loci.formats.in

Class TecanReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.TecanReader

All Implemented Interfaces:

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

public class TecanReader
extends FormatReader

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	TecanReader.Channel
(package private) class	TecanReader.Image

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.ArrayList<TecanReader.Channel>	channels
private java.util.ArrayList<java.lang.String>	extraFiles
private MinimalTiffReader	helperReader
private java.lang.String	imageDirectory
private java.util.ArrayList<TecanReader.Image>	images
private static org.slf4j.Logger	LOGGER
private java.lang.Integer	maxCycle
private java.lang.Integer	maxField
private int	plateColumns
private java.lang.String	plateName
private int	plateRows
private static java.lang.String[]	SPREADSHEET_KEYS

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 and Description
TecanReader() Constructs a new Tecan Spark Cyto reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
private void	findAllFiles(loci.common.Location root, java.util.ArrayList<java.lang.String> files)
private void	findExtraMetadata()
private void	findImages(java.sql.Connection conn, java.util.HashMap<java.lang.Integer,java.lang.String> wells)
private void	findPlateDimensions(java.sql.Connection conn)
private java.lang.String	getImageFile(java.lang.String file) Turn a relative image file path into an absolute 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.
java.lang.String[]	getUsedFiles(boolean noPixels) Returns an array of filenames needed to open this dataset.
private java.util.HashMap<java.lang.Integer,java.lang.String>	getWellLabels(java.sql.Connection conn)
private java.lang.Integer[]	getWellLink(java.sql.PreparedStatement linkQuery, java.lang.String imagingResultID) Get the well identifier and field indexfor the given Id in the ImagingResult table.
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.
private int	lookupChannelIndex(java.lang.String name)
private TecanReader.Image	lookupImage(int series, int plane, boolean overlay, boolean result)
private java.lang.String	makeWellLabel(int row, int col)
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 java.sql.Connection	openConnection()
private java.sql.Connection	openConnection(java.lang.String file)
private void	parseSpreadsheet()

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, 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, 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

LOGGER

private static final org.slf4j.Logger LOGGER

SPREADSHEET_KEYS

private static final java.lang.String[] SPREADSHEET_KEYS

plateRows

private int plateRows

plateColumns

private int plateColumns

plateName

private transient java.lang.String plateName

images

private java.util.ArrayList<TecanReader.Image> images

helperReader

private transient MinimalTiffReader helperReader

channels

private transient java.util.ArrayList<TecanReader.Channel> channels

imageDirectory

private java.lang.String imageDirectory

extraFiles

private java.util.ArrayList<java.lang.String> extraFiles

maxField

private java.lang.Integer maxField

maxCycle

private java.lang.Integer maxCycle

Constructor Detail

TecanReader

public TecanReader()

Constructs a new Tecan Spark Cyto reader.

Method Detail

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.

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

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

getUsedFiles

public java.lang.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 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

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

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.

See Also:

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

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

openConnection

private java.sql.Connection openConnection()
                                    throws java.io.IOException

Throws:

java.io.IOException

openConnection

private java.sql.Connection openConnection(java.lang.String file)
                                    throws java.io.IOException

Throws:

java.io.IOException

findExtraMetadata

private void findExtraMetadata()

parseSpreadsheet

private void parseSpreadsheet()

makeWellLabel

private java.lang.String makeWellLabel(int row,
                                       int col)

findPlateDimensions

private void findPlateDimensions(java.sql.Connection conn)
                          throws java.sql.SQLException

Throws:

java.sql.SQLException

getWellLabels

private java.util.HashMap<java.lang.Integer,java.lang.String> getWellLabels(java.sql.Connection conn)
                                                                     throws java.sql.SQLException

Throws:

java.sql.SQLException

findImages

private void findImages(java.sql.Connection conn,
                        java.util.HashMap<java.lang.Integer,java.lang.String> wells)
                 throws java.sql.SQLException

Throws:

java.sql.SQLException

getWellLink

private java.lang.Integer[] getWellLink(java.sql.PreparedStatement linkQuery,
                                        java.lang.String imagingResultID)
                                 throws java.sql.SQLException

Get the well identifier and field indexfor the given Id in the ImagingResult table.

Parameters:

imagingResultID -

Returns:

well ID

Throws:

java.sql.SQLException

lookupImage

private TecanReader.Image lookupImage(int series,
                                      int plane,
                                      boolean overlay,
                                      boolean result)

lookupChannelIndex

private int lookupChannelIndex(java.lang.String name)

getImageFile

private java.lang.String getImageFile(java.lang.String file)

Turn a relative image file path into an absolute path. Storing relative paths and one copy of the parent directory saves some space in the memo file, especially for large plates.

Parameters:

file - relative path to an image file

Returns:

absolute path to the image file

findAllFiles

private void findAllFiles(loci.common.Location root,
                          java.util.ArrayList<java.lang.String> files)