org.nd4j.linalg.api.ndarray.INDArray Java Examples

@Test
public void testAdaMax() {
    int rows = 10;
    int cols = 2;


    AdaMaxUpdater grad = new AdaMaxUpdater(new AdaMax());
    grad.setStateViewArray(Nd4j.zeros(1, 2 * rows * cols), new long[] {rows, cols}, 'c', true);
    INDArray W = Nd4j.zeros(rows, cols);
    Distribution dist = Nd4j.getDistributions().createNormal(1e-3, 1e-3);
    for (int i = 0; i < W.rows(); i++)
        W.putRow(i, Nd4j.create(dist.sample(W.columns())));

    for (int i = 0; i < 5; i++) {
        //            String learningRates = String.valueOf("\nAdaMax\n " + grad.getGradient(W, i)).replaceAll(";", "\n");
        //            System.out.println(learningRates);
        W.addi(Nd4j.randn(rows, cols));
    }
}
 

@Override
public Map<String, INDArray> getGradientsFromFlattened(NeuralNetConfiguration conf, INDArray gradientView) {
    org.deeplearning4j.nn.conf.ocnn.OCNNOutputLayer ocnnOutputLayer = ( org.deeplearning4j.nn.conf.ocnn.OCNNOutputLayer) conf.getLayer();
    Map<String, INDArray> params = Collections.synchronizedMap(new LinkedHashMap<String, INDArray>());
    val nIn = ocnnOutputLayer.getNIn();
    val hiddenLayer = ocnnOutputLayer.getHiddenSize();

    val firstLayerWeightLength =  hiddenLayer;
    val secondLayerLength = nIn * hiddenLayer;

    INDArray weightView = gradientView.get(point(0),interval(0, firstLayerWeightLength))
            .reshape('f',1,hiddenLayer);
    INDArray vView = gradientView.get(point(0),
            NDArrayIndex.interval(firstLayerWeightLength,firstLayerWeightLength + secondLayerLength))
            .reshape('f',nIn,hiddenLayer);
    params.put(W_KEY, weightView);
    params.put(V_KEY,vView);
    params.put(R_KEY,gradientView.get(point(0),point(gradientView.length() - 1)));
    return params;

}
 

@Test
public void testLinspaceDerivative() throws Exception {

   String basePath = "/two_points_approx_deriv_numpy/";
    INDArray linspace = Nd4j.createNpyFromInputStream(new ClassPathResource(basePath + "x.npy").getInputStream());
    INDArray yLinspace = Nd4j.createNpyFromInputStream(new ClassPathResource(basePath + "y.npy").getInputStream());
    Function<INDArray,INDArray> f = new Function<INDArray, INDArray>() {
        @Override
        public INDArray apply(INDArray indArray) {
            return indArray.add(1);
        }
    };

    INDArray test = TwoPointApproximation
            .approximateDerivative(f,linspace,null,yLinspace,
                    Nd4j.create(new double[] {Float.MIN_VALUE
                            ,Float.MAX_VALUE}));

    INDArray npLoad = Nd4j.createNpyFromInputStream(new ClassPathResource(basePath + "approx_deriv_small.npy").getInputStream());
    assertEquals(npLoad,test);
    System.out.println(test);

}
 

@Test
public void testTimeSeriesEval() {

    int[] shape = {2, 4, 3};
    Nd4j.getRandom().setSeed(12345);
    INDArray labels = Nd4j.getExecutioner().exec(new BernoulliDistribution(Nd4j.createUninitialized(shape), 0.5));
    INDArray predicted = Nd4j.rand(shape);
    INDArray mask = Nd4j.getExecutioner().exec(new BernoulliDistribution(Nd4j.createUninitialized(shape), 0.5));

    EvaluationBinary eb1 = new EvaluationBinary();
    eb1.eval(labels, predicted, mask);

    EvaluationBinary eb2 = new EvaluationBinary();
    for (int i = 0; i < shape[2]; i++) {
        INDArray l = labels.get(NDArrayIndex.all(), NDArrayIndex.all(), NDArrayIndex.point(i));
        INDArray p = predicted.get(NDArrayIndex.all(), NDArrayIndex.all(), NDArrayIndex.point(i));
        INDArray m = mask.get(NDArrayIndex.all(), NDArrayIndex.all(), NDArrayIndex.point(i));

        eb2.eval(l, p, m);
    }

    assertEquals(eb2.stats(), eb1.stats());
}
 

public INDArray scoreArray(INDArray labels, INDArray preOutput, IActivation activationFn, INDArray mask) {
    if (labels.size(1) != preOutput.size(1)) {
        throw new IllegalArgumentException(
                        "Labels array numColumns (size(1) = " + labels.size(1) + ") does not match output layer"
                                        + " number of outputs (nOut = " + preOutput.size(1) + ") ");

    }
    INDArray scoreArr;
    //INDArray output = Nd4j.getExecutioner().execAndReturn(Nd4j.getOpFactory().createTransform(activationFn, preOutput.dup()));
    INDArray output = activationFn.getActivation(preOutput.dup(), true);
    scoreArr = output.subi(labels);
    Nd4j.getExecutioner().execAndReturn(Nd4j.getOpFactory().createTransform("abs", scoreArr));

    //Weighted loss function
    if (weights != null) {
        if (weights.length() != output.size(1)) {
            throw new IllegalStateException("Weights vector (length " + weights.length()
                            + ") does not match output.size(1)=" + output.size(1));
        }
        scoreArr.muliRowVector(weights);
    }

    if (mask != null) {
        LossUtil.applyMask(scoreArr, mask);
    }
    return scoreArr;
}
 

@Override
public void potrf(INDArray A, boolean lower) {

    // FIXME: int cast
    if (A.columns() > Integer.MAX_VALUE)
        throw new ND4JArraySizeException();

    byte uplo = (byte) (lower ? 'L' : 'U'); // upper or lower part of the factor desired ?
    int n = (int) A.columns();

    INDArray INFO = Nd4j.createArrayFromShapeBuffer(Nd4j.getDataBufferFactory().createInt(1),
                    Nd4j.getShapeInfoProvider().createShapeInformation(new int[] {1, 1}).getFirst());

    if (A.data().dataType() == DataBuffer.Type.DOUBLE)
        dpotrf(uplo, n, A, INFO);
    else if (A.data().dataType() == DataBuffer.Type.FLOAT)
        spotrf(uplo, n, A, INFO);
    else
        throw new UnsupportedOperationException();

    if (INFO.getInt(0) < 0) {
        throw new Error("Parameter #" + INFO.getInt(0) + " to potrf() was not valid");
    } else if (INFO.getInt(0) > 0) {
        throw new Error("The matrix is not positive definite! (potrf fails @ order " + INFO.getInt(0) + ")");
    }

    return;
}
 

/**
 * This method calculates 'phi' which is the probability
 * density function (see Bishop 23)
 * @param diffSquared This is the 'x-mu' term of the Gaussian distribution (distance between 'x' and the mean value of the distribution).
 * @param sigma This is the standard deviation of the Gaussian distribution.
 * @return This returns an array of shape [nsamples, nlabels, ndistributions] which contains the probability density (phi) for each of the
 *         samples * labels * distributions for the given x, sigma, mu.
 */
private INDArray phi(INDArray diffSquared, INDArray sigma) {
    // 1/sqrt(2PIs^2) * e^((in-u)^2/2*s^2)
    INDArray minustwovariance = sigma.mul(sigma).muli(2).negi();

    // This is phi_i(x,mu,sigma)
    INDArray likelihoods = Transforms.exp(diffSquared.divi(minustwovariance))
                    .divi(Transforms.pow(sigma.mul(SQRT_TWO_PI), (double) mLabelWidth));

    return likelihoods;
}
 

/**
 * This op fills Z with binomial distribution over given trials with single given probability for all trials
 * @param z
 * @param trials
 * @param probability
 */
public BinomialDistribution(@NonNull INDArray z, int trials, double probability) {
    super(z, z, z);
    this.trials = trials;
    this.probability = probability;
    this.extraArgs = new Object[] {(double) this.trials, this.probability};
}
 

@Test
public void basicBroadcastTest_1() {
    val x = Nd4j.create(DataType.FLOAT, 3, 5);
    val y = Nd4j.createFromArray(new float[]{1.f, 1.f, 1.f, 1.f, 1.f});
    val e = Nd4j.create(DataType.FLOAT, 3, 5).assign(1.f);

    // inplace setup
    val op = new AddOp(new INDArray[]{x, y}, new INDArray[]{x});

    Nd4j.exec(op);

    assertEquals(e, x);
}
 

/**
 * Computes a gaussian kernel
 * given a vector of squared distance distances
 *
 * @param d the data
 * @param beta
 * @return
 */
public Pair<Double, INDArray> hBeta(INDArray d, double beta) {
    INDArray P = exp(d.neg().muli(beta));
    double sumP = P.sumNumber().doubleValue();
    double logSumP = FastMath.log(sumP);
    Double H = logSumP + ((beta * (d.mul(P).sumNumber().doubleValue())) / sumP);
    P.divi(sumP);
    return new Pair<>(H, P);
}
 

@Test
public void testSum6d() {
    INDArray arr6 = Nd4j.ones(1, 1, 4, 4, 4, 4);
    INDArray arr6s = arr6.sum(2, 3);
    for (int i = 0; i < arr6s.length(); i++)
        assertEquals(16, arr6s.getDouble(i), 1e-1);

}
 

@Test
public void testDup() {
    SameDiff sameDiff = SameDiff.create();
    INDArray arr = Transforms.sigmoid(Nd4j.linspace(1, 8, 8)).reshape(2, 2, 2);
    SDVariable x = sameDiff.var("x", arr);
    SDVariable y = sameDiff.var("y", arr);
    SameDiff tg2 = sameDiff.dup();
}
 

public static ReduceOp createDistanceFunctionOp(Distance distanceFunction, INDArray x, INDArray y){
    switch (distanceFunction){
        case COSINE_DISTANCE:
            return new CosineDistance(x,y);
        case COSINE_SIMILARITY:
            return new CosineSimilarity(x,y);
        case DOT:
            return new Dot(x,y);
        case EUCLIDEAN:
            return new EuclideanDistance(x,y);
        case JACCARD:
            return new JaccardDistance(x,y);
        case MANHATTAN:
            return new ManhattanDistance(x,y);
        default:
            throw new IllegalStateException("Unknown distance function: " + distanceFunction);
    }
}
 

private INDArray permuteImageOrder(INDArray input) {
    if (!imageLoadingStepConfig.initialImageLayoutMatchesFinal()) {
        return ImagePermuter.permuteOrder(input,
                imageLoadingStepConfig.getImageProcessingInitialLayout(),
                imageLoadingStepConfig.getImageProcessingRequiredLayout());
    } else {
        return input;
    }
}
 

@Test
public void testElementWiseVertexForwardAdd() {
    int batchsz = 24;
    int featuresz = 17;
    ComputationGraphConfiguration cgc = new NeuralNetConfiguration.Builder().graphBuilder()
                    .addInputs("input1", "input2", "input3")
                    .addLayer("denselayer",
                                    new DenseLayer.Builder().nIn(featuresz).nOut(1).activation(Activation.IDENTITY)
                                                    .build(),
                                    "input1")
                    /* denselayer is not actually used, but it seems that you _need_ to have trainable parameters, otherwise, you get
                     * Invalid shape: Requested INDArray shape [1, 0] contains dimension size values < 1 (all dimensions must be 1 or more)
                     * at org.nd4j.linalg.factory.Nd4j.checkShapeValues(Nd4j.java:4877)
                     * at org.nd4j.linalg.factory.Nd4j.create(Nd4j.java:4867)
                     * at org.nd4j.linalg.factory.Nd4j.create(Nd4j.java:4820)
                     * at org.nd4j.linalg.factory.Nd4j.create(Nd4j.java:3948)
                     * at org.deeplearning4j.nn.graph.ComputationGraph.init(ComputationGraph.java:409)
                     * at org.deeplearning4j.nn.graph.ComputationGraph.init(ComputationGraph.java:341)
                     */
                    .addVertex("elementwiseAdd", new ElementWiseVertex(ElementWiseVertex.Op.Add), "input1",
                                    "input2", "input3")
                    .addLayer("Add", new ActivationLayer.Builder().activation(Activation.IDENTITY).build(),
                                    "elementwiseAdd")
                    .setOutputs("Add", "denselayer").build();

    ComputationGraph cg = new ComputationGraph(cgc);
    cg.init();


    INDArray input1 = Nd4j.rand(batchsz, featuresz);
    INDArray input2 = Nd4j.rand(batchsz, featuresz);
    INDArray input3 = Nd4j.rand(batchsz, featuresz);

    INDArray target = input1.dup().addi(input2).addi(input3);

    INDArray output = cg.output(input1, input2, input3)[0];
    INDArray squared = output.sub(target.castTo(output.dataType()));
    double rms = squared.mul(squared).sumNumber().doubleValue();
    Assert.assertEquals(0.0, rms, this.epsilon);
}
 

@Test
    public void testScore() throws Exception {
        EnvironmentContext context = EnvironmentFactory.getContext();
        Future<?> task = context.doTask(() -> {
            LinkedList<KeyValue<IActivation, ActivationFunction>> activetionList = new LinkedList<>();
            activetionList.add(new KeyValue<>(new ActivationSigmoid(), new SigmoidActivationFunction()));
//            activetionList.add(new KeyValue<>(new ActivationSoftmax(), new SoftMaxActivationFunction()));
            for (KeyValue<IActivation, ActivationFunction> keyValue : activetionList) {
                INDArray array = Nd4j.linspace(-2.5D, 2.0D, 10).reshape(5, 2);
                INDArray marks = Nd4j.create(new double[] { 0D, 1D, 0D, 1D, 0D, 1D, 0D, 1D, 0D, 1D }).reshape(5, 2);
                ILossFunction oldFunction = getOldFunction(marks);
                double value = oldFunction.computeScore(marks, array.dup(), keyValue.getKey(), null, false);

                Nd4jMatrix input = getMatrix(array.dup());
                Nd4jMatrix output = new Nd4jMatrix(Nd4j.zeros(input.getRowSize(), input.getColumnSize()));
                ActivationFunction function = keyValue.getValue();
                function.forward(input, output);
                LossFunction newFunction = getNewFunction(marks, function);
                newFunction.doCache(getMatrix(marks), output);
                double score = newFunction.computeScore(getMatrix(marks), output, null);

                System.out.println(value);
                System.out.println(score);

                if (Math.abs(value - score) > MathUtility.EPSILON) {
                    Assert.fail();
                }
            }
        });
        task.get();
    }
 

/**
 * Check the Moore-Penrose conditions for pseudo-matrices.
 *
 * @param A Initial matrix
 * @param B Pseudo-Inverse of {@code A}
 * @param precision Precision when comparing matrix elements
 */
private void checkMoorePenroseConditions(INDArray A, INDArray B, double precision) {
    // ABA=A (AB need not be the general identity matrix, but it maps all column vectors of A to themselves)
    assertTrue(A.equalsWithEps(A.mmul(B).mmul(A), precision));
    // BAB=B (B is a weak inverse for the multiplicative semigroup)
    assertTrue(B.equalsWithEps(B.mmul(A).mmul(B), precision));
    // (AB)^T=AB (AB is Hermitian)
    assertTrue((A.mmul(B)).transpose().equalsWithEps(A.mmul(B), precision));
    // (BA)^T=BA (BA is also Hermitian)
    assertTrue((B.mmul(A)).transpose().equalsWithEps(B.mmul(A), precision));
}
 

@Before
public void randomData() {
    Nd4j.getRandom().setSeed(12345);
    batchSize = 13;
    batchCount = 20;
    lastBatch = batchSize / 2;
    INDArray origFeatures = Nd4j.rand(batchCount * batchSize + lastBatch, 10);
    INDArray origLabels = Nd4j.rand(batchCount * batchSize + lastBatch, 3);
    data = new DataSet(origFeatures, origLabels);
    stdScaler = new NormalizerStandardize();
    minMaxScaler = new NormalizerMinMaxScaler();
}
 

private INDArray copyIfNecessary(INDArray arr) {
    //See also: Shape.toMmulCompatible - want same conditions here and there
    //Check if matrix values are contiguous in memory. If not: dup
    //Contiguous for c if: stride[0] == shape[1] and stride[1] = 1
    //Contiguous for f if: stride[0] == 1 and stride[1] == shape[0]
    if (arr.ordering() == 'c' && (arr.stride(0) != arr.size(1) || arr.stride(1) != 1))
        return arr.dup();
    else if (arr.ordering() == 'f' && (arr.stride(0) != 1 || arr.stride(1) != arr.size(0)))
        return arr.dup();
    else if (arr.elementWiseStride() < 1)
        return arr.dup();
    return arr;
}
 

@Test
public void testIMax4() {
    INDArray array1 = Nd4j.linspace(1, 1000, 128000).reshape(128, 1000);

    long time1 = System.currentTimeMillis();
    INDArray  argMax = Nd4j.argMax(array1, 0,1);
    long time2 = System.currentTimeMillis();

    System.out.println("Execution time: " + (time2 - time1));

    assertEquals(127999f, argMax.getFloat(0), 0.001f);
}
 

@Test
public void testVariableRenaming2() {

    SameDiff sd = SameDiff.create();
    SDVariable v1 = sd.placeHolder("x", DataType.FLOAT, 3, 4);
    SDVariable v2 = sd.var("y", Nd4j.rand(DataType.FLOAT, 4, 5));
    SDVariable v3 = v1.mmul("oldName", v2);
    SDVariable v4 = v3.std("out", false);

    INDArray out = sd.outputSingle(Collections.singletonMap("x", Nd4j.rand(DataType.FLOAT, 3, 4)), "out");

    sd.setTrainingConfig(TrainingConfig.builder()
            .updater(new Adam(1e-3))
            .dataSetFeatureMapping("x")
            .markLabelsUnused()
            .build());

    sd.fit(new DataSet(Nd4j.rand(DataType.FLOAT, 3, 4), null));
    v3.rename("newName");
    sd.fit(new DataSet(Nd4j.rand(DataType.FLOAT, 3, 4), null));
}
 

/**
 * Get a peak at the features of the {@code iterator}'s first batch using the given instances.
 *
 * @return Features of the first batch
 */
protected INDArray getFirstBatchFeatures(Instances data) throws Exception {
  final DataSetIterator it = getDataSetIterator(data, CacheMode.NONE);
  if (!it.hasNext()) {
    throw new RuntimeException("Iterator was unexpectedly empty.");
  }
  final INDArray features = Utils.getNext(it).getFeatures();
  it.reset();
  return features;
}
 

private void knn(KDNode node, HyperRect rect, List<Pair<Float, INDArray>> best, int _disc) {
    if (node == null || rect == null || rect.minDistance(currentPoint, minDistance) > currentDistance)
        return;
    int _discNext = (_disc + 1) % dims;
    float distance = Nd4j.getExecutioner().execAndReturn(new EuclideanDistance(currentPoint,node.point, minDistance)).getFinalResult()
            .floatValue();

    if (distance <= currentDistance) {
        best.add(Pair.of(distance, node.getPoint()));
    }

    HyperRect lower = rect.getLower(node.point, _disc);
    HyperRect upper = rect.getUpper(node.point, _disc);
    knn(node.getLeft(), lower, best, _discNext);
    knn(node.getRight(), upper, best, _discNext);
}
 

@Test
public void testNDArrayToWritablesArray() throws Exception {
    INDArray arr = Nd4j.arange(5);
    List<Writable> expected = Arrays.asList((Writable) new NDArrayWritable(arr));
    List<Writable> actual = new NDArrayToWritablesFunction(true).call(arr);
    assertEquals(expected, actual);
}
 

@Test
public void testDescriptiveStats() {
    OpExecutioner opExecutioner = Nd4j.getExecutioner();
    INDArray x = Nd4j.linspace(1, 5, 5);

    Mean mean = new Mean(x);
    opExecutioner.exec(mean);
    assertEquals(getFailureMessage(), 3.0, mean.getFinalResult().doubleValue(), 1e-1);

    Variance variance = new Variance(x.dup(), true);
    opExecutioner.exec(variance);
    assertEquals(getFailureMessage(), 2.5, variance.getFinalResult().doubleValue(), 1e-1);
}
 

@Test
public void testRepeatVector() {

    double[] arr = new double[] {1., 2., 3., 1., 2., 3., 1., 2., 3., 1., 2., 3.};
    INDArray expectedOut = Nd4j.create(arr, new long[] {1, 3, REPEAT}, 'f');
    INDArray input = Nd4j.create(new double[] {1., 2., 3.}, new long[] {1, 3});
    Layer layer = getRepeatVectorLayer();

    INDArray output = layer.activate(input, false, LayerWorkspaceMgr.noWorkspaces());
    assertTrue(Arrays.equals(expectedOut.shape(), output.shape()));
    assertEquals(expectedOut, output);

    INDArray epsilon = Nd4j.ones(1,3,4);

    Pair<Gradient, INDArray> out = layer.backpropGradient(epsilon, LayerWorkspaceMgr.noWorkspaces());
    INDArray outEpsilon = out.getSecond();
    INDArray expectedEpsilon = Nd4j.create(new double[] {4., 4., 4.}, new long[] {1, 3});
    assertEquals(expectedEpsilon, outEpsilon);
}
 

@Override
public INDArray sort(INDArray x, boolean descending) {
    if (x.isScalar())
        return x;

    if (x.data().dataType() == DataBuffer.Type.FLOAT) {
        NativeOpsHolder.getInstance().getDeviceNativeOps().sortFloat(null, (FloatPointer) x.data().addressPointer(), (LongPointer) x.shapeInfoDataBuffer().addressPointer(), descending);
    } else if (x.data().dataType() == DataBuffer.Type.DOUBLE) {
        NativeOpsHolder.getInstance().getDeviceNativeOps().sortDouble(null, (DoublePointer) x.data().addressPointer(), (LongPointer) x.shapeInfoDataBuffer().addressPointer(), descending);
    } else {
        throw new UnsupportedOperationException("Unknown dataype " + x.data().dataType());
    }
    return x;
}
 

/**
 * Inplace compression of INDArray
 *
 * @param array
 */
@Override
public void compressi(INDArray array) {
    // TODO: lift this restriction
    if (array.isView())
        throw new UnsupportedOperationException("Impossible to apply inplace compression on View");

    array.setData(compress(array.data()));
    array.markAsCompressed(true);
}
 

@Override
public INDArray computeScoreArray(INDArray labels, INDArray preOutput, IActivation activationFn, INDArray mask) {
    INDArray scoreArr = scoreArray(labels, preOutput, activationFn, mask);
    BooleanIndexing.replaceWhere(scoreArr, 0.0, Conditions.lessThan(0.0));//max(0,1-y*yhat)
    scoreArr.muli(scoreArr);
    return scoreArr.sum(true,1);
}
 

@Test
public void vpTreeTest() throws Exception {
    INDArray matrix = Nd4j.rand(new int[] {400,10});
    INDArray rowVector = matrix.getRow(70);
    INDArray resultArr = Nd4j.zeros(400,1);
    Executor executor = Executors.newSingleThreadExecutor();
    VPTree vpTree = new VPTree(matrix);
    System.out.println("Ran!");
}