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java.lang.Objectloci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.OIFReader
public class OIFReader
OIFReader is the file format reader for Fluoview FV 1000 OIF files.
Field Summary | |
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protected String[] |
code
|
protected int |
imageDepth
|
protected String[] |
size
|
protected BMPReader |
thumbReader
Helper reader to open the thumbnail. |
protected TiffReader[] |
tiffReader
Helper reader to open TIFF files. |
protected Vector |
tiffs
Names of every TIFF file to open. |
protected Vector |
usedFiles
List of files in the current OIF dataset. |
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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OIFReader()
Constructs a new OIF reader. |
Method Summary | |
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void |
close()
Closes currently open file(s) and frees allocated memory. |
void |
close(boolean fileOnly)
Closes the currently open file. |
int |
fileGroupOption(String id)
Returns an int indicating that we cannot, must, or might group the files in a given dataset. |
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.). |
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). |
BufferedImage |
openThumbImage(int no)
Obtains a thumbnail for the specified image from the current file. |
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 |
Field Detail |
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protected Vector tiffs
protected TiffReader[] tiffReader
protected BMPReader thumbReader
protected Vector usedFiles
protected String[] size
protected String[] code
protected int imageDepth
Constructor Detail |
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public OIFReader()
Method Detail |
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public boolean isThisType(byte[] block)
IFormatReader
public int fileGroupOption(String id) throws FormatException, IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
in class FormatReader
FormatException
IOException
public byte[] openBytes(int no, byte[] buf) throws FormatException, IOException
IFormatReader
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.public BufferedImage openThumbImage(int no) throws FormatException, IOException
IFormatReader
openThumbImage
in interface IFormatReader
openThumbImage
in class FormatReader
FormatException
IOException
public String[] getUsedFiles()
IFormatReader
getUsedFiles
in interface IFormatReader
getUsedFiles
in class FormatReader
public void close(boolean fileOnly) throws IOException
IFormatReader
IFormatHandler.close()
.
close
in interface IFormatReader
close
in class FormatReader
IOException
public void close() throws IOException
IFormatHandler
close
in interface IFormatHandler
close
in class FormatReader
IOException
protected void initFile(String id) throws FormatException, IOException
FormatReader
initFile
in class FormatReader
FormatException
IOException
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