loci.formats.in
Class MetamorphReader

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatReader
          extended by loci.formats.in.BaseTiffReader
              extended by 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