| Modifier and Type | Method and Description |
|---|---|
protected static ArrayList<ViewSetup> |
SpimRegistrationSequence.createViewSetups(SPIMConfiguration conf)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
protected static BasicImgLoader |
SpimRegistrationSequence.createImageLoader(SPIMConfiguration conf,
ArrayList<ViewSetup> setups)
Deprecated.
|
protected static ViewRegistrations |
SpimRegistrationSequence.createViewRegistrations(SPIMConfiguration conf,
ArrayList<ViewSetup> setups)
Deprecated.
|
protected static int |
SpimRegistrationSequence.getViewSetupId(ArrayList<ViewSetup> setups,
int angle,
int illumination,
int channel)
Deprecated.
find ViewSetup index corresponding to given (angle, illumination,
channel) triple.
|
| Constructor and Description |
|---|
SetupLoader(ViewSetup setup) |
| Constructor and Description |
|---|
HuiskenImageLoader(File file,
HashMap<Integer,ViewSetup> setups)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<ViewSetup> |
SpimDataExample2.createSetups() |
| Modifier and Type | Method and Description |
|---|---|
int |
ViewSetup.compareTo(ViewSetup o)
Compares the
ids. |
| Modifier and Type | Method and Description |
|---|---|
static HashMap<Integer,Angle> |
ViewSetups.getAllAngles(Collection<? extends ViewSetup> setups) |
static HashMap<Integer,Channel> |
ViewSetups.getAllChannels(Collection<? extends ViewSetup> setups) |
static HashMap<Integer,Illumination> |
ViewSetups.getAllIlluminations(Collection<? extends ViewSetup> setups) |
static HashMap<Integer,Tile> |
ViewSetups.getAllTiles(Collection<? extends ViewSetup> setups) |
| Constructor and Description |
|---|
SequenceDescription(TimePoints timepoints,
Collection<ViewSetup> setups) |
SequenceDescription(TimePoints timepoints,
Collection<ViewSetup> setups,
ImgLoader imgLoader) |
SequenceDescription(TimePoints timepoints,
Collection<ViewSetup> setups,
ImgLoader imgLoader,
MissingViews missingViews) |
SequenceDescription(TimePoints timepoints,
Map<Integer,ViewSetup> setups) |
SequenceDescription(TimePoints timepoints,
Map<Integer,ViewSetup> setups,
ImgLoader imgLoader) |
SequenceDescription(TimePoints timepoints,
Map<Integer,ViewSetup> setups,
ImgLoader imgLoader,
MissingViews missingViews) |
ViewDescription(int timepointId,
int setupId,
boolean present,
AbstractSequenceDescription<? extends ViewSetup,?,?> sequenceDescription) |
| Modifier and Type | Method and Description |
|---|---|
protected ArrayList<ViewSetup> |
StackList.createViewSetups()
|
protected ArrayList<ViewSetup> |
DHM.createViewSetups(DHMMetaData meta)
|
protected ArrayList<ViewSetup> |
LightSheetZ1.createViewSetups(LightSheetZ1MetaData meta)
|
protected ArrayList<ViewSetup> |
MicroManager.createViewSetups(MultipageTiffReader meta)
|
protected ArrayList<ViewSetup> |
SlideBook6.createViewSetups(SlideBook6MetaData meta)
|
| Modifier and Type | Method and Description |
|---|---|
protected ArrayList<ViewSetup> |
Interest_Point_Registration.getListOfViewSetupPresentInAllSubsets(List<GlobalOptimizationSubset> subsets,
GlobalOptimizationType type) |
| Modifier and Type | Field and Description |
|---|---|
protected Map<ViewSetup,ViewSetup> |
Fusion.newViewsetups
Maps from an old Viewsetup to a new ViewSetup that is created by the fusion
|
protected Map<ViewSetup,ViewSetup> |
Fusion.newViewsetups
Maps from an old Viewsetup to a new ViewSetup that is created by the fusion
|
| Modifier and Type | Method and Description |
|---|---|
protected abstract Map<ViewSetup,ViewSetup> |
Fusion.createNewViewSetups(BoundingBoxGUI bb)
Set up the list of new viewsetups that are created with this fusion.
|
protected abstract Map<ViewSetup,ViewSetup> |
Fusion.createNewViewSetups(BoundingBoxGUI bb)
Set up the list of new viewsetups that are created with this fusion.
|
List<ViewSetup> |
Fusion.getNewViewSetups() |
| Modifier and Type | Method and Description |
|---|---|
static boolean |
Resave_HDF5.loadDimensions(SpimData2 spimData,
List<ViewSetup> viewsetups) |
| Modifier and Type | Method and Description |
|---|---|
static ViewSetup |
SpimData2.getViewSetup(List<? extends ViewSetup> list,
Channel c,
Angle a,
Illumination i) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<ViewSetup> |
SpimData2.getAllViewSetups(Collection<? extends ViewDescription> vds) |
static ArrayList<ViewSetup> |
SpimData2.getAllViewSetupsSorted(SpimData data,
List<? extends ViewId> viewIds) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<ViewId> |
SpimData2.getAllViewIdsSorted(SpimData data,
List<? extends ViewSetup> setups,
List<? extends TimePoint> tps) |
static ViewSetup |
SpimData2.getViewSetup(List<? extends ViewSetup> list,
Channel c,
Angle a,
Illumination i) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
AbstractImgLoader.updateXMLMetaData(ViewSetup setup,
boolean forceUpdate)
Updates one specific ViewSetup using the imageMetaDataCache
|
| Modifier and Type | Method and Description |
|---|---|
void |
AbstractImgLoader.updateXMLMetaData(List<? extends ViewSetup> setups,
boolean forceUpdate)
Updates a list of ViewSetups using the imageMetaDataCache
|
| Modifier and Type | Method and Description |
|---|---|
protected Map<ViewSetup,ViewSetup> |
EfficientBayesianBased.createNewViewSetups(BoundingBoxGUI bb) |
protected Map<ViewSetup,ViewSetup> |
EfficientBayesianBased.createNewViewSetups(BoundingBoxGUI bb) |
| Modifier and Type | Method and Description |
|---|---|
<T extends RealType<T> & NativeType<T>> |
Save3dTIFF.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs) |
<T extends RealType<T> & NativeType<T>> |
ImgExport.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs)
Exports the image (min and max intensity will be computed)
|
<T extends RealType<T> & NativeType<T>> |
ExportSpimData2TIFF.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs) |
<T extends RealType<T> & NativeType<T>> |
ExportSpimData2HDF5.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs) |
<T extends RealType<T> & NativeType<T>> |
DisplayImage.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs) |
<T extends RealType<T> & NativeType<T>> |
AppendSpimData2HDF5.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs) |
<T extends RealType<T> & NativeType<T>> |
AppendSpimData2.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs) |
<T extends RealType<T> & NativeType<T>> |
Save3dTIFF.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max) |
<T extends RealType<T> & NativeType<T>> |
ImgExport.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max)
Exports the image using a predefined min/max
|
<T extends RealType<T> & NativeType<T>> |
ExportSpimData2TIFF.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max) |
<T extends RealType<T> & NativeType<T>> |
ExportSpimData2HDF5.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max) |
<T extends RealType<T> & NativeType<T>> |
DisplayImage.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max) |
<T extends RealType<T> & NativeType<T>> |
AppendSpimData2HDF5.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max) |
<T extends RealType<T> & NativeType<T>> |
AppendSpimData2.exportImage(RandomAccessibleInterval<T> img,
BoundingBoxGUI bb,
TimePoint tp,
ViewSetup vs,
double min,
double max) |
String |
XMLTIFFImgTitler.getImageTitle(TimePoint tp,
ViewSetup vs) |
String |
ImgTitler.getImageTitle(TimePoint tp,
ViewSetup vs) |
String |
FixedNameImgTitler.getImageTitle(TimePoint tp,
ViewSetup vs) |
String |
DefaultImgTitler.getImageTitle(TimePoint tp,
ViewSetup vs) |
| Modifier and Type | Method and Description |
|---|---|
static void |
AppendSpimData2.appendSpimData2(SpimData2 spimData,
List<TimePoint> timepointsToProcess,
List<ViewSetup> newViewSetups)
Assembles a new SpimData2 based on the timepoints and viewsetups.
|
static SpimData2 |
ExportSpimData2TIFF.assembleSpimData2(List<TimePoint> timepointsToProcess,
List<ViewSetup> viewSetupsToProcess,
File basePath)
Assembles a new SpimData2 based on the timepoints and viewsetups.
|
protected SpimData2 |
ExportSpimData2TIFF.createSpimData2(List<TimePoint> timepointsToProcess,
List<ViewSetup> viewSetupsToProcess,
Resave_TIFF.Parameters params) |
static Set<Angle> |
XMLTIFFImgTitler.getAllAngles(List<ViewSetup> viewSetups) |
static Set<Channel> |
XMLTIFFImgTitler.getAllChannels(List<ViewSetup> viewSetups) |
static Set<Illumination> |
XMLTIFFImgTitler.getAllIlluminations(List<ViewSetup> viewSetups) |
static ExportSpimData2TIFF.FileNamePattern |
ExportSpimData2TIFF.getFileNamePattern(List<TimePoint> timepoints,
List<ViewSetup> viewSetups,
boolean compress) |
protected static Pair<SpimData2,HashMap<ViewId,Partition>> |
ExportSpimData2HDF5.initSpimData(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups,
Generic_Resave_HDF5.Parameters params,
Map<Integer,ExportMipmapInfo> perSetupExportMipmapInfo) |
void |
Save3dTIFF.setXMLData(List<TimePoint> timepointsToProcess,
List<ViewSetup> newViewSetups) |
void |
ImgExport.setXMLData(List<TimePoint> timepointsToProcess,
List<ViewSetup> newViewSetups) |
void |
ExportSpimData2TIFF.setXMLData(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups) |
void |
ExportSpimData2HDF5.setXMLData(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups) |
void |
DisplayImage.setXMLData(List<TimePoint> timepointsToProcess,
List<ViewSetup> newViewSetups) |
void |
AppendSpimData2HDF5.setXMLData(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups) |
void |
AppendSpimData2.setXMLData(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups) |
| Constructor and Description |
|---|
XMLTIFFImgTitler(List<TimePoint> newTimepoints,
List<ViewSetup> newViewSetups) |
| Modifier and Type | Method and Description |
|---|---|
static Map<ViewSetup,ViewSetup> |
WeightedAverageFusion.assembleNewViewSetupsFusion(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
String newAngleName,
String newIlluminationName)
Creates one new Angle and one new Illumination for the fused dataset.
|
static Map<ViewSetup,ViewSetup> |
WeightedAverageFusion.assembleNewViewSetupsFusion(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
String newAngleName,
String newIlluminationName)
Creates one new Angle and one new Illumination for the fused dataset.
|
static Map<ViewSetup,ViewSetup> |
WeightedAverageFusion.assembleNewViewSetupsSequential(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb)
Duplicates all Angles and Illuminations that are processed.
|
static Map<ViewSetup,ViewSetup> |
WeightedAverageFusion.assembleNewViewSetupsSequential(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb)
Duplicates all Angles and Illuminations that are processed.
|
protected Map<ViewSetup,ViewSetup> |
WeightedAverageFusion.createNewViewSetups(BoundingBoxGUI bb) |
protected Map<ViewSetup,ViewSetup> |
WeightedAverageFusion.createNewViewSetups(BoundingBoxGUI bb) |
| Constructor and Description |
|---|
ProcessIndependent(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
ImgExport export,
Map<ViewSetup,ViewSetup> newViewsetups) |
ProcessIndependent(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
ImgExport export,
Map<ViewSetup,ViewSetup> newViewsetups) |
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