Package net.preibisch.mvrecon.process.export

Class ExportN5Api

java.lang.Object

net.preibisch.mvrecon.process.export.ExportN5Api

All Implemented Interfaces:

Calibrateable, ImgExport

public class ExportN5Api
extends Object
implements ImgExport, Calibrateable

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	defaultAdvancedBlockSize
static boolean	defaultBDV
static int	defaultBlocksizeFactorX_H5
static int	defaultBlocksizeFactorX_N5
static int	defaultBlocksizeFactorY_H5
static int	defaultBlocksizeFactorY_N5
static int	defaultBlocksizeFactorZ_H5
static int	defaultBlocksizeFactorZ_N5
static int	defaultBlocksizeX_H5
static int	defaultBlocksizeX_N5
static int	defaultBlocksizeY_H5
static int	defaultBlocksizeY_N5
static int	defaultBlocksizeZ_H5
static int	defaultBlocksizeZ_N5
static String	defaultDatasetName
static boolean	defaultManuallyAssignViewId
static boolean	defaultMultiRes
static int	defaultOmeZarrDim
static boolean	defaultOmeZarrOneContainer
static int	defaultOption
static String	defaultPathURI
static int	defaultTpId
static boolean	defaultUseSharding
static int	defaultVSId
static String	defaultXMLOutURI

Constructor Summary

Constructors

Constructor	Description
ExportN5Api()

Method Summary

Modifier and Type	Method	Description
int[]	blocksize()	specify the desired 3d blocksize used for the Lazy instances
int[]	computeBlocksizeFactor()
static int[][]	estimateMultiResPyramid(net.imglib2.Dimensions dimensions, double aniso)
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> boolean	exportImage(net.imglib2.algorithm.blocks.BlockSupplier<T> blockSupplierIn, net.imglib2.Interval bb, double downsamplingF, double anisoF, String title, Group<? extends mpicbg.spim.data.sequence.ViewDescription> fusionGroup)	Exports the image using a predefined min/max
boolean	finish()	Called last when the fusion is finished (e.g. to write the XML)
String	getDescription()
double[]	getPixelSize()
String	getUnit()
ImgExport	newInstance()
boolean	queryParameters(FusionExportInterface fusion)
void	setCalibration(double[] pixelSize, String unit)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

defaultPathURI

public static String defaultPathURI

defaultOption

public static int defaultOption

defaultDatasetName

public static String defaultDatasetName

defaultOmeZarrDim

public static int defaultOmeZarrDim

defaultOmeZarrOneContainer

public static boolean defaultOmeZarrOneContainer

defaultBDV

public static boolean defaultBDV

defaultMultiRes

public static boolean defaultMultiRes

defaultXMLOutURI

public static String defaultXMLOutURI

defaultManuallyAssignViewId

public static boolean defaultManuallyAssignViewId

defaultTpId

public static int defaultTpId

defaultVSId

public static int defaultVSId

defaultBlocksizeX_N5

public static int defaultBlocksizeX_N5

defaultBlocksizeY_N5

public static int defaultBlocksizeY_N5

defaultBlocksizeZ_N5

public static int defaultBlocksizeZ_N5

defaultBlocksizeX_H5

public static int defaultBlocksizeX_H5

defaultBlocksizeY_H5

public static int defaultBlocksizeY_H5

defaultBlocksizeZ_H5

public static int defaultBlocksizeZ_H5

defaultAdvancedBlockSize

public static boolean defaultAdvancedBlockSize

defaultBlocksizeFactorX_N5

public static int defaultBlocksizeFactorX_N5

defaultBlocksizeFactorY_N5

public static int defaultBlocksizeFactorY_N5

defaultBlocksizeFactorZ_N5

public static int defaultBlocksizeFactorZ_N5

defaultBlocksizeFactorX_H5

public static int defaultBlocksizeFactorX_H5

defaultBlocksizeFactorY_H5

public static int defaultBlocksizeFactorY_H5

defaultBlocksizeFactorZ_H5

public static int defaultBlocksizeFactorZ_H5

defaultUseSharding

public static boolean defaultUseSharding

Constructor Details

ExportN5Api

public ExportN5Api()

Method Details

finish

public boolean finish()

Description copied from interface: ImgExport

Called last when the fusion is finished (e.g. to write the XML)

Specified by:

finish in interface ImgExport

Returns:

- true if the spimdata was modified, otherwise false

blocksize

public int[] blocksize()

Description copied from interface: ImgExport

specify the desired 3d blocksize used for the Lazy instances

Specified by:

blocksize in interface ImgExport

Returns:

- the desired 3d blocksize

computeBlocksizeFactor

public int[] computeBlocksizeFactor()

newInstance

public ImgExport newInstance()

Specified by:

newInstance in interface ImgExport

getDescription

public String getDescription()

Specified by:

getDescription in interface ImgExport

Returns:

- to be displayed in the generic dialog

exportImage

public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
boolean exportImage(net.imglib2.algorithm.blocks.BlockSupplier<T> blockSupplierIn,
 net.imglib2.Interval bb,
 double downsamplingF,
 double anisoF,
 String title,
 Group<? extends mpicbg.spim.data.sequence.ViewDescription> fusionGroup)

Description copied from interface: ImgExport

Exports the image using a predefined min/max

Specified by:

exportImage in interface ImgExport

Type Parameters:

T - pixel type

Parameters:

blockSupplierIn - - Note, in rare cases this can be null (i.e. do nothing)

bb - - the bounding box used to fuse this image

downsamplingF - - how much it was downsampled (or NaN if not)

anisoF - - how much the z-dimension was scaled (or NaN if not)

title - - the name of the image

fusionGroup - - which views are part of this fusion

Returns:

success? true or false

queryParameters

public boolean queryParameters(FusionExportInterface fusion)

Specified by:

queryParameters in interface ImgExport

setCalibration

public void setCalibration(double[] pixelSize,
 String unit)

Specified by:

setCalibration in interface Calibrateable

getUnit

public String getUnit()

Specified by:

getUnit in interface Calibrateable

getPixelSize

public double[] getPixelSize()

Specified by:

getPixelSize in interface Calibrateable

estimateMultiResPyramid

public static int[][] estimateMultiResPyramid(net.imglib2.Dimensions dimensions,
 double aniso)