| Package | Description |
|---|---|
| bdv | |
| bdv.export | |
| bdv.export.n5 | |
| bdv.gui | |
| bdv.ij | |
| bdv.ij.export.tiles | |
| bdv.tools | |
| bigwarp | |
| mpicbg.spim.io | |
| spim.fiji.plugin.resave |
| Modifier and Type | Method and Description |
|---|---|
static BigDataViewer |
BigDataViewer.open(AbstractSpimData<?> spimData,
String windowTitle,
ProgressWriter progressWriter,
ViewerOptions options) |
static BigDataViewer |
BigDataViewer.open(ArrayList<ConverterSetup> converterSetups,
ArrayList<SourceAndConverter<?>> sources,
int numTimepoints,
CacheControl cache,
String windowTitle,
ProgressWriter progressWriter,
ViewerOptions options) |
static BigDataViewer |
BigDataViewer.open(String xmlFilename,
String windowTitle,
ProgressWriter progressWriter,
ViewerOptions options) |
| Constructor and Description |
|---|
BigDataViewer(ArrayList<ConverterSetup> converterSetups,
ArrayList<SourceAndConverter<?>> sources,
AbstractSpimData<?> spimData,
int numTimepoints,
CacheControl cache,
String windowTitle,
ProgressWriter progressWriter,
ViewerOptions options) |
| Modifier and Type | Class and Description |
|---|---|
class |
ProgressWriterConsole |
class |
ProgressWriterNull |
class |
SubTaskProgressWriter |
| Modifier and Type | Field and Description |
|---|---|
protected ProgressWriter |
SubTaskProgressWriter.progressWriter |
| Modifier and Type | Method and Description |
|---|---|
static void |
WriteSequenceToHdf5.writeHdf5File(AbstractSequenceDescription<?,?,?> seq,
int[][] resolutions,
int[][] subdivisions,
boolean deflate,
File hdf5File,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
int numCellCreatorThreads,
ProgressWriter progressWriter)
Create a hdf5 file containing image data from all views and all
timepoints in a chunked, mipmaped representation.
|
static void |
WriteSequenceToHdf5.writeHdf5File(AbstractSequenceDescription<?,?,?> seq,
Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
boolean deflate,
File hdf5File,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
int numCellCreatorThreads,
ProgressWriter progressWriter)
Create a hdf5 file containing image data from all views and all
timepoints in a chunked, mipmaped representation.
|
static void |
WriteSequenceToHdf5.writeHdf5PartitionFile(AbstractSequenceDescription<?,?,?> seq,
Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
boolean deflate,
Partition partition,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
int numCellCreatorThreads,
ProgressWriter progressWriter)
Create a hdf5 partition file containing image data for a subset of views
and timepoints in a chunked, mipmaped representation.
|
static <T extends RealType<T> & NativeType<T>,D> |
ExportScalePyramid.writeScalePyramid(RandomAccessibleInterval<T> img,
T type,
ExportMipmapInfo mipmapInfo,
ExportScalePyramid.DatasetIO<D,T> io,
ExecutorService executorService,
int numThreads,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
ProgressWriter progressWriter)
Write an image to a chunked mipmap representation.
|
static void |
WriteSequenceToHdf5.writeViewToHdf5PartitionFile(RandomAccessibleInterval<UnsignedShortType> img,
int timepointIdPartition,
int setupIdPartition,
ExportMipmapInfo mipmapInfo,
boolean writeMipmapInfo,
boolean deflate,
bdv.export.IHDF5Access writerQueue,
ExecutorService executorService,
int numThreads,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
ProgressWriter progressWriter)
Write a single view to a hdf5 partition file, in a chunked, mipmaped
representation.
|
static void |
WriteSequenceToHdf5.writeViewToHdf5PartitionFile(RandomAccessibleInterval<UnsignedShortType> img,
Partition partition,
int timepointIdPartition,
int setupIdPartition,
ExportMipmapInfo mipmapInfo,
boolean writeMipmapInfo,
boolean deflate,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
int numCellCreatorThreads,
ProgressWriter progressWriter)
Write a single view to a hdf5 partition file, in a chunked, mipmaped
representation.
|
| Constructor and Description |
|---|
SubTaskProgressWriter(ProgressWriter progressWriter,
double startCompletionRatio,
double endCompletionRatio) |
| Modifier and Type | Method and Description |
|---|---|
static void |
WriteSequenceToN5.writeN5File(AbstractSequenceDescription<?,?,?> seq,
Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
org.janelia.saalfeldlab.n5.Compression compression,
File n5File,
ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
ExportScalePyramid.AfterEachPlane afterEachPlane,
int numCellCreatorThreads,
ProgressWriter progressWriter)
Create a n5 group containing image data from all views and all
timepoints in a chunked, mipmaped representation.
|
| Constructor and Description |
|---|
BigwarpLandmarkSelectionPanel(BigWarp.BigWarpData<T> data,
List<SourceAndConverter<T>> sources,
String fieldOfViewOption,
List<Interval> outputIntervalList,
List<String> matchedPtNames,
Interpolation interp,
double[] offsetIn,
double[] resolution,
boolean isVirtual,
int nThreads,
ProgressWriter progressWriter)
Displays a dialog showing point matches
|
| Modifier and Type | Method and Description |
|---|---|
static <T> List<ij.ImagePlus> |
ApplyBigwarpPlugin.runExport(BigWarp.BigWarpData<T> data,
List<SourceAndConverter<T>> sources,
String fieldOfViewOption,
List<Interval> outputIntervalList,
List<String> matchedPtNames,
Interpolation interp,
double[] offsetIn,
double[] resolution,
boolean isVirtual,
int nThreads,
ProgressWriter progressWriter,
boolean show,
boolean wait,
ApplyBigwarpPlugin.WriteDestinationOptions writeOpts) |
static <S,T extends NativeType<T> & NumericType<T>> |
ApplyBigwarpPlugin.runN5Export(BigWarp.BigWarpData<S> data,
List<SourceAndConverter<S>> sources,
String fieldOfViewOption,
Interval outputInterval,
Interpolation interp,
double[] offset,
double[] resolution,
String unit,
ProgressWriter progressWriter,
ApplyBigwarpPlugin.WriteDestinationOptions writeOpts,
ExecutorService exec) |
| Modifier and Type | Method and Description |
|---|---|
void |
CellVoyagerDataExporter.export(File seqFile,
File hdf5File,
int[][] resolutions,
int[][] chunks,
ProgressWriter progressWriter)
Export the target dataset to a xml/hd5 file couple.
|
| Constructor and Description |
|---|
RecordMaxProjectionDialog(Frame owner,
ViewerPanel viewer,
ProgressWriter progressWriter) |
RecordMovieDialog(Frame owner,
ViewerPanel viewer,
ProgressWriter progressWriter) |
| Modifier and Type | Field and Description |
|---|---|
protected ProgressWriter |
BigWarpExporter.progress |
| Modifier and Type | Method and Description |
|---|---|
static <T extends NumericType<T> & NativeType<T>> |
BigWarpRealExporter.copyToImageStack(RandomAccessible<T> rai,
Interval itvl,
ProgressWriter progress) |
static <T extends NumericType<T>> |
BigWarpExporter.copyToImageStackBySlice(RandomAccessible<T> raible,
Interval itvl,
ImgFactory<T> factory,
int nThreads,
ProgressWriter progress) |
static <T extends NumericType<T>> |
BigWarpExporter.copyToImageStackBySlice(RandomAccessible<T> ra,
Interval itvl,
RandomAccessibleInterval<T> target,
int nThreads,
ProgressWriter progress) |
static <T extends NumericType<T>> |
BigWarpExporter.copyToImageStackIterOrder(RandomAccessible<T> raible,
Interval itvl,
ImgFactory<T> factory,
int nThreads,
ProgressWriter progress) |
static <T extends NumericType<T>> |
BigWarpExporter.copyToImageStackIterOrder(RandomAccessible<T> ra,
Interval itvl,
RandomAccessibleInterval<T> target,
int nThreads,
ProgressWriter progress) |
static <T> BigWarpExporter<?> |
BigWarpExporter.getExporter(BigWarp.BigWarpData<T> bwData,
List<SourceAndConverter<T>> transformedSources,
Interpolation interp,
ProgressWriter progressWriter) |
| Constructor and Description |
|---|
BigWarp(BigWarp.BigWarpData<T> data,
String windowTitle,
BigWarpViewerOptions options,
ProgressWriter progressWriter) |
BigWarp(BigWarp.BigWarpData<T> data,
String windowTitle,
ProgressWriter progressWriter) |
BigWarpARGBExporter(List<SourceAndConverter<ARGBType>> sources,
List<ConverterSetup> convSetups,
int[] movingSourceIndexList,
int[] targetSourceIndexList,
Interpolation interp,
ProgressWriter progress) |
BigWarpExporter(List<SourceAndConverter<T>> sourcesIn,
List<ConverterSetup> convSetups,
int[] movingSourceIndexList,
int[] targetSourceIndexList,
Interpolation interp,
ProgressWriter progress) |
BigWarpRealExporter(List<SourceAndConverter<T>> sources,
List<ConverterSetup> convSetups,
int[] movingSourceIndexList,
int[] targetSourceIndexList,
Interpolation interp,
T baseType,
boolean needConversion,
ProgressWriter progress) |
BigWarpRealExporter(List<SourceAndConverter<T>> sources,
List<ConverterSetup> convSetups,
int[] movingSourceIndexList,
int[] targetSourceIndexList,
Interpolation interp,
T baseType,
ProgressWriter progress) |
| Modifier and Type | Method and Description |
|---|---|
static ProgressWriter |
IOFunctions.getProgressWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
ProgressWriterIJ |
| Modifier and Type | Method and Description |
|---|---|
static Pair<SpimData2,List<String>> |
Resave_HDF5.createXMLObject(SpimData2 spimData,
List<ViewId> viewIds,
Generic_Resave_HDF5.Parameters params,
ProgressWriter progressWriter,
boolean useRightAway) |
static void |
Generic_Resave_HDF5.writeHDF5(AbstractSpimData<?> spimData,
Generic_Resave_HDF5.Parameters params,
ProgressWriter progressWriter) |
static void |
Resave_TIFF.writeTIFF(SpimData spimData,
List<ViewId> viewIds,
String path,
boolean compress,
ProgressWriter progressWriter) |
static <T extends AbstractSpimData<A>,A extends AbstractSequenceDescription<?,?,? super ImgLoader>> |
Generic_Resave_HDF5.writeXML(T spimData,
XmlIoAbstractSpimData<A,T> io,
Generic_Resave_HDF5.Parameters params,
ProgressWriter progressWriter) |
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