CELL/EDGE_INTENSITY: improved description for added functionalities

epitools · Jul 26, 2018 · 8fc8058 · 8fc8058
1 parent 0e503b2
commit 8fc8058
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Showing 2 changed files with 17 additions and 12 deletions.
diff --git a/CellGraph/src/plugins/davhelle/cellgraph/overlays/CellIntensityOverlay.java b/CellGraph/src/plugins/davhelle/cellgraph/overlays/CellIntensityOverlay.java
@@ -30,7 +30,7 @@
 import com.vividsolutions.jts.geom.Point;
 
 /**
- * Overlay to measure the intensity of individual cells.
+ * Overlay to measure the junction intensity for each cell.
  * Currently the measurement geometry is a difference
  * between the positive and negative buffer of the cell
  * geometry. The size of the buffer is set by the user.
@@ -45,7 +45,14 @@ public class CellIntensityOverlay extends StGraphOverlay implements EzVarListene
 	 * Description string for GUI
 	 */
 	public static final String DESCRIPTION = 
-			"Measures cell border intensity";
+			"Overlay to measure the junction intensity for each cell.<br/><br>" + 
+			"Currently the measurement geometry is the difference<br/>" + 
+			"between the positive and negative buffer of the cell<br/>" + 
+			"geometry. The size of the buffer is set by the user.<br/>" + 
+			"The end geometry is a ring geometry.<br/><br>" + 
+			"NOTE: more conservative measure available through: <br>"
+			+ "    EDGE_INTENSITY > ring_mode (i.e. edge union <br/>"
+			+ "intersected with cell geometry)";
 
 	/**
 	 * JTS class to convert JTS Geometries to AWT Shapes

diff --git a/CellGraph/src/plugins/davhelle/cellgraph/overlays/EdgeIntensityOverlay.java b/CellGraph/src/plugins/davhelle/cellgraph/overlays/EdgeIntensityOverlay.java
@@ -48,16 +48,14 @@ public class EdgeIntensityOverlay extends StGraphOverlay{
 			" the underlying intensity (I). Save the intensities via<br/>" +
 			" the layer option menu as XLS.<br/><br/>" +
 
-			"(i) [Measure relative intensity] computes a ratio by<br/>" +
-			" dividing the original value through intensities of<br/>" +
-			" neighboring edges and cells:<br/><br/>" +
-			"  relative_edge_intensity = <br/>" +
-			"    (edge - avg_cell_background) / <br/>" +
-			"    (avg_neighbor_edges - avg_cell_background)<br/><br/>" +
-
-			"(i) The color gradient is normalized by frame.<br/><br/>" + 
-
-			"(w) [Measure all frames] can take very long!";
+			"[Measure relative intensity] computes a ratio between<br/>" +
+			" the original edge intensity (E) and the intensities of<br/>" +
+			" neighboring edges (NE) and cell backgrounds (CB):<br/><blockquote>" +
+			"  rel.intensity = (E - avg.CB) / (avg.NE - avg.CB)</blockquote>" +
+			"NOTE:<br/>" +
+			"- The color gradient is normalized by frame.<br/>" + 
+			"- [ring mode] edge union intersected with cell area<br/>"+
+			"- [Measure all frames] may take very long!";
 
 	/**
 	 * JTS to AWT shape writer