start improving the tiling strategy and usage

src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java

@@ -57,4 +57,6 @@ public interface TensorSpec {
     public Axes getAxesInfo();
 
     public String getDataType();
+
+    public boolean isImage();
 }

src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV04.java

@@ -177,4 +177,12 @@ public String getDataType() {
 	public int[] getHaloArr() {
 		return this.axes.getHaloArr();
 	}
+
+	@Override
+	public boolean isImage() {
+		if (axes.getAxesOrder().contains("x") && axes.getAxesOrder().contains("y"))
+			return true;
+		else
+			return false;
+	}
 }

src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV05.java

@@ -180,4 +180,12 @@ public String getDataType() {
 	public int[] getHaloArr() {
 		return this.axes.getHaloArr();
 	}
+
+	@Override
+	public boolean isImage() {
+		if (axes.getAxesOrder().contains("x") && axes.getAxesOrder().contains("y"))
+			return true;
+		else
+			return false;
+	}
 }

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

@@ -186,11 +186,11 @@ public void checkPatchSpecs(LinkedHashMap<String, PatchSpec> patchSpecs) throws
     	for (Entry<String, PatchSpec> spec : patchSpecs.entrySet()) {
     		int[] nGrid = spec.getValue().getTileGrid();
     		TensorSpec tt = this.descriptor.findInputTensor(spec.getKey());
-    		if (grid == null && tt.getTiling()) {
+    		if (grid == null && this.descriptor.isTilingAllowed()) {
     			grid = nGrid;
     			firstName = spec.getKey();
     		}
-    		if (tt.getTiling() && !compareTwoArrays(nGrid, grid)){
+    		if (this.descriptor.isTilingAllowed() && !compareTwoArrays(nGrid, grid)){
     			throw new IllegalArgumentException("All the input images must be processed with the same number of patches.\n"
 						+ "The relationship between the patch size and image size should be the same for every input that allows patching/tiling.\n"
 						+ "Tensors '" + firstName + "' and '" + spec.getKey() + "' need different number of patches to "
@@ -247,7 +247,7 @@ private List<TensorSpec> findOutputImageTensorSpec()
     private LinkedHashMap<String, PatchSpec> computePatchSpecsForEveryTensor(List<TensorSpec> tensors, List<Tensor<T>> images){
     	LinkedHashMap<String, PatchSpec> patchInfoList = new LinkedHashMap<String, PatchSpec>();
     	for (int i = 0; i < tensors.size(); i ++)
-    		patchInfoList.put(tensors.get(i).getName(), computePatchSpecs(tensors.get(i), images.get(i)));
+    		patchInfoList.put(tensors.get(i).getTensorID(), computePatchSpecs(tensors.get(i), images.get(i)));
     	return patchInfoList;
     }
 
@@ -272,7 +272,7 @@ public LinkedHashMap<String, PatchSpec> getOutputTensorsTileSpecs() throws Illeg
 		for (int i = 0; i < outTensors.size(); i ++) {
     		String refTensor = outTensors.get(i).getShape().getReferenceInput();
     		PatchSpec refSpec = refTensor == null ? inputTilesSpecs.values().stream().findFirst().get() : inputTilesSpecs.get(refTensor);
-    		patchInfoList.put(outTensors.get(i).getName(), computePatchSpecsForOutputTensor(outTensors.get(i), refSpec));
+    		patchInfoList.put(outTensors.get(i).getTensorID(), computePatchSpecsForOutputTensor(outTensors.get(i), refSpec));
 		}
 		outputTilesSpecs = patchInfoList;
     	return outputTilesSpecs;
@@ -331,8 +331,8 @@ private PatchSpec computePatchSpecs(TensorSpec spec, RandomAccessibleInterval<T>
         int[][] paddingSize = new int[2][tileSize.length];
         // REgard that the input halo represents the output halo + offset 
         // and must be divisible by 0.5. 
-        float[] halo = spec.getHalo();
-        if (!descriptor.isPyramidal() && spec.getTiling()) {
+        int[] halo = spec.getHaloArr();
+        if (!descriptor.isPyramidal() && this.descriptor.isTilingAllowed()) {
         	// In the case that padding is asymmetrical, the left upper padding has the extra pixel
             for (int i = 0; i < halo.length; i ++) {paddingSize[0][i] = (int) Math.ceil(halo[i]);}
             // In the case that padding is asymmetrical, the right bottom padding has one pixel less
@@ -373,7 +373,7 @@ private PatchSpec computePatchSpecsForOutputTensor(TensorSpec tensorSpec, PatchS
         paddingSize[1] = arrayToWantedAxesOrderAddZeros(paddingSize[1], ogAxes, tensorSpec.getAxesOrder());
         long[] tileSize;
         long[] shapeLong;
-        if (tensorSpec.getShape().getReferenceInput() == null && !tensorSpec.getTiling()) {
+        if (tensorSpec.getShape().getReferenceInput() == null && !this.descriptor.isTilingAllowed()) {
         	shapeLong = Arrays.stream(tensorSpec.getTileSize()).mapToLong(i -> i).toArray();
         	tileSize = shapeLong;
         } else if (tensorSpec.getShape().getReferenceInput() == null) {

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

@@ -0,0 +1,18 @@
+package io.bioimage.modelrunner.tiling;
+
+import java.util.List;
+
+import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
+
+public class TileCalculator {
+
+	private final List<TileInfo> tileInfoList;
+
+	private final ModelDescriptor descriptor;
+
+	private TileCalculator(ModelDescriptor descriptor, List<TileInfo> tileInfoList) {
+		this.descriptor = descriptor;
+		this.tileInfoList = tileInfoList;
+	}
+
+}

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

@@ -160,22 +160,4 @@ public List<long[]> getRoiPostionsInImage() {
     	return this.roiPositionsInImage;
     }
 
-    @Override
-    public String toString()
-    {
-    	return "";
-    	/*
-    	String[] paddingStrArr = new String[patchPaddingSize[0].length];
-    	for (int i = 0; i < paddingStrArr.length; i ++)
-    		paddingStrArr[i] = patchPaddingSize[0][i] + "," + patchPaddingSize[1][i];
-        StringBuilder builder = new StringBuilder();
-        builder.append("PatchSpec of '" + tensorName + "'"
-        		+ "[patchInputSize=").append(Arrays.toString(this.tileSize))
-                .append(", patchGridSize=").append(Arrays.toString(patchGridSize))
-                .append(", patchPaddingSize=").append(Arrays.toString(paddingStrArr))
-                .append("]");
-        return builder.toString();
-        */
-    }
-
 }

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

@@ -0,0 +1,61 @@
+package io.bioimage.modelrunner.tiling;
+
+public class TileInfo {
+
+
+	private final String name;
+
+	private final long[] imDims;
+
+	private final long[] proposedTileDims;
+
+	private final String imAxesOrder;
+
+	private final String tileAxesOrder;
+
+	private TileInfo(String tensorName, long[] imDims, String imAxesOrder, long[] proposedTileDims, String tileAxesOrder) {
+		this.name = tensorName;
+		this.imAxesOrder = imAxesOrder;
+		this.imDims = imDims;
+		this.proposedTileDims = proposedTileDims;
+		this.tileAxesOrder = tileAxesOrder;
+	}
+
+	/**
+	 * @return the name
+	 */
+	public String getName() {
+		return name;
+	}
+
+	/**
+	 * @return the imDims
+	 */
+	public long[] getImageDimensions() {
+		return imDims;
+	}
+
+	/**
+	 * @return the proposedTileDims
+	 */
+	public long[] getProposedTileDimensions() {
+		return proposedTileDims;
+	}
+
+	/**
+	 * @return the imAxesOrder
+	 */
+	public String getImageAxesOrder() {
+		return imAxesOrder;
+	}
+
+	/**
+	 * @return the tileAxesOrder
+	 */
+	public String getTileAxesOrder() {
+		return tileAxesOrder;
+	}
+
+
+
+}