add more comments

src/main/java/io/bioimage/modelrunner/tiling/PatchSpec.java

@@ -65,7 +65,9 @@ public class PatchSpec
      *        sequence sizes.
      * @param patchPaddingSize
      *        The padding size used on each patch.
-    * @return The create patch specification.
+     * @param tensorDims
+     * 		  The original size of the image/tensor that is going to be tiled
+     * @return The create patch specification.
      */
     public static PatchSpec create(String tensorName, long[] patchInputSize, int[] patchGridSize, 
     		int[][] patchPaddingSize, long[] tensorDims)

src/main/java/io/bioimage/modelrunner/utils/IndexingUtils.java

@@ -33,7 +33,7 @@ public class IndexingUtils
 {
 
 	/**
-	 * Obtain a flat index position from a multidimensional index position
+	 * Obtain a flat index position from a multidimensional index position, assumes row major (C-order)
 	 * 
 	 * @param ind
 	 *            the multidimensional indexes
@@ -75,7 +75,7 @@ public static void main(String[] args) {
 	}
 
 	/**
-	 * Obtain a flat index position from a multidimensional index position
+	 * Obtain a flat index position from a multidimensional index position, assumes row major (C-order)
 	 * 
 	 * @param ind
 	 *            the multidimensional indexes
@@ -97,10 +97,10 @@ public static int multidimensionalIntoFlatIndex( long[] ind, long[] size )
 	}
 
 	/**
-	 * Obtain a flat index position from a multidimensional index position
+	 * Obtain the multidimensional position corresponding to a flat position in an nd array
 	 * 
-	 * @param ind
-	 * 			  the index of the position as if it was a flat array
+	 * @param flat
+	 * 			  flat position in an nd-array, assumes row major (C-order)
 	 * @param size
 	 *            size of the tensor
 	 * @return the multidimensional indexes
@@ -121,10 +121,10 @@ public static long[] flatIntoMultidimensionalIndex( long flat, long[] size )
 	}
 
 	/**
-	 * Obtain a flat index position from a multidimensional index position
+	 * Obtain the multidimensional position corresponding to a flat position in an nd array
 	 * 
-	 * @param ind
-	 * 			  the index of the position as if it was a flat array
+	 * @param flat
+	 * 			  flat position in an nd-array, assumes row major (C-order)
 	 * @param size
 	 *            size of the tensor
 	 * @return the multidimensional indexes