| Modifier and Type | Field and Description |
|---|---|
protected List<TimePoint> |
AbstractSpimSource.timePointsOrdered |
| 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 | Field and Description |
|---|---|
protected List<TimePoint> |
SourceInfoOverlayRenderer.timePointsOrdered |
| Modifier and Type | Method and Description |
|---|---|
void |
SourceInfoOverlayRenderer.setTimePointsOrdered(List<TimePoint> timePointsOrdered) |
| Modifier and Type | Method and Description |
|---|---|
TimePoint |
BasicViewDescription.getTimePoint() |
| Modifier and Type | Method and Description |
|---|---|
Map<Integer,TimePoint> |
TimePoints.getTimePoints() |
List<TimePoint> |
TimePoints.getTimePointsOrdered() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
TimePoints.setTimePoints(Collection<TimePoint> timepoints) |
protected void |
TimePoints.setTimePoints(Map<Integer,TimePoint> timepoints) |
| Constructor and Description |
|---|
TimePoints(Collection<TimePoint> timepoints) |
TimePoints(Map<Integer,TimePoint> timepoints) |
| Modifier and Type | Method and Description |
|---|---|
protected String[] |
Duplicate_Transformation.assembleTimepoints(List<TimePoint> timepoints) |
| Modifier and Type | Field and Description |
|---|---|
protected List<TimePoint> |
Fusion.timepointsToProcess |
| Modifier and Type | Method and Description |
|---|---|
List<TimePoint> |
Fusion.getTimepointsToProcess() |
| Modifier and Type | Method and Description |
|---|---|
abstract HashMap<ViewId,List<InterestPoint>> |
InterestPointDetection.findInterestPoints(TimePoint tp)
Perform the interestpoint detection for one timepoint
|
HashMap<ViewId,List<InterestPoint>> |
DifferenceOfMean.findInterestPoints(TimePoint t) |
HashMap<ViewId,List<InterestPoint>> |
DifferenceOfGaussian.findInterestPoints(TimePoint t) |
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<TimePoint> |
GenericLoadParseQueryXML.timepointsToProcess |
| Modifier and Type | Method and Description |
|---|---|
List<TimePoint> |
GenericLoadParseQueryXML.getTimePointsToProcess() |
| Modifier and Type | Method and Description |
|---|---|
protected static String[] |
GenericLoadParseQueryXML.buildTimepointList(List<TimePoint> tpList,
boolean addTitle) |
| Modifier and Type | Method and Description |
|---|---|
static String |
Resave_TIFF.listAllTimePoints(List<TimePoint> timePointsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<TimePoint> |
SpimData2.getAllTimePointsSorted(Collection<? extends ViewDescription> vds) |
static ArrayList<TimePoint> |
SpimData2.getAllTimePointsSorted(SpimData data,
Collection<? extends ViewId> viewIds) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<ViewId> |
SpimData2.getAllViewIdsSorted(SpimData data,
List<? extends ViewSetup> setups,
List<? extends TimePoint> tps) |
| Modifier and Type | Method and Description |
|---|---|
static int |
ViewSetupExplorerPanel.getBDVTimePointIndex(TimePoint t,
AbstractSpimData<?> data) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<ViewDescription> |
FusionHelper.assembleInputData(SpimData2 spimData,
TimePoint timepoint,
Channel channel,
List<ViewId> viewIdsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
protected String[] |
AutomaticBoundingBox.assembleTimepoints(List<TimePoint> timepoints) |
| Constructor and Description |
|---|
MinFilterThreshold(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
Channel channel,
TimePoint timepoint,
BoundingBoxGUI bb,
double background,
int discardedObjectSize,
boolean loadSequentially,
boolean displaySegmentationImage) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
ProcessForDeconvolution.fuseStacksAndGetPSFs(TimePoint timepoint,
Channel channel,
ImgFactory<FloatType> imgFactory,
int osemIndex,
double osemspeedup,
ProcessForDeconvolution.WeightType weightType,
HashMap<Channel,ChannelPSF> extractPSFLabels,
long[] psfSize,
HashMap<Channel,ArrayList<Pair<Pair<Angle,Illumination>,String>>> psfFiles,
boolean transformLoadedPSFs)
Fuses one stack, i.e.
|
protected ArrayList<double[]> |
ProcessForDeconvolution.getLocationsOfCorrespondingBeads(TimePoint tp,
ViewDescription inputData,
String label) |
| 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 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 |
|---|---|
<T extends RealType<T> & NativeType<T>> |
ProcessSequential.fuseStack(T type,
InterpolatorFactory<T,RandomAccessible<T>> interpolatorFactory,
TimePoint timepoint,
Channel channel)
Fuses one stack, i.e.
|
<T extends RealType<T> & NativeType<T>> |
ProcessParalell.fuseStack(T type,
InterpolatorFactory<T,RandomAccessible<T>> interpolatorFactory,
TimePoint timepoint,
Channel channel)
Fuses one stack, i.e.
|
<T extends RealType<T> & NativeType<T>> |
ProcessIndependent.fuseStack(T type,
InterpolatorFactory<T,RandomAccessible<T>> interpolatorFactory,
TimePoint timepoint,
Channel channel)
Fuses one stack, i.e.
|
abstract <T extends RealType<T> & NativeType<T>> |
ProcessFusion.fuseStack(T type,
InterpolatorFactory<T,RandomAccessible<T>> interpolatorFactory,
TimePoint timepoint,
Channel channel) |
| Modifier and Type | Method and Description |
|---|---|
TimePoint |
ReferenceTimepointRegistration.getReferenceTimepoint() |
| Modifier and Type | Method and Description |
|---|---|
protected static HashSet<ViewId> |
ReferenceTimepointRegistration.assembleFixedTiles(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess,
TimePoint referenceTimepoint)
All tiles of the reference timepoint are fixed, nothing else
|
protected HashMap<ViewId,MatchPointList> |
GlobalOptimizationType.getInterestPoints(TimePoint timepoint)
Creates lists of input points for the registration, based on the current transformation of the views
Note: this always duplicates the location array from the input List> InterestPoint < !!!
|
| Constructor and Description |
|---|
ReferenceTimepointRegistration(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess,
TimePoint referenceTimepoint,
boolean considerTimePointsAsUnit) |
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