Add CallbackInputData.

CallbackInputData is very generic loader, which is right now useful for Hdf5 reading.

The callback which is required to be implemented, must return pixel data at pixel specified by the x, y and z coordinates.

src/main/java/cz/it4i/qcmp/io/CallbackInputData.java

+package cz.it4i.qcmp.io;
+
+import cz.it4i.qcmp.data.V3i;
+
+public class CallbackInputData extends InputData {
+
+    private final String cacheHint;
+    private final LoadCallback pixelLoadCallback;
+
+    /**
+     * Interface defining method for pixel data loading.
+     */
+    public interface LoadCallback {
+        /**
+         * Callback to load pixel value at specified position.
+         *
+         * @param x X position.
+         * @param y Y position.
+         * @param z Z position.
+         * @return Pixel value at specified position.
+         */
+        int getValueAt(final int x, final int y, final int z);
+    }
+
+    public CallbackInputData(final LoadCallback pixelLoadCallback,
+                             final V3i dimensions,
+                             final String cacheHint) {
+        this.pixelLoadCallback = pixelLoadCallback;
+        this.cacheHint = cacheHint;
+        setDataLoaderType(DataLoaderType.CallbackLoader);
+        setPixelType(PixelType.Gray16);
+        setDimension(dimensions);
+    }
+
+    @Override
+    public String getCacheFileName() {
+        return cacheHint;
+    }
+
+    public final LoadCallback getPixelLoadCallback() {
+        return pixelLoadCallback;
+    }
+}

src/main/java/cz/it4i/qcmp/io/InputData.java

@@ -11,7 +11,8 @@ public abstract class InputData {
         RawDataLoader,
         SCIFIOLoader,
         ImageJBufferLoader,
-        FlatBufferLoader
+        FlatBufferLoader,
+        CallbackLoader
     }
 
     public enum PixelType {

src/main/java/cz/it4i/qcmp/io/loader/CallbackLoader.java

+package cz.it4i.qcmp.io.loader;
+
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.CallbackInputData;
+
+import java.io.IOException;
+import java.util.Arrays;
+
+public class CallbackLoader extends BasicLoader implements IPlaneLoader {
+
+    private final CallbackInputData callbackInputData;
+    private final CallbackInputData.LoadCallback pixelLoad;
+
+    public CallbackLoader(final CallbackInputData callbackInputData) {
+        super(callbackInputData.getDimensions());
+        this.callbackInputData = callbackInputData;
+        this.pixelLoad = callbackInputData.getPixelLoadCallback();
+    }
+
+    @Override
+    protected int valueAt(final int plane, final int x, final int y, final int width) {
+        return pixelLoad.getValueAt(x, y, plane);
+    }
+
+
+    @Override
+    public int[] loadPlaneData(final int plane) {
+        final int planePixelCount = dims.getX() * dims.getY();
+        final int[] planeData = new int[planePixelCount];
+
+        int index = 0;
+        for (int y = 0; y < dims.getY(); y++) {
+            for (int x = 0; x < dims.getX(); x++) {
+                planeData[index++] = pixelLoad.getValueAt(x, y, plane);
+            }
+        }
+        return planeData;
+    }
+
+    @Override
+    public int[] loadPlanesU16Data(final int[] planes) throws IOException {
+        if (planes.length < 1) {
+            return new int[0];
+        } else if (planes.length == 1) {
+            return loadPlaneData(planes[0]);
+        } else if (planes.length == dims.getZ()) {
+            return loadAllPlanesU16Data();
+        }
+        final int planePixelCount = dims.getX() * dims.getY();
+        final long totalValueCount = (long) planePixelCount * (long) planes.length;
+        if (totalValueCount > (long) Integer.MAX_VALUE) {
+            throw new IOException("Unable to load image data for planes, file size is too big.");
+        }
+
+        Arrays.sort(planes);
+
+        final int[] destBuffer = new int[(int) totalValueCount];
+        int index = 0;
+        for (final int plane : planes) {
+            for (int y = 0; y < dims.getY(); y++) {
+                for (int x = 0; x < dims.getX(); x++) {
+                    destBuffer[index++] = pixelLoad.getValueAt(x, y, plane);
+                }
+            }
+        }
+        return destBuffer;
+    }
+
+    @Override
+    public int[] loadAllPlanesU16Data() throws IOException {
+        final long totalValueCount = dims.multiplyTogether();
+        if (totalValueCount > (long) Integer.MAX_VALUE) {
+            throw new IOException("Unable to load all image data, file size is too big.");
+        }
+
+        final int[] destBuffer = new int[(int) totalValueCount];
+        int index = 0;
+        for (int z = 0; z < dims.getZ(); z++) {
+            for (int y = 0; y < dims.getY(); y++) {
+                for (int x = 0; x < dims.getX(); x++) {
+                    destBuffer[index++] = pixelLoad.getValueAt(x, y, z);
+                }
+            }
+        }
+
+        return destBuffer;
+    }
+
+    @Override
+    public int[][] loadRowVectors(final int vectorSize, final Range<Integer> planeRange) {
+        return loadRowVectorsImplByValueAt(vectorSize, planeRange);
+    }
+
+    @Override
+    public int[][] loadBlocks(final V2i blockDim, final Range<Integer> planeRange) {
+        return loadBlocksImplByValueAt(blockDim, planeRange);
+    }
+
+    @Override
+    public int[][] loadVoxels(final V3i voxelDim, final Range<Integer> planeRange) {
+        return loadVoxelsImplByValueAt(voxelDim, planeRange);
+    }
+}

src/main/java/cz/it4i/qcmp/io/loader/PlaneLoaderFactory.java

 package cz.it4i.qcmp.io.loader;
 
-import cz.it4i.qcmp.io.BufferInputData;
-import cz.it4i.qcmp.io.FileInputData;
-import cz.it4i.qcmp.io.FlatBufferInputData;
-import cz.it4i.qcmp.io.InputData;
+import cz.it4i.qcmp.io.*;
 
 public final class PlaneLoaderFactory {
 
@@ -24,6 +21,8 @@ public final class PlaneLoaderFactory {
                 return new ImageJBufferLoader((BufferInputData) inputDataInfo);
             case FlatBufferLoader:
                 return new FlatBufferLoader((FlatBufferInputData) inputDataInfo);
+            case CallbackLoader:
+                return new CallbackLoader((CallbackInputData) inputDataInfo);
             default:
                 throw new Exception("Unsupported data loader.");
         }