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

Example 41 with BufferedDataContainer

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

the class StatisticCalculatorTest method createRandomTableWithMissingValues.

private static BufferedDataTable createRandomTableWithMissingValues(final int cols, final int rows) {
    long currentTimeMillis = System.currentTimeMillis();
    System.out.println("Using seed: " + currentTimeMillis);
    Random random = new Random(currentTimeMillis);
    DataTableSpecCreator creator = new DataTableSpecCreator();
    for (int i = 0; i < cols; i++) {
        creator.addColumns(new DataColumnSpecCreator("" + i, DoubleCell.TYPE).createSpec());
    }
    final BufferedDataContainer container = EXEC_CONTEXT.createDataContainer(creator.createSpec());
    for (int i = 0; i < rows; i++) {
        DataCell[] rowVals = new DataCell[cols];
        for (int j = 0; j < cols; j++) {
            rowVals[j] = random.nextDouble() > 0.66 ? new DoubleCell(random.nextDouble()) : DataType.getMissingCell();
        }
        container.addRowToTable(new DefaultRow(Integer.toString(i), rowVals));
        if (i % 1000 == 0) {
            System.out.println("Added row: " + i);
        }
    }
    container.close();
    return container.getTable();
}

Example 42 with BufferedDataContainer

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

the class LogisticRegressionContent method createCoeffStatisticsTablePortObject.

/**
 * Creates a BufferedDataTable with the
 * @param exec The execution context
 * @return a port object
 */
public BufferedDataTable createCoeffStatisticsTablePortObject(final ExecutionContext exec) {
    DataTableSpec tableOutSpec = LogRegCoordinator.createCoeffStatisticsTableSpec();
    BufferedDataContainer dc = exec.createDataContainer(tableOutSpec);
    List<DataCell> logits = this.getLogits();
    List<String> parameters = this.getParameters();
    int c = 0;
    for (DataCell logit : logits) {
        Map<String, Double> coefficients = this.getCoefficients(logit);
        Map<String, Double> stdErrs;
        Map<String, Double> zScores;
        Map<String, Double> pValues;
        if (m_covMat == null) {
            HashMap<String, Double> emptyMap = new HashMap<>();
            stdErrs = emptyMap;
            zScores = emptyMap;
            pValues = emptyMap;
        } else {
            stdErrs = this.getStandardErrors(logit);
            zScores = this.getZScores(logit);
            pValues = this.getPValues(logit);
        }
        for (String parameter : parameters) {
            List<DataCell> cells = new ArrayList<>();
            cells.add(new StringCell(logit.toString()));
            cells.add(new StringCell(parameter));
            cells.add(new DoubleCell(coefficients.get(parameter)));
            if (m_covMat != null) {
                cells.add(new DoubleCell(stdErrs.get(parameter)));
                cells.add(new DoubleCell(zScores.get(parameter)));
                cells.add(new DoubleCell(pValues.get(parameter)));
            } else {
                cells.add(NOT_INVERTIBLE_MISSING);
                cells.add(NOT_INVERTIBLE_MISSING);
                cells.add(NOT_INVERTIBLE_MISSING);
            }
            c++;
            dc.addRowToTable(new DefaultRow("Row" + c, cells));
        }
        List<DataCell> cells = new ArrayList<>();
        cells.add(new StringCell(logit.toString()));
        cells.add(new StringCell("Constant"));
        cells.add(new DoubleCell(this.getIntercept(logit)));
        if (m_covMat != null) {
            cells.add(new DoubleCell(this.getInterceptStdErr(logit)));
            cells.add(new DoubleCell(this.getInterceptZScore(logit)));
            cells.add(new DoubleCell(this.getInterceptPValue(logit)));
        } else {
            cells.add(NOT_INVERTIBLE_MISSING);
            cells.add(NOT_INVERTIBLE_MISSING);
            cells.add(NOT_INVERTIBLE_MISSING);
        }
        c++;
        dc.addRowToTable(new DefaultRow("Row" + c, cells));
    }
    dc.close();
    return dc.getTable();
}

Example 43 with BufferedDataContainer

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

the class AbstractColumnTableSorterTest method setUp.

/**
 * @throws java.lang.Exception
 */
@SuppressWarnings("rawtypes")
@Before
public void setUp() throws Exception {
    @SuppressWarnings("unchecked") NodeFactory<NodeModel> dummyFactory = (NodeFactory) new VirtualParallelizedChunkPortObjectInNodeFactory(new PortType[0]);
    m_exec = new ExecutionContext(new DefaultNodeProgressMonitor(), new Node(dummyFactory), SingleNodeContainer.MemoryPolicy.CacheOnDisc, new HashMap<Integer, ContainerTable>());
    DataColumnSpec[] colSpecs = new DataColumnSpec[] { new DataColumnSpecCreator(FEATURE1, DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator(FEATURE2, DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator(STRING_FEATURE, StringCell.TYPE).createSpec(), new DataColumnSpecCreator(CLASS, StringCell.TYPE).createSpec() };
    DataTableSpec spec = new DataTableSpec(colSpecs);
    final BufferedDataContainer container = m_exec.createDataContainer(spec);
    int i = 0;
    container.addRowToTable(creatRow(i++, 1, 8, "A", "AClass8"));
    container.addRowToTable(creatRow(i++, 2, 2, "Z", "ZClass2"));
    container.addRowToTable(creatRow(i++, 3, 5, "B", "BClass5"));
    container.addRowToTable(creatRow(i++, 4, 0, "E", "EClass0"));
    container.addRowToTable(creatRow(i++, 5, 1, "F", "FClass1"));
    container.addRowToTable(creatRow(i++, 6, 7, "G", "GClass7"));
    container.addRowToTable(creatRow(i++, 7, 9, "H", "HClass9"));
    container.addRowToTable(creatRow(i++, 8, 8, null, "Class8"));
    container.close();
    testTable = container.getTable();
    final BufferedDataContainer emptyContainer = m_exec.createDataContainer(spec);
    emptyContainer.close();
    emptyTestTable = emptyContainer.getTable();
    MemoryAlertSystemTest.forceGC();
}

Example 44 with BufferedDataContainer

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

the class EndifNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] rawInData, final ExecutionContext exec) throws Exception {
    if (m_enableHiliting) {
        // create empty hilite translation map (so we correctly
        // handle the internals even if we return with a IBPO:
        Map<RowKey, Set<RowKey>> map = new HashMap<RowKey, Set<RowKey>>();
        m_hiliteTranslator.setMapper(new DefaultHiLiteMapper(map));
    }
    if (rawInData[0] instanceof InactiveBranchPortObject) {
        return new PortObject[] { rawInData[1] };
    }
    if (rawInData[1] instanceof InactiveBranchPortObject) {
        return new PortObject[] { rawInData[0] };
    }
    // no inactive branch - check compatibility of specs - which in
    // this case must be BFT Specs!
    DataTableSpec spec0 = (DataTableSpec) (rawInData[0].getSpec());
    DataTableSpec spec1 = (DataTableSpec) (rawInData[1].getSpec());
    if (spec0.equalStructure(spec1)) {
        // concatenate tables and return result
        BufferedDataTable[] inData = new BufferedDataTable[2];
        inData[0] = (BufferedDataTable) rawInData[0];
        inData[1] = (BufferedDataTable) rawInData[1];
        int totalRowCount = 0;
        for (BufferedDataTable t : inData) {
            totalRowCount += t.getRowCount();
        }
        AppendedRowsTable out = new AppendedRowsTable((m_isAppendSuffix ? m_suffix : null), inData);
        // note, this iterator throws runtime exceptions when canceled.
        AppendedRowsIterator it = out.iterator(exec, totalRowCount);
        BufferedDataContainer c = exec.createDataContainer(out.getDataTableSpec());
        try {
            while (it.hasNext()) {
                // may throw exception, also sets progress
                c.addRowToTable(it.next());
            }
        } catch (AppendedRowsIterator.RuntimeCanceledExecutionException rcee) {
            throw rcee.getCause();
        } finally {
            c.close();
        }
        if (it.getNrRowsSkipped() > 0) {
            setWarningMessage("Filtered out " + it.getNrRowsSkipped() + " duplicate row id(s).");
        }
        if (m_enableHiliting) {
            // create hilite translation map
            Map<RowKey, Set<RowKey>> map = new HashMap<RowKey, Set<RowKey>>();
            // map of all RowKeys and duplicate RowKeys in the resulting table
            Map<RowKey, RowKey> dupMap = it.getDuplicateNameMap();
            for (Map.Entry<RowKey, RowKey> e : dupMap.entrySet()) {
                // if a duplicate key
                if (!e.getKey().equals(e.getValue())) {
                    Set<RowKey> set = Collections.singleton(e.getValue());
                    // put duplicate key and original key into map
                    map.put(e.getKey(), set);
                } else {
                    // skip duplicate keys
                    if (!dupMap.containsKey(new RowKey(e.getKey().getString() + m_suffix))) {
                        Set<RowKey> set = Collections.singleton(e.getValue());
                        map.put(e.getKey(), set);
                    }
                }
            }
            m_hiliteTranslator.setMapper(new DefaultHiLiteMapper(map));
        }
        return new BufferedDataTable[] { c.getTable() };
    }
    throw new Exception("Both input ports have data but the tables " + "have incompatible specs");
}

Example 45 with BufferedDataContainer

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

the class AdapterNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inObjects, final ExecutionContext exec) throws Exception {
    if (getNrInPorts() == 0 && getNrOutPorts() == 1) {
        // assume simple source node with one table output
        BufferedDataContainer cnt = exec.createDataContainer(createDefaultOutputSpec());
        cnt.addRowToTable(new DefaultRow(RowKey.createRowKey(0), new DataCell[] { new StringCell("Cell-1.1"), new IntCell(12), new DoubleCell(1.3) }));
        cnt.addRowToTable(new DefaultRow(RowKey.createRowKey(1), new DataCell[] { new StringCell("Cell-2.1"), new IntCell(22), new DoubleCell(2.3) }));
        cnt.addRowToTable(new DefaultRow(RowKey.createRowKey(2), new DataCell[] { new StringCell("Cell-3.1"), new IntCell(32), new DoubleCell(3.3) }));
        cnt.close();
        return new BufferedDataTable[] { cnt.getTable() };
    }
    return inObjects;
}