guiTimeseries_Model.java [src/java/cfa] Revision: d64a7042d7439a9588a71182bd8d9ce267822aa4 Date: Wed Jun 04 12:09:06 MDT 2014
package cfa;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Stroke;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Rectangle2D;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.CategoryAxis;
import org.jfree.chart.axis.DateAxis;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.axis.ValueAxis;
import org.jfree.chart.plot.CategoryPlot;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.category.BarRenderer;
import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.chart.title.LegendTitle;
import org.jfree.data.category.DefaultCategoryDataset;
import org.jfree.data.time.Day;
import org.jfree.data.time.Month;
import org.jfree.data.time.TimeSeries;
import org.jfree.data.time.Year;
import org.jfree.data.xy.XYDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
/**
* Last Updated: 3-June-2014
* @author Tyler Wible
* @since 24-June-2011
*/
public class guiTimeseries_Model {
//Inputs
String mainFolder = "C:/Projects/TylerWible/CodeDirectories/NetBeans/CSIP/data/CFA";
String organizationName = "USGS";//"Colorado Dept. of Public Health & Environment";//
String stationID = "06764880";//"000028";//
String stationName = "South Platte River at Roscoe, Nebr.";//"BIG THOMPSON R NEAR MOUTH";//
String wqTest = "flow";//"00600 Total nitrogen, water, unfiltered, milligrams per liter, mg/L";
String beginDate = "";
String endDate = "";
String timeStep = "Daily";//"Yearly";//"Monthly";//
String method = "Max";//"Min";//"Average";//"Total";//
int numBins = 10;
String period1Begin = "";
String period1End = "";
String period2Begin = "";
String period2End = "";
String period3Begin = "";
String period3End = "";
boolean medianTF = false;
String userData = "";//"Date\tFlow\n1999-04-29\t8.3\n1999-05-09\t60.2\n1999-05-29\t20.1";//
boolean mergeDatasets = false;//true;//
String mergeMethod = "user";//"public";//"max";//"average";//"min";//
//Outputs
String len = "-1";
String start = "?";
String end = "?";
String units = "?";
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 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 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 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;
//Gets
public File getParagraph() {
return new File(mainFolder, "timeseries_summary.txt");
}
public String getMonthlyGraph() {
return "timeseries_monthlygraph.jpg";
}
public String getGraph() {
return "timeseries_graph.jpg";
}
public String getBoxplot() {
return "timeseries_boxplot.jpg";
}
public String getHistogram() {
return "timeseries_histogram.jpg";
}
public String getLen(){
return len;
}
public String getStart(){
return start;
}
public String getEnd(){
return end;
}
public String getUnits(){
return units;
}
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 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 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 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);
}
//Sets
public void setMainFolder(String mainFolder) {
this.mainFolder = mainFolder;
}
public void setOrganizationName(String organizationName) {
this.organizationName = organizationName;
}
public void setBeginDate(String beginDate) {
this.beginDate = beginDate;
}
public void setEndDate(String endDate) {
this.endDate = endDate;
}
public void setStationName(String stationName) {
this.stationName = stationName;
}
public void setStationID(String stationID) {
this.stationID = stationID;
}
public void setWQtest(String wqTest) {
this.wqTest = wqTest;
}
public void setTimeStep(String timeStep) {
this.timeStep = timeStep;
}
public void setMethod(String method) {
this.method = method;
}
public void setNumberOfBins(int numBins) {
this.numBins = numBins;
}
public void setPeriod1Begin(String period1Begin) {
this.period1Begin = period1Begin;
}
public void setPeriod1End(String period1End) {
this.period1End = period1End;
}
public void setPeriod2Begin(String period2Begin) {
this.period2Begin = period2Begin;
}
public void setPeriod2End(String period2End) {
this.period2End = period2End;
}
public void setPeriod3Begin(String period3Begin) {
this.period3Begin = period3Begin;
}
public void setPeriod3End(String period3End) {
this.period3End = period3End;
}
public void setMedianTF(boolean medianTF) {
this.medianTF = medianTF;
}
public void setUserData(String userData) {
this.userData = userData;
}
public void setMergeDatasets(boolean mergeDatasets) {
this.mergeDatasets = mergeDatasets;
}
public void setMergeMethod(String mergeMethod) {
this.mergeMethod = mergeMethod;
}
/**
* Computes the daily/monthly/yearly max/min/average/total of the daily dataset provided
* @param dailyData a string array with column1 = dates (yyyy-mm-dd format), column2 = value
* @param timeStep the desired timestep "daily", "monthly", or "yearly"
* @param method the desired method "max", "min", "average", or "total"
* @return a new string[][] with column 1 = dates (yyyy-mm-dd format for "daily" timeStep,
* yyyy-mm format for "monthly" timeStep, and yyyy format for "yearly" timeStep) and column2 = values
*/
private String[][] computeFlowMethod(String[][] dailyData, String timeStep, String method){
String[][] newData = new String[0][2];
if(dailyData.length > 0){
if(timeStep.equalsIgnoreCase("daily")){
return dailyData;
}else if(timeStep.equalsIgnoreCase("monthly")){
//Compute the method on the unique monthYears
newData = computeMethod(dailyData, method, 7);
}else if(timeStep.equalsIgnoreCase("yearly")){
//Compute the method on the unique monthYears
newData = computeMethod(dailyData, method, 4);
}
}
return newData;
}
/**
* Computes the method on the dailyData provided substring-ing the dates from 0-dateLimit to
* get a unique set of time periods on which to perform the method
* @param dailyData a string array with column1 = dates (yyyy-mm-dd format), column2 = value
* @param method the desired method "max", "min", "average", or "total"
* @param dateLimit an integer for the limit of the date substring (typically 4 or 7 for the
* format yyyy-mm-dd resulting in yyyy and yyyy-mm respectively)
* @return a new string[][] with column 1 = dates (yyyy-mm-dd format for "daily" timeStep,
* yyyy-mm format for "monthly" timeStep, and yyyy format for "yearly" timeStep) and column2 = values
*/
private String[][] computeMethod(String[][] dailyData, String method, int dateLimit){
DoubleMath doubleMath = new DoubleMath();
//Find the unique set of months/years for which the method is desired for
ArrayList<String> uniqueTimeStep = new ArrayList<String>();
String previousMonthYear = dailyData[0][0].substring(0,dateLimit);
uniqueTimeStep.add(previousMonthYear);
for(int i=1; i<dailyData.length; i++){
//Check if current monthYear is the same or different from the previous
String currentMonthYear = dailyData[i][0].substring(0,dateLimit);
if(!previousMonthYear.equalsIgnoreCase(currentMonthYear)){
uniqueTimeStep.add(currentMonthYear);
previousMonthYear = currentMonthYear;
}
}
//Loop through daily data, pull out each uniqueTimeStep's dataset and perform the method on that dataset
String[][] newData = new String[uniqueTimeStep.size()][2];
ArrayList<Double> currentMonthData = new ArrayList<Double>();
int ctr=0;
for(int i=0; i<dailyData.length; i++){
if(uniqueTimeStep.get(ctr).equals(dailyData[i][0].substring(0, dateLimit))){
//If current data = current month, add it to the dataset
currentMonthData.add(Double.parseDouble(dailyData[i][1]));
}else{
//If current data != current month, calculate method on the current month's dataset, save the result and reset the dataset
newData[ctr][0] = uniqueTimeStep.get(ctr);
if(method.equalsIgnoreCase("max")){
newData[ctr][1] = String.valueOf(doubleMath.max(currentMonthData));
}else if(method.equalsIgnoreCase("average")){
newData[ctr][1] = String.valueOf(doubleMath.Average(currentMonthData));
}else if(method.equalsIgnoreCase("min")){
newData[ctr][1] = String.valueOf(doubleMath.min(currentMonthData));
}else if(method.equalsIgnoreCase("total")){
newData[ctr][1] = String.valueOf(doubleMath.sum(currentMonthData));
}
//Reset the dataset and add the current data to it as the new month's data
currentMonthData.clear();
currentMonthData.add(Double.parseDouble(dailyData[i][1]));
ctr++;
}
//If on the last point calculate the method on the current dataset
if(i == dailyData.length-1){
newData[ctr][0] = uniqueTimeStep.get(ctr);
if(method.equalsIgnoreCase("max")){
newData[ctr][1] = String.valueOf(doubleMath.max(currentMonthData));
}else if(method.equalsIgnoreCase("average")){
newData[ctr][1] = String.valueOf(doubleMath.Average(currentMonthData));
}else if(method.equalsIgnoreCase("min")){
newData[ctr][1] = String.valueOf(doubleMath.min(currentMonthData));
}else if(method.equalsIgnoreCase("total")){
newData[ctr][1] = String.valueOf(doubleMath.sum(currentMonthData));
}
}
}
return newData;
}
/**
* 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(ArrayList<Double> dataList, String flag) {
DoubleMath doubleMath = new DoubleMath();
double temp1 = doubleMath.round(doubleMath.Min_Max(dataList, true),3);//Call Max function
double temp2 = doubleMath.round(doubleMath.Min_Max(dataList, false),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.Average(dataList),3);//Call Mean function
double temp7 = doubleMath.round(doubleMath.StandardDeviationSample(dataList),3);//Call standard deviation
double temp8 = doubleMath.round(doubleMath.VarianceSample(dataList), 3);
double temp9 = doubleMath.round(doubleMath.SkewnessSample(dataList),8);
if(flag.equalsIgnoreCase("all")){
max = temp1;
min = temp2;
upperQuartile = temp3;
lowerQuartile = temp4;
median = temp5;
mean = temp6;
standardDeviation = temp7;
variance = temp8;
skew = temp9;
}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;
}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;
}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;
}
}
/**
* Graph the timeseries and user data and save the resulting graph to the specified location
* @param sortedData the String[][] containing sorted data for the timeseries
* (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
* timeseries (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
* @param units the units of the current graph to be used in labeling for the lengend
* @param medianTF if true then the median value will be plotted for period analyses, if false the mean (average) will be used
*/
private void createTimeseriesGraph(String[][] sortedData,
String[][] sortedData_user,
Color color,
Color color2,
boolean showLine,
String yAxisTitle,
String units,
boolean medianTF) throws ParseException {
//Change analysis period dates into calendar objects
SimpleDateFormat desiredDateFormat = new SimpleDateFormat("yyyy-MM-dd");
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 = desiredDateFormat.parse(period1Begin);
period1End_date = desiredDateFormat.parse(period1End);
}
if(!period2Begin.isEmpty() && !period2End.isEmpty()){
period2Begin_date = desiredDateFormat.parse(period2Begin);
period2End_date = desiredDateFormat.parse(period2End);
}
if(!period3Begin.isEmpty() && !period3End.isEmpty()){
period3Begin_date = desiredDateFormat.parse(period3Begin);
period3End_date = desiredDateFormat.parse(period3End);
}
//Create TimeSeries graph of merged data
TimeSeries series = new TimeSeries(stationID + ": Data");
ArrayList<Double> period1 = new ArrayList<>();
ArrayList<Double> period2 = new ArrayList<>();
ArrayList<Double> period3 = new ArrayList<>();
for(int i=0; i < sortedData.length; i++) {
double value = Double.parseDouble(sortedData[i][1]);
String tmpStr = sortedData[i][0];
if(timeStep.equalsIgnoreCase("daily")){
double d = Double.parseDouble(tmpStr.substring(8));
double m = Double.parseDouble(tmpStr.substring(5,7));
double y = Double.parseDouble(tmpStr.substring(0,4));
int day = (int)d;
int month = (int)m;
int year = (int)y;
Day date = new Day(day,month,year);//day,month,year
series.add(date, value);
}else if(timeStep.equalsIgnoreCase("monthly")){
desiredDateFormat = new SimpleDateFormat("yyyy-MM");
double m = Double.parseDouble(tmpStr.substring(5,7));
double y = Double.parseDouble(tmpStr.substring(0,4));
int month = (int)m;
int year = (int)y;
Month date = new Month(month,year);//month,year
series.add(date, value);
}else if(timeStep.equalsIgnoreCase("yearly")){
desiredDateFormat = new SimpleDateFormat("yyyy");
double y = Double.parseDouble(tmpStr.substring(0,4));
int year = (int)y;
Year date = new Year(year);//year
series.add(date, value);
}
//Check periods
Date newDate = desiredDateFormat.parse(tmpStr);
if(newDate.compareTo(period1Begin_date) >= 0 && newDate.compareTo(period1End_date) <= 0){
period1.add(value);
}else if(newDate.compareTo(period2Begin_date) >= 0 && newDate.compareTo(period2End_date) <= 0){
period2.add(value);
}else if(newDate.compareTo(period3Begin_date) >= 0 && newDate.compareTo(period3End_date) <= 0){
period3.add(value);
}
}
//Create Time Series graph of user data
TimeSeries series2 = new TimeSeries(stationID + ": User Data");
for(int i=0; i < sortedData_user.length; i++) {
double value = Double.parseDouble(sortedData_user[i][1]);
String tmpStr = sortedData_user[i][0];
if(timeStep.equalsIgnoreCase("daily")){
double d = Double.parseDouble(tmpStr.substring(8));
double m = Double.parseDouble(tmpStr.substring(5,7));
double y = Double.parseDouble(tmpStr.substring(0,4));
int day = (int)d;
int month = (int)m;
int year = (int)y;
Day date = new Day(day,month,year);//day,month,year
series2.add(date, value);
}else if(timeStep.equalsIgnoreCase("monthly")){
double m = Double.parseDouble(tmpStr.substring(5,7));
double y = Double.parseDouble(tmpStr.substring(0,4));
int month = (int)m;
int year = (int)y;
Month date = new Month(month,year);//month,year
series2.add(date, value);
}else if(timeStep.equalsIgnoreCase("yearly")){
double y = Double.parseDouble(tmpStr.substring(0,4));
int year = (int)y;
Year date = new Year(year);//year
series2.add(date, value);
}
}
//Create renderer, and axis for timeseries graph
Graphing graphing = new Graphing();
XYPlot plotTime = new XYPlot();
boolean showLegend = false;
//Create user data points
if(sortedData_user.length != 0){//only show user points if it is not zero
plotTime = graphing.graphTimeData(plotTime, series, showLine, color, false, false, false, true, 0);
plotTime = graphing.graphTimeData(plotTime, series2, showLine, color2, false, false, false, true, 1);
showLegend = true;
}else{
plotTime = graphing.graphTimeData(plotTime, series, showLine, color, false, false, false, true, 0);
}
//Create period analysis average lines
if(!period1Begin.isEmpty() && !period1End.isEmpty()){
CalculateStatistics(period1,"period1");
double value = mean_period1;
String label = "Average";
if(medianTF){
value = median_period1;
label = "Median";
}
TimeSeries periodSeries = new TimeSeries("Period 1 " + label + ": " + value + " " + units);
//Set Start Point
double d = Double.parseDouble(period1Begin.substring(8));
double m = Double.parseDouble(period1Begin.substring(5,7));
double y = Double.parseDouble(period1Begin.substring(0,4));
int day = (int)d;
int month = (int)m;
int year = (int)y;
Day date = new Day(day,month,year);//day,month,year
periodSeries.add(date, value);
//Set End Point
d = Double.parseDouble(period1End.substring(8));
m = Double.parseDouble(period1End.substring(5,7));
y = Double.parseDouble(period1End.substring(0,4));
day = (int)d;
month = (int)m;
year = (int)y;
date = new Day(day,month,year);//day,month,year
periodSeries.add(date, value);
plotTime = graphing.graphTimeData(plotTime, periodSeries, true, Color.RED, false, false, true, true, 2);
showLegend = true;
}
if(!period2Begin.isEmpty() && !period2End.isEmpty()){
CalculateStatistics(period2,"period2");
double value = mean_period2;
String label = "Average";
if(medianTF){
value = median_period2;
label = "Median";
}
TimeSeries periodSeries = new TimeSeries("Period 2 " + label + ": " + value + " " + units);
//Set Start Point
double d = Double.parseDouble(period2Begin.substring(8));
double m = Double.parseDouble(period2Begin.substring(5,7));
double y = Double.parseDouble(period2Begin.substring(0,4));
int day = (int)d;
int month = (int)m;
int year = (int)y;
Day date = new Day(day,month,year);//day,month,year
periodSeries.add(date, value);
//Set End Point
d = Double.parseDouble(period2End.substring(8));
m = Double.parseDouble(period2End.substring(5,7));
y = Double.parseDouble(period2End.substring(0,4));
day = (int)d;
month = (int)m;
year = (int)y;
date = new Day(day,month,year);//day,month,year
periodSeries.add(date, value);
plotTime = graphing.graphTimeData(plotTime, periodSeries, true, Color.BLACK, false, false, true, true, 3);
showLegend = true;
}
if(!period3Begin.isEmpty() && !period3End.isEmpty()){
CalculateStatistics(period3,"period3");
double value = mean_period3;
String label = "Average";
if(medianTF){
value = median_period3;
label = "Median";
}
TimeSeries periodSeries = new TimeSeries("Period 3 " + label + ": " + value + " " + units);
//Set Start Point
double d = Double.parseDouble(period3Begin.substring(8));
double m = Double.parseDouble(period3Begin.substring(5,7));
double y = Double.parseDouble(period3Begin.substring(0,4));
int day = (int)d;
int month = (int)m;
int year = (int)y;
Day date = new Day(day,month,year);//day,month,year
periodSeries.add(date, value);
//Set End Point
d = Double.parseDouble(period3End.substring(8));
m = Double.parseDouble(period3End.substring(5,7));
y = Double.parseDouble(period3End.substring(0,4));
day = (int)d;
month = (int)m;
year = (int)y;
date = new Day(day,month,year);//day,month,year
periodSeries.add(date, value);
plotTime = graphing.graphTimeData(plotTime, periodSeries, true, Color.LIGHT_GRAY, 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 title = "Time Series for Station: " + stationID + "; " + stationName;
JFreeChart chart = new JFreeChart(title, 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 = mainFolder + 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){
Graphing graphing = new Graphing();
//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 IQR = upperQuartile - lowerQuartile;
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 = 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.add(5, value);
}
//Upper outliers
if(value > (upperQuartile + 1.5*IQR) && value < (lowerQuartile + 3*IQR)){
outliers.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);
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.DARK_GRAY);
if(outliers.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 = mainFolder + 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 a histogram of the timeseries and user data and save the resulting graph to the specified location
* @param sortedData the String[][] containing sorted data for the timeseries
* (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
* timeseries (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,
Color color,
String xAxisTitle){
//Initialize other classes
Graphing graphing = new Graphing();
DoubleMath doubleMath = new DoubleMath();
//Retrieve Data
double[] data = new double[sortedData.length];
for(int i=0; i < sortedData.length; i++) {
data[i] = Double.parseDouble(sortedData[i][1]);
}
double[] data_user = new double[sortedData_user.length];
for(int i=0; i < sortedData_user.length; i++) {
data_user[i] = Double.parseDouble(sortedData_user[i][1]);
}
//Determine bin range
double interval = (max - min) / numBins;
double[] lowerLimit = new double[numBins];
double[] upperLimit = new double[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();
for(int j=0; j<numBins; j++){
//Count data within the bin range
int count = 0;
for(int i=0; i < sortedData.length; i++) {
if(data[i] > lowerLimit[j] && data[i] <= upperLimit[j]){
count++;
}
}
double[] binCenter = {lowerLimit[j], upperLimit[j]};
double temp = doubleMath.Average(binCenter)*100;
String categoryTitle = String.valueOf(Math.round(temp/100));
dataset.addValue(count, "All Data", categoryTitle);
if(sortedData_user.length > 0){
//Count user data within the bin range
count = 0;
for(int i=0; i < sortedData_user.length; i++) {
if(data_user[i] > lowerLimit[j] && data[i] <= upperLimit[j]){
count++;
}
}
dataset.addValue(count, "User Data", categoryTitle);
}
}
//Define renderer properties for bar graph
BarRenderer renderer = new BarRenderer();
renderer.setDrawBarOutline(false);
renderer.setSeriesPaint(0, color);
if(sortedData_user.length > 0){
renderer.setSeriesPaint(1, Color.GRAY);
}
//Define axis and properties
NumberAxis numberaxis = new NumberAxis("Count");
CategoryAxis Xaxis = new CategoryAxis(xAxisTitle);
//Graph the dataset using the renderer and create a chart
CategoryPlot plot = new CategoryPlot(dataset, Xaxis, numberaxis, renderer);
//Set extra plot preferences
graphing.setCategoryAxisPreferences(plot);
//Create the chart with the plot
String graphTitle = "Histogram for Station: " + stationID + "; " + stationName;
JFreeChart chart = new JFreeChart(graphTitle, graphing.titleFont, plot, false);
//Save resulting graph for use later
try{
String path = mainFolder + 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 timeseries 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 color the color of the merged 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 createTimeseriesMonthlyGraph(String[][] sortedData,
Color color,
String yAxisTitle) throws ParseException {
//Convert sortedData to monthly data
sortedData = computeFlowMethod(sortedData, "Monthly", "Average");
//Calculate monthly averages for the entire dataset
XYSeries series = new XYSeries(stationID + ": Data");
for(int j=1; j<=12; j++){
double flow = 0;
double ctr = 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){
flow = flow + value;
ctr = ctr + 1;
}
}
series.add(j, flow/ctr);
}
//Create renderer, and axis for timeseries graph
Graphing graphing = new Graphing();
XYPlot plot = new XYPlot();
int seriesIndex = 0;
XYDataset xyDataset = new XYSeriesCollection(series);
XYItemRenderer renderer = new XYLineAndShapeRenderer(true, false);
renderer.setSeriesPaint(seriesIndex, color);
renderer.setSeriesVisibleInLegend(seriesIndex, false);
renderer.setSeriesStroke(seriesIndex,
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);
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
DoubleArray doubleArray = new DoubleArray();
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.graphSeries(plot, currentYearData, Color.lightGray, seriesIndex);
seriesIndex++;
int nextYear = Integer.parseInt(currentYear) + 1;
if(finalYear.compareToIgnoreCase(String.valueOf(nextYear)) >= 0){
currentYear = String.valueOf(nextYear);
}else{
moreYears = false;
}
}
//Create Y Axis
ValueAxis rangeAxis = new NumberAxis(yAxisTitle);
plot.setRangeAxis(0, rangeAxis);
//Create X Axis
NumberAxis domainAxis = new NumberAxis("Month");
domainAxis.setRange(1, 12);
NumberTickUnit temp = new NumberTickUnit(1);
domainAxis.setTickUnit(temp);
plot.setDomainAxis(0, domainAxis);
//Set extra plot preferences
plot = graphing.setAxisPreferences(plot);
//Create the chart with the plot and a legend
String title = "Monthly Averages for Station: " + stationID + "; " + stationName;
JFreeChart chart = new JFreeChart(title, graphing.titleFont, plot, false);
//Save resulting graph for use later
try{
String path = mainFolder + 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 dynamically created paragraph to be displayed to the user along with the LDC graph
* @param dynamicParagraph string array to be written as each line of the text file
* @param partialpath the partial folder path of the file to be written
* @throws IOException
*/
private void writeSummary(String[] dynamicParagraph, String partialpath) throws IOException{
String path = partialpath + File.separator + "timeseries_summary.txt";
FileWriter writer = new FileWriter(path, false);
PrintWriter print_line = new PrintWriter(writer);
//Output data to text file
for(int i = 0; i < dynamicParagraph.length; i++) {
print_line.printf("%s" + "%n", dynamicParagraph[i]);
}
print_line.close();
writer.close();
System.out.println("Text File located at:\t" + path);
}
/**
* 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
* @throws IOException
* @throws InterruptedException
*/
public void run() throws IOException, InterruptedException, ParseException {
//Inputs
//assert args.length > 0;
//String mainFolder = args[0];
//String fileName = args[1];
//String organizationName = args[2];
//String stationID = args[3];
//String stationName = args[4];
//String wqTest = args[5];
//String beginDate = args[6];
//String endDate = args[7];
//String timeStep = args[8];
//String method = args[9];
//If no date input, make it the maximum of available data
if(beginDate == null || beginDate.equalsIgnoreCase("")){
beginDate = "1900-01-01";
}
if(endDate == null || endDate.equalsIgnoreCase("")){
// Pull current date for upper limit of data search
DateFormat desiredDateFormat = new SimpleDateFormat("yyyy-MM-dd");
Date currentDate = new Date();
endDate = desiredDateFormat.format(currentDate);
}
//Artificial limit due to the properties of the Jfreechart object "Date"
if(beginDate.compareToIgnoreCase("1900-01-01") < 0){
beginDate = "1900-01-01";
}
if(endDate.compareToIgnoreCase("1900-01-01") < 0){
endDate = "1900-01-01";
}
//Initialize graph variables
String yAxisTitle = "y axis";
String monthlyYaxisTitle = "y axis";
String WQlabel = "??";
String graphUnits = "??";
Color color = Color.black, color2 = Color.black;
boolean showLine = true;
Data data = new Data();
String[][] sortableData = new String[0][2];
if(wqTest.equalsIgnoreCase("flow")){
//Check if any flow data exists
sortableData = data.extractFlowData(mainFolder, organizationName, stationID, beginDate, endDate, userData);
//Define other graph information
graphUnits = "cfs";
yAxisTitle = timeStep + " " + method + " Flow [" + graphUnits + "]";
monthlyYaxisTitle = "Monthly Average Flow [" + graphUnits + "]";
color = Color.blue;
color2 = Color.DARK_GRAY;
showLine = true;
}else{
//Search for WQ data
Object[] returnArray = data.extractWQdata(mainFolder, organizationName, stationID, beginDate, endDate, userData, wqTest);
sortableData = (String[][]) returnArray[0];
graphUnits = (String) returnArray[1];
WQlabel = (String) returnArray[2];
//Define other graph information
yAxisTitle = timeStep + " " + method + " " + WQlabel + " [" + graphUnits + "]";
monthlyYaxisTitle = "Monthly Average " + WQlabel + " [" + graphUnits + "]";
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){
User_Data user_Data = new User_Data();
sortableData_user = user_Data.readUserFile(userData, beginDate, endDate);
}
//Sort the Data by date to remove duplicate date entries
DoubleArray doubleArray = new DoubleArray();
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){
String database = "USGS";
if(!organizationName.equals("USGS")){
database = "STORET";
}
errorMessage.add("There is no available " + wqTest + " data in the " + database + " database for station '" + stationID + "' and the specified date range.");
}
if(sortedData_user.length == 0){
errorMessage.add("There is no available uploaded data for station '" + stationID + "' and the specified date range");
}
writeError(errorMessage);
}
//Create monthly average chart from daily data before it is converted to another timestep
this.start = sortedData_combined[0][0];
this.end = sortedData_combined[sortedData_combined.length - 1][0];
createTimeseriesMonthlyGraph(sortedData_combined, color, monthlyYaxisTitle);//this is here because it needs to operate on the original daily data
//Perform analysis method on data
sortedData_combined = computeFlowMethod(sortedData_combined, timeStep, method);
sortedData_user = computeFlowMethod(sortedData_user, timeStep, method);
//Calculate stats of data
ArrayList<Double> dataList = new ArrayList<>();
for(int i=0; i<sortedData_combined.length; i++){
dataList.add(Double.parseDouble(sortedData_combined[i][1]));
}
CalculateStatistics(dataList, "all");
//Graph the timeseries data
createTimeseriesGraph(sortedData_combined, sortedData_user, color, color2, showLine, yAxisTitle, graphUnits, medianTF);
createTimeseriesBoxplot(sortedData_combined, yAxisTitle);
createTimeseriesHistogram(sortedData_combined, sortedData_user, color, yAxisTitle);
//Create dynamic summary paragraph
this.len = String.valueOf(sortedData_combined.length);
this.units = graphUnits;
//Create the correct dynamic paragraph
String[] dynamic_paragraph = new String[9];
dynamic_paragraph[0] = "Time Series Graph Overview: ";
dynamic_paragraph[1] = "A time series graph is a straight scale graphing of available flow data with the oldest date on the bottom left and the most recent date on the bottom right with flows on the y axis. This can be useful to identify hydrographs from storm runoff for small time frames (ie. less than a couple days worth of data points)";
dynamic_paragraph[2] = "";
dynamic_paragraph[3] = "";
dynamic_paragraph[4] = "References:";
dynamic_paragraph[6] = "Cleland, B. R. November 2003. TMDL Development from the 'Bottom Up' Part III: Duration Curves and Wet-Weather Assessments. National TMDL Science and Policy 2003.";
dynamic_paragraph[7] = "Cleland, B. R. August 2007. An Approach for Using Load Duration Curves in the Development of TMDLs. National TMDL Science and Policy 2007.";
//Get today's date for the source reference
DateFormat desiredDateFormat = new SimpleDateFormat("yyyy-MM-dd");
Date currentDate = new Date();
String today = desiredDateFormat.format(currentDate);
if(organizationName.equals("USGS")){
dynamic_paragraph[5] = "Stream flow data and water quality test data courtesy of the U.S. Geological Survey, National Water Information System: Web Interface. http://waterdata.usgs.gov/nwis, accessed " + today;
}else{
dynamic_paragraph[5] = "Stream flow data and water quality test data courtesy of the U.S. Environmental Protection Agency, STORET. http://www.epa.gov/storet/index.html accessed " + today;
}
//Write dynamic Paragraph to text file
writeSummary(dynamic_paragraph, mainFolder);
}
public static void main(String[] args) throws IOException, InterruptedException, Exception {
guiTimeseries_Model timeseries_Model = new guiTimeseries_Model();
//Run model
timeseries_Model.run();
}
}