Examples with Pair org.apache.commons.math3.util.Pair used on opensource projects

Example 16 with Pair

use of org.apache.commons.math3.util.Pair in project Remindy by abicelis.

the class UnprogrammedTaskViewHolder method onClick.

@Override
public void onClick(View view) {
    int id = view.getId();
    switch(id) {
        case R.id.item_task_unprogrammed_container:
            Pair[] pairs = new Pair[1];
            pairs[0] = new Pair<View, String>(mCategoryIcon, mFragment.getResources().getString(R.string.transition_task_list_category));
            //pairs[1] = new Pair<View, String>(mTitle, mFragment.getResources().getString(R.string.transition_task_list_title));
            //pairs[2] = new Pair<View, String>(mDescription, mFragment.getResources().getString(R.string.transition_task_list_description));
            ActivityOptionsCompat options = ActivityOptionsCompat.makeSceneTransitionAnimation(mFragment.getActivity(), pairs);
            Intent openTaskDetailActivity = new Intent(mFragment.getActivity(), TaskDetailActivity.class);
            openTaskDetailActivity.putExtra(TaskDetailActivity.TASK_ID_TO_DISPLAY, mCurrent.getId());
            openTaskDetailActivity.putExtra(TaskDetailActivity.TASK_POSITION, mReminderPosition);
            if (mClickListener != null) {
                mClickListener.onItemClicked(mReminderPosition, openTaskDetailActivity, options.toBundle());
            }
            break;
    }
}

Example 17 with Pair

use of org.apache.commons.math3.util.Pair in project Remindy by abicelis.

the class ProgrammedOneTimeTaskViewHolder method onClick.

@Override
public void onClick(View view) {
    int id = view.getId();
    switch(id) {
        case R.id.item_task_programmed_one_time_container:
            Pair[] pairs = new Pair[1];
            pairs[0] = new Pair<View, String>(mCategoryIcon, mFragment.getResources().getString(R.string.transition_task_list_category));
            //pairs[1] = new Pair<View, String>(mTitle, mFragment.getResources().getString(R.string.transition_task_list_title));
            //pairs[2] = new Pair<View, String>(mDescription, mFragment.getResources().getString(R.string.transition_task_list_description));
            ActivityOptionsCompat options = ActivityOptionsCompat.makeSceneTransitionAnimation(mFragment.getActivity(), pairs);
            Intent openTaskDetailActivity = new Intent(mFragment.getActivity(), TaskDetailActivity.class);
            openTaskDetailActivity.putExtra(TaskDetailActivity.TASK_ID_TO_DISPLAY, mCurrent.getId());
            openTaskDetailActivity.putExtra(TaskDetailActivity.TASK_POSITION, mReminderPosition);
            if (mClickListener != null) {
                mClickListener.onItemClicked(mReminderPosition, openTaskDetailActivity, options.toBundle());
            }
            break;
    }
}

Example 18 with Pair

use of org.apache.commons.math3.util.Pair in project Remindy by abicelis.

the class ImageAttachmentViewHolder method launchImageViewAttachmentActivity.

private void launchImageViewAttachmentActivity() {
    Pair[] pairs = new Pair[1];
    pairs[0] = new Pair<View, String>(mImage, mActivity.getResources().getString(R.string.transition_image_attachment_image));
    ActivityOptionsCompat options = ActivityOptionsCompat.makeSceneTransitionAnimation(mActivity, pairs);
    Intent goToViewImageAttachmentActivity = new Intent(mActivity, ViewImageAttachmentActivity.class);
    goToViewImageAttachmentActivity.putExtra(ViewImageAttachmentActivity.IMAGE_ATTACHMENT_EXTRA, mCurrent);
    goToViewImageAttachmentActivity.putExtra(ViewImageAttachmentActivity.HOLDER_POSITION_EXTRA, mPosition);
    mActivity.startActivityForResult(goToViewImageAttachmentActivity, ViewImageAttachmentActivity.VIEW_IMAGE_ATTACHMENT_REQUEST_CODE, options.toBundle());
}

Example 19 with Pair

use of org.apache.commons.math3.util.Pair in project GDSC-SMLM by aherbert.

the class ApacheLVMFitter method computeFit.

public FitStatus computeFit(double[] y, final double[] y_fit, double[] a, double[] a_dev) {
    int n = y.length;
    try {
        // Different convergence thresholds seem to have no effect on the resulting fit, only the number of
        // iterations for convergence
        final double initialStepBoundFactor = 100;
        final double costRelativeTolerance = 1e-10;
        final double parRelativeTolerance = 1e-10;
        final double orthoTolerance = 1e-10;
        final double threshold = Precision.SAFE_MIN;
        // Extract the parameters to be fitted
        final double[] initialSolution = getInitialSolution(a);
        // TODO - Pass in more advanced stopping criteria.
        // Create the target and weight arrays
        final double[] yd = new double[n];
        final double[] w = new double[n];
        for (int i = 0; i < n; i++) {
            yd[i] = y[i];
            w[i] = 1;
        }
        LevenbergMarquardtOptimizer optimizer = new LevenbergMarquardtOptimizer(initialStepBoundFactor, costRelativeTolerance, parRelativeTolerance, orthoTolerance, threshold);
        //@formatter:off
        LeastSquaresBuilder builder = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(getMaxEvaluations()).start(initialSolution).target(yd).weight(new DiagonalMatrix(w));
        if (f instanceof ExtendedNonLinearFunction && ((ExtendedNonLinearFunction) f).canComputeValuesAndJacobian()) {
            // Compute together, or each individually
            builder.model(new ValueAndJacobianFunction() {

                final ExtendedNonLinearFunction fun = (ExtendedNonLinearFunction) f;

                public Pair<RealVector, RealMatrix> value(RealVector point) {
                    final double[] p = point.toArray();
                    final Pair<double[], double[][]> result = fun.computeValuesAndJacobian(p);
                    return new Pair<RealVector, RealMatrix>(new ArrayRealVector(result.getFirst(), false), new Array2DRowRealMatrix(result.getSecond(), false));
                }

                public RealVector computeValue(double[] params) {
                    return new ArrayRealVector(fun.computeValues(params), false);
                }

                public RealMatrix computeJacobian(double[] params) {
                    return new Array2DRowRealMatrix(fun.computeJacobian(params), false);
                }
            });
        } else {
            // Compute separately
            builder.model(new MultivariateVectorFunctionWrapper((NonLinearFunction) f, a, n), new MultivariateMatrixFunctionWrapper((NonLinearFunction) f, a, n));
        }
        LeastSquaresProblem problem = builder.build();
        Optimum optimum = optimizer.optimize(problem);
        final double[] parameters = optimum.getPoint().toArray();
        setSolution(a, parameters);
        iterations = optimum.getIterations();
        evaluations = optimum.getEvaluations();
        if (a_dev != null) {
            try {
                double[][] covar = optimum.getCovariances(threshold).getData();
                setDeviationsFromMatrix(a_dev, covar);
            } catch (SingularMatrixException e) {
                // Matrix inversion failed. In order to return a solution 
                // return the reciprocal of the diagonal of the Fisher information 
                // for a loose bound on the limit 
                final int[] gradientIndices = f.gradientIndices();
                final int nparams = gradientIndices.length;
                GradientCalculator calculator = GradientCalculatorFactory.newCalculator(nparams);
                double[][] alpha = new double[nparams][nparams];
                double[] beta = new double[nparams];
                calculator.findLinearised(nparams, y, a, alpha, beta, (NonLinearFunction) f);
                FisherInformationMatrix m = new FisherInformationMatrix(alpha);
                setDeviations(a_dev, m.crlb(true));
            }
        }
        // Compute function value
        if (y_fit != null) {
            Gaussian2DFunction f = (Gaussian2DFunction) this.f;
            f.initialise0(a);
            f.forEach(new ValueProcedure() {

                int i = 0;

                public void execute(double value) {
                    y_fit[i] = value;
                }
            });
        }
        // As this is unweighted then we can do this to get the sum of squared residuals
        // This is the same as optimum.getCost() * optimum.getCost(); The getCost() function
        // just computes the dot product anyway.
        value = optimum.getResiduals().dotProduct(optimum.getResiduals());
    } catch (TooManyEvaluationsException e) {
        return FitStatus.TOO_MANY_EVALUATIONS;
    } catch (TooManyIterationsException e) {
        return FitStatus.TOO_MANY_ITERATIONS;
    } catch (ConvergenceException e) {
        // Occurs when QR decomposition fails - mark as a singular non-linear model (no solution)
        return FitStatus.SINGULAR_NON_LINEAR_MODEL;
    } catch (Exception e) {
        // TODO - Find out the other exceptions from the fitter and add return values to match. 
        return FitStatus.UNKNOWN;
    }
    return FitStatus.OK;
}

Example 20 with Pair

use of org.apache.commons.math3.util.Pair in project GDSC-SMLM by aherbert.

the class PCPALMMolecules method performDistanceAnalysis.

private void performDistanceAnalysis(double[][] intraHist, int p99) {
    // We want to know the fraction of distances between molecules at the 99th percentile
    // that are intra- rather than inter-molecule.
    // Do single linkage clustering of closest pair at this distance and count the number of 
    // links that are inter and intra.
    // Convert molecules for clustering
    ArrayList<ClusterPoint> points = new ArrayList<ClusterPoint>(molecules.size());
    for (Molecule m : molecules) // Precision was used to store the molecule ID
    points.add(ClusterPoint.newClusterPoint((int) m.precision, m.x, m.y, m.photons));
    ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), ClusteringAlgorithm.PARTICLE_SINGLE_LINKAGE, new IJTrackProgress());
    IJ.showStatus("Clustering to check inter-molecule distances");
    engine.setTrackJoins(true);
    ArrayList<Cluster> clusters = engine.findClusters(points, intraHist[0][p99]);
    IJ.showStatus("");
    if (clusters != null) {
        double[] intraIdDistances = engine.getIntraIdDistances();
        double[] interIdDistances = engine.getInterIdDistances();
        int all = interIdDistances.length + intraIdDistances.length;
        log("  * Fraction of inter-molecule particle linkage @ %s nm = %s %%", Utils.rounded(intraHist[0][p99], 4), (all > 0) ? Utils.rounded(100.0 * interIdDistances.length / all, 4) : "0");
        // Show a double cumulative histogram plot
        double[][] intraIdHist = Maths.cumulativeHistogram(intraIdDistances, false);
        double[][] interIdHist = Maths.cumulativeHistogram(interIdDistances, false);
        // Plot
        String title = TITLE + " molecule linkage distance";
        Plot2 plot = new Plot2(title, "Distance", "Frequency", intraIdHist[0], intraIdHist[1]);
        double max = (intraIdHist[1].length > 0) ? intraIdHist[1][intraIdHist[1].length - 1] : 0;
        if (interIdHist[1].length > 0)
            max = FastMath.max(max, interIdHist[1][interIdHist[1].length - 1]);
        plot.setLimits(0, intraIdHist[0][intraIdHist[0].length - 1], 0, max);
        plot.setColor(Color.blue);
        plot.addPoints(interIdHist[0], interIdHist[1], Plot2.LINE);
        plot.setColor(Color.black);
        Utils.display(title, plot);
    } else {
        log("Aborted clustering to check inter-molecule distances");
    }
}