Added seed picker tool and improved Seeds structure

Adapted RW UI for grayscale support. Task: #284 (http://github.com/CellDynamics/QuimP/issues/284) Reworked SeedPicker Changed UI Added conversion to stack and grayscale image. Task: #239 Added conversion from grayscale to Seeds Task: #284 Changes in UI Task: #284 Added exception on empty roi seeds Task: #284 Almost finished
CellDynamics · Jan 10, 2018 · 3e6211a · 3e6211a
1 parent c4aa3b7
commit 3e6211a
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Showing 14 changed files with 878 additions and 234 deletions.
diff --git a/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/ProbabilityMaps.java b/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/ProbabilityMaps.java
@@ -20,7 +20,7 @@
 public class ProbabilityMaps extends ListMap<RealMatrix> {
 
   /**
-   * 
+   * Default constructor.
    */
   public ProbabilityMaps() {
     super();
@@ -36,6 +36,7 @@ public ProbabilityMaps() {
    * @throws IllegalArgumentException if size is not equal
    */
   public double[][][] convertTo3dMatrix(Object key) {
+    // TODO consider using ImageStack here
     List<RealMatrix> maps = get(key);
     // Can be null if points not found
     if (maps == null || maps.isEmpty()) {

diff --git a/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/PropagateSeeds.java b/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/PropagateSeeds.java
@@ -546,8 +546,9 @@ public Seeds propagateSeed(ImageProcessor previous, ImageProcessor org, double s
       big.fill();
       double stepsshrink = shrinkPower / stepSize; // total shrink/step size
       double stepsexp = (expandPower) / stepSize; // total shrink/step size
+      Seeds ret = new Seeds(2);
 
-      List<Outline> outlines = getOutline(previous);
+      List<Outline> outlines = getOutline(previous); // this supports grayscales
 
       // save extra debug info if property set
       if (QuimP.SUPER_DEBUG) {
@@ -577,6 +578,7 @@ public Seeds propagateSeed(ImageProcessor previous, ImageProcessor org, double s
         small.fill(fr);
         small.drawRoi(fr);
         // small.resetRoi();
+        ret.put(SeedTypes.FOREGROUNDS, small);
       }
 
       for (Outline o : outlines) {
@@ -596,8 +598,6 @@ public Seeds propagateSeed(ImageProcessor previous, ImageProcessor org, double s
       }
       big.invert();
       // store seeds if option ticked
-      Seeds ret = new Seeds(2);
-      ret.put(SeedTypes.FOREGROUNDS, small);
       ret.put(SeedTypes.BACKGROUND, getTrueBackground(big, org));
       if (storeSeeds) {
         seeds.add(ret);
@@ -610,7 +610,7 @@ public Seeds propagateSeed(ImageProcessor previous, ImageProcessor org, double s
     /**
      * Convert mask to outline.
      * 
-     * @param previous image to outline. White object on black background.
+     * @param previous image to be converted outline. White object on black background.
      * @return List of Outline for current frame
      * @see TrackOutline
      */
@@ -729,8 +729,9 @@ public ImagePlus getCompositeSeed(ImagePlus org, int offset) throws RandomWalkEx
 
     for (Seeds p : seeds) {
       // just in case convert to byte
-      // FIXME compile foregorunds from all images
-      ImageProcessor fg = (ImageProcessor) p.get(SeedTypes.FOREGROUNDS, 1).convertToByte(true);
+      // ImageProcessor fg = (ImageProcessor) p.get(SeedTypes.FOREGROUNDS, 1).convertToByte(true);
+      ImageProcessor fg = SeedProcessor.flatten(p, SeedTypes.FOREGROUNDS, 1).convertToByte(true);
+      fg.threshold(0); // need 255 not real value of map
       ImageProcessor bg = (ImageProcessor) p.get(SeedTypes.BACKGROUND, 1).convertToByte(true);
       // make colors transparent
       bg.multiply(colorScaling);

diff --git a/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkModel.java b/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkModel.java
@@ -43,7 +43,11 @@ public enum SeedSource {
     /**
      * Seed from binary mask image read from Qconf file.
      */
-    QconfFile
+    QconfFile,
+    /**
+     * ROIs
+     */
+    Rois
   }
 
   /**
@@ -76,6 +80,16 @@ public String[] getFilteringMethods() {
     return Arrays.stream(Filters.values()).map(Enum::name).toArray(String[]::new);
   }
 
+  /**
+   * Get seed sources defined in {@link SeedSource}.
+   * 
+   * @return array of seed sources
+   * @see SeedSource
+   */
+  public String[] getSeedSources() {
+    return Arrays.stream(SeedSource.values()).map(Enum::name).toArray(String[]::new);
+  }
+
   /**
    * Image to process.
    */
@@ -116,7 +130,37 @@ public void setOriginalImage(ImagePlus originalImage) {
   /**
    * Selected seed source. Depending on value some of fields may be invalid.
    */
-  public SeedSource seedSource;
+  private SeedSource selectedSeedSource;
+
+  /**
+   * SeedSource getter.
+   * 
+   * @return the seedSource
+   * @see SeedSource
+   */
+  public SeedSource getSelectedSeedSource() {
+    return selectedSeedSource;
+  }
+
+  /**
+   * SeedSource setter.
+   * 
+   * @param selectedSeedSource the selectedSeedSource to set
+   */
+  public void setSelectedSeedSource(SeedSource selectedSeedSource) {
+    this.selectedSeedSource = selectedSeedSource;
+  }
+
+  /**
+   * SeedSource setter.
+   * 
+   * @param selectedSeedSource index of SeedSource to set according to order returned by
+   *        {@link #getSeedSources()}
+   */
+  public void setSelectedSeedSource(int selectedSeedSource) {
+    this.selectedSeedSource = SeedSource.valueOf(getSeedSources()[selectedSeedSource]);
+  }
+
   /**
    * Seed given by RGB image selected from IJ. Valid for all seed sources.
    */
@@ -361,7 +405,7 @@ public void setSelectedFilteringPostMethod(int selectedFilteringPostMethod) {
   public RandomWalkModel() {
     algOptions = new RandomWalkOptions();
     originalImage = null;
-    seedSource = SeedSource.RGBImage;
+    setSelectedSeedSource(SeedSource.RGBImage);
     seedImage = null;
     qconfFile = null;
     selectedShrinkMethod = Propagators.NONE;
@@ -386,18 +430,18 @@ public RandomWalkModel() {
   @Override
   public String toString() {
     return "RandomWalkModel [params=" + algOptions + ", originalImage=" + originalImage
-            + ", seedSource=" + seedSource + ", seedImage=" + seedImage + ", qconfFile=" + qconfFile
-            + ", selectedShrinkMethod=" + selectedShrinkMethod + ", shrinkPower=" + shrinkPower
-            + ", expandPower=" + expandPower + ", estimateBackground=" + estimateBackground
-            + ", selectedFilteringMethod=" + selectedFilteringMethod + ", hatFilter=" + hatFilter
-            + ", alev=" + alev + ", num=" + num + ", window=" + window
-            + ", selectedFilteringPostMethod=" + selectedFilteringPostMethod + ", showSeeds="
-            + showSeeds + ", showPreview=" + showPreview + ", getShrinkMethods()="
-            + Arrays.toString(getShrinkMethods()) + ", getFilteringMethods()="
-            + Arrays.toString(getFilteringMethods()) + ", getselectedShrinkMethod()="
-            + getselectedShrinkMethod() + ", getSelectedFilteringMethod()="
-            + getSelectedFilteringMethod() + ", getSelectedFilteringPostMethod()="
-            + getSelectedFilteringPostMethod() + "]";
+            + ", seedSource=" + getSelectedSeedSource() + ", seedImage=" + seedImage
+            + ", qconfFile=" + qconfFile + ", selectedShrinkMethod=" + selectedShrinkMethod
+            + ", shrinkPower=" + shrinkPower + ", expandPower=" + expandPower
+            + ", estimateBackground=" + estimateBackground + ", selectedFilteringMethod="
+            + selectedFilteringMethod + ", hatFilter=" + hatFilter + ", alev=" + alev + ", num="
+            + num + ", window=" + window + ", selectedFilteringPostMethod="
+            + selectedFilteringPostMethod + ", showSeeds=" + showSeeds + ", showPreview="
+            + showPreview + ", getShrinkMethods()=" + Arrays.toString(getShrinkMethods())
+            + ", getFilteringMethods()=" + Arrays.toString(getFilteringMethods())
+            + ", getselectedShrinkMethod()=" + getselectedShrinkMethod()
+            + ", getSelectedFilteringMethod()=" + getSelectedFilteringMethod()
+            + ", getSelectedFilteringPostMethod()=" + getSelectedFilteringPostMethod() + "]";
   }
 
   /*
@@ -420,7 +464,7 @@ public int hashCode() {
     result = prime * result + ((algOptions == null) ? 0 : algOptions.hashCode());
     result = prime * result + ((qconfFile == null) ? 0 : qconfFile.hashCode());
     result = prime * result + ((seedImage == null) ? 0 : seedImage.getTitle().hashCode());
-    result = prime * result + ((seedSource == null) ? 0 : seedSource.hashCode());
+    result = prime * result + ((selectedSeedSource == null) ? 0 : selectedSeedSource.hashCode());
     result = prime * result
             + ((selectedFilteringMethod == null) ? 0 : selectedFilteringMethod.hashCode());
     result = prime * result
@@ -493,7 +537,7 @@ public boolean equals(Object obj) {
     } else if (!seedImage.getTitle().equals(other.seedImage.getTitle())) {
       return false;
     }
-    if (seedSource != other.seedSource) {
+    if (selectedSeedSource != other.selectedSeedSource) {
       return false;
     }
     if (selectedFilteringMethod != other.selectedFilteringMethod) {

diff --git a/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkOptions.java b/src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkOptions.java
@@ -88,7 +88,7 @@ public RandomWalkOptions() {
     alpha = 4e2;
     beta = 2 * 25;
     gamma[0] = 100;
-    gamma[1] = 300;
+    gamma[1] = 0;
     iter = 10000;
     dt = 0.1;
     relim = new double[] { 8e-3, 10 * 8e-3 };