From 5bd310ee80465b3886a64128fb083b5e9a2f6ffe Mon Sep 17 00:00:00 2001
From: Tor-Einar Skog <tor-einar.skog@nibio.no>
Date: Mon, 20 Dec 2021 12:29:36 +0100
Subject: [PATCH] First working version with separate cutoffs per phase
---
.../yellowstemborertempmodel/DataMatrix.java | 8 +-
.../YellowStemborerTempModel.java | 130 +++++++++++++-----
.../YellowStemborerTempModelTest.java | 40 ++++--
3 files changed, 130 insertions(+), 48 deletions(-)
diff --git a/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/DataMatrix.java b/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/DataMatrix.java
index f4dcd06..17d2e76 100644
--- a/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/DataMatrix.java
+++ b/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/DataMatrix.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2016 NIBIO <http://www.nibio.no/>.
+ * Copyright (c) 2021 NIBIO <http://www.nibio.no/>.
*
* This file is part of PsilaRosaeTempModel.
* PsilaRosaeTempModel is free software: you can redistribute it and/or modify
@@ -22,7 +22,7 @@ package no.nibio.vips.model.yellowstemborertempmodel;
import no.nibio.vips.util.DateMap;
/**
- * @copyright 2016 <a href="http://www.nibio.no/">NIBIO</a>
+ * @copyright 2021 <a href="http://www.nibio.no/">NIBIO</a>
* @author Tor-Einar Skog <tor-einar.skog@nibio.no>
*/
public class DataMatrix extends DateMap{
@@ -31,4 +31,8 @@ public class DataMatrix extends DateMap{
public final static String DAILY_CONTRIB = "DC";
public final static String HEAT_SUM = "HEAT_SUM";
public final static String PHASE = "PHASE";
+ public final static String PHASE_EGG ="EGG";
+ public final static String PHASE_LARVAE ="LARVAE";
+ public final static String PHASE_PUPA ="PUPA";
+ public final static String PHASE_ADULT ="ADULT";
}
diff --git a/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModel.java b/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModel.java
index 7244505..4180168 100644
--- a/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModel.java
+++ b/src/main/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModel.java
@@ -26,6 +26,7 @@ import java.text.DecimalFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
@@ -58,17 +59,21 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
private TimeZone timeZone;
private DataMatrix dataMatrix;
private Date biofixDate;
- private String[] phases = {"EGG","LARVAE","PUPA","ADULT"};
+ private final String[] phases = {
+ DataMatrix.PHASE_EGG,
+ DataMatrix.PHASE_LARVAE,
+ DataMatrix.PHASE_PUPA,
+ DataMatrix.PHASE_ADULT
+ };
+ // DD aggregation cutoff values for each phase
+ private Double[] dd_lower = {13.0,12.0,15.0,13.0};
+ private Double[] dd_upper = {36.0, 34.0,36.0,36.0};
- // Threshold values
- // TODO: ADJUST with actual biologically sensible defaults
- private Double dd_lower = 0.0;
- private Double dd_upper = 40.0;
+ // Heat sum thresholds for each phase
+ private Double[] heatRequirements = {113.0, 370.0, 188.0, 25.0};
- private Double THRESHOLD_1 = 260.0; // Egg to larvae
- private Double THRESHOLD_2 = 360.0; // Larvae to pupa
- private Double THRESHOLD_3 = 560.0; // Pupa to adult
+ private String observedPhase = DataMatrix.PHASE_EGG;
public YellowStemborerTempModel()
{
@@ -79,7 +84,7 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
@Override
public List<Result> getResult() throws ModelExcecutionException {
this.calculateTemperatureSum();
-
+ //System.out.println(this.dataMatrix.toCSV());
List<Result> retVal = new ArrayList<>();
Date currentDate = this.dataMatrix.getFirstDateWithParameterValue(DataMatrix.HEAT_SUM);
Calendar cal = Calendar.getInstance(this.timeZone);
@@ -94,35 +99,35 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
Double DAILY_CONTRIB = this.dataMatrix.getParamDoubleValueForDate(currentDate, DataMatrix.DAILY_CONTRIB);
Double HEAT_SUM = this.dataMatrix.getParamDoubleValueForDate(currentDate, DataMatrix.HEAT_SUM);
+ String PHASE = this.dataMatrix.getParamStringValueForDate(currentDate, DataMatrix.PHASE);
result.setValue(CommonNamespaces.NS_WEATHER, DataMatrix.TND, dFormat.format(TNDCurrentDate));
result.setValue(CommonNamespaces.NS_WEATHER, DataMatrix.TXD, dFormat.format(TXDCurrentDate));
result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.DAILY_CONTRIB, dFormat.format(DAILY_CONTRIB));
result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.HEAT_SUM, dFormat.format(HEAT_SUM));
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), "THRESHOLD_1", dFormat.format(this.THRESHOLD_1));
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), "THRESHOLD_2", dFormat.format(this.THRESHOLD_2));
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), "THRESHOLD_3", dFormat.format(this.THRESHOLD_3));
+ result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.PHASE, PHASE);
+ result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), "thresholdLarvae", dFormat.format(this.heatRequirements[0]));
+ result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), "thresholdPupa", dFormat.format(this.heatRequirements[0] + this.heatRequirements[1]));
+ result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), "thresholdAdult", dFormat.format(this.heatRequirements[0] + this.heatRequirements[1] + this.heatRequirements[2]));
+ result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.PHASE, PHASE);
+ Integer warningStatus = Result.WARNING_STATUS_NO_WARNING;
- Integer warningStatus = Result.WARNING_STATUS_NO_RISK;
- if(HEAT_SUM < this.THRESHOLD_1)
+ if(PHASE.equals(DataMatrix.PHASE_EGG))
{
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.PHASE, this.phases[0]);
+ warningStatus = Result.WARNING_STATUS_NO_RISK;
}
- if(HEAT_SUM >= this.THRESHOLD_1)
+ if(PHASE.equals(DataMatrix.PHASE_LARVAE))
{
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.PHASE, this.phases[1]);
warningStatus = Result.WARNING_STATUS_MINOR_RISK;
}
- if(HEAT_SUM >= this.THRESHOLD_2)
+ if(PHASE.equals(DataMatrix.PHASE_PUPA))
{
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.PHASE, this.phases[2]);
- warningStatus = Result.WARNING_STATUS_HIGH_RISK;
+ warningStatus = Result.WARNING_STATUS_MINOR_RISK;
}
- if(HEAT_SUM >= this.THRESHOLD_3)
+ if(PHASE.equals(DataMatrix.PHASE_ADULT))
{
- result.setValue(YellowStemborerTempModel.MODEL_ID.toString(), DataMatrix.PHASE, this.phases[3]);
- warningStatus = Result.WARNING_STATUS_NO_WARNING;
+ warningStatus = Result.WARNING_STATUS_HIGH_RISK;
}
result.setWarningStatus(warningStatus);
retVal.add(result);
@@ -236,6 +241,8 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
"\t\t}\n" +
"]}\n";
}
+
+
@Override
public void setConfiguration(ModelConfiguration config) throws ConfigValidationException {
@@ -243,26 +250,47 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
// Adjusting defaults
try
{
- if(config.getConfigParameter("THRESHOLD_1") != null)
+ if(config.getConfigParameter("heatRequirements") != null)
{
- this.THRESHOLD_1 = this.modelUtil.getDouble(config.getConfigParameter("THRESHOLD_1"));
- }
- if(config.getConfigParameter("THRESHOLD_2") != null)
- {
- this.THRESHOLD_2 = this.modelUtil.getDouble(config.getConfigParameter("THRESHOLD_2"));
- }
- if(config.getConfigParameter("THRESHOLD_3") != null)
- {
- this.THRESHOLD_3 = this.modelUtil.getDouble(config.getConfigParameter("THRESHOLD_3"));
+ this.heatRequirements = this.modelUtil.getDoubleArray(config.getConfigParameter("heatRequirements"));
+ if(this.heatRequirements.length != 4)
+ {
+ throw new ConfigValidationException("ERROR: Array of heat requirements has " + this.dd_lower.length + " elements, should be 4");
+ }
}
if(config.getConfigParameter("dd_lower") != null)
{
- this.dd_lower = this.modelUtil.getDouble(config.getConfigParameter("dd_lower"));
+ this.dd_lower = this.modelUtil.getDoubleArray(config.getConfigParameter("dd_lower"));
+ if(this.dd_lower.length != 4)
+ {
+ throw new ConfigValidationException("ERROR: Array of lower cutoffs has " + this.dd_lower.length + " elements, should be 4");
+ }
}
if(config.getConfigParameter("dd_upper") != null)
{
- this.dd_upper = this.modelUtil.getDouble(config.getConfigParameter("dd_upper"));
+ this.dd_upper = this.modelUtil.getDoubleArray(config.getConfigParameter("dd_upper"));
+ if(this.dd_upper.length != 4)
+ {
+ throw new ConfigValidationException("ERROR: Array of upper cutoffs has " + this.dd_upper.length + " elements, should be 4");
+ }
}
+ if(config.getConfigParameter("observedPhase") != null)
+ {
+ if(!(config.getConfigParameter("observedPhase") instanceof String))
+ {
+ throw new ConfigValidationException("ERROR: Input parameter \"configParameter\" is " + config.getConfigParameter("observedPhase").getClass().getName() + ", must be a String");
+ }
+ String inputObservedPhase = (String) config.getConfigParameter("observedPhase");
+ if(Arrays.asList(phases).contains(inputObservedPhase))
+ {
+ this.observedPhase = inputObservedPhase;
+ }
+ else
+ {
+ throw new ConfigValidationException("ERROR: observedPhase \"" + inputObservedPhase + "\" is not among the valid phases (" + String.join(",", phases) + ")");
+ }
+
+ }
}
catch(ClassCastException ex)
{
@@ -338,7 +366,15 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
Date lastDate = this.dataMatrix.getLastDateWithParameterValue(DataMatrix.TND);
Calendar cal = Calendar.getInstance(this.timeZone);
- Double sum = 0.0;
+ String currentPhase = this.observedPhase;
+
+ Double sum = currentPhase.equals(DataMatrix.PHASE_EGG) ? 0.0
+ : currentPhase.equals(DataMatrix.PHASE_LARVAE) ? this.heatRequirements[0]
+ : currentPhase.equals(DataMatrix.PHASE_PUPA) ? this.heatRequirements[0] + this.heatRequirements[1]
+ : this.heatRequirements[0] + this.heatRequirements[1] + this.heatRequirements[2];
+
+ List<String> phasesList = Arrays.asList(this.phases);
+
while(today.compareTo(lastDate) <= 0)
{
WeatherObservation todayMinTemp = (WeatherObservation)this.dataMatrix.getParamValueForDate(today, DataMatrix.TND);
@@ -348,10 +384,30 @@ public class YellowStemborerTempModel extends I18nImpl implements Model {
throw new ModelExcecutionException("Missing weather data at " + today + ": " + (todayMinTemp == null ? "TND ": "") + (todayMaxTemp == null ? "TXD ": ""));
}
//System.out.println("today=" + today + ",todayTemp=" + todayTemp);
- Double dailyContribution = nlc.calculateSingleSineWaveWithCutoff(todayMinTemp.getValue(), todayMaxTemp.getValue(), this.dd_lower, this.dd_upper);
+ Double current_dd_lower = this.dd_lower[phasesList.indexOf(currentPhase)];
+ Double current_dd_upper = this.dd_upper[phasesList.indexOf(currentPhase)];
+ Double dailyContribution = nlc.calculateSingleSineWaveWithCutoff(todayMinTemp.getValue(), todayMaxTemp.getValue(), current_dd_lower, current_dd_upper);
this.dataMatrix.setParamDoubleValueForDate(today, DataMatrix.DAILY_CONTRIB, dailyContribution);
sum += dailyContribution;
this.dataMatrix.setParamDoubleValueForDate(today, DataMatrix.HEAT_SUM, sum);
+ // Check phase transition
+ if(sum >= this.heatRequirements[0] + this.heatRequirements[1] + this.heatRequirements[2])
+ {
+ currentPhase = DataMatrix.PHASE_ADULT;
+ }
+ else if(sum >= this.heatRequirements[0] + this.heatRequirements[1])
+ {
+ currentPhase = DataMatrix.PHASE_PUPA;
+ }
+ else if(sum >= this.heatRequirements[0])
+ {
+ currentPhase = DataMatrix.PHASE_LARVAE;
+ }
+ else
+ {
+ currentPhase = DataMatrix.PHASE_EGG;
+ }
+ this.dataMatrix.setParamStringValueForDate(today, DataMatrix.PHASE, currentPhase);
cal.setTime(today);
cal.add(Calendar.DATE, 1);
today = cal.getTime();
diff --git a/src/test/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModelTest.java b/src/test/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModelTest.java
index 1d85d40..a37f366 100644
--- a/src/test/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModelTest.java
+++ b/src/test/java/no/nibio/vips/model/yellowstemborertempmodel/YellowStemborerTempModelTest.java
@@ -50,26 +50,48 @@ public class YellowStemborerTempModelTest {
@Test
public void testGetResult() throws Exception {
System.out.println("getResult");
+
+ // REQUIRED
WeatherDataFileReader wfr = new WeatherDataFileReader();
+ // Weather data files can be placed in ("src/test/resources")
ModelConfiguration config = wfr.getModelConfigurationWithWeatherData("/test_data_2019.json", YellowStemborerTempModel.MODEL_ID.toString());
+ // The timezone is used to set daily temperatures and biofix date correctly
config.setConfigParameter("timeZone", "GMT+05:30");
+ // The date for when to start calculating heat sums
config.setConfigParameter("biofixDate", "2019-01-05");
- config.setConfigParameter("THRESHOLD_1", 290.0);
- config.setConfigParameter("THRESHOLD_2", 390.0);
- config.setConfigParameter("THRESHOLD_3", 590);
- config.setConfigParameter("dd_lower", 15);
- config.setConfigParameter("dd_upper", 31.1);
+
+ // OPTIONAL
+ // The observed phase at biofix date. Default is EGG
+ config.setConfigParameter("observedPhase", DataMatrix.PHASE_EGG);
+
+ // Heat requirement for transitioning out of [EGG,LARVAE,PUPA,ADULT] phases
+ Double[] heatRequirements = {113.0, 370.0, 188.0, 25.0};
+ // Lower and upper cutoffs for [EGG,LARVAE,PUPA,ADULT] phases
+ Double[] dd_lower = {13.0,12.0,15.0,13.0};
+ Double[] dd_upper = {36.0, 34.0,36.0,36.0};
+ config.setConfigParameter("heatRequirements", heatRequirements);
+ config.setConfigParameter("dd_lower", dd_lower);
+ config.setConfigParameter("dd_upper", dd_upper);
+
+
+
+
+ //config.setConfigParameter("observedPhase", "Donald Duck");
+
// Print the config
- System.out.println(config.toJSON());
+ //System.out.println(config.toJSON());
+
+ // Run the test
YellowStemborerTempModel instance = new YellowStemborerTempModel();
instance.setConfiguration(config);
List<Result> result = instance.getResult();
assertNotNull(result);
+
// Print the result
- //ObjectMapper mapper = new ObjectMapper();
- //System.out.println(mapper.writeValueAsString(result));
- //result.forEach(r->System.out.println(r));
+ /*ObjectMapper mapper = new ObjectMapper();
+ System.out.println(mapper.writeValueAsString(result));
+ result.forEach(r->System.out.println(r));*/
}
--
GitLab