loci.formats.in

Class TissueFAXSReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.TissueFAXSReader

All Implemented Interfaces:

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

public class TissueFAXSReader
extends FormatReader

Reader for TissueFAXS format from TissueGnostics.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	TissueFAXSReader.Channel
(package private) class	TissueFAXSReader.ScanRegion

Field Summary

Fields

Modifier and Type	Field and Description
private static org.slf4j.Logger	LOGGER
private java.util.List<java.lang.String>	pixelsFiles
private java.util.List<TissueFAXSReader.ScanRegion>	regions
private static int	WAVE_MAX
private static int	WAVE_MIN

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
TissueFAXSReader() Constructs a new TissueGnostics TissueFAXS reader.

Method Summary

Modifier and Type	Method and Description
byte[]	applyTransformation(byte[] tile, int regionID, int level, int channel, int zIndex, int fovRow, int fovColumn) Extension point for doing something to an FOV immediately after decompression, before any stitching or cropping.
void	close(boolean fileOnly) Closes the currently open file.
private void	copyCorrectionImageToBuffer(TissueFAXSReader.ScanRegion region, loci.common.Region dest, int[] zct, byte[] buf)
private void	copyRegion(loci.common.Region srcRegion, byte[] src, loci.common.Region destRegion, byte[] dest, int tileWidth)
private void	copyRegionToBuffer(TissueFAXSReader.ScanRegion region, int level, loci.common.Region dest, int[] zct, byte[] buf)
private void	findDBFiles() If a .tfcyto file was provided, then that is the only file that should be read.
private java.util.List<TissueFAXSReader.ScanRegion>	getAllRegions(int t)
private Codec	getCodec(int compression)
private CodecOptions	getCodecOptions(TissueFAXSReader.ScanRegion region)
private int	getLevel()
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
private TissueFAXSReader.ScanRegion	getRegion()
private TissueFAXSReader.ScanRegion	getRegion(int t)
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
private boolean	isCorrectionImage(TissueFAXSReader.ScanRegion r)
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 java.sql.Connection	openConnection(java.lang.String file)
private byte[][]	splitFOVs(TissueFAXSReader.ScanRegion region, byte[] tile, int scale) The largest resolution stores one field of view (FOV) per tile.

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, fileGroupOption, 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, 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, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, 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

LOGGER

private static final org.slf4j.Logger LOGGER

WAVE_MIN

private static final int WAVE_MIN

See Also:

Constant Field Values

WAVE_MAX

private static final int WAVE_MAX

See Also:

Constant Field Values

pixelsFiles

private java.util.List<java.lang.String> pixelsFiles

regions

private java.util.List<TissueFAXSReader.ScanRegion> regions

Constructor Detail

TissueFAXSReader

public TissueFAXSReader()

Constructs a new TissueGnostics TissueFAXS reader.

Method Detail

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 FormatReader

Throws:

java.io.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 FormatReader

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 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

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.

See Also:

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

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

findDBFiles

private void findDBFiles()

If a .tfcyto file was provided, then that is the only file that should be read. If an .aqproj file was provided, look for all associated .tfcyto files.

getAllRegions

private java.util.List<TissueFAXSReader.ScanRegion> getAllRegions(int t)
                                                           throws FormatException

Throws:

FormatException

getRegion

private TissueFAXSReader.ScanRegion getRegion()
                                       throws FormatException

Throws:

FormatException

getRegion

private TissueFAXSReader.ScanRegion getRegion(int t)
                                       throws FormatException

Throws:

FormatException

isCorrectionImage

private boolean isCorrectionImage(TissueFAXSReader.ScanRegion r)

getLevel

private int getLevel()
              throws FormatException

Throws:

FormatException

getCodec

private Codec getCodec(int compression)
                throws UnsupportedCompressionException

Throws:

UnsupportedCompressionException

getCodecOptions

private CodecOptions getCodecOptions(TissueFAXSReader.ScanRegion region)

splitFOVs

private byte[][] splitFOVs(TissueFAXSReader.ScanRegion region,
                           byte[] tile,
                           int scale)

The largest resolution stores one field of view (FOV) per tile. Each sub-resolution has the same tile size as the largest resolution, so the number of FOVs stored in one tile increases as the resolutions get smaller. For example, with a tile size of 2048x2048 and a downsample factor of 4, resolution 1 will have 16 (4x4) FOVs per tile, with each FOV being 512x512. However, none of the FOV positions or overlaps are taken into account. So the first step in assembling a sub-resolution is to split each tile into its component FOVs. Then each FOV can be repositioned according to its associated stitching rectangle and overlap. This method only splits the given tile into component FOVs. This is not necessary for the largest resolution, only sub-resolutions.

copyRegionToBuffer

private void copyRegionToBuffer(TissueFAXSReader.ScanRegion region,
                                int level,
                                loci.common.Region dest,
                                int[] zct,
                                byte[] buf)
                         throws FormatException,
                                java.io.IOException

Throws:

FormatException

java.io.IOException

copyRegion

private void copyRegion(loci.common.Region srcRegion,
                        byte[] src,
                        loci.common.Region destRegion,
                        byte[] dest,
                        int tileWidth)

copyCorrectionImageToBuffer

private void copyCorrectionImageToBuffer(TissueFAXSReader.ScanRegion region,
                                         loci.common.Region dest,
                                         int[] zct,
                                         byte[] buf)
                                  throws FormatException,
                                         java.io.IOException

Throws:

FormatException

java.io.IOException

openConnection

private java.sql.Connection openConnection(java.lang.String file)
                                    throws java.io.IOException

Throws:

java.io.IOException

applyTransformation

public byte[] applyTransformation(byte[] tile,
                                  int regionID,
                                  int level,
                                  int channel,
                                  int zIndex,
                                  int fovRow,
                                  int fovColumn)

Extension point for doing something to an FOV immediately after decompression, before any stitching or cropping. Overriding this in a subclass could be used to apply a correction image. Currently this method is a no-op.