loci.formats.in

Class MicromanagerReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.MicromanagerReader

All Implemented Interfaces:

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

public class MicromanagerReader
extends FormatReader

MicromanagerReader is the file format reader for Micro-Manager files.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	MicromanagerReader.Index
(package private) class	MicromanagerReader.MicromanagerHandler SAX handler for parsing Acqusition.xml.
(package private) class	MicromanagerReader.Position

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DATE_FORMAT
private static int	JSON_TAG
private static int	MAX_MAJOR_VERSION Defines maximum Micro-Manager version supported.
private static java.lang.String	MAX_VERSION
private static java.lang.String	METADATA File containing extra metadata.
private static int	MM_JSON_TAG
private java.util.Vector<MicromanagerReader.Position>	positions
private boolean	spim
private int	start
private MinimalTiffReader	tiffReader Helper reader for TIFF files.
private static java.lang.String	XML Optional file containing additional acquisition parameters.

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
MicromanagerReader() Constructs a new Micromanager reader.

Method Summary

Modifier and Type	Method and Description
private void	buildTIFFList(int posIndex)
private void	buildTIFFList(int posIndex, java.lang.String baseTiff) Populate the list of TIFF files using the given file name as a pattern.
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 java.lang.String	getNextLine(byte[] buf)
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 java.lang.String	getPrefixMetadataName(java.lang.String baseName)
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
private void	handleKeyValue(java.lang.String key, java.lang.String value) Process a piece of metadata represented by a key/value pair.
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 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 void	parseKeyAndValue(java.lang.String key, java.lang.String value, int digits, int plane, int nPlanes)
private void	parsePosition(int posIndex)
private void	parsePosition(java.lang.String jsonData, int posIndex)
private void	parseXMLFile() Parse metadata values from the Acqusition.xml file.
private void	populateMetadata()
void	populateMetadataStore(java.lang.String[] jsonData)
private void	setupReader() Initialize the TIFF reader with the first non-null file in the current 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, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, 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, 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

Field Detail

DATE_FORMAT

public static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

METADATA

private static final java.lang.String METADATA

File containing extra metadata.

See Also:

Constant Field Values

JSON_TAG

private static final int JSON_TAG

See Also:

Constant Field Values

MM_JSON_TAG

private static final int MM_JSON_TAG

See Also:

Constant Field Values

MAX_MAJOR_VERSION

private static final int MAX_MAJOR_VERSION

Defines maximum Micro-Manager version supported. Anything acquired with a version after 1.4.22 (especially 2.x.x) is expected to not work reliably.

See Also:

Constant Field Values

MAX_VERSION

private static final java.lang.String MAX_VERSION

See Also:

Constant Field Values

XML

private static final java.lang.String XML

Optional file containing additional acquisition parameters. (And yes, the spelling is correct.)

See Also:

Constant Field Values

tiffReader

private MinimalTiffReader tiffReader

Helper reader for TIFF files.

positions

private java.util.Vector<MicromanagerReader.Position> positions

start

private int start

spim

private boolean spim

Constructor Detail

MicromanagerReader

public MicromanagerReader()

Constructs a new Micromanager reader.

Method Detail

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.

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

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

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

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)

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

public 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

populateMetadata

private void populateMetadata()
                       throws FormatException,
                              java.io.IOException

Throws:

FormatException

java.io.IOException

populateMetadataStore

public void populateMetadataStore(java.lang.String[] jsonData)
                           throws FormatException,
                                  java.io.IOException

Throws:

FormatException

java.io.IOException

parsePosition

private void parsePosition(int posIndex)
                    throws java.io.IOException,
                           FormatException

Throws:

java.io.IOException

FormatException

parseKeyAndValue

private void parseKeyAndValue(java.lang.String key,
                              java.lang.String value,
                              int digits,
                              int plane,
                              int nPlanes)

buildTIFFList

private void buildTIFFList(int posIndex)
                    throws FormatException

Throws:

FormatException

parsePosition

private void parsePosition(java.lang.String jsonData,
                           int posIndex)
                    throws java.io.IOException,
                           FormatException

Throws:

java.io.IOException

FormatException

buildTIFFList

private void buildTIFFList(int posIndex,
                           java.lang.String baseTiff)

Populate the list of TIFF files using the given file name as a pattern.

parseXMLFile

private void parseXMLFile()
                   throws java.io.IOException

Parse metadata values from the Acqusition.xml file.

Throws:

java.io.IOException

setupReader

private void setupReader()

Initialize the TIFF reader with the first non-null file in the current series.

getPrefixMetadataName

private java.lang.String getPrefixMetadataName(java.lang.String baseName)

handleKeyValue

private void handleKeyValue(java.lang.String key,
                            java.lang.String value)

Process a piece of metadata represented by a key/value pair. Mostly this just adds to the original metadata table, but is also helpful for handling specific keys consistently independent of which file/INI table the key and value came from.

getNextLine

private java.lang.String getNextLine(byte[] buf)
                              throws java.io.UnsupportedEncodingException

Throws:

java.io.UnsupportedEncodingException