guiTimeseries_Model.java [src/java/m/cfa/timeseries] Revision: dcd7855a1c5c790e25d21d768e7dc4b21435f39d Date: Wed Dec 15 12:56:29 MST 2021
package m.cfa.timeseries;
import WaterData.WaterData;
import WaterData.WaterDataInterface;
import WaterData.WaterQualityInfo;
import csip.Executable;
import m.cfa.FlowStatistics;
import m.cfa.DoubleArray;
import m.cfa.DoubleMath;
import m.cfa.Graphing;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Paint;
import java.awt.Stroke;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Rectangle2D;
import java.io.File;
import java.io.IOException;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.AxisLocation;
import org.jfree.chart.axis.CategoryAxis;
import org.jfree.chart.axis.CategoryLabelPositions;
import org.jfree.chart.axis.DateAxis;
import org.jfree.chart.axis.LogarithmicAxis;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.axis.ValueAxis;
import org.jfree.chart.block.BlockBorder;
import org.jfree.chart.plot.CategoryPlot;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.LookupPaintScale;
import org.jfree.chart.renderer.category.BarRenderer;
import org.jfree.chart.renderer.xy.XYBlockRenderer;
import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.chart.title.LegendTitle;
import org.jfree.chart.title.PaintScaleLegend;
import org.jfree.data.category.DefaultCategoryDataset;
import org.jfree.data.time.Day;
import org.jfree.data.time.TimeSeries;
import org.jfree.data.xy.AbstractXYZDataset;
import org.jfree.data.xy.XYDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import org.jfree.data.xy.XYZDataset;
import org.jfree.ui.RectangleEdge;
import org.jfree.ui.RectangleInsets;
/**
* Last Updated: 9-April-2019
* @author Tyler Wible
* @since 24-June-2011
*/
public class guiTimeseries_Model {
//Inputs
String directory = "E:/Projects/TylerWible_repos/NetBeans/data/CFA/Timeseries";
String database = "USGS";//"CDWR";//"STORET";//"CDSN";//"UserData";//
String orgId = "n/a";//"n/a";//"21COL001";//"CITYFTCO_WQX";//"n/a";//
String stationId = "06764880";//"CLAGRECO";//"000028";//"1EFF";//"n/a";//
String stationName = "South Platte River at Roscoe, Nebr.";//"Cache La Poudre Near Greeley";//"BIG THOMPSON R NEAR MOUTH";//"n/a";//"n/a";//
String wqTest = "flow";//"00600 Total nitrogen, water, unfiltered, milligrams per liter -- mg/L";//"00625 Ammonia-nitrogen as N -- mg/L";//
String startDate = "";
String endDate = "";
String timeStep = "Daily";//"Yearly";//"Monthly";//
String method = "Max";//"Min";//"Average";//"Total";//
int numBins = 10;
boolean logarithmicBinsTF = true;
String seasonBegin = "06-01";//"MM-dd"
String seasonEnd = "09-30";//"MM-dd"
String period1Begin = "";
String period1End = "";
String period2Begin = "";
String period2End = "";
String period3Begin = "";
String period3End = "";
boolean medianTF = false;
boolean envelopeTF = true;
boolean rasterTF = true;
boolean rasterLogarithmicBinsTF = true;
double highPercentile = 0.75;
double lowPercentile = 0.25;
boolean showMonthlyStatsTF = false;
boolean calcFlowStatisticsFileTF = true;
boolean waterYearTF = false;
boolean calcCDPHElowflowTF = true;
String CDPHE_lowFlowType = "dflow-all";//"extreme-value";//"biological";//"human-health";//"reg31";//
int CDPHE_m = 4;//m-day average //only used if CDPHE_lowFlowType == "all" or "extreme-value" or "biological"
int CDPHE_R = 10;//R-year return period for cdphe flows //only used if CDPHE_lowFlowType == "all" or "extreme-value" or "biological"
String CDPHE_waterYearBegin = "04-01";//"MM-dd" //only used if CDPHE_lowFlowType == "all" or "extreme-value"
int CDPHE_clusterLength = 120; //only used if CDPHE_lowFlowType == "all" or "biological"
int CDPHE_clusterCountMax = 5; //only used if CDPHE_lowFlowType == "all" or "biological"
boolean mergeDatasets = false;//true;//
String mergeMethod = "user";//"public";//"max";//"average";//"min";//
String userData = "";//"Date\tFlow\n1999-04-29\t8.3\n1999-05-09\t60.2\n1999-05-29\t20.1";//
//Outputs
String len = "-1";
String start = "?";
String end = "?";
String units = "?";
String dataSource = "?";
double extremeValueDFLOW = -1;
double biologicalDFLOW_all = -1;
double biologicalDFLOW_jan = -1;
double biologicalDFLOW_feb = -1;
double biologicalDFLOW_mar = -1;
double biologicalDFLOW_apr = -1;
double biologicalDFLOW_may = -1;
double biologicalDFLOW_jun = -1;
double biologicalDFLOW_jul = -1;
double biologicalDFLOW_aug = -1;
double biologicalDFLOW_sep = -1;
double biologicalDFLOW_oct = -1;
double biologicalDFLOW_nov = -1;
double biologicalDFLOW_dec = -1;
int biologicalYear_jan = -1;
int biologicalYear_feb = -1;
int biologicalYear_mar = -1;
int biologicalYear_apr = -1;
int biologicalYear_may = -1;
int biologicalYear_jun = -1;
int biologicalYear_jul = -1;
int biologicalYear_aug = -1;
int biologicalYear_sep = -1;
int biologicalYear_oct = -1;
int biologicalYear_nov = -1;
int biologicalYear_dec = -1;
double humanHealthDFLOW = -1;
String reg31DFLOWsummary = "?";
double max = -1;
double min = -1;
double upperQuartile = -1;
double lowerQuartile = -1;
double median = -1;
double mean = -1;
double standardDeviation = -1;
double variance = -1;
double skew = -1;
double coeffvar = -1;
double kendallCorlCoeff = -1;
String len_seasonal = "-1";
double max_seasonal = -1;
double min_seasonal = -1;
double upperQuartile_seasonal = -1;
double lowerQuartile_seasonal = -1;
double median_seasonal = -1;
double mean_seasonal = -1;
double standardDeviation_seasonal = -1;
double variance_seasonal = -1;
double skew_seasonal = -1;
double coeffvar_seasonal = -1;
double kendallCorlCoeff_seasonal = -1;
String len_period1 = "-1";
double max_period1 = -1;
double min_period1 = -1;
double upperQuartile_period1 = -1;
double lowerQuartile_period1 = -1;
double median_period1 = -1;
double mean_period1 = -1;
double standardDeviation_period1 = -1;
double variance_period1 = -1;
double skew_period1 = -1;
double coeffvar_period1 = -1;
double kendallCorlCoeff_period1 = -1;
String len_period2 = "-1";
double max_period2 = -1;
double min_period2 = -1;
double upperQuartile_period2 = -1;
double lowerQuartile_period2 = -1;
double median_period2 = -1;
double mean_period2 = -1;
double standardDeviation_period2 = -1;
double variance_period2 = -1;
double skew_period2 = -1;
double coeffvar_period2 = -1;
double kendallCorlCoeff_period2 = -1;
String len_period3 = "-1";
double max_period3 = -1;
double min_period3 = -1;
double upperQuartile_period3 = -1;
double lowerQuartile_period3 = -1;
double median_period3 = -1;
double mean_period3 = -1;
double standardDeviation_period3 = -1;
double variance_period3 = -1;
double skew_period3 = -1;
double coeffvar_period3 = -1;
double kendallCorlCoeff_period3 = -1;
//Gets
public File getParagraph(){ return new File(directory, "timeseries_summary.txt"); }
public File getFlowStatistics_summary() {
FlowStatistics flowStats = new FlowStatistics();
return new File(directory, flowStats.getFlowStatistics_summary());
}
public File getTimeseriesOutput(){ return new File(directory, "timeseries_graph.out"); }//for use with JSHighCharts
public File getBoxplotOutput(){ return new File(directory, "timeseries_boxplot.out"); }//for use with JSHighCharts
public File getMonthlyTimeseriesOutput(){ return new File(directory, "timeseries_monthlygraph.out"); }//for use with JSHighCharts
// public File getMonthlyBoxplotOutput(){ return new File(directory, "timeseries_monthlyboxplot.out"); }//for use with JSHighCharts
public File getTimeseriesEnvelopeOutput(){ return new File(directory, "timeseries_envelope.out"); }//for use with JSHighCharts
public File getHistogramOutput(){ return new File(directory, "timeseries_histogram.outt"); }//for use with JSHighCharts
public File getCDFoutput(){ return new File(directory, "timeseries_cdf.out"); }//for use with JSHighCharts
public String getGraph(){ return "timeseries_graph.jpg"; }
public String getBoxplot(){ return "timeseries_boxplot.jpg"; }
public String getTimeseriesEnvelope(){ return "timeseries_envelope.jpg"; }
public String getTimeseriesRaster(){ return "timeseries_raster.jpg"; }
public String getMonthlyGraph(){ return "timeseries_monthlygraph.jpg"; }
public String getHistogram(){ return "timeseries_histogram.jpg"; }
public String getCDF(){ return "timeseries_cdf.jpg"; }
public String getLen(){ return len; }
public String getStart(){ return start; }
public String getEnd(){ return end; }
public String getUnits(){ return units; }
public String getDataSource(){ return dataSource; }
public String getCDPHE_ExtremeValueDFLOW(){ return String.valueOf(extremeValueDFLOW); }
public String getCDPHE_BiologicalDFLOW_all(){ return String.valueOf(biologicalDFLOW_all); }
public String getCDPHE_BiologicalDFLOW_jan(){ return String.valueOf(biologicalDFLOW_jan); }
public String getCDPHE_BiologicalDFLOW_feb(){ return String.valueOf(biologicalDFLOW_feb); }
public String getCDPHE_BiologicalDFLOW_mar(){ return String.valueOf(biologicalDFLOW_mar); }
public String getCDPHE_BiologicalDFLOW_apr(){ return String.valueOf(biologicalDFLOW_apr); }
public String getCDPHE_BiologicalDFLOW_may(){ return String.valueOf(biologicalDFLOW_may); }
public String getCDPHE_BiologicalDFLOW_jun(){ return String.valueOf(biologicalDFLOW_jun); }
public String getCDPHE_BiologicalDFLOW_jul(){ return String.valueOf(biologicalDFLOW_jul); }
public String getCDPHE_BiologicalDFLOW_aug(){ return String.valueOf(biologicalDFLOW_aug); }
public String getCDPHE_BiologicalDFLOW_sep(){ return String.valueOf(biologicalDFLOW_sep); }
public String getCDPHE_BiologicalDFLOW_oct(){ return String.valueOf(biologicalDFLOW_oct); }
public String getCDPHE_BiologicalDFLOW_nov(){ return String.valueOf(biologicalDFLOW_nov); }
public String getCDPHE_BiologicalDFLOW_dec(){ return String.valueOf(biologicalDFLOW_dec); }
public String getCDPHE_BiologicalYear_jan(){ return String.valueOf(biologicalYear_jan); }
public String getCDPHE_BiologicalYear_feb(){ return String.valueOf(biologicalYear_feb); }
public String getCDPHE_BiologicalYear_mar(){ return String.valueOf(biologicalYear_mar); }
public String getCDPHE_BiologicalYear_apr(){ return String.valueOf(biologicalYear_apr); }
public String getCDPHE_BiologicalYear_may(){ return String.valueOf(biologicalYear_may); }
public String getCDPHE_BiologicalYear_jun(){ return String.valueOf(biologicalYear_jun); }
public String getCDPHE_BiologicalYear_jul(){ return String.valueOf(biologicalYear_jul); }
public String getCDPHE_BiologicalYear_aug(){ return String.valueOf(biologicalYear_aug); }
public String getCDPHE_BiologicalYear_sep(){ return String.valueOf(biologicalYear_sep); }
public String getCDPHE_BiologicalYear_oct(){ return String.valueOf(biologicalYear_oct); }
public String getCDPHE_BiologicalYear_nov(){ return String.valueOf(biologicalYear_nov); }
public String getCDPHE_BiologicalYear_dec(){ return String.valueOf(biologicalYear_dec); }
public String getCDPHE_HumanHealthDFLOW(){ return String.valueOf(humanHealthDFLOW); }
public String getCDPHE_Reg31DFLOWsummary(){ return String.valueOf(reg31DFLOWsummary); }
public String getMax(){ return String.valueOf(max); }
public String getMin(){ return String.valueOf(min); }
public String getUpperQuartile(){ return String.valueOf(upperQuartile); }
public String getLowerQuartile(){ return String.valueOf(lowerQuartile); }
public String getMedian(){ return String.valueOf(median); }
public String getMean(){ return String.valueOf(mean); }
public String getStandardDeviation(){ return String.valueOf(standardDeviation); }
public String getVariance(){ return String.valueOf(variance); }
public String getSkewness(){ return String.valueOf(skew); }
public String getCoefficientOfVariation(){ return String.valueOf(coeffvar); }
public String getKendallCorrelationCoefficient(){ return String.valueOf(kendallCorlCoeff); }
public String getLen_seasonal(){ return len_seasonal; }
public String getMax_seasonal(){ return String.valueOf(max_seasonal); }
public String getMin_seasonal(){ return String.valueOf(min_seasonal); }
public String getUpperQuartile_seasonal(){ return String.valueOf(upperQuartile_seasonal); }
public String getLowerQuartile_seasonal(){ return String.valueOf(lowerQuartile_seasonal); }
public String getMedian_seasonal(){ return String.valueOf(median_seasonal); }
public String getMean_seasonal(){ return String.valueOf(mean_seasonal); }
public String getStandardDeviation_seasonal(){ return String.valueOf(standardDeviation_seasonal); }
public String getVariance_seasonal(){ return String.valueOf(variance_seasonal); }
public String getSkewness_seasonal(){ return String.valueOf(skew_seasonal); }
public String getCoefficientOfVariation_seasonal(){ return String.valueOf(coeffvar_seasonal); }
public String getKendallCorrelationCoefficient_seasonal(){ return String.valueOf(kendallCorlCoeff_seasonal); }
public String getLen_period1(){ return len_period1; }
public String getMax_period1(){ return String.valueOf(max_period1); }
public String getMin_period1(){ return String.valueOf(min_period1); }
public String getUpperQuartile_period1(){ return String.valueOf(upperQuartile_period1); }
public String getLowerQuartile_period1(){ return String.valueOf(lowerQuartile_period1); }
public String getMedian_period1(){ return String.valueOf(median_period1); }
public String getMean_period1(){ return String.valueOf(mean_period1); }
public String getStandardDeviation_period1(){ return String.valueOf(standardDeviation_period1); }
public String getVariance_period1(){ return String.valueOf(variance_period1); }
public String getSkewness_period1(){ return String.valueOf(skew_period1); }
public String getCoefficientOfVariation_period1(){ return String.valueOf(coeffvar_period1); }
public String getKendallCorrelationCoefficient_period1(){ return String.valueOf(kendallCorlCoeff_period1); }
public String getLen_period2(){ return len_period2; }
public String getMax_period2(){ return String.valueOf(max_period2); }
public String getMin_period2(){ return String.valueOf(min_period2); }
public String getUpperQuartile_period2(){ return String.valueOf(upperQuartile_period2); }
public String getLowerQuartile_period2(){ return String.valueOf(lowerQuartile_period2); }
public String getMedian_period2(){ return String.valueOf(median_period2); }
public String getMean_period2(){ return String.valueOf(mean_period2); }
public String getStandardDeviation_period2(){ return String.valueOf(standardDeviation_period2); }
public String getVariance_period2(){ return String.valueOf(variance_period2); }
public String getSkewness_period2(){ return String.valueOf(skew_period2); }
public String getCoefficientOfVariation_period2(){ return String.valueOf(coeffvar_period2); }
public String getKendallCorrelationCoefficient_period2(){ return String.valueOf(kendallCorlCoeff_period2); }
public String getLen_period3(){ return len_period3; }
public String getMax_period3(){ return String.valueOf(max_period3); }
public String getMin_period3(){ return String.valueOf(min_period3); }
public String getUpperQuartile_period3(){ return String.valueOf(upperQuartile_period3); }
public String getLowerQuartile_period3(){ return String.valueOf(lowerQuartile_period3); }
public String getMedian_period3(){ return String.valueOf(median_period3); }
public String getMean_period3(){ return String.valueOf(mean_period3); }
public String getStandardDeviation_period3(){ return String.valueOf(standardDeviation_period3); }
public String getVariance_period3(){ return String.valueOf(variance_period3); }
public String getSkewness_period3(){ return String.valueOf(skew_period3); }
public String getCoefficientOfVariation_period3(){ return String.valueOf(coeffvar_period3); }
public String getKendallCorrelationCoefficient_period3(){ return String.valueOf(kendallCorlCoeff_period3); }
//Sets
public void setDirectory(String directory_str){ directory = directory_str; }
public void setDatabase(String database_str){ database = database_str; }
public void setOrganizationID(String orgId_str){ orgId = orgId_str; }
public void setStartDate(String startDate_str){ startDate = startDate_str; }
public void setEndDate(String endDate_str){ endDate = endDate_str; }
public void setStationName(String stationName_str){ stationName = stationName_str; }
public void setStationId(String stationId_str){ stationId = stationId_str; }
public void setWQtest(String wqTest_str){ wqTest = wqTest_str; }
public void setTimeStep(String timeStep_str){ timeStep = timeStep_str; }
public void setMethod(String method_str){ method = method_str; }
public void setNumberOfBins(int numBins_int){ numBins = numBins_int; }
public void setLogarithmicHistogramBins(boolean logarithmicBins_TF){ logarithmicBinsTF = logarithmicBins_TF; }
public void setSeasonBegin(String seasonBegin_str){ seasonBegin = seasonBegin_str; }
public void setSeasonEnd(String seasonEnd_str){ seasonEnd = seasonEnd_str; }
public void setPeriod1Begin(String period1Begin_str){ period1Begin = period1Begin_str; }
public void setPeriod1End(String period1End_str){ period1End = period1End_str; }
public void setPeriod2Begin(String period2Begin_str){ period2Begin = period2Begin_str; }
public void setPeriod2End(String period2End_str){ period2End = period2End_str; }
public void setPeriod3Begin(String period3Begin_str){ period3Begin = period3Begin_str; }
public void setPeriod3End(String period3End_str){ period3End = period3End_str; }
public void setMedianTF(boolean median_TF){ medianTF = median_TF; }
public void setEnvelopeTF(boolean envelope_TF){ envelopeTF = envelope_TF; }
public void setRasterTF(boolean raster_TF){ rasterTF = raster_TF; }
public void setRasterLogarithmicBinsTF(boolean rasterLogarithmicBins_TF){ rasterLogarithmicBinsTF = rasterLogarithmicBins_TF; }
public void setHighPercentile(double highPercentile_dbl){ highPercentile = highPercentile_dbl; }
public void setLowPercentile(double lowPercentile_dbl){ lowPercentile = lowPercentile_dbl; }
public void setShowMonthlyStatsTF(boolean showMonthlyStats_TF){ showMonthlyStatsTF = showMonthlyStats_TF; }
public void setCalcFlowStatisticsFileTF(boolean calcFlowStatisticsFile_TF){ calcFlowStatisticsFileTF = calcFlowStatisticsFile_TF; }
public void setWaterYear_TF(boolean waterYear_TF){ waterYearTF = waterYear_TF; }
public void setCalcCDPHElowflowTF(boolean calcCDPHElowflow_TF){ calcCDPHElowflowTF = calcCDPHElowflow_TF; }
public void setCDPHE_lowFlowType(String CDPHE_lowFlowType_str){ CDPHE_lowFlowType = CDPHE_lowFlowType_str; }
public void setCDPHE_m(int CDPHE_m_int){ CDPHE_m = CDPHE_m_int; }
public void setCDPHE_R(int CDPHE_R_int){ CDPHE_R = CDPHE_R_int; }
public void setCDPHE_waterYearBegin(String CDPHE_waterYearBegin_str){ CDPHE_waterYearBegin = CDPHE_waterYearBegin_str; }
public void setCDPHE_clusterLength(int CDPHE_clusterLength_int){ CDPHE_clusterLength = CDPHE_clusterLength_int; }
public void setCDPHE_clusterCountMax(int CDPHE_clusterCountMax_int){ CDPHE_clusterCountMax = CDPHE_clusterCountMax_int; }
public void setMergeDatasets(boolean mergeDatasets_TF){ mergeDatasets = mergeDatasets_TF; }
public void setMergeMethod(String mergeMethod_str){ mergeMethod = mergeMethod_str; }
public void setUserData(String userData_str){ userData = userData_str; }
/**
* Main statistics function calls other functions to calculate each statistic value then stores the results as global variables
* @param dataList data on which statistical values are desired
* @param flag a flag for which results the statistics will be stored to, either "all", "period1", "period2", or "period3"
*/
private void CalculateStatistics(String[][] data, String flag) {
//Convert into double list
ArrayList<Double> dataList = new ArrayList<>();
for(int i=0; i<data.length; i++){
dataList.add(Double.parseDouble(data[i][1]));
}
//Calculate statistics
double temp1 = DoubleMath.round(DoubleMath.max(dataList),3);//Call Max function
double temp2 = DoubleMath.round(DoubleMath.min(dataList),3);//Call Min function
double temp3 = DoubleMath.round(DoubleMath.Percentile_function(dataList,0.75),3);//Call Upper Quartile function
double temp4 = DoubleMath.round(DoubleMath.Percentile_function(dataList,0.25),3);//Call Lower Quartile function
double temp5 = DoubleMath.round(DoubleMath.median(dataList),3);//Call Median function
double temp6 = DoubleMath.round(DoubleMath.meanArithmetic(dataList),3);//Call Mean function
double temp7 = DoubleMath.round(DoubleMath.StandardDeviationSample(dataList),3);//Call standard deviation function
double temp8 = DoubleMath.round(DoubleMath.VarianceSample(dataList),3);//Call variance function
double temp9 = DoubleMath.round(DoubleMath.SkewnessSample(dataList),8);//Call skewness function
double temp10 = DoubleMath.round(DoubleMath.CoefficientOfVariation(dataList),3);//call coefficient of variation function
double temp11 = DoubleMath.round(DoubleMath.KendallCorrelationCoefficient(dataList), 4);
if(flag.equalsIgnoreCase("all")){
max = temp1;
min = temp2;
upperQuartile = temp3;
lowerQuartile = temp4;
median = temp5;
mean = temp6;
standardDeviation = temp7;
variance = temp8;
skew = temp9;
coeffvar = temp10;
kendallCorlCoeff = temp11;
}else if(flag.equalsIgnoreCase("seasonal")){
len_seasonal = String.valueOf(data.length);
max_seasonal = temp1;
min_seasonal = temp2;
upperQuartile_seasonal = temp3;
lowerQuartile_seasonal = temp4;
median_seasonal = temp5;
mean_seasonal = temp6;
standardDeviation_seasonal = temp7;
variance_seasonal = temp8;
skew_seasonal = temp9;
coeffvar_seasonal = temp10;
kendallCorlCoeff_seasonal = temp11;
}else if(flag.equalsIgnoreCase("period1")){
max_period1 = temp1;
min_period1 = temp2;
upperQuartile_period1 = temp3;
lowerQuartile_period1 = temp4;
median_period1 = temp5;
mean_period1 = temp6;
standardDeviation_period1 = temp7;
variance_period1 = temp8;
skew_period1 = temp9;
coeffvar_period1 = temp10;
kendallCorlCoeff_period1 = temp11;
}else if(flag.equalsIgnoreCase("period2")){
max_period2 = temp1;
min_period2 = temp2;
upperQuartile_period2 = temp3;
lowerQuartile_period2 = temp4;
median_period2 = temp5;
mean_period2 = temp6;
standardDeviation_period2 = temp7;
variance_period2 = temp8;
skew_period2 = temp9;
coeffvar_period2 = temp10;
kendallCorlCoeff_period2 = temp11;
}else if(flag.equalsIgnoreCase("period3")){
max_period3 = temp1;
min_period3 = temp2;
upperQuartile_period3 = temp3;
lowerQuartile_period3 = temp4;
median_period3 = temp5;
mean_period3 = temp6;
standardDeviation_period3 = temp7;
variance_period3 = temp8;
skew_period3 = temp9;
coeffvar_period3 = temp10;
kendallCorlCoeff_period3 = temp11;
}
}
/**
* Graph the time series and user data and save the resulting graph to the specified location
* @param sortedData the String[][] containing sorted data for the time series
* (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm if
* timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param sortedData_user the String[][] containing sorted user data for the
* time series (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm
* if timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param period1Data the String[][] containing sorted data for the time
* series contained by period1 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period2Data the String[][] containing sorted data for the time
* series contained by period2 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period3Data the String[][] containing sorted data for the time
* series contained by period3 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param color the color of the merged dataset (Java.Color)
* @param color2 the color of the user dataset (Java.Color)
* @param showLine a boolean, if true lines will be shown on the graph, if false only shapes for the data
* @param yAxisTitle the String label for the y axis of the graph
*/
private void createTimeseriesGraph(String[][] sortedData,
String[][] sortedData_user,
String[][] period1Data,
String[][] period2Data,
String[][] period3Data,
Color color,
Color color2,
boolean showLine,
String yAxisTitle) throws ParseException, IOException {
DateFormat periodDateFormat = DoubleArray.getDateFormat("daily", false);
Date jfreeChartDateLimit = periodDateFormat.parse("1900-01-01");
//Re-Format graphing data for output for use with JHighChart
Date period1Begin_date = new Date();
Date period1End_date = new Date();
Date period2Begin_date = new Date();
Date period2End_date = new Date();
Date period3Begin_date = new Date();
Date period3End_date = new Date();
if(!period1Begin.isEmpty() && !period1End.isEmpty()){
period1Begin_date = periodDateFormat.parse(period1Begin);
period1End_date = periodDateFormat.parse(period1End);
}
if(!period2Begin.isEmpty() && !period2End.isEmpty()){
period2Begin_date = periodDateFormat.parse(period2Begin);
period2End_date = periodDateFormat.parse(period2End);
}
if(!period3Begin.isEmpty() && !period3End.isEmpty()){
period3Begin_date = periodDateFormat.parse(period3Begin);
period3End_date = periodDateFormat.parse(period3End);
}
String[][] graphData = new String[sortedData.length][5];
DateFormat desiredDateFormat = DoubleArray.getDateFormat(timeStep, false);
for(int i=0; i<sortedData.length; i++){
Date newDate = desiredDateFormat.parse(sortedData[i][0]);
graphData[i][0] = sortedData[i][0];
graphData[i][1] = sortedData[i][1];
//Period1
if(newDate.compareTo(period1Begin_date) >= 0 && newDate.compareTo(period1End_date) <= 0){
if(medianTF){
graphData[i][2] = String.valueOf(median_period1);
}else{
graphData[i][2] = String.valueOf(mean_period1);
}
}else{
graphData[i][2] = "-1";
}
//Period2
if(newDate.compareTo(period2Begin_date) >= 0 && newDate.compareTo(period2End_date) <= 0){
if(medianTF){
graphData[i][3] = String.valueOf(median_period2);
}else{
graphData[i][3] = String.valueOf(mean_period2);
}
}else{
graphData[i][3] = "-1";
}
//Period3
if(newDate.compareTo(period3Begin_date) >= 0 && newDate.compareTo(period3End_date) <= 0){
if(medianTF){
graphData[i][4] = String.valueOf(median_period3);
}else{
graphData[i][4] = String.valueOf(mean_period3);
}
}else{
graphData[i][4] = "-1";
}
}
//Write output for JHighChart timeseries for use on eRAMS
Arrays.sort(graphData, new m.cfa.DateComparator());
DoubleArray.writeTimeSeries(directory, graphData, timeStep, getTimeseriesOutput().getName(), false);
//Create TimeSeries graph of merged data
XYPlot plotTime = new XYPlot();
boolean showLegend = false;
TimeSeries series = Graphing.createTimeSeriesFromData(sortedData, stationId + ": Data", timeStep);
TimeSeries series2 = Graphing.createTimeSeriesFromData(sortedData_user, stationId + ": User Data", timeStep);
//Create user data points
if(sortedData_user.length != 0){//only show user points if it is not zero
plotTime = Graphing.addTimeseriesData(plotTime, series, showLine, color, false, false, false, true, 0);
plotTime = Graphing.addTimeseriesData(plotTime, series2, showLine, color2, false, false, false, true, 1);
showLegend = true;
}else{
plotTime = Graphing.addTimeseriesData(plotTime, series, showLine, color, false, false, false, true, 0);
}
//Create period analysis average lines
if(period1Data.length > 0){
len_period1 = String.valueOf(period1Data.length);
double value = mean_period1;
String label = "Mean";
if(medianTF){
value = median_period1;
label = "Median";
}
TimeSeries periodSeries = new TimeSeries("Period 1 " + label + ": " + value + " " + units);
//artificial limit for JFreeCharts' "Day" class
Date period1Begin_Date = desiredDateFormat.parse(period1Begin);
if(period1Begin_Date.compareTo(jfreeChartDateLimit) >= 0){
periodSeries.add(new Day(period1Begin_Date), value);
}
Date period1End_Date = desiredDateFormat.parse(period1End);
if(period1End_Date.compareTo(jfreeChartDateLimit) >= 0){
periodSeries.add(new Day(period1End_Date), value);
}
plotTime = Graphing.addTimeseriesData(plotTime, periodSeries, true, Color.red, false, false, true, true, 2);
showLegend = true;
}
if(period2Data.length > 0){
len_period2 = String.valueOf(period2Data.length);
double value = mean_period2;
String label = "Mean";
if(medianTF){
value = median_period2;
label = "Median";
}
TimeSeries periodSeries = new TimeSeries("Period 2 " + label + ": " + value + " " + units);
//artificial limit for JFreeCharts' "Day" class
Date period2Begin_Date = desiredDateFormat.parse(period2Begin);
if(period2Begin_Date.compareTo(jfreeChartDateLimit) >= 0){
periodSeries.add(new Day(period2Begin_Date), value);
}
Date period2End_Date = desiredDateFormat.parse(period2End);
if(period2End_Date.compareTo(jfreeChartDateLimit) >= 0){
periodSeries.add(new Day(period2End_Date), value);
}
plotTime = Graphing.addTimeseriesData(plotTime, periodSeries, true, new Color(255, 135, 0), false, false, true, true, 3);//gold
showLegend = true;
}
if(period3Data.length > 0){
len_period3 = String.valueOf(period3Data.length);
double value = mean_period3;
String label = "Mean";
if(medianTF){
value = median_period3;
label = "Median";
}
TimeSeries periodSeries = new TimeSeries("Period 3 " + label + ": " + value + " " + units);
//artificial limit for JFreeCharts' "Day" class
Date period3Begin_Date = desiredDateFormat.parse(period3Begin);
if(period3Begin_Date.compareTo(jfreeChartDateLimit) >= 0){
periodSeries.add(new Day(period3Begin_Date), value);
}
Date period3End_Date = desiredDateFormat.parse(period3End);
if(period3End_Date.compareTo(jfreeChartDateLimit) >= 0){
periodSeries.add(new Day(period3End_Date), value);
}
plotTime = Graphing.addTimeseriesData(plotTime, periodSeries, true, Color.green, false, false, true, true, 4);
showLegend = true;
}
//Create Y Axis
ValueAxis rangeTime = new NumberAxis(yAxisTitle);
plotTime.setRangeAxis(0, rangeTime);
//Create X Axis
DateAxis domainTime = new DateAxis("Date");
domainTime.setLowerMargin(0.05);
domainTime.setUpperMargin(0.05);
plotTime.setDomainAxis(0, domainTime);
//Set extra plot preferences
plotTime = Graphing.setTimeAxisPreferences(plotTime);
//Create the chart with the plot and a legend
String graphTitle = "Time Series for " + database + " Station: " + stationId + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, Graphing.titleFont, plotTime, showLegend);
//Set legend Font
if(showLegend){
LegendTitle legendTitle = chart.getLegend();
legendTitle.setItemFont(Graphing.masterFont);
}
//Save resulting graph for use later
try{
String path = directory + File.separator + getGraph();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
/**
* Creates a boxplot of the timeseries data to be displayed next to a summary of the statistics of the timeseries data
* @param yAxisTitle a String of the title for the Y axis of the boxplot
*/
private void createTimeseriesBoxplot(String[][] data, String yAxisTitle) throws IOException{
//Prep. boxplot data for output function
ArrayList<ArrayList<Double>> boxplotOutliers = new ArrayList<>();
ArrayList<Double> outliers = new ArrayList<>();// Get daily outliers
double IQR = upperQuartile - lowerQuartile;// Find IQR
for (int i = 0; i < data.length; i++){
double value = Double.parseDouble(data[i][1]);
if(value < (lowerQuartile - 1.5 * IQR) || value > (upperQuartile + 1.5 * IQR)){
outliers.add(value);
}
}
boxplotOutliers.add(outliers);
double[][] boxplotData = {{max},{upperQuartile},{median},{lowerQuartile},{min}};
//Write output for JHighChart boxplot for use on eRAMS
DoubleArray.writeBoxplot(directory, boxplotOutliers, boxplotData, getBoxplotOutput().getName());
//Create boxplot of the timeseries data
XYPlot plot = new XYPlot();
//Create X Axis
ValueAxis xAxis = new NumberAxis("");
xAxis.setRange(0, 10);
xAxis.setLabelFont(Graphing.masterFont);
xAxis.setTickLabelFont(Graphing.masterFont);
xAxis.setTickLabelsVisible(false);
plot.setDomainAxis(0, xAxis);
ValueAxis yAxis = new NumberAxis(yAxisTitle);
yAxis.setLabelFont(Graphing.masterFont);
yAxis.setTickLabelFont(Graphing.masterFont);
plot.setRangeAxis(0, yAxis);
//Calculate and add Median to dataset
XYSeries median_series = new XYSeries("Median");
median_series.add(5, median);
//Create median Line
XYDataset median_scatter = new XYSeriesCollection(median_series);
XYItemRenderer renderer_median = new XYLineAndShapeRenderer(false, true);
renderer_median.setSeriesShape(0, new Rectangle2D.Double(-4.0, 0.0, 8.0, 1));//new Ellipse2D.Double(-4, -4, 8, 8));
renderer_median.setSeriesPaint(0, Color.red);
renderer_median.setSeriesVisibleInLegend(0, false);
plot.setDataset(0, median_scatter);
plot.setRenderer(0, renderer_median);
//Create quartile Box shapes for the box plot
//Create XYSeries for the box shape
XYSeries shapeSeries = new XYSeries("Shape");
shapeSeries.add(5, lowerQuartile);
shapeSeries.add(5, upperQuartile);
//Create the quartile rectangle shape
XYDataset shapeDataset = new XYSeriesCollection(shapeSeries);
XYItemRenderer renderer_shape = new XYLineAndShapeRenderer(true, false);
Stroke thickness = new BasicStroke(10, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
renderer_shape.setSeriesStroke(0, thickness);
renderer_shape.setSeriesPaint(0, Color.blue);
renderer_shape.setSeriesVisibleInLegend(0, false);
plot.setDataset(1, shapeDataset);
plot.setRenderer(1, renderer_shape);
//Creates 1.5 * Interquartile Range (IQR) lines
//Create XYSeries for the min-max lines
double lowerLimit = lowerQuartile - 1.5*IQR;
double upperLimit = upperQuartile + 1.5*IQR;
if(lowerLimit < min){
lowerLimit = min;
}
if(upperLimit > max){
upperLimit = max;
}
XYSeries lineSeries = new XYSeries("Line");
lineSeries.add(5, lowerLimit);
lineSeries.add(5, upperLimit);
//Create the 1.5*IQR lines
XYDataset lineDataset = new XYSeriesCollection(lineSeries);
XYItemRenderer lineRenderer = new XYLineAndShapeRenderer(true, true);
Stroke thickness2 = new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
lineRenderer.setSeriesStroke(0, thickness2);
lineRenderer.setSeriesShape(0, new Rectangle2D.Double(-10.0, 0.0, 20.0, 1));
lineRenderer.setSeriesPaint(0, Color.black);
lineRenderer.setSeriesVisibleInLegend(0, false);
plot.setDataset(2, lineDataset);
plot.setRenderer(2, lineRenderer);
//Calculate and create Outliers (# < lowerQuartile - 1.5*IQR or # > upperQuartile + 1.5*IQR)
//Calculate and create Extreme Outliers (# < lowerQuartile - 3*IQR or # > upperQuartile + 3*IQR)
XYSeries outliers_XY = new XYSeries("Outliers");
XYSeries extremeOutliers = new XYSeries("Extreme Outliers");
for(int i=0; i<data.length; i++){
double value = Double.parseDouble(data[i][1]);
//Lower outliers
if(value < (lowerQuartile - 1.5*IQR) && value > (lowerQuartile - 3*IQR)){
outliers_XY.add(5, value);
}
//Upper outliers
if(value > (upperQuartile + 1.5*IQR) && value < (lowerQuartile + 3*IQR)){
outliers_XY.add(5, value);
}
//Extreme Lower outliers
if(value < (lowerQuartile - 3*IQR)){
extremeOutliers.add(5, value);
}
//Extreme Upper outliers
if(value > (lowerQuartile + 3*IQR)){
extremeOutliers.add(5, value);
}
}
//Create outlier scatter
XYDataset outlier_scatter = new XYSeriesCollection(outliers_XY);
XYItemRenderer renderer_outlier = new XYLineAndShapeRenderer(false, true);
renderer_outlier.setSeriesShape(0, new Ellipse2D.Double(-2.0, 2.0, 4.0, 4.0));
renderer_outlier.setSeriesPaint(0, Color.darkGray);
if(outliers_XY.isEmpty()){
renderer_outlier.setSeriesVisibleInLegend(0, false);
}
plot.setDataset(3, outlier_scatter);
plot.setRenderer(3, renderer_outlier);
//Create extreme outlier scatter
XYDataset extremeOutlier_scatter = new XYSeriesCollection(extremeOutliers);
XYItemRenderer renderer_ExtremeOutlier = new XYLineAndShapeRenderer(false, true);
renderer_ExtremeOutlier.setSeriesShape(0, new Ellipse2D.Double(-2.0, 2.0, 4.0, 4.0));
renderer_ExtremeOutlier.setSeriesPaint(0, Color.red);
if(extremeOutliers.isEmpty()){
renderer_ExtremeOutlier.setSeriesVisibleInLegend(0, false);
}
plot.setDataset(4, extremeOutlier_scatter);
plot.setRenderer(4, renderer_ExtremeOutlier);
//Put the line on the first Domain and first Range
plot.mapDatasetToDomainAxis(0, 0);
plot.mapDatasetToRangeAxis(0, 0);
//Set extra plot preferences
plot.setOutlinePaint(Color.black);
plot.setDomainGridlinePaint(Color.white);
plot.setRangeGridlinePaint(Color.black);
//Create the chart with the plot and a legend
JFreeChart chart = new JFreeChart("Boxplot of Timeseries Data", Graphing.titleFont, plot, true);
//Save resulting graph for use later
try{
String path = directory + File.separator + getBoxplot();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 200, 400);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
/**
* Graph the quantile plot CDF of the time series data and save the resulting graph to the specified location.
* @param sortedData the String[][] containing sorted data for the time series
* (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm if
* timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param sortedData_user the String[][] containing sorted user data for the
* time series (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm
* if timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param period1Data the String[][] containing sorted data for the time
* series contained by period1 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period2Data the String[][] containing sorted data for the time
* series contained by period2 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period3Data the String[][] containing sorted data for the time
* series contained by period3 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param color the color of the merged dataset (Java.Color)
* @param color2 the color of the user dataset (Java.Color)
* @param xAxisTitle the String label for the x axis of the graph
*/
private void createTimeseriesCDF(String[][] sortedData,
String[][] sortedData_user,
String[][] period1Data,
String[][] period2Data,
String[][] period3Data,
Color color,
Color color2,
String xAxisTitle) throws ParseException, IOException {
double[][] xyRanks = DoubleArray.weibullPlottingPosition(sortedData);
double[][] xyRanks_user = DoubleArray.weibullPlottingPosition(sortedData_user);
double[][] xyRanks_period1 = DoubleArray.weibullPlottingPosition(period1Data);
double[][] xyRanks_period2 = DoubleArray.weibullPlottingPosition(period2Data);
double[][] xyRanks_period3 = DoubleArray.weibullPlottingPosition(period3Data);
//Calculate cdf for the entire dataset
XYSeries series = new XYSeries(stationId + ": Data");
XYSeries series_user = new XYSeries(stationId + ": User Data");
XYSeries period1_series = new XYSeries(stationId + ": Period 1");
XYSeries period2_series = new XYSeries(stationId + ": Period 2");
XYSeries period3_series = new XYSeries(stationId + ": Period 3");
String[][] cdfData = new String[xyRanks.length][8];
for(int i=0; i<xyRanks.length; i++){
double x = xyRanks[i][1]; //flow
double y = 1 - (xyRanks[i][0]/100); //rank
series.add(x, y);
cdfData[i][0] = String.valueOf(x);
cdfData[i][1] = String.valueOf(y);
//Add user data (if any)
if(i < xyRanks_user.length){
x = xyRanks_user[i][1]; //flow
y = 1 - (xyRanks_user[i][0]/100); //rank
series_user.add(x, y);
}
//Add period 1 data (if any)
if(i < xyRanks_period1.length){
x = xyRanks_period1[i][1]; //flow
y = 1 - (xyRanks_period1[i][0]/100); //rank
period1_series.add(x, y);
cdfData[i][2] = String.valueOf(x);
cdfData[i][3] = String.valueOf(y);
}else{
cdfData[i][2] = "-1";
cdfData[i][3] = "-1";
}
//Add period 2 data (if any)
if(i < xyRanks_period2.length){
x = xyRanks_period2[i][1]; //flow
y = 1 - (xyRanks_period2[i][0]/100); //rank
period2_series.add(x, y);
cdfData[i][4] = String.valueOf(x);
cdfData[i][5] = String.valueOf(y);
}else{
cdfData[i][4] = "-1";
cdfData[i][5] = "-1";
}
//Add period 3 data (if any)
if(i < xyRanks_period3.length){
x = xyRanks_period3[i][1]; //flow
y = 1 - (xyRanks_period3[i][0]/100); //rank
period3_series.add(x, y);
cdfData[i][6] = String.valueOf(x);
cdfData[i][7] = String.valueOf(y);
}else{
cdfData[i][6] = "-1";
cdfData[i][7] = "-1";
}
}
//Save cdf data for JHighCharts
DoubleArray.writeXYseries(directory, cdfData, getCDFoutput().getName());
//Create renderer, and axis for timeseries graph
XYPlot plot = new XYPlot();
XYDataset xyDataset = new XYSeriesCollection(series);
XYDataset xyDataset_user = new XYSeriesCollection(series_user);
XYDataset xyDataset_period1 = new XYSeriesCollection(period1_series);
XYDataset xyDataset_period2 = new XYSeriesCollection(period2_series);
XYDataset xyDataset_period3 = new XYSeriesCollection(period3_series);
XYItemRenderer renderer = new XYLineAndShapeRenderer(true, false);
renderer.setSeriesPaint(0, color);
//Set the line data, renderer, and axis into plot
plot.setDataset(0, xyDataset);
plot.setRenderer(0, renderer);
boolean legendTF = false;
if(sortedData_user.length > 0){
XYItemRenderer renderer_user = new XYLineAndShapeRenderer(true, false);
renderer_user.setSeriesPaint(0, color2);
plot.setDataset(1, xyDataset_user);
plot.setRenderer(1, renderer_user);
legendTF = true;
}
if(period1Data.length > 0){
XYItemRenderer renderer_period1 = new XYLineAndShapeRenderer(true, false);
renderer_period1.setSeriesPaint(0, Color.red);
plot.setDataset(2, xyDataset_period1);
plot.setRenderer(2, renderer_period1);
legendTF = true;
}
if(period2Data.length > 0){
XYItemRenderer renderer_period2 = new XYLineAndShapeRenderer(true, false);
renderer_period2.setSeriesPaint(0, new Color(255, 135, 0));//gold
plot.setDataset(3, xyDataset_period2);
plot.setRenderer(3, renderer_period2);
legendTF = true;
}
if(period3Data.length > 0){
XYItemRenderer renderer_period3 = new XYLineAndShapeRenderer(true, false);
renderer_period3.setSeriesPaint(0, Color.green);
plot.setDataset(4, xyDataset_period3);
plot.setRenderer(4, renderer_period3);
legendTF = true;
}
//Map the line to the first Domain and first Range
plot.mapDatasetToDomainAxis(0, 0);
plot.mapDatasetToRangeAxis(0, 0);
//Create Y Axis
ValueAxis rangeAxis = new NumberAxis("Non-Exceedance");
rangeAxis.setRange(0, 1);
plot.setRangeAxis(0, rangeAxis);
//Create X Axis
LogarithmicAxis xAxis = new LogarithmicAxis(xAxisTitle);
xAxis.setAllowNegativesFlag(true);
plot.setDomainAxis(0, xAxis);
//Set extra plot preferences
plot = Graphing.setLogXaxisPreferences(plot);
//Create the charts out of the plots
String graphTitle = "CDF for " + database + " Station: " + stationId + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, Graphing.titleFont, plot, legendTF);
//Set legend Font
if(legendTF){
LegendTitle legendTitle = chart.getLegend();
legendTitle.setItemFont(Graphing.masterFont);
}
//Save monthly timeseries graph for use later
try{
String path = directory + File.separator + getCDF();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
/**
* Graph the time series verses the month/day for each year (calender or water year depends on waterYearTF)
* and long term average/median and user data and save the resulting graph to the specified location.
* @param sortedData the String[][] containing sorted data for the time series
* (column 1 = dates (yyyy-mm-dd), column 2 = value
* @param period1Data the String[][] containing sorted data for the time series
* contained by period1 (column 1 = dates (yyyy-mm-dd), column 2 = value
* @param period2Data the String[][] containing sorted data for the time series
* contained by period1 (column 1 = dates (yyyy-mm-dd), column 2 = value
* @param period3Data the String[][] containing sorted data for the time series
* contained by period1 (column 1 = dates (yyyy-mm-dd), column 2 = value
* @param yAxisTitle the String label for the y axis of the graph
*/
private void createTimeseriesEnvelopeGraph(String[][] sortedData,
String[][] period1Data,
String[][] period2Data,
String[][] period3Data,
String yAxisTitle,
boolean logYaxis_TF) throws IOException, ParseException {
//Initialize variables
DateFormat desiredDateFormat = DoubleArray.getDateFormat("daily", false);
String[][] graphData = new String[366][6];
String[] dayList = new String[366];
int seriesIndex = 0;
String periodTitle = "Mean";
if(medianTF){ periodTitle = "Median"; }
//Plot each year and the long term average and the most recent year
XYPlot plot = new XYPlot();
TimeSeries median_TS = new TimeSeries("All Data: Median");
TimeSeries mean_TS = new TimeSeries("All Data: Mean");
TimeSeries period1_TS = new TimeSeries("Period 1: " + periodTitle);
TimeSeries period2_TS = new TimeSeries("Period 2: " + periodTitle);
TimeSeries period3_TS = new TimeSeries("Period 3: " + periodTitle);
String currentDate_str = "2000-01-01";
if(waterYearTF) currentDate_str = "1999-10-01";
for(int j=1; j<=366; j++){
ArrayList<Double> dateData = new ArrayList<>();
ArrayList<Double> dateData_period1 = new ArrayList<>();
ArrayList<Double> dateData_period2 = new ArrayList<>();
ArrayList<Double> dateData_period3 = new ArrayList<>();
dayList[j-1] = String.valueOf(j);
for(int i=0; i<sortedData.length; i++){
String month_day = sortedData[i][0].substring(5);
if(month_day.equalsIgnoreCase(currentDate_str.substring(5))){
dateData.add(Double.parseDouble(sortedData[i][1]));
}
}
for(int i=0; i<period1Data.length; i++){
String month_day = period1Data[i][0].substring(5);
if(month_day.equalsIgnoreCase(currentDate_str.substring(5))){
dateData_period1.add(Double.parseDouble(period1Data[i][1]));
}
}
for(int i=0; i<period2Data.length; i++){
String month_day = period2Data[i][0].substring(5);
if(month_day.equalsIgnoreCase(currentDate_str.substring(5))){
dateData_period2.add(Double.parseDouble(period2Data[i][1]));
}
}
for(int i=0; i<period3Data.length; i++){
String month_day = period3Data[i][0].substring(5);
if(month_day.equalsIgnoreCase(currentDate_str.substring(5))){
dateData_period3.add(Double.parseDouble(period3Data[i][1]));
}
}
//Calculate average/median
double dayValue_median = DoubleMath.median(dateData);
double dayValue_mean = DoubleMath.meanArithmetic(dateData);
Day currentDay = new Day(desiredDateFormat.parse(currentDate_str));
median_TS.add(currentDay, dayValue_median);
mean_TS.add(currentDay, dayValue_mean);
graphData[j-1][0] = currentDate_str;
graphData[j-1][1] = String.valueOf(dayValue_median);
graphData[j-1][2] = String.valueOf(dayValue_mean);
//Check for period 1 data
double dayValue_period1 = -1;
if(!dateData_period1.isEmpty()){
if(medianTF){
dayValue_period1 = DoubleMath.median(dateData_period1);
}else{
dayValue_period1 = DoubleMath.meanArithmetic(dateData_period1);
}
period1_TS.add(currentDay, dayValue_period1);
}
graphData[j-1][3] = String.valueOf(dayValue_period1);
//Check for period 2 data
double dayValue_period2 = -1;
if(!dateData_period2.isEmpty()){
if(medianTF){
dayValue_period2 = DoubleMath.median(dateData_period2);
}else{
dayValue_period2 = DoubleMath.meanArithmetic(dateData_period2);
}
period2_TS.add(currentDay, dayValue_period2);
}
graphData[j-1][4] = String.valueOf(dayValue_period2);
//Check for period 3 data
double dayValue_period3 = -1;
if(!dateData_period3.isEmpty()){
if(medianTF){
dayValue_period3 = DoubleMath.median(dateData_period3);
}else{
dayValue_period3 = DoubleMath.meanArithmetic(dateData_period3);
}
period3_TS.add(currentDay, dayValue_period3);
}
graphData[j-1][5] = String.valueOf(dayValue_period3);
//Move to the next day
currentDate_str = DoubleArray.getDay(currentDate_str, 1);
}
//Create renderer, and axis for timeseries graph
plot = Graphing.addTimeseriesData(plot, median_TS, true, Color.gray, false, false, true, true, seriesIndex);
seriesIndex++;
plot = Graphing.addTimeseriesData(plot, mean_TS, true, Color.black, false, false, true, true, seriesIndex);
seriesIndex++;
if(!period1_TS.isEmpty()){
plot = Graphing.addTimeseriesData(plot, period1_TS, true, Color.red, false, false, true, true, seriesIndex);
seriesIndex++;
}
if(!period2_TS.isEmpty()){
plot = Graphing.addTimeseriesData(plot, period2_TS, true, new Color(255, 135, 0), false, false, true, true, seriesIndex);
seriesIndex++;
}
if(!period3_TS.isEmpty()){
plot = Graphing.addTimeseriesData(plot, period3_TS, true, Color.green, false, false, true, true, seriesIndex);
seriesIndex++;
}
int recentYear = seriesIndex;
seriesIndex++;//Increase series so the most recent month can be plotted second
//Calculate Flow statistics for each year in time period
boolean moreYears = sortedData.length > 0;
String firstYear = sortedData[0][0].substring(0,4);
String finalYear = sortedData[sortedData.length - 1][0].substring(0,4);
String currentYear = sortedData[sortedData.length - 1][0].substring(0,4);
if(waterYearTF){
Date firstDate = desiredDateFormat.parse(sortedData[0][0]);
Date firstWaterYear = desiredDateFormat.parse(firstYear + "-10-01");
if(firstDate.before(firstWaterYear)){
firstYear = String.valueOf(Integer.parseInt(firstYear) - 1);
}
Date lastDate = desiredDateFormat.parse(sortedData[sortedData.length - 1][0]);
Date lastWaterYear = desiredDateFormat.parse(finalYear + "-09-30");
if(lastDate.after(lastWaterYear)){
finalYear = String.valueOf(Integer.parseInt(finalYear) + 1);
}
}
//Graph a line for each year of data in analysis period
String[][] mostRecentYearData = new String[0][2];
while(moreYears){
String[][] partialData = new String[0][2];
if(waterYearTF){
//Get current water year's data
String previousYear = String.valueOf(Integer.parseInt(currentYear) - 1);
partialData = DoubleArray.getPeriodData(sortedData, previousYear + "-10-01", currentYear + "-09-30");
}else{
//Get current calendar year's data
partialData = DoubleArray.getYearsData(sortedData, currentYear);
}
//Get current year's data and graph it
for(int i=0; i<partialData.length; i++){
String month_day = partialData[i][0].substring(5);
if(waterYearTF){
Date currentDate = desiredDateFormat.parse("2000-" + month_day);
Date waterYearEndDate = desiredDateFormat.parse("2000-09-30");
if(currentDate.after(waterYearEndDate)){
partialData[i][0] = "1999-" + month_day;
}else{
partialData[i][0] = "2000-" + month_day;
}
}else{
partialData[i][0] = "2000-" + month_day;
}
}
TimeSeries currentYear_TS = Graphing.createTimeSeriesFromData(partialData, "temp", "daily");
plot = Graphing.addTimeseriesData(plot, currentYear_TS, true, Color.lightGray, false, false, false, false, seriesIndex);
seriesIndex++;
if(waterYearTF){
Date currentStartDate = desiredDateFormat.parse(currentYear + "-10-01");
Date finalWaterYear = desiredDateFormat.parse(finalYear + "-10-01");
if(currentStartDate.equals(finalWaterYear)){
mostRecentYearData = partialData;
}
}else {
if(currentYear.equalsIgnoreCase(finalYear)){
mostRecentYearData = partialData;
}
}
//Save results for output for JHighCharts
String[] partialDayData = new String[dayList.length];
int ctr = 0;
currentDate_str = "2000-01-01";
if(waterYearTF) currentDate_str = "1999-10-01";
for(int i=0; i<dayList.length; i++){
partialDayData[i] = "-1";//value
try{
String month_day = partialData[ctr][0].substring(5);
if(month_day.equalsIgnoreCase(currentDate_str.substring(5))){
partialDayData[i] = partialData[ctr][1];//value
ctr++;
}
}catch(IndexOutOfBoundsException e){
//do nothing as it already has a -1 value
}
currentDate_str = DoubleArray.getDay(currentDate_str, 1);
}
graphData = DoubleArray.appendcolumn_Matrix(graphData, partialDayData);//Add day values (aka y points)
//Check to stop looping
if(waterYearTF){
//For water year comparison
String previousYear = String.valueOf(Integer.parseInt(currentYear) - 1);
Date currentStartDate = desiredDateFormat.parse(previousYear + "-10-01");
Date firstWaterYear = desiredDateFormat.parse(firstYear + "-10-01");
if(currentStartDate.after(firstWaterYear)){
currentYear = String.valueOf(previousYear);
}else{
moreYears = false;
}
}else{
//For calendar year comparison
int previousYear = Integer.parseInt(currentYear) - 1;
if(firstYear.compareToIgnoreCase(String.valueOf(previousYear)) <= 0){
currentYear = String.valueOf(previousYear);
}else{
moreYears = false;
}
}
}
//Re-add the most recent year to the graph so it renders on top
TimeSeries finalYear_TS = Graphing.createTimeSeriesFromData(mostRecentYearData, String.valueOf(finalYear), "daily");
plot = Graphing.addTimeseriesData(plot, finalYear_TS, true, Color.cyan, false, false, true, true, recentYear);
//Output monthly boxplot and timeseries data for use with JHighCharts
if(rasterTF || envelopeTF){
DoubleArray.writeTimeSeries(directory, graphData, "daily", getTimeseriesEnvelopeOutput().getName(), false);
}
//Check if the user desires a raster graph
if(rasterTF){
createTimeseriesRasterGraph(graphData, yAxisTitle);
}
//Check if the user desires an envelope graph
if(envelopeTF){
//Create Y Axis
if(logYaxis_TF){
LogarithmicAxis rangeAxis = new LogarithmicAxis(yAxisTitle);
rangeAxis.setAllowNegativesFlag(true);
plot.setRangeAxis(0, rangeAxis);
}else{
ValueAxis rangeAxis = new NumberAxis(yAxisTitle);
plot.setRangeAxis(0, rangeAxis);
}
//Create X Axis
String xAxisTitle = "Calendar Year";
if(waterYearTF) xAxisTitle = "Water Year (10-01 to 9-30)";
DateAxis domainTime = new DateAxis(xAxisTitle);
domainTime.setLowerMargin(0.05);
domainTime.setUpperMargin(0.05);
SimpleDateFormat xlabelDateFormat = new SimpleDateFormat("MMM");
domainTime.setDateFormatOverride(xlabelDateFormat);
plot.setDomainAxis(0, domainTime);
//Set extra plot preferences
plot = Graphing.setAxisPreferences(plot);
//Create the charts out of the plots
String graphTitle = "Time Series Range for " + database + " Station: " + stationId + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, Graphing.titleFont, plot, true);
//Set legend Font
LegendTitle legendTitle = chart.getLegend();
legendTitle.setItemFont(Graphing.masterFont);
//Save monthly timeseries graph for use later
try{
String path = directory + File.separator + getTimeseriesEnvelope();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
}
/**
* Graph the time series (z) verses the month/day (x) per each year (y)
* and save the resulting graph to the specified location.
*/
private void createTimeseriesRasterGraph(String[][] envelopePlotData, String zAxisTitle) throws IOException {
//Manipulate envelope plot data into raster plot data format
ArrayList<Double> tempData_dayOfYear = new ArrayList<>();
ArrayList<Double> tempData_year = new ArrayList<>();
ArrayList<Double> tempData_value = new ArrayList<>();
ArrayList<Double> tempData_noZeros = new ArrayList<>();
double currentYear = Double.parseDouble(end.substring(0,4));
for(int j=6; j< envelopePlotData[0].length; j++){//skip data columns 0=date, 1=median, 2=average, 3=period1, 4=period2, 5=period3 to get to the individual year(s) data
for(int i=0; i<366; i++){//day loop
double value = Double.parseDouble(envelopePlotData[i][j]);
if(value > -1){
tempData_dayOfYear.add((double) i+1);
tempData_year.add(currentYear);
tempData_value.add(value);
if(value > 0){
tempData_noZeros.add(value);
}
}
}
currentYear--;
}
double[][] rasterData = new double[tempData_dayOfYear.size()][3];
for(int i=0; i<tempData_dayOfYear.size(); i++){
rasterData[i][0] = tempData_dayOfYear.get(i);
rasterData[i][1] = tempData_year.get(i);
rasterData[i][2] = tempData_value.get(i);
}
double tempMin = DoubleMath.min(tempData_value);
double tempMax = DoubleMath.max(tempData_value);
//Renderer
XYZDataset xyzRasterData = new XYZArrayDataset(rasterData);
XYBlockRenderer renderer = new XYBlockRenderer();
LookupPaintScale paintScale = new LookupPaintScale(tempMin, tempMax, Color.lightGray);
Paint[] contourColors = getFullRainBowScale(170);
//Color Scale
double value = tempMax;
double delta = (tempMax - tempMin)/(contourColors.length -1);
if(rasterLogarithmicBinsTF){
value = Math.log(tempMax);
delta = (Math.log(tempMax) - Math.log(tempMin))/(contourColors.length -1);
if(tempMin == 0){
delta = (Math.log(tempMax) - Math.log(DoubleMath.min(tempData_noZeros)))/(contourColors.length -1);
}
}
for(int i=0; i<contourColors.length; i++){
if(rasterLogarithmicBinsTF){
paintScale.add(Math.exp(value), contourColors[i]);
}else{
paintScale.add(value, contourColors[i]);
}
value = value - delta;
}
paintScale.add(0, Color.blue);
renderer.setPaintScale(paintScale);
//Put the line data, renderer, and axis into plot
XYPlot plot = new XYPlot();
plot.setDataset(0, xyzRasterData);
plot.setRenderer(0, renderer);
//Put the line on the first Domain and first Range
plot.mapDatasetToDomainAxis(0, 0);
plot.mapDatasetToRangeAxis(0, 0);
//Create Y Axis
ValueAxis rangeAxis = new NumberAxis("Year");
rangeAxis.setRange(Double.parseDouble(start.substring(0,4)), Double.parseDouble(end.substring(0,4)));
rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
plot.setRangeAxis(0, rangeAxis);
//Create X Axis
String xAxisTitle = "Day of Calendar Year";
if(waterYearTF) xAxisTitle = "Day of Water Year (10-01 to 9-30)";
ValueAxis domainAxis = new NumberAxis(xAxisTitle);
domainAxis.setLowerMargin(0.0);
domainAxis.setUpperMargin(0.0);
plot.setDomainAxis(0, domainAxis);
//Set extra plot preferences
plot = Graphing.setAxisPreferences(plot);
//Create the charts out of the plots
String graphTitle = "Raster Graph for " + database + " Station: " + stationId + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, Graphing.titleFont, plot, false);
//Add scale/legend
NumberAxis scaleAxis = new NumberAxis(zAxisTitle);
if(rasterLogarithmicBinsTF){
scaleAxis = new LogarithmicAxis(zAxisTitle);
}
scaleAxis.setAxisLinePaint(Color.white);
scaleAxis.setTickMarkPaint(Color.white);
scaleAxis.setTickLabelFont(Graphing.masterFont);
scaleAxis.setLabelFont(Graphing.masterFont);
PaintScaleLegend legend = new PaintScaleLegend(paintScale, scaleAxis);
legend.setAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
legend.setAxisOffset(5.0);
legend.setMargin(new RectangleInsets(5, 5, 5, 5));
legend.setFrame(new BlockBorder(Color.black));
legend.setPadding(new RectangleInsets(10, 10, 10, 10));
legend.setPosition(RectangleEdge.RIGHT);
chart.addSubtitle(legend);
//Save monthly timeseries graph for use later
try{
String path = directory + File.separator + getTimeseriesRaster();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
private static class XYZArrayDataset extends AbstractXYZDataset{
double[][] data; //{{x1, y1, z1}, {x2, y2, z2}, ...{xN, yN, zN}}
int rowCount = 0;
int columnCount = 0;
XYZArrayDataset(double[][] data){
this.data = data;
rowCount = data.length;
columnCount = data[0].length;
}
@Override
public int getSeriesCount(){
return 1;
}
@Override
public Comparable getSeriesKey(int series){
return "serie";
}
@Override
public int getItemCount(int series){
return rowCount;
}
@Override
public double getXValue(int series,int item){
return data[item][0];
}
@Override
public double getYValue(int series,int item){
return data[item][1];
}
@Override
public double getZValue(int series,int item){
return data[item][2];
}
@Override
public Number getX(int series,int item){
return data[item][0];
}
@Override
public Number getY(int series,int item){
return data[item][1];
}
@Override
public Number getZ(int series,int item){
return data[item][2];
}
}
private static Paint[] getFullRainBowScale(double colorValue){
// minimum of about 200 to not have perceptible steps in color scale
// whether or not perceptible color gradients show depend upon the
// legend size and the monitor settings
int ncolor = 360;
Color [] rainbow = new Color[ncolor];
// divide the color wheel up into more than ncolor pieces
// but don't go all of the way around the wheel, or the first color
// will repeat. The 60 value is about a minimum of 40, or the
// red color will repeat. Too large a value, and there will be no magenta.
// float x = (float) (1./(ncolor + 170.));
float x = (float) (1./(ncolor + colorValue));
for (int i=0; i < rainbow.length; i++){
rainbow[i] = new Color( Color.HSBtoRGB((i)*x,1.0F,1.0F));
}
return rainbow;
}
/**
* Graph a histogram of the time series and user data and save the resulting graph to the specified location
* @param sortedData the String[][] containing sorted data for the time series
* (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm if
* timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param sortedData_user the String[][] containing sorted user data for the
* time series (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm
* if timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param period1Data the String[][] containing sorted data for the time
* series contained by period1 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period2Data the String[][] containing sorted data for the time
* series contained by period2 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period3Data the String[][] containing sorted data for the time
* series contained by period3 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param color the color of the graph for flow (blue) or water quality (magenta)
* @param xAxisTitle the String label for the y axis of the graph
*/
private void createTimeseriesHistogram(String[][] sortedData,
String[][] sortedData_user,
String[][] period1Data,
String[][] period2Data,
String[][] period3Data,
Color color,
String xAxisTitle) throws IOException{
//Determine bin type (arithmetic/logarithmic) and then range
double[] lowerLimit = new double[numBins];
double[] upperLimit = new double[numBins];
if(logarithmicBinsTF){
if(min != 0){
double exponent = (Math.log10(max) - Math.log10(min)) / numBins;
for(int i=0; i<numBins; i++){
if(i == 0){
lowerLimit[i] = 0;
}else{
lowerLimit[i] = upperLimit[i-1];
}
upperLimit[i] = min * Math.pow(10, exponent * (i+1));
}
}else{
double exponent = Math.log10(max) / numBins;
for(int i=0; i<numBins; i++){
if(i == 0){
lowerLimit[i] = 0;
}else{
lowerLimit[i] = upperLimit[i-1];
}
upperLimit[i] = Math.pow(10, exponent * (i+1));
}
}
}else{
double interval = (max - min) / numBins;
for(int i=0; i<numBins; i++){
lowerLimit[i] = min + i*interval;
upperLimit[i] = min + (i+1)*interval;
}
}
//Create TimeSeries graph
DefaultCategoryDataset dataset = new DefaultCategoryDataset();
String[][] histogramData = new String[numBins][5];
boolean legendTF = false;
for(int j=0; j<numBins; j++){
//Count data within the bin range
int count = 0;
for(int i=0; i < sortedData.length; i++) {
double value = Double.parseDouble(sortedData[i][1]);
if(value > lowerLimit[j] && value <= upperLimit[j]){
count++;
}
}
String categoryTitle = String.valueOf(DoubleMath.round(lowerLimit[j],1)) + " to " + String.valueOf(DoubleMath.round(upperLimit[j],1));
dataset.addValue(count, "All Data", categoryTitle);
histogramData[j][0] = categoryTitle;
histogramData[j][1] = String.valueOf(count);
//Count user data within the bin range
if(sortedData_user.length > 0){
count = 0;
for(int i=0; i < sortedData_user.length; i++) {
double value = Double.parseDouble(sortedData_user[i][1]);
if(value > lowerLimit[j] && value <= upperLimit[j]){
count++;
}
}
dataset.addValue(count, "User Data", categoryTitle);
}
//Count period 1 data within the bin range
if(period1Data.length > 0){
count = 0;
for(int i=0; i < period1Data.length; i++) {
double value = Double.parseDouble(period1Data[i][1]);
if(value > lowerLimit[j] && value <= upperLimit[j]){
count++;
}
}
dataset.addValue(count, "Period 1 Data", categoryTitle);
histogramData[j][2] = String.valueOf(count);
legendTF = true;
}else{
histogramData[j][2] = "-1";
}
//Count period 2 data within the bin range
if(period2Data.length > 0){
count = 0;
for(int i=0; i < period2Data.length; i++) {
double value = Double.parseDouble(period2Data[i][1]);
if(value > lowerLimit[j] && value <= upperLimit[j]){
count++;
}
}
dataset.addValue(count, "Period 2 Data", categoryTitle);
histogramData[j][3] = String.valueOf(count);
legendTF = true;
}else{
histogramData[j][3] = "-1";
}
//Count period 3 data within the bin range
if (period3Data.length > 0) {
count = 0;
for (int i = 0; i < period3Data.length; i++) {
double value = Double.parseDouble(period3Data[i][1]);
if (value > lowerLimit[j] && value <= upperLimit[j]) {
count++;
}
}
dataset.addValue(count, "Period 3 Data", categoryTitle);
histogramData[j][4] = String.valueOf(count);
legendTF = true;
}else{
histogramData[j][4] = "-1";
}
}
//Save histogram data for JHighCharts
DoubleArray.writeXYseries(directory, histogramData, getHistogramOutput().getName());
//Define renderer properties for bar graph
int seriesIndex = 0;
BarRenderer renderer = new BarRenderer();
renderer.setDrawBarOutline(false);
renderer.setSeriesPaint(seriesIndex, color);
seriesIndex++;
if(sortedData_user.length > 0){
renderer.setSeriesPaint(seriesIndex, Color.gray);
seriesIndex++;
}
if(period1Data.length > 0){
renderer.setSeriesPaint(seriesIndex, Color.red);
seriesIndex++;
}
if(period2Data.length > 0){
renderer.setSeriesPaint(seriesIndex, new Color(255, 135, 0));//gold
seriesIndex++;
}
if(period3Data.length > 0){
renderer.setSeriesPaint(seriesIndex, Color.green);
seriesIndex++;
}
//Define axis and properties
NumberAxis yAxis = new NumberAxis("Count");
CategoryAxis xAxis = new CategoryAxis(xAxisTitle);
xAxis.setCategoryLabelPositions(CategoryLabelPositions.DOWN_45);
//Graph the dataset using the renderer and create a chart
CategoryPlot plot = new CategoryPlot(dataset, xAxis, yAxis, renderer);
//Set extra plot preferences
plot = Graphing.setCategoryAxisPreferences(plot);
//Create the chart with the plot
String graphTitle = "Histogram for " + database + " Station: " + stationId + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, Graphing.titleFont, plot, legendTF);
//Set legend Font
if(legendTF){
LegendTitle legendTitle = chart.getLegend();
legendTitle.setItemFont(Graphing.masterFont);
}
//Save resulting graph for use later
try{
String path = directory + File.separator + getHistogram();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
/**
* Graph the monthly average time series and user data and save the resulting graph to the specified location.
* Also creates a boxplot for each month's data in a new graph
* @param sortedData the String[][] containing sorted data for the time series
* (column 1 = dates (yyyy-mm-dd if timeStep = "daily", yyyy-mm if
* timeStep = "monthly", yyyy if timeStep = "yearly") column 2 = value
* @param period1Data the String[][] containing sorted data for the time
* series contained by period1 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period2Data the String[][] containing sorted data for the time
* series contained by period2 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param period3Data the String[][] containing sorted data for the time
* series contained by period3 (column 1 = dates (yyyy-mm-dd if timeStep =
* "daily", yyyy-mm if timeStep = "monthly", yyyy if timeStep = "yearly")
* column 2 = value
* @param yAxisTitle the String label for the y axis of the graph
*/
private void createTimeseriesMonthlyGraph(String[][] sortedData,
String[][] period1Data,
String[][] period2Data,
String[][] period3Data,
String yAxisTitle) throws IOException {
//Convert sortedData to monthly data
sortedData = DoubleArray.computeFlowMethod(sortedData, "Monthly", "Average", false);
period1Data = DoubleArray.computeFlowMethod(period1Data, "Monthly", "Average", false);
period2Data = DoubleArray.computeFlowMethod(period2Data, "Monthly", "Average", false);
period3Data = DoubleArray.computeFlowMethod(period3Data, "Monthly", "Average", false);
//Calculate monthly averages for the entire dataset
XYPlot plot = new XYPlot();
XYSeries series = new XYSeries(stationId + ": Data");
XYSeries period1_series = new XYSeries(stationId + ": Period 1 Data");
XYSeries period2_series = new XYSeries(stationId + ": Period 2 Data");
XYSeries period3_series = new XYSeries(stationId + ": Period 3 Data");
// ArrayList<ArrayList<Double>> boxplotOutliers = new ArrayList<>();
// double[][] boxplotData = new double[5][12];
String[][] monthXYdata = new String[12][8];
boolean showOutliers = false, showExtremeOutliers = false;
int seriesIndex = 0;
for(int j=1; j<=12; j++){
ArrayList<Double> monthlyData = new ArrayList<>();
double flow = 0, flow1 = 0, flow2 = 0, flow3 = 0;
double ctr = 0, ctr1 = 0, ctr2 = 0, ctr3 = 0;
for(int i=0; i<sortedData.length; i++){
double month = Double.parseDouble(sortedData[i][0].substring(5));
double value = Double.parseDouble(sortedData[i][1]);
int month_int = (int) month;
if(month_int == j){
monthlyData.add(value);
flow = flow + value;
ctr = ctr + 1;
}
if(i < period1Data.length){
month_int = (int) Double.parseDouble(period1Data[i][0].substring(5));
value = Double.parseDouble(period1Data[i][1]);
if(month_int == j){
flow1 = flow1 + value;
ctr1 = ctr1 + 1;
}
}
if(i < period2Data.length){
month_int = (int) Double.parseDouble(period2Data[i][0].substring(5));
value = Double.parseDouble(period2Data[i][1]);
if(month_int == j){
flow2 = flow2 + value;
ctr2 = ctr2 + 1;
}
}
if(i < period3Data.length){
month_int = (int) Double.parseDouble(period3Data[i][0].substring(5));
value = Double.parseDouble(period3Data[i][1]);
if(month_int == j){
flow3 = flow3 + value;
ctr3 = ctr3 + 1;
}
}
}
//Calculate monthly average
if(ctr == 0){ctr = 1;} //prevent divide by zero problems
series.add(j, flow/ctr);
monthXYdata[j-1][0] = String.valueOf(j);
monthXYdata[j-1][1] = String.valueOf(flow/ctr);
monthXYdata[j-1][2] = String.valueOf(j);
monthXYdata[j-1][3] = "-1";
monthXYdata[j-1][4] = String.valueOf(j);
monthXYdata[j-1][5] = "-1";
monthXYdata[j-1][6] = String.valueOf(j);
monthXYdata[j-1][7] = "-1";
//Check for period data
if(period1Data.length > 0){
if(ctr1 == 0){ctr1 = 1;} //prevent divide by zero problems
period1_series.add(j, flow1/ctr1);
monthXYdata[j-1][3] = String.valueOf(flow1/ctr1);
}
if(period2Data.length > 0){
if(ctr2 == 0){ctr2 = 1;} //prevent divide by zero problems
period2_series.add(j, flow2/ctr2);
monthXYdata[j-1][5] = String.valueOf(flow2/ctr2);
}
if(period3Data.length > 0){
if(ctr3 == 0){ctr3 = 1;} //prevent divide by zero problems
period3_series.add(j, flow3/ctr3);
monthXYdata[j-1][7] = String.valueOf(flow3/ctr3);
}
//Create Monthly boxplot
if(monthlyData.size() > 4){
//Create quartile rectangle, min-max line, and median line
Object[] returnArray = Graphing.boxplot_shapes(plot, j, monthlyData, seriesIndex, showOutliers, showExtremeOutliers);
plot = (XYPlot) returnArray[0];
showOutliers = (boolean) returnArray[1];
showExtremeOutliers = (boolean) returnArray[2];
seriesIndex = (int) returnArray[3];
// ArrayList<Double> outliers = (ArrayList<Double>) returnArray[4];
// double[] currentBoxplotData = (double[]) returnArray[5];
//
// //Store additional results for use with JHighCharts
// boxplotOutliers.add(outliers);
// boxplotData[0][j-1] = currentBoxplotData[0];
// boxplotData[1][j-1] = currentBoxplotData[1];
// boxplotData[2][j-1] = currentBoxplotData[2];
// boxplotData[3][j-1] = currentBoxplotData[3];
// boxplotData[4][j-1] = currentBoxplotData[4];
}
}
// //Check to show legend on boxplot graph
// boolean showBoxplotLegend = false;
// if(showOutliers || showExtremeOutliers){
// showBoxplotLegend = true;
// }
//Create renderer, and axis for timeseries graph
XYDataset xyDataset = new XYSeriesCollection(series);
XYDataset xyDataset_period1 = new XYSeriesCollection(period1_series);
XYDataset xyDataset_period2 = new XYSeriesCollection(period2_series);
XYDataset xyDataset_period3 = new XYSeriesCollection(period3_series);
XYItemRenderer renderer = new XYLineAndShapeRenderer(true, false);
renderer.setSeriesPaint(0, Color.black);
renderer.setSeriesStroke(0,
new BasicStroke(
3.0f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND,
1.0f, new float[] {6.0f, 0.0f}, 0.0f
));
//Set the line data, renderer, and axis into plot
plot.setDataset(seriesIndex, xyDataset);
plot.setRenderer(seriesIndex, renderer);
boolean legendTF = false;
seriesIndex++;
//Add period data (if any)
if(period1Data.length > 0){
XYItemRenderer renderer_period1 = new XYLineAndShapeRenderer(true, false);
renderer_period1.setSeriesPaint(0, Color.red);
plot.setDataset(seriesIndex, xyDataset_period1);
plot.setRenderer(seriesIndex, renderer_period1);
legendTF = true;
seriesIndex++;
}
if(period2Data.length > 0){
XYItemRenderer renderer_period2 = new XYLineAndShapeRenderer(true, false);
renderer_period2.setSeriesPaint(0, new Color(255, 135, 0));//gold
plot.setDataset(seriesIndex, xyDataset_period2);
plot.setRenderer(seriesIndex, renderer_period2);
legendTF = true;
seriesIndex++;
}
if(period3Data.length > 0){
XYItemRenderer renderer_period3 = new XYLineAndShapeRenderer(true, false);
renderer_period3.setSeriesPaint(0, Color.green);
plot.setDataset(seriesIndex, xyDataset_period3);
plot.setRenderer(seriesIndex, renderer_period3);
legendTF = true;
seriesIndex++;
}
//Map the line to the first Domain and first Range
plot.mapDatasetToDomainAxis(0, 0);
plot.mapDatasetToRangeAxis(0, 0);
//Graph a line for each year of monthly data in time period
String[] monthList = {"1","2","3","4","5","6","7","8","9","10","11","12"};
String currentYear = start.substring(0,4);
String finalYear = end.substring(0,4);
boolean moreYears = sortedData.length > 0;
while(moreYears){
//Get current year's data and graph it
String[][] partialData = DoubleArray.getYearsData(sortedData, currentYear);
double[][] currentYearData = new double[partialData.length][2];
for(int i=0; i<partialData.length; i++){
currentYearData[i][0] = Double.parseDouble(partialData[i][0].substring(5));//month
currentYearData[i][1] = Double.parseDouble(partialData[i][1]);//value
}
Graphing.addXYSeries(plot, currentYearData, Color.lightGray, seriesIndex);
seriesIndex++;
//Save results for output for JHighCharts
String[] partialMonthData = new String[12];
int ctr = 0;
for(int i=0; i<12; i++){
partialMonthData[i] = "-1";//value
try{
double month = Double.parseDouble(partialData[ctr][0].substring(5));//month
int month_int = (int) month;
if(month_int == (i+1)){
partialMonthData[i] = partialData[ctr][1];//value
ctr++;
}
}catch(IndexOutOfBoundsException e){
//do nothing as it already has a -1 value
}
}
monthXYdata = DoubleArray.appendcolumn_Matrix(monthXYdata, monthList);//Add list of months (aka x points)
monthXYdata = DoubleArray.appendcolumn_Matrix(monthXYdata, partialMonthData);//Add month values (aka y points)
//Determine the next data year to continue looping over
int nextYear = Integer.parseInt(currentYear) + 1;
if(finalYear.compareToIgnoreCase(String.valueOf(nextYear)) >= 0){
currentYear = String.valueOf(nextYear);
}else{
moreYears = false;
}
}
//Output monthly boxplot and timeseries data for use with JHighCharts
DoubleArray.writeXYseries(directory, monthXYdata, getMonthlyTimeseriesOutput().getName());
// DoubleArray.writeBoxplot(directory, boxplotOutliers, boxplotData, getMonthlyBoxplotOutput().getName());
//Create Y Axis
ValueAxis rangeAxis = new NumberAxis(yAxisTitle);
plot.setRangeAxis(0, rangeAxis);
//Create X Axis
NumberTickUnit temp = new NumberTickUnit(1);
NumberAxis domainAxis = new NumberAxis("Calendar Month");
domainAxis.setRange(0.75, 12.25);
domainAxis.setTickUnit(temp);
plot.setDomainAxis(0, domainAxis);
//Set extra plot preferences
plot = Graphing.setAxisPreferences(plot);
//Create the charts out of the plots
String graphTitle = "Monthly Averages for " + database + " Station: " + stationId + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, Graphing.titleFont, plot, legendTF);
//Set legend Font
if(legendTF){
LegendTitle legendTitle = chart.getLegend();
legendTitle.setItemFont(Graphing.masterFont);
}
//Save monthly timeseries graph for use later
try{
String path = directory + File.separator + getMonthlyGraph();
ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
System.out.println("JFreeChart created properly at: " + path);
}catch(IOException e){
System.err.println("A problem occurred while trying to creating the chart.");
}
}
/**
* Writes out the error message, if any, for finding the file and then exits the program
* @param error string array to be written as each line of an error message
* @throws IOException
*/
public void writeError(ArrayList<String> error) throws IOException{
//Output data to text file
String errorContents = error.get(0);
for(int i=1; i<error.size(); i++){
errorContents = errorContents + "\n" + error.get(i);
}
throw new IOException("Error encountered. Please see the following message for details: \n" + errorContents);
}
/**
* Primary TimeSeries
* It calls the subfunctions based on user selection/inputs.
* Calls STORET or USGS database queries and their respective subfunctions
* @param e DFLOW executable file
* @throws IOException
* @throws InterruptedException
* @throws java.text.ParseException
*/
public void run(Executable e) throws IOException, InterruptedException, ParseException, Exception {
//If no date input, make it the maximum of available data
if(startDate == null || startDate.equalsIgnoreCase("")){
startDate = "1850-01-01";
}
if(endDate == null || endDate.equalsIgnoreCase("")){
// Pull current date for upper limit of data search
DateFormat desiredDateFormat = DoubleArray.getDateFormat("daily", false);
Date currentDate = new Date();
endDate = desiredDateFormat.format(currentDate);
}
//Initialize graph variables
String yAxisTitle = "y axis";
String monthlyYaxisTitle = "y axis";
Color color = Color.black, color2 = Color.black;
boolean showLine = true;
String[][] sortableData = new String[0][2];
if(wqTest.equalsIgnoreCase("flow")){
//Check if any flow data exists
WaterDataInterface waterLib = WaterData.getNewWaterDataInterface(database, userData);
sortableData = waterLib.extractFlowData_formatted(directory, orgId, stationId, startDate, endDate);
dataSource = waterLib.getDataSourceCitation();
//Define other graph information
units = "cfs";
if(timeStep.equalsIgnoreCase("Daily")){
yAxisTitle = timeStep + " Flow [cfs]";
}else{
yAxisTitle = timeStep + " " + method + " Flow [cfs]";
}
monthlyYaxisTitle = "Monthly Average Flow [cfs]";
color = Color.blue;
color2 = Color.darkGray;
showLine = true;
}else{
//Search for WQ data
WaterDataInterface waterLib = WaterData.getNewWaterDataInterface(database, userData);
sortableData = waterLib.extractWaterQualityData_formatted(directory, orgId, stationId, startDate, endDate, wqTest);
dataSource = waterLib.getDataSourceCitation();
//Get Units and conversion for current WQ test
String[] resultArray = WaterQualityInfo.getWqTestDataInfo(wqTest, database);
//String wqCode = resultArray[0];
String wqLabel = resultArray[1];
units = resultArray[2];
//double ldcConversion = Double.parseDouble(resultArray[3]);
//String ldcEndUnits = resultArray[4];
//Define other graph information
if(timeStep.equalsIgnoreCase("Daily")){
yAxisTitle = timeStep + " " + wqLabel + " [" + units + "]";
}else{
yAxisTitle = timeStep + " " + method + " " + wqLabel + " [" + units + "]";
}
monthlyYaxisTitle = "Monthly Average " + wqLabel + " [" + units + "]";
color = Color.magenta;
color2 = Color.blue;
showLine = false;
}
//Check if merging the datasets is desired, if so get the user data
String[][] sortableData_user = new String[0][0];
if(mergeDatasets){
WaterDataInterface waterLibUser = WaterData.getNewWaterDataInterface("UserData", userData);
if(wqTest.equalsIgnoreCase("flow")){
sortableData = waterLibUser.extractFlowData_formatted(directory, orgId, stationId, startDate, endDate);
}else{
sortableData = waterLibUser.extractWaterQualityData_formatted(directory, orgId, stationId, startDate, endDate, wqTest);
}
}
//Sort the Data by date to remove duplicate date entries
String[][] sortedData = DoubleArray.removeDuplicateDates(sortableData);
String[][] sortedData_user = DoubleArray.removeDuplicateDates(sortableData_user);
//Merge the two datasets (if user data is empty nothing will be merged)
String[][] sortedData_combined = DoubleArray.mergeData(sortedData, sortedData_user, mergeMethod);
if(sortedData_combined.length == 0){
ArrayList<String> errorMessage = new ArrayList<>();
if(sortableData.length == 0){
errorMessage.add("There is no available " + wqTest + " data in the " + database + " database for station '" + stationId + "' and the specified date range.");
if(database.equalsIgnoreCase("CDWR")){
errorMessage.add("The CDWR database is sensitive to the begin date used, try specifying a later begin date");
}
}
if(sortedData_user.length == 0){
errorMessage.add("There is no available uploaded data for station '" + stationId + "' and the specified date range");
}
writeError(errorMessage);
}
//Save analysis results
start = sortedData_combined[0][0];
end = sortedData_combined[sortedData_combined.length - 1][0];
//Get period data for analyses
String[][] period1Data = DoubleArray.getPeriodData(sortedData_combined, period1Begin, period1End);
String[][] period2Data = DoubleArray.getPeriodData(sortedData_combined, period2Begin, period2End);
String[][] period3Data = DoubleArray.getPeriodData(sortedData_combined, period3Begin, period3End);
String[][] seasonalData = DoubleArray.getSeasonalData(sortedData_combined, seasonBegin, seasonEnd);
//Perform operations on daily data before it is converted to the user desired timeStep
createTimeseriesMonthlyGraph(sortedData_combined, period1Data, period2Data, period3Data, monthlyYaxisTitle);
FlowStatistics flowStats = new FlowStatistics();
if(wqTest.equalsIgnoreCase("flow")){
//Create Envelope Graph
if(envelopeTF || rasterTF){
createTimeseriesEnvelopeGraph(sortedData_combined, period1Data, period2Data, period3Data, yAxisTitle, true);
}
//Calculate Hydrologic Indicators of Alteration
if(calcFlowStatisticsFileTF){
flowStats.calculateAllStatisticsSummaries(directory, stationId, stationName, sortedData_combined, highPercentile, lowPercentile, 0, 0, showMonthlyStatsTF,
seasonBegin, seasonEnd, period1Begin, period1End, period2Begin, period2End, period3Begin, period3End, waterYearTF);
}
//Calculate CDPHE design low flow
if(calcCDPHElowflowTF){
CDPHE_lowFlowStats cdphe_lowflow = new CDPHE_lowFlowStats();
DFLOW_lowFlowStats dflow_lowflow = new DFLOW_lowFlowStats();
if(CDPHE_lowFlowType.equalsIgnoreCase("extreme-value")){
//Calculate the Extreme-value based design flow:
extremeValueDFLOW = cdphe_lowflow.CDPHE_ExtremeValue(sortedData_combined, CDPHE_m, CDPHE_R, CDPHE_waterYearBegin);
}if(CDPHE_lowFlowType.equalsIgnoreCase("dflow-extreme-value")){
//Calculate the Extreme-value based design flow:
extremeValueDFLOW = dflow_lowflow.DFLOW_ExtremeValue(e, directory, sortedData_combined, CDPHE_m, CDPHE_R);
}else if(CDPHE_lowFlowType.equalsIgnoreCase("biological")){
//Calculate the Biologically based design flow:
double[] biologial_flows = cdphe_lowflow.CDPHE_Biological(sortedData_combined, CDPHE_m, CDPHE_R, CDPHE_clusterLength, CDPHE_clusterCountMax);
biologicalDFLOW_all = biologial_flows[0];
biologicalDFLOW_jan = biologial_flows[1];
biologicalDFLOW_feb = biologial_flows[2];
biologicalDFLOW_mar = biologial_flows[3];
biologicalDFLOW_apr = biologial_flows[4];
biologicalDFLOW_may = biologial_flows[5];
biologicalDFLOW_jun = biologial_flows[6];
biologicalDFLOW_jul = biologial_flows[7];
biologicalDFLOW_aug = biologial_flows[8];
biologicalDFLOW_sep = biologial_flows[9];
biologicalDFLOW_oct = biologial_flows[10];
biologicalDFLOW_nov = biologial_flows[11];
biologicalDFLOW_dec = biologial_flows[12];
}else if(CDPHE_lowFlowType.equalsIgnoreCase("dflow-biological")){
//Calculate the Biologically based design flow:
double[][] biologial_flows = dflow_lowflow.DFLOW_Biological(e, directory, sortedData_combined, CDPHE_m, CDPHE_R, CDPHE_clusterLength, CDPHE_clusterCountMax);
biologicalDFLOW_all = biologial_flows[0][0];
biologicalDFLOW_jan = biologial_flows[0][1];
biologicalDFLOW_feb = biologial_flows[0][2];
biologicalDFLOW_mar = biologial_flows[0][3];
biologicalDFLOW_apr = biologial_flows[0][4];
biologicalDFLOW_may = biologial_flows[0][5];
biologicalDFLOW_jun = biologial_flows[0][6];
biologicalDFLOW_jul = biologial_flows[0][7];
biologicalDFLOW_aug = biologial_flows[0][8];
biologicalDFLOW_sep = biologial_flows[0][9];
biologicalDFLOW_oct = biologial_flows[0][10];
biologicalDFLOW_nov = biologial_flows[0][11];
biologicalDFLOW_dec = biologial_flows[0][12];
biologicalYear_jan = (int) biologial_flows[1][1];
biologicalYear_feb = (int) biologial_flows[1][2];
biologicalYear_mar = (int) biologial_flows[1][3];
biologicalYear_apr = (int) biologial_flows[1][4];
biologicalYear_may = (int) biologial_flows[1][5];
biologicalYear_jun = (int) biologial_flows[1][6];
biologicalYear_jul = (int) biologial_flows[1][7];
biologicalYear_aug = (int) biologial_flows[1][8];
biologicalYear_sep = (int) biologial_flows[1][9];
biologicalYear_oct = (int) biologial_flows[1][10];
biologicalYear_nov = (int) biologial_flows[1][11];
biologicalYear_dec = (int) biologial_flows[1][12];
}else if(CDPHE_lowFlowType.equalsIgnoreCase("human-health")){
//Calculate the Human-health based design flow:
humanHealthDFLOW = cdphe_lowflow.CDPHE_HumanHealth(sortedData_combined);
}else if(CDPHE_lowFlowType.equalsIgnoreCase("dflow-human-health")){
//Calculate the Human-health based design flow:
humanHealthDFLOW = dflow_lowflow.DFLOW_HumanHealth(e, directory, sortedData_combined);
}else if(CDPHE_lowFlowType.equalsIgnoreCase("reg31")){
//Calcualte the Regulation 31 summary of design flows:
reg31DFLOWsummary = cdphe_lowflow.CDPHE_REG31(sortedData_combined);
}else if(CDPHE_lowFlowType.equalsIgnoreCase("dflow-reg31")){
//Calcualte the Regulation 31 summary of design flows:
reg31DFLOWsummary = dflow_lowflow.DFLOW_REG31(e, directory, sortedData_combined);
}else if(CDPHE_lowFlowType.equalsIgnoreCase("all")){
//Calculate all design flows
extremeValueDFLOW = cdphe_lowflow.CDPHE_ExtremeValue(sortedData_combined, CDPHE_m, CDPHE_R, CDPHE_waterYearBegin);
double[] biologial_flows = cdphe_lowflow.CDPHE_Biological(sortedData_combined, CDPHE_m, CDPHE_R, CDPHE_clusterLength, CDPHE_clusterCountMax);
biologicalDFLOW_all = biologial_flows[0];
biologicalDFLOW_jan = biologial_flows[1];
biologicalDFLOW_feb = biologial_flows[2];
biologicalDFLOW_mar = biologial_flows[3];
biologicalDFLOW_apr = biologial_flows[4];
biologicalDFLOW_may = biologial_flows[5];
biologicalDFLOW_jun = biologial_flows[6];
biologicalDFLOW_jul = biologial_flows[7];
biologicalDFLOW_aug = biologial_flows[8];
biologicalDFLOW_sep = biologial_flows[9];
biologicalDFLOW_oct = biologial_flows[10];
biologicalDFLOW_nov = biologial_flows[11];
biologicalDFLOW_dec = biologial_flows[12];
humanHealthDFLOW = cdphe_lowflow.CDPHE_HumanHealth(sortedData_combined);
reg31DFLOWsummary = cdphe_lowflow.CDPHE_REG31(sortedData_combined);
}else if(CDPHE_lowFlowType.equalsIgnoreCase("dflow-all")){
//Calculate all design flows
extremeValueDFLOW = dflow_lowflow.DFLOW_ExtremeValue(e, directory, sortedData_combined, CDPHE_m, CDPHE_R);
double[][] biologial_flows = dflow_lowflow.DFLOW_Biological(e, directory, sortedData_combined, CDPHE_m, CDPHE_R, CDPHE_clusterLength, CDPHE_clusterCountMax);
biologicalDFLOW_all = biologial_flows[0][0];
biologicalDFLOW_jan = biologial_flows[0][1];
biologicalDFLOW_feb = biologial_flows[0][2];
biologicalDFLOW_mar = biologial_flows[0][3];
biologicalDFLOW_apr = biologial_flows[0][4];
biologicalDFLOW_may = biologial_flows[0][5];
biologicalDFLOW_jun = biologial_flows[0][6];
biologicalDFLOW_jul = biologial_flows[0][7];
biologicalDFLOW_aug = biologial_flows[0][8];
biologicalDFLOW_sep = biologial_flows[0][9];
biologicalDFLOW_oct = biologial_flows[0][10];
biologicalDFLOW_nov = biologial_flows[0][11];
biologicalDFLOW_dec = biologial_flows[0][12];
biologicalYear_jan = (int) biologial_flows[1][1];
biologicalYear_feb = (int) biologial_flows[1][2];
biologicalYear_mar = (int) biologial_flows[1][3];
biologicalYear_apr = (int) biologial_flows[1][4];
biologicalYear_may = (int) biologial_flows[1][5];
biologicalYear_jun = (int) biologial_flows[1][6];
biologicalYear_jul = (int) biologial_flows[1][7];
biologicalYear_aug = (int) biologial_flows[1][8];
biologicalYear_sep = (int) biologial_flows[1][9];
biologicalYear_oct = (int) biologial_flows[1][10];
biologicalYear_nov = (int) biologial_flows[1][11];
biologicalYear_dec = (int) biologial_flows[1][12];
humanHealthDFLOW = dflow_lowflow.DFLOW_HumanHealth(e, directory, sortedData_combined);
reg31DFLOWsummary = dflow_lowflow.DFLOW_REG31(e, directory, sortedData_combined);
}
}
}else{
//Report that there cannot be flow statistics for water quality data
String[][] errorMessage = {{"Error"," Cannot compute flow statistics as indicators of hydrologic alteration using water quality data."},{"This output is only applicable for flow analysis.",""}};
flowStats.writeStatsSummaryFile(directory, errorMessage);
}
//Perform analysis method on data
sortedData_combined = DoubleArray.computeFlowMethod(sortedData_combined, timeStep, method, false);
sortedData_user = DoubleArray.computeFlowMethod(sortedData_user, timeStep, method, false);
period1Data = DoubleArray.computeFlowMethod(period1Data, timeStep, method, false);
period2Data = DoubleArray.computeFlowMethod(period2Data, timeStep, method, false);
period3Data = DoubleArray.computeFlowMethod(period3Data, timeStep, method, false);
seasonalData = DoubleArray.computeFlowMethod(seasonalData, timeStep, method, false);
//CalculateStatistics
CalculateStatistics(sortedData_combined, "all");
CalculateStatistics(period1Data, "period1");
CalculateStatistics(period2Data, "period2");
CalculateStatistics(period3Data, "period3");
CalculateStatistics(seasonalData, "seasonal");
//Graph the timeseries data
createTimeseriesGraph(sortedData_combined, sortedData_user, period1Data, period2Data, period3Data, color, color2, showLine, yAxisTitle);
createTimeseriesBoxplot(sortedData_combined, yAxisTitle);
createTimeseriesHistogram(sortedData_combined, sortedData_user, period1Data, period2Data, period3Data, color, yAxisTitle);
createTimeseriesCDF(sortedData_combined, sortedData_user, period1Data, period2Data, period3Data, color, color2, yAxisTitle);
len = String.valueOf(sortedData_combined.length);
}
public static void main(String[] args) throws IOException, InterruptedException, Exception {
//Run model
guiTimeseries_Model timeseries_Model = new guiTimeseries_Model();
timeseries_Model.run(null);
}
}