| 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.
|
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 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 |
|---|---|
AbstractSequenceDescription<?,?,?> |
ViewSetupWrapper.getSourceSequence()
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
int |
SetupAggregator.add(BasicViewSetup sourceSetup,
AbstractSequenceDescription<?,?,?> sourceSequence,
ViewRegistrations sourceRegs,
int[][] resolutions,
int[][] subdivisions)
Deprecated.
Add a new
BasicViewSetup to the aggregator. |
| Constructor and Description |
|---|
ViewSetupWrapper(int id,
AbstractSequenceDescription<?,?,?> sourceSequence,
BasicViewSetup sourceSetup)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
CatmaidImageLoader |
XmlIoCatmaidImageLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Modifier and Type | Field and Description |
|---|---|
protected AbstractSequenceDescription<?,?,?> |
Hdf5ImageLoader.sequenceDescription |
| Modifier and Type | Method and Description |
|---|---|
Hdf5ImageLoader |
XmlIoHdf5ImageLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Constructor and Description |
|---|
Hdf5ImageLoader(File hdf5File,
ArrayList<Partition> hdf5Partitions,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
Hdf5ImageLoader(File hdf5File,
ArrayList<Partition> hdf5Partitions,
AbstractSequenceDescription<?,?,?> sequenceDescription,
boolean doOpen) |
Hdf5ImageLoader(File hdf5File,
ch.systemsx.cisd.hdf5.IHDF5Reader existingHdf5Reader,
ArrayList<Partition> hdf5Partitions,
AbstractSequenceDescription<?,?,?> sequenceDescription,
boolean doOpen) |
| Modifier and Type | Method and Description |
|---|---|
ImarisImageLoader<?,?,?> |
XmlIoImarisImageLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Constructor and Description |
|---|
ImarisImageLoader(File hdf5File,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Modifier and Type | Method and Description |
|---|---|
N5ImageLoader |
XmlIoN5ImageLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Constructor and Description |
|---|
N5ImageLoader(File n5File,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Modifier and Type | Method and Description |
|---|---|
OpenConnectomeImageLoader |
XmlIoOpenConnectomeImageLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Modifier and Type | Method and Description |
|---|---|
RemoteImageLoader |
XmlIoRemoteImageLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Constructor and Description |
|---|
RemoteImageLoaderMetaData(Hdf5ImageLoader imgLoader,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Modifier and Type | Class and Description |
|---|---|
class |
SequenceDescriptionMinimal |
| Constructor and Description |
|---|
CropDialog(Frame owner,
ViewerPanel viewer,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Modifier and Type | Method and Description |
|---|---|
<S extends AbstractSequenceDescription<?,?,?>> |
Loader.load() |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractSpimData<S extends AbstractSequenceDescription<?,?,?>> |
class |
XmlIoAbstractSpimData<S extends AbstractSequenceDescription<?,?,?>,T extends AbstractSpimData<S>> |
| Modifier and Type | Class and Description |
|---|---|
class |
XmlIoAbstractSequenceDescription<V extends BasicViewSetup,T extends AbstractSequenceDescription<V,?,?>> |
| Modifier and Type | Field and Description |
|---|---|
protected AbstractSequenceDescription<? extends V,?,?> |
BasicViewDescription.sequenceDescription |
| Modifier and Type | Method and Description |
|---|---|
static <V extends BasicViewSetup> |
AbstractSequenceDescriptionUtils.changeIds(AbstractSequenceDescription<V,?,?> seq,
int... oldIdToNewIdMap) |
static <V extends BasicViewSetup> |
AbstractSequenceDescriptionUtils.changeIds(AbstractSequenceDescription<V,?,?> seq,
Map<Integer,Integer> oldIdToNewIdMap) |
T |
XmlIoBasicImgLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
| Constructor and Description |
|---|
BasicViewDescription(int timepointId,
int setupId,
boolean present,
AbstractSequenceDescription<? extends V,?,?> sequenceDescription)
TODO
|
| Modifier and Type | Class and Description |
|---|---|
class |
SequenceDescription |
| Constructor and Description |
|---|
ViewDescription(int timepointId,
int setupId,
boolean present,
AbstractSequenceDescription<? extends ViewSetup,?,?> sequenceDescription) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<Specify_Calibration.Cal> |
Specify_Calibration.findCalibrations(AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>> spimData,
List<ViewId> viewIds) |
| 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
|
| Modifier and Type | Method and Description |
|---|---|
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) |
| Modifier and Type | Field and Description |
|---|---|
protected AbstractSequenceDescription<?,?,?> |
LegacyStackImgLoader.sequenceDescription |
| Modifier and Type | Method and Description |
|---|---|
protected StackImgLoaderLOCI |
XmlIoStackImgLoaderLOCI.createImgLoader(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
protected StackImgLoaderIJ |
XmlIoStackImgLoaderIJ.createImgLoader(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
protected abstract T |
XmlIoStackImgLoader.createImgLoader(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
T |
XmlIoStackImgLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
SlideBook6ImgLoader |
XmlIoSlideBook6ImgLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
MicroManagerImgLoader |
XmlIoMicroManagerImgLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
LightSheetZ1ImgLoader |
XmlIoLightSheetZ1ImgLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
DHMImgLoader |
XmlIoDHMImgLoader.fromXml(org.jdom2.Element elem,
File basePath,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
protected static Angle |
LegacySlideBook6ImgLoader.getAngle(AbstractSequenceDescription<?,?,?> seqDesc,
ViewId view) |
protected static Angle |
LegacyLightSheetZ1ImgLoader.getAngle(AbstractSequenceDescription<?,?,?> seqDesc,
ViewId view) |
| Constructor and Description |
|---|
DHMImgLoader(File directory,
String stackDir,
String amplitudeDir,
String phaseDir,
List<String> timepoints,
List<String> zPlanes,
String extension,
int ampChannelId,
int phaseChannelId,
AbstractSequenceDescription<? extends BasicViewSetup,? extends BasicViewDescription<?>,?> sd) |
LegacyDHMImgLoader(File directory,
String stackDir,
String amplitudeDir,
String phaseDir,
List<String> timepoints,
List<String> zPlanes,
String extension,
int ampChannelId,
int phaseChannelId,
AbstractSequenceDescription<? extends BasicViewSetup,? extends BasicViewDescription<?>,?> sd) |
LegacyLightSheetZ1ImgLoader(File cziFile,
ImgFactory<? extends NativeType<?>> imgFactory,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
LegacyMicroManagerImgLoader(File mmFile,
AbstractSequenceDescription<? extends BasicViewSetup,? extends BasicViewDescription<?>,?> sequenceDescription) |
LegacySlideBook6ImgLoader(File sldFile,
ImgFactory<? extends NativeType<?>> imgFactory,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
LegacyStackImgLoader(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription)
For a local initialization without the XML
|
LegacyStackImgLoaderIJ(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
LegacyStackImgLoaderLOCI(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
LightSheetZ1ImgLoader(File cziFile,
ImgFactory<? extends NativeType<?>> imgFactory,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
MicroManagerImgLoader(File mmFile,
AbstractSequenceDescription<? extends BasicViewSetup,? extends BasicViewDescription<?>,?> sequenceDescription) |
SlideBook6ImgLoader(File sldFile,
ImgFactory<? extends NativeType<?>> imgFactory,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
StackImgLoaderIJ(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
StackImgLoaderLOCI(File path,
String fileNamePattern,
ImgFactory<? extends NativeType<?>> imgFactory,
int layoutTP,
int layoutChannels,
int layoutIllum,
int layoutAngles,
AbstractSequenceDescription<?,?,?> sequenceDescription) |
Copyright © 2015–2021 Fiji. All rights reserved.