loci.formats.in

Class TextReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.TextReader

All Implemented Interfaces:

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

public class TextReader
extends FormatReader

Reader for text files containing tables of data. All image planes are stored in memory as 32-bit floats until the file is closed, so very large text documents will require commensurate available RAM. Text format is flexible, but assumed to be in tabular form with a consistent number of columns, and a labeled header line immediately preceding the data.

Author:

Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String[]	channels List of channel labels.
private float[][]	data Because we have no way of indexing into the text file efficiently in general, we cheat and store the entire file's data in a giant array.
private static java.lang.String	LABEL_X
private static java.lang.String	LABEL_Y
private static boolean	LITTLE_ENDIAN
private int	row Current row number.
private int	rowLength Number of tokens per row.
private int	sizeX Image width.
private int	sizeY Image height.
private static long	TIME_OFFSET How often to report progress during initialization, in milliseconds.
private int	xIndex Column index for X coordinate.
private int	yIndex Column index for Y coordinate.

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
TextReader() Constructs a new text reader.

Method Summary

Modifier and Type	Method and Description
private void	assignValues(double[] rowData) Assigns values from the given row into the data array.
private long	checkTime(long time, int no, long pos, long len)
void	close(boolean fileOnly) Closes the currently open file.
java.lang.String	getChannelLabel(int c) Gets the label for the given channel.
java.lang.Class<?>	getNativeDataType() Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
private java.lang.String[]	getNextLine(java.util.List<java.lang.String> lines)
private boolean	getRowData(java.lang.String[] tokens, double[] rowData) Parses numerical row data from the given tokens.
private int	getX(double[] rowData)
private int	getY(double[] rowData)
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
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.
java.lang.Object	openPlane(int no, int x, int y, int w, int h) Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
private int	parseFileHeader(java.util.List<java.lang.String> lines) Parses the file looking for the file header.
private void	parseHeaderRow(java.lang.String[] tokens) Populates rowLength, xIndex, yIndex, and channels.
private void	parseTableData(java.util.List<java.lang.String> lines, int linesToSkip) Reads the tabular data into the data array.
private void	populateCoreMetadata(int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT) Populates the CoreMetadata values.
private java.util.List<java.lang.String>	readFile(java.lang.String id)

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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, 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, 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, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

LITTLE_ENDIAN

private static final boolean LITTLE_ENDIAN

See Also:

Constant Field Values

LABEL_X

private static final java.lang.String LABEL_X

See Also:

Constant Field Values

LABEL_Y

private static final java.lang.String LABEL_Y

See Also:

Constant Field Values

TIME_OFFSET

private static final long TIME_OFFSET

How often to report progress during initialization, in milliseconds.

See Also:

Constant Field Values

data

private float[][] data

Because we have no way of indexing into the text file efficiently in general, we cheat and store the entire file's data in a giant array.

row

private int row

Current row number.

rowLength

private int rowLength

Number of tokens per row.

xIndex

private int xIndex

Column index for X coordinate.

yIndex

private int yIndex

Column index for Y coordinate.

channels

private java.lang.String[] channels

List of channel labels.

sizeX

private int sizeX

Image width.

sizeY

private int sizeY

Image height.

Constructor Detail

TextReader

public TextReader()

Constructs a new text reader.

Method Detail

getChannelLabel

public java.lang.String getChannelLabel(int c)

Gets the label for the given channel.

isThisType

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

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

java.io.IOException

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.

openPlane

public java.lang.Object openPlane(int no,
                                  int x,
                                  int y,
                                  int w,
                                  int h)
                           throws FormatException,
                                  java.io.IOException

Description copied from interface: IFormatReader

Obtains the specified image plane (or sub-image thereof) in the reader's native data structure. For most readers this is a byte array; however, some readers call external APIs that work with other types such as BufferedImage. The openPlane method exists to maintain generality and efficiency while avoiding pollution of the API with AWT-specific logic.

Specified by:

openPlane in interface IFormatReader

Overrides:

openPlane in class FormatReader

Throws:

FormatException

java.io.IOException

See Also:

FormatReader, BufferedImageReader

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

getNativeDataType

public java.lang.Class<?> getNativeDataType()

Description copied from interface: IFormatHandler

Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object). For most readers this type will be a byte array; however, some readers call external APIs that work with other types such as BufferedImage.

Specified by:

getNativeDataType in interface IFormatHandler

Overrides:

getNativeDataType in class FormatHandler

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

readFile

private java.util.List<java.lang.String> readFile(java.lang.String id)
                                           throws java.io.IOException

Throws:

java.io.IOException

parseFileHeader

private int parseFileHeader(java.util.List<java.lang.String> lines)
                     throws FormatException

Parses the file looking for the file header. Determines image extents (sets sizeX and sizeY). Determines channel names (populates channels array).

Returns:

number of rows in the header

Throws:

FormatException

parseTableData

private void parseTableData(java.util.List<java.lang.String> lines,
                            int linesToSkip)

Reads the tabular data into the data array.

populateCoreMetadata

private void populateCoreMetadata(int sizeX,
                                  int sizeY,
                                  int sizeZ,
                                  int sizeC,
                                  int sizeT)

Populates the CoreMetadata values.

getRowData

private boolean getRowData(java.lang.String[] tokens,
                           double[] rowData)

Parses numerical row data from the given tokens.

Parameters:

tokens - list of token strings to parse

rowData - array to fill in with the data; length must match tokens

Returns:

true if the data could be parsed

parseHeaderRow

private void parseHeaderRow(java.lang.String[] tokens)

Populates rowLength, xIndex, yIndex, and channels.

assignValues

private void assignValues(double[] rowData)

Assigns values from the given row into the data array.

checkTime

private long checkTime(long time,
                       int no,
                       long pos,
                       long len)

getX

private int getX(double[] rowData)

getY

private int getY(double[] rowData)

getNextLine

private java.lang.String[] getNextLine(java.util.List<java.lang.String> lines)