Examples with DefaultRow org.knime.core.data.def.DefaultRow used on opensource projects

Example 66 with DefaultRow

use of org.knime.core.data.def.DefaultRow in project knime-core by knime.

the class EntropyCalculator method createScoreTable.

private static DataTable createScoreTable(final Map<RowKey, RowKey> referenceMap, final Map<RowKey, Set<RowKey>> clusteringMap) {
    ArrayList<DefaultRow> sortedRows = new ArrayList<DefaultRow>();
    // number of different clusters in reference clustering, used for
    // normalization
    int clusterCardinalityInReference = (new HashSet<RowKey>(referenceMap.values())).size();
    double normalization = Math.log(clusterCardinalityInReference) / Math.log(2.0);
    int totalSize = 0;
    for (Map.Entry<RowKey, Set<RowKey>> e : clusteringMap.entrySet()) {
        int size = e.getValue().size();
        DataCell sizeCell = new IntCell(size);
        totalSize += size;
        double entropy = entropy(referenceMap, e.getValue());
        DataCell entropyCell = new DoubleCell(entropy);
        DataCell normEntropy = new DoubleCell(entropy / normalization);
        DataCell quality = DataType.getMissingCell();
        RowKey clusterID = e.getKey();
        DefaultRow row = new DefaultRow(clusterID, sizeCell, entropyCell, normEntropy, quality);
        sortedRows.add(row);
    }
    Collections.sort(sortedRows, new Comparator<DefaultRow>() {

        @Override
        public int compare(final DefaultRow o1, final DefaultRow o2) {
            double e1 = ((DoubleValue) o1.getCell(2)).getDoubleValue();
            double e2 = ((DoubleValue) o2.getCell(2)).getDoubleValue();
            return e1 < e2 ? -1 : e1 > e2 ? 1 : 0;
        }
    });
    DataRow[] rows = sortedRows.toArray(new DataRow[0]);
    DataTableSpec tableSpec = getScoreTableSpec();
    DataContainer container = new DataContainer(tableSpec);
    for (DataRow r : rows) {
        container.addRowToTable(r);
    }
    // last row contains overall quality values
    double entropy = getEntropy(referenceMap, clusteringMap);
    double quality = getQuality(referenceMap, clusteringMap);
    DataCell entropyCell = new DoubleCell(entropy);
    DataCell normEntropy = new DoubleCell(entropy / normalization);
    DataCell qualityCell = new DoubleCell(quality);
    DataCell size = new IntCell(totalSize);
    RowKey clusterID = new RowKey("Overall");
    int uniquifier = 1;
    while (clusteringMap.containsKey(clusterID)) {
        clusterID = new RowKey("Overall (#" + (uniquifier++) + ")");
    }
    DefaultRow row = new DefaultRow(clusterID, size, entropyCell, normEntropy, qualityCell);
    container.addRowToTable(row);
    container.close();
    return container.getTable();
}

Example 67 with DefaultRow

use of org.knime.core.data.def.DefaultRow in project knime-core by knime.

the class PolyRegLearnerNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inData, final ExecutionContext exec) throws Exception {
    BufferedDataTable inTable = (BufferedDataTable) inData[0];
    DataTableSpec inSpec = inTable.getDataTableSpec();
    final int colCount = inSpec.getNumColumns();
    String[] selectedCols = computeSelectedColumns(inSpec);
    Set<String> hash = new HashSet<String>(Arrays.asList(selectedCols));
    m_colSelected = new boolean[colCount];
    for (int i = 0; i < colCount; i++) {
        m_colSelected[i] = hash.contains(inTable.getDataTableSpec().getColumnSpec(i).getName());
    }
    final int rowCount = inTable.getRowCount();
    String[] temp = new String[m_columnNames.length + 1];
    System.arraycopy(m_columnNames, 0, temp, 0, m_columnNames.length);
    temp[temp.length - 1] = m_settings.getTargetColumn();
    FilterColumnTable filteredTable = new FilterColumnTable(inTable, temp);
    final DataArray rowContainer = new DefaultDataArray(filteredTable, 1, m_settings.getMaxRowsForView());
    // handle the optional PMML input
    PMMLPortObject inPMMLPort = m_pmmlInEnabled ? (PMMLPortObject) inData[1] : null;
    PortObjectSpec[] outputSpec = configure((inPMMLPort == null) ? new PortObjectSpec[] { inData[0].getSpec(), null } : new PortObjectSpec[] { inData[0].getSpec(), inPMMLPort.getSpec() });
    Learner learner = new Learner((PMMLPortObjectSpec) outputSpec[0], 0d, m_settings.getMissingValueHandling() == MissingValueHandling.fail, m_settings.getDegree());
    try {
        PolyRegContent polyRegContent = learner.perform(inTable, exec);
        m_betas = fillBeta(polyRegContent);
        m_meanValues = polyRegContent.getMeans();
        ColumnRearranger crea = new ColumnRearranger(inTable.getDataTableSpec());
        crea.append(getCellFactory(inTable.getDataTableSpec().findColumnIndex(m_settings.getTargetColumn())));
        PortObject[] bdt = new PortObject[] { createPMMLModel(inPMMLPort, inSpec), exec.createColumnRearrangeTable(inTable, crea, exec.createSilentSubExecutionContext(.2)), polyRegContent.createTablePortObject(exec.createSubExecutionContext(0.2)) };
        m_squaredError /= rowCount;
        if (polyRegContent.getWarningMessage() != null) {
            setWarningMessage(polyRegContent.getWarningMessage());
        }
        double[] stdErrors = PolyRegViewData.mapToArray(polyRegContent.getStandardErrors(), m_columnNames, m_settings.getDegree(), polyRegContent.getInterceptStdErr());
        double[] tValues = PolyRegViewData.mapToArray(polyRegContent.getTValues(), m_columnNames, m_settings.getDegree(), polyRegContent.getInterceptTValue());
        double[] pValues = PolyRegViewData.mapToArray(polyRegContent.getPValues(), m_columnNames, m_settings.getDegree(), polyRegContent.getInterceptPValue());
        m_viewData = new PolyRegViewData(m_meanValues, m_betas, stdErrors, tValues, pValues, m_squaredError, polyRegContent.getAdjustedRSquared(), m_columnNames, m_settings.getDegree(), m_settings.getTargetColumn(), rowContainer);
        return bdt;
    } catch (ModelSpecificationException e) {
        final String origWarning = getWarningMessage();
        final String warning = (origWarning != null && !origWarning.isEmpty()) ? (origWarning + "\n") : "" + e.getMessage();
        setWarningMessage(warning);
        final ExecutionContext subExec = exec.createSubExecutionContext(.1);
        final BufferedDataContainer empty = subExec.createDataContainer(STATS_SPEC);
        int rowIdx = 1;
        for (final String column : m_columnNames) {
            for (int d = 1; d <= m_settings.getDegree(); ++d) {
                empty.addRowToTable(new DefaultRow("Row" + rowIdx++, new StringCell(column), new IntCell(d), new DoubleCell(0.0d), DataType.getMissingCell(), DataType.getMissingCell(), DataType.getMissingCell()));
            }
        }
        empty.addRowToTable(new DefaultRow("Row" + rowIdx, new StringCell("Intercept"), new IntCell(0), new DoubleCell(0.0d), DataType.getMissingCell(), DataType.getMissingCell(), DataType.getMissingCell()));
        double[] nans = new double[m_columnNames.length * m_settings.getDegree() + 1];
        Arrays.fill(nans, Double.NaN);
        m_betas = new double[nans.length];
        // Mean only for the linear tags
        m_meanValues = new double[nans.length / m_settings.getDegree()];
        m_viewData = new PolyRegViewData(m_meanValues, m_betas, nans, nans, nans, m_squaredError, Double.NaN, m_columnNames, m_settings.getDegree(), m_settings.getTargetColumn(), rowContainer);
        empty.close();
        ColumnRearranger crea = new ColumnRearranger(inTable.getDataTableSpec());
        crea.append(getCellFactory(inTable.getDataTableSpec().findColumnIndex(m_settings.getTargetColumn())));
        BufferedDataTable rearrangerTable = exec.createColumnRearrangeTable(inTable, crea, exec.createSubProgress(0.6));
        PMMLPortObject model = createPMMLModel(inPMMLPort, inTable.getDataTableSpec());
        PortObject[] bdt = new PortObject[] { model, rearrangerTable, empty.getTable() };
        return bdt;
    }
}

Example 68 with DefaultRow

use of org.knime.core.data.def.DefaultRow in project knime-core by knime.

the class HierarchicalClusterNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected BufferedDataTable[] execute(final BufferedDataTable[] data, final ExecutionContext exec) throws Exception {
    // determine the indices of the selected columns
    List<String> inlcludedCols = m_selectedColumns.getIncludeList();
    int[] selectedColIndices = new int[inlcludedCols.size()];
    for (int count = 0; count < selectedColIndices.length; count++) {
        selectedColIndices[count] = data[0].getDataTableSpec().findColumnIndex(inlcludedCols.get(count));
    }
    BufferedDataTable inputData = data[0];
    if (inputData.size() > 65500) {
        throw new RuntimeException("At most 65,500 patterns can be clustered");
    }
    DataTable outputData = null;
    if (DistanceFunction.Names.Manhattan.toString().equals(m_distFunctionName.getStringValue())) {
        m_distFunction = ManhattanDist.MANHATTEN_DISTANCE;
    } else {
        m_distFunction = EuclideanDist.EUCLIDEAN_DISTANCE;
    }
    // generate initial clustering
    // which means that every data point is one cluster
    List<ClusterNode> clusters = initClusters(inputData, exec);
    // store the distance per each fusion step
    DataContainer fusionCont = exec.createDataContainer(createFusionSpec());
    int iterationStep = 0;
    final HalfFloatMatrix cache;
    if (m_cacheDistances.getBooleanValue()) {
        cache = new HalfFloatMatrix((int) inputData.size(), false);
        cache.fill(Float.NaN);
    } else {
        cache = null;
    }
    double max = inputData.size();
    // the number of clusters at the beginning is equal to the number
    // of data rows (each row is a cluster)
    int numberDataRows = clusters.size();
    while (clusters.size() > 1) {
        // checks if number clusters to generate output table is reached
        if (m_numClustersForOutput.getIntValue() == clusters.size()) {
            outputData = createResultTable(inputData, clusters, exec);
        }
        exec.setProgress((numberDataRows - clusters.size()) / (double) numberDataRows, clusters.size() + " clusters left to merge.");
        iterationStep++;
        exec.setProgress(iterationStep / max, "Iteration " + iterationStep + ", " + clusters.size() + " clusters remaining");
        // calculate distance between all clusters
        float currentSmallestDist = Float.MAX_VALUE;
        ClusterNode currentClosestCluster1 = null;
        ClusterNode currentClosestCluster2 = null;
        // subprogress for loop
        double availableProgress = (1.0 / numberDataRows);
        ExecutionContext subexec = exec.createSubExecutionContext(availableProgress);
        for (int i = 0; i < clusters.size(); i++) {
            exec.checkCanceled();
            ClusterNode node1 = clusters.get(i);
            for (int j = i + 1; j < clusters.size(); j++) {
                final float dist;
                ClusterNode node2 = clusters.get(j);
                // and average linkage supported.
                if (m_linkageType.getStringValue().equals(Linkage.SINGLE.name())) {
                    dist = calculateSingleLinkageDist(node1, node2, cache, selectedColIndices);
                } else if (m_linkageType.getStringValue().equals(Linkage.AVERAGE.name())) {
                    dist = calculateAverageLinkageDist(node1, node2, cache, selectedColIndices);
                } else {
                    dist = calculateCompleteLinkageDist(node1, node2, cache, selectedColIndices);
                }
                if (dist < currentSmallestDist) {
                    currentClosestCluster1 = node1;
                    currentClosestCluster2 = node2;
                    currentSmallestDist = dist;
                }
            }
        }
        subexec.setProgress(1.0);
        // make one cluster of the two closest
        ClusterNode newNode = new ClusterNode(currentClosestCluster1, currentClosestCluster2, currentSmallestDist);
        clusters.remove(currentClosestCluster1);
        clusters.remove(currentClosestCluster2);
        clusters.add(newNode);
        // store the distance per each fusion step
        fusionCont.addRowToTable(new DefaultRow(// row key
        Integer.toString(clusters.size()), // x-axis scatter plotter
        new IntCell(clusters.size()), // y-axis scatter plotter
        new DoubleCell(newNode.getDist())));
    // // print number clusters and their data points
    // LOGGER.debug("Iteration " + iterationStep + ":");
    // LOGGER.debug(" Number Clusters: " + clusters.size());
    // printClustersDataRows(clusters);
    }
    if (clusters.size() > 0) {
        m_rootNode = clusters.get(0);
    }
    fusionCont.close();
    // if there was no input data create an empty output data
    if (outputData == null) {
        outputData = createResultTable(inputData, clusters, exec);
    }
    m_dataArray = new DefaultDataArray(inputData, 1, (int) inputData.size());
    m_fusionTable = new DefaultDataArray(fusionCont.getTable(), 1, iterationStep);
    return new BufferedDataTable[] { exec.createBufferedDataTable(outputData, exec) };
}

Example 69 with DefaultRow

use of org.knime.core.data.def.DefaultRow in project knime-core by knime.

the class DecTreePredictorNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
public PortObject[] execute(final PortObject[] inPorts, final ExecutionContext exec) throws CanceledExecutionException, Exception {
    exec.setMessage("Decision Tree Predictor: Loading predictor...");
    PMMLPortObject port = (PMMLPortObject) inPorts[INMODELPORT];
    List<Node> models = port.getPMMLValue().getModels(PMMLModelType.TreeModel);
    if (models.isEmpty()) {
        String msg = "Decision Tree evaluation failed: " + "No tree model found.";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
    }
    PMMLDecisionTreeTranslator trans = new PMMLDecisionTreeTranslator();
    port.initializeModelTranslator(trans);
    DecisionTree decTree = trans.getDecisionTree();
    decTree.resetColorInformation();
    BufferedDataTable inData = (BufferedDataTable) inPorts[INDATAPORT];
    // get column with color information
    String colorColumn = null;
    for (DataColumnSpec s : inData.getDataTableSpec()) {
        if (s.getColorHandler() != null) {
            colorColumn = s.getName();
            break;
        }
    }
    decTree.setColorColumn(colorColumn);
    exec.setMessage("Decision Tree Predictor: start execution.");
    PortObjectSpec[] inSpecs = new PortObjectSpec[] { inPorts[0].getSpec(), inPorts[1].getSpec() };
    DataTableSpec outSpec = createOutTableSpec(inSpecs);
    BufferedDataContainer outData = exec.createDataContainer(outSpec);
    long coveredPattern = 0;
    long nrPattern = 0;
    long rowCount = 0;
    final long numberRows = inData.size();
    exec.setMessage("Classifying...");
    List<String> predictionValues = getPredictionStrings((PMMLPortObjectSpec) inPorts[INMODELPORT].getSpec());
    for (DataRow thisRow : inData) {
        DataCell cl = null;
        LinkedHashMap<String, Double> classDistrib = null;
        try {
            Pair<DataCell, LinkedHashMap<DataCell, Double>> pair = decTree.getWinnerAndClasscounts(thisRow, inData.getDataTableSpec());
            cl = pair.getFirst();
            LinkedHashMap<DataCell, Double> classCounts = pair.getSecond();
            classDistrib = getDistribution(classCounts);
            if (coveredPattern < m_maxNumCoveredPattern.getIntValue()) {
                // remember this one for HiLite support
                decTree.addCoveredPattern(thisRow, inData.getDataTableSpec());
                coveredPattern++;
            } else {
                // too many patterns for HiLite - at least remember color
                decTree.addCoveredColor(thisRow, inData.getDataTableSpec());
            }
            nrPattern++;
        } catch (Exception e) {
            LOGGER.error("Decision Tree evaluation failed: " + e.getMessage());
            throw e;
        }
        if (cl == null) {
            LOGGER.error("Decision Tree evaluation failed: result empty");
            throw new Exception("Decision Tree evaluation failed.");
        }
        DataCell[] newCells = new DataCell[outSpec.getNumColumns()];
        int numInCells = thisRow.getNumCells();
        for (int i = 0; i < numInCells; i++) {
            newCells[i] = thisRow.getCell(i);
        }
        if (m_showDistribution.getBooleanValue()) {
            assert predictionValues.size() >= newCells.length - 1 - numInCells : "Could not determine the prediction values: " + newCells.length + "; " + numInCells + "; " + predictionValues;
            for (int i = numInCells; i < newCells.length - 1; i++) {
                String predClass = predictionValues.get(i - numInCells);
                if (classDistrib != null && classDistrib.get(predClass) != null) {
                    newCells[i] = new DoubleCell(classDistrib.get(predClass));
                } else {
                    newCells[i] = new DoubleCell(0.0);
                }
            }
        }
        newCells[newCells.length - 1] = cl;
        outData.addRowToTable(new DefaultRow(thisRow.getKey(), newCells));
        rowCount++;
        if (rowCount % 100 == 0) {
            exec.setProgress(rowCount / (double) numberRows, "Classifying... Row " + rowCount + " of " + numberRows);
        }
        exec.checkCanceled();
    }
    if (coveredPattern < nrPattern) {
        // let the user know that we did not store all available pattern
        // for HiLiting.
        this.setWarningMessage("Tree only stored first " + m_maxNumCoveredPattern.getIntValue() + " (of " + nrPattern + ") rows for HiLiting!");
    }
    outData.close();
    m_decTree = decTree;
    exec.setMessage("Decision Tree Predictor: end execution.");
    return new BufferedDataTable[] { outData.getTable() };
}

Example 70 with DefaultRow

use of org.knime.core.data.def.DefaultRow in project knime-core by knime.

the class PCANodeModel method createCovarianceTable.

/**
 * create data table from covariance matrix.
 *
 * @param exec
 *            execution context
 * @param m
 *            covariance matrix
 * @param inputColumnNames
 *            names of input columns the matrix was created from
 * @return table
 */
public static BufferedDataTable createCovarianceTable(final ExecutionContext exec, final double[][] m, final String[] inputColumnNames) {
    final BufferedDataContainer bdt = exec.createDataContainer(createCovarianceMatrixSpec(inputColumnNames));
    for (int i = 0; i < m.length; i++) {
        final DataCell[] cells = new DataCell[inputColumnNames.length];
        for (int j = 0; j < m[i].length; j++) {
            cells[j] = new DoubleCell(m[i][j]);
        }
        bdt.addRowToTable(new DefaultRow(inputColumnNames[i], cells));
    }
    bdt.close();
    final BufferedDataTable covarianceTable = bdt.getTable();
    return covarianceTable;
}