BigWarpInit (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bigwarp.BigWarpInit

```
public class BigWarpInit
extends Object
```

Constructor Summary

Constructors
Constructor and Description

BigWarpInit()

Constructors
Constructor and Description
`BigWarpInit()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static <T> BigWarp.BigWarpData<?>`	`add(BigWarp.BigWarpData bwdata, AbstractSpimData<?> data, int setupId, int numTimepoints, boolean isMoving)`
`static <T> int`	`add(BigWarp.BigWarpData bwdata, ij.ImagePlus ip, int setupId, int numTimepoints, boolean isMoving)`
`static <T> BigWarp.BigWarpData<?>`	`add(BigWarp.BigWarpData bwdata, Source<T> src, int setupId, int numTimepoints, boolean isMoving)`
`static SpimData`	`addToData(BigWarp.BigWarpData<?> bwdata, boolean isMoving, int setupId, String rootPath, String dataset)`
`static BigWarp.BigWarpData<?>`	`createBigWarpData(AbstractSpimData<?>[] spimDataPList, AbstractSpimData<?>[] spimDataQList)`
`static BigWarp.BigWarpData<?>`	`createBigWarpData(AbstractSpimData<?>[] spimDataPList, AbstractSpimData<?>[] spimDataQList, String[] names)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	`createBigWarpData(AbstractSpimData<?> spimDataP, AbstractSpimData<?> spimDataQ)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	`createBigWarpData(ImagePlusLoader loaderP, ImagePlusLoader loaderQ)`
`static BigWarp.BigWarpData<?>`	`createBigWarpData(ImagePlusLoader loaderP, ImagePlusLoader loaderQ, String[] names)`
`static BigWarp.BigWarpData<?>`	`createBigWarpData(Loader loaderP, Loader loaderQ)` Create `BigWarp.BigWarpData` from two `Loaders` that generate `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	`createBigWarpData(Loader loaderP, Loader loaderQ, String[] namesIn)` Create `BigWarp.BigWarpData` from two `Loaders` that generate `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	`createBigWarpData(Source<?>[] movingSourceList, Source<?>[] fixedSourceList, String[] names)` Create `BigWarp.BigWarpData` from two `AbstractSpimData`.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromImagePlusXML(ij.ImagePlus[] impP, String xmlFilenameQ)` Create `BigWarp.BigWarpData` from an `ImagePlus` array and an XML file.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromImagePlusXML(ij.ImagePlus impP, String xmlFilenameQ)` Create `BigWarp.BigWarpData` from an `ImagePlus` and an XML file.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromImages(ij.ImagePlus[] impP, ij.ImagePlus impQ)` Create `BigWarp.BigWarpData` from one `ImagePlus` array (moving) and one `ImagePlus` (target).
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromImages(ij.ImagePlus[] impP, ij.ImagePlus[] impQ)` Create `BigWarp.BigWarpData` from two `ImagePlus` arrays.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromImages(ij.ImagePlus impP, ij.ImagePlus impQ)` Create `BigWarp.BigWarpData` from two `ImagePluses`.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromImages(ij.ImagePlus impP, ij.ImagePlus[] impQ)` Create `BigWarp.BigWarpData` from one `ImagePlus` (moving) and one `ImagePlus` array (target).
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromXML(String xmlFilenameP, String xmlFilenameQ)` Create `BigWarp.BigWarpData` from two XML files.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromXMLImagePlus(String xmlFilenameP, ij.ImagePlus impQ)` Create `BigWarp.BigWarpData` from an xml file and an `ImagePlus`.
`static BigWarp.BigWarpData<?>`	`createBigWarpDataFromXMLImagePlus(String xmlFilenameP, ij.ImagePlus[] impQ)` Create `BigWarp.BigWarpData` from an xml file and an `ImagePlus` array.
`static <T> BigWarp.BigWarpData<T>`	`initData()`
`static void`	`initSetup(Source<?> src, int setupId, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)`
`static void`	`initSetups(AbstractSpimData<?> spimData, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)`
`static void`	`initSourceARGB(Source<ARGBType> src, int setupId, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)`
`static <T extends RealType<T>> void`	`initSourceReal(Source<T> src, int setupId, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)`
`static Source<?>`	`loadN5Source(String n5Root, String n5Dataset)`
`static String[]`	`namesFromImagePlus(ij.ImagePlus imp)` Create a `String` array of names from an `ImagePlus`.
`static String[]`	`namesFromImagePluses(ij.ImagePlus impP, ij.ImagePlus impQ)` Create a `String` array of names from two `ImagePlus`es, essentially concatenating the results from calling `namesFromImagePlus` with each.
`static <T extends org.janelia.saalfeldlab.n5.metadata.N5Metadata> Source<?>`	`openAsSource(org.janelia.saalfeldlab.n5.N5Reader n5, T meta, boolean isVolatile)`
`static Source<?>`	`openAsSourceMulti(org.janelia.saalfeldlab.n5.N5Reader n5, org.janelia.saalfeldlab.n5.metadata.MultiscaleMetadata<?> multiMeta, boolean isVolatile)`
`static ArrayList<SourceAndConverter<?>>`	`wrapSourcesAsRenamable(List<SourceAndConverter<?>> sources, String[] names)`

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

Constructor Detail
- BigWarpInit
```
public BigWarpInit()
```

Method Detail

initSetups

public static void initSetups(AbstractSpimData<?> spimData,
                              List<ConverterSetup> converterSetups,
                              List<SourceAndConverter<?>> sources)

initSetup

public static void initSetup(Source<?> src,
                             int setupId,
                             List<ConverterSetup> converterSetups,
                             List<SourceAndConverter<?>> sources)

initSourceARGB

public static void initSourceARGB(Source<ARGBType> src,
                                  int setupId,
                                  List<ConverterSetup> converterSetups,
                                  List<SourceAndConverter<?>> sources)

initSourceReal

public static <T extends RealType<T>> void initSourceReal(Source<T> src,
                                                          int setupId,
                                                          List<ConverterSetup> converterSetups,
                                                          List<SourceAndConverter<?>> sources)

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(AbstractSpimData<?>[] spimDataPList,
                                                       AbstractSpimData<?>[] spimDataQList)

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(Source<?>[] movingSourceList,
                                                       Source<?>[] fixedSourceList,
                                                       String[] names)

Create BigWarp.BigWarpData from two AbstractSpimData.

Parameters:: movingSourceList - array of moving SpimData; fixedSourceList - array of fixed SpimData; names - array of source names
Returns:: BigWarpData the data

add

public static <T> int add(BigWarp.BigWarpData bwdata,
                          ij.ImagePlus ip,
                          int setupId,
                          int numTimepoints,
                          boolean isMoving)

add

public static <T> BigWarp.BigWarpData<?> add(BigWarp.BigWarpData bwdata,
                                             Source<T> src,
                                             int setupId,
                                             int numTimepoints,
                                             boolean isMoving)

add

public static <T> BigWarp.BigWarpData<?> add(BigWarp.BigWarpData bwdata,
                                             AbstractSpimData<?> data,
                                             int setupId,
                                             int numTimepoints,
                                             boolean isMoving)

addToData

public static SpimData addToData(BigWarp.BigWarpData<?> bwdata,
                                 boolean isMoving,
                                 int setupId,
                                 String rootPath,
                                 String dataset)

loadN5Source

public static Source<?> loadN5Source(String n5Root,
                                     String n5Dataset)

openAsSource

public static <T extends org.janelia.saalfeldlab.n5.metadata.N5Metadata> Source<?> openAsSource(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                                                                T meta,
                                                                                                boolean isVolatile)

openAsSourceMulti

public static Source<?> openAsSourceMulti(org.janelia.saalfeldlab.n5.N5Reader n5,
                                          org.janelia.saalfeldlab.n5.metadata.MultiscaleMetadata<?> multiMeta,
                                          boolean isVolatile)

initData

public static <T> BigWarp.BigWarpData<T> initData()

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(AbstractSpimData<?>[] spimDataPList,
                                                       AbstractSpimData<?>[] spimDataQList,
                                                       String[] names)

Create BigWarp.BigWarpData from two AbstractSpimData.

Parameters:: spimDataPList - array of moving SpimData; spimDataQList - array of fixed SpimData; names - array of source names
Returns:: BigWarpData

wrapSourcesAsRenamable

public static ArrayList<SourceAndConverter<?>> wrapSourcesAsRenamable(List<SourceAndConverter<?>> sources,
                                                                      String[] names)

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(AbstractSpimData<?> spimDataP,
                                                       AbstractSpimData<?> spimDataQ)

Create BigWarp.BigWarpData from two AbstractSpimData.

Parameters:: spimDataP - array of moving SpimData; spimDataQ - array of fixed SpimData
Returns:: BigWarpData

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(ImagePlusLoader loaderP,
                                                       ImagePlusLoader loaderQ)

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(ImagePlusLoader loaderP,
                                                       ImagePlusLoader loaderQ,
                                                       String[] names)

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(Loader loaderP,
                                                       Loader loaderQ)

Create BigWarp.BigWarpData from two Loaders that generate AbstractSpimData.

Parameters:: loaderP - moving image source loader; loaderQ - fixed image source loader
Returns:: BigWarpData

createBigWarpData

public static BigWarp.BigWarpData<?> createBigWarpData(Loader loaderP,
                                                       Loader loaderQ,
                                                       String[] namesIn)

Create BigWarp.BigWarpData from two Loaders that generate AbstractSpimData.

Parameters:: loaderP - moving image source loader; loaderQ - fixed image source loader; namesIn - list of names
Returns:: BigWarpData

createBigWarpDataFromXML

public static BigWarp.BigWarpData<?> createBigWarpDataFromXML(String xmlFilenameP,
                                                              String xmlFilenameQ)

Create BigWarp.BigWarpData from two XML files.

Parameters:: xmlFilenameP - moving source XML; xmlFilenameQ - fixed source XML
Returns:: BigWarpData

createBigWarpDataFromImages

public static BigWarp.BigWarpData<?> createBigWarpDataFromImages(ij.ImagePlus impP,
                                                                 ij.ImagePlus impQ)

Create BigWarp.BigWarpData from two ImagePluses.

Parameters:: impP - moving source ImagePlus; impQ - fixed source ImagePlus
Returns:: BigWarpData

createBigWarpDataFromImages
```
public static BigWarp.BigWarpData<?> createBigWarpDataFromImages(ij.ImagePlus[] impP,
                                                                 ij.ImagePlus[] impQ)
```
Create BigWarp.BigWarpData from two ImagePlus arrays.

Parameters:

impP - array of moving sources ImagePlus

impQ - array of fixed sources ImagePlus

Returns:

BigWarpData

createBigWarpDataFromImages
```
public static BigWarp.BigWarpData<?> createBigWarpDataFromImages(ij.ImagePlus impP,
                                                                 ij.ImagePlus[] impQ)
```
Create BigWarp.BigWarpData from one ImagePlus (moving) and one ImagePlus array (target).

Parameters:

impP - moving source ImagePlus

impQ - array of fixed sources ImagePlus

Returns:

BigWarpData

createBigWarpDataFromImages
```
public static BigWarp.BigWarpData<?> createBigWarpDataFromImages(ij.ImagePlus[] impP,
                                                                 ij.ImagePlus impQ)
```
Create BigWarp.BigWarpData from one ImagePlus array (moving) and one ImagePlus (target).

Parameters:

impP - array of fixed sources ImagePlus

impQ - fixed source ImagePlus

Returns:

BigWarpData

createBigWarpDataFromXMLImagePlus

public static BigWarp.BigWarpData<?> createBigWarpDataFromXMLImagePlus(String xmlFilenameP,
                                                                       ij.ImagePlus impQ)

Create BigWarp.BigWarpData from an xml file and an ImagePlus.

Parameters:: xmlFilenameP - movingSource XML; impQ - fixed source ImagePlus
Returns:: BigWarpData

createBigWarpDataFromXMLImagePlus
```
public static BigWarp.BigWarpData<?> createBigWarpDataFromXMLImagePlus(String xmlFilenameP,
                                                                       ij.ImagePlus[] impQ)
```
Create BigWarp.BigWarpData from an xml file and an ImagePlus array.

Parameters:

xmlFilenameP - movingSource XML

impQ - array of fixed sources ImagePlus

Returns:

BigWarpData

createBigWarpDataFromImagePlusXML

public static BigWarp.BigWarpData<?> createBigWarpDataFromImagePlusXML(ij.ImagePlus impP,
                                                                       String xmlFilenameQ)

Create BigWarp.BigWarpData from an ImagePlus and an XML file.

Parameters:: impP - moving source ImagePlus; xmlFilenameQ - fixed source XML
Returns:: BigWarpData

createBigWarpDataFromImagePlusXML

public static BigWarp.BigWarpData<?> createBigWarpDataFromImagePlusXML(ij.ImagePlus[] impP,
                                                                       String xmlFilenameQ)

Create BigWarp.BigWarpData from an ImagePlus array and an XML file.

Parameters:: impP - array of moving sources ImagePlus; xmlFilenameQ - fixed source XML
Returns:: BigWarpData

namesFromImagePluses
```
public static String[] namesFromImagePluses(ij.ImagePlus impP,
                                            ij.ImagePlus impQ)
```
Create a String array of names from two ImagePluses, essentially concatenating the results from calling namesFromImagePlus with each.

Parameters:

impP - first image to generate names from

impQ - second image to generate names from

Returns:

String array of names from both images

namesFromImagePlus
```
public static String[] namesFromImagePlus(ij.ImagePlus imp)
```
Create a String array of names from an ImagePlus. Each channel is given its own name, in the format of [title]-[channel #], unless there is only one channel.

Parameters:

imp - image to generate names from

Returns:

String array of names

Class BigWarpInit

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BigWarpInit

Method Detail

initSetups

initSetup

initSourceARGB

initSourceReal

createBigWarpData

createBigWarpData

add

add

add

addToData

loadN5Source

openAsSource

openAsSourceMulti

initData

createBigWarpData

wrapSourcesAsRenamable

createBigWarpData

createBigWarpData

createBigWarpData

createBigWarpData

createBigWarpData

createBigWarpDataFromXML

createBigWarpDataFromImages

createBigWarpDataFromImages

createBigWarpDataFromImages

createBigWarpDataFromImages

createBigWarpDataFromXMLImagePlus

createBigWarpDataFromXMLImagePlus

createBigWarpDataFromImagePlusXML

createBigWarpDataFromImagePlusXML

namesFromImagePluses

namesFromImagePlus