ome::files::in::OMETIFFReader Member List

This is the complete list of members for ome::files::in::OMETIFFReader, including all inherited members.

addTIFF(const boost::filesystem::path &tiff)	ome::files::in::OMETIFFReader	protected
ome::assertId(const boost::optional< boost::filesystem::path > &id, bool notNull=true)	ome::files::FormatHandler	inlinestatic
ome::files::FormatHandler::assertId(const boost::optional< boost::filesystem::path > &id, bool notNull=true)	ome::files::FormatHandler	inlinestatic
cachedMetadata	ome::files::in::OMETIFFReader	mutableprotected
cachedMetadataFile	ome::files::in::OMETIFFReader	mutableprotected
cacheMetadata(const boost::filesystem::path &id) const	ome::files::in::OMETIFFReader	protected
CAN_GROUP enum value	ome::files::FormatReader
CANNOT_GROUP enum value	ome::files::FormatReader
ome::checkSuffix(const boost::filesystem::path &name, const boost::filesystem::path &suffix)	ome::files::FormatHandler	inlinestatic
ome::checkSuffix(const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes)	ome::files::FormatHandler	inlinestatic
ome::checkSuffix(const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes, const std::vector< boost::filesystem::path > &compression_suffixes)	ome::files::FormatHandler	inlinestatic
ome::files::FormatHandler::checkSuffix(const boost::filesystem::path &name, const boost::filesystem::path &suffix)	ome::files::FormatHandler	inlinestatic
ome::files::FormatHandler::checkSuffix(const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes)	ome::files::FormatHandler	inlinestatic
ome::files::FormatHandler::checkSuffix(const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes, const std::vector< boost::filesystem::path > &compression_suffixes)	ome::files::FormatHandler	inlinestatic
cleanMetadata(ome::xml::meta::OMEXMLMetadata &meta)	ome::files::in::OMETIFFReader	private
close(bool fileOnly=false)	ome::files::in::OMETIFFReader	virtual
closeTIFF(const boost::filesystem::path &tiff)	ome::files::in::OMETIFFReader	protected
companionFiles	ome::files::detail::FormatReader	protected
core	ome::files::detail::FormatReader	protected
coreIndex	ome::files::detail::FormatReader	mutableprotected
coreIndexToSeries(dimension_size_type index) const	ome::files::detail::FormatReader	virtual
coremetadata_list_type typedef	ome::files::detail::FormatReader	protected
currentId	ome::files::detail::FormatReader	protected
datasetDescription	ome::files::detail::FormatReader	protected
domains	ome::files::detail::FormatReader	protected
FileGroupOption enum name	ome::files::FormatReader
fileGroupOption(const std::string &id)	ome::files::in::OMETIFFReader	virtual
files	ome::files::in::OMETIFFReader	protected
filterMetadata	ome::files::detail::FormatReader	protected
findUsedFiles(const ome::xml::meta::OMEXMLMetadata &meta, const boost::filesystem::path &currentId, const boost::filesystem::path &currentDir, const boost::optional< std::string > &currentUUID)	ome::files::in::OMETIFFReader	private
fixDimensions(ome::xml::meta::BaseMetadata::index_type series)	ome::files::in::OMETIFFReader	private
fixOMEROMetadata(ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)	ome::files::in::OMETIFFReader	private
flattenedResolutions	ome::files::detail::FormatReader	protected
ome::FormatHandler()	ome::files::FormatHandler	inlineprotected
ome::files::FormatHandler::FormatHandler()	ome::files::FormatHandler	inlineprotected
FormatReader(const ReaderProperties &)	ome::files::detail::FormatReader	protected
ome::files::FormatReader::FormatReader()	ome::files::FormatReader	inlineprotected
getAcquisitionDates(const ome::xml::meta::OMEXMLMetadata &meta, std::vector< boost::optional< ome::xml::model::primitives::Timestamp >> &timestamps)	ome::files::in::OMETIFFReader	private
getAdvancedSeriesUsedFiles(bool noPixels=false) const	ome::files::detail::FormatReader	virtual
getAdvancedUsedFiles(bool noPixels=false) const	ome::files::detail::FormatReader	virtual
getBitsPerPixel() const	ome::files::detail::FormatReader	virtual
getCompressionSuffixes() const	ome::files::detail::FormatReader	virtual
getCoreIndex() const	ome::files::detail::FormatReader	virtual
getCoreMetadata(dimension_size_type index) const	ome::files::detail::FormatReader	inlineprotected
getCoreMetadata(dimension_size_type index)	ome::files::detail::FormatReader	inlineprotected
getCoreMetadataList() const	ome::files::detail::FormatReader	virtual
getCurrentFile() const	ome::files::detail::FormatReader	virtual
getDatasetStructureDescription() const	ome::files::detail::FormatReader	virtual
getDimensionOrder() const	ome::files::detail::FormatReader	virtual
getDomains() const	ome::files::in::OMETIFFReader	virtual
getEffectiveSizeC() const	ome::files::detail::FormatReader	virtual
getFormat() const	ome::files::detail::FormatReader	virtual
getFormatDescription() const	ome::files::detail::FormatReader	virtual
getGlobalMetadata() const	ome::files::detail::FormatReader	virtual
getImageCount() const	ome::files::detail::FormatReader	virtual
getIndex(dimension_size_type z, dimension_size_type c, dimension_size_type t) const	ome::files::detail::FormatReader	virtual
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	ome::files::detail::FormatReader	virtual
getLookupTable(dimension_size_type plane, VariantPixelBuffer &buf) const	ome::files::in::OMETIFFReader	protectedvirtual
getMetadataOptions() const	ome::files::detail::FormatReader	virtual
getMetadataOptions()	ome::files::detail::FormatReader	virtual
getMetadataStore() const	ome::files::detail::FormatReader	virtual
getMetadataStore()	ome::files::detail::FormatReader	virtual
getMetadataStoreForConversion()	ome::files::in::OMETIFFReader
getMetadataStoreForDisplay()	ome::files::in::OMETIFFReader
getMetadataValue(const std::string &field) const	ome::files::detail::FormatReader	virtual
getModuloC()	ome::files::detail::FormatReader	virtual
getModuloC() const	ome::files::detail::FormatReader	virtual
getModuloT()	ome::files::detail::FormatReader	virtual
getModuloT() const	ome::files::detail::FormatReader	virtual
getModuloZ()	ome::files::detail::FormatReader	virtual
getModuloZ() const	ome::files::detail::FormatReader	virtual
getOptimalTileHeight(dimension_size_type channel) const	ome::files::in::OMETIFFReader	virtual
ome::files::detail::FormatReader::getOptimalTileHeight() const	ome::files::detail::FormatReader	virtual
getOptimalTileWidth(dimension_size_type channel) const	ome::files::in::OMETIFFReader	virtual
ome::files::detail::FormatReader::getOptimalTileWidth() const	ome::files::detail::FormatReader	virtual
getPixelType() const	ome::files::detail::FormatReader	virtual
getPlane() const	ome::files::detail::FormatReader	virtual
getPossibleDomains(const std::string &id) const	ome::files::detail::FormatReader	virtual
getRequiredDirectories(const std::vector< std::string > &files) const	ome::files::detail::FormatReader	virtual
getResolution() const	ome::files::detail::FormatReader	virtual
getResolutionCount() const	ome::files::detail::FormatReader	virtual
getRGBChannelCount(dimension_size_type channel) const	ome::files::detail::FormatReader	virtual
getSeries() const	ome::files::detail::FormatReader	virtual
getSeriesCount() const	ome::files::detail::FormatReader	virtual
getSeriesMetadata() const	ome::files::detail::FormatReader	virtual
getSeriesMetadataValue(const MetadataMap::key_type &field) const	ome::files::detail::FormatReader	virtual
getSeriesUsedFiles(bool noPixels) const	ome::files::in::OMETIFFReader	virtual
getSizeC() const	ome::files::detail::FormatReader	virtual
getSizeT() const	ome::files::detail::FormatReader	virtual
getSizeX() const	ome::files::detail::FormatReader	virtual
getSizeY() const	ome::files::detail::FormatReader	virtual
getSizeZ() const	ome::files::detail::FormatReader	virtual
getSuffixes() const	ome::files::detail::FormatReader	virtual
getSupportedMetadataLevels()	ome::files::detail::FormatReader	virtual
getThumbSize() const	ome::files::detail::FormatReader	protected
getThumbSizeX() const	ome::files::detail::FormatReader	virtual
getThumbSizeY() const	ome::files::detail::FormatReader	virtual
getTIFF(const boost::filesystem::path &tiff) const	ome::files::in::OMETIFFReader	protected
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)	ome::files::in::OMETIFFReader	private
getUnderlyingReaders() const	ome::files::detail::FormatReader	virtual
getUsedFiles(bool noPixels=false) const	ome::files::detail::FormatReader	virtual
getZCTCoords(dimension_size_type index) const	ome::files::detail::FormatReader	virtual
getZCTModuloCoords(dimension_size_type index) const	ome::files::detail::FormatReader	virtual
group	ome::files::detail::FormatReader	protected
hasCompanionFiles() const	ome::files::detail::FormatReader	virtual
hasFlattenedResolutions() const	ome::files::detail::FormatReader	virtual
hasSPW	ome::files::in::OMETIFFReader	protected
ifdAtIndex(dimension_size_type plane) const	ome::files::in::OMETIFFReader	protected
in	ome::files::detail::FormatReader	protected
indexedAsRGB	ome::files::detail::FormatReader	protected
initFile(const boost::filesystem::path &id)	ome::files::in::OMETIFFReader	virtual
invalid_file_map typedef	ome::files::in::OMETIFFReader	protected
invalidFiles	ome::files::in::OMETIFFReader	protected
isFalseColor() const	ome::files::detail::FormatReader	virtual
isFilenameThisTypeImpl(const boost::filesystem::path &name) const	ome::files::in::OMETIFFReader	protectedvirtual
isGroupFiles() const	ome::files::detail::FormatReader	virtual
isIndexed() const	ome::files::detail::FormatReader	virtual
isInterleaved() const	ome::files::detail::FormatReader	virtual
isInterleaved(dimension_size_type subC) const	ome::files::detail::FormatReader	virtual
isLittleEndian() const	ome::files::detail::FormatReader	virtual
isMetadataComplete() const	ome::files::detail::FormatReader	virtual
isMetadataFiltered() const	ome::files::detail::FormatReader	virtual
isNormalized() const	ome::files::detail::FormatReader	virtual
isOrderCertain() const	ome::files::detail::FormatReader	virtual
isOriginalMetadataPopulated() const	ome::files::detail::FormatReader	virtual
isRGB(dimension_size_type channel) const	ome::files::detail::FormatReader	virtual
isSingleFile(const boost::filesystem::path &id) const	ome::files::in::OMETIFFReader	virtual
isStreamThisTypeImpl(std::istream &stream) const	ome::files::detail::FormatReader	protectedvirtual
isThisType(const boost::filesystem::path &name, bool open) const	ome::files::in::OMETIFFReader	virtual
ome::files::detail::FormatReader::isThisType(const uint8_t *begin, std::size_t length) const	ome::files::detail::FormatReader	virtual
ome::files::detail::FormatReader::isThisType(const uint8_t *begin, const uint8_t *end) const	ome::files::detail::FormatReader	virtual
ome::files::detail::FormatReader::isThisType(std::istream &stream) const	ome::files::detail::FormatReader	virtual
isThumbnailSeries() const	ome::files::detail::FormatReader	virtual
isUsedFile(const boost::filesystem::path &file)	ome::files::detail::FormatReader	protectedvirtual
logger	ome::files::in::OMETIFFReader	mutableprotected
makeFilterMetadata()	ome::files::detail::FormatReader	protectedvirtual
metadata	ome::files::detail::FormatReader	protected
MetadataConfigurable()	ome::files::MetadataConfigurable	protected
metadataFile	ome::files::in::OMETIFFReader	protected
metadataOptions	ome::files::detail::FormatReader	protected
metadataStore	ome::files::detail::FormatReader	protected
MUST_GROUP enum value	ome::files::FormatReader
normalizeData	ome::files::detail::FormatReader	protected
OMETIFFReader()	ome::files::in::OMETIFFReader
openBytes(dimension_size_type plane, VariantPixelBuffer &buf) const	ome::files::detail::FormatReader	virtual
openBytes(dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const	ome::files::detail::FormatReader	virtual
openBytesImpl(dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const	ome::files::in::OMETIFFReader	protectedvirtual
openThumbBytes(dimension_size_type plane, VariantPixelBuffer &buf) const	ome::files::detail::FormatReader	virtual
plane	ome::files::detail::FormatReader	mutableprotected
readerProperties	ome::files::detail::FormatReader	protected
readMetadata(const ome::files::tiff::TIFF &tiff)	ome::files::in::OMETIFFReader	protected
readMetadata(const boost::filesystem::path &id)	ome::files::in::OMETIFFReader	protected
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)	ome::files::detail::FormatReader	protectedvirtual
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)	ome::files::detail::FormatReader	protectedvirtual
resolution	ome::files::detail::FormatReader	mutableprotected
saveOriginalMetadata	ome::files::detail::FormatReader	protected
series	ome::files::detail::FormatReader	mutableprotected
seriesFileSamplesPerPixel(const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)	ome::files::in::OMETIFFReader	private
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)	ome::files::in::OMETIFFReader	private
seriesToCoreIndex(dimension_size_type series) const	ome::files::detail::FormatReader	virtual
setCoreIndex(dimension_size_type index) const	ome::files::detail::FormatReader	virtual
setFlattenedResolutions(bool flatten)	ome::files::detail::FormatReader	virtual
setGroupFiles(bool group)	ome::files::detail::FormatReader	virtual
setId(const boost::filesystem::path &id)	ome::files::detail::FormatReader	virtual
setMetadataFiltered(bool filter)	ome::files::detail::FormatReader	virtual
setMetadataOptions(const MetadataOptions &options)	ome::files::detail::FormatReader	virtual
setMetadataStore(std::shared_ptr<::ome::xml::meta::MetadataStore > &store)	ome::files::detail::FormatReader	virtual
setNormalized(bool normalize)	ome::files::detail::FormatReader	virtual
setOriginalMetadataPopulated(bool populate)	ome::files::detail::FormatReader	virtual
setPlane(dimension_size_type plane) const	ome::files::detail::FormatReader	virtual
setResolution(dimension_size_type resolution) const	ome::files::detail::FormatReader	virtual
setSeries(dimension_size_type series) const	ome::files::detail::FormatReader	virtual
suffixNecessary	ome::files::detail::FormatReader	protected
suffixSufficient	ome::files::detail::FormatReader	protected
tiff_map typedef	ome::files::in::OMETIFFReader	protected
tiffs	ome::files::in::OMETIFFReader	mutableprotected
usedFiles	ome::files::in::OMETIFFReader	protected
uuid_file_map typedef	ome::files::in::OMETIFFReader	protected
validTIFF(const boost::filesystem::path &tiff) const	ome::files::in::OMETIFFReader	protected
~FormatHandler()	ome::files::FormatHandler	inlinevirtual
~FormatReader()	ome::files::detail::FormatReader	virtual
~MetadataConfigurable()	ome::files::MetadataConfigurable	virtual
~OMETIFFReader()	ome::files::in::OMETIFFReader	virtual