Examples with DataTable org.knime.core.data.DataTable used on opensource projects

Example 26 with DataTable

use of org.knime.core.data.DataTable in project knime-core by knime.

the class PCAApplyNodeModel method execute.

/**
 * Performs the PCA.
 *
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inData, final ExecutionContext exec) throws Exception {
    final PCAModelPortObject model = (PCAModelPortObject) inData[MODEL_INPORT];
    final int dimensions = m_dimSelection.getNeededDimensions();
    if (dimensions == -1) {
        throw new IllegalArgumentException("Number of dimensions not correct configured");
    }
    if (m_failOnMissingValues.getBooleanValue()) {
        for (final DataRow row : (DataTable) inData[DATA_INPORT]) {
            for (int i = 0; i < m_inputColumnIndices.length; i++) {
                if (row.getCell(m_inputColumnIndices[i]).isMissing()) {
                    throw new IllegalArgumentException("data table contains missing values");
                }
            }
        }
    }
    final Matrix eigenvectors = EigenValue.getSortedEigenVectors(model.getEigenVectors(), model.getEigenvalues(), dimensions);
    final DataColumnSpec[] specs = PCANodeModel.createAddTableSpec((DataTableSpec) inData[DATA_INPORT].getSpec(), dimensions);
    final int dim = dimensions;
    final CellFactory fac = new CellFactory() {

        @Override
        public DataCell[] getCells(final DataRow row) {
            return PCANodeModel.convertInputRow(eigenvectors, row, model.getCenter(), m_inputColumnIndices, dim, m_failOnMissingValues.getBooleanValue());
        }

        @Override
        public DataColumnSpec[] getColumnSpecs() {
            return specs;
        }

        @Override
        public void setProgress(final int curRowNr, final int rowCount, final RowKey lastKey, final ExecutionMonitor texec) {
            texec.setProgress((double) curRowNr / rowCount, "converting input row " + curRowNr + " of " + rowCount);
        }
    };
    final ColumnRearranger cr = new ColumnRearranger((DataTableSpec) inData[DATA_INPORT].getSpec());
    cr.append(fac);
    if (m_removeOriginalCols.getBooleanValue()) {
        cr.remove(m_inputColumnNames);
    }
    final BufferedDataTable result = exec.createColumnRearrangeTable((BufferedDataTable) inData[DATA_INPORT], cr, exec);
    final PortObject[] out = { result };
    return out;
}

Example 27 with DataTable

use of org.knime.core.data.DataTable in project knime-core by knime.

the class EndcaseNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inData, final ExecutionContext exec) throws Exception {
    Vector<BufferedDataTable> tables = new Vector<BufferedDataTable>();
    for (int i = 0; i < getNrInPorts(); i++) {
        if (inData[i] != null) {
            // if connected...
            if (!(inData[i] instanceof InactiveBranchPortObject)) {
                // ...and active, add it:
                tables.add((BufferedDataTable) inData[i]);
            }
        }
    }
    if (tables.size() == 0) {
        // be connected!)
        assert inData[0] instanceof InactiveBranchPortObject;
        if (m_enableHiliting) {
            // create empty hilite translation map (so we correctly
            // handle the internals).
            Map<RowKey, Set<RowKey>> map = new HashMap<RowKey, Set<RowKey>>();
            m_hiliteTranslator.setMapper(new DefaultHiLiteMapper(map));
        }
        return new PortObject[] { inData[0] };
    }
    assert tables.size() > 0;
    // check compatibility of specs against first spec in list
    for (int i = 1; i < tables.size(); i++) {
        if (!(tables.get(0).getSpec().equalStructure(tables.get(i).getSpec()))) {
            // incompatible - refuse to execute
            throw new Exception("The data table structures of the active " + "ports are not compatible.");
        }
    }
    int totalRowCount = 0;
    DataTable[] dtables = new DataTable[tables.size()];
    int i = 0;
    for (BufferedDataTable t : tables) {
        totalRowCount += t.getRowCount();
        dtables[i] = t;
        i++;
    }
    AppendedRowsTable out = new AppendedRowsTable((m_isAppendSuffix ? m_suffix : null), dtables);
    // 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 (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() };
}

Example 28 with DataTable

use of org.knime.core.data.DataTable in project knime-core by knime.

the class CorrelationComputeNodeView method modelChanged.

/**
 * {@inheritDoc}
 */
@Override
protected void modelChanged() {
    DataTable table = getNodeModel().getCorrelationTable();
    tableChanged(table);
}

Example 29 with DataTable

use of org.knime.core.data.DataTable in project knime-core by knime.

the class ReadTableNodeModel method configure.

/**
 * {@inheritDoc}
 */
@Override
protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException {
    String warning = CheckUtils.checkSourceFile(m_fileName.getStringValue());
    if (warning != null) {
        setWarningMessage(warning);
    }
    InputStream in = null;
    try {
        in = openInputStream();
        DataTableSpec spec = peekDataTableSpec(in);
        if (spec == null) {
            // if written with 1.3.x and before
            in.close();
            in = openInputStream();
            LOGGER.debug("Table spec is not first entry in input file, " + "need to deflate entire file");
            DataTable outTable = DataContainer.readFromStream(in);
            spec = outTable.getDataTableSpec();
        }
        return new DataTableSpec[] { spec };
    } catch (IOException ioe) {
        String message = ioe.getMessage();
        if (message == null) {
            message = "Unable to read spec from file, " + "no detailed message available.";
        }
        throw new InvalidSettingsException(message);
    } finally {
        if (in != null) {
            try {
                in.close();
            } catch (IOException ioe) {
            // ignore
            }
        }
    }
}

Example 30 with DataTable

use of org.knime.core.data.DataTable in project knime-core by knime.

the class HiLiteCollectorNodeView method modelChanged.

/**
 * {@inheritDoc}
 */
@Override
public void modelChanged() {
    DataTable data = super.getNodeModel().getHiLiteAnnotationsTable();
    m_table.setDataTable(data);
    HiLiteHandler hdl = super.getNodeModel().getInHiLiteHandler(0);
    m_table.setHiLiteHandler(hdl);
    m_table.setColumnWidth(50);
}