Example usage for org.apache.commons.math3.analysis.function Abs Abs

Introduction

In this page you can find the example usage for org.apache.commons.math3.analysis.function Abs Abs.

Prototype

Abs

Source Link

Usage

From source file:edu.stanford.cfuller.colocalization3d.correction.PositionCorrector.java

/**
* Applies an existing correction to the positions of a set of objects, using a specified reference
* and correction channel.//from w ww.j ava 2 s. c  om
* 
* @param imageObjects                  A Vector containing all the ImageObjects to be corrected.
* @param c                             The Correction object to be used, which could have been generated with determineCorrection, or loaded from disk.
* @return                              A RealVector with one entry per ImageObject, containing the corrected scalar distance between the object in the reference channel and the channel being corrected.
*/
public RealVector applyCorrection(Correction c, java.util.List<ImageObject> imageObjects) {

    int referenceChannel = this.parameters.getIntValueForKey(REF_CH_PARAM);

    int channelToCorrect = this.parameters.getIntValueForKey(CORR_CH_PARAM);

    RealVector diffs = new ArrayRealVector(imageObjects.size(), 0.0);
    RealVector averageVectorDiffs = null;

    for (int i = 0; i < imageObjects.size(); i++) {

        diffs.setEntry(i, imageObjects.get(i).getScalarDifferenceBetweenChannels(referenceChannel,
                channelToCorrect, this.pixelToDistanceConversions));

        if (i == 0) {
            averageVectorDiffs = imageObjects.get(i)
                    .getVectorDifferenceBetweenChannels(referenceChannel, channelToCorrect).copy();

        } else {
            averageVectorDiffs = averageVectorDiffs.add(imageObjects.get(i)
                    .getVectorDifferenceBetweenChannels(referenceChannel, channelToCorrect).map(new Abs()));
        }

    }

    averageVectorDiffs.mapDivideToSelf(imageObjects.size());
    averageVectorDiffs = averageVectorDiffs.ebeMultiply(this.pixelToDistanceConversions);

    java.util.logging.Logger.getLogger("edu.stanford.cfuller.colocalization3d")
            .info("mean separation uncorrected = " + diffs.getL1Norm() / diffs.getDimension());
    java.util.logging.Logger.getLogger("edu.stanford.cfuller.colocalization3d")
            .info("mean separation components uncorrected = " + averageVectorDiffs.toString());

    RealVector newDiffs = new ArrayRealVector(imageObjects.size(), 0.0);

    if (this.parameters.getBooleanValueForKey("correct_images")) {

        for (int i = 0; i < imageObjects.size(); i++) {

            try {

                newDiffs.setEntry(i, this.correctSingleObjectVectorDifference(c, imageObjects.get(i),
                        referenceChannel, channelToCorrect).getNorm());

                imageObjects.get(i).setCorrectionSuccessful(true);

            } catch (UnableToCorrectException e) {

                newDiffs.setEntry(i, -1.0 * Double.MAX_VALUE);

                imageObjects.get(i).setCorrectionSuccessful(false);

            }

        }

        java.util.logging.Logger.getLogger("edu.stanford.cfuller.colocalization3d")
                .info("mean separation corrected = " + newDiffs.getL1Norm() / newDiffs.getDimension());

    } else {
        newDiffs = diffs;
    }

    return newDiffs;
}

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