Method computeP

JSAT/src/jsat/datatransform/visualization/TSNE.java:348–516

@param d the dataset to search @param ex the source of threads for parallel computation @param rand source of randomness @param knn the number of neighbors to search for @param nearMe each row is the set of knn indices returned by the NN search @param nearMePij the symmetrized neighbor probability @

(DataSet d, ExecutorService ex, Random rand, final int knn, final int[][] nearMe, final double[][] nearMePij, final DistanceMetric dm, final double perplexity)

     * @param perplexity the perplexity value for the effective nearest neighbor search and weighting
     */
    protected static void computeP(DataSet d, ExecutorService ex, Random rand, final int knn, final int[][] nearMe, final double[][] nearMePij, final DistanceMetric dm, final double perplexity)
    {
        @SuppressWarnings("unchecked")
        final List<Vec> vecs = d.getDataVectors();
        final List<Double> accelCache = dm.getAccelerationCache(vecs, ex);
        final int N = vecs.size();
        
        final VPTreeMV<Vec> vp = new VPTreeMV<Vec>(vecs, dm, VPTree.VPSelection.Random, rand, 2, 1, ex);
        
        final List<List<? extends VecPaired<Vec, Double>>> neighbors = new ArrayList<List<? extends VecPaired<Vec, Double>>>(N);
        for(int i = 0; i < N; i++)
            neighbors.add(null);
        
        
        
        //new scope b/c I don't want to leark the silly vecIndex thing
        {
            //Used to map vecs back to their index so we can store only the ones we need in nearMe
            final IdentityHashMap<Vec, Integer> vecIndex = new IdentityHashMap<Vec, Integer>(N);
            for(int i = 0; i < N; i++)
                vecIndex.put(vecs.get(i), i);

            final CountDownLatch latch = new CountDownLatch(SystemInfo.LogicalCores);

            for (int id = 0; id < SystemInfo.LogicalCores; id++)
            {
                final int ID = id;
                ex.submit(new Runnable()
                {
                    @Override
                    public void run()
                    {
                        for (int i = ID; i < N; i += SystemInfo.LogicalCores)//lets pre-compute the 3u nearesst neighbors used in eq(1)
                        {
                            Vec x_i = vecs.get(i);
                            List<? extends VecPaired<Vec, Double>> closest = vp.search(x_i, knn+1);//+1 b/c self is closest
                            neighbors.set(i, closest);
                            for (int j = 1; j < closest.size(); j++)
                            {
                                nearMe[i][j - 1] = vecIndex.get(closest.get(j).getVector());
                            }
                        }
                        latch.countDown();
                    }
                });
            }

            try
            {
                latch.await();
            }
            catch (InterruptedException ex1)
            {
                Logger.getLogger(TSNE.class.getName()).log(Level.SEVERE, null, ex1);
            }

        }
        //Now lets figure out everyone's sigmas