Add remove rois (#10)

* add example script to remove rois
* changes following @ppouchin 's suggestions in PR
* adds me as a contributor

pom.xml

@@ -11,7 +11,7 @@
 
     <groupId>fr.igred</groupId>
     <artifactId>omero_macro-extensions</artifactId>
-    <version>1.1.0</version>
+    <version>1.2.0</version>
 
     <name>ImageJ OMERO macro extensions</name>
     <description>Plugin providing macro extensions for OMERO.</description>
@@ -53,6 +53,10 @@
             <name>Pierre Pouchin</name>
             <email>[email protected]</email>
         </contributor>
+        <contributor>
+            <name>Romain Guiet</name>
+            <email>[email protected]</email>
+        </contributor>
     </contributors>
 
     <mailingLists>

src/main/java/fr/igred/ij/plugin/OMEROMacroExtension.java

@@ -45,6 +45,7 @@
 import java.nio.file.Files;
 import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -89,6 +90,7 @@ public class OMEROMacroExtension implements PlugIn, MacroExtension {
             newDescriptor("getImage", this, ARG_NUMBER),
             newDescriptor("getROIs", this, ARG_NUMBER, ARG_NUMBER + ARG_OPTIONAL, ARG_STRING + ARG_OPTIONAL),
             newDescriptor("saveROIs", this, ARG_NUMBER, ARG_STRING + ARG_OPTIONAL),
+            newDescriptor("removeROIs", this, ARG_NUMBER, ARG_STRING + ARG_OPTIONAL),
             newDescriptor("sudo", this, ARG_STRING),
             newDescriptor("endSudo", this),
             newDescriptor("disconnect", this),
@@ -965,6 +967,29 @@ public int saveROIs(ImagePlus imp, long id, String property) {
         return result;
     }
 
+    /**
+     * removes the ROIs of the image in OMERO.
+     *
+     * @param id       The image ID on OMERO.
+     *
+     * @return The 1 if at least one ROI has been deleted
+     */
+    public int removeROIs(long id) {
+
+        int removed = 0;
+        try {
+            ImageWrapper image = client.getImage(id);
+            List<ROIWrapper> rois = image.getROIs(client);
+            for (ROIWrapper roi : rois) {
+                client.delete(roi);
+                removed++;
+            }
+        } catch (ServiceException | AccessException | ExecutionException | OMEROServerError | InterruptedException e) {
+            IJ.error("Could not remove image ROIs: " + e.getMessage());
+        }
+        return removed;
+    }
+
 
     /**
      * Disconnects from OMERO.
@@ -979,6 +1004,7 @@ public void disconnect() {
     public void run(String arg) {
         if (!IJ.macroRunning()) {
             IJ.error("Cannot install extensions from outside a macro!");
+            //TODO print API
             return;
         }
         Functions.registerExtensions(this);
@@ -1162,6 +1188,12 @@ public String handleExtension(String name, Object[] args) {
                 results = String.valueOf(nROIs);
                 break;
 
+            case "removeROIs":
+                id = ((Double) args[0]).longValue();
+                int removed = removeROIs(id);
+                results = String.valueOf(removed);
+                break;
+
             case "sudo":
                 sudo((String) args[0]);
                 break;

src/main/resources/script_templates/OMERO/Macro_Extensions/Remove_rois_dataset.ijm

@@ -0,0 +1,25 @@
+// @String(label="Username") USERNAME
+// @String(label="Password", style='password') PASSWORD
+// @String(label="Host", value='wss://workshop.openmicroscopy.org/omero-ws') HOST
+// @Integer(label="Port", value=4064) PORT
+// @Integer(label="Dataset ID", value=2331) dataset_id
+
+run("OMERO Extensions");
+
+connected = Ext.connectToOMERO(HOST, PORT, USERNAME, PASSWORD);
+
+
+
+if(connected == "true") {
+    images = Ext.list("images", "dataset", dataset_id);
+    image_ids = split(images, ",");
+
+    for(i=0; i<image_ids.length; i++) {
+	    // Open the image
+        Ext.removeROIs(image_ids[i])
+    }
+}
+
+
+Ext.disconnect();
+print("processing done");

src/test/java/fr/igred/ij/plugin/OMEROExtensionTest.java

@@ -18,6 +18,9 @@
 
 import fr.igred.omero.Client;
 import fr.igred.omero.annotations.TableWrapper;
+import fr.igred.omero.exception.AccessException;
+import fr.igred.omero.exception.OMEROServerError;
+import fr.igred.omero.exception.ServiceException;
 import ij.ImagePlus;
 import ij.gui.Overlay;
 import ij.gui.Roi;
@@ -39,6 +42,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -284,10 +288,14 @@ void testSaveAndGetROIs() {
         int savedROIs = ext.saveROIs(imp, 1L, "");
         overlay.clear();
         int loadedROIs = ext.getROIs(imp, 1L, true, "");
+        ext.removeROIs(1L);
+        int clearedROIs = ext.getROIs(imp, 1L, true, "");
+
 
         assertEquals(1, savedROIs);
         assertEquals(1, loadedROIs);
         assertEquals(1, imp.getOverlay().size());
+        assertEquals(0, clearedROIs);
     }