Merge pull request #194 from mianalysis/develop

Develop
mianalysis · Jun 17, 2024 · c3b527c · c3b527c
2 parents 30e238f + 636bffd
commit c3b527c
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diff --git a/mia-algorithms/pom.xml b/mia-algorithms/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-algorithms</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-algorithms</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-bonej/pom.xml b/mia-bonej/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-bonej</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-bonej</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-coordinates/pom.xml b/mia-coordinates/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-coordinates</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-coordinates</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-core/pom.xml b/mia-core/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-core</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-core</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/Categories.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/Categories.java
@@ -68,6 +68,9 @@ public class Categories {
         public final static Category OBJECTS_RELATE_MERGE = new Category("Merge",
                         "Modules used for combining either different objects into one or combining objects from different collections into a single collection.",
                         OBJECTS_RELATE);
+        public final static Category OBJECTS_TRACK = new Category("Track",
+                        "Modules tracking objects between frames.  Establishes parent-child relationships, with parent track objects acting as links for all instances of that track.",
+                        OBJECTS);
         public final static Category OBJECTS_TRANSFORM = new Category("Transform",
                         "Modules capable of updating coordinates of existing objects.  These operations can include hole filling and masking.",
                         OBJECTS);

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/Module.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/Module.java
@@ -585,7 +585,7 @@ public void writeProgressStatus(int count, int total, String featureBeingProcess
 
     public static void writeProgressStatus(int count, int total, String featureBeingProcessed, String moduleName) {
         if (verbose)
-            writeStatus("Processed " + count + " of " + total + " " + featureBeingProcessed + " ("
+            writeStatus(count + "/" + total + " " + featureBeingProcessed + " ("
                     + Math.floorDiv(100 * count, total) + "%)", moduleName);
     }
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/Obj.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/Obj.java
@@ -10,7 +10,6 @@
 import ij.IJ;
 import ij.ImagePlus;
 import ij.gui.Roi;
-import io.github.mianalysis.mia.MIA;
 import io.github.mianalysis.mia.object.coordinates.Point;
 import io.github.mianalysis.mia.object.coordinates.volume.PointOutOfRangeException;
 import io.github.mianalysis.mia.object.coordinates.volume.Volume;
@@ -208,7 +207,7 @@ public Obj getParent(String name) {
         // If the first parent was the only one listed, returning this
         if (elements.length == 1)
             return parent;
-
+             
         // If there are additional parents listed, re-constructing the string and
         // running this method on the parent
         StringBuilder stringBuilder = new StringBuilder();
@@ -235,7 +234,10 @@ public void addParent(String name, Obj parent) {
 
     public void removeParent(String name) {
         parents.remove(name);
+    }
 
+    public void removeParent(Obj parent) {
+        parents.remove(parent.getName());
     }
 
     public LinkedHashMap<String, Objs> getChildren() {
@@ -249,8 +251,7 @@ public Objs getChildren(String name) {
         // Getting the first set of children
         Objs allChildren = children.get(elements[0]);
         if (allChildren == null)
-            return new Objs(elements[0], spatCal, objCollection.getNFrames(), objCollection.getFrameInterval(),
-                    objCollection.getTemporalUnit());
+            return new Objs(elements[0], objCollection);
 
         // If the first set of children was the only one listed, returning this
         if (elements.length == 1)
@@ -267,8 +268,7 @@ public Objs getChildren(String name) {
 
         // Going through each child in the current set, then adding all their children
         // to the output set
-        Objs outputChildren = new Objs(name, allChildren.getSpatialCalibration(),
-                objCollection.getNFrames(), objCollection.getFrameInterval(), objCollection.getTemporalUnit());
+        Objs outputChildren = new Objs(name, allChildren);
         for (Obj child : allChildren.values()) {
             Objs currentChildren = child.getChildren(stringBuilder.toString());
             for (Obj currentChild : currentChildren.values())
@@ -294,8 +294,7 @@ public void removeChildren(String name) {
     public void addChild(Obj child) {
         String childName = child.getName();
 
-        children.computeIfAbsent(childName, k -> new Objs(childName, child.getSpatialCalibration(),
-                objCollection.getNFrames(), objCollection.getFrameInterval(), objCollection.getTemporalUnit()));
+        children.computeIfAbsent(childName, k -> new Objs(childName, child.getObjectCollection()));
         children.get(childName).add(child);
 
     }
@@ -329,8 +328,7 @@ public void removePartners(String name) {
     public void addPartner(Obj partner) {
         String partnerName = partner.getName();
 
-        partners.computeIfAbsent(partnerName, k -> new Objs(partnerName, partner.getSpatialCalibration(),
-                objCollection.getNFrames(), objCollection.getFrameInterval(), objCollection.getTemporalUnit()));
+        partners.computeIfAbsent(partnerName, k -> new Objs(partnerName, partner.getObjectCollection()));
         partners.get(partnerName).add(partner);
     }
 
@@ -344,6 +342,60 @@ public void removePartner(String name) {
         partners.remove(name);
     }
 
+    /**
+     * Returns any partners that happened in previous frames
+     */
+    public Objs getPreviousPartners(String name) {
+        Objs allPartners = getPartners(name);
+
+        if (allPartners == null)
+            return new Objs(name, objCollection);
+
+        Objs previousPartners = new Objs(name, allPartners);
+        for (Obj partner : allPartners.values())
+            if (partner.getT() < T)
+                previousPartners.add(partner);
+
+        return previousPartners;
+
+    }
+
+    /**
+     * Returns any partners that happen in following frames
+     */
+    public Objs getSimultaneousPartners(String name) {
+        Objs allPartners = getPartners(name);
+
+        if (allPartners == null)
+            return new Objs(name, objCollection);
+
+        Objs simultaneousPartners = new Objs(name, allPartners);
+        for (Obj partner : allPartners.values())
+            if (partner.getT() == T)
+                simultaneousPartners.add(partner);
+
+        return simultaneousPartners;
+
+    }
+
+    /**
+     * Returns any partners that happen in following frames
+     */
+    public Objs getNextPartners(String name) {
+        Objs allPartners = getPartners(name);
+
+        if (allPartners == null)
+            return new Objs(name, objCollection);
+
+        Objs nextPartners = new Objs(name, allPartners);
+        for (Obj partner : allPartners.values())
+            if (partner.getT() > T)
+                nextPartners.add(partner);
+
+        return nextPartners;
+
+    }
+
     /**
      * Removes itself from any other objects as a parent or child.
      */
@@ -406,7 +458,6 @@ public Roi getRoi(int slice) {
         if (rois.containsKey(slice))
             return (Roi) rois.get(slice).clone();
 
-        MIA.log.writeDebug("ID "+ID);
         Roi roi = super.getRoi(slice);
 
         if (roi == null)

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java
@@ -737,8 +737,6 @@ public Roi getRoi(int slice) {
 
         Roi roi = new ThresholdToSelection().convert(ipr);
         double[][] extents = sliceVol.getExtents(true, false);
-        MIA.log.writeDebug("ROI "+roi);
-        MIA.log.writeDebug("Ex "+extents);
         roi.translate(extents[0][0], extents[1][0]);
 
         return roi;

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/process/ColourFactory.java b/mia-core/src/main/java/io/github/mianalysis/mia/process/ColourFactory.java
@@ -375,8 +375,6 @@ public static HashMap<Integer, Float> getObjectMetadataHues(Objs objects, String
             H = metadataHues.get(metadataItem.getValue());
             hues.put(ID, H);
 
-            // MIA.log.writeDebug(metadataItem.getName());
-
         }
 
         return hues;

diff --git a/mia-deepimagej/pom.xml b/mia-deepimagej/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-deepimagej</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-deepimagej</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-macros/pom.xml b/mia-macros/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-macros</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-macros</name>
     <url>https://github.com/mianalysis/mia</url>
@@ -127,13 +127,13 @@
         <dependency>
             <groupId>io.github.mianalysis</groupId>
             <artifactId>mia-core</artifactId>
-            <version>1.6.0</version>
+            <version>1.6.1</version>
         </dependency>
 
         <dependency>
             <groupId>io.github.mianalysis</groupId>
             <artifactId>mia-modules</artifactId>
-            <version>1.6.0</version>
+            <version>1.6.1</version>
         </dependency>
     </dependencies>
 

diff --git a/mia-modules/pom.xml b/mia-modules/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.0</version>
+        <version>1.6.1</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-modules</artifactId>
-    <version>1.6.0</version>
+    <version>1.6.1</version>
     <packaging>jar</packaging>
     <name>mia-modules</name>
     <url>https://github.com/mianalysis/mia</url>
@@ -127,7 +127,7 @@
         <dependency>
             <groupId>io.github.mianalysis</groupId>
             <artifactId>mia-core</artifactId>
-            <version>1.6.0</version>
+            <version>1.6.1</version>
         </dependency>
 
         <dependency>
@@ -188,7 +188,7 @@
         <dependency>
             <groupId>sc.fiji</groupId>
             <artifactId>TrackMate</artifactId>
-            <version>7.10.0</version>
+            <version>7.12.2</version>
             <scope>${scp}</scope>
         </dependency>
 

diff --git a/...main/java/io/github/mianalysis/mia/lostandfound/objects/relate/TrackObjectsLostFound.java b/...main/java/io/github/mianalysis/mia/lostandfound/objects/relate/TrackObjectsLostFound.java
@@ -6,7 +6,7 @@
 import org.scijava.plugin.Plugin;
 
 import io.github.mianalysis.mia.module.lostandfound.LostAndFoundItem;
-import io.github.mianalysis.mia.module.objects.relate.TrackObjects;
+import io.github.mianalysis.mia.module.objects.track.TrackObjects;
 
 @Plugin(type = LostAndFoundItem.class, priority = Priority.LOW, visible = true)
 public class TrackObjectsLostFound extends LostAndFoundItem {

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/inputoutput/LoadObjectsFromROIs.java b/...odules/src/main/java/io/github/mianalysis/mia/module/inputoutput/LoadObjectsFromROIs.java
@@ -22,7 +22,7 @@
 import io.github.mianalysis.mia.module.Category;
 import io.github.mianalysis.mia.module.Module;
 import io.github.mianalysis.mia.module.Modules;
-import io.github.mianalysis.mia.module.objects.relate.TrackObjects;
+import io.github.mianalysis.mia.module.objects.track.TrackObjects;
 import io.github.mianalysis.mia.object.Obj;
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.Workspace;

diff --git a/.../src/main/java/io/github/mianalysis/mia/module/objects/convert/ConvertImageToObjects.java b/.../src/main/java/io/github/mianalysis/mia/module/objects/convert/ConvertImageToObjects.java
@@ -9,7 +9,7 @@
 import io.github.mianalysis.mia.module.Modules;
 import io.github.mianalysis.mia.module.objects.detect.IdentifyObjects;
 import io.github.mianalysis.mia.module.objects.measure.intensity.MeasureObjectIntensity;
-import io.github.mianalysis.mia.module.objects.relate.TrackObjects;
+import io.github.mianalysis.mia.module.objects.track.TrackObjects;
 import io.github.mianalysis.mia.object.Obj;
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.VolumeTypesInterface;

diff --git a/...src/main/java/io/github/mianalysis/mia/module/objects/detect/ManuallyIdentifyObjects.java b/...src/main/java/io/github/mianalysis/mia/module/objects/detect/ManuallyIdentifyObjects.java
@@ -76,7 +76,7 @@
 import io.github.mianalysis.mia.module.Module;
 import io.github.mianalysis.mia.module.Modules;
 import io.github.mianalysis.mia.module.images.transform.ExtractSubstack;
-import io.github.mianalysis.mia.module.objects.relate.TrackObjects;
+import io.github.mianalysis.mia.module.objects.track.TrackObjects;
 import io.github.mianalysis.mia.object.Obj;
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.VolumeTypesInterface;
@@ -548,7 +548,6 @@ static void applyTemporalInterpolation(Image binaryImage) {
             ImagePlus sliceIpl = ExtractSubstack.extractSubstack(binaryIpl,"Substack","1-1", z + "-" + z, "1-" + nFrames);
             // ImagePlus sliceIpl = SubHyperstackMaker.makeSubhyperstack(binaryIpl, "1-1", z + "-" + z, "1-" + nFrames);
             ImageStack sliceIst = sliceIpl.getStack();
-            MIA.log.writeDebug(sliceIst.size());
 
             if (!checkStackForInterpolation(sliceIst))
                 continue;

diff --git a/...src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutParent.java b/...src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutParent.java
@@ -127,17 +127,20 @@ protected Status process(Workspace workspace) {
         while (iterator.hasNext()) {
             Obj inputObject = iterator.next();
 
-            LinkedHashMap<String, Obj> parents = inputObject.getParents(true);
+            Obj parentObject = inputObject.getParent(parentObjectName);
+            // LinkedHashMap<String, Obj> parents = inputObject.getParents(true);
             switch (filterMethod) {
                 case FilterMethods.WITH_PARENT:
-                    if (parents.get(parentObjectName) != null) {
+                    if (parentObject != null) {
+                        // if (parents.get(parentObjectName) != null) {
                         count++;
                         if (remove)
                             processRemoval(inputObject, outputObjects, iterator);
                     }
                     break;
                 case FilterMethods.WITHOUT_PARENT:
-                    if (parents.get(parentObjectName) == null) {
+                    if (parentObject == null) {
+                        // if (parents.get(parentObjectName) == null) {
                         count++;
                         if (remove)
                             processRemoval(inputObject, outputObjects, iterator);