loci.formats.in
Class OMETiffReader
java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.BaseTiffReader
loci.formats.in.OMETiffReader
- All Implemented Interfaces:
- IFormatHandler, IFormatReader, StatusReporter
public class OMETiffReader
- extends BaseTiffReader
OMETiffReader is the file format reader for
OME-TIFF
files.
- Source code:
- Trac,
SVN
Fields inherited from class loci.formats.FormatReader |
collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION |
Method Summary |
String[] |
getUsedFiles()
Returns an array of filenames needed to open this dataset. |
protected void |
initMetadataStore()
Populates the metadata store using the data parsed in
BaseTiffReader.initStandardMetadata() along with some further parsing done in
the method itself. |
protected void |
initStandardMetadata()
Parses standard metadata. |
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.in.BaseTiffReader |
get16BitLookupTable, get8BitLookupTable, getImageCreationDate, getImageDescription, getImageName, getMetadataValue, getTiffDimensions, initFile, initMetadata, isThisType, put, put, put, put, put, put, put, put, put, put, putInt, swapIfRequired |
Methods inherited from class loci.formats.FormatReader |
addMeta, checkBytes, close, close, fileGroupOption, 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, 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 |
SAX_FACTORY
public static final SAXParserFactory SAX_FACTORY
- Factory for generating SAX parsers.
OMETiffReader
public OMETiffReader()
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
initMetadataStore
protected void initMetadataStore()
- Description copied from class:
BaseTiffReader
- Populates the metadata store using the data parsed in
BaseTiffReader.initStandardMetadata()
along with some further parsing done in
the method itself.
All calls to the active MetadataStore
should be made in this
method and only in this method. This is especially important for
sub-classes that override the getters for pixel set array size, etc.
- Overrides:
initMetadataStore
in class BaseTiffReader
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.
isThisType
public boolean isThisType(String name,
boolean open)
- Description copied from class:
FormatHandler
- Checks if a file matches the type of this format handler.
The default implementation checks filename suffixes against
those known for this format (the open parameter does nothing).
- Specified by:
isThisType
in interface IFormatHandler
- Overrides:
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.