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

MetamorphReader()
Constructs a new Metamorph reader.

Method Summary

void	close()
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)
protected String	getImageCreationDate() Retrieves the image creation date.
protected String	getImageName() Retrieves the image name from the TIFF.
String[]	getUsedFiles()
protected void	initFile(String id)
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)
byte[]	openBytes(int no, byte[] buf)

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)

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class BaseTiffReader

close

public void close()
           throws IOException

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

Specified by:

fileGroupOption in interface loci.formats.IFormatReader

Overrides:

fileGroupOption in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

getUsedFiles

public String[] getUsedFiles()

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

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class BaseTiffReader

Throws:

loci.formats.FormatException

IOException

initFile

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

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