Commit 6178d9ae authored by Tor-Einar Skog's avatar Tor-Einar Skog
Browse files

Documentation updates

parent 76c3ffef
Model_GENPHENOLO
# Generic Phenology model
The model aims to be a generic model for phenology prediction of a number of species of plants and insects. It is based on the assumption that the development of the specimen is temperature driven. Its general nature requires the user to provide both weather data and the specific characteristics data for the species/variant at hand.
**© 2021** NIBIO, the Norwegian Institute of Bioeconomy Research
**Authors:** Bhabesh Bhabani Mukhopadyay and Tor-Einar Skog
Input data:
* Weather data
* Phenhology phases and their heat requirements
* Day degree calculation method
See a full example of input data for Fall Armyworm [here]("docs/input_data_example.md")
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......@@ -40,9 +40,8 @@ public class DataMatrix extends DateMap
public final static String PARAM_HEAT_REQUIREMENT = "HEATREQ";
public final static String PLANTATION_DATA = "plantationData";
public final static String PARAM_SOWINGDATE = "startDate";
public final static String PARAM_PLANTATION_DATA = "plantationData";
public final static String PARAM_BIOFIX = "startDate";
......
......@@ -273,6 +273,7 @@ public class PhenologyModel extends I18nImpl implements Model{
this.timeZone = TimeZone.getTimeZone((String) config.getConfigParameter("timeZone"));
Collections.sort(observations);
dateSowTrimmed = trimmedDate(wUtil.pragmaticAdjustmentToMidnight(plantationData.getStartDate(),timeZone),timeZone);
for(WeatherObservation weatherObj: observations)
{
......@@ -282,7 +283,7 @@ public class PhenologyModel extends I18nImpl implements Model{
Double HTT = 0.0; /* Hourly Tharmal Time */
Double TM = 0.0; /* Mean Temperature */
dateSowTrimmed = trimmedDate(wUtil.pragmaticAdjustmentToMidnight(plantationData.getStartDate(),timeZone),timeZone);
weatherObj.setTimeMeasured(wUtil.pragmaticAdjustmentToMidnight(woTime, timeZone));
......
......@@ -5,8 +5,6 @@
*/
package no.nibio.vips.model.phenology;
import no.nibio.vips.model.phenology.Plantation;
import no.nibio.vips.model.phenology.PhenologyModel;
import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.type.TypeReference;
......@@ -17,7 +15,6 @@ import java.io.BufferedInputStream;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.logging.Level;
......@@ -105,6 +102,7 @@ public class PhenologyModelTest {
config.setConfigParameter("plantationData", plantDBData);
PhenologyModel instance = new PhenologyModel();
//System.out.println(config.toJSON());
instance.setConfiguration(config);
List<Result> result = instance.getResult();
......@@ -367,7 +365,7 @@ public class PhenologyModelTest {
plant.setTypeName(all.get("typeName").asText());
plant.setSpeciesLatinName(all.get("speciesName").asText());
plant.setStartDate((Date)mapper.convertValue(all.get(DataMatrix.PARAM_SOWINGDATE).asText(), new TypeReference<Date>(){}));
plant.setStartDate((Date)mapper.convertValue(all.get(DataMatrix.PARAM_BIOFIX).asText(), new TypeReference<Date>(){}));
} catch (IOException ex) {
Logger.getLogger(PhenologyModelTest.class.getName()).log(Level.SEVERE, null, ex);
......
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