java.lang.Object
- gov.nih.mipav.view.dialogs.AlgorithmParameters

Direct Known Subclasses:

DataProvenanceParameters
```
public class AlgorithmParameters
extends java.lang.Object
```
This class standardizes the parameter names given to many common parameters used in algorithms. It also provides helper methods to store/retrieve those common parameters.

See Also:

JDialogGaussianBlur

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`currentInputImageLabelNumber`	Counter used to track the number of input images stored (aka used) by an algorithm.
`static java.lang.String`	`DO_OUTPUT_NEW_IMAGE`	Label used for the parameter indicating whether an algorithm should output a new image.
`static java.lang.String`	`DO_PROCESS_3D_AS_25D`	Label used for the parameter indicating whether an algorithm should process a 3D image as a set of 2D slices instead of a 3D volume.
`static java.lang.String`	`DO_PROCESS_RGB`	Label used for the parameter indicating whether to process the each channel of an RGB image (ignored for grayscale images).
`static java.lang.String`	`DO_PROCESS_SEPARABLE`	Label used for the parameter indicating whether separable convolution kernels should be used in an algorithm.
`static java.lang.String`	`DO_PROCESS_WHOLE_IMAGE`	Label used for the parameter indicating whether the whole image should be processed (`true`), or just areas within VOIs (`false`).
`static java.lang.String`	`INPUT_IMAGE_LABEL_BASE`	The base of parameter labels used for an algorithm's input image(s).
`static java.lang.String`	`NUM_ITERATIONS`	Label used for the parameter indicating the number of iterations to perform in a script action.
`protected ParameterTable`	`params`	The list of parameters selected by the user in an algorithm's dialog, or the list of parameters to use to setup the dialog GUI.
`static java.lang.String`	`RESULT_IMAGE`	Label used in ActionDiscovery system for main result image of an algorithm.
`static java.lang.String`	`SIGMA_DO_Z_RES_CORRECTION`	Label used for the parameter indicating whether to correct the gaussian's standard deviation Z dimension using the ratio of the X and Z resolutions.
`static java.lang.String`	`SIGMAS`	Label used for the parameter indicating the unnormalized/uncorrected gaussian standard deviation to be used.
`static java.lang.String`	`USE_OPENCL`	Label used for boolean param indicating whether the algorithm should try to use OpenCL.

Constructor Summary

Constructors
Constructor	Description
`AlgorithmParameters()`	Creates a new AlgorithmParameters object to be used to record the current parameters entered into the algorithm's GUI by the user.
`AlgorithmParameters(ParameterTable parsedParams)`	Creates a new AlgorithmParameters object to be used to set up the algorithm's GUI from stored parameters.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`doOutputNewImage()`	DOCUMENT ME!
`boolean`	`doProcess3DAs25D()`	DOCUMENT ME!
`boolean[]`	`doProcessRGB()`	DOCUMENT ME!
`boolean`	`doProcessSeparable()`	DOCUMENT ME!
`boolean`	`doProcessWholeImage()`	DOCUMENT ME!
`boolean`	`doSigmaResolutionCorrection()`	DOCUMENT ME!
`static java.lang.String`	`getInputImageLabel(int inputImageNumber)`	Returns the label which should be used for an input image parameter.
`int`	`getNumIterations()`	DOCUMENT ME!
`ParameterTable`	`getParams()`	Retrieves the list of parameters to either be used to run the script or store settings for future executions of the algorithm in a script.
`float[]`	`getUnnormalizedSigmas()`	DOCUMENT ME!
`protected static boolean`	`isImageStoredInRecorder(ModelImage image)`	Returns whether an image has been registered in the script recorder.
`ModelImage`	`retrieveImage(java.lang.String imageParamLabel)`	Returns an image with a particular parameter name.
`ModelImage`	`retrieveInputImage()`	Returns the first input image for the algorithm.
`ModelImage`	`retrieveInputImage(int inputImageNumber)`	Returns one of the algorithm's input images.
`void`	`setColorOptionsGUI(JPanelColorChannels colorChannelPanel)`	Sets the color channel GUI panel, based on the script action's parameters.
`void`	`setOutputOptionsGUI(JPanelAlgorithmOutputOptions outputOptionsPanel)`	Sets up the algorithm output options panel components (whole image vs.
`void`	`setSigmasGUI(JPanelSigmas sigmaPanel)`	Sets up the GUI containing the sigmas used in an algorithm (usually Gaussian sigmas), based on the script action's parameters.
`void`	`storeColorOptions(boolean processRed, boolean processGreen, boolean processBlue)`	Stores the values of color channel processing options in the parameter table.
`void`	`storeColorOptions(JPanelColorChannels colorChannelPanel)`	Stores the values from the color channel panel in the parameter table.
`java.lang.String`	`storeImage(ModelImage image, java.lang.String paramLabel)`	Stores an input image in the list of parameters for the algorithm.
`java.lang.String`	`storeImageInRecorder(ModelImage image)`	Store an image in the script recorder image variable table.
`static java.lang.String`	`storeImageInRunner(ModelImage image)`	Store an image in the script runner image variable table.
`java.lang.String`	`storeInputImage(ModelImage inputImage)`	Stores an input image in the list of parameters for the algorithm.
`void`	`storeNumIterations(int numIters)`	DOCUMENT ME!
`java.lang.String`	`storeOutputImageParams(ModelImage outputImage, boolean isNewImage)`	Stores information about the output of images for this algorithm in the parameter table.
`void`	`storeProcess3DAs25D(boolean doProcess3DAs25D)`
`void`	`storeProcessingOptions(boolean doWholeImage, boolean do25D)`	Stores options for how an algorithm should process images in the parameter table.
`void`	`storeProcessSeparable(boolean doProcessSep)`	Stores options for an algorithm using a kernel that can process dimensions separately.
`void`	`storeProcessWholeImage(boolean doWholeImage)`	Stores whether the whole image or just VOI regions should be processed in the parameter table.
`void`	`storeSigmas(float[] sigmas, boolean isZCorrectionEnabled)`	Stores an algorithm's sigmas in the parameter table.
`void`	`storeSigmas(JPanelSigmas sigmaPanel)`	Stores an algorithm's sigmas in the parameter table.
`void`	`storeWaterShed(float[] sigmas, boolean isZCorrectionEnabled)`	Stores an algorithm's sigmas in the parameter table.
`void`	`tryToStoreResultImageInRunner(ModelImage resultImage)`	DOCUMENT ME!

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

- Field Detail
  - INPUT_IMAGE_LABEL_BASE
```
public static final java.lang.String INPUT_IMAGE_LABEL_BASE
```
    The base of parameter labels used for an algorithm's input image(s). Append a '_1' to get the first image, for example.
    
    See Also:
    
    getInputImageLabel(int), Constant Field Values
  - DO_OUTPUT_NEW_IMAGE
```
public static final java.lang.String DO_OUTPUT_NEW_IMAGE
```
    Label used for the parameter indicating whether an algorithm should output a new image.
    
    See Also:
    
    Constant Field Values
  - DO_PROCESS_WHOLE_IMAGE
```
public static final java.lang.String DO_PROCESS_WHOLE_IMAGE
```
    Label used for the parameter indicating whether the whole image should be processed (true), or just areas within VOIs (false).
    
    See Also:
    
    Constant Field Values
  - DO_PROCESS_SEPARABLE
```
public static final java.lang.String DO_PROCESS_SEPARABLE
```
    Label used for the parameter indicating whether separable convolution kernels should be used in an algorithm.
    
    See Also:
    
    Constant Field Values
  - DO_PROCESS_3D_AS_25D
```
public static final java.lang.String DO_PROCESS_3D_AS_25D
```
    Label used for the parameter indicating whether an algorithm should process a 3D image as a set of 2D slices instead of a 3D volume.
    
    See Also:
    
    Constant Field Values
  - SIGMAS
```
public static final java.lang.String SIGMAS
```
    Label used for the parameter indicating the unnormalized/uncorrected gaussian standard deviation to be used.
    
    See Also:
    
    Constant Field Values
  - SIGMA_DO_Z_RES_CORRECTION
```
public static final java.lang.String SIGMA_DO_Z_RES_CORRECTION
```
    Label used for the parameter indicating whether to correct the gaussian's standard deviation Z dimension using the ratio of the X and Z resolutions.
    
    See Also:
    
    Constant Field Values
  - DO_PROCESS_RGB
```
public static final java.lang.String DO_PROCESS_RGB
```
    Label used for the parameter indicating whether to process the each channel of an RGB image (ignored for grayscale images).
    
    See Also:
    
    Constant Field Values
  - NUM_ITERATIONS
```
public static final java.lang.String NUM_ITERATIONS
```
    Label used for the parameter indicating the number of iterations to perform in a script action.
    
    See Also:
    
    Constant Field Values
  - RESULT_IMAGE
```
public static final java.lang.String RESULT_IMAGE
```
    Label used in ActionDiscovery system for main result image of an algorithm.
    
    See Also:
    
    Constant Field Values
  - USE_OPENCL
```
public static final java.lang.String USE_OPENCL
```
    Label used for boolean param indicating whether the algorithm should try to use OpenCL.
    
    See Also:
    
    Constant Field Values
  - currentInputImageLabelNumber
```
protected int currentInputImageLabelNumber
```
    Counter used to track the number of input images stored (aka used) by an algorithm. This is only used while recording parameters from an algorithm's GUI.
  - params
```
protected ParameterTable params
```
    The list of parameters selected by the user in an algorithm's dialog, or the list of parameters to use to setup the dialog GUI. This depends on whether this object is being used to store parameters or to make use of previously stored parameters.
- Constructor Detail
  - AlgorithmParameters
```
public AlgorithmParameters()
```
    Creates a new AlgorithmParameters object to be used to record the current parameters entered into the algorithm's GUI by the user.
  - AlgorithmParameters
```
public AlgorithmParameters(ParameterTable parsedParams)
```
    Creates a new AlgorithmParameters object to be used to set up the algorithm's GUI from stored parameters.
    
    Parameters:
    
    parsedParams - stored parameters which should be used to set up the algorithm's variables/GUI.
- Method Detail
  - getInputImageLabel
```
public static java.lang.String getInputImageLabel(int inputImageNumber)
```
    Returns the label which should be used for an input image parameter.
    
    Parameters:
    
    inputImageNumber - Number indicating which input image this is.
    
    Returns:
    
    The label/name which should be used for this input image in the parameter table.
  - storeImageInRecorder
```
public java.lang.String storeImageInRecorder(ModelImage image)
```
    Store an image in the script recorder image variable table. Used to store input/output images while recording a script. Should not be used while running a script.
    
    Parameters:
    
    image - The image to store in the variable table.
    
    Returns:
    
    The image placeholder variable assigned to the image by the variable table.
  - storeImageInRunner
```
public static java.lang.String storeImageInRunner(ModelImage image)
```
    Store an image in the script runner image variable table. Used to store input/output images while running a script. Should not be used while recording a script.
    
    Parameters:
    
    image - The image to store in the variable table.
    
    Returns:
    
    The image placeholder variable assigned to the image by the variable table.
  - doOutputNewImage
```
public boolean doOutputNewImage()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - doProcess3DAs25D
```
public boolean doProcess3DAs25D()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - doProcessRGB
```
public boolean[] doProcessRGB()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - doProcessSeparable
```
public boolean doProcessSeparable()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - doProcessWholeImage
```
public boolean doProcessWholeImage()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - doSigmaResolutionCorrection
```
public boolean doSigmaResolutionCorrection()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getNumIterations
```
public int getNumIterations()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getParams
```
public ParameterTable getParams()
```
    Retrieves the list of parameters to either be used to run the script or store settings for future executions of the algorithm in a script.
    
    Returns:
    
    The table of parameters for this algorithm.
  - getUnnormalizedSigmas
```
public float[] getUnnormalizedSigmas()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - retrieveImage
```
public ModelImage retrieveImage(java.lang.String imageParamLabel)
```
    Returns an image with a particular parameter name.
    
    Parameters:
    
    imageParamLabel - The parameter label of the image to retrieve.
    
    Returns:
    
    The requested image.
  - retrieveInputImage
```
public ModelImage retrieveInputImage()
```
    Returns the first input image for the algorithm.
    
    Returns:
    
    The first input image.
    
    See Also:
    
    getInputImageLabel(int)
  - retrieveInputImage
```
public ModelImage retrieveInputImage(int inputImageNumber)
```
    Returns one of the algorithm's input images.
    
    Parameters:
    
    inputImageNumber - A number indicating which input image should be retrieved.
    
    Returns:
    
    The inputImageNumber-th input image.
  - setColorOptionsGUI
```
public void setColorOptionsGUI(JPanelColorChannels colorChannelPanel)
```
    Sets the color channel GUI panel, based on the script action's parameters. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    colorChannelPanel - The color channel panel to set the values of.
  - setOutputOptionsGUI
```
public void setOutputOptionsGUI(JPanelAlgorithmOutputOptions outputOptionsPanel)
```
    Sets up the algorithm output options panel components (whole image vs. VOI and new image vs. replace), based on the script action's parameters. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    outputOptionsPanel - The algorithm output options panel to set the values of.
  - setSigmasGUI
```
public void setSigmasGUI(JPanelSigmas sigmaPanel)
```
    Sets up the GUI containing the sigmas used in an algorithm (usually Gaussian sigmas), based on the script action's parameters. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    sigmaPanel - The sigmas panel to set up based on the parameters.
  - storeColorOptions
```
public void storeColorOptions(JPanelColorChannels colorChannelPanel)
                       throws ParserException
```
    Stores the values from the color channel panel in the parameter table. This function is used when recording a script. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    colorChannelPanel - The color channel panel to extract the options from.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeColorOptions
```
public void storeColorOptions(boolean processRed,
                              boolean processGreen,
                              boolean processBlue)
                       throws ParserException
```
    Stores the values of color channel processing options in the parameter table. This function is used when recording a script. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    processRed - Whether the red channel of a color image should be processed.
    
    processGreen - Whether the green channel of a color image should be processed.
    
    processBlue - Whether the blue channel of a color image should be processed.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeImage
```
public java.lang.String storeImage(ModelImage image,
                                   java.lang.String paramLabel)
                            throws ParserException
```
    Stores an input image in the list of parameters for the algorithm.
    
    Parameters:
    
    image - The image to store.
    
    paramLabel - The label to give to the new image parameter.
    
    Returns:
    
    The image placeholder variable assigned to the image by the variable table.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeInputImage
```
public java.lang.String storeInputImage(ModelImage inputImage)
                                 throws ParserException
```
    Stores an input image in the list of parameters for the algorithm. This image is stored with a new parameter label incremented with each new call to this method.
    
    Parameters:
    
    inputImage - The input image to store.
    
    Returns:
    
    The image placeholder variable assigned to the image by the variable table.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeNumIterations
```
public void storeNumIterations(int numIters)
                        throws ParserException
```
    DOCUMENT ME!
    
    Parameters:
    
    numIters - DOCUMENT ME!
    
    Throws:
    
    ParserException - DOCUMENT ME!
  - storeOutputImageParams
```
public java.lang.String storeOutputImageParams(ModelImage outputImage,
                                               boolean isNewImage)
                                        throws ParserException
```
    Stores information about the output of images for this algorithm in the parameter table. It first stores whether a new output image should be generated by the algorithm, and then (if a new image should be generated) stores the new output image in the variable table.
    
    Parameters:
    
    outputImage - The result image generated by the algorithm (may be null if isNewImage is false.
    
    isNewImage - Whether the algorithm should output a new image when it is executed.
    
    Returns:
    
    The new image placeholder variable assigned to the result image (or null if no output image should be generated).
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeProcess3DAs25D
```
public void storeProcess3DAs25D(boolean doProcess3DAs25D)
                         throws ParserException
```
    Parameters:
    
    doProcess3DAs25D - Whether to process 3D images in 2.5D mode (slice by slice).
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
    
    See Also:
    
    storeProcessingOptions(boolean,boolean)
  - storeProcessingOptions
```
public void storeProcessingOptions(boolean doWholeImage,
                                   boolean do25D)
                            throws ParserException
```
    Stores options for how an algorithm should process images in the parameter table. This function is used when recording a script. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    doWholeImage - Whether to process the whole image or just VOI regions.
    
    do25D - Whether to process 3D images in 2.5D mode (slice by slice).
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeProcessSeparable
```
public void storeProcessSeparable(boolean doProcessSep)
                           throws ParserException
```
    Stores options for an algorithm using a kernel that can process dimensions separately.
    
    Parameters:
    
    doProcessSep - Whether to use a separable filter kernel.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeProcessWholeImage
```
public void storeProcessWholeImage(boolean doWholeImage)
                            throws ParserException
```
    Stores whether the whole image or just VOI regions should be processed in the parameter table. This function is used when recording a script. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    doWholeImage - Whether to process the whole image or just VOI regions.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameter.
    
    See Also:
    
    storeProcessingOptions(boolean,boolean)
  - storeSigmas
```
public void storeSigmas(JPanelSigmas sigmaPanel)
                 throws ParserException
```
    Stores an algorithm's sigmas in the parameter table. This function is used when recording a script. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    sigmaPanel - The sigma GUI panel to extract the parameters from.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeSigmas
```
public void storeSigmas(float[] sigmas,
                        boolean isZCorrectionEnabled)
                 throws ParserException
```
    Stores an algorithm's sigmas in the parameter table. This function is used when recording a script. This is a helper function used to handle parameters common to many algorithms.
    
    Parameters:
    
    sigmas - The unnormalized sigmas (must be a 3D array).
    
    isZCorrectionEnabled - Whether adjustment of the Z sigma should be performed based on the ratio of x resolution to z resolution.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - storeWaterShed
```
public void storeWaterShed(float[] sigmas,
                           boolean isZCorrectionEnabled)
                    throws ParserException
```
    Stores an algorithm's sigmas in the parameter table. This function is used when recording a script. This is a for the WaterShed algorithm.
    
    Parameters:
    
    sigmas - The unnormalized sigmas (must be a 3D array).
    
    isZCorrectionEnabled - Whether adjustment of the Z sigma should be performed based on the ratio of x resolution to z resolution.
    
    Throws:
    
    ParserException - If there is a problem creating one of the new parameters.
  - tryToStoreResultImageInRunner
```
public void tryToStoreResultImageInRunner(ModelImage resultImage)
                                   throws ParserException
```
    DOCUMENT ME!
    
    Parameters:
    
    resultImage - DOCUMENT ME!
    
    Throws:
    
    ParserException - DOCUMENT ME!
  - isImageStoredInRecorder
```
protected static boolean isImageStoredInRecorder(ModelImage image)
```
    Returns whether an image has been registered in the script recorder. If it has not been used, it must be specified externally when this script is run later.
    
    Parameters:
    
    image - The image to look for in the recorder's image table.
    
    Returns:
    
    True if the image has been stored in the recorder's image table, false otherwise.

Class AlgorithmParameters

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

INPUT_IMAGE_LABEL_BASE

DO_OUTPUT_NEW_IMAGE

DO_PROCESS_WHOLE_IMAGE

DO_PROCESS_SEPARABLE

DO_PROCESS_3D_AS_25D

SIGMAS

SIGMA_DO_Z_RES_CORRECTION

DO_PROCESS_RGB

NUM_ITERATIONS

RESULT_IMAGE

USE_OPENCL

currentInputImageLabelNumber

params

Constructor Detail

AlgorithmParameters

AlgorithmParameters

Method Detail

getInputImageLabel

storeImageInRecorder

storeImageInRunner

doOutputNewImage

doProcess3DAs25D

doProcessRGB

doProcessSeparable

doProcessWholeImage

doSigmaResolutionCorrection

getNumIterations

getParams

getUnnormalizedSigmas

retrieveImage

retrieveInputImage

retrieveInputImage

setColorOptionsGUI

setOutputOptionsGUI

setSigmasGUI

storeColorOptions

storeColorOptions

storeImage

storeInputImage

storeNumIterations

storeOutputImageParams

storeProcess3DAs25D

storeProcessingOptions

storeProcessSeparable

storeProcessWholeImage

storeSigmas

storeSigmas

storeWaterShed

tryToStoreResultImageInRunner

isImageStoredInRecorder