bioformats  5.1.8
FormatWriter.h
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37 
38 #ifndef OME_BIOFORMATS_DETAIL_FORMATWRITER_H
39 #define OME_BIOFORMATS_DETAIL_FORMATWRITER_H
40 
41 #include <ome/bioformats/FormatWriter.h>
42 #include <ome/bioformats/FormatHandler.h>
43 
44 #include <map>
45 
46 namespace ome
47 {
48  namespace bioformats
49  {
50  namespace detail
51  {
52 
57  {
59  typedef std::map<std::string,
60  std::set<ome::xml::model::enums::PixelType> > codec_pixel_type_map;
61 
63  std::string name;
65  std::string description;
67  std::vector<boost::filesystem::path> suffixes;
69  std::vector<boost::filesystem::path> compression_suffixes;
71  std::set<std::string> compression_types;
73  codec_pixel_type_map codec_pixel_types;
75  bool stacks;
76 
83  WriterProperties(const std::string& name,
84  const std::string& description):
85  name(name),
86  description(description),
87  suffixes(),
88  compression_suffixes(),
89  compression_types(),
90  codec_pixel_types(),
91  stacks()
92  {
93  compression_suffixes.push_back(boost::filesystem::path(""));
94  }
95  };
96 
109  virtual public ::ome::bioformats::FormatHandler
110  {
111  protected:
114 
116  boost::optional<boost::filesystem::path> currentId;
117 
119  ome::compat::shared_ptr<std::ostream> out;
120 
123 
126 
128  boost::optional<std::string> compression;
129 
131  boost::optional<bool> interleaved;
132 
135 
138 
143  ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve> metadataRetrieve;
144 
145  protected:
148 
149  private:
151  FormatWriter (const FormatWriter&);
152 
154  FormatWriter&
155  operator= (const FormatWriter&);
156 
157  public:
159  virtual
160  ~FormatWriter();
161 
162  // Documented in superclass.
163  bool
164  isThisType(const boost::filesystem::path& name,
165  bool open = true) const;
166 
175  virtual
177  getSeriesCount() const;
178 
179  // Documented in superclass.
180  void
182  const VariantPixelBuffer& buf);
183 
185 
186  // Documented in superclass.
187  void
189  VariantPixelBuffer& buf);
190 
191  // Documented in superclass.
192  void
193  setSeries(dimension_size_type series) const;
194 
195  // Documented in superclass.
197  getSeries() const;
198 
199  // Documented in superclass.
200  void
201  setPlane(dimension_size_type plane) const;
202 
203  // Documented in superclass.
205  getPlane() const;
206 
207  // Documented in superclass.
208  bool
209  canDoStacks() const;
210 
211  // Documented in superclass.
212  void
213  setMetadataRetrieve(ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>& retrieve);
214 
215  // Documented in superclass.
216  const ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>&
217  getMetadataRetrieve() const;
218 
219  // Documented in superclass.
220  ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>&
222 
228  virtual
230  getImageCount() const;
231 
242  virtual
243  bool
244  isRGB(dimension_size_type channel) const;
245 
251  virtual
253  getSizeX() const;
254 
260  virtual
262  getSizeY() const;
263 
269  virtual
271  getSizeZ() const;
272 
278  virtual
280  getSizeT() const;
281 
287  virtual
289  getSizeC() const;
290 
296  virtual
298  getPixelType() const;
299 
309  virtual
311  getBitsPerPixel() const;
312 
324  virtual
326  getEffectiveSizeC() const;
327 
339  virtual
342 
346  virtual
347  const std::string&
348  getDimensionOrder() const;
349 
353  virtual
357  dimension_size_type t) const;
358 
362  virtual
363  ome::compat::array<dimension_size_type, 3>
364  getZCTCoords(dimension_size_type index) const;
365 
366  // Documented in superclass.
367  void
369 
370  // Documented in superclass.
372  getFramesPerSecond() const;
373 
374  // Documented in superclass.
375  const std::set<ome::xml::model::enums::PixelType>&
376  getPixelTypes() const;
377 
378  // Documented in superclass.
379  const std::set<ome::xml::model::enums::PixelType>&
380  getPixelTypes(const std::string& codec) const;
381 
382  // Documented in superclass.
383  bool
385 
386  // Documented in superclass.
387  bool
389  const std::string& codec) const;
390 
391  // Documented in superclass.
392  const std::set<std::string>&
393  getCompressionTypes() const ;
394 
395  // Documented in superclass.
396  void
397  setCompression(const std::string& compression);
398 
399  // Documented in superclass.
400  const boost::optional<std::string>&
401  getCompression() const;
402 
403  // Documented in superclass.
404  void
405  setInterleaved(bool interleaved);
406 
407  // Documented in superclass.
408  const boost::optional<bool>&
409  getInterleaved() const;
410 
411  // Documented in superclass.
412  void
413  changeOutputFile(const boost::filesystem::path& id);
414 
415  // Documented in superclass.
416  void
417  setWriteSequentially(bool sequential = true);
418 
419  // Documented in superclass.
420  bool
421  getWriteSequentially() const;
422 
423  // Documented in superclass.
424  void
425  setId(const boost::filesystem::path& id);
426 
427  // Documented in superclass.
428  void
429  close(bool fileOnly = false);
430 
431  // Documented in superclass.
432  const std::string&
433  getFormat() const;
434 
435  // Documented in superclass.
436  const std::string&
437  getFormatDescription() const;
438 
439  // Documented in superclass.
440  const std::vector<boost::filesystem::path>&
441  getSuffixes() const;
442 
443  // Documented in superclass.
444  const std::vector<boost::filesystem::path>&
445  getCompressionSuffixes() const;
446  };
447 
448  }
449  }
450 }
451 
452 #endif // OME_BIOFORMATS_DETAIL_FORMATWRITER_H
453 
454 /*
455  * Local Variables:
456  * mode:C++
457  * End:
458  */
void setSeries(dimension_size_type series) const
Set the active series.
Definition: FormatWriter.cpp:177
bool getWriteSequentially() const
Check if planes are written sequentially.
Definition: FormatWriter.cpp:332
void setLookupTable(dimension_size_type plane, const VariantPixelBuffer &buf)
Set the color lookup table associated with the current series.
Definition: FormatWriter.cpp:157
virtual ~FormatWriter()
Destructor.
Definition: FormatWriter.cpp:95
codec_pixel_type_map codec_pixel_types
Supported pixel types.
Definition: FormatWriter.h:73
uint32_t pixel_size_type
Size type for pixel bit depths.
Definition: Types.h:62
WriterProperties(const std::string &name, const std::string &description)
Constructor.
Definition: FormatWriter.h:83
const std::set< ome::xml::model::enums::PixelType > & getPixelTypes() const
Get supported pixel types.
Definition: FormatWriter.cpp:254
Interface for all biological file format readers and writers.
Definition: FormatHandler.h:64
virtual pixel_size_type getBitsPerPixel() const
Get the number of valid bits per pixel.
Definition: FormatWriter.cpp:430
boost::optional< bool > interleaved
Subchannel interleaving enabled.
Definition: FormatWriter.h:131
virtual dimension_size_type getImageCount() const
Determine the number of image planes in the current series.
Definition: FormatWriter.cpp:361
virtual dimension_size_type getSizeZ() const
Get the size of the Z dimension.
Definition: FormatWriter.cpp:393
bool sequential
Planes are written sequentially.
Definition: FormatWriter.h:134
const std::vector< boost::filesystem::path > & getCompressionSuffixes() const
Get the default compression suffixes for this file format.
Definition: FormatWriter.cpp:514
dimension_size_type getPlane() const
Get the active plane.
Definition: FormatWriter.cpp:234
const WriterProperties & writerProperties
Writer properties specific to the derived file format.
Definition: FormatWriter.h:113
virtual dimension_size_type getIndex(dimension_size_type z, dimension_size_type c, dimension_size_type t) const
Get the linear index of a Z, C and T coordinate.
Definition: FormatWriter.cpp:470
virtual dimension_size_type getSizeC() const
Get the size of the C dimension.
Definition: FormatWriter.cpp:413
const boost::optional< bool > & getInterleaved() const
Set subchannel interleaving.
Definition: FormatWriter.cpp:312
const std::vector< boost::filesystem::path > & getSuffixes() const
Get the default file suffixes for this file format.
Definition: FormatWriter.cpp:508
std::vector< boost::filesystem::path > compression_suffixes
Filename compression suffixes this format can handle.
Definition: FormatWriter.h:69
void saveBytes(dimension_size_type plane, VariantPixelBuffer &buf)
Save an image plane.
Definition: FormatWriter.cpp:166
Interface for all biological file format writers (default behaviour).
Definition: FormatWriter.h:108
uint16_t frame_rate_type
Frame rate type.
Definition: FormatWriter.h:86
Interface for all biological file format writers.
Definition: FormatWriter.h:82
virtual dimension_size_type getSizeT() const
Get the size of the T dimension.
Definition: FormatWriter.cpp:403
dimension_size_type series
Current series.
Definition: FormatWriter.h:122
bool isThisType(const boost::filesystem::path &name, bool open=true) const
Check if the given file is a valid instance of this file format.
Definition: FormatWriter.cpp:142
FormatWriter & operator=(const FormatWriter &)
Assignment operator (deleted).
std::set< std::string > compression_types
Supported compression types.
Definition: FormatWriter.h:71
void setFramesPerSecond(frame_rate_type rate)
Set the frame rate to use when writing.
Definition: FormatWriter.cpp:242
virtual dimension_size_type getEffectiveSizeC() const
Get the effective size of the C dimension.
Definition: FormatWriter.cpp:437
virtual ome::compat::array< dimension_size_type, 3 > getZCTCoords(dimension_size_type index) const
Get the Z, C and T coordinate of a linear index.
Definition: FormatWriter.cpp:484
virtual bool isRGB(dimension_size_type channel) const
Does a channel contain subchannels?
Definition: FormatWriter.cpp:367
virtual dimension_size_type getRGBChannelCount(dimension_size_type channel) const
Get the number of channels required for a call to saveBytes().
Definition: FormatWriter.cpp:444
std::vector< boost::filesystem::path > suffixes
Filename suffixes this format can handle.
Definition: FormatWriter.h:67
Open Microscopy Environment C++ implementation.
Definition: CoreMetadata.cpp:40
virtual const std::string & getDimensionOrder() const
Get the dimension order.
Definition: FormatWriter.cpp:463
void close(bool fileOnly=false)
Close the currently open file.
Definition: FormatWriter.cpp:129
virtual void saveBytes(dimension_size_type plane, VariantPixelBuffer &buf)=0
Save an image plane.
bool stacks
Stacks are supported.
Definition: FormatWriter.h:75
void changeOutputFile(const boost::filesystem::path &id)
Switch the output file for the current dataset.
Definition: FormatWriter.cpp:318
bool canDoStacks() const
Get whether or not the writer can save multiple images in a single file.
Definition: FormatWriter.cpp:526
const std::set< std::string > & getCompressionTypes() const
Get supported compression types.
Definition: FormatWriter.cpp:520
virtual dimension_size_type getSeriesCount() const
Get the number of image series in this file.
Definition: FormatWriter.cpp:151
void setMetadataRetrieve(ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > &retrieve)
Set the default metadata store for this writer.
Definition: FormatWriter.cpp:338
dimension_size_type getSeries() const
Get the active series.
Definition: FormatWriter.cpp:202
std::string description
Format description.
Definition: FormatWriter.h:65
frame_rate_type getFramesPerSecond() const
Get the frame rate to use when writing.
Definition: FormatWriter.cpp:248
const std::string & getFormat() const
Get the name of this file format.
Definition: FormatWriter.cpp:496
PixelType enumeration.
Definition: PixelType.h:69
void setPlane(dimension_size_type plane) const
Set the active plane.
Definition: FormatWriter.cpp:210
const ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > & getMetadataRetrieve() const
Get the current metadata store for this writer.
Definition: FormatWriter.cpp:349
dimension_size_type plane
Current plane.
Definition: FormatWriter.h:125
frame_rate_type framesPerSecond
The frames per second to use when writing.
Definition: FormatWriter.h:137
virtual ome::xml::model::enums::PixelType getPixelType() const
Get the pixel type.
Definition: FormatWriter.cpp:423
const std::string & getFormatDescription() const
Get the description of this file format.
Definition: FormatWriter.cpp:502
Buffer for all pixel types.
Definition: VariantPixelBuffer.h:75
void setId(const boost::filesystem::path &id)
Set the current file name.
Definition: FormatWriter.cpp:107
boost::optional< std::string > compression
The compression type to use.
Definition: FormatWriter.h:128
FormatWriter()
Constructor.
Definition: FormatWriter.h:90
std::map< std::string, std::set< ome::xml::model::enums::PixelType > > codec_pixel_type_map
Map of codec to pixel types.
Definition: FormatWriter.h:60
std::string name
Format name.
Definition: FormatWriter.h:63
void setCompression(const std::string &compression)
Set the compression type to use when writing.
Definition: FormatWriter.cpp:286
boost::optional< boost::filesystem::path > currentId
The identifier (path) of the currently open file.
Definition: FormatWriter.h:116
virtual dimension_size_type getSizeY() const
Get the size of the Y dimension.
Definition: FormatWriter.cpp:383
std::size_t dimension_size_type
Size type for image dimensions.
Definition: Types.h:59
bool isSupportedType(ome::xml::model::enums::PixelType type) const
Check if the pixel type is supported.
Definition: FormatWriter.cpp:271
ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > metadataRetrieve
Current metadata store.
Definition: FormatWriter.h:143
Properties specific to a particular writer.
Definition: FormatWriter.h:56
const boost::optional< std::string > & getCompression() const
Get the compression type to use when writing.
Definition: FormatWriter.cpp:300
virtual dimension_size_type getSizeX() const
Get the size of the X dimension.
Definition: FormatWriter.cpp:373
void setWriteSequentially(bool sequential=true)
Write planes sequentially.
Definition: FormatWriter.cpp:326
void setInterleaved(bool interleaved)
Set subchannel interleaving.
Definition: FormatWriter.cpp:306
ome::compat::shared_ptr< std::ostream > out
Current output.
Definition: FormatWriter.h:119