Initial commit

.gitignore

+target/
+nbproject/
+classes/

README.md

+Model_MAIZEPHENO

doc/readme.txt

+Tag-V3 : Separation logic based on algorithmId

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<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.nibio.vips.model</groupId>
+    <artifactId>Model_PHYNOLOGYM</artifactId>
+    <version>1.0-SNAPSHOT</version>
+    <packaging>jar</packaging>
+    <dependencies>
+        <dependency>
+            <groupId>no.nibio.vips.common</groupId>
+            <artifactId>VIPSCommon</artifactId>
+            <version>1.0-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.3.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-params</artifactId>
+            <version>5.3.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.3.1</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+    <name>Model_PHYNOLOGYM</name>
+</project>
\ No newline at end of file

src/main/java/no/nibio/vips/model/phenology/DataMatrix.java

+/*
+ * 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.
+ */
+package no.nibio.vips.model.phenology;
+
+import no.nibio.vips.util.DateMap;
+
+/**
+ *
+ * @author wildfly
+ */
+public class DataMatrix extends DateMap
+{
+     public final static String  TEMPERATURE_MEAN              =   "TM";           //  Mean Temperature
+     public final static String  TEMPERATURE_MAX               =   "TX";           //  Max Temperature
+     public final static String  TEMPERATURE_MIN               =   "TN";           //  Min Temperature
+     public final static String  TEMPERATURE_DAILY_TIME        =   "DTT";          //  Daily Temperature Time
+     
+     public final static String  TEMP_NON_NEGATIVE              =   "NON_NEG";
+     public final static Double  BASE_TEMP_VALUE                =   10.0;
+     
+     public final static String  PARAM_PHENOLOGYM_VARIETY       =   "VARIETY";
+     public final static String  PARAM_PHENOLOGYM_PHASE         =   "PHASE";
+     public final static String  PARAM_HEAT_SUM                 =   "HEATSUM";
+     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";
+
+     
+     
+     
+     
+     
+     
+}

src/main/java/no/nibio/vips/model/phenology/PhenologyModelStore.java

+/*
+ * 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.
+ */
+package no.nibio.vips.model.phenology;
+
+/**
+ *
+ * @author wildfly
+ */
+public class PhenologyModelStore {
+    
+    private PhenologyModelStore(){ }
+    private static PhenologyModelStore instance = null;
+    
+    private static void activateStore()
+    {
+        
+    }
+    
+    public Double dayDegreeModel(Double tm_daily, Double heatSum, Double baseTempValue)
+    {
+            Double              tm_nonNegative      =   getNonNegative(tm_daily, baseTempValue); //tm_nonNegative + ((tm_calculate < 0)? 0 : tm_calculate);
+                                heatSum             =   heatSum + tm_nonNegative;
+            return heatSum;                    
+    }
+    
+    
+    
+    public Double hourlyMeanWithBaseMaxAndOptTemp(Double tm, Double tb, Double tOpt, Double tu)
+    {
+        Double f1, f2, f3, f4   =   0.0;
+        Double p1, p2, p3, p4   =   0.0;
+        Double htt              =   0.0;
+        
+        f1 =    tm   -  tb;
+        f2 =    tOpt - tb;
+        f3 =    tu  - tm;
+        f4 =    tu  - tOpt;
+        
+        p1  =   f1 / f2;
+        p2  =   f3 / f4;
+        p3  =   f4/ f2;
+        p4  =   Math.pow(p2, p3);
+        
+        htt = (tm < tb)? 0.0 : (tm<tb)? 0.0 : (p1 * f2 * p4 );
+        
+        return htt;
+        
+    }
+    
+    
+        /**
+     * 
+     * @param tm_daily
+     * @return 
+     */
+    public Double getNonNegative(Double tm_daily, Double baseTempValue){
+            Double              tm_calculate        =   0.0;
+            Double              tm_nonNegative      =   0.0;
+                                tm_calculate        =   tm_daily - baseTempValue;
+                                tm_nonNegative      =   tm_nonNegative + ((tm_calculate < 0)? 0 : tm_calculate);
+        
+        return tm_nonNegative;
+    }
+    
+    public static PhenologyModelStore getInstance()
+    {
+        if(instance == null)
+        {
+            instance    =   new PhenologyModelStore();
+            
+        }
+        
+        return instance;
+    }
+}

src/main/java/no/nibio/vips/model/phenology/Plant.java

+/*
+ * 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.
+ */
+package no.nibio.vips.model.phenology;
+
+import java.util.Date;
+import java.util.List;
+
+/**
+ *
+ * @author wildfly
+ */
+public class Plant {
+   private String              speciesLatinName;
+    private String              typeName;
+    private Double              baseTemp;
+    private Double              optTemp;                                        /* Optimum temperature */
+    private Double              upperTemp;                                      /* Upper temperature */    
+    private Integer             logIntervalId;
+    private Integer             algorithmId;
+    private Date                startDate;
+    private String[]            weatherParams;
+    
+    private List<Plantation>    plantations;
+
+    public String getSpeciesLatinName() {
+        return speciesLatinName;
+    }
+
+    public void setSpeciesLatinName(String speciesLatinName) {
+        this.speciesLatinName = speciesLatinName;
+    }
+
+    public String getTypeName() {
+        return typeName;
+    }
+
+    public void setTypeName(String typeName) {
+        this.typeName = typeName;
+    }
+
+    public Double getBaseTemp() {
+        return baseTemp;
+    }
+
+    public void setBaseTemp(Double baseTemp) {
+        this.baseTemp = baseTemp;
+    }
+
+    public Double getOptTemp() {
+        return optTemp;
+    }
+
+    public void setOptTemp(Double optTemp) {
+        this.optTemp = optTemp;
+    }
+
+    public Double getUpperTemp() {
+        return upperTemp;
+    }
+
+    public void setUpperTemp(Double upperTemp) {
+        this.upperTemp = upperTemp;
+    }
+
+    public Integer getLogIntervalId() {
+        return logIntervalId;
+    }
+
+    public void setLogIntervalId(Integer logIntervalId) {
+        this.logIntervalId = logIntervalId;
+    }
+
+    public Integer getAlgorithmId() {
+        return algorithmId;
+    }
+
+    public void setAlgorithmId(Integer algorithmId) {
+        this.algorithmId = algorithmId;
+    }
+
+    public Date getStartDate() {
+        return startDate;
+    }
+
+    public void setStartDate(Date startDate) {
+        this.startDate = startDate;
+    }
+
+    public List<Plantation> getPlantations() {
+        return plantations;
+    }
+
+    public void setPlantations(List<Plantation> plantations) {
+        this.plantations = plantations;
+    }
+
+    public String[] getWeatherParams() {
+        return weatherParams;
+    }
+
+    public void setWeatherParams(String[] weatherParams) {
+        this.weatherParams = weatherParams;
+    }
+
+    @Override
+    public String toString() {
+        return "Plant{" + "speciesLatinName=" + speciesLatinName + ", typeName=" + typeName + ", baseTemp=" + baseTemp + ", optTemp=" + optTemp + ", upperTemp=" + upperTemp + ", logIntervalId=" + logIntervalId + ", algorithmId=" + algorithmId + ", startDate=" + startDate + ", weatherParams=" + weatherParams + ", plantations=" + plantations + '}';
+    }
+
+
+        
+}

src/main/java/no/nibio/vips/model/phenology/Plantation.java

+/*
+ * 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.
+ */
+package no.nibio.vips.model.phenology;
+
+import java.util.Date;
+
+/**
+ *
+ * @author wildfly
+ */
+public class Plantation {
+    private String  typeName;
+    private String  phaseName;
+    private Double  heatReq;
+
+    public Plantation() {
+    }
+
+    public Plantation(String typeName, String phaseName, Double heatReq) {
+        this.typeName = typeName;
+        this.phaseName = phaseName;
+        this.heatReq = heatReq;
+        } 
+    
+      public Plantation(String phaseName, Double heatReq) {
+        this.phaseName = phaseName;
+        this.heatReq = heatReq;
+        }  
+    
+    public String getTypeName() {
+        return typeName;
+    }
+
+    public void setTypeName(String typeName) {
+        this.typeName = typeName;
+    }
+
+    public String getPhaseName() {
+        return phaseName;
+    }
+
+    public void setPhaseName(String phaseName) {
+        this.phaseName = phaseName;
+    }
+
+    public Double getHeatReq() {
+        return heatReq;
+    }
+
+    public void setHeatReq(Double heatReq) {
+        this.heatReq = heatReq;
+    }
+
+    @Override
+    public String toString() {
+        return "Plantation{" + "typeName=" + typeName + ", phaseName=" + phaseName + ", heatReq=" + heatReq + '}';
+    }
+
+}

src/main/resources/dataset/plantationData.json

+{
+   "species":
+            [
+                {
+                    "speciesLatinName"          : "Zea mays",
+                    "baseTemp"                  : "10",
+                    "weatherLogIntervalId"      : "2",
+                    "weatherParameters"         : ["TN","TX","TM"],
+                    "dayDegreeAlgorithmId"      : "1",
+                    "typeNames"                 :
+                                                [
+                                                    {
+                                                        "typeName"          : "TESTVARIETY 2",
+                                                        "baseTemp"          : "10",
+                                                        "weatherLogIntervalId"      : "2",
+                                                        "weatherParameters" : ["TN","TX","TM"],
+                                                        "dayDegreeAlgorithmId"      :"1",
+                                                        "phaseInfo"     :
+                                                                        [
+                                                                            {
+                                                                                "phaseName": "VE",
+                                                                                "heatReq"  : "66.67"
+                                                                            },
+                                                                            {
+                                                                                "phaseName": "V2",
+                                                                                 "heatReq"  : "111.11"
+                                                                            },
+                                                                            {
+                                                                                "phaseName": "V3",
+                                                                                "heatReq"  : "194.44"
+                                                                            },
+                                                                            {
+                                                                                "phaseName": "V4-V6",
+                                                                                "heatReq"  : "263.89"
+                                                                            }, 
+                                                                            {
+                                                                                "phaseName": "V7-V9",
+                                                                                "heatReq"  : "338.89"
+                                                                            }, 
+                                                                            {
+                                                                                "phaseName": "V10",
+                                                                                "heatReq"  : "411.11"
+                                                                            }, 
+                                                                            {
+                                                                                "phaseName": "VT",
+                                                                                "heatReq"  : "630.55"
+                                                                            }, 
+                                                                            {
+                                                                                "phaseName": "R2",
+                                                                                "heatReq"  : "922.22"
+                                                                            }, 
+                                                                            {
+                                                                                "phaseName": "R5",
+                                                                                "heatReq"  : "1361.11"
+                                                                            }, 
+                                                                            {
+                                                                                "phaseName": "R6",
+                                                                                "heatReq"  : "1500"
+                                                                            }
+
+                                                                        ]
+                                                    }
+                                                ]
+                }
+            ]
+
+}
\ No newline at end of file

src/main/resources/no/nibio/vips/model/phenology/texts.properties

+name=Fall Army Worm - Phenology Model
+license= Copyright (c) 2020 NIBIO <http://www.nibio.no/>. \
+\
+This file is part of Altenaria Model. \
+ Altenaria Model 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. \
+\
+MamestraBrassicaeModel 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 Altenaria Model.  If not, see <http://www.nibio.no/licenses/>.
+
+statusInterpretation=TODO
+
+usage=Description of required input parameters:\n\
+timeZone - What timezone the calculation is for. Necessary to calculate daily values from the provided hourly values. \
+See this list of time zones: http://en.wikipedia.org/wiki/List_of_tz_database_time_zones (Column "TZ")\n\
+observations - list of weather data. The following parameters are required:\n\
+* TM - Average temperature (Degrees Celcius)
+
+sampleconfig=TODO
+description=TODO

src/main/resources/no/nibio/vips/model/phenology/texts_nb.properties

+name=Fall Army Worm - Phenology Model
+license= Copyright (c) 2020 NIBIO <http://www.nibio.no/>. \
+\
+This file is part of Altenaria Model. \
+ Altenaria Model 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. \
+\
+MamestraBrassicaeModel 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 Altenaria Model.  If not, see <http://www.nibio.no/licenses/>.
+
+statusInterpretation=TODO
+
+usage=Description of required input parameters:\n\
+timeZone - What timezone the calculation is for. Necessary to calculate daily values from the provided hourly values. \
+See this list of time zones: http://en.wikipedia.org/wiki/List_of_tz_database_time_zones (Column "TZ")\n\
+observations - list of weather data. The following parameters are required:\n\
+* TM - Average temperature (Degrees Celcius)
+
+sampleconfig=TODO
+description=TODO
\ No newline at end of file

src/test/resources/dataset01/plantationData_01.json

+[
+    {
+        "maizeVarity"        : "COMMON",
+        "phaseName": "V2",
+        "baseTemp" : "B101",
+        "heatReq"  : "200"
+    },
+    {
+        "maizeVarity"       : "COMMON",
+        "phaseName": "V6",
+        "baseTemp" : "B101",
+        "heatReq"  : "475"
+    },
+     {
+        "maizeVarity"       : "COMMON",
+        "phaseName": "V12",
+        "baseTemp" : "B101",
+        "heatReq"  : "870"
+    },
+     {
+        "maizeVarity"       : "COMMON",
+        "phaseName": "VT",
+        "baseTemp" : "B101",
+        "heatReq"  : "1135"
+    }, 
+    {
+        "maizeVarity"       : "COMMON",
+        "phaseName": "R1",
+        "baseTemp" : "B101",
+        "heatReq"  : "1400"
+    }, 
+    {
+        "maizeVarity" : "COMMON",
+        "phaseName": "R6",
+        "baseTemp" : "B201",
+        "heatReq"  : "2700"
+    }
+ 
+]

src/test/resources/dataset01/plantationData_02.json

+{
+    "speciesLatinName"        : "Zea mays",
+    "typeName"                : "TESTVARIETY 2",
+    "baseTemp"                : "10",
+    "phaseInfo":
+[
+    {
+        "phaseName": "VE",
+        "heatReq"  : "66.67"
+    },
+    {
+        "phaseName": "V2",
+         "heatReq"  : "111.11"
+    },
+     {
+        "phaseName": "V3",
+        "heatReq"  : "194.44"
+    },
+     {
+        "phaseName": "V4-V6",
+        "heatReq"  : "263.89"
+    }, 
+    {
+        "phaseName": "V7-V9",
+        "heatReq"  : "338.89"
+    }, 
+    {
+        "phaseName": "V10",
+        "heatReq"  : "411.11"
+    }, 
+    {
+        "phaseName": "VT",
+        "heatReq"  : "630.55"
+    }, 
+    {
+        "phaseName": "R2",
+        "heatReq"  : "922.22"
+    }, 
+    {
+        "phaseName": "R5",
+        "heatReq"  : "1361.11"
+    }, 
+    {
+        "phaseName": "R6",
+        "heatReq"  : "1500"
+    }
+ 
+]
+}
\ No newline at end of file

src/test/resources/dataset01/plantationData_03.json

+{
+   "species":
+            [
+                {
+                    "speciesLatinName"          : "Zea mays",
+                    "baseTemp"                  : "10",
+                    "weatherLogIntervalId"      : "2",
+                    "weatherParameters"         : ["TN","TX","TM"],
+                    "dayDegreeAlgorithmId"      : "1",
+                    "typeNames"                 :
+                                                [
+                                                    {
+                                                        "typeName"          : "TESTVARIETY 2",
+                                                        "baseTemp"          : "10",
+                                                        "weatherLogIntervalId"      : "2",
+                                                        "weatherParameters" : ["TN","TX","TM"],
+                                                        "dayDegreeAlgorithmId"      :"1",
+                                                        "phaseInfo"     :
+                                                                        [