/**
   * Fairly straightforward: the task here is to reassemble the rows of the affinity matrix. The
   * tricky part is that any specific element in the list of elements which does NOT lay on the
   * diagonal will be so because it did not drop below the sensitivity threshold, hence it was not
   * "cut".
   *
   * <p>On the flip side, there will be many entries whose coordinate is now set to the diagonal,
   * indicating they were previously affinity entries whose sensitivities were below the threshold,
   * and hence were "cut" - set to 0 at their original coordinates, and had their values added to
   * the diagonal entry (hence the numerous entries with the coordinate of the diagonal).
   *
   * @throws Exception
   */
  @Test
  public void testEigencutsAffinityCutsReducer() throws Exception {
    Configuration conf = new Configuration();
    Path affinity = new Path("affinity");
    Path sensitivity = new Path("sensitivity");
    conf.set(EigencutsKeys.AFFINITY_PATH, affinity.getName());
    conf.setInt(EigencutsKeys.AFFINITY_DIMENSIONS, this.affinity.length);

    // since we need the working paths to distinguish the vertex types,
    // we can't use the mapper (since we have no way of manually setting
    // the Context.workingPath() )
    Map<Text, List<VertexWritable>> data = buildMapData(affinity, sensitivity, this.sensitivity);

    // now, set up the combiner
    EigencutsAffinityCutsCombiner combiner = new EigencutsAffinityCutsCombiner();
    DummyRecordWriter<Text, VertexWritable> comWriter =
        new DummyRecordWriter<Text, VertexWritable>();
    Reducer<Text, VertexWritable, Text, VertexWritable>.Context comContext =
        DummyRecordWriter.build(combiner, conf, comWriter, Text.class, VertexWritable.class);

    // perform the combining
    for (Map.Entry<Text, List<VertexWritable>> entry : data.entrySet()) {
      combiner.reduce(entry.getKey(), entry.getValue(), comContext);
    }

    // finally, set up the reduction writers
    EigencutsAffinityCutsReducer reducer = new EigencutsAffinityCutsReducer();
    DummyRecordWriter<IntWritable, VectorWritable> redWriter =
        new DummyRecordWriter<IntWritable, VectorWritable>();
    Reducer<Text, VertexWritable, IntWritable, VectorWritable>.Context redContext =
        DummyRecordWriter.build(reducer, conf, redWriter, Text.class, VertexWritable.class);

    // perform the reduction
    for (Text key : comWriter.getKeys()) {
      reducer.reduce(key, comWriter.getValue(key), redContext);
    }

    // now, check that the affinity matrix is correctly formed
    for (IntWritable row : redWriter.getKeys()) {
      List<VectorWritable> results = redWriter.getValue(row);
      // there should only be 1 vector
      assertEquals("Only one vector with a given row number", 1, results.size());
      Vector therow = results.get(0).get();
      for (Vector.Element e : therow.all()) {
        // check the diagonal
        if (row.get() == e.index()) {
          assertEquals(
              "Correct diagonal sum of cuts",
              sumOfRowCuts(row.get(), this.sensitivity),
              e.get(),
              EPSILON);
        } else {
          // not on the diagonal...if it was an element labeled to be cut,
          // it should have a value of 0. Otherwise, it should have kept its
          // previous value
          if (this.sensitivity[row.get()][e.index()] == 0.0) {
            // should be what it was originally
            assertEquals(
                "Preserved element", this.affinity[row.get()][e.index()], e.get(), EPSILON);
          } else {
            // should be 0
            assertEquals("Cut element", 0.0, e.get(), EPSILON);
          }
        }
      }
    }
  }
  /**
   * This is by far the trickiest step. However, an easy condition is if we have only two vertices -
   * indicating vertices on the diagonal of the two matrices - then we simply exit (since the
   * algorithm does not operate on the diagonal; it makes no sense to perform cuts by isolating data
   * points from themselves).
   *
   * <p>If there are four points, then first we must separate the two which belong to the affinity
   * matrix from the two that are sensitivities. In theory, each pair should have exactly the same
   * value (symmetry). If the sensitivity is below a certain threshold, then we set the two values
   * of the affinity matrix to 0 (but not before adding the affinity values to the diagonal, so as
   * to maintain the overall sum of the row of the affinity matrix).
   *
   * @throws Exception
   */
  @Test
  public void testEigencutsAffinityCutsCombiner() throws Exception {
    Configuration conf = new Configuration();
    Path affinity = new Path("affinity");
    Path sensitivity = new Path("sensitivity");
    conf.set(EigencutsKeys.AFFINITY_PATH, affinity.getName());
    conf.setInt(EigencutsKeys.AFFINITY_DIMENSIONS, this.affinity.length);

    // since we need the working paths to distinguish the vertex types,
    // we can't use the mapper (since we have no way of manually setting
    // the Context.workingPath() )
    Map<Text, List<VertexWritable>> data = buildMapData(affinity, sensitivity, this.sensitivity);

    // now, set up the combiner
    EigencutsAffinityCutsCombiner combiner = new EigencutsAffinityCutsCombiner();
    DummyRecordWriter<Text, VertexWritable> redWriter =
        new DummyRecordWriter<Text, VertexWritable>();
    Reducer<Text, VertexWritable, Text, VertexWritable>.Context redContext =
        DummyRecordWriter.build(combiner, conf, redWriter, Text.class, VertexWritable.class);

    // perform the combining
    for (Map.Entry<Text, List<VertexWritable>> entry : data.entrySet()) {
      combiner.reduce(entry.getKey(), entry.getValue(), redContext);
    }

    // test the number of cuts, there should be 2
    assertEquals(
        "Number of cuts detected",
        4,
        redContext.getCounter(EigencutsAffinityCutsJob.CUTSCOUNTER.NUM_CUTS).getValue());

    // loop through all the results; let's see if they match up to our
    // affinity matrix (and all the cuts appear where they should
    Map<Text, List<VertexWritable>> results = redWriter.getData();
    for (Map.Entry<Text, List<VertexWritable>> entry : results.entrySet()) {
      List<VertexWritable> row = entry.getValue();
      IntWritable key = new IntWritable(Integer.parseInt(entry.getKey().toString()));

      double calcDiag = 0.0;
      double trueDiag = sumOfRowCuts(key.get(), this.sensitivity);
      for (VertexWritable e : row) {

        // should the value have been cut, e.g. set to 0?
        if (key.get() == e.getCol()) {
          // we have our diagonal
          calcDiag += e.getValue();
        } else if (this.sensitivity[key.get()][e.getCol()] == 0.0) {
          // no, corresponding affinity should have same value as before
          assertEquals(
              "Preserved affinity value",
              this.affinity[key.get()][e.getCol()],
              e.getValue(),
              EPSILON);
        } else {
          // yes, corresponding affinity value should be 0
          assertEquals("Cut affinity value", 0.0, e.getValue(), EPSILON);
        }
      }
      // check the diagonal has the correct sum
      assertEquals("Diagonal sum from cuts", trueDiag, calcDiag, EPSILON);
    }
  }