Uses of Class mpicbg.spim.data.generic.AbstractSpimData (Fiji Javadocs 0-SNAPSHOT API)

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Packages that use AbstractSpimData
Package	Description
bdv
bdv.ij
bdv.spimdata
bdv.spimdata.tools
bdv.util
bigwarp
bigwarp.loader
mpicbg.spim.data
mpicbg.spim.data.generic
spim.fiji.plugin
spim.fiji.plugin.queryXML
spim.fiji.plugin.resave
spim.fiji.spimdata
spim.fiji.spimdata.explorer
spim.fiji.spimdata.explorer.popup
spim.fiji.spimdata.explorer.registration
spim.process.fusion.boundingbox

Uses of AbstractSpimData in bdv

Methods in bdv with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static void`	BigDataViewer.`initSetups(AbstractSpimData<?> spimData, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)`
`static BigDataViewer`	BigDataViewer.`open(AbstractSpimData<?> spimData, String windowTitle, ProgressWriter progressWriter, ViewerOptions options)`

Constructors in bdv with parameters of type AbstractSpimData
Constructor and Description
`AbstractSpimSource(AbstractSpimData<?> spimData, int setupId, String name)`
`BigDataViewer(ArrayList<ConverterSetup> converterSetups, ArrayList<SourceAndConverter<?>> sources, AbstractSpimData<?> spimData, int numTimepoints, CacheControl cache, String windowTitle, ProgressWriter progressWriter, ViewerOptions options)`
`SpimSource(AbstractSpimData<?> spimData, int setup, String name)`
`VolatileSpimSource(AbstractSpimData<?> spimData, int setup, String name)`

Uses of AbstractSpimData in bdv.ij

Methods in bdv.ij that return AbstractSpimData
Modifier and Type	Method and Description
`protected AbstractSpimData<?>`	OpenImagePlusPlugIn.`load(ij.ImagePlus imp, ArrayList<ConverterSetup> converterSetups, ArrayList<SourceAndConverter<?>> sources, int setup_id_offset)`

Uses of AbstractSpimData in bdv.spimdata

Subclasses of AbstractSpimData in bdv.spimdata
Modifier and Type	Class and Description
`class`	`SpimDataMinimal`

Methods in bdv.spimdata with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static boolean`	WrapBasicImgLoader.`removeWrapperIfPresent(AbstractSpimData<?> spimData)`
`static boolean`	WrapBasicImgLoader.`wrapImgLoaderIfNecessary(AbstractSpimData<?> spimData)` If the `image loader` of `spimData` is not a `ViewerImgLoader`, then replace it with a wrapper that presents it as `ViewerImgLoader`.

Uses of AbstractSpimData in bdv.spimdata.tools

Methods in bdv.spimdata.tools with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static Map<String,Map<Integer,Integer>>`	ChangeAttributeId.`assignNewAttributeIds(AbstractSpimData<?> spimData, Map<String,Set<Integer>> idsInUse)` For the specified `spimData` data set, re-assign attribute id's that are already in use.
`static Map<Integer,Integer>`	ChangeViewSetupId.`assignNewViewSetupIds(AbstractSpimData<?> spimData, Set<Integer> idsInUse)` For the specified `spimData` data set, re-assign setup id's that are already in use.
`static void`	ChangeAttributeId.`changeAttributeId(AbstractSpimData<?> spimData, String attributeName, int oldAttributeId, int newAttributeId)` TODO
`static void`	ChangeViewSetupId.`changeViewSetupId(AbstractSpimData<?> spimData, int oldViewSetupId, int newViewSetupId)` TODO

Uses of AbstractSpimData in bdv.util

Methods in bdv.util with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static List<BdvStackSource<?>>`	BdvFunctions.`show(AbstractSpimData<?> spimData)`
`static List<BdvStackSource<?>>`	BdvFunctions.`show(AbstractSpimData<?> spimData, BdvOptions options)`

Uses of AbstractSpimData in bigwarp

Methods in bigwarp with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static <T> BigWarp.BigWarpData<?>`	BigWarpInit.`add(BigWarp.BigWarpData bwdata, AbstractSpimData<?> data, int setupId, int numTimepoints, boolean isMoving)`
`static <T> BigWarpExporter<T>`	BigWarpBatchTransformFOV.`applyBigWarpHelper(AbstractSpimData<?>[] spimDataP, AbstractSpimData<?>[] spimDataQ, ij.ImagePlus impP, LandmarkTableModel ltm, Interpolation interpolation)`
`static <T> BigWarpExporter<T>`	BigWarpBatchTransformFOV.`applyBigWarpHelper(AbstractSpimData<?>[] spimDataP, AbstractSpimData<?>[] spimDataQ, ij.ImagePlus impP, LandmarkTableModel ltm, Interpolation interpolation)`
`static BigWarp.BigWarpData<?>`	BigWarpInit.`createBigWarpData(AbstractSpimData<?>[] spimDataPList, AbstractSpimData<?>[] spimDataQList)`
`static BigWarp.BigWarpData<?>`	BigWarpInit.`createBigWarpData(AbstractSpimData<?>[] spimDataPList, AbstractSpimData<?>[] spimDataQList)`
`static BigWarp.BigWarpData<?>`	BigWarpInit.`createBigWarpData(AbstractSpimData<?>[] spimDataPList, AbstractSpimData<?>[] spimDataQList, String[] names)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	BigWarpInit.`createBigWarpData(AbstractSpimData<?>[] spimDataPList, AbstractSpimData<?>[] spimDataQList, String[] names)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	BigWarpInit.`createBigWarpData(AbstractSpimData<?> spimDataP, AbstractSpimData<?> spimDataQ)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	BigWarpInit.`createBigWarpData(AbstractSpimData<?> spimDataP, AbstractSpimData<?> spimDataQ)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static void`	BigWarpInit.`initSetups(AbstractSpimData<?> spimData, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)`

Uses of AbstractSpimData in bigwarp.loader

Methods in bigwarp.loader that return AbstractSpimData
Modifier and Type Method and Description

<S extends AbstractSequenceDescription<?,?,?>> AbstractSpimData<S>[] Loader.load()
Uses of AbstractSpimData in mpicbg.spim.data

Subclasses of AbstractSpimData in mpicbg.spim.data
Modifier and Type Class and Description

class SpimData

Uses of AbstractSpimData in mpicbg.spim.data.generic

Classes in mpicbg.spim.data.generic with type parameters of type AbstractSpimData
Modifier and Type	Class and Description
`class`	`XmlIoAbstractSpimData<S extends AbstractSequenceDescription<?,?,?>,T extends AbstractSpimData<S>>`

Uses of AbstractSpimData in spim.fiji.plugin

Methods in spim.fiji.plugin with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static void`	Display_View.`display(AbstractSpimData<?> spimData, ViewId viewId, int pixelType, String name, boolean virtual)`
`static ArrayList<Specify_Calibration.Cal>`	Specify_Calibration.`findCalibrations(AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>> spimData, List<ViewId> viewIds)`

Uses of AbstractSpimData in spim.fiji.plugin.queryXML

Classes in spim.fiji.plugin.queryXML with type parameters of type AbstractSpimData
Modifier and Type	Class and Description
`class`	`GenericLoadParseQueryXML<AS extends AbstractSpimData<S>,S extends AbstractSequenceDescription<V,D,L>,V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader,X extends XmlIoAbstractSpimData<S,AS>>` Interface for interactive parsing of spimdata XMLs

Fields in spim.fiji.plugin.queryXML declared as AbstractSpimData
Modifier and Type	Field and Description
`protected AS`	GenericLoadParseQueryXML.`data`

Uses of AbstractSpimData in spim.fiji.plugin.resave

Methods in spim.fiji.plugin.resave with type parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static <T extends AbstractSpimData<A>,A extends AbstractSequenceDescription<?,?,? super ImgLoader>> void`	Generic_Resave_HDF5.`writeXML(T spimData, XmlIoAbstractSpimData<A,T> io, Generic_Resave_HDF5.Parameters params, ProgressWriter progressWriter)`

Methods in spim.fiji.plugin.resave with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static ArrayList<Partition>`	Generic_Resave_HDF5.`getPartitions(AbstractSpimData<?> spimData, Generic_Resave_HDF5.Parameters params)`
`static Map<Integer,ExportMipmapInfo>`	Generic_Resave_HDF5.`getPerSetupExportMipmapInfo(AbstractSpimData<?> spimData, Generic_Resave_HDF5.Parameters params)`
`static void`	Generic_Resave_HDF5.`writeHDF5(AbstractSpimData<?> spimData, Generic_Resave_HDF5.Parameters params, ProgressWriter progressWriter)`

Uses of AbstractSpimData in spim.fiji.spimdata

Subclasses of AbstractSpimData in spim.fiji.spimdata
Modifier and Type Class and Description

class SpimData2
Extends the SpimData class; has additonally detections

Uses of AbstractSpimData in spim.fiji.spimdata.explorer

Classes in spim.fiji.spimdata.explorer with type parameters of type AbstractSpimData
Modifier and Type	Interface and Description
`interface`	`SelectedViewDescriptionListener<AS extends AbstractSpimData<?>>`
`class`	`ViewSetupExplorer<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>>`
`class`	`ViewSetupExplorerInfoBox<AS extends AbstractSpimData<?>>`
`class`	`ViewSetupExplorerPanel<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>>`
`class`	`ViewSetupTableModel<AS extends AbstractSpimData<?>>`

Fields in spim.fiji.spimdata.explorer declared as AbstractSpimData
Modifier and Type	Field and Description
`protected AS`	ViewSetupExplorerPanel.`data`

Methods in spim.fiji.spimdata.explorer with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static int`	ViewSetupExplorerPanel.`getBDVSourceIndex(BasicViewSetup vs, AbstractSpimData<?> data)`
`static int`	ViewSetupExplorerPanel.`getBDVTimePointIndex(TimePoint t, AbstractSpimData<?> data)`
`static void`	ViewSetupExplorerPanel.`setFusedModeSimple(BigDataViewer bdv, AbstractSpimData<?> data)`
`static void`	ViewSetupExplorerPanel.`updateBDV(BigDataViewer bdv, boolean colorMode, AbstractSpimData<?> data, BasicViewDescription<? extends BasicViewSetup> firstVD, Collection<? extends BasicViewDescription<? extends BasicViewSetup>> selectedRows)`

Uses of AbstractSpimData in spim.fiji.spimdata.explorer.popup

Method parameters in spim.fiji.spimdata.explorer.popup with type arguments of type AbstractSpimData
Modifier and Type	Method and Description
`JMenuItem`	VisualizeDetectionsPopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JComponent`	ViewExplorerSetable.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JMenuItem`	SpecifyCalibrationPopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JMenuItem`	ResavePopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JMenuItem`	ReorientSamplePopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JMenuItem`	MaxProjectPopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JComponent`	FusionPopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JComponent`	BoundingBoxPopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`
`JMenuItem`	ApplyTransformationPopup.`setViewExplorer(ViewSetupExplorerPanel<? extends AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>>,?> panel)`

Uses of AbstractSpimData in spim.fiji.spimdata.explorer.registration

Classes in spim.fiji.spimdata.explorer.registration with type parameters of type AbstractSpimData
Modifier and Type	Class and Description
`class`	`RegistrationExplorer<AS extends AbstractSpimData<?>,X extends XmlIoAbstractSpimData<?,AS>>`

Uses of AbstractSpimData in spim.process.fusion.boundingbox

Methods in spim.process.fusion.boundingbox with parameters of type AbstractSpimData
Modifier and Type	Method and Description
`static Pair<BigDataViewer,Boolean>`	BigDataViewerBoundingBox.`getBDV(AbstractSpimData<?> spimData, Collection<ViewId> viewIdsToProcess)`

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