From 1cd3087b3518e76e36fc8630cdc30828e967a282 Mon Sep 17 00:00:00 2001
From: Vojtech Moravec <vojtech.moravec.st@vsb.cz>
Date: Tue, 11 Aug 2020 15:00:14 +0200
Subject: [PATCH] Add new loader type, FlatBufferLoader.
This loader is quite similiar to ImageJBufferLoader, except that
different plane data are stored in a single flat array.
To handle this situation with different loader help us prevent future
IndexOutOfBounds exceptions.
---
.../azgracompress/io/FlatBufferInputData.java | 52 +++++++++
.../io/loader/FlatBufferLoader.java | 110 ++++++++++++++++++
.../io/loader/PlaneLoaderFactory.java | 3 +
3 files changed, 165 insertions(+)
create mode 100644 src/main/java/azgracompress/io/FlatBufferInputData.java
create mode 100644 src/main/java/azgracompress/io/loader/FlatBufferLoader.java
diff --git a/src/main/java/azgracompress/io/FlatBufferInputData.java b/src/main/java/azgracompress/io/FlatBufferInputData.java
new file mode 100644
index 0000000..b6eef34
--- /dev/null
+++ b/src/main/java/azgracompress/io/FlatBufferInputData.java
@@ -0,0 +1,52 @@
+package azgracompress.io;
+
+import azgracompress.data.V3i;
+
+/**
+ * Input data backed by the single buffer object.
+ * In this buffer all the dataset pixels are stored.
+ */
+public class FlatBufferInputData extends InputData {
+ /**
+ * Reference to the buffer.
+ */
+ private final Object imageBuffer;
+
+ /**
+ * Name of the image used in caching.
+ */
+ private final String cacheHint;
+
+ /**
+ * Create input data backed by buffer object.
+ *
+ * @param imageBuffer Image buffer reference.
+ * @param imageDimensions Image dimensions.
+ * @param pixelType Image pixel type.
+ * @param cacheHint Name of the image used in caching.
+ */
+ public FlatBufferInputData(final Object imageBuffer,
+ final V3i imageDimensions,
+ final PixelType pixelType,
+ final String cacheHint) {
+ this.imageBuffer = imageBuffer;
+ setDataLoaderType(DataLoaderType.ImageJBufferLoader);
+ setDimension(imageDimensions);
+ setPixelType(pixelType);
+ this.cacheHint = cacheHint;
+ }
+
+ /**
+ * Get buffer with the image plane data.
+ *
+ * @return Pointer to pixel buffer.
+ */
+ public Object getPixelBuffer() {
+ return imageBuffer;
+ }
+
+ @Override
+ public String getCacheFileName() {
+ return cacheHint;
+ }
+}
diff --git a/src/main/java/azgracompress/io/loader/FlatBufferLoader.java b/src/main/java/azgracompress/io/loader/FlatBufferLoader.java
new file mode 100644
index 0000000..81e5d6c
--- /dev/null
+++ b/src/main/java/azgracompress/io/loader/FlatBufferLoader.java
@@ -0,0 +1,110 @@
+package azgracompress.io.loader;
+
+import azgracompress.data.Range;
+import azgracompress.data.V2i;
+import azgracompress.data.V3i;
+import azgracompress.io.FlatBufferInputData;
+import azgracompress.utilities.TypeConverter;
+
+import java.io.IOException;
+import java.util.Arrays;
+
+/**
+ * This loader is used when the entire dataset is stored in single buffer (array).
+ */
+public class FlatBufferLoader extends BasicLoader implements IPlaneLoader {
+ /**
+ * Flat buffer information.
+ */
+ private final FlatBufferInputData bufferInputData;
+
+ /**
+ * Pixel count in single plane.
+ */
+ private final int planePixelCount;
+
+ public FlatBufferLoader(final FlatBufferInputData bufferDataInfo) {
+ super(bufferDataInfo.getDimensions());
+ this.bufferInputData = bufferDataInfo;
+ planePixelCount = dims.getX() * dims.getY();
+ }
+
+ @Override
+ public boolean supportParallelLoading() {
+ return true;
+ }
+
+ private void copyShortArrayIntoBuffer(short[] srcArray,
+ final int srcOffset,
+ int[] destBuffer,
+ final int destOffset,
+ final int copyLen) {
+ for (int i = 0; i < copyLen; i++) {
+ destBuffer[destOffset + i] = TypeConverter.shortToInt(srcArray[srcOffset + i]);
+ }
+ }
+
+ @Override
+ protected int valueAt(final int plane, final int offset) {
+ return TypeConverter.shortToInt(((short[]) bufferInputData.getPixelBuffer())[(plane * planePixelCount) + offset]);
+ }
+
+ @Override
+ public int[] loadPlaneData(final int plane) throws IOException {
+ final short[] flatBuffer = ((short[]) bufferInputData.getPixelBuffer());
+ final int offset = plane * planePixelCount;
+ final int[] planeData = new int[planePixelCount];
+ for (int i = 0; i < planePixelCount; i++) {
+ planeData[i] = TypeConverter.shortToInt(flatBuffer[offset + i]);
+ }
+ 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 == bufferInputData.getDimensions().getZ()) { // Maybe?
+ return loadAllPlanesU16Data();
+ }
+ 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 short[] flatBuffer = (short[]) bufferInputData.getPixelBuffer();
+ int[] destBuffer = new int[(int) totalValueCount];
+ int destOffset = 0;
+ for (final int planeIndex : planes) {
+ final int planeOffset = planeIndex * planePixelCount;
+ copyShortArrayIntoBuffer(flatBuffer, planeOffset, destBuffer, destOffset, planePixelCount);
+ destOffset += planePixelCount;
+ }
+ return destBuffer;
+ }
+
+ @Override
+ public int[] loadAllPlanesU16Data() {
+ final short[] flatBuffer = (short[]) bufferInputData.getPixelBuffer();
+ return TypeConverter.shortArrayToIntArray(flatBuffer);
+ }
+
+ @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) throws IOException {
+ return loadVoxelsImplByValueAt(voxelDim, planeRange);
+ }
+}
diff --git a/src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java b/src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java
index 6783ba6..b34f67e 100644
--- a/src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java
+++ b/src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java
@@ -2,6 +2,7 @@ package azgracompress.io.loader;
import azgracompress.io.BufferInputData;
import azgracompress.io.FileInputData;
+import azgracompress.io.FlatBufferInputData;
import azgracompress.io.InputData;
public final class PlaneLoaderFactory {
@@ -21,6 +22,8 @@ public final class PlaneLoaderFactory {
return new SCIFIOLoader((FileInputData) inputDataInfo);
case ImageJBufferLoader:
return new ImageJBufferLoader((BufferInputData) inputDataInfo);
+ case FlatBufferLoader:
+ return new FlatBufferLoader((FlatBufferInputData) inputDataInfo);
default:
throw new Exception("Unsupported data loader.");
}
--
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