loci.plugins.util

Class ImageProcessorReader

java.lang.Object

loci.formats.ReaderWrapper

loci.plugins.util.ImageProcessorReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class ImageProcessorReader
extends ReaderWrapper

A low-level reader for ImageProcessor objects. For a higher-level reader that returns ImagePlus objects, see ImagePlusReader instead.

Field Summary

Fields inherited from class loci.formats.ReaderWrapper

reader

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
ImageProcessorReader() Constructs an ImageProcessorReader around a new image reader.
ImageProcessorReader(IFormatReader r) Constructs an ImageProcessorReader with the given reader.

Method Summary

Modifier and Type	Method and Description
private byte[][]	convertTo8Bit(short[][] shortTable)
private ij.process.LUT	createColorModel()
java.lang.Class<?>	getNativeDataType() Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
static ImageProcessorReader	makeImageProcessorReader(IFormatReader r) Converts the given reader into a ImageProcessorReader, wrapping if needed.
java.lang.Object	openPlane(int no, int x, int y, int w, int h) Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
ij.process.ImageProcessor[]	openProcessors(int no) Creates an ImageJ image processor object for the image plane at the given position.
ij.process.ImageProcessor[]	openProcessors(int no, int x, int y, int w, int h) Returns an array of ImageProcessors that represent the given slice.
ij.process.ImageProcessor[]	openThumbProcessors(int no)

Methods inherited from class loci.formats.ReaderWrapper

close, close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getTileCodec, getTileCodecOptions, getTileColumns, getTileRows, 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, openBytes, openBytes, openBytes, openBytes, openCompressedBytes, openCompressedBytes, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImageProcessorReader

public ImageProcessorReader()

Constructs an ImageProcessorReader around a new image reader.

ImageProcessorReader

public ImageProcessorReader(IFormatReader r)

Constructs an ImageProcessorReader with the given reader.

Method Detail

makeImageProcessorReader

public static ImageProcessorReader makeImageProcessorReader(IFormatReader r)

Converts the given reader into a ImageProcessorReader, wrapping if needed.

openProcessors

public ij.process.ImageProcessor[] openProcessors(int no)
                                           throws FormatException,
                                                  java.io.IOException

Creates an ImageJ image processor object for the image plane at the given position.

Parameters:

no - Position of image plane.

Throws:

FormatException

java.io.IOException

openThumbProcessors

public ij.process.ImageProcessor[] openThumbProcessors(int no)
                                                throws FormatException,
                                                       java.io.IOException

Throws:

FormatException

java.io.IOException

openProcessors

public ij.process.ImageProcessor[] openProcessors(int no,
                                                  int x,
                                                  int y,
                                                  int w,
                                                  int h)
                                           throws FormatException,
                                                  java.io.IOException

Returns an array of ImageProcessors that represent the given slice. There is one ImageProcessor per RGB channel; i.e., length of returned array == getRGBChannelCount().

Parameters:

no - Position of image plane.

Throws:

FormatException

java.io.IOException

getNativeDataType

public java.lang.Class<?> getNativeDataType()

Description copied from interface: IFormatHandler

Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object). For most readers this type will be a byte array; however, some readers call external APIs that work with other types such as BufferedImage.

Specified by:

getNativeDataType in interface IFormatHandler

Overrides:

getNativeDataType in class ReaderWrapper

openPlane

public java.lang.Object openPlane(int no,
                                  int x,
                                  int y,
                                  int w,
                                  int h)
                           throws FormatException,
                                  java.io.IOException

Description copied from interface: IFormatReader

Obtains the specified image plane (or sub-image thereof) in the reader's native data structure. For most readers this is a byte array; however, some readers call external APIs that work with other types such as BufferedImage. The openPlane method exists to maintain generality and efficiency while avoiding pollution of the API with AWT-specific logic.

Specified by:

openPlane in interface IFormatReader

Overrides:

openPlane in class ReaderWrapper

Throws:

FormatException

java.io.IOException

See Also:

FormatReader, BufferedImageReader

createColorModel

private ij.process.LUT createColorModel()
                                 throws FormatException,
                                        java.io.IOException

Throws:

FormatException

java.io.IOException

convertTo8Bit

private byte[][] convertTo8Bit(short[][] shortTable)