From 0ba0d1b4d5ba8d339fc9c62223a95dc6b64702dc Mon Sep 17 00:00:00 2001
From: Florian M <florian@scm.io>
Date: Tue, 16 Apr 2024 11:45:11 +0200
Subject: [PATCH 1/2] Fix reading CompressedSegmentation with uint32 data

---
 .../scalableminds/util/tools/ByteUtils.scala   | 15 +++++++++++++++
 .../CompressedSegmentation.scala               | 18 +++++++++---------
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/util/src/main/scala/com/scalableminds/util/tools/ByteUtils.scala b/util/src/main/scala/com/scalableminds/util/tools/ByteUtils.scala
index 9583051b704..8a0ff93f002 100644
--- a/util/src/main/scala/com/scalableminds/util/tools/ByteUtils.scala
+++ b/util/src/main/scala/com/scalableminds/util/tools/ByteUtils.scala
@@ -20,4 +20,19 @@ trait ByteUtils {
     }
     result.reverse
   }
+
+  /**
+    *
+    * @param i a 32 bit number
+    * @return i as array of 8 bytes, little endian
+    */
+  def intToBytes(i: Int): Array[Byte] = {
+    var w = i
+    val result = new Array[Byte](4)
+    for (i <- 3 to 0 by -1) {
+      result(i) = (w & 0xFF).toByte
+      w >>= 4
+    }
+    result.reverse
+  }
 }
diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala
index 3633bbcd925..c742f5d4c5a 100644
--- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala
+++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/precomputed/compressedsegmentation/CompressedSegmentation.scala
@@ -48,11 +48,11 @@ trait CompressedSegmentation[T <: AnyVal] extends ByteUtils {
           val bitmask = (1 << encodedBits) - 1
           for (z <- zmin until zmax) {
             for (y <- ymin until ymax) {
-              var outindex = (z * (volumeSize(1)) + y) * volumeSize(0) + xmin
-              var bitpos = blockSize.x * ((z - zmin) * (blockSize.y) + (y - ymin)) * encodedBits
-              for (x <- xmin until xmax) {
+              var outindex = (z * volumeSize(1) + y) * volumeSize(0) + xmin
+              var bitpos = blockSize.x * ((z - zmin) * blockSize.y + (y - ymin)) * encodedBits
+              for (_ <- xmin until xmax) {
                 val bitshift = bitpos % 32
-                val arraypos = bitpos / (32)
+                val arraypos = bitpos / 32
                 var bitval = 0
                 if (encodedBits > 0) {
                   bitval = (input(encodedValueStart + arraypos) >> bitshift) & bitmask
@@ -76,7 +76,7 @@ trait CompressedSegmentation[T <: AnyVal] extends ByteUtils {
       .flatMap(channel => decompressChannel(input.drop(input(channel)), volumeSize, blockSize))
       .toArray
 
-  def valueAsLong(v: T): Long
+  def valueToBytes(v: T): Array[Byte]
 
   def decompress(encodedBytes: Array[Byte], volumeSize: Array[Int], blockSize: Vec3Int)(
       implicit c: ClassTag[T]): Array[Byte] = {
@@ -87,8 +87,8 @@ trait CompressedSegmentation[T <: AnyVal] extends ByteUtils {
     }
     val input32 = new Array[Int](encodedBytes.length / 4)
     ByteBuffer.wrap(encodedBytes).order(ByteOrder.LITTLE_ENDIAN).asIntBuffer().get(input32)
-    val values = decompressChannels(input32, vs, blockSize)
-    values.flatMap(v => longToBytes(valueAsLong(v)))
+    val values: Array[T] = decompressChannels(input32, vs, blockSize)
+    values.flatMap(v => valueToBytes(v))
   }
 }
 
@@ -101,7 +101,7 @@ object CompressedSegmentation32 extends CompressedSegmentation[Int] {
   override def readValue(input: Array[Int], position: Int): Int =
     input(position)
 
-  override def valueAsLong(v: Int): Long = v.toLong
+  def valueToBytes(v: Int): Array[Byte] = intToBytes(v)
 }
 
 object CompressedSegmentation64 extends CompressedSegmentation[Long] {
@@ -113,5 +113,5 @@ object CompressedSegmentation64 extends CompressedSegmentation[Long] {
   override def readValue(input: Array[Int], position: Int): Long =
     ByteBuffer.wrap(ByteBuffer.allocate(8).putInt(input(position + 1)).putInt(input(position)).array()).getLong
 
-  override def valueAsLong(v: Long): Long = v
+  def valueToBytes(v: Long): Array[Byte] = longToBytes(v)
 }

From 6146eeb75c41ae858ffa3415bba58b166f730522 Mon Sep 17 00:00:00 2001
From: Florian M <florian@scm.io>
Date: Tue, 16 Apr 2024 11:49:54 +0200
Subject: [PATCH 2/2] changelog

---
 CHANGELOG.unreleased.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
index 64501ba90c7..5b86ca25a04 100644
--- a/CHANGELOG.unreleased.md
+++ b/CHANGELOG.unreleased.md
@@ -33,6 +33,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug where users that have no team memberships were omitted from the user list. [#7721](https://github.com/scalableminds/webknossos/pull/7721)
 - Added an appropriate placeholder to be rendered in case the timetracking overview is otherwise empty. [#7736](https://github.com/scalableminds/webknossos/pull/7736)
 - The overflow menu in the layer settings tab for layers with long names can now be opened comfortably. [#7747](https://github.com/scalableminds/webknossos/pull/7747)
+- Fixed a bug where segmentation data looked scrambled when reading uint32 segmentation layers with CompressedSegmentation codec. [#7757](https://github.com/scalableminds/webknossos/pull/7757)
 
 ### Removed