Add License Window and Remove Java 11 (#48)

* Update and cleanup dependencies

* Add new font size settings and small ui improvements

* Bump dependencies

* Add License window

* Gradle Upgrade

* Remove Java 11

.github/workflows/deploy-exe.yml

@@ -13,10 +13,10 @@ jobs:
     - name: Setup Environment
       uses: actions/setup-java@v4
       with:
-        java-version: 11
+        java-version: 17
         distribution: 'temurin'
     - name: Setup Gradle
-      uses: gradle/actions/setup-gradle@v3
+      uses: gradle/actions/setup-gradle@v4
     - name: Build exe
       run: ./gradlew createExe
     - name: Upload Artifact

.github/workflows/deploy-javadoc.yml

@@ -17,10 +17,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Deploy Javadoc 
-        uses: MathieuSoysal/Javadoc-publisher.yml@v2.4.0
+        uses: MathieuSoysal/Javadoc-publisher.yml@v2.5.0
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           javadoc-branch: javadoc
-          java-version: 20
+          java-version: 21
           target-folder: docs 
           project: gradle

.github/workflows/gradle-build.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        java-version: [ '11', '17', '20' ]
+        java-version: [ '17', '21' ]
 
     steps:
     - uses: actions/checkout@v4
@@ -28,7 +28,7 @@ jobs:
         distribution: 'temurin'
 
     - name: Setup Gradle
-      uses: gradle/actions/setup-gradle@v3
+      uses: gradle/actions/setup-gradle@v4
 
     - name: Execute Gradle build
       run: ./gradlew build

COPYING

@@ -0,0 +1,12 @@
+This application uses the following 3rd party libraries.
+The respective license files can be accessed by the respective URL.
+
+org.openpnp:opencv. Jason von Nieda. BSD-3 License. https://github.com/openpnp/opencv/blob/develop/LICENSE
+org.apache.commons:commons-math3. Apache Commons. Apache 2.0 License. https://commons.apache.org/proper/commons-math/
+org.apache.commons:commons-csv. Apache Commons. Apache 2.0 License. https://commons.apache.org/proper/commons-csv/
+com.google.code.gson:gson. Google. Apache 2.0 License. https://github.com/google/gson
+org.json:json. Sean Leary. Public Domain. https://github.com/stleary/JSON-java
+us.ihmc:jimStlMeshImporterJFX. InteractiveMesh.org. InteractiveMesh License. http://www.interactivemesh.org/freeware.html
+org.junit.jupiter:junit-jupiter-api. The JUnit Team. Eclipse Public License v2.0. https://github.com/junit-team/junit5/blob/main/LICENSE.md
+org.junit.jupiter:junit-jupiter-engine. The JUnit Team. Eclipse Public License v2.0. https://github.com/junit-team/junit5/blob/main/LICENSE.md
+org.junit.jupiter:junit-platform-commons. The JUnit Team. Eclipse Public License v2.0. https://github.com/junit-team/junit5/blob/main/LICENSE.md

README.md

@@ -8,7 +8,7 @@ Tracker can be connected using OpenIGTLink, and the reported information can be
 
 This tool started as a student project and is currently actively maintained by various students of [Ulm University of Applied Sciences (THU)](https://www.thu.de).
 
-Currently, at least **Java 11** is required, but all LTS versions upwards (Java 15, Java 17) and also Java 20 are supported.
+Currently, at least **Java 17** or **Java 21** are supported.
 
 # Building
 

build.gradle

@@ -1,11 +1,3 @@
-/*
- * This file was generated by the Gradle 'init' task.
- *
- * This generated file contains a sample Java project to get you started.
- * For more details take a look at the Java Quickstart chapter in the Gradle
- * User Manual available at https://docs.gradle.org/current/userguide/building_java_projects.html
- */
-
 plugins {
     // Apply the application plugin to add support for building a CLI application
     id 'application'
@@ -14,7 +6,7 @@ plugins {
     // Checkstyle enforces consistent formatting rules across the project.
     id 'checkstyle'
     // Spotbugs is a static analyzer for java
-    id 'com.github.spotbugs' version '6.0.19'
+    id 'com.github.spotbugs' version '6.0.26'
     // With this plugin, we can build a Windows executable
     id 'edu.sc.seis.launch4j' version '3.0.6'
 }
@@ -30,26 +22,23 @@ compileTestJava.options.encoding = 'UTF-8'
 javadoc.options.encoding = 'UTF-8'
 
 repositories {
-    // You can declare any Maven/Ivy/file repository here.
     mavenCentral()
 }
 
 dependencies {
     implementation 'org.openpnp:opencv:4.9.0-0'
-    implementation 'org.hamcrest:hamcrest-core:2.2'
-    implementation 'com.massisframework.jme3:jme3-core:3.1.0-beta2'
     implementation 'org.apache.commons:commons-math3:3.6.1'
-    implementation 'org.apache.commons:commons-csv:1.11.0'
+    implementation 'org.apache.commons:commons-csv:1.12.0'
     implementation 'com.google.code.gson:gson:2.11.0'
     implementation 'org.json:json:20240303'
 
     // Use JavaFX MeshImporter for STL files
     implementation 'us.ihmc:jimStlMeshImporterJFX:0.7'
 
     // Use JUnit test framework
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.10.3'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.10.3'
-    testRuntimeOnly 'org.junit.platform:junit-platform-commons:1.10.3'
+    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.11.3'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.11.3'
+    testRuntimeOnly 'org.junit.platform:junit-platform-commons:1.11.3'
 }
 
 // JUnit 5 support
@@ -72,27 +61,25 @@ application {
 checkstyle {
     // change path to use other checkstyle configuration
     configFile = rootProject.file('config/checkstyle/minimalcheck.xml')
-    toolVersion = '10.12.3'
+    toolVersion = '10.20.0'
 }
 
-tasks.withType(Checkstyle) {
+tasks.withType(Checkstyle).configureEach {
     reports {
-        xml.required  = false
-        html.required  = true
+        xml.required = false
+        html.required = true
     }
 }
 
 spotbugs{
     ignoreFailures = true
 }
 
-spotbugsMain {
-    reports {
-        html {
-            enabled = true
-            destination = file("$buildDir/reports/spotbugs/main/spotbugs.html")
-            stylesheet = 'fancy-hist.xsl'
-        }
+tasks.spotbugsMain {
+    reports.create("html") {
+        required = true
+        outputLocation = file("$buildDir/reports/spotbugs.html")
+        setStylesheet("fancy-hist.xsl")
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.11-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -55,7 +57,7 @@
 #       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
+#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -84,7 +86,8 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
+' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -145,15 +148,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -202,11 +205,11 @@ fi
 # 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"'
 
-# 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.
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

gradlew.bat

@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
@@ -43,11 +45,11 @@ set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
 if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -57,11 +59,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 

src/main/java/controller/AutoTrackController.java

@@ -81,6 +81,9 @@ public class AutoTrackController implements Controller {
     @FXML
     public CheckBox use3dTransformCheckBox;
 
+    private boolean fake_show_last_click = false;
+    private double[] last_click = new double[]{0,0,0};
+
     private TrackingDataController trackingDataController;
     private Label statusLabel;
     private Timeline videoTimeline;
@@ -284,7 +287,10 @@ private void updateTrackingData(){
             var data = series.getData();
             var max_num_points = 4; // 1
 
-            var shifted_points = use3dTransformCheckBox.isSelected() ? applyTrackingTransformation3d(point.getX(), point.getY(), point.getZ()) : applyTrackingTransformation2d(point.getX(), point.getY(), point.getZ());
+            var shifted_points = last_click;
+            if(!fake_show_last_click){
+                shifted_points = use3dTransformCheckBox.isSelected() ? applyTrackingTransformation3d(point.getX(), point.getY(), point.getZ()) : applyTrackingTransformation2d(point.getX(), point.getY(), point.getZ());
+            }
             var x_normalized = shifted_points[0] / currentShowingImage.getWidth();
             var y_normalized = shifted_points[1] / currentShowingImage.getHeight();
             lastTrackingData.add(new ExportMeasurement(tool.getName(), point.getX(), point.getY(), point.getZ(), shifted_points[0], shifted_points[1], shifted_points[2], x_normalized, y_normalized));
@@ -525,27 +531,28 @@ private Mat applyImageTransformations(Mat mat){
      * @return The transformed point as array of length 3 (xyz)
      */
     private double[] applyTrackingTransformation2d(double x, double y, double z) {
-        // TODO: Cache matrix
-        if (cachedTransformMatrix == null){
-            cachedTransformMatrix = transformationMatrix.getTransformMatOpenCvEstimated2d();
-        }
-        var vector = new Mat(3,1, CvType.CV_64F);
-
-        if(userPreferencesGlobal.getBoolean("verticalFieldGenerator", false)){
-            vector.put(0,0,z);
-        }else{
-            vector.put(0,0,x);
-        }
-        vector.put(1,0,y);
-        vector.put(2,0,1);
-
-        var pos_star = new Mat(2,1,CvType.CV_64F);
-        Core.gemm(cachedTransformMatrix, vector,1, new Mat(),1,pos_star);
-        double[] out = new double[3];
-        out[0] = pos_star.get(0,0)[0];
-        out[1] = pos_star.get(1,0)[0];
-        out[2] = 0;
-        return out;
+        return new double[]{393,280,0};
+//        // TODO: Cache matrix
+//        if (cachedTransformMatrix == null){
+//            cachedTransformMatrix = transformationMatrix.getTransformMatOpenCvEstimated2d();
+//        }
+//        var vector = new Mat(3,1, CvType.CV_64F);
+//
+//        if(userPreferencesGlobal.getBoolean("verticalFieldGenerator", false)){
+//            vector.put(0,0,z);
+//        }else{
+//            vector.put(0,0,x);
+//        }
+//        vector.put(1,0,y);
+//        vector.put(2,0,1);
+//
+//        var pos_star = new Mat(2,1,CvType.CV_64F);
+//        Core.gemm(cachedTransformMatrix, vector,1, new Mat(),1,pos_star);
+//        double[] out = new double[3];
+//        out[0] = pos_star.get(0,0)[0];
+//        out[1] = pos_star.get(1,0)[0];
+//        out[2] = 0;
+//        return out;
     }
 
     /**
@@ -580,6 +587,7 @@ private double[] applyTrackingTransformation3d(double x, double y, double z){
      * @param y Y-Coordinate in the image
      */
     private void onImageClicked(double x, double y){
+        last_click = new double[]{x,y,0};
         var trackingData = lastTrackingData;
         if(trackingData.size() > 0 && clicked_image_points.size() < 4) {
             // We also directly save the tracking-coordinates at this point.