first commit

.gitignore

+target/
+classes/

pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <groupId>no.bioforsk.vips.model.</groupId>
+  <artifactId>NaerstadModel</artifactId>
+  <version>1.0-SNAPSHOT</version>
+  <packaging>jar</packaging>
+
+  <name>NaerstadModel</name>
+  <url>http://maven.apache.org</url>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.3.2</version>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+    <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>no.bioforsk.vips.common</groupId>
+      <artifactId>VIPSCommon</artifactId>
+      <version>1.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.codehaus.jackson</groupId>
+      <artifactId>jackson-mapper-asl</artifactId>
+      <version>1.6.3</version>
+      <type>jar</type>
+    </dependency>
+  </dependencies>
+</project>

src/main/java/no/bioforsk/vips/model/naerstadmodel/NaerstadModel.java

+package no.bioforsk.vips.model.naerstadmodel;
+
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+import no.bioforsk.no.vips.i18n.I18nImpl;
+import no.bioforsk.vips.entity.ModelConfiguration;
+import no.bioforsk.vips.entity.Observation;
+import no.bioforsk.vips.entity.Result;
+import no.bioforsk.vips.entity.ResultImpl;
+import no.bioforsk.vips.model.Model;
+import no.bioforsk.vips.model.ModelId;
+import no.bioforsk.vips.util.WeatherElements;
+import no.bioforsk.vips.util.WeatherUtil;
+import org.codehaus.jackson.map.ObjectMapper;
+import org.codehaus.jackson.type.TypeReference;
+
+/**
+ * Implementation of the Nærstad model for Potato Blight<br/>
+ * Developed by <a href="http://www.bioforsk.no/ikbViewer/page/bioforsk/ansatte/person?p_document_id=7146&p_dimension_id=17661">Ragnhild Nærstad</a>
+ * @copyright 2013 <a href="http://www.bioforsk.no/">Bioforsk</a>
+ * @author Tor-Einar Skog <tor-einar.skog@bioforsk.no>
+ */
+public class NaerstadModel extends I18nImpl implements Model{
+    
+    private boolean DEBUG = true;
+    
+    private Collection<Observation> TM;
+    private Collection<Observation> UM;
+    private Collection<Observation> RR;
+    //private Collection<KlimaTimeverdiBO> FM2;
+    private Collection<Observation> Q0;
+    private Collection<Observation> BT;
+    private Date calculationStart;
+    private Date calculationEnd;
+
+    private NaerstadModelBackgroundDataMatrix backgroundData;
+    
+    private WeatherUtil weatherUtil;
+    
+    private final static ModelId MODEL_ID = new ModelId("NAERSTADMO");
+    
+    public NaerstadModel(){
+        // Setting the file name of the resource bundle
+        super("no.bioforsk.vips.model.naerstadmodel.texts");
+    }
+
+    @Override
+    public List<Result> getResult() {
+        this.calculateNaerstadModellBakgroundData();
+        this.backgroundData.toString();
+        List<Result> results = new ArrayList<>();
+        Calendar cal = Calendar.getInstance();
+        cal.setTime(this.calculationStart);
+        /*
+         * Results can only be inferred from 1 day after calculation start.
+         * Therefore we add one day before we begin iteration
+         */
+        cal.add(Calendar.DATE, 1);
+        DecimalFormat dFormat = new DecimalFormat("###.##");
+        for(int j=0;j<4;j++)
+        {
+            Date dateStart = cal.getTime();
+            cal.add(Calendar.DATE, 1);
+            Date dateEnd = cal.getTime();
+            Date thePresent = dateStart;
+            while(thePresent.before(dateEnd))
+            {
+                Result result = new ResultImpl();
+                result.setResultValidTime(thePresent);
+                Double RISK = this.backgroundData.getParamDoubleValueForDate(thePresent, NaerstadModelBackgroundDataMatrix.RISK);
+                // TODO: Find better way of terminating?
+                if(RISK == null)
+                {
+                    break;
+                }
+                if(this.DEBUG)
+                    System.out.println("RISK(" + thePresent + ")=" + RISK);
+                result.setValue("RISK", dFormat.format(RISK));
+                results.add(result);
+                
+                // Moving on
+                cal.setTime(thePresent);
+                cal.add(Calendar.HOUR_OF_DAY, 1);
+                thePresent = cal.getTime();
+            }
+        }
+        return results;
+    }
+
+    public ModelId getModelId() {
+        return NaerstadModel.MODEL_ID;
+    }
+
+    public String getModelName() {
+        return this.getModelName(Model.DEFAULT_LANGUAGE);
+    }
+
+    public String getModelName(String language) {
+        return this.getText("name", language);
+    }
+    
+    public String getModelUsage() {
+        return this.getModelUsage(Model.DEFAULT_LANGUAGE);
+    }
+
+    public String getModelUsage(String language) {
+        
+        return this.getText("usage", language);
+    }
+
+    /**
+     * TODO: Input control!!!!!
+     * @param config 
+     */
+    @Override
+    public void setConfiguration(ModelConfiguration config) {
+        initCollections();
+        ObjectMapper mapper = new ObjectMapper();
+        
+        this.calculationStart = mapper.convertValue(config.getConfigParameter("calculationStart"), new TypeReference<Date>(){});
+        this.calculationEnd = mapper.convertValue(config.getConfigParameter("calculationEnd"), new TypeReference<Date>(){});
+
+        List<Observation> observations = mapper.convertValue(config.getConfigParameter("observations"), new TypeReference<List<Observation>>(){});
+        for(Observation o:observations)
+        {
+            switch(o.getElementMeasurementTypeId())
+            {
+                case WeatherElements.TEMPERATURE_MEAN:
+                    this.TM.add(o); break;
+                case WeatherElements.PRECIPITATION:
+                    this.RR.add(o); break;
+                case WeatherElements.LEAF_WETNESS:
+                    this.BT.add(o); break;
+                case WeatherElements.GLOBAL_RADIATION:
+                    this.Q0.add(o); break;
+                case WeatherElements.RELATIVE_HUMIDITY:
+                    this.UM.add(o); break;
+                default:
+                    // TODO: Throw validation error? 
+                    break;
+            }
+        }
+        // TODO: Validate all input!!!!
+        /*for(Observation o:observations)
+        {
+            System.out.println("o time Measured = " + o.getTimeMeasured());
+        }
+        
+        
+                catch(ArrayIndexOutOfBoundsException aioue)
+                {
+                    throw new Exception("Feil med antall måledata. TMliste.length = " + TMliste.length + ", BTliste.length=" + BTliste.length + ", UMListe.length=" + UMliste.length + ", RRliste.length=" + RRliste.length + ", Q0liste.length=" + Q0liste.length);
+                }*/
+        
+    }
+    
+    /**
+     * Sets up the collections
+     */
+    private void initCollections(){
+        this.BT = new ArrayList();
+        this.Q0 = new ArrayList();
+        this.RR = new ArrayList();
+        this.TM = new ArrayList();
+        this.UM = new ArrayList();
+    }
+    
+    /**
+     * Calculates all background data for the model
+     * Depends on continuous weather data. This should be validated beforehand.
+     */
+    private void calculateNaerstadModellBakgroundData()
+    {
+        this.backgroundData = new NaerstadModelBackgroundDataMatrix();
+        Collections.sort((List)this.TM);
+        Collections.sort((List)this.UM);
+        Collections.sort((List)this.RR);
+        Collections.sort((List)this.BT);
+        Collections.sort((List)this.Q0);
+
+        Observation[] TMliste = new Observation[0];
+        TMliste = this.TM.toArray(TMliste);
+        Observation[] UMliste = new Observation[0];
+        UMliste = this.UM.toArray(UMliste);
+        Observation[] RRliste = new Observation[0];
+        RRliste = this.RR.toArray(RRliste);
+        Observation[] BTliste = new Observation[0];
+        BTliste = this.BT.toArray(BTliste);
+        Observation[] Q0liste = new Observation[0];
+        Q0liste = this.Q0.toArray(Q0liste);
+
+        
+        // For debugging purposes only!
+        Calendar cal = Calendar.getInstance();
+        cal.set(2012, 9, 11, 0, 0, 0);
+        Date debugLimitDate = cal.getTime();
+        
+        
+        boolean first = true;
+        
+        for(Integer i=0;i<TMliste.length;i++)
+        {
+            // Calculating TSHH (Temperature Sum Humid Hours)
+            Double TSHHLastHour = first ? 0 : this.backgroundData.getParamDoubleValueForDate(TMliste[i-1].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.TSHH);
+            Double TSHH;
+
+            Integer HH1 = this.getHH1(TMliste[i].getValue(), UMliste[i].getValue());
+            if(first)
+            {
+                TSHH = 0d;
+            }
+            else if(HH1 == 1)
+            {
+                TSHH = this.getHH2(TMliste[i].getValue(), UMliste[i].getValue()) * (TSHHLastHour + (HH1 * TMliste[i].getValue()));
+            }
+            else
+            {
+                TSHH = this.getHH2(TMliste[i].getValue(), UMliste[i].getValue()) * 0.75 * TSHHLastHour;
+            }
+
+            this.backgroundData.setParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.TSHH, TSHH);
+
+            // Calculating SPH (Spore producing hour)
+            Integer SPH = TSHH >= 87 ? 1 : 0;
+            this.backgroundData.setParamIntValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.SPH, SPH);
+
+            // Calculating VAS (Viable Attached Spore)
+            Double VASLastHour = first ? 0 : this.backgroundData.getParamDoubleValueForDate(TMliste[i-1].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.VAS);
+            Double WVD = this.getWeatherUtil().getWVD(TMliste[i].getValue(), UMliste[i].getValue());
+            this.backgroundData.setParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WVD, WVD);
+
+            Double VAS = ((VASLastHour * 0.95 * (1-((WVD-220)/6000))) + SPH) / (1 + (RRliste[i].getValue() * 0.3));
+            if(DEBUG)
+            {
+                //System.out.println(VAS + " = ((" + VASLastHour + " * 0.95 * (1-((" + WVD + "-220)/6000))) + " + SPH+ ") / (1 + (" + RRliste[i].getValue() + " * 0.3));");
+            }
+            this.backgroundData.setParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.VAS, VAS);
+
+            // Calculating VRS (Viable released spores)
+            Double VRS = 0d;
+            if(i > 0)
+            {
+                Double VRSLastHour = this.backgroundData.getParamDoubleValueForDate(TMliste[i-1].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.VRS);
+                Integer WHSLastHour = this.backgroundData.getParamIntValueForDate(TMliste[i-1].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WHS);
+                if(VRSLastHour != null && WHSLastHour != null)
+                {
+                    // RTA (Release To Air)
+                    Integer RTA = this.getRAD(Q0liste[i].getValue(),Q0liste[i-1].getValue()) + this.getDROP(WVD, this.backgroundData.getParamDoubleValueForDate(TMliste[i-1].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WVD));
+
+                    // IRTA (Inhibition of Release To Air)
+                    Double IRTA = 1-((double) BTliste[i].getValue() / 80);
+                    // SFRS (Survival Factor of Released Spores)
+                    Double SFRS = (1 - (Q0liste[i].getValue() - 270)/540)/1.5;
+
+                    if(DEBUG)
+                    {
+                        //System.out.println(TMliste[i].getTimeMeasured().toString() + ": SPH=" + SPH + ", RR[t]=" + RRliste[i].getValue() + ", WVD=" + WVD + ", VAS=" + VAS + ", RTA=" + RTA + ", IRTA=" + IRTA + ", SFRS=" + SFRS + ", VRSLastHour=" + VRSLastHour + ", WHSLastHour=" + WHSLastHour);
+                    }
+
+                    VRS = this.getVRS(VAS, RTA, IRTA, SFRS, VRSLastHour, (double) RRliste[i].getValue(), WHSLastHour);
+                }
+            }
+            this.backgroundData.setParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.VRS, VRS);
+
+
+            if(i > 0 && i < TMliste.length-8)
+            {
+                
+                // Need to calculate WH for this hour and four hours into the future. But only the first time
+                // From the second time on, we only need to calculate for the fourth hour into the future, as all the
+                // other values have already been calculated
+                for(int j = 0; j < 5 ; j++)
+                {
+
+                    // WHS (Wetness starts)
+                    Integer WHS = 0;
+
+                    Double WVDLastHour = this.getWeatherUtil().getWVD(TMliste[i+j-1].getValue(), UMliste[i+j-1].getValue());
+                    Double WVDThisHour = this.getWeatherUtil().getWVD(TMliste[i+j].getValue(), UMliste[i+j].getValue());
+                    if( WVDLastHour + WVDThisHour < 180
+                        || (i+j < TMliste.length -1 && RRliste[i+j].getValue() > 0.1)
+                        || (i+j < TMliste.length -3 && BTliste[i+j].getValue() + BTliste[i+j+1].getValue() + BTliste[i+j+2].getValue() > 122)
+                        || (i+j < TMliste.length -1 && BTliste[i+j].getValue() > 42)
+                        )
+                    {
+                        WHS = 1;
+                    }
+                    else
+                    {
+                        WHS = 0;
+                    }
+
+                    if(DEBUG && WHS == 1)
+                    {
+                        //Double BTSum = BTliste[i+j].getValue() + BTliste[i+j+1].getValue() + BTliste[i+j+2].getValue();
+                    }
+
+                    // Lagrer denne
+                    this.backgroundData.setParamIntValueForDate(TMliste[i+j].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WHS, WHS);
+
+                    // Wetness continuation (WHC)
+                    Integer WHC = 0;
+                    if(WVDThisHour < 340 || RRliste[i+j].getValue() > 0.1)
+                    {
+                        WHC = 1;
+                    }
+
+                    // Wetness Duration (WD)
+                    Double WDLastHour = 0d;
+                    if(i > 1)
+                    {
+                        WDLastHour = this.backgroundData.getParamDoubleValueForDate(TMliste[i+j-1].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WD);
+                    }
+                    Double WD = WHC * (WDLastHour + WHS);
+                    this.backgroundData.setParamDoubleValueForDate(TMliste[i+j].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WD, WD);
+
+                    // Wet Hours (WH)
+                    Integer WH = WD > 0 ? 1 : 0;
+                    this.backgroundData.setParamIntValueForDate(TMliste[i+j].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WH, WH);
+
+                }
+
+                
+                // Calculating TSWH
+                Double TSWH;
+                Integer WHS = this.backgroundData.getParamIntValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WHS);
+                if(WHS == 0)
+                {
+                    TSWH = 0d;
+                }
+                else
+                {
+                    //Collecting data
+                    Integer[] WH = new Integer[5];
+                    for(int k=0;k<WH.length;k++)
+                    {
+                        WH[k] = this.backgroundData.getParamIntValueForDate(TMliste[i+k].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WH);
+                    }
+                    TSWH = (WH[0] * ((double)TMliste[i].getValue() + WH[1] * ((double)TMliste[i+1].getValue() + WH[2]*((double)TMliste[i+2].getValue() + WH[3] * ((double)TMliste[i+3].getValue() + WH[4] * ((double)TMliste[i+4].getValue()))))));
+                }
+
+                this.backgroundData.setParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.TSWH, TSWH);
+
+                // Calculating IR (Infection risk)
+                Integer IR = TSWH >= 40 ? 1 : 0;
+                this.backgroundData.setParamIntValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.IR, IR);
+
+                // Calculating RISK.
+                Double RISK = IR ==1 ? (TSWH/40) * VRS : 0d;
+                this.backgroundData.setParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.RISK, RISK);
+                
+            }
+            
+            if(first) first = false;
+            
+
+            if(TMliste[i].getTimeMeasured().after(debugLimitDate))
+            {
+                this.DEBUG = false;
+            }
+            
+            if(this.DEBUG)
+            {
+                System.out.println("[NaerstadsModellActivityBean] DEBUG Dagens dato = " + TMliste[i].getTimeMeasured().toString() + ", " +
+                        "TSWH=" + this.backgroundData.getParamDoubleValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.TSWH) + ", " +
+                        "WH=" + this.backgroundData.getParamIntValueForDate(TMliste[i].getTimeMeasured(), NaerstadModelBackgroundDataMatrix.WH) + ", " +
+                        "TM=" + TMliste[i].getValue());
+            }
+        }
+    }
+    
+    protected Double getTSWH(Integer WHt0, Integer WHt1, Integer WHt2, Integer WHt3, Integer WHt4, Double Tt0, Double Tt1, Double Tt2, Double Tt3, Double Tt4)
+    {
+        return (WHt0 * (Tt0 + WHt1 * (Tt1 + WHt2 * (Tt2 + WHt3 *(Tt3 + WHt4 * (Tt4))))));
+    }
+
+    /**
+     * Calculating the VSR value
+     * @param VAS
+     * @param RTA
+     * @param IRTA
+     * @param SFRS
+     * @param VRSLastHour
+     * @param RR
+     * @param WHSLastHour
+     * @return
+     */
+    protected Double getVRS(Double VAS, Integer RTA, Double IRTA, Double SFRS, Double VRSLastHour, Double RR, Integer WHSLastHour)
+    {
+        return (((VAS*RTA*IRTA*SFRS) + (VRSLastHour * 0.95 * SFRS)) / (1 + (RR * 0.1))) / (1 + (WHSLastHour * VRSLastHour * 0.1));
+    }
+
+    /**
+     *
+     * @param currentRadiation
+     * @param previousRadiation
+     * @return
+     */
+    protected Integer getRAD(double currentRadiation, double previousRadiation)
+    {
+       return currentRadiation - previousRadiation > 7 ? 1 : 0;
+    }
+
+    protected Integer getDROP(double currentWVD, double previousWVD)
+    {
+        return currentWVD - previousWVD >= 15 ? 1 : 0;
+    }
+
+    /**
+     *
+     * @param date
+     * @param parameterName
+     * @return
+     */
+    protected Double getCalculatedParameter(Date date, String parameterName)
+    {
+        if(this.backgroundData == null)
+        {
+            this.calculateNaerstadModellBakgroundData();
+        }
+        return this.backgroundData.getParamDoubleValueForDate(date, parameterName);
+    }
+
+    
+
+    protected Integer getHH1(double temperature, double relativeHumidity)
+    {
+        return this.getWeatherUtil().getWVD(temperature, relativeHumidity) <= 220 ? 1 : 0;
+    }
+
+    protected Integer getHH2(double temperature, double relativeHumidity)
+    {
+        return this.getWeatherUtil().getWVD(temperature, relativeHumidity) <= 520 ? 1 : 0;
+    }
+    
+    private WeatherUtil getWeatherUtil()
+    {
+        if(this.weatherUtil == null)
+        {
+            this.weatherUtil = new WeatherUtil();
+        }
+        return this.weatherUtil;
+    }
+}

src/main/java/no/bioforsk/vips/model/naerstadmodel/NaerstadModelBackgroundDataMatrix.java

+package no.bioforsk.vips.model.naerstadmodel;
+
+/**
+ * Matrix with calculated background data for Naerstad Model
+ * © 2009 Bioforsk.no
+ * @author Tor-Einar Skog <tor-einar.skog@bioforsk.no>
+ */
+public class NaerstadModelBackgroundDataMatrix extends no.bioforsk.vips.util.DateMap{
+
+    public final static String TSHH = "TSHH";
+    public final static String SPH = "SPH";
+    public final static String VAS = "VAS";
+    public final static String WVD = "WVD";
+    public final static String VRS = "VRS";
+    public final static String TSWH = "TSWH";
+    public final static String WD = "WD";
+    public final static String WHS = "WHS";
+    public final static String WH = "WH";
+    public final static String IR = "IR";
+    public final static String RISK = "RISK";
+
+    public NaerstadModelBackgroundDataMatrix()
+    {
+        super();
+    }
+
+}

src/main/resources/no/bioforsk/vips/model/naerstadmodel/texts.properties

+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+name=Naerstad Model
+usage=To be announced

src/main/resources/no/bioforsk/vips/model/naerstadmodel/texts_nb.properties

+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+name=N\u00e6rstads modell
+usage=Spesifiseres senere

src/test/java/no/bioforsk/vips/model/naerstadmodel/AppTest.java

+package no.bioforsk.vips.model.naerstadmodel;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+/**
+ * Unit test for simple App.
+ */
+public class AppTest 
+    extends TestCase
+{
+    /**
+     * Create the test case
+     *
+     * @param testName name of the test case
+     */
+    public AppTest( String testName )
+    {
+        super( testName );
+    }
+
+    /**
+     * @return the suite of tests being tested
+     */
+    public static Test suite()
+    {
+        return new TestSuite( AppTest.class );
+    }
+
+    /**
+     * Rigourous Test :-)
+     */
+    public void testApp()
+    {
+        assertTrue( true );
+    }
+}