Package adams.data.filter

Class RemoveNoise<T extends DataContainer & Mergeable>

  • Type Parameters:
    T - the data to process
    All Implemented Interfaces:
    CleanUpHandler, Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, ShallowCopySupporter<Filter>, SizeOfHandler, Filter<T>, Serializable, Comparable
    public class RemoveNoise<T extends DataContainer & Mergeable>
extends AbstractFilter<T>
    A filter that removes noise from the data with a user-supplied noise level algorithm.

    Valid options are: 

    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -denoiser <gcms.data.noise.AbstractDenoiser [options]> (property: denoiser)
         The denoiser algorithm to use for removing the noise from the data.
         default: gcms.data.noise.MedianHeightDifference -factor-sd 2.0 -thr2 -1.0 -savitzky "gcms.data.filter.SavitzkyGolay -polynomial 2 -derivative 0 -left 3 -right 3 -optimize 15" -derivative "gcms.data.filter.Derivative -order 2 -scaling -1.0"
 
    -invert (property: invert)
         If set to true, non-noise will be removed instead of noise.
    Default options for gcms.data.noise.MedianHeightDifference (-denoiser/denoiser): 
    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -zero (property: zeroNoise)
         If set to true, the abundances of noisy points will be set to zero instead
          of being completely removed from the data.
 
    -factor-sd <double> (property: thresholdSdFactor)
         The factor to multiply the height median (thr_sd) with in order to obtain
          the threshold below signals are considered being noise.
         default: 2
 
    -thr2 <double> (property: threshold2)
         A user-supplied threshold (= thr_2) that is applied to the abundances of
          the original input data, use -1 to disable.
         default: -1.0
 
    -savitzky <gcms.data.filter.AbstractFilter [options]> (property: savitzkyGolay)
         The Savitzky-Golay filter setup to use in smoothing the data beforehand.
         default: gcms.data.filter.SavitzkyGolay -polynomial 2 -derivative 0 -left 3 -right 3 -optimize 15
 
    -derivative <gcms.data.filter.AbstractFilter [options]> (property: derivative)
         The Derivative filter to use (always uses 2nd derivative).
         default: gcms.data.filter.Derivative -order 2 -scaling -1.0
 
    -regions (property: recordRegions)
         If set to true, the elution regions will be recorded as well.
 
    Default options for gcms.data.filter.SavitzkyGolay (-savitzky/savitzkyGolay):
 
    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -polynomial <int> (property: polynomialOrder)
         The polynomial order to use, must be at least 2.
         default: 2
 
    -derivative <int> (property: derivativeOrder)
         The order of the derivative to use, >= 0.
         default: 1
 
    -left <int> (property: numPointsLeft)
         The number of points left of a data point, >= 0.
         default: 3
 
    -right <int> (property: numPointsRight)
         The number of points right of a data point, >= 0.
         default: 3
 
    -optimize <int> (property: optimizeWindowSize)
         The maximum window size to optimize (odd, positive number); uses the Durbin-Watson
          statistic to determine the best window size, ie, number of points left
         and right of the points being smoothed; the data must be oscillating around
          zero, ie, passed through the Derivative filter.
         default: -1
 
    

 
    Default options for gcms.data.filter.Derivative (-derivative/derivative):
 
    

 
    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    

 
    -order <int> (property: order)
         The order of the derivative to calculate.
         default: 1
 
    

 
    -scaling <double> (property: scalingRange)
         The range to scale the abundances to after each derivation step; use 0 to
          turn off and -1 to set it to the input range.
         default: 0.0
 
    
 
    

    

    Version:
    

    $Revision$
    

    Author:
    

    fracpete (fracpete at waikato dot ac dot nz)
    

    See Also:
    

    Serialized Form
    

    

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        m_Invert
        

        protected boolean m_Invert
        

        indicates whether to invert behavior, i.e., to remove non-noise instead
 of noise.
        

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      Constructor Detail
      




        

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        RemoveNoise
        

        public RemoveNoise()
        

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      Method Detail
      












        

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        setDenoiser
        

        public void setDenoiser​(AbstractDenoiser value)
        

        Sets the denoiser algorithm.
        

        

        Parameters:
        

        value - the algorithm
        

        

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        getDenoiser
        

        public AbstractDenoiser getDenoiser()
        

        Returns the current denoiser algorithm.
        

        

        Returns:
        

        the algorithm
        

        

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        denoiserTipText
        

        public String denoiserTipText()
        

        Returns the tip text for this property.
        

        

        Returns:
        

        tip text for this property suitable for
                        displaying in the GUI or for listing the options.
        

        

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        setInvert
        

        public void setInvert​(boolean value)
        

        Sets whether the behavior should be inverted, i.e., removing non-noise.
        

        

        Parameters:
        

        value - true if non-noise should be removed
        

        

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        getInvert
        

        public boolean getInvert()
        

        Returns whether non-noise is removed (= true) or the actual noise.
        

        

        Returns:
        

        true if non-noise is removed
        

        

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        invertTipText
        

        public String invertTipText()
        

        Returns the tip text for this property.
        

        

        Returns:
        

        tip text for this property suitable for
                        displaying in the GUI or for listing the options.
        

        

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