diff --git a/.vscode/launch.json b/.vscode/launch.json index 8e7f918d9..c3017fe31 100644 --- a/.vscode/launch.json +++ b/.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" } ] } \ No newline at end of file diff --git a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/activecontour/ActiveContour.java b/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/activecontour/ActiveContour.java deleted file mode 100644 index 9730425d0..000000000 --- a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/activecontour/ActiveContour.java +++ /dev/null @@ -1,75 +0,0 @@ -package io.github.mianalysis.mia.process.activecontour; - -import java.awt.Polygon; - -import ij.IJ; -import ij.ImageJ; -import ij.ImagePlus; -import ij.gui.Overlay; -import ij.gui.Roi; -import ij.plugin.Duplicator; -import io.github.mianalysis.mia.process.activecontour.energies.BendingEnergy; -import io.github.mianalysis.mia.process.activecontour.energies.ElasticEnergy; -import io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection; -import io.github.mianalysis.mia.process.activecontour.energies.PathEnergy; -import io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser; -import io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection; -import io.github.mianalysis.mia.process.activecontour.visualisation.GridOverlay; - -/** - * Created by Stephen on 08/09/2016. - */ -public class ActiveContour { - public static void main(String[] args) throws InterruptedException { - new ImageJ(); - IJ.runMacro("waitForUser"); - - ImagePlus ipl = IJ.getImage(); - Roi roi = ipl.getRoi(); - - Polygon roiPoly = roi.getPolygon(); - int[] xCoords = roiPoly.xpoints; - int[] yCoords = roiPoly.ypoints; - - // Reducing the number of points per contour - int div = 5; - int[] xCoordsSub = new int[(int) Math.floor(xCoords.length/div)]; - int[] yCoordsSub = new int[(int) Math.floor(yCoords.length/div)]; - - for (int i=0;i objects = transform.getObjects(10000, 100); - transform.addDetectedObjectsOverlay(ipl, objects); - - ipl.show(); - IJ.runMacro("waitForUser"); - - } - public CircleTransform(ImageProcessor ipr, String[] parameterRanges) { super(ipr); diff --git a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/RectangleTransform.java b/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/RectangleTransform.java index 32c3f77ea..3033e2c62 100644 --- a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/RectangleTransform.java +++ b/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 objects = transform.getObjects(8000, 500); - // transform.addDetectedObjectsOverlay(ipl, objects); - - ipl.show(); - IJ.runMacro("waitForUser"); - - } - public RectangleTransform(ImageProcessor ipr, String[] parameterRanges) { super(ipr); diff --git a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/SphereTransform.java b/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/SphereTransform.java index 25d1653a6..c2d12cc50 100644 --- a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/SphereTransform.java +++ b/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); diff --git a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/skeleton/Skeleton.java b/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/skeleton/Skeleton.java index b4a9de737..d88909b50 100644 --- a/mia-algorithms/src/main/java/io/github/mianalysis/mia/process/skeleton/Skeleton.java +++ b/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 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 longestPath = skeleton.getLongestPath(); -// CurvatureCalculator curvatureCalculator = new CurvatureCalculator(longestPath); -// curvatureCalculator.setFittingMethod(CurvatureCalculator.FittingMethod.LOESS); -// curvatureCalculator.setLoessNNeighbours(10); -// curvatureCalculator.setLoessIterations(10000); -// curvatureCalculator.setLoessAccuracy(1); -// TreeMap curvature = curvatureCalculator.getCurvature(); -// curvatureCalculator.showOverlay(ipl,new int[]{1,1,1},2); -// -// } - public Skeleton(ImagePlus ipl) { for (int x=0;x//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; diff --git a/mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiAlgorithm.java b/mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiAlgorithm.java index ffe1a5aad..b50903009 100644 --- a/mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiAlgorithm.java +++ b/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() { } /* ********************************************************* */ diff --git a/mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiTest.java b/mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiTest.java index 0614655d2..936e5401b 100644 --- a/mia-algorithms/src/main/java/signalprocesser/voronoi/VoronoiTest.java +++ b/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 diff --git a/mia-algorithms/src/main/java/signalprocesser/voronoi/statusstructure/binarysearchtreeimpl/debug/DebugTree.java b/mia-algorithms/src/main/java/signalprocesser/voronoi/statusstructure/binarysearchtreeimpl/debug/DebugTree.java index af1e978d4..7199f9b50 100644 --- a/mia-algorithms/src/main/java/signalprocesser/voronoi/statusstructure/binarysearchtreeimpl/debug/DebugTree.java +++ b/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 diff --git a/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/CountryData.java b/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/CountryData.java index 4b138d140..a4af00b90 100644 --- a/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/CountryData.java +++ b/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/CountryData.java @@ -39,12 +39,7 @@ public class CountryData { public static final String INDEX_FILE = PATH_TO_COUNTRYDATA + "/fileindex.dat"; public static final Pattern PATTERN_COORDLINE = Pattern.compile("^[ ]*([0-9E.-]*)[ ]*,[ ]*([0-9E.-]*)[ ]*$"); - - public static void main(String args[]) throws IOException, URISyntaxException { - // Call country data generation to generate mapping data - //CountryDataGeneration.main(args); - } - + public static ArrayList getCountryList() throws IOException { // Open the index file InputStream stream = CountryData.class.getResourceAsStream(INDEX_FILE); diff --git a/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/TestSuite.java b/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/TestSuite.java index e5b1bae7c..da2f22d8e 100644 --- a/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/TestSuite.java +++ b/mia-algorithms/src/main/java/signalprocesser/voronoi/tools/TestSuite.java @@ -1495,20 +1495,7 @@ private void optLetterGenerationActionPerformed(java.awt.event.ActionEvent evt) panelGenerationSelection.validate(); panelGenerationSelection.repaint(); }//GEN-LAST:event_optLetterGenerationActionPerformed - - public static void main(String args[]) { - // Set look and feel - try { - UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); - } catch (Exception e) { - displayError(null, e); - } - // Load test form - TestSuite dialog = new TestSuite(true, new javax.swing.JFrame()); - dialog.setVisible(true); - } - private void runTestSuite(final RunTestSeries testseries) { // Update status lblStatus.setText("Starting test suite run..."); diff --git a/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/tools/EllipsoidCalculator.java b/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/tools/EllipsoidCalculator.java index 85c2e5dab..a131b746a 100644 --- a/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/tools/EllipsoidCalculator.java +++ b/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/tools/EllipsoidCalculator.java @@ -15,90 +15,6 @@ public class EllipsoidCalculator { private final Volume volume; private Ellipsoid ell; - public static void main(String[] args) { - SpatCal spatCal = new SpatCal(1, 1, "px", 200, 200, 20); - Volume vol = new Volume(VolumeType.POINTLIST, spatCal); - - try { - vol.add(83, 81, 4); - vol.add(84, 81, 4); - vol.add(84, 82, 4); - vol.add(85, 82, 4); - vol.add(84, 80, 5); - vol.add(84, 81, 5); - vol.add(84, 82, 5); - vol.add(85, 80, 5); - vol.add(85, 81, 5); - vol.add(85, 82, 5); - vol.add(85, 83, 5); - vol.add(85, 84, 5); - vol.add(86, 80, 5); - vol.add(86, 81, 5); - vol.add(86, 82, 5); - vol.add(86, 83, 5); - vol.add(86, 84, 5); - vol.add(87, 82, 5); - vol.add(87, 83, 5); - vol.add(87, 84, 5); - vol.add(87, 85, 5); - vol.add(88, 83, 5); - vol.add(88, 84, 5); - vol.add(88, 85, 5); - vol.add(85, 83, 6); - vol.add(86, 81, 6); - vol.add(86, 82, 6); - vol.add(86, 83, 6); - vol.add(86, 84, 6); - vol.add(86, 85, 6); - vol.add(87, 82, 6); - vol.add(87, 83, 6); - vol.add(87, 84, 6); - vol.add(87, 85, 6); - vol.add(88, 84, 6); - vol.add(88, 85, 6); - vol.add(83, 83, 7); - - vol.add(84, 82, 7); - vol.add(84, 83, 7); - vol.add(84, 84, 7); - vol.add(85, 82, 7); - vol.add(85, 83, 7); - vol.add(85, 84, 7); - vol.add(85, 85, 7); - vol.add(86, 82, 7); - vol.add(86, 83, 7); - vol.add(86, 84, 7); - vol.add(86, 85, 7); - vol.add(87, 82, 7); - vol.add(87, 83, 7); - vol.add(87, 84, 7); - vol.add(87, 85, 7); - vol.add(88, 85, 7); - - // vol.add(83,82,4); - // vol.add(83,83,4); - // vol.add(84,83,4); - // vol.add(85,81,4); - // vol.add(85,83,4); - // vol.add(83,84,7); - // vol.add(84,85,7); - // vol.add(84,86,7); - // vol.add(85,86,7); - // vol.add(89,85,7); - // vol.add(89,85,7); - - } catch (PointOutOfRangeException e) { - } - - EllipsoidCalculator calculator = new EllipsoidCalculator(vol, 1000); - double[] ori = calculator.getOrientationRads(); - System.out.println("Ori " + ori[0] + "_" + ori[1]); - - double sphericity = calculator.getSphericity(); - System.out.println("Sphericity " + sphericity); - - } - /** * This constructor is package-private. As such, it's intended for testing only. * diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/MIA.java b/mia-core/src/main/java/io/github/mianalysis/mia/MIA.java index df05f5b94..56ca2aea6 100644 --- a/mia-core/src/main/java/io/github/mianalysis/mia/MIA.java +++ b/mia-core/src/main/java/io/github/mianalysis/mia/MIA.java @@ -61,28 +61,6 @@ public abstract class MIA { */ protected static final boolean imagePlusMode = true; - // public static void main(String[] args) throws Exception { - // debug = true; - - // try { - // if (args.length == 0) { - // System.err.println("No workflow file path specified as command line - // argument"); - // } else if (args.length == 1) { - // Analysis analysis = AnalysisReader.loadModules(new File(args[0])); - // new AnalysisRunner().run(analysis); - // } else if (args.length == 2) { - // Analysis analysis = AnalysisReader.loadModules(new File(args[0])); - // analysis.getModules().getInputControl().updateParameterValue(InputControl.INPUT_PATH, - // args[1]); - // new AnalysisRunner().run(analysis); - // } - - // } catch (Exception e) { - // MIA.log.writeError(e); - // } - // } - private static String extractVersion() { // Determining the version number from the pom file try { diff --git a/mia-deepimagej/src/main/java/io/github/mianalysis/mia/process/deepimagej/PrepareDeepImageJ.java b/mia-deepimagej/src/main/java/io/github/mianalysis/mia/process/deepimagej/PrepareDeepImageJ.java index e7fc8dd86..75aa1e1ed 100644 --- a/mia-deepimagej/src/main/java/io/github/mianalysis/mia/process/deepimagej/PrepareDeepImageJ.java +++ b/mia-deepimagej/src/main/java/io/github/mianalysis/mia/process/deepimagej/PrepareDeepImageJ.java @@ -472,10 +472,10 @@ else if (runStage == 2) int minID = 0; while (iter.hasNext()) { Object nx = iter.next(); - // MIA.log.writeDebug("OUTPUT " + nx); if (nx != null && nx instanceof ImagePlus && ((ImagePlus) nx).getProcessor() != null) { ImagePlus currIpl = (ImagePlus) nx; currIpl.hide(); + if (currIpl.getID() < minID) { ipl = currIpl; minID = currIpl.getID(); diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/ImageLoader.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/ImageLoader.java index 21a52fa3b..c48c657d3 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/ImageLoader.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/ImageLoader.java @@ -425,14 +425,6 @@ public class ImageLoader & NativeType> extends Module { */ public static final String MAX_INPUT_INTENSITY = "Maximum input intensity"; - public static void main(String[] args) throws io.scif.FormatException, IOException { - SCIFIO scifio = new SCIFIO(); - String path = "C:\\Users\\steph\\Desktop\\lumen_area.tif"; - Reader reader = scifio.initializer().initializeReader(new FileLocation(path)); - Plane plane = reader.openPlane(0, 0); - System.out.println(plane.getLengths()[0]); - } - public ImageLoader(Modules modules) { super("Load image", modules); } diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitActiveContours.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitActiveContours.java index f4d5dbb63..2fd3042cb 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitActiveContours.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitActiveContours.java @@ -444,20 +444,6 @@ void addParameterDescriptions() { parameters.get(SHOW_CONTOURS_REALTIME).setDescription("When selected, the contour evolution will be displayed on the input image in realtime. This may be useful for optimising weight parameters."); } - - public static void main(String[] args) { - BalloonEnergy balloonEnergy = new BalloonEnergy(1); - - Vertex node1 = new Vertex(50, 20); - Vertex node2 = new Vertex(53, 18); - Vertex node3 = new Vertex(54, 14); - - node2.setLeftNeighbour(node1); - node2.setRightNeighbour(node3); - - balloonEnergy.getEnergy(node2); - - } } class BalloonEnergy extends Energy { diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateManyToMany.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateManyToMany.java index 197634c47..dea6bdd53 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateManyToMany.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateManyToMany.java @@ -54,11 +54,6 @@ // return new SparseCostMatrix( cc, kk, number, m ); // } // -// public static void main(String[] args) { -// new RelateOneToOne().testSparseIsNonSparse(); -// -// } -// // public final void testSparseIsNonSparse() { // final int n = 4; // final int m = 6; diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateOneToOne.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateOneToOne.java index 52dc94f7d..699f1d1a7 100644 --- a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateOneToOne.java +++ b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/RelateOneToOne.java @@ -54,11 +54,6 @@ // return new SparseCostMatrix( cc, kk, number, m ); // } // -// public static void main(String[] args) { -// new RelateOneToOne().testSparseIsNonSparse(); -// -// } -// // public final void testSparseIsNonSparse() { // final int n = 4; // final int m = 6; diff --git a/mia-plugin/pom.xml.versionsBackup b/mia-plugin/pom.xml.versionsBackup deleted file mode 100644 index c08a2f5a1..000000000 --- a/mia-plugin/pom.xml.versionsBackup +++ /dev/null @@ -1,246 +0,0 @@ - - 4.0.0 - - - io.github.mianalysis - pom-mia - 1.5.0-SNAPSHOT - - - io.github.mianalysis - mia-plugin - 1.5.0-SNAPSHOT - jar - mia-plugin - https://github.com/mianalysis/mia - 2017 - ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets. - - University of Bristol - - - - - GNU General Public License v3+ - http://www.gnu.org/licenses/gpl.html - repo - - - - - - sjcross - Stephen Cross - - founder - lead - developer - debugger - reviewer - support - maintainer - - - - jdjfisher - Jordan Fisher - - developer - - - - glmfisher - Gemma Fisher - - reviewer - support - - - - - - - Gemma Fisher - - support - - - glmfisher - - - - - - GitHub Issues - https://github.com/mianalysis/mia/issues - - - - UTF-8 - false - 1.8 - 1.8 - compile - GNU General Public License v3+ - Stephen Cross - - 3.2.0 - 1.15.0 - 5.11.0 - 1.1.6 - - - - - Image.sc Forum - https://forum.image.sc/tag/modular-image-analysis - - - - - scm:git:git://github.com/mianalysis/mia - scm:git:git@github.com:mianalysis/mia - HEAD - https://github.com/mianalysis/mia - - - - GitHub Actions - https://github.com/mianalysis/mia - - - - - scijava.public - https://maven.scijava.org/content/groups/public - - - - jitpack.io - https://jitpack.io - - - - - - io.github.mianalysis - mia-core - ${project.version} - - - - io.github.mianalysis - mia-modules - ${project.version} - - - - io.github.mianalysis - mia-macros - ${project.version} - - - - io.github.mianalysis - mia-algorithms - ${project.version} - - - - - - - org.sonatype.plugins - nexus-staging-maven-plugin - - - - org.apache.maven.plugins - maven-source-plugin - - - - org.apache.maven.plugins - maven-javadoc-plugin - - - - org.apache.maven.plugins - maven-gpg-plugin - - - - org.apache.maven.plugins - maven-jar-plugin - 2.6 - - MIA_-${project.version} - - - true - true - io.github.mianalysis.mia.MIA_ - - - - - - - - org.apache.maven.plugins - maven-shade-plugin - 3.2.1 - - - package - - shade - - - - - - - *:* - - META-INF/*.SF - META-INF/*.DSA - META-INF/*.RSA - - - - - - - - org.apache.maven.plugins - maven-dependency-plugin - 3.0.0 - - - copy-dependencies - package - - copy-dependencies - - - provided - runtime - - - commons-codec,commons-collections4,commons-compress,commons-io,commons-math3,slf4j-api,xml-apis - - - ${project.build.directory}/mia-dependencies/ - false - false - true - - - - - - - \ No newline at end of file diff --git a/mia-plugin/src/main/java/io/github/mianalysis/mia/module/images/process/threshold/LiveManualThreshold.java b/mia-plugin/src/main/java/io/github/mianalysis/mia/module/images/process/threshold/LiveManualThreshold.java index 0e28ef934..aae492cfc 100644 --- a/mia-plugin/src/main/java/io/github/mianalysis/mia/module/images/process/threshold/LiveManualThreshold.java +++ b/mia-plugin/src/main/java/io/github/mianalysis/mia/module/images/process/threshold/LiveManualThreshold.java @@ -89,18 +89,6 @@ public class LiveManualThreshold extends Module { public interface BinaryLogic extends BinaryLogicInterface { } - public static void main(String[] args) { - // Creating a new instance of ImageJ - new ij.ImageJ(); - - // Launching MIA - new ImageJ().command().run("io.github.mianalysis.mia.MIA", false); - - // Adding the current module to MIA's list of available modules. - AvailableModules.addModuleName(LiveManualThreshold.class); - - } - public LiveManualThreshold(Modules modules) { // The first argument is the name by which the module will be seen in the GUI. super("Live manual threshold", modules); diff --git a/mia-plugin/src/main/java/io/github/mianalysis/mia/module/objects/filter/LiveFilterByMeasurement.java b/mia-plugin/src/main/java/io/github/mianalysis/mia/module/objects/filter/LiveFilterByMeasurement.java index a13543642..8376ddf76 100644 --- a/mia-plugin/src/main/java/io/github/mianalysis/mia/module/objects/filter/LiveFilterByMeasurement.java +++ b/mia-plugin/src/main/java/io/github/mianalysis/mia/module/objects/filter/LiveFilterByMeasurement.java @@ -68,18 +68,6 @@ public class LiveFilterByMeasurement extends AbstractObjectFilter { public interface FilterMethods extends AbstractNumericObjectFilter.FilterMethods { } - public static void main(String[] args) { - // Creating a new instance of ImageJ - new ij.ImageJ(); - - // Launching MIA - new ImageJ().command().run("io.github.mianalysis.mia.MIA", false); - - // Adding the current module to MIA's list of available modules. - AvailableModules.addModuleName(LiveFilterByMeasurement.class); - - } - public LiveFilterByMeasurement(Modules modules) { // The first argument is the name by which the module will be seen in the GUI. super("Live measurement filter", modules);