correct small bug and ad setters and getters

bioimage-io · Oct 25, 2023 · 5d36645 · 5d36645
1 parent 0dde1d1
commit 5d36645
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Showing 2 changed files with 45 additions and 20 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/tiling/PatchGridCalculator.java b/src/main/java/io/bioimage/modelrunner/tiling/PatchGridCalculator.java
@@ -141,7 +141,6 @@ public LinkedHashMap<String, PatchSpec> getInputTensorsTileSpecs() throws Illega
     	if (this.inputTilesSpecs != null)
     		return inputTilesSpecs;
     	List<TensorSpec> inputTensors = findInputImageTensorSpec();
-    	List<TensorSpec> outputTensors = findOutputImageTensorSpec();
         List<Tensor<T>> inputImages = inputTensors.stream()
         		.filter(k -> this.inputValuesMap.get(k.getName()) != null)
         		.map(k -> this.inputValuesMap.get(k.getName())).collect(Collectors.toList());
@@ -235,17 +234,17 @@ private LinkedHashMap<String, PatchSpec> computePatchSpecsForEveryTensor(List<Te
     	return patchInfoList;
     }
 
-    public LinkedHashMap<String, PatchSpec> getOutputTensorsTileSpecs(List<TensorSpec> outTensors,
-    		Map<String, PatchSpec> inSpecs) throws IllegalArgumentException {
+    public LinkedHashMap<String, PatchSpec> getOutputTensorsTileSpecs() throws IllegalArgumentException {
+    	if (this.inputTilesSpecs == null)
+    		throw new IllegalArgumentException("Please first calculate the tile specs for the input tensors. Call: "
+					+ "getInputTensorsTileSpecs()");
     	if (this.outputTilesSpecs != null)
     		return outputTilesSpecs;
+    	List<TensorSpec> outTensors = findOutputImageTensorSpec();
     	LinkedHashMap<String, PatchSpec> patchInfoList = new LinkedHashMap<String, PatchSpec>();
 		for (int i = 0; i < outTensors.size(); i ++) {
     		String refTensor = outTensors.get(i).getShape().getReferenceInput();
-    		PatchSpec refSpec = refTensor == null ? inSpecs.values().stream().findFirst().get() : inSpecs.get(refTensor);
-    		if (refSpec == null)
-    			throw new IllegalArgumentException("Please first calculate the tile specs for th einput tensors. Call: "
-    					+ "getInputTensorsTileSpecs()");
+    		PatchSpec refSpec = refTensor == null ? inputTilesSpecs.values().stream().findFirst().get() : inputTilesSpecs.get(refTensor);
     		patchInfoList.put(outTensors.get(i).getName(), computePatchSpecsForOutputTensor(outTensors.get(i), refSpec));
 		}
 		outputTilesSpecs = patchInfoList;
@@ -336,29 +335,29 @@ private PatchSpec computePatchSpecs(TensorSpec spec, RandomAccessibleInterval<T>
         return PatchSpec.create(spec.getName(), tileSize, patchGridSize, paddingSize, rai.dimensionsAsLongArray());
     }
 
-    private PatchSpec computePatchSpecsForOutputTensor(TensorSpec spec, PatchSpec refSpec)
+    private PatchSpec computePatchSpecsForOutputTensor(TensorSpec tensorSpec, PatchSpec refTilesSpec)
     {
-    	int[] inputTileGrid = refSpec.getPatchGridSize();
+    	int[] inputTileGrid = refTilesSpec.getPatchGridSize();
         // REgard that the input halo represents the output halo + offset 
         // and must be divisible by 0.5. 
-        int[][] paddingSize = refSpec.getPatchPaddingSize();
+        int[][] paddingSize = refTilesSpec.getPatchPaddingSize();
         int[] tileSize;
         long[] shapeLong;
-        if (spec.getShape().getReferenceInput() == null) {
-        	tileSize = spec.getShape().getPatchRecomendedSize();
-        	shapeLong = LongStream.range(0, spec.getAxesOrder().length())
+        if (tensorSpec.getShape().getReferenceInput() == null) {
+        	tileSize = tensorSpec.getShape().getPatchRecomendedSize();
+        	shapeLong = LongStream.range(0, tensorSpec.getAxesOrder().length())
         			.map(i -> (tileSize[(int) i] - paddingSize[0][(int) i] - paddingSize[0][(int) i]) * inputTileGrid[(int) i])
         			.toArray();
         } else {
-        	tileSize = IntStream.range(0, spec.getAxesOrder().length())
-            		.map(i -> (int) (refSpec.getPatchInputSize()[i] * spec.getShape().getScale()[i] + 2 * spec.getShape().getOffset()[i]))
+        	tileSize = IntStream.range(0, tensorSpec.getAxesOrder().length())
+            		.map(i -> (int) (refTilesSpec.getPatchInputSize()[i] * tensorSpec.getShape().getScale()[i] + 2 * tensorSpec.getShape().getOffset()[i]))
             		.toArray();
-        	shapeLong = LongStream.range(0, spec.getAxesOrder().length())
-            		.map(i -> (int) (refSpec.getPatchInputSize()[(int) i] * spec.getShape().getScale()[(int) i] 
-            				+ 2 * spec.getShape().getOffset()[(int) i])).toArray();
+        	shapeLong = LongStream.range(0, tensorSpec.getAxesOrder().length())
+            		.map(i -> (int) (refTilesSpec.getTensorDims()[(int) i] * tensorSpec.getShape().getScale()[(int) i] 
+            				+ 2 * tensorSpec.getShape().getOffset()[(int) i])).toArray();
         }
 
-        return PatchSpec.create(spec.getName(), tileSize, inputTileGrid, paddingSize, shapeLong);
+        return PatchSpec.create(tensorSpec.getName(), tileSize, inputTileGrid, paddingSize, shapeLong);
     }
 
     /**

diff --git a/src/main/java/io/bioimage/modelrunner/tiling/TileGrid.java b/src/main/java/io/bioimage/modelrunner/tiling/TileGrid.java
@@ -62,9 +62,11 @@ private TileGrid()
 
     /**
      */
-    public static TileGrid create(PatchSpec tileSpecs, long[] imageDims)
+    public static TileGrid create(PatchSpec tileSpecs)
     {
         TileGrid ps = new TileGrid();
+        ps.tensorName = tileSpecs.getTensorName();
+        long[] imageDims = tileSpecs.getTensorDims();
         int[] gridSize = tileSpecs.getPatchGridSize();
         ps.tileSize = tileSpecs.getPatchInputSize();
         int tileCount = Arrays.stream(gridSize).reduce(1, (a, b) -> a * b);
@@ -87,6 +89,30 @@ public static TileGrid create(PatchSpec tileSpecs, long[] imageDims)
         }
         return ps;
     }
+
+    public String getTensorName() {
+    	return tensorName;
+    }
+
+    public int[] getTileSize() {
+    	return this.tileSize;
+    }
+
+    public int[] getRoiSize() {
+    	return this.roiSize;
+    }
+
+    public List<long[]> getTilePostionsInImage() {
+    	return this.tilePostionsInImage;
+    }
+
+    public List<long[]> getRoiPositionsInTile() {
+    	return this.roiPositionsInTile;
+    }
+
+    public List<long[]> getRoiPostionsInImage() {
+    	return this.roiPositionsInImage;
+    }
 
     @Override
     public String toString()