| Modifier and Type | Method and Description |
|---|---|
SpimData2 |
StackList.createDataset() |
SpimData2 |
SlideBook6.createDataset() |
SpimData2 |
MultiViewDatasetDefinition.createDataset()
This method is supposed to (interactively, ideally ImageJ-macroscriptable)
query all necessary data from the user to build up a SpimData object and
save it as an XML file.
|
SpimData2 |
MicroManager.createDataset() |
SpimData2 |
LightSheetZ1.createDataset() |
SpimData2 |
DHM.createDataset() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
LightSheetZ1.fixBioformats(SpimData2 spimData,
File cziFile,
LightSheetZ1MetaData meta) |
| Modifier and Type | Method and Description |
|---|---|
Pair<SpimData2,String> |
Define_Multi_View_Dataset.defineDataset(boolean save) |
| Modifier and Type | Method and Description |
|---|---|
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) |
protected void |
Duplicate_Transformation.duplicateTransformations(int transformations,
ViewId sourceViewId,
ViewId targetViewId,
SpimData2 spimData) |
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 Histogram |
ThinOut_Detections.plotHistogram(SpimData2 spimData,
List<ViewId> viewIds,
ChannelProcessThinOut channel) |
static Visualize_Detections.Params |
Visualize_Detections.queryDetails(SpimData2 spimData,
List<ViewId> viewIds) |
static Pair<String,String> |
Interactive_Remove_Detections.queryLabelAndNewLabel(SpimData2 spimData,
ViewDescription vd) |
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 |
Interactive_Remove_Detections.removeDetections(SpimData2 spimData,
ViewDescription vd,
int projectionDim,
String label,
String newLabel) |
protected static Img<UnsignedShortType> |
Visualize_Detections.renderSegmentations(SpimData2 data,
ViewId viewId,
String label,
int detections,
Interval interval,
double downsample) |
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 SpimData2 |
Fusion.spimData |
| 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 |
|---|---|
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) |
protected RandomAccessibleInterval<FloatType> |
DifferenceOf.openAndDownsample(SpimData2 spimData,
ViewDescription vd,
AffineTransform3D t) |
| 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 |
|---|---|
protected SpimData2 |
InterestPointRegistration.getSpimData() |
| 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) |
| Constructor and Description |
|---|
InteractiveProjections(SpimData2 spimData,
ViewDescription vd,
String label,
String newLabel,
int projectionDim) |
| 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 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.
|
| Modifier and Type | Method and Description |
|---|---|
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) |
| 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 boolean |
Resave_HDF5.loadDimensions(SpimData2 spimData,
List<ViewSetup> viewsetups) |
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.
|
| Modifier and Type | Method and Description |
|---|---|
SpimData2 |
XmlIoSpimData2.fromXml(org.jdom2.Element root,
File xmlFile) |
| Modifier and Type | Method and Description |
|---|---|
void |
XmlIoSpimData2.save(SpimData2 spimData,
String xmlFilename) |
static String |
SpimData2.saveXML(SpimData2 data,
String xmlFileName,
String clusterExtension) |
org.jdom2.Element |
XmlIoSpimData2.toXml(SpimData2 spimData,
File xmlFileDirectory) |
| Modifier and Type | Class and Description |
|---|---|
class |
InterestPointExplorer<AS extends SpimData2,X extends XmlIoAbstractSpimData<?,AS>> |
| 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 SpimData2 |
BoundingBoxGUI.spimData |
| Modifier and Type | Method and Description |
|---|---|
static boolean |
BoundingBoxGUI.computeMaxBoundingBoxDimensions(SpimData2 spimData,
List<ViewId> viewIdsToProcess,
double[] minBB,
double[] maxBB) |
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) |
protected static void |
PreDefinedBoundingBox.update(SpimData2 spimData,
Choice choice,
Label label1,
Label label2) |
| 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 SpimData2 |
ProcessForDeconvolution.spimData |
| Modifier and Type | Method and Description |
|---|---|
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 |
|---|---|
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) |
| 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 void |
AppendSpimData2.appendSpimData2(SpimData2 spimData,
List<TimePoint> timepointsToProcess,
List<ViewSetup> newViewSetups)
Assembles a new SpimData2 based on the timepoints and viewsetups.
|
boolean |
Save3dTIFF.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
boolean |
ImgExport.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData)
Parse the additional parameters added before within the bounding box dialog
|
boolean |
ExportSpimData2TIFF.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
boolean |
ExportSpimData2HDF5.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
boolean |
DisplayImage.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
boolean |
AppendSpimData2HDF5.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
boolean |
AppendSpimData2.parseAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
void |
Save3dTIFF.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
void |
ImgExport.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData)
Query additional parameters within the bounding box dialog
|
void |
ExportSpimData2TIFF.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
void |
ExportSpimData2HDF5.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
void |
DisplayImage.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
void |
AppendSpimData2HDF5.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
void |
AppendSpimData2.queryAdditionalParameters(GenericDialog gd,
SpimData2 spimData) |
boolean |
Save3dTIFF.queryParameters(SpimData2 spimData,
boolean is16bit) |
boolean |
ImgExport.queryParameters(SpimData2 spimData,
boolean is16bit)
Query the necessary parameters for the fusion (new dialog has to be made)
|
boolean |
ExportSpimData2TIFF.queryParameters(SpimData2 spimData,
boolean is16bit) |
boolean |
ExportSpimData2HDF5.queryParameters(SpimData2 spimData,
boolean is16bit) |
boolean |
DisplayImage.queryParameters(SpimData2 spimData,
boolean is16bit) |
boolean |
AppendSpimData2HDF5.queryParameters(SpimData2 spimData,
boolean is16bit) |
boolean |
AppendSpimData2.queryParameters(SpimData2 spimData,
boolean is16bit) |
| Modifier and Type | Field and Description |
|---|---|
protected SpimData2 |
ProcessFusion.spimData |
| 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.
|
static <T extends RealType<T>> |
ProcessFusion.getImage(T type,
SpimData2 spimData,
ViewId view,
boolean normalize) |
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 |
|---|---|
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 |
|---|---|
SpimData2 |
GlobalOptimizationType.getSpimData() |
| 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
|
<M extends Model<M>> |
GlobalOptimizationSubset.computeGlobalOpt(M model,
GlobalOptimizationType type,
SpimData2 spimData,
List<ChannelProcess> channelsToProcess,
String description) |
protected <M extends Model<M>> |
GlobalOptimizationSubset.computeMapBackModel(HashMap<ViewId,Tile<M>> tiles,
GlobalOptimizationType type,
SpimData2 spimData) |
| 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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