ome-files  0.1.1
OMETIFFReader.h
1 /*
2  * #%L
3  * OME-FILES C++ library for image IO.
4  * Copyright © 2015 Open Microscopy Environment:
5  * - Massachusetts Institute of Technology
6  * - National Institutes of Health
7  * - University of Dundee
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37 
38 #ifndef OME_FILES_IN_OMETIFFREADER_H
39 #define OME_FILES_IN_OMETIFFREADER_H
40 
41 #include <ome/files/in/MinimalTIFFReader.h>
42 #include <ome/files/tiff/ImageJMetadata.h>
43 
44 #include <ome/common/log.h>
45 
46 #include <ome/xml/meta/BaseMetadata.h>
47 
48 namespace ome
49 {
50 
51  namespace xml
52  {
53  namespace meta
54  {
55  class OMEXMLMetadata;
56  }
57  }
58 
59  namespace files
60  {
61  namespace in
62  {
63 
68  {
69  using detail::FormatReader::isThisType;
70  using ::ome::files::FormatReader::getOptimalTileWidth;
71  using ::ome::files::FormatReader::getOptimalTileHeight;
72 
73  protected:
76 
78  typedef std::map<std::string, boost::filesystem::path> uuid_file_map;
79 
81  typedef std::map<boost::filesystem::path, boost::filesystem::path> invalid_file_map;
82 
84  typedef std::map<boost::filesystem::path, ome::compat::shared_ptr<ome::files::tiff::TIFF> > tiff_map;
85 
87  uuid_file_map files;
88 
90  invalid_file_map invalidFiles;
91 
92  // Mutable to allow opening TIFFs when const.
94  mutable tiff_map tiffs;
95 
97  boost::filesystem::path metadataFile;
98 
100  std::vector<boost::filesystem::path> usedFiles;
101 
103  bool hasSPW;
104 
105  public:
107  OMETIFFReader();
108 
110  virtual
111  ~OMETIFFReader();
112 
113  // Documented in superclass.
114  bool
115  isSingleFile(const boost::filesystem::path& id) const;
116 
117  // Documented in superclass.
118  bool
119  isThisType(const boost::filesystem::path& name,
120  bool open) const;
121 
122  protected:
123  // Documented in superclass.
124  bool
125  isFilenameThisTypeImpl(const boost::filesystem::path& name) const;
126 
127  // Documented in superclass.
128  void
129  getLookupTable(dimension_size_type plane,
130  VariantPixelBuffer& buf) const;
131 
132  // Documented in superclass.
133  void
134  openBytesImpl(dimension_size_type plane,
135  VariantPixelBuffer& buf,
139  dimension_size_type h) const;
140 
148  const ome::compat::shared_ptr<const tiff::IFD>
149  ifdAtIndex(dimension_size_type plane) const;
150 
156  void
157  addTIFF(const boost::filesystem::path& tiff);
158 
170  const ome::compat::shared_ptr<const ome::files::tiff::TIFF>
171  getTIFF(const boost::filesystem::path& tiff) const;
172 
180  void
181  closeTIFF(const boost::filesystem::path& tiff);
182 
183  public:
184  // Documented in superclass.
185  void
186  close(bool fileOnly = false);
187 
188  const std::vector<std::string>&
189  getDomains() const;
190 
191  // Documented in superclass.
192  const std::vector<boost::filesystem::path>
193  getSeriesUsedFiles(bool noPixels) const;
194 
195  // Documented in superclass.
197  fileGroupOption(const std::string& id);
198 
199  // Documented in superclass.
201  getOptimalTileWidth(dimension_size_type channel) const;
202 
203  // Documented in superclass.
205  getOptimalTileHeight(dimension_size_type channel) const;
206 
207  // Documented in superclass.
208  void
209  initFile(const boost::filesystem::path& id);
210 
211  private:
222  void
223  findUsedFiles(const ome::xml::meta::OMEXMLMetadata& meta,
224  const boost::filesystem::path& currentId,
225  const boost::filesystem::path& currentDir,
226  const boost::optional<std::string>& currentUUID);
227 
237  void
238  getAcquisitionDates(const ome::xml::meta::OMEXMLMetadata& meta,
239  std::vector<boost::optional<ome::xml::model::primitives::Timestamp> >& timestamps);
240 
248  void
249  cleanMetadata(ome::xml::meta::OMEXMLMetadata& meta);
250 
259  seriesFileSamplesPerPixel(const ome::xml::meta::OMEXMLMetadata& meta,
261 
274  void
275  seriesIndexStart(const ome::xml::meta::OMEXMLMetadata& meta,
277  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& zIndexStart,
278  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tIndexStart,
279  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& cIndexStart);
280 
294  bool
295  getTiffDataValues(const ome::xml::meta::OMEXMLMetadata& meta,
298  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tdIFD,
303 
314  void
315  fixOMEROMetadata(ome::xml::meta::OMEXMLMetadata& meta,
317 
329  void
330  fixDimensions(ome::xml::meta::BaseMetadata::index_type series);
331 
332  public:
343  ome::compat::shared_ptr< ome::xml::meta::MetadataStore>
344  getMetadataStoreForConversion();
345 
355  ome::compat::shared_ptr< ome::xml::meta::MetadataStore>
356  getMetadataStoreForDisplay();
357  };
358 
359 
360  }
361  }
362 }
363 
364 #endif // OME_FILES_IN_OMETIFFREADER_H
365 
366 /*
367  * Local Variables:
368  * mode:C++
369  * End:
370  */
logging::sources::severity_logger_mt< logging::trivial::severity_level > Logger
std::size_t dimension_size_type
Size type for image dimensions.
Definition: Types.h:59
std::map< boost::filesystem::path, ome::compat::shared_ptr< ome::files::tiff::TIFF > > tiff_map
Map filename to open TIFF handle.
Definition: OMETIFFReader.h:84
FileGroupOption
File grouping options.
Definition: FormatReader.h:77
bool hasSPW
Has screen-plate-well metadata.
Definition: OMETIFFReader.h:103
invalid_file_map invalidFiles
Invalid filename to valid filename mapping.
Definition: OMETIFFReader.h:90
uuid_file_map files
UUID to filename mapping.
Definition: OMETIFFReader.h:87
tiff_map tiffs
Open TIFF files.
Definition: OMETIFFReader.h:94
TIFF reader with support for OME-XML metadata.
Definition: OMETIFFReader.h:67
Interface for all biological file format readers (default behaviour).
Definition: FormatReader.h:107
ome::common::Logger logger
Message logger.
Definition: OMETIFFReader.h:75
std::map< boost::filesystem::path, boost::filesystem::path > invalid_file_map
Map filename to another file.
Definition: OMETIFFReader.h:81
boost::filesystem::path metadataFile
Metadata file.
Definition: OMETIFFReader.h:97
std::map< std::string, boost::filesystem::path > uuid_file_map
Map UUID to filename.
Definition: OMETIFFReader.h:78
Buffer for all pixel types.
Definition: VariantPixelBuffer.h:75
std::vector< boost::filesystem::path > usedFiles
Used files.
Definition: OMETIFFReader.h:100