finish the scafold for directly running models from the bioimage.io

bioimage-io · Oct 25, 2023 · 2a023e2 · 2a023e2
1 parent f080bb1
commit 2a023e2
Showing 1 changed file with 18 additions and 5 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/model/Model.java b/src/main/java/io/bioimage/modelrunner/model/Model.java
@@ -504,10 +504,11 @@ public void runModel( List< Tensor < ? > > inTensors, List< Tensor < ? > > outTe
 	 * @param inputTensors
 	 * @return
 	 * @throws ValidationException 
+	 * @throws RunModelException 
 	 * @throws Exception 
 	 */
 	public <T extends RealType<T> & NativeType<T>, R extends RealType<R> & NativeType<R>> 
-	List<Tensor<T>> runBioimageioModelOnImgLib2WithTiling(List<Tensor<R>> inputTensors) throws ValidationException {
+	List<Tensor<T>> runBioimageioModelOnImgLib2WithTiling(List<Tensor<R>> inputTensors) throws ValidationException, RunModelException {
 		if (descriptor == null && modelFolder == null)
 			throw new IllegalArgumentException("");
 		else if (descriptor == null && !(new File(modelFolder, Constants.RDF_FNAME).isFile()))
@@ -521,7 +522,7 @@ else if (descriptor == null)
 
 	@SuppressWarnings("unchecked")
 	private <T extends RealType<T> & NativeType<T>, R extends RealType<R> & NativeType<R>> 
-	void runTiling(List<Tensor<R>> inputTensors, PatchGridCalculator<R> tileGrid) {
+	void runTiling(List<Tensor<R>> inputTensors, PatchGridCalculator<R> tileGrid) throws RunModelException {
 		LinkedHashMap<String, PatchSpec> inTileSpecs = tileGrid.getInputTensorsTileSpecs();
 		LinkedHashMap<String, PatchSpec> outTileSpecs = tileGrid.getOutputTensorsTileSpecs();
 		List<Tensor<T>> outputTensors = new ArrayList<Tensor<T>>();
@@ -538,7 +539,7 @@ void runTiling(List<Tensor<R>> inputTensors, PatchGridCalculator<R> tileGrid) {
 	}
 
 	private <T extends RealType<T> & NativeType<T>, R extends RealType<R> & NativeType<R>> 
-	void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors, PatchGridCalculator<R> tileGrid) {
+	void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors, PatchGridCalculator<R> tileGrid) throws RunModelException {
 		LinkedHashMap<String, PatchSpec> inTileSpecs = tileGrid.getInputTensorsTileSpecs();
 		LinkedHashMap<String, PatchSpec> outTileSpecs = tileGrid.getOutputTensorsTileSpecs();
 		Map<Object, TileGrid> inTileGrids = inTileSpecs.entrySet().stream()
@@ -551,7 +552,7 @@ void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors, Patch
 
 		for (int j = 0; j < nTiles; j ++) {
 			int tileCount = j + 0;
-			IntStream.range(0, inputTensors.size()).mapToObj(i -> {
+			List<Tensor<?>> inputTileList = IntStream.range(0, inputTensors.size()).mapToObj(i -> {
 				if (!inputTensors.get(i).isImage())
 					return inputTensors.get(i);
 				RandomAccessibleInterval<R> tileRai = Views.interval(
@@ -564,7 +565,19 @@ void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors, Patch
 						Intervals.expand(inputTensors.get(i).getData(), 50));
 						*/
 				return Tensor.build(inputTensors.get(i).getName(), inputTensors.get(i).getAxesOrderString(), tileRai);
-			});
+			}).collect(Collectors.toList());
+
+			List<Tensor<?>> outputTileList = IntStream.range(0, outputTensors.size()).mapToObj(i -> {
+				if (!outputTensors.get(i).isImage())
+					return outputTensors.get(i);
+				RandomAccessibleInterval<T> tileRai = Views.interval(
+						Views.extendBorder(outputTensors.get(i).getData()), 
+						outTileGrids.get(outputTensors.get(i).getName()).getTilePostionsInImage().get(tileCount),
+						(long[]) outTileGrids.get(outputTensors.get(i).getName()).getTileSize());
+				return Tensor.build(outputTensors.get(i).getName(), outputTensors.get(i).getAxesOrderString(), tileRai);
+			}).collect(Collectors.toList());
+
+			this.runModel(inputTileList, outputTileList);
 		}
 
 	}