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:
IFormatHandler, IFormatReader, 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()
          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: IFormatReader
Checks if the given block is a valid header for this file format.

Specified by:
isThisType in interface IFormatReader
Overrides:
isThisType in class BaseTiffReader

close

public void close()
           throws IOException
Description copied from interface: IFormatHandler
Closes currently open file(s) and frees allocated memory.

Specified by:
close in interface IFormatHandler
Overrides:
close in class FormatReader
Throws:
IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
                           IOException
Description copied from interface: IFormatReader
Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:
fileGroupOption in interface IFormatReader
Overrides:
fileGroupOption in class FormatReader
Throws:
FormatException
IOException

getUsedFiles

public String[] getUsedFiles()
Description copied from interface: IFormatReader
Returns an array of filenames needed to open this dataset.

Specified by:
getUsedFiles in interface IFormatReader
Overrides:
getUsedFiles in class FormatReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        IOException
Description copied from interface: IFormatReader
Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Specified by:
openBytes in interface 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:
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 FormatException,
                        IOException
Description copied from class: 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:
FormatException
IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws 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:
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