Package net.preibisch.mvrecon.process.n5api

Class N5ApiTools

java.lang.Object

net.preibisch.mvrecon.process.n5api.N5ApiTools

public class N5ApiTools
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	N5ApiTools.MultiResolutionLevelInfo

Constructor Summary

Constructors

Constructor	Description
N5ApiTools()

Method Summary

Modifier and Type	Method	Description
static Map<Integer,org.janelia.saalfeldlab.n5.DataType>	assembleDataTypes(mpicbg.spim.data.generic.AbstractSpimData<?> data, Collection<Integer> viewSetupIds)
static HashMap<Integer,long[]>	assembleDimensions(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static List<long[][]>	assembleJobs(long[] dimensions, int[] blockSize)
static List<long[][]>	assembleJobs(long[] dimensions, int[] blockSize, int[] computeBlockSize)
static List<long[][]>	assembleJobs(mpicbg.spim.data.sequence.ViewId viewId, long[] dimensions, int[] blockSize)
static List<long[][]>	assembleJobs(mpicbg.spim.data.sequence.ViewId viewId, long[] dimensions, int[] blockSize, int[] computeBlockSize)
static List<long[][]>	assembleJobs(mpicbg.spim.data.sequence.ViewId viewId, N5ApiTools.MultiResolutionLevelInfo mrInfo)
static List<long[][]>	assembleJobs(mpicbg.spim.data.sequence.ViewId viewId, N5ApiTools.MultiResolutionLevelInfo mrInfo, int[] computeBlockSize)
static List<long[][]>	assembleJobs(N5ApiTools.MultiResolutionLevelInfo mrInfo)
static List<long[][]>	assembleJobs(N5ApiTools.MultiResolutionLevelInfo mrInfo, int[] computeBlockSize)
static ArrayList<mpicbg.spim.data.sequence.ViewSetup>	assembleViewSetups(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static int	channelIndex(Group<? extends mpicbg.spim.data.sequence.ViewDescription> queryGroup, ArrayList<mpicbg.spim.data.sequence.Channel> channels)
static ArrayList<mpicbg.spim.data.sequence.Channel>	channels(List<? extends Group<? extends mpicbg.spim.data.sequence.ViewDescription>> fusionGroups)
static int[]	computeRelativeDownsampling(int[][] downsamplings, int level)
static String	createBDVPath(String bdvString, int level, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static String	createBDVPath(mpicbg.spim.data.sequence.ViewId viewId, int level, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static String	createDownsampledBDVPath(String s0path, int level, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static String[]	exportOptions()
static mpicbg.spim.data.sequence.ViewId	getViewId(String bdvString)
static mpicbg.spim.data.sequence.ViewId	gridBlockToViewId(long[][] gridBlock)
static Function<long[][],String>	gridToDatasetBdv(int level, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static BiFunction<long[][],Integer,String>	gridToDatasetBdv(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static int[][]	mipMapInfoToDownsamplings(Map<Integer,bdv.export.ExportMipmapInfo> mipmaps)
static <T extends net.imglib2.type.NativeType<T>> void	resaveS0Block(SpimData2 data, org.janelia.saalfeldlab.n5.N5Writer n5, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType, org.janelia.saalfeldlab.n5.DataType dataType, Function<long[][],String> gridBlockToDataset, long[][] gridBlock)
static N5ApiTools.MultiResolutionLevelInfo[]	setupBdvDatasetsHDF5(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, mpicbg.spim.data.sequence.ViewId viewId, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensions, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings)
static N5ApiTools.MultiResolutionLevelInfo[]	setupBdvDatasetsN5(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, mpicbg.spim.data.sequence.ViewId viewId, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensions, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings)
static N5ApiTools.MultiResolutionLevelInfo[]	setupBdvDatasetsOMEZARR_ResaveRaw(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, mpicbg.spim.data.sequence.ViewId viewId, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensions, double[] resolutionS0, String resolutionUnit, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings, boolean useSharding, int[] shardSize)
static N5ApiTools.MultiResolutionLevelInfo[]	setupMultiResolutionPyramid(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, Function<Integer,String> levelToDataset, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensionsS0, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings)
static N5ApiTools.MultiResolutionLevelInfo[]	setupMultiResolutionPyramid(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, Function<Integer,String> levelToDataset, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensionsS0, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings, boolean useSharding, int[] shardSize)
static N5ApiTools.MultiResolutionLevelInfo[]	setupMultiResolutionPyramid(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, mpicbg.spim.data.sequence.ViewId viewId, BiFunction<mpicbg.spim.data.sequence.ViewId,Integer,String> viewIdToDataset, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensionsS0, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings, boolean useSharding, int[] shardSize)
static int	timepointIndex(Group<? extends mpicbg.spim.data.sequence.ViewDescription> queryGroup, ArrayList<mpicbg.spim.data.sequence.TimePoint> timepoints)
static ArrayList<mpicbg.spim.data.sequence.TimePoint>	timepoints(List<? extends Group<? extends mpicbg.spim.data.sequence.ViewDescription>> fusionGroups)
static Function<mpicbg.spim.data.sequence.ViewId,String>	viewIdToDatasetBdv(int level, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static BiFunction<mpicbg.spim.data.sequence.ViewId,Integer,String>	viewIdToDatasetBdv(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)
static <T extends net.imglib2.type.NativeType<T> & net.imglib2.type.numeric.RealType<T>> void	writeDownsampledBlock(org.janelia.saalfeldlab.n5.N5Writer n5, N5ApiTools.MultiResolutionLevelInfo mrInfo, N5ApiTools.MultiResolutionLevelInfo mrInfoPreviousScale, long[][] gridBlock)
static <T extends net.imglib2.type.NativeType<T> & net.imglib2.type.numeric.RealType<T>> void	writeDownsampledBlock5dOMEZARR(org.janelia.saalfeldlab.n5.N5Writer n5, N5ApiTools.MultiResolutionLevelInfo mrInfo, N5ApiTools.MultiResolutionLevelInfo mrInfoPreviousScale, long[][] gridBlock, long currentChannelIndex, long currentTPIndex)

Methods inherited from class java.lang.Object

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

Constructor Details

N5ApiTools

public N5ApiTools()

Method Details

gridBlockToViewId

public static mpicbg.spim.data.sequence.ViewId gridBlockToViewId(long[][] gridBlock)

gridToDatasetBdv

public static Function<long[][],String> gridToDatasetBdv(int level,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

Parameters:

level - - the downsampling level

storageType - - N5 or HDF5 (soon Zarr)

Returns:

a Function that maps the gridBlock to a N5 dataset name

viewIdToDatasetBdv

public static Function<mpicbg.spim.data.sequence.ViewId,String> viewIdToDatasetBdv(int level,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

Parameters:

level - - the downsampling level

storageType - - N5 or HDF5 (soon Zarr)

Returns:

a Function that maps the ViewId to a N5 dataset name

viewIdToDatasetBdv

public static BiFunction<mpicbg.spim.data.sequence.ViewId,Integer,String> viewIdToDatasetBdv(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

Parameters:

storageType - - N5 or HDF5 (soon Zarr)

Returns:

a Function that maps (ViewId, level) to a N5 dataset name

gridToDatasetBdv

public static BiFunction<long[][],Integer,String> gridToDatasetBdv(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

Parameters:

storageType - - N5 or HDF5 (soon Zarr)

Returns:

a Function that maps (gridBlock, level) to a N5 dataset name

getViewId

public static mpicbg.spim.data.sequence.ViewId getViewId(String bdvString)

createBDVPath

public static String createBDVPath(String bdvString,
 int level,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

createBDVPath

public static String createBDVPath(mpicbg.spim.data.sequence.ViewId viewId,
 int level,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

createDownsampledBDVPath

public static String createDownsampledBDVPath(String s0path,
 int level,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType)

setupMultiResolutionPyramid

public static N5ApiTools.MultiResolutionLevelInfo[] setupMultiResolutionPyramid(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 Function<Integer,String> levelToDataset,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensionsS0,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings)

setupMultiResolutionPyramid

public static N5ApiTools.MultiResolutionLevelInfo[] setupMultiResolutionPyramid(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 Function<Integer,String> levelToDataset,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensionsS0,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings,
 boolean useSharding,
 int[] shardSize)

setupMultiResolutionPyramid

public static N5ApiTools.MultiResolutionLevelInfo[] setupMultiResolutionPyramid(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 mpicbg.spim.data.sequence.ViewId viewId,
 BiFunction<mpicbg.spim.data.sequence.ViewId,Integer,String> viewIdToDataset,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensionsS0,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings,
 boolean useSharding,
 int[] shardSize)

exportOptions

public static String[] exportOptions()

setupBdvDatasetsHDF5

public static N5ApiTools.MultiResolutionLevelInfo[] setupBdvDatasetsHDF5(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 mpicbg.spim.data.sequence.ViewId viewId,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensions,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings)

setupBdvDatasetsOMEZARR_ResaveRaw

public static N5ApiTools.MultiResolutionLevelInfo[] setupBdvDatasetsOMEZARR_ResaveRaw(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 mpicbg.spim.data.sequence.ViewId viewId,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensions,
 double[] resolutionS0,
 String resolutionUnit,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings,
 boolean useSharding,
 int[] shardSize)

setupBdvDatasetsN5

public static N5ApiTools.MultiResolutionLevelInfo[] setupBdvDatasetsN5(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 mpicbg.spim.data.sequence.ViewId viewId,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensions,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings)

writeDownsampledBlock

public static <T extends net.imglib2.type.NativeType<T> & net.imglib2.type.numeric.RealType<T>>
void writeDownsampledBlock(org.janelia.saalfeldlab.n5.N5Writer n5,
 N5ApiTools.MultiResolutionLevelInfo mrInfo,
 N5ApiTools.MultiResolutionLevelInfo mrInfoPreviousScale,
 long[][] gridBlock)

writeDownsampledBlock5dOMEZARR

public static <T extends net.imglib2.type.NativeType<T> & net.imglib2.type.numeric.RealType<T>>
void writeDownsampledBlock5dOMEZARR(org.janelia.saalfeldlab.n5.N5Writer n5,
 N5ApiTools.MultiResolutionLevelInfo mrInfo,
 N5ApiTools.MultiResolutionLevelInfo mrInfoPreviousScale,
 long[][] gridBlock,
 long currentChannelIndex,
 long currentTPIndex)

assembleJobs

public static List<long[][]> assembleJobs(N5ApiTools.MultiResolutionLevelInfo mrInfo)

assembleJobs

public static List<long[][]> assembleJobs(N5ApiTools.MultiResolutionLevelInfo mrInfo,
 int[] computeBlockSize)

assembleJobs

public static List<long[][]> assembleJobs(mpicbg.spim.data.sequence.ViewId viewId,
 N5ApiTools.MultiResolutionLevelInfo mrInfo)

assembleJobs

public static List<long[][]> assembleJobs(mpicbg.spim.data.sequence.ViewId viewId,
 N5ApiTools.MultiResolutionLevelInfo mrInfo,
 int[] computeBlockSize)

assembleJobs

public static List<long[][]> assembleJobs(long[] dimensions,
 int[] blockSize)

assembleJobs

public static List<long[][]> assembleJobs(long[] dimensions,
 int[] blockSize,
 int[] computeBlockSize)

assembleJobs

public static List<long[][]> assembleJobs(mpicbg.spim.data.sequence.ViewId viewId,
 long[] dimensions,
 int[] blockSize)

assembleJobs

public static List<long[][]> assembleJobs(mpicbg.spim.data.sequence.ViewId viewId,
 long[] dimensions,
 int[] blockSize,
 int[] computeBlockSize)

computeRelativeDownsampling

public static int[] computeRelativeDownsampling(int[][] downsamplings,
 int level)

resaveS0Block

public static <T extends net.imglib2.type.NativeType<T>>
void resaveS0Block(SpimData2 data,
 org.janelia.saalfeldlab.n5.N5Writer n5,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType,
 org.janelia.saalfeldlab.n5.DataType dataType,
 Function<long[][],String> gridBlockToDataset,
 long[][] gridBlock)

assembleDataTypes

public static Map<Integer,org.janelia.saalfeldlab.n5.DataType> assembleDataTypes(mpicbg.spim.data.generic.AbstractSpimData<?> data,
 Collection<Integer> viewSetupIds)

mipMapInfoToDownsamplings

public static int[][] mipMapInfoToDownsamplings(Map<Integer,bdv.export.ExportMipmapInfo> mipmaps)

assembleDimensions

public static HashMap<Integer,long[]> assembleDimensions(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

assembleViewSetups

public static ArrayList<mpicbg.spim.data.sequence.ViewSetup> assembleViewSetups(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

timepoints

public static ArrayList<mpicbg.spim.data.sequence.TimePoint> timepoints(List<? extends Group<? extends mpicbg.spim.data.sequence.ViewDescription>> fusionGroups)

channels

public static ArrayList<mpicbg.spim.data.sequence.Channel> channels(List<? extends Group<? extends mpicbg.spim.data.sequence.ViewDescription>> fusionGroups)

channelIndex

public static int channelIndex(Group<? extends mpicbg.spim.data.sequence.ViewDescription> queryGroup,
 ArrayList<mpicbg.spim.data.sequence.Channel> channels)

timepointIndex

public static int timepointIndex(Group<? extends mpicbg.spim.data.sequence.ViewDescription> queryGroup,
 ArrayList<mpicbg.spim.data.sequence.TimePoint> timepoints)