bdv.export.n5

Class WriteSequenceToN5

java.lang.Object

bdv.export.n5.WriteSequenceToN5

public class WriteSequenceToN5
extends Object

Author:

Tobias Pietzsch, John Bogovic

Constructor Summary

Constructors

Constructor and Description
WriteSequenceToN5()

Method Summary

Modifier and Type

Method and Description

static void

writeN5File(AbstractSequenceDescription<?,?,?> seq, Map<Integer,ExportMipmapInfo> perSetupMipmapInfo, org.janelia.saalfeldlab.n5.Compression compression, File n5File, ExportScalePyramid.LoopbackHeuristic loopbackHeuristic, ExportScalePyramid.AfterEachPlane afterEachPlane, int numCellCreatorThreads, ProgressWriter progressWriter) Create a n5 group containing image data from all views and all timepoints in a chunked, mipmaped representation.

Methods inherited from class java.lang.Object

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

Constructor Detail

WriteSequenceToN5

public WriteSequenceToN5()

Method Detail

writeN5File

public static void writeN5File(AbstractSequenceDescription<?,?,?> seq,
                               Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
                               org.janelia.saalfeldlab.n5.Compression compression,
                               File n5File,
                               ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
                               ExportScalePyramid.AfterEachPlane afterEachPlane,
                               int numCellCreatorThreads,
                               ProgressWriter progressWriter)
                        throws IOException

Create a n5 group containing image data from all views and all timepoints in a chunked, mipmaped representation.

Parameters:

seq - description of the sequence to be stored as hdf5. (The AbstractSequenceDescription contains the number of setups and timepoints as well as an BasicImgLoader that provides the image data, Registration information is not needed here, that will go into the accompanying xml).

perSetupMipmapInfo - this maps from setup id to ExportMipmapInfo for that setup. The ExportMipmapInfo contains for each mipmap level, the subsampling factors and subdivision block sizes.

compression - n5 compression scheme.

n5File - n5 root.

loopbackHeuristic - heuristic to decide whether to create each resolution level by reading pixels from the original image or by reading back a finer resolution level already written to the hdf5. may be null (in this case always use the original image).

afterEachPlane - this is called after each "plane of chunks" is written, giving the opportunity to clear caches, etc.

numCellCreatorThreads - The number of threads that will be instantiated to generate cell data. Must be at least 1. (In addition the cell creator threads there is one writer thread that saves the generated data to HDF5.)

progressWriter - completion ratio and status output will be directed here.

Throws:

IOException