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Copy whole shards when writing v3, instead of individual chunks #6

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Aug 30, 2024
+15 −11
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Copy whole shards when writing v3, instead of individual chunks #6

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26 changes: 15 additions & 11 deletions src/main/java/com/glencoesoftware/zarr/Convert.java
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Original file line number Diff line number Diff line change
Expand Up @@ -290,8 +290,6 @@ public void convertToV3() throws Exception {
System.arraycopy(originalChunkSizes, 0, chunkSizes, 0, chunkSizes.length);

int[] gridPosition = new int[] {0, 0, 0, 0, 0};
int tileX = chunkSizes[chunkSizes.length - 2];
int tileY = chunkSizes[chunkSizes.length - 1];

DataType type = tile.getDataType();

Expand Down Expand Up @@ -367,10 +365,16 @@ else if (codecName.equals("blosc")) {
.build()
);

for (int t=0; t<shape[0]; t+=originalChunkSizes[0]) {
for (int c=0; c<shape[1]; c+=originalChunkSizes[1]) {
for (int z=0; z<shape[2]; z+=originalChunkSizes[2]) {

// if sharding is used, these will be the shard dimensions
int tileX = chunkSizes[chunkSizes.length - 2];
int tileY = chunkSizes[chunkSizes.length - 1];

for (int t=0; t<shape[0]; t+=chunkSizes[0]) {
for (int c=0; c<shape[1]; c+=chunkSizes[1]) {
for (int z=0; z<shape[2]; z+=chunkSizes[2]) {
// copy each chunk, keeping the original chunk sizes
// if sharding is used, whole shards are copied at once, not individual chunks
for (int y=0; y<shape[4]; y+=tileY) {
for (int x=0; x<shape[3]; x+=tileX) {
gridPosition[4] = y;
Expand All @@ -379,26 +383,26 @@ else if (codecName.equals("blosc")) {
gridPosition[1] = c;
gridPosition[0] = t;
LOGGER.debug("copying chunk of size {} at position {}",
Arrays.toString(originalChunkSizes), Arrays.toString(gridPosition));
Arrays.toString(chunkSizes), Arrays.toString(gridPosition));

// adjust the chunk size to handle edges
// otherwise the array writing will throw an exception if the
// array shape is not an exact multiple of the chunk size
int[] thisChunkSize = new int[originalChunkSizes.length];
System.arraycopy(originalChunkSizes, 0, thisChunkSize, 0, thisChunkSize.length);
int[] thisChunkSize = new int[chunkSizes.length];
System.arraycopy(chunkSizes, 0, thisChunkSize, 0, thisChunkSize.length);
if (x + tileX > shape[3]) {
thisChunkSize[3] = shape[3] - x;
}
if (y + tileY > shape[4]) {
thisChunkSize[4] = shape[4] - y;
}
if (z + originalChunkSizes[2] > shape[2]) {
if (z + chunkSizes[2] > shape[2]) {
thisChunkSize[2] = shape[2] - z;
}
if (c + originalChunkSizes[1] > shape[1]) {
if (c + chunkSizes[1] > shape[1]) {
thisChunkSize[1] = shape[1] - c;
}
if (t + originalChunkSizes[0] > shape[0]) {
if (t + chunkSizes[0] > shape[0]) {
thisChunkSize[0] = shape[0] - t;
}
Object bytes = tile.read(thisChunkSize, gridPosition);
Expand Down