loci.formats.in

Class TextReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.TextReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

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.

Source code:

Trac, Gitweb

Author:

Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields inherited from class loci.formats.FormatReader

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

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, 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

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
String	getChannelLabel(int c) Gets the label for the given channel.
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).
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
boolean	isThisType(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.
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.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, close, coreIndexToSeries, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getSuffixes

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

Constructor Detail

TextReader

public TextReader()

Constructs a new text reader.

Method Detail

getChannelLabel

public String getChannelLabel(int c)

Gets the label for the given channel.

isThisType

public boolean isThisType(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 FormatReader

Throws:

IOException

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

Specified by:

openBytes in class FormatReader

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.

openPlane

public Object openPlane(int no,
               int x,
               int y,
               int w,
               int h)
                 throws FormatException,
                        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

IOException

See Also:

FormatReader, BufferedImageReader

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 FormatReader

Throws:

IOException

getNativeDataType

public 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(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 FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

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