Refactoring

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

@@ -9,7 +9,6 @@
 import gred.nucleus.files.Directory;
 import ij.ImagePlus;
 import ij.gui.TextRoi;
-import ij.io.FileSaver;
 import ij.plugin.ContrastEnhancer;
 import ij.plugin.ZProjector;
 import ij.process.ImageConverter;
@@ -29,6 +28,7 @@
 import java.util.concurrent.ExecutionException;
 import java.util.regex.Pattern;
 
+import static gred.nucleus.utils.ImageSaver.saveFile;
 import static loci.plugins.BF.openImagePlus;
 
 
@@ -176,18 +176,6 @@ public void run() {
 	}
 
 
-	/**
-	 * Save the ImagePlus Z-projection image
-	 *
-	 * @param imagePlusInput image to save
-	 * @param pathFile       path to save the image
-	 */
-	public void saveFile(ImagePlus imagePlusInput, String pathFile) {
-		FileSaver fileSaver = new FileSaver(imagePlusInput);
-		fileSaver.saveAsTiff(pathFile);
-	}
-
-
 	public void saveProjectionOMERO(Client client, Long output)
 	throws AccessException, ServiceException, ExecutionException, OMEROServerError, IOException {
 		long                 datasetID;
@@ -218,7 +206,7 @@ public void saveProjectionOMERO(Client client, Long output)
 	 *
 	 * @return Z projection
 	 */
-	private ImagePlus projectionMax(ZProjector project) {
+	private static ImagePlus projectionMax(ZProjector project) {
 		project.setMethod(ZProjector.MAX_METHOD);
 		project.doProjection();
 		return project.getProjection();

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

@@ -187,7 +187,7 @@ public ImagePlus getImageChannel(int channelNumber) throws IOException, FormatEx
 	}
 
 
-	public ImagePlus getImageChannelOMERO(int channelNumber, ImageWrapper image, Client client)
+	public static ImagePlus getImageChannelOMERO(int channelNumber, ImageWrapper image, Client client)
 	throws ServiceException, AccessException, ExecutionException {
 		int[] cBound = {channelNumber, channelNumber};
 		return image.toImagePlus(client, null, null, cBound, null, null);
@@ -603,16 +603,6 @@ public void cropKernels3() {
 	}
 
 
-	/**
-	 * Getter for the outputFile ArrayList
-	 *
-	 * @return outputFile: ArrayList of String for the path of the output files created.
-	 */
-	public List<String> getOutputFileList() {
-		return new ArrayList<>(outputFile);
-	}
-
-
 	/**
 	 * Getter for the boxCoordinates
 	 *
@@ -631,7 +621,7 @@ public List<String> getFileCoordinates() {
 	 *
 	 * @return The segmented binary image.
 	 */
-	private ImagePlus generateSegmentedImage(ImagePlus imagePlusInput, int threshold) {
+	private static ImagePlus generateSegmentedImage(ImagePlus imagePlusInput, int threshold) {
 		ImageStack imageStackInput     = imagePlusInput.getStack();
 		ImagePlus  imagePlusSegmented  = imagePlusInput.duplicate();
 		ImageStack imageStackSegmented = imagePlusSegmented.getStack();
@@ -718,16 +708,6 @@ public String getSpecificImageInfo() {
 	}
 
 
-	/**
-	 * Getter column name for the tab delimited file
-	 *
-	 * @return columns name for output text file
-	 */
-	public String getColumnNames() {
-		return HEADERS;
-	}
-
-
 	/**
 	 * Write analysis info in output text file
 	 */
@@ -815,13 +795,4 @@ public void boxIntersection() {
 	}
 
 
-	/**
-	 * Set a list of boxes
-	 *
-	 * @param boxes list of boxes
-	 */
-	public void setBoxes(Map<Double, ? extends Box> boxes) {
-		this.boxes = new HashMap<>(boxes);
-	}
-
 }

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

@@ -57,11 +57,6 @@ public class AutoCropCalling {
 	private String typeThresholding = "Otsu";
 
 
-	/** Constructor Create the output directory if it doesn't exist. */
-	public AutoCropCalling() {
-	}
-
-
 	public AutoCropCalling(AutocropParameters autocropParameters) {
 		this.autocropParameters = autocropParameters;
 		this.outputCropGeneralInfo = autocropParameters.getAnalysisParameters() + HEADERS;

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

@@ -43,10 +43,6 @@ public class AutocropParameters extends PluginParameters {
 	private boolean boxesRegrouping             = true;
 
 
-	public AutocropParameters() {
-	}
-
-
 	/**
 	 * Constructor with default parameter
 	 *
@@ -58,70 +54,6 @@ public AutocropParameters(String inputFolder, String outputFolder) {
 	}
 
 
-	/**
-	 * Constructor with box size modifications
-	 *
-	 * @param inputFolder  Path folder containing Images
-	 * @param outputFolder Path folder output analyse
-	 * @param xCropBoxSize Number of voxels add in x axis around object
-	 * @param yCropBoxSize Number of voxels add in z axis around object
-	 * @param zCropBoxSize Number of stack add in z axis around object
-	 */
-	public AutocropParameters(String inputFolder, String outputFolder,
-	                          int xCropBoxSize,
-	                          int yCropBoxSize,
-	                          int zCropBoxSize,
-	                          int numberFontSize,
-	                          int thresholdOTSUComputing,
-	                          int channelToComputeThreshold) {
-		super(inputFolder, outputFolder);
-		this.xCropBoxSize = xCropBoxSize;
-		this.yCropBoxSize = yCropBoxSize;
-		this.zCropBoxSize = zCropBoxSize;
-		this.numberFontSize = numberFontSize;
-		this.thresholdOTSUComputing = thresholdOTSUComputing;
-		this.channelToComputeThreshold = channelToComputeThreshold;
-	}
-
-
-	/**
-	 * Constructor with all manual parameters
-	 *
-	 * @param inputFolder               Path folder containing Images
-	 * @param outputFolder              Path folder output analyse
-	 * @param xCropBoxSize              Number of voxels add in x axis around object
-	 * @param yCropBoxSize              Number of voxels add in z axis around object
-	 * @param zCropBoxSize              Number of stack add in z axis around object
-	 * @param channelToComputeThreshold Channel number to compute OTSU
-	 * @param slicesOTSUComputing       Slice start to compute OTSU
-	 * @param thresholdOTSUComputing    Minimum OTSU threshold used
-	 * @param maxVolumeNucleus          Volume maximum of objects detected
-	 * @param minVolumeNucleus          Volume minimum of objects detected
-	 */
-	public AutocropParameters(String inputFolder, String outputFolder,
-	                          int xCropBoxSize,
-	                          int yCropBoxSize,
-	                          int zCropBoxSize,
-	                          int numberFontSize,
-	                          int slicesOTSUComputing,
-	                          int thresholdOTSUComputing,
-	                          int channelToComputeThreshold,
-	                          int minVolumeNucleus,
-	                          int maxVolumeNucleus) {
-
-		super(inputFolder, outputFolder);
-		this.xCropBoxSize = xCropBoxSize;
-		this.yCropBoxSize = yCropBoxSize;
-		this.zCropBoxSize = zCropBoxSize;
-		this.numberFontSize = numberFontSize;
-		this.thresholdOTSUComputing = thresholdOTSUComputing;
-		this.slicesOTSUComputing = slicesOTSUComputing;
-		this.channelToComputeThreshold = channelToComputeThreshold;
-		this.maxVolumeNucleus = maxVolumeNucleus;
-		this.minVolumeNucleus = minVolumeNucleus;
-	}
-
-
 	/**
 	 * Constructor with all manual parameters 2
 	 *
@@ -166,48 +98,6 @@ public AutocropParameters(String inputFolder, String outputFolder,
 	}
 
 
-	/**
-	 * Constructor with box size modification and slice number used to start OTSU threshold calculation to last slice
-	 *
-	 * @param inputFolder               Path folder containing Images
-	 * @param outputFolder              Path folder output analyse
-	 * @param xCropBoxSize              Number of voxels add in x axis around object
-	 * @param yCropBoxSize              Number of voxels add in z axis around object
-	 * @param zCropBoxSize              Number of stack add in z axis around object
-	 * @param channelToComputeThreshold Channel number to compute OTSU
-	 * @param slicesOTSUComputing       Slice start to compute OTSU
-	 * @param thresholdOTSUComputing    Minimum OTSU threshold used
-	 * @param maxVolumeNucleus          Volume maximum of objects detected
-	 * @param minVolumeNucleus          Volume minimum of objects detected
-	 */
-	public AutocropParameters(String inputFolder, String outputFolder,
-	                          double xCal,
-	                          double yCal,
-	                          double zCal,
-	                          int xCropBoxSize,
-	                          int yCropBoxSize,
-	                          int zCropBoxSize,
-	                          int numberFontSize,
-	                          int slicesOTSUComputing,
-	                          int thresholdOTSUComputing,
-	                          int channelToComputeThreshold,
-	                          int minVolumeNucleus,
-	                          int maxVolumeNucleus) {
-
-		super(inputFolder, outputFolder, xCal, yCal, zCal);
-		this.xCropBoxSize = xCropBoxSize;
-		this.yCropBoxSize = yCropBoxSize;
-		this.zCropBoxSize = zCropBoxSize;
-		this.numberFontSize = numberFontSize;
-		this.thresholdOTSUComputing = thresholdOTSUComputing;
-		this.slicesOTSUComputing = slicesOTSUComputing;
-		this.channelToComputeThreshold = channelToComputeThreshold;
-		this.maxVolumeNucleus = maxVolumeNucleus;
-		this.minVolumeNucleus = minVolumeNucleus;
-
-	}
-
-
 	/**
 	 * Constructor with box size modification and slice number used to start OTSU threshold calculation to last slice
 	 *

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

@@ -9,8 +9,6 @@
 import fr.igred.omero.repository.ProjectWrapper;
 import gred.nucleus.files.Directory;
 import gred.nucleus.files.FilesNames;
-import ij.ImagePlus;
-import ij.io.FileSaver;
 import loci.formats.FormatException;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
@@ -28,6 +26,8 @@
 import java.util.concurrent.ExecutionException;
 import java.util.regex.Pattern;
 
+import static gred.nucleus.utils.ImageSaver.saveFile;
+
 
 public class CropFromCoordinates {
 	/** Logger */
@@ -70,12 +70,6 @@ public CropFromCoordinates(String pathToCoordinates) {
 	}
 
 
-	public static void saveFile(ImagePlus imagePlusInput, String pathFile) {
-		FileSaver fileSaver = new FileSaver(imagePlusInput);
-		fileSaver.saveAsTiff(pathFile);
-	}
-
-
 	private Map<File, File> gatherFilePairs() {
 		File coordinateDir = new File(pathToCoordinates);
 		File rawDir        = new File(pathToRaw);
@@ -153,7 +147,7 @@ public void runFromOMERO(String rawDatasetIDAndChannel, String outputProjectID,
 	}
 
 
-	public Map<Double, Box> readCoordinatesTXT(File boxesFile) {
+	public static Map<Double, Box> readCoordinatesTXT(File boxesFile) {
 		Map<Double, Box> boxLists = new HashMap<>();
 
 		try (Scanner scanner = new Scanner(boxesFile)) {

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

@@ -10,7 +10,6 @@
 import gred.nucleus.files.Directory;
 import ij.ImagePlus;
 import ij.gui.ImageRoi;
-import ij.io.FileSaver;
 import ij.plugin.Duplicator;
 import ij.plugin.LutLoader;
 import ij.process.ImageConverter;
@@ -36,6 +35,8 @@
 import java.util.Map;
 import java.util.concurrent.ExecutionException;
 
+import static gred.nucleus.utils.ImageSaver.saveFile;
+
 
 public class GenerateOverlay {
 	/** Logger */
@@ -64,18 +65,6 @@ public GenerateOverlay(String pathToProjection, String pathToDic) {
 	}
 
 
-	/**
-	 * Save output file in tiff format for OMERO
-	 *
-	 * @param imagePlusInput image to save
-	 * @param pathFile       path to save image
-	 */
-	public static void saveFile(ImagePlus imagePlusInput, String pathFile) {
-		FileSaver fileSaver = new FileSaver(imagePlusInput);
-		fileSaver.saveAsTiff(pathFile);
-	}
-
-
 	private Map<File, File> gatherFilePairs() {
 		File projectionDir = new File(pathToProjection);
 		File dicDir        = new File(pathToDic);

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

@@ -29,13 +29,13 @@ public CLIActionOptionCmdLine(String[] args) {
 			isTrue(availableActionCMD(cmd.getOptionValue("action")));
 		} catch (ParseException exp) {
 			System.console().writer().println(exp.getMessage() + "\n");
-			System.console().writer().println(super.getHelperInfo());
+			System.console().writer().println(getHelperInfo());
 			System.exit(1);
 		} catch (Exception exp) {
 			System.console().writer().println("Action option \"" +
 			                                  cmd.getOptionValue("action") +
 			                                  "\" not available" + "\n");
-			System.console().writer().println(super.getHelperInfo());
+			System.console().writer().println(getHelperInfo());
 			System.exit(1);
 		}
 	}

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

@@ -111,13 +111,13 @@ public CLIActionOptionOMERO(String[] argument) {
 			isTrue(availableActionOMERO(cmd.getOptionValue("action")));
 		} catch (ParseException exp) {
 			System.console().writer().println(exp.getMessage() + "\n");
-			System.console().writer().println(super.getHelperInfo());
+			System.console().writer().println(getHelperInfo());
 			System.exit(1);
 		} catch (Exception exp) {
 			System.console().writer().println("Action option \"" +
 			                                  cmd.getOptionValue("action") +
 			                                  "\" not available" + "\n");
-			System.console().writer().println(super.getHelperInfo());
+			System.console().writer().println(getHelperInfo());
 			System.exit(1);
 		}
 	}

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

@@ -122,7 +122,7 @@ public CLIActionOptions(String[] argument) {
 
 
 	/** @return : helper info */
-	public String getHelperInfo() {
+	public static String getHelperInfo() {
 		return "More details for available actions:\n" +
 		       "java -jar nucleusj-" + NJ_VERSION + ".jar -h \n" +
 		       "java -jar nucleusj-" + NJ_VERSION + ".jar -help \n\n" +

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

@@ -7,7 +7,7 @@
 
 
 /** Class to generate helper */
-public class CLIHelper {
+public final class CLIHelper {
 
 	private CLIHelper() {
 		// DO NOTHING
@@ -249,7 +249,7 @@ private static void specificAction(String action) {
 				exampleCMD = exampleArgument.split(" ");
 				CLIActionOptions wrongAction = new CLIActionOptions(exampleCMD);
 				System.console().writer().println("Invalid action \"" + action + "\" :\n");
-				System.console().writer().println(wrongAction.getHelperInfo());
+				System.console().writer().println(CLIActionOptions.getHelperInfo());
 				break;
 		}
 	}