loci.formats.in

Class CellVoyagerReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.CellVoyagerReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class CellVoyagerReader
extends FormatReader

A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).

This reader opens the dataset generated by the Yokagawa Cellvoyager automated microscope. The user should point the reader to the file named MeasurementResult.xml in the dataset folder.

The file format itself consists of several nested folder containing a lot of - sometimes redundant - information. This specific reader exploits the following files:

• MeasurementResult.xml that contains high level information about image geometry, well (if any) organization, fields arrangement, etc..
• MeasurementResult.ome.xml is a malformed OME xml file that contains information on one of the numerous TIF files that compose the pixel data. It is used to easily extract common metadata.
• All the TIF files in the Image folder: They contain the pixel data itself. Each well (if any) can have several Areas (fields in the HCS vocable), in turn composed of several tiles that are to be stitched border to border, without the possibility of a more subtle stitching process.

This reader stitches each area on the fly upon loading. It yields one series per well x area. If there is 20 wells each made of 2 areas, 40 series will be available.

This reader version was derived from reverse-engineering data files generated on a system hosted by the imaging facility of the Institut Pasteur, Paris (Imagopole / PFID). It spits file versioned 1.0. The file format contains several obvious typos, notably in some XML tags, and as mentionned above, the ome.xml is malformed. It is likely that that subsequent versions of the CellVoyager format will fix these problems, alas incapacitating this reader. Should it happen, mail the author to help them update this reader.

Author:

Jean-Yves Tinevez Oct-Nov 2013, Melissa Linkert

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	CellVoyagerReader.AreaInfo
private static class	CellVoyagerReader.ChannelInfo
private static class	CellVoyagerReader.FieldInfo
private static class	CellVoyagerReader.WellInfo

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<CellVoyagerReader.ChannelInfo>	channelInfos
private java.lang.String	imageFolder
private java.lang.String	measurementResultFile
private java.lang.String	omeMeasurementFile
private static java.lang.String	SINGLE_TIFF_PATH_BUILDER
private java.util.List<java.lang.Integer>	timePoints
private java.util.List<CellVoyagerReader.WellInfo>	wells

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
CellVoyagerReader()

Method Summary

Modifier and Type	Method and Description
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
private static org.w3c.dom.Element	getChild(org.w3c.dom.Element parent, java.lang.String childName)
private static org.w3c.dom.Element	getChild(org.w3c.dom.Element parent, java.lang.String[] path)
private static java.util.List<org.w3c.dom.Element>	getChildren(org.w3c.dom.Element parent, java.lang.String name)
private static java.lang.String	getChildText(org.w3c.dom.Element parent, java.lang.String childName)
private static java.lang.String	getChildText(org.w3c.dom.Element parent, java.lang.String[] path)
int	getRequiredDirectories(java.lang.String[] files) Returns the number of parent directories that are important when processing the given list of files.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
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.
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format reader.
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 CellVoyagerReader.AreaInfo	readArea(org.w3c.dom.Element areaEl, int startingFieldIndex, double pixelWidth, double pixelHeight, int tileWidth, int tileHeight)
private CellVoyagerReader.ChannelInfo	readChannel(org.w3c.dom.Element channelEl)
private CellVoyagerReader.FieldInfo	readField(org.w3c.dom.Element fieldEl)
private double	readFrameInterval(org.w3c.dom.Document document)
private void	readInfo(org.w3c.dom.Document msDocument, org.w3c.dom.Document omeDocument)
private java.util.List<java.lang.Integer>	readTimePoints(org.w3c.dom.Document document)
private CellVoyagerReader.WellInfo	readWellInfo(org.w3c.dom.Element wellEl, double pixelWidth, double pixelHeight, int tileWidth, int tileHeight)
private int[]	seriesToWellArea(int series) Returns the well index (in the field wells) and the area index (in the field CellVoyagerReader.WellInfo.areas corresponding to the specified series.

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, close, coreIndexToSeries, flattenHashtables, get16BitLookupTable, get8BitLookupTable, 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, 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, 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.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

SINGLE_TIFF_PATH_BUILDER

private static final java.lang.String SINGLE_TIFF_PATH_BUILDER

See Also:

Constant Field Values

imageFolder

private java.lang.String imageFolder

channelInfos

private java.util.List<CellVoyagerReader.ChannelInfo> channelInfos

wells

private java.util.List<CellVoyagerReader.WellInfo> wells

timePoints

private java.util.List<java.lang.Integer> timePoints

measurementResultFile

private java.lang.String measurementResultFile

omeMeasurementFile

private java.lang.String omeMeasurementFile

Constructor Detail

CellVoyagerReader

public CellVoyagerReader()

Method Detail

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.

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.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

java.io.IOException

See Also:

FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP

getRequiredDirectories

public int getRequiredDirectories(java.lang.String[] files)
                           throws FormatException,
                                  java.io.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

java.io.IOException

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.

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

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

seriesToWellArea

private int[] seriesToWellArea(int series)

Returns the well index (in the field wells) and the area index (in the field CellVoyagerReader.WellInfo.areas corresponding to the specified series.

Parameters:

series - the desired series.

Returns:

the corresponding well index and area index, as a 2-element array of int[] { well, area }.

readInfo

private void readInfo(org.w3c.dom.Document msDocument,
                      org.w3c.dom.Document omeDocument)
               throws FormatException

Throws:

FormatException

readChannel

private CellVoyagerReader.ChannelInfo readChannel(org.w3c.dom.Element channelEl)

readWellInfo

private CellVoyagerReader.WellInfo readWellInfo(org.w3c.dom.Element wellEl,
                                                double pixelWidth,
                                                double pixelHeight,
                                                int tileWidth,
                                                int tileHeight)

readArea

private CellVoyagerReader.AreaInfo readArea(org.w3c.dom.Element areaEl,
                                            int startingFieldIndex,
                                            double pixelWidth,
                                            double pixelHeight,
                                            int tileWidth,
                                            int tileHeight)

readField

private CellVoyagerReader.FieldInfo readField(org.w3c.dom.Element fieldEl)

readTimePoints

private java.util.List<java.lang.Integer> readTimePoints(org.w3c.dom.Document document)

readFrameInterval

private double readFrameInterval(org.w3c.dom.Document document)

getChild

private static final org.w3c.dom.Element getChild(org.w3c.dom.Element parent,
                                                  java.lang.String childName)

getChild

private static final org.w3c.dom.Element getChild(org.w3c.dom.Element parent,
                                                  java.lang.String[] path)

getChildren

private static final java.util.List<org.w3c.dom.Element> getChildren(org.w3c.dom.Element parent,
                                                                     java.lang.String name)

getChildText

private static final java.lang.String getChildText(org.w3c.dom.Element parent,
                                                   java.lang.String[] path)

getChildText

private static final java.lang.String getChildText(org.w3c.dom.Element parent,
                                                   java.lang.String childName)