Examples with Interval org.knime.base.node.preproc.discretization.caim2.Interval used on opensource projects

Example 1 with Interval

use of org.knime.base.node.preproc.discretization.caim2.Interval in project knime-core by knime.

the class DiscretizationApplyNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inData, final ExecutionContext exec) throws Exception {
    DiscretizationModel discrModel = (DiscretizationModel) inData[MODEL_INPORT];
    // if an empty model was received, just return the input data
    if (discrModel.getSchemes().length == 0) {
        return new PortObject[] { inData[DATA_INPORT] };
    }
    // create an output table that replaces the included columns by
    // interval values from the model
    BufferedDataTable resultTable = CAIMDiscretizationNodeModel.createResultTable(exec, (BufferedDataTable) inData[DATA_INPORT], discrModel);
    return new BufferedDataTable[] { resultTable };
}

Example 2 with Interval

use of org.knime.base.node.preproc.discretization.caim2.Interval in project knime-core by knime.

the class CAIMDiscretizationNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inData, final ExecutionContext exec) throws Exception {
    // measure the time
    long startTime = System.currentTimeMillis();
    // empty model
    if (m_includedColumnNames.getIncludeList() == null || m_includedColumnNames.getIncludeList().size() == 0) {
        return new PortObject[] { inData[0], new DiscretizationModel() };
    }
    LOGGER.debug("Start discretizing.");
    // as the algorithm is for binary class problems only
    // (positive, negative) the algorithm is performed for each class value
    // labeled as positive class and the rest as negative
    exec.setProgress(0.0, "Preparing...");
    // check input data
    BufferedDataTable data = (BufferedDataTable) inData[0];
    // get class column index
    m_classifyColumnIndex = data.getDataTableSpec().findColumnIndex(m_classColumnName.getStringValue());
    assert m_classifyColumnIndex > -1;
    // create the class - index mapping
    createClassFromToIndexMaps(data.getDataTableSpec());
    // create the array with the result discretization schemes for
    // each included column
    DiscretizationScheme[] resultSchemes = new DiscretizationScheme[m_includedColumnNames.getIncludeList().size()];
    // for all included columns do the discretization
    int currentColumn = 0;
    for (String includedColumnName : m_includedColumnNames.getIncludeList()) {
        LOGGER.debug("Process column: " + includedColumnName);
        exec.setProgress("Discretizing column '" + includedColumnName + "'");
        ExecutionContext subExecPerColumn = exec.createSubExecutionContext(1.0D / m_includedColumnNames.getIncludeList().size());
        subExecPerColumn.checkCanceled();
        // never discretize the column index (should never happen)
        if (m_classColumnName.getStringValue().equals(includedColumnName)) {
            continue;
        }
        // determine the column index of the current column
        int columnIndex = data.getDataTableSpec().findColumnIndex(includedColumnName);
        DataColumnDomain domain = data.getDataTableSpec().getColumnSpec(columnIndex).getDomain();
        double minValue = ((DoubleValue) domain.getLowerBound()).getDoubleValue();
        double maxValue = ((DoubleValue) domain.getUpperBound()).getDoubleValue();
        // find all distinct values of the column and create
        // a table with all possible interval boundaries (midpoint value of
        // adjacent values)
        subExecPerColumn.setProgress("Find possible boundaries.");
        BoundaryScheme boundaryScheme = null;
        // create subExec for sorting
        ExecutionContext subExecSort = subExecPerColumn.createSubExecutionContext(0.1);
        // long t1 = System.currentTimeMillis();
        if (m_classOptimizedVersion) {
            boundaryScheme = createAllIntervalBoundaries(data, columnIndex, subExecSort);
        } else {
            boundaryScheme = createAllIntervalBoundaries2(data, columnIndex, subExecSort);
        }
        subExecSort.setProgress(1.0D);
        // long t2 = System.currentTimeMillis() - t1;
        // LOGGER.error("Create boundaries time: " + (t2 / 1000.0)
        // + " optimized: " + m_classOptimizedVersion);
        // LOGGER.error("Boundaries: " + boundaryScheme.getHead());
        LinkedDouble allIntervalBoundaries = boundaryScheme.getHead();
        // create the initial discretization scheme
        DiscretizationScheme discretizationScheme = new DiscretizationScheme(new Interval(minValue, maxValue, true, true));
        double globalCAIM = 0;
        // performe the iterative search for the best intervals
        int numInsertedBounds = 0;
        double currentCAIM = 0;
        // create subExec for inserted bounds
        ExecutionContext subExecBounds = subExecPerColumn.createSubExecutionContext(0.9);
        while (currentCAIM > globalCAIM || numInsertedBounds < m_classValues.length - 1) {
            subExecPerColumn.checkCanceled();
            // create subExec for counting
            ExecutionContext subExecCount = subExecBounds.createSubExecutionContext(1.0D / m_classValues.length);
            // LOGGER.debug("Inserted bounds: " + numInsertedBounds);
            // LOGGER.debug("intervall boundaries: " +
            // allIntervalBoundaries);
            // for all possible interval boundaries
            // insert each one, calculate the caim value and add
            // the one with the biggest caim
            LinkedDouble intervalBoundary = allIntervalBoundaries.m_next;
            currentCAIM = 0;
            LinkedDouble bestBoundary = null;
            long currentCountedBoundaries = 0;
            while (intervalBoundary != null) {
                subExecPerColumn.checkCanceled();
                // set progress
                currentCountedBoundaries++;
                subExecCount.setProgress((double) currentCountedBoundaries / (double) boundaryScheme.getNumBoundaries(), "Count for possible boundary " + currentCountedBoundaries + " of " + boundaryScheme.getNumBoundaries());
                // LOGGER.debug("current caim: " + currentCAIM);
                DiscretizationScheme tentativeDS = new DiscretizationScheme(discretizationScheme);
                tentativeDS.insertBound(intervalBoundary.m_value);
                // create the quanta matrix
                QuantaMatrix2D quantaMatrix = new QuantaMatrix2D(tentativeDS, m_classValueToIndexMap);
                // pass the data for filling the matrix
                quantaMatrix.countData(data, columnIndex, m_classifyColumnIndex);
                // calculate the caim
                double caim = quantaMatrix.calculateCaim();
                if (caim > currentCAIM) {
                    currentCAIM = caim;
                    bestBoundary = intervalBoundary;
                }
                intervalBoundary = intervalBoundary.m_next;
            }
            // if there is no best boundary, break the first while loop
            if (bestBoundary == null) {
                break;
            }
            // in this case accept the best discretization scheme
            if (currentCAIM > globalCAIM || numInsertedBounds < m_classValues.length) {
                int numIntervals = discretizationScheme.getNumIntervals();
                discretizationScheme.insertBound(bestBoundary.m_value);
                // remove the linked list element from the list
                bestBoundary.remove();
                globalCAIM = currentCAIM;
                if (numIntervals < discretizationScheme.getNumIntervals()) {
                    numInsertedBounds++;
                    subExecPerColumn.setProgress("Inserted bound " + numInsertedBounds);
                // LOGGER.debug("Inserted boundary: "
                // + bestBoundary.m_value);
                } else {
                    throw new IllegalStateException("Only usefull bounds should be inserted: " + bestBoundary.m_value);
                }
            }
            subExecCount.setProgress(1.0D);
        }
        resultSchemes[currentColumn] = discretizationScheme;
        subExecBounds.setProgress(1.0D);
        // ensure the full progress is set for this iteration
        subExecPerColumn.setProgress(1.0D);
        currentColumn++;
    }
    // set the model
    DataTableSpec modelSpec = createModelSpec(m_includedColumnNames, data.getDataTableSpec());
    m_discretizationModel = new DiscretizationModel(resultSchemes, modelSpec);
    // create an output table that replaces the included columns by
    // interval values
    BufferedDataTable resultTable = createResultTable(exec, data, m_discretizationModel);
    // log the runtime of the execute method
    long runtime = System.currentTimeMillis() - startTime;
    LOGGER.debug("Binning runtime: " + (runtime / 1000.0) + " sec.");
    return new PortObject[] { resultTable, m_discretizationModel };
}

Example 3 with Interval

use of org.knime.base.node.preproc.discretization.caim2.Interval in project vcell by virtualcell.

the class ConstructTIRFGeometry method run.

@Override
public void run() {
    // Calculate constant d in TIRF exponential decay function
    // Angle of incidence in radians
    theta = theta * 2 * Math.PI / 360;
    // Refractive index of glass
    final double n1 = 1.52;
    // Refractive index of cytosol
    final double n2 = 1.38;
    final double d = lambda * Math.pow((Math.pow(n1, 2) * Math.pow(Math.sin(theta), 2) - Math.pow(n2, 2)), -0.5) / (4 * Math.PI);
    System.out.println("d: " + d);
    final double fluorPerMolecule = 250;
    // Get frame of interest to define geometry
    long maxX = data.dimension(0) - 1;
    long maxY = data.dimension(1) - 1;
    Interval interval = Intervals.createMinMax(0, 0, sliceIndex, maxX, maxY, sliceIndex);
    RandomAccessibleInterval<T> croppedRAI = ops.transform().crop(data, interval, true);
    // Subtract lowest pixel value
    IterableInterval<T> dataII = Views.iterable(croppedRAI);
    double min = ops.stats().min(dataII).getRealDouble();
    Cursor<T> dataCursor = dataII.cursor();
    while (dataCursor.hasNext()) {
        double val = dataCursor.next().getRealDouble();
        dataCursor.get().setReal(val - min);
    }
    // Perform Gaussian blur
    RandomAccessibleInterval<T> blurredRAI = ops.filter().gauss(croppedRAI, 2);
    IterableInterval<T> blurredII = Views.iterable(blurredRAI);
    // Segment slice by threshold and fill holes
    IterableInterval<BitType> thresholded = ops.threshold().huang(blurredII);
    Img<BitType> thresholdedImg = ops.convert().bit(thresholded);
    RandomAccessibleInterval<BitType> thresholdedRAI = ops.morphology().fillHoles(thresholdedImg);
    // Get the largest region
    RandomAccessibleInterval<LabelingType<ByteType>> labeling = ops.labeling().cca(thresholdedRAI, ConnectedComponents.StructuringElement.EIGHT_CONNECTED);
    LabelRegions<ByteType> labelRegions = new LabelRegions<>(labeling);
    Iterator<LabelRegion<ByteType>> iterator = labelRegions.iterator();
    LabelRegion<ByteType> maxRegion = iterator.next();
    while (iterator.hasNext()) {
        LabelRegion<ByteType> currRegion = iterator.next();
        if (currRegion.size() > maxRegion.size()) {
            maxRegion = currRegion;
        }
    }
    // Generate z index map
    double iMax = ops.stats().max(dataII).getRealDouble();
    Img<UnsignedShortType> dataImg = ops.convert().uint16(dataII);
    Img<UnsignedShortType> zMap = ops.convert().uint16(ops.create().img(dataII));
    LabelRegionCursor cursor = maxRegion.localizingCursor();
    RandomAccess<UnsignedShortType> zMapRA = zMap.randomAccess();
    RandomAccess<UnsignedShortType> dataRA = dataImg.randomAccess();
    while (cursor.hasNext()) {
        cursor.fwd();
        zMapRA.setPosition(cursor);
        dataRA.setPosition(cursor);
        double val = dataRA.get().getRealDouble();
        // Log of 0 is undefined
        if (val < 1) {
            val = 1;
        }
        int z = (int) Math.round(-d * Math.log(val / iMax) / zRes);
        zMapRA.get().set(z);
    }
    System.out.println("6");
    // Use map to construct 3D geometry
    // Add 5 slices of padding on top
    int maxZ = (int) ops.stats().max(zMap).getRealDouble() + 5;
    long[] resultDimensions = { maxX + 1, maxY + 1, maxZ };
    Img<BitType> result = new ArrayImgFactory<BitType>().create(resultDimensions, new BitType());
    RandomAccess<BitType> resultRA = result.randomAccess();
    System.out.println(maxZ);
    cursor.reset();
    while (cursor.hasNext()) {
        cursor.fwd();
        zMapRA.setPosition(cursor);
        int zIndex = zMapRA.get().get();
        int[] position = { cursor.getIntPosition(0), cursor.getIntPosition(1), zIndex };
        while (position[2] < maxZ) {
            resultRA.setPosition(position);
            resultRA.get().set(true);
            position[2]++;
        }
    }
    output = datasetService.create(result);
    CalibratedAxis[] axes = new DefaultLinearAxis[] { new DefaultLinearAxis(Axes.X), new DefaultLinearAxis(Axes.Y), new DefaultLinearAxis(Axes.Z) };
    output.setAxes(axes);
    System.out.println("Done constructing geometry");
}