loci.formats.in

Class BrukerReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BrukerReader

All Implemented Interfaces:

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

public class BrukerReader
extends FormatReader

BrukerReader is the file format reader for Bruker MRI files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.ArrayList<java.lang.String>	allFiles
private int	bits
private static java.lang.String	DATE_FORMAT
private java.lang.String[]	imageNames
private java.lang.String[]	institutions
private boolean	isFloat
private int	lastSeries
private int	ni
private int	nr
private int	ns
private java.lang.String[]	ordering
private java.util.ArrayList<java.lang.String>	pixelsFiles
private loci.common.RandomAccessInputStream	seriesStream
private boolean	signed
private java.lang.String[]	sizes
private java.lang.String[]	timestamps
private java.lang.String[]	users

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, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
BrukerReader() Constructs a new Bruker 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.
int	getRequiredDirectories(java.lang.String[] files) Returns the number of parent directories that are important when processing the given list of files.
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.).
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(java.lang.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	parseLines(java.lang.String[] lines)

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, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, 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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, 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

Field Detail

DATE_FORMAT

private static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

pixelsFiles

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

allFiles

private java.util.ArrayList<java.lang.String> allFiles

lastSeries

private int lastSeries

seriesStream

private loci.common.RandomAccessInputStream seriesStream

sizes

private java.lang.String[] sizes

ordering

private java.lang.String[] ordering

ni

private int ni

nr

private int nr

ns

private int ns

bits

private int bits

signed

private boolean signed

isFloat

private boolean isFloat

imageNames

private java.lang.String[] imageNames

institutions

private java.lang.String[] institutions

users

private java.lang.String[] users

timestamps

private java.lang.String[] timestamps

Constructor Detail

BrukerReader

public BrukerReader()

Constructs a new Bruker reader.

Method Detail

getRequiredDirectories

public int getRequiredDirectories(java.lang.String[] files)
                           throws FormatException,
                                  java.io.IOException

Description copied from interface: IFormatReader

Returns the number of parent directories that are important when processing the given list of files. The number of directories is relative to the common parent. For example, given a list with these two files: /path/to/file/foo /path/to/file/that/is/related A return value of 0 indicates that "/path/to/file/" is irrelevant. A return value of 1 indicates that "/path/to/" is irrelevant. Return values less than 0 are invalid. All listed files are assumed to belong to datasets of the same format.

Specified by:

getRequiredDirectories in interface IFormatReader

Overrides:

getRequiredDirectories in class FormatReader

Throws:

FormatException

java.io.IOException

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

isThisType

public boolean isThisType(java.lang.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 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 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.

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

See Also:

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

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

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

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

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

parseLines

private void parseLines(java.lang.String[] lines)