MetamorphReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.MinimalTiffReader
    - - loci.formats.in.BaseTiffReader
      - loci.formats.in.MetamorphReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
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 and 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 static org.slf4j.Logger`	`LOGGER` Logger for this class.
`static String`	`LONG_DATE_FORMAT`
`private static int`	`METAMORPH_ID`
`private int`	`mmPlanes`
`static String[]`	`ND_SUFFIX`
`private String`	`ndFilename`
`private int`	`openFiles`
`static String`	`SHORT_DATE_FORMAT`
`private Double`	`sizeX`
`private Double`	`sizeY`
`private List<String>`	`stageNames`
`private Length[]`	`stageX`
`private Length[]`	`stageY`
`private double`	`stepSize`
`static String[]`	`STK_SUFFIX`
`private MetamorphReader[][]`	`stkReaders`
`private String[][]`	`stks` List of STK files in the dataset.
`private double`	`tempZ`
`private static int`	`UIC1TAG`
`private static int`	`UIC2TAG`
`private static int`	`UIC3TAG`
`private static int`	`UIC4TAG`
`private boolean`	`validZ`
`private double[]`	`wave`
`private List<String>`	`waveNames`
`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
equalStrips, ifds, lastPlane, noSubresolutions, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description

MetamorphReader()
Constructs a new Metamorph reader.

Constructors
Constructor and Description
`MetamorphReader()` Constructs a new Metamorph reader.

Method Summary

Methods
Modifier and Type	Method and 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 int indicating that we cannot, must, or might group the files in a given dataset.
`private String`	`getComment(int i, int no)`
`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`	`getRealSTKFile(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 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 this is a single-file format.
`boolean`	`isThisType(RandomAccessInputStream stream)` Checks if the given stream is a valid stream for this file format.
`boolean`	`isThisType(String name, boolean open)` Checks if a file matches the type of this format reader.
`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 void`	`readPlaneData()`
`private TiffRational`	`readRational(RandomAccessInputStream s)`
`private TiffRational`	`readRational(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, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader
get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, openThumbBytes, reopenFile, setResolutionLevel

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, 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, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

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
  - 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
```
  - 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
  - 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
  - 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 Length[] stageX
```
  - stageY
```
private 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 Detail
  - MetamorphReader
```
public MetamorphReader()
```
    Constructs a new Metamorph reader.
- Method Detail
  - 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
    
    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(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 MinimalTiffReader
    
    Throws:
    
    IOException
  - isSingleFile
```
public boolean isSingleFile(String id)
                     throws FormatException,
                            IOException
```
    Description copied from interface: IFormatReader
    
    Returns true if this is a single-file format.
    
    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 int indicating that we cannot, must, or might group the files in a given dataset.
    
    Specified by:
    
    fileGroupOption in interface IFormatReader
    
    Overrides:
    
    fileGroupOption in class FormatReader
    
    Throws:
    
    FormatException
    
    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.
    
    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 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.
    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: 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 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(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
  - 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.
  - 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(RandomAccessInputStream s)
                           throws IOException
```
    Throws:
    
    IOException
  - readRational
```
private TiffRational readRational(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)
```

Class MetamorphReader

Field Summary

Fields inherited from class loci.formats.in.BaseTiffReader

Fields inherited from class loci.formats.in.MinimalTiffReader

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.in.BaseTiffReader

Methods inherited from class loci.formats.in.MinimalTiffReader

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Methods inherited from interface loci.formats.IMetadataConfigurable

Field Detail

LOGGER

SHORT_DATE_FORMAT

LONG_DATE_FORMAT

ND_SUFFIX

STK_SUFFIX

METAMORPH_ID

UIC1TAG

UIC2TAG

UIC3TAG

UIC4TAG

imageName

imageCreationDate

emWavelength

wave

binning

zoom

stepSize

exposureTime

waveNames

stageNames

internalStamps

zDistances

stageX

stageY

zStart

sizeX

sizeY

tempZ

validZ

gain

mmPlanes

stkReaders

stks

ndFilename

canLookForND

firstSeriesChannels

bizarreMultichannelAcquisition

openFiles

hasStagePositions

hasChipOffsets

hasAbsoluteZ

hasAbsoluteZValid

Constructor Detail

MetamorphReader

Method Detail

isThisType

isThisType

isSingleFile

fileGroupOption

getSeriesUsedFiles

openBytes

close

initFile

initStandardMetadata

getRealSTKFile

getFirstComment

getComment

makeImageName

parseUIC2Tags

parseUIC4Tags

readStagePositions

readRationals

readStageLabels