FakeReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.FakeReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
```
public class FakeReader
extends FormatReader
```
FakeReader is the file format reader for faking input data. It is mainly useful for testing.
Examples:
- showinf 'multi-series&series=11&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake' -series 9
- showinf '8bit-signed&pixelType=int8&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '16bit-signed&pixelType=int16&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '16bit-unsigned&pixelType=uint16&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '32bit-signed&pixelType=int32&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '32bit-unsigned&pixelType=uint32&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '32bit-floating&pixelType=float&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf '64bit-floating&pixelType=double&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
- showinf 'SPW&plates=2&plateRows=3&plateCols=3&fields=8&plateAcqs=5.fake'
- showinf 'SPW&screens=2&plates=1&plateRows=3&plateCols=3&fields=1&plateAcqs=1.fake'
- showinf 'Plate&screens=0&plates=1&plateRows=3&plateCols=3&fields=8&plateAcqs=5.fake'
- showinf 'regions&points=10&ellipses=5&rectangles=10.fake'
- showinf 'pyramid&sizeX=10000&sizeY=10000&resolutions=5&resolutionScale=2.fake' -noflat -resolution 4

Field Summary

Fields
Modifier and Type	Field and Description
`private int`	`ac` Channel of last opened image plane.
`private static boolean`	`ANN_BOOLEAN_VALUE`
`private static java.lang.String`	`ANN_COMMENT_VALUE`
`private static java.lang.Double`	`ANN_DOUBLE_VALUE`
`private static long`	`ANN_LONG_VALUE`
`private static java.lang.String`	`ANN_TAG_VALUE`
`private static java.lang.String`	`ANN_TERM_VALUE`
`private static ome.xml.model.primitives.Timestamp`	`ANN_TIME_VALUE`
`private static java.lang.String`	`ANN_XML_VALUE_END`
`private static java.lang.String`	`ANN_XML_VALUE_START`
`private int`	`annBool`
`private int`	`annComment`
`private int`	`annDouble`
`private int`	`annLong`
`private int`	`annMap`
`private static java.lang.String`	`ANNOTATION_NAMESPACE`
`private static java.lang.String`	`ANNOTATION_PREFIX`
`private int`	`annotationBoolCount`
`private int`	`annotationCommentCount`
`private int`	`annotationCount`
`private int`	`annotationDoubleCount`
`private int`	`annotationLongCount`
`private int`	`annotationMapCount`
`private int`	`annotationTagCount`
`private int`	`annotationTermCount`
`private int`	`annotationTimeCount`
`private int`	`annotationXmlCount`
`private int`	`annTag`
`private int`	`annTerm`
`private int`	`annTime`
`private int`	`annXml`
`static int`	`BOX_SIZE`
`static java.lang.String`	`DEFAULT_DIMENSION_ORDER`
`static int`	`DEFAULT_PIXEL_TYPE`
`static int`	`DEFAULT_RESOLUTION_SCALE`
`static int`	`DEFAULT_RGB_CHANNEL_COUNT`
`static java.lang.String`	`DEFAULT_RGB_DIMENSION_ORDER`
`static int`	`DEFAULT_SIZE_C`
`static int`	`DEFAULT_SIZE_T`
`static int`	`DEFAULT_SIZE_X`
`static int`	`DEFAULT_SIZE_Y`
`static int`	`DEFAULT_SIZE_Z`
`private int`	`ellipses`
`private ome.units.quantity.Time`	`exposureTime` exposure time per plane info
`private java.util.List<java.lang.String>`	`fakeSeries` List of used files if the fake is a SPW structure
`private int`	`fields`
`private int[][]`	`indexToValue` For indexed color, mapping from indices to values and vice versa.
`private java.lang.String`	`iniFile` Properties companion file which can be associated with this fake file
`private int`	`labels`
`private int`	`lines`
`private short[][][]`	`lut16` 16-bit lookup table, if indexed color, one per channel.
`private byte[][][]`	`lut8` 8-bit lookup table, if indexed color, one per channel.
`private int`	`masks`
`private OMEXMLMetadata`	`omeXmlMetadata`
`private OMEXMLService`	`omeXmlService`
`private ome.units.quantity.Length`	`physicalSizeX`
`private ome.units.quantity.Length`	`physicalSizeY`
`private ome.units.quantity.Length`	`physicalSizeZ`
`private int`	`plateAcqs`
`private int`	`plateCols`
`private int`	`plateRows`
`private int`	`plates`
`private int`	`points`
`private int`	`polygons`
`private int`	`polylines`
`private int`	`rectangles`
`private static java.lang.String`	`ROI_PREFIX`
`private static int`	`ROI_SPACING`
`private int`	`roiCount`
`private double`	`scaleFactor` Scale factor for gradient, if any.
`private int`	`screens`
`private static long`	`SEED`
`private static java.lang.String`	`SHAPE_PREFIX`
`private int`	`sizeC`
`private int`	`sizeT`
`private int`	`sizeX`
`private int`	`sizeY`
`private int`	`sizeZ`
`private int`	`sleepInitFile`
`private int`	`sleepOpenBytes`
`private static java.lang.String`	`TOKEN_SEPARATOR`
`private int[][]`	`valueToIndex` For indexed color, mapping from indices to values and vice versa.

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 and Description

FakeReader()
Constructs a new fake reader.

Constructors
Constructor and Description
`FakeReader()` Constructs a new fake reader.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close(boolean fileOnly)` Closes the currently open file.
`private void`	`createIndexMap(int num)` Creates a mapping between indices and color values.
`private java.lang.String[]`	`extractTokensFromFakeSeries(java.lang.String path)`
`private void`	`fillAcquisitionDate(MetadataStore store, java.lang.String date, int imageIndex)`
`private void`	`fillAnnotations(MetadataStore store, int imageIndex)`
`private void`	`fillExposureTime(MetadataStore store)`
`private void`	`fillPhysicalSizes(MetadataStore store)`
`private void`	`fillRegions(MetadataStore store, int imageIndex)`
`private void`	`findLogFiles()`
`short[][]`	`get16BitLookupTable()` Gets the 16-bit color lookup table associated with the most recently opened image.
`byte[][]`	`get8BitLookupTable()` Gets the 8-bit color lookup table associated with the most recently opened image.
`OMEXMLMetadata`	`getOmeXmlMetadata()`
`OMEXMLService`	`getOmeXmlService()`
`private java.lang.String`	`getPoints(int i)`
`java.lang.String[]`	`getSeriesUsedFiles(boolean noPixels)` Returns an array of filenames needed to open the current series.
`private java.lang.Double`	`getX(int i)`
`private java.lang.Double`	`getY(int i)`
`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.
`private boolean`	`isSPWStructure(java.lang.String path)`
`boolean`	`isThisType(java.lang.String name, boolean open)` Checks if a file matches the type of this format reader.
`private java.util.List<java.lang.String>`	`listFakeSeries(java.lang.String traversedDirectory)` Traverses a fake file folder structure indicated by traversedDirectory
`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 int`	`parseColor(java.lang.String value)`
`private ome.units.quantity.Length`	`parsePhysicalSize(java.lang.String s, java.lang.String defaultUnit)`
`private ome.units.quantity.Length`	`parsePosition(java.lang.String axis, int s, int index, loci.common.IniTable table)`
`private void`	`parseSeriesTable(loci.common.IniTable table, MetadataStore store, int newSeries)` Translate key/value pairs from the INI table for the specified series.
`private int`	`populateSPW(MetadataStore store, int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)`
`static int[]`	`readSpecialPixels(byte[] plane)` Read byte-encoded metadata from the given plane.
`static int[]`	`readSpecialPixels(byte[] plane, int pixelType, boolean little)` Read byte-encoded metadata from the given plane.
`static int[]`	`readSpecialPixels(byte[] plane, int pixelType, boolean little, int rgb, boolean interleaved)` Read byte-encoded metadata from the given plane.
`void`	`reopenFile()` Reopen any files that were closed, and which are expected to be open while the reader is open.
`private static void`	`shuffle(int c, int[] array)` Fisher-Yates shuffle with constant seeds to ensure reproducibility.
`(package private) static void`	`sleep(java.lang.String msg, int ms)`
`private int[]`	`toSPWCoordinates(int seriesIndex)` Convert the given series (Image) index to a WellSample, Well, and Plate index.

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, 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, 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, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, 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.IFormatHandler
getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader
getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

- Field Detail
  - ANN_LONG_VALUE
```
private static final long ANN_LONG_VALUE
```
    See Also:
    
    Constant Field Values
  - ANN_DOUBLE_VALUE
```
private static final java.lang.Double ANN_DOUBLE_VALUE
```
  - ANNOTATION_PREFIX
```
private static final java.lang.String ANNOTATION_PREFIX
```
    See Also:
    
    Constant Field Values
  - ANNOTATION_NAMESPACE
```
private static final java.lang.String ANNOTATION_NAMESPACE
```
    See Also:
    
    Constant Field Values
  - ANN_TERM_VALUE
```
private static final java.lang.String ANN_TERM_VALUE
```
    See Also:
    
    Constant Field Values
  - ANN_TAG_VALUE
```
private static final java.lang.String ANN_TAG_VALUE
```
    See Also:
    
    Constant Field Values
  - ANN_TIME_VALUE
```
private static final ome.xml.model.primitives.Timestamp ANN_TIME_VALUE
```
  - ANN_BOOLEAN_VALUE
```
private static final boolean ANN_BOOLEAN_VALUE
```
    See Also:
    
    Constant Field Values
  - ANN_COMMENT_VALUE
```
private static final java.lang.String ANN_COMMENT_VALUE
```
    See Also:
    
    Constant Field Values
  - ANN_XML_VALUE_START
```
private static final java.lang.String ANN_XML_VALUE_START
```
    See Also:
    
    Constant Field Values
  - ANN_XML_VALUE_END
```
private static final java.lang.String ANN_XML_VALUE_END
```
    See Also:
    
    Constant Field Values
  - ROI_PREFIX
```
private static final java.lang.String ROI_PREFIX
```
    See Also:
    
    Constant Field Values
  - SHAPE_PREFIX
```
private static final java.lang.String SHAPE_PREFIX
```
    See Also:
    
    Constant Field Values
  - BOX_SIZE
```
public static final int BOX_SIZE
```
    See Also:
    
    Constant Field Values
  - ROI_SPACING
```
private static final int ROI_SPACING
```
    See Also:
    
    Constant Field Values
  - DEFAULT_SIZE_X
```
public static final int DEFAULT_SIZE_X
```
    See Also:
    
    Constant Field Values
  - DEFAULT_SIZE_Y
```
public static final int DEFAULT_SIZE_Y
```
    See Also:
    
    Constant Field Values
  - DEFAULT_SIZE_Z
```
public static final int DEFAULT_SIZE_Z
```
    See Also:
    
    Constant Field Values
  - DEFAULT_SIZE_C
```
public static final int DEFAULT_SIZE_C
```
    See Also:
    
    Constant Field Values
  - DEFAULT_SIZE_T
```
public static final int DEFAULT_SIZE_T
```
    See Also:
    
    Constant Field Values
  - DEFAULT_PIXEL_TYPE
```
public static final int DEFAULT_PIXEL_TYPE
```
    See Also:
    
    Constant Field Values
  - DEFAULT_RGB_CHANNEL_COUNT
```
public static final int DEFAULT_RGB_CHANNEL_COUNT
```
    See Also:
    
    Constant Field Values
  - DEFAULT_DIMENSION_ORDER
```
public static final java.lang.String DEFAULT_DIMENSION_ORDER
```
    See Also:
    
    Constant Field Values
  - DEFAULT_RGB_DIMENSION_ORDER
```
public static final java.lang.String DEFAULT_RGB_DIMENSION_ORDER
```
    See Also:
    
    Constant Field Values
  - DEFAULT_RESOLUTION_SCALE
```
public static final int DEFAULT_RESOLUTION_SCALE
```
    See Also:
    
    Constant Field Values
  - TOKEN_SEPARATOR
```
private static final java.lang.String TOKEN_SEPARATOR
```
    See Also:
    
    Constant Field Values
  - SEED
```
private static final long SEED
```
    See Also:
    
    Constant Field Values
  - sizeX
```
private int sizeX
```
  - sizeY
```
private int sizeY
```
  - sizeZ
```
private int sizeZ
```
  - sizeC
```
private int sizeC
```
  - sizeT
```
private int sizeT
```
  - exposureTime
```
private ome.units.quantity.Time exposureTime
```
    exposure time per plane info
  - physicalSizeX
```
private ome.units.quantity.Length physicalSizeX
```
  - physicalSizeY
```
private ome.units.quantity.Length physicalSizeY
```
  - physicalSizeZ
```
private ome.units.quantity.Length physicalSizeZ
```
  - annBool
```
private int annBool
```
  - annComment
```
private int annComment
```
  - annDouble
```
private int annDouble
```
  - annLong
```
private int annLong
```
  - annMap
```
private int annMap
```
  - annTime
```
private int annTime
```
  - annTag
```
private int annTag
```
  - annTerm
```
private int annTerm
```
  - annXml
```
private int annXml
```
  - annotationCount
```
private int annotationCount
```
  - annotationBoolCount
```
private int annotationBoolCount
```
  - annotationCommentCount
```
private int annotationCommentCount
```
  - annotationDoubleCount
```
private int annotationDoubleCount
```
  - annotationLongCount
```
private int annotationLongCount
```
  - annotationMapCount
```
private int annotationMapCount
```
  - annotationTagCount
```
private int annotationTagCount
```
  - annotationTermCount
```
private int annotationTermCount
```
  - annotationTimeCount
```
private int annotationTimeCount
```
  - annotationXmlCount
```
private int annotationXmlCount
```
  - ellipses
```
private int ellipses
```
  - labels
```
private int labels
```
  - lines
```
private int lines
```
  - masks
```
private int masks
```
  - points
```
private int points
```
  - polygons
```
private int polygons
```
  - polylines
```
private int polylines
```
  - rectangles
```
private int rectangles
```
  - roiCount
```
private int roiCount
```
  - scaleFactor
```
private double scaleFactor
```
    Scale factor for gradient, if any.
  - lut8
```
private byte[][][] lut8
```
    8-bit lookup table, if indexed color, one per channel.
  - lut16
```
private short[][][] lut16
```
    16-bit lookup table, if indexed color, one per channel.
  - indexToValue
```
private int[][] indexToValue
```
    For indexed color, mapping from indices to values and vice versa.
  - valueToIndex
```
private int[][] valueToIndex
```
    For indexed color, mapping from indices to values and vice versa.
  - ac
```
private int ac
```
    Channel of last opened image plane.
  - iniFile
```
private java.lang.String iniFile
```
    Properties companion file which can be associated with this fake file
  - fakeSeries
```
private java.util.List<java.lang.String> fakeSeries
```
    List of used files if the fake is a SPW structure
  - omeXmlMetadata
```
private OMEXMLMetadata omeXmlMetadata
```
  - omeXmlService
```
private OMEXMLService omeXmlService
```
  - screens
```
private transient int screens
```
  - plates
```
private transient int plates
```
  - plateRows
```
private transient int plateRows
```
  - plateCols
```
private transient int plateCols
```
  - fields
```
private transient int fields
```
  - plateAcqs
```
private transient int plateAcqs
```
  - sleepOpenBytes
```
private int sleepOpenBytes
```
  - sleepInitFile
```
private int sleepInitFile
```
- Constructor Detail
  - FakeReader
```
public FakeReader()
```
    Constructs a new fake reader.
- Method Detail
  - sleep
```
static void sleep(java.lang.String msg,
                  int ms)
```
  - readSpecialPixels
```
public static int[] readSpecialPixels(byte[] plane)
```
    Read byte-encoded metadata from the given plane.
    
    See Also:
    
    readSpecialPixels(byte[], int, boolean, int, boolean)
  - readSpecialPixels
```
public static int[] readSpecialPixels(byte[] plane,
                                      int pixelType,
                                      boolean little)
```
    Read byte-encoded metadata from the given plane.
    
    See Also:
    
    readSpecialPixels(byte[], int, boolean, int, boolean)
  - readSpecialPixels
```
public static int[] readSpecialPixels(byte[] plane,
                                      int pixelType,
                                      boolean little,
                                      int rgb,
                                      boolean interleaved)
```
    Read byte-encoded metadata from the given plane.
    FakeReader encodes the following information in the upper-left section of each plane: series, plane number, Z index, C index, T index. Given an image plane generated by FakeReader (or by anything that follows the same encoding rules), this method decodes the above information and returns it as an array of integers.
    Note that the above numbers are encoded as valid pixels, so that the information is still retrievable after conversion to a pixel-oriented image format (this allows to use the class for testing the ImageJ plugin). Among other things, this implies that the maximum encodable values depend on the pixel type.
    Note:
    In the case of indexed color data, the returned values will be the indices of the actual values in the relevant lookup table (see get8BitLookupTable() and get16BitLookupTable()).
    
    Parameters:
    
    plane - an image plane as a byte array
    
    pixelType - the pixel type of the image; see FormatTools
    
    little - true if the byte order is little-endian, false otherwise
    
    rgb - the RGB channel count
    
    interleaved - true if the channels are interleaved, false otherwise
    
    Returns:
    
    an array of integers representing, in order: series; plane number; Z index; C index, T index
  - get8BitLookupTable
```
public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.
    
    Specified by:
    
    get8BitLookupTable in interface IFormatReader
    
    Overrides:
    
    get8BitLookupTable in class FormatReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.
    
    Specified by:
    
    get16BitLookupTable in interface IFormatReader
    
    Overrides:
    
    get16BitLookupTable in class FormatReader
    
    Throws:
    
    FormatException
    
    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 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.
    
    java.io.IOException - if there was a problem reading the file.
  - 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.
  - 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
  - findLogFiles
```
private void findLogFiles()
```
  - 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
  - getOmeXmlMetadata
```
public OMEXMLMetadata getOmeXmlMetadata()
```
  - getOmeXmlService
```
public OMEXMLService getOmeXmlService()
```
  - 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
  - reopenFile
```
public void reopenFile()
                throws java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.
    
    Specified by:
    
    reopenFile in interface IFormatReader
    
    Overrides:
    
    reopenFile in class FormatReader
    
    Throws:
    
    java.io.IOException
  - fillPhysicalSizes
```
private void fillPhysicalSizes(MetadataStore store)
```
  - fillExposureTime
```
private void fillExposureTime(MetadataStore store)
```
  - fillAcquisitionDate
```
private void fillAcquisitionDate(MetadataStore store,
                                 java.lang.String date,
                                 int imageIndex)
```
  - fillAnnotations
```
private void fillAnnotations(MetadataStore store,
                             int imageIndex)
```
  - getX
```
private java.lang.Double getX(int i)
```
  - getY
```
private java.lang.Double getY(int i)
```
  - getPoints
```
private java.lang.String getPoints(int i)
```
  - fillRegions
```
private void fillRegions(MetadataStore store,
                         int imageIndex)
```
  - parseSeriesTable
```
private void parseSeriesTable(loci.common.IniTable table,
                              MetadataStore store,
                              int newSeries)
```
    Translate key/value pairs from the INI table for the specified series.
  - toSPWCoordinates
```
private int[] toSPWCoordinates(int seriesIndex)
```
    Convert the given series (Image) index to a WellSample, Well, and Plate index. This should match the ordering used by XMLMockObjects.
    
    Parameters:
    
    seriesIndex - the index of the series/Image
    
    Returns:
    
    an array of length 3 containing the WellSample, Well, and Plate indices (in order), or null if SPW metadata was not defined
  - extractTokensFromFakeSeries
```
private java.lang.String[] extractTokensFromFakeSeries(java.lang.String path)
```
  - isSPWStructure
```
private boolean isSPWStructure(java.lang.String path)
```
  - populateSPW
```
private int populateSPW(MetadataStore store,
                        int screens,
                        int plates,
                        int rows,
                        int cols,
                        int fields,
                        int acqs,
                        boolean withMicrobeam)
```
  - createIndexMap
```
private void createIndexMap(int num)
```
    Creates a mapping between indices and color values.
  - listFakeSeries
```
private java.util.List<java.lang.String> listFakeSeries(java.lang.String traversedDirectory)
```
    Traverses a fake file folder structure indicated by traversedDirectory
  - shuffle
```
private static void shuffle(int c,
                            int[] array)
```
    Fisher-Yates shuffle with constant seeds to ensure reproducibility.
  - parseColor
```
private int parseColor(java.lang.String value)
```
  - parsePosition
```
private ome.units.quantity.Length parsePosition(java.lang.String axis,
                                                int s,
                                                int index,
                                                loci.common.IniTable table)
```
  - parsePhysicalSize
```
private ome.units.quantity.Length parsePhysicalSize(java.lang.String s,
                                                    java.lang.String defaultUnit)
```

Class FakeReader

Field Summary

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.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

Methods inherited from interface loci.formats.ICompressedTileReader

Field Detail

ANN_LONG_VALUE

ANN_DOUBLE_VALUE

ANNOTATION_PREFIX

ANNOTATION_NAMESPACE

ANN_TERM_VALUE

ANN_TAG_VALUE

ANN_TIME_VALUE

ANN_BOOLEAN_VALUE

ANN_COMMENT_VALUE

ANN_XML_VALUE_START

ANN_XML_VALUE_END

ROI_PREFIX

SHAPE_PREFIX

BOX_SIZE

ROI_SPACING

DEFAULT_SIZE_X

DEFAULT_SIZE_Y

DEFAULT_SIZE_Z

DEFAULT_SIZE_C

DEFAULT_SIZE_T

DEFAULT_PIXEL_TYPE

DEFAULT_RGB_CHANNEL_COUNT

DEFAULT_DIMENSION_ORDER

DEFAULT_RGB_DIMENSION_ORDER

DEFAULT_RESOLUTION_SCALE

TOKEN_SEPARATOR

SEED

sizeX

sizeY

sizeZ

sizeC

sizeT

exposureTime

physicalSizeX

physicalSizeY

physicalSizeZ

annBool

annComment

annDouble

annLong

annMap

annTime

annTag

annTerm

annXml

annotationCount

annotationBoolCount

annotationCommentCount

annotationDoubleCount

annotationLongCount

annotationMapCount

annotationTagCount

annotationTermCount

annotationTimeCount

annotationXmlCount

ellipses

labels

lines

masks

points

polygons

polylines

rectangles

roiCount

scaleFactor

lut8