ChannelMerger (Bio-Formats API)

java.lang.Object
- loci.formats.ReaderWrapper
- - loci.formats.ChannelMerger

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
public class ChannelMerger
extends ReaderWrapper
```
Logic to automatically merge channels in a file.

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
`ChannelMerger()` Constructs a ChannelMerger around a new image reader.
`ChannelMerger(IFormatReader r)` Constructs a ChannelMerger with the given reader.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`canMerge()` Determines whether the channels in the file can be merged.
`String`	`getDimensionOrder()` Gets a five-character string representing the dimension order in which planes will be returned.
`int`	`getImageCount()` Determines the number of image planes in the current file.
`int`	`getIndex(int z, int c, int t)` Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
`int`	`getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT)` Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes).
`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)`.
`int`	`getOriginalIndex(int no)` Returns the image number in the original dataset that corresponds to the given image number.
`int[]`	`getZCTCoords(int index)` Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
`int[]`	`getZCTModuloCoords(int index)` Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value.
`boolean`	`isIndexed()` Gets whether the image planes are indexed color.
`boolean`	`isInterleaved()` Gets whether or not the channels are interleaved.
`boolean`	`isRGB()` Checks if the image planes in the file have more than one channel per `IFormatReader.openBytes(int)` call.
`static ChannelMerger`	`makeChannelMerger(IFormatReader r)` Converts the given reader into a ChannelMerger, wrapping if needed.
`byte[]`	`openBytes(int no)` Obtains the specified image plane from the current file as a byte array.
`byte[]`	`openBytes(int no, byte[] buf)` Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
`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.
`byte[]`	`openBytes(int no, int x, int y, int w, int h)` Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).

Methods inherited from class loci.formats.ReaderWrapper
close, close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDomains, getEffectiveSizeC, getFormat, getGlobalMetadata, 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, getUnderlyingReaders, getUsedFiles, getUsedFiles, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, 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
  - ChannelMerger
```
public ChannelMerger()
```
    Constructs a ChannelMerger around a new image reader.
  - ChannelMerger
```
public ChannelMerger(IFormatReader r)
```
    Constructs a ChannelMerger with the given reader.
- Method Detail
  - makeChannelMerger
```
public static ChannelMerger makeChannelMerger(IFormatReader r)
```
    Converts the given reader into a ChannelMerger, wrapping if needed.
  - canMerge
```
public boolean canMerge()
```
    Determines whether the channels in the file can be merged.
  - getOriginalIndex
```
public int getOriginalIndex(int no)
                     throws FormatException,
                            IOException
```
    Returns the image number in the original dataset that corresponds to the given image number.
    
    Parameters:
    
    no - is an image number greater than or equal to 0 and less than getImageCount()
    
    Returns:
    
    the corresponding image number in the original (unmerged) data.
    
    Throws:
    
    FormatException
    
    IOException
  - getImageCount
```
public int getImageCount()
```
    Description copied from interface: IFormatReader
    
    Determines the number of image planes in the current file.
    
    Specified by:
    
    getImageCount in interface IFormatReader
    
    Overrides:
    
    getImageCount in class ReaderWrapper
  - getDimensionOrder
```
public String getDimensionOrder()
```
    Description copied from interface: IFormatReader
    Gets a five-character string representing the dimension order in which planes will be returned. Valid orders are:
    - XYCTZ
    - XYCZT
    - XYTCZ
    - XYTZC
    - XYZCT
    - XYZTC
    In cases where the channels are interleaved (e.g., CXYTZ), C will be the first dimension after X and Y (e.g., XYCTZ) and the IFormatReader.isInterleaved() method will return true.
    Specified by:
    
    getDimensionOrder in interface IFormatReader
    
    Overrides:
    
    getDimensionOrder in class ReaderWrapper
  - isInterleaved
```
public boolean isInterleaved()
```
    Description copied from interface: IFormatReader
    
    Gets whether or not the channels are interleaved. This method exists because X and Y must appear first in the dimension order. For interleaved data, IFormatReader.getDimensionOrder() returns XYCTZ or XYCZT, and this method returns true. Note that this flag returns whether or not the data returned by IFormatReader.openBytes(int) is interleaved. In most cases, this will match the interleaving in the original file, but for some formats (e.g. TIFF) channel re-ordering is done internally and the return value of this method will not match what is in the original file.
    
    Specified by:
    
    isInterleaved in interface IFormatReader
    
    Overrides:
    
    isInterleaved in class ReaderWrapper
  - isRGB
```
public boolean isRGB()
```
    Description copied from interface: IFormatReader
    
    Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call. This method returns true if and only if IFormatReader.getRGBChannelCount() returns a value greater than 1.
    
    Specified by:
    
    isRGB in interface IFormatReader
    
    Overrides:
    
    isRGB in class ReaderWrapper
  - isIndexed
```
public boolean isIndexed()
```
    Description copied from interface: IFormatReader
    
    Gets whether the image planes are indexed color. This value has no impact on IFormatReader.getSizeC(), IFormatReader.getEffectiveSizeC() or IFormatReader.getRGBChannelCount().
    
    Specified by:
    
    isIndexed in interface IFormatReader
    
    Overrides:
    
    isIndexed in class ReaderWrapper
  - openBytes
```
public byte[] openBytes(int no)
                 throws FormatException,
                        IOException
```
    Description copied from interface: IFormatReader
    
    Obtains the specified image plane from the current file as a byte array.
    
    Specified by:
    
    openBytes in interface IFormatReader
    
    Overrides:
    
    openBytes in class ReaderWrapper
    
    Throws:
    
    FormatException
    
    IOException
    
    See Also:
    
    IFormatReader.openBytes(int, byte[])
  - openBytes
```
public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        IOException
```
    Description copied from interface: IFormatReader
    
    Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
    
    Specified by:
    
    openBytes in interface IFormatReader
    
    Overrides:
    
    openBytes in class ReaderWrapper
    
    Parameters:
    
    no - the image index within the file.
    
    buf - a pre-allocated buffer.
    
    Returns:
    
    the pre-allocated buffer buf for convenience.
    
    Throws:
    
    FormatException - if there was a problem parsing the metadata of the file.
    
    IOException - if there was a problem reading the file.
  - openBytes
```
public byte[] openBytes(int no,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        IOException
```
    Description copied from interface: IFormatReader
    
    Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
    
    Specified by:
    
    openBytes in interface IFormatReader
    
    Overrides:
    
    openBytes in class ReaderWrapper
    
    Throws:
    
    FormatException
    
    IOException
  - openBytes
```
public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        IOException
```
    Description copied from interface: IFormatReader
    
    Obtains a sub-image of the specified image plane into a pre-allocated byte array.
    
    Specified by:
    
    openBytes in interface IFormatReader
    
    Overrides:
    
    openBytes in class ReaderWrapper
    
    Parameters:
    
    no - the image index within the file.
    
    buf - a pre-allocated buffer.
    
    x - X coordinate of the upper-left corner of the sub-image
    
    y - Y coordinate of the upper-left corner of the sub-image
    
    w - width of the sub-image
    
    h - height of the sub-image
    
    Returns:
    
    the pre-allocated buffer buf for convenience.
    
    Throws:
    
    FormatException - if there was a problem parsing the metadata of the file.
    
    IOException - if there was a problem reading the file.
  - getIndex
```
public int getIndex(int z,
                    int c,
                    int t,
                    int moduloZ,
                    int moduloC,
                    int moduloT)
```
    Description copied from interface: IFormatReader
    
    Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes). Note that the Z, C and T coordinates take the modulo dimension sizes into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.
    
    Specified by:
    
    getIndex in interface IFormatReader
    
    Overrides:
    
    getIndex in class ReaderWrapper
  - getIndex
```
public int getIndex(int z,
                    int c,
                    int t)
```
    Description copied from interface: IFormatReader
    
    Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
    
    Specified by:
    
    getIndex in interface IFormatReader
    
    Overrides:
    
    getIndex in class ReaderWrapper
  - getZCTCoords
```
public int[] getZCTCoords(int index)
```
    Description copied from interface: IFormatReader
    
    Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
    
    Specified by:
    
    getZCTCoords in interface IFormatReader
    
    Overrides:
    
    getZCTCoords in class ReaderWrapper
  - getZCTModuloCoords
```
public int[] getZCTModuloCoords(int index)
```
    Description copied from interface: IFormatReader
    
    Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value. Note that the Z, C and T coordinates are not the same as those returned by getZCTCoords(int) because the size of the modulo dimensions is taken into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.
    
    Specified by:
    
    getZCTModuloCoords in interface IFormatReader
    
    Overrides:
    
    getZCTModuloCoords in class ReaderWrapper
  - getNativeDataType
```
public 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

Class ChannelMerger

Field Summary

Fields inherited from class loci.formats.ReaderWrapper

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.ReaderWrapper

Methods inherited from class java.lang.Object

Constructor Detail

ChannelMerger

ChannelMerger

Method Detail

makeChannelMerger

canMerge

getOriginalIndex

getImageCount

getDimensionOrder

isInterleaved

isRGB

isIndexed

openBytes

openBytes

openBytes

openBytes

getIndex

getIndex

getZCTCoords

getZCTModuloCoords

getNativeDataType