Changeset 3879

Timestamp:

Oct 26, 2007, 11:01:46 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #797: Enhance performance for LOWESS and Medin-ratio plug-ins

Location:

trunk/src/plugins/core/net/sf/basedb/plugins

Files:

• LowessNormalization.java (modified) (5 diffs)
• MedianRatioNormalization.java (modified) (1 diff)

trunk/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java

@@ -334 +334 @@
     Expression ch2 = Dynamic.column(VirtualColumn.channel(2));
     // A = log10(sqrt(ch1 * ch2))
-    Expression A = Expressions.log10(Expressions.sqrt(Expressions.multiply(ch1, ch2)));
+    Expression pseudoA = Expressions.multiply(ch1, ch2);
+    Expression A = Expressions.log10(Expressions.sqrt(pseudoA));
 
     // Create restriction: ch1 > 0 and ch2 > 0
@@ -363 +364 @@
     query.restrict(bioAssayRestriction);
     query.order(Orders.asc(block));
-    query.order(Orders.asc(A));
+    query.order(Orders.asc(pseudoA));
       
     // Normalize one bioassay at a time
@@ -428 +429 @@
               SpotData spot = data.get(fromIndex + j);
               double factor = Math.exp(smoothCurve.get(j) * 0.5);
-              double newCh1 = spot.ch1/factor;
-              double newCh2 = spot.ch2*factor;
-              batcher.insert(bioassayColumn, spot.position, (float) newCh1, (float) newCh2);
+              batcher.insert(bioassayColumn, spot.position, (float)(spot.ch1/factor), (float)(spot.ch2*factor));
             }
             normalizedSpots += smoothCurve.size();
@@ -645 +644 @@
     final double A;
     final int block;
-    static final double LN2 = Math.log(2);
+    static final double INV_LN2 = 1 / Math.log(2);
 
     public SpotData(int position, float ch1, float ch2, int block)
@@ -653 +652 @@
       this.ch2 = ch2;
       this.block = block;
-      this.M = Math.log(ch1 / ch2) / LN2;
+      this.M = Math.log(ch1 / ch2) * INV_LN2;
       this.A = Math.log10(Math.sqrt(ch1 * ch2));
     }

trunk/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -429 +429 @@
               
               // Correct all spot intensities
-              float sqrtMedRatio = (float)Math.sqrt(median);
-              float invSqrtMedRatio = 1 / sqrtMedRatio;
+              double sqrtMedRatio = Math.sqrt(median);
+              double invSqrtMedRatio = 1 / sqrtMedRatio;
               for (int j = fromIndex; j < toIndex; ++j)
               {
                 SpotData spot = data.get(j);
-                double newCh1 = spot.ch1 * invSqrtMedRatio;
-                double newCh2 = spot.ch2 * sqrtMedRatio;
-                batcher.insert(bioassayColumn, spot.position, (float)newCh1, (float)newCh2);
+                float newCh1 = (float)(spot.ch1 * invSqrtMedRatio);
+                float newCh2 = (float)(spot.ch2 * sqrtMedRatio);
+                batcher.insert(bioassayColumn, spot.position, newCh1, newCh2);
               }
             }