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java.lang.Objectloci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.BaseTiffReader
loci.formats.in.MetamorphReader
public class MetamorphReader
Reader is the file format reader for Metamorph STK files.
Field Summary |
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Fields inherited from class loci.formats.in.BaseTiffReader |
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ifds |
Fields inherited from class loci.formats.FormatReader |
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collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION |
Fields inherited from class loci.formats.FormatHandler |
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currentId, debug, debugLevel, format, statusListeners, suffixes |
Fields inherited from interface loci.formats.IFormatReader |
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CAN_GROUP, CANNOT_GROUP, MUST_GROUP |
Constructor Summary | |
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MetamorphReader()
Constructs a new Metamorph reader. |
Method Summary | |
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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 |
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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.FormatHandler |
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addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface loci.formats.IFormatHandler |
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getFormat, getSuffixes, isThisType, isThisType, setId |
Methods inherited from interface loci.formats.StatusReporter |
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addStatusListener, getStatusListeners, removeStatusListener |
Constructor Detail |
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public MetamorphReader()
Method Detail |
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public boolean isThisType(byte[] block)
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class BaseTiffReader
public void close() throws IOException
IFormatHandler
close
in interface IFormatHandler
close
in class FormatReader
IOException
public int fileGroupOption(String id) throws FormatException, IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
in class FormatReader
FormatException
IOException
public String[] getUsedFiles()
IFormatReader
getUsedFiles
in interface IFormatReader
getUsedFiles
in class FormatReader
public byte[] openBytes(int no, byte[] buf) throws FormatException, IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class BaseTiffReader
no
- the image index within the file.buf
- a pre-allocated buffer.
buf
for convenience.
FormatException
- if there was a problem parsing the metadata of the
file.
IOException
- if there was a problem reading the file.protected void initFile(String id) throws FormatException, IOException
FormatReader
initFile
in class BaseTiffReader
FormatException
IOException
protected void initStandardMetadata() throws FormatException, IOException
BaseTiffReader
initStandardMetadata
in class BaseTiffReader
FormatException
IOException
protected String getImageName()
BaseTiffReader
getImageName
in class BaseTiffReader
protected String getImageCreationDate()
BaseTiffReader
getImageCreationDate
in class BaseTiffReader
public static String decodeDate(int julian)
public static String decodeTime(int millis)
public static String intFormat(int myint, int digits)
public static String intFormatMax(int myint, int maxint)
myint
- integer to formatmaxint
- max of "myint"
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