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

Example 31 with Pair

use of org.apache.commons.math3.util.Pair in project gatk by broadinstitute.

the class CoverageModelEMWorkspace method updateCopyRatioPosteriorExpectationsLocal.

/**
     * Local implementation of the E-step update of copy ratio posteriors
     *
     * @return a {@link SubroutineSignal} containing the update size (key: "error_norm")
     */
public SubroutineSignal updateCopyRatioPosteriorExpectationsLocal(final double admixingRatio) {
    /* step 1. fetch copy ratio emission data */
    final List<List<CoverageModelCopyRatioEmissionData>> copyRatioEmissionData = fetchCopyRatioEmissionDataLocal();
    /* step 2. run the forward-backward algorithm and calculate copy ratio posteriors */
    final INDArray sampleReadDepths = Transforms.exp(sampleMeanLogReadDepths, true);
    final List<CopyRatioExpectations> copyRatioPosteriorResults = sampleIndexStream().parallel().mapToObj(si -> copyRatioExpectationsCalculator.getCopyRatioPosteriorExpectations(CopyRatioCallingMetadata.builder().sampleName(processedSampleNameList.get(si)).sampleSexGenotypeData(processedSampleSexGenotypeData.get(si)).sampleCoverageDepth(sampleReadDepths.getDouble(si)).emissionCalculationStrategy(EmissionCalculationStrategy.HYBRID_POISSON_GAUSSIAN).build(), processedTargetList, copyRatioEmissionData.get(si))).collect(Collectors.toList());
    /* update log chain posterior expectation */
    sampleLogChainPosteriors.assign(Nd4j.create(copyRatioPosteriorResults.stream().mapToDouble(CopyRatioExpectations::getLogChainPosteriorProbability).toArray(), new int[] { numSamples, 1 }));
    /* sent the results back to workers */
    final ImmutablePair<INDArray, INDArray> copyRatioPosteriorDataPair = convertCopyRatioLatentPosteriorExpectationsToNDArray(copyRatioPosteriorResults);
    final INDArray log_c_st = copyRatioPosteriorDataPair.left;
    final INDArray var_log_c_st = copyRatioPosteriorDataPair.right;
    /* partition the pair of (log_c_st, var_log_c_st), sent the result to workers via broadcast-hash-map */
    pushToWorkers(mapINDArrayPairToBlocks(log_c_st.transpose(), var_log_c_st.transpose()), (p, cb) -> cb.cloneWithUpdatedCopyRatioPosteriors(p.get(cb.getTargetSpaceBlock()).left.transpose(), p.get(cb.getTargetSpaceBlock()).right.transpose(), admixingRatio));
    cacheWorkers("after E-step update of copy ratio posteriors");
    /* collect subroutine signals */
    final List<SubroutineSignal> sigs = mapWorkersAndCollect(CoverageModelEMComputeBlock::getLatestMStepSignal);
    final double errorNormInfinity = Collections.max(sigs.stream().map(sig -> sig.<Double>get(StandardSubroutineSignals.RESIDUAL_ERROR_NORM)).collect(Collectors.toList()));
    return SubroutineSignal.builder().put(StandardSubroutineSignals.RESIDUAL_ERROR_NORM, errorNormInfinity).build();
}

Example 32 with Pair

use of org.apache.commons.math3.util.Pair in project pyramid by cheng-li.

the class Sampling method rotate.

/**
     * sample desired size from first to last with given probabilities
     * if one pass is not enough, rotate
     * assume non-zero probabilities
     */
public static Set<Integer> rotate(List<Pair<Integer, Double>> probs, int size) {
    Set<Integer> res = new HashSet<>();
    if (size == 0) {
        return res;
    }
    // if not enough candidates, return all
    if (probs.size() < size) {
        probs.stream().forEach(pair -> res.add(pair.getFirst()));
        return res;
    }
    boolean next = true;
    while (next) {
        for (Pair<Integer, Double> pair : probs) {
            int dataIndex = pair.getFirst();
            double prob = pair.getSecond();
            if (res.size() == size) {
                next = false;
                break;
            }
            if (!res.contains(dataIndex)) {
                BinomialDistribution distribution = new BinomialDistribution(1, prob);
                int sample = distribution.sample();
                if (sample == 1) {
                    res.add(dataIndex);
                }
            }
        }
    }
    return res;
}

Example 33 with Pair

use of org.apache.commons.math3.util.Pair in project druid by druid-io.

the class BenchmarkColumnValueGenerator method initDistribution.

private void initDistribution() {
    BenchmarkColumnSchema.ValueDistribution distributionType = schema.getDistributionType();
    ValueType type = schema.getType();
    List<Object> enumeratedValues = schema.getEnumeratedValues();
    List<Double> enumeratedProbabilities = schema.getEnumeratedProbabilities();
    List<Pair<Object, Double>> probabilities = new ArrayList<>();
    switch(distributionType) {
        case SEQUENTIAL:
            // not random, just cycle through numbers from start to end, or cycle through enumerated values if provided
            distribution = new SequentialDistribution(schema.getStartInt(), schema.getEndInt(), schema.getEnumeratedValues());
            break;
        case UNIFORM:
            distribution = new UniformRealDistribution(schema.getStartDouble(), schema.getEndDouble());
            break;
        case DISCRETE_UNIFORM:
            if (enumeratedValues == null) {
                enumeratedValues = new ArrayList<>();
                for (int i = schema.getStartInt(); i < schema.getEndInt(); i++) {
                    Object val = convertType(i, type);
                    enumeratedValues.add(val);
                }
            }
            // give them all equal probability, the library will normalize probabilities to sum to 1.0
            for (int i = 0; i < enumeratedValues.size(); i++) {
                probabilities.add(new Pair<>(enumeratedValues.get(i), 0.1));
            }
            distribution = new EnumeratedTreeDistribution<>(probabilities);
            break;
        case NORMAL:
            distribution = new NormalDistribution(schema.getMean(), schema.getStandardDeviation());
            break;
        case ROUNDED_NORMAL:
            NormalDistribution normalDist = new NormalDistribution(schema.getMean(), schema.getStandardDeviation());
            distribution = new RealRoundingDistribution(normalDist);
            break;
        case ZIPF:
            int cardinality;
            if (enumeratedValues == null) {
                Integer startInt = schema.getStartInt();
                cardinality = schema.getEndInt() - startInt;
                ZipfDistribution zipf = new ZipfDistribution(cardinality, schema.getZipfExponent());
                for (int i = 0; i < cardinality; i++) {
                    probabilities.add(new Pair<>((Object) (i + startInt), zipf.probability(i)));
                }
            } else {
                cardinality = enumeratedValues.size();
                ZipfDistribution zipf = new ZipfDistribution(enumeratedValues.size(), schema.getZipfExponent());
                for (int i = 0; i < cardinality; i++) {
                    probabilities.add(new Pair<>(enumeratedValues.get(i), zipf.probability(i)));
                }
            }
            distribution = new EnumeratedTreeDistribution<>(probabilities);
            break;
        case ENUMERATED:
            for (int i = 0; i < enumeratedValues.size(); i++) {
                probabilities.add(new Pair<>(enumeratedValues.get(i), enumeratedProbabilities.get(i)));
            }
            distribution = new EnumeratedTreeDistribution<>(probabilities);
            break;
        default:
            throw new UnsupportedOperationException("Unknown distribution type: " + distributionType);
    }
    if (distribution instanceof AbstractIntegerDistribution) {
        ((AbstractIntegerDistribution) distribution).reseedRandomGenerator(seed);
    } else if (distribution instanceof AbstractRealDistribution) {
        ((AbstractRealDistribution) distribution).reseedRandomGenerator(seed);
    } else if (distribution instanceof EnumeratedDistribution) {
        ((EnumeratedDistribution) distribution).reseedRandomGenerator(seed);
    }
}

Example 34 with Pair

use of org.apache.commons.math3.util.Pair in project android-topeka by googlesamples.

the class SignInFragment method performSignInWithTransition.

private void performSignInWithTransition(View v) {
    final Activity activity = getActivity();
    if (v == null || ApiLevelHelper.isLowerThan(Build.VERSION_CODES.LOLLIPOP)) {
        // Don't run a transition if the passed view is null
        CategorySelectionActivity.start(activity, mPlayer);
        activity.finish();
        return;
    }
    if (ApiLevelHelper.isAtLeast(Build.VERSION_CODES.LOLLIPOP)) {
        activity.getWindow().getSharedElementExitTransition().addListener(new TransitionListenerAdapter() {

            @Override
            public void onTransitionEnd(Transition transition) {
                activity.finish();
            }
        });
        final Pair[] pairs = TransitionHelper.createSafeTransitionParticipants(activity, true, new Pair<>(v, activity.getString(R.string.transition_avatar)));
        @SuppressWarnings("unchecked") ActivityOptionsCompat activityOptions = ActivityOptionsCompat.makeSceneTransitionAnimation(activity, pairs);
        CategorySelectionActivity.start(activity, mPlayer, activityOptions);
    }
}

Example 35 with Pair

use of org.apache.commons.math3.util.Pair in project android-topeka by googlesamples.

the class TransitionHelper method createSafeTransitionParticipants.

/**
     * Create the transition participants required during a activity transition while
     * avoiding glitches with the system UI.
     *
     * @param activity The activity used as start for the transition.
     * @param includeStatusBar If false, the status bar will not be added as the transition
     * participant.
     * @return All transition participants.
     */
@TargetApi(Build.VERSION_CODES.LOLLIPOP)
public static Pair<View, String>[] createSafeTransitionParticipants(@NonNull Activity activity, boolean includeStatusBar, @Nullable Pair... otherParticipants) {
    // Avoid system UI glitches as described here:
    // https://plus.google.com/+AlexLockwood/posts/RPtwZ5nNebb
    View decor = activity.getWindow().getDecorView();
    View statusBar = null;
    if (includeStatusBar) {
        statusBar = decor.findViewById(android.R.id.statusBarBackground);
    }
    View navBar = decor.findViewById(android.R.id.navigationBarBackground);
    // Create pair of transition participants.
    List<Pair> participants = new ArrayList<>(3);
    addNonNullViewToTransitionParticipants(statusBar, participants);
    addNonNullViewToTransitionParticipants(navBar, participants);
    // only add transition participants if there's at least one none-null element
    if (otherParticipants != null && !(otherParticipants.length == 1 && otherParticipants[0] == null)) {
        participants.addAll(Arrays.asList(otherParticipants));
    }
    //noinspection unchecked
    return participants.toArray(new Pair[participants.size()]);
}