From ef5dabdc4ac85ef0d4ddbc7b86227ba373e0aa71 Mon Sep 17 00:00:00 2001
From: Vojtech Moravec <vojtech.moravec.st@vsb.cz>
Date: Tue, 3 Dec 2019 08:45:48 +0100
Subject: [PATCH] Dump HDF5 chunks.
---
src/main/java/bdv/server/CellHandler.java | 26 +++++++++++++++--------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/src/main/java/bdv/server/CellHandler.java b/src/main/java/bdv/server/CellHandler.java
index 6d110e1..cb8c97a 100644
--- a/src/main/java/bdv/server/CellHandler.java
+++ b/src/main/java/bdv/server/CellHandler.java
@@ -2,6 +2,7 @@ package bdv.server;
import java.awt.image.BufferedImage;
import java.io.*;
+import java.nio.ByteBuffer;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
@@ -12,6 +13,7 @@ import javax.servlet.http.HttpServletResponse;
import compression.U16;
import compression.data.Chunk3D;
+import compression.data.ChunkIO;
import compression.data.V3i;
import compression.data.V3l;
import compression.quantization.scalar.ScalarQuantizer;
@@ -165,18 +167,19 @@ public class CellHandler extends ContextHandler {
cell = cache.getLoadingVolatileCache().get(key, cacheHints, new VolatileCellLoader<>(loader, timepoint, setup, level, cellDims, cellMin));
}
-
@SuppressWarnings("unchecked")
short[] data = ((VolatileCell<VolatileShortArray>) cell).getData().getCurrentStorageArray();
- Chunk3D boxChunk = new Chunk3D(new V3i(cellDims[0], cellDims[1], cellDims[2]), data);
- boxChunk.setOffsets(cellMin[0], cellMin[1], cellMin[2]);
- //System.out.println(boxChunk.toString());
- // TODO(Moravec): When chunking boxes of non-uniform dimensions, some data cells are missed!
- if (cellDims[0] != 16 || cellDims[1] != 16 || cellDims[2] != 16) {
- boxChunk.divideIntoChunks(new V3i(2, 2, 2));
- }
- //boxChunk.divideIntoChunks(new V3i(3,3,3));
+
+// // Stupidity just testing chunking
+// {
+// Chunk3D dataBox = new Chunk3D(new V3i(cellDims[0], cellDims[1], cellDims[2]),
+// new V3l(cellMin[0], cellMin[1], cellMin[1]), data);
+// Chunk3D[] chunks = dataBox.divideIntoChunks(new V3i(3));
+// dataBox.zeroData();
+// dataBox.reconstructFromChunks(chunks);
+// data = dataBox.getDataAsShort();
+// }
if (compressionParams.shouldCompressData()) {
assert (quantizer != null) : "Compressor wasn't created";
@@ -229,10 +232,15 @@ public class CellHandler extends ContextHandler {
}
if (compressionParams.shouldDumpRequestData()) {
+ // Normal data dump
+ /*
FileOutputStream dumpStream = new FileOutputStream(compressionParams.getDumpFile(), true);
dumpStream.write(buf);
dumpStream.flush();
dumpStream.close();
+ */
+ // Dumping HDF5 3D chunks
+ ChunkIO.saveChunks(cellDims, cellMin, buf, compressionParams.getDumpFile());
}
transferedDataSize += buf.length;
--
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