Fix agglomerate mapping (#4904)

* load additional element * also load additional element for offset based handling * remove unnecessary size check * update changelog
scalableminds · Nov 4, 2020 · a623fa8 · a623fa8
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commit a623fa8
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -20,6 +20,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Fixed
 - Fixed the disappearing of dataset settings after switching between view mode and annotation mode. [#4845](https://github.com/scalableminds/webknossos/pull/4845)
+- Fixed a rare error in the agglomerate mapping for large datasets. [#4904](https://github.com/scalableminds/webknossos/pull/4904)
 
 ### Removed
 -
diff --git a/...s-datastore/app/com/scalableminds/webknossos/datastore/storage/AgglomerateFileCache.scala b/...s-datastore/app/com/scalableminds/webknossos/datastore/storage/AgglomerateFileCache.scala
@@ -70,9 +70,8 @@ class AgglomerateIdCache(val maxEntries: Int, val standardBlockSize: Int) extend
     def handleUncachedAgglomerate(): Long = {
       val minId =
         if (segmentId < ULong(standardBlockSize / 2)) ULong(0) else segmentId - ULong(standardBlockSize / 2)
-      val blockSize = spire.math.min(size - minId, ULong(standardBlockSize))
 
-      val agglomerateIds = readFromFile(reader, dataSet, minId.toLong, blockSize.toLong)
+      val agglomerateIds = readFromFile(reader, dataSet, minId.toLong, standardBlockSize)
 
       agglomerateIds.zipWithIndex.foreach {
         case (id, index) => put(index + minId.toLong, id)
@@ -151,15 +150,15 @@ class BoundingBoxCache(val cache: mutable.HashMap[(Long, Long, Long), BoundingBo
       readHDF: (IHDF5Reader, Long, Long) => Array[Long]): Array[Long] = {
     val readerRange = getReaderRange(request)
     if (readerRange._2 - readerRange._1 < maxReaderRange) {
-      val agglomerateIds = readHDF(reader, readerRange._1.toLong, (readerRange._2 - readerRange._1).toLong)
+      val agglomerateIds = readHDF(reader, readerRange._1.toLong, (readerRange._2 - readerRange._1).toLong + 1)
       input.map(i => if (i == ULong(0)) 0L else agglomerateIds((i - readerRange._1).toInt))
     } else {
       var offset = readerRange._1
       val result = Array.ofDim[Long](input.length)
       val isTransformed = Array.fill(input.length)(false)
       while (offset <= readerRange._2) {
         val agglomerateIds =
-          readHDF(reader, offset.toLong, spire.math.min(maxReaderRange, readerRange._2 - offset).toLong)
+          readHDF(reader, offset.toLong, spire.math.min(maxReaderRange, readerRange._2 - offset).toLong + 1)
         for (i <- input.indices) {
           val inputElement = input(i)
           if (!isTransformed(i) && inputElement >= offset && inputElement < offset + maxReaderRange) {