| Package | Description |
|---|---|
| bdv.gui | |
| bdv.ij | |
| bigwarp | |
| bigwarp.loader | |
| bigwarp.source |
| Constructor and Description |
|---|
BigwarpLandmarkSelectionPanel(BigWarp.BigWarpData<T> data,
List<SourceAndConverter<T>> sources,
String fieldOfViewOption,
List<Interval> outputIntervalList,
List<String> matchedPtNames,
Interpolation interp,
double[] offsetIn,
double[] resolution,
boolean isVirtual,
int nThreads,
ProgressWriter progressWriter)
Displays a dialog showing point matches
|
| 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<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 double[] |
ApplyBigwarpPlugin.getResolution(BigWarp.BigWarpData<?> bwData,
String resolutionOption,
double[] resolutionSpec) |
static String |
ApplyBigwarpPlugin.getUnit(BigWarp.BigWarpData<?> bwData,
String resolutionOption) |
static <T> List<ij.ImagePlus> |
ApplyBigwarpPlugin.runExport(BigWarp.BigWarpData<T> data,
List<SourceAndConverter<T>> sources,
String fieldOfViewOption,
List<Interval> outputIntervalList,
List<String> matchedPtNames,
Interpolation interp,
double[] offsetIn,
double[] resolution,
boolean isVirtual,
int nThreads,
ProgressWriter progressWriter,
boolean show,
boolean wait,
ApplyBigwarpPlugin.WriteDestinationOptions writeOpts) |
static <S,T extends NativeType<T> & NumericType<T>> |
ApplyBigwarpPlugin.runN5Export(BigWarp.BigWarpData<S> data,
List<SourceAndConverter<S>> sources,
String fieldOfViewOption,
Interval outputInterval,
Interpolation interp,
double[] offset,
double[] resolution,
String unit,
ProgressWriter progressWriter,
ApplyBigwarpPlugin.WriteDestinationOptions writeOpts,
ExecutorService exec) |
| Modifier and Type | Field and Description |
|---|---|
protected BigWarp.BigWarpData<T> |
BigWarp.data |
| Modifier and Type | Method and Description |
|---|---|
static <T> BigWarp.BigWarpData<?> |
BigWarpInit.add(BigWarp.BigWarpData bwdata,
AbstractSpimData<?> data,
int setupId,
int numTimepoints,
boolean isMoving) |
static <T> BigWarp.BigWarpData<?> |
BigWarpInit.add(BigWarp.BigWarpData bwdata,
Source<T> src,
int setupId,
int numTimepoints,
boolean isMoving) |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(AbstractSpimData<?>[] spimDataPList,
AbstractSpimData<?>[] spimDataQList) |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(AbstractSpimData<?>[] spimDataPList,
AbstractSpimData<?>[] spimDataQList,
String[] names)
Create
BigWarp.BigWarpData from two AbstractSpimData. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(AbstractSpimData<?> spimDataP,
AbstractSpimData<?> spimDataQ)
Create
BigWarp.BigWarpData from two AbstractSpimData. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(ImagePlusLoader loaderP,
ImagePlusLoader loaderQ) |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(ImagePlusLoader loaderP,
ImagePlusLoader loaderQ,
String[] names) |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(Loader loaderP,
Loader loaderQ)
|
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(Loader loaderP,
Loader loaderQ,
String[] namesIn)
|
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpData(Source<?>[] movingSourceList,
Source<?>[] fixedSourceList,
String[] names)
Create
BigWarp.BigWarpData from two AbstractSpimData. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromImagePlusXML(ij.ImagePlus[] impP,
String xmlFilenameQ)
Create
BigWarp.BigWarpData from an ImagePlus array and an XML
file. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromImagePlusXML(ij.ImagePlus impP,
String xmlFilenameQ)
Create
BigWarp.BigWarpData from an ImagePlus and an XML file. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromImages(ij.ImagePlus[] impP,
ij.ImagePlus impQ)
|
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromImages(ij.ImagePlus[] impP,
ij.ImagePlus[] impQ)
Create
BigWarp.BigWarpData from two ImagePlus arrays. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromImages(ij.ImagePlus impP,
ij.ImagePlus impQ)
Create
BigWarp.BigWarpData from two ImagePluses. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromImages(ij.ImagePlus impP,
ij.ImagePlus[] impQ)
|
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromXML(String xmlFilenameP,
String xmlFilenameQ)
Create
BigWarp.BigWarpData from two XML files. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromXMLImagePlus(String xmlFilenameP,
ij.ImagePlus impQ)
Create
BigWarp.BigWarpData from an xml file and an ImagePlus. |
static BigWarp.BigWarpData<?> |
BigWarpInit.createBigWarpDataFromXMLImagePlus(String xmlFilenameP,
ij.ImagePlus[] impQ)
Create
BigWarp.BigWarpData from an xml file and an ImagePlus
array. |
BigWarp.BigWarpData<T> |
BigWarp.getData() |
static <T> BigWarp.BigWarpData<T> |
BigWarpInit.initData() |
| Modifier and Type | Method and Description |
|---|---|
static <T> BigWarp.BigWarpData<?> |
BigWarpInit.add(BigWarp.BigWarpData bwdata,
AbstractSpimData<?> data,
int setupId,
int numTimepoints,
boolean isMoving) |
static <T> int |
BigWarpInit.add(BigWarp.BigWarpData bwdata,
ij.ImagePlus ip,
int setupId,
int numTimepoints,
boolean isMoving) |
static <T> BigWarp.BigWarpData<?> |
BigWarpInit.add(BigWarp.BigWarpData bwdata,
Source<T> src,
int setupId,
int numTimepoints,
boolean isMoving) |
static SpimData |
BigWarpInit.addToData(BigWarp.BigWarpData<?> bwdata,
boolean isMoving,
int setupId,
String rootPath,
String dataset) |
static <T> BigWarpExporter<?> |
BigWarpExporter.getExporter(BigWarp.BigWarpData<T> bwData,
List<SourceAndConverter<T>> transformedSources,
Interpolation interp,
ProgressWriter progressWriter) |
static void |
BigWarpExporter.updateBrightnessContrast(ij.ImagePlus imp,
BigWarp.BigWarpData<?> bwdata,
int[] indexList) |
static <T> List<SourceAndConverter<T>> |
BigWarp.wrapSourcesAsTransformed(List<SourceAndConverter<T>> sources,
int ndims,
BigWarp.BigWarpData<?> data) |
| Constructor and Description |
|---|
BigWarp(BigWarp.BigWarpData<T> data,
String windowTitle,
BigWarpViewerOptions options,
ProgressWriter progressWriter) |
BigWarp(BigWarp.BigWarpData<T> data,
String windowTitle,
ProgressWriter progressWriter) |
SourceInfoDialog(Frame owner,
BigWarp.BigWarpData<?> bwData)
Instantiates and displays a JFrame that lists information on
the opened sources.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ImagePlusLoader.update(BigWarp.BigWarpData<?> data) |
| Modifier and Type | Field and Description |
|---|---|
protected BigWarp.BigWarpData<?> |
WarpMagnitudeSource.sourceData |
protected BigWarp.BigWarpData<?> |
JacobianDeterminantSource.sourceData |
protected BigWarp.BigWarpData<?> |
GridSource.sourceData |
| Constructor and Description |
|---|
GridSource(String name,
BigWarp.BigWarpData<?> data,
T t,
RealTransform warp) |
JacobianDeterminantSource(String name,
BigWarp.BigWarpData<?> data,
T t) |
WarpMagnitudeSource(String name,
BigWarp.BigWarpData<?> data,
T t) |
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