diff --git a/resources/model-constants.json b/resources/model-constants.json
index 7e6f89a65aa2eac338bb9c83a2890b7792979e9b..0360133f838f673e086532b203f2040b3928a5bb 100644
--- a/resources/model-constants.json
+++ b/resources/model-constants.json
@@ -9,6 +9,8 @@
"Pulse":{ "Intensive":{ "Value":-30 }, "Reduced":{ "Value":-70 }, "None":{ "Value":-100 } }
},
"Tillage":{ "Intensive":{ "Value":100 }, "Reduced":{ "Value":150 }, "None":{ "Value":200 } },
+ "TillageEffectDays":{ "Value":30 },
+ "TillageEffectAfter" : { "Intensive":{ "Value":150 }, "Reduced":{ "Value":150 }, "None":{ "Value":200 } },
"CropSusceptibility":{ "Sensitive":{ "Value":1.5 }, "Normal":{ "Value":1 }, "Resistant":{ "Value":0.5 } },
"DiseaseProgress":{ "[0,9]":{ "Value":1 }, "[10,19]":{ "Value":1 }, "[20,29]":{ "Value":1 }, "[30,44]":{ "Value":1.1 }, "[45,[":{ "Value":1.2 } },
"SporeDevelopment":{
@@ -42,6 +44,8 @@
"Pulse":{ "Intensive":{ "Value":-30 }, "Reduced":{ "Value":-70 }, "None":{ "Value":-100 } }
},
"Tillage":{ "Intensive":{ "Value":100 }, "Reduced":{ "Value":150 }, "None":{ "Value":200 } },
+ "TillageEffectDays":{ "Value":30 },
+ "TillageEffectAfter" : { "Intensive":{ "Value":150 }, "Reduced":{ "Value":150 }, "None":{ "Value":200 } },
"CropSusceptibility":{ "Sensitive":{ "Value":1.5 }, "Normal":{ "Value":1 }, "Resistant":{ "Value":0.5 } },
"DiseaseProgress":{ "[0,9]":{ "Value":1 }, "[10,19]":{ "Value":1 }, "[20,29]":{ "Value":1 }, "[30,44]":{ "Value":1 }, "[45,[":{ "Value":1.2 } },
"SporeDevelopment":{
@@ -76,6 +80,8 @@
"Pulse":{ "Intensive":{ "Value":-50 }, "Reduced":{ "Value":-100 }, "None":{ "Value":-100 } }
},
"Tillage":{ "Intensive":{ "Value":100 }, "Reduced":{ "Value":150 }, "None":{ "Value":200 } },
+ "TillageEffectDays":{ "Value":30 },
+ "TillageEffectAfter" : { "Intensive":{ "Value":150 }, "Reduced":{ "Value":150 }, "None":{ "Value":200 } },
"CropSusceptibility":{ "Sensitive":{ "Value":1.5 }, "Normal":{ "Value":1 }, "Resistant":{ "Value":0.5 } },
"DiseaseProgress":{ "[0,9]":{ "Value":1 }, "[10,19]":{ "Value":1 }, "[20,29]":{ "Value":1 }, "[30,44]":{ "Value":1.1 }, "[45,[":{ "Value":1.2 } },
"SporeDevelopment":{
diff --git a/src/main/java/fi/luke/vips/model/cerealmodels/FinnCerealModels.java b/src/main/java/fi/luke/vips/model/cerealmodels/FinnCerealModels.java
index 65f5f348c064e2d3dfd2d07764ff43282d0526a9..5dbd8166eec0c1de5d6ffa4b15ab1fc418918b00 100644
--- a/src/main/java/fi/luke/vips/model/cerealmodels/FinnCerealModels.java
+++ b/src/main/java/fi/luke/vips/model/cerealmodels/FinnCerealModels.java
@@ -117,8 +117,13 @@ public class FinnCerealModels implements Model {
List<Result> resultList = new ArrayList<>();
// reset model
Double accumulatedRisk = 0.0;
+ // sowing date now presumed to be the first date in the data set
+ // XXX this may be a bad idea
+ Date firstDate = dailyTemperature2.get(0).getTimeMeasured();
+ m.setSowingDay(firstDate);
for(int i=0; i < dailyTemperature2.size(); i++) {
Date currentDate = dailyTemperature2.get(i).getTimeMeasured();
+ m.setCurrentDay(currentDate);
Result r = new ResultImpl();
m.setTemperature(dailyTemperature2.get(i).getValue());
r.setValue(pathogen, "ATemp", ""+dailyTemperature2.get(i).getValue());
@@ -325,6 +330,12 @@ public class FinnCerealModels implements Model {
} else {
m.setDailyLeafWetnessDuration(d);
}
+ Boolean b = (Boolean)arg0.getConfigParameter("timeTillageEffects");
+ if(b == null) {
+ m.setTimeTillageEffects(true);
+ } else {
+ m.setTimeTillageEffects(b);
+ }
// weather information
ObjectMapper objectMapper = new ObjectMapper();
diff --git a/src/main/java/fi/uef/envi/mtt/model/diseasepressure/BaseRisk.java b/src/main/java/fi/uef/envi/mtt/model/diseasepressure/BaseRisk.java
index 3349680c8e702a9085712cf7b135a31bc63ed2cf..24206cd393e704c895a004dee3715b55e14d6392 100644
--- a/src/main/java/fi/uef/envi/mtt/model/diseasepressure/BaseRisk.java
+++ b/src/main/java/fi/uef/envi/mtt/model/diseasepressure/BaseRisk.java
@@ -7,6 +7,7 @@ package fi.uef.envi.mtt.model.diseasepressure;
import java.io.File;
import java.io.IOException;
+import java.util.Calendar;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
@@ -37,6 +38,7 @@ public class BaseRisk implements Risk {
private String tillageType;
private String cropSusceptibilityType;
private String pathogenType;
+ private boolean tillageEffect;
private static ObjectMapper mapper = new ObjectMapper();
public BaseRisk() throws JsonProcessingException, IOException {
@@ -52,8 +54,13 @@ public class BaseRisk implements Risk {
throw new NullPointerException("[node = null]");
this.node = node;
+ this.tillageEffect = true;
}
+ public void setTillageEffect(boolean b) {
+ tillageEffect=b;
+ }
+
public void setPathogen(String type) {
this.pathogenType = type;
}
@@ -65,7 +72,7 @@ public class BaseRisk implements Risk {
public void setTillage(String type) {
this.tillageType = type;
}
-
+
public void setCropSusceptibility(String type) {
this.cropSusceptibilityType = type;
}
@@ -120,7 +127,11 @@ public class BaseRisk implements Risk {
double a = n.asDouble();
- n = pathogenTypeNode.get("Tillage");
+ if(tillageEffect) {
+ n = pathogenTypeNode.get("Tillage");
+ } else {
+ n = pathogenTypeNode.get("TillageEffectAfter");
+ }
if (n == null)
throw new NullPointerException("Tillage not found [pathogenType = "
@@ -168,4 +179,28 @@ public class BaseRisk implements Risk {
return (a + b) * c;
}
+
+ public boolean isTillageInEffect(Calendar sowingDay, Calendar currentDay) {
+ // TODO Auto-generated method stub
+ JsonNode pathogenTypeNode = node.get(pathogenType);
+ JsonNode n = pathogenTypeNode.get("TillageEffectDays");
+ if (n == null)
+ throw new NullPointerException(
+ "Value not found [pathogenType = "
+ + pathogenType + "; TillageEffectDays ]");
+
+ n = n.get("Value");
+ if (n == null)
+ throw new NullPointerException(
+ "Value not found [pathogenType = "
+ + pathogenType + "; TillageEffectDays ]");
+ int days = n.asInt();
+ // less days since sowing than the maximum that the tillage is in effect
+ return (currentDay.get(Calendar.DAY_OF_YEAR) < (sowingDay.get(Calendar.DAY_OF_YEAR)+days));
+ }
+
+ public boolean getTillageEffect() {
+ // TODO Auto-generated method stub
+ return tillageEffect;
+ }
}
diff --git a/src/main/java/fi/uef/envi/mtt/model/diseasepressure/DiseasePressureModel.java b/src/main/java/fi/uef/envi/mtt/model/diseasepressure/DiseasePressureModel.java
index 8342d9f9ad67771f9d0762fbc46cfe23bb532236..f4f6c45e677fc6a39307ca727ea81dae85928593 100644
--- a/src/main/java/fi/uef/envi/mtt/model/diseasepressure/DiseasePressureModel.java
+++ b/src/main/java/fi/uef/envi/mtt/model/diseasepressure/DiseasePressureModel.java
@@ -10,6 +10,8 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
+import java.util.Calendar;
+import java.util.Date;
import java.util.List;
import com.fasterxml.jackson.databind.JsonNode;
@@ -42,17 +44,37 @@ public class DiseasePressureModel {
private SporeSpreading sporeSpreading;
private InfectionProbability infectionProbability;
private ObjectMapper mapper = new ObjectMapper();
+ private Calendar sowingDay, currentDay;
+ // if timeTillageEffects is true, then the model keeps track of how long it has been
+ // since tillage, and at certain point stops using the Tillage configuration value
+ // and starts using the TillageEffectAfter -value.
+ // if timeTillageEffects is false, the value of Tillage field in the configuration is used
+ // always. The default is true if sowing date is given, false otherwise
+ private boolean timeTillageEffects;
public DiseasePressureModel() {
this(DiseasePressureModel.class.getClassLoader().getResourceAsStream(
- Options.MODEL_CONSTANTS_FILE));
+ Options.MODEL_CONSTANTS_FILE), new Date());
}
+ public DiseasePressureModel(Date date) {
+ this(DiseasePressureModel.class.getClassLoader().getResourceAsStream(
+ Options.MODEL_CONSTANTS_FILE), date);
+ }
+
+ public DiseasePressureModel(File file, Date date) throws FileNotFoundException {
+ this(new FileInputStream(file), date);
+ }
+
public DiseasePressureModel(File file) throws FileNotFoundException {
- this(new FileInputStream(file));
+ this(new FileInputStream(file), new Date());
}
public DiseasePressureModel(InputStream stream) {
+ this(stream, new Date());
+ }
+
+ public DiseasePressureModel(InputStream stream, Date sowingDay) {
JsonNode node;
try {
@@ -61,6 +83,18 @@ public class DiseasePressureModel {
throw new RuntimeException(e);
}
+ this.sowingDay = Calendar.getInstance();
+ this.currentDay = Calendar.getInstance();
+ timeTillageEffects = false;
+ if(sowingDay != null) {
+ this.sowingDay.setTime(sowingDay);
+ this.currentDay.setTime(sowingDay);
+ timeTillageEffects = true;
+ }
+// this.sowingDay.set(Calendar.HOUR_OF_DAY,0);
+// this.sowingDay.set(Calendar.MINUTE,0);
+// this.sowingDay.set(Calendar.SECOND,0);
+// this.sowingDay.set(Calendar.MILLISECOND,1);
baseRisk = new BaseRisk(node);
dailyRisk = new DailyRisk();
accumulatedRisk = new AccumulatedRisk(node);
@@ -125,8 +159,29 @@ public class DiseasePressureModel {
public void setLeafIsWet(List<Boolean> leafIsWet) {
sporeSpreading.setLeafIsWet(leafIsWet);
}
+
+ public void setSowingDay(Date d) {
+ sowingDay.setTime(d);
+ }
+ public void setCurrentDay(Date d) {
+// if(currentDay == null) {
+// currentDay = Calendar.getInstance();
+// }
+ currentDay.setTime(d);
+// currentDay.set(Calendar.HOUR_OF_DAY,0);
+// currentDay.set(Calendar.HOUR,0);
+// currentDay.set(Calendar.MINUTE,0);
+// currentDay.set(Calendar.MILLISECOND,1);
+ }
+
public double getBaseRisk() {
+ // tillage is not timed, thus it is always on.
+ if(!timeTillageEffects) {
+ baseRisk.setTillageEffect(true);
+ } else if(baseRisk.getTillageEffect()) {
+ baseRisk.setTillageEffect(baseRisk.isTillageInEffect(sowingDay,currentDay));
+ }
return baseRisk.compute();
}
@@ -137,6 +192,14 @@ public class DiseasePressureModel {
public double getAccumulatedRisk() {
return accumulatedRisk.compute();
}
+
+ public boolean isTimeTillageEffects() {
+ return timeTillageEffects;
+ }
+
+ public void setTimeTillageEffects(boolean timeTillageEffects) {
+ this.timeTillageEffects = timeTillageEffects;
+ }
diff --git a/src/test/java/fi/luke/vips/model/cerealmodels/FinnCerealModelsTest.java b/src/test/java/fi/luke/vips/model/cerealmodels/FinnCerealModelsTest.java
index 51550203c6b88db64f4cf74f37f0f5bd9215f327..61cbf0161b4619529ff7611cb549f266c3126c9a 100644
--- a/src/test/java/fi/luke/vips/model/cerealmodels/FinnCerealModelsTest.java
+++ b/src/test/java/fi/luke/vips/model/cerealmodels/FinnCerealModelsTest.java
@@ -136,6 +136,7 @@ public class FinnCerealModelsTest {
m.setConfigParameter("rh", rh);
m.setConfigParameter("windspeed", windSpeedAll);
+ m.setConfigParameter("timeTillageEffects", new Boolean(false));
m.setConfigParameter("precedingCrop","Wheat");
m.setConfigParameter("tillageMethod","Intensive");
m.setConfigParameter("diseaseSusceptibility","Normal");