public abstract class BaseTiffReader extends MinimalTiffReader
Modifier and Type | Field and Description |
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static java.lang.String[] |
DATE_FORMATS |
protected static org.slf4j.Logger |
LOGGER
Logger for this class.
|
canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit
core
coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
BaseTiffReader(java.lang.String name,
java.lang.String suffix)
Constructs a new BaseTiffReader.
|
BaseTiffReader(java.lang.String name,
java.lang.String[] suffixes)
Constructs a new BaseTiffReader.
|
Modifier and Type | Method and Description |
---|---|
static java.lang.String |
getExifTagName(int tag) |
protected java.lang.String |
getImageCreationDate()
Retrieves the image creation date.
|
private java.lang.String |
getResolutionUnitFromComment(IFD ifd)
Extracts the resolution unit symbol from the comment field
|
protected void |
initFile(java.lang.String id)
Initializes the given file (parsing header information, etc.).
|
protected void |
initMetadata()
Populates the metadata hashtable and metadata store.
|
protected void |
initMetadataStore()
Populates the metadata store using the data parsed in
initStandardMetadata() along with some further parsing done in
the method itself. |
protected void |
initStandardMetadata()
Parses standard metadata.
|
protected void |
put(java.lang.String key,
boolean value) |
protected void |
put(java.lang.String key,
byte value) |
protected void |
put(java.lang.String key,
char value) |
protected void |
put(java.lang.String key,
double value) |
protected void |
put(java.lang.String key,
float value) |
protected void |
put(java.lang.String key,
IFD ifd,
int tag) |
protected void |
put(java.lang.String key,
int value) |
protected void |
put(java.lang.String key,
long value) |
protected void |
put(java.lang.String key,
java.lang.Object value) |
protected void |
put(java.lang.String key,
short value) |
protected void |
putInt(java.lang.String key,
IFD ifd,
int tag) |
protected void |
putString(java.lang.String key,
IFD ifd,
int tag) |
close, get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, isThisType, openBytes, openThumbBytes, reopenFile, setResolutionLevel
coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions
protected static final org.slf4j.Logger LOGGER
public static final java.lang.String[] DATE_FORMATS
public BaseTiffReader(java.lang.String name, java.lang.String suffix)
public BaseTiffReader(java.lang.String name, java.lang.String[] suffixes)
protected void initMetadata() throws FormatException, java.io.IOException
FormatException
java.io.IOException
protected void initStandardMetadata() throws FormatException, java.io.IOException
FormatException
java.io.IOException
protected void initMetadataStore() throws FormatException
initStandardMetadata()
along with some further parsing done in
the method itself.
All calls to the active MetadataStore
should be made in this
method and only in this method. This is especially important for
sub-classes that override the getters for pixel set array size, etc.FormatException
private java.lang.String getResolutionUnitFromComment(IFD ifd)
ifd
- The IFD
null
if the information is not
availableprotected java.lang.String getImageCreationDate()
protected void put(java.lang.String key, java.lang.Object value)
protected void put(java.lang.String key, int value)
protected void put(java.lang.String key, boolean value)
protected void put(java.lang.String key, byte value)
protected void put(java.lang.String key, char value)
protected void put(java.lang.String key, double value)
protected void put(java.lang.String key, float value)
protected void put(java.lang.String key, long value)
protected void put(java.lang.String key, short value)
protected void put(java.lang.String key, IFD ifd, int tag)
protected void putInt(java.lang.String key, IFD ifd, int tag)
protected void putString(java.lang.String key, IFD ifd, int tag)
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
SubResolutionFormatReader
initFile
in class MinimalTiffReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the filepublic static java.lang.String getExifTagName(int tag)
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