ApplyBigwarpPlugin (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bdv.ij.ApplyBigwarpPlugin

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class ApplyBigwarpPlugin
extends Object
implements ij.plugin.PlugIn
```
Apply a bigwarp transform to a 2d or 3d ImagePlus

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class ApplyBigwarpPlugin.WriteDestinationOptions

Nested Classes
Modifier and Type	Class and Description
`static class`	`ApplyBigwarpPlugin.WriteDestinationOptions`

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`LANDMARK_POINT_CUBE_PHYSICAL`
`static String`	`LANDMARK_POINT_CUBE_PIXEL`
`static String`	`LANDMARK_POINTS`
`static String`	`MOVING`
`static String`	`MOVING_WARPED`
`static String`	`SPECIFIED`
`static String`	`SPECIFIED_PHYSICAL`
`static String`	`SPECIFIED_PIXEL`
`static String`	`TARGET`
`static String`	`UNION_TARGET_MOVING`

Constructor Summary

Constructors
Constructor and Description

ApplyBigwarpPlugin()

Constructors
Constructor and Description
`ApplyBigwarpPlugin()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static <T> List<ij.ImagePlus>`	`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>`	`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>`	`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`	`fillMatchedPointNames(List<String> ptList, LandmarkTableModel landmarks, String fieldOfViewPointFilter)`
`static org.janelia.saalfeldlab.n5.Compression`	`getCompression(String compressionArg)`
`static List<Double[]>`	`getMatchedPoints(LandmarkTableModel landmarks, String fieldOfViewPointFilter)`
`static List<Interval>`	`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>`	`getPixelInterval(ij.ImagePlus movingIp, ij.ImagePlus targetIp, LandmarkTableModel landmarks, InvertibleRealTransform transform, String fieldOfViewOption, String fieldOfViewPointFilter, double[] fovSpec, double[] offsetSpec, double[] outputResolution)`
`static Interval`	`getPixelInterval(Source<?> source, LandmarkTableModel landmarks, InvertibleRealTransform transform, String fieldOfViewOption, double[] outputResolution)`
`static double[]`	`getPixelOffset(String fieldOfViewOption, double[] offsetSpec, double[] outputResolution, Interval outputInterval)` Get the offset in pixels given the output resolution and interval
`static double[]`	`getResolution(BigWarp.BigWarpData<?> bwData, String resolutionOption, double[] resolutionSpec)`
`static double[]`	`getResolution(ij.ImagePlus movingIp, ij.ImagePlus targetIp, String resolutionOption, double[] resolutionSpec)` Returns the resolution of the output given input options
`static double[]`	`getResolution(Source<?> source, String resolutionOption, double[] resolutionSpec)`
`static String`	`getUnit(BigWarp.BigWarpData<?> bwData, String resolutionOption)`
`static void`	`main(String[] args)`
`static int[]`	`parseBlockSize(String blockSizeArg, int nd)`
`static double[]`	`resolutionFromSource(Source<?> src)`
`void`	`run(String arg)`
`static <T> List<ij.ImagePlus>`	`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>> void`	`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)`
`static boolean`	`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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- TARGET
```
public static final String TARGET
```
  See Also:
  
  Constant Field Values
- MOVING
```
public static final String MOVING
```
  See Also:
  
  Constant Field Values
- MOVING_WARPED
```
public static final String MOVING_WARPED
```
  See Also:
  
  Constant Field Values
- UNION_TARGET_MOVING
```
public static final String UNION_TARGET_MOVING
```
  See Also:
  
  Constant Field Values
- SPECIFIED
```
public static final String SPECIFIED
```
  See Also:
  
  Constant Field Values
- SPECIFIED_PHYSICAL
```
public static final String SPECIFIED_PHYSICAL
```
  See Also:
  
  Constant Field Values
- SPECIFIED_PIXEL
```
public static final String SPECIFIED_PIXEL
```
  See Also:
  
  Constant Field Values
- LANDMARK_POINTS
```
public static final String LANDMARK_POINTS
```
  See Also:
  
  Constant Field Values
- LANDMARK_POINT_CUBE_PHYSICAL
```
public static final String LANDMARK_POINT_CUBE_PHYSICAL
```
  See Also:
  
  Constant Field Values
- LANDMARK_POINT_CUBE_PIXEL
```
public static final String LANDMARK_POINT_CUBE_PIXEL
```
  See Also:
  
  Constant Field Values

Constructor Detail
- ApplyBigwarpPlugin
```
public ApplyBigwarpPlugin()
```

Method Detail

main

public static void main(String[] args)
                 throws IOException

Throws:: IOException

validateInput

public static boolean 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)

getResolution

public static double[] getResolution(Source<?> source,
                                     String resolutionOption,
                                     double[] resolutionSpec)

getUnit

public static String getUnit(BigWarp.BigWarpData<?> bwData,
                             String resolutionOption)

getResolution

public static double[] getResolution(BigWarp.BigWarpData<?> bwData,
                                     String resolutionOption,
                                     double[] resolutionSpec)

getResolution

public static double[] getResolution(ij.ImagePlus movingIp,
                                     ij.ImagePlus targetIp,
                                     String resolutionOption,
                                     double[] resolutionSpec)

Returns the resolution of the output given input options

Parameters:: movingIp - the moving ImagePlus; targetIp - the target ImagePlus; resolutionOption - the resolution option; resolutionSpec - the resolution (if applicable)
Returns:: the output image resolution

getPixelInterval

public static List<Interval> getPixelInterval(ij.ImagePlus movingIp,
                                              ij.ImagePlus targetIp,
                                              LandmarkTableModel landmarks,
                                              InvertibleRealTransform transform,
                                              String fieldOfViewOption,
                                              String fieldOfViewPointFilter,
                                              double[] fovSpec,
                                              double[] offsetSpec,
                                              double[] outputResolution)

getPixelInterval

public static Interval getPixelInterval(Source<?> source,
                                        LandmarkTableModel landmarks,
                                        InvertibleRealTransform transform,
                                        String fieldOfViewOption,
                                        double[] outputResolution)

resolutionFromSource

public static double[] resolutionFromSource(Source<?> src)

getPixelInterval

public static List<Interval> 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

Parameters:: bwData - the BigWarpData; landmarks - the landmarks; fieldOfViewOption - the field of view option; fieldOfViewPointFilter - the regexp for filtering landmarks points by name; fovSpec - the field of view specification; offsetSpec - the offset specification; outputResolution - the resolution of the output image
Returns:: the output interval

fillMatchedPointNames

public static void fillMatchedPointNames(List<String> ptList,
                                         LandmarkTableModel landmarks,
                                         String fieldOfViewPointFilter)

getMatchedPoints

public static List<Double[]> getMatchedPoints(LandmarkTableModel landmarks,
                                              String fieldOfViewPointFilter)

getPixelOffset

public static double[] getPixelOffset(String fieldOfViewOption,
                                      double[] offsetSpec,
                                      double[] outputResolution,
                                      Interval outputInterval)

Get the offset in pixels given the output resolution and interval

Parameters:: fieldOfViewOption - the field of view option; offsetSpec - the offset specification; outputResolution - the resolution of the output image; outputInterval - the output interval
Returns:: the offset

apply

public static List<ij.ImagePlus> 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)

apply

public static List<ij.ImagePlus> 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)

apply

public static <T> List<ij.ImagePlus> 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)

runExport

public static <T> List<ij.ImagePlus> 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)

runN5Export

public static <S,T extends NativeType<T> & NumericType<T>> void 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)

run
```
public void run(String arg)
```
Specified by:

run in interface ij.plugin.PlugIn

parseBlockSize

public static int[] parseBlockSize(String blockSizeArg,
                                   int nd)

getCompression

public static org.janelia.saalfeldlab.n5.Compression getCompression(String compressionArg)

Class ApplyBigwarpPlugin

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TARGET

MOVING

MOVING_WARPED

UNION_TARGET_MOVING

SPECIFIED

SPECIFIED_PHYSICAL

SPECIFIED_PIXEL

LANDMARK_POINTS

LANDMARK_POINT_CUBE_PHYSICAL

LANDMARK_POINT_CUBE_PIXEL

Constructor Detail

ApplyBigwarpPlugin

Method Detail

main

validateInput

getResolution

getUnit

getResolution

getResolution

getPixelInterval

getPixelInterval

resolutionFromSource

getPixelInterval

fillMatchedPointNames

getMatchedPoints

getPixelOffset

apply

apply

apply

runExport

runN5Export

run

parseBlockSize

getCompression