Package net.preibisch.mvrecon.fiji.datasetmanager

Class OMEZARR

java.lang.Object

net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

All Implemented Interfaces:

MultiViewDatasetDefinition

public class OMEZARR
extends Object
implements MultiViewDatasetDefinition

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	OMEZARR.MultipleOMEZARRListChooser
protected static interface	OMEZARR.URIListChooser
protected static class	OMEZARR.WildcardDirectoryListChooser

Field Summary

Fields

Modifier and Type	Field	Description
static String	defaultDir
static String	defaultDirectory
static int	defaultURIListChoice
static int	defaultZarrChoice

Constructor Summary

Constructors

Constructor	Description
OMEZARR()

Method Summary

Modifier and Type	Method	Description
SpimData2	createDataset(String xmlFileName)	This method is supposed to (interactively, ideally ImageJ-macroscriptable) query all necessary data from the user to build up a SpimData object and save it as an XML file.
String	getExtendedDescription()	An explanation for the user what exactly this MultiViewDatasetDefinition supports and how it needs to be stored.
String	getTitle()	Defines the title under which it will be displayed in the list of available multi-view dataset definitions
protected static boolean	hasCommonScale(Map<String,net.imglib2.util.Pair<org.janelia.saalfeldlab.n5.DatasetAttributes,net.imglib2.util.Pair<mpicbg.spim.data.sequence.VoxelDimensions,double[]>>> attr)
static void	main(String[] args)
OMEZARR	newInstance()
boolean	supportsRemoteXMLLocation()
protected static HashMap<mpicbg.spim.data.sequence.ViewId,AllenOMEZarrLoader.OMEZARREntry>	updateViewSetup(String dataset, Collection<mpicbg.spim.data.sequence.ViewSetup> viewSetups, net.imglib2.util.Pair<org.janelia.saalfeldlab.n5.DatasetAttributes,net.imglib2.util.Pair<mpicbg.spim.data.sequence.VoxelDimensions,double[]>> meta, int angleId, int channelId, int illumId, int tileId, int tpId, long sizeT, int numDimensions)

Methods inherited from class java.lang.Object

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

Field Details

defaultDirectory

public static String defaultDirectory

defaultDir

public static String defaultDir

defaultZarrChoice

public static int defaultZarrChoice

defaultURIListChoice

public static int defaultURIListChoice

Constructor Details

OMEZARR

public OMEZARR()

Method Details

supportsRemoteXMLLocation

public boolean supportsRemoteXMLLocation()

Specified by:

supportsRemoteXMLLocation in interface MultiViewDatasetDefinition

Returns:

if the XML can be stored somewhere else but where the data is located

getTitle

public String getTitle()

Description copied from interface: MultiViewDatasetDefinition

Defines the title under which it will be displayed in the list of available multi-view dataset definitions

Specified by:

getTitle in interface MultiViewDatasetDefinition

Returns:

the title

getExtendedDescription

public String getExtendedDescription()

Description copied from interface: MultiViewDatasetDefinition

An explanation for the user what exactly this MultiViewDatasetDefinition supports and how it needs to be stored. Up to 15 lines will be displayed with 80 characters each. No newline characters are allowed.

Specified by:

getExtendedDescription in interface MultiViewDatasetDefinition

Returns:

description

createDataset

public SpimData2 createDataset(String xmlFileName)

Description copied from interface: MultiViewDatasetDefinition

This method is supposed to (interactively, ideally ImageJ-macroscriptable) query all necessary data from the user to build up a SpimData object and save it as an XML file.

Specified by:

createDataset in interface MultiViewDatasetDefinition

Parameters:

xmlFileName - - the filename of the XML that was selected (no path!)

Returns:

- the saved SpimData2 object

updateViewSetup

protected static HashMap<mpicbg.spim.data.sequence.ViewId,AllenOMEZarrLoader.OMEZARREntry> updateViewSetup(String dataset,
 Collection<mpicbg.spim.data.sequence.ViewSetup> viewSetups,
 net.imglib2.util.Pair<org.janelia.saalfeldlab.n5.DatasetAttributes,net.imglib2.util.Pair<mpicbg.spim.data.sequence.VoxelDimensions,double[]>> meta,
 int angleId,
 int channelId,
 int illumId,
 int tileId,
 int tpId,
 long sizeT,
 int numDimensions)

hasCommonScale

protected static boolean hasCommonScale(Map<String,net.imglib2.util.Pair<org.janelia.saalfeldlab.n5.DatasetAttributes,net.imglib2.util.Pair<mpicbg.spim.data.sequence.VoxelDimensions,double[]>>> attr)

newInstance

public OMEZARR newInstance()

Specified by:

newInstance in interface MultiViewDatasetDefinition

Returns:

- a new instance of this implementation

main

public static void main(String[] args)