Handle different possible divisions by zero and remove unused variables/methods

Author: ppouchin

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

@@ -78,9 +78,6 @@ public class AutoCrop {
 	/** The path of the image to be processed */
 	private final String             imageFilePath;
 
-	/** File to process (Image input) */
-	private final File currentFile;
-	
 	/** Raw image */
 	private ImagePlus        rawImg;
 	/** Segmented image */
@@ -114,7 +111,6 @@ public class AutoCrop {
 	public AutoCrop(File imageFile, String outputFilesPrefix, AutocropParameters autocropParametersAnalyse)
 	throws IOException, FormatException {
 		this.autocropParameters = autocropParametersAnalyse;
-		this.currentFile = imageFile;
 		this.imageFilePath = imageFile.getAbsolutePath();
 		this.outputDirPath = autocropParameters.getOutputFolder();
 		this.outputFilesPrefix = outputFilesPrefix;
@@ -130,7 +126,6 @@ public AutoCrop(File imageFile, String outputFilesPrefix, AutocropParameters aut
 
 	public AutoCrop(ImageWrapper image, AutocropParameters autocropParametersAnalyse, Client client)
 	throws ServiceException, AccessException, ExecutionException {
-		this.currentFile = new File(image.getName());
 		this.autocropParameters = autocropParametersAnalyse;
 		this.outputDirPath = autocropParameters.getOutputFolder();
 		this.outputFilesPrefix = FilenameUtils.removeExtension(image.getName());
@@ -154,7 +149,6 @@ public AutoCrop(File imageFile,
 	                Map<Double, Box> boxes)
 	throws IOException, FormatException {
 		this.autocropParameters = autocropParametersAnalyse;
-		this.currentFile = imageFile;
 		this.imageFilePath = imageFile.getAbsolutePath();
 		this.outputDirPath = autocropParameters.getOutputFolder();
 		this.outputFilesPrefix = outputFilesPrefix;

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

@@ -92,12 +92,14 @@ private Map<File, File> gatherFilePairs() {
 	private LUT getNucleiLUT() throws IOException {
 		InputStream    in = getClass().getResourceAsStream("/overlay/LUT.txt");
 		BufferedReader br = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8));
-		BufferedWriter bw = new BufferedWriter(new FileWriter("./tmp-LUT.txt"));
-		String         l;
-		while ((l = br.readLine()) != null) {
-			bw.write(l + "\n");
+		try (BufferedWriter bw = new BufferedWriter(new FileWriter("./tmp-LUT.txt"))) {
+			String l = br.readLine();
+			while(l != null) {
+				bw.write(l);
+				bw.newLine();
+				l = br.readLine();
+			}
 		}
-		bw.close();
 		LUT fire = LutLoader.openLut("./tmp-LUT.txt");
 		Files.delete(Paths.get("./tmp-LUT.txt"));
 		return fire;

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

@@ -244,11 +244,6 @@ private static void specificAction(String action) {
 				break;
 
 			default:
-				exampleArgument = "-action segmentation " +
-				                  "-input path/to/input/folder/ " +
-				                  "-output path/to/output/folder/ ";
-				exampleCMD = exampleArgument.split(" ");
-				CLIActionOptions wrongAction = new CLIActionOptions(exampleCMD);
 				System.console().writer().println("Invalid action \"" + action + "\" :\n");
 				System.console().writer().println(CLIActionOptions.getHelperInfo());
 				break;

src/main/java/gred/nucleus/core/ChromocentersEnhancement.java

@@ -128,7 +128,7 @@ private static double[] computeContrast(ImagePlus imagePlusRaw, ImagePlus imageP
 					neighborVolumeTotal += tRegionAdjacencyGraph[i][j];
 				}
 			}
-			if (tContrast[i] <= 0) {
+			if (tContrast[i] <= 0 || neighborVolumeTotal == 0) {
 				tContrast[i] = 0;
 			} else {
 				tContrast[i] /= neighborVolumeTotal;

src/main/java/gred/nucleus/core/Measure3D.java

@@ -82,49 +82,6 @@ public Measure3D(ImagePlus[] imageSegs, ImagePlus rawImage, double xCal, double
 	}
 
 
-	/**
-	 * Scan of image and if the voxel belong to the object of interest, looking, if in his neighborhood there are voxel
-	 * value == 0 then it is a boundary voxel. Adding the surface of the face of the voxel frontier, which are in
-	 * contact with the background of the image, to the surface total.
-	 *
-	 * @param label label of the interest object
-	 *
-	 * @return the surface
-	 */
-	public double computeSurfaceObject(double label) {
-		ImageStack imageStackInput = imageSegs[0].getStack();
-		double     surfaceArea     = 0, voxelValue, neighborVoxelValue;
-		for (int k = 1; k < imageSegs[0].getStackSize(); ++k) {
-			for (int i = 1; i < imageSegs[0].getWidth(); ++i) {
-				for (int j = 1; j < imageSegs[0].getHeight(); ++j) {
-					voxelValue = imageStackInput.getVoxel(i, j, k);
-					if (voxelValue == label) {
-						for (int kk = k - 1; kk <= k + 1; kk += 2) {
-							neighborVoxelValue = imageStackInput.getVoxel(i, j, kk);
-							if (voxelValue != neighborVoxelValue) {
-								surfaceArea += xCal * yCal;
-							}
-						}
-						for (int ii = i - 1; ii <= i + 1; ii += 2) {
-							neighborVoxelValue = imageStackInput.getVoxel(ii, j, k);
-							if (voxelValue != neighborVoxelValue) {
-								surfaceArea += yCal * zCal;
-							}
-						}
-						for (int jj = j - 1; jj <= j + 1; jj += 2) {
-							neighborVoxelValue = imageStackInput.getVoxel(i, jj, k);
-							if (voxelValue != neighborVoxelValue) {
-								surfaceArea += xCal * zCal;
-							}
-						}
-					}
-				}
-			}
-		}
-		return surfaceArea;
-	}
-	
-	
 	/**
 	 * This Method compute the volume of each segmented objects in imagePlus
 	 *
@@ -474,7 +431,7 @@ public static double computeIntensityRHF(ImagePlus imagePlusInput
 				}
 			}
 		}
-		return chromocenterIntensity / nucleusIntensity;
+		return nucleusIntensity != 0 ? chromocenterIntensity / nucleusIntensity : 0;
 	}
 
 
@@ -716,7 +673,7 @@ private double meanIntensity() {
 			numberOfVoxel += hist.getValue();
 			mean += hist.getKey() * hist.getValue();
 		}
-		return mean / numberOfVoxel;
+		return numberOfVoxel != 0 ? mean / numberOfVoxel : 0;
 	}
 
 
@@ -740,8 +697,7 @@ private double meanIntensityBackground() {
 				}
 			}
 		}
-		meanIntensity /= voxelCounted;
-		return meanIntensity;
+		return voxelCounted != 0 ? meanIntensity / voxelCounted : 0;
 	}
 
 
@@ -891,7 +847,6 @@ public String nucleusParameter3D() {
 		histogramSegmentedNucleus();
 
 		double   volume         = computeVolumeObjectML();
-		double   surfaceArea    = computeSurfaceObject(255);
 		double   surfaceAreaNew = computeComplexSurface();
 		double[] tEigenValues   = computeEigenValue3D(255);
 		compute2dParameters();
@@ -912,9 +867,9 @@ public String nucleusParameter3D() {
 		          + medianIntensityNucleus() + ","
 		          + medianIntensityBackground() + ","
 		          + rawImage.getHeight() * rawImage.getWidth() * rawImage.getNSlices() + ","
-		          + computeEigenValue3D(255)[0] + ","
-		          + computeEigenValue3D(255)[1] + ","
-		          + computeEigenValue3D(255)[2] + ","
+		          + tEigenValues[0] + ","
+		          + tEigenValues[1] + ","
+		          + tEigenValues[2] + ","
 		          + getAspectRatio() + ","
 		          + getCirculairty();
 		return results;

src/main/java/gred/nucleus/core/NucleusSegmentation.java

@@ -83,31 +83,6 @@ public class NucleusSegmentation {
 	private       ImagePlus[]            imageSeg;
 
 
-	/**
-	 * Constructor for the segmentation analysis for a single image.
-	 *
-	 * @param imgRaw                 raw image to analyse
-	 * @param vMin                   minimum volume of detected object
-	 * @param vMax                   maximum volume of detected object
-	 * @param segmentationParameters list the parameters for the analyse
-	 *
-	 * @throws IOException
-	 * @throws FormatException
-	 */
-	public NucleusSegmentation(ImagePlus imgRaw,
-	                           int vMin,
-	                           int vMax,
-	                           SegmentationParameters segmentationParameters)
-	throws IOException, FormatException {
-		this.vMin = vMin;
-		this.vMax = vMax;
-		this.segmentationParameters = segmentationParameters;
-		this.imgRaw = imgRaw;
-		this.imgRaw = getImageChannel(0);
-		this.imgRawTransformed = this.imgRaw;
-	}
-	
-	
 	/**
 	 * Constructor for the segmentation analysis for a folder containing images.
 	 *

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

@@ -184,7 +184,7 @@ public boolean isCalibrationSelected() {
 	@Override
 	public void itemStateChanged(ItemEvent e) {
 		if (e.getSource() == convexHullDetection) {
-			Boolean isConvexHullDetection = convexHullDetection.isSelected();
+			boolean isConvexHullDetection = convexHullDetection.isSelected();
 		} else if (e.getSource() == addCalibrationBox) {
 			if (addCalibrationBox.isSelected()) {
 

src/main/java/gred/nucleus/process/ChromocenterCalling.java

@@ -17,15 +17,21 @@
 import loci.common.DebugTools;
 import loci.formats.FormatException;
 import loci.plugins.BF;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.io.IOException;
+import java.lang.invoke.MethodHandles;
 import java.nio.file.Files;
 import java.util.List;
 import java.util.concurrent.ExecutionException;
 
 
 public class ChromocenterCalling {
+	/** Logger */
+	private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+	
 	private final ChromocenterParameters chromocenterParameters;
 
 	private String         prefix;
@@ -77,7 +83,7 @@ public void runSeveralImages2() throws IOException, FormatException {
 			file.mkdir();
 		}
 		// TODO A REFAIRE C EST MOCHE !!!!
-		System.out.println("size: " + directoryInput.getNumberFiles());
+		LOGGER.info("size: {}", directoryInput.getNumberFiles());
 
 		if (isGui) {
 			progress = new Progress("Images Analysis: ", directoryInput.getNumberFiles());
@@ -139,7 +145,7 @@ public void SegmentationOMERO(String inputDirectoryRaw,
 			if ("Image".equals(param[0]) && "Image".equals(param1[0])) {
 				runOneImageOMERO(imageID, maskID, outputDirectory, client);
 			} else if ("Dataset".equals(param[0]) && "Dataset".equals(param1[0])) {
-				String             dataset_name = client.getDataset(imageID).getName();
+				String             datasetName = client.getDataset(imageID).getName();
 				List<ImageWrapper> images;
 				List<ImageWrapper> masks;
 				/* get raw images and masks datasets*/
@@ -148,8 +154,8 @@ public void SegmentationOMERO(String inputDirectoryRaw,
 				/* get images List */
 				images = imageDataset.getImages(client);
 				/* Create Dataset named NodeJOMERO */
-				outDataset = new DatasetWrapper("NODeJ_" + dataset_name, "");
-				DatasetWrapper outDatasetGradient = new DatasetWrapper("NODeJ_" + dataset_name + "_Gradient", "");
+				outDataset = new DatasetWrapper("NODeJ_" + datasetName, "");
+				DatasetWrapper outDatasetGradient = new DatasetWrapper("NODeJ_" + datasetName + "_Gradient", "");
 				project = client.getProject(Long.parseLong(outputDirectory));
 				/* Add Dataset To the Project */
 				Long datasetId = project.addDataset(client, outDataset).getId();
@@ -164,7 +170,7 @@ public void SegmentationOMERO(String inputDirectoryRaw,
 						/* Get the mask with the same name */
 						masks = maskDataset.getImages(client, imageName);
 						/* Run Segmentation */
-						runSeveralImagesOMERO(image, masks.get(0), dataset_name, client);
+						runSeveralImagesOMERO(image, masks.get(0), datasetName, client);
 						/* Import Segmented cc to the Dataset*/
 						outDataset.importImages(client, segImg);
 						outDatasetGradient.importImages(client, gradImg);
@@ -218,8 +224,7 @@ public void runOneImageOMERO(Long inputDirectoryRaw, Long inputDirectorySeg, Str
 		ImagePlus[] rawImage = {image.toImagePlus(client)};
 		ImagePlus[] segImage = {mask.toImagePlus(client)};
 
-		String diffDir  = chromocenterParameters.outputFolder + "gradientImage";
-		String segCcDir = chromocenterParameters.outputFolder + "SegCC";
+		String diffDir = chromocenterParameters.outputFolder + "gradientImage";
 
 		FilesNames outPutFilesNames = new FilesNames(imageName);
 		this.prefix = outPutFilesNames.prefixNameFile();
@@ -283,8 +288,7 @@ public void runSeveralImagesOMERO(ImageWrapper image, ImageWrapper mask, String
 		ImagePlus[] rawImage = {image.toImagePlus(client)};
 		ImagePlus[] segImage = {mask.toImagePlus(client)};
 
-		String diffDir  = chromocenterParameters.outputFolder + "gradientImage";
-		String segCcDir = chromocenterParameters.outputFolder + "SegCC";
+		String diffDir = chromocenterParameters.outputFolder + "gradientImage";
 
 		FilesNames outPutFilesNames = new FilesNames(imageName);
 
@@ -318,45 +322,6 @@ public void runSeveralImagesOMERO(ImageWrapper image, ImageWrapper mask, String
 	}
 
 
-	/**
-	 * Run the Chromocenter segmentation on a single image
-	 *
-	 * @throws IOException
-	 * @throws FormatException
-	 */
-	public void just3D() throws IOException, FormatException {
-		DebugTools.enableLogging("OFF");
-		Directory directoryInput = new Directory(chromocenterParameters.getInputFolder());
-		directoryInput.listImageFiles(chromocenterParameters.getInputFolder());
-		directoryInput.checkIfEmpty();
-		String rhfChoice            = "Volume";
-		String nameFileChromocenter = chromocenterParameters.outputFolder + "CcParameters.tab";
-		
-		String segCcDir = chromocenterParameters.outputFolder;
-		
-		// TODO A REFAIRE C EST MOCHE !!!!
-		System.out.println("size: " + directoryInput.getNumberFiles());
-		
-		for (short i = 0; i < directoryInput.getNumberFiles(); ++i) {
-			File   currentFile = directoryInput.getFile(i);
-			String fileImg     = currentFile.toString();
-			
-			ImagePlus[] raw = BF.openImagePlus(currentFile.getAbsolutePath());
-			imageType(raw[0]);
-			String outputFileName = segCcDir + File.separator + currentFile.getName();
-			ImagePlus[] segNuc = BF.openImagePlus(chromocenterParameters.segInputFolder +
-			                                      File.separator +
-			                                      currentFile.getName());
-			
-			NucleusChromocentersAnalysis.compute3DParameters(rhfChoice,
-			                                                 raw[0],
-			                                                 segNuc[0],
-			                                                 IJ.openImage(outputFileName),
-			                                                 chromocenterParameters);
-		}
-	}
-	
-	
 	/**
 	 * @param img
 	 */