Develop

.vscode/launch.json

@@ -1,60 +1,11 @@
 {
     "configurations": [
-        {
-            "type": "java",
-            "name": "AnalysisReader",
-            "request": "launch",
-            "mainClass": "io.github.mianalysis.mia.process.analysishandling.AnalysisReader",
-            "projectName": "mia-core"
-        },
-        {
-            "type": "java",
-            "name": "MinimalExample",
-            "request": "launch",
-            "mainClass": "io.github.mianalysis.mia.module.MinimalExample",
-            "projectName": "mia-modules"
-        },
-        {
-            "type": "java",
-            "name": "MinimalExample",
-            "request": "launch",
-            "mainClass": "MinimalExample",
-            "projectName": "pom-mia"
-        },
-        {
-            "type": "java",
-            "name": "MinimalExample",
-            "request": "launch",
-            "mainClass": "io.github.mianalysis.example.MinimalExample",
-            "projectName": "mia-examples"
-        },
-        {
-            "type": "java",
-            "name": "MIA",
-            "request": "launch",
-            "mainClass": "io.github.mianalysis.mia.MIA",
-            "projectName": "mia-core"
-        },
         {
             "type": "java",
             "name": "MIA_",
             "request": "launch",
             "mainClass": "io.github.mianalysis.mia.MIA_",
             "projectName": "mia-plugin"
-        },
-        {
-            "type": "java",
-            "name": "MIA",
-            "request": "launch",
-            "mainClass": "io.github.mianalysis.mia.MIA",
-            "projectName": "mia"
-        },
-        {
-            "type": "java",
-            "name": "RunScript",
-            "request": "launch",
-            "mainClass": "io.github.mianalysis.mia.module.script.RunScript",
-            "projectName": "mia"
         }
     ]
 }

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/CircleTransform.java

@@ -1,13 +1,9 @@
 package io.github.mianalysis.mia.process.houghtransform.transforms;
 
-import java.util.ArrayList;
 import java.util.concurrent.LinkedBlockingQueue;
 import java.util.concurrent.ThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
 import ij.process.ImageProcessor;
 import io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator;
 import io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter;
@@ -17,23 +13,6 @@
  * Created by sc13967 on 12/01/2018.
  */
 public class CircleTransform extends AbstractTransform {
-    public static void main(String[] args) {
-        new ImageJ();
-        ImagePlus ipl = IJ.openImage("C:/Users/steph/Desktop/TEST_HoughCircle.tif");
-        ImageProcessor ipr = ipl.getProcessor();
-
-        CircleTransform transform = new CircleTransform(ipr, new String[]{"150-300-5","100-200","60-70-5"});
-        transform.setnThreads(4);
-        transform.run();
-
-        ArrayList<double[]> objects = transform.getObjects(10000, 100);
-        transform.addDetectedObjectsOverlay(ipl, objects);
-
-        ipl.show();
-        IJ.runMacro("waitForUser");
-
-    }
-
     public CircleTransform(ImageProcessor ipr, String[] parameterRanges) {
         super(ipr);
 

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/RectangleTransform.java

@@ -4,9 +4,6 @@
 import java.util.concurrent.ThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
 import ij.process.ImageProcessor;
 import io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator;
 import io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter;
@@ -16,26 +13,6 @@
  * Created by sc13967 on 12/01/2018.
  */
 public class RectangleTransform extends AbstractTransform {
-    public static void main(String[] args) {
-        new ImageJ();
-        ImagePlus ipl = IJ.openImage("C:/Users/steph/Desktop/TEST_HoughRectangle.tif");
-        ImageProcessor ipr = ipl.getProcessor();
-        String[] parameterRanges = new String[] { "0-end", "0-end", "70", "130-170-5", "0-360-60" };
-
-        RectangleTransform transform = new RectangleTransform(ipr, parameterRanges);
-        transform.setnThreads(4);
-        transform.run();
-
-        transform.getAccumulatorAsImage().show();
-
-        // ArrayList<double[]> objects = transform.getObjects(8000, 500);
-        // transform.addDetectedObjectsOverlay(ipl, objects);
-
-        ipl.show();
-        IJ.runMacro("waitForUser");
-
-    }
-
     public RectangleTransform(ImageProcessor ipr, String[] parameterRanges) {
         super(ipr);
 

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/SphereTransform.java

@@ -14,19 +14,6 @@
  * Created by sc13967 on 12/01/2018.
  */
 public class SphereTransform extends AbstractTransform {
-
-    // public static void main(String[] args) {
-    //     new ImageJ();
-    //     ImagePlus ipl = IJ.openImage("C:/Users/steph/Desktop/TEST_HoughSphere.tif");
-    //     ImageStack ist = ipl.getStack();
-    //     String[] paramRanges = new String[] { "0-end", "0-end", "0-end", "15-25-1" };
-    //     SphereTransform sht = new SphereTransform(ist, paramRanges);
-    //     sht.run();
-    //     sht.getAccumulatorAsImage().show();
-    //     sht.addDetectedObjectsOverlay(ipl, sht.getObjects(10, 100));
-    //     ipl.show();
-    // }
-
     public SphereTransform(ImageStack ist, String[] parameterRanges) {
         super(ist);
 

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/skeleton/Skeleton.java

@@ -17,26 +17,6 @@ public class Skeleton extends VertexCollection {
     private double longestDistance;
     private ArrayList<Vertex> longestPath;
 
-
-//    public static void main(String[] args) {
-//        new ImageJ();
-//
-//        ImagePlus ipl = IJ.openImage("C:\\Users\\sc13967\\Downloads\\FakeFish.tif");
-//        ipl.show();
-//
-//        Skeleton skeleton = new Skeleton(ipl);
-//
-//        LinkedHashSet<Vertex> longestPath = skeleton.getLongestPath();
-//        CurvatureCalculator curvatureCalculator = new CurvatureCalculator(longestPath);
-//        curvatureCalculator.setFittingMethod(CurvatureCalculator.FittingMethod.LOESS);
-//        curvatureCalculator.setLoessNNeighbours(10);
-//        curvatureCalculator.setLoessIterations(10000);
-//        curvatureCalculator.setLoessAccuracy(1);
-//        TreeMap<Double,Double> curvature = curvatureCalculator.getCurvature();
-//        curvatureCalculator.showOverlay(ipl,new int[]{1,1,1},2);
-//
-//    }
-
     public Skeleton(ImagePlus ipl) {
         for (int x=0;x<ipl.getWidth();x++) {
             for (int y=0;y<ipl.getHeight();y++) {

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/string/CommaSeparatedStringInterpreter.java

@@ -7,13 +7,6 @@
 import java.util.regex.Pattern;
 
 public class CommaSeparatedStringInterpreter {
-    public static void main(String[] args) {
-        firstValue("7-(end-3)");
-        // for (int i:interpretIntegers("20-(end-3)", true, 12)) {
-        // System.out.println(i);
-        // }
-    }
-
     public static int firstValue(String range) {
         Matcher matcher = Pattern.compile("[0-9]+").matcher(range);
 

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/voxel/SphereShell.java

@@ -1,30 +1,10 @@
 package io.github.mianalysis.mia.process.voxel;
 
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
-import ij.ImageStack;
-
 public class SphereShell extends AbstractSphere {
     public enum Connectivity {
         SIX, TWENTY_SIX;
     }
 
-    public static void main(String[] args) {
-        SphereShell sphereShell = new SphereShell(46,Connectivity.TWENTY_SIX);
-        int[] x = sphereShell.getX();
-        int[] y = sphereShell.getY();
-        int[] z = sphereShell.getZ();
-
-        new ImageJ();
-        ImagePlus ipl = IJ.createImage("", 100, 100, 100, 8);
-        ImageStack ist = ipl.getStack();
-        for (int i = 0; i < x.length; i++) {
-            ist.setVoxel(x[i] + 50, y[i] + 50, z[i] + 50, 255);
-        }
-        ipl.show();
-    }
-
     public SphereShell(int r, Connectivity connectivity) {
         for (int xx = -r; xx < r+1; xx++) {
             for (int yy = -r; yy < r+1; yy++) {

mia-algorithms/src/main/java/io/github/mianalysis/mia/process/voxel/SphereSolid.java

@@ -1,26 +1,6 @@
 package io.github.mianalysis.mia.process.voxel;
 
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
-import ij.ImageStack;
-
 public class SphereSolid extends AbstractSphere {
-    public static void main(String[] args) {
-        SphereSolid sphereSolid = new SphereSolid(45);
-        int[] x = sphereSolid.getX();
-        int[] y = sphereSolid.getY();
-        int[] z = sphereSolid.getZ();
-
-        new ImageJ();
-        ImagePlus ipl = IJ.createImage("", 100, 100, 100, 8);
-        ImageStack ist = ipl.getStack();
-        for (int i = 0; i < x.length; i++) {
-            ist.setVoxel(x[i] + 50, y[i] + 50, z[i] + 50, 255);
-        }
-        ipl.show();
-    }
-
     public SphereSolid(int r) {
         for (int xx = -r; xx < r; xx++) {
             for (int yy = -r; yy < r; yy++) {

mia-algorithms/src/main/java/signalprocesser/shared/StatusDialog.java

@@ -110,10 +110,6 @@ private void initComponents() {
     }
     // </editor-fold>//GEN-END:initComponents
 
-    public static void main(String args[]) {
-        StatusDialog dialog = new StatusDialog(new JFrame(), "Title", "Caption");
-        dialog.setVisible(true);
-    }
 
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JLabel lblCaption;

mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiAlgorithm.java

@@ -31,14 +31,7 @@
 import signalprocesser.voronoi.statusstructure.VLinkedNode;
 
 public class VoronoiAlgorithm {
-
-    /* ********************************************************* */
-    // Test Main Function
-
-    public static void main(String[] args) {
-        VoronoiTest.main(args);
-    }
-
+
     private VoronoiAlgorithm() { }
 
     /* ********************************************************* */

mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiTest.java

@@ -106,20 +106,7 @@ public class VoronoiTest extends javax.swing.JFrame {
     private TestRepresentationWrapper representationwrapper = new TestRepresentationWrapper();
 
     private AbstractRepresentation representation;
-
-    public static void main(String args[]) {
-        // Set look and feel
-        try {
-            UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
-        } catch (Exception e) {
-            displayError(null, e);
-        }
 
-        // Load the application
-        VoronoiTest frame = new VoronoiTest();
-        frame.setVisible(true);
-    }
-
     /** Creates new form MainFrame */
     public VoronoiTest() {
         // Inital components

mia-algorithms/src/main/java/signalprocesser/voronoi/statusstructure/binarysearchtreeimpl/debug/DebugTree.java

@@ -159,18 +159,7 @@ public void windowClosed(java.awt.event.WindowEvent evt) {
     private void formWindowClosed(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_formWindowClosed
         //System.exit(0);
     }//GEN-LAST:event_formWindowClosed
-
-    public static void main(String args[]) {
-        DebugTree app = new DebugTree(new javax.swing.JFrame());
-        app.setVisible(true);
-        VInternalNode node = new VInternalNode();
-        VLeafNode leaf1 = new VLeafNode(new VSiteEvent(new VPoint(1,2)));
-        VLeafNode leaf2 = new VLeafNode(new VSiteEvent(new VPoint(1,2)));
-        node.setLeft(leaf1);
-        node.setRight(leaf2);
-        app.setRootNode(node, 10);
-    }
-
+
     // Variables declaration - do not modify//GEN-BEGIN:variables
     // End of variables declaration//GEN-END:variables