ome-files  0.1.1
FormatWriter.h
1 /*
2  * #%L
3  * OME-FILES C++ library for image IO.
4  * Copyright © 2006 - 2015 Open Microscopy Environment:
5  * - Massachusetts Institute of Technology
6  * - National Institutes of Health
7  * - University of Dundee
8  * - Board of Regents of the University of Wisconsin-Madison
9  * - Glencoe Software, Inc.
10  * %%
11  * Redistribution and use in source and binary forms, with or without
12  * modification, are permitted provided that the following conditions are met:
13  *
14  * 1. Redistributions of source code must retain the above copyright notice,
15  * this list of conditions and the following disclaimer.
16  * 2. Redistributions in binary form must reproduce the above copyright notice,
17  * this list of conditions and the following disclaimer in the documentation
18  * and/or other materials provided with the distribution.
19  *
20  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
21  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
22  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
23  * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
24  * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
25  * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
26  * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
27  * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
28  * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
29  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
30  * POSSIBILITY OF SUCH DAMAGE.
31  *
32  * The views and conclusions contained in the software and documentation are
33  * those of the authors and should not be interpreted as representing official
34  * policies, either expressed or implied, of any organization.
35  * #L%
36  */
37 
38 #ifndef OME_FILES_DETAIL_FORMATWRITER_H
39 #define OME_FILES_DETAIL_FORMATWRITER_H
40 
41 #include <ome/files/FormatWriter.h>
42 #include <ome/files/FormatHandler.h>
43 
44 #include <map>
45 
46 namespace ome
47 {
48  namespace files
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::files::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
181  setLookupTable(dimension_size_type plane,
182  const VariantPixelBuffer& buf);
183 
185 
186  // Documented in superclass.
187  void
188  saveBytes(dimension_size_type plane,
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>&
221  getMetadataRetrieve();
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
341  getRGBChannelCount(dimension_size_type channel) const;
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
368  setFramesPerSecond(frame_rate_type rate);
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
384  isSupportedType(ome::xml::model::enums::PixelType type) const;
385 
386  // Documented in superclass.
387  bool
388  isSupportedType(ome::xml::model::enums::PixelType type,
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_FILES_DETAIL_FORMATWRITER_H
453 
454 /*
455  * Local Variables:
456  * mode:C++
457  * End:
458  */
const WriterProperties & writerProperties
Writer properties specific to the derived file format.
Definition: FormatWriter.h:113
Interface for all biological file format writers.
Definition: FormatWriter.h:82
bool sequential
Planes are written sequentially.
Definition: FormatWriter.h:134
uint32_t pixel_size_type
Size type for pixel bit depths.
Definition: Types.h:62
std::size_t dimension_size_type
Size type for image dimensions.
Definition: Types.h:59
WriterProperties(const std::string &name, const std::string &description)
Constructor.
Definition: FormatWriter.h:83
dimension_size_type getIndex(const std::string &order, dimension_size_type zSize, dimension_size_type cSize, dimension_size_type tSize, dimension_size_type num, dimension_size_type z, dimension_size_type c, dimension_size_type t)
Get the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
Definition: FormatTools.cpp:365
std::set< std::string > compression_types
Supported compression types.
Definition: FormatWriter.h:71
virtual void saveBytes(dimension_size_type plane, VariantPixelBuffer &buf)=0
Save an image plane.
boost::optional< boost::filesystem::path > currentId
The identifier (path) of the currently open file.
Definition: FormatWriter.h:116
Interface for all biological file format writers (default behaviour).
Definition: FormatWriter.h:108
ome::compat::shared_ptr< std::ostream > out
Current output.
Definition: FormatWriter.h:119
boost::optional< bool > interleaved
Subchannel interleaving enabled.
Definition: FormatWriter.h:131
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
dimension_size_type series
Current series.
Definition: FormatWriter.h:122
boost::optional< std::string > compression
The compression type to use.
Definition: FormatWriter.h:128
Properties specific to a particular writer.
Definition: FormatWriter.h:56
ome::compat::array< dimension_size_type, 3 > getZCTCoords(const std::string &order, dimension_size_type zSize, dimension_size_type cSize, dimension_size_type tSize, dimension_size_type num, dimension_size_type index)
Get the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value...
Definition: FormatTools.cpp:422
frame_rate_type framesPerSecond
The frames per second to use when writing.
Definition: FormatWriter.h:137
codec_pixel_type_map codec_pixel_types
Supported pixel types.
Definition: FormatWriter.h:73
ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > metadataRetrieve
Current metadata store.
Definition: FormatWriter.h:143
std::string name
Format name.
Definition: FormatWriter.h:63
std::vector< boost::filesystem::path > suffixes
Filename suffixes this format can handle.
Definition: FormatWriter.h:67
dimension_size_type plane
Current plane.
Definition: FormatWriter.h:125
bool stacks
Stacks are supported.
Definition: FormatWriter.h:75
std::vector< boost::filesystem::path > compression_suffixes
Filename compression suffixes this format can handle.
Definition: FormatWriter.h:69
std::string description
Format description.
Definition: FormatWriter.h:65
uint16_t frame_rate_type
Frame rate type.
Definition: FormatWriter.h:86
Buffer for all pixel types.
Definition: VariantPixelBuffer.h:75
Interface for all biological file format readers and writers.
Definition: FormatHandler.h:64