Added debug routines

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)

src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkSegmentation.java

@@ -2,6 +2,8 @@
 
 import java.awt.Color;
 import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.security.InvalidParameterException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -22,6 +24,7 @@
 
 import ij.IJ;
 import ij.ImagePlus;
+import ij.ImageStack;
 import ij.plugin.ImageCalculator;
 import ij.process.BinaryProcessor;
 import ij.process.ByteProcessor;
@@ -968,6 +971,7 @@ protected RealMatrix getMeanSeedLocal(ImageProcessor mask, int localMeanMaskSize
    *         not contain BG map.
    */
   protected ProbabilityMaps solver(Seeds seeds, RealMatrix[] gradients) {
+    ImageStack debugPm = null;
     RealMatrix diffIfg = null; // normalised squared differences to mean seed intensities for FG
     // store number of iterations performed for each object. These numbers are used for stopping
     // iterations earlier for background object
@@ -1077,18 +1081,21 @@ protected ProbabilityMaps solver(Seeds seeds, RealMatrix[] gradients) {
       // specified relError and after weighting it dominates leaving only original object seed as
       // segmented object. Here we stop segmenting background after certain number of iterations but
       // not relErr. This is how we have it solved in MAtlab
-      if (userBckPoints.contains(seedsPointsFg.get(cell)) && iterations.size() > 0) {
+      if (true && (userBckPoints.contains(seedsPointsFg.get(cell)) && iterations.size() > 0)) {
         // just use average of iters for BCK
         iter = iterations.stream().mapToInt(Integer::intValue).max().getAsInt() / iterations.size();
         // FIXME This can be disabled, then BCK will need more iterations but sometimes results are
         // better
+        // potential pitfall is if user mark BG far from cell, then small number of iters is not
+        // enough to flood whole background (but it will work because during comparison bck is on 0
+        // and FG segmentation rather does not leave object
         iter /= (currentSweep + 1);
       } else { // object - use specified number of iters
         iter = params.iter / (currentSweep + 1);
       }
       // main loop here we simulate diffusion process in time
       outerloop: for (i = 0; i < iter; i++) {
-        if (i % 50 == 0) {
+        if (i % relErrStep == 0) {
           LOGGER.info("Iter: " + i);
         } else {
           LOGGER.trace("Iter: " + i);
@@ -1157,6 +1164,19 @@ protected ProbabilityMaps solver(Seeds seeds, RealMatrix[] gradients) {
             break outerloop;
           }
         }
+        // store probabilities over iterations
+        if (QuimP.SUPER_DEBUG) {
+          debugPm =
+                  (debugPm == null) ? new ImageStack(fg.getColumnDimension(), fg.getRowDimension())
+                          : debugPm;
+          if (i > 1000) {
+            if (i % 50 == 0) {
+              debugPm.addSlice(QuimPArrayUtils.realMatrix2ImageProcessor(fg));
+            }
+          } else {
+            debugPm.addSlice(QuimPArrayUtils.realMatrix2ImageProcessor(fg));
+          }
+        }
         // remember FG map for this iteration to use it to compute relative error in next iteration
         QuimPArrayUtils.copy2darray(fg2d, tmpFglast2d);
       } // iter
@@ -1168,6 +1188,16 @@ protected ProbabilityMaps solver(Seeds seeds, RealMatrix[] gradients) {
       } else {
         ret.put(SeedTypes.FOREGROUNDS, fg);
       }
+      // save stack of probability maps (over iterations) for each processed object separately
+      if (QuimP.SUPER_DEBUG) {
+        if (debugPm != null) {
+          ImagePlus debugIm = new ImagePlus("debug", debugPm);
+          String tmp = System.getProperty("java.io.tmpdir");
+          Path p = Paths.get(tmp, "Rw_ProbMap-cell_" + cell);
+          IJ.saveAsTiff(debugIm, p.toString());
+          debugPm = null; // next object
+        }
+      }
     } // cell
     return ret;
   }

src/test/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkSegmentationPluginRun.java

@@ -27,8 +27,8 @@ public static void main(String[] args) throws InterruptedException {
     // "open(\"src/test/Resources-static/ticket209gh/fluoreszenz-test.tif\")");
     // IJ.runMacro("open(\"src/test/Resources-static/ticket209gh/segmented_color.tif\")");
 
-    IJ.openImage("src/test/Resources-static/PropagateSeeds/stack.tif").show();
-    IJ.openImage("src/test/Resources-static/PropagateSeeds/stack-mask.tif").show();
+    // IJ.openImage("src/test/Resources-static/PropagateSeeds/stack.tif").show();
+    // IJ.openImage("src/test/Resources-static/PropagateSeeds/stack-mask.tif").show();
 
     // IJ.openImage("src/test/Resources-static/Stack_cut.tif").show();
 
@@ -40,10 +40,66 @@ public static void main(String[] args) throws InterruptedException {
     // + "selectedFilteringMethod:NONE,hatFilter:false,alev:0.9,num:1,window:15,"
     // + "selectedFilteringPostMethod:MEDIAN,showSeeds:false,showPreview:false,"
     // + "paramFile:(null)}");
-    obj.run("");
+
+    // obj.run("");
 
     // ************** Run **************
     // example1();
+    example2();
+  }
+
+  /**
+   * Super debug.
+   * 
+   * <p>Save selected number of fg and bg prob maps to stack for each iteration.
+   */
+  public static void example2() {
+    System.setProperty("quimpconfig.superDebug", "true");
+    new ImageJ();
+    RandomWalkSegmentationPlugin_ obj = new RandomWalkSegmentationPlugin_();
+    //!> example 1
+    IJ.openImage(
+            "/home/baniuk/Desktop/Tests/284/Stack_1frame.tif")
+            .show();
+    IJ.openImage("/home/baniuk/Desktop/Tests/284/SEED_Stack_1frame.tif")
+            .show();
+    obj.run("opts={"
+            + "algOptions:{"
+            + "alpha:400.0,"
+            + "beta:50.0,"
+            + "gamma:[100.0,0.0],"
+            + "iter:10000," // !
+            + "dt:0.1,"
+            + "relim:[0.00200,0.02],"
+            + "useLocalMean:false,"
+            + "localMeanMaskSize:23,"
+            + "maskLimit:false"
+            + "},"
+            + "originalImageName:(Stack_1frame.tif),"
+            + "selectedSeedSource:RGBImage,"
+            + "seedImageName:(SEED_Stack_1frame.tif),"
+            + "qconfFile:(null),"
+            + "selectedShrinkMethod:NONE,"
+            + "shrinkPower:17.0,"
+            + "expandPower:15.0,"
+            + "scaleSigma:0.3,"
+            + "scaleMagn:4.0,"
+            + "scaleEqNormalsDist:12.0,"
+            + "scaleCurvDistDist:12.0,"
+            + "estimateBackground:false,"
+            + "selectedFilteringMethod:NONE,"
+            + "hatFilter:false,alev:0.9,num:1,window:15,"
+            + "selectedFilteringPostMethod:NONE,"
+            + "showSeeds:false,"
+            + "showPreview:false,"
+            + "showProbMaps:false,"
+            + "paramFile:(null)}");
+    IJ.runMacro("selectWindow(\"Segmented_Stack_1frame.tif\");");
+    IJ.runMacro("run(\"Outline\");");
+    IJ.runMacro("run(\"Merge Channels...\", \""
+            + "c1=Segmented_Stack_1frame.tif "
+            + "c4=Stack_1frame.tif create keep\");");
+    //!<
   }
 
   /**