| Package | Description |
|---|---|
| bdv.gui | |
| bdv.ij | |
| bdv.viewer | |
| bigwarp | |
| bigwarp.landmarks | |
| bigwarp.landmarks.actions | |
| bigwarp.scripts | |
| bigwarp.source | |
| bigwarp.transforms |
| Modifier and Type | Field and Description |
|---|---|
protected LandmarkTableModel |
BigWarpLandmarkPanel.tableModel |
| Modifier and Type | Method and Description |
|---|---|
LandmarkTableModel |
BigWarpLandmarkPanel.getTableModel() |
| Modifier and Type | Method and Description |
|---|---|
void |
BigWarpLandmarkPanel.setTableModel(LandmarkTableModel tableModel) |
| Constructor and Description |
|---|
BigWarpLandmarkPanel(LandmarkTableModel tableModel) |
JTableChecking(LandmarkTableModel tableModel) |
| Modifier and Type | Method and Description |
|---|---|
static <T> List<ij.ImagePlus> |
ApplyBigwarpPlugin.apply(BigWarp.BigWarpData<T> bwData,
LandmarkTableModel landmarks,
String tranformTypeOption,
String fieldOfViewOption,
String fieldOfViewPointFilter,
String resolutionOption,
double[] resolutionSpec,
double[] fovSpec,
double[] offsetSpec,
Interpolation interp,
boolean isVirtual,
int nThreads,
boolean wait,
ApplyBigwarpPlugin.WriteDestinationOptions writeOpts) |
static List<ij.ImagePlus> |
ApplyBigwarpPlugin.apply(ij.ImagePlus movingIp,
ij.ImagePlus targetIp,
LandmarkTableModel landmarks,
String tranformTypeOption,
String fieldOfViewOption,
String fieldOfViewPointFilter,
String resolutionOption,
double[] resolutionSpec,
double[] fovSpec,
double[] offsetSpec,
Interpolation interp,
boolean isVirtual,
boolean wait,
int nThreads) |
static List<ij.ImagePlus> |
ApplyBigwarpPlugin.apply(ij.ImagePlus movingIp,
ij.ImagePlus targetIp,
LandmarkTableModel landmarks,
String tranformTypeOption,
String fieldOfViewOption,
String fieldOfViewPointFilter,
String resolutionOption,
double[] resolutionSpec,
double[] fovSpec,
double[] offsetSpec,
Interpolation interp,
boolean isVirtual,
int nThreads,
boolean wait,
ApplyBigwarpPlugin.WriteDestinationOptions writeOpts) |
static void |
ApplyBigwarpPlugin.fillMatchedPointNames(List<String> ptList,
LandmarkTableModel landmarks,
String fieldOfViewPointFilter) |
static List<Double[]> |
ApplyBigwarpPlugin.getMatchedPoints(LandmarkTableModel landmarks,
String fieldOfViewPointFilter) |
static List<Interval> |
ApplyBigwarpPlugin.getPixelInterval(BigWarp.BigWarpData<?> bwData,
LandmarkTableModel landmarks,
InvertibleRealTransform transform,
String fieldOfViewOption,
String fieldOfViewPointFilter,
double[] fovSpec,
double[] offsetSpec,
double[] outputResolution)
Returns the interval in pixels of the output given input options
|
static List<Interval> |
ApplyBigwarpPlugin.getPixelInterval(ij.ImagePlus movingIp,
ij.ImagePlus targetIp,
LandmarkTableModel landmarks,
InvertibleRealTransform transform,
String fieldOfViewOption,
String fieldOfViewPointFilter,
double[] fovSpec,
double[] offsetSpec,
double[] outputResolution) |
static Interval |
ApplyBigwarpPlugin.getPixelInterval(Source<?> source,
LandmarkTableModel landmarks,
InvertibleRealTransform transform,
String fieldOfViewOption,
double[] outputResolution) |
<T> void |
BigWarpToDeformationFieldPlugIn.runFromBigWarpInstance(LandmarkTableModel landmarkModel,
List<SourceAndConverter<T>> sources,
int[] targetSourceIndexList) |
static ij.ImagePlus |
BigWarpToDeformationFieldPlugIn.toImagePlus(LandmarkTableModel ltm,
boolean ignoreAffine,
long[] dims,
double[] spacing,
int nThreads) |
static boolean |
ApplyBigwarpPlugin.validateInput(ij.ImagePlus movingIp,
ij.ImagePlus targetIp,
LandmarkTableModel landmarks,
String fieldOfViewOption,
String resolutionOption,
double[] resolutionSpec,
double[] fovSpec,
double[] offsetSpec,
Interpolation interp,
boolean isVirtual,
int nThreads) |
static void |
BigWarpToDeformationFieldPlugIn.writeN5(String n5BasePath,
LandmarkTableModel ltm,
long[] dims,
double[] spacing,
int[] spatialBlockSize,
org.janelia.saalfeldlab.n5.Compression compression,
int nThreads) |
static void |
BigWarpToDeformationFieldPlugIn.writeN5(String n5BasePath,
String n5Dataset,
LandmarkTableModel ltm,
long[] dims,
double[] spacing,
int[] spatialBlockSize,
org.janelia.saalfeldlab.n5.Compression compression,
int nThreads) |
| Modifier and Type | Field and Description |
|---|---|
protected LandmarkTableModel |
BigWarpOverlay.landmarkModel |
| Modifier and Type | Method and Description |
|---|---|
static void |
LandmarkPointMenu.updateBigwarp(BigWarp<?> bw,
LandmarkTableModel model) |
| Modifier and Type | Field and Description |
|---|---|
protected LandmarkTableModel |
BigWarp.landmarkModel |
| Modifier and Type | Method and Description |
|---|---|
static <T> BigWarpExporter<T> |
BigWarpBatchTransformFOV.applyBigWarpHelper(AbstractSpimData<?>[] spimDataP,
AbstractSpimData<?>[] spimDataQ,
ij.ImagePlus impP,
LandmarkTableModel ltm,
Interpolation interpolation) |
static void |
BigWarp.updateRowSelection(LandmarkTableModel landmarkModel,
JTable table,
boolean isMoving,
int lastRowEdited) |
| Modifier and Type | Method and Description |
|---|---|
LandmarkTableModel |
LandmarkTableModel.invert()
Returns a new LandmarkTableModel but makes the moving points fixed and vice versa.
|
| Modifier and Type | Method and Description |
|---|---|
int |
LandmarkGridGenerator.fill(LandmarkTableModel ltm) |
| Modifier and Type | Field and Description |
|---|---|
protected LandmarkTableModel |
AbstractPointEdit.ltm |
| Constructor and Description |
|---|
AbstractPointEdit(LandmarkTableModel ltm) |
AddPointEdit(LandmarkTableModel ltm,
int index,
double[] pt,
boolean isMoving) |
DeleteRowEdit(LandmarkTableModel ltm,
int index) |
ModifyPointEdit(LandmarkTableModel ltm,
int index,
double[] oldpt,
double[] newpt,
boolean isMoving) |
| Modifier and Type | Method and Description |
|---|---|
static void |
RescaleLandmarks.scaleLandmarks(LandmarkTableModel ltm,
double[] scales,
boolean isMoving) |
| Modifier and Type | Method and Description |
|---|---|
double |
WarpMagnitudeSource.getMax(LandmarkTableModel lm) |
double |
JacobianDeterminantSource.getMax(LandmarkTableModel lm) |
| Modifier and Type | Method and Description |
|---|---|
WrappedIterativeInvertibleRealTransform<?> |
TpsTransformSolver.solve(LandmarkTableModel landmarkTable) |
WrappedIterativeInvertibleRealTransform<?> |
TpsTransformSolver.solve(LandmarkTableModel landmarkTable,
int indexChanged) |
| Constructor and Description |
|---|
BigWarpTransform(LandmarkTableModel tableModel) |
BigWarpTransform(LandmarkTableModel tableModel,
String transformType) |
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