Merge pull request #26 from petebankhead/dev

Faster Mat to NDArray channels-first conversion

src/main/java/qupath/ext/djl/DjlTools.java

@@ -1,5 +1,5 @@
 /*-
- * Copyright 2022 QuPath developers, University of Edinburgh
+ * Copyright 2022-2024 QuPath developers, University of Edinburgh
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -29,7 +29,6 @@
 import java.util.Set;
 
 import ai.djl.Device;
-import org.bytedeco.javacpp.Loader;
 import org.bytedeco.javacpp.PointerScope;
 import org.bytedeco.javacpp.indexer.BooleanIndexer;
 import org.bytedeco.javacpp.indexer.ByteIndexer;
@@ -41,6 +40,7 @@
 import org.bytedeco.javacpp.indexer.UByteIndexer;
 import org.bytedeco.javacpp.indexer.UShortIndexer;
 import org.bytedeco.opencv.global.opencv_core;
+import org.bytedeco.opencv.global.opencv_dnn;
 import org.bytedeco.opencv.opencv_core.Mat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -389,7 +389,6 @@ static Mat predict(Model model, Mat mat) throws TranslateException {
 
 	/**
 	 * Convert an Opencv {@link Mat} to a Deep Java Library {@link NDArray}.
-	 * Note that this ass
 	 * @param manager an {@link NDManager}, required to create the NDArray
 	 * @param mat the mat to convert
 	 * @param ndLayout a layout string for the NDArray, e.g. "CHW"; currently, HW must appear together (in that order)
@@ -408,10 +407,15 @@ public static NDArray matToNDArray(NDManager manager, Mat mat, String ndLayout)
 		// TODO: Check what this order is!!!
 		NDArray array = null;
 		if (indC > indHW || shape.get(indC) == 1) {
+			// Channels-last, or single-channel
 			var buffer = mat.createBuffer();
 			array = manager.create(buffer, shape, dataType);			
+		} else if ("NCHW".equals(ndLayout) || "CHW".equals(ndLayout)) {
+			// Channels-first - an OpenCV blob is defined to have the order NCHW
+			array = manager.create(opencv_dnn.blobFromImage(mat).createBuffer(), shape, dataType);
 		} else {
-			var shapeDims = shape.getShape();
+			// Really awkward strategy to handle channels in an uncommon place (shouldn't actually occur?)
+			var shapeDims = shape.getShape().clone();
 			shapeDims[indC] = 1;
 			var shapeChannel = new Shape(shapeDims, shape.getLayout());