public class ZipReader extends FormatReader
Modifier and Type | Field and Description |
---|---|
private String |
entryName |
private ArrayList<String> |
mappedFiles |
private ImageReader |
reader |
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
ZipReader() |
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
short[][] |
get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
byte[][] |
get8BitLookupTable()
Gets the 8-bit color lookup table associated with
the most recently opened image.
|
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
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.
|
void |
setGroupFiles(boolean groupFiles)
Specifies whether or not to force grouping in multi-file formats.
|
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, 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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries
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
private transient ImageReader reader
private String entryName
public byte[][] get8BitLookupTable() throws FormatException, IOException
IFormatReader
IFormatReader.isIndexed()
returns
false, then this may return null. Also, if IFormatReader.getPixelType()
returns
anything other than FormatTools.INT8
or FormatTools.UINT8
,
this method will return null.get8BitLookupTable
in interface IFormatReader
get8BitLookupTable
in class FormatReader
FormatException
IOException
public short[][] get16BitLookupTable() throws FormatException, IOException
IFormatReader
IFormatReader.isIndexed()
returns
false, then this may return null. Also, if IFormatReader.getPixelType()
returns
anything other than FormatTools.INT16
or FormatTools.UINT16
, this method will return null.get16BitLookupTable
in interface IFormatReader
get16BitLookupTable
in class FormatReader
FormatException
IOException
public void setGroupFiles(boolean groupFiles)
IFormatReader
setGroupFiles
in interface IFormatReader
setGroupFiles
in class FormatReader
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class FormatReader
no
- 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 void close(boolean fileOnly) throws IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
IOException
protected void initFile(String id) throws FormatException, IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.IOException
- if an I/O error occurs processing the fileCopyright © 2016 Open Microscopy Environment