Serialized Form
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Package io.scif
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Class io.scif.AbstractMetadata extends AbstractHasSource implements Serializable
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Class io.scif.DefaultMetadata extends AbstractMetadata implements Serializable
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Serialized Fields
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format
Format format
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Class io.scif.DefaultMetaTable extends HashMap<String,Object> implements Serializable
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Serialized Fields
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filtered
boolean filtered
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Class io.scif.DependencyException extends Exception implements Serializable
- serialVersionUID:
- -7836244849086491562L
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Serialized Fields
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failureClass
Class<? extends org.scijava.service.Service> failureClass
The class that was used in a failed instantiation.
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Class io.scif.FormatException extends Exception implements Serializable
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Class io.scif.MissingLibraryException extends FormatException implements Serializable
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Class io.scif.UnsupportedCompressionException extends FormatException implements Serializable
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Package io.scif.common
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Class io.scif.common.IniList extends ArrayList<IniTable> implements Serializable
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Class io.scif.common.IniTable extends HashMap<String,String> implements Serializable
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Package io.scif.config
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Class io.scif.config.SCIFIOConfig extends HashMap<String,Object> implements Serializable
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Serialized Fields
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bufferedReading
boolean bufferedReading
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compression
String compression
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computeMinMax
boolean computeMinMax
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failIfOverwriting
boolean failIfOverwriting
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filterMetadata
boolean filterMetadata
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fps
int fps
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group
boolean group
Whether or not to group multi-file formats. -
imgFactoryHeuristic
ImgFactoryHeuristic imgFactoryHeuristic
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imgModes
SCIFIOConfig.ImgMode[] imgModes
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level
MetadataLevel level
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logService
org.scijava.log.LogService logService
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model
ColorModel model
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openAll
boolean openAll
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openDataset
boolean openDataset
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options
CodecOptions options
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planeConverter
PlaneConverter planeConverter
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range
Range range
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region
ImageRegion region
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saveOriginalMetadata
boolean saveOriginalMetadata
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writeRGB
boolean writeRGB
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writeSequential
boolean writeSequential
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Package io.scif.enumeration
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Class io.scif.enumeration.EnumException extends RuntimeException implements Serializable
- serialVersionUID:
- -4969429871517178079L
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Package io.scif.filters
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Class io.scif.filters.AbstractMetadataWrapper extends AbstractMetadata implements Serializable
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Serialized Fields
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meta
Metadata meta
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Class io.scif.filters.ChannelFillerMetadata extends AbstractMetadataWrapper implements Serializable
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Serialized Fields
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initializeService
InitializeService initializeService
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lutLength
int lutLength
Number of components in the wrapped color table
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Class io.scif.filters.DimensionSwapperMetadata extends AbstractMetadataWrapper implements Serializable
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Serialized Fields
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outputOrder
List<net.imagej.axis.AxisType>[] outputOrder
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Class io.scif.filters.FileStitcherMetadata extends AbstractMetadataWrapper implements Serializable
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Serialized Fields
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imgMeta
ImageMetadata imgMeta
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Class io.scif.filters.PlaneSeparatorMetadata extends AbstractMetadataWrapper implements Serializable
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Serialized Fields
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splitTypes
Set<net.imagej.axis.AxisType> splitTypes
List of Axes to separate.
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Package io.scif.formats
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Class io.scif.formats.APNGFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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actl
APNGFormat.ACTLChunk actl
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iend
APNGFormat.IENDChunk iend
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ihdr
APNGFormat.IHDRChunk ihdr
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littleEndian
boolean littleEndian
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plte
APNGFormat.PLTEChunk plte
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separateDefault
boolean separateDefault
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signed
boolean signed
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Class io.scif.formats.AVIFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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bmpBitsPerPixel
short bmpBitsPerPixel
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bmpColorsUsed
int bmpColorsUsed
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bmpCompression
int bmpCompression
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bmpScanLineSize
int bmpScanLineSize
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bmpWidth
int bmpWidth
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bytesPerPlane
int bytesPerPlane
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lastDims
int[] lastDims
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lastPlane
ByteArrayPlane lastPlane
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lastPlaneIndex
long lastPlaneIndex
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lengths
List<Long> lengths
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lut
net.imglib2.display.ColorTable lut
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offsets
List<Long> offsets
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Class io.scif.formats.BMPFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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compression
int compression
Compression type -
global
long global
Offset to image data. -
invertY
boolean invertY
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palette
net.imglib2.display.ColorTable8 palette
The palette for indexed color images.
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Class io.scif.formats.DICOMFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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date
String date
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imagesPerFile
int imagesPerFile
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imageType
String imageType
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inverted
boolean inverted
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isDeflate
boolean isDeflate
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isJP2K
boolean isJP2K
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isJPEG
boolean isJPEG
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isRLE
boolean isRLE
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lut16
net.imglib2.display.ColorTable16 lut16
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lut8
net.imglib2.display.ColorTable8 lut8
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maxPixelValue
int maxPixelValue
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oddLocations
boolean oddLocations
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offsets
long[] offsets
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originalDate
String originalDate
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originalInstance
String originalInstance
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originalSeries
int originalSeries
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originalTime
String originalTime
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pixelSizeX
String pixelSizeX
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pixelSizeY
String pixelSizeY
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pixelSizeZ
Double pixelSizeZ
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rescaleIntercept
double rescaleIntercept
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rescaleSlope
double rescaleSlope
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time
String time
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Class io.scif.formats.EPSFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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binary
boolean binary
Flag indicating binary data. -
ifds
IFDList ifds
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isTiff
boolean isTiff
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start
int start
Starting line of pixel data.
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Class io.scif.formats.FITSFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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pixelOffset
long pixelOffset
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Class io.scif.formats.GIFFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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blockSize
int blockSize
Block size. -
cachedTable
net.imglib2.display.ColorTable8 cachedTable
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dispose
int dispose
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ih
int ih
Current image rectangle. -
interlace
boolean interlace
Interlace flag. -
iw
int iw
Current image rectangle. -
ix
int ix
Current image rectangle. -
iy
int iy
Current image rectangle. -
lastDispose
int lastDispose
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transIndex
int transIndex
Transparent color index. -
transparency
boolean transparency
Use transparent color.
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Class io.scif.formats.ICSFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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hasInstrumentData
boolean hasInstrumentData
True if instrument information was discovered. -
icsId
String icsId
ICS file name -
icsLocation
org.scijava.io.location.Location icsLocation
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idsId
String idsId
IDS file name -
idsLocation
org.scijava.io.location.Location idsLocation
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keyValPairs
Map<String,String> keyValPairs
ICS Metadata -
offset
long offset
Offset to pixel data -
storedRGB
boolean storedRGB
True if this planes were stored in RGB order. -
versionTwo
boolean versionTwo
Whether this file is ICS version 2, and thus does not have an IDS companion
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Class io.scif.formats.ImageIOFormat.Metadata extends AbstractMetadata implements Serializable
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Class io.scif.formats.JPEG2000Format.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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lastIndex
JPEG2000Format.Index lastIndex
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pixelsOffset
long pixelsOffset
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resolutionLevels
Integer resolutionLevels
The number of JPEG 2000 resolution levels the file has.
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Class io.scif.formats.JPEGFormat.Metadata extends ImageIOFormat.Metadata implements Serializable
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Class io.scif.formats.JPEGTileFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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decoder
JPEGTileDecoder decoder
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Class io.scif.formats.KontronFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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height
long height
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width
long width
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Class io.scif.formats.MicromanagerFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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positions
List<MicromanagerFormat.Position> positions
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Class io.scif.formats.MinimalTIFFFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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equalStrips
boolean equalStrips
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ifds
IFDList ifds
List of IFDs for the current TIFF. -
j2kCodecOptions
JPEG2000CodecOptions j2kCodecOptions
Codec options to use when decoding JPEG 2000 data. -
lastPlane
long lastPlane
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noSubresolutions
boolean noSubresolutions
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resolutionLevels
Integer resolutionLevels
Number of JPEG 2000 resolution levels. -
subResolutionIFDs
List<IFDList> subResolutionIFDs
List of sub-resolution IFDs for each IFD in the current TIFF with the same order asifds. -
thumbnailIFDs
IFDList thumbnailIFDs
List of thumbnail IFDs for the current TIFF. -
tiffParser
TiffParser tiffParser
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use64Bit
boolean use64Bit
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Class io.scif.formats.MNGFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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datasetInfo
io.scif.formats.MNGFormat.MNGDatasetInfo datasetInfo
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isJNG
boolean isJNG
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Class io.scif.formats.NRRDFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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dataFile
org.scijava.io.location.Location dataFile
Location of data file, if the current extension is 'nhdr'. -
encoding
String encoding
Data encoding. -
helper
Reader helper
Helper format for reading pixel data. -
initializeHelper
boolean initializeHelper
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lookForCompanion
boolean lookForCompanion
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offset
long offset
Offset to pixel data. -
pixelSizes
String[] pixelSizes
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Class io.scif.formats.PCXFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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bytesPerLine
int bytesPerLine
Number of bytes per scan line - may be different than image width. -
lut
net.imglib2.display.ColorTable8 lut
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nColorPlanes
int nColorPlanes
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offset
long offset
Offset to pixel data.
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Class io.scif.formats.PGMFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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offset
long offset
Offset to pixel data. -
rawBits
boolean rawBits
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Class io.scif.formats.ScancoISQFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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creationDate
LocalDate creationDate
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dataOffset
int dataOffset
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energy
int energy
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firstSlicePosition
int firstSlicePosition
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height
int height
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intensity
int intensity
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maxDataValue
int maxDataValue
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measurementIndex
int measurementIndex
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minDataValue
int minDataValue
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muScaling
int muScaling
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patientIndex
int patientIndex
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patientName
String patientName
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physicalDepth
int physicalDepth
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physicalHeight
int physicalHeight
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physicalWidth
int physicalWidth
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projections
int projections
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reconstructionAlgorithm
int reconstructionAlgorithm
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referenceLine
int referenceLine
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samples
int samples
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samplingTime
int samplingTime
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scanDistance
int scanDistance
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scannerId
int scannerId
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scannerType
int scannerType
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site
int site
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sliceBytes
int sliceBytes
Number of bytes in a single slice of the image -
slices
int slices
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sliceSpacing
int sliceSpacing
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sliceThickness
int sliceThickness
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voxelDepth
double voxelDepth
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voxelHeight
double voxelHeight
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voxelWidth
double voxelWidth
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width
int width
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Class io.scif.formats.StratecPQCTFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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deviceName
String deviceName
Name of device used in imaging -
height
short height
Height in pixels -
leftEdge
short leftEdge
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measurementDate
Date measurementDate
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measurementInfo
String measurementInfo
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objectSize
double objectSize
Size of the sample in mm -
patientAge
int patientAge
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patientBirthDate
Date patientBirthDate
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patientId
String patientId
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patientMeasurementNumber
short patientMeasurementNumber
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patientName
String patientName
Patient name (surname, forename) -
patientNumber
int patientNumber
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resolution
double resolution
Image resolution in mm. Same for X and Y axes -
sliceDistance
double sliceDistance
Distance between slices (mm) -
slices
short slices
Number of slicesNB in theory the format supports 3D files, but they are are exceedingly rare. However slice number is still often used in metadata. People take individual images of the same object, and mark down slice info as if they were in the same stack.
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sliceStart
double sliceStart
Position of the first slice (mm) -
topEdge
short topEdge
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width
short width
Width in pixels
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Class io.scif.formats.TestImgFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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axes
String[] axes
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falseColor
boolean falseColor
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images
int images
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indexed
boolean indexed
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interleavedDims
int interleavedDims
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lengths
long[] lengths
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little
boolean little
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lutLength
int lutLength
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luts
net.imglib2.display.ColorTable[][] luts
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metadataComplete
boolean metadataComplete
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orderCertain
boolean orderCertain
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pixelType
String pixelType
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planarDims
int planarDims
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scaleFactor
int scaleFactor
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scales
double[] scales
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thumbnail
boolean thumbnail
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thumbSizeX
int thumbSizeX
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thumbSizeY
int thumbSizeY
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units
String[] units
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valueToIndex
int[][] valueToIndex
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Class io.scif.formats.TIFFFormat.Metadata extends MinimalTIFFFormat.Metadata implements Serializable
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Serialized Fields
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calibrationUnit
String calibrationUnit
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colorTable
List<net.imglib2.display.ColorTable> colorTable
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companionFile
org.scijava.io.location.Location companionFile
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creationDate
String creationDate
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description
String description
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experimenterEmail
String experimenterEmail
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experimenterFirstName
String experimenterFirstName
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experimenterLastName
String experimenterLastName
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imageDescription
String imageDescription
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lut
byte[][] lut
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populateImageMetadata
boolean populateImageMetadata
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timeIncrement
Double timeIncrement
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xOrigin
Integer xOrigin
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yOrigin
Integer yOrigin
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Class io.scif.formats.TIFFJAIFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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numPages
int numPages
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r
org.scijava.util.ReflectedUniverse r
Reflection tool for JAI calls.
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Package io.scif.formats.qt
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Class io.scif.formats.qt.LegacyQTFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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image
Image image
Image containing current frame. -
qtJavaService
QTJavaService qtJavaService
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times
int[] times
Time offset for each frame.
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Class io.scif.formats.qt.NativeQTFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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altCodec
String altCodec
Some movies use two video codecs -- this is the second codec. -
altPlanes
int altPlanes
Number of frames that use the alternate codec. -
bitsPerPixel
int bitsPerPixel
Pixel depth. -
canUsePrevious
boolean canUsePrevious
Flag indicating whether we can safely use prevPixels. -
chunkSizes
List<Integer> chunkSizes
Number of bytes in each plane. -
codec
String codec
Video codec used by this movie. -
flip
boolean flip
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interlaced
boolean interlaced
Set to true if the scanlines in a plane are interlaced (mjpb only). -
offsets
List<Integer> offsets
Offsets to each plane's pixel data. -
pixelBytes
long pixelBytes
Total number of bytes of pixel data. -
pixelOffset
long pixelOffset
Offset to start of pixel data. -
prevPixels
byte[] prevPixels
Pixel data for the previous image plane. -
prevPlane
long prevPlane
Previous plane number. -
rawSize
int rawSize
Raw plane size, in bytes. -
scale
int scale
Amount to subtract from each offset. -
spork
boolean spork
Flag indicating whether the resource and data fork are separated.
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Class io.scif.formats.qt.PICTFormat.Metadata extends AbstractMetadata implements Serializable
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Serialized Fields
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rowBytes
int rowBytes
Number of bytes in a row of pixel data (variable). -
versionOne
boolean versionOne
Whether or not the file is PICT v1.
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Package io.scif.formats.tiff
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Class io.scif.formats.tiff.IFD extends HashMap<Integer,Object> implements Serializable
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Serialized Fields
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log
org.scijava.log.LogService log
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Class io.scif.formats.tiff.IFDList extends ArrayList<IFD> implements Serializable
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Class io.scif.formats.tiff.TiffRational extends Number implements Serializable
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Serialized Fields
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denom
long denom
Components of the rational's fractional representation. -
numer
long numer
Components of the rational's fractional representation.
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Package io.scif.gui
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Class io.scif.gui.ImageViewer extends JFrame implements Serializable
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Serialized Fields
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anim
boolean anim
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canCloseReader
boolean canCloseReader
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context
org.scijava.Context context
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filename
String filename
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fileSave
JMenuItem fileSave
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fileView
JMenuItem fileView
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formatService
FormatService formatService
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fps
int fps
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guiService
GUIService guiService
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icon
ImageIcon icon
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iconLabel
JLabel iconLabel
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images
BufferedImage[] images
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initializeService
InitializeService initializeService
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logService
org.scijava.log.LogService logService
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myReader
Reader myReader
Current format reader. -
myWriter
Writer myWriter
Current format writer. -
nSlider
JSlider nSlider
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pane
JPanel pane
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probeLabel
JLabel probeLabel
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sb
StringBuffer sb
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sliderPanel
JPanel sliderPanel
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Class io.scif.gui.PreviewPane extends JPanel implements Serializable
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Serialized Fields
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formatLabel
JLabel formatLabel
Labels containing thumbnail and dimensional information. -
formatText
String formatText
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formatTip
String formatTip
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icon
ImageIcon icon
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iconLabel
JLabel iconLabel
Labels containing thumbnail and dimensional information. -
iconText
String iconText
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iconTip
String iconTip
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initializeService
InitializeService initializeService
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lastId
String lastId
Last ID loaded. -
loader
Thread loader
Thumbnail loading thread. -
loaderAlive
boolean loaderAlive
Flag indicating whether loader thread should keep running. -
loadId
String loadId
Current ID to load. -
logService
org.scijava.log.LogService logService
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npText
String npText
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reader
Reader reader
Reader for use when loading thumbnails. -
refresher
Runnable refresher
Method for syncing the view to the model. -
resLabel
JLabel resLabel
Labels containing thumbnail and dimensional information. -
resText
String resText
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resTip
String resTip
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typeLabel
JLabel typeLabel
Labels containing thumbnail and dimensional information. -
typeText
String typeText
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typeTip
String typeTip
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zctLabel
JLabel zctLabel
Labels containing thumbnail and dimensional information. -
zctTip
String zctTip
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Class io.scif.gui.TwoChannelColorSpace extends ColorSpace implements Serializable
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Package io.scif.img
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Class io.scif.img.ImgIOException extends net.imglib2.exception.ImgLibException implements Serializable
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Class io.scif.img.Range extends ArrayList<Long> implements Serializable
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Package io.scif.services
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Class io.scif.services.ServiceException extends Exception implements Serializable
- serialVersionUID:
- 7402442944895106504L
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