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Fix invalid checksum error #1380

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merged 2 commits into from
Aug 23, 2024
Merged

Fix invalid checksum error #1380

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08d367c
Allow shuffle to be applied even with data is not a multiple of the e…
Aug 22, 2024
b320279
Add unit test to test that shuffle gets applied to data that is not a…
Aug 22, 2024
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40 changes: 23 additions & 17 deletions cdm/core/src/main/java/ucar/nc2/filter/Shuffle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ public int getId() {

@Override
public byte[] encode(byte[] dataIn) {
if (dataIn.length % elemSize != 0 || elemSize <= 1) {
if (elemSize <= 1) {
return dataIn;
}

Expand All @@ -56,29 +56,35 @@ public byte[] encode(byte[] dataIn) {
}
}

int leftoverBytes = dataIn.length % this.elemSize;
System.arraycopy(dataIn, dataIn.length - leftoverBytes, result, result.length - leftoverBytes, leftoverBytes);

return result;
}

@Override
public byte[] decode(byte[] dataIn) {
if (dataIn.length % this.elemSize == 0 && this.elemSize > 1) {
int nElems = dataIn.length / this.elemSize;
byte[] result = new byte[dataIn.length];

for (int j = 0; j < this.elemSize; ++j) {
int sourceIndex = j * nElems;
int destIndex = j;
for (int i = 0; i < nElems; ++i) {
result[destIndex] = dataIn[sourceIndex];
sourceIndex++;
destIndex += this.elemSize;
}
}

return result;
} else {
if (elemSize <= 1) {
return dataIn;
}

int nElems = dataIn.length / this.elemSize;
byte[] result = new byte[dataIn.length];

for (int j = 0; j < this.elemSize; ++j) {
int sourceIndex = j * nElems;
int destIndex = j;
for (int i = 0; i < nElems; ++i) {
result[destIndex] = dataIn[sourceIndex];
sourceIndex++;
destIndex += this.elemSize;
}
}

int leftoverBytes = dataIn.length % this.elemSize;
System.arraycopy(dataIn, dataIn.length - leftoverBytes, result, result.length - leftoverBytes, leftoverBytes);

return result;
}

public static class Provider implements FilterProvider {
Expand Down
22 changes: 22 additions & 0 deletions cdm/core/src/test/java/ucar/nc2/filter/TestFilters.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
import ucar.unidata.io.RandomAccessFile;

import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
Expand Down Expand Up @@ -59,6 +60,27 @@ public void testShuffle() throws IOException {
testEncodeDecode(filter, "shuffle");
}

@Test
public void shouldShuffleDoublesAndLeaveIntAtEnd() throws IOException {
ByteBuffer bb = ByteBuffer.allocate(2 * 8 + 4);
bb.putDouble(-1.0);
bb.putDouble(1.0);
// to represent a checksum at the end of a chunk of doubles
bb.putInt(12345);
byte[] bytes = bb.array();

Map<String, Object> props = new HashMap<>();
props.put("id", "shuffle");
props.put("elementsize", 8);
Filter filter = new Shuffle(props);

byte[] expected = new byte[] {-65, 63, -16, -16, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 48, 57};
byte[] encoded = filter.encode(bytes);
assertThat(encoded).isEqualTo(expected);
byte[] decoded = filter.decode(encoded);
assertThat(decoded).isEqualTo(bytes);
}

@Test
public void testChecksum32() throws IOException {
// test Adler32
Expand Down
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