Package loci.formats.in

Class MetamorphReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.MetamorphReader

All Implemented Interfaces:

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

public class MetamorphReader
extends BaseTiffReader

Reader is the file format reader for Metamorph STK files.

Author:

Eric Kjellman egkjellman at wisc.edu, Melissa Linkert melissa at glencoesoftware.com, Curtis Rueden ctrueden at wisc.edu, Sebastien Huart Sebastien dot Huart at curie.fr

Field Summary

Fields

Modifier and Type	Field	Description
private String	binning
private boolean	bizarreMultichannelAcquisition
private boolean	canLookForND
private long[]	emWavelength	The TIFF's emWavelength
private Double	exposureTime
private boolean[]	firstSeriesChannels
private Double	gain
private boolean	hasAbsoluteZ
private boolean	hasAbsoluteZValid
private boolean	hasChipOffsets
private boolean	hasStagePositions
private String	imageCreationDate	The TIFF's creation date
private String	imageName	The TIFF's name
private long[]	internalStamps
private boolean	isHCS
private static final org.slf4j.Logger	LOGGER	Logger for this class.
static final String	LONG_DATE_FORMAT
private static final int	METAMORPH_ID
private int	mmPlanes
private static final String	ND_ENCODING
static final String[]	ND_SUFFIX
private String	ndFilename
private static final String	NDINFOFILE_VER1
private static final String	NDINFOFILE_VER2
private int	openFiles
static final String	SHORT_DATE_FORMAT
private Double	sizeX
private Double	sizeY
private String[]	stageLabels
private List<String>	stageNames
private ome.units.quantity.Length[]	stageX
private ome.units.quantity.Length[]	stageY
private double	stepSize
static final String[]	STK_SUFFIX
private MetamorphReader[][]	stkReaders
private String[][]	stks	List of STK files in the dataset.
private double	tempZ
private static final int	UIC1TAG
private static final int	UIC2TAG
private static final int	UIC3TAG
private static final int	UIC4TAG
private boolean	validZ
private double[]	wave
private List<String>	waveNames
static final Pattern	WELL_COORDS
private double[]	zDistances
private double	zoom
private double	zStart

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS

Fields inherited from class loci.formats.in.MinimalTiffReader

canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
MetamorphReader()	Constructs a new Metamorph reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
static String	decodeDate(int julian)	Converts a Julian date value into a human-readable string.
static String	decodeTime(int millis)	Converts a time value in milliseconds into a human-readable string.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
private String	getComment(int i, int no)
String[]	getDomains()	Returns the list of domains represented by the current file.
private String	getFirstComment(int i)	Returns the TIFF comment from the first IFD of the first STK file in the given series.
private String	getKey(int id)
private String	getNDVersionSuffix(loci.common.Location ndfile)	Parses the given ND file to determined the version and return the expected file suffix
private String	getRealSTKFile(loci.common.Location l)	Check that the given STK file exists.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
protected ome.units.quantity.Length[]	getStageX()
protected ome.units.quantity.Length[]	getStageY()
private Map.Entry<Integer,Integer>	getWellCoords(String label)
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
protected void	initStandardMetadata()	Parses standard metadata.
static String	intFormat(int myint, int digits)	Formats an integer value with leading 0s if needed.
static String	intFormatMax(int myint, int maxint)	Formats an integer with leading 0 using maximum sequence number.
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.
private String	locateFirstValidFile()	Locates the first valid file in the STK arrays.
private String	makeImageName(int i)	Create an appropriate name for the given series.
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	parseUIC1Tags(long uic1offset, int uic1count)	UIC1 entry parser
(package private) void	parseUIC2Tags(long uic2offset)	Populates metadata fields with some contained in MetaMorph UIC2 Tag.
private void	parseUIC4Tags(long uic4offset)	UIC4 metadata parser UIC4 Table contains per-plane blocks of metadata stage X/Y positions, camera chip offsets, stage labels...
(package private) void	readAbsoluteZValid()
private static String	readCString(loci.common.RandomAccessInputStream s, int n)	Read a null-terminated string.
private void	readPlaneData()
private TiffRational	readRational(loci.common.RandomAccessInputStream s)
private TiffRational	readRational(loci.common.RandomAccessInputStream s, long offset)
private void	readRationals(String[] labels)
(package private) void	readStageLabels()
private void	readStagePositions()
private void	setCanLookForND(boolean v)

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initMetadata, initMetadataStore, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initTiffParser, openThumbBytes, reopenFile, setResolutionLevel

Methods inherited from class loci.formats.SubResolutionFormatReader

coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, 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, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, 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, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

SHORT_DATE_FORMAT

public static final String SHORT_DATE_FORMAT

See Also:

• Constant Field Values

LONG_DATE_FORMAT

public static final String LONG_DATE_FORMAT

See Also:

• Constant Field Values

ND_SUFFIX

public static final String[] ND_SUFFIX

STK_SUFFIX

public static final String[] STK_SUFFIX

WELL_COORDS

public static final Pattern WELL_COORDS

METAMORPH_ID

private static final int METAMORPH_ID

See Also:

• Constant Field Values

UIC1TAG

private static final int UIC1TAG

See Also:

• Constant Field Values

UIC2TAG

private static final int UIC2TAG

See Also:

• Constant Field Values

UIC3TAG

private static final int UIC3TAG

See Also:

• Constant Field Values

UIC4TAG

private static final int UIC4TAG

See Also:

• Constant Field Values

NDINFOFILE_VER1

private static final String NDINFOFILE_VER1

See Also:

• Constant Field Values

NDINFOFILE_VER2

private static final String NDINFOFILE_VER2

See Also:

• Constant Field Values

ND_ENCODING

private static final String ND_ENCODING

See Also:

• Constant Field Values

imageName

private String imageName

The TIFF's name

imageCreationDate

private String imageCreationDate

The TIFF's creation date

emWavelength

private long[] emWavelength

The TIFF's emWavelength

isHCS

private boolean isHCS

stageLabels

private String[] stageLabels

wave

private double[] wave

binning

private String binning

zoom

private double zoom

stepSize

private double stepSize

exposureTime

private Double exposureTime

waveNames

private List<String> waveNames

stageNames

private List<String> stageNames

internalStamps

private long[] internalStamps

zDistances

private double[] zDistances

stageX

private ome.units.quantity.Length[] stageX

stageY

private ome.units.quantity.Length[] stageY

zStart

private double zStart

sizeX

private Double sizeX

sizeY

private Double sizeY

tempZ

private double tempZ

validZ

private boolean validZ

gain

private Double gain

mmPlanes

private int mmPlanes

stkReaders

private MetamorphReader[][] stkReaders

stks

private String[][] stks

List of STK files in the dataset.

ndFilename

private String ndFilename

canLookForND

private boolean canLookForND

firstSeriesChannels

private boolean[] firstSeriesChannels

bizarreMultichannelAcquisition

private boolean bizarreMultichannelAcquisition

openFiles

private int openFiles

hasStagePositions

private boolean hasStagePositions

hasChipOffsets

private boolean hasChipOffsets

hasAbsoluteZ

private boolean hasAbsoluteZ

hasAbsoluteZValid

private boolean hasAbsoluteZValid

Constructor Details

MetamorphReader

public MetamorphReader()

Constructs a new Metamorph reader.

Method Details

getDomains

public String[] getDomains()

Description copied from interface: IFormatReader

Returns the list of domains represented by the current file.

Specified by:

getDomains in interface IFormatReader

Overrides:

getDomains in class FormatReader

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 MinimalTiffReader

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

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

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

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

Overrides:

openBytes in class MinimalTiffReader

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 MinimalTiffReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Description copied from class: SubResolutionFormatReader

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 BaseTiffReader

Throws:

FormatException - if a parsing error occurs processing the file.

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

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
IOException

Description copied from class: BaseTiffReader

Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

FormatException

IOException

getRealSTKFile

private String getRealSTKFile(loci.common.Location l)

Check that the given STK file exists. If it does, then return the absolute path. If it does not, then apply various formatting rules until an existing file is found.

Returns:

the absolute path of an STK file, or null if no STK file is found.

getFirstComment

private String getFirstComment(int i)
                        throws IOException

Returns the TIFF comment from the first IFD of the first STK file in the given series.

Throws:

IOException

getComment

private String getComment(int i,
 int no)
                   throws IOException

Throws:

IOException

makeImageName

private String makeImageName(int i)

Create an appropriate name for the given series.

parseUIC2Tags

void parseUIC2Tags(long uic2offset)
            throws IOException

Populates metadata fields with some contained in MetaMorph UIC2 Tag. (for each plane: 6 integers: zdistance numerator, zdistance denominator, creation date, creation time, modif date, modif time)

Parameters:

uic2offset - offset to UIC2 (33629) tag entries not a regular tiff tag (6*N entries, N being the tagCount)

Throws:

IOException

parseUIC4Tags

private void parseUIC4Tags(long uic4offset)
                    throws IOException

UIC4 metadata parser UIC4 Table contains per-plane blocks of metadata stage X/Y positions, camera chip offsets, stage labels...

Parameters:

uic4offset - offset of UIC4 table (not tiff-compliant)

Throws:

IOException

getStageX

protected ome.units.quantity.Length[] getStageX()

getStageY

protected ome.units.quantity.Length[] getStageY()

readStagePositions

private void readStagePositions()
                         throws IOException

Throws:

IOException

readRationals

private void readRationals(String[] labels)
                    throws IOException

Throws:

IOException

readStageLabels

void readStageLabels()
              throws IOException

Throws:

IOException

readAbsoluteZValid

void readAbsoluteZValid()
                 throws IOException

Throws:

IOException

parseUIC1Tags

private void parseUIC1Tags(long uic1offset,
 int uic1count)
                    throws IOException

UIC1 entry parser

Parameters:

uic1offset - offset as found in the tiff tag 33628 (UIC1Tag)

uic1count - number of entries in UIC1 table (not tiff-compliant)

Throws:

IOException

decodeDate

public static String decodeDate(int julian)

Converts a Julian date value into a human-readable string.

decodeTime

public static String decodeTime(int millis)

Converts a time value in milliseconds into a human-readable string. Note that the date and time are handled separately, so this method is only concerned with the time of day. The time of day in milliseconds is stored as a 32-bit int in Metamorph files, but is expected to be a positive integer less than the number of milliseconds in one day.

Parameters:

millis - milliseconds elapsed in the relevant day

See Also:

• decodeDate(int)

intFormat

public static String intFormat(int myint,
 int digits)

Formats an integer value with leading 0s if needed.

intFormatMax

public static String intFormatMax(int myint,
 int maxint)

Formats an integer with leading 0 using maximum sequence number.

Parameters:

myint - integer to format

maxint - max of "myint"

Returns:

String

locateFirstValidFile

private String locateFirstValidFile()

Locates the first valid file in the STK arrays.

Returns:

Path to the first valid file.

readRational

private TiffRational readRational(loci.common.RandomAccessInputStream s)
                           throws IOException

Throws:

IOException

readRational

private TiffRational readRational(loci.common.RandomAccessInputStream s,
 long offset)
                           throws IOException

Throws:

IOException

setCanLookForND

private void setCanLookForND(boolean v)

readPlaneData

private void readPlaneData()
                    throws IOException

Throws:

IOException

getKey

private String getKey(int id)

getWellCoords

private Map.Entry<Integer,Integer> getWellCoords(String label)

readCString

private static String readCString(loci.common.RandomAccessInputStream s,
 int n)
                           throws IOException

Read a null-terminated string. Read at most n characters if the null character is not found.

Throws:

IOException

getNDVersionSuffix

private String getNDVersionSuffix(loci.common.Location ndfile)
                           throws IOException

Parses the given ND file to determined the version and return the expected file suffix

Parameters:

ndfile - The ND file which should be parsed

Returns:

The file suffix to be used for associated files based on the ND version

Throws:

IOException