Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found
Select Git revision
  • feature/vips-test
  • main
  • release
  • v1.0.1
  • v1.0.2
  • v1.0.3
  • v1.1.0
  • v1.1.1
  • v1.1.10
  • v1.1.11
  • v1.1.12
  • v1.1.13
  • v1.1.14
  • v1.1.15
  • v1.1.16
  • v1.1.17
  • v1.1.18
  • v1.1.19
  • v1.1.2
  • v1.1.20
  • v1.1.21
  • v1.1.22
  • v1.1.23
  • v1.1.3
  • v1.1.4
  • v1.1.5
  • v1.1.6
  • v1.1.7
  • v1.1.8
  • v1.1.9
30 results

Target

Select target project
  • VIPS/models/java/Model_ALTERNARIA
1 result
Select Git revision
  • feature/vips-test
  • main
  • release
  • v1.0.1
  • v1.0.2
  • v1.0.3
  • v1.1.0
  • v1.1.1
  • v1.1.10
  • v1.1.11
  • v1.1.12
  • v1.1.13
  • v1.1.14
  • v1.1.15
  • v1.1.16
  • v1.1.17
  • v1.1.18
  • v1.1.19
  • v1.1.2
  • v1.1.20
  • v1.1.21
  • v1.1.22
  • v1.1.23
  • v1.1.3
  • v1.1.4
  • v1.1.5
  • v1.1.6
  • v1.1.7
  • v1.1.8
  • v1.1.9
30 results
Show changes
Commits on Source (27)
Hide whitespace changes
Inline Side-by-side
Showing
with 655 additions and 565 deletions
.gitignore
View file @ 6dd8400a
target/
.idea
\ No newline at end of file
.idea
.vscode
\ No newline at end of file
README.md
View file @ 6dd8400a
# AlternariaModel
# AlternariaModel (TOMCAST)
<p><img src="src/main/resources/images/ef-20200421-altenaria.jpg" description="Photo: Bilde: S. Abrahamsen, NLR"/></p>
<p>TOMCAST is based on a model that was originally developed for leaf spot diseases in tomato. The model that is used here is tested and adapted to be used against early blight in potato in Denmark (Alternaria solani). The model calculates daily risk values (DSV: Disease Severity Values) based on temperature and leaf wetness the previous day. DSV represents the risk of attack of early blight the previous 24 hours. Daily values of DSV are accumulated until a threshold value is reached, and treatment is recommended. When a spray is performed and entered into the model, accumulation of DSV is reset and starts over at 0.</p>
<p>The model will be evaluated in potato and carrots in Norway in 2020, and is only available for private warnings. Based on experience from other countries, the threshold for a warning to be issued is set to 20.</p>
<h3>When to initiate the model</h3>
<p>Potato plants vary in susceptibility during the season, and gradually become more susceptible. This means that the requirement for protection against early blight vary accordingly. The model is started when the first symptoms are visible, and first treatment is performed (below 0,1% attack).</p>
<h3>Interpretation of results</h3>
<p>The model will be green (no risk) until it reaches 15. From this value the warning will be yellow (possible risk) until the threshold is reached, and the warning turns red (risk of infection).</p>
<img src="src/main/resources/images/ef-20200421-altenaria.jpg" description="Photo: S. Abrahamsen, NLR"/>
### Development
_Photo: S. Abrahamsen, NLR_
TOMCAST is based on a model that was originally developed for leaf spot diseases in tomato. The model that is used here is tested and adapted to be used against early blight in potato in Denmark (Alternaria solani). The model calculates daily risk values (DSV: Disease Severity Values) based on temperature and leaf wetness the previous day. DSV represents the risk of attack of early blight the previous 24 hours. Daily values of DSV are accumulated until a threshold value is reached, and treatment is recommended. When a spray is performed and entered into the model, accumulation of DSV is reset and starts over at 0.
## Configurable parameters
### Lower temperature threshold for DSV
Default value: 13.0 (as in the original TOMCAST model)
### DSV (Daily Severity Value) Threshold for high infection risk
Default value: 20
## When to initiate the model
Potato plants vary in susceptibility during the season, and gradually become more susceptible. This means that the requirement for protection against early blight vary accordingly. The model is started when the first symptoms are visible, and first treatment is performed (below 0,1% attack).
## Interpretation of results
The model will be green (no risk) until it reaches 15. From this value the warning will be yellow (possible risk) until the threshold is reached, and the warning turns red (risk of infection).
## Development
Requirements:
* Maven
* Java 11
Clone Gitlab repository
```
$ git clone https://gitlab.nibio.no/VIPS/models/java/Model_ALTERNARIA.git
$ cd Model_ALTERNARIA
```
Build
```
$ mvn install
```
\ No newline at end of file
pom.xml
View file @ 6dd8400a
......@@ -5,19 +5,19 @@
<parent>
<groupId>no.nibio.vips</groupId>
<artifactId>vips-parent-pom</artifactId>
<version>1.0.0</version>
<version>1.1.0</version>
</parent>
<groupId>no.nibio.vips.model</groupId>
<artifactId>AlternariaModel</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.1.11-SNAPSHOT</version>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>no.nibio.vips</groupId>
<artifactId>VIPSCommon</artifactId>
<version>2.0.3</version>
<version>2.1.1</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
......
src/main/java/no/nibio/vips/model/alternariamodel/AlternariaModel.java
View file @ 6dd8400a
......@@ -39,13 +39,17 @@ package no.nibio.vips.model.alternariamodel;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.BufferedInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Scanner;
import java.util.TimeZone;
import java.util.logging.Level;
import java.util.logging.Logger;
......@@ -62,133 +66,139 @@ import no.nibio.vips.util.CommonNamespaces;
import no.nibio.vips.util.ModelUtil;
import no.nibio.vips.util.WeatherUtil;
/**
*
* @author bhabesh
*/
public class AlternariaModel extends I18nImpl implements Model{
public final static Logger LOGGER = Logger.getLogger(AlternariaModel.class.getName());
public final static String NAME_MODEL_ID = "ALTERNARIA";
public final static ModelId MODEL_ID = new ModelId(NAME_MODEL_ID);
public final static int THRESHOLD_LW = 30; // Threshold for leave wetness
public final static int THRESHOLD_DSV_MAX = 20; // Threshold Minimum for DSV
public final static int THRESHOLD_DSV_DIFF_MIN_MAX = 5; // Threshold Maximum for DSV
public final static String YES = "Y"; // Spray Date
public final static String NO = "N";
private final ModelUtil modelUtil;
private DataMatrix dataMatrix;
private TimeZone timeZone;
public AlternariaModel()
{
public class AlternariaModel extends I18nImpl implements Model {
public final static Logger LOGGER = Logger.getLogger(AlternariaModel.class.getName());
public final static String NAME_MODEL_ID = "ALTERNARIA";
public final static ModelId MODEL_ID = new ModelId(NAME_MODEL_ID);
public final static int THRESHOLD_LW = 30; // Threshold for leave wetness
private Double THRESHOLD_DSV_MAX = 20.0; // Threshold Minimum for DSV
public final static int THRESHOLD_DSV_DIFF_MIN_MAX = 5; // Threshold Maximum for DSV
private Double THRESHOLD_DSV_TEMP_MIN = 13.0; // Minimum temp for getting a DSV value
public final static String YES = "Y"; // Spray Date
public final static String NO = "N";
private final ModelUtil modelUtil;
private DataMatrix dataMatrix;
private TimeZone timeZone;
public AlternariaModel() {
super("no.nibio.vips.model.alternariamodel.texts");
this.modelUtil = new ModelUtil();
this.modelUtil = new ModelUtil();
}
@Override
public List<Result> getResult() throws ModelExcecutionException
{
public List<Result> getResult() throws ModelExcecutionException {
/**
* method name : getResult
* @param :
* @return : java.util.List<no.nibio.vips.entity.Result>
*
* @param :
* @return : java.util.List<no.nibio.vips.entity.Result>
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
//throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
//TODO write proper list of result object
//Date currentDate = this.dataMatrix.getFirstDateWithParameterValue(DataMatrix.LEAF_WETNESS_DURATION);
List<Result> results = new ArrayList<>();
Date currentDate = this.dataMatrix.getFirstDateWithParameterValue(DataMatrix.TEMPERATURE_MEAN);
Date endDate = this.dataMatrix.getLastDateWithParameterValue(DataMatrix.TEMPERATURE_MEAN);
DecimalFormat dFormat = new DecimalFormat("###.##");
DecimalFormat iFormat = new DecimalFormat("###");
Calendar cal = Calendar.getInstance(timeZone);
int accumulatedDSV = 0;
while(currentDate.before(endDate))
{
Result result = new ResultImpl();
if(null == dataMatrix.getParamStringValueForDate(currentDate, DataMatrix.SPRAYING_DATE))
{
// DO Nothing -- Consider same accumulatedDSV
}
else
{
if(dataMatrix.getParamStringValueForDate(currentDate, DataMatrix.SPRAYING_DATE).equals(YES))
{
accumulatedDSV = 0;
}
else
{
accumulatedDSV = accumulatedDSV + dataMatrix.getParamIntValueForDate(currentDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE);
}
}
result.setValidTimeStart(currentDate);
result.setWarningStatus(getWarningStatus(accumulatedDSV));
result.setValue(CommonNamespaces.NS_WEATHER, DataMatrix.TEMPERATURE_MEAN, dFormat.format(this.dataMatrix.getParamValueForDate(currentDate, DataMatrix.TEMPERATURE_MEAN)));
result.setValue(NAME_MODEL_ID, DataMatrix.WET_HOUR, iFormat.format(this.dataMatrix.getParamValueForDate(currentDate, DataMatrix.LEAF_WETNESS_DURATION)));
result.setValue(NAME_MODEL_ID, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE_SUM, iFormat.format(accumulatedDSV));
result.setValue(NAME_MODEL_ID, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE, iFormat.format(this.dataMatrix.getParamValueForDate(currentDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE)));
result.setValue(NAME_MODEL_ID, DataMatrix.THRESHOLD_DSV_BASE, String.valueOf(THRESHOLD_DSV_MAX - THRESHOLD_DSV_DIFF_MIN_MAX));
result.setValue(NAME_MODEL_ID, DataMatrix.THRESHOLD_DSV_MAX, String.valueOf(THRESHOLD_DSV_MAX));
results.add(result);
// throw new UnsupportedOperationException("Not supported yet."); //To change
// body of generated methods, choose Tools | Templates.
// TODO write proper list of result object
// Date currentDate =
// this.dataMatrix.getFirstDateWithParameterValue(DataMatrix.LEAF_WETNESS_DURATION);
List<Result> results = new ArrayList<>();
Date currentDate = this.dataMatrix.getFirstDateWithParameterValue(DataMatrix.TEMPERATURE_MEAN);
Date endDate = this.dataMatrix.getLastDateWithParameterValue(DataMatrix.TEMPERATURE_MEAN);
DecimalFormat dFormat = new DecimalFormat("###.##");
DecimalFormat iFormat = new DecimalFormat("###");
Calendar cal = Calendar.getInstance(timeZone);
int accumulatedDSV = 0;
while (currentDate.before(endDate)) {
Result result = new ResultImpl();
if (null == dataMatrix.getParamStringValueForDate(currentDate, DataMatrix.SPRAYING_DATE)) {
// DO Nothing -- Consider same accumulatedDSV
} else {
if (dataMatrix.getParamStringValueForDate(currentDate, DataMatrix.SPRAYING_DATE).equals(YES)) {
accumulatedDSV = 0;
} else
{
accumulatedDSV = accumulatedDSV
+ dataMatrix.getParamIntValueForDate(currentDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE);
}
}
result.setValidTimeStart(currentDate);
result.setWarningStatus(getWarningStatus(accumulatedDSV));
result.setValue(CommonNamespaces.NS_WEATHER, DataMatrix.TEMPERATURE_MEAN,
dFormat.format(this.dataMatrix.getParamValueForDate(currentDate, DataMatrix.TEMPERATURE_MEAN)));
result.setValue(NAME_MODEL_ID, DataMatrix.WET_HOUR, iFormat
.format(this.dataMatrix.getParamValueForDate(currentDate, DataMatrix.LEAF_WETNESS_DURATION)));
result.setValue(NAME_MODEL_ID, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE_SUM, iFormat.format(accumulatedDSV));
result.setValue(NAME_MODEL_ID, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE, iFormat.format(
this.dataMatrix.getParamValueForDate(currentDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE)));
result.setValue(NAME_MODEL_ID, DataMatrix.THRESHOLD_DSV_BASE,
String.valueOf(THRESHOLD_DSV_MAX - THRESHOLD_DSV_DIFF_MIN_MAX));
result.setValue(NAME_MODEL_ID, DataMatrix.THRESHOLD_DSV_MAX, String.valueOf(THRESHOLD_DSV_MAX));
result.setValue(NAME_MODEL_ID, DataMatrix.THRESHOLD_DSV_TEMP_MIN, String.valueOf(this.THRESHOLD_DSV_TEMP_MIN));
results.add(result);
cal.setTime(currentDate);
cal.add(Calendar.DATE, 1);
currentDate = cal.getTime();
currentDate = cal.getTime();
}
//LOGGER.log(Level.INFO, "DataMatrix-Value 03: "+dataMatrix);
// LOGGER.log(Level.INFO, "DataMatrix-Value 03: "+dataMatrix);
return results;
}
@Override
public ModelId getModelId()
{
public ModelId getModelId() {
/**
* method name : getModelId
* @param :
* @return : no.nibio.vips.model.ModelId
*
* @param :
* @return : no.nibio.vips.model.ModelId
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
//throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
// throw new UnsupportedOperationException("Not supported yet."); //To change
// body of generated methods, choose Tools | Templates.
return AlternariaModel.MODEL_ID;
}
@Override
public String getModelName()
{
public String getModelName() {
/**
* method name : getModelName
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getModelName(Model.DEFAULT_LANGUAGE);
}
......@@ -196,64 +206,64 @@ public class AlternariaModel extends I18nImpl implements Model{
/**
*
* @param language
* @return
* @return
*/
@Override
public String getModelName(String language)
{
public String getModelName(String language) {
/**
* method name : getModelName
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getText("name", language);
}
@Override
public String getLicense()
{
/**
* method name : getLicense
* @param :
* @return : java.lang.String
*
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getText("license", Model.DEFAULT_LANGUAGE);
public String getLicense() {
return this.modelUtil.getTextFromFileInJar(this.getClass(), "/LICENSE_header.txt");
}
@Override
public String getCopyright()
{
public String getCopyright() {
/**
* method name : getCopyright
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return "(c) 2020 NIBIO (http://www.nibio.no/). Contact: post@nibio.no";
}
@Override
public String getModelDescription()
{
public String getModelDescription() {
/**
* method name : getModelDescription
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getModelDescription(Model.DEFAULT_LANGUAGE);
}
......@@ -261,507 +271,456 @@ public class AlternariaModel extends I18nImpl implements Model{
/**
*
* @param language
* @return
* @return
*/
@Override
public String getModelDescription(String language)
{
public String getModelDescription(String language) {
/**
* method name : getModelDescription
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
try
{
return this.modelUtil.getTextWithBase64EncodedImages(this.getText("description", language), this.getClass());
}
catch (IOException ex)
{
try {
return this.modelUtil.getTextWithBase64EncodedImages(this.getText("description", language),
this.getClass());
} catch (IOException ex) {
return this.getText("description", language);
}
}
@Override
public String getWarningStatusInterpretation()
{
public String getWarningStatusInterpretation() {
/**
* method name : getWarningStatusInterpretation
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getWarningStatusInterpretation(Model.DEFAULT_LANGUAGE);
}
@Override
public String getWarningStatusInterpretation(String language)
{
public String getWarningStatusInterpretation(String language) {
/**
* method name : getWarningStatusInterpretation
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getText("statusInterpretation", language);
}
@Override
public String getModelUsage()
{
public String getModelUsage() {
/**
* method name : getModelUsage
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getModelUsage(Model.DEFAULT_LANGUAGE);
}
@Override
public String getModelUsage(String language)
{
public String getModelUsage(String language) {
/**
* method name : getModelUsage
* @param :
* @return : java.lang.String
*
* @param :
* @return : java.lang.String
*
* purpose :
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
* date : Expression date is undefined on line 20, column 19 in
* Templates/Classes/Code/GeneratedMethodBody. Expression time is
* undefined on line 20, column 27 in
* Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getText("usage", language);
}
/**
* TODO
* @return
*
*
* @return a Json configuration example
*/
@Override
public String getSampleConfig()
{
/**
* method name : getSampleConfig
* @param :
* @return : java.lang.String
*
* purpose :
*
* date : Expression date is undefined on line 20, column 19 in Templates/Classes/Code/GeneratedMethodBody. Expression time is undefined on line 20, column 27 in Templates/Classes/Code/GeneratedMethodBody.
*/
return this.getText("sampleconfig", Model.DEFAULT_LANGUAGE);
public String getSampleConfig() {
return this.modelUtil.getTextFromFileInJar(this.getClass(), "/sample_config.json");
}
/**
*
* @param config
* @throws ConfigValidationException
* @throws ConfigValidationException
*/
@Override
public void setConfiguration(ModelConfiguration config) throws ConfigValidationException
{
List<WeatherObservation> altenariaWeatherListDaily = new ArrayList<WeatherObservation>();
dataMatrix = new DataMatrix();
ObjectMapper mapper = new ObjectMapper();
timeZone = TimeZone.getTimeZone((String)config.getConfigParameter("timeZone"));
WeatherUtil weatherUtil = new WeatherUtil();
List<WeatherObservation> observations = modelUtil.extractWeatherObservationList(config.getConfigParameter("observations"));
List<Date> sprayingDates = null;
List<WeatherObservation> altenariaWeatherLIstHourly_tm = new ArrayList<WeatherObservation>();
List<WeatherObservation> altenariaWeatherLIstHourly_lw = new ArrayList<WeatherObservation>();
Date dateHourlyTm_currentDay = null;
Date dateHourlyTm_previousDay = null;
Date dateHourlyLw_currentDay = null;
Date dateHourlyLw_previousDay = null;
public void setConfiguration(ModelConfiguration config) throws ConfigValidationException {
List<WeatherObservation> altenariaWeatherListDaily = new ArrayList<WeatherObservation>();
dataMatrix = new DataMatrix();
ObjectMapper mapper = new ObjectMapper();
timeZone = TimeZone.getTimeZone((String) config.getConfigParameter("timeZone"));
WeatherUtil weatherUtil = new WeatherUtil();
List<WeatherObservation> observations = modelUtil
.extractWeatherObservationList(config.getConfigParameter("observations"));
List<Date> sprayingDates = null;
List<WeatherObservation> altenariaWeatherLIstHourly_tm = new ArrayList<WeatherObservation>();
List<WeatherObservation> altenariaWeatherLIstHourly_lw = new ArrayList<WeatherObservation>();
try
{
this.THRESHOLD_DSV_TEMP_MIN = config.getConfigParameter(DataMatrix.THRESHOLD_DSV_TEMP_MIN) != null ? modelUtil.getDouble(config.getConfigParameter(DataMatrix.THRESHOLD_DSV_TEMP_MIN)): this.THRESHOLD_DSV_TEMP_MIN;
this.THRESHOLD_DSV_MAX = config.getConfigParameter(DataMatrix.THRESHOLD_DSV_MAX) != null ? modelUtil.getDouble(config.getConfigParameter(DataMatrix.THRESHOLD_DSV_MAX)) : this.THRESHOLD_DSV_MAX;
}
catch(ClassCastException ex)
{
throw new ConfigValidationException(ex.getMessage());
}
Date dateHourlyTm_currentDay = null;
Date dateHourlyTm_previousDay = null;
Date dateHourlyLw_currentDay = null;
Date dateHourlyLw_previousDay = null;
WeatherUtil wUtil = new WeatherUtil();
// Setting timezone
// Setting timezone
this.timeZone = TimeZone.getTimeZone((String) config.getConfigParameter("timeZone"));
sprayingDates = (null == mapper.convertValue(config.getConfigParameter(DataMatrix.SPRAYING_DATES), new TypeReference<List<Date>>(){}))
? null
: mapper.convertValue(config.getConfigParameter(DataMatrix.SPRAYING_DATES), new TypeReference<List<Date>>(){});
sprayingDates = (null == mapper.convertValue(config.getConfigParameter(DataMatrix.SPRAYING_DATES),
new TypeReference<List<Date>>() {
}))
? null
: mapper.convertValue(config.getConfigParameter(DataMatrix.SPRAYING_DATES),
new TypeReference<List<Date>>() {
});
int count = 0;
int count = 0;
Collections.sort(observations);
for(WeatherObservation weatherObj: observations)
{
weatherObj.setTimeMeasured(wUtil.pragmaticAdjustmentToMidnight(weatherObj.getTimeMeasured(), timeZone));
Date sprayDate = null;
switch(weatherObj.getElementMeasurementTypeId())
{
case DataMatrix.TEMPERATURE_MEAN:
dateHourlyTm_currentDay = trimmedDate(weatherObj.getTimeMeasured(),timeZone);
if(weatherObj.getLogIntervalId().equals(WeatherObservation.LOG_INTERVAL_ID_1H))
{
WeatherObservation altanariaWeatherBO_tm_hourly = weatherObj;
if (
(null != dateHourlyTm_currentDay )
&& (null != dateHourlyTm_previousDay)
&& dateHourlyTm_currentDay.after (
dateHourlyTm_previousDay
)
)
{
double counterTMHourly = 0;
//TODO calculation of accumulation value and add to daily
for(WeatherObservation wo: altenariaWeatherLIstHourly_tm)
{
counterTMHourly = counterTMHourly + wo.getValue();
for (WeatherObservation weatherObj : observations) {
}
//average value of temperature for a day
dataMatrix.setParamDoubleValueForDate ( dateHourlyTm_previousDay
, DataMatrix.TEMPERATURE_MEAN
, (
counterTMHourly
/
altenariaWeatherLIstHourly_tm.size()
)
);
//discard old value for next day and start fresh
altenariaWeatherLIstHourly_tm = new ArrayList<WeatherObservation>();
}
weatherObj.setTimeMeasured(wUtil.pragmaticAdjustmentToMidnight(weatherObj.getTimeMeasured(), timeZone));
altenariaWeatherLIstHourly_tm.add(altanariaWeatherBO_tm_hourly);
}
Date sprayDate = null;
switch (weatherObj.getElementMeasurementTypeId()) {
case DataMatrix.TEMPERATURE_MEAN:
dateHourlyTm_currentDay = trimmedDate(weatherObj.getTimeMeasured(), timeZone);
if (weatherObj.getLogIntervalId().equals(WeatherObservation.LOG_INTERVAL_ID_1H)) {
WeatherObservation altanariaWeatherBO_tm_hourly = weatherObj;
if ((null != dateHourlyTm_currentDay)
&& (null != dateHourlyTm_previousDay)
&& dateHourlyTm_currentDay.after(
dateHourlyTm_previousDay)) {
double counterTMHourly = 0;
// TODO calculation of accumulation value and add to daily
for (WeatherObservation wo : altenariaWeatherLIstHourly_tm) {
counterTMHourly = counterTMHourly + wo.getValue();
if(weatherObj.getLogIntervalId().equals(WeatherObservation.LOG_INTERVAL_ID_1D))
{
if (
(null == dataMatrix.getParamDoubleValueForDate(dateHourlyTm_currentDay, DataMatrix.TEMPERATURE_MEAN) )
||
((dataMatrix.getParamDoubleValueForDate(dateHourlyTm_currentDay, DataMatrix.TEMPERATURE_MEAN)).intValue() == 0)
)
{
dataMatrix.setParamDoubleValueForDate (
weatherObj.getTimeMeasured() //TODO - Might be the date need to be trimmed
, DataMatrix.TEMPERATURE_MEAN
, weatherObj.getValue()
);
}
// average value of temperature for a day
dataMatrix.setParamDoubleValueForDate(dateHourlyTm_previousDay, DataMatrix.TEMPERATURE_MEAN,
(counterTMHourly
/
altenariaWeatherLIstHourly_tm.size()));
// discard old value for next day and start fresh
altenariaWeatherLIstHourly_tm = new ArrayList<WeatherObservation>();
}
break;
case DataMatrix.LEAF_WETNESS_DURATION:
dateHourlyLw_currentDay = trimmedDate(weatherObj.getTimeMeasured(),timeZone);
if(weatherObj.getLogIntervalId().equals(WeatherObservation.LOG_INTERVAL_ID_1H))
{
WeatherObservation altanariaWeatherBO_lw_hourly = weatherObj;
if(
null != dateHourlyLw_currentDay
&& null != dateHourlyLw_previousDay
&& dateHourlyLw_currentDay.after(dateHourlyLw_previousDay)
)
{
int counterLwHourly = 0;
for(WeatherObservation wo: altenariaWeatherLIstHourly_lw)
{
if(wo.getValue() >= THRESHOLD_LW )
{
counterLwHourly = counterLwHourly + 1;
}
}
dataMatrix.setParamIntValueForDate(
dateHourlyLw_previousDay
, DataMatrix.LEAF_WETNESS_DURATION
, counterLwHourly
);
altenariaWeatherLIstHourly_lw = new ArrayList<WeatherObservation>();
altenariaWeatherLIstHourly_tm.add(altanariaWeatherBO_tm_hourly);
}
if (weatherObj.getLogIntervalId().equals(WeatherObservation.LOG_INTERVAL_ID_1D)) {
if ((null == dataMatrix.getParamDoubleValueForDate(dateHourlyTm_currentDay,
DataMatrix.TEMPERATURE_MEAN))
||
((dataMatrix.getParamDoubleValueForDate(dateHourlyTm_currentDay,
DataMatrix.TEMPERATURE_MEAN)).intValue() == 0)) {
dataMatrix.setParamDoubleValueForDate(
weatherObj.getTimeMeasured() // TODO - Might be the date need to be trimmed
, DataMatrix.TEMPERATURE_MEAN, weatherObj.getValue());
}
}
break;
case DataMatrix.LEAF_WETNESS_DURATION:
dateHourlyLw_currentDay = trimmedDate(weatherObj.getTimeMeasured(), timeZone);
if (weatherObj.getLogIntervalId().equals(WeatherObservation.LOG_INTERVAL_ID_1H)) {
WeatherObservation altanariaWeatherBO_lw_hourly = weatherObj;
if (null != dateHourlyLw_currentDay
&& null != dateHourlyLw_previousDay
&& dateHourlyLw_currentDay.after(dateHourlyLw_previousDay)) {
int counterLwHourly = 0;
for (WeatherObservation wo : altenariaWeatherLIstHourly_lw) {
if (wo.getValue() >= THRESHOLD_LW) {
counterLwHourly = counterLwHourly + 1;
}
}
altenariaWeatherLIstHourly_lw.add(altanariaWeatherBO_lw_hourly);
dataMatrix.setParamIntValueForDate(
dateHourlyLw_previousDay, DataMatrix.LEAF_WETNESS_DURATION, counterLwHourly);
altenariaWeatherLIstHourly_lw = new ArrayList<WeatherObservation>();
}
break;
}
if(null != sprayingDates && sprayingDates.size() != 0)
{
for (Date spDate:sprayingDates)
{
spDate = trimmedDate(spDate, timeZone);
if(
(null != spDate && (null != dateHourlyTm_previousDay ) && (null != dateHourlyLw_previousDay))
&&
(
( spDate.compareTo(dateHourlyTm_previousDay)== 0 || spDate.before(dateHourlyTm_previousDay) )
|| ( spDate.compareTo(dateHourlyLw_previousDay)== 0 || spDate.before(dateHourlyLw_previousDay) )
)
)
{
sprayDate = trimmedDate(spDate, timeZone);
}
altenariaWeatherLIstHourly_lw.add(altanariaWeatherBO_lw_hourly);
}
break;
}
if (null != sprayingDates && sprayingDates.size() != 0) {
for (Date spDate : sprayingDates) {
spDate = trimmedDate(spDate, timeZone);
if ((null != spDate && (null != dateHourlyTm_previousDay) && (null != dateHourlyLw_previousDay))
&&
((spDate.compareTo(dateHourlyTm_previousDay) == 0
|| spDate.before(dateHourlyTm_previousDay))
|| (spDate.compareTo(dateHourlyLw_previousDay) == 0
|| spDate.before(dateHourlyLw_previousDay)))) {
sprayDate = trimmedDate(spDate, timeZone);
}
}
}
}
//Setting DSV values to dataMatrix
setDSV(dataMatrix
, dateHourlyTm_previousDay
, DataMatrix.TEMPERATURE_MEAN
, dateHourlyLw_previousDay
, DataMatrix.LEAF_WETNESS_DURATION
, sprayDate
);
// Setting DSV values to dataMatrix
setDSV(dataMatrix, dateHourlyTm_previousDay, DataMatrix.TEMPERATURE_MEAN, dateHourlyLw_previousDay,
DataMatrix.LEAF_WETNESS_DURATION, sprayDate);
dateHourlyTm_previousDay = dateHourlyTm_currentDay;
dateHourlyLw_previousDay = dateHourlyLw_currentDay;
}
//LOGGER.log(Level.INFO, dataMatrix.toString());
// LOGGER.log(Level.INFO, dataMatrix.toString());
}
/**
* method name : getDSV
* method name : getDSV
*
* @param temp
* @param lw
* @return
* purpose : DSV (Daily Severity Value) calculation based on mean temperature
* and Leaf Wetness
* @return
* purpose : DSV (Daily Severity Value) calculation based on mean
* temperature
* and Leaf Wetness
*/
public int getDSV_DAILY(double temp, int lw )
{
public int getDSV_DAILY(double temp, int lw) {
int dsvResult = 0;
if ((temp >= 10 && temp <= 17) && (lw <= 6)) dsvResult = 0;
if ((temp >= 10 && temp <= 17) && (lw >= 7 && lw <= 15 )) dsvResult = 1;
if ((temp >= 10 && temp <= 17) && (lw >= 16 && lw <= 20 )) dsvResult = 2;
if ((temp >= 10 && temp <= 17) && (lw > 21 )) dsvResult = 3;
if ((temp >= 18 && temp <= 20) && (lw <= 3 )) dsvResult = 0;
if ((temp >= 18 && temp <= 20) && (lw >= 4 && lw <= 8 )) dsvResult = 1;
if ((temp >= 18 && temp <= 20) && (lw >= 9 && lw <= 15)) dsvResult = 2;
if ((temp >= 18 && temp <= 20) && (lw >= 16 && lw <= 22)) dsvResult = 3;
if ((temp >= 18 && temp <= 20) && (lw >= 23)) dsvResult = 4;
if ((temp >= 21 && temp <= 25) && (lw <= 2 )) dsvResult = 0;
if ((temp >= 21 && temp <= 25) && (lw >= 3 && lw <= 5 )) dsvResult = 1;
if ((temp >= 21 && temp <= 25) && (lw >= 6 && lw <= 12)) dsvResult = 2;
if ((temp >= 21 && temp <= 25) && (lw >= 13 && lw <= 20)) dsvResult = 3;
if ((temp >= 21 && temp <= 25) && (lw >= 21)) dsvResult = 4;
if ((temp >= 26 && temp <= 29) && (lw <= 3)) dsvResult = 0;
if ((temp >= 26 && temp <= 29) && (lw >= 4 && lw <= 8)) dsvResult = 1;
if ((temp >= 26 && temp <= 29) && (lw >= 9 && lw <= 15)) dsvResult = 2;
if ((temp >= 26 && temp <= 29) && (lw >= 16 && lw <= 22)) dsvResult = 3;
if ((temp >= 26 && temp <= 29) && (lw >= 23 )) dsvResult = 4;
if ((temp >= this.THRESHOLD_DSV_TEMP_MIN && temp <= 17) && (lw <= 6))
dsvResult = 0;
if ((temp >= this.THRESHOLD_DSV_TEMP_MIN && temp <= 17) && (lw >= 7 && lw <= 15))
dsvResult = 1;
if ((temp >= this.THRESHOLD_DSV_TEMP_MIN && temp <= 17) && (lw >= 16 && lw <= 20))
dsvResult = 2;
if ((temp >= this.THRESHOLD_DSV_TEMP_MIN && temp <= 17) && (lw > 21))
dsvResult = 3;
if ((temp >= 18 && temp <= 20) && (lw <= 3))
dsvResult = 0;
if ((temp >= 18 && temp <= 20) && (lw >= 4 && lw <= 8))
dsvResult = 1;
if ((temp >= 18 && temp <= 20) && (lw >= 9 && lw <= 15))
dsvResult = 2;
if ((temp >= 18 && temp <= 20) && (lw >= 16 && lw <= 22))
dsvResult = 3;
if ((temp >= 18 && temp <= 20) && (lw >= 23))
dsvResult = 4;
if ((temp >= 21 && temp <= 25) && (lw <= 2))
dsvResult = 0;
if ((temp >= 21 && temp <= 25) && (lw >= 3 && lw <= 5))
dsvResult = 1;
if ((temp >= 21 && temp <= 25) && (lw >= 6 && lw <= 12))
dsvResult = 2;
if ((temp >= 21 && temp <= 25) && (lw >= 13 && lw <= 20))
dsvResult = 3;
if ((temp >= 21 && temp <= 25) && (lw >= 21))
dsvResult = 4;
if ((temp >= 26 && temp <= 29) && (lw <= 3))
dsvResult = 0;
if ((temp >= 26 && temp <= 29) && (lw >= 4 && lw <= 8))
dsvResult = 1;
if ((temp >= 26 && temp <= 29) && (lw >= 9 && lw <= 15))
dsvResult = 2;
if ((temp >= 26 && temp <= 29) && (lw >= 16 && lw <= 22))
dsvResult = 3;
if ((temp >= 26 && temp <= 29) && (lw >= 23))
dsvResult = 4;
return dsvResult;
}
/**
* Get a trimmed date without hour,minute,second,milli second
*
* @param date
* @return
* @return
*/
private Date trimmedDate(Date date, TimeZone timezone)
{
Date resultDate = date;
Calendar calendar = Calendar.getInstance();
private Date trimmedDate(Date date, TimeZone timezone) {
Date resultDate = date;
Calendar calendar = Calendar.getInstance();
calendar.setTimeZone(timezone);
calendar.setTime(resultDate);
calendar.set(Calendar.HOUR_OF_DAY, 0);
calendar.set(Calendar.MINUTE,0);
calendar.set(Calendar.SECOND,0);
calendar.set(Calendar.MILLISECOND,0);
return calendar.getTime();
calendar.set(Calendar.MINUTE, 0);
calendar.set(Calendar.SECOND, 0);
calendar.set(Calendar.MILLISECOND, 0);
return calendar.getTime();
}
/**
* Set DSV values to the DataMatrix in HashMap
*
* @param dataMatrix
* @param tmDate
* @param tmFlag
* @param lwDate
* @param lwFlag
* @param lwFlag
*/
private void setDSV(
DataMatrix dataMatrix, Date tmDate, String tmFlag, Date lwDate, String lwFlag, Date sprayDate)
{
int resultDSV_tm = 0;
int resultDSV_lw = 0;
if((null != tmDate) && (null != lwDate))
{
resultDSV_tm = getDSV_DAILY(
getMeanTeamperature(dataMatrix,tmDate,tmFlag)
,
getLeafWetnessHour(dataMatrix,tmDate,lwFlag)
);
dataMatrix.setParamStringValueForDate(tmDate, DataMatrix.SPRAYING_DATE, NO);
dataMatrix.setParamIntValueForDate(tmDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE, resultDSV_tm);
if(null != sprayDate )
{
if (tmDate.compareTo(sprayDate)== 0 || sprayDate.before(tmDate))
{
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, YES);
}
else if(null == sprayDate || sprayDate.after(tmDate))
{
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, NO);
}
}
resultDSV_lw = getDSV_DAILY(
getMeanTeamperature(dataMatrix,lwDate,tmFlag)
,
getLeafWetnessHour(dataMatrix,lwDate,lwFlag)
);
dataMatrix.setParamStringValueForDate(lwDate, DataMatrix.SPRAYING_DATE, NO);
dataMatrix.setParamIntValueForDate(lwDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE, resultDSV_lw);
if(null != sprayDate)
{
if ((lwDate.compareTo(sprayDate)== 0) || sprayDate.before(lwDate))
{
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, YES);
}
else if(null == sprayDate || sprayDate.after(lwDate))
{
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, NO);
}
}
DataMatrix dataMatrix, Date tmDate, String tmFlag, Date lwDate, String lwFlag, Date sprayDate) {
int resultDSV_tm = 0;
int resultDSV_lw = 0;
if ((null != tmDate) && (null != lwDate)) {
resultDSV_tm = getDSV_DAILY(
getMeanTeamperature(dataMatrix, tmDate, tmFlag),
getLeafWetnessHour(dataMatrix, tmDate, lwFlag));
dataMatrix.setParamStringValueForDate(tmDate, DataMatrix.SPRAYING_DATE, NO);
dataMatrix.setParamIntValueForDate(tmDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE, resultDSV_tm);
if (null != sprayDate) {
if (tmDate.compareTo(sprayDate) == 0 || sprayDate.before(tmDate)) {
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, YES);
} else if (null == sprayDate || sprayDate.after(tmDate)) {
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, NO);
}
}
resultDSV_lw = getDSV_DAILY(
getMeanTeamperature(dataMatrix, lwDate, tmFlag),
getLeafWetnessHour(dataMatrix, lwDate, lwFlag));
dataMatrix.setParamStringValueForDate(lwDate, DataMatrix.SPRAYING_DATE, NO);
dataMatrix.setParamIntValueForDate(lwDate, DataMatrix.DAILY_DISEASE_SEVERITY_VALUE, resultDSV_lw);
if (null != sprayDate) {
if ((lwDate.compareTo(sprayDate) == 0) || sprayDate.before(lwDate)) {
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, YES);
} else if (null == sprayDate || sprayDate.after(lwDate)) {
dataMatrix.setParamStringValueForDate(sprayDate, DataMatrix.SPRAYING_DATE, NO);
}
}
}
}
/**
*
* @param dataMatrix
* @param tmDate
* @param tmFlag
* @return
* @return
*/
private double getMeanTeamperature ( DataMatrix dataMatrix
, Date tmDate
, String tmFlag
)
{
return (null == dataMatrix.getParamDoubleValueForDate(tmDate, tmFlag))
? 0.0
: dataMatrix.getParamDoubleValueForDate(tmDate, tmFlag);
private double getMeanTeamperature(DataMatrix dataMatrix, Date tmDate, String tmFlag) {
return (null == dataMatrix.getParamDoubleValueForDate(tmDate, tmFlag))
? 0.0
: dataMatrix.getParamDoubleValueForDate(tmDate, tmFlag);
}
/**
*
* @param dataMatrix
* @param lwDate
* @param lwFlag
* @return
* @return
*/
private int getLeafWetnessHour(
DataMatrix dataMatrix
, Date lwDate
, String lwFlag
)
{
return (null == dataMatrix.getParamIntValueForDate(lwDate, lwFlag))
? 0
: dataMatrix.getParamIntValueForDate(lwDate, lwFlag);
private int getLeafWetnessHour(
DataMatrix dataMatrix, Date lwDate, String lwFlag) {
return (null == dataMatrix.getParamIntValueForDate(lwDate, lwFlag))
? 0
: dataMatrix.getParamIntValueForDate(lwDate, lwFlag);
}
private Integer getWarningStatus(Integer accumulatedDSV)
{
Integer result = 0;
/*
Hint of warning system
1 = Missing data (Blue) - OK
2 = No Risk (Green) – From 0 to DSV-threshold minus 5
private Integer getWarningStatus(Integer accumulatedDSV) {
Integer result = 0;
3 = Possible Risk (Yellow) – From DSV-threshold minus 5 to DSV-threshold
/*
* Hint of warning system
* 1 = Missing data (Blue) - OK
*
* 2 = No Risk (Green) – From 0 to DSV-threshold minus 5
*
* 3 = Possible Risk (Yellow) – From DSV-threshold minus 5 to DSV-threshold
*
* 4 = High Risk (Red) – {Above DSV-threshold
*/
4 = High Risk (Red) – {Above DSV-threshold
*/
if (accumulatedDSV >= 0)
{
if(accumulatedDSV >= THRESHOLD_DSV_MAX)
{
if (accumulatedDSV >= 0) {
if (accumulatedDSV >= THRESHOLD_DSV_MAX) {
result = Result.WARNING_STATUS_HIGH_RISK;
}
else
{
} else {
// e.g. 20 -- 30
if((accumulatedDSV < THRESHOLD_DSV_MAX) && (accumulatedDSV >= (THRESHOLD_DSV_MAX - THRESHOLD_DSV_DIFF_MIN_MAX)) )
{
if ((accumulatedDSV < THRESHOLD_DSV_MAX)
&& (accumulatedDSV >= (THRESHOLD_DSV_MAX - THRESHOLD_DSV_DIFF_MIN_MAX))) {
result = Result.WARNING_STATUS_MINOR_RISK;
}
else
{
if(accumulatedDSV < (THRESHOLD_DSV_MAX - THRESHOLD_DSV_DIFF_MIN_MAX))
{
} else {
if (accumulatedDSV < (THRESHOLD_DSV_MAX - THRESHOLD_DSV_DIFF_MIN_MAX)) {
result = Result.WARNING_STATUS_NO_RISK;
}
}
}
} else {
result = Result.WARNING_STATUS_NO_WARNING_MISSING_DATA;
}
else
{
result = Result.WARNING_STATUS_NO_WARNING_MISSING_DATA;
}
return result;
}
}
src/main/java/no/nibio/vips/model/alternariamodel/DataMatrix.java
View file @ 6dd8400a
......@@ -3,7 +3,7 @@
* Organization : NIBIO, Ås
* Department : VIPS
*
* Author : bhabesh
* Author : bhabesh & Tor-Einar Skog
*
*
* File Name : DataMatrix.java
......@@ -16,22 +16,23 @@
*/
/*
*
Copyright (c) 2016 NIBIO <http://www.nibio.no/>.
This file is part of AlternariaModel.
AlternariaModel is free software: you can redistribute it and/or modify
it under the terms of the NIBIO Open Source License as published by
NIBIO, either version 1 of the License, or (at your option) any
later version.
AlternariaModel is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
NIBIO Open Source License for more details.
You should have received a copy of the NIBIO Open Source License
along with AlternariaModel. If not, see <http://www.nibio.no/licenses/>.
*
* Copyright (c) 2020-2024 NIBIO <http://www.nibio.no/>.
*
* This file is part of AlternariaModel.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
......@@ -42,6 +43,7 @@ import no.nibio.vips.util.DateMap;
/**
*
* @author bhabesh
* @author Tor-Einar Skog <tor-einar.skog@nibio.no>
*/
public class DataMatrix extends DateMap{
public final static String WET_HOUR = "WH"; // Leaf wetness 2 m, minutes per hour
......@@ -53,8 +55,8 @@ public class DataMatrix extends DateMap{
public final static String SPRAYING_DATE = "sprayingDate"; // Spray Date
public final static String THRESHOLD_DSV_BASE = "THRESHOLD_DSV_BASE"; // THRESHOLD_DSV_BASE
public final static String THRESHOLD_DSV_MAX = "THRESHOLD_DSV_MAX"; // THRESHOLD_DSV_MAX
public final static String THRESHOLD_DSV_MAX = "thresholdDSVMax"; // THRESHOLD_DSV_MAX
public final static String THRESHOLD_DSV_TEMP_MIN = "thresholdDSVTempMin";
......
src/main/resources/LICENSE_header.txt 0 → 100644
View file @ 6dd8400a
Copyright (C) 2024 Tor-Einar Skog <tor-einar.skog@nibio.no>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
src/main/resources/no/nibio/vips/model/alternariamodel/texts.properties
View file @ 6dd8400a
......@@ -26,35 +26,3 @@ observations - list of weather data. The following parameters are required:\n\
* TM - Average temperature (Degrees Celcius)\n\
* BT - Leaf wetness (Minutes/hour) (IF you don't have leaf wetness, you must provide UM (relative humidity). Then we will calculate the leaf wetness.\n\
sprayingDate - (Optional) Farmers can choose multiple spraying dates (upto four spraying dates).
license= Copyright (c) 2020 NIBIO <http://www.nibio.no/>. \n \nThis file is part of AlternariaModel. \nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU Affero General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\nGNU Affero General Public License for more details.\n\nYou should have received a copy of the GNU Affero General Public License\nalong with this program. If not, see <https://www.gnu.org/licenses/>.
sampleconfig={ \n\
\t "loginInfo": { \n\
\t\t "username": "example", \n\
\t\t "password": "example" \n\
\t }, \n\
\t "modelId": "ALTERNARIA", \n\
\t "configParameters": { \n\
\t "timeZone": "Europe/Oslo", \n\
\t "observations": [ \n\
\t { \n\
\t\t "elementMeasurementTypeId": "TM", \n\
\t\t "logIntervalId": 1, \n\
\t\t "timeMeasured": "2018-08-11T00:00:00+02:00", \n\
\t\t "value": 10.46 \n\
\t }, \n\
\t { \n\
\t\t "elementMeasurementTypeId": "BT", \n\
\t\t "logIntervalId": 1, \n\
\t\t "timeMeasured": "2018-08-11T00:00:00+02:00", \n\
\t\t "value": 60.0 \n\
\t } \n\
\t ], \n\
\t "sprayingDates": [ \n\
\t\t "2018-07-02T22:00:00Z", \n\
\t\t "2018-07-30T22:00:00Z", \n\
\t\t "2018-09-04T22:00:00Z" \n\
\t ] \n\
\t } \n\
} \n\
src/main/resources/no/nibio/vips/model/alternariamodel/texts_nb.properties
View file @ 6dd8400a
......@@ -19,4 +19,3 @@ name=TOMCAST (FAST - Dew) modell for Alternaria
description= <p>{{filename="/images/ef-20200421-altenaria.jpg" description="Photo: Bilde: S. Abrahamsen, NLR"}}</p>\n<p>TOMCAST er basert p&aring; en modell utviklet for varsling av bladflekksjukdommer i tomat. Versjonen som blir brukt her er testet og tilpasset t&oslash;rrflekksjuke i potet (Alternaria solani) i Danmark. Modellen beregner daglige risikoverdier (DSV: Disease Severity Value) basert p&aring; temperatur og bladfuktighet siste d&oslash;gn. DSV representerer risikoen for angrep av t&oslash;rrflekksjuke siste d&oslash;gn. Daglige DSV-verdier blir summert frem til en terskel er n&aring;dd og behandling er anbefalt. Modellen er laget slik at akkumulering av DSV nullstilles n&aring;r spr&oslash;yting gjennomf&oslash;res, og akkumulering starter p&aring; nytt fra 0.</p>\n<p>Modellen er under utpr&oslash;ving i 2020, og vil bli testet b&aring;de i gulrot og i potet. Det vil kun v&aelig;re mulig &aring; starte private varler for denne modellen. Basert p&aring; erfaringer fra andre land er terskelverdien for r&oslash;dt varsel satt til 20.</p>\n<h3>Oppstart av varsel</h3>\n<p>Potetplanter varierer i mottakelighet for t&oslash;rrflekksjuke gjennom sesongen, og de blir gradvis mer og mer mottakelige. Dette betyr at behovet for beskyttelse ogs&aring; varierer tilsvarende. Modellen startes n&aring;r man ser de f&oslash;rste symptomene p&aring; t&oslash;rrflekksjuke og gjennomf&oslash;rer f&oslash;rste behandling (under 0,1% angrep).</p>\n<h3>Tolking av varsel</h3>\n<p>Modellen vil vise gr&oslash;nt (ingen fare) frem til den akkumulerte risikoverdien er 15. Fra denne verdien frem til terskelverdien (20) vil varselet v&aelig;re gult (mulig fare), og deretter g&aring; over til r&oslash;dt (fare).</p>
statusInterpretation=Modellen vil vise gr\u00f8nt (ingen fare) frem til den akkumulerte risikoverdien er 15. Fra denne verdien frem til terskelverdien (20) vil varselet v\u00e6re gult (mulig fare), og deretter g\u00e5 over til r\u00f8dt (fare).
usage=TODO
license=Copyright (c) 2020 NIBIO <http://www.nibio.no/>. \n \nThis file is part of AlternariaModel. \nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU Affero General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\nGNU Affero General Public License for more details.\n\nYou should have received a copy of the GNU Affero General Public License\nalong with this program. If not, see <https://www.gnu.org/licenses/>.
src/main/resources/sample_config.json 0 → 100644
View file @ 6dd8400a
{
"loginInfo": {
"username": "example",
"password": "example"
},
"modelId": "ALTERNARIA",
"configParameters": {
"sprayingDates": [
"2018-07-02T22:00:00Z",
"2018-07-30T22:00:00Z",
"2018-09-04T22:00:00Z"
],
"thresholdDSVTempMin": "10.0",
"thresholdDSVMax": "20.0",
"timeZone": "Europe/Oslo",
"observations": [
{
"elementMeasurementTypeId": "TM",
"logIntervalId": 1,
"timeMeasured": "2018-08-11T00:00:00+02:00",
"value": 10.46
},
{
"elementMeasurementTypeId": "BT",
"logIntervalId": 1,
"timeMeasured": "2018-08-11T00:00:00+02:00",
"value": 60
}
]
}
}
\ No newline at end of file
src/test/java/no/nibio/vips/model/alternariamodel/AlternariaModelTest.java
View file @ 6dd8400a
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
* Copyright (c) 2020 NIBIO <http://www.nibio.no/>.
This file is part of AlternariaModel.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package no.nibio.vips.model.alternariamodel;
......@@ -25,6 +37,7 @@ import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.BeforeAll;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.DynamicTest.stream;
/**
*
......@@ -104,6 +117,90 @@ public class AlternariaModelTest {
*/
}
@org.junit.jupiter.api.Test
public void testGetResultWithThresholdDSVTempMin() throws Exception {
System.out.println("getResultWithThresholdDSVTempMin");
ModelConfiguration config = this.getConfiguration(getWeatherDataFile());
config.setConfigParameter("sprayingDates", this.getConfigurationSprayingDates(getResetDataFile()));
config.setConfigParameter(DataMatrix.THRESHOLD_DSV_TEMP_MIN, 10.0);
AlternariaModel instance = new AlternariaModel();
instance.setConfiguration(config);
List<Result> result = instance.getResult();
assertNotNull(result);
config.setConfigParameter(DataMatrix.THRESHOLD_DSV_TEMP_MIN, "10.0");
instance.setConfiguration(config);
result = instance.getResult();
assertNotNull(result);
/*
for(Result res:result)
{
// LOGGER.log(Level.INFO, res.toString());
System.out.println(res.toString());
}*/
config.setConfigParameter(DataMatrix.THRESHOLD_DSV_TEMP_MIN, "13.0");
//System.out.println(config.toJSON());
instance.setConfiguration(config);
result = instance.getResult();
assertNotNull(result);
/*
for(Result res:result)
{
// LOGGER.log(Level.INFO, res.toString());
System.out.println(res.toString());
} */
}
@org.junit.jupiter.api.Test
public void testGetResultWithThresholdDSVMax() throws Exception {
System.out.println("getResultWithThresholdDSVMax");
ModelConfiguration config = this.getConfiguration(getWeatherDataFile());
config.setConfigParameter("sprayingDates", this.getConfigurationSprayingDates(getResetDataFile()));
config.setConfigParameter(DataMatrix.THRESHOLD_DSV_MAX, 21);
AlternariaModel instance = new AlternariaModel();
instance.setConfiguration(config);
List<Result> result = instance.getResult();
assertNotNull(result);
config.setConfigParameter(DataMatrix.THRESHOLD_DSV_MAX, "21");
instance.setConfiguration(config);
result = instance.getResult();
assertNotNull(result);
/*
for(Result res:result)
{
// LOGGER.log(Level.INFO, res.toString());
System.out.println(res.toString());
}*/
config.setConfigParameter(DataMatrix.THRESHOLD_DSV_MAX, "13.0");
//System.out.println(config.toJSON());
instance.setConfiguration(config);
result = instance.getResult();
assertNotNull(result);
/*
for(Result res:result)
{
// LOGGER.log(Level.INFO, res.toString());
System.out.println(res.toString());
} */
}
/**
......@@ -149,9 +246,8 @@ public class AlternariaModelTest {
public void testGetLicense() {
System.out.println("getLicense");
AlternariaModel instance = new AlternariaModel();
String expResult = "";
String result = instance.getLicense();
assertNotNull(result);
assertTrue(result.contains("GNU Affero"));
}
/**
......@@ -251,15 +347,13 @@ public class AlternariaModelTest {
/**
* Test of getSampleConfig method, of class AlternariaModel.
* TODO - Recheck the functionality
*/
@org.junit.jupiter.api.Test
public void testGetSampleConfig() {
System.out.println("getSampleConfig");
AlternariaModel instance = new AlternariaModel();
String expResult = "";
String result = instance.getSampleConfig();
assertNotNull(result);
assertTrue(result.contains("configParameters"));
}
/**
......