loci.formats.in

Class FakeReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FakeReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

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'

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 String	ANN_COMMENT_VALUE
private static Double	ANN_DOUBLE_VALUE
private static long	ANN_LONG_VALUE
private static String	ANN_TAG_VALUE
private static String	ANN_TERM_VALUE
private static Timestamp	ANN_TIME_VALUE
private static String	ANN_XML_VALUE_END
private static String	ANN_XML_VALUE_START
private static String	ANNOTATION_NAMESPACE
private static String	ANNOTATION_PREFIX
static int	BOX_SIZE
static String	DEFAULT_DIMENSION_ORDER
static int	DEFAULT_PIXEL_TYPE
static int	DEFAULT_RGB_CHANNEL_COUNT
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 Time	exposureTime exposure time per plane info
private List<String>	fakeSeries List of used files if the fake is a SPW structure
private int[][]	indexToValue For indexed color, mapping from indices to values and vice versa.
private String	iniFile Properties companion file which can be associated with this fake file
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 OMEXMLMetadata	omeXmlMetadata
private OMEXMLService	omeXmlService
private Length	physicalSizeX
private Length	physicalSizeY
private Length	physicalSizeZ
private double	scaleFactor Scale factor for gradient, if any.
private static long	SEED
private static 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, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, 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.

Method Summary

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 String[]	extractTokensFromFakeSeries(String path)
private void	fillExposureTime(MetadataStore store)
private void	fillPhysicalSizes(MetadataStore store)
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()
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 this is a single-file format.
private boolean	isSPWStructure(String path)
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format reader.
private List<String>	listFakeSeries(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(String value)
private Length	parseLength(String value, String defaultUnit)
private int	populateSPW(MetadataStore store, int screens, int plates, int rows, int cols, int fields, int acqs)
private static void	shuffle(int c, int[] array) Fisher-Yates shuffle with constant seeds to ensure reproducibility.

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, 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, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

ANN_LONG_VALUE

private static final long ANN_LONG_VALUE

See Also:

Constant Field Values

ANN_DOUBLE_VALUE

private static final Double ANN_DOUBLE_VALUE

ANNOTATION_PREFIX

private static final String ANNOTATION_PREFIX

See Also:

Constant Field Values

ANNOTATION_NAMESPACE

private static final String ANNOTATION_NAMESPACE

See Also:

Constant Field Values

ANN_TERM_VALUE

private static final String ANN_TERM_VALUE

See Also:

Constant Field Values

ANN_TAG_VALUE

private static final String ANN_TAG_VALUE

See Also:

Constant Field Values

ANN_TIME_VALUE

private static final 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 String ANN_COMMENT_VALUE

See Also:

Constant Field Values

ANN_XML_VALUE_START

private static final String ANN_XML_VALUE_START

See Also:

Constant Field Values

ANN_XML_VALUE_END

private static final String ANN_XML_VALUE_END

See Also:

Constant Field Values

BOX_SIZE

public static final int BOX_SIZE

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 String DEFAULT_DIMENSION_ORDER

See Also:

Constant Field Values

TOKEN_SEPARATOR

private static final String TOKEN_SEPARATOR

See Also:

Constant Field Values

SEED

private static final long SEED

See Also:

Constant Field Values

exposureTime

private Time exposureTime

exposure time per plane info

physicalSizeX

private Length physicalSizeX

physicalSizeY

private Length physicalSizeY

physicalSizeZ

private Length physicalSizeZ

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 String iniFile

Properties companion file which can be associated with this fake file

fakeSeries

private List<String> fakeSeries

List of used files if the fake is a SPW structure

omeXmlMetadata

private OMEXMLMetadata omeXmlMetadata

omeXmlService

private OMEXMLService omeXmlService

Constructor Detail

FakeReader

public FakeReader()

Constructs a new fake reader.

Method Detail

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   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

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     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

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 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.

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

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.

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

findLogFiles

private void findLogFiles()

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

getOmeXmlMetadata

public OMEXMLMetadata getOmeXmlMetadata()

getOmeXmlService

public OMEXMLService getOmeXmlService()

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

fillPhysicalSizes

private void fillPhysicalSizes(MetadataStore store)

fillExposureTime

private void fillExposureTime(MetadataStore store)

extractTokensFromFakeSeries

private String[] extractTokensFromFakeSeries(String path)

isSPWStructure

private boolean isSPWStructure(String path)

populateSPW

private int populateSPW(MetadataStore store,
              int screens,
              int plates,
              int rows,
              int cols,
              int fields,
              int acqs)

createIndexMap

private void createIndexMap(int num)

Creates a mapping between indices and color values.

listFakeSeries

private List<String> listFakeSeries(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(String value)

parseLength

private Length parseLength(String value,
                 String defaultUnit)