public class LiFlimReader extends FormatReader
Modifier and Type | Class and Description |
---|---|
private class |
LiFlimReader.ROI |
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
BACKGROUND_TABLE |
private java.lang.String |
backgroundC |
private java.lang.String |
backgroundDatatype |
private java.lang.String |
backgroundF |
private java.lang.String |
backgroundP |
private java.lang.String |
backgroundT |
private java.lang.String |
backgroundX |
private java.lang.String |
backgroundY |
private java.lang.String |
backgroundZ |
static java.lang.String |
C_KEY |
private java.lang.String |
channels |
private java.lang.String |
compression |
static java.lang.String |
COMPRESSION_GZIP |
static java.lang.String |
COMPRESSION_KEY |
static java.lang.String |
COMPRESSION_NONE |
private java.lang.String |
DarkImage |
static java.lang.String |
DarkImage_KEY |
private long |
dataOffset
Offset to start of pixel data.
|
private java.lang.String |
datatype |
static java.lang.String |
DATATYPE_INT16 |
static java.lang.String |
DATATYPE_INT32 |
static java.lang.String |
DATATYPE_INT8 |
static java.lang.String |
DATATYPE_KEY |
static java.lang.String |
DATATYPE_REAL32 |
static java.lang.String |
DATATYPE_REAL64 |
static java.lang.String |
DATATYPE_UINT12 |
static java.lang.String |
DATATYPE_UINT16 |
static java.lang.String |
DATATYPE_UINT32 |
static java.lang.String |
DATATYPE_UINT8 |
private java.lang.Double |
exposureTime |
private ome.units.unit.Unit<ome.units.quantity.Time> |
exposureTimeUnit |
static java.lang.String |
F_KEY |
private java.lang.String |
frequencies |
private java.io.DataInputStream |
gz
Stream to use for reading gzip-compressed pixel data.
|
private boolean |
gzip
True if gzip compression was used to deflate the pixels.
|
private int |
gzPos
Image number indicating position in gzip stream.
|
private int |
gzSeries
Series number indicating position in gzip stream.
|
static java.lang.String |
INFO_TABLE |
private loci.common.IniList |
ini
Parsed configuration data.
|
static java.lang.String[] |
KNOWN_VERSIONS |
static java.lang.String |
LAYOUT_TABLE |
private int |
numRegions |
static java.lang.String |
P_KEY |
private java.lang.String |
phases |
private java.util.Map<java.lang.Integer,LiFlimReader.ROI> |
rois |
private java.util.Map<java.lang.Integer,java.lang.String> |
stampValues |
static java.lang.String |
T_KEY |
static java.lang.String |
TIMESTAMP_KEY |
private java.lang.String |
timestamps |
private boolean |
TypeUINT12
if DataType is UINT12, data is compressed in 12 bits.
|
private java.io.DataInputStream |
UINT12stream |
private int |
UINT12streamPos |
private int |
UINT12streamSeries |
private java.lang.String |
version |
static java.lang.String |
VERSION_KEY |
static java.lang.String |
X_KEY |
private java.lang.String |
xLen |
static java.lang.String |
Y_KEY |
private java.lang.String |
yLen |
static java.lang.String |
Z_KEY |
private java.lang.String |
zLen |
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 |
---|
LiFlimReader()
Constructs a new LI-FLIM reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
private static byte[] |
convert12to16(byte[] image) |
private int |
getPixelTypeFromString(java.lang.String type) |
private void |
initCoreMetadata() |
protected void |
initFile(java.lang.String id)
Initializes the given file (parsing header information, etc.).
|
private void |
initOMEMetadata() |
private void |
initOriginalMetadata() |
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 |
parseHeader() |
private void |
prepareGZipStream(int no) |
private void |
prepareUINT12Stream(int no)
Similar to Gzip, make a DataInputstream for UINT12 data
|
private void |
skip(java.io.InputStream is,
long num) |
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, getCurrentCore, 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, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, 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
public static final java.lang.String INFO_TABLE
public static final java.lang.String LAYOUT_TABLE
public static final java.lang.String BACKGROUND_TABLE
public static final java.lang.String VERSION_KEY
public static final java.lang.String COMPRESSION_KEY
public static final java.lang.String DATATYPE_KEY
public static final java.lang.String C_KEY
public static final java.lang.String X_KEY
public static final java.lang.String Y_KEY
public static final java.lang.String Z_KEY
public static final java.lang.String P_KEY
public static final java.lang.String F_KEY
public static final java.lang.String T_KEY
public static final java.lang.String DarkImage_KEY
public static final java.lang.String TIMESTAMP_KEY
public static final java.lang.String[] KNOWN_VERSIONS
public static final java.lang.String COMPRESSION_NONE
public static final java.lang.String COMPRESSION_GZIP
public static final java.lang.String DATATYPE_UINT8
public static final java.lang.String DATATYPE_INT8
public static final java.lang.String DATATYPE_UINT16
public static final java.lang.String DATATYPE_INT16
public static final java.lang.String DATATYPE_UINT32
public static final java.lang.String DATATYPE_INT32
public static final java.lang.String DATATYPE_REAL32
public static final java.lang.String DATATYPE_REAL64
public static final java.lang.String DATATYPE_UINT12
private long dataOffset
private loci.common.IniList ini
private java.lang.String version
private java.lang.String compression
private java.lang.String datatype
private java.lang.String channels
private java.lang.String xLen
private java.lang.String yLen
private java.lang.String zLen
private java.lang.String phases
private java.lang.String frequencies
private java.lang.String timestamps
private java.lang.String DarkImage
private java.lang.String backgroundDatatype
private java.lang.String backgroundX
private java.lang.String backgroundY
private java.lang.String backgroundC
private java.lang.String backgroundZ
private java.lang.String backgroundT
private java.lang.String backgroundP
private java.lang.String backgroundF
private int numRegions
private java.util.Map<java.lang.Integer,LiFlimReader.ROI> rois
private java.util.Map<java.lang.Integer,java.lang.String> stampValues
private java.lang.Double exposureTime
private ome.units.unit.Unit<ome.units.quantity.Time> exposureTimeUnit
private boolean gzip
private java.io.DataInputStream gz
private int gzPos
private int gzSeries
private boolean TypeUINT12
private java.io.DataInputStream UINT12stream
private int UINT12streamPos
private int UINT12streamSeries
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, java.io.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.java.io.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the fileprivate void parseHeader() throws java.io.IOException
java.io.IOException
private void initOriginalMetadata()
private void initCoreMetadata() throws FormatException
FormatException
private void initOMEMetadata()
private int getPixelTypeFromString(java.lang.String type) throws FormatException
FormatException
private void prepareGZipStream(int no) throws java.io.IOException
java.io.IOException
private void prepareUINT12Stream(int no) throws java.io.IOException
java.io.IOException
private static byte[] convert12to16(byte[] image)
private void skip(java.io.InputStream is, long num) throws java.io.IOException
java.io.IOException
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