loci.formats.in

Class TrestleReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.TrestleReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class TrestleReader
extends BaseTiffReader

TrestleReader is the file format reader for Trestle slide datasets.

Field Summary

Fields

Modifier and Type	Field and Description
private ArrayList<String>	files
private static org.slf4j.Logger	LOGGER Logger for this class.
private int[]	overlaps
private String	roiDrawFile
private String	roiFile

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS

Fields inherited from class loci.formats.in.MinimalTiffReader

equalStrips, ifds, lastPlane, noSubresolutions, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
TrestleReader() Constructs a new Trestle reader.

Method Summary

Modifier and Type	Method and Description
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.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
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(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format reader.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h) Obtains a sub-image of the specified image plane into a pre-allocated byte array.
private void	parseROIs(MetadataStore store)

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initMetadata, put, put, put, put, put, put, put, put, put, put, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

get16BitLookupTable, get8BitLookupTable, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, openThumbBytes, reopenFile, setResolutionLevel

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

files

private ArrayList<String> files

roiFile

private String roiFile

roiDrawFile

private String roiDrawFile

overlaps

private int[] overlaps

Constructor Detail

TrestleReader

public TrestleReader()

Constructs a new Trestle reader.

Method Detail

isThisType

public boolean isThisType(String name,
                          boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class MinimalTiffReader

Throws:

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
                           IOException

Description copied from interface: IFormatReader

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class MinimalTiffReader

Parameters:

no - the image index within the file.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

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.

See Also:

IFormatReader.openBytes(int, byte[], int, int, int, int)

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class MinimalTiffReader

Throws:

IOException

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class MinimalTiffReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class MinimalTiffReader

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException

Description copied from class: FormatReader

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:

initFile in class BaseTiffReader

Throws:

FormatException - if a parsing error occurs processing the file.

IOException - if an I/O error occurs processing the file

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()
                          throws FormatException

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

Throws:

FormatException

parseROIs

private void parseROIs(MetadataStore store)
                throws FormatException,
                       IOException

Throws:

FormatException

IOException