Merge pull request #197 from mianalysis/develop

Develop

mia-algorithms/pom.xml

@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.3</version>
+        <version>1.6.4</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-algorithms</artifactId>
-    <version>1.6.3</version>
+    <version>1.6.4</version>
     <packaging>jar</packaging>
     <name>mia-algorithms</name>
     <url>https://github.com/mianalysis/mia</url>

mia-bonej/pom.xml

@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.3</version>
+        <version>1.6.4</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-bonej</artifactId>
-    <version>1.6.3</version>
+    <version>1.6.4</version>
     <packaging>jar</packaging>
     <name>mia-bonej</name>
     <url>https://github.com/mianalysis/mia</url>

mia-coordinates/pom.xml

@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.3</version>
+        <version>1.6.4</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-coordinates</artifactId>
-    <version>1.6.3</version>
+    <version>1.6.4</version>
     <packaging>jar</packaging>
     <name>mia-coordinates</name>
     <url>https://github.com/mianalysis/mia</url>

mia-core/pom.xml

@@ -6,12 +6,12 @@
     <parent>
         <groupId>io.github.mianalysis</groupId>
         <artifactId>pom-mia</artifactId>
-        <version>1.6.3</version>
+        <version>1.6.4</version>
     </parent>
 
     <groupId>io.github.mianalysis</groupId>
     <artifactId>mia-core</artifactId>
-    <version>1.6.3</version>
+    <version>1.6.4</version>
     <packaging>jar</packaging>
     <name>mia-core</name>
     <url>https://github.com/mianalysis/mia</url>

mia-core/src/main/java/io/github/mianalysis/mia/module/objects/filter/AbstractObjectFilter.java

@@ -221,15 +221,15 @@ public PartnerRefs updateAndGetPartnerRefs() {
 
         switch ((String) parameters.getValue(FILTER_MODE, workspace)) {
             case FilterModes.MOVE_FILTERED:
-                String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
+                String outputObjectsName = parameters.getValue(OUTPUT_FILTERED_OBJECTS, workspace);
 
                 // Getting references up to this location
                 PartnerRefs currentRefs = modules.getPartnerRefs(this);
 
                 // Adding relationships
-                String[] partnerNames = currentRefs.getPartnerNamesArray(inputObjectsName);
+                String[] partnerNames = currentRefs.getPartnerNamesArray(outputObjectsName);
                 for (String partnerName : partnerNames)
-                    returnedRefs.add(partnerRefs.getOrPut(inputObjectsName, partnerName));
+                    returnedRefs.add(partnerRefs.getOrPut(outputObjectsName, partnerName));
 
                 break;
         }

mia-core/src/main/java/io/github/mianalysis/mia/module/workflow/ModuleIsEnabled.java

@@ -65,7 +65,7 @@ public interface TestModes {
 
     public boolean testDoRedirect(Workspace workspace) {
         String testMode = parameters.getValue(TEST_MODE,workspace);
-        Module testModule = parameters.getValue(TEST_MODULE,workspace);
+        Module testModule = modules.getModuleByID(parameters.getValue(TEST_MODULE,workspace));
 
         if (testModule == null)
             return false;

mia-core/src/main/java/io/github/mianalysis/mia/object/Measurement.java

@@ -26,6 +26,10 @@ public Measurement(String name, double value) {
         this.value = value;
     }
 
+    public Measurement duplicate() {
+        return new Measurement(getName(), getValue());
+    }
+
 
     // GETTERS AND SETTERS
 

mia-core/src/main/java/io/github/mianalysis/mia/object/Obj.java

@@ -207,7 +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();
@@ -622,6 +622,47 @@ public void clearAllCoordinates() {
         rois = new HashMap<>();
     }
 
+    public Obj duplicate(Objs newCollection, boolean duplicateRelationships, boolean duplicateMeasurement,
+            boolean duplicateMetadata) {
+        Obj newObj = new Obj(newCollection, getID(), this);
+
+        // Duplicating coordinates
+        newObj.setCoordinateSet(getCoordinateSet().duplicate());
+
+        // Duplicating relationships
+        if (duplicateRelationships) {
+            for (Obj parent : parents.values()) {
+                newObj.addParent(parent);
+                parent.addChild(this);
+            }
+
+            for (Objs currChildren : children.values())
+                for (Obj child : currChildren.values()) {
+                    newObj.addChild(child);
+                    child.addParent(newObj);
+                }
+
+            for (Objs currPartners : partners.values())
+                for (Obj partner : currPartners.values()) {
+                    newObj.addPartner(partner);
+                    partner.addPartner(newObj);
+                }
+        }
+
+        // Duplicating measurements
+        if (duplicateMeasurement)
+            for (Measurement measurement : measurements.values())
+                newObj.addMeasurement(measurement.duplicate());
+
+        // Duplicating metadata
+        if (duplicateMetadata)
+            for (ObjMetadata metadataItem : metadata.values())
+                newObj.addMetadataItem(metadataItem.duplicate());
+
+        return newObj;
+
+    }
+
     @Override
     public int hashCode() {
         // Updating the hash for time-point. Measurements and relationships aren't

mia-core/src/main/java/io/github/mianalysis/mia/object/ObjMetadata.java

@@ -26,6 +26,10 @@ public ObjMetadata(String name, String value) {
         this.value = value;
     }
 
+    public ObjMetadata duplicate() {
+        return new ObjMetadata(getName(), getValue());
+    }
+
 
     // GETTERS AND SETTERS
 

mia-core/src/main/java/io/github/mianalysis/mia/object/Objs.java

@@ -1,5 +1,6 @@
 package io.github.mianalysis.mia.object;
 
+import java.awt.Color;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
@@ -9,6 +10,7 @@
 import ij.ImagePlus;
 import ij.measure.Calibration;
 import ij.measure.ResultsTable;
+import ij.process.LUT;
 import io.github.mianalysis.mia.module.Module;
 import io.github.mianalysis.mia.module.Modules;
 import io.github.mianalysis.mia.object.coordinates.Point;
@@ -40,7 +42,8 @@ public class Objs extends LinkedHashMap<Integer, Obj> {
     private double frameInterval;
     private Unit<Time> temporalUnit;
 
-    public Objs(String name, double dppXY, double dppZ, String units, int width, int height, int nSlices, int nFrames, double frameInterval, Unit<Time> temporalUnit) {
+    public Objs(String name, double dppXY, double dppZ, String units, int width, int height, int nSlices, int nFrames,
+            double frameInterval, Unit<Time> temporalUnit) {
         this.name = name;
         this.spatCal = new SpatCal(dppXY, dppZ, units, width, height, nSlices);
         this.nFrames = nFrames;
@@ -208,7 +211,7 @@ public int getLargestID() {
         for (Obj obj : values())
             if (obj.getID() > largestID)
                 largestID = obj.getID();
-        
+
         return largestID;
 
     }
@@ -227,7 +230,8 @@ public Obj getAsSingleObject() {
                 try {
                     newObj.add(point.duplicate());
                 } catch (PointOutOfRangeException e) {
-                    // This shouldn't occur, as the points are from a collection with the same dimensions
+                    // This shouldn't occur, as the points are from a collection with the same
+                    // dimensions
                     e.printStackTrace();
                 }
 
@@ -239,7 +243,8 @@ public Image convertToImage(String outputName, HashMap<Integer, Float> hues, int
         return convertToImage(outputName, hues, bitDepth, nanBackground, false);
     }
 
-    public Image convertToImage(String outputName, HashMap<Integer, Float> hues, int bitDepth, boolean nanBackground, boolean verbose) {
+    public Image convertToImage(String outputName, HashMap<Integer, Float> hues, int bitDepth, boolean nanBackground,
+            boolean verbose) {
         // Create output image
         Image image = createImage(outputName, bitDepth);
 
@@ -251,8 +256,9 @@ public Image convertToImage(String outputName, HashMap<Integer, Float> hues, int
         int count = 0;
         for (Obj object : values()) {
             object.addToImage(image, hues.get(object.getID()));
-            Module.writeProgressStatus(++count, size(), "objects", "Object collection");
-        }            
+            if (verbose)
+                Module.writeProgressStatus(++count, size(), "objects", "Object collection");
+        }
 
         // Assigning the spatial cal from the cal
         spatCal.setImageCalibration(image.getImagePlus());
@@ -279,8 +285,26 @@ public Image convertToImageRandomColours() {
 
     }
 
+    public Image convertToImageBinary() {
+        HashMap<Integer, Float> hues = ColourFactory.getSingleColourValues(this, ColourFactory.SingleColours.WHITE);
+        Image dispImage = convertToImage(name, hues, 8, false);
+
+        if (dispImage == null)
+            return null;
+        if (dispImage.getImagePlus() == null)
+            return null;
+
+        ImagePlus dispIpl = dispImage.getImagePlus();
+        dispIpl.setLut(LUT.createLutFromColor(Color.WHITE));
+        dispIpl.setPosition(1, 1, 1);
+        dispIpl.updateChannelAndDraw();
+
+        return dispImage;
+
+    }
+
     public Image convertToImageIDColours() {
-        HashMap<Integer, Float> hues = ColourFactory.getIDHues(this,false);
+        HashMap<Integer, Float> hues = ColourFactory.getIDHues(this, false);
         Image dispImage = convertToImage(name, hues, 32, false);
 
         if (dispImage == null)
@@ -289,7 +313,7 @@ public Image convertToImageIDColours() {
             return null;
 
         ImagePlus dispIpl = dispImage.getImagePlus();
-        dispIpl.setLut(LUTs.Random(true,false));
+        dispIpl.setLut(LUTs.Random(true, false));
         dispIpl.setPosition(1, 1, 1);
         dispIpl.updateChannelAndDraw();
 
@@ -369,7 +393,7 @@ public Obj getByEqualsIgnoreNameAndID(Obj referenceObj) {
         for (Obj testObj : values())
             if (testObj.equalsIgnoreNameAndID(referenceObj))
                 return testObj;
-        
+
         return null;
 
     }
@@ -381,7 +405,8 @@ public void resetCollection() {
 
     /**
      * Displays measurement values from a specific Module
-     * @param module The module for which measurements will be displayed
+     * 
+     * @param module  The module for which measurements will be displayed
      * @param modules The collection of modules in which this module resides
      */
     public void showMeasurements(Module module, Modules modules) {
@@ -471,7 +496,8 @@ public void showAllMeasurements() {
 
     /**
      * Displays metadata values from a specific Module
-     * @param module The module for which metadata will be displayed
+     * 
+     * @param module  The module for which metadata will be displayed
      * @param modules The collection of modules in which this module resides
      */
     public void showMetadata(Module module, Modules modules) {
@@ -487,7 +513,7 @@ public void showMetadata(Module module, Modules modules) {
         LinkedHashSet<String> metadataNames = new LinkedHashSet<>();
         for (ObjMetadataRef metadataRef : metadataRefs.values()) {
             if (metadataRef.getObjectsName().equals(name))
-            metadataNames.add(metadataRef.getName());
+                metadataNames.add(metadataRef.getName());
         }
 
         // Iterating over each measurement, adding all the values
@@ -642,16 +668,15 @@ public Objs getObjectsInFrame(String outputObjectsName, int frame) {
         outputObjects.setNFrames(1);
 
         // Iterating over objects, getting those in this frame
-        for (Obj obj:values()) {
-            if (obj.getT() == frame) {   
+        for (Obj obj : values()) {
+            if (obj.getT() == frame) {
                 Obj outputObject = new Obj(outputObjects, obj.getVolumeType(), obj.getID());
                 outputObject.setCoordinateSet(obj.getCoordinateSet().duplicate());
                 outputObject.setT(0);
                 outputObjects.add(outputObject);
             }
         }
 
-
         return outputObjects;
 
     }
@@ -671,11 +696,32 @@ public Unit<Time> getTemporalUnit() {
     public void setNFrames(int nFrames) {
         this.nFrames = nFrames;
     }
+
+    public Objs duplicate(String newObjectsName, boolean duplicateRelationships, boolean duplicateMeasurement,
+            boolean duplicateMetadata, boolean addOriginalDuplicateRelationship) {
+        Objs newObjs = new Objs(newObjectsName, this);
+
+        for (Obj obj : values()) {
+            Obj newObj = obj.duplicate(newObjs, duplicateRelationships, duplicateMeasurement, duplicateMetadata);
+
+            newObjs.add(newObj);
+
+            if (addOriginalDuplicateRelationship) {
+                newObj.addParent(obj);
+                obj.addChild(newObj);
+            }
+        }
+
+        newObjs.maxID = this.maxID;
+
+        return newObjs;
+
+    }
 }
 
 // clear all
 // print'HelloWorld'
 // if{
-//         'theSkyIsGreen'
-//              getMeasurements
+// 'theSkyIsGreen'
+// getMeasurements
 // }

mia-core/src/main/java/io/github/mianalysis/mia/object/image/Image.java

@@ -41,6 +41,8 @@ public abstract class Image<T extends RealType<T> & NativeType<T>> {
 
     public abstract ImageRenderer getRenderer();
 
+    public abstract void clear();
+
     public abstract void setRenderer(ImageRenderer imageRenderer);
 
     public abstract void show(String title, @Nullable LUT lut, boolean normalise, boolean composite);

mia-core/src/main/java/io/github/mianalysis/mia/object/image/ImagePlusImage.java

@@ -262,6 +262,11 @@ public synchronized static ImageStack getSetStack(ImagePlus inputImagePlus, int
         }
     }
 
+    @Override
+    public void clear() {
+        imagePlus = null;
+    }
+
     @Override
     public int hashCode() {
         int hash = 1;