Updated version number to 1.7.0-SNAPSHOT

mianalysis · Nov 15, 2024 · 3500a2f · 3500a2f
1 parent 9775e5b
commit 3500a2f
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Showing 15 changed files with 60 additions and 37 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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-algorithms</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-bonej</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-coordinates</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-core</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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/system/GlobalVariables.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/system/GlobalVariables.java
@@ -22,6 +22,7 @@
 import io.github.mianalysis.mia.object.parameters.Parameters;
 import io.github.mianalysis.mia.object.parameters.SeparatorP;
 import io.github.mianalysis.mia.object.parameters.text.StringP;
+import io.github.mianalysis.mia.object.parameters.text.TextAreaP;
 import io.github.mianalysis.mia.object.refs.collections.ImageMeasurementRefs;
 import io.github.mianalysis.mia.object.refs.collections.MetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ObjMeasurementRefs;
@@ -30,17 +31,22 @@
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
 
-
 /**
-* Create fixed values which can be accessed by text entry parameters from all modules.  Use of global variables allows the same value to be used across multiple different modules without the need to explicitly type it.  Global variables are accessed with the notation "V{[NAME]}", where "[NAME]" is replaced with the name of the relevant variable.  Global variables can be used by any text or numeric parameter.
-*/
+ * Create fixed values which can be accessed by text entry parameters from all
+ * modules. Use of global variables allows the same value to be used across
+ * multiple different modules without the need to explicitly type it. Global
+ * variables are accessed with the notation "V{[NAME]}", where "[NAME]" is
+ * replaced with the name of the relevant variable. Global variables can be used
+ * by any text or numeric parameter.
+ */
 @Plugin(type = Module.class, priority = Priority.LOW, visible = true)
 public class GlobalVariables extends Module {
     public static final String VARIABLE_SEPARATOR = "Variable settings";
 
-	/**
-	* Add a new global variable.  Added variables can be removed using the "Remove" button.
-	*/
+    /**
+     * Add a new global variable. Added variables can be removed using the "Remove"
+     * button.
+     */
     public static final String ADD_NEW_VARIABLE = "Add new variable";
     public static final String VARIABLE_NAME = "Variable name";
     public static final String VARIABLE_TYPE = "Variable type";
@@ -50,6 +56,7 @@ public class GlobalVariables extends Module {
     public static final String VARIABLE_FOLDER = "Variable folder";
     public static final String VARIABLE_CHOICES = "Variable choices";
     public static final String VARIABLE_CHOICE = "Variable choice";
+    public static final String VARIABLE_TEXT_AREA = "Variable text";
     public static final String STORE_AS_METADATA_ITEM = "Store as metadata item";
 
     protected static final HashMap<StringP, String> globalVariables = new HashMap<>();
@@ -60,8 +67,9 @@ public interface VariableTypes {
         String FILE = "File";
         String FOLDER = "Folder";
         String TEXT = "Text";
+        String TEXT_AREA = "Text area";
 
-        String[] ALL = new String[] { BOOLEAN, CHOICE, FILE, FOLDER, TEXT };
+        String[] ALL = new String[] { BOOLEAN, CHOICE, FILE, FOLDER, TEXT, TEXT_AREA };
 
     }
 
@@ -191,6 +199,9 @@ public Status process(Workspace workspace) {
                     case VariableTypes.TEXT:
                         workspace.getMetadata().put(variableName, collection.getValue(VARIABLE_VALUE, workspace));
                         break;
+                    case VariableTypes.TEXT_AREA:
+                        workspace.getMetadata().put(variableName, collection.getValue(VARIABLE_TEXT_AREA, workspace));
+                        break;
                 }
             }
         }
@@ -212,6 +223,7 @@ protected void initialiseParameters() {
         parameterCollection.add(new StringP(VARIABLE_CHOICES, this));
         parameterCollection.add(new ChoiceP(VARIABLE_CHOICE, this, "", new String[0]));
         parameterCollection.add(new BooleanP(STORE_AS_METADATA_ITEM, this, false));
+        parameterCollection.add(new TextAreaP(VARIABLE_TEXT_AREA, this, true));
 
         parameters.add(new ParameterGroup(ADD_NEW_VARIABLE, this, parameterCollection, 1, getUpdaterAndGetter()));
 
@@ -250,6 +262,9 @@ public Parameters updateAndGetParameters() {
                     case VariableTypes.TEXT:
                         globalVariables.put(variableName, collection.getValue(VARIABLE_VALUE, workspace));
                         break;
+                    case VariableTypes.TEXT_AREA:
+                        globalVariables.put(variableName, collection.getValue(VARIABLE_TEXT_AREA, workspace));
+                        break;
                 }
 
             } else if (globalVariables.containsKey(variableName)) {
@@ -272,8 +287,8 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
     }
 
     @Override
-    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
-	return null; 
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {
+        return null;
     }
 
     @Override
@@ -340,7 +355,11 @@ void addParameterDescriptions() {
                 + "\" parameter.  The variable will be set to the full path to this folder.  Note: backslash characters will be escaped (i.e. \"\\\" will appear as \"\\\\\").</li>"
 
                 + "<li>\"" + VariableTypes.TEXT + "\" Specify a fixed text value for this variable using the \""
-                + VARIABLE_VALUE + "\" parameter.</li></ul>");
+                + VARIABLE_VALUE + "\" parameter.</li></ul>"
+
+                + "<li>\"" + VariableTypes.TEXT_AREA + "\" Specify a fixed text value for this variable using the \""
+                + VARIABLE_TEXT_AREA
+                + "\" parameter.  This simply provides a larger, multiline area in which text can be entered.</li></ul>");
 
         collection.get(VARIABLE_BOOLEAN).setDescription("Boolean value for the corresponding global variable when \""
                 + VARIABLE_TYPE + "\" is in \"" + VariableTypes.BOOLEAN + "\" mode.");
@@ -395,6 +414,9 @@ public Parameters updateAndGet(Parameters params) {
                     case VariableTypes.TEXT:
                         returnedParameters.add(params.getParameter(VARIABLE_VALUE));
                         break;
+                    case VariableTypes.TEXT_AREA:
+                        returnedParameters.add(params.getParameter(VARIABLE_TEXT_AREA));
+                        break;
                 }
                 returnedParameters.add(params.getParameter(STORE_AS_METADATA_ITEM));
 

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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-deepimagej</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-macros</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+            <version>1.7.0-SNAPSHOT</version>
         </dependency>
 
         <dependency>
             <groupId>io.github.mianalysis</groupId>
             <artifactId>mia-modules</artifactId>
-            <version>1.6.13-SNAPSHOT</version>
+            <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-modules</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+            <version>1.7.0-SNAPSHOT</version>
         </dependency>
 
         <dependency>

diff --git a/...n/java/io/github/mianalysis/mia/module/images/measure/abstrakt/MeasurementCalculator.java b/...n/java/io/github/mianalysis/mia/module/images/measure/abstrakt/MeasurementCalculator.java
@@ -3,6 +3,7 @@
 import java.util.Collection;
 import java.util.List;
 
+import io.github.mianalysis.mia.MIA;
 import io.github.mianalysis.mia.module.Module;
 import io.github.mianalysis.mia.module.Modules;
 import io.github.mianalysis.mia.object.Obj;

diff --git a/...github/mianalysis/mia/module/objects/measure/miscellaneous/CalculateStatsForChildren.java b/...github/mianalysis/mia/module/objects/measure/miscellaneous/CalculateStatsForChildren.java
@@ -171,7 +171,7 @@ public static void processObject(Obj parentObject, String childObjectsName, Stri
                 String name = getFullName(childObjectsName, measurement, Measurements.MIN);
                 parentObject.addMeasurement(new Measurement(name, cs.getMin()));
             }
-
+            
             if (statsToCalculate[3]) {
                 String name = getFullName(childObjectsName, measurement, Measurements.MAX);
                 parentObject.addMeasurement(new Measurement(name, cs.getMax()));

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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-plugin</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>mia-plugin</name>
     <url>https://github.com/mianalysis/mia</url>

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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-ptbiop</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-samj</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+        <version>1.7.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-stardist</artifactId>
-    <version>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</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>1.6.13-SNAPSHOT</version>
+    <version>1.7.0-SNAPSHOT</version>
     <packaging>pom</packaging>
     <name>pom-mia</name>
     <url>https://github.com/mianalysis/mia</url>