Refactor GUI package

ppouchin · ppouchin · commit 62502b643d99 · 2025-07-30T23:51:47.000+02:00
diff --git a/src/main/java/fr/igred/nucleus/NucleusJ.java b/src/main/java/fr/igred/nucleus/NucleusJ.java
@@ -22,7 +22,7 @@
 import fr.igred.nucleus.cli.CLIHelper;
 import fr.igred.nucleus.cli.CLIRunAction;
 import fr.igred.nucleus.cli.CLIRunActionOMERO;
-import fr.igred.nucleus.dialogs.MainGui;
+import fr.igred.nucleus.gui.MainGui;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
diff --git a/src/main/java/fr/igred/nucleus/core/ChromocenterEnhancement.java b/src/main/java/fr/igred/nucleus/core/ChromocenterEnhancement.java
@@ -38,13 +38,13 @@
  *
  * @author Tristan Dubos and Axel Poulet
  */
-public final class ChromocentersEnhancement {
+public final class ChromocenterEnhancement {
 	/** Logger */
 	private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 	
 	
 	/** Private constructor to prevent instantiation */
-	private ChromocentersEnhancement() {
+	private ChromocenterEnhancement() {
 		// This class should not be instantiated
 	}
 	
diff --git a/src/main/java/fr/igred/nucleus/dialogs/package-info.java b/src/main/java/fr/igred/nucleus/dialogs/package-info.java
diff --git a/src/main/java/fr/igred/nucleus/gui/AutocropConfigDialog.java b/src/main/java/fr/igred/nucleus/gui/AutocropConfigDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import javax.swing.BorderFactory;
 import javax.swing.Box;
diff --git a/src/main/java/fr/igred/nucleus/gui/AutocropDialog.java b/src/main/java/fr/igred/nucleus/gui/AutocropDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.nucleus.Version;
 import fr.igred.omero.exception.AccessException;
diff --git a/src/main/java/fr/igred/nucleus/gui/ChromocenterAnalysisDialog.java b/src/main/java/fr/igred/nucleus/gui/ChromocenterAnalysisDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
@@ -57,7 +57,7 @@
  *
  * @author pouletaxel
  */
-public class ChromocentersAnalysisPipelineBatchDialog extends JFrame implements ItemListener {
+public class ChromocenterAnalysisDialog extends JFrame implements ItemListener {
 	private static final long         serialVersionUID        = 896147828956284745L;
 	private final        JTextField   jTextFieldWorkDirectory = new JTextField();
 	private final        JTextField   jTextFieldRawData       = new JTextField();
@@ -106,7 +106,7 @@ public class ChromocentersAnalysisPipelineBatchDialog extends JFrame implements
 	
 	
 	/** Architecture of the graphical windows */
-	public ChromocentersAnalysisPipelineBatchDialog(IDialogListener dialogListener) {
+	public ChromocenterAnalysisDialog(IDialogListener dialogListener) {
 		final String font = "Albertus";
 		container = super.getContentPane();
 		JLabel      jLabelWorkDirectory  = new JLabel("Work directory and data directory choice:");
diff --git a/src/main/java/fr/igred/nucleus/gui/ChromocenterSegmentationDialog.java b/src/main/java/fr/igred/nucleus/gui/ChromocenterSegmentationDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
@@ -47,7 +47,7 @@
  *
  * @author Poulet Axel
  */
-public class ChromocenterSegmentationPipelineBatchDialog extends JFrame implements ItemListener {
+public class ChromocenterSegmentationDialog extends JFrame implements ItemListener {
 	private static final long serialVersionUID = -1605324416480852307L;
 	
 	private final transient IDialogListener dialogListener;
@@ -67,7 +67,7 @@ public class ChromocenterSegmentationPipelineBatchDialog extends JFrame implemen
 	
 	
 	/** Architecture of the graphical windows */
-	public ChromocenterSegmentationPipelineBatchDialog(IDialogListener dialogListener) {
+	public ChromocenterSegmentationDialog(IDialogListener dialogListener) {
 		this.dialogListener = dialogListener;
 		Container container;
 		JLabel    jLabelWorkDirectory;
diff --git a/src/main/java/fr/igred/nucleus/gui/ComputeParametersDialog.java b/src/main/java/fr/igred/nucleus/gui/ComputeParametersDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
diff --git a/src/main/java/fr/igred/nucleus/gui/CropFromCoordinatesDialog.java b/src/main/java/fr/igred/nucleus/gui/CropFromCoordinatesDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.nucleus.Version;
 import fr.igred.omero.exception.AccessException;
diff --git a/src/main/java/fr/igred/nucleus/gui/GenerateOverlayDialog.java b/src/main/java/fr/igred/nucleus/gui/GenerateOverlayDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.nucleus.Version;
 import fr.igred.omero.exception.AccessException;
diff --git a/src/main/java/fr/igred/nucleus/gui/GuiAnalysis.java b/src/main/java/fr/igred/nucleus/gui/GuiAnalysis.java
@@ -20,7 +20,6 @@
 
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.nucleus.dialogs.IDialogListener;
 import ij.IJ;
 import ij.Prefs;
 
diff --git a/src/main/java/fr/igred/nucleus/gui/IDialogListener.java b/src/main/java/fr/igred/nucleus/gui/IDialogListener.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
diff --git a/src/main/java/fr/igred/nucleus/gui/MainGui.java b/src/main/java/fr/igred/nucleus/gui/MainGui.java
@@ -15,13 +15,13 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 
 import fr.igred.nucleus.Version;
 import fr.igred.nucleus.plugins.AutocropPlugin;
-import fr.igred.nucleus.plugins.ChromocenterSegmentationBatchPlugin;
-import fr.igred.nucleus.plugins.ChromocentersAnalysisBatchPlugin;
+import fr.igred.nucleus.plugins.ChromocenterSegmentationPlugin;
+import fr.igred.nucleus.plugins.ChromocenterAnalysisPlugin;
 import fr.igred.nucleus.plugins.ComputeParametersPlugin;
 import fr.igred.nucleus.plugins.CropFromCoordinatesPlugin;
 import fr.igred.nucleus.plugins.GenerateOverlayPlugin;
@@ -101,8 +101,8 @@ private enum PluginButton {
 		OVERLAY("Overlay", new GenerateOverlayPlugin()),
 		COMPUTE_PARAMS("Compute Parameters Nuc", new ComputeParametersPlugin()),
 		NODEJ("NODeJ", new NODeJ()),
-		CC_SEGMENT("Chromocenter Segmentation", new ChromocenterSegmentationBatchPlugin()),
-		COMPUTE_CC_PARAMS("Compute Parameters Spots", new ChromocentersAnalysisBatchPlugin());
+		CC_SEGMENT("Chromocenter Segmentation", new ChromocenterSegmentationPlugin()),
+		COMPUTE_CC_PARAMS("Compute Parameters Spots", new ChromocenterAnalysisPlugin());
 		
 		private final String label;
 		private final PlugIn plugin;
diff --git a/src/main/java/fr/igred/nucleus/gui/SegmentationConfigDialog.java b/src/main/java/fr/igred/nucleus/gui/SegmentationConfigDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.nucleus.Version;
 import fr.igred.nucleus.utils.ConvexHullDetection;
diff --git a/src/main/java/fr/igred/nucleus/gui/SegmentationDialog.java b/src/main/java/fr/igred/nucleus/gui/SegmentationDialog.java
@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-package fr.igred.nucleus.dialogs;
+package fr.igred.nucleus.gui;
 
 import fr.igred.nucleus.Version;
 import fr.igred.omero.exception.AccessException;
diff --git a/src/main/java/fr/igred/nucleus/gui/package-info.java b/src/main/java/fr/igred/nucleus/gui/package-info.java
@@ -16,5 +16,5 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/** This package contains GUI classes. */
+/** This package contains GUI classes to create dialogs and windows. */
 package fr.igred.nucleus.gui;
diff --git a/src/main/java/fr/igred/nucleus/plugins/AutocropPlugin.java b/src/main/java/fr/igred/nucleus/plugins/AutocropPlugin.java
@@ -19,9 +19,9 @@
 
 import fr.igred.nucleus.autocrop.AutoCropCalling;
 import fr.igred.nucleus.autocrop.AutocropParameters;
-import fr.igred.nucleus.dialogs.AutocropConfigDialog;
-import fr.igred.nucleus.dialogs.AutocropDialog;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.gui.AutocropConfigDialog;
+import fr.igred.nucleus.gui.AutocropDialog;
+import fr.igred.nucleus.gui.IDialogListener;
 import fr.igred.omero.Client;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
 import fr.igred.omero.exception.AccessException;
diff --git a/src/main/java/fr/igred/nucleus/plugins/ChromocenterAnalysisPlugin.java b/src/main/java/fr/igred/nucleus/plugins/ChromocenterAnalysisPlugin.java
@@ -24,8 +24,8 @@
 import fr.igred.omero.repository.ImageWrapper;
 import fr.igred.nucleus.core.ChromocenterAnalysis;
 import fr.igred.nucleus.core.NucleusChromocentersAnalysis;
-import fr.igred.nucleus.dialogs.ChromocentersAnalysisPipelineBatchDialog;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.gui.ChromocenterAnalysisDialog;
+import fr.igred.nucleus.gui.IDialogListener;
 import fr.igred.nucleus.io.FileList;
 import ij.IJ;
 import ij.ImagePlus;
@@ -52,11 +52,11 @@
 /**
  * @author Tristan Dubos and Axel Poulet
  */
-public class ChromocentersAnalysisBatchPlugin implements PlugIn, IDialogListener {
+public class ChromocenterAnalysisPlugin implements PlugIn, IDialogListener {
 	/** Logger */
 	private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 	
-	private ChromocentersAnalysisPipelineBatchDialog chromocentersPipelineBatchDialog;
+	private ChromocenterAnalysisDialog chromocentersPipelineBatchDialog;
 	
 	
 	public static void deleteFolder(String folderPathString) throws IOException {
@@ -83,7 +83,7 @@ public void run(String arg) {
 		if (IJ.versionLessThan("1.32c")) {
 			return;
 		}
-		chromocentersPipelineBatchDialog = new ChromocentersAnalysisPipelineBatchDialog(this);
+		chromocentersPipelineBatchDialog = new ChromocenterAnalysisDialog(this);
 	}
 	
 	
diff --git a/src/main/java/fr/igred/nucleus/plugins/ChromocenterSegmentationPlugin.java b/src/main/java/fr/igred/nucleus/plugins/ChromocenterSegmentationPlugin.java
@@ -17,9 +17,9 @@
  */
 package fr.igred.nucleus.plugins;
 
-import fr.igred.nucleus.core.ChromocentersEnhancement;
-import fr.igred.nucleus.dialogs.ChromocenterSegmentationPipelineBatchDialog;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.core.ChromocenterEnhancement;
+import fr.igred.nucleus.gui.ChromocenterSegmentationDialog;
+import fr.igred.nucleus.gui.IDialogListener;
 import fr.igred.nucleus.io.FileList;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
@@ -42,15 +42,15 @@
 /**
  * @author Tristan Dubos and Axel Poulet
  */
-public class ChromocenterSegmentationBatchPlugin implements PlugIn, IDialogListener {
+public class ChromocenterSegmentationPlugin implements PlugIn, IDialogListener {
 	/** Logger */
 	private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 	
-	private ChromocenterSegmentationPipelineBatchDialog ccSegDialog;
+	private ChromocenterSegmentationDialog ccSegDialog;
 	
 	/* This method is used by plugins.config */
 	public void run(String arg) {
-		ccSegDialog = new ChromocenterSegmentationPipelineBatchDialog(this);
+		ccSegDialog = new ChromocenterSegmentationDialog(this);
 	}
 	
 	
@@ -112,8 +112,8 @@ private void processOneNucleus(ImagePlus imagePlusInput, ImagePlus imagePlusSegm
 		} else {
 			calibration = imagePlusInput.getCalibration();
 		}
-		ImagePlus imagePlusContrast = ChromocentersEnhancement.applyEnhanceChromocenters(imagePlusInput,
-		                                                                                 imagePlusSegmented);
+		ImagePlus imagePlusContrast = ChromocenterEnhancement.applyEnhanceChromocenters(imagePlusInput,
+		                                                                                imagePlusSegmented);
 		imagePlusContrast.setTitle(imagePlusInput.getTitle());
 		imagePlusContrast.setCalibration(calibration);
 		saveFile(imagePlusContrast, workDirectory + File.separator + "ContrastDataNucleus");
diff --git a/src/main/java/fr/igred/nucleus/plugins/ComputeParametersPlugin.java b/src/main/java/fr/igred/nucleus/plugins/ComputeParametersPlugin.java
@@ -21,8 +21,8 @@
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.nucleus.core.ComputeNucleiParameters;
-import fr.igred.nucleus.dialogs.ComputeParametersDialog;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.gui.ComputeParametersDialog;
+import fr.igred.nucleus.gui.IDialogListener;
 import ij.IJ;
 import ij.Prefs;
 import ij.measure.Calibration;
diff --git a/src/main/java/fr/igred/nucleus/plugins/CropFromCoordinatesPlugin.java b/src/main/java/fr/igred/nucleus/plugins/CropFromCoordinatesPlugin.java
@@ -28,8 +28,8 @@
 import fr.igred.omero.roi.GenericShapeWrapper;
 import fr.igred.omero.roi.ROIWrapper;
 import fr.igred.nucleus.autocrop.CropFromCoordinates;
-import fr.igred.nucleus.dialogs.CropFromCoordinatesDialog;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.gui.CropFromCoordinatesDialog;
+import fr.igred.nucleus.gui.IDialogListener;
 import fr.igred.nucleus.io.FilesNames;
 import ij.IJ;
 import ij.ImagePlus;
diff --git a/src/main/java/fr/igred/nucleus/plugins/GenerateOverlayPlugin.java b/src/main/java/fr/igred/nucleus/plugins/GenerateOverlayPlugin.java
@@ -24,8 +24,8 @@
 import fr.igred.omero.repository.DatasetWrapper;
 import fr.igred.omero.repository.ImageWrapper;
 import fr.igred.nucleus.autocrop.GenerateOverlay;
-import fr.igred.nucleus.dialogs.GenerateOverlayDialog;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.gui.GenerateOverlayDialog;
+import fr.igred.nucleus.gui.IDialogListener;
 import ij.IJ;
 import ij.Prefs;
 import ij.plugin.PlugIn;
diff --git a/src/main/java/fr/igred/nucleus/plugins/NODeJ.java b/src/main/java/fr/igred/nucleus/plugins/NODeJ.java
@@ -22,7 +22,7 @@
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.nucleus.dialogs.IDialogListener;
+import fr.igred.nucleus.gui.IDialogListener;
 import fr.igred.nucleus.gui.GuiAnalysis;
 import fr.igred.nucleus.process.ChromocenterCalling;
 import ij.IJ;
diff --git a/src/main/java/fr/igred/nucleus/plugins/SegmentationPlugin.java b/src/main/java/fr/igred/nucleus/plugins/SegmentationPlugin.java
@@ -25,9 +25,9 @@
 import fr.igred.omero.repository.DatasetWrapper;
 import fr.igred.omero.repository.ImageWrapper;
 import fr.igred.omero.repository.ProjectWrapper;
-import fr.igred.nucleus.dialogs.IDialogListener;
-import fr.igred.nucleus.dialogs.SegmentationConfigDialog;
-import fr.igred.nucleus.dialogs.SegmentationDialog;
+import fr.igred.nucleus.gui.IDialogListener;
+import fr.igred.nucleus.gui.SegmentationConfigDialog;
+import fr.igred.nucleus.gui.SegmentationDialog;
 import fr.igred.nucleus.segmentation.SegmentationCalling;
 import fr.igred.nucleus.segmentation.SegmentationParameters;
 import ij.IJ;

Original file line number	Diff line number	Diff line change
`@@ -38,13 +38,13 @@`
`38`	`38`	`*`
`39`	`39`	`* @author Tristan Dubos and Axel Poulet`
`40`	`40`	`*/`
`41`		`-public final class ChromocentersEnhancement {`
	`41`	`+public final class ChromocenterEnhancement {`
`42`	`42`	`/** Logger */`
`43`	`43`	`private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());`
`44`	`44`
`45`	`45`
`46`	`46`	`/** Private constructor to prevent instantiation */`
`47`		`- private ChromocentersEnhancement() {`
	`47`	`+ private ChromocenterEnhancement() {`
`48`	`48`	`// This class should not be instantiated`
`49`	`49`	`}`
`50`	`50`