public class FujiReader extends FormatReader
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSIONCOMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixesCAN_GROUP, CANNOT_GROUP, MUST_GROUP| Constructor and Description |
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FujiReader()
Constructs a new Fuji reader.
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| Modifier and Type | Method and Description |
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void |
close(boolean fileOnly)
Closes the currently open file.
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int |
fileGroupOption(String id)
Returns an int indicating that we cannot, must, or might group the files
in a given dataset.
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String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
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protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
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boolean |
isSingleFile(String id)
Returns true if this is a single-file format.
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boolean |
isThisType(RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
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boolean |
isThisType(String name,
boolean open)
Checks if a file matches the type of this format reader.
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byte[] |
openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane
into a pre-allocated byte array.
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addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeriescheckSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixesclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetFormat, getNativeDataType, getSuffixespublic boolean isThisType(String name, boolean open)
FormatReaderFormatReader.isThisType(RandomAccessInputStream).isThisType in interface IFormatReaderisThisType in class FormatReaderopen - If true, and the file extension is insufficient to determine
the file type, the (existing) file is opened for further analysis.public boolean isThisType(RandomAccessInputStream stream) throws IOException
IFormatReaderisThisType in interface IFormatReaderisThisType in class FormatReaderIOExceptionpublic boolean isSingleFile(String id) throws FormatException, IOException
IFormatReaderisSingleFile in interface IFormatReaderisSingleFile in class FormatReaderFormatExceptionIOExceptionpublic byte[] openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
throws FormatException,
IOException
IFormatReaderopenBytes in interface IFormatReaderopenBytes in class FormatReaderno - the image index within the file.buf - a pre-allocated buffer.x - X coordinate of the upper-left corner of the sub-imagey - Y coordinate of the upper-left corner of the sub-imagew - width of the sub-imageh - height of the sub-imagebuf for convenience.FormatException - if there was a problem parsing the metadata of the
file.IOException - if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)public String[] getSeriesUsedFiles(boolean noPixels)
IFormatReadergetSeriesUsedFiles in interface IFormatReadergetSeriesUsedFiles in class FormatReaderpublic int fileGroupOption(String id) throws FormatException, IOException
IFormatReaderfileGroupOption in interface IFormatReaderfileGroupOption in class FormatReaderFormatExceptionIOExceptionpublic void close(boolean fileOnly)
throws IOException
IFormatReaderCloseable.close().close in interface IFormatReaderclose in class FormatReaderIOExceptionprotected void initFile(String id) throws FormatException, IOException
FormatReaderinitFile in class FormatReaderFormatException - if a parsing error occurs processing the file.IOException - if an I/O error occurs processing the fileCopyright © 2014 Open Microscopy Environment