Merge branch 'extraspanel' into develop

mianalysis · Aug 13, 2024 · 7d89810 · 7d89810
2 parents 5599f55 + 20ced11
commit 7d89810
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Showing 82 changed files with 1,192 additions and 6,635 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -1,5 +1,33 @@
 {
     "configurations": [
+        {
+            "type": "java",
+            "name": "MenDemo",
+            "request": "launch",
+            "mainClass": "io.github.mianalysis.mia.gui.regions.workflowmodules.MenDemo",
+            "projectName": "mia-plugin"
+        },
+        {
+            "type": "java",
+            "name": "Test",
+            "request": "launch",
+            "mainClass": "io.github.mianalysis.mia.gui.regions.editingpanel.Test",
+            "projectName": "mia-plugin"
+        },
+        {
+            "type": "java",
+            "name": "EditingPanel",
+            "request": "launch",
+            "mainClass": "io.github.mianalysis.mia.gui.regions.editingpanel.EditingPanel",
+            "projectName": "mia-plugin"
+        },
+        {
+            "type": "java",
+            "name": "ProjectImage",
+            "request": "launch",
+            "mainClass": "io.github.mianalysis.mia.module.images.transform.ProjectImage",
+            "projectName": "mia-modules"
+        },
         {
             "type": "java",
             "name": "CommaSeparatedStringInterpreter",

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/MIAHeadless.java b/mia-core/src/main/java/io/github/mianalysis/mia/MIAHeadless.java
@@ -2,7 +2,6 @@
 
 import java.awt.GraphicsEnvironment;
 import java.io.File;
-import java.io.IOException;
 import java.util.LinkedHashMap;
 
 import org.scijava.ItemVisibility;
@@ -109,18 +108,10 @@ public void run() {
                 applyGlobalVariables(modules, variables);
 
             // Running analysis
-            Thread t = new Thread(() -> {
-                try {
-                    new AnalysisRunner().run(modules);
+            new AnalysisRunner().run(modules);
 
-                    if (GraphicsEnvironment.isHeadless())
-                        java.lang.System.exit(0);
-
-                } catch (InterruptedException | IOException e) {
-                    MIA.log.writeError(e);
-                }
-            });
-            t.start();
+            if (GraphicsEnvironment.isHeadless())
+                java.lang.System.exit(0);
 
         } catch (Exception e) {
             e.printStackTrace();

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/lostandfound/LostAndFound.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/lostandfound/LostAndFound.java
@@ -3,7 +3,6 @@
 import java.util.HashMap;
 import java.util.List;
 
-import org.scijava.InstantiableException;
 import org.scijava.plugin.PluginInfo;
 
 import io.github.mianalysis.mia.MIA;

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/system/Colours.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/system/Colours.java
@@ -24,8 +24,11 @@ public class Colours {
     private static final Color RED = new Color(217, 66, 66); // #d94242
     private static final Color RED_DM = new Color(225,106,106); // #e16a6a
 
+    private static final Color LIGHT_GREY = new Color(210, 210, 210); // #d2d2d2
+    private static final Color LIGHT_GREY_DM = new Color(66, 66, 66); // #424242
+
     private static final Color DARK_GREY = new Color(66, 66, 66); // #424242
-    private static final Color DARK_GREY_DM = new Color(66, 66, 66); // #424242
+    private static final Color DARK_GREY_DM = new Color(190, 190, 190); // #bebebe
 
     public static Color getLightBlue(boolean darkMode) {
         if (darkMode)
@@ -69,6 +72,13 @@ public static Color getRed(boolean darkMode) {
             return RED;
     }
 
+    public static Color getLightGrey(boolean darkMode) {
+        if (darkMode)
+            return LIGHT_GREY_DM;
+        else
+            return LIGHT_GREY;
+    }
+
     public static Color getDarkGrey(boolean darkMode) {
         if (darkMode)
             return DARK_GREY_DM;

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/process/analysishandling/AnalysisRunner.java b/mia-core/src/main/java/io/github/mianalysis/mia/process/analysishandling/AnalysisRunner.java
@@ -106,7 +106,7 @@ public void run(Modules modules, boolean clearMemoryAtEnd) throws InterruptedExc
 
         }
 
-        for (Workspace workspace : workspaces)            
+        for (Workspace workspace : workspaces)       
             pool.submit(createRunnable(modules, workspace, exporter, clearMemoryAtEnd));
 
         // Telling the pool not to accept any more jobs and to wait until all queued
@@ -351,6 +351,15 @@ Runnable createRunnable(Modules modules, Workspace workspace, Exporter exporter,
                 workspace.clearAllObjects(true);
 
             }
+
+            // Thread currThread = Thread.currentThread();
+            // System.out.println("Parent "+currThread.getName());
+            // Thread[] group = new Thread[currThread.activeCount()];
+            // currThread.enumerate(group);
+            // for (Thread item:group) {
+            //     item.stop(null);
+            //     System.out.println("    Child "+item.getName());
+            // }
         };
     }
 

diff --git a/...src/main/java/io/github/mianalysis/mia/module/images/process/WekaPixelClassification.java b/...src/main/java/io/github/mianalysis/mia/module/images/process/WekaPixelClassification.java
@@ -316,6 +316,8 @@ public Status process(Workspace workspace) {
             RGBStackConverter.convertToRGB(inputImagePlus);
         }
 
+        inputImagePlus.duplicate().show();
+
         // Converting the bit depth to an integer
         int bitDepth = Integer.parseInt(outputBitDepth);
 

diff --git a/...modules/src/main/java/io/github/mianalysis/mia/module/objects/detect/IdentifyObjects.java b/...modules/src/main/java/io/github/mianalysis/mia/module/objects/detect/IdentifyObjects.java
@@ -27,6 +27,7 @@
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.VolumeTypesInterface;
 import io.github.mianalysis.mia.object.Workspace;
+import io.github.mianalysis.mia.object.coordinates.Point;
 import io.github.mianalysis.mia.object.coordinates.volume.SpatCal;
 import io.github.mianalysis.mia.object.image.Image;
 import io.github.mianalysis.mia.object.image.ImageFactory;
@@ -442,6 +443,7 @@ public static Objs process(Image inputImage, String outputObjectsName, boolean b
             }
         }
 
+
         return outputObjects;
 
     }

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/system/TestBigImage.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/system/TestBigImage.java
@@ -1,5 +1,7 @@
 package io.github.mianalysis.mia.module.system;
 
+import java.util.Random;
+
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
 
@@ -24,6 +26,9 @@
 import net.imagej.ImgPlus;
 import net.imagej.axis.Axes;
 import net.imagej.axis.DefaultLinearAxis;
+import net.imglib2.Cursor;
+import net.imglib2.RandomAccess;
+import net.imglib2.cache.img.DiskCachedCellImg;
 import net.imglib2.cache.img.DiskCachedCellImgFactory;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
@@ -61,10 +66,11 @@ public Status process(Workspace workspace) {
 
         int w = 2000;
         int h = 2000;
-        int d = 3000;
+        int d = 20;
 
-        ImgPlus<FloatType> img = new ImgPlus<>(
-                new DiskCachedCellImgFactory<>(new FloatType()).create(new int[] { 2000, 2000, 2, 20, 40 }));
+        DiskCachedCellImg dcImage = new DiskCachedCellImgFactory<>(new FloatType())
+                .create(new int[] { 2000, 2000, 1, 400, 30 });
+        ImgPlus<FloatType> img = new ImgPlus<>(dcImage);
         // ImgPlus<FloatType> img = (ImgPlus<FloatType>)
         // ImgPlusTools.createNewImgPlus(w, h, 0, d, 0, 0.2, 0.1, "um",
         // new FloatType());
@@ -77,16 +83,32 @@ public Status process(Workspace workspace) {
 
         // Creating a ramp intensity gradient along the x-axis, so operations can be
         // tested
-        // RandomAccess ra = img.randomAccess();
+        RandomAccess ra = img.randomAccess();
         // Random random = new Random();
-        // for (int i = 0; i < 1000000; i++) {
+        // for (int i = 0; i < 10000; i++) {
         // int x = (int) Math.floor(random.nextDouble() * w);
         // int y = (int) Math.floor(random.nextDouble() * h);
         // int z = (int) Math.floor(random.nextDouble() * d);
-        // ra.setPosition(new int[] { x, y, z });
+        // ra.setPosition(new int[] { x, y, z, 0, 0 });
         // ((FloatType) ra.get()).set(1000);
         // }
-        // Cursor<T> c = img.cursor();
+        for (int x = 0; x < 10; x++) {
+            for (int y = 0; y < 20; y++) {
+                ra.setPosition(new int[] { x, y, 0, 0, 0 });
+                ((FloatType) ra.get()).set(1000);
+            }
+        }
+
+        dcImage.shutdown();
+
+        for (int x = 100; x < 120; x++) {
+            for (int y = 100; y < 110; y++) {
+                ra.setPosition(new int[] { x, y, 0, 0, 0 });
+                ((FloatType) ra.get()).set(1000);
+            }
+        }
+
+        // Cursor<FloatType> c = img.cursor();
         // while (c.hasNext()) {
         // c.fwd();
         // ((FloatType) c.get()).set(c.getFloatPosition(0));
@@ -129,8 +151,8 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
     }
 
     @Override
-    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
-	return null; 
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {
+        return null;
     }
 
     @Override

diff --git a/mia-plugin/pom.xml b/mia-plugin/pom.xml
@@ -169,7 +169,7 @@
         <dependency>
             <groupId>com.formdev</groupId>
             <artifactId>flatlaf</artifactId>
-            <version>3.4</version>
+            <version>3.5</version>
             <scope>${scp}</scope>
         </dependency>