DatasetDimensions (imglib2-imaris-bridge 9.7.2.0 API)

java.lang.Object
- com.bitplane.xt.DatasetDimensions

```
public final class DatasetDimensions
extends Object
```
Dimensions of an ImarisDataset.
Stores the 5D XYZCT dimensions of the underlying Imaris dataset, as well as the mapping from Imaris to ImgLib2 dimensions.
In Imaris, datasets are always 5D: for example, a 2D dataset (without channel or time) is represented as 5D with size=1 along Z, C, T axes. In ImgLib2, there is a distinction between a 2D image and a 5D image with size=1 along the 3rd, 4th, and 5th dimension. Therefore, there are several ways to represent such an Imaris dataset in ImgLib2. Which way is chosen is specified by the mapping from Imaris to ImgLib2 dimensions, as well as (redundantly) the #getAxisOrder axis order (of the ImgLib2 representation).

Author:

Tobias Pietzsch

Constructor Summary

Constructors
Constructor and Description
`DatasetDimensions(Imaris.IDataSetPrx dataset, ImarisAxesOptions.Axis... includeAxes)` Create `DatasetDimensions` from the given Imaris `IDataSetPrx`.
`DatasetDimensions(int sx, int sy, int sz, int sc, int st)` Create `DatasetDimensions`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`dimC()` Get the index of the channel dimension in the ImgLib2 representation.
`int`	`dimT()` Get the index of the time dimension in the ImgLib2 representation.
`int`	`dimX()` Get the index of the X dimension in the ImgLib2 representation.
`int`	`dimY()` Get the index of the Y dimension in the ImgLib2 representation.
`int`	`dimZ()` Get the index of the Z dimension in the ImgLib2 representation.
`AxisOrder`	`getAxisOrder()` Returns the `AxisOrder` of the ImgLib2 representation.
`int[]`	`getImarisDimensions()` Returns the 5D dimensions of the dataset on the imaris side.
`int[]`	`getMapDimensions()` Get the mapping between dimension indices in the Imaris and in the ImgLib2 representation.
`boolean`	`hasC()` Returns `true` if the ImgLib2 representation has a channel dimension.
`boolean`	`hasT()` Returns `true` if the ImgLib2 representation has a time dimension.
`boolean`	`hasZ()` Returns `true` if the ImgLib2 representation has a Z dimension.
`int`	`sizeC()` Returns the number of channels.
`int`	`sizeT()` Returns the number of timepoints.
`int`	`sizeX()` Returns the size along X.
`int`	`sizeY()` Returns the size along Y.
`int`	`sizeZ()` Returns the size along Z.
`String`	`toString()`

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

- Constructor Detail
  - DatasetDimensions
```
public DatasetDimensions(int sx,
                         int sy,
                         int sz,
                         int sc,
                         int st)
```
    Create DatasetDimensions.
    Sizes s≤0 indicate missing dimensions. For example, new DatasetDimension(new UnsignedByteType(), 300, 200, 0, 0, 0) represents a 2D ImgLib2 image with axes [X,Y]. The size along missing dimensions (Z, C, T in this example) is set to s=1 on the Imaris side.
    
    Parameters:
    
    sx - size in X dimension
    
    sy - size in Y dimension
    
    sz - size in Z dimension
    
    sc - size in C (channel) dimension
    
    st - size in T (time) dimension
  - DatasetDimensions
```
public DatasetDimensions(Imaris.IDataSetPrx dataset,
                         ImarisAxesOptions.Axis... includeAxes)
                  throws Imaris.Error
```
    Create DatasetDimensions from the given Imaris IDataSetPrx.
    The optional includeAxes arguments specify which axes must be included (at least) in the ImgLib2 representation.
    In Imaris, datasets are always 5D: for example, a 2D dataset (without channel or time) is represented as 5D with size=1 along Z, C, T axes. In ImgLib2, there is a distinction between a 2D image and a 5D image with size=1 along the 3rd, 4th, and 5th dimension. Therefore, there are several ways to represent such an Imaris dataset in ImgLib2. Which way is chosen is specified by the mapping from Imaris to ImgLib2 dimensions, as well as (redundantly) the #getAxisOrder axis order (of the ImgLib2 representation).
    By default, axes Z, C, and T are not represented in ImgLib2 if the dataset size along those axes is s=1. By specifying these axes as includeAxes arguments, this can be overridden. For example, an Imaris dataset with size {100, 100, 1, 1, 1} would be represented as a 2D ImgLib2 image with size {100, 100}. Specifying includeAxes = Z, T, would result in a 4D ImgLib2 image with size {100,100,1,1}.
    
    Throws:
    
    Imaris.Error
- Method Detail
  - getMapDimensions
```
public int[] getMapDimensions()
```
    Get the mapping between dimension indices in the Imaris and in the ImgLib2 representation.
    The returned int[5] array maps Imaris dimension indices to imglib2 dimension indices. If i is dimension index from Imaris (0..4 means X,Y,Z,C,T) then mapDimensions[i] is the corresponding imglib2 dimension, e.g., in imagePyramid.
    For imglib2 dimensions, Imaris dimensions with size=1 maybe skipped. E.g., for a XYC image mapDimensions = {0,1,-1,2,-1}.
  - getImarisDimensions
```
public int[] getImarisDimensions()
```
    Returns the 5D dimensions of the dataset on the imaris side.
  - getAxisOrder
```
public AxisOrder getAxisOrder()
```
    Returns the AxisOrder of the ImgLib2 representation. The returned value will be one of XY, XYZ, XYC, XYT, XYZC, XYZT, XYCT, XYZCT.
  - dimX
```
public int dimX()
```
    Get the index of the X dimension in the ImgLib2 representation. (This is always 0.)
  - sizeX
```
public int sizeX()
```
    Returns the size along X.
  - dimY
```
public int dimY()
```
    Get the index of the Y dimension in the ImgLib2 representation. (This is always 1.)
  - sizeY
```
public int sizeY()
```
    Returns the size along Y.
  - hasZ
```
public boolean hasZ()
```
    Returns true if the ImgLib2 representation has a Z dimension.
  - dimZ
```
public int dimZ()
```
    Get the index of the Z dimension in the ImgLib2 representation.
    
    Returns:
    
    the index of the Z dimension, or -1 if the ImgLib2 representation doesn't have Z
  - sizeZ
```
public int sizeZ()
```
    Returns the size along Z. If the ImgLib2 representation does not have a Z dimension, returns 1.
  - hasC
```
public boolean hasC()
```
    Returns true if the ImgLib2 representation has a channel dimension.
  - dimC
```
public int dimC()
```
    Get the index of the channel dimension in the ImgLib2 representation.
    
    Returns:
    
    the index of the channel dimension, or -1 if the ImgLib2 representation doesn't have channels
  - sizeC
```
public int sizeC()
```
    Returns the number of channels. If the ImgLib2 representation does not have channels, returns 1.
  - hasT
```
public boolean hasT()
```
    Returns true if the ImgLib2 representation has a time dimension.
  - dimT
```
public int dimT()
```
    Get the index of the time dimension in the ImgLib2 representation.
    
    Returns:
    
    the index of the time dimension, or -1 if the ImgLib2 representation doesn't have a time dimension.
  - sizeT
```
public int sizeT()
```
    Returns the number of timepoints. If the ImgLib2 representation does not have timepoints, return 1.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class DatasetDimensions

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DatasetDimensions

DatasetDimensions

Method Detail

getMapDimensions

getImarisDimensions

getAxisOrder

dimX

sizeX

dimY

sizeY

hasZ

dimZ

sizeZ

hasC

dimC

sizeC

hasT

dimT

sizeT

toString