Package loci.formats.in

Class ScanrReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ScanrReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class ScanrReader
extends FormatReader

ScanrReader is the file format reader for Olympus ScanR datasets.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	ScanrReader.ScanrHandler

Field Summary

Fields

Modifier and Type	Field	Description
private static final String	ACQUISITION_FILE
private final List<String>	channelNames
private Double	deltaT
private static final String	EXPERIMENT_FILE
private final List<Double>	exposures
private int	fieldColumns
private ome.units.quantity.Length[]	fieldPositionX
private ome.units.quantity.Length[]	fieldPositionY
private int	fieldRows
private boolean	foundPositions
private static final String[]	METADATA_SUFFIXES
private final List<String>	metadataFiles
private Double	pixelSize
private String	plateName
private MinimalTiffReader	reader
private Map<Integer,String[]>	seriesFiles
static final String	SKIP_MISSING_WELLS
static final boolean	SKIP_MISSING_WELLS_DEFAULT
private String[]	tiffs
private int	tileHeight
private int	tileWidth
private int	wellColumns
private int	wellCount
private Map<String,Integer>	wellLabels
private Map<Integer,Integer>	wellNumbers
private int	wellRows
private static final String	XML_FILE

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	Description
ScanrReader()	Constructs a new ScanR reader.

Method Summary

Modifier and Type	Method	Description
private void	adjustWellDimensions()
void	close(boolean fileOnly)	Closes the currently open file.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
private String	getBlock(int index, String axis)
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(String name, boolean open)	Checks if a file matches the type of this format reader.
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.
boolean	skipMissingWells()

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, 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, 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.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

XML_FILE

private static final String XML_FILE

See Also:

• Constant Field Values

EXPERIMENT_FILE

private static final String EXPERIMENT_FILE

See Also:

• Constant Field Values

ACQUISITION_FILE

private static final String ACQUISITION_FILE

See Also:

• Constant Field Values

METADATA_SUFFIXES

private static final String[] METADATA_SUFFIXES

SKIP_MISSING_WELLS

public static final String SKIP_MISSING_WELLS

See Also:

• Constant Field Values

SKIP_MISSING_WELLS_DEFAULT

public static final boolean SKIP_MISSING_WELLS_DEFAULT

See Also:

• Constant Field Values

metadataFiles

private final List<String> metadataFiles

wellRows

private int wellRows

wellColumns

private int wellColumns

fieldRows

private int fieldRows

fieldColumns

private int fieldColumns

wellCount

private int wellCount

channelNames

private final List<String> channelNames

wellLabels

private Map<String,Integer> wellLabels

wellNumbers

private Map<Integer,Integer> wellNumbers

plateName

private String plateName

pixelSize

private Double pixelSize

tileWidth

private int tileWidth

tileHeight

private int tileHeight

tiffs

private String[] tiffs

reader

private MinimalTiffReader reader

foundPositions

private boolean foundPositions

fieldPositionX

private ome.units.quantity.Length[] fieldPositionX

fieldPositionY

private ome.units.quantity.Length[] fieldPositionY

exposures

private final List<Double> exposures

deltaT

private Double deltaT

seriesFiles

private Map<Integer,String[]> seriesFiles

Constructor Details

ScanrReader

public ScanrReader()

Constructs a new ScanR reader.

Method Details

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
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

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
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

IOException

See Also:

• FormatTools.MUST_GROUP
• FormatTools.CAN_GROUP
• FormatTools.CANNOT_GROUP

isThisType

public boolean isThisType(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

Parameters:

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 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:

IOException

getSeriesUsedFiles

public 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 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

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 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.

IOException - if there was a problem reading the file.

See Also:

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

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

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

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

skipMissingWells

public boolean skipMissingWells()

getBlock

private String getBlock(int index,
 String axis)

adjustWellDimensions

private void adjustWellDimensions()