| 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 | Class and Description |
|---|---|
class |
ViewSetupWrapper
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 |
|---|---|
static ArrayList<Partition> |
Partition.split(List<TimePoint> timepoints,
List<? extends BasicViewSetup> setups,
int timepointsPerPartition,
int setupsPerPartition,
String basename)
Split a sequence into partitions, each containing a specified number of
timepoints and setups.
|
| Modifier and Type | Method and Description |
|---|---|
protected BasicViewDescription<BasicViewSetup> |
SequenceDescriptionMinimal.createViewDescription(int timepointId,
int setupId) |
| Constructor and Description |
|---|
SequenceDescriptionMinimal(TimePoints timepoints,
Map<Integer,? extends BasicViewSetup> setups,
BasicImgLoader imgLoader,
MissingViews missingViews) |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractSequenceDescription<V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader>
A SPIM sequence consisting of a list of timepoints and a list of view setups.
|
class |
BasicViewDescription<V extends BasicViewSetup>
TODO
|
class |
XmlIoAbstractSequenceDescription<V extends BasicViewSetup,T extends AbstractSequenceDescription<V,?,?>> |
class |
XmlIoBasicViewSetup<T extends BasicViewSetup> |
class |
XmlIoBasicViewSetups<T extends BasicViewSetup>
Writes and reads collections of a specific
BasicViewSetup subclass as
an XML section. |
| 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) |
static <V extends BasicViewSetup,D extends BasicViewDescription<V>> |
BasicViewDescription.markMissingViews(Map<ViewId,D> viewDescriptions,
MissingViews missingViews) |
| Modifier and Type | Class and Description |
|---|---|
class |
ViewSetup
A collection of parameters describing the setup for a particular stack coming
from a SPIM microscope (angle, illumination direction, etc).
|
| 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 Map<Integer,ExportMipmapInfo> |
Resave_HDF5.proposeMipmaps(List<? extends BasicViewSetup> viewsetups) |
| Modifier and Type | Method and Description |
|---|---|
static Dimensions |
ViewSetupUtils.getSize(BasicViewSetup setup) |
static Dimensions |
ViewSetupUtils.getSizeOrLoad(BasicViewSetup setup,
TimePoint t,
ImgLoader loader) |
static VoxelDimensions |
ViewSetupUtils.getVoxelSize(BasicViewSetup setup) |
static VoxelDimensions |
ViewSetupUtils.getVoxelSizeOrLoad(BasicViewSetup setup,
TimePoint t,
ImgLoader loader) |
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<BasicViewDescription<? extends BasicViewSetup>> |
ViewSetupTableModel.elements |
protected BasicViewDescription<? extends BasicViewSetup> |
ViewSetupExplorerPanel.firstSelectedVD |
protected HashSet<BasicViewDescription<? extends BasicViewSetup>> |
ViewSetupExplorerPanel.selectedRows |
| Modifier and Type | Method and Description |
|---|---|
protected ArrayList<BasicViewDescription<? extends BasicViewSetup>> |
ViewSetupTableModel.elements() |
BasicViewDescription<? extends BasicViewSetup> |
ViewSetupExplorerPanel.firstSelectedVD() |
ArrayList<BasicViewDescription<? extends BasicViewSetup>> |
ViewSetupTableModel.getElements() |
HashSet<BasicViewDescription<? extends BasicViewSetup>> |
ViewSetupExplorerPanel.getSelectedRows() |
List<BasicViewDescription<? extends BasicViewSetup>> |
ViewSetupExplorerPanel.selectedRows() |
| Modifier and Type | Method and Description |
|---|---|
static int |
ViewSetupExplorerPanel.getBDVSourceIndex(BasicViewSetup vs,
AbstractSpimData<?> data) |
| Modifier and Type | Method and Description |
|---|---|
void |
SelectedViewDescriptionListener.seletedViewDescription(BasicViewDescription<? extends BasicViewSetup> viewDescription) |
static void |
ViewSetupExplorerPanel.updateBDV(BigDataViewer bdv,
boolean colorMode,
AbstractSpimData<?> data,
BasicViewDescription<? extends BasicViewSetup> firstVD,
Collection<? extends BasicViewDescription<? extends BasicViewSetup>> selectedRows) |
static void |
ViewSetupExplorerPanel.updateBDV(BigDataViewer bdv,
boolean colorMode,
AbstractSpimData<?> data,
BasicViewDescription<? extends BasicViewSetup> firstVD,
Collection<? extends BasicViewDescription<? extends BasicViewSetup>> selectedRows) |
| Modifier and Type | Method and Description |
|---|---|
void |
InterestPointExplorer.seletedViewDescription(BasicViewDescription<? extends BasicViewSetup> viewDescription) |
| Modifier and Type | Method and Description |
|---|---|
void |
RegistrationExplorer.seletedViewDescription(BasicViewDescription<? extends BasicViewSetup> viewDescription) |
| 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) |
LegacyMicroManagerImgLoader(File mmFile,
AbstractSequenceDescription<? extends BasicViewSetup,? extends BasicViewDescription<?>,?> sequenceDescription) |
MicroManagerImgLoader(File mmFile,
AbstractSequenceDescription<? extends BasicViewSetup,? extends BasicViewDescription<?>,?> sequenceDescription) |
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