annotation of main algorithms

src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java

@@ -62,7 +62,7 @@
 import boa.plugins.plugins.segmenters.BacteriaIntensity;
 import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
 import boa.plugins.plugins.segmenters.MutationSegmenter;
-import boa.plugins.plugins.trackers.LAPTracker;
+import boa.plugins.plugins.trackers.MutationTracker;
 import boa.plugins.plugins.trackers.MicrochannelTracker;
 import boa.plugins.plugins.trackers.bacteria_in_microchannel_tracker.BacteriaClosedMicrochannelTrackerLocalCorrections;
 import boa.plugins.plugins.transformations.AutoRotationXY;
@@ -176,9 +176,9 @@ public static Experiment generateXPFluo(String name, String outputDir, boolean s
         //bacteria.setProcessingScheme(new SegmentAndTrack(new BacteriaClosedMicrochannelTrackerLocalCorrections(new BacteriaFluo()).setCostParameters(0.1, 0.5)));
         bacteria.setProcessingScheme(new SegmentThenTrack(new BacteriaIntensity(), new BacteriaClosedMicrochannelTrackerLocalCorrections().setCostParameters(0.1, 0.5)));
         mutation.setProcessingScheme(new SegmentAndTrack(
-                new LAPTracker().setCompartimentStructure(1).setSegmenter(
+                new MutationTracker().setCompartimentStructure(1).setSegmenter(
                         new MutationSegmenter(0.65, 0.5, 0.55).setScale(2.5) 
-                ).setSpotQualityThreshold(1).setLinkingMaxDistance(0.4, 0.41).setGapParameters(0.4, 0.1, 3).setTrackLength(10, 0)
+                ).setSpotQualityThreshold(1).setLinkingMaxDistance(0.4, 0.41).setGapParameters(0.4, 0.1, 3)
         ).addPreFilters(new BandPass(0, 8, 0, 5) // was 10
         ).addPostFilters(new FeatureFilter(new Quality(), 0.6, true, true))); 
 

src/main/java/boa/core/generateXP/GenerateXP.java

@@ -73,7 +73,7 @@
 import boa.plugins.plugins.track_post_filter.RemoveTracksStartingAfterFrame;
 import boa.plugins.plugins.track_post_filter.TrackLengthFilter;
 import boa.plugins.plugins.trackers.bacteria_in_microchannel_tracker.BacteriaClosedMicrochannelTrackerLocalCorrections;
-import boa.plugins.plugins.trackers.LAPTracker;
+import boa.plugins.plugins.trackers.MutationTracker;
 import boa.plugins.plugins.trackers.MicrochannelTracker;
 import boa.plugins.plugins.trackers.ObjectIdxTracker;
 import boa.plugins.plugins.transformations.AutoRotationXY;
@@ -496,10 +496,10 @@ public static void setParametersFluo(Experiment xp, boolean processing, boolean
             );
             // modification of scaling: lap * 2.5, gauss * scale (=2) quality * 2.23
             mutation.setProcessingScheme(new SegmentAndTrack(
-                    new LAPTracker().setCompartimentStructure(1).setSegmenter(
+                    new MutationTracker().setCompartimentStructure(1).setSegmenter(
                         new MutationSegmenter(2.25, 1.625, 1.8).setScale(2.5, 3)  // was 0.9, 0.65, 0.9, scale was 2 for mutH
                 ).setSpotQualityThreshold(3.122) // 4.46 for mutH ? 
-                            .setLinkingMaxDistance(0.8, 0.82).setGapParameters(0.8, 0.15, 3).setTrackLength(8, 14)
+                            .setLinkingMaxDistance(0.8, 0.82).setGapParameters(0.8, 0.15, 3)
             ).addPreFilters(new BandPass(0, 10, 0, 5) // was 10
             ).addPostFilters(new FeatureFilter(new Quality(), 2.23, true, true))); // was 1
         }
@@ -575,7 +575,6 @@ public static void setParametersPhase(Experiment xp, boolean processing, boolean
                             new BacteriaClosedMicrochannelTrackerLocalCorrections()
                             .setSegmenter(new BacteriaIntensityPhase())
                             .setCostParameters(0.2, 2)
-                            .setCorrectMotherCell(false)
                     ).addTrackPreFilters(
                         new SubtractBackgroundMicrochannels(),
                         new NormalizeTrack(1, true)

src/main/java/boa/gui/GUI.java

@@ -190,6 +190,7 @@ public class GUI extends javax.swing.JFrame implements ImageObjectListener, User
     public GUI() {
         //logger.info("DBMaker: {}", checkClass("org.mapdb.DBMaker"));
         ToolTipManager.sharedInstance().setInitialDelay(100);
+        ToolTipManager.sharedInstance().setDismissDelay(Integer.MAX_VALUE);
         logger.info("Creating GUI instance...");
         this.instance=this;
         initComponents();

src/main/java/boa/plugins/ToolTip.java

@@ -24,11 +24,15 @@
  * @author jollion
  */
 public interface ToolTip{
+    /**
+     * The returned tooltip string will be formatted as html in a box with a fixed with, so the \"<html>\" tag is not needed, and line skipping will be automatically managed
+     * @return the string that will be displayed as a tool tip when scrolling over the name of the plugin
+     */
     public String getToolTipText();
-    public static int tooltipWidth = 750;
+    public static int TOOL_TIP_BOX_WIDTH = 750;
     public static String formatToolTip(String toolTip) {
         if (toolTip.startsWith("<html>")) toolTip = toolTip.replace("<html>", "");
         if (toolTip.endsWith("</html>")) toolTip = toolTip.replace("</html>", "");
-        return "<html><div style=\"width:"+tooltipWidth+"px\">" + toolTip + "</div></html>";
+        return "<html><div style=\"width:"+TOOL_TIP_BOX_WIDTH+"px\">" + toolTip + "</div></html>";
     }
 }

src/main/java/boa/plugins/TrackParametrizable.java

@@ -50,8 +50,23 @@
  * @param <S> segmenter type
  */
 public interface TrackParametrizable<S extends Segmenter> {
-    @FunctionalInterface public static interface ApplyToSegmenter<S> { public void apply(StructureObject parent, S segmenter);}
+    @FunctionalInterface public static interface ApplyToSegmenter<S> { 
+        /**
+         * Parametrizes the {@param segmenter}
+         * This method may be called asynchronously with different pairs of {@param parent}/{@param segmenter}
+         * @param parent parent object from the parent track used to create the {@link boa.plugins.TrackParametrizable.ApplyToSegmenter apply to segmenter object} See: {@link #getApplyToSegmenter(int, java.util.List, boa.plugins.Segmenter, java.util.concurrent.ExecutorService) }. This is not necessary the segmentation parent that will be used as argument in {@link boa.plugins.Segmenter#runSegmenter(boa.image.Image, int, boa.data_structure.StructureObjectProcessing) }
+         * @param segmenter Segmenter instance that will be parametrized, prior to call the method {@link boa.plugins.Segmenter#runSegmenter(boa.image.Image, int, boa.data_structure.StructureObjectProcessing) }
+         */
+        public void apply(StructureObject parent, S segmenter);
+    }
+    /**
+     * 
+     * @param structureIdx index of the structure to be segmented via call to {@link boa.plugins.Segmenter#runSegmenter(boa.image.Image, int, boa.data_structure.StructureObjectProcessing) }
+     * @param parentTrack parent track (elements are parent of structure {@param structureIdx}
+     * @return ApplyToSegmenter object that will parametrize Segmenter instances before call to {@link boa.plugins.Segmenter#runSegmenter(boa.image.Image, int, boa.data_structure.StructureObjectProcessing) }
+     */
     public ApplyToSegmenter run(int structureIdx, List<StructureObject> parentTrack);
+
     // + static helpers methods
     public static <S extends Segmenter> ApplyToSegmenter<S> getApplyToSegmenter(int structureIdx, List<StructureObject> parentTrack, S segmenter, ExecutorService executor) {
         if (segmenter instanceof TrackParametrizable) {

src/main/java/boa/plugins/plugins/segmenters/MutationSegmenter.java

@@ -23,13 +23,8 @@
 import boa.configuration.parameters.BoundedNumberParameter;
 import boa.configuration.parameters.NumberParameter;
 import boa.configuration.parameters.Parameter;
-import boa.configuration.parameters.ParameterUtils;
-import boa.configuration.parameters.PluginParameter;
 import boa.data_structure.Region;
 import boa.data_structure.RegionPopulation;
-import boa.data_structure.RegionPopulation.MeanIntensity;
-import boa.data_structure.RegionPopulation.Or;
-import boa.data_structure.RegionPopulation.Overlap;
 import boa.data_structure.StructureObject;
 import boa.data_structure.StructureObjectProcessing;
 import boa.data_structure.Voxel;
@@ -71,25 +66,33 @@
 import static boa.image.processing.WatershedTransform.watershed;
 import boa.image.processing.neighborhood.CylindricalNeighborhood;
 import boa.image.processing.neighborhood.Neighborhood;
+import boa.plugins.ToolTip;
 import boa.utils.Utils;
 
 /**
  *
  * @author jollion
  */
-public class MutationSegmenter implements Segmenter, UseMaps, ManualSegmenter, ObjectSplitter, ParameterSetup {
+public class MutationSegmenter implements Segmenter, UseMaps, ManualSegmenter, ObjectSplitter, ParameterSetup, ToolTip {
     public List<Image> intermediateImages;
     public static boolean debug = false;
     public static boolean displayImages = false;
     ArrayNumberParameter scale = new ArrayNumberParameter("Scale", 0, new BoundedNumberParameter("Scale", 1, 2, 1, 5)).setSorted(true);
-    NumberParameter smoothScale = new BoundedNumberParameter("Smooth scale", 1, 2, 1, 5);
-    NumberParameter minSpotSize = new BoundedNumberParameter("Min. Spot Size (Voxels)", 0, 5, 1, null);
-    NumberParameter thresholdHigh = new NumberParameter("Threshold for Seeds", 2, 2.25);
-    NumberParameter thresholdLow = new NumberParameter("Threshold for propagation", 2, 1.63);
-    NumberParameter intensityThreshold = new NumberParameter("Intensity Threshold for Seeds", 2, 1.8); // 
+    NumberParameter smoothScale = new BoundedNumberParameter("Smooth scale", 1, 2, 1, 5).setToolTipText("Scale (in pixels) for gaussian smooth");
+    NumberParameter minSpotSize = new BoundedNumberParameter("Min. Spot Size (Voxels)", 0, 5, 1, null).setToolTipText("In pixels: spots under this size will be removed");
+    NumberParameter thresholdHigh = new NumberParameter("Threshold for Seeds", 2, 2.25).setToolTipText("Higher value will increase false negative and decrease false positives.<br /> Laplacian Threshold for seed selection");
+    NumberParameter thresholdLow = new NumberParameter("Threshold for propagation", 2, 1.63).setToolTipText("Lower value will yield in larger spots.<br /> Laplacian Threshold for watershed propagation: propagation stops at this value.");
+    NumberParameter intensityThreshold = new NumberParameter("Intensity Threshold for Seeds", 2, 1.8).setToolTipText("Higher value will increase false negative and decrease false positives.<br /> Laplacian Threshold for seed selection"); 
     boolean planeByPlane = false;
     Parameter[] parameters = new Parameter[]{scale, smoothScale, minSpotSize, thresholdHigh,  thresholdLow, intensityThreshold};
     ProcessingVariables pv = new ProcessingVariables();
+    protected String toolTip = "<b>Spot Detection</b>. <br /> "
+            + "<ul><li>Input image is scaled by removing the mean value and dividing by the standard-deviation value of the background signal within the segmentation parent</li>"
+            + "<li>Spots are detected using a seeded watershed algorithm in the laplacian transform.</li> "
+            + "<li>Seeds are set on regional maxima of the laplacian transform, within the mask of the segmentation parent, with laplacian value superior to <em>Threshold for Seeds</em> and gaussian value superior to <em>Intensity Threshold for Seeds</em></li>"
+            + "<li>If several scales are provided, the laplacian scale space will be computed (3D for 2D input, and 4D for 3D input) and the seeds will be 3D/4D local extrema in the scale space in order to determine at the same time their scale and spatial localization</li>"
+            + "<li>Watershed propagation is done within the segmentation parent mask until laplacian values reach <em>Threshold for propagation</em></li>"
+            + "<li>A quality parameter in computed as √(laplacian x gaussian) at the center of the spot</li><ul>";
 
     public MutationSegmenter() {}
 
@@ -136,12 +139,18 @@ public boolean canBeTested(String p) {
     public void setTestParameter(String p) {
         testParam = p;
     }
-
+    /**
+     * See {@link #run(boa.image.Image, boa.data_structure.StructureObjectProcessing, double[], int, double, double, double, java.util.List) }
+     * @param input
+     * @param structureIdx
+     * @param parent
+     * @return 
+     */
     @Override
     public RegionPopulation runSegmenter(Image input, int structureIdx, StructureObjectProcessing parent) {
         return run(input, parent, getScale(), minSpotSize.getValue().intValue(), thresholdHigh.getValue().doubleValue(), thresholdLow.getValue().doubleValue(), intensityThreshold.getValue().doubleValue(), intermediateImages);
     }
-    
+
     /*public RegionPopulation run(Image input, StructureObjectProcessing parent, double[] scale, int minSpotSize, double thresholdHigh , double thresholdLow, double intensityThreshold, List<Image> intermediateImages) {
         if (input.getSizeZ()>1) {
             // tester sur average, max, ou plan par plan
@@ -187,6 +196,7 @@ public Image getScaledInput() {
         protected Image getSmoothedMap() {
             if (smooth==null) throw new RuntimeException("Smooth map not initialized");
             if (!smoothScaled) {
+                if (!smooth.sameDimensions(input)) smooth = smooth.cropWithOffset(input.getBoundingBox()); // map was computed on parent that differs from segmentation parent
                 ImageOperations.affineOperation2WithOffset(smooth, smooth, smoothScale/ms[1], -ms[0]);
                 smoothScaled=true;
             }
@@ -196,18 +206,37 @@ protected Image getSmoothedMap() {
         protected Image[] getLaplacianMap() {
             if (lap==null) throw new RuntimeException("Laplacian map not initialized");
             if (!lapScaled) {
-                for (int i = 0; i<lap.length; ++i) ImageOperations.affineOperation2WithOffset(lap[i], lap[i], 1/ms[1], 0); // no additive coefficient
+                for (int i = 0; i<lap.length; ++i) {
+                    if (!lap[i].sameDimensions(input)) lap[i] = lap[i].cropWithOffset(input.getBoundingBox()); // map was computed on parent that differs from segmentation parent
+                    ImageOperations.affineOperation2WithOffset(lap[i], lap[i], 1/ms[1], 0);
+                } // no additive coefficient
                 lapScaled=true;
             }
             return lap;
         }
     }
+    /**
+     * Spots are detected using a seeded watershed algorithm in the laplacian transform
+     * Input image is scaled by removing the mean value and dividing by the standard-deviation value of the background within the segmentation parent
+     * Seeds are set on regional maxima of the laplacian transform, within the mask of {@param parent}, with laplacian value superior to {@param thresholdSeeds} and gaussian value superior to {@param intensityThreshold}
+     * If several scales are provided, the laplacian scale space will be computed (3D for 2D input, and 4D for 3D input) and the seeds will be 3D/4D local extrema in the scale space in order to determine at the same time their scale and spatial localization
+     * Watershed propagation is done within the mask of {@param parent} until laplacian values reach {@param thresholdPropagation}
+     * A quality parameter in computed as √(laplacian x gaussian) at the center of the spot
+     * @param input pre-diltered image from wich spots will be detected
+     * @param parent segmentation parent
+     * @param scale scale for laplacian filtering, corresponds to size of the objects to be detected, if several, objects will be detected in the scale space
+     * @param minSpotSize under this size spots will be erased
+     * @param thresholdSeeds minimal laplacian value to segment a spot
+     * @param thresholdPropagation laplacian value at the border of spots
+     * @param intensityThreshold minimal gaussian value to semgent a spot
+     * @param intermediateImages for testing purpose
+     * @return segmented spots
+     */
     public RegionPopulation run(Image input, StructureObjectProcessing parent, double[] scale, int minSpotSize, double thresholdSeeds, double thresholdPropagation, double intensityThreshold, List<Image> intermediateImages) {
         Arrays.sort(scale);
         ImageMask parentMask = parent.getMask().getSizeZ()!=input.getSizeZ() ? new ImageMask2D(parent.getMask()) : parent.getMask();
         this.pv.initPV(input, parentMask, smoothScale.getValue().doubleValue()) ;
         if (pv.smooth==null || pv.lap==null) setMaps(computeMaps(input, input));
-        // TODO: test is Use Scale is taken into acount.
 
         Image smooth = pv.getSmoothedMap();
         Image[] lapSPZ = ((List<Image>)Image.mergeImagesInZ(Arrays.asList(pv.getLaplacianMap()))).toArray(new Image[0]); // in case there are several z
@@ -294,6 +323,7 @@ public RegionPopulation run(Image input, StructureObjectProcessing parent, doubl
         }
         return pop;
     }
+
     private static void setCenterAndQuality(Image map, Image map2, RegionPopulation pop, int z) {
         SubPixelLocalizator.setSubPixelCenter(map, pop.getRegions(), true); // lap -> better in case of close objects
         for (Region o : pop.getRegions()) { // quality criterion : sqrt (smooth * lap)
@@ -431,4 +461,8 @@ public RegionPopulation splitObject(StructureObject parent, int structureIdx, Re
     public void setSplitVerboseMode(boolean verbose) {
         manualSplitVerbose=verbose;
     }
+    @Override
+    public String getToolTipText() {
+       return toolTip;
+    }
 }