ImageReader (Bio-Formats API)

java.lang.Object
- loci.formats.ImageReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
```
public class ImageReader
extends java.lang.Object
implements IFormatReader
```
ImageReader is the master file format reader for all supported formats. It uses one instance of each reader subclass (specified in readers.txt, or other class list source) to identify file formats and read data.

Author:

Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`allowOpen`
`private int`	`current` Current form index.
`private java.lang.String`	`currentId` Name of current file.
`private static ClassList<IFormatReader>`	`defaultClasses` Default list of reader classes, for use with noargs constructor.
`private static org.slf4j.Logger`	`LOGGER`
`private static java.util.concurrent.atomic.AtomicBoolean`	`raisedException`
`private IFormatReader[]`	`readers` List of supported file format readers.
`private java.lang.String[]`	`suffixes` Valid suffixes for this file format.

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description
`ImageReader()` Constructs a new ImageReader with the default list of reader classes from readers.txt.
`ImageReader(ClassList<IFormatReader> classList)` Constructs a new ImageReader from the given list of reader classes.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()`
`void`	`close(boolean fileOnly)` Closes the currently open file.
`int`	`coreIndexToSeries(int index)` Returns the series corresponding to the specified core index.
`int`	`fileGroupOption(java.lang.String id)` Returns an indication of whether the files in a multi-file dataset can be handled individually.
`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.
`FileInfo[]`	`getAdvancedSeriesUsedFiles(boolean noPixels)` Returns an array of FileInfo objects representing the files needed to open the current series.
`FileInfo[]`	`getAdvancedUsedFiles(boolean noPixels)` Returns an array of FileInfo objects representing the files needed to open this dataset.
`int`	`getBitsPerPixel()` Gets the number of valid bits per pixel.
`int`	`getCoreIndex()` Return the index into CoreMetadata of the current resolution/series.
`java.util.List<CoreMetadata>`	`getCoreMetadataList()` Obtains the core metadata values for the current file.
`java.lang.String`	`getCurrentFile()` Returns the current file.
`java.lang.String`	`getDatasetStructureDescription()` Returns a short description of the dataset structure.
`static ClassList<IFormatReader>`	`getDefaultReaderClasses()`
`java.lang.String`	`getDimensionOrder()` Gets a five-character string representing the dimension order in which planes will be returned.
`java.lang.String[]`	`getDomains()` Returns the list of domains represented by the current file.
`int`	`getEffectiveSizeC()` Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
`java.lang.String`	`getFormat()` Gets the name of this file format.
`java.lang.String`	`getFormat(java.lang.String id)` Gets a string describing the file format for the given file.
`java.util.Hashtable<java.lang.String,java.lang.Object>`	`getGlobalMetadata()` Obtains the hashtable containing the metadata field/value pairs from the current file.
`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).
`MetadataOptions`	`getMetadataOptions()`
`MetadataStore`	`getMetadataStore()` Retrieves the current metadata store for this reader.
`java.lang.Object`	`getMetadataStoreRoot()` Retrieves the current metadata store's root object.
`java.lang.Object`	`getMetadataValue(java.lang.String field)` Obtains the specified metadata field's value for the current file.
`Modulo`	`getModuloC()`
`Modulo`	`getModuloT()`
`Modulo`	`getModuloZ()`
`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)`.
`int`	`getOptimalTileHeight()` Returns the optimal sub-image height for use with openBytes.
`int`	`getOptimalTileWidth()` Returns the optimal sub-image width for use with openBytes.
`int`	`getPixelType()` Gets the pixel type.
`java.lang.String[]`	`getPossibleDomains(java.lang.String id)` Returns a list of scientific domains in which this format is used.
`IFormatReader`	`getReader()` Gets the reader used to open the current file.
`IFormatReader`	`getReader(java.lang.Class<? extends IFormatReader> c)` Gets the file format reader instance matching the given class.
`IFormatReader`	`getReader(java.lang.String id)` Gets the reader used to open the given file.
`IFormatReader[]`	`getReaders()` Gets all constituent file format readers.
`int`	`getRequiredDirectories(java.lang.String[] files)` Returns the number of parent directories that are important when processing the given list of files.
`int`	`getResolution()` Get the current resolution level.
`int`	`getResolutionCount()` Return the number of resolutions for the current series.
`int`	`getRGBChannelCount()` Gets the number of channels returned with each call to openBytes.
`int`	`getSeries()` Gets the currently active series.
`int`	`getSeriesCount()` Gets the number of series in this file.
`java.util.Hashtable<java.lang.String,java.lang.Object>`	`getSeriesMetadata()` Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
`java.lang.Object`	`getSeriesMetadataValue(java.lang.String field)` Obtains the specified metadata field's value for the current series in the current file.
`java.lang.String[]`	`getSeriesUsedFiles()` Returns an array of filenames needed to open the current series.
`java.lang.String[]`	`getSeriesUsedFiles(boolean noPixels)` Returns an array of filenames needed to open the current series.
`int`	`getSizeC()` Gets the size of the C dimension.
`int`	`getSizeT()` Gets the size of the T dimension.
`int`	`getSizeX()` Gets the size of the X dimension.
`int`	`getSizeY()` Gets the size of the Y dimension.
`int`	`getSizeZ()` Gets the size of the Z dimension.
`java.lang.String[]`	`getSuffixes()` Gets the default file suffixes for this file format.
`java.util.Set<MetadataLevel>`	`getSupportedMetadataLevels()`
`int`	`getThumbSizeX()` Get the size of the X dimension for the thumbnail.
`int`	`getThumbSizeY()` Get the size of the Y dimension for the thumbnail.
`IFormatReader[]`	`getUnderlyingReaders()` Retrieves all underlying readers.
`java.lang.String[]`	`getUsedFiles()` Returns an array of filenames needed to open this dataset.
`java.lang.String[]`	`getUsedFiles(boolean noPixels)` Returns an array of filenames needed to open this dataset.
`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`	`hasCompanionFiles()` Returns true if this format supports multi-file datasets.
`boolean`	`hasFlattenedResolutions()` Return whether or not resolution flattening is enabled.
`boolean`	`isFalseColor()` Returns false if `IFormatReader.isIndexed()` is false, or if `IFormatReader.isIndexed()` is true and the lookup table represents "real" color data.
`boolean`	`isGroupFiles()` Returns true if we should group files in multi-file formats.
`boolean`	`isIndexed()` Gets whether the image planes are indexed color.
`boolean`	`isInterleaved()` Gets whether or not the channels are interleaved.
`boolean`	`isInterleaved(int subC)` Gets whether or not the given sub-channel is interleaved.
`boolean`	`isLittleEndian()` Gets whether the data is in little-endian format.
`boolean`	`isMetadataComplete()` Returns true if this format's metadata is completely parsed.
`boolean`	`isMetadataFiltered()` Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
`boolean`	`isNormalized()` Returns true if we should normalize float data.
`private boolean`	`isOmero(java.lang.String id)`
`boolean`	`isOrderCertain()` Gets whether the dimension order and sizes are known, or merely guesses.
`boolean`	`isOriginalMetadataPopulated()` Returns true if we should save proprietary metadata in the MetadataStore.
`boolean`	`isRGB()` Checks if the image planes in the file have more than one channel per `IFormatReader.openBytes(int)` call.
`boolean`	`isSingleFile(java.lang.String id)` Returns true if the named file is expected to be the only file in the dataset.
`boolean`	`isThisType(byte[] block)` Checks if the given block is a valid header for this file format.
`private boolean`	`isThisType(IFormatReader reader, byte[] block)`
`private boolean`	`isThisType(IFormatReader reader, loci.common.RandomAccessInputStream rais)`
`private boolean`	`isThisType(IFormatReader reader, java.lang.String name, boolean allowOpen)`
`boolean`	`isThisType(loci.common.RandomAccessInputStream stream)` Checks if the given stream is a valid stream for this file format.
`boolean`	`isThisType(java.lang.String name)` Checks if the given string is a valid filename for this file format.
`boolean`	`isThisType(java.lang.String name, boolean open)` Checks if the given file is a valid instance of this file format.
`boolean`	`isThumbnailSeries()` Gets whether the current series is a lower resolution copy of a different series.
`private void`	`logIsThisTypeError(IFormatReader reader, java.lang.Exception e)`
`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).
`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.
`byte[]`	`openThumbBytes(int no)` Obtains a thumbnail for the specified image plane from the current file, as a byte array.
`void`	`reopenFile()` Reopen any files that were closed, and which are expected to be open while the reader is open.
`int`	`seriesToCoreIndex(int series)` Returns the first core index corresponding to the specified series.
`void`	`setAllowOpenFiles(boolean allowOpen)` Toggles whether or not file system access is allowed when doing type detection.
`void`	`setCoreIndex(int no)` Set the current resolution/series (ignores subresolutions).
`void`	`setFlattenedResolutions(boolean flattened)` Set whether or not to flatten resolutions into individual series.
`void`	`setGroupFiles(boolean group)` Specifies whether or not to force grouping in multi-file formats.
`void`	`setId(java.lang.String id)` Sets the current file name.
`void`	`setMetadataFiltered(boolean filter)` Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
`void`	`setMetadataOptions(MetadataOptions options)`
`void`	`setMetadataStore(MetadataStore store)` Sets the default metadata store for this reader.
`void`	`setNormalized(boolean normalize)` Specifies whether or not to normalize float data.
`void`	`setOriginalMetadataPopulated(boolean populate)` Specifies whether or not to save proprietary metadata in the MetadataStore.
`void`	`setResolution(int no)` Set the resolution level.
`void`	`setSeries(int no)` Activates the specified series.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - LOGGER
```
private static final org.slf4j.Logger LOGGER
```
  - defaultClasses
```
private static ClassList<IFormatReader> defaultClasses
```
    Default list of reader classes, for use with noargs constructor.
  - readers
```
private IFormatReader[] readers
```
    List of supported file format readers.
  - suffixes
```
private java.lang.String[] suffixes
```
    Valid suffixes for this file format. Populated the first time getSuffixes() is called.
  - currentId
```
private java.lang.String currentId
```
    Name of current file.
  - current
```
private int current
```
    Current form index.
  - allowOpen
```
private boolean allowOpen
```
  - raisedException
```
private static java.util.concurrent.atomic.AtomicBoolean raisedException
```
- Constructor Detail
  - ImageReader
```
public ImageReader()
```
    Constructs a new ImageReader with the default list of reader classes from readers.txt.
  - ImageReader
```
public ImageReader(ClassList<IFormatReader> classList)
```
    Constructs a new ImageReader from the given list of reader classes.
- Method Detail
  - getDefaultReaderClasses
```
public static ClassList<IFormatReader> getDefaultReaderClasses()
```
  - isOmero
```
private boolean isOmero(java.lang.String id)
```
  - setAllowOpenFiles
```
public void setAllowOpenFiles(boolean allowOpen)
```
    Toggles whether or not file system access is allowed when doing type detection. By default, file system access is allowed.
  - getFormat
```
public java.lang.String getFormat(java.lang.String id)
                           throws FormatException,
                                  java.io.IOException
```
    Gets a string describing the file format for the given file.
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getReader
```
public IFormatReader getReader(java.lang.String id)
                        throws FormatException,
                               java.io.IOException
```
    Gets the reader used to open the given file.
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getReader
```
public IFormatReader getReader()
```
    Gets the reader used to open the current file.
  - getReader
```
public IFormatReader getReader(java.lang.Class<? extends IFormatReader> c)
```
    Gets the file format reader instance matching the given class.
  - getReaders
```
public IFormatReader[] getReaders()
```
    Gets all constituent file format readers.
  - getSupportedMetadataLevels
```
public java.util.Set<MetadataLevel> getSupportedMetadataLevels()
```
    Specified by:
    
    getSupportedMetadataLevels in interface IMetadataConfigurable
  - getMetadataOptions
```
public MetadataOptions getMetadataOptions()
```
    Specified by:
    
    getMetadataOptions in interface IMetadataConfigurable
  - setMetadataOptions
```
public void setMetadataOptions(MetadataOptions options)
```
    Specified by:
    
    setMetadataOptions in interface IMetadataConfigurable
    
    See Also:
    
    IMetadataConfigurable.setMetadataOptions(MetadataOptions)
  - isThisType
```
public boolean isThisType(java.lang.String name,
                          boolean open)
```
    Description copied from interface: IFormatReader
    
    Checks if the given file is a valid instance of this file format.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    open - If true, and the file extension is insufficient to determine the file type, the file may be opened for further analysis, or other relatively expensive file system operations (such as file existence tests and directory listings) may be performed. If false, file system access is not allowed.
  - isThisType
```
public boolean isThisType(byte[] block)
```
    Description copied from interface: IFormatReader
    
    Checks if the given block is a valid header for this file format.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    See Also:
    
    IFormatReader.isThisType(RandomAccessInputStream)
  - isThisType
```
public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    Parameters:
    
    stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.
    
    Returns:
    
    true if the file represented by the stream can be read by this reader; false otherwise.
    
    Throws:
    
    java.io.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
  - 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
  - getSizeX
```
public int getSizeX()
```
    Description copied from interface: IFormatReader
    
    Gets the size of the X dimension.
    
    Specified by:
    
    getSizeX in interface IFormatReader
  - getSizeY
```
public int getSizeY()
```
    Description copied from interface: IFormatReader
    
    Gets the size of the Y dimension.
    
    Specified by:
    
    getSizeY in interface IFormatReader
  - getSizeC
```
public int getSizeC()
```
    Description copied from interface: IFormatReader
    
    Gets the size of the C dimension.
    
    Specified by:
    
    getSizeC in interface IFormatReader
  - getSizeZ
```
public int getSizeZ()
```
    Description copied from interface: IFormatReader
    
    Gets the size of the Z dimension.
    
    Specified by:
    
    getSizeZ in interface IFormatReader
  - getSizeT
```
public int getSizeT()
```
    Description copied from interface: IFormatReader
    
    Gets the size of the T dimension.
    
    Specified by:
    
    getSizeT in interface IFormatReader
  - getPixelType
```
public int getPixelType()
```
    Description copied from interface: IFormatReader
    
    Gets the pixel type.
    
    Specified by:
    
    getPixelType in interface IFormatReader
    
    Returns:
    
    the pixel type as an enumeration from FormatTools static pixel types such as FormatTools.INT8.
  - getBitsPerPixel
```
public int getBitsPerPixel()
```
    Description copied from interface: IFormatReader
    
    Gets the number of valid bits per pixel. The number of valid bits per pixel is always less than or equal to the number of bits per pixel that correspond to IFormatReader.getPixelType().
    
    Specified by:
    
    getBitsPerPixel in interface IFormatReader
  - getEffectiveSizeC
```
public int getEffectiveSizeC()
```
    Description copied from interface: IFormatReader
    
    Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
    
    Specified by:
    
    getEffectiveSizeC in interface IFormatReader
  - getRGBChannelCount
```
public int getRGBChannelCount()
```
    Description copied from interface: IFormatReader
    
    Gets the number of channels returned with each call to openBytes. The most common case where this value is greater than 1 is for interleaved RGB data, such as a 24-bit color image plane. However, it is possible for this value to be greater than 1 for non-interleaved data, such as an RGB TIFF with Planar rather than Chunky configuration.
    
    Specified by:
    
    getRGBChannelCount in interface IFormatReader
  - 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
  - isFalseColor
```
public boolean isFalseColor()
```
    Description copied from interface: IFormatReader
    
    Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data. Returns true if IFormatReader.isIndexed() is true and the lookup table is only present to aid in visualization.
    
    Specified by:
    
    isFalseColor in interface IFormatReader
  - get8BitLookupTable
```
public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if 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.
    
    Specified by:
    
    get8BitLookupTable in interface IFormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if 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.
    
    Specified by:
    
    get16BitLookupTable in interface IFormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getModuloZ
```
public Modulo getModuloZ()
```
    Specified by:
    
    getModuloZ in interface IFormatReader
  - getModuloC
```
public Modulo getModuloC()
```
    Specified by:
    
    getModuloC in interface IFormatReader
  - getModuloT
```
public Modulo getModuloT()
```
    Specified by:
    
    getModuloT in interface IFormatReader
  - getThumbSizeX
```
public int getThumbSizeX()
```
    Description copied from interface: IFormatReader
    
    Get the size of the X dimension for the thumbnail.
    
    Specified by:
    
    getThumbSizeX in interface IFormatReader
  - getThumbSizeY
```
public int getThumbSizeY()
```
    Description copied from interface: IFormatReader
    
    Get the size of the Y dimension for the thumbnail.
    
    Specified by:
    
    getThumbSizeY in interface IFormatReader
  - isLittleEndian
```
public boolean isLittleEndian()
```
    Description copied from interface: IFormatReader
    
    Gets whether the data is in little-endian format.
    
    Specified by:
    
    isLittleEndian in interface IFormatReader
  - getDimensionOrder
```
public java.lang.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
  - isOrderCertain
```
public boolean isOrderCertain()
```
    Description copied from interface: IFormatReader
    
    Gets whether the dimension order and sizes are known, or merely guesses.
    
    Specified by:
    
    isOrderCertain in interface IFormatReader
  - isThumbnailSeries
```
public boolean isThumbnailSeries()
```
    Description copied from interface: IFormatReader
    
    Gets whether the current series is a lower resolution copy of a different series.
    
    Specified by:
    
    isThumbnailSeries in interface IFormatReader
  - 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
  - isInterleaved
```
public boolean isInterleaved(int subC)
```
    Description copied from interface: IFormatReader
    
    Gets whether or not the given sub-channel is interleaved. This method exists because some data with multiple rasterized sub-dimensions within C have one sub-dimension interleaved, and the other not—e.g., SDTReader handles spectral-lifetime data with interleaved lifetime bins and non-interleaved spectral channels.
    
    Specified by:
    
    isInterleaved in interface IFormatReader
  - openBytes
```
public byte[] openBytes(int no)
                 throws FormatException,
                        java.io.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
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    IFormatReader.openBytes(int, byte[])
  - openBytes
```
public byte[] openBytes(int no,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - openBytes
```
public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        java.io.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
    
    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.
    
    java.io.IOException - if there was a problem reading the file.
  - openBytes
```
public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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
    
    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.
    
    java.io.IOException - if there was a problem reading the file.
  - 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
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    FormatReader, BufferedImageReader
  - openThumbBytes
```
public byte[] openThumbBytes(int no)
                      throws FormatException,
                             java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Obtains a thumbnail for the specified image plane from the current file, as a byte array.
    
    Specified by:
    
    openThumbBytes in interface IFormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getSeriesCount
```
public int getSeriesCount()
```
    Description copied from interface: IFormatReader
    
    Gets the number of series in this file.
    
    Specified by:
    
    getSeriesCount in interface IFormatReader
  - setSeries
```
public void setSeries(int no)
```
    Description copied from interface: IFormatReader
    
    Activates the specified series. This also resets the resolution to 0.
    
    Specified by:
    
    setSeries in interface IFormatReader
  - getSeries
```
public int getSeries()
```
    Description copied from interface: IFormatReader
    
    Gets the currently active series.
    
    Specified by:
    
    getSeries in interface IFormatReader
  - getUsedFiles
```
public java.lang.String[] getUsedFiles()
```
    Description copied from interface: IFormatReader
    
    Returns an array of filenames needed to open this dataset. The first element in the array is expected to be the path passed to IFormatHandler.setId(String). The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.
    
    Specified by:
    
    getUsedFiles in interface IFormatReader
  - getUsedFiles
```
public java.lang.String[] getUsedFiles(boolean noPixels)
```
    Description copied from interface: IFormatReader
    
    Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.
    
    Specified by:
    
    getUsedFiles in interface IFormatReader
  - getSeriesUsedFiles
```
public java.lang.String[] getSeriesUsedFiles()
```
    Description copied from interface: IFormatReader
    
    Returns an array of filenames needed to open the current series. The first element in the array is expected to be the path passed to IFormatHandler.setId(String). The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.
    
    Specified by:
    
    getSeriesUsedFiles in interface IFormatReader
  - getSeriesUsedFiles
```
public java.lang.String[] getSeriesUsedFiles(boolean noPixels)
```
    Description copied from interface: IFormatReader
    
    Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.
    
    Specified by:
    
    getSeriesUsedFiles in interface IFormatReader
  - getAdvancedUsedFiles
```
public FileInfo[] getAdvancedUsedFiles(boolean noPixels)
```
    Description copied from interface: IFormatReader
    
    Returns an array of FileInfo objects representing the files needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.
    
    Specified by:
    
    getAdvancedUsedFiles in interface IFormatReader
  - getAdvancedSeriesUsedFiles
```
public FileInfo[] getAdvancedSeriesUsedFiles(boolean noPixels)
```
    Description copied from interface: IFormatReader
    
    Returns an array of FileInfo objects representing the files needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.
    
    Specified by:
    
    getAdvancedSeriesUsedFiles in interface IFormatReader
  - 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
  - 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
  - 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
  - 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
  - getMetadataValue
```
public java.lang.Object getMetadataValue(java.lang.String field)
```
    Description copied from interface: IFormatReader
    
    Obtains the specified metadata field's value for the current file.
    
    Specified by:
    
    getMetadataValue in interface IFormatReader
    
    Parameters:
    
    field - the name associated with the metadata field
    
    Returns:
    
    the value, or null if the field doesn't exist
  - getSeriesMetadataValue
```
public java.lang.Object getSeriesMetadataValue(java.lang.String field)
```
    Description copied from interface: IFormatReader
    
    Obtains the specified metadata field's value for the current series in the current file.
    
    Specified by:
    
    getSeriesMetadataValue in interface IFormatReader
    
    Parameters:
    
    field - the name associated with the metadata field
    
    Returns:
    
    the value, or null if the field doesn't exist
  - getGlobalMetadata
```
public java.util.Hashtable<java.lang.String,java.lang.Object> getGlobalMetadata()
```
    Description copied from interface: IFormatReader
    
    Obtains the hashtable containing the metadata field/value pairs from the current file.
    
    Specified by:
    
    getGlobalMetadata in interface IFormatReader
    
    Returns:
    
    the hashtable containing all non-series-specific metadata from the file
  - getSeriesMetadata
```
public java.util.Hashtable<java.lang.String,java.lang.Object> getSeriesMetadata()
```
    Description copied from interface: IFormatReader
    
    Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
    
    Specified by:
    
    getSeriesMetadata in interface IFormatReader
  - getCoreMetadataList
```
public java.util.List<CoreMetadata> getCoreMetadataList()
```
    Description copied from interface: IFormatReader
    
    Obtains the core metadata values for the current file.
    
    Specified by:
    
    getCoreMetadataList in interface IFormatReader
  - close
```
public void close(boolean fileOnly)
           throws java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().
    
    Specified by:
    
    close in interface IFormatReader
    
    Throws:
    
    java.io.IOException
  - setGroupFiles
```
public void setGroupFiles(boolean group)
```
    Description copied from interface: IFormatReader
    
    Specifies whether or not to force grouping in multi-file formats.
    
    Specified by:
    
    setGroupFiles in interface IFormatReader
    
    See Also:
    
    IFormatReader.fileGroupOption(String), IFormatReader.isGroupFiles()
  - isGroupFiles
```
public boolean isGroupFiles()
```
    Description copied from interface: IFormatReader
    
    Returns true if we should group files in multi-file formats.
    
    Specified by:
    
    isGroupFiles in interface IFormatReader
    
    See Also:
    
    IFormatReader.setGroupFiles(boolean), IFormatReader.fileGroupOption(String)
  - fileGroupOption
```
public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.
    
    Specified by:
    
    fileGroupOption in interface IFormatReader
    
    Parameters:
    
    id - a file in the multi-file dataset
    
    Returns:
    
    an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP
  - isMetadataComplete
```
public boolean isMetadataComplete()
```
    Description copied from interface: IFormatReader
    
    Returns true if this format's metadata is completely parsed.
    
    Specified by:
    
    isMetadataComplete in interface IFormatReader
  - setNormalized
```
public void setNormalized(boolean normalize)
```
    Description copied from interface: IFormatReader
    
    Specifies whether or not to normalize float data.
    
    Specified by:
    
    setNormalized in interface IFormatReader
  - isNormalized
```
public boolean isNormalized()
```
    Description copied from interface: IFormatReader
    
    Returns true if we should normalize float data.
    
    Specified by:
    
    isNormalized in interface IFormatReader
  - setOriginalMetadataPopulated
```
public void setOriginalMetadataPopulated(boolean populate)
```
    Description copied from interface: IFormatReader
    
    Specifies whether or not to save proprietary metadata in the MetadataStore.
    
    Specified by:
    
    setOriginalMetadataPopulated in interface IFormatReader
  - isOriginalMetadataPopulated
```
public boolean isOriginalMetadataPopulated()
```
    Description copied from interface: IFormatReader
    
    Returns true if we should save proprietary metadata in the MetadataStore.
    
    Specified by:
    
    isOriginalMetadataPopulated in interface IFormatReader
  - getCurrentFile
```
public java.lang.String getCurrentFile()
```
    Description copied from interface: IFormatReader
    
    Returns the current file.
    
    Specified by:
    
    getCurrentFile in interface IFormatReader
  - setMetadataFiltered
```
public void setMetadataFiltered(boolean filter)
```
    Description copied from interface: IFormatReader
    
    Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
    
    Specified by:
    
    setMetadataFiltered in interface IFormatReader
  - isMetadataFiltered
```
public boolean isMetadataFiltered()
```
    Description copied from interface: IFormatReader
    
    Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
    
    Specified by:
    
    isMetadataFiltered in interface IFormatReader
  - setMetadataStore
```
public void setMetadataStore(MetadataStore store)
```
    Description copied from interface: IFormatReader
    
    Sets the default metadata store for this reader.
    
    Specified by:
    
    setMetadataStore in interface IFormatReader
    
    Parameters:
    
    store - a metadata store implementation.
  - getMetadataStore
```
public MetadataStore getMetadataStore()
```
    Description copied from interface: IFormatReader
    
    Retrieves the current metadata store for this reader. You can be assured that this method will never return a null metadata store.
    
    Specified by:
    
    getMetadataStore in interface IFormatReader
    
    Returns:
    
    A metadata store implementation.
  - getMetadataStoreRoot
```
public java.lang.Object getMetadataStoreRoot()
```
    Description copied from interface: IFormatReader
    
    Retrieves the current metadata store's root object. It is guaranteed that all file parsing has been performed by the reader prior to retrieval. Requests for a full populated root object should be made using this method.
    
    Specified by:
    
    getMetadataStoreRoot in interface IFormatReader
    
    Returns:
    
    Current metadata store's root object fully populated.
  - getUnderlyingReaders
```
public IFormatReader[] getUnderlyingReaders()
```
    Description copied from interface: IFormatReader
    
    Retrieves all underlying readers. Returns null if there are no underlying readers.
    
    Specified by:
    
    getUnderlyingReaders in interface IFormatReader
  - isSingleFile
```
public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.
    
    Specified by:
    
    isSingleFile in interface IFormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getRequiredDirectories
```
public int getRequiredDirectories(java.lang.String[] files)
                           throws FormatException,
                                  java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Returns the number of parent directories that are important when processing the given list of files. The number of directories is relative to the common parent. For example, given a list with these two files: /path/to/file/foo /path/to/file/that/is/related A return value of 0 indicates that "/path/to/file/" is irrelevant. A return value of 1 indicates that "/path/to/" is irrelevant. Return values less than 0 are invalid. All listed files are assumed to belong to datasets of the same format.
    
    Specified by:
    
    getRequiredDirectories in interface IFormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getDatasetStructureDescription
```
public java.lang.String getDatasetStructureDescription()
```
    Description copied from interface: IFormatReader
    
    Returns a short description of the dataset structure.
    
    Specified by:
    
    getDatasetStructureDescription in interface IFormatReader
  - hasCompanionFiles
```
public boolean hasCompanionFiles()
```
    Description copied from interface: IFormatReader
    
    Returns true if this format supports multi-file datasets.
    
    Specified by:
    
    hasCompanionFiles in interface IFormatReader
  - getPossibleDomains
```
public java.lang.String[] getPossibleDomains(java.lang.String id)
                                      throws FormatException,
                                             java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Returns a list of scientific domains in which this format is used.
    
    Specified by:
    
    getPossibleDomains in interface IFormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getDomains
```
public java.lang.String[] getDomains()
```
    Description copied from interface: IFormatReader
    
    Returns the list of domains represented by the current file.
    
    Specified by:
    
    getDomains in interface IFormatReader
  - getOptimalTileWidth
```
public int getOptimalTileWidth()
```
    Description copied from interface: IFormatReader
    
    Returns the optimal sub-image width for use with openBytes.
    
    Specified by:
    
    getOptimalTileWidth in interface IFormatReader
  - getOptimalTileHeight
```
public int getOptimalTileHeight()
```
    Description copied from interface: IFormatReader
    
    Returns the optimal sub-image height for use with openBytes.
    
    Specified by:
    
    getOptimalTileHeight in interface IFormatReader
  - getCoreIndex
```
public int getCoreIndex()
```
    Description copied from interface: IFormatReader
    
    Return the index into CoreMetadata of the current resolution/series.
    
    Specified by:
    
    getCoreIndex in interface IFormatReader
  - setCoreIndex
```
public void setCoreIndex(int no)
```
    Description copied from interface: IFormatReader
    
    Set the current resolution/series (ignores subresolutions). Equivalent to setSeries, but with flattened resolutions always set to false.
    
    Specified by:
    
    setCoreIndex in interface IFormatReader
  - seriesToCoreIndex
```
public int seriesToCoreIndex(int series)
```
    Description copied from interface: IFormatReader
    
    Returns the first core index corresponding to the specified series.
    
    Specified by:
    
    seriesToCoreIndex in interface IFormatReader
  - coreIndexToSeries
```
public int coreIndexToSeries(int index)
```
    Description copied from interface: IFormatReader
    
    Returns the series corresponding to the specified core index.
    
    Specified by:
    
    coreIndexToSeries in interface IFormatReader
  - getResolutionCount
```
public int getResolutionCount()
```
    Description copied from interface: IPyramidHandler
    
    Return the number of resolutions for the current series. Resolutions are stored in descending order, so the largest resolution is first and the smallest resolution is last.
    
    Specified by:
    
    getResolutionCount in interface IPyramidHandler
  - setResolution
```
public void setResolution(int no)
```
    Description copied from interface: IPyramidHandler
    
    Set the resolution level.
    
    Specified by:
    
    setResolution in interface IPyramidHandler
    
    See Also:
    
    IPyramidHandler.getResolutionCount()
  - getResolution
```
public int getResolution()
```
    Description copied from interface: IPyramidHandler
    
    Get the current resolution level.
    
    Specified by:
    
    getResolution in interface IPyramidHandler
    
    See Also:
    
    IPyramidHandler.getResolutionCount()
  - hasFlattenedResolutions
```
public boolean hasFlattenedResolutions()
```
    Description copied from interface: IFormatReader
    
    Return whether or not resolution flattening is enabled.
    
    Specified by:
    
    hasFlattenedResolutions in interface IFormatReader
  - setFlattenedResolutions
```
public void setFlattenedResolutions(boolean flattened)
```
    Description copied from interface: IFormatReader
    
    Set whether or not to flatten resolutions into individual series.
    
    Specified by:
    
    setFlattenedResolutions in interface IFormatReader
  - isThisType
```
public boolean isThisType(java.lang.String name)
```
    Description copied from interface: IFormatHandler
    
    Checks if the given string is a valid filename for this file format.
    
    Specified by:
    
    isThisType in interface IFormatHandler
  - getFormat
```
public java.lang.String getFormat()
```
    Description copied from interface: IFormatHandler
    
    Gets the name of this file format.
    
    Specified by:
    
    getFormat in interface IFormatHandler
  - getSuffixes
```
public java.lang.String[] getSuffixes()
```
    Description copied from interface: IFormatHandler
    
    Gets the default file suffixes for this file format.
    
    Specified by:
    
    getSuffixes in interface IFormatHandler
  - 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
  - setId
```
public void setId(java.lang.String id)
           throws FormatException,
                  java.io.IOException
```
    Description copied from interface: IFormatHandler
    
    Sets the current file name.
    
    Specified by:
    
    setId in interface IFormatHandler
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - reopenFile
```
public void reopenFile()
                throws java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.
    
    Specified by:
    
    reopenFile in interface IFormatReader
    
    Throws:
    
    java.io.IOException
  - close
```
public void close()
           throws java.io.IOException
```
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable
    
    Throws:
    
    java.io.IOException
  - isThisType
```
private boolean isThisType(IFormatReader reader,
                           java.lang.String name,
                           boolean allowOpen)
```
  - isThisType
```
private boolean isThisType(IFormatReader reader,
                           byte[] block)
```
  - isThisType
```
private boolean isThisType(IFormatReader reader,
                           loci.common.RandomAccessInputStream rais)
```
  - logIsThisTypeError
```
private void logIsThisTypeError(IFormatReader reader,
                                java.lang.Exception e)
```

Class ImageReader

Field Summary

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LOGGER

defaultClasses

readers

suffixes

currentId

current

allowOpen

raisedException

Constructor Detail

ImageReader

ImageReader

Method Detail

getDefaultReaderClasses

isOmero

setAllowOpenFiles

getFormat

getReader

getReader

getReader

getReaders

getSupportedMetadataLevels

getMetadataOptions

setMetadataOptions

isThisType

isThisType

isThisType

getImageCount

isRGB

getSizeX

getSizeY

getSizeC

getSizeZ

getSizeT

getPixelType

getBitsPerPixel

getEffectiveSizeC

getRGBChannelCount

isIndexed

isFalseColor

get8BitLookupTable

get16BitLookupTable

getModuloZ

getModuloC

getModuloT

getThumbSizeX

getThumbSizeY

isLittleEndian

getDimensionOrder

isOrderCertain

isThumbnailSeries

isInterleaved

isInterleaved

openBytes

openBytes

openBytes

openBytes

openPlane

openThumbBytes

getSeriesCount

setSeries

getSeries

getUsedFiles

getUsedFiles

getSeriesUsedFiles

getSeriesUsedFiles

getAdvancedUsedFiles

getAdvancedSeriesUsedFiles

getIndex

getIndex

getZCTCoords

getZCTModuloCoords

getMetadataValue

getSeriesMetadataValue