bioformats  5.1.6
OMETIFFReader.h
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3  * OME-BIOFORMATS C++ library for image IO.
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37 
38 #ifndef OME_BIOFORMATS_IN_OMETIFFREADER_H
39 #define OME_BIOFORMATS_IN_OMETIFFREADER_H
40 
41 #include <ome/bioformats/in/MinimalTIFFReader.h>
42 #include <ome/bioformats/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 bioformats
60  {
61  namespace in
62  {
63 
68  {
70  using ::ome::bioformats::FormatReader::getOptimalTileWidth;
71  using ::ome::bioformats::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::bioformats::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
130  VariantPixelBuffer& buf) const;
131 
132  // Documented in superclass.
133  void
135  VariantPixelBuffer& buf,
139  dimension_size_type h) const;
140 
148  const ome::compat::shared_ptr<const tiff::IFD>
150 
156  void
157  addTIFF(const boost::filesystem::path& tiff);
158 
170  const ome::compat::shared_ptr<const ome::bioformats::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.
202 
203  // Documented in superclass.
206 
207  // Documented in superclass.
208  void
209  initFile(const boost::filesystem::path& id);
210 
211  private:
222  void
224  const boost::filesystem::path& currentId,
225  const boost::filesystem::path& currentDir,
226  const boost::optional<std::string>& currentUUID);
227 
237  void
239  std::vector<boost::optional<ome::xml::model::primitives::Timestamp> >& timestamps);
240 
248  void
250 
261 
274  void
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
298  boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tdIFD,
303 
314  void
317 
329  void
331 
332  public:
343  ome::compat::shared_ptr< ome::xml::meta::MetadataStore>
345 
355  ome::compat::shared_ptr< ome::xml::meta::MetadataStore>
357  };
358 
359 
360  }
361  }
362 }
363 
364 #endif // OME_BIOFORMATS_IN_OMETIFFREADER_H
365 
366 /*
367  * Local Variables:
368  * mode:C++
369  * End:
370  */
Interface for all biological file format readers (default behaviour).
Definition: FormatReader.h:107
bool hasSPW
Has screen-plate-well metadata.
Definition: OMETIFFReader.h:103
logging::sources::severity_logger_mt< logging::trivial::severity_level > Logger
Message logger.
Definition: log.h:98
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:1044
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:362
void addTIFF(const boost::filesystem::path &tiff)
Add a TIFF file to the internal TIFF map.
Definition: OMETIFFReader.cpp:1302
void fixOMEROMetadata(ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)
Fix invalid OMERO OME-TIFF metadata.
Definition: OMETIFFReader.cpp:1192
ome::common::Logger logger
Message logger.
Definition: OMETIFFReader.h:75
ome::compat::shared_ptr< ome::xml::meta::MetadataStore > getMetadataStoreForDisplay()
Get a MetadataStore suitable for display.
Definition: OMETIFFReader.cpp:1355
invalid_file_map invalidFiles
Invalid filename to valid filename mapping.
Definition: OMETIFFReader.h:90
const std::vector< boost::filesystem::path > getSeriesUsedFiles(bool noPixels) const
Get the files used by the active series.
Definition: OMETIFFReader.cpp:336
bool isFilenameThisTypeImpl(const boost::filesystem::path &name) const
isThisType file implementation for readers.
Definition: OMETIFFReader.cpp:263
TIFF reader with support for OME-XML metadata.
Definition: OMETIFFReader.h:67
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:420
void fixDimensions(ome::xml::meta::BaseMetadata::index_type series)
Attempt to correct logically inconsistent dimensions.
Definition: OMETIFFReader.cpp:1227
std::map< boost::filesystem::path, boost::filesystem::path > invalid_file_map
Map filename to another file.
Definition: OMETIFFReader.h:81
uuid_file_map files
UUID to filename mapping.
Definition: OMETIFFReader.h:87
const ome::compat::shared_ptr< const ome::bioformats::tiff::TIFF > getTIFF(const boost::filesystem::path &tiff) const
Get a an open TIFF file from the internal TIFF map.
Definition: OMETIFFReader.cpp:1308
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:1287
tiff_map tiffs
Open TIFF files.
Definition: OMETIFFReader.h:94
void close(bool fileOnly=false)
Close the currently open file.
Definition: OMETIFFReader.cpp:196
bool isSingleFile(const boost::filesystem::path &id) const
Is this a single-file format?
Definition: OMETIFFReader.cpp:214
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:966
virtual ~OMETIFFReader()
Destructor.
Definition: OMETIFFReader.cpp:184
void closeTIFF(const boost::filesystem::path &tiff)
Close an open TIFF file from the internal TIFF map.
Definition: OMETIFFReader.cpp:1325
Open Microscopy Environment C++ implementation.
Definition: CoreMetadata.cpp:40
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) const
Check if the given file is a valid instance of this file format.
Definition: OMETIFFReader.cpp:253
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:1074
std::vector< boost::filesystem::path > usedFiles
Used files.
Definition: OMETIFFReader.h:100
void getLookupTable(dimension_size_type plane, VariantPixelBuffer &buf) const
Get the color lookup table associated with an image plane.
Definition: OMETIFFReader.cpp:1265
A metadata store implementation for constructing and manipulating OME-XML DOMs for the current versio...
Definition: OMEXMLMetadata.h:67
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.
void cleanMetadata(ome::xml::meta::OMEXMLMetadata &meta)
Clean up OME-XML metadata.
Definition: OMETIFFReader.cpp:1063
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:1126
ome::compat::shared_ptr< ome::xml::meta::MetadataStore > getMetadataStoreForConversion()
Get a MetadataStore suitable for writing.
Definition: OMETIFFReader.cpp:1336
dimension_size_type getOptimalTileHeight() const
Get the optimal sub-image height.
Definition: FormatReader.cpp:1172
const std::vector< std::string > & getDomains() const
Get the domains represented by the current file.
Definition: OMETIFFReader.cpp:329
boost::optional< boost::filesystem::path > currentId
The identifier (path) of the currently open file.
Definition: FormatReader.h:118
FileGroupOption
File grouping options.
Definition: FormatReader.h:77
std::map< boost::filesystem::path, ome::compat::shared_ptr< ome::bioformats::tiff::TIFF > > tiff_map
Map filename to open TIFF handle.
Definition: OMETIFFReader.h:84
OMETIFFReader()
Constructor.
Definition: OMETIFFReader.cpp:167
dimension_size_type series
The number of the current series (non-flattened).
Definition: FormatReader.h:140
std::map< std::string, boost::filesystem::path > uuid_file_map
Map UUID to filename.
Definition: OMETIFFReader.h:78
dimension_size_type getOptimalTileWidth() const
Get the optimal sub-image width.
Definition: FormatReader.cpp:1159
Buffer for all pixel types.
Definition: VariantPixelBuffer.h:75
boost::filesystem::path metadataFile
Metadata file.
Definition: OMETIFFReader.h:97
const ome::compat::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:304
Boost.Log compatibility.
std::size_t dimension_size_type
Size type for image dimensions.
Definition: Types.h:59
std::size_t index_type
Index into an array.
Definition: BaseMetadata.h:64
A numeric type constrained to a subrange (or subranges) of its range limits.
Definition: ConstrainedNumeric.h:119
void initFile(const boost::filesystem::path &id)
Initialize the given file.
Definition: OMETIFFReader.cpp:399
Xerces-C modern C++ wrapper.
Definition: Base.h:53