improve border management of tiles

bioimage-io · Oct 25, 2023 · ba55595 · ba55595
1 parent c537907
commit ba55595
Showing 1 changed file with 8 additions and 10 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/tiling/TileGrid.java b/src/main/java/io/bioimage/modelrunner/tiling/TileGrid.java
@@ -22,14 +22,10 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 import java.util.stream.IntStream;
+import java.util.stream.LongStream;
 
 import io.bioimage.modelrunner.utils.IndexingUtils;
-import net.imglib2.img.Img;
-import net.imglib2.img.array.ArrayImgFactory;
-import net.imglib2.type.NativeType;
-import net.imglib2.util.Util;
 
 /**
  * Calculate all the coordinates for the tiles for a specific tensor in the image that wants to
@@ -66,9 +62,10 @@ private TileGrid()
 
     /**
      */
-    public static TileGrid create(PatchSpec tileSpecs, int[] gridSize)
+    public static TileGrid create(PatchSpec tileSpecs, long[] imageDims)
     {
         TileGrid ps = new TileGrid();
+        int[] gridSize = tileSpecs.getPatchGridSize();
         ps.tileSize = tileSpecs.getPatchInputSize();
         int tileCount = Arrays.stream(gridSize).reduce(1, (a, b) -> a * b);
 
@@ -80,11 +77,12 @@ public static TileGrid create(PatchSpec tileSpecs, int[] gridSize)
                     .map(i -> patchSize[i] - padSize[0][i] - padSize[1][i]).toArray();
 			ps.roiSize = roiSize;
 			ps.roiPositionsInTile.add(IntStream.range(0, padSize[0].length).mapToLong(i -> (long) padSize[0][i]).toArray());
-        	long[] roiStart = IntStream.range(0, patchIndex.length)
-                    .map(i -> roiSize[i] * patchIndex[i]).mapToLong(i -> (long) i).toArray();
+        	long[] roiStart = LongStream.range(0, patchIndex.length)
+                    .map(i -> Math.min(roiSize[(int) i] * patchIndex[(int) i], imageDims[(int) i] - roiSize[(int) i])).toArray();
 			ps.roiPositionsInImage.add(roiStart);
-        	long[] patchStart = IntStream.range(0, patchIndex.length)
-                    .map(i -> roiSize[i] * patchIndex[i] - padSize[0][i]).mapToLong(i -> (long) i).toArray();
+        	long[] patchStart = LongStream.range(0, patchIndex.length)
+                    .map(i -> Math.min(roiSize[(int) i] * patchIndex[(int) i] - padSize[0][(int) i], imageDims[(int) i] - roiSize[(int) i]))
+                    .toArray();
         	ps.tilePostionsInImage.add(patchStart);
         }
         return ps;