Merge remote-tracking branch 'origin/27.04.26-2' into 27.04.26-2

src/ecoparasite/Application.java

@@ -6,86 +6,48 @@ import ecoparasite.input.InputFileException;
 import ecoparasite.input.RawData;
 import ecoparasite.input.RawDataOverflow;
 import ecoparasite.nettoyage.Nettoyage;
-import ecoparasite.poisson.Mackerel;
 import ecoparasite.poisson.MackerelSerra;
-import ecoparasite.poisson.Merlu;
 import ecoparasite.poisson.Poisson;
-import ecoparasite.population.Population;
-import ecoparasite.population.PopulationArgInterval;
-import ecoparasite.population.PopulationParsing;
 import ecoparasite.representation.ValeursXY;
 import ecoparasite.svg.IncorrectAxesPointsException;
 import ecoparasite.svg.SVGBuilder;
 import ecoparasite.svg.SVGFactory;
 import ecoparasite.svg.elements.Element;
 
-import java.io.File;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.function.BiConsumer;
 import java.util.function.Function;
 
 public class Application {
 
-    static final String[] VALID_FILES = {"Campagne/mackerel.97442.csv", "Campagne/merlu2018_75164.csv","Combinés/ParasitesPeru2021.csv"};
+    public static void main(String[] args) throws InputFileException, RawDataOverflow {
 
-    public static void validFileName(File dir, HashSet<String> listeName){
+        RawData rawMackerel = InputFactory.readData("test2.csv", ",");
 
-        File[] liste = dir.listFiles();
-
-        for (File item : liste) {
-            if (!item.isDirectory()){
-                listeName.add(item.getName());
-            } else {
-                validFileName(new File(dir.getName()+ "/" + item.getName()), listeName);
-            }
-        }
-
-    }
-
-    public static String validFile(){
-
-        Scanner sc = new Scanner(System.in);
-        String name = "";
-        boolean isValid = false;
-
-        /*
-        File dir = new File("data");
-
-        HashSet<String> listeName = new HashSet<>();
-
-        Application.validFileName(dir,listeName);
-        */
-
-        while (!isValid) {
-            System.out.println("Veuillez rentrez le nom du fichier :");
-            name = sc.nextLine();
-
-            for (int i = 0; i < 3; i++) {
-                if (name.contains(VALID_FILES[i])){
-                    isValid = true;
-                    break;
-                }
-            }
-        }
-
-        return name;
-    }
-
-    public static void MackerelFile(String name) throws InputFileException, RawDataOverflow {
-
-        RawData rawMackerel = InputFactory.readData(name);
-
-        HashSet<Poisson> mackerelSet = Mackerel.parse(rawMackerel);
+        HashSet<Poisson> mackerelSet = MackerelSerra.parse(rawMackerel);
 
+        System.out.println( "Avant nettoyage et complétion" );
         System.out.println( mackerelSet );
 
         Function<Poisson,Double> getLength = Poisson::getLength;
         Function<Poisson,Double> getInfes = Poisson::getInfestation;
         BiConsumer<Poisson,Double> setInfes = Poisson::setInfestation;
 
+        mackerelSet = Nettoyage.nettoieColumns( mackerelSet, Poisson::getLength, Poisson::setLength, false );
+        mackerelSet = Completion.completeColumnsMoyenne( mackerelSet, Poisson::getLength, Poisson::setLength );
+
+        System.out.println( "Après Nettoyage et complétion de la longueur du poisson." );
+        System.out.println( mackerelSet );
+
         mackerelSet = Nettoyage.nettoieColumns( mackerelSet, getInfes, setInfes, false );
         mackerelSet = Completion.completeColumnsLinear( mackerelSet, getLength, getInfes, setInfes );
 
+        System.out.println( "Après Nettoyage et complétion du taux d'infestation des poissons" );
+        System.out.println( mackerelSet );
+
+        // Conversion des valeurs.
         HashSet<ValeursXY> mackerelXY = ValeursXY.convertToXY( mackerelSet, getLength, getInfes );
         HashMap<String, ArrayList<Double>> axes = SVGBuilder.calcPointAxes( mackerelXY );
         System.out.println( axes );
@@ -101,122 +63,8 @@ public class Application {
         // Sauvegarde pour plus tard.
         double[] ABCoef = Completion.getLinearCoef(mackerelSet, getLength, getInfes);
 
-        ArrayList<Element> SVGElements = axesInstance.buildAll( "Length", "Infestation", mackerelXY, ABCoef[0], ABCoef[1] );
+        ArrayList<Element> SVGElements = axesInstance.buildAll( "Length (mm)", "Taux d'infestation", mackerelXY, ABCoef[0], ABCoef[1] );
         SVGFactory.createSVG( SVGElements );
-    }
-
-    public static void MerluFile(String name) throws InputFileException, RawDataOverflow {
-
-        RawData rawMerlu = InputFactory.readData(name);
-
-        HashSet<Poisson> merluSet = Merlu.parse(rawMerlu);
-
-        System.out.println( merluSet );
-
-        Function<Poisson,Double> getLength = Poisson::getLength;
-        Function<Poisson,Double> getInfes = Poisson::getInfestation;
-        BiConsumer<Poisson,Double> setInfes = Poisson::setInfestation;
-
-        merluSet = Nettoyage.nettoieColumns( merluSet, getInfes, setInfes, false );
-        merluSet = Completion.completeColumnsLinear( merluSet, getLength, getInfes, setInfes );
-
-        HashSet<ValeursXY> merluXY = ValeursXY.convertToXY( merluSet, getLength, getInfes );
-        HashMap<String, ArrayList<Double>> axes = SVGBuilder.calcPointAxes( merluXY );
-        System.out.println( axes );
-
-        SVGBuilder axesInstance;
-        try {
-            axesInstance = new SVGBuilder(axes);
-        } catch (IncorrectAxesPointsException e) {
-            System.out.println( "Mauvais format communiqué" );
-            return;
-        }
-
-        // Sauvegarde pour plus tard.
-        double[] ABCoef = Completion.getLinearCoef(merluSet, getLength, getInfes);
-
-        ArrayList<Element> SVGElements = axesInstance.buildAll( "Length", "Infestation", merluXY, ABCoef[0], ABCoef[1] );
-        SVGFactory.createSVG( SVGElements );
-    }
-
-    public static void PopPeru(String name) throws InputFileException,RawDataOverflow{
-
-        RawData popRaw; int index;
-        try {
-            popRaw = InputFactory.readData(name , "," );
-        } catch(InputFileException e) {
-            System.out.println(e.getMessage());
-            return;
-        }
-
-        HashSet<Population> popSet = PopulationParsing.parseParasitesPeru(popRaw);
-
-        index = 1;
-        for( Population p: popSet){
-            System.out.println(String.valueOf(index++) + p);
-        }
-
-        // Nettoyage de la taille.
-        Function<Population,Double> getLength = population -> {
-            return population.getTotal().getLength() != null ? population.getTotal().getLength().transformToDouble() : null;
-        };
-        BiConsumer<Population,Double> setLength = (population, aDouble) -> {
-            population.getTotal().setLength(aDouble != null ? new PopulationArgInterval(aDouble,aDouble) : null);
-        };
-
-        Function<Population,Double> getInfes = population -> {
-            return population.getTotal().getAbondance() != null ? population.getTotal().getPrevalence().transformToDouble() : null;
-        };
-
-        popSet = Nettoyage.nettoieColumns(popSet, getLength, setLength, false);
-        System.out.println("---");
-        index = 1;
-        for( Population p: popSet){
-            System.out.println(String.valueOf(index++) + p);
-        }
-
-        // Complétion de la masse.
-        popSet = Completion.completeColumnsMoyenne(popSet, getLength, setLength);
-        System.out.println("---");
-        for( Population p: popSet){
-            System.out.println(String.valueOf(index++) + p);
-        }
-
-        HashSet<ValeursXY> popXY = ValeursXY.convertToXY( popSet, getLength, getInfes );
-        HashMap<String, ArrayList<Double>> axes = SVGBuilder.calcPointAxes( popXY );
-        System.out.println( axes );
-
-        SVGBuilder axesInstance;
-        try {
-            axesInstance = new SVGBuilder(axes);
-        } catch (IncorrectAxesPointsException e) {
-            System.out.println( "Mauvais format communiqué" );
-            return;
-        }
-
-
-        ArrayList<Element> elements = new ArrayList<>();
-
-        elements.addAll(axesInstance.buildAxes("Taille en mm", "Abondance"));
-        elements.addAll(axesInstance.buildXTicks());
-        elements.addAll(axesInstance.buildYTicks());
-        elements.addAll(axesInstance.buildPoints(popXY));
-
-        SVGFactory.createSVG(elements);
-    }
-
-    public static void main(String[] args) throws InputFileException, RawDataOverflow {
-
-        String nameFile = Application.validFile();
-
-        if (nameFile.contains("mackerel")) {
-            MackerelFile(nameFile);
-        } else if (nameFile.contains("merlu")){
-            MerluFile(nameFile);
-        } else if (nameFile.contains("Peru")) {
-            PopPeru(nameFile);
-        }
-
 
     }
 }

src/ecoparasite/svg/SVGBuilder.java

@@ -98,17 +98,17 @@ public class SVGBuilder {
         Coordonnees right = getResizer().resize( maxPointsX, beginAxeY );
 
         // Axes
-        elements.add( new Line( bottom, top, ElementsFactory.COLOR_BLACK, 2 ) );
-        elements.add( new Line( left, right, ElementsFactory.COLOR_BLACK, 2 ) );
+        elements.add( new Line( bottom, top, ElementsFactory.COLOR_WHITE, 2 ) );
+        elements.add( new Line( left, right, ElementsFactory.COLOR_WHITE, 2 ) );
 
         // Labels.
         elements.add( new Text(
            new Coordonnees( right.getX() + OFFSET_TEXT_AXISX_X, right.getY() + OFFSET_TEXT_AXISX_Y ),
-           XLabel, ElementsFactory.COLOR_BLACK, ElementsFactory.AXES_TEXT_SIZE
+           XLabel, ElementsFactory.COLOR_WHITE, ElementsFactory.AXES_TEXT_SIZE
         ) );
         elements.add( new Text(
                 new Coordonnees( top.getX() + OFFSET_TEXT_AXISY_X, top.getY() + OFFSET_TEXT_AXISY_Y ),
-                YLabel, ElementsFactory.COLOR_BLACK, ElementsFactory.AXES_TEXT_SIZE
+                YLabel, ElementsFactory.COLOR_WHITE, ElementsFactory.AXES_TEXT_SIZE
         ));
 
         return elements;
@@ -130,12 +130,12 @@ public class SVGBuilder {
             elements.add(new Line(
                     coords,
                     new Coordonnees( coords.getX(), coords.getY() + OFFSET_TICK ),
-                    ElementsFactory.COLOR_BLACK, 1
+                    ElementsFactory.COLOR_WHITE, 1
             ));
             elements.add(new Text(
                new Coordonnees( coords.getX() + OFFSET_TEXT_X, coords.getY() + OFFSET_TEXT_Y ),
                 X.toString(),
-                ElementsFactory.COLOR_BLACK,
+                ElementsFactory.COLOR_WHITE,
                 SIZE_TICK_TEXT
             ));
         }
@@ -158,12 +158,12 @@ public class SVGBuilder {
             elements.add(new Line(
                     new Coordonnees(coords.getX() + OFFSET_TICK, coords.getY() ),
                     coords,
-                    ElementsFactory.COLOR_BLACK, 1
+                    ElementsFactory.COLOR_WHITE, 1
             ));
             elements.add(new Text(
                     new Coordonnees( coords.getX() + OFFSET_TEXT_X, coords.getY() + OFFSET_TEXT_Y ),
                     Y.toString(),
-                    ElementsFactory.COLOR_BLACK,
+                    ElementsFactory.COLOR_WHITE,
                     SIZE_TICK_TEXT
             ));
         }

src/ecoparasite/svg/elements/ElementsFactory.java

@@ -12,6 +12,7 @@ public class ElementsFactory {
 
     final public static int AXES_TEXT_SIZE = 10;
 
+    final public static String COLOR_WHITE = "white";
     final public static String COLOR_RED = "red";
     final public static String COLOR_BLUE = "blue";
     final public static String COLOR_BLACK = "black";