Examples with TimeSeriesCollection org.jfree.data.time.TimeSeriesCollection used on opensource projects

Example 26 with TimeSeriesCollection

use of org.jfree.data.time.TimeSeriesCollection in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method writeDetailedFactorAnalysis.

private boolean writeDetailedFactorAnalysis(ExpressionExperiment ee, OutputStream os) throws Exception {
    SVDValueObject svdo = svdService.getSvdFactorAnalysis(ee.getId());
    if (svdo == null)
        return false;
    if (svdo.getFactors().isEmpty() && svdo.getDates().isEmpty()) {
        return false;
    }
    Map<Integer, Map<Long, Double>> factorCorrelations = svdo.getFactorCorrelations();
    // Map<Integer, Map<Long, Double>> factorPvalues = svdo.getFactorPvalues();
    Map<Integer, Double> dateCorrelations = svdo.getDateCorrelations();
    assert ee.getId().equals(svdo.getId());
    // need the experimental design
    ee = expressionExperimentService.thawLite(ee);
    int maxWidth = 30;
    Map<Long, String> efs = this.getFactorNames(ee, maxWidth);
    Map<Long, ExperimentalFactor> efIdMap = EntityUtils.getIdMap(ee.getExperimentalDesign().getExperimentalFactors());
    Collection<Long> continuousFactors = new HashSet<>();
    for (ExperimentalFactor ef : ee.getExperimentalDesign().getExperimentalFactors()) {
        boolean isContinous = ExperimentalDesignUtils.isContinuous(ef);
        if (isContinous) {
            continuousFactors.add(ef.getId());
        }
    }
    /*
         * Make plots of the dates vs. PCs, factors vs. PCs.
         */
    int MAX_COMP = 3;
    Map<Long, List<JFreeChart>> charts = new LinkedHashMap<>();
    ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme());
    /*
         * FACTORS
         */
    String componentShorthand = "PC";
    for (Integer component : factorCorrelations.keySet()) {
        if (component >= MAX_COMP)
            break;
        String xaxisLabel = componentShorthand + (component + 1);
        for (Long efId : factorCorrelations.get(component).keySet()) {
            /*
                 * Should not happen.
                 */
            if (!efs.containsKey(efId)) {
                log.warn("No experimental factor with id " + efId);
                continue;
            }
            if (!svdo.getFactors().containsKey(efId)) {
                // this should not happen.
                continue;
            }
            boolean isCategorical = !continuousFactors.contains(efId);
            Map<Long, String> categories = new HashMap<>();
            if (isCategorical) {
                this.getCategories(efIdMap, efId, categories);
            }
            if (!charts.containsKey(efId)) {
                charts.put(efId, new ArrayList<JFreeChart>());
            }
            Double a = factorCorrelations.get(component).get(efId);
            // unique?
            String plotname = (efs.get(efId) == null ? "?" : efs.get(efId)) + " " + xaxisLabel;
            if (a != null && !Double.isNaN(a)) {
                String title = plotname + " " + String.format("%.2f", a);
                List<Double> values = svdo.getFactors().get(efId);
                Double[] eigenGene = this.getEigenGene(svdo, component);
                assert values.size() == eigenGene.length;
                /*
                     * Plot eigengene vs values, add correlation to the plot
                     */
                JFreeChart chart;
                if (isCategorical) {
                    /*
                         * Categorical factor
                         */
                    // use the absolute value of the correlation, since direction is arbitrary.
                    title = plotname + " " + String.format("r=%.2f", Math.abs(a));
                    DefaultMultiValueCategoryDataset dataset = new DefaultMultiValueCategoryDataset();
                    /*
                         * What this code does is organize the factor values by the groups.
                         */
                    Map<String, List<Double>> groupedValues = new TreeMap<>();
                    for (int i = 0; i < values.size(); i++) {
                        Long fvId = values.get(i).longValue();
                        String fvValue = categories.get(fvId);
                        if (fvValue == null) {
                            // is this all we need to do?
                            continue;
                        }
                        if (!groupedValues.containsKey(fvValue)) {
                            groupedValues.put(fvValue, new ArrayList<Double>());
                        }
                        groupedValues.get(fvValue).add(eigenGene[i]);
                        if (log.isDebugEnabled())
                            log.debug(fvValue + " " + values.get(i));
                    }
                    for (String key : groupedValues.keySet()) {
                        dataset.add(groupedValues.get(key), plotname, key);
                    }
                    // don't show the name of the X axis: it's redundant with the title.
                    NumberAxis rangeAxis = new NumberAxis(xaxisLabel);
                    rangeAxis.setAutoRangeIncludesZero(false);
                    // rangeAxis.setAutoRange( false );
                    rangeAxis.setAutoRangeMinimumSize(4.0);
                    // rangeAxis.setRange( new Range( -2, 2 ) );
                    CategoryPlot plot = new CategoryPlot(dataset, new CategoryAxis(null), rangeAxis, new ScatterRenderer());
                    plot.setRangeGridlinesVisible(false);
                    plot.setDomainGridlinesVisible(false);
                    chart = new JFreeChart(title, new Font("SansSerif", Font.BOLD, 12), plot, false);
                    ScatterRenderer renderer = (ScatterRenderer) plot.getRenderer();
                    float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP);
                    renderer.setSeriesFillPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f));
                    renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
                    renderer.setUseOutlinePaint(false);
                    renderer.setUseFillPaint(true);
                    renderer.setDefaultFillPaint(Color.white);
                    CategoryAxis domainAxis = plot.getDomainAxis();
                    domainAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);
                } else {
                    /*
                         * Continuous value factor
                         */
                    DefaultXYDataset series = new DefaultXYDataset();
                    series.addSeries(plotname, new double[][] { ArrayUtils.toPrimitive(values.toArray(new Double[] {})), ArrayUtils.toPrimitive(eigenGene) });
                    // don't show x-axis label, which would otherwise be efs.get( efId )
                    chart = ChartFactory.createScatterPlot(title, null, xaxisLabel, series, PlotOrientation.VERTICAL, false, false, false);
                    XYPlot plot = chart.getXYPlot();
                    plot.setRangeGridlinesVisible(false);
                    plot.setDomainGridlinesVisible(false);
                    XYItemRenderer renderer = plot.getRenderer();
                    renderer.setDefaultPaint(Color.white);
                    renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
                    float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP);
                    renderer.setSeriesPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f));
                    plot.setRenderer(renderer);
                }
                chart.getTitle().setFont(new Font("SansSerif", Font.BOLD, 12));
                charts.get(efId).add(chart);
            }
        }
    }
    /*
         * DATES
         */
    charts.put(-1L, new ArrayList<JFreeChart>());
    for (Integer component : dateCorrelations.keySet()) {
        String xaxisLabel = componentShorthand + (component + 1);
        List<Date> dates = svdo.getDates();
        if (dates.isEmpty())
            break;
        long secspan = ubic.basecode.util.DateUtil.numberOfSecondsBetweenDates(dates);
        if (component >= MAX_COMP)
            break;
        Double a = dateCorrelations.get(component);
        if (a != null && !Double.isNaN(a)) {
            Double[] eigenGene = svdo.getvMatrix().getColObj(component);
            /*
                 * Plot eigengene vs values, add correlation to the plot
                 */
            TimeSeries series = new TimeSeries("Dates vs. eigen" + (component + 1));
            int i = 0;
            for (Date d : dates) {
                // if span is less than an hour, retain the minute.
                if (secspan < 60 * 60) {
                    series.addOrUpdate(new Minute(d), eigenGene[i++]);
                } else {
                    series.addOrUpdate(new Hour(d), eigenGene[i++]);
                }
            }
            TimeSeriesCollection dataset = new TimeSeriesCollection();
            dataset.addSeries(series);
            JFreeChart chart = ChartFactory.createTimeSeriesChart("Dates: " + xaxisLabel + " " + String.format("r=%.2f", a), null, xaxisLabel, dataset, false, false, false);
            XYPlot xyPlot = chart.getXYPlot();
            chart.getTitle().setFont(new Font("SansSerif", Font.BOLD, 12));
            // standard renderer makes lines.
            XYDotRenderer renderer = new XYDotRenderer();
            renderer.setDefaultFillPaint(Color.white);
            renderer.setDotHeight(3);
            renderer.setDotWidth(3);
            // has no effect, need dotheight.
            renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3));
            float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP);
            renderer.setSeriesPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f));
            ValueAxis domainAxis = xyPlot.getDomainAxis();
            domainAxis.setVerticalTickLabels(true);
            xyPlot.setRenderer(renderer);
            xyPlot.setRangeGridlinesVisible(false);
            xyPlot.setDomainGridlinesVisible(false);
            charts.get(-1L).add(chart);
        }
    }
    /*
         * Plot in a grid, with each factor as a column. FIXME What if we have too many factors to fit on the screen?
         */
    int columns = (int) Math.ceil(charts.size());
    int perChartSize = ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX;
    BufferedImage image = new BufferedImage(columns * perChartSize, MAX_COMP * perChartSize, BufferedImage.TYPE_INT_ARGB);
    Graphics2D g2 = image.createGraphics();
    int currentX = 0;
    int currentY = 0;
    for (Long id : charts.keySet()) {
        for (JFreeChart chart : charts.get(id)) {
            this.addChartToGraphics(chart, g2, currentX, currentY, perChartSize, perChartSize);
            if (currentY + perChartSize < MAX_COMP * perChartSize) {
                currentY += perChartSize;
            } else {
                currentY = 0;
                currentX += perChartSize;
            }
        }
    }
    os.write(ChartUtils.encodeAsPNG(image));
    return true;
}

Example 27 with TimeSeriesCollection

use of org.jfree.data.time.TimeSeriesCollection in project nimbus by nimbus-org.

the class TimeSeriesCollectionFactoryService method createDataset.

/**
 * データセットを生成する。<p>
 *
 * @param dsConditions データセット条件配列
 * @return データセット
 * @exception DatasetCreateException
 */
public Dataset createDataset(DatasetCondition[] dsConditions) throws DatasetCreateException {
    DatasetConnection connection = createConnection(dsConditions);
    TimeSeriesCollection dataset = new TimeSeriesCollection();
    try {
        List cursors = connection.getSeriesCursorList();
        if (cursors == null) {
            return dataset;
        }
        Calendar workCal = Calendar.getInstance();
        Holder inOut = new Holder();
        Record record = new Record();
        DoubleList sameDateValues = null;
        OHLCList ohlcList = null;
        for (int i = 0, imax = cursors.size(); i < imax; i++) {
            TimeSeriesCursor cursor = (TimeSeriesCursor) cursors.get(i);
            String series = cursor.getSeriesName();
            Class timePeriodClass = (Class) timePeriodClassMap.get(series);
            int periodType = 0;
            TimeSeries timeSeries = null;
            if (collateDataType != 0) {
                if (timePeriodClass == null) {
                    timePeriodClass = Millisecond.class;
                }
                timeSeries = new TimeSeries(series, timePeriodClass);
            } else {
                if (timePeriodClass != null) {
                    timeSeries = new TimeSeries(series, timePeriodClass);
                } else {
                    timeSeries = new TimeSeries(series);
                    timePeriodClass = timeSeries.getTimePeriodClass();
                    if (timePeriodClass == null) {
                        timePeriodClass = Millisecond.class;
                    }
                }
            }
            periodType = convertPeriodType(timePeriodClass);
            double value = 0d;
            if (sameDateValues != null) {
                sameDateValues.clear();
            }
            if (ohlcList != null) {
                ohlcList.clear();
            }
            inOut.clear();
            record.clear();
            Date date = null;
            boolean hasNext = cursor.next();
            while (hasNext) {
                // 同値の最後のデータを追加する際に使う日付
                if (inOut.date == null || inOut.preDate == null) {
                    inOut.preDate = inOut.date;
                } else {
                    inOut.preDate.setTime(inOut.date.getTime());
                }
                date = cursor.getDate();
                if (date == null) {
                    throw new DatasetCreateException("date is null.");
                }
                value = cursor.getValue();
                boolean wasNull = cursor.wasNull();
                if (!wasNull) {
                    inOut.date = date;
                    if (isAutoTimesharing) {
                        // 自動時分割を行う
                        if (inOut.preDate != null && inOut.preDate.equals(date)) {
                            // 同じ時間の値を溜め込む
                            record.setDate(date);
                            record.add(value);
                            hasNext = cursor.next();
                            if (hasNext) {
                                continue;
                            }
                        } else {
                            record.setPeriodMillis(getPeriodMillis(workCal, inOut.lastDate, inputDataField, inputDataPeriod));
                            // 溜め込んだ同じ時間の値をTimeSeriesに追加
                            inOut.date = inOut.preDate;
                            double tmpValue = Double.NaN;
                            while (record.hasNext()) {
                                if (inOut.date == null || inOut.preDate == null) {
                                    inOut.preDate = (Date) inOut.date.clone();
                                } else {
                                    inOut.preDate.setTime(inOut.date.getTime());
                                }
                                inOut.date = record.nextDate();
                                tmpValue = record.nextValue();
                                addTimeSeries(date, tmpValue, workCal, timeSeries, periodType, false, inOut);
                            }
                            record.clear();
                            inOut.date = date;
                        }
                    }
                }
                if (hasNext) {
                    hasNext = cursor.next();
                }
                if (!hasNext) {
                    // collateDataTypeが設定されていない(0)時はすでにすべての値が追加されているので処理する必要なし
                    if (collateDataType != 0) {
                        if (isAutoTimesharing && record.size() != 0) {
                            record.setPeriodMillis(getPeriodMillis(workCal, inOut.lastDate, inputDataField, inputDataPeriod));
                            // 溜め込んだ同じ時間の値をTimeSeriesに追加
                            inOut.date = inOut.preDate;
                            double tmpValue = Double.NaN;
                            while (record.hasNext()) {
                                if (inOut.date == null || inOut.preDate == null) {
                                    inOut.preDate = (Date) inOut.date.clone();
                                } else {
                                    inOut.preDate.setTime(inOut.date.getTime());
                                }
                                inOut.date = record.nextDate();
                                tmpValue = record.nextValue();
                                addTimeSeries(date, tmpValue, workCal, timeSeries, periodType, wasNull && !record.hasNext(), inOut);
                            }
                            record.clear();
                            inOut.date = date;
                        } else {
                            // 現在の値を追加
                            addTimeSeries(date, value, workCal, timeSeries, periodType, false, inOut);
                        }
                    }
                    if (!wasNull) {
                        // 最後の期間の値を追加
                        addTimeSeries(date, value, workCal, timeSeries, periodType, true, inOut);
                    }
                } else if (!wasNull) {
                    // 現在の値を追加
                    addTimeSeries(date, value, workCal, timeSeries, periodType, false, inOut);
                }
            }
            dataset.addSeries(timeSeries);
            timePeriodClass = null;
            cursor.close();
        }
    } finally {
        connection.close();
    }
    return dataset;
}

Example 28 with TimeSeriesCollection

use of org.jfree.data.time.TimeSeriesCollection in project nimbus by nimbus-org.

the class MovingAverageFactoryService method createDataset.

public Dataset createDataset(DatasetCondition[] dsConditions) throws DatasetCreateException {
    if (dsConditions == null || dsConditions.length == 0) {
        return null;
    }
    Dataset dataset = null;
    try {
        dataset = datasetFactory.createDataset(dsConditions);
    } catch (DatasetCreateException e) {
        throw new MovingAverageCreateException(e);
    }
    Dataset datasetMV = dataset;
    if (dataset instanceof TimeSeriesCollection) {
        final List seriesList = ((TimeSeriesCollection) dataset).getSeries();
        final int seriesLength = seriesList.size();
        final TimeSeriesCollection newCollection = new TimeSeriesCollection();
        for (int i = 0; i < periodCounts.length; i++) {
            for (int j = 0; j < seriesLength; j++) {
                TimeSeries series = (TimeSeries) seriesList.get(j);
                series = MovingAverage.createMovingAverage(series, series.getKey() + (suffixs == null ? "" : suffixs[i]), (int) periodCounts[i], (int) (skips == null ? 0 : skips[i]));
                newCollection.addSeries(series);
            }
        }
        datasetMV = newCollection;
    } else if (dataset instanceof XYDataset) {
        XYSeriesCollection newCollection = new XYSeriesCollection();
        XYDataset inDataset = (XYDataset) dataset;
        for (int i = 0; i < periodCounts.length; i++) {
            for (int j = 0; j < inDataset.getSeriesCount(); j++) {
                XYSeries series = MovingAverage.createMovingAverage(inDataset, j, inDataset.getSeriesKey(j) + (suffixs == null ? "" : suffixs[i]), periodCounts[i], skips == null ? 0 : skips[i]);
                newCollection.addSeries(series);
            }
        }
        datasetMV = newCollection;
    }
    return datasetMV;
}

Example 29 with TimeSeriesCollection

use of org.jfree.data.time.TimeSeriesCollection in project ta4j by ta4j.

the class CandlestickChartWithChopIndicator method createChopDataset.

private static TimeSeriesCollection createChopDataset(BarSeries series) {
    ChopIndicator indicator = new ChopIndicator(series, CHOP_INDICATOR_TIMEFRAME, CHOP_SCALE_VALUE);
    TimeSeriesCollection dataset = new TimeSeriesCollection();
    org.jfree.data.time.TimeSeries chartTimeSeries = new org.jfree.data.time.TimeSeries("CHOP_14");
    for (int i = 0; i < series.getBarCount(); i++) {
        Bar bar = series.getBar(i);
        if (i < CHOP_INDICATOR_TIMEFRAME)
            continue;
        chartTimeSeries.add(new Second(new Date(bar.getEndTime().toEpochSecond() * 1000)), indicator.getValue(i).doubleValue());
    }
    dataset.addSeries(chartTimeSeries);
    return dataset;
}

Example 30 with TimeSeriesCollection

use of org.jfree.data.time.TimeSeriesCollection in project ta4j by ta4j.

the class CandlestickChartWithChopIndicator method main.

public static void main(String[] args) {
    series = CsvTradesLoader.loadBitstampSeries();
    /*
         * Create the OHLC dataset from the data series
         */
    OHLCDataset ohlcDataset = createOHLCDataset(series);
    /*
         * Create volume dataset
         */
    TimeSeriesCollection xyDataset = createAdditionalDataset(series);
    /*
         * add the CHOP Indicator
         */
    TimeSeriesCollection chopSeries = createChopDataset(series);
    /*
         * Display the chart
         */
    displayChart(ohlcDataset, xyDataset, chopSeries);
}