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java.lang.Objectloci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.ICSReader
public class ICSReader
ICSReader is the file format reader for ICS (Image Cytometry Standard) files. More information on ICS can be found at http://libics.sourceforge.net
Field Summary | |
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protected int |
bitsPerPixel
Number of bits per pixel. |
protected String |
currentIcsId
Current filename. |
protected String |
currentIdsId
|
protected byte[] |
data
Image data. |
protected Location |
icsIn
Current ICS file. |
protected boolean |
versionTwo
Flag indicating whether current file is v2.0. |
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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ICSReader()
Constructs a new ICSReader. |
Method Summary | |
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void |
close()
Closes currently open file(s) and frees allocated memory. |
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). |
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 String currentIcsId
protected String currentIdsId
protected Location icsIn
protected int bitsPerPixel
protected boolean versionTwo
protected byte[] data
Constructor Detail |
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public ICSReader()
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 String[] getUsedFiles()
IFormatReader
getUsedFiles
in interface IFormatReader
getUsedFiles
in class FormatReader
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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