loci.formats.in

Class PerkinElmerReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.PerkinElmerReader

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.StatusReporter

public class PerkinElmerReader
extends loci.formats.FormatReader

PerkinElmerReader is the file format reader for PerkinElmer files.

Source code:

Trac, SVN

Author:

Melissa Linkert linkert at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String[]	files Tiff files to open.
protected TiffReader[]	tiff Helper reader.

Fields inherited from class loci.formats.FormatReader

collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

currentId, debug, debugLevel, format, statusListeners, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
PerkinElmerReader() Constructs a new PerkinElmer reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes currently open file(s) and frees allocated memory.
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.String id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
java.lang.String[]	getUsedFiles() Returns an array of filenames needed to open this dataset.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isThisType(byte[] block) Checks if the given block is a valid header for this file format.
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format handler.
byte[]	openBytes(int no, byte[] buf) Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries

Methods inherited from class loci.formats.FormatHandler

addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace

Methods inherited from class java.lang.Object

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

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getSuffixes, isThisType, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

Field Detail

tiff

protected TiffReader[] tiff

Helper reader.

files

protected java.lang.String[] files

Tiff files to open.

Constructor Detail

PerkinElmerReader

public PerkinElmerReader()

Constructs a new PerkinElmer reader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

Description copied from interface: loci.formats.IFormatReader

Checks if the given block is a valid header for this file format.

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws loci.formats.FormatException,
                           java.io.IOException

Description copied from interface: loci.formats.IFormatReader

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:

fileGroupOption in interface loci.formats.IFormatReader

Overrides:

fileGroupOption in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

java.io.IOException

openBytes

public byte[] openBytes(int no,
               byte[] buf)
                 throws loci.formats.FormatException,
                        java.io.IOException

Description copied from interface: loci.formats.IFormatReader

Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Parameters:

no - the image index within the file.

buf - a pre-allocated buffer.

Returns:

the pre-allocated buffer buf for convenience.

Throws:

loci.formats.FormatException - if there was a problem parsing the metadata of the file.

java.io.IOException - if there was a problem reading the file.

getUsedFiles

public java.lang.String[] getUsedFiles()

Description copied from interface: loci.formats.IFormatReader

Returns an array of filenames needed to open this dataset.

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.FormatReader

close

public void close(boolean fileOnly)
           throws java.io.IOException

Description copied from interface: loci.formats.IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling IFormatHandler.close().

Specified by:

close in interface loci.formats.IFormatReader

Overrides:

close in class loci.formats.FormatReader

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Description copied from interface: loci.formats.IFormatHandler

Closes currently open file(s) and frees allocated memory.

Specified by:

close in interface loci.formats.IFormatHandler

Overrides:

close in class loci.formats.FormatReader

Throws:

java.io.IOException

isThisType

public boolean isThisType(java.lang.String name,
                 boolean open)

Description copied from class: loci.formats.FormatHandler

Checks if a file matches the type of this format handler. The default implementation checks filename suffixes against those known for this format (the open parameter does nothing).

Specified by:

isThisType in interface loci.formats.IFormatHandler

Overrides:

isThisType in class loci.formats.FormatHandler

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis. Does nothing in the default implementation.

initFile

protected void initFile(java.lang.String id)
                 throws loci.formats.FormatException,
                        java.io.IOException

Description copied from class: loci.formats.FormatReader

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

java.io.IOException