public class OBFReader extends FormatReader
Modifier and Type | Class and Description |
---|---|
private class |
OBFReader.Frame |
private class |
OBFReader.Stack |
Modifier and Type | Field and Description |
---|---|
private OBFReader.Frame |
currentInflatedFrame |
private static String |
FILE_MAGIC_STRING |
private Inflater |
inflater |
private static boolean |
LITTLE_ENDIAN |
private static short |
MAGIC_NUMBER |
private static int |
MAXIMAL_NUMBER_OF_DIMENSIONS |
private static String |
STACK_MAGIC_STRING |
private List<OBFReader.Stack> |
stacks |
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 |
---|
OBFReader() |
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
private int |
getBitsPerPixel(int type) |
private ArrayList<Element> |
getChildNodes(Element root) |
private boolean |
getCompression(int compression) |
private int |
getFileVersion(loci.common.RandomAccessInputStream stream) |
private long |
getLength(long length) |
private int |
getPixelType(int type) |
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
private long |
initStack(long current,
int fileVersion) |
boolean |
isThisType(loci.common.RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
byte[] |
openBytes(int no,
byte[] buffer,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane
into a pre-allocated byte array.
|
private String |
readString() |
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, get16BitLookupTable, get8BitLookupTable, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, 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 static final boolean LITTLE_ENDIAN
private static final String FILE_MAGIC_STRING
private static final String STACK_MAGIC_STRING
private static final short MAGIC_NUMBER
private static final int MAXIMAL_NUMBER_OF_DIMENSIONS
private List<OBFReader.Stack> stacks
private OBFReader.Frame currentInflatedFrame
private transient Inflater inflater
private int getFileVersion(loci.common.RandomAccessInputStream stream) throws IOException
IOException
public boolean isThisType(loci.common.RandomAccessInputStream stream) throws IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
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 fileprivate long initStack(long current, int fileVersion) throws FormatException, IOException
FormatException
IOException
private int getPixelType(int type) throws FormatException
FormatException
private int getBitsPerPixel(int type) throws FormatException
FormatException
private long getLength(long length) throws FormatException
FormatException
private boolean getCompression(int compression) throws FormatException
FormatException
private String readString() throws IOException
IOException
public byte[] openBytes(int no, byte[] buffer, 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.buffer
- 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.public void close(boolean fileOnly) throws IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
IOException
Copyright © 2017 Open Microscopy Environment