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Prevent multiple loading of DatasetAttributes in N5OMEZarrImageLoader #100

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Prevent multiple loading of DatasetAttributes in N5OMEZarrImageLoader #100

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637e2a5
Prevent multiple loading of DatasetAttributes in N5OMEZarrImageLoader
tischi Jun 17, 2022
d346477
Change loading strategy to volatile, which appears more reponsive in BDV
tischi Jun 17, 2022
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23 changes: 12 additions & 11 deletions src/main/java/org/embl/mobie/io/ome/zarr/loaders/N5OMEZarrImageLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,7 @@
import java.io.IOException;
import java.util.*;
import java.util.concurrent.Callable;
import java.util.concurrent.ConcurrentHashMap;

import static org.embl.mobie.io.ome.zarr.util.OmeZarrMultiscales.MULTI_SCALE_KEY;

Expand Down Expand Up @@ -98,6 +99,7 @@ public class N5OMEZarrImageLoader implements ViewerImgLoader, MultiResolutionImg
private ZarrAxes zarrAxes;
List<ZarrAxis> zarrAxesList;
private BlockingFetchQueues<Callable<?>> queue;
private ConcurrentHashMap< String, DatasetAttributes > pathToAttributes = new ConcurrentHashMap<>();

/**
* The sequenceDescription and viewRegistrations are known already, typically read from xml.
Expand Down Expand Up @@ -220,8 +222,7 @@ private void initSetups() throws IOException {
String pathName = "labels/" + label;
multiscales = getMultiscale(pathName);
for (OmeZarrMultiscales multiscale : multiscales) {
DatasetAttributes attributes = getDatasetAttributes(multiscale.datasets[0].path);
attributes = getDatasetAttributes(pathName + "/" + multiscale.datasets[0].path);
DatasetAttributes attributes = getDatasetAttributes(pathName + "/" + multiscale.datasets[0].path);

setupToMultiscale.put(setupId, multiscale);
setupToAttributes.put(setupId, attributes);
Expand All @@ -244,8 +245,13 @@ private void initSetups() throws IOException {
* @return
* @throws IOException
*/
private DatasetAttributes getDatasetAttributes(String pathName) throws IOException {
return n5.getDatasetAttributes(pathName);
private synchronized DatasetAttributes getDatasetAttributes(String pathName) throws IOException {
if ( ! pathToAttributes.containsKey( pathName ) )
{
final DatasetAttributes attributes = n5.getDatasetAttributes( pathName );
pathToAttributes.put( pathName, attributes );
}
return pathToAttributes.get( pathName );
}

/**
Expand Down Expand Up @@ -510,11 +516,6 @@ private int[] fillBlockSize(DatasetAttributes attributes) {
return tmp;
}

private SimpleCacheArrayLoader<?> createCacheArrayLoader(final N5Reader n5, final String pathName, int channel, int timepointId, CellGrid grid) throws IOException {
final DatasetAttributes attributes = n5.getDatasetAttributes(pathName);
return new N5OMEZarrCacheArrayLoader<>(n5, pathName, channel, timepointId, attributes, grid, zarrAxes);
}

private class SetupImgLoader<T extends NativeType<T>, V extends Volatile<T> & NativeType<V>>
extends AbstractViewerSetupImgLoader<T, V>
implements MultiResolutionSetupImgLoader<T> {
Expand Down Expand Up @@ -565,7 +566,7 @@ private double[][] readMipmapResolutions() throws IOException {

@Override
public RandomAccessibleInterval<V> getVolatileImage(final int timepointId, final int level, final ImgLoaderHint... hints) {
return prepareCachedImage(timepointId, level, LoadingStrategy.BUDGETED, volatileType);
return prepareCachedImage(timepointId, level, LoadingStrategy.VOLATILE, volatileType);
}

@Override
Expand Down Expand Up @@ -627,7 +628,7 @@ private <T extends NativeType<T>> RandomAccessibleInterval<T> prepareCachedImage
final int priority = numMipmapLevels() - 1 - level;
final CacheHints cacheHints = new CacheHints(loadingStrategy, priority, false);

final SimpleCacheArrayLoader<?> loader = createCacheArrayLoader(n5, pathName, setupToChannel.get(setupId), timepointId, grid);
final SimpleCacheArrayLoader<?> loader = new N5OMEZarrCacheArrayLoader<>(n5, pathName, setupToChannel.get(setupId), timepointId, attributes, grid, zarrAxes);
return cache.createImg(grid, timepointId, setupId, level, cacheHints, loader, type);
} catch (IOException e) {
log.error(String.format(
Expand Down