loci.formats.in

Class MIASReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.MIASReader

All Implemented Interfaces:

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

public class MIASReader
extends FormatReader

MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	MIASReader.AnalysisFile

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<MIASReader.AnalysisFile>	analysisFiles
private int[]	bpp
private byte[]	cachedTileBuffer Cached tile buffer to avoid re-allocations when reading tiles.
private java.util.Map<java.lang.String,java.lang.String>	overlayFiles
private java.util.Map<java.lang.String,java.lang.Integer>	overlayPlanes
private boolean	parseMasks Whether or not mask pixel data should be parsed in setId.
private MinimalTiffReader[][]	readers Delegate readers.
private java.lang.String	resultFile Path to file containing analysis results for all plates.
private java.util.List<MIASReader.AnalysisFile>	roiFiles
private java.lang.String	templateFile
private java.lang.String[][]	tiffs TIFF files - indexed by well and file.
private int	tileCols
private int	tileHeight
private int	tileRows
private int	tileWidth
private int	wellColumns
private int[]	wellNumber

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, 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
MIASReader() Constructs a new MIAS 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.
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.
private ome.xml.model.primitives.Color	getChannelColorFromFile(java.lang.String file) Get the color associated with the given file's channel.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
private int[]	getPositionFromFile(java.lang.String file) Returns an array of length 5 that contains the well, time point, Z and channel indices corresponding to the given analysis file.
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.
private byte[]	getTile(int well, int no, int row, int col, loci.common.Region intersection)
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(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(java.lang.String filename, 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.
void	parseMasks(MetadataStore overlayStore) Parse masks into a separate overlay-specific MetadataStore.
private int	parseMasks(MetadataStore store, int series, int roi, java.lang.String overlayTiff) Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
private void	parseTemplateFile(MetadataStore store) Parse metadata from the Nugenesistemplate.txt file.
boolean	populateMaskPixels(int imageIndex, int roiIndex, int shapeIndex, MetadataStore store) Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
private void	populateROI(java.util.List<java.lang.String> columns, java.lang.String[] data, int series, int roi, int time, int z, MetadataStore store)
void	setAutomaticallyParseMasks(boolean parse) Toggle whether or not Mask pixel data should be parsed in setId.

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, 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

Field Detail

tiffs

private java.lang.String[][] tiffs

TIFF files - indexed by well and file.

readers

private MinimalTiffReader[][] readers

Delegate readers.

resultFile

private java.lang.String resultFile

Path to file containing analysis results for all plates.

analysisFiles

private java.util.List<MIASReader.AnalysisFile> analysisFiles

roiFiles

private java.util.List<MIASReader.AnalysisFile> roiFiles

wellNumber

private int[] wellNumber

tileRows

private int tileRows

tileCols

private int tileCols

tileWidth

private int tileWidth

tileHeight

private int tileHeight

wellColumns

private int wellColumns

bpp

private int[] bpp

templateFile

private java.lang.String templateFile

overlayFiles

private final java.util.Map<java.lang.String,java.lang.String> overlayFiles

overlayPlanes

private final java.util.Map<java.lang.String,java.lang.Integer> overlayPlanes

parseMasks

private boolean parseMasks

Whether or not mask pixel data should be parsed in setId.

cachedTileBuffer

private byte[] cachedTileBuffer

Cached tile buffer to avoid re-allocations when reading tiles.

Constructor Detail

MIASReader

public MIASReader()

Constructs a new MIAS reader.

Method Detail

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 filename,
                          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.

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

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

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 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.

java.io.IOException - if there was a problem reading the file.

See Also:

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

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

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

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

getChannelColorFromFile

private ome.xml.model.primitives.Color getChannelColorFromFile(java.lang.String file)
                                                        throws FormatException,
                                                               java.io.IOException

Get the color associated with the given file's channel. The file must be one of the Well_mode_z_t_AllModesOverlay.tif files in //results/

Throws:

FormatException

java.io.IOException

getPositionFromFile

private int[] getPositionFromFile(java.lang.String file)

Returns an array of length 5 that contains the well, time point, Z and channel indices corresponding to the given analysis file.

populateROI

private void populateROI(java.util.List<java.lang.String> columns,
                         java.lang.String[] data,
                         int series,
                         int roi,
                         int time,
                         int z,
                         MetadataStore store)

getTile

private byte[] getTile(int well,
                       int no,
                       int row,
                       int col,
                       loci.common.Region intersection)
                throws FormatException,
                       java.io.IOException

Throws:

FormatException

java.io.IOException

parseTemplateFile

private void parseTemplateFile(MetadataStore store)
                        throws java.io.IOException

Parse metadata from the Nugenesistemplate.txt file.

Throws:

java.io.IOException

parseMasks

public void parseMasks(MetadataStore overlayStore)
                throws FormatException,
                       java.io.IOException

Parse masks into a separate overlay-specific MetadataStore.

Throws:

FormatException

java.io.IOException

parseMasks

private int parseMasks(MetadataStore store,
                       int series,
                       int roi,
                       java.lang.String overlayTiff)
                throws FormatException,
                       java.io.IOException

Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.

Returns:

the number of masks parsed

Throws:

FormatException

java.io.IOException

populateMaskPixels

public boolean populateMaskPixels(int imageIndex,
                                  int roiIndex,
                                  int shapeIndex,
                                  MetadataStore store)
                           throws FormatException,
                                  java.io.IOException

Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.

Returns:

true if the mask was populated successfully.

Throws:

FormatException

java.io.IOException

setAutomaticallyParseMasks

public void setAutomaticallyParseMasks(boolean parse)
                                throws FormatException

Toggle whether or not Mask pixel data should be parsed in setId. By default, it is not parsed.

Throws:

FormatException