PlateSeries

Object
- acquifer.core.PlateSeries

```
public class PlateSeries
extends Object
```
A PlateSeries holds a collection of PlatePlane, with identical subpositions.
It thus can be used to represent a hyperstack of plate-montages.
A PlateSeris can also be constructed from a 2D-array of ImagePlane, first the ImagePlanes are grouped into PlatePlanes, and the collection of PlatePlanes generates the PlateSeries. Indexing would thus be like myPlateSeries[platePlaneIndex][imagePlaneIndex].

PlateSeries are mutable, one can add, remove and reorder ImagePlanes

Constructor Summary

Constructors
Constructor and Description
`PlateSeries(ImagePlane[][] groupedImagePlanes)` Constructs a PlateSeries from a 2D array of ImagePlanes.
`PlateSeries(ImagePlane[][] groupedImagePlanes, Comparator<PlatePlane> sortOrder)` Constructs a PlateSeries from a 2D array of ImagePlanes.
`PlateSeries(PlatePlane[] listPlatePlanes)` Constructs a PlateSeries from a list of PlatePlanes.
`PlateSeries(PlatePlane[] listPlatePlanes, Comparator<PlatePlane> sortOrder)` Constructs a PlateSeries from a list of PlatePlanes with optional sorting of the PlatePlanes.
`PlateSeries(PlateSeries plateSeries)` Clone constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`PlateSeries`	`clone()` Create an independant clone of the PlateSeries instance.
`File`	`getDirectory()` Get the directory containing this PlateSeries.
`PlatePlane[]`	`getListPlatePlanes()` Return a copy of the list of PlatePlanes contained in this PlateSeries.
`int`	`getNumberOfChannels()`
`int`	`getNumberOfPlanes()` Return the number of PlatePlane in the PlateSeries.
`int`	`getNumberOfTimepoints()`
`int`	`getNumberOfZslices()`
`PlatePlane`	`getPlatePlane(int i)` Get the Plane at index i (0-based) in the PlateSeries.
`Set<Integer>`	`getSetChannels()`
`Set<Integer>`	`getSetColumns()`
`Set<Character>`	`getSetRows()`
`Comparator<PlatePlane>`	`getSortOrder()`
`int`	`getSubPosition()` Return the subposition of this PlateSeries.
`static PlateSeries[]`	`groupByPlateSeries(Dataset dataset)` Group the ImagePlanes in a dataset as PlateSeries, each corresponding to a hyperstack of plate montages.
`void`	`removePlane(int i)` Remove the PlatePlane at index i (0-based).
`void`	`sort(Comparator<PlatePlane> sortOrder)` Reorder the PlatePlane in the PlateSeries (in-place sort).
`String`	`toString()`

Methods inherited from class Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - PlateSeries
```
public PlateSeries(PlatePlane[] listPlatePlanes)
```
    Constructs a PlateSeries from a list of PlatePlanes.
    The order of the PlatePlane in the resulting PlateSeries is identical to the order of the array of PlatePlanes.
  - PlateSeries
```
public PlateSeries(PlatePlane[] listPlatePlanes,
                   Comparator<PlatePlane> sortOrder)
```
    Constructs a PlateSeries from a list of PlatePlanes with optional sorting of the PlatePlanes.
    
    Parameters:
    
    sortOrder - can be null.
  - PlateSeries
```
public PlateSeries(ImagePlane[][] groupedImagePlanes)
```
    Constructs a PlateSeries from a 2D array of ImagePlanes.
    The order of the PlatePlane in the PlateSeries corresponds to the order in the array of ImagePlane.
    All ImagePlanes in the array must have an identical subPosition index and reside in the same directory.
    The inner-groups corresponds to ImagePlanes with by identical CZT (ie PlatePlanes), the outer group is thus a group of PlatePlanes.
  - PlateSeries
```
public PlateSeries(ImagePlane[][] groupedImagePlanes,
                   Comparator<PlatePlane> sortOrder)
```
    Constructs a PlateSeries from a 2D array of ImagePlanes.
    All ImagePlanes in the array must have an identical subPosition index and reside in the same directory.
    The inner-groups corresponds to ImagePlanes with by identical CZT (ie PlatePlanes), the outer group is thus a group of PlatePlanes.
  - PlateSeries
```
public PlateSeries(PlateSeries plateSeries)
```
    Clone constructor.
    The returned copy is independent from the original one.
- Method Detail
  - clone
```
public PlateSeries clone()
```
    Create an independant clone of the PlateSeries instance.
    Changes to the original PlateSeries are thus not reflected in the clone. (e.g. sorting)
    
    Overrides:
    
    clone in class Object
  - getDirectory
```
public File getDirectory()
```
    Get the directory containing this PlateSeries.
  - getSubPosition
```
public int getSubPosition()
```
    Return the subposition of this PlateSeries.
    All ImagePlane in this PlateSeries have the same subposition.
  - getSortOrder
```
public Comparator<PlatePlane> getSortOrder()
```
  - getSetChannels
```
public Set<Integer> getSetChannels()
```
  - getSetRows
```
public Set<Character> getSetRows()
```
  - getSetColumns
```
public Set<Integer> getSetColumns()
```
  - getNumberOfChannels
```
public int getNumberOfChannels()
```
  - getNumberOfZslices
```
public int getNumberOfZslices()
```
  - getNumberOfTimepoints
```
public int getNumberOfTimepoints()
```
  - getListPlatePlanes
```
public PlatePlane[] getListPlatePlanes()
```
    Return a copy of the list of PlatePlanes contained in this PlateSeries.
  - getPlatePlane
```
public PlatePlane getPlatePlane(int i)
```
    Get the Plane at index i (0-based) in the PlateSeries.
  - getNumberOfPlanes
```
public int getNumberOfPlanes()
```
    Return the number of PlatePlane in the PlateSeries.
  - removePlane
```
public void removePlane(int i)
```
    Remove the PlatePlane at index i (0-based).
  - sort
```
public void sort(Comparator<PlatePlane> sortOrder)
```
    Reorder the PlatePlane in the PlateSeries (in-place sort).
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - groupByPlateSeries
```
public static PlateSeries[] groupByPlateSeries(Dataset dataset)
```
    Group the ImagePlanes in a dataset as PlateSeries, each corresponding to a hyperstack of plate montages.
    There is always 1 PlateSeries per subposition.

Class PlateSeries

Constructor Summary

Method Summary

Methods inherited from class Object

Constructor Detail

PlateSeries

PlateSeries

PlateSeries

PlateSeries

PlateSeries

Method Detail

clone

getDirectory

getSubPosition

getSortOrder

getSetChannels

getSetRows

getSetColumns

getNumberOfChannels

getNumberOfZslices

getNumberOfTimepoints

getListPlatePlanes

getPlatePlane

getNumberOfPlanes

removePlane

sort

toString

groupByPlateSeries