2DDatafield<T>::difference_type difference_type;
143  typedef typename T2DDatafield<T>::size_type size_type;
144  typedef typename T2DDatafield<T>::range_iterator range_iterator;
145  typedef typename T2DDatafield<T>::const_range_iterator const_range_iterator;
146  typedef typename T2DDatafield<T>::range_iterator_with_boundary_flag range_iterator_with_boundary_flag;
147  typedef typename T2DDatafield<T>::const_range_iterator_with_boundary_flag const_range_iterator_with_boundary_flag;
148 
149  typedef typename T2DDatafield<T>::data_array data_array;
150 
152 
158  T2DImage(const C2DBounds& size, const T* init_data);
159 
165  T2DImage(const C2DBounds& size, const std::vector<T>& init_data);
171  T2DImage(const C2DBounds& size, const CAttributedData& attr);
172 
177  T2DImage(const C2DBounds& size);
178 
182  T2DImage(const T2DImage& orig);
183 
188  T2DImage(const T2DDatafield<T>& orig);
189 
195  T2DImage(const T2DDatafield<T>& orig, const CAttributedData& attr);
196 
197  T2DImage();
198 
202  virtual C2DImage* clone() const __attribute__((warn_unused_result));
203 
205  const_reference operator()(size_t x, size_t y) const {
206  return m_image(x,y);
207  }
208 
210  reference operator()(size_t x, size_t y){
211  return m_image(x,y);
212  }
213 
215  const_reference operator[](size_t idx) const {
216  return m_image[idx];
217  }
218 
220  reference operator[](size_t idx){
221  return m_image[idx];
222  }
223 
225  const_reference operator()(const C2DBounds& l) const{
226  return m_image(l.x,l.y);
227  }
228 
230  reference operator()(const C2DBounds& l){
231  return m_image(l.x,l.y);
232  }
233 
235  const_iterator begin()const {
236  return m_image.begin();
237  }
238 
240  const_iterator end()const {
241  return m_image.end();
242  }
243 
245  iterator begin() {
246  return m_image.begin();
247  }
248 
250  iterator end() {
251  return m_image.end();
252  }
253 
255  const_iterator begin_at(size_t x, size_t y)const {
256  return m_image.begin_at(x, y);
257  }
258 
260  iterator begin_at(size_t x, size_t y) {
261  return m_image.begin_at(x, y);
262  }
263 
265  range_iterator begin_range(const C2DBounds& begin, const C2DBounds& end) {
266  return m_image.begin_range(begin, end);
267  }
268 
270  range_iterator end_range(const C2DBounds& begin, const C2DBounds& end){
271  return m_image.end_range(begin, end);
272  }
273 
275  const_range_iterator begin_range(const C2DBounds& begin, const C2DBounds& end)const {
276  return m_image.begin_range(begin, end);
277  }
278 
280  const_range_iterator end_range(const C2DBounds& begin, const C2DBounds& end) const{
281  return m_image.end_range(begin, end);
282  }
283 
285  size_t size() const;
286 
288  const T2DDatafield<T>& data() const;
289 
291  void get_data_line_x(size_t y, std::vector<T>& buffer) const;
292 
294  void get_data_line_y(size_t x, std::vector<T>& buffer) const;
295 
297  void put_data_line_x(size_t y, const std::vector<T>& buffer);
298 
300  void put_data_line_y(size_t x, const std::vector<T>& buffer);
301 
307  C2DFVector get_gradient(size_t idx) const;
308 
314  C2DFVector get_gradient(const C2DFVector& p) const;
315 
317  std::pair<double, double> get_minmax_intensity() const;
318 
319  void make_single_ref();
320 private:
321  T2DDatafield<T> m_image;
322 };
323 
328 class CImageComparePrinter: public TFilter<int> {
329 public:
330  template <typename T, typename S>
331  int operator () (const T2DImage<T>& src, const T2DImage<S>& ref) const {
332  typename T2DImage<T>::const_iterator si = src.begin();
333  typename T2DImage<T>::const_iterator se = src.end();
334  typename T2DImage<S>::const_iterator ri = ref.begin();
335 
336  while (si != se)
337  cvdebug() << *si++ << " expect " << *ri++ << "\n";
338  return 0;
339  }
340 };
341 
345 template <typename S>
346 struct plugin_data_type<T2DImage<S> > {
347  typedef C2DImage type;
348 };
350 
360 EXPORT_2D bool operator == (const C2DImage& a, const C2DImage& b);
361 
366 inline bool operator != (const C2DImage& a, const C2DImage& b)
367 {
368  return ! (a == b );
369 }
370 
371 
377 
385 public:
386  template <typename T>
387  P2DImage operator () (const T2DImage<T>& image) const {
388  return P2DImage(new T2DImage<T>(image));
389  }
390 };
391 
394 
397 
400 
403 
406 
409 
412 
413 #ifdef LONG_64BIT
416 
419 #endif
420 
423 
426 
435 template <>
436 struct Binder<C2DImage> {
438  typedef __bind_all<T2DImage> Derived;
439 };
440 
441 //@endcond INTERNAL
442 
454 template <typename O>
455 struct FConvert2DImageToPixeltypeO: public TFilter<T2DImage<O> > {
456 
462  template <typename T>
463  T2DImage<O> operator () (const T2DImage<T> &image) const {
464  T2DImage<O> result(image.get_size(), image);
465  copy(image.begin(), image.end(), result.begin());
466  return result;
467  }
468 
475  T2DImage<O> operator () (const C2DImage &image) const {
476  return filter(*this, image);
477  }
478 
485  T2DImage<O> operator () (P2DImage image) const {
486  return filter(*this, *image);
487  }
488 };
489 
490 
498 
499 
501 
502 #endif
C2DImage::Pointer P2DImage
Shared pointer representation of the 2D Image.
Definition: 2d/image.hh:110
CDebugSink & cvdebug()
Definition: msgstream.hh:216
std::map< std::string, C2DImageSeriesGroup > C2DImageGroupedSeries
Definition: 2d/image.hh:118
T2DImage< signed int > C2DSIImage
2D image with signed 32 bit integer values
Definition: 2d/image.hh:408
functor to convert an image with an abitrary pixel type to single floating point pixels ...
Definition: 2d/image.hh:455
2D Vector field
iterator end()
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:250
std::vector< C2DImageSeries > C2DImageSeriesGroup
Definition: 2d/image.hh:117
EPixelType
Definition: pixeltype.hh:32
functor to copy an image into paointer representation
Definition: 2d/image.hh:384
T2DImage< double > C2DDImage
2D image with double precsion floating point values
Definition: 2d/image.hh:425
base class for all filer type functors.
Definition: core/filter.hh:68
T y
second element
Definition: 2d/vector.hh:56
This is the template version of a 2D image that is used for holding real data.
Definition: 2d/image.hh:129
class EXPORT_CORE CMeans private
#define NS_MIA_BEGIN
conveniance define to start the mia namespace
Definition: defines.hh:33
A collection of attributes.
Definition: attributes.hh:255
T2DImage< unsigned short > C2DUSImage
2D image with unsigned 16 bit integer values
Definition: 2d/image.hh:405
T2DImage< float > C2DFImage
2D image with single precsion floating point values
Definition: 2d/image.hh:422
static F::result_type filter(const F &f, const B &b)
Definition: core/filter.hh:250
const_iterator end() const
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:240
EXPORT_2D bool operator==(const C2DImage &a, const C2DImage &b)
bool operator!=(const C2DImage &a, const C2DImage &b)
Definition: 2d/image.hh:366
range_iterator begin_range(const C2DBounds &begin, const C2DBounds &end)
forwarding function to access the specified range of the underlying T2DDatafield
Definition: 2d/image.hh:265
reference operator[](size_t idx)
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:220
T2DImage< signed short > C2DSSImage
2D image with signed 16 bit integer values
Definition: 2d/image.hh:402
#define EXPORT_2D
Definition: defines2d.hh:37
iterator begin_at(size_t x, size_t y)
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:260
iterator begin()
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:245
const_range_iterator begin_range(const C2DBounds &begin, const C2DBounds &end) const
forwarding function to access the specified range of the underlying T2DDatafield
Definition: 2d/image.hh:275
T2DImage< unsigned int > C2DUIImage
2D image with unsigned 32 bit integer values
Definition: 2d/image.hh:411
EXPORT_2D C2DFVectorfield get_gradient(const C2DImage &image)
const_iterator begin() const
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:235
std::shared_ptr< C2DImage > Pointer
2D Image pointer type
Definition: 2d/image.hh:57
static const char * data_descr
Definition: 2d/image.hh:51
A class to hold data on a regular 2D grid.
Definition: 2d/datafield.hh:53
C2DImage Super
define the super class of this class for generic processing
Definition: 2d/image.hh:132
const_reference operator[](size_t idx) const
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:215
T2DImage< unsigned char > C2DUBImage
2D image with unsigned 8 bit integer values
Definition: 2d/image.hh:399
reference operator()(size_t x, size_t y)
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:210
const_iterator begin_at(size_t x, size_t y) const
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:255
std::shared_ptr< C2DImageSeries > P2DImageSeries
Definition: 2d/image.hh:115
range_iterator end_range(const C2DBounds &begin, const C2DBounds &end)
forwarding function to access the specified range of the underlying T2DDatafield
Definition: 2d/image.hh:270
FConvert2DImageToPixeltypeO< float > FCopy2DImageToFloatRepn
short name for 2DImage to float pixel repn copy functor
Definition: 2d/image.hh:497
const_range_iterator end_range(const C2DBounds &begin, const C2DBounds &end) const
forwarding function to access the specified range of the underlying T2DDatafield
Definition: 2d/image.hh:280
This is the base class for 2D images that can hold generic pixel data.
Definition: 2d/image.hh:47
C2DBounds dimsize_type
a definition of the image dimension type for
Definition: 2d/image.hh:54
T2DImage< bool > C2DBitImage
2D image with binary values
Definition: 2d/image.hh:393
T2DImage< signed char > C2DSBImage
2D image with signed 8 bit integer values
Definition: 2d/image.hh:396
a class to print out the intensity values of two images to compare them
Definition: 2d/image.hh:328
::std::vector< typename __holder_type_dispatch< T >::type > data_array
type for the flat reprentation of the 2D data field
Definition: 2d/datafield.hh:58
const C2DBounds & get_size() const
std::vector< P2DImage > C2DImageSeries
helper type for image series
Definition: 2d/image.hh:113
T2DImage< signed long > C2DSLImage
2D image with signed 64 bit integer values
Definition: 2d/image.hh:415
T2DImage< unsigned long > C2DULImage
2D image with unsigned 64 bit integer values
Definition: 2d/image.hh:418
const_reference operator()(const C2DBounds &l) const
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:225
reference operator()(const C2DBounds &l)
forwarding function to access the underlying T2DDatafield
Definition: 2d/image.hh:230
T x
first element
Definition: 2d/vector.hh:53
#define NS_MIA_END
conveniance define to end the mia namespace
Definition: defines.hh:36