Package gov.nih.mipav.view.dialogs

Class AlgorithmParameters

java.lang.Object
gov.nih.mipav.view.dialogs.AlgorithmParameters
Direct Known Subclasses:
DataProvenanceParameters
public class AlgorithmParameters extends 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:

  • Field Details

    • INPUT_IMAGE_LABEL_BASE

      public static final 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.
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    • DO_OUTPUT_NEW_IMAGE

      public static final String DO_OUTPUT_NEW_IMAGE
      Label used for the parameter indicating whether an algorithm should output a new image.
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    • DO_PROCESS_WHOLE_IMAGE

      public static final 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).
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    • DO_PROCESS_SEPARABLE

      public static final String DO_PROCESS_SEPARABLE
      Label used for the parameter indicating whether separable convolution kernels should be used in an algorithm.
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    • DO_PROCESS_3D_AS_25D

      public static final 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.
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    • SIGMAS

      public static final String SIGMAS
      Label used for the parameter indicating the unnormalized/uncorrected gaussian standard deviation to be used.
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    • SIGMA_DO_Z_RES_CORRECTION

      public static final 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.
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    • DO_PROCESS_RGB

      public static final String DO_PROCESS_RGB
      Label used for the parameter indicating whether to process the each channel of an RGB image (ignored for grayscale images).
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    • NUM_ITERATIONS

      public static final String NUM_ITERATIONS
      Label used for the parameter indicating the number of iterations to perform in a script action.
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    • RESULT_IMAGE

      public static final String RESULT_IMAGE
      Label used in ActionDiscovery system for main result image of an algorithm.
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    • USE_OPENCL

      public static final String USE_OPENCL
      Label used for boolean param indicating whether the algorithm should try to use OpenCL.
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    • 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 Details

    • 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 Details

    • getInputImageLabel

      public static 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 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 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()
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      Returns:
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    • doProcess3DAs25D

      public boolean doProcess3DAs25D()
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      Returns:
      DOCUMENT ME!

    • doProcessRGB

      public boolean[] doProcessRGB()
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      Returns:
      DOCUMENT ME!

    • doProcessSeparable

      public boolean doProcessSeparable()
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      Returns:
      DOCUMENT ME!

    • doProcessWholeImage

      public boolean doProcessWholeImage()
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      Returns:
      DOCUMENT ME!

    • doSigmaResolutionCorrection

      public boolean doSigmaResolutionCorrection()
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      Returns:
      DOCUMENT ME!

    • getNumIterations

      public int getNumIterations()
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      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()
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      Returns:
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    • retrieveImage

      public ModelImage retrieveImage(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.
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    • 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 String storeImage(ModelImage image, 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 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
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      Parameters:
      numIters - DOCUMENT ME!
      Throws:
      ParserException - DOCUMENT ME!

    • storeOutputImageParams

      public 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.
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    • 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.
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    • 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
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      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.