loci.formats.in

Class XLEFReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

loci.formats.in.XLEFReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class XLEFReader
extends LMSFileReader

XLEFReader is the file format reader for Leica Microsystems' XLEF files.

Author:

Melissa Linkert melissa at glencoesoftware.com, Constanze Wendlandt constanze.wendlandt at leica-microsystems.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static class	XLEFReader.PathComparator Helper class to sort file paths by name and depth

Nested classes/interfaces inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

LMSFileReader.ImageFormat

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<LMSFileReader>	readers

Fields inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

associatedXmlDoc, log, metaTemp, OLD_PHYSICAL_SIZE_DEFAULT, OLD_PHYSICAL_SIZE_KEY

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, 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, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
XLEFReader() Constructs a new Leica XLEF reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
LMSFileReader.ImageFormat	getImageFormat() Returns the file format in which actual image bytes are stored
private int	getReaderIndex(int seriesIndex) Returns the index of the correct reader for the series index.
private byte[]	getRgbChannel(int channel, byte[] in) Returns single channel data for an rgb plane
private int	getSeriesPerReaderIndex(int series) Returns the index of the series (tile) in the corresponding reader
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
java.lang.String[]	getUsedFiles(boolean noPixels) Returns an array of filenames needed to open this dataset.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
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.
byte[]	openBytes(int no, int x, int y, int w, int h) Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
private byte[]	openBytesJpeg(int no, byte[] buf, int x, int y, int w, int h) Gets bytes of jpeg images.
void	reopenFile() Reopen any files that were closed, and which are expected to be open while the reader is open.
private void	setMetadataOfMultipleImagesReaders()
private void	sortMultipleImagesReaders() Sorts frames of all MultipleImagesReaders as per core dimension sizes and order
private void	sortPaths(java.util.List<java.lang.String> paths) Sorts file paths by name and depth and moves current file path to the beginning
private int	sum(int[] arr, int start, int end) Sums up all values of an array, from start index to (including) end index
private void	transformBytes8To16(byte[] in, byte[] out, int outRes) Transforms an 8bit byte array to a 16bit byte array, optionally with bit upscaling (8-16bit)

Methods inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

addSeriesMeta, addSeriesMetaList, fileExists, getCore, makeFilterMetadata, setCore, translateMetadata, translateMetadata, useOldPhysicalSizeCalculation

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, close, coreIndexToSeries, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

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

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

readers

private java.util.List<LMSFileReader> readers

Constructor Detail

XLEFReader

public XLEFReader()

Constructs a new Leica XLEF reader.

Method Detail

openBytes

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

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

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.

java.io.IOException - if there was a problem reading the file.

openBytes

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

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class FormatReader

Throws:

FormatException

java.io.IOException

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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 FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

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

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

java.io.IOException

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

java.io.IOException

See Also:

FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP

getUsedFiles

public java.lang.String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class FormatReader

getSeriesUsedFiles

public java.lang.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. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

close

public void close(boolean fileOnly)
           throws java.io.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 LMSFileReader

Throws:

java.io.IOException

reopenFile

public void reopenFile()
                throws java.io.IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

java.io.IOException

getImageFormat

public LMSFileReader.ImageFormat getImageFormat()

Description copied from class: LMSFileReader

Returns the file format in which actual image bytes are stored

Specified by:

getImageFormat in class LMSFileReader

getReaderIndex

private int getReaderIndex(int seriesIndex)

Returns the index of the correct reader for the series index. Currently, tilescans are treated as if each tile was an own series (like in LIFReader), so one reader may contain multiple series.

Parameters:

seriesIndex - index of series

Returns:

reader which contains the series

getSeriesPerReaderIndex

private int getSeriesPerReaderIndex(int series)

Returns the index of the series (tile) in the corresponding reader

Parameters:

series - index of the series over all readers

Returns:

openBytesJpeg

private byte[] openBytesJpeg(int no,
                             byte[] buf,
                             int x,
                             int y,
                             int w,
                             int h)
                      throws FormatException,
                             java.io.IOException

Gets bytes of jpeg images. Originally monochrome images that were stored by LASX as 24bit (RGB) jpegs are transformed to monochrome again (upscaled to their original bit depth)

Parameters:

no - the plane index within the current series

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:

Throws:

FormatException

java.io.IOException

sortMultipleImagesReaders

private void sortMultipleImagesReaders()
                                throws FormatException

Sorts frames of all MultipleImagesReaders as per core dimension sizes and order

Throws:

FormatException

setMetadataOfMultipleImagesReaders

private void setMetadataOfMultipleImagesReaders()

transformBytes8To16

private void transformBytes8To16(byte[] in,
                                 byte[] out,
                                 int outRes)

Transforms an 8bit byte array to a 16bit byte array, optionally with bit upscaling (8-16bit)

Parameters:

in - 8bit buffer with data

out - 16bit buffer to be filled

outRes - resolution to which data shall be upscaled (8-16)

getRgbChannel

private byte[] getRgbChannel(int channel,
                             byte[] in)

Returns single channel data for an rgb plane

Parameters:

channel - Index of channel that shall be read

in - channel separated buffer

sum

private int sum(int[] arr,
                int start,
                int end)

Sums up all values of an array, from start index to (including) end index

Parameters:

arr -

start - first array position whose value shall be added

end - last array position whose value shall be added

Returns:

sortPaths

private void sortPaths(java.util.List<java.lang.String> paths)

Sorts file paths by name and depth and moves current file path to the beginning

Parameters:

paths -