Merge branch 'develop'

mianalysis · Oct 29, 2024 · 905fcac · 905fcac
2 parents 063678d + c1c9589
commit 905fcac
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Showing 15 changed files with 66 additions and 80 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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-algorithms</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-bonej</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-coordinates</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-core</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</version>
     <packaging>jar</packaging>
     <name>mia-core</name>
     <url>https://github.com/mianalysis/mia</url>

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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-deepimagej</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-macros</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</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>1.6.11</version>
+            <version>1.6.12</version>
         </dependency>
 
         <dependency>
             <groupId>io.github.mianalysis</groupId>
             <artifactId>mia-modules</artifactId>
-            <version>1.6.11</version>
+            <version>1.6.12</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>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-modules</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</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>1.6.11</version>
+            <version>1.6.12</version>
         </dependency>
 
         <dependency>

diff --git a/mia-plugin/pom.xml b/mia-plugin/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-plugin</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</version>
     <packaging>jar</packaging>
     <name>mia-plugin</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-plugin/src/main/java/io/github/mianalysis/mia/process/selectors/ClassSelector.java b/mia-plugin/src/main/java/io/github/mianalysis/mia/process/selectors/ClassSelector.java
@@ -9,8 +9,6 @@
 import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
-import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.LinkedList;
 import java.util.Set;
 import java.util.TreeSet;
@@ -50,12 +48,13 @@ public class ClassSelector implements ActionListener, KeyListener {
     private SortedListModel<String> searchListModel = new SortedListModel<>();
     private JList<String> searchList = new JList<>(searchListModel);
     private String lastSelectedClass = null;
-    private ActiveList activeList = ActiveList.FULL;
-
-    private enum ActiveList {
-        FULL, CURRENT, RECENT, SEARCH
-    }
 
+    // Tab names
+    private static final String ALL_CLASSES = "All classes";
+    private static final String CURRENT = "Current classes";
+    private static final String RECENT = "Recent classes";
+    private static final String SEARCH = "Search";
+
     // GUI buttons
     private static final String CREATE_CLASS = "+";
     private static final String APPLY_CLASS = "Apply class";
@@ -101,58 +100,31 @@ public void windowClosing(WindowEvent e) {
         tabbedPane = new JTabbedPane();
         frame.add(tabbedPane, c);
 
+        currentList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
         fullList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        fullList.addListSelectionListener(new ListSelectionListener() {
-            @Override
-            public void valueChanged(ListSelectionEvent e) {
-                activeList = ActiveList.FULL;
-            }
-        });
+        recentList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+        searchList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
         JScrollPane fullListScrollPane = new JScrollPane(fullList);
         fullListScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
         fullListScrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
         fullListScrollPane.getVerticalScrollBar().setUnitIncrement(10);
         fullListScrollPane.setViewportBorder(BorderFactory.createEmptyBorder());
-        tabbedPane.add("All classes", fullListScrollPane);
-
-        currentList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        currentList.addListSelectionListener(new ListSelectionListener() {
-            @Override
-            public void valueChanged(ListSelectionEvent e) {
-                activeList = ActiveList.CURRENT;
-            }
-        });
+        tabbedPane.add(ALL_CLASSES, fullListScrollPane);
 
         JScrollPane currentListScrollPane = new JScrollPane(currentList);
         currentListScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
         currentListScrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
         currentListScrollPane.getVerticalScrollBar().setUnitIncrement(10);
         currentListScrollPane.setViewportBorder(BorderFactory.createEmptyBorder());
-        tabbedPane.add("Current classes", currentListScrollPane);
-
-        recentList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        recentList.addListSelectionListener(new ListSelectionListener() {
-            @Override
-            public void valueChanged(ListSelectionEvent e) {
-                activeList = ActiveList.RECENT;
-            }
-        });
+        tabbedPane.add(CURRENT, currentListScrollPane);
 
         JScrollPane recentListScrollPane = new JScrollPane(recentList);
         recentListScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
         recentListScrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
         recentListScrollPane.getVerticalScrollBar().setUnitIncrement(10);
         recentListScrollPane.setViewportBorder(BorderFactory.createEmptyBorder());
-        tabbedPane.add("Recent classes", recentListScrollPane);
-
-        searchList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        searchList.addListSelectionListener(new ListSelectionListener() {
-            @Override
-            public void valueChanged(ListSelectionEvent e) {
-                activeList = ActiveList.SEARCH;
-            }
-        });
+        tabbedPane.add(RECENT, recentListScrollPane);        
 
         JPanel searchPane = new JPanel();
         searchPane.setLayout(new BoxLayout(searchPane, BoxLayout.PAGE_AXIS));
@@ -192,7 +164,7 @@ public void removeUpdate(DocumentEvent e) {
             }
         });
         searchPane.add(searchField);
-        tabbedPane.add("Search", searchPane);
+        tabbedPane.add(SEARCH, searchPane);
 
         JButton createClassButton = new JButton(CREATE_CLASS);
         createClassButton.addActionListener(this);
@@ -254,8 +226,10 @@ void saveRecentClassesToPrefs() {
     public void actionPerformed(ActionEvent e) {
         switch (e.getActionCommand()) {
             case (APPLY_CLASS):
+                String activeList = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
+
                 switch (activeList) {
-                    case FULL:
+                    case ALL_CLASSES:
                         lastSelectedClass = fullList.getSelectedValue();
                         currentListModel.add(lastSelectedClass);
                         recentListModel.add(lastSelectedClass);

diff --git a/mia-plugin/src/main/java/io/github/mianalysis/mia/process/selectors/ObjectSelector.java b/mia-plugin/src/main/java/io/github/mianalysis/mia/process/selectors/ObjectSelector.java
@@ -843,7 +843,7 @@ public void addToExistingObject() {
                 return;
             }
         }
-        
+
         // If no ROI was found, this will add it as a new ROI
         ObjRoi objRoi = new ObjRoi(ID, roi, displayIpl.getT() - 1, displayIpl.getZ() - 1,
                 assignedClass);
@@ -867,14 +867,14 @@ public void changeObjectClass() {
                 } catch (Exception e) {
                 }
             assignedClass = classSelector.getLastSelectedClass();
+
         }
 
         // Get selected ROIs
         List<ObjRoi> selected = list.getSelectedValuesList();
 
-        for (ObjRoi objRoi : selected) {
+        for (ObjRoi objRoi : selected)
             objRoi.setAssignedClass(assignedClass);
-        }
 
         listModel.redraw();
 
@@ -1095,12 +1095,24 @@ public void addToOverlay(ObjRoi objRoi) {
                 break;
         }
 
-        switch ((String) overlayMode.getSelectedItem()) {
-            case OverlayModes.FILL:
-                overlayRoi.setFillColor(new Color(colour.getRed(), colour.getGreen(), colour.getBlue(), 64));
+        switch (overlayRoi.getType()) {
+            // Lines are a special case when it comes to rendering
+            case Roi.LINE:
+            case Roi.FREELINE:
+            case Roi.POLYLINE:
+                overlayRoi.setStrokeColor(new Color(colour.getRed(), colour.getGreen(), colour.getBlue(), 64));
                 break;
-            case OverlayModes.OUTLINES:
-                overlayRoi.setStrokeColor(colour);
+
+            // Everything else is rendered as the normal fill or outlines
+            default:
+                switch ((String) overlayMode.getSelectedItem()) {
+                    case OverlayModes.FILL:
+                        overlayRoi.setFillColor(new Color(colour.getRed(), colour.getGreen(), colour.getBlue(), 64));
+                        break;
+                    case OverlayModes.OUTLINES:
+                        overlayRoi.setStrokeColor(colour);
+                        break;
+                }
                 break;
         }
 

diff --git a/mia-ptbiop/pom.xml b/mia-ptbiop/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-ptbiop</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</version>
     <packaging>jar</packaging>
     <name>mia-ptbiop</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-samj/pom.xml b/mia-samj/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-samj</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</version>
     <packaging>jar</packaging>
     <name>mia-samj</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-stardist/pom.xml b/mia-stardist/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.11</version>
+        <version>1.6.12</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-stardist</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</version>
     <packaging>jar</packaging>
     <name>mia-stardist</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/pom.xml b/pom.xml
@@ -12,7 +12,7 @@
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>pom-mia</artifactId>
-    <version>1.6.11</version>
+    <version>1.6.12</version>
     <packaging>pom</packaging>
     <name>pom-mia</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/target/site/dependencies.html b/target/site/dependencies.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<!-- Generated by Apache Maven Doxia Site Renderer 1.8.1 from org.apache.maven.plugins:maven-project-info-reports-plugin:3.0.0:dependencies at 2024-10-24 -->
+<!-- Generated by Apache Maven Doxia Site Renderer 1.8.1 from org.apache.maven.plugins:maven-project-info-reports-plugin:3.0.0:dependencies at 2024-10-29 -->
 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
@@ -24,8 +24,8 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2024-10-24</span>
-          &nbsp;| <span id="projectVersion">Version: 1.6.11</span>
+        <span id="publishDate">Last Published: 2024-10-29</span>
+          &nbsp;| <span id="projectVersion">Version: 1.6.12</span>
       </div>
       <div class="xright"><a href="./" title="pom-mia">pom-mia</a>      </div>
       <div class="clear">
@@ -2529,7 +2529,7 @@ <h2><a name="Project_Dependency_Graph"></a>Project Dependency Graph</h2>
 <div class="section">
 <h3><a name="Dependency_Tree"></a>Dependency Tree</h3>
 <ul>
-<li>io.github.mianalysis:pom-mia:pom:1.6.11 <img id="_img1" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep0', '_img1' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep0" style="display:none">
+<li>io.github.mianalysis:pom-mia:pom:1.6.12 <img id="_img1" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep0', '_img1' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep0" style="display:none">
 <table border="0" class="bodyTable">
 <tr class="a">
 <th>pom-mia</th></tr>