writeN5File
public static void writeN5File(mpicbg.spim.data.generic.sequence.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