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

Example 51 with CanceledExecutionException

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

the class AppendedRowsIterator method initNextRow.

/**
 * Get next row internally.
 */
private void initNextRow() {
    // reached end of table's iterator - take next
    if (!m_curIterator.hasNext()) {
        do {
            if (m_curItIndex < m_iteratorSuppliers.length - 1) {
                initNextTable();
            } else {
                // final end
                m_nextRow = null;
                // reached end of this table
                return;
            }
        } while (!m_curIterator.hasNext());
    }
    // row from table
    DataRow baseRow = m_curIterator.next();
    m_curRowIndex++;
    boolean keyHasChanged = false;
    RowKey origKey = baseRow.getKey();
    RowKey key = origKey;
    while (m_duplicateMap.containsKey(key)) {
        if (m_exec != null) {
            try {
                m_exec.checkCanceled();
            } catch (CanceledExecutionException cee) {
                throw new RuntimeCanceledExecutionException(cee);
            }
        }
        switch(m_duplPolicy) {
            case Fail:
                assert false : "Duplicate checking is done in the BDT";
                throw new RuntimeException("Duplicate key \"" + key + "\"");
            case Skip:
                if (!m_hasPrintedError) {
                    LOGGER.warn("Table contains duplicate entry \"" + key.toString() + "\", skipping this row. " + "Suppress further warnings.");
                    m_hasPrintedError = true;
                }
                if (!m_curIterator.hasNext()) {
                    // end of one table reached
                    // note, this causes one more call on the stack
                    // (but who wants to concatenate 60000 tables...)
                    initNextRow();
                    return;
                }
                if (m_exec != null) {
                    m_nrRowsSkipped++;
                    String message = "Skipping row " + m_curRowIndex + " (\"" + key.toString() + "\")";
                    if (m_totalRowCount > 0L) {
                        m_exec.setProgress(m_curRowIndex / (double) m_totalRowCount, message);
                    } else {
                        m_exec.setMessage(message);
                    }
                }
                // row from table
                baseRow = m_curIterator.next();
                m_curRowIndex++;
                // stays false! rows have been skipped.
                keyHasChanged = false;
                origKey = baseRow.getKey();
                key = origKey;
                break;
            case AppendSuffix:
                // first time we come here
                if (!keyHasChanged && m_exec != null) {
                    String message = "Unifying row " + m_curRowIndex + " (\"" + key.toString() + "\")";
                    if (m_totalRowCount > 0L) {
                        m_exec.setProgress(m_curRowIndex / (double) m_totalRowCount, message);
                    } else {
                        m_exec.setMessage(message);
                    }
                }
                keyHasChanged = true;
                String newId = key.toString() + m_suffix;
                key = new RowKey(newId);
                // to do duplicate handling.
                break;
            default:
                throw new RuntimeException("Unknown policy: " + m_duplPolicy);
        }
    }
    switch(m_duplPolicy) {
        case Fail:
            // to do a efficient duplicate checking
            break;
        default:
            m_duplicateMap.put(key, origKey);
    }
    if (m_exec != null) {
        try {
            m_exec.checkCanceled();
        } catch (CanceledExecutionException cee) {
            throw new RuntimeCanceledExecutionException(cee);
        }
        String message = "Adding row " + m_curRowIndex + " (\"" + key.toString() + "\"" + (keyHasChanged ? " uniquified)" : ")");
        if (m_totalRowCount > 0L) {
            m_exec.setProgress(m_curRowIndex / (double) m_totalRowCount, message);
        } else {
            m_exec.setMessage(message);
        }
    }
    DataRow nextRow;
    if (m_curMissingCells != null) {
        // no missing cells implies the base row is complete
        assert (m_curMissingCells.length + baseRow.getNumCells() == m_spec.getNumColumns());
        // row enlarged by "missing" columns
        DataRow filledBaseRow = new AppendedColumnRow(baseRow, m_curMissingCells);
        nextRow = new ResortedCellsRow(filledBaseRow, m_curMapping);
    } else {
        nextRow = baseRow;
    }
    if (keyHasChanged) {
        DataCell[] cells = new DataCell[nextRow.getNumCells()];
        for (int i = 0; i < cells.length; i++) {
            cells[i] = nextRow.getCell(i);
        }
        m_nextRow = new DefaultRow(key, cells);
    } else {
        m_nextRow = nextRow;
    }
}

Example 52 with CanceledExecutionException

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

the class TreeEnsembleLearner method learnEnsemble.

public TreeEnsembleModel learnEnsemble(final ExecutionMonitor exec) throws CanceledExecutionException, ExecutionException {
    final int nrModels = m_config.getNrModels();
    final RandomData rd = m_config.createRandomData();
    final ThreadPool tp = KNIMEConstants.GLOBAL_THREAD_POOL;
    final AtomicReference<Throwable> learnThrowableRef = new AtomicReference<Throwable>();
    @SuppressWarnings("unchecked") final Future<TreeLearnerResult>[] modelFutures = new Future[nrModels];
    final int procCount = 3 * Runtime.getRuntime().availableProcessors() / 2;
    final Semaphore semaphore = new Semaphore(procCount);
    Callable<TreeLearnerResult[]> learnCallable = new Callable<TreeLearnerResult[]>() {

        @Override
        public TreeLearnerResult[] call() throws Exception {
            final TreeLearnerResult[] results = new TreeLearnerResult[nrModels];
            for (int i = 0; i < nrModels; i++) {
                semaphore.acquire();
                finishedTree(i - procCount, exec);
                checkThrowable(learnThrowableRef);
                RandomData rdSingle = TreeEnsembleLearnerConfiguration.createRandomData(rd.nextLong(Long.MIN_VALUE, Long.MAX_VALUE));
                ExecutionMonitor subExec = exec.createSubProgress(0.0);
                modelFutures[i] = tp.enqueue(new TreeLearnerCallable(subExec, rdSingle, learnThrowableRef, semaphore));
            }
            for (int i = 0; i < procCount; i++) {
                semaphore.acquire();
                finishedTree(nrModels - 1 + i - procCount, exec);
            }
            for (int i = 0; i < nrModels; i++) {
                try {
                    results[i] = modelFutures[i].get();
                } catch (Exception e) {
                    learnThrowableRef.compareAndSet(null, e);
                }
            }
            return results;
        }

        private void finishedTree(final int treeIndex, final ExecutionMonitor progMon) {
            if (treeIndex > 0) {
                progMon.setProgress(treeIndex / (double) nrModels, "Tree " + treeIndex + "/" + nrModels);
            }
        }
    };
    TreeLearnerResult[] modelResults = tp.runInvisible(learnCallable);
    checkThrowable(learnThrowableRef);
    AbstractTreeModel[] models = new AbstractTreeModel[nrModels];
    m_rowSamples = new RowSample[nrModels];
    m_columnSampleStrategies = new ColumnSampleStrategy[nrModels];
    for (int i = 0; i < nrModels; i++) {
        models[i] = modelResults[i].m_treeModel;
        m_rowSamples[i] = modelResults[i].m_rowSample;
        m_columnSampleStrategies[i] = modelResults[i].m_rootColumnSampleStrategy;
    }
    m_ensembleModel = new TreeEnsembleModel(m_config, m_data.getMetaData(), models, m_data.getTreeType());
    return m_ensembleModel;
}

Example 53 with CanceledExecutionException

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

the class IrlsLearner method learn.

/**
 * {@inheritDoc}
 */
@Override
public LogRegLearnerResult learn(final TrainingData<ClassificationTrainingRow> trainingData, final ExecutionMonitor exec) throws CanceledExecutionException, InvalidSettingsException {
    exec.checkCanceled();
    int iter = 0;
    boolean converged = false;
    final int tcC = trainingData.getTargetDimension() + 1;
    final int rC = trainingData.getFeatureCount() - 1;
    final RealMatrix beta = MatrixUtils.createRealMatrix(1, (tcC - 1) * (rC + 1));
    Double loglike = 0.0;
    Double loglikeOld = 0.0;
    exec.setMessage("Iterative optimization. Processing iteration 1.");
    // main loop
    while (iter < m_maxIter && !converged) {
        RealMatrix betaOld = beta.copy();
        loglikeOld = loglike;
        // Do heavy work in a separate thread which allows to interrupt it
        // note the queue may block if no more threads are available (e.g. thread count = 1)
        // as soon as we stall in 'get' this thread reduces the number of running thread
        Future<Double> future = ThreadPool.currentPool().enqueue(new Callable<Double>() {

            @Override
            public Double call() throws Exception {
                final ExecutionMonitor progMon = exec.createSubProgress(1.0 / m_maxIter);
                irlsRls(trainingData, beta, rC, tcC, progMon);
                progMon.setProgress(1.0);
                return likelihood(trainingData.iterator(), beta, rC, tcC, exec);
            }
        });
        try {
            loglike = future.get();
        } catch (InterruptedException e) {
            future.cancel(true);
            exec.checkCanceled();
            throw new RuntimeException(e);
        } catch (ExecutionException e) {
            if (e.getCause() instanceof RuntimeException) {
                throw (RuntimeException) e.getCause();
            } else {
                throw new RuntimeException(e.getCause());
            }
        }
        if (Double.isInfinite(loglike) || Double.isNaN(loglike)) {
            throw new RuntimeException(FAILING_MSG);
        }
        exec.checkCanceled();
        // test for decreasing likelihood
        while ((Double.isInfinite(loglike) || Double.isNaN(loglike) || loglike < loglikeOld) && iter > 0) {
            converged = true;
            for (int k = 0; k < beta.getColumnDimension(); k++) {
                if (abs(beta.getEntry(0, k) - betaOld.getEntry(0, k)) > m_eps * abs(betaOld.getEntry(0, k))) {
                    converged = false;
                    break;
                }
            }
            if (converged) {
                break;
            }
            // half the step size of beta
            beta.setSubMatrix((beta.add(betaOld)).scalarMultiply(0.5).getData(), 0, 0);
            exec.checkCanceled();
            loglike = likelihood(trainingData.iterator(), beta, rC, tcC, exec);
            exec.checkCanceled();
        }
        // test for convergence
        converged = true;
        for (int k = 0; k < beta.getColumnDimension(); k++) {
            if (abs(beta.getEntry(0, k) - betaOld.getEntry(0, k)) > m_eps * abs(betaOld.getEntry(0, k))) {
                converged = false;
                break;
            }
        }
        iter++;
        LOGGER.debug("#Iterations: " + iter);
        LOGGER.debug("Log Likelihood: " + loglike);
        StringBuilder betaBuilder = new StringBuilder();
        for (int i = 0; i < beta.getColumnDimension() - 1; i++) {
            betaBuilder.append(Double.toString(beta.getEntry(0, i)));
            betaBuilder.append(", ");
        }
        if (beta.getColumnDimension() > 0) {
            betaBuilder.append(Double.toString(beta.getEntry(0, beta.getColumnDimension() - 1)));
        }
        LOGGER.debug("beta: " + betaBuilder.toString());
        exec.checkCanceled();
        exec.setMessage("Iterative optimization. #Iterations: " + iter + " | Log-likelihood: " + DoubleFormat.formatDouble(loglike) + ". Processing iteration " + (iter + 1) + ".");
    }
    StringBuilder warnBuilder = new StringBuilder();
    if (iter >= m_maxIter) {
        warnBuilder.append("The algorithm did not reach convergence after the specified number of epochs. " + "Setting the epoch limit higher might result in a better model.");
    }
    // The covariance matrix
    RealMatrix covMat = null;
    if (m_calcCovMatrix) {
        try {
            covMat = new QRDecomposition(A).getSolver().getInverse().scalarMultiply(-1);
        } catch (SingularMatrixException sme) {
            if (warnBuilder.length() > 0) {
                warnBuilder.append("\n");
            }
            warnBuilder.append("The covariance matrix could not be calculated because the" + " observed fisher information matrix was singular.");
        }
    }
    RealMatrix betaMat = MatrixUtils.createRealMatrix(tcC - 1, rC + 1);
    for (int i = 0; i < beta.getColumnDimension(); i++) {
        int r = i / (rC + 1);
        int c = i % (rC + 1);
        betaMat.setEntry(r, c, beta.getEntry(0, i));
    }
    m_warning = warnBuilder.length() > 0 ? warnBuilder.toString() : null;
    return new LogRegLearnerResult(betaMat, covMat, iter, loglike);
}

Example 54 with CanceledExecutionException

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

the class ARFFTableTest method testCreateDataTableSpecFromARFFfileFOO.

/**
 * tests the creatoion of a table spec from a nice ARFF file.
 *
 * @throws IOException if.
 * @throws InvalidSettingsException when.
 */
public void testCreateDataTableSpecFromARFFfileFOO() throws IOException, InvalidSettingsException {
    File tempFile = File.createTempFile("ARFFReaderUnitTest", "mini");
    tempFile.deleteOnExit();
    Writer out = new BufferedWriter(new FileWriter(tempFile));
    out.write(ARFF_FOO);
    out.close();
    try {
        DataTableSpec tSpec = ARFFTable.createDataTableSpecFromARFFfile(tempFile.toURI().toURL(), null);
        assertEquals(tSpec.getNumColumns(), 8);
        assertEquals(tSpec.getColumnSpec(0).getName().toString(), "col1");
        assertEquals(tSpec.getColumnSpec(1).getName().toString(), "COL1");
        assertEquals(tSpec.getColumnSpec(2).getName().toString(), "col2");
        assertEquals(tSpec.getColumnSpec(3).getName().toString(), "COL2");
        assertEquals(tSpec.getColumnSpec(4).getName().toString(), "col3");
        assertEquals(tSpec.getColumnSpec(5).getName().toString(), "col4");
        assertEquals(tSpec.getColumnSpec(6).getName().toString(), "col5");
        assertEquals(tSpec.getColumnSpec(7).getName().toString(), "col6");
        assertEquals(tSpec.getColumnSpec(0).getType(), DoubleCell.TYPE);
        assertEquals(tSpec.getColumnSpec(1).getType(), DoubleCell.TYPE);
        assertEquals(tSpec.getColumnSpec(2).getType(), DoubleCell.TYPE);
        assertEquals(tSpec.getColumnSpec(3).getType(), DoubleCell.TYPE);
        assertEquals(tSpec.getColumnSpec(4).getType(), IntCell.TYPE);
        assertEquals(tSpec.getColumnSpec(5).getType(), StringCell.TYPE);
        assertEquals(tSpec.getColumnSpec(6).getType(), StringCell.TYPE);
        assertEquals(tSpec.getColumnSpec(7).getType(), StringCell.TYPE);
        assertNull(tSpec.getColumnSpec(0).getDomain().getValues());
        assertNull(tSpec.getColumnSpec(1).getDomain().getValues());
        assertNull(tSpec.getColumnSpec(2).getDomain().getValues());
        assertNull(tSpec.getColumnSpec(3).getDomain().getValues());
        assertNull(tSpec.getColumnSpec(4).getDomain().getValues());
        assertNull(tSpec.getColumnSpec(5).getDomain().getValues());
        assertNull(tSpec.getColumnSpec(6).getDomain().getValues());
        assertEquals(tSpec.getColumnSpec(7).getDomain().getValues().size(), 5);
    } catch (CanceledExecutionException cee) {
    // if you cancel during the test I will not fail!
    }
}

Example 55 with CanceledExecutionException

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

the class ARFFTableTest method testARFFwithMissingSpace.

/**
 * Customer file. Weka is able to read it. We failed on the missing space
 * in the last "@attribute" line.
 *
 * @throws IOException some time.
 * @throws InvalidSettingsException sometimes.
 */
public void testARFFwithMissingSpace() throws IOException, InvalidSettingsException {
    final String missingSpace = "@relation kredit_bereinigt\n" + "\n" + "@attribute REPAYMENT_PROBLEM {0,1}\n" + /* Col 0*/
    "@attribute RSV {0,1}\n" + /* Col 1*/
    "@attribute GENDER {0,1}\n" + /* Col 2*/
    "@attribute AGE real\n" + /* Col 3*/
    "@attribute PHONE {0,1}\n" + /* Col 4*/
    "@attribute NUMBER_CHILDREN real\n" + /* Col 5*/
    "@attribute ADDRESS_CHANGED {0,1}\n" + /* Col 6*/
    "@attribute GUARANTOR {0,1}\n" + /* Col 7*/
    "@attribute JOB_DURATION real\n" + /* Col 8*/
    "@attribute INCOME real\n" + /* Col 9*/
    "@attribute DISP_INCOME real\n" + /* Col 10*/
    "@attribute RENTAL_FEE real\n" + /* Col 11*/
    "@attribute CAR {0,1}\n" + /* Col 12*/
    "@attribute OTHER_CONTRACTS {0,1}\n" + /* Col 13*/
    "@attribute OTHER_LOANS {0,1}\n" + /* Col 14*/
    "@attribute EXPENSE real\n" + /* Col 15*/
    "@attribute SAVINGS {0,1}\n" + /* following line is missing a space */
    "@attribute STOCK{0,1}\n" + /* Col 17*/
    "\n" + "@data\n" + "1,1,1,27,0,1,1,1,2,2900,1335,330,1,0,0,1565,1,0\n" + "1,1,0,28,1,0,1,0,20,2000,1100,150,0,1,0,900,1,0\n";
    File tempFile = File.createTempFile("ARFFReaderUnitTest", "missSpace");
    tempFile.deleteOnExit();
    Writer out = new BufferedWriter(new FileWriter(tempFile));
    out.write(missingSpace);
    out.close();
    try {
        ARFFTable table = new ARFFTable(tempFile.toURI().toURL(), ARFFTable.createDataTableSpecFromARFFfile(tempFile.toURI().toURL(), null), "Row");
        assertEquals(table.getDataTableSpec().getNumColumns(), 18);
        assertEquals(table.getDataTableSpec().getColumnSpec(0).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(1).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(2).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(3).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(4).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(5).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(6).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(7).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(8).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(9).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(10).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(11).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(12).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(13).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(14).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(15).getType(), DoubleCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(16).getType(), StringCell.TYPE);
        assertEquals(table.getDataTableSpec().getColumnSpec(17).getType(), StringCell.TYPE);
        /*
        + "1,1,1,27,0,1,1,1,2,2900,1335,330,1,0,0,1565,1,0\n"
*/
        DataRow row;
        RowIterator rIter = table.iterator();
        assertTrue(rIter.hasNext());
        row = rIter.next();
        assertEquals(row.getKey().toString(), "Row0");
        assertEquals(row.getCell(0).toString(), "1");
        assertEquals(row.getCell(1).toString(), "1");
        assertEquals(row.getCell(2).toString(), "1");
        assertEquals(row.getCell(3).toString(), "27.0");
        assertEquals(row.getCell(4).toString(), "0");
        assertEquals(row.getCell(5).toString(), "1.0");
        assertEquals(row.getCell(6).toString(), "1");
        assertEquals(row.getCell(7).toString(), "1");
        assertEquals(row.getCell(8).toString(), "2.0");
        assertEquals(row.getCell(9).toString(), "2900.0");
        assertEquals(row.getCell(10).toString(), "1335.0");
        assertEquals(row.getCell(11).toString(), "330.0");
        assertEquals(row.getCell(12).toString(), "1");
        assertEquals(row.getCell(13).toString(), "0");
        assertEquals(row.getCell(14).toString(), "0");
        assertEquals(row.getCell(15).toString(), "1565.0");
        assertEquals(row.getCell(16).toString(), "1");
        assertEquals(row.getCell(17).toString(), "0");
        /*
 *         + "1,1,0,28,1,0,1,0,20,2000,1100,150,0,1,0,900,1,0\n";
 */
        assertTrue(rIter.hasNext());
        row = rIter.next();
        assertEquals(row.getKey().toString(), "Row1");
        assertEquals(row.getCell(0).toString(), "1");
        assertEquals(row.getCell(1).toString(), "1");
        assertEquals(row.getCell(2).toString(), "0");
        assertEquals(row.getCell(3).toString(), "28.0");
        assertEquals(row.getCell(4).toString(), "1");
        assertEquals(row.getCell(5).toString(), "0.0");
        assertEquals(row.getCell(6).toString(), "1");
        assertEquals(row.getCell(7).toString(), "0");
        assertEquals(row.getCell(8).toString(), "20.0");
        assertEquals(row.getCell(9).toString(), "2000.0");
        assertEquals(row.getCell(10).toString(), "1100.0");
        assertEquals(row.getCell(11).toString(), "150.0");
        assertEquals(row.getCell(12).toString(), "0");
        assertEquals(row.getCell(13).toString(), "1");
        assertEquals(row.getCell(14).toString(), "0");
        assertEquals(row.getCell(15).toString(), "900.0");
        assertEquals(row.getCell(16).toString(), "1");
        assertEquals(row.getCell(17).toString(), "0");
        assertFalse(rIter.hasNext());
    } catch (CanceledExecutionException cee) {
    // no exec monitor, no cancel
    }
}