Package net.preibisch.mvrecon.process.n5api

Class SpimData2Tools

java.lang.Object

net.preibisch.mvrecon.process.n5api.SpimData2Tools

public class SpimData2Tools
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	SpimData2Tools.InstantiateViewSetup
static class	SpimData2Tools.InstantiateViewSetupBigStitcher
static class	SpimData2Tools.InstantiateViewSetupBigStitcherSpark

Constructor Summary

Constructors

Constructor	Description
SpimData2Tools()

Method Summary

Modifier and Type	Method	Description
static SpimData2	createNewSpimDataForFusion(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType, URI n5PathURI, URI xmlOutPathURI, Map<mpicbg.spim.data.sequence.ViewId,AllenOMEZarrLoader.OMEZARREntry> viewIdToPath, ArrayList<mpicbg.spim.data.sequence.ViewSetup> setups, ArrayList<mpicbg.spim.data.sequence.TimePoint> tps)
static String	listAllTimePoints(List<mpicbg.spim.data.sequence.TimePoint> timePointsToProcess)
static SpimData2	reduceSpimData2(SpimData2 oldSpimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)	Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and keeping the basepath (i.e. interest points still work) Note: PSF's will be lost.
static SpimData2	reduceSpimData2(SpimData2 oldSpimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, URI basePath)	Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and changing the base path (you still need to save to materialize the returned object!)
static N5ApiTools.MultiResolutionLevelInfo[]	writeBDVMetaData(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType, org.janelia.saalfeldlab.n5.DataType dataType, long[] dimensions, org.janelia.saalfeldlab.n5.Compression compression, int[] blockSize, int[][] downsamplings, mpicbg.spim.data.sequence.ViewId viewId, URI n5PathURI, URI xmlOutPathURI, SpimData2Tools.InstantiateViewSetup instantiateViewSetup)
static net.imglib2.util.Pair<Boolean,Boolean>	writeSpimData(mpicbg.spim.data.sequence.ViewId viewId, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType, long[] dimensions, URI n5PathURI, URI xmlOutPathURI, AllenOMEZarrLoader.OMEZARREntry omeZarrEntry, SpimData2Tools.InstantiateViewSetup instantiateViewSetup)

Methods inherited from class java.lang.Object

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

Constructor Details

SpimData2Tools

public SpimData2Tools()

Method Details

writeBDVMetaData

public static N5ApiTools.MultiResolutionLevelInfo[] writeBDVMetaData(org.janelia.saalfeldlab.n5.N5Writer driverVolumeWriter,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType,
 org.janelia.saalfeldlab.n5.DataType dataType,
 long[] dimensions,
 org.janelia.saalfeldlab.n5.Compression compression,
 int[] blockSize,
 int[][] downsamplings,
 mpicbg.spim.data.sequence.ViewId viewId,
 URI n5PathURI,
 URI xmlOutPathURI,
 SpimData2Tools.InstantiateViewSetup instantiateViewSetup)
                                                              throws mpicbg.spim.data.SpimDataException,
IOException

Throws:

mpicbg.spim.data.SpimDataException

IOException

writeSpimData

public static net.imglib2.util.Pair<Boolean,Boolean> writeSpimData(mpicbg.spim.data.sequence.ViewId viewId,
 org.janelia.saalfeldlab.n5.universe.StorageFormat storageType,
 long[] dimensions,
 URI n5PathURI,
 URI xmlOutPathURI,
 AllenOMEZarrLoader.OMEZARREntry omeZarrEntry,
 SpimData2Tools.InstantiateViewSetup instantiateViewSetup)
                                                            throws mpicbg.spim.data.SpimDataException

Throws:

mpicbg.spim.data.SpimDataException

createNewSpimDataForFusion

public static SpimData2 createNewSpimDataForFusion(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType,
 URI n5PathURI,
 URI xmlOutPathURI,
 Map<mpicbg.spim.data.sequence.ViewId,AllenOMEZarrLoader.OMEZARREntry> viewIdToPath,
 ArrayList<mpicbg.spim.data.sequence.ViewSetup> setups,
 ArrayList<mpicbg.spim.data.sequence.TimePoint> tps)

reduceSpimData2

public static SpimData2 reduceSpimData2(SpimData2 oldSpimData,
 List<mpicbg.spim.data.sequence.ViewId> viewIds)

Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and keeping the basepath (i.e. interest points still work) Note: PSF's will be lost.

Parameters:

oldSpimData - - the original SpimData

viewIds - - the views to keep

Returns:

- reduced SpimData2

reduceSpimData2

public static SpimData2 reduceSpimData2(SpimData2 oldSpimData,
 List<mpicbg.spim.data.sequence.ViewId> viewIds,
 URI basePath)

Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and changing the base path (you still need to save to materialize the returned object!) Note: PSF's will be lost.

Parameters:

oldSpimData - - the original SpimData

viewIds - - the views to keep

basePath - - the new base path (can be null); if you set a new base path it will load all interest points so the new SpimData2 object can be saved including these points

Returns:

- reduced SpimData2

listAllTimePoints

public static String listAllTimePoints(List<mpicbg.spim.data.sequence.TimePoint> timePointsToProcess)