loci.formats.in.LeicaMicrosystemsMetadata

Class MultipleImagesReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

All Implemented Interfaces:

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

public class MultipleImagesReader
extends LMSFileReader

MultipleImagesReader presents a number of image files as one image reference

Author:

Constanze Wendlandt constanze.wendlandt at leica-microsystems.com

Nested Class Summary

Nested classes/interfaces inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

LMSFileReader.ImageFormat

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	dimensionsSwapped
private LMSFileReader.ImageFormat	imageFormat
private int	imageIndex
private java.util.List<FormatReader>	readers
private int	series
private int	tileCount

Fields inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

associatedXmlDoc, log, metaTemp, OLD_PHYSICAL_SIZE_DEFAULT, OLD_PHYSICAL_SIZE_KEY

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, 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
MultipleImagesReader(XlifDocument xlif, int imageIndex)

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	getBitsPerPixel() Gets the number of valid bits per pixel.
LMSFileReader.ImageFormat	getImageFormat() Returns the file format in which actual image bytes are stored
int	getPixelType() Gets the pixel type.
int	getRGBChannelCount() Gets the number of channels returned with each call to openBytes.
int	getSizeC() Gets the size of the C dimension.
private void	initReaders(java.util.List<java.lang.String> ids) Creates an internal reader for each image file
boolean	isRGB() Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
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	reopenFile() Reopen any files that were closed, and which are expected to be open while the reader is open.
void	setCoreMetadata(CoreMetadata cmd)
void	setMetadataTempBuffer(MetadataTempBuffer metaTemp)
void	setSeries(int no) Sets the field MultipleImagesReader.series.
void	swapDimensions() Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder

Methods inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

addSeriesMeta, addSeriesMetaList, fileExists, getCore, makeFilterMetadata, setCore, translateMetadata, translateMetadata, useOldPhysicalSizeCalculation

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, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, 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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, 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

readers

private java.util.List<FormatReader> readers

imageFormat

private LMSFileReader.ImageFormat imageFormat

tileCount

private int tileCount

dimensionsSwapped

private boolean dimensionsSwapped

series

private int series

imageIndex

private int imageIndex

Constructor Detail

MultipleImagesReader

public MultipleImagesReader(XlifDocument xlif,
                            int imageIndex)
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException

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.

setSeries

public void setSeries(int no)

Sets the field MultipleImagesReader.series. Needs to be called before calling MultipleImagesReader.openBytes()

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class FormatReader

getRGBChannelCount

public int getRGBChannelCount()

Description copied from interface: IFormatReader

Gets the number of channels returned with each call to openBytes. The most common case where this value is greater than 1 is for interleaved RGB data, such as a 24-bit color image plane. However, it is possible for this value to be greater than 1 for non-interleaved data, such as an RGB TIFF with Planar rather than Chunky configuration.

Specified by:

getRGBChannelCount in interface IFormatReader

Overrides:

getRGBChannelCount in class FormatReader

getBitsPerPixel

public int getBitsPerPixel()

Description copied from interface: IFormatReader

Gets the number of valid bits per pixel. The number of valid bits per pixel is always less than or equal to the number of bits per pixel that correspond to IFormatReader.getPixelType().

Specified by:

getBitsPerPixel in interface IFormatReader

Overrides:

getBitsPerPixel in class FormatReader

getPixelType

public int getPixelType()

Description copied from interface: IFormatReader

Gets the pixel type.

Specified by:

getPixelType in interface IFormatReader

Overrides:

getPixelType in class FormatReader

Returns:

the pixel type as an enumeration from FormatTools static pixel types such as FormatTools.INT8.

getSizeC

public int getSizeC()

Description copied from interface: IFormatReader

Gets the size of the C dimension.

Specified by:

getSizeC in interface IFormatReader

Overrides:

getSizeC in class FormatReader

isRGB

public boolean isRGB()

Description copied from interface: IFormatReader

Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call. This method returns true if and only if IFormatReader.getRGBChannelCount() returns a value greater than 1.

Specified by:

isRGB in interface IFormatReader

Overrides:

isRGB 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 LMSFileReader

Throws:

java.io.IOException

initReaders

private void initReaders(java.util.List<java.lang.String> ids)
                  throws FormatException,
                         java.io.IOException

Creates an internal reader for each image file

Parameters:

ids - list of file ids

Throws:

FormatException

java.io.IOException

getImageFormat

public LMSFileReader.ImageFormat getImageFormat()

Description copied from class: LMSFileReader

Returns the file format in which actual image bytes are stored

Specified by:

getImageFormat in class LMSFileReader

setMetadataTempBuffer

public void setMetadataTempBuffer(MetadataTempBuffer metaTemp)

setCoreMetadata

public void setCoreMetadata(CoreMetadata cmd)

swapDimensions

public void swapDimensions()
                    throws FormatException

Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder

Parameters:

cmd - corresponding CoreMetadata (expecting that all tiles have the same dimension sizes)

Throws:

FormatException

reopenFile

public void reopenFile()
                throws java.io.IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

java.io.IOException