.gitignore

@@ -51,6 +51,7 @@ cmake-build-*/
 
 # IntelliJ
 out/
+.idea
 
 # mpeltonen/sbt-idea plugin
 .idea_modules/

.gitlab-ci.yml

-image: gradle:jdk16
+image: openjdk:17-alpine
+
+variables:
+  GRADLE_OPTS: "-Dorg.gradle.daemon=false"
 
 before_script:
   - export GRADLE_USER_HOME=`pwd`/.gradle
@@ -8,11 +11,30 @@ cache:
     - .gradle/wrapper
     - .gradle/caches
 
+stages:
+  - build
+  - test
+
+build:
+  stage: build
+  script: ./gradlew --build-cache assemble
+  cache:
+    key: "$CI_COMMIT_REF_NAME"
+    policy: push
+    paths:
+      - build
+      - .gradle
+
 java:
   stage: test
-  script:
-    - gradle test
+  script: ./gradlew test
   artifacts:
     when: always
     reports:
       junit: build/test-results/test/**/TEST-*.xml
+  cache:
+    key: "$CI_COMMIT_REF_NAME"
+    policy: pull
+    paths:
+      - build
+      - .gradle
\ No newline at end of file

README.md

@@ -4,7 +4,6 @@
 
 Ce projet est l'occasion de travailler sur la représentation et la manipulation d'images. Ces images seront constituées de pixels caractérisés par une couleur représentant un niveau de gris.
 
-## Membres du projet
+## Membre du projet
 
-- NOM, prénom, numéro de groupe, du premier participant
-- NOM, prénom, numéro de groupe, du deuxième participant
+- NOM, prénom

build.gradle

 plugins {
+    id 'java'
     id 'application'
-    id "org.openjfx.javafxplugin" version "0.0.10"
+    id "org.openjfx.javafxplugin" version "0.0.14"
 }
 
+group 'M2_BIO_INFO'
+version '1.0-SNAPSHOT'
+
 javafx {
-    version = "17"
+    version = "20"
     modules = [ 'javafx.controls', 'javafx.fxml' ]
 }
 
@@ -12,16 +16,21 @@ repositories {
     mavenCentral()
 }
 
-dependencies {
-    testImplementation('org.junit.jupiter:junit-jupiter-api:5.7.2',
-            'org.hamcrest:hamcrest-library:2.2', 'net.obvj:junit-utils:1.3.1')
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.7.2'
-}
-
 test {
     useJUnitPlatform()
 }
 
+dependencies {
+    testRuntimeOnly("org.junit.platform:junit-platform-launcher") {
+        because("Only needed to run tests in a version of IntelliJ IDEA that bundles older versions")
+    }
+    testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine")
+    testImplementation("org.assertj:assertj-core:3.24.2")
+    testImplementation("org.junit.jupiter:junit-jupiter:5.10.0")
+}
+
+
+
 application {
-    mainClassName = "Main"
+    mainClass.set("Main")
 }

gradle/wrapper/gradle-wrapper.properties

 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

-#!/usr/bin/env sh
+#!/bin/sh
 
 #
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,67 +17,101 @@
 #
 
 ##############################################################################
-##
-##  Gradle start up script for UN*X
-##
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # Attempt to set APP_HOME
+
 # Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
 
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+DEFAULT_JVM_OPTS='-Dfile.encoding=UTF-8 "-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "`uname`" in
-  CYGWIN* )
-    cygwin=true
-    ;;
-  Darwin* )
-    darwin=true
-    ;;
-  MSYS* | MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
@@ -87,9 +121,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -98,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
+    JAVACMD=java
     which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
@@ -106,80 +140,105 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
-    if [ $? -eq 0 ] ; then
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
-            MAX_FD="$MAX_FD_LIMIT"
-        fi
-        ulimit -n $MAX_FD
-        if [ $? -ne 0 ] ; then
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
-        fi
-    else
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
-    fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
 fi
 
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
 
 # For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
-    # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
 
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
         fi
-        i=`expr $i + 1`
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
     done
-    case $i in
-        0) set -- ;;
-        1) set -- "$args0" ;;
-        2) set -- "$args0" "$args1" ;;
-        3) set -- "$args0" "$args1" "$args2" ;;
-        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
-    esac
 fi
 
-# Escape application args
-save () {
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
-    echo " "
-}
-APP_ARGS=`save "$@"`
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
 
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
 
 exec "$JAVACMD" "$@"

src/main/java/ByteGrayColor.java

@@ -10,6 +10,8 @@ public class ByteGrayColor implements GrayColor {
     private static final int MAXIMUM_GRAY_LEVEL = 255;
     private static final int OPACITY = 1;
 
+    // TODO : add static ByteGrayColors WHITE and BLACK
+
     private final int grayLevel;
 
 
@@ -35,7 +37,7 @@ public class ByteGrayColor implements GrayColor {
 
     @Override
     public Color getColor(){
-        double component = grayLevel / (double) MAXIMUM_GRAY_LEVEL;
+        double component = getLuminosity();
         return new Color(component, component, component, OPACITY);
     }
 
@@ -51,7 +53,7 @@ public class ByteGrayColor implements GrayColor {
         if (this == o) return true;
         if (this.getClass() != o.getClass()) return false;
         ByteGrayColor color = (ByteGrayColor) o;
-        return this.compareTo(color) == 0;
+        return grayLevel == color.grayLevel;
     }
 
 }

src/test/java/ByteGrayColorTest.java

+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.closeTo;
-import static org.hamcrest.Matchers.is;
+import static org.assertj.core.api.Assertions.*;
 
 public class ByteGrayColorTest {
   @Test
+  @Disabled
   public void testGetLuminosity_whenColorCreatedWithGrayLevel(){
     ByteGrayColor black = new ByteGrayColor(0);
     ByteGrayColor white = new ByteGrayColor(255);
-    assertThat(black.getLuminosity(), is(closeTo(0.,.0001)));
-    assertThat(white.getLuminosity(), is(closeTo(1.,.0001)));
+    assertThat(black.getLuminosity()).isCloseTo(0., within(.01));
+    assertThat(white.getLuminosity()).isCloseTo(1., within(.01));
   }
 
   @Test
+  @Disabled
   public void testGetLuminosity_whenColorCreatedWithLuminosity(){
     ByteGrayColor color1 = new ByteGrayColor(.25);
     ByteGrayColor color2 = new ByteGrayColor(.75);
-    assertThat(color1.getLuminosity(), is(closeTo(.25,.01)));
-    assertThat(color2.getLuminosity(), is(closeTo(.75,.01)));
+    assertThat(color1.getLuminosity()).isCloseTo(.25, within(.01));
+    assertThat(color2.getLuminosity()).isCloseTo(.75, within(.01));
+  }
+
+  @Test
+  @Disabled
+  public void testCompareTo_whenColorsCreatedWithGrayLevel(){
+    ByteGrayColor color1 = new ByteGrayColor(100);
+    ByteGrayColor color2 = new ByteGrayColor(150);
+    ByteGrayColor color3 = new ByteGrayColor(200);
+    ByteGrayColor sameGrayLevelAsColor1 = new ByteGrayColor(100);
+    assertThat(color1.compareTo(color2)).isNegative();
+    assertThat(color2.compareTo(color3)).isNegative();
+    assertThat(color1.compareTo(color3)).isNegative();
+    assertThat(color2.compareTo(color1)).isPositive();
+    assertThat(color1.compareTo(sameGrayLevelAsColor1)).isZero();
+    assertThat(color1.compareTo(color2)).isEqualTo(sameGrayLevelAsColor1.compareTo(color2));
+  }
+
+  @Test
+  @Disabled
+  public void testCompareTo_whenColorsCreatedWithLuminosity(){
+    ByteGrayColor color1 = new ByteGrayColor(0.20);
+    ByteGrayColor color2 = new ByteGrayColor(0.60);
+    ByteGrayColor color3 = new ByteGrayColor(0.80);
+    ByteGrayColor sameLuminosityAsColor1 = new ByteGrayColor(0.20);
+    assertThat(color1.compareTo(color2)).isNegative();
+    assertThat(color2.compareTo(color3)).isNegative();
+    assertThat(color1.compareTo(color3)).isNegative();
+    assertThat(color2.compareTo(color1)).isPositive();
+    assertThat(color1.compareTo(sameLuminosityAsColor1)).isZero();
+    assertThat(color1.compareTo(color2)).isEqualTo(sameLuminosityAsColor1.compareTo(color2));
+  }
+
+  @Test
+  @Disabled
+  public void testCompareTo_whenColorsCreatedWithLuminosityAndGrayLevel(){
+    ByteGrayColor color1 = new ByteGrayColor(0.);
+    ByteGrayColor color2 = new ByteGrayColor(150);
+    ByteGrayColor color3 = new ByteGrayColor(1.);
+    assertThat(color1.compareTo(color2)).isNegative();
+    assertThat(color2.compareTo(color3)).isNegative();
+    assertThat(color1.compareTo(color3)).isNegative();
+    assertThat(color2.compareTo(color1)).isPositive();
   }
 }

src/test/java/MatrixGrayImageTest.java

+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.equalTo;
-import static org.hamcrest.Matchers.is;
-
+import static org.assertj.core.api.Assertions.*;
 
 class MatrixGrayImageTest {
 
     @Test
-    void getWidth() {
-        assertThat(new MatrixGrayImage(0,0).getWidth(), is(equalTo(0)));
-        assertThat(new MatrixGrayImage(10,20).getWidth(), is(equalTo(10)));
-        assertThat(new MatrixGrayImage(400,300).getWidth(), is(equalTo(400)));
+    @Disabled
+    void testGetWidth() {
+        assertThat(new MatrixGrayImage(0,0).getWidth()).isEqualTo(0);
+        assertThat(new MatrixGrayImage(10,20).getWidth()).isEqualTo(10);
+        assertThat(new MatrixGrayImage(400,300).getWidth()).isEqualTo(400);
+    }
+
+    @Test
+    @Disabled
+    void testGetHeight() {
+        assertThat(new MatrixGrayImage(0,0).getHeight()).isEqualTo(0);
+        assertThat(new MatrixGrayImage(10,20).getHeight()).isEqualTo(20);
+        assertThat(new MatrixGrayImage(400,300).getHeight()).isEqualTo(300);
     }
 
     @Test
-    void getHeight() {
-        assertThat(new MatrixGrayImage(0,0).getHeight(), is(equalTo(0)));
-        assertThat(new MatrixGrayImage(10,20).getHeight(), is(equalTo(20)));
-        assertThat(new MatrixGrayImage(400,300).getHeight(), is(equalTo(300)));
+    @Disabled
+    void testGetPixel_whenPixelHasBeenSet() {
+        GrayColor grey1 = new ByteGrayColor(0.2);
+        GrayColor grey2 = new ByteGrayColor(0.8);
+        MatrixGrayImage image = new MatrixGrayImage(10, 10);
+        image.setPixel(grey1, 1, 1);
+        assertThat(image.getPixelGrayColor(1,1)).isEqualTo(grey1);
+        image.setPixel(grey2, 3, 9);
+        assertThat(image.getPixelGrayColor(3,9)).isEqualTo(grey2);
     }
 }
\ No newline at end of file