| Package | Description |
|---|---|
| bdv.export | |
| bdv.export.n5 | |
| bdv.ij | |
| bdv.ij.export | |
| bdv.spimdata.tools | |
| spim.fiji.plugin.resave | |
| spim.process.fusion.export |
| Modifier and Type | Method and Description |
|---|---|
static ExportMipmapInfo |
ProposeMipmaps.proposeMipmaps(BasicViewSetup setup)
Propose number of mipmap levels as well subsampling factors and chunk
size for each level, based on the image and voxel size of the given
setup.
|
static ExportMipmapInfo |
ProposeMipmaps.proposeMipmaps(BasicViewSetup setup,
int maxNumElements)
Propose number of mipmap levels as well subsampling factors and chunk
size for each level, based on the image and voxel size of the given
setup.
|
| Modifier and Type | Method and Description |
|---|---|
static Map<Integer,ExportMipmapInfo> |
ProposeMipmaps.proposeMipmaps(AbstractSequenceDescription<?,?,?> seq)
Propose number of mipmap levels as well subsampling factors and chunk
size for each level, for each setup of the given sequence.
|
| Modifier and Type | Method and Description |
|---|---|
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.
|
| Modifier and Type | Method and Description |
|---|---|
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 void |
WriteSequenceToHdf5.writeHdf5PartitionLinkFile(AbstractSequenceDescription<?,?,?> seq,
Map<Integer,ExportMipmapInfo> perSetupMipmapInfo)
Create a hdf5 master file linking to image data from all views and all
timepoints.
|
static void |
WriteSequenceToHdf5.writeHdf5PartitionLinkFile(AbstractSequenceDescription<?,?,?> seq,
Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
ArrayList<Partition> partitions,
File hdf5File)
Create a hdf5 master file linking to image data from all views and all
timepoints.
|
| 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.
|
| Modifier and Type | Method and Description |
|---|---|
protected ExportImagePlusPlugIn.Parameters |
ExportImagePlusPlugIn.getParameters(double impMin,
double impMax,
ExportMipmapInfo autoMipmapSettings) |
protected ExportImagePlusAsN5PlugIn.Parameters |
ExportImagePlusAsN5PlugIn.getParameters(ExportMipmapInfo autoMipmapSettings) |
| Modifier and Type | Field and Description |
|---|---|
protected Map<Integer,ExportMipmapInfo> |
SetupAggregator.perSetupMipmapInfo
Deprecated.
|
protected Map<Integer,ExportMipmapInfo> |
Scripting.PartitionedSequenceWriter.perSetupMipmapInfo |
| Modifier and Type | Method and Description |
|---|---|
Map<Integer,ExportMipmapInfo> |
SetupAggregator.getPerSetupMipmapInfo()
Deprecated.
Get the aggregated per-setup
ExportMipmapInfos. |
| Modifier and Type | Method and Description |
|---|---|
static Map<Integer,ExportMipmapInfo> |
MergePartitionList.getHdf5PerSetupExportMipmapInfos(AbstractSequenceDescription<?,?,?> seq)
Return map from setup id to
ExportMipmapInfo for the
Hdf5ImageLoader of the specified
AbstractSequenceDescription. |
| Modifier and Type | Method and Description |
|---|---|
static Map<Integer,ExportMipmapInfo> |
Generic_Resave_HDF5.getPerSetupExportMipmapInfo(AbstractSpimData<?> spimData,
Generic_Resave_HDF5.Parameters params) |
static Map<Integer,ExportMipmapInfo> |
Resave_HDF5.proposeMipmaps(List<? extends BasicViewSetup> viewsetups) |
| Modifier and Type | Method and Description |
|---|---|
static Generic_Resave_HDF5.Parameters |
Generic_Resave_HDF5.getParameters(ExportMipmapInfo autoMipmapSettings,
boolean askForXMLPath,
boolean is16bit) |
static Generic_Resave_HDF5.Parameters |
Generic_Resave_HDF5.getParameters(ExportMipmapInfo autoMipmapSettings,
boolean askForXMLPath,
String dialogTitle,
boolean is16bit) |
| Modifier and Type | Method and Description |
|---|---|
protected static Pair<SpimData2,HashMap<ViewId,Partition>> |
ExportSpimData2HDF5.initSpimData(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups,
Generic_Resave_HDF5.Parameters params,
Map<Integer,ExportMipmapInfo> perSetupExportMipmapInfo) |
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