| Modifier and Type | Field and Description |
|---|---|
protected Set<ViewId> |
AbstractSpimSource.missingViews |
protected Map<ViewId,ViewRegistration> |
AbstractSpimSource.viewRegistrations |
| Modifier and Type | Method and Description |
|---|---|
RandomAccessibleInterval<UnsignedShortType> |
LegacyStackImageLoader.getImage(ViewId view)
Deprecated.
|
| Constructor and Description |
|---|
LegacyStackImageLoader(HashMap<ViewId,String> filenames,
boolean useImageJOpener)
Deprecated.
|
StackImageLoader(HashMap<ViewId,String> filenames,
boolean useImageJOpener)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
RandomAccessibleInterval<UnsignedShortType> |
LegacyTileImgLoader.getImage(ViewId view) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Partition.contains(ViewId viewId)
Does this partition contain the given
view
(timepoint-setup pair)? |
static String |
Util.getCellsPath(ViewId viewId,
int level) |
static String |
Util.getGroupPath(ViewId viewId,
int level) |
| Constructor and Description |
|---|
ViewLevelId(ViewId viewId,
int level) |
| Modifier and Type | Method and Description |
|---|---|
RandomAccessibleInterval<T> |
AbstractLegacyViewerImgLoader.getImage(ViewId view) |
RandomAccessibleInterval<T> |
LegacyViewerImgLoader.getImage(ViewId view,
int level) |
RandomAccessibleInterval<V> |
LegacyViewerImgLoader.getVolatileImage(ViewId view,
int level) |
| Modifier and Type | Method and Description |
|---|---|
AffineTransform3D |
CropImgLoader.getCroppedTransform(ViewId view) |
| Modifier and Type | Class and Description |
|---|---|
class |
BasicViewDescription<V extends BasicViewSetup>
TODO
|
| Modifier and Type | Method and Description |
|---|---|
Map<ViewId,D> |
AbstractSequenceDescription.getViewDescriptions() |
| Modifier and Type | Method and Description |
|---|---|
static <V extends BasicViewSetup,D extends BasicViewDescription<V>> |
BasicViewDescription.markMissingViews(Map<ViewId,D> viewDescriptions,
MissingViews missingViews) |
| Modifier and Type | Method and Description |
|---|---|
RandomAccessibleInterval<FloatType> |
LegacyImgLoader.getFloatImage(ViewId view,
boolean normalize)
Get
FloatType image. |
RandomAccessibleInterval<T> |
LegacyBasicImgLoader.getImage(ViewId view)
Get the un-normalized image of the default
pixel
type of this BasicImgLoader. |
Dimensions |
LegacyImgLoader.getImageSize(ViewId view)
Get the size of an image.
|
VoxelDimensions |
LegacyImgLoader.getVoxelSize(ViewId view)
Get the voxel size of an image.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ViewRegistration |
| Modifier and Type | Method and Description |
|---|---|
Map<ViewId,ViewRegistration> |
ViewRegistrations.getViewRegistrations() |
| Modifier and Type | Method and Description |
|---|---|
ViewRegistration |
ViewRegistrations.getViewRegistration(ViewId viewId) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
ViewRegistrations.setViewRegistrations(Map<ViewId,ViewRegistration> registrations) |
| Constructor and Description |
|---|
ViewRegistrations(Map<ViewId,ViewRegistration> registrations) |
| Modifier and Type | Class and Description |
|---|---|
class |
ViewDescription |
| Modifier and Type | Method and Description |
|---|---|
Set<ViewId> |
MissingViews.getMissingViews() |
| Modifier and Type | Method and Description |
|---|---|
int |
ViewId.compareTo(ViewId o)
|
ViewDescription |
SequenceDescription.getViewDescription(ViewId view)
convenience method.
|
| Modifier and Type | Method and Description |
|---|---|
protected static void |
ViewIdUtils.changeViewsetupIds(Collection<? extends ViewId> viewIds,
Map<Integer,Integer> oldIdToNewIdMap) |
protected void |
MissingViews.setMissingViews(Set<ViewId> missingViews) |
| Constructor and Description |
|---|
MissingViews(Collection<? extends ViewId> missingViews) |
| Modifier and Type | Method and Description |
|---|---|
protected static ViewRegistrations |
StackList.createViewRegistrations(Map<ViewId,ViewDescription> viewDescriptionList,
double minResolution)
Assembles the
ViewRegistration object consisting of a list of ViewRegistrations for all ViewDescriptions that are present |
| Modifier and Type | Method and Description |
|---|---|
static void |
Display_View.display(AbstractSpimData<?> spimData,
ViewId viewId,
int pixelType,
String name,
boolean virtual) |
protected void |
Duplicate_Transformation.duplicateTransformations(int transformations,
ViewId sourceViewId,
ViewId targetViewId,
SpimData2 spimData) |
static void |
Apply_Transformation.preConcatenateTransform(SpimData spimData,
ViewId viewId,
AffineTransform3D model,
String name) |
protected static Img<UnsignedShortType> |
Visualize_Detections.renderSegmentations(SpimData2 data,
ViewId viewId,
String label,
int detections,
Interval interval,
double downsample) |
static void |
Apply_Transformation.setModelToCalibration(SpimData spimData,
ViewId viewId,
double minResolution) |
static void |
Apply_Transformation.setModelToIdentity(SpimData spimData,
ViewId viewId) |
| Modifier and Type | Method and Description |
|---|---|
static void |
Specify_Calibration.applyCal(Specify_Calibration.Cal maxCal,
SpimData spimData,
List<ViewId> viewIds) |
protected boolean |
Interest_Point_Registration.askForFixedTiles(GlobalOptimizationSubset subset,
GlobalOptimizationType type,
Set<ViewId> fixedTiles,
String title) |
static double |
Apply_Transformation.assembleAllMetaData(SequenceDescription sequenceDescription,
Collection<? extends ViewId> viewIdsToProcess)
Should be called before registration to make sure all metadata is right
|
BoundingBox |
Define_Bounding_Box.defineBoundingBox(SpimData2 data,
List<ViewId> viewIds) |
BoundingBox |
Define_Bounding_Box.defineBoundingBox(SpimData2 data,
List<ViewId> viewIds,
String clusterExtension,
String xmlFileName,
boolean saveXML) |
boolean |
Interest_Point_Detection.detectInterestPoints(SpimData2 data,
List<ViewId> viewIds)
Does just the detection, no saving
|
boolean |
Interest_Point_Detection.detectInterestPoints(SpimData2 data,
List<ViewId> viewIds,
String xmlFileName,
boolean saveXML) |
boolean |
Interest_Point_Detection.detectInterestPoints(SpimData2 data,
List<ViewId> viewIds,
String clusterExtension,
String xmlFileName,
boolean saveXML) |
static ArrayList<Specify_Calibration.Cal> |
Specify_Calibration.findCalibrations(AbstractSpimData<? extends AbstractSequenceDescription<?,?,?>> spimData,
List<ViewId> viewIds) |
boolean |
Image_Fusion.fuse(SpimData2 data,
List<ViewId> viewIds) |
boolean |
Image_Fusion.fuse(SpimData2 data,
List<ViewId> viewIds,
String clusterExtension,
String xmlFileName,
boolean saveXML) |
static String[] |
Interest_Point_Registration.getAllInterestPointLabelsForChannel(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
Channel channel)
Goes through all ViewDescriptions and checks all available labels for interest point detection
|
static String[] |
Interest_Point_Registration.getAllInterestPointLabelsForChannel(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
Channel channel,
String doWhat)
Goes through all ViewDescriptions and checks all available labels for interest point detection
|
static ArrayList<ChannelProcessThinOut> |
ThinOut_Detections.getChannelsAndLabels(SpimData2 spimData,
List<ViewId> viewIds) |
static boolean |
ThinOut_Detections.getThinOutThresholds(SpimData2 spimData,
List<ViewId> viewIds,
List<ChannelProcessThinOut> channels) |
static <T extends RealType<T> & NativeType<T>> |
Max_Project.maxProject(SpimData data,
List<? extends ViewId> viewIds,
T type) |
static Histogram |
ThinOut_Detections.plotHistogram(SpimData2 spimData,
List<ViewId> viewIds,
ChannelProcessThinOut channel) |
Map<ViewDescription,Pair<double[],String>> |
Apply_Transformation.queryBigDataViewer(SpimData data,
List<ViewId> viewIds,
ApplyParameters params) |
static Visualize_Detections.Params |
Visualize_Detections.queryDetails(SpimData2 spimData,
List<ViewId> viewIds) |
ApplyParameters |
Apply_Transformation.queryParams(SpimData data,
List<ViewId> viewIds) |
Map<ViewDescription,Pair<double[],String>> |
Apply_Transformation.queryRotationAxis(SpimData data,
List<ViewId> viewIds,
ApplyParameters params) |
Map<ViewDescription,Pair<double[],String>> |
Apply_Transformation.queryString(SpimData data,
List<ViewId> viewIds,
ApplyParameters params) |
boolean |
Interest_Point_Registration.register(SpimData2 data,
List<ViewId> viewIds) |
boolean |
Interest_Point_Registration.register(SpimData2 data,
List<ViewId> viewIds,
String xmlFileName,
boolean saveXML) |
boolean |
Interest_Point_Registration.register(SpimData2 data,
List<ViewId> viewIds,
String clusterExtension,
String xmlFileName,
boolean saveXML) |
static boolean |
ThinOut_Detections.thinOut(SpimData2 spimData,
List<ViewId> viewIds,
List<ChannelProcessThinOut> channels,
boolean save) |
static void |
Visualize_Detections.visualize(SpimData2 spimData,
List<ViewId> viewIds,
ArrayList<ChannelProcess> channelsToProcess,
int detections,
double downsample,
boolean displayInput) |
| Modifier and Type | Field and Description |
|---|---|
protected List<ViewId> |
Fusion.viewIdsToProcess
which ViewId to process, set in queryParameters
|
| Modifier and Type | Method and Description |
|---|---|
abstract Fusion |
Fusion.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Constructor and Description |
|---|
Fusion(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
protected ViewId |
DifferenceOf.getViewSelection(String dialogHeader,
String text,
Channel channel)
Figure out which view to use for the interactive preview
|
| 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) |
List<ViewId> |
InterestPointDetection.getViewIdsToProcess() |
| Modifier and Type | Method and Description |
|---|---|
abstract InterestPointDetection |
InterestPointDetection.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
DifferenceOfMean |
DifferenceOfMean.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
DifferenceOfGaussian |
DifferenceOfGaussian.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Constructor and Description |
|---|
DifferenceOf(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
DifferenceOfGaussian(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
DifferenceOfMean(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
InterestPointDetection(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
List<ViewId> |
InterestPointRegistration.getViewIdsToProcess() |
| Modifier and Type | Method and Description |
|---|---|
abstract InterestPointRegistration |
InterestPointRegistration.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Constructor and Description |
|---|
InterestPointRegistration(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess)
Instantiate the interest point registration.
|
| Modifier and Type | Method and Description |
|---|---|
protected List<InterestPoint> |
InteractiveProjections.loadInterestPoints(SpimData2 spimData,
ViewId id,
String label) |
| Modifier and Type | Method and Description |
|---|---|
static SpimData2 |
Resave_TIFF.assemblePartialSpimData2(SpimData2 spimData,
List<ViewId> viewIds,
File basePath,
List<String> filesToCopy)
Assembles a new SpimData2 based on the subset of timepoints and viewsetups as selected by the user.
|
static Pair<SpimData2,List<String>> |
Resave_HDF5.createXMLObject(SpimData2 spimData,
List<ViewId> viewIds,
Generic_Resave_HDF5.Parameters params,
ProgressWriter progressWriter,
boolean useRightAway) |
static Pair<SpimData2,List<String>> |
Resave_TIFF.createXMLObject(SpimData2 spimData,
List<ViewId> viewIds,
Resave_TIFF.Parameters params) |
static SpimData2 |
Resave_HDF5.reduceSpimData2(SpimData2 oldSpimData,
List<ViewId> viewIds)
Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader.
|
static void |
Resave_TIFF.writeTIFF(SpimData spimData,
List<ViewId> viewIds,
String path,
boolean compress,
ProgressWriter progressWriter) |
| Modifier and Type | Method and Description |
|---|---|
static HashMap<String,Integer> |
GUIHelper.assembleRegistrationNames(SpimData data,
List<ViewId> viewIds) |
| Modifier and Type | Method and Description |
|---|---|
static ViewId |
SpimData2.getViewId(SequenceDescription seqDesc,
TimePoint t,
Channel c,
Angle a,
Illumination i) |
| 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 |
|---|---|
List<ViewId> |
ViewSetupExplorerPanel.selectedRowsViewId() |
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<Pair<InterestPointList,ViewId>> |
InterestPointExplorerPanel.delete |
| Modifier and Type | Method and Description |
|---|---|
List<CorrespondingInterestPoints> |
InterestPointExplorerPanel.getCorrespondingInterestPoints(ViewInterestPoints vip,
ViewId v,
String label) |
List<InterestPoint> |
InterestPointExplorerPanel.getInterestPoints(ViewInterestPoints vip,
ViewId v,
String label) |
protected int |
InterestPointTableModel.numCorrespondences(ViewInterestPoints vip,
ViewId v,
String label) |
protected int |
InterestPointTableModel.numCorresponding(ViewInterestPoints vip,
ViewId v,
String label) |
protected int |
InterestPointTableModel.numDetections(ViewInterestPoints vip,
ViewId v,
String label) |
| Modifier and Type | Method and Description |
|---|---|
protected static Angle |
LegacySlideBook6ImgLoader.getAngle(AbstractSequenceDescription<?,?,?> seqDesc,
ViewId view) |
protected static Angle |
LegacyLightSheetZ1ImgLoader.getAngle(AbstractSequenceDescription<?,?,?> seqDesc,
ViewId view) |
protected File |
LegacyStackImgLoader.getFile(ViewId view) |
RandomAccessibleInterval<FloatType> |
LegacyStackImgLoaderLOCI.getFloatImage(ViewId view,
boolean normalize)
Get
FloatType image normalized to the range [0,1]. |
RandomAccessibleInterval<FloatType> |
LegacyStackImgLoaderIJ.getFloatImage(ViewId view,
boolean normalize)
Get
FloatType image normalized to the range [0,1]. |
RandomAccessibleInterval<FloatType> |
LegacySlideBook6ImgLoader.getFloatImage(ViewId view,
boolean normalize) |
RandomAccessibleInterval<FloatType> |
LegacyMicroManagerImgLoader.getFloatImage(ViewId view,
boolean normalize) |
RandomAccessibleInterval<FloatType> |
LegacyLightSheetZ1ImgLoader.getFloatImage(ViewId view,
boolean normalize) |
RandomAccessibleInterval<FloatType> |
LegacyDHMImgLoader.getFloatImage(ViewId view,
boolean normalize) |
RandomAccessibleInterval<UnsignedShortType> |
LegacyStackImgLoaderLOCI.getImage(ViewId view)
Get
UnsignedShortType un-normalized image. |
RandomAccessibleInterval<UnsignedShortType> |
LegacyStackImgLoaderIJ.getImage(ViewId view)
Get
UnsignedShortType un-normalized image. |
RandomAccessibleInterval<UnsignedShortType> |
LegacySlideBook6ImgLoader.getImage(ViewId view) |
RandomAccessibleInterval<UnsignedShortType> |
LegacyMicroManagerImgLoader.getImage(ViewId view) |
RandomAccessibleInterval<UnsignedShortType> |
LegacyLightSheetZ1ImgLoader.getImage(ViewId view) |
RandomAccessibleInterval<UnsignedShortType> |
LegacyDHMImgLoader.getImage(ViewId view) |
Dimensions |
AbstractImgLoader.getImageSize(ViewId view) |
VoxelDimensions |
AbstractImgLoader.getVoxelSize(ViewId view) |
protected void |
LegacyStackImgLoaderLOCI.loadMetaData(ViewId view) |
protected void |
LegacyStackImgLoaderIJ.loadMetaData(ViewId view) |
protected void |
LegacySlideBook6ImgLoader.loadMetaData(ViewId view) |
protected void |
LegacyMicroManagerImgLoader.loadMetaData(ViewId view) |
protected void |
LegacyLightSheetZ1ImgLoader.loadMetaData(ViewId view) |
protected void |
LegacyDHMImgLoader.loadMetaData(ViewId view) |
protected abstract void |
AbstractImgLoader.loadMetaData(ViewId view)
Loads only the metadata from the image, should call updateMetaDataCache( ...
|
protected <T extends RealType<T> & NativeType<T>> |
LegacyLightSheetZ1ImgLoader.openCZI(T type,
ViewId view) |
protected <T extends RealType<T> & NativeType<T>> |
LegacyStackImgLoaderLOCI.openLOCI(File path,
T type,
ViewId view) |
protected <T extends RealType<T> & NativeType<T>> |
LegacySlideBook6ImgLoader.openSLD(T type,
ViewId view) |
protected void |
AbstractImgLoader.updateMetaDataCache(ViewId viewId,
int w,
int h,
int d,
double calX,
double calY,
double calZ)
Updates the cached imageMetaData
|
| Modifier and Type | Class and Description |
|---|---|
class |
ViewInterestPointLists
Maps from a String label to a list of interest points for a specific viewid
|
| Modifier and Type | Field and Description |
|---|---|
protected Map<ViewId,ViewInterestPointLists> |
ViewInterestPoints.interestPointCollectionLookup |
| Modifier and Type | Method and Description |
|---|---|
ViewId |
CorrespondingInterestPoints.getCorrespondingViewId() |
| Modifier and Type | Method and Description |
|---|---|
Map<ViewId,ViewInterestPointLists> |
ViewInterestPoints.getViewInterestPoints() |
| Modifier and Type | Method and Description |
|---|---|
ViewInterestPointLists |
ViewInterestPoints.getViewInterestPointLists(ViewId viewId) |
| Modifier and Type | Method and Description |
|---|---|
void |
ViewInterestPoints.createViewInterestPoints(Map<ViewId,ViewDescription> viewDescriptions)
Assembles the
ViewInterestPoints object consisting of a list of ViewInterestPointLists objects for all ViewDescriptions that are present |
ViewInterestPoints |
XmlIoViewInterestPoints.fromXml(org.jdom2.Element allInterestPointLists,
File basePath,
Map<ViewId,ViewDescription> viewDescriptions) |
| Constructor and Description |
|---|
CorrespondingInterestPoints(int detectionId,
ViewId correspondingViewId,
String correspondingLabel,
int correspondingDetectionId) |
| Constructor and Description |
|---|
ViewInterestPoints(Map<ViewId,ViewInterestPointLists> interestPointCollectionLookup) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<ViewDescription> |
FusionHelper.assembleInputData(SpimData2 spimData,
TimePoint timepoint,
Channel channel,
List<ViewId> viewIdsToProcess) |
| Modifier and Type | Field and Description |
|---|---|
protected List<ViewId> |
BoundingBoxGUI.viewIdsToProcess
which viewIds to process, set in queryParameters
|
| Modifier and Type | Method and Description |
|---|---|
static boolean |
BoundingBoxGUI.computeMaxBoundingBoxDimensions(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
double[] minBB,
double[] maxBB) |
static Pair<BigDataViewer,Boolean> |
BigDataViewerBoundingBox.getBDV(AbstractSpimData<?> spimData,
Collection<ViewId> viewIdsToProcess) |
PreDefinedBoundingBox |
PreDefinedBoundingBox.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
BoundingBoxGUI |
BoundingBoxGUI.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
BigDataViewerBoundingBox |
BigDataViewerBoundingBox.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
AutomaticReorientation |
AutomaticReorientation.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
AutomaticBoundingBox |
AutomaticBoundingBox.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Constructor and Description |
|---|
AutomaticBoundingBox(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
AutomaticReorientation(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
BigDataViewerBoundingBox(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
BoundingBoxGUI(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
BoundingBoxGUI(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBox bb) |
PreDefinedBoundingBox(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| 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 | Field and Description |
|---|---|
protected HashMap<ViewId,ArrayImg<T,?>> |
ExtractPSF.originalPSFs |
protected HashMap<ViewId,ArrayImg<T,?>> |
ExtractPSF.pointSpreadFunctions |
protected ArrayList<ViewId> |
ExtractPSF.viewIds |
protected List<ViewId> |
ProcessForDeconvolution.viewIdsToProcess |
| Modifier and Type | Method and Description |
|---|---|
HashMap<ViewId,ArrayImg<T,?>> |
ExtractPSF.getInputCalibrationPSFs() |
HashMap<ViewId,ArrayImg<T,?>> |
ExtractPSF.getPSFMap() |
HashMap<ViewId,RandomAccessibleInterval<FloatType>> |
ProcessForDeconvolution.getTransformedImgs() |
HashMap<ViewId,RandomAccessibleInterval<FloatType>> |
ProcessForDeconvolution.getTransformedWeights() |
HashMap<ViewId,ViewId> |
ExtractPSF.getViewIdMapping() |
HashMap<ViewId,ViewId> |
ExtractPSF.getViewIdMapping() |
ArrayList<ViewId> |
ExtractPSF.getViewIdsForPSFs() |
| Modifier and Type | Method and Description |
|---|---|
void |
ExtractPSF.extractNextImg(RandomAccessibleInterval<T> img,
ViewId viewId,
AffineTransform3D model,
ArrayList<double[]> locations,
long[] psfSize) |
ArrayImg<T,?> |
ExtractPSF.getTransformedPSF(ViewId viewId)
Returns the transformed PSF.
|
| Modifier and Type | Method and Description |
|---|---|
static <T extends RealType<T> & NativeType<T>> |
ExtractPSF.loadAndTransformPSFs(ArrayList<Pair<Pair<Angle,Illumination>,String>> filenames,
ArrayList<ViewDescription> viewDesc,
T type,
HashMap<ViewId,AffineTransform3D> models) |
Fusion |
EfficientBayesianBased.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Constructor and Description |
|---|
EfficientBayesianBased(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
ProcessForDeconvolution(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
int[] blendingBorder,
int[] blendingRange) |
| 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) |
| Modifier and Type | Method and Description |
|---|---|
static <T extends RealType<T>> |
ProcessFusion.getImage(T type,
ImgLoader imgLoader,
ViewId view,
boolean normalize) |
static <T extends RealType<T>> |
ProcessFusion.getImage(T type,
SpimData2 spimData,
ViewId view,
boolean normalize) |
| 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.assembleNewViewSetupsSequential(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb)
Duplicates all Angles and Illuminations that are processed.
|
WeightedAverageFusion |
WeightedAverageFusion.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess) |
| Constructor and Description |
|---|
ProcessFusion(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
boolean useBlending,
boolean useContentBased) |
ProcessIndependent(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
ImgExport export,
Map<ViewSetup,ViewSetup> newViewsetups) |
ProcessParalell(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
boolean useBlending,
boolean useContentBased) |
ProcessSequential(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
BoundingBoxGUI bb,
boolean useBlending,
boolean useContentBased,
int numSequentialViews) |
WeightedAverageFusion(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
WeightedAverageFusion.WeightedAvgFusionType type) |
| Modifier and Type | Method and Description |
|---|---|
ViewId |
PairwiseMatch.getViewIdA() |
ViewId |
PairwiseMatch.getViewIdB() |
| Modifier and Type | Method and Description |
|---|---|
protected static <M extends Model<M>> |
GlobalOpt.assignViewsToTiles(M model,
List<ViewId> views,
boolean considerTimePointsAsUnit) |
static <M extends Model<M>> |
GlobalOpt.compute(M model,
GlobalOptimizationType registrationType,
GlobalOptimizationSubset subset,
boolean considerTimePointsAsUnit)
Computes a global optimization based on the corresponding points
|
ArrayList<ViewId> |
PairwiseMatch.getBothViewIds() |
| Modifier and Type | Method and Description |
|---|---|
protected static <M extends Model<M>> |
GlobalOpt.addAndFixTiles(List<ViewId> views,
HashMap<ViewId,Tile<M>> map,
GlobalOptimizationType registrationType,
GlobalOptimizationSubset subset,
boolean considerTimePointsAsUnit) |
protected static <M extends Model<M>> |
GlobalOpt.addAndFixTiles(List<ViewId> views,
HashMap<ViewId,Tile<M>> map,
GlobalOptimizationType registrationType,
GlobalOptimizationSubset subset,
boolean considerTimePointsAsUnit) |
protected static <M extends Model<M>> |
GlobalOpt.assignViewsToTiles(M model,
List<ViewId> views,
boolean considerTimePointsAsUnit) |
| Constructor and Description |
|---|
PairwiseMatch(ViewId viewIdA,
ViewId viewIdB,
MatchPointList listA,
MatchPointList listB) |
| Modifier and Type | Method and Description |
|---|---|
CenterOfMass |
CenterOfMass.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Constructor and Description |
|---|
CenterOfMass(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
RGLDM |
RGLDM.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Constructor and Description |
|---|
RGLDM(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
GeometricHashing |
GeometricHashing.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Constructor and Description |
|---|
GeometricHashing(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
IterativeClosestPoint |
IterativeClosestPoint.newInstance(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Constructor and Description |
|---|
IterativeClosestPoint(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
| Modifier and Type | Method and Description |
|---|---|
ViewId |
ReferenceTimepointRegistration.getMapBackReferenceTile(GlobalOptimizationSubset set) |
ViewId |
GlobalOptimizationType.getMapBackReferenceTile(GlobalOptimizationSubset set)
In case there is one tile which would be reference tile, return this one - can be null.
|
| 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
|
Set<ViewId> |
GlobalOptimizationType.getFixedTiles() |
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 < !!!
|
List<ViewId> |
GlobalOptimizationSubset.getViews() |
| Modifier and Type | Method and Description |
|---|---|
boolean |
GlobalOptimizationType.isFixedTile(ViewId viewId) |
protected static boolean |
GlobalOptimizationType.isValid(ViewId viewId,
MatchPointList list) |
void |
GlobalOptimizationType.setMapBackReferenceTile(GlobalOptimizationSubset set,
ViewId referenceTile) |
| 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 <M extends Model<M>> |
GlobalOptimizationSubset.computeMapBackModel(HashMap<ViewId,Tile<M>> tiles,
GlobalOptimizationType type,
SpimData2 spimData) |
void |
GlobalOptimizationType.setFixedTiles(Set<ViewId> fixedTiles) |
void |
GlobalOptimizationType.setMapBackReferenceTiles(Map<GlobalOptimizationSubset,ViewId> referenceTiles) |
| Constructor and Description |
|---|
AllToAllRegistration(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess,
boolean considerTimePointsAsUnit) |
AllToAllRegistrationWithRange(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess,
int range,
boolean considerTimePointsAsUnit) |
GlobalOptimizationType(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess,
boolean considerTimePointsAsUnit) |
IndividualTimepointRegistration(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess) |
ReferenceTimepointRegistration(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
List<ChannelProcess> channelsToProcess,
TimePoint referenceTimepoint,
boolean considerTimePointsAsUnit) |
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