DGtal  1.3.beta
GenericReader.h
1 
17 #pragma once
18 
31 #if defined(GenericReader_RECURSES)
32 #error Recursive header files inclusion detected in GenericReader.h
33 #else // defined(GenericReader_RECURSES)
34 
35 #define GenericReader_RECURSES
36 
37 #if !defined GenericReader_h
38 
39 #define GenericReader_h
40 
42 // Inclusions
43 #include <iostream>
44 #include <vector>
45 #include "DGtal/images/CImage.h"
46 #include "DGtal/base/Common.h"
47 #include "DGtal/io/readers/VolReader.h"
48 #include "DGtal/io/readers/LongvolReader.h"
49 #include "DGtal/io/readers/PPMReader.h"
50 #include "DGtal/io/readers/PGMReader.h"
51 #include "DGtal/io/readers/RawReader.h"
52 #include "DGtal/io/readers/STBReader.h"
53 #ifdef WITH_HDF5
54 #include "DGtal/io/readers/HDF5Reader.h"
55 #endif
56 #ifdef WITH_ITK
57 #include "DGtal/io/readers/DicomReader.h"
58 #include "DGtal/io/readers/ITKReader.h"
59 #endif
60 #include "DGtal/io/colormaps/BasicColorToScalarFunctors.h"
61 
63 
64 namespace DGtal
65 {
66 
68  // template class GenericReader
98  template <typename TContainer, int Tdim=TContainer::Point::dimension, typename TValue = typename TContainer::Value>
100  {
102 
113  static TContainer import(const std::string &filename,
114  std::vector<unsigned int> dimSpace= std::vector<unsigned int > () );
115 
128  template <typename TFunctor>
129  static TContainer importWithValueFunctor(
130  const std::string & filename, const TFunctor & aFunctor,
131  std::vector<unsigned int> dimSpace =
132  std::vector<unsigned int>() )
133  {
136  DGtal::IOException dgtalio;
137  const std::string extension =
138  filename.substr( filename.find_last_of( "." ) + 1 );
139 
140  if ( extension == "raw" )
141  {
142  for ( unsigned int i = 0; i < dimSpace.size(); i++ )
143  ASSERT( dimSpace[ i ] != 0 );
144  typename TContainer::Point const pt;
145  for ( unsigned int i = 0; i < dimSpace.size(); i++ )
146  pt[ i ] = dimSpace[ i ];
147 
148  return RawReader<TContainer, TFunctor>::template importRaw<TValue>(
149  filename, pt, aFunctor );
150  }
151 
152  trace.error() << "Extension " << extension
153  << " not yet implemented in DGtal GenericReader."
154  << std::endl;
155  throw dgtalio;
156  }
157 
173  template <typename TFunctor>
174  static TContainer importWithColorFunctor(
175  const std::string & filename, const TFunctor & aFunctor,
176  std::vector<unsigned int> dimSpace =
177  std::vector<unsigned int>() )
178 
179  {
182  typename TContainer::Value>));
183 
184  DGtal::IOException dgtalio;
185  const std::string extension =
186  filename.substr( filename.find_last_of( "." ) + 1 );
187 
188  if ( extension == "raw" )
189  {
190  for ( unsigned int i = 0; i < dimSpace.size(); i++ )
191  ASSERT( dimSpace[ i ] != 0 );
192  typename TContainer::Point const pt;
193  for ( unsigned int i = 0; i < dimSpace.size(); i++ )
194  pt[ i ] = dimSpace[ i ];
196  DGtal::Color>( filename, pt, aFunctor );
197  }
198 
199  trace.error() << "Extension " << extension
200  << " not yet implemented in DGtal GenericReader."
201  << std::endl;
202  throw dgtalio;
203  }
204  };
205 
206 
211  template <typename TContainer, typename TValue>
212  struct GenericReader<TContainer, 3, TValue>
213  {
227  static TContainer import(const std::string &filename, unsigned int x=0,
228  unsigned int y=0, unsigned int z=0);
229 
230 
231 
244  template<typename TFunctor>
245  static TContainer importWithValueFunctor(const std::string &filename,
246  const TFunctor &aFunctor,
247  unsigned int x=0,
248  unsigned int y=0, unsigned int z=0)
249  {
251  DGtal::IOException dgtalio;
252  const std::string extension = filename.substr(filename.find_last_of(".") + 1);
253 
254  if ( extension == "vol" )
255  {
256  return VolReader<TContainer, TFunctor>::importVol( filename, aFunctor );
257  }
258  else if ( extension == "longvol" )
259  {
260  return LongvolReader<TContainer, TFunctor>::importLongvol( filename, aFunctor );
261  }
262  else if ( extension == "pgm3d" || extension == "pgm3D" || extension == "p3d" || extension == "pgm" )
263  {
264  return PGMReader<TContainer, TFunctor>::importPGM3D(filename, aFunctor);
265  }
266  else if ( extension == "raw" )
267  {
268  ASSERT( x != 0 && y != 0 && z != 0 );
269  typename TContainer::Point const pt (x, y, z);
270  return RawReader< TContainer, TFunctor >::template importRaw<TValue>( filename, pt, aFunctor );
271  }
272 
273 #ifdef WITH_HDF5
274  if ( extension == "h5" )
275  return HDF5Reader<TContainer, TFunctor>::importHDF5_3D(filename, "UInt8Array3D", aFunctor);
276 #endif
277 
278 #ifdef WITH_ITK
279  if ( extension == "dcm" )
280  {
281  return DicomReader<TContainer, TFunctor>::importDicom(filename, aFunctor);
282  }
283  else if (std::find(ITK_IO_IMAGE_EXT.begin(), ITK_IO_IMAGE_EXT.end(), extension) != ITK_IO_IMAGE_EXT.end() )
284  {
285  return ITKReader<TContainer>::importITK( filename, aFunctor );
286  }
287 #endif
288 
289  trace.error() << "Extension " << extension<< " in 3D, not yet implemented in DGtal GenericReader." << std::endl;
290  throw dgtalio;
291  }
292  };
293 
294 
295 
300  template <typename TContainer>
301  struct GenericReader<TContainer, 3 , DGtal::uint32_t>
302  {
316  static TContainer import(const std::string &filename, unsigned int x=0,
317  unsigned int y=0, unsigned int z=0);
318 
319 
320 
333  template<typename TFunctor>
334  static TContainer importWithValueFunctor(const std::string &filename,
335  const TFunctor &aFunctor,
336  unsigned int x=0,
337  unsigned int y=0, unsigned int z=0)
338  {
340  DGtal::IOException dgtalio;
341  const std::string extension = filename.substr( filename.find_last_of(".") + 1 );
342 
343  if ( extension == "longvol" )
344  {
345  return LongvolReader<TContainer, TFunctor>::importLongvol( filename, aFunctor );
346  }
347  else if ( extension == "raw" )
348  {
349  ASSERT( x != 0 && y != 0 && z != 0 );
350  typename TContainer::Point const pt (x, y, z);
351  return RawReader< TContainer, TFunctor >::importRaw32 ( filename, pt, aFunctor );
352  }
353 
354 #ifdef WITH_ITK
355  if ( extension == "dcm" )
356  {
357  return DicomReader<TContainer, TFunctor>::importDicom(filename, aFunctor);
358  }
359  else if ( extension == "mha" || extension == "mhd" )
360  {
361  return ITKReader<TContainer>::importITK( filename, aFunctor );
362  }
363 #endif
364 
365  trace.error() << "Extension " << extension<< " not yet implemented in DGtal GenericReader." << std::endl;
366  throw dgtalio;
367  }
368  };
369 
370 
371 
372 
377  template <typename TContainer>
378  struct GenericReader<TContainer, 3 , DGtal::uint64_t>
379  {
388  static TContainer import(const std::string &filename);
389 
390  };
391 
392 
397  template <typename TContainer, typename TValue>
398  struct GenericReader<TContainer, 2, TValue>
399  {
401 
413  static TContainer import(const std::string &filename, unsigned int x=0,
414  unsigned int y=0);
415 
416 
428  template<typename TFunctor>
429  static TContainer importWithColorFunctor(const std::string &filename,
430  const TFunctor &aFunctor,
431  unsigned int x=0,
432  unsigned int y=0)
433  {
435  DGtal::IOException dgtalio;
436  //Getting image extension
437  const std::string extension = filename.substr( filename.find_last_of(".") + 1 );
438 
439  if ( extension == "ppm" )
440  {
441  return PPMReader<TContainer, TFunctor>::importPPM(filename, aFunctor);
442  }
443  else if ( extension == "raw" )
444  {
445  ASSERT( x != 0 && y != 0 );
446  typename TContainer::Point const pt (x,y);
447  return RawReader< TContainer, TFunctor >::template importRaw<DGtal::Color>( filename, pt, aFunctor);
448  }
449  else if ( extension == "gif" || extension == "jpg" || extension == "png" || extension == "jpeg" || extension == "bmp" || extension == "tga" )
450  {
452  return reader.import( filename, aFunctor );
453  }
454 
455  trace.error() << "Extension " << extension<< " in 2D, not yet implemented in DGtal GenericReader." << std::endl;
456  throw dgtalio;
457  }
458 
459 
471  template<typename TFunctor>
472  static TContainer importWithValueFunctor(const std::string &filename,
473  const TFunctor &aFunctor, unsigned int x=0,
474  unsigned int y=0)
475  {
477 
478  DGtal::IOException dgtalio;
479  //Getting image extension
480  const std::string extension = filename.substr( filename.find_last_of(".") + 1 );
481 
482  if ( extension == "raw" )
483  {
484  ASSERT( x!= 0 && y != 0);
485  typename TContainer::Point const pt (x,y);
486  return RawReader< TContainer, TFunctor >::importRaw8( filename, pt, aFunctor );
487  }
488  else if ( extension == "pgm" )
489  {
490  return PGMReader<TContainer, TFunctor>::importPGM(filename, aFunctor);
491  }
492 
493 #ifdef WITH_HDF5
494  if (extension=="h5")
495  return HDF5Reader<TContainer, TFunctor>::importHDF5(filename, "image8bit", aFunctor);
496 #endif
497 
498  trace.error() << "Extension " << extension<< " not yet implemented in DGtal GenericReader." << std::endl;
499  throw dgtalio;
500 
501  }
502 
503  };
504 
509  template <typename TContainer>
510  struct GenericReader<TContainer, 2, DGtal::uint32_t>
511  {
513 
525  static TContainer import(const std::string &filename,unsigned int x=0,
526  unsigned int y=0 );
527 
528 
540  template<typename TFunctor>
541  static TContainer importWithColorFunctor(const std::string &filename,
542  const TFunctor &aFunctor, unsigned int x=0,
543  unsigned int y=0)
544  {
545 
547  DGtal::IOException dgtalio;
548  //Getting image extension
549  const std::string extension = filename.substr(filename.find_last_of(".") + 1);
550 
551  if ( extension == "ppm" )
552  {
553  return PPMReader<TContainer, TFunctor>::importPPM(filename, aFunctor);
554  }
555  else if ( extension == "raw" )
556  {
557  ASSERT( x != 0 && y != 0 );
558  typename TContainer::Point const pt (x,y);
559  return RawReader< TContainer, TFunctor >::template importRaw<DGtal::Color>( filename, pt, aFunctor);
560  }
561  else if ( extension == "tga" || extension == "jpg" || extension == "png" || extension == "jpeg" || extension == "bmp" )
562  {
564  return reader.import( filename, aFunctor );
565  }
566 
567  trace.error() << "Extension " << extension<< " not yet implemented in DGtal GenericReader." << std::endl;
568  throw dgtalio;
569  }
570 
571 
582  template<typename TFunctor>
583  static TContainer importWithValueFunctor(const std::string &filename,
584  const TFunctor &aFunctor, unsigned int x=0,
585  unsigned int y=0)
586  {
588 
589  DGtal::IOException dgtalio;
590  //Getting image extension
591  const std::string extension = filename.substr(filename.find_last_of(".") + 1);
592 
593  if ( extension == "raw" )
594  {
595  ASSERT( x != 0 && y != 0);
596  typename TContainer::Point const pt (x,y);
597  return RawReader< TContainer, TFunctor >::importRaw8 ( filename, pt, aFunctor );
598  }
599  else if ( extension == "pgm ")
600  {
601  return PGMReader<TContainer, TFunctor>::importPGM(filename, aFunctor);
602  }
603 
604 #ifdef WITH_HDF5
605  if (extension=="h5")
606  return HDF5Reader<TContainer, TFunctor>::importHDF5(filename, "image8bit", aFunctor);
607 #endif
608 
609  trace.error() << "Extension " << extension<< " not yet implemented in DGtal GenericReader." << std::endl;
610  throw dgtalio;
611 
612  }
613 
614  };
615 
616 
617 } // namespace DGtal
618 
619 
621 // Includes inline functions.
622 #include "DGtal/io/readers/GenericReader.ih"
623 
624 // //
626 
627 #endif // !defined GenericReader_h
628 
629 #undef GenericReader_RECURSES
630 #endif // else defined(GenericReader_RECURSES)
DGtal::HDF5Reader::importHDF5
static ImageContainer importHDF5(const std::string &aFilename, const std::string &aDataset, const Functor &aFunctor=Functor(), bool topbotomOrder=true)
DGtal::ITK_IO_IMAGE_EXT
const auto ITK_IO_IMAGE_EXT
Definition: ITKIOTrait.h:48
DGtal::VolReader::importVol
static ImageContainer importVol(const std::string &filename, const Functor &aFunctor=Functor())
DGtal::GenericReader< TContainer, 3, DGtal::uint32_t >::importWithValueFunctor
static TContainer importWithValueFunctor(const std::string &filename, const TFunctor &aFunctor, unsigned int x=0, unsigned int y=0, unsigned int z=0)
Definition: GenericReader.h:334
DGtal::uint32_t
boost::uint32_t uint32_t
unsigned 32-bit integer.
Definition: BasicTypes.h:63
DGtal::Trace::error
std::ostream & error()
DGtal::Color
Structure representing an RGB triple with alpha component.
Definition: Color.h:67
DGtal::STBReader::import
static ImageContainer import(const std::string &filename, const Functor &aFunctor=Functor())
DGtal::GenericReader::importWithValueFunctor
static TContainer importWithValueFunctor(const std::string &filename, const TFunctor &aFunctor, std::vector< unsigned int > dimSpace=std::vector< unsigned int >())
Definition: GenericReader.h:129
DGtal::RawReader
Aim: Raw binary import of an Image.
Definition: RawReader.h:93
DGtal::trace
Trace trace
Definition: Common.h:154
DGtal::GenericReader< TContainer, 2, TValue >::importWithValueFunctor
static TContainer importWithValueFunctor(const std::string &filename, const TFunctor &aFunctor, unsigned int x=0, unsigned int y=0)
Definition: GenericReader.h:472
DGtal::STBReader
Aim: Image reader using the stb_image.h header only code.
Definition: STBReader.h:61
DGtal::GenericReader
Aim: Provide a mechanism to load with the bestloader according to an image (2D or 3D) filename (by pa...
Definition: GenericReader.h:99
DGtal::GenericReader< TContainer, 2, DGtal::uint32_t >::importWithColorFunctor
static TContainer importWithColorFunctor(const std::string &filename, const TFunctor &aFunctor, unsigned int x=0, unsigned int y=0)
Definition: GenericReader.h:541
DGtal::GenericReader< TContainer, 3, TValue >::importWithValueFunctor
static TContainer importWithValueFunctor(const std::string &filename, const TFunctor &aFunctor, unsigned int x=0, unsigned int y=0, unsigned int z=0)
Definition: GenericReader.h:245
DGtal::PPMReader::importPPM
static ImageContainer importPPM(const std::string &aFilename, const Functor &aFunctor=functors::ColorRGBEncoder< Value >(), bool topbotomOrder=true)
DGtal::RawReader::importRaw8
static ImageContainer importRaw8(const std::string &filename, const Vector &extent, const Functor &aFunctor=Functor())
DGtal
DGtal is the top-level namespace which contains all DGtal functions and types.
DGtal::PGMReader::importPGM
static ImageContainer importPGM(const std::string &aFilename, const Functor &aFunctor=Functor(), bool topbotomOrder=true)
DGtal::GenericReader::importWithColorFunctor
static TContainer importWithColorFunctor(const std::string &filename, const TFunctor &aFunctor, std::vector< unsigned int > dimSpace=std::vector< unsigned int >())
Definition: GenericReader.h:174
DGtal::DicomReader::importDicom
static ImageContainer importDicom(const std::string &aFilename, const Functor &aFunctor=Functor())
DGtal::uint64_t
boost::uint64_t uint64_t
unsigned 64-bit integer.
Definition: BasicTypes.h:65
DGtal::RawReader::importRaw32
static ImageContainer importRaw32(const std::string &filename, const Vector &extent, const Functor &aFunctor=Functor())
DGtal::GenericReader::BOOST_CONCEPT_ASSERT
BOOST_CONCEPT_ASSERT((concepts::CImage< TContainer >))
DGtal::PGMReader::importPGM3D
static ImageContainer importPGM3D(const std::string &aFilename, const Functor &aFunctor=Functor())
DGtal::LongvolReader::importLongvol
static ImageContainer importLongvol(const std::string &filename, const Functor &aFunctor=Functor())
DGtal::GenericReader< TContainer, 2, DGtal::uint32_t >::importWithValueFunctor
static TContainer importWithValueFunctor(const std::string &filename, const TFunctor &aFunctor, unsigned int x=0, unsigned int y=0)
Definition: GenericReader.h:583
DGtal::GenericReader< TContainer, 2, TValue >::importWithColorFunctor
static TContainer importWithColorFunctor(const std::string &filename, const TFunctor &aFunctor, unsigned int x=0, unsigned int y=0)
Definition: GenericReader.h:429
DGtal::IOException
Definition: Exceptions.h:52
Point
MyPointD Point
Definition: testClone2.cpp:383
DGtal::concepts::CUnaryFunctor
Aim: Defines a unary functor, which associates arguments to results.
Definition: CUnaryFunctor.h:89
Value
double Value
Definition: testSimpleRandomAccessRangeFromPoint.cpp:38
DGtal::HDF5Reader::importHDF5_3D
static ImageContainer importHDF5_3D(const std::string &aFilename, const std::string &aDataset, const Functor &aFunctor=Functor())
DGtal::ITKReader::importITK
static Image importITK(const std::string &filename, const TFunctor &aFunctor=TFunctor(), bool shiftDomainUsingOrigin=true)
DGtal::concepts::CImage
Aim: Defines the concept describing a read/write image, having an output iterator.
Definition: CImage.h:102