ome-files  0.3.1
OMETIFFReader.h
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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/TIFF.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  {
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, std::shared_ptr<ome::files::tiff::TIFF>> tiff_map;
85 
88 
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 
106  mutable std::shared_ptr<::ome::xml::meta::OMEXMLMetadata> cachedMetadata;
107 
112  mutable boost::filesystem::path cachedMetadataFile;
113 
114  public:
116  OMETIFFReader();
117 
119  virtual
120  ~OMETIFFReader();
121 
122  // Documented in superclass.
123  bool
124  isSingleFile(const boost::filesystem::path& id) const;
125 
126  // Documented in superclass.
127  bool
128  isThisType(const boost::filesystem::path& name,
129  bool open) const;
130 
131  protected:
132  // Documented in superclass.
133  bool
134  isFilenameThisTypeImpl(const boost::filesystem::path& name) const;
135 
136  // Documented in superclass.
137  void
139  VariantPixelBuffer& buf) const;
140 
141  // Documented in superclass.
142  void
144  VariantPixelBuffer& buf,
148  dimension_size_type h) const;
149 
157  const std::shared_ptr<const tiff::IFD>
159 
165  void
166  addTIFF(const boost::filesystem::path& tiff);
167 
179  const std::shared_ptr<const ome::files::tiff::TIFF>
180  getTIFF(const boost::filesystem::path& tiff) const;
181 
188  bool
189  validTIFF(const boost::filesystem::path& tiff) const;
190 
198  void
199  closeTIFF(const boost::filesystem::path& tiff);
200 
207  std::shared_ptr<::ome::xml::meta::OMEXMLMetadata>
209 
217  std::shared_ptr<::ome::xml::meta::OMEXMLMetadata>
218  readMetadata(const boost::filesystem::path& id);
219 
232  std::shared_ptr<::ome::xml::meta::OMEXMLMetadata>
233  cacheMetadata(const boost::filesystem::path& id) const;
234 
235  public:
236  // Documented in superclass.
237  void
238  close(bool fileOnly = false);
239 
240  const std::vector<std::string>&
241  getDomains() const;
242 
243  // Documented in superclass.
244  const std::vector<boost::filesystem::path>
245  getSeriesUsedFiles(bool noPixels) const;
246 
247  // Documented in superclass.
249  fileGroupOption(const std::string& id);
250 
251  // Documented in superclass.
254 
255  // Documented in superclass.
258 
259  // Documented in superclass.
260  void
261  initFile(const boost::filesystem::path& id);
262 
263  private:
274  void
276  const boost::filesystem::path& currentId,
277  const boost::filesystem::path& currentDir,
278  const boost::optional<std::string>& currentUUID);
279 
289  void
291  std::vector<boost::optional<ome::xml::model::primitives::Timestamp>>& timestamps);
292 
300  void
302 
313 
326  void
329  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& zIndexStart,
330  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tIndexStart,
331  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& cIndexStart);
332 
346  bool
350  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tdIFD,
355 
366  void
369 
381  void
383 
384  public:
400  std::shared_ptr< ome::xml::meta::MetadataStore>
402 
420  std::shared_ptr< ome::xml::meta::MetadataStore>
422  };
423 
424 
425  }
426  }
427 }
428 
429 #endif // OME_FILES_IN_OMETIFFREADER_H
430 
431 /*
432  * Local Variables:
433  * mode:C++
434  * End:
435  */
boost::filesystem::path cachedMetadataFile
Cached metadata file location (for re-using parsed metadata).
Definition: OMETIFFReader.h:112
const std::vector< std::string > & getDomains() const
Get the domains represented by the current file.
Definition: OMETIFFReader.cpp:351
logging::sources::severity_logger_mt< logging::trivial::severity_level > Logger
void fixOMEROMetadata(ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)
Fix invalid OMERO OME-TIFF metadata.
Definition: OMETIFFReader.cpp:1293
const std::vector< boost::filesystem::path > getSeriesUsedFiles(bool noPixels) const
Get the files used by the active series.
Definition: OMETIFFReader.cpp:358
const std::shared_ptr< const tiff::IFD > ifdAtIndex(dimension_size_type plane) const
Get the IFD index for a plane in the current series.
Definition: OMETIFFReader.cpp:326
Tagged Image File Format (TIFF).
Definition: TIFF.h:154
std::size_t dimension_size_type
Size type for image dimensions.
Definition: Types.h:58
dimension_size_type seriesFileSamplesPerPixel(const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)
Get the samples per pixel from the first IFD for a series.
bool validTIFF(const boost::filesystem::path &tiff) const
Check if a cached TIFF is valid (can be opened).
Definition: OMETIFFReader.cpp:1450
bool isSingleFile(const boost::filesystem::path &id) const
Is this a single-file format?
Definition: OMETIFFReader.cpp:220
void getLookupTable(dimension_size_type plane, VariantPixelBuffer &buf) const
Get the color lookup table associated with an image plane.
Definition: OMETIFFReader.cpp:1366
FileGroupOption
File grouping options.
Definition: FormatReader.h:79
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
FormatReader::FileGroupOption fileGroupOption(const std::string &id)
Returns an enum indicating that we cannot, must, or might group the files in this dataset...
Definition: OMETIFFReader.cpp:382
void cleanMetadata(ome::xml::meta::OMEXMLMetadata &meta)
Clean up OME-XML metadata.
Definition: OMETIFFReader.cpp:1164
uuid_file_map files
UUID to filename mapping.
Definition: OMETIFFReader.h:87
dimension_size_type series
The number of the current series (non-flattened).
Definition: FormatReader.h:140
bool isThisType(const boost::filesystem::path &name, bool open) const
Check if the given file is a valid instance of this file format.
Definition: OMETIFFReader.cpp:263
dimension_size_type getOptimalTileWidth() const
Get the optimal sub-image width.
Definition: FormatReader.cpp:1148
tiff_map tiffs
Open TIFF files.
Definition: OMETIFFReader.h:94
dimension_size_type plane
The number of the current plane in the current series.
Definition: FormatReader.h:148
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: FormatReader.cpp:412
OMETIFFReader()
Constructor.
Definition: OMETIFFReader.cpp:171
void getAcquisitionDates(const ome::xml::meta::OMEXMLMetadata &meta, std::vector< boost::optional< ome::xml::model::primitives::Timestamp >> &timestamps)
Get acquisition dates for each image.
Definition: OMETIFFReader.cpp:1145
bool isFilenameThisTypeImpl(const boost::filesystem::path &name) const
isThisType file implementation for readers.
Definition: OMETIFFReader.cpp:273
TIFF reader with support for OME-XML metadata.
Definition: OMETIFFReader.h:67
void close(bool fileOnly=false)
Close the currently open file.
Definition: OMETIFFReader.cpp:202
std::map< boost::filesystem::path, std::shared_ptr< ome::files::tiff::TIFF > > tiff_map
Map filename to open TIFF handle.
Definition: OMETIFFReader.h:84
void fixDimensions(ome::xml::meta::BaseMetadata::index_type series)
Attempt to correct logically inconsistent dimensions.
Definition: OMETIFFReader.cpp:1328
std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > cachedMetadata
Cached metadata (for re-using parsed metadata).
Definition: OMETIFFReader.h:106
void seriesIndexStart(const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &zIndexStart, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &tIndexStart, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &cIndexStart)
Get starting index for each dimension.
Definition: OMETIFFReader.cpp:1175
std::shared_ptr< ome::xml::meta::MetadataStore > getMetadataStoreForDisplay()
Get a MetadataStore suitable for display.
Definition: OMETIFFReader.cpp:1539
std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > cacheMetadata(const boost::filesystem::path &id) const
Read and cache metadata.
Definition: OMETIFFReader.cpp:1489
void initFile(const boost::filesystem::path &id)
Initialize the given file.
Definition: OMETIFFReader.cpp:419
Interface for all biological file format readers (default behaviour).
Definition: FormatReader.h:107
ome::common::Logger logger
Message logger.
Definition: OMETIFFReader.h:75
std::shared_ptr< ome::xml::meta::MetadataStore > getMetadataStoreForConversion()
Get a MetadataStore suitable for writing.
Definition: OMETIFFReader.cpp:1533
std::map< boost::filesystem::path, boost::filesystem::path > invalid_file_map
Map filename to another file.
Definition: OMETIFFReader.h:81
virtual ~OMETIFFReader()
Destructor.
Definition: OMETIFFReader.cpp:190
boost::optional< boost::filesystem::path > currentId
The identifier (path) of the currently open file.
Definition: FormatReader.h:118
boost::filesystem::path metadataFile
Metadata file.
Definition: OMETIFFReader.h:97
bool getTiffDataValues(const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series, ome::xml::meta::BaseMetadata::index_type tiffData, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &tdIFD, ome::xml::model::primitives::NonNegativeInteger &numPlanes, ome::xml::model::primitives::NonNegativeInteger &firstZ, ome::xml::model::primitives::NonNegativeInteger &firstT, ome::xml::model::primitives::NonNegativeInteger &firstC)
Get values from a TiffData element.
Definition: OMETIFFReader.cpp:1227
std::map< std::string, boost::filesystem::path > uuid_file_map
Map UUID to filename.
Definition: OMETIFFReader.h:78
const std::shared_ptr< const ome::files::tiff::TIFF > getTIFF(const boost::filesystem::path &tiff) const
Get a an open TIFF file from the internal TIFF map.
Definition: OMETIFFReader.cpp:1409
std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > readMetadata(const ome::files::tiff::TIFF &tiff)
Read metadata into metadata store from an open TIFF.
Definition: OMETIFFReader.cpp:1468
void closeTIFF(const boost::filesystem::path &tiff)
Close an open TIFF file from the internal TIFF map.
Definition: OMETIFFReader.cpp:1457
dimension_size_type getOptimalTileHeight() const
Get the optimal sub-image height.
Definition: FormatReader.cpp:1161
void findUsedFiles(const ome::xml::meta::OMEXMLMetadata &meta, const boost::filesystem::path &currentId, const boost::filesystem::path &currentDir, const boost::optional< std::string > &currentUUID)
Get UUID to file associations and used files.
Definition: OMETIFFReader.cpp:1055
Buffer for all pixel types.
Definition: VariantPixelBuffer.h:75
void openBytesImpl(dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const
Obtain a sub-image of an image plane.
Definition: OMETIFFReader.cpp:1388
std::vector< boost::filesystem::path > usedFiles
Used files.
Definition: OMETIFFReader.h:100
void addTIFF(const boost::filesystem::path &tiff)
Add a TIFF file to the internal TIFF map.
Definition: OMETIFFReader.cpp:1403