Package loci.formats.in

Class ZeissXRMReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ZeissXRMReader

All Implemented Interfaces:

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

public class ZeissXRMReader
extends FormatReader

ZeissXRMReader is the file format reader for Zeiss X-Ray Microscopy .txm and .txrm files.

Field Summary

Fields

Modifier and Type	Field	Description
private static final String	AUTORECON_PATH
private double[]	current
private static final String	DATASET
private static final String	DATESTAMP
private String[]	datestamps
private double[]	exposureTimes
private static final String	GENERAL_PARAMS
private static final String	IMAGE_DETAILS
private static final String	IMAGE_INFO_PATH
private List<String>	imagePaths
private Double	pixelSize
private POIService	poi
private static final String	POSITIONS
private static final String	PROJECTION
private static final String	RECON_SETTINGS
private static final String	RECON_SETTINGS_PATH
private static final String	REFERENCE_PATH
private static final String	SOURCE_ASSEMBLY
private double[]	voltage
private double[]	xPos
private double[]	yPos
private double[]	zPos

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
ZeissXRMReader()	Constructs a new Zeiss XRM reader.

Method Summary

Modifier and Type	Method	Description
private void	addMetadataList(double[] v, String key)	Add each double value in an array to the original metadata table, using the given key.
private void	addMetadataList(double[] v, String key, boolean formatDoubles)	Add each double value in an array to the original metadata table, using the given key.
void	close(boolean fileOnly)	Closes the currently open file.
private String	formatDouble(double v)	Format double value to 2 decimal places, rounding to nearest.
private String	getMetadataPixelType(int dataType)
private int	getPixelType(int dataType)	Convert an XRM data type to a Bio-Formats pixel type.
private String	getYesNo(loci.common.RandomAccessInputStream stream)
private void	handleTXMMetadata(String name, loci.common.RandomAccessInputStream stream)	Parse metadata fields specific to .txm files.
private void	handleTXRMMetadata(String name, loci.common.RandomAccessInputStream stream)	Parse metadata fields specific to .txrm files.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private void	initPOIService()
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.
private double[]	readAsDoubles(loci.common.RandomAccessInputStream stream)
private String	readAsString(loci.common.RandomAccessInputStream stream)

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, 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

DATESTAMP

private static final String DATESTAMP

See Also:

• Constant Field Values

IMAGE_INFO_PATH

private static final String IMAGE_INFO_PATH

See Also:

• Constant Field Values

RECON_SETTINGS_PATH

private static final String RECON_SETTINGS_PATH

See Also:

• Constant Field Values

AUTORECON_PATH

private static final String AUTORECON_PATH

See Also:

• Constant Field Values

REFERENCE_PATH

private static final String REFERENCE_PATH

See Also:

• Constant Field Values

POSITIONS

private static final String POSITIONS

See Also:

• Constant Field Values

DATASET

private static final String DATASET

See Also:

• Constant Field Values

RECON_SETTINGS

private static final String RECON_SETTINGS

See Also:

• Constant Field Values

IMAGE_DETAILS

private static final String IMAGE_DETAILS

See Also:

• Constant Field Values

SOURCE_ASSEMBLY

private static final String SOURCE_ASSEMBLY

See Also:

• Constant Field Values

GENERAL_PARAMS

private static final String GENERAL_PARAMS

See Also:

• Constant Field Values

PROJECTION

private static final String PROJECTION

See Also:

• Constant Field Values

poi

private transient POIService poi

imagePaths

private List<String> imagePaths

pixelSize

private transient Double pixelSize

exposureTimes

private transient double[] exposureTimes

current

private transient double[] current

voltage

private transient double[] voltage

xPos

private transient double[] xPos

yPos

private transient double[] yPos

zPos

private transient double[] zPos

datestamps

private transient String[] datestamps

Constructor Details

ZeissXRMReader

public ZeissXRMReader()

Constructs a new Zeiss XRM reader.

Method Details

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

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)

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

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

handleTXMMetadata

private void handleTXMMetadata(String name,
 loci.common.RandomAccessInputStream stream)
                        throws IOException

Parse metadata fields specific to .txm files.

Throws:

IOException

handleTXRMMetadata

private void handleTXRMMetadata(String name,
 loci.common.RandomAccessInputStream stream)
                         throws IOException

Parse metadata fields specific to .txrm files.

Throws:

IOException

initPOIService

private void initPOIService()
                     throws FormatException,
IOException

Throws:

FormatException

IOException

getPixelType

private int getPixelType(int dataType)
                  throws FormatException

Convert an XRM data type to a Bio-Formats pixel type.

Throws:

FormatException

getMetadataPixelType

private String getMetadataPixelType(int dataType)
                             throws FormatException

Throws:

FormatException

readAsString

private String readAsString(loci.common.RandomAccessInputStream stream)
                     throws IOException

Throws:

IOException

getYesNo

private String getYesNo(loci.common.RandomAccessInputStream stream)
                 throws IOException

Throws:

IOException

readAsDoubles

private double[] readAsDoubles(loci.common.RandomAccessInputStream stream)
                        throws IOException

Throws:

IOException

addMetadataList

private void addMetadataList(double[] v,
 String key)

Add each double value in an array to the original metadata table, using the given key. Double values are not formatted.

addMetadataList

private void addMetadataList(double[] v,
 String key,
 boolean formatDoubles)

Add each double value in an array to the original metadata table, using the given key. Double values are formatted to 2 decimal places if the formatDoubles parameter is true.

formatDouble

private String formatDouble(double v)

Format double value to 2 decimal places, rounding to nearest.