Merge branch 'BIO_ICT_olugins-have-optional-emptyImg-check-disable'

CellTrackingChallenge · Nov 22, 2023 · 6bf4723 · 6bf4723
2 parents d107a06 + 4593d06
commit 6bf4723
Showing 1 changed file with 17 additions and 5 deletions.
diff --git a/src/main/java/net/celltrackingchallenge/measures/TrackDataCache.java b/src/main/java/net/celltrackingchallenge/measures/TrackDataCache.java
@@ -84,11 +84,23 @@ public void setupSimilarAs(final TrackDataCache _referenceCache)
 			throw new NullPointerException("No existing (null) template/reference cache has been supplied.");
 
 		noOfDigits = _referenceCache.noOfDigits;
+		shouldComplainOnEmptyImages = _referenceCache.shouldComplainOnEmptyImages;
+		overlapRatio = _referenceCache.overlapRatio;
 	}
 
-	///specifies how many digits are to be expected in the input filenames
+	/** specifies how many digits are to be expected in the input filenames */
 	public int noOfDigits = 3;
 
+	/** specifies if the processing should stop when an input image with no segmentation/detection is found,
+	    it's advisable to stop on empty images, the code may assume at places that there's always at least
+	    one segmentation mask found in every image and definitively the code assumes that there's at least
+	    one mask in a whole sequence (otherwise division by zero will occur) */
+	public boolean shouldComplainOnEmptyImages = true;
+
+	/** specifies what relative proportion of the area of a GT marker must be covered in order to declare a match,
+	    it's advisable to avoid going below 0.5, the code may assume at places that overlapRatio >= 0.5 */
+	public double overlapRatio = 0.5;
+
 	///GT and RES paths combination for which this cache is valid, null means invalid
 	private String gtPath = null;
 	///GT and RES paths combination for which this cache is valid, null means invalid
@@ -522,14 +534,14 @@ public void ClassifyLabels(IterableInterval<UnsignedShortType> gt_img,
 	{
 		//default behavior is to be very strict:
 		//  complain whenever empty result or GT image is found
-		ClassifyLabels(gt_img,res_img, true, levels.size(), 0.5);
+		ClassifyLabels(gt_img,res_img, shouldComplainOnEmptyImages, levels.size(), overlapRatio);
 	}
 
 	public void ClassifyLabels(IterableInterval<UnsignedShortType> gt_img,
 	                           RandomAccessibleInterval<UnsignedShortType> res_img,
 	                           final boolean shouldComplainOnEmptyImages)
 	{
-		ClassifyLabels(gt_img,res_img, shouldComplainOnEmptyImages, levels.size(), 0.5);
+		ClassifyLabels(gt_img,res_img, shouldComplainOnEmptyImages, levels.size(), overlapRatio);
 	}
 
 	public void ClassifyLabels(IterableInterval<UnsignedShortType> gt_img,
@@ -538,7 +550,7 @@ public void ClassifyLabels(IterableInterval<UnsignedShortType> gt_img,
 	{
 		//default behavior is to be very strict:
 		//  complain whenever empty result or GT image is found
-		ClassifyLabels(gt_img,res_img, true, time, 0.5);
+		ClassifyLabels(gt_img,res_img, true, time, overlapRatio);
 	}
 
 	public void ClassifyLabels(IterableInterval<UnsignedShortType> gt_img,
@@ -548,7 +560,7 @@ public void ClassifyLabels(IterableInterval<UnsignedShortType> gt_img,
 	{
 		//default behavior is to be very strict:
 		//  complain whenever empty result or GT image is found
-		ClassifyLabels(gt_img,res_img, shouldComplainOnEmptyImages, time, 0.5);
+		ClassifyLabels(gt_img,res_img, shouldComplainOnEmptyImages, time, overlapRatio);
 	}
 
 	@SuppressWarnings("unchecked")