Added object metadata to modules

This allows text items to be stored with objects and exported to Excel
mianalysis · May 9, 2024 · 66c6d03 · 66c6d03
1 parent 6685859
commit 66c6d03
Show file tree

Hide file tree

Showing 232 changed files with 2,003 additions and 170 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>1.5.3-SNAPSHOT</version>
+        <version>1.6.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-algorithms</artifactId>
-    <version>1.5.3-SNAPSHOT</version>
+    <version>1.6.0-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>1.5.3-SNAPSHOT</version>
+        <version>1.6.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-bonej</artifactId>
-    <version>1.5.3-SNAPSHOT</version>
+    <version>1.6.0-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>mia-bonej</name>
     <url>https://github.com/mianalysis/mia</url>

diff --git a/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/FitEllipsoid.java b/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/FitEllipsoid.java
@@ -32,6 +32,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.process.exceptions.IntegerOverflowException;
@@ -502,6 +503,11 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
 
     }
 
+    @Override
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
     @Override
     public MetadataRefs updateAndGetMetadataReferences() {
         return null;

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>1.5.3-SNAPSHOT</version>
+        <version>1.6.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-coordinates</artifactId>
-    <version>1.5.3-SNAPSHOT</version>
+    <version>1.6.0-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>1.5.3-SNAPSHOT</version>
+        <version>1.6.0-SNAPSHOT</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-core</artifactId>
-    <version>1.5.3-SNAPSHOT</version>
+    <version>1.6.0-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/Module.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/Module.java
@@ -22,12 +22,14 @@
 import io.github.mianalysis.mia.object.refs.ImageMeasurementRef;
 import io.github.mianalysis.mia.object.refs.MetadataRef;
 import io.github.mianalysis.mia.object.refs.ObjMeasurementRef;
+import io.github.mianalysis.mia.object.refs.ObjMetadataRef;
 import io.github.mianalysis.mia.object.refs.ParentChildRef;
 import io.github.mianalysis.mia.object.refs.PartnerRef;
 import io.github.mianalysis.mia.object.refs.abstrakt.Ref;
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -44,6 +46,7 @@ public abstract class Module extends Ref implements Comparable, SciJavaPlugin {
     protected Parameters parameters = new Parameters();
     protected ImageMeasurementRefs imageMeasurementRefs = new ImageMeasurementRefs();
     protected ObjMeasurementRefs objectMeasurementRefs = new ObjMeasurementRefs();
+    protected ObjMetadataRefs objectMetadataRefs = new ObjMetadataRefs();
     protected MetadataRefs metadataRefs = new MetadataRefs();
     protected ParentChildRefs parentChildRefs = new ParentChildRefs();
     protected PartnerRefs partnerRefs = new PartnerRefs();
@@ -150,6 +153,18 @@ public Module(String name, Modules modules) {
      */
     public abstract ObjMeasurementRefs updateAndGetObjectMeasurementRefs();
 
+    /**
+     * Metadata added to any objects by this module are reported by adding their
+     * reference to an ObjMetadataRefs collection. When no metadata items are added
+     * by this module, this method can simply return "null". These references tell
+     * downstream modules what metadata items are available for each object of a
+     * specific object collection. Returned references should be the original copies
+     * stored in the local "objectMetadataRefs" object.
+     * 
+     * @return Object metadata references currently active for this module
+     */
+    public abstract ObjMetadataRefs updateAndGetObjectMetadataRefs();
+
     /**
      * Values added to the workspace's metadata collection by this module are
      * reported by adding their reference to a MetadataRefs collection. When no
@@ -245,6 +260,10 @@ public void addObjectMeasurementRef(ObjMeasurementRef ref) {
         objectMeasurementRefs.add(ref);
     }
 
+    public void addObjectMetadataRef(ObjMetadataRef ref) {
+        objectMetadataRefs.add(ref);
+    }
+
     public ImageMeasurementRef getImageMeasurementRef(String name) {
         return imageMeasurementRefs.getOrPut(name);
     }
@@ -257,6 +276,10 @@ public ObjMeasurementRef getObjectMeasurementRef(String name) {
         return objectMeasurementRefs.getOrPut(name);
     }
 
+    public ObjMetadataRef getObjectMetadataRef(String name) {
+        return objectMetadataRefs.getOrPut(name);
+    }
+
     public MetadataRef getMetadataRef(String name) {
         return metadataRefs.getOrPut(name);
     }
@@ -501,6 +524,14 @@ public Module duplicate(Modules newModules) {
             newObjMeasurementRefs.add(newRef);
         }
 
+        ObjMetadataRefs newObjMetadataRefs = newModule.objectMetadataRefs;
+        for (ObjMetadataRef ref : objectMetadataRefs.values()) {
+            ObjMetadataRef newRef = ref.duplicate();
+            if (newRef == null)
+                continue;
+            newObjMetadataRefs.add(newRef);
+        }
+
         ImageMeasurementRefs newImageMeasurementRefs = newModule.imageMeasurementRefs;
         for (ImageMeasurementRef ref : imageMeasurementRefs.values()) {
             ImageMeasurementRef newRef = ref.duplicate();
@@ -621,7 +652,7 @@ public void setAttributesFromXML(Node node) {
                 MIA.log.writeWarning("    Module name: \"" + name + "\"");
                 MIA.log.writeWarning("    Workflow version: " + workflowVersion);
                 MIA.log.writeWarning("    Plugin version: " + getVersionNumber());
-                MIA.log.writeWarning("    Status: " + resultsWarning+".");
+                MIA.log.writeWarning("    Status: " + resultsWarning + ".");
 
             }
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/Modules.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/Modules.java
@@ -26,9 +26,11 @@
 import io.github.mianalysis.mia.object.parameters.objects.RemovedObjectsP;
 import io.github.mianalysis.mia.object.refs.ImageMeasurementRef;
 import io.github.mianalysis.mia.object.refs.ObjMeasurementRef;
+import io.github.mianalysis.mia.object.refs.ObjMetadataRef;
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.refs.collections.Refs;
@@ -264,6 +266,64 @@ void addObjectMeasurementRefs(Module module, ObjMeasurementRefs measurementRefs,
         }
     }
 
+    public ObjMetadataRefs getObjectMetadataRefs(String objectName) {
+        return getObjectMetadataRefs(objectName, null);
+
+    }
+
+    public ObjMetadataRefs getObjectMetadataRefs(String objectName, Module cutoffModule) {
+        ObjMetadataRefs metadataRefs = new ObjMetadataRefs();
+
+        // If this is a distant relative there will be "//" in the name that need to be
+        // removed
+        if (objectName.contains("//"))
+            objectName = objectName.substring(objectName.lastIndexOf("//") + 3);
+
+        addObjectMetadataRefs(inputControl, metadataRefs, objectName);
+        addObjectMetadataRefs(outputControl, metadataRefs, objectName);
+
+        // Iterating over all modules, collecting any measurements for the current
+        // objects
+        for (Module module : this) {
+            if (module == cutoffModule)
+                break;
+            if (!module.isEnabled() | !module.isRunnable())
+                continue;
+                addObjectMetadataRefs(module, metadataRefs, objectName);
+        }
+
+        return metadataRefs;
+
+    }
+
+    public boolean objectsExportMetadata(String objectName) {
+        ObjMetadataRefs refCollection = getObjectMetadataRefs(objectName);
+
+        for (ObjMetadataRef ref : refCollection.values()) {
+            if (ref.isExportIndividual() && ref.isExportGlobal())
+                return true;
+        }
+
+        return false;
+
+    }
+
+    void addObjectMetadataRefs(Module module, ObjMetadataRefs metadataRefs, String objectName) {
+        if (!module.isEnabled())
+            return;
+            ObjMetadataRefs currentMetadataRefs = module.updateAndGetObjectMetadataRefs();
+        if (currentMetadataRefs == null)
+            return;
+
+        for (ObjMetadataRef ref : currentMetadataRefs.values()) {
+            if (ref.getObjectsName() == null)
+                continue;
+            if (ref.getObjectsName().equals(objectName))
+            metadataRefs.put(ref.getName(), ref);
+
+        }
+    }
+
     public MetadataRefs getMetadataRefs() {
         return getMetadataRefs(null);
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/core/InputControl.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/core/InputControl.java
@@ -34,6 +34,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -550,6 +551,11 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
         return null;
     }
 
+    @Override
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
     @Override
     public MetadataRefs updateAndGetMetadataReferences() {
         MetadataRefs returnedRefs = new MetadataRefs();

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/core/OutputControl.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/core/OutputControl.java
@@ -32,6 +32,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -701,6 +702,11 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
         return null;
     }
 
+    @Override
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
     @Override
     public MetadataRefs updateAndGetMetadataReferences() {
         return null;

diff --git a/...re/src/main/java/io/github/mianalysis/mia/module/objects/filter/AbstractObjectFilter.java b/...re/src/main/java/io/github/mianalysis/mia/module/objects/filter/AbstractObjectFilter.java
@@ -20,6 +20,7 @@
 import io.github.mianalysis.mia.object.parameters.objects.OutputObjectsP;
 import io.github.mianalysis.mia.object.refs.ObjMeasurementRef;
 import io.github.mianalysis.mia.object.refs.collections.ObjMeasurementRefs;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/script/RunMacro.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/script/RunMacro.java
@@ -39,6 +39,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -372,6 +373,11 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
         return null;
     }
 
+    @Override
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
     @Override
     public MetadataRefs updateAndGetMetadataReferences() {
         return null;

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/script/RunMacroOnObjects.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/script/RunMacroOnObjects.java
@@ -37,6 +37,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -361,7 +362,12 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
     }
 
     @Override
-public MetadataRefs updateAndGetMetadataReferences() {
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
+    @Override
+    public MetadataRefs updateAndGetMetadataReferences() {
 return null;
     }
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/system/GUISeparator.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/system/GUISeparator.java
@@ -14,6 +14,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -168,7 +169,12 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
     }
 
     @Override
-public MetadataRefs updateAndGetMetadataReferences() {
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
+    @Override
+    public MetadataRefs updateAndGetMetadataReferences() {
 return null;
     }
 

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
@@ -25,6 +25,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -266,6 +267,11 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
         return null;
     }
 
+    @Override
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
     @Override
     public MetadataRefs updateAndGetMetadataReferences() {
         Workspace workspace = null;

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/module/workflow/AddPause.java b/mia-core/src/main/java/io/github/mianalysis/mia/module/workflow/AddPause.java
@@ -21,6 +21,7 @@
 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;
+import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
@@ -149,7 +150,12 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
     }
 
     @Override
-public MetadataRefs updateAndGetMetadataReferences() {
+    public ObjMetadataRefs updateAndGetObjectMetadataRefs() {  
+	return null; 
+    }
+
+    @Override
+    public MetadataRefs updateAndGetMetadataReferences() {
 return null;
     }