CurveCollection (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.slim.fit.CurveCollection

All Implemented Interfaces:

CurveReporter
```
public class CurveCollection
extends Object
implements CurveReporter
```
Data structure for managing a collection of curves. The main purpose of this structure is to create subsampled curve sets at a resolution for each order of magnitude—e.g., for a 256 x 256 image, the collection constructs 128 x 128, 64 x 64, 32 x 32, 16 x 16, 8 x 8, 4 x 4, 2 x 2 and 1 x 1 subsampled images—by summing neighboring curves.

Author:

Curtis Rueden

Field Summary

Fields
Modifier and Type	Field and Description
`protected Vector`	`curveListeners`
`protected ICurveFitter[][][]`	`curves` Curve fit data, dimensioned [maxDepth][numRows][numCols].
`protected int`	`depth` Total number of samplings, counting full-resolution image.
`protected int`	`numCols` Full image resolution.
`protected int`	`numRows` Full image resolution.

Constructor Summary

Constructors
Constructor and Description
`CurveCollection(ICurveFitter[][] curveFitters)` Creates an object to manage the given collection of curves.
`CurveCollection(int[][][] data, Class curveFitterClass, int binRadius, int firstIndex, int lastIndex)` Creates an object to manage a collection of curves for the given data.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCurveListener(CurveListener l)`
`void`	`computeCurves()` Computes subsamplings.
`void`	`fireCurveEvent(CurveEvent e)`
`ICurveFitter[][]`	`getCurves()` Gets the collection of curves at full resolution.
`ICurveFitter[][]`	`getCurves(int depth)` Gets the collection of curves subsampled at the given depth.
`boolean[][]`	`getFixed()` Gets which parameters should be fixed, versus allowed to converge.
`int`	`getNumCols()` Gets the full X resolution.
`int`	`getNumRows()` Gets the full Y resolution.
`int`	`getSubsamplingDepth()` Gets the maximum subsampling depth of the curve collection.
`static ICurveFitter[][]`	`makeCurveFitters(int[][][] data, Class curveFitterClass, int binRadius, int firstIndex, int lastIndex)` Creates a list of curve fitters using the given data as a source.
`static ICurveFitter`	`newCurveFitter(Class c)`
`void`	`removeCurveListener(CurveListener l)`
`void`	`setComponentCount(int numExp)` Sets how many exponentials are expected to be fitted.
`void`	`setFixed(boolean[][] fixed)` Sets which parameters should be fixed, versus allowed to converge.

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

- Field Detail
  - numRows
```
protected int numRows
```
    Full image resolution.
  - numCols
```
protected int numCols
```
    Full image resolution.
  - depth
```
protected int depth
```
    Total number of samplings, counting full-resolution image.
  - curves
```
protected ICurveFitter[][][] curves
```
    Curve fit data, dimensioned [maxDepth][numRows][numCols].
  - curveListeners
```
protected Vector curveListeners
```
- Constructor Detail
  - CurveCollection
```
public CurveCollection(int[][][] data,
                       Class curveFitterClass,
                       int binRadius,
                       int firstIndex,
                       int lastIndex)
```
    Creates an object to manage a collection of curves for the given data.
    
    Parameters:
    
    data - Data array dimensioned [numRows][numCols][timeBins].
    
    curveFitterClass - Class representing the type of curve fitters to use (e.g., loci.slim.fit.GACurveFitter or loci.slim.fit.LMCurveFitter).
    
    binRadius - Radius of neighboring pixels to bin, to improve signal-to-noise ratio.
  - CurveCollection
```
public CurveCollection(ICurveFitter[][] curveFitters)
```
    Creates an object to manage the given collection of curves.
    
    Parameters:
    
    curveFitters - Array of curve fitters dimensioned [numRows][numCols].
- Method Detail
  - computeCurves
```
public void computeCurves()
```
    Computes subsamplings.
  - getNumRows
```
public int getNumRows()
```
    Gets the full Y resolution.
  - getNumCols
```
public int getNumCols()
```
    Gets the full X resolution.
  - getCurves
```
public ICurveFitter[][] getCurves()
```
    Gets the collection of curves at full resolution.
  - getCurves
```
public ICurveFitter[][] getCurves(int depth)
```
    Gets the collection of curves subsampled at the given depth. For example, for a 256 x 256 image, getCurves(2) returns a 64 x 64 subsampling.
    
    Throws:
    
    IllegalArgumentException - if the subsampling depth is greater than getSubsamplingDepth()
  - getSubsamplingDepth
```
public int getSubsamplingDepth()
```
    Gets the maximum subsampling depth of the curve collection. For example, for a 250 x 200 image, the depth is 8 because there exist samplings at 250 x 200, 125 x 100, 62 x 50, 31 x 25, 15 x 12, 7 x 6, 3 x 3 and 1 x 1.
  - setComponentCount
```
public void setComponentCount(int numExp)
```
    Sets how many exponentials are expected to be fitted. Currently, more than 2 is not supported.
  - setFixed
```
public void setFixed(boolean[][] fixed)
```
    Sets which parameters should be fixed, versus allowed to converge.
  - getFixed
```
public boolean[][] getFixed()
```
    Gets which parameters should be fixed, versus allowed to converge.
  - addCurveListener
```
public void addCurveListener(CurveListener l)
```
    Specified by:
    
    addCurveListener in interface CurveReporter
  - removeCurveListener
```
public void removeCurveListener(CurveListener l)
```
    Specified by:
    
    removeCurveListener in interface CurveReporter
  - fireCurveEvent
```
public void fireCurveEvent(CurveEvent e)
```
    Specified by:
    
    fireCurveEvent in interface CurveReporter
  - makeCurveFitters
```
public static ICurveFitter[][] makeCurveFitters(int[][][] data,
                                                Class curveFitterClass,
                                                int binRadius,
                                                int firstIndex,
                                                int lastIndex)
```
    Creates a list of curve fitters using the given data as a source.
  - newCurveFitter
```
public static ICurveFitter newCurveFitter(Class c)
```

Class CurveCollection

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

numRows

numCols

depth

curves

curveListeners

Constructor Detail

CurveCollection

CurveCollection

Method Detail

computeCurves

getNumRows

getNumCols

getCurves

getCurves

getSubsamplingDepth

setComponentCount

setFixed

getFixed

addCurveListener

removeCurveListener

fireCurveEvent

makeCurveFitters

newCurveFitter