reorganize tiling so it lays inside the bioimageio package

src/main/java/io/bioimage/modelrunner/bioimageio/ImageInfo.java → src/main/java/io/bioimage/modelrunner/bioimageio/tiling/ImageInfo.java

@@ -1,4 +1,4 @@
-package io.bioimage.modelrunner.bioimageio;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 public class ImageInfo {
 

src/main/java/io/bioimage/modelrunner/tiling/ImgLib2Utils.java → src/main/java/io/bioimage/modelrunner/bioimageio/tiling/ImgLib2Utils.java

@@ -17,7 +17,7 @@
  * limitations under the License.
  * #L%
  */
-package io.bioimage.modelrunner.tiling;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 import java.util.stream.LongStream;
 

src/main/java/io/bioimage/modelrunner/tiling/PatchSpec.java → src/main/java/io/bioimage/modelrunner/bioimageio/tiling/PatchSpec.java

@@ -17,11 +17,10 @@
  * limitations under the License.
  * #L%
  */
-package io.bioimage.modelrunner.tiling;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
 /**
  * Patch specification providing information about the patch size and patch grid size.
@@ -69,7 +68,7 @@ public class PatchSpec
      * 		  The original size of the image/tensor that is going to be tiled
      * @return The create patch specification.
      */
-    public static PatchSpec create(String tensorName, long[] patchInputSize, int[] patchGridSize, 
+    protected static PatchSpec create(String tensorName, long[] patchInputSize, int[] patchGridSize, 
     		int[][] patchPaddingSize, long[] nonTiledTensorDims)
     {
         PatchSpec ps = new PatchSpec();
@@ -85,38 +84,26 @@ private PatchSpec()
     {
     }
 
-    /**
-     * Return the PatchSpec corresponding to the tensor called by the name defined
-     * @param specs
-     * 	list of patch specs
-     * @param name
-     * 	name of the tensor of interest
-     * @return the patch specs of the tensor if interest
-     */
-    public static PatchSpec getPatchSpecFromListByName(List<PatchSpec> specs, String name) {
-    	return specs.stream().filter(pp -> pp.getTensorName().equals(name)).findAny().orElse(null);
-    }
-
     /**
      * GEt the name of the tensor
      * @return the name of the tensor
      */
-    public String getTensorName() {
+    protected String getTensorName() {
     	return tensorName;
     }
 
     /**
      * The dimensions of the tensor
      * @return the dimensions of the tensor that is going to be tiled
      */
-    public long[] getNonTiledTensorDims() {
+    protected long[] getNonTiledTensorDims() {
     	return nonTiledTensorDims;
     }
 
     /**
      * @return Input patch size. The patch taken from the input sequence including the halo.
      */
-    public long[] getTileSize()
+    protected long[] getTileSize()
     {
         return patchInputSize;
     }
@@ -125,15 +112,15 @@ public long[] getTileSize()
      * @return The patch grid size. The number of patches in each axis used to cover the entire sequence. It should be computed from the output patch and input
      *         sequence sizes.
      */
-    public int[] getTileGrid()
+    protected int[] getTileGrid()
     {
         return patchGridSize;
     }
 
     /**
      * @return The padding size used on each patch.
      */
-    public int[][] getPadding()
+    protected int[][] getPadding()
     {
         return patchPaddingSize;
     }

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

@@ -1,4 +1,4 @@
-package io.bioimage.modelrunner.bioimageio;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -12,7 +12,7 @@
 import io.bioimage.modelrunner.bioimageio.description.Axis;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
 import io.bioimage.modelrunner.bioimageio.description.TensorSpec;
-import io.bioimage.modelrunner.tiling.TileInfo;
+import io.bioimage.modelrunner.bioimageio.tiling.TileInfo;
 import io.bioimage.modelrunner.utils.Constants;
 
 public class TileCalculator {

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

@@ -17,7 +17,7 @@
  * limitations under the License.
  * #L%
  */
-package io.bioimage.modelrunner.tiling;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -81,7 +81,7 @@ private TileGrid()
      * @return an instance of {@link TileGrid} that contains the information about where the tiles need to be 
      * 	positioned with respect to the original image
      */
-    public static TileGrid create(PatchSpec tileSpecs)
+    protected static TileGrid create(PatchSpec tileSpecs)
     {
         TileGrid ps = new TileGrid();
         ps.tensorName = tileSpecs.getTensorName();
@@ -114,23 +114,23 @@ public static TileGrid create(PatchSpec tileSpecs)
      * 
      * @return name of the tensor that is going to be processed
      */
-    public String getTensorName() {
+    protected String getTensorName() {
     	return tensorName;
     }
 
     /**
      * 
      * @return size of the tile that is going to be used to process the image
      */
-    public long[] getTileSize() {
+    protected long[] getTileSize() {
     	return this.tileSize;
     }
 
     /**
      * 
      * @return size of the roi of each of the tiles that is going to be used to process the image
      */
-    public int[] getRoiSize() {
+    protected int[] getRoiSize() {
     	return this.roiSize;
     }
 
@@ -140,15 +140,15 @@ public int[] getRoiSize() {
      * respect to the original image of the tensor.
      * The positions might be negative as the image that is going to be processed might have padding on the edges
      */
-    public List<long[]> getTilePostionsInImage() {
+    protected List<long[]> getTilePostionsInImage() {
     	return this.tilePostionsInImage;
     }
 
     /**
      * 
      * @return the positions of the roi in each of the tiles that are going to be used
      */
-    public List<long[]> getRoiPositionsInTile() {
+    protected List<long[]> getRoiPositionsInTile() {
     	return this.roiPositionsInTile;
     }
 
@@ -157,7 +157,7 @@ public List<long[]> getRoiPositionsInTile() {
      * @return the positions of the roi of each of the tiles in the original image. Where the ROIs are
      * inserted on the original image.
      */
-    public List<long[]> getRoiPostionsInImage() {
+    protected List<long[]> getRoiPostionsInImage() {
     	return this.roiPositionsInImage;
     }
 

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

@@ -1,4 +1,4 @@
-package io.bioimage.modelrunner.tiling;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 public class TileInfo {
 

src/main/java/io/bioimage/modelrunner/tiling/TileMaker.java → src/main/java/io/bioimage/modelrunner/bioimageio/tiling/TileMaker.java

@@ -1,4 +1,4 @@
-package io.bioimage.modelrunner.tiling;
+package io.bioimage.modelrunner.bioimageio.tiling;
 
 import java.util.ArrayList;
 import java.util.Arrays;

src/main/java/io/bioimage/modelrunner/model/Model.java

@@ -28,16 +28,13 @@
 import java.net.MalformedURLException;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 import java.util.stream.Collectors;
-import java.util.stream.IntStream;
-import java.util.stream.LongStream;
 
-import io.bioimage.modelrunner.bioimageio.ImageInfo;
-import io.bioimage.modelrunner.bioimageio.TileCalculator;
+import io.bioimage.modelrunner.bioimageio.tiling.ImageInfo;
+import io.bioimage.modelrunner.bioimageio.tiling.TileCalculator;
 import io.bioimage.modelrunner.bioimageio.bioengine.BioEngineAvailableModels;
 import io.bioimage.modelrunner.bioimageio.bioengine.BioengineInterface;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
@@ -46,27 +43,24 @@
 import io.bioimage.modelrunner.bioimageio.description.exceptions.ModelSpecsException;
 import io.bioimage.modelrunner.bioimageio.description.weights.ModelWeight;
 import io.bioimage.modelrunner.bioimageio.description.weights.WeightFormat;
+import io.bioimage.modelrunner.bioimageio.tiling.PatchSpec;
+import io.bioimage.modelrunner.bioimageio.tiling.TileGrid;
+import io.bioimage.modelrunner.bioimageio.tiling.TileInfo;
+import io.bioimage.modelrunner.bioimageio.tiling.TileMaker;
 import io.bioimage.modelrunner.engine.DeepLearningEngineInterface;
 import io.bioimage.modelrunner.engine.EngineInfo;
 import io.bioimage.modelrunner.engine.EngineLoader;
 import io.bioimage.modelrunner.exceptions.LoadEngineException;
 import io.bioimage.modelrunner.exceptions.LoadModelException;
 import io.bioimage.modelrunner.exceptions.RunModelException;
 import io.bioimage.modelrunner.tensor.Tensor;
-import io.bioimage.modelrunner.tiling.PatchSpec;
-import io.bioimage.modelrunner.tiling.TileGrid;
-import io.bioimage.modelrunner.tiling.TileInfo;
-import io.bioimage.modelrunner.tiling.TileMaker;
 import io.bioimage.modelrunner.utils.Constants;
 import io.bioimage.modelrunner.versionmanagement.InstalledEngines;
-import net.imglib2.FinalInterval;
-import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.FloatType;
-import net.imglib2.view.Views;
 
 /**
  * Class that manages a Deep Learning model to load it and run it.