Crop from coordinates (#3)

* Updated simple-omero-client to 5.14.1
* Changed String password to char (simple-omero-client update)
* Added "From OMERO" option to CropFromCoordinate, Changed buttons style.
* Backend for "OMERO option" in CropFromCoordinates.
* Changed the way to save ROIs, Changed Label of "Boxes regrouping".
* Fixed CropFromCoordinatesDialog name and serialVersionUID
* Save autocrop ROIs even if ROIs are already present

---------

Co-authored-by: SafarbatiSami <[email protected]>

pom.xml

@@ -90,7 +90,7 @@
 		<dependency>
 			<groupId>fr.igred</groupId>
 			<artifactId>simple-omero-client</artifactId>
-			<version>5.7.0</version>
+			<version>5.14.1</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
 		<dependency>

src/main/java/gred/nucleus/autocrop/AutoCrop.java

@@ -454,6 +454,7 @@ public void cropKernelsOMERO(ImageWrapper image, Long[] outputsDat, Client clien
 		info.append(getSpecificImageInfo()).append(HEADERS);
 		for (int c = 0; c < this.channelNumbers; c++) {
 			DatasetWrapper dataset = client.getDataset(outputsDat[c]);
+			List<ROIWrapper> rois = new ArrayList<>(this.boxes.size());
 			for (Map.Entry<Double, Box> entry : new TreeMap<>(this.boxes).entrySet()) {
 				int i = entry.getKey().intValue();
 				LOGGER.info("Processing box number: {} (OMERO)", i);
@@ -481,7 +482,8 @@ public void cropKernelsOMERO(ImageWrapper image, Long[] outputsDat, Client clien
 					shapes.add(rectangle);
 				}
 				ROIWrapper roi = new ROIWrapper(shapes);
-				image.saveROI(client, roi);
+				roi.setName(String.valueOf(i));
+				rois.add(roi);
 				ImagePlus   croppedImage = image.toImagePlus(client, xBound, yBound, cBound, zBound, null);
 				Calibration cal          = this.rawImg.getCalibration();
 				croppedImage.setCalibration(cal);
@@ -527,6 +529,7 @@ public void cropKernelsOMERO(ImageWrapper image, Long[] outputsDat, Client clien
 					                        zMax);
 				}
 			}
+			image.saveROIs(client, rois);
 		}
 		this.infoImageAnalysis += info.toString();
 	}

src/main/java/gred/nucleus/cli/CLIRunActionOMERO.java

@@ -31,7 +31,7 @@ public class CLIRunActionOMERO {
 	Client      client  = new Client();
 
 	/** OMERO password connection */
-	String mdp;
+	char[] mdp;
 
 	/** OMERO type of data to analyse : image data dataset tag */
 	String dataType;
@@ -126,11 +126,11 @@ public static void autoCropOMERO(String inputDirectory,
 
 	public void getOMEROPassword() {
 		if (this.cmd.hasOption("password")) {
-			this.mdp = this.cmd.getOptionValue("password");
+			this.mdp = this.cmd.getOptionValue("password").toCharArray();
 		} else {
 			System.console().writer().println("Enter password: ");
 			Console con = System.console();
-			this.mdp = String.valueOf(con.readPassword());
+			this.mdp = con.readPassword();
 		}
 	}
 

src/main/java/gred/nucleus/dialogs/AutocropDialog.java

@@ -261,8 +261,8 @@ public AutocropDialog(IDialogListener dialogListener) {
 		jTextFieldHostname.setText("omero.gred-clermont.fr");
 		jTextFieldPort.setText("4064");
 
-		jTextFieldUsername.setText("demo");
-		jPasswordField.setText("Isim@42");
+		jTextFieldUsername.setText("");
+		jPasswordField.setText("");
 		jTextFieldGroup.setText("553");
 
 		jComboBoxDataType.setSelectedIndex(3);
@@ -311,8 +311,8 @@ public String getUsername() {
 	}
 
 
-	public String getPassword() {
-		return String.valueOf(jPasswordField.getPassword());
+	public char[] getPassword() {
+		return jPasswordField.getPassword();
 	}