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Fix Duplicate File Deletes when running Detect Interest Points with --overlappingOnly #51

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Fix Duplicate File Deletes when running Detect Interest Points with --overlappingOnly #51

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be07892
fix multiple file deletes with --overlappingOnly
indecisiveuser Sep 16, 2025
41d8d66
Merge branch 'JaneliaSciComp:main' into overlap_only_patch
indecisiveuser Dec 2, 2025
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12 changes: 12 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,15 @@
/.settings/
/.idea/
affine-fusion
clear-interestpoints
clear-registrations
create-fusion-container
detect-interestpoints
downsample
match-interestpoints
nonrigid-fusion
resave
solver
split-images
stitching
transform-points
17 changes: 12 additions & 5 deletions src/main/java/net/preibisch/bigstitcher/spark/SparkInterestPointDetection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,8 @@
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.stream.Collectors;
import java.util.Set;
import java.util.HashSet;

import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
Expand Down Expand Up @@ -662,6 +664,11 @@ public Void call() throws Exception
rddResult.count();

final List<Tuple3<ViewId, long[][], String>> results = rddResult.collect();
final Set<String> datasetSet = new HashSet<String>();
for (Tuple3<ViewId, long[][], String> res : results) {
datasetSet.add(res._3());
}
final List<String> datasetNoDups = new ArrayList<>(datasetSet);

// assemble all interest point intervals per ViewId
final HashMap< ViewId, List< List< InterestPoint > > > interestPointsPerViewId = new HashMap<>();
Expand Down Expand Up @@ -704,18 +711,18 @@ public Void call() throws Exception
{
System.out.println( "Deleting temporary Spark files ... ");

final JavaRDD<Tuple3<ViewId, long[][], String>> rdd = sc.parallelize( results, Math.min( Spark.maxPartitions, results.size() ) );
final JavaRDD<String> rdd = sc.parallelize( datasetNoDups, Math.min( Spark.maxPartitions, datasetNoDups.size() ) );

rdd.foreach( boundingBox ->
{
final N5Writer n5WriterLocal = URITools.instantiateN5Writer( StorageFormat.N5, tempURI );

if ( n5WriterLocal.datasetExists( tempDataset + "/" + boundingBox._3() + "/points" ))
if ( n5WriterLocal.datasetExists( tempDataset + "/" + boundingBox + "/points" ))
{
n5WriterLocal.remove( tempDataset + "/" + boundingBox._3() + "/points" );
n5WriterLocal.remove( tempDataset + "/" + boundingBox + "/points" );

if ( n5WriterLocal.datasetExists( tempDataset + "/" + boundingBox._3() + "/intensities" ) )
n5WriterLocal.remove( tempDataset + "/" + boundingBox._3() + "/intensities" );
if ( n5WriterLocal.datasetExists( tempDataset + "/" + boundingBox + "/intensities" ) )
n5WriterLocal.remove( tempDataset + "/" + boundingBox + "/intensities" );

n5WriterLocal.close();
}
Expand Down