public class NativeND2Reader extends FormatReader
Modifier and Type | Class and Description |
---|---|
(package private) static class |
NativeND2Reader.ChunkMapEntry |
Modifier and Type | Field and Description |
---|---|
private ND2Handler |
backupHandler |
private static int |
BUFFER_SIZE |
private Map<String,Integer> |
channelColors |
private Codec |
codec
Codec to use when decompressing pixel data.
|
private int[] |
colors |
private ArrayList<Double> |
exposureTime |
private int |
fieldIndex |
private boolean |
isJPEG
Whether or not the pixel data is compressed using JPEG 2000.
|
private boolean |
isLossless
Whether or not the pixel data is losslessly compressed.
|
private int |
lastChannel |
static long |
ND2_MAGIC_BYTES_1 |
static long |
ND2_MAGIC_BYTES_2 |
private int |
nXFields |
private long[][] |
offsets
Array of image offsets.
|
private long |
pfsOffset |
private long |
pfsStateOffset |
private int |
positionCount |
private ArrayList<ome.units.quantity.Length> |
posX |
private ArrayList<ome.units.quantity.Length> |
posY |
private ArrayList<ome.units.quantity.Length> |
posZ |
private Double |
refractiveIndex |
private boolean |
split |
private ArrayList<String> |
textChannelNames |
private boolean |
textData |
private ArrayList<Double> |
textEmissionWavelengths |
private double |
trueSizeX |
private double |
trueSizeY |
private Double |
trueSizeZ |
private ArrayList<Double> |
tsT |
static boolean |
USE_CHUNKMAP_DEFAULT |
static String |
USE_CHUNKMAP_KEY |
private Boolean |
useZ |
private long |
xOffset |
private long |
yOffset |
private long |
zOffset |
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 |
---|
NativeND2Reader()
Constructs a new ND2 reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
private void |
copyPixels(int x,
int y,
int w,
int h,
int bpp,
int scanlinePad,
byte[] pix,
byte[] buf,
boolean split) |
private Codec |
createCodec(boolean isJPEG) |
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.
|
private int |
getScanlinePad() |
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
boolean |
isThisType(loci.common.RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
private void |
iterateIn(loci.common.RandomAccessInputStream in,
Long stop)
Function for iterating through ND2 metaAttributes
|
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.
|
private void |
parseText(String textString,
int offsetCount,
boolean useDimensions) |
private void |
populateMetadataStore(ND2Handler handler) |
static String |
sanitizeControl(String s)
Remove control and invalid characters from the given string.
|
boolean |
useChunkMap() |
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, 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
public static final long ND2_MAGIC_BYTES_1
public static final long ND2_MAGIC_BYTES_2
private static final int BUFFER_SIZE
public static final String USE_CHUNKMAP_KEY
public static final boolean USE_CHUNKMAP_DEFAULT
private long[][] offsets
private boolean isJPEG
private Codec codec
private boolean isLossless
private int positionCount
private int fieldIndex
private long xOffset
private long yOffset
private long zOffset
private long pfsOffset
private long pfsStateOffset
private ArrayList<ome.units.quantity.Length> posX
private ArrayList<ome.units.quantity.Length> posY
private ArrayList<ome.units.quantity.Length> posZ
private boolean split
private int lastChannel
private int[] colors
private Boolean useZ
private int nXFields
private ND2Handler backupHandler
private double trueSizeX
private double trueSizeY
private Double trueSizeZ
private boolean textData
private Double refractiveIndex
public boolean useChunkMap()
public boolean isThisType(loci.common.RandomAccessInputStream stream) throws IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class FormatReader
IOException
public byte[][] get8BitLookupTable()
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
public short[][] get16BitLookupTable()
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
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 fileprivate void iterateIn(loci.common.RandomAccessInputStream in, Long stop)
in
- stream of bytes from filestop
- position where to stopprivate void populateMetadataStore(ND2Handler handler) throws FormatException
FormatException
private Codec createCodec(boolean isJPEG)
private void copyPixels(int x, int y, int w, int h, int bpp, int scanlinePad, byte[] pix, byte[] buf, boolean split) throws IOException
IOException
public static String sanitizeControl(String s)
private int getScanlinePad()
private void parseText(String textString, int offsetCount, boolean useDimensions)
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