TIFF reader with support for ImageJ extensions. More...
#include <ome/bioformats/in/TIFFReader.h>
Inheritance diagram for ome::bioformats::in::TIFFReader: Collaboration diagram for ome::bioformats::in::TIFFReader:Public Member Functions | |
| TIFFReader () | |
| Constructor. | |
| virtual | ~TIFFReader () |
| Destructor. | |
| void | close (bool fileOnly=false) |
| Close the currently open file. More... | |
| Public Member Functions inherited from ome::bioformats::in::MinimalTIFFReader | |
| MinimalTIFFReader () | |
| Constructor. | |
| MinimalTIFFReader (const ome::bioformats::detail::ReaderProperties &readerProperties) | |
| Constructor with reader properties (for derived readers). | |
| virtual | ~MinimalTIFFReader () |
| Destructor. | |
| void | getLookupTable (dimension_size_type plane, VariantPixelBuffer &buf) const |
| Get the color lookup table associated with an image plane. More... | |
| ome::compat::shared_ptr< ome::bioformats::tiff::TIFF > | getTIFF () |
| Get open TIFF file. More... | |
| const ome::compat::shared_ptr< ome::bioformats::tiff::TIFF > | getTIFF () const |
| Get open TIFF file. More... | |
| Public Member Functions inherited from ome::bioformats::detail::FormatReader | |
| virtual | ~FormatReader () |
| Destructor. | |
| const std::set< MetadataOptions::MetadataLevel > & | getSupportedMetadataLevels () |
| Get the supported metadata levels. More... | |
| void | setMetadataOptions (const MetadataOptions &options) |
| Set metadata options. More... | |
| const MetadataOptions & | getMetadataOptions () const |
| Get metadata options. More... | |
| MetadataOptions & | getMetadataOptions () |
| Get metadata options. More... | |
| const MetadataMap & | getGlobalMetadata () const |
| Get global metadata map. More... | |
| const MetadataMap::value_type & | getMetadataValue (const std::string &field) const |
| Get a global metadata value. More... | |
| const MetadataMap & | getSeriesMetadata () const |
| Get series metadata map. More... | |
| const MetadataMap::value_type & | getSeriesMetadataValue (const MetadataMap::key_type &field) const |
| Get a series metadata value. More... | |
| bool | isThisType (const boost::filesystem::path &name, bool open=true) const |
| Check if the given file is a valid instance of this file format. More... | |
| bool | isThisType (const uint8_t *begin, std::size_t length) const |
| Check if the given buffer is a valid header for this file format. More... | |
| bool | isThisType (const uint8_t *begin, const uint8_t *end) const |
| Check if the given buffer is a valid header for this file format. More... | |
| bool | isThisType (std::istream &stream) const |
| Check if the given input stream is a valid stream for this file format. More... | |
| dimension_size_type | getImageCount () const |
| Determine the number of image planes in the current series. More... | |
| bool | isRGB (dimension_size_type channel) const |
| Check if the image planes for a channel have more than one sub-channel per openBytes() call. More... | |
| dimension_size_type | getSizeX () const |
| Get the size of the X dimension. More... | |
| dimension_size_type | getSizeY () const |
| Get the size of the Y dimension. More... | |
| dimension_size_type | getSizeZ () const |
| Get the size of the Z dimension. More... | |
| dimension_size_type | getSizeT () const |
| Get the size of the T dimension. More... | |
| dimension_size_type | getSizeC () const |
| Get the size of the C dimension. More... | |
| ome::xml::model::enums::PixelType | getPixelType () const |
| Get the pixel type. More... | |
| pixel_size_type | getBitsPerPixel () const |
| Get the number of valid bits per pixel. More... | |
| dimension_size_type | getEffectiveSizeC () const |
| Get the effective size of the C dimension. More... | |
| dimension_size_type | getRGBChannelCount (dimension_size_type channel) const |
| Get the number of channels returned for a call to openBytes(). More... | |
| bool | isIndexed () const |
| Get whether the image planes are indexed color. More... | |
| bool | isFalseColor () const |
| Get whether the image planes are false color. More... | |
| Modulo & | getModuloZ () |
| Get the Modulo subdivision of the Z dimension. More... | |
| const Modulo & | getModuloZ () const |
| Get the Modulo subdivision of the Z dimension. More... | |
| Modulo & | getModuloT () |
| Get the Modulo subdivision of the T dimension. More... | |
| const Modulo & | getModuloT () const |
| Get the Modulo subdivision of the T dimension. More... | |
| Modulo & | getModuloC () |
| Get the Modulo subdivision of the C dimension. More... | |
| const Modulo & | getModuloC () const |
| Get the Modulo subdivision of the C dimension. More... | |
| dimension_size_type | getThumbSizeX () const |
| Get the thumbnail size of the X dimension. More... | |
| dimension_size_type | getThumbSizeY () const |
| Get the thumbnail size of the Y dimension. More... | |
| bool | isLittleEndian () const |
| Get whether the data is in little-endian format. More... | |
| const std::string & | getDimensionOrder () const |
| Get the dimension order. More... | |
| bool | isOrderCertain () const |
| Get whether the dimension order and sizes are known, or merely guesses. More... | |
| bool | isThumbnailSeries () const |
| Get whether the current series is a lower resolution copy of a different series. More... | |
| bool | isInterleaved () const |
| Get whether or not the channels are interleaved. More... | |
| bool | isInterleaved (dimension_size_type subC) const |
| Get whether or not the given channel is interleaved. More... | |
| void | openBytes (dimension_size_type plane, VariantPixelBuffer &buf) const |
| Obtain an image plane. More... | |
| void | openBytes (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. More... | |
| void | openThumbBytes (dimension_size_type plane, VariantPixelBuffer &buf) const |
| Obtain a thumbnail of an image plane. More... | |
| dimension_size_type | getSeriesCount () const |
| Get the number of image series in this file. More... | |
| void | setSeries (dimension_size_type series) const |
| Set the active series. More... | |
| dimension_size_type | getSeries () const |
| Get the active series. More... | |
| void | setPlane (dimension_size_type plane) const |
| Set the active plane. More... | |
| dimension_size_type | getPlane () const |
| Get the active plane. More... | |
| void | setGroupFiles (bool group) |
| Set file grouping. More... | |
| bool | isGroupFiles () const |
| Get file grouping. More... | |
| FileGroupOption | fileGroupOption (const std::string &id) |
| Returns an enum indicating that we cannot, must, or might group the files in this dataset. More... | |
| bool | isMetadataComplete () const |
| Get status of metadata parsing. More... | |
| void | setNormalized (bool normalize) |
| Set float normalization. More... | |
| bool | isNormalized () const |
| Get float normalization. More... | |
| void | setOriginalMetadataPopulated (bool populate) |
| Specifies whether or not to save proprietary metadata in the MetadataStore. | |
| bool | isOriginalMetadataPopulated () const |
| Get proprietary metadata storage. More... | |
| const std::vector< boost::filesystem::path > | getUsedFiles (bool noPixels=false) const |
| Get the files used by this dataset. More... | |
| const std::vector< boost::filesystem::path > | getSeriesUsedFiles (bool noPixels=false) const |
| Get the files used by the active series. More... | |
| std::vector< FileInfo > | getAdvancedUsedFiles (bool noPixels=false) const |
| Get the files used by this dataset. More... | |
| std::vector< FileInfo > | getAdvancedSeriesUsedFiles (bool noPixels=false) const |
| Get the files used by the active series. More... | |
| const boost::optional< boost::filesystem::path > & | getCurrentFile () const |
| Get the currently open file. More... | |
| 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. More... | |
| dimension_size_type | getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t, dimension_size_type moduloZ, dimension_size_type moduloC, dimension_size_type moduloT) const |
Get the linear index of a Z, C, T, ModuloZ, ModuloC and ModuloT coordinate. More... | |
| ome::compat::array< dimension_size_type, 3 > | getZCTCoords (dimension_size_type index) const |
Get the Z, C and T coordinate of a linear index. More... | |
| ome::compat::array< dimension_size_type, 6 > | getZCTModuloCoords (dimension_size_type index) const |
Get the Z, C, T, ModuloZ, ModuloC and ModuloT coordinate of a linear index. More... | |
| const std::vector< ome::compat::shared_ptr< ::ome::bioformats::CoreMetadata > > & | getCoreMetadataList () const |
| Get the core metadata. More... | |
| void | setMetadataFiltered (bool filter) |
| Set metadata filtering. More... | |
| bool | isMetadataFiltered () const |
| Get metadata filtering. More... | |
| void | setMetadataStore (ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > &store) |
| Set the default metadata store for this reader. More... | |
| const ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > & | getMetadataStore () const |
| Get the current metadata store for this reader. More... | |
| ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > & | getMetadataStore () |
| Get the current metadata store for this reader. More... | |
| std::vector< ome::compat::shared_ptr< ::ome::bioformats::FormatReader > > | getUnderlyingReaders () const |
| Get all underlying readers. More... | |
| bool | isSingleFile (const boost::filesystem::path &id) const |
| Is this a single-file format? More... | |
| uint32_t | getRequiredDirectories (const std::vector< std::string > &files) const |
| Get required parent directories. More... | |
| const std::string & | getDatasetStructureDescription () const |
| Get a short description of the dataset structure. More... | |
| const std::vector< std::string > & | getPossibleDomains (const std::string &id) const |
| Get the possible domains represented in which this format is used. More... | |
| bool | hasCompanionFiles () const |
| Does this format support multi-file datasets? More... | |
| const std::vector< std::string > & | getDomains () const |
| Get the domains represented by the current file. More... | |
| dimension_size_type | getOptimalTileWidth (dimension_size_type channel) const |
| Get the optimal sub-image width. More... | |
| dimension_size_type | getOptimalTileHeight (dimension_size_type channel) const |
| Get the optimal sub-image height. More... | |
| dimension_size_type | getOptimalTileWidth () const |
| Get the optimal sub-image width. More... | |
| dimension_size_type | getOptimalTileHeight () const |
| Get the optimal sub-image height. More... | |
| dimension_size_type | seriesToCoreIndex (dimension_size_type series) const |
| Get the first core index corresponding to the specified series. More... | |
| dimension_size_type | coreIndexToSeries (dimension_size_type index) const |
| Get the series corresponding to the specified core index. More... | |
| dimension_size_type | getCoreIndex () const |
| Get the CoreMetadata index of the current resolution/series. More... | |
| void | setCoreIndex (dimension_size_type index) const |
| Set the current resolution/series (ignoring sub-resolutions). More... | |
| dimension_size_type | getResolutionCount () const |
| Get the number of resolutions for the current series. More... | |
| void | setResolution (dimension_size_type resolution) const |
| Set the active resolution level. More... | |
| dimension_size_type | getResolution () const |
| Get the active resolution level. More... | |
| bool | hasFlattenedResolutions () const |
| Get resolution flattening. More... | |
| void | setFlattenedResolutions (bool flatten) |
| Set resolution flattening. More... | |
| void | setId (const boost::filesystem::path &id) |
| Set the current file name. More... | |
| const std::string & | getFormat () const |
| Get the name of this file format. More... | |
| const std::string & | getFormatDescription () const |
| Get the description of this file format. More... | |
| const std::vector< boost::filesystem::path > & | getSuffixes () const |
| Get the default file suffixes for this file format. More... | |
| const std::vector< boost::filesystem::path > & | getCompressionSuffixes () const |
| Get the default compression suffixes for this file format. More... | |
| Public Member Functions inherited from ome::bioformats::FormatHandler | |
| virtual | ~FormatHandler () |
| Destructor. | |
| Public Member Functions inherited from ome::bioformats::MetadataConfigurable | |
| virtual | ~MetadataConfigurable () |
| Destructor. | |
Protected Member Functions | |
| void | readIFDs () |
| Read metadata from IFDs. | |
| Protected Member Functions inherited from ome::bioformats::in::MinimalTIFFReader | |
| void | initFile (const boost::filesystem::path &id) |
| Initialize the given file. More... | |
| bool | isFilenameThisTypeImpl (const boost::filesystem::path &name) const |
| isThisType file implementation for readers. More... | |
| 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. More... | |
| 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. More... | |
| Protected Member Functions inherited from ome::bioformats::detail::FormatReader | |
| FormatReader (const ReaderProperties &) | |
| Constructor. | |
| virtual bool | isUsedFile (const boost::filesystem::path &file) |
| Check if a file is in the used files list. More... | |
| virtual void | readPlane (std::istream &source, VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h, dimension_size_type samples) |
| Read a raw plane. More... | |
| virtual void | readPlane (std::istream &source, VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h, dimension_size_type scanlinePad, dimension_size_type samples) |
| Read a raw plane with scanline padding. More... | |
| virtual ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > | makeFilterMetadata () |
| Create a configured FilterMetadata instance. More... | |
| const CoreMetadata & | getCoreMetadata (dimension_size_type index) const |
| Get CoreMetadata by core index. More... | |
| CoreMetadata & | getCoreMetadata (dimension_size_type index) |
| Get CoreMetadata by core index. More... | |
| virtual bool | isStreamThisTypeImpl (std::istream &stream) const |
| isThisType stream implementation for readers. More... | |
| ome::compat::array< dimension_size_type, 2 > | getThumbSize () const |
| Get the thumbnail size of the X and Y dimensions. More... | |
| Protected Member Functions inherited from ome::bioformats::FormatReader | |
| FormatReader () | |
| Constructor. | |
| Protected Member Functions inherited from ome::bioformats::FormatHandler | |
| FormatHandler () | |
| Constructor. | |
| Protected Member Functions inherited from ome::bioformats::MetadataConfigurable | |
| MetadataConfigurable () | |
| Constructor. | |
Protected Attributes | |
| boost::optional< tiff::ImageJMetadata > | ijmeta |
| ImageJ metadata. | |
| Protected Attributes inherited from ome::bioformats::in::MinimalTIFFReader | |
| ome::compat::shared_ptr< ome::bioformats::tiff::TIFF > | tiff |
| Underlying TIFF file. | |
| tiff::SeriesIFDRange | seriesIFDRange |
| Mapping between series index and start and end IFD as a half-open range. | |
| Protected Attributes inherited from ome::bioformats::detail::FormatReader | |
| const ReaderProperties & | readerProperties |
| Reader properties specific to the derived file format. | |
| boost::optional< boost::filesystem::path > | currentId |
| The identifier (path) of the currently open file. | |
| ome::compat::shared_ptr< std::istream > | in |
| Current input. | |
| ::ome::bioformats::MetadataMap | metadata |
| Mapping of metadata key/value pairs. | |
| dimension_size_type | coreIndex |
| The number of the current series (flattened). More... | |
| dimension_size_type | series |
| The number of the current series (non-flattened). More... | |
| dimension_size_type | plane |
| The number of the current plane in the current series. More... | |
| coremetadata_list_type | core |
| Core metadata values. | |
| dimension_size_type | resolution |
| The number of the current resolution. More... | |
| bool | flattenedResolutions |
| Whether or not resolutions are flattened. | |
| bool | suffixNecessary |
| Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format. | |
| bool | suffixSufficient |
| Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format. | |
| bool | companionFiles |
| Whether this format supports multi-file datasets. | |
| std::string | datasetDescription |
| Short description of the structure of the dataset. | |
| bool | normalizeData |
| Whether or not to normalize float data. | |
| bool | filterMetadata |
| Whether or not to filter out invalid metadata. | |
| bool | saveOriginalMetadata |
| Whether or not to save proprietary metadata in the MetadataStore. | |
| bool | indexedAsRGB |
| Whether or not MetadataStore sets C = 3 for indexed color images. | |
| bool | group |
| Whether or not to group multi-file formats. | |
| std::vector< std::string > | domains |
| List of domains in which this format is used. | |
| ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > | metadataStore |
| Current metadata store. More... | |
| MetadataOptions | metadataOptions |
| Metadata parsing options. | |
Additional Inherited Members | |
| Public Types inherited from ome::bioformats::FormatReader | |
| enum | FileGroupOption { MUST_GROUP, CAN_GROUP, CANNOT_GROUP } |
| File grouping options. More... | |
| Static Public Member Functions inherited from ome::bioformats::FormatHandler | |
| static bool | checkSuffix (const boost::filesystem::path &name, const boost::filesystem::path &suffix) |
| Perform suffix matching for the given filename. More... | |
| static bool | checkSuffix (const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes) |
| Perform suffix matching for the given filename. More... | |
| static bool | checkSuffix (const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes, const std::vector< boost::filesystem::path > &compression_suffixes) |
| Perform suffix matching for the given filename. More... | |
| static void | assertId (const boost::optional< boost::filesystem::path > &id, bool notNull=true) |
| Assert that the current file is valid. More... | |
| Protected Types inherited from ome::bioformats::detail::FormatReader | |
| typedef std::vector< ome::compat::shared_ptr< ::ome::bioformats::CoreMetadata > > | coremetadata_list_type |
| List type for storing CoreMetadata. | |
Detailed Description
TIFF reader with support for ImageJ extensions.
Member Function Documentation
|
virtual |
Close the currently open file.
- Parameters
-
fileOnly close the open file only if true, or else free all internal state iffalse.
Reimplemented from ome::bioformats::in::MinimalTIFFReader.
References ome::bioformats::in::MinimalTIFFReader::close(), and ijmeta.
Referenced by ~TIFFReader().
Here is the caller graph for this function:The documentation for this class was generated from the following files:
- ome/bioformats/in/TIFFReader.h
- ome/bioformats/in/TIFFReader.cpp
