Push 16bit conversion deeper into loading mechanism

saalfeldlab · Nov 21, 2024 · 22f0561 · 22f0561
1 parent 914c7b1
commit 22f0561
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Showing 2 changed files with 15 additions and 22 deletions.
diff --git a/render-app/src/main/java/org/janelia/alignment/loader/N5SliceLoader.java b/render-app/src/main/java/org/janelia/alignment/loader/N5SliceLoader.java
@@ -10,6 +10,8 @@
 import java.net.URLDecoder;
 import java.nio.charset.Charset;
 
+import net.imglib2.loops.LoopBuilder;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
 import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5FSReader;
@@ -170,6 +172,10 @@ public abstract B buildImageProcessor(final int width,
 
         public abstract RandomAccessibleInterval<A> setupTarget(B forImageProcessor);
 
+        protected A convert(final A pixel) {
+            return pixel;
+        }
+
         public ImageProcessor load(final N5Reader reader,
                                    final String dataSet,
                                    final int width,
@@ -186,15 +192,8 @@ public ImageProcessor load(final N5Reader reader,
             if (xAndYOffsets != null) {
                 slice = Views.offsetInterval(slice, xAndYOffsets, new long[] {0,1});
             }
-            final IntervalView<Pair<A, A>> pairView =  Views.interval(Views.pair(slice, target),
-                                                                      target);
-            final IterableInterval<Pair<A, A>> pairs = Views.flatIterable(pairView);
 
-            pairs.forEach(pair -> {
-                final A fromPixel = pair.getA();
-                final A toPixel = pair.getB();
-                toPixel.set(fromPixel);
-            });
+            LoopBuilder.setImages(slice, target).forEachPixel((s, t) -> t.set(convert(s)));
 
             return imageProcessor;
         }
@@ -232,6 +231,13 @@ public RandomAccessibleInterval<ShortType> setupTarget(final ShortProcessor forI
                             forImageProcessor.getWidth(),
                             forImageProcessor.getHeight());
                 }
+
+                @Override
+                // Since all 16bit HDF5 slices we open are converted .dat files, we need to properly convert the pixel values
+                protected ShortType convert(final ShortType pixel) {
+                    pixel.set(UnsignedShortType.getCodedSignedShortChecked(32768 - pixel.get()));
+                    return pixel;
+                }
             };
 
     public static Helper<FloatType, FloatProcessor> FLOAT_HELPER =

diff --git a/render-ws-spark-client/src/main/java/org/janelia/render/client/spark/n5/ShortN5Client.java b/render-ws-spark-client/src/main/java/org/janelia/render/client/spark/n5/ShortN5Client.java
@@ -206,8 +206,7 @@ private static void saveRenderStack(final JavaSparkContext sc,
                         .flatIterable(
                                 Views.interval(
                                         ArrayImgs.unsignedShorts(
-                                        		(short[])convert16bit( currentProcessor ).getPixels(),
-                                                //(short[]) currentProcessor.getPixels(),
+                                                (short[]) currentProcessor.getPixels(),
                                                 currentProcessor.getWidth(),
                                                 currentProcessor.getHeight()),
                                         outSlice));
@@ -223,16 +222,4 @@ private static void saveRenderStack(final JavaSparkContext sc,
             N5Utils.saveNonEmptyBlock(block, anotherN5Writer, datasetName, gridBlock.gridPosition, new UnsignedShortType(0));
         });
     }
-
-    public static ShortProcessor convert16bit( final ShortProcessor currentProcessor )
-    {
-    	final short[] array = (short[])currentProcessor.getPixels();
-
-        for (int i = 0; i < array.length; ++i) {
-            final short value = array[i];
-            array[i] = (value == 0) ? 0 : UnsignedShortType.getCodedSignedShort(32768 - array[i]);
-        }
-
-    	return currentProcessor;
-    }
 }