Examples with IJVarInfos org.vcell.imagej.helper.VCellHelper.IJVarInfos used on opensource projects

Example 1 with IJVarInfos

use of org.vcell.imagej.helper.VCellHelper.IJVarInfos in project vcell by virtualcell.

the class NikitaTest method run.

@Override
public void run() {
    try {
        // Find the port that a separately running VCell client is listening on
        System.out.println("vcell service port=" + vcellHelper.findVCellApiServerPort());
    } catch (Exception e) {
        uiService.showDialog("Activate VCell client ImageJ service\nTools->'Start Fiji (ImageJ) service'\n" + e.getMessage(), "Couldn't contact VCell client", MessageType.ERROR_MESSAGE);
        return;
    }
    String theCacheKey = null;
    VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.valueOf(modelType), vCellUser, vCellModel, application, simulation, null, null);
    try {
        ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false, vcms, null);
        if (vcmsr.size() == 0) {
            throw new Exception("No Results for search found");
        }
        theCacheKey = vcmsr.get(0).getCacheKey();
        System.out.println("theCacheKey=" + theCacheKey);
    } catch (Exception e) {
        uiService.showDialog(modelType + ", " + vCellUser + ", " + vCellModel + ", " + application + ", " + simulation + ", null, null\n" + e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
        return;
    }
    IJDataList timePointData = null;
    // there is 1 timePoint
    int[] timePointIndexes = new int[1];
    int theTimePointIndex = 0;
    timePointIndexes[theTimePointIndex] = timePoint;
    try {
        timePointData = vcellHelper.getTimePointData(theCacheKey, variable, VARTYPE_POSTPROC.NotPostProcess, timePointIndexes, 0);
    } catch (Exception e) {
        uiService.showDialog(modelType + ", " + vCellUser + ", " + vCellModel + ", " + application + ", " + simulation + ", " + variable + ", " + timePoint + "\n" + e.getMessage(), "Get Data failed", MessageType.ERROR_MESSAGE);
        return;
    }
    double[] theTimePointData = timePointData.ijData[theTimePointIndex].getDoubleData();
    Range xAxisRange = null;
    int[] dataIndexes = new int[endIndex - startIndex + 1];
    // This is just for JFreeChart
    double[] dataIndexesDouble = new double[dataIndexes.length];
    for (int i = startIndex; i <= endIndex; i++) {
        dataIndexes[i - startIndex] = i;
        dataIndexesDouble[i - startIndex] = i;
        xAxisRange = Range.expandToInclude(xAxisRange, dataIndexesDouble[i - startIndex]);
    }
    Range yAxisRange = null;
    double[] chartTheseDataPoints = new double[dataIndexes.length];
    for (int i = 0; i < dataIndexes.length; i++) {
        chartTheseDataPoints[i] = theTimePointData[dataIndexes[i]];
        yAxisRange = Range.expandToInclude(yAxisRange, chartTheseDataPoints[i]);
    // ijTimeSeriesJobResults.data[0/*index of "r"*/][i+1/*data, skip 0 because it holds copy of times*/][0/*0 always because we had only 1 timePoint=22.0*/]
    }
    try {
        // LINE plot of data at 1 timePoint along defined indexes
        // Create JFreechart x,y axis arrays for plotting x=data indexes, y=dataPoint values
        double[][] data = new double[][] { dataIndexesDouble, chartTheseDataPoints };
        String title = "LINE Plot at time=" + timePoint;
        String xAxisLabel = "distance";
        String yAxisLabel = "val";
        DefaultXYDataset xyDataset = new DefaultXYDataset();
        xyDataset.addSeries("data1", data);
        JFreeChart chart = ChartFactory.createXYLineChart(title, xAxisLabel, yAxisLabel, xyDataset, PlotOrientation.VERTICAL, false, false, false);
        // Y
        chart.getXYPlot().getDomainAxis().setRange(xAxisRange);
        // X
        chart.getXYPlot().getRangeAxis().setRange(yAxisRange);
        ChartPanel chartPanel = new ChartPanel(chart);
        JFrame frame = new JFrame("Chart");
        // frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.getContentPane().add(chartPanel);
        // Display the window.
        frame.pack();
        frame.setVisible(true);
    } catch (Exception e) {
        uiService.showDialog("LINE PlotGet Data failed\n" + e.getMessage(), MessageType.ERROR_MESSAGE);
        return;
    }
    IJTimeSeriesJobResults timeSeries = null;
    try {
        IJVarInfos simulationInfo = vcellHelper.getSimulationInfo(theCacheKey);
        double[] times = simulationInfo.getTimes();
        timeSeries = vcellHelper.getTimeSeries(new String[] { variable }, new int[] { dataIndexes[0] }, times[0], 1, times[times.length - 1], false, false, 0, Integer.parseInt(theCacheKey));
    } catch (Exception e) {
        uiService.showDialog("TIME Plot Get Data failed\n" + e.getMessage(), MessageType.ERROR_MESSAGE);
        return;
    }
    try {
        // TIME plot of data at 1 timePoint along defined indexes
        // Create JFreechart x,y axis arrays for plotting x=data indexes, y=dataPoint values
        double[][] data = new double[][] { timeSeries.data[0][0], timeSeries.data[0][1] };
        String title = "TIME Plot at dataIndex=" + dataIndexes[0];
        String xAxisLabel = "time";
        String yAxisLabel = "val";
        DefaultXYDataset xyDataset = new DefaultXYDataset();
        xyDataset.addSeries("data1", data);
        JFreeChart chart = ChartFactory.createXYLineChart(title, xAxisLabel, yAxisLabel, xyDataset, PlotOrientation.VERTICAL, false, false, false);
        // chart.getXYPlot().getDomainAxis().setRange(yAxisRange);//Y
        // chart.getXYPlot().getRangeAxis().setRange(xAxisRange);//X
        ChartPanel chartPanel = new ChartPanel(chart);
        JFrame frame = new JFrame("Chart");
        // frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.getContentPane().add(chartPanel);
        // Display the window.
        frame.pack();
        frame.setVisible(true);
    } catch (Exception e) {
        uiService.showDialog("TIME Plot show chart failed\n" + e.getMessage(), MessageType.ERROR_MESSAGE);
        return;
    }
}

Example 2 with IJVarInfos

use of org.vcell.imagej.helper.VCellHelper.IJVarInfos in project vcell by virtualcell.

the class LinePlot method run.

@Override
public void run() {
    try {
        // Find the port that a separately running VCell client is listening on
        System.out.println("vcell service port=" + vcellHelper.findVCellApiServerPort());
    } catch (Exception e) {
        uiService.showDialog("Activate VCell client ImageJ service\nTools->'Start Fiji (ImageJ) service'\n" + e.getMessage(), "Couldn't contact VCell client", MessageType.ERROR_MESSAGE);
        return;
    }
    String theCacheKey = null;
    VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.valueOf(modelType), vCellUser, vCellModel, application, simulation, null, null);
    try {
        ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false, vcms, null);
        if (vcmsr.size() == 0) {
            throw new Exception("No Results for search found");
        }
        theCacheKey = vcmsr.get(0).getCacheKey();
        System.out.println("theCacheKey=" + theCacheKey);
    } catch (Exception e) {
        uiService.showDialog(modelType + ", " + vCellUser + ", " + vCellModel + ", " + application + ", " + simulation + ", null, null\n" + e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
        return;
    }
    IJDataList timePointData = null;
    // there is 1 timePoint
    int[] timePointIndexes = new int[1];
    int theTimePointIndex = 0;
    timePointIndexes[theTimePointIndex] = timePoint;
    try {
        timePointData = vcellHelper.getTimePointData(theCacheKey, variable, VARTYPE_POSTPROC.NotPostProcess, timePointIndexes, 0);
    } catch (Exception e) {
        uiService.showDialog(modelType + ", " + vCellUser + ", " + vCellModel + ", " + application + ", " + simulation + ", " + variable + ", " + timePoint + "\n" + e.getMessage(), "Get Data failed", MessageType.ERROR_MESSAGE);
        return;
    }
    double[] theTimePointData = timePointData.ijData[theTimePointIndex].getDoubleData();
    Range xAxisRange = null;
    int[] dataIndexes = new int[endIndex - startIndex + 1];
    // This is just for JFreeChart
    double[] dataIndexesDouble = new double[dataIndexes.length];
    for (int i = startIndex; i <= endIndex; i++) {
        dataIndexes[i - startIndex] = i;
        dataIndexesDouble[i - startIndex] = i;
        xAxisRange = Range.expandToInclude(xAxisRange, dataIndexesDouble[i - startIndex]);
    }
    Range yAxisRange = null;
    double[] chartTheseDataPoints = new double[dataIndexes.length];
    for (int i = 0; i < dataIndexes.length; i++) {
        chartTheseDataPoints[i] = theTimePointData[dataIndexes[i]];
        yAxisRange = Range.expandToInclude(yAxisRange, chartTheseDataPoints[i]);
    // ijTimeSeriesJobResults.data[0/*index of "r"*/][i+1/*data, skip 0 because it holds copy of times*/][0/*0 always because we had only 1 timePoint=22.0*/]
    }
    try {
        // LINE plot of data at 1 timePoint along defined indexes
        // Create JFreechart x,y axis arrays for plotting x=data indexes, y=dataPoint values
        double[][] data = new double[][] { dataIndexesDouble, chartTheseDataPoints };
        String title = "LINE Plot at time=" + timePoint;
        String xAxisLabel = "distance";
        String yAxisLabel = "val";
        DefaultXYDataset xyDataset = new DefaultXYDataset();
        xyDataset.addSeries("data1", data);
        JFreeChart chart = ChartFactory.createXYLineChart(title, xAxisLabel, yAxisLabel, xyDataset, PlotOrientation.VERTICAL, false, false, false);
        // Y
        chart.getXYPlot().getDomainAxis().setRange(xAxisRange);
        // X
        chart.getXYPlot().getRangeAxis().setRange(yAxisRange);
        ChartPanel chartPanel = new ChartPanel(chart);
        JFrame frame = new JFrame("Chart");
        // frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.getContentPane().add(chartPanel);
        // Display the window.
        frame.pack();
        frame.setVisible(true);
    } catch (Exception e) {
        uiService.showDialog("LINE PlotGet Data failed\n" + e.getMessage(), MessageType.ERROR_MESSAGE);
        return;
    }
    IJTimeSeriesJobResults timeSeries = null;
    try {
        IJVarInfos simulationInfo = vcellHelper.getSimulationInfo(theCacheKey);
        double[] times = simulationInfo.getTimes();
        timeSeries = vcellHelper.getTimeSeries(new String[] { variable }, new int[] { dataIndexes[0] }, times[0], 1, times[times.length - 1], false, false, 0, Integer.parseInt(theCacheKey));
    } catch (Exception e) {
        uiService.showDialog("TIME Plot Get Data failed\n" + e.getMessage(), MessageType.ERROR_MESSAGE);
        return;
    }
    try {
        // TIME plot of data at 1 timePoint along defined indexes
        // Create JFreechart x,y axis arrays for plotting x=data indexes, y=dataPoint values
        double[][] data = new double[][] { timeSeries.data[0][0], timeSeries.data[0][1] };
        String title = "TIME Plot at dataIndex=" + dataIndexes[0];
        String xAxisLabel = "time";
        String yAxisLabel = "val";
        DefaultXYDataset xyDataset = new DefaultXYDataset();
        xyDataset.addSeries("data1", data);
        JFreeChart chart = ChartFactory.createXYLineChart(title, xAxisLabel, yAxisLabel, xyDataset, PlotOrientation.VERTICAL, false, false, false);
        // chart.getXYPlot().getDomainAxis().setRange(yAxisRange);//Y
        // chart.getXYPlot().getRangeAxis().setRange(xAxisRange);//X
        ChartPanel chartPanel = new ChartPanel(chart);
        JFrame frame = new JFrame("Chart");
        // frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.getContentPane().add(chartPanel);
        // Display the window.
        frame.pack();
        frame.setVisible(true);
    } catch (Exception e) {
        uiService.showDialog("TIME Plot show chart failed\n" + e.getMessage(), MessageType.ERROR_MESSAGE);
        return;
    }
}