FeatureStackArray (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- trainableSegmentation.FeatureStackArray

```
public class FeatureStackArray
extends Object
```
This class stores the feature stacks of a set of input slices. It can be used so for 2D stacks or as the container of 3D features (by using a feature stack per section).

Author:

Ignacio Arganda-Carreras (iarganda@mit.edu)

Constructor Summary

Constructors
Constructor and Description
`FeatureStackArray(ij.ImagePlus inputImage, ij.ImagePlus filters)` Create a feature stack array based on specific filters
`FeatureStackArray(int num)` Initialize a feature stack list of a specific size (with default values for the rest of parameters).
`FeatureStackArray(int num, float minimumSigma, float maximumSigma, boolean useNeighbors, int membraneSize, int membranePatchSize, boolean[] enabledFeatures)` Initialize a feature stack list of a specific size

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`FeatureStack`	`get(int n)` Get n-th stack in the array (remember n>=0)
`boolean[]`	`getEnabledFeatures()` Get the features enabled for the reference stack
`int`	`getHeight()` Get the height of the feature stacks.
`String`	`getLabel(int index)` Get a specific label of the reference stack
`int`	`getNumOfFeatures()` Get the number of features of the reference stack (consistent all along the array)
`int`	`getReferenceSliceIndex()` Get the index of the reference slice in the feature stack array.
`int`	`getSize()` Get the number of feature stacks
`int`	`getWidth()` Get the width of the feature stacks.
`boolean`	`isEmpty()` Check if the array has not been yet initialized
`boolean`	`isOldColorFormat()` Check if the old color format is used.
`boolean`	`isOldoldHessianFormatFormat()` Check if the old Hessian format is used.
`boolean`	`isRGB()` Return if image stacks are RGB or grayscale.
`boolean`	`reorderFeatures(Instances data)` Reorder the features of each stack based on the order of attributes given by a set of instances.
`void`	`resetReference()` Reset the reference index (used when the are changes in the features)
`void`	`set(FeatureStack fs, int index)` Set a member of the list
`void`	`setEnabledFeatures(boolean[] newFeatures)` Set the features enabled for the reference stack
`void`	`setMaximumSigma(float sigma)` Set maximum sigma.
`void`	`setMembranePatchSize(int patchSize)` Set membrane patch size.
`void`	`setMembraneSize(int thickness)` Set expected membrane thickness
`void`	`setMinimumSigma(float sigma)` Set minimum sigma.
`void`	`setOldColorFormat(boolean oldColorFormat)` Set the use of the old color format.
`void`	`setOldHessianFormat(boolean oldHessianFormat)` Specify the use of the old (wrong) Hessian format (fixed in version 3.2.25 of TWS)
`void`	`setReference(int index)` Set the reference index (used when the are changes in the features).
`void`	`setUseNeighbors(boolean useNeighbors)` Set the use of neighbor features.
`void`	`shutDownNow()` Shut down the executor service
`Callable<Boolean>`	`updateFeatures(FeatureStack fs)` Update features of a feature stack (to be submitted to an Executor Service)
`boolean`	`updateFeaturesMT()` Update all feature stacks in the list (multi-thread fashion)
`boolean`	`updateFeaturesMT(boolean[] update)` Update specific feature stacks in the list (multi-thread fashion)
`boolean`	`useNeighborhood()` Check if neighbor features are used.

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

- Constructor Detail
  - FeatureStackArray
```
public FeatureStackArray(int num)
```
    Initialize a feature stack list of a specific size (with default values for the rest of parameters).
    
    Parameters:
    
    num - number of elements in the list
  - FeatureStackArray
```
public FeatureStackArray(int num,
                         float minimumSigma,
                         float maximumSigma,
                         boolean useNeighbors,
                         int membraneSize,
                         int membranePatchSize,
                         boolean[] enabledFeatures)
```
    Initialize a feature stack list of a specific size
    
    Parameters:
    
    num - number of elements in the list
    
    minimumSigma - minimum sigma value (usually filter radius)
    
    maximumSigma - maximum sigma value (usually filter radius)
    
    useNeighbors - flag to use neighbor features
    
    membraneSize - expected membrane thickness
    
    membranePatchSize - membrane patch size
    
    enabledFeatures - array of flags to enable features
  - FeatureStackArray
```
public FeatureStackArray(ij.ImagePlus inputImage,
                         ij.ImagePlus filters)
```
    Create a feature stack array based on specific filters
    
    Parameters:
    
    inputImage - original image
    
    filters - stack of filters to apply to the original image in order to create the features
- Method Detail
  - getSize
```
public int getSize()
```
    Get the number of feature stacks
    
    Returns:
    
    number of feature stacks stored in the array
  - get
```
public FeatureStack get(int n)
```
    Get n-th stack in the array (remember n>=0)
    
    Parameters:
    
    n - position of the stack to get
    
    Returns:
    
    feature stack of the corresponding slice
  - isRGB
```
public boolean isRGB()
```
    Return if image stacks are RGB or grayscale.
    
    Returns:
    
    true if image feature stacks are RGB, false if grayscale
  - set
```
public void set(FeatureStack fs,
                int index)
```
    Set a member of the list
    
    Parameters:
    
    fs - new feature stack
    
    index - index of the new feature stack in the array
  - updateFeaturesMT
```
public boolean updateFeaturesMT(boolean[] update)
```
    Update specific feature stacks in the list (multi-thread fashion)
    
    Parameters:
    
    update - boolean array indicating which feature stack to update
    
    Returns:
    
    false if any feature stack was not properly updated
  - updateFeaturesMT
```
public boolean updateFeaturesMT()
```
    Update all feature stacks in the list (multi-thread fashion)
    
    Returns:
    
    false if error, true otherwise
  - updateFeatures
```
public Callable<Boolean> updateFeatures(FeatureStack fs)
```
    Update features of a feature stack (to be submitted to an Executor Service)
    
    Parameters:
    
    fs - feature stack to be updated
    
    Returns:
    
    true if everything went correct
  - resetReference
```
public void resetReference()
```
    Reset the reference index (used when the are changes in the features)
  - setReference
```
public void setReference(int index)
```
    Set the reference index (used when the are changes in the features).
    
    Parameters:
    
    index - reference index
  - shutDownNow
```
public void shutDownNow()
```
    Shut down the executor service
  - isEmpty
```
public boolean isEmpty()
```
    Check if the array has not been yet initialized
    
    Returns:
    
    true if the array has been initialized
  - getNumOfFeatures
```
public int getNumOfFeatures()
```
    Get the number of features of the reference stack (consistent all along the array)
    
    Returns:
    
    number of features on each feature stack of the array
  - getLabel
```
public String getLabel(int index)
```
    Get a specific label of the reference stack
    
    Parameters:
    
    index - slice index (>=1)
    
    Returns:
    
    label name
  - getEnabledFeatures
```
public boolean[] getEnabledFeatures()
```
    Get the features enabled for the reference stack
    
    Returns:
    
    features to be calculated on each stack
  - setEnabledFeatures
```
public void setEnabledFeatures(boolean[] newFeatures)
```
    Set the features enabled for the reference stack
    
    Parameters:
    
    newFeatures - boolean flags for the features to use
  - setMembraneSize
```
public void setMembraneSize(int thickness)
```
    Set expected membrane thickness
    
    Parameters:
    
    thickness - expected membrane thickness in pixels
  - setMembranePatchSize
```
public void setMembranePatchSize(int patchSize)
```
    Set membrane patch size.
    
    Parameters:
    
    patchSize - membrange patch size in pixels
  - setMaximumSigma
```
public void setMaximumSigma(float sigma)
```
    Set maximum sigma.
    
    Parameters:
    
    sigma - maximum sigma
  - setMinimumSigma
```
public void setMinimumSigma(float sigma)
```
    Set minimum sigma.
    
    Parameters:
    
    sigma - minimum sigma
  - setUseNeighbors
```
public void setUseNeighbors(boolean useNeighbors)
```
    Set the use of neighbor features.
    
    Parameters:
    
    useNeighbors -
  - useNeighborhood
```
public boolean useNeighborhood()
```
    Check if neighbor features are used.
    
    Returns:
    
    true if neighbor features are used
  - getReferenceSliceIndex
```
public int getReferenceSliceIndex()
```
    Get the index of the reference slice in the feature stack array.
    
    Returns:
    
    index of the reference slice in the feature stack array
  - getWidth
```
public int getWidth()
```
    Get the width of the feature stacks.
    
    Returns:
    
    width of the feature stacks or -1 if not initialized yet.
  - getHeight
```
public int getHeight()
```
    Get the height of the feature stacks.
    
    Returns:
    
    height of the feature stacks or -1 if not initialized yet.
  - setOldColorFormat
```
public void setOldColorFormat(boolean oldColorFormat)
```
    Set the use of the old color format.
    
    Parameters:
    
    oldColorFormat - true if old color format is to be used
  - isOldColorFormat
```
public boolean isOldColorFormat()
```
    Check if the old color format is used.
    
    Returns:
    
    true if the old color format is used
  - setOldHessianFormat
```
public void setOldHessianFormat(boolean oldHessianFormat)
```
    Specify the use of the old (wrong) Hessian format (fixed in version 3.2.25 of TWS)
    
    Parameters:
    
    oldHessianFormat - true if old Hessian format is to be used
  - isOldoldHessianFormatFormat
```
public boolean isOldoldHessianFormatFormat()
```
    Check if the old Hessian format is used.
    
    Returns:
    
    true if the old Hessian format is used
  - reorderFeatures
```
public boolean reorderFeatures(Instances data)
```
    Reorder the features of each stack based on the order of attributes given by a set of instances.
    
    Parameters:
    
    data - set of instances to get the order from
    
    Returns:
    
    true if reordering was possible

Class FeatureStackArray

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FeatureStackArray

FeatureStackArray

FeatureStackArray

Method Detail

getSize

get

isRGB

set

updateFeaturesMT

updateFeaturesMT

updateFeatures

resetReference

setReference

shutDownNow

isEmpty

getNumOfFeatures

getLabel

getEnabledFeatures

setEnabledFeatures

setMembraneSize

setMembranePatchSize

setMaximumSigma

setMinimumSigma

setUseNeighbors

useNeighborhood

getReferenceSliceIndex

getWidth

getHeight

setOldColorFormat

isOldColorFormat

setOldHessianFormat

isOldoldHessianFormatFormat

reorderFeatures