Package loci.formats.in

Class CV7000Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.CV7000Reader

All Implemented Interfaces:

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

public class CV7000Reader
extends FormatReader

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	CV7000Reader.Channel
(package private) class	CV7000Reader.Field
(package private) class	CV7000Reader.LightSource
(package private) class	CV7000Reader.MeasurementDataHandler
(package private) class	CV7000Reader.MeasurementDetailHandler
(package private) class	CV7000Reader.MeasurementSettingsHandler
(package private) class	CV7000Reader.MinMax
(package private) class	CV7000Reader.Plane
(package private) class	CV7000Reader.WPIHandler

Field Summary

Fields

Modifier and Type	Field	Description
private Map<String,Boolean>	acquiredWells
private List<String>	allFiles
private ArrayList<CV7000Reader.Channel>	channels
private String	detailPath
static final boolean	DUPLICATE_PLANES_DEFAULT
static final String	DUPLICATE_PLANES_KEY
private String	endTime
private ArrayList<String>	extraFiles
private int	fields
private ArrayList<CV7000Reader.LightSource>	lightSources
private static final org.slf4j.Logger	LOGGER
private static final String	MEASUREMENT_DETAIL
private static final String	MEASUREMENT_FILE
private String	measurementPath
private ArrayList<CV7000Reader.Plane>	planeData
private static final String	POST_PROCESS
private MinimalTiffReader	reader
private int[][]	reversePlaneLookup
private String	settingsPath
private String	startTime
private String	wppPath

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
CV7000Reader()	Constructs a new Yokogawa CV7000 reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
boolean	duplicatePlanes()
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
private int	getChannelIndex(CV7000Reader.Plane p)
int	getRequiredDirectories(String[] files)	Returns the number of parent directories that are important when processing the given list of files.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
String[]	getUsedFiles(boolean noPixels)	Returns an array of filenames needed to open this dataset.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
private boolean	isWellAcquired(int row, int col)
private CV7000Reader.Channel	lookupChannel(CV7000Reader.Plane p)
private CV7000Reader.Plane	lookupPlane(int series, int no)
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 String	readSanitizedXML(String filename)

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, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

DUPLICATE_PLANES_KEY

public static final String DUPLICATE_PLANES_KEY

See Also:

• Constant Field Values

DUPLICATE_PLANES_DEFAULT

public static final boolean DUPLICATE_PLANES_DEFAULT

See Also:

• Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

MEASUREMENT_FILE

private static final String MEASUREMENT_FILE

See Also:

• Constant Field Values

MEASUREMENT_DETAIL

private static final String MEASUREMENT_DETAIL

See Also:

• Constant Field Values

POST_PROCESS

private static final String POST_PROCESS

See Also:

• Constant Field Values

allFiles

private List<String> allFiles

reader

private MinimalTiffReader reader

wppPath

private String wppPath

detailPath

private String detailPath

measurementPath

private String measurementPath

settingsPath

private String settingsPath

planeData

private ArrayList<CV7000Reader.Plane> planeData

reversePlaneLookup

private int[][] reversePlaneLookup

lightSources

private ArrayList<CV7000Reader.LightSource> lightSources

channels

private ArrayList<CV7000Reader.Channel> channels

fields

private int fields

startTime

private String startTime

endTime

private String endTime

extraFiles

private ArrayList<String> extraFiles

acquiredWells

private transient Map<String,Boolean> acquiredWells

Constructor Details

CV7000Reader

public CV7000Reader()

Constructs a new Yokogawa CV7000 reader.

Method Details

duplicatePlanes

public boolean duplicatePlanes()

getRequiredDirectories

public int getRequiredDirectories(String[] files)
                           throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns the number of parent directories that are important when processing the given list of files. The number of directories is relative to the common parent. For example, given a list with these two files: /path/to/file/foo /path/to/file/that/is/related A return value of 0 indicates that "/path/to/file/" is irrelevant. A return value of 1 indicates that "/path/to/" is irrelevant. Return values less than 0 are invalid. All listed files are assumed to belong to datasets of the same format.

Specified by:

getRequiredDirectories in interface IFormatReader

Overrides:

getRequiredDirectories in class FormatReader

Throws:

FormatException

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

getUsedFiles

public String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. 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:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class FormatReader

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

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

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

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

getChannelIndex

private int getChannelIndex(CV7000Reader.Plane p)

lookupChannel

private CV7000Reader.Channel lookupChannel(CV7000Reader.Plane p)

readSanitizedXML

private String readSanitizedXML(String filename)
                         throws IOException

Throws:

IOException

isWellAcquired

private boolean isWellAcquired(int row,
 int col)

lookupPlane

private CV7000Reader.Plane lookupPlane(int series,
 int no)