Examples with BufferedDataContainer org.knime.core.node.BufferedDataContainer used on opensource projects

Example 91 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class CovarianceMatrixCalculatorTest method computeCovarianceOfRandomData.

/**
 * Computes a set of random double
 *
 * @throws InvalidSettingsException
 * @throws CanceledExecutionException
 */
@Test
public void computeCovarianceOfRandomData() throws InvalidSettingsException, CanceledExecutionException {
    long currentTimeMillis = System.currentTimeMillis();
    System.out.println("Mahalanobis test random seed: " + currentTimeMillis);
    final Random random = new Random(currentTimeMillis);
    double[][] data = new double[TEST_TABLE_SIZE][];
    BufferedDataContainer inTableCont = generateData(random, data, SPEC_4);
    inTableCont.close();
    BufferedDataTable inTable = inTableCont.getTable();
    // test the covariance matrix computation
    CovarianceMatrixCalculator covMatrixCalculator = new CovarianceMatrixCalculator(SPEC_4, SPEC_4.getColumnNames());
    BufferedDataContainer covDataContainer = m_exec.createDataContainer(covMatrixCalculator.getResultSpec());
    RealMatrix covMatrixUnderTest = covMatrixCalculator.computeCovarianceMatrix(m_exec, inTable, covDataContainer);
    covDataContainer.close();
    Covariance covariance = new Covariance(data);
    RealMatrix referenceCovarianceMatrix = covariance.getCovarianceMatrix();
    BufferedDataTable covTableUnderTest = covDataContainer.getTable();
    assertCovarianceMatrixEquality(covMatrixUnderTest, referenceCovarianceMatrix, covTableUnderTest, SPEC_4, true);
}

Example 92 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class CovarianceMatrixCalculatorTest method computeCovarianceOfRandomDataWithMissingValues.

/**
 * Tests the covariance computation on data with missing values
 *
 * @throws InvalidSettingsException
 * @throws CanceledExecutionException
 */
@Test
public void computeCovarianceOfRandomDataWithMissingValues() throws InvalidSettingsException, CanceledExecutionException {
    long currentTimeMillis = System.currentTimeMillis();
    System.out.println("Mahalanobis test random seed: " + currentTimeMillis);
    final Random random = new Random(47);
    double[][] data = new double[10][];
    BufferedDataContainer inTableCont = generateData(random, data, SPEC_2);
    // add two rows with missing values, at the end both should be ignored
    DataCell[] row = new DataCell[2];
    row[0] = new DoubleCell(random.nextDouble());
    row[1] = DataType.getMissingCell();
    inTableCont.addRowToTable(new DefaultRow(new RowKey("Missing!1"), row));
    row[1] = new DoubleCell(random.nextDouble());
    row[0] = DataType.getMissingCell();
    inTableCont.addRowToTable(new DefaultRow(new RowKey("Missing!2"), row));
    inTableCont.close();
    BufferedDataTable inTable = inTableCont.getTable();
    // As the missing row should be ignored the test the covariance matrix computation should be the same
    CovarianceMatrixCalculator covMatrixCalculator = new CovarianceMatrixCalculator(SPEC_2, SPEC_2.getColumnNames());
    BufferedDataContainer covDataContainer = m_exec.createDataContainer(covMatrixCalculator.getResultSpec());
    RealMatrix covMatrixUnderTest = covMatrixCalculator.computeCovarianceMatrix(m_exec, inTable, covDataContainer);
    covDataContainer.close();
    Covariance covariance = new Covariance(data);
    RealMatrix referenceCovarianceMatrix = covariance.getCovarianceMatrix();
    BufferedDataTable covTableUnderTest = covDataContainer.getTable();
    // The diagonal is the variance which also changes considering missing values...
    // but we check only the part of the covariance matrix at the top right triangle.
    assertCovarianceMatrixEquality(covMatrixUnderTest, referenceCovarianceMatrix, covTableUnderTest, SPEC_2, false);
}

Example 93 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class StatisticCalculatorTest method setUp.

/**
 * @throws java.lang.Exception
 */
@Before
public void setUp() throws Exception {
    DataColumnSpec[] colSpecs = new DataColumnSpec[] { new DataColumnSpecCreator(FEATURE1, DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator(FEATURE2, DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator(STRING_FEATURE, StringCell.TYPE).createSpec() };
    DataTableSpec spec = new DataTableSpec(colSpecs);
    final BufferedDataContainer container = EXEC_CONTEXT.createDataContainer(spec);
    int i = 0;
    // values second row : miss,1,1,1,3,4,5,8    mean: 3
    // values 3rd row : miss,miss,A,B,E,F,G,H,Z  mean: F
    container.addRowToTable(creatRow(i++, 1, 1d, "A"));
    container.addRowToTable(creatRow(i++, 1, 1d, "Z"));
    container.addRowToTable(creatRow(i++, 2, 3d, "B"));
    container.addRowToTable(creatRow(i++, 2, 5d, "G"));
    container.addRowToTable(creatRow(i++, 2, 1d, "E"));
    container.addRowToTable(creatRow(i++, 6, 4d, "F"));
    container.addRowToTable(creatRow(i++, 7, null, "H"));
    container.addRowToTable(creatRow(i++, 8, null, null));
    container.addRowToTable(creatRow(i++, 8, 8d, null));
    container.close();
    testTable = container.getTable();
}

Example 94 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class BlobsInSetCellPartiallySingletonsWorkflowTest method createBDT.

/**
 * {@inheritDoc}
 */
@Override
protected BufferedDataTable createBDT(final ExecutionContext exec) {
    DataType t = ListCell.getCollectionType(DataType.getType(DataCell.class));
    BufferedDataContainer c = exec.createDataContainer(new DataTableSpec(new DataColumnSpecCreator("Sequence", t).createSpec()));
    LargeBlobCell singleton = new LargeBlobCell("singleton", LargeBlobCell.SIZE_OF_CELL);
    for (int i = 0; i < ROW_COUNT; i++) {
        String s = "someName_" + i;
        // every other a ordinary string cell
        Collection<DataCell> cells = new ArrayList<DataCell>();
        for (int j = 0; j < 4; j++) {
            String val = "Row_" + i + "; Cell index " + j;
            switch(j) {
                case 0:
                    cells.add(singleton);
                    break;
                case 1:
                case 3:
                    cells.add(new StringCell(val));
                    break;
                case 2:
                    cells.add(new LargeBlobCell(val, LargeBlobCell.SIZE_OF_CELL));
                    break;
                default:
                    fail("invalid index");
            }
        }
        ListCell cell = CollectionCellFactory.createListCell(cells);
        c.addRowToTable(new DefaultRow(s, cell));
    }
    c.close();
    return c.getTable();
}

Example 95 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class OneBlobManyTimesInTableWorkflowTest method createBDT.

/**
 * {@inheritDoc}
 */
@Override
public BufferedDataTable createBDT(final ExecutionContext exec) {
    BufferedDataContainer c = exec.createDataContainer(new DataTableSpec(new DataColumnSpecCreator("Blobs", LargeBlobCell.TYPE).createSpec()));
    LargeBlobCell cell = new LargeBlobCell("This is a big cell", LargeBlobCell.SIZE_OF_CELL);
    for (int i = 0; i < ROW_COUNT; i++) {
        String s = "someName_" + i;
        c.addRowToTable(new DefaultRow(s, cell));
    }
    c.close();
    return c.getTable();
}