ImgUtils (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.util.ImgUtils

```
public class ImgUtils
extends Object
```
Static utilities for handling and manipulation of RandomAccessibleIntervals

Author:

Cameron Arshadi

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static List<Interval>`	`createIntervals(long[] sourceDimensions, long[] blockDimensions)` Partition the source dimensions into a list of `Interval`s with given dimensions.
`static <T extends RealType<T>> RandomAccessibleInterval<T>`	`getCtSlice(Dataset dataset, int channelIndex, int frameIndex)` Get a view of the `Dataset` at the specified channel and frame.
`static <T extends RealType<T>> RandomAccessibleInterval<T>`	`getCtSlice3d(Dataset dataset, int channelIndex, int frameIndex)` Get a 3D view of a `Dataset` at the specified channel and frame.
`static int`	`maxDimension(long[] dimensions)`
`static boolean`	`outOfBounds(long[] pos, long[] min, long[] max)` Checks if pos is outside the bounds given by min and max
`static <T extends NumericType<T>> ij.ImagePlus`	`raiToImp(RandomAccessibleInterval<T> rai, String title)` Convert a `RandomAccessibleInterval` to an `ImagePlus`.
`static <T> List<IntervalView<T>>`	`splitIntoBlocks(RandomAccessibleInterval<T> source, long[] blockDimensions)` Partition the source rai into a list of `IntervalView` with given dimensions.
`static <T> RandomAccessibleInterval<T>`	`subInterval(RandomAccessibleInterval<T> img, Localizable p1, Localizable p2, long padPixels)` Get an N-D sub-interval of an N-D image, given two corner points and specified padding.
`static <T> RandomAccessibleInterval<T>`	`subVolume(RandomAccessibleInterval<T> img, long x1, long y1, long z1, long x2, long y2, long z2, long padPixels)` Get a 3D sub-volume of an image, given two corner points and specified padding.

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

- Method Detail
  - maxDimension
```
public static int maxDimension(long[] dimensions)
```
    Parameters:
    
    dimensions -
    
    Returns:
    
    the index of the largest dimension
  - subVolume
```
public static <T> RandomAccessibleInterval<T> subVolume(RandomAccessibleInterval<T> img,
                                                        long x1,
                                                        long y1,
                                                        long z1,
                                                        long x2,
                                                        long y2,
                                                        long z2,
                                                        long padPixels)
```
    Get a 3D sub-volume of an image, given two corner points and specified padding. If the input is 2D, a singleton dimension is added. If necessary, the computed sub-volume is clamped at the min and max of each dimension of the input interval.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    img - the source interval
    
    x1 - x-coordinate of the first corner point
    
    y1 - y-coordinate of the first corner point
    
    z1 - z-coordinate of the first corner point
    
    x2 - x-coordinate of the second corner point
    
    y2 - y-cooridnate of the second corner point
    
    z2 - z-coordinate of the second corner point
    
    padPixels - the amount of padding in each dimension, in pixels
    
    Returns:
    
    the subvolume
  - subInterval
```
public static <T> RandomAccessibleInterval<T> subInterval(RandomAccessibleInterval<T> img,
                                                          Localizable p1,
                                                          Localizable p2,
                                                          long padPixels)
```
    Get an N-D sub-interval of an N-D image, given two corner points and specified padding. If necessary, the computed sub-interval is clamped at the min and max of each dimension of the input interval.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    img - the source interval
    
    p1 - the first corner point
    
    p2 - the second corner point
    
    padPixels - the amount of padding in each dimension, in pixels
    
    Returns:
    
    the sub-interval
  - splitIntoBlocks
```
public static <T> List<IntervalView<T>> splitIntoBlocks(RandomAccessibleInterval<T> source,
                                                        long[] blockDimensions)
```
    Partition the source rai into a list of IntervalView with given dimensions. If the block dimensions are not multiples of the image dimensions, some blocks will have truncated dimensions.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    source - the source rai
    
    blockDimensions - the target block size
    
    Returns:
    
    the list of blocks
  - createIntervals
```
public static List<Interval> createIntervals(long[] sourceDimensions,
                                             long[] blockDimensions)
```
    Partition the source dimensions into a list of Intervals with given dimensions. If the block dimensions are not multiples of the image dimensions, some blocks will have slightly different dimensions.
    
    Parameters:
    
    sourceDimensions - the source dimensions
    
    blockDimensions - the target block size
    
    Returns:
    
    the list of Intervals
  - raiToImp
```
public static <T extends NumericType<T>> ij.ImagePlus raiToImp(RandomAccessibleInterval<T> rai,
                                                               String title)
```
    Convert a RandomAccessibleInterval to an ImagePlus. If the input has 3 dimensions, the 3rd dimension is treated as depth.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    rai - the source rai
    
    title - the title for the converted ImagePlus
    
    Returns:
    
    the ImagePlus
  - getCtSlice3d
```
public static <T extends RealType<T>> RandomAccessibleInterval<T> getCtSlice3d(Dataset dataset,
                                                                               int channelIndex,
                                                                               int frameIndex)
```
    Get a 3D view of a Dataset at the specified channel and frame. If the Dataset is 2D, a singleton dimension is added.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    dataset - the input Dataset
    
    channelIndex - the channel position, 0-indexed
    
    frameIndex - the time position, 0-indexed
    
    Returns:
    
    the view rai
  - getCtSlice
```
public static <T extends RealType<T>> RandomAccessibleInterval<T> getCtSlice(Dataset dataset,
                                                                             int channelIndex,
                                                                             int frameIndex)
```
    Get a view of the Dataset at the specified channel and frame.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    dataset - the input Dataset
    
    channelIndex - the channel position, 0-indexed
    
    frameIndex - the time position, 0-indexed
    
    Returns:
    
    the view rai
  - outOfBounds
```
public static boolean outOfBounds(long[] pos,
                                  long[] min,
                                  long[] max)
```
    Checks if pos is outside the bounds given by min and max
    
    Parameters:
    
    pos - the position to check
    
    min - the minimum of the interval
    
    max - the maximum of the interval
    
    Returns:
    
    true if pos is out of bounds, false otherwise

Class ImgUtils

Method Summary

Methods inherited from class java.lang.Object

Method Detail

maxDimension

subVolume

subInterval

splitIntoBlocks

createIntervals

raiToImp

getCtSlice3d

getCtSlice

outOfBounds