loci.formats.in

Class MetamorphReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseTiffReader

loci.formats.in.MetamorphReader

All Implemented Interfaces:

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

public class MetamorphReader
extends BaseTiffReader

Reader is the file format reader for Metamorph STK files.

Source code:

Trac, SVN

Author:

Eric Kjellman egkjellman at wisc.edu, Melissa Linkert linkert at wisc.edu, Curtis Rueden ctrueden at wisc.edu, Sebastien Huart Sebastien dot Huart at curie.fr

Field Summary

Fields inherited from class loci.formats.in.BaseTiffReader

ifds

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
MetamorphReader() Constructs a new Metamorph reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes currently open file(s) and frees allocated memory.
static String	decodeDate(int julian) Converts a Julian date value into a human-readable string.
static String	decodeTime(int millis) Converts a time value in milliseconds into a human-readable string.
int	fileGroupOption(String id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
protected String	getImageCreationDate() Retrieves the image creation date.
protected String	getImageName() Retrieves the image name from the TIFF.
String[]	getUsedFiles() Returns an array of filenames needed to open this dataset.
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
protected void	initStandardMetadata() Parses standard metadata.
static String	intFormat(int myint, int digits) Formats an integer value with leading 0s if needed.
static String	intFormatMax(int myint, int maxint) Formats an integer with leading 0 using maximum sequence number.
boolean	isThisType(byte[] block) Checks if the given block is a valid header for this file format.
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.in.BaseTiffReader

get16BitLookupTable, get8BitLookupTable, getImageDescription, getMetadataValue, getTiffDimensions, initMetadata, initMetadataStore, put, put, put, put, put, put, put, put, put, put, putInt, swapIfRequired

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, close, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, 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, 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, isThisType, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

Constructor Detail

MetamorphReader

public MetamorphReader()

Constructs a new Metamorph 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.

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class BaseTiffReader

close

public void close()
           throws 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:

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws loci.formats.FormatException,
                           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

IOException

getUsedFiles

public 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

openBytes

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

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class BaseTiffReader

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.

IOException - if there was a problem reading the file.

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
                        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 BaseTiffReader

Throws:

loci.formats.FormatException

IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws loci.formats.FormatException,
                                    IOException

Description copied from class: BaseTiffReader

Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

loci.formats.FormatException

IOException

getImageName

protected String getImageName()

Description copied from class: BaseTiffReader

Retrieves the image name from the TIFF.

Overrides:

getImageName in class BaseTiffReader

Returns:

the image name.

getImageCreationDate

protected String getImageCreationDate()

Description copied from class: BaseTiffReader

Retrieves the image creation date.

Overrides:

getImageCreationDate in class BaseTiffReader

Returns:

the image creation date.

decodeDate

public static String decodeDate(int julian)

Converts a Julian date value into a human-readable string.

decodeTime

public static String decodeTime(int millis)

Converts a time value in milliseconds into a human-readable string.

intFormat

public static String intFormat(int myint,
               int digits)

Formats an integer value with leading 0s if needed.

intFormatMax

public static String intFormatMax(int myint,
                  int maxint)

Formats an integer with leading 0 using maximum sequence number.

Parameters:

myint - integer to format

maxint - max of "myint"

Returns:

String