correct small errors and add TODO

bioimage-io · Oct 26, 2023 · a0a7e3a · a0a7e3a
1 parent 6d617fd
commit a0a7e3a
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Showing 3 changed files with 9 additions and 19 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java
@@ -238,20 +238,8 @@ public String getDisplayableStepMinConstraints() {
     	return minStr + "    " + stepStr;
     }
 
-    /**
-     * REturn an array containing the optimal patch for the given sequence.
-     * An optimal patch has the arbitrary requirement of not being bigger than
-     * 10^6 pixels
-     * @param seqSize
-     * 	array containing the size of the sequence with the axes order "xyczb"
-     * @return the array with the pathc of interest
-     */
-    public int[] getOptimalPatch(int[] seqSize) {
-    	String seqSizeAxes = "XYCZB";
-    	return getOptimalPatch(seqSize, seqSizeAxes);
-    }
-
-    /**
+    /** TODO this method does not realy required to be non-static because the instance already
+     * contains the axes order, maybe separate two methods
      * REturn an array containing the optimal patch for the given sequence.
      * @param seqSize
      * 	array containing the size of the sequence with the axes order defined
@@ -564,11 +552,13 @@ public void setTotalHalo(float[] totalHalo){
      * patch for the selected image
      * @param imSize
      * 	size of the image. The order is Width, Height, Channel, Slices, time
+     * @param axesOrder
+     * 	the axes order of the imSize parameter
      * @return the String containing a patch in the format 256,256,3
      */
-    public String getDisplayableOptimalPatch(int[] imSize) {
+    public String getDisplayableOptimalPatch(int[] imSize, String axesOrder) {
     	// Remove the B axes from the optimal patch size and get the String representation
-    	String patchStr = getDisplayableSizesString(getOptimalPatch(imSize));
+    	String patchStr = getDisplayableSizesString(getOptimalPatch(imSize, axesOrder));
     	return patchStr;
     }
 

diff --git a/src/main/java/io/bioimage/modelrunner/model/Model.java b/src/main/java/io/bioimage/modelrunner/model/Model.java
@@ -525,7 +525,7 @@ List<Tensor<T>> runBioimageioModelOnImgLib2WithTiling(List<Tensor<R>> inputTenso
 		else if (descriptor == null && !(new File(modelFolder, Constants.RDF_FNAME).isFile()))
 			throw new IllegalArgumentException("");
 		else if (descriptor == null)
-			descriptor = ModelDescriptor.readFromLocalFile(modelFolder + File.separator + Constants.RDF_FNAME);
+			descriptor = ModelDescriptor.readFromLocalFile(modelFolder + File.separator + Constants.RDF_FNAME, false);
 		PatchGridCalculator<R> tileGrid = PatchGridCalculator.build(descriptor, inputTensors);
 		return runTiling(inputTensors, tileGrid);
 	}
@@ -592,7 +592,7 @@ void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors, Patch
 		}
 	}
 
-	public static <T extends NativeType<T> & RealType<T>> void main(String[] args) throws IOException, ValidationException, LoadEngineException, RunModelException {
+	public static <T extends NativeType<T> & RealType<T>> void main(String[] args) throws IOException, ValidationException, LoadEngineException, RunModelException, LoadModelException {
 		String mm = "C:\\Users\\angel\\OneDrive\\Documentos\\pasteur\\git\\model-runner-java\\models\\StarDist H&E Nuclei Segmentation_06092023_020924\\";
 		Img<FloatType> im = ArrayImgs.floats(new long[] {1, 511, 512, 3});
 		ImagePlus imp = IJ.openImage(mm + File.separator + "sample_input_0.tif");

diff --git a/src/main/java/io/bioimage/modelrunner/tiling/PatchGridCalculator.java b/src/main/java/io/bioimage/modelrunner/tiling/PatchGridCalculator.java
@@ -275,7 +275,7 @@ private PatchSpec computePatchSpecs(TensorSpec spec, RandomAccessibleInterval<T>
     	for (int i = 0; i < intShape.length; i ++) intShape[i] = (int) rai.dimensionsAsLongArray()[i];
     	if (spec.getProcessingPatch() == null) {
 			try {
-				spec.setTileSizeForTensorAndImageSize(spec.getOptimalPatch(intShape), intShape);
+				spec.setTileSizeForTensorAndImageSize(spec.getOptimalPatch(intShape, spec.getAxesOrder()), intShape);
 			} catch (Exception e) {
 				throw new IllegalArgumentException("Tensor dimensions of tensor named '" + spec.getName() + "' "
 						+ "are not compatible with the requirements set by the"