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java.lang.Objectloci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.PerkinElmerReader
public class PerkinElmerReader
PerkinElmerReader is the file format reader for PerkinElmer files.
Field Summary | |
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protected String[] |
files
Tiff files to open. |
protected TiffReader[] |
tiff
Helper reader. |
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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PerkinElmerReader()
Constructs a new PerkinElmer 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. |
boolean |
isThisType(String name,
boolean open)
Checks if a file matches the type of this format handler. |
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, 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, setId |
Methods inherited from interface loci.formats.StatusReporter |
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addStatusListener, getStatusListeners, removeStatusListener |
Field Detail |
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protected TiffReader[] tiff
protected String[] files
Constructor Detail |
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public PerkinElmerReader()
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(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
public boolean isThisType(String name, boolean open)
FormatHandler
isThisType
in interface IFormatHandler
isThisType
in class FormatHandler
open
- If true, and the file extension is insufficient to determine
the file type, the (existing) file is opened for further analysis.
Does nothing in the default implementation.protected void initFile(String id) throws FormatException, IOException
FormatReader
initFile
in class FormatReader
FormatException
IOException
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