Updated version number

mianalysis · Sep 17, 2024 · 0ac1caf · 0ac1caf
1 parent 628a2d3
commit 0ac1caf
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Showing 29 changed files with 105 additions and 6,011 deletions.
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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-algorithms</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-bonej</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-coordinates</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-core</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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/object/coordinates/volume/Volume.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java
@@ -274,23 +274,6 @@ public boolean is2D() {
         return spatCal.nSlices == 1;
     }
 
-    @Deprecated
-    public ArrayList<Integer> getXCoords() {
-        return getPoints().stream().map(Point::getX).collect(Collectors.toCollection(ArrayList::new));
-
-    }
-
-    @Deprecated
-    public ArrayList<Integer> getYCoords() {
-        return getPoints().stream().map(Point::getY).collect(Collectors.toCollection(ArrayList::new));
-    }
-
-    @Deprecated
-    public ArrayList<Integer> getZCoords() {
-        return getPoints().stream().map(Point::getZ).collect(Collectors.toCollection(ArrayList::new));
-
-    }
-
     @Deprecated
     public double[] getX(boolean pixelDistances) {
         if (pixelDistances)

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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-deepimagej</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-macros</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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>1.6.8</version>
+            <version>1.6.9</version>
         </dependency>
 
         <dependency>
             <groupId>io.github.mianalysis</groupId>
             <artifactId>mia-modules</artifactId>
-            <version>1.6.8</version>
+            <version>1.6.9</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>1.6.8</version>
+        <version>1.6.9</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-modules</artifactId>
-    <version>1.6.8</version>
+    <version>1.6.9</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>1.6.8</version>
+            <version>1.6.9</version>
         </dependency>
 
         <dependency>

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java
@@ -32,6 +32,7 @@
 import io.github.mianalysis.mia.object.Obj;
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.Workspace;
+import io.github.mianalysis.mia.object.coordinates.Point;
 import io.github.mianalysis.mia.object.image.Image;
 import io.github.mianalysis.mia.object.parameters.BooleanP;
 import io.github.mianalysis.mia.object.parameters.ChildObjectsP;
@@ -291,19 +292,16 @@ public void filterObjectsOnImageEdge(Objs inputObjects, @Nullable Objs outputObj
         while (iterator.hasNext()) {
             Obj inputObject = iterator.next();
 
-            ArrayList<Integer> x = inputObject.getXCoords();
-            ArrayList<Integer> y = inputObject.getYCoords();
-            ArrayList<Integer> z = inputObject.getZCoords();
-
-            for (int i = 0; i < x.size(); i++) {
-                if (x.get(i) == minX | x.get(i) == maxX | y.get(i) == minY | y.get(i) == maxY) {
+            for (Point<Integer> pt:inputObject.getCoordinateSet()) {
+            // for (int i = 0; i < x.size(); i++) {
+                if (pt.x == minX || pt.x == maxX || pt.y == minY || pt.y == maxY) {
                     if (remove)
                         processRemoval(inputObject, outputObjects, iterator);
                     break;
                 }
 
                 // Only consider Z if the user requested this
-                if (includeZ && (z.get(i) == minZ | z.get(i) == maxZ)) {
+                if (includeZ && (pt.z == minZ || pt.z == maxZ)) {
                     if (remove)
                         processRemoval(inputObject, outputObjects, iterator);
                     break;

diff --git a/...dules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java b/...dules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java
@@ -3,20 +3,22 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 
-import com.drew.lang.annotations.Nullable;
-
-import io.github.mianalysis.mia.module.Modules;
-import io.github.mianalysis.mia.module.Module;
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
-import io.github.mianalysis.mia.module.Category;
+
+import com.drew.lang.annotations.Nullable;
+
 import io.github.mianalysis.mia.module.Categories;
+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.object.Obj;
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.Workspace;
+import io.github.mianalysis.mia.object.coordinates.Point;
 import io.github.mianalysis.mia.object.parameters.BooleanP;
-import io.github.mianalysis.mia.object.parameters.SeparatorP;
 import io.github.mianalysis.mia.object.parameters.Parameters;
+import io.github.mianalysis.mia.object.parameters.SeparatorP;
 import io.github.mianalysis.mia.object.parameters.text.IntegerP;
 import io.github.mianalysis.mia.object.refs.collections.ImageMeasurementRefs;
 import io.github.mianalysis.mia.object.refs.collections.MetadataRefs;
@@ -158,18 +160,14 @@ public static boolean hasContactWithEdge(Obj obj, int maxContact, boolean[] remo
             maxY = Integer.MAX_VALUE;
         if (!removalEdges[3])
             maxX = Integer.MAX_VALUE;
-
-        ArrayList<Integer> x = obj.getXCoords();
-        ArrayList<Integer> y = obj.getYCoords();
-        ArrayList<Integer> z = obj.getZCoords();
-
+
         int count = 0;
-        for (int i = 0; i < x.size(); i++) {
-            if (x.get(i) == minX | x.get(i) == maxX | y.get(i) == minY | y.get(i) == maxY)
+        for (Point<Integer> pt:obj.getCoordinateSet()) {
+            if (pt.x == minX || pt.x == maxX || pt.y == minY || pt.y == maxY)
                 count++;
 
             // Only consider Z if the user requested this
-            if (includeZ && (z.get(i) == minZ | z.get(i) == maxZ))
+            if (includeZ && (pt.z == minZ | pt.z == maxZ))
                 count++;
 
             // Check if the maximum number of contacts with the edge has been made

diff --git a/...ava/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java b/...ava/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java
@@ -183,20 +183,15 @@ public static CumStat[] measureWeightedCentre(Obj object, Image image, boolean a
         CumStat csY = new CumStat();
         CumStat csZ = new CumStat();
 
-        // Getting pixel coordinates
-        ArrayList<Integer> x = object.getXCoords();
-        ArrayList<Integer> y = object.getYCoords();
-        ArrayList<Integer> z = object.getZCoords();
         int tPos = object.getT();
 
         // Running through all pixels in this object and adding the intensity to the
         // MultiCumStat object
-        for (int i = 0; i < x.size(); i++) {
-            ipl.setPosition(1, z.get(i) + 1, tPos + 1);
-            csX.addMeasure(x.get(i), ipl.getProcessor().getPixelValue(x.get(i), y.get(i)));
-            csY.addMeasure(y.get(i), ipl.getProcessor().getPixelValue(x.get(i), y.get(i)));
-            csZ.addMeasure(z.get(i), ipl.getProcessor().getPixelValue(x.get(i), y.get(i)));
-
+        for (Point<Integer> pt:object.getCoordinateSet()) {
+            ipl.setPosition(1, pt.z + 1, tPos + 1);
+            csX.addMeasure(pt.x, ipl.getProcessor().getPixelValue(pt.x, pt.y));
+            csY.addMeasure(pt.y, ipl.getProcessor().getPixelValue(pt.x, pt.y));
+            csZ.addMeasure(pt.z, ipl.getProcessor().getPixelValue(pt.x, pt.y));
         }
 
         if (addMeasurements) {