From 040dc2404e841638c056ee996c9b47cf549084ca Mon Sep 17 00:00:00 2001
From: Florian M <florian@scm.io>
Date: Thu, 30 Jan 2025 16:25:47 +0100
Subject: [PATCH 1/4] Fix merging editable mappings where self-merge is
generated; fix compacted update action writes
---
conf/application.conf | 2 +-
.../EditableMappingUpdater.scala | 42 ++++++++++++-------
.../tracings/volume/VolumeUpdateActions.scala | 3 +-
3 files changed, 31 insertions(+), 16 deletions(-)
diff --git a/conf/application.conf b/conf/application.conf
index a775b1ae0a3..f62ca861b1b 100644
--- a/conf/application.conf
+++ b/conf/application.conf
@@ -161,7 +161,7 @@ features {
exportTiffMaxVolumeMVx = 1024
exportTiffMaxEdgeLengthVx = 8192
defaultToLegacyBindings = false
- editableMappingsEnabled = false
+ editableMappingsEnabled = true
# The only valid item value is currently "ConnectomeView":
optInTabs = []
openIdConnectEnabled = false
diff --git a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala
index ea2a6f620e8..65419d8b75c 100644
--- a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala
+++ b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala
@@ -334,13 +334,15 @@ class EditableMappingUpdater(
agglomerateId2 <- agglomerateIdForSegmentId(segmentId2) ?~> "Failed to look up agglomerate ids for merge action segments"
agglomerateGraph1 <- agglomerateGraphForIdWithFallback(mapping, agglomerateId1) ?~> s"Failed to get agglomerate graph for id $agglomerateId1"
agglomerateGraph2 <- agglomerateGraphForIdWithFallback(mapping, agglomerateId2) ?~> s"Failed to get agglomerate graph for id $agglomerateId2"
- _ <- bool2Fox(agglomerateGraph2.segments.contains(segmentId2)) ?~> s"Segment $segmentId2 as queried by position ${update.segmentPosition2} is not contained in fetched agglomerate graph for agglomerate $agglomerateId2"
+ _ <- bool2Fox(agglomerateGraph2.segments.contains(segmentId2)) ?~> s"Segment $segmentId2 as queried by position ${update.segmentPosition2} is not contained in fetched agglomerate graph for agglomerate $agglomerateId2. actionTimestamp: ${update.actionTimestamp}, graph segments: ${agglomerateGraph2.segments}"
mergedGraphOpt = mergeGraph(agglomerateGraph1, agglomerateGraph2, segmentId1, segmentId2)
_ <- Fox.runOptional(mergedGraphOpt) { mergedGraph =>
for {
_ <- updateSegmentToAgglomerate(agglomerateGraph2.segments, agglomerateId1) ?~> s"Failed to update segment to agglomerate buffer"
_ = updateAgglomerateGraph(agglomerateId1, mergedGraph)
- _ = updateAgglomerateGraph(agglomerateId2, AgglomerateGraph(List.empty, List.empty, List.empty, List.empty))
+ _ = if (agglomerateId1 != agglomerateId2)
+ // The second agglomerate vanishes, all its segments have been moved to agglomerateId1
+ updateAgglomerateGraph(agglomerateId2, AgglomerateGraph(List.empty, List.empty, List.empty, List.empty))
} yield ()
}
} yield mapping
@@ -349,19 +351,31 @@ class EditableMappingUpdater(
agglomerateGraph2: AgglomerateGraph,
segmentId1: Long,
segmentId2: Long): Option[AgglomerateGraph] = {
- val segment1IsValid = agglomerateGraph1.segments.contains(segmentId1)
- val segment2IsValid = agglomerateGraph2.segments.contains(segmentId2)
- if (segment1IsValid && segment2IsValid) {
+ val newEdgeAffinity = 255.0f
+ val newEdge = AgglomerateEdge(segmentId1, segmentId2)
+ if (agglomerateGraph1 == agglomerateGraph2) {
+ // Agglomerate is merged with itself. Insert new edge anyway, if it does not exist yet
val newEdge = AgglomerateEdge(segmentId1, segmentId2)
- val newEdgeAffinity = 255.0f
- Some(
- AgglomerateGraph(
- segments = agglomerateGraph1.segments ++ agglomerateGraph2.segments,
- edges = newEdge +: (agglomerateGraph1.edges ++ agglomerateGraph2.edges),
- affinities = newEdgeAffinity +: (agglomerateGraph1.affinities ++ agglomerateGraph2.affinities),
- positions = agglomerateGraph1.positions ++ agglomerateGraph2.positions
- ))
- } else None
+ if (agglomerateGraph1.edges.contains(newEdge)) {
+ Some(agglomerateGraph1)
+ } else {
+ Some(
+ agglomerateGraph1.copy(edges = newEdge +: agglomerateGraph1.edges,
+ affinities = newEdgeAffinity +: agglomerateGraph1.affinities))
+ }
+ } else {
+ val segment1IsValid = agglomerateGraph1.segments.contains(segmentId1)
+ val segment2IsValid = agglomerateGraph2.segments.contains(segmentId2)
+ if (segment1IsValid && segment2IsValid) {
+ Some(
+ AgglomerateGraph(
+ segments = agglomerateGraph1.segments ++ agglomerateGraph2.segments,
+ edges = newEdge +: (agglomerateGraph1.edges ++ agglomerateGraph2.edges),
+ affinities = newEdgeAffinity +: (agglomerateGraph1.affinities ++ agglomerateGraph2.affinities),
+ positions = agglomerateGraph1.positions ++ agglomerateGraph2.positions
+ ))
+ } else None
+ }
}
def revertToVersion(sourceVersion: Long)(implicit ec: ExecutionContext): Fox[Unit] =
diff --git a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeUpdateActions.scala b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeUpdateActions.scala
index c4e5fae0be6..9307df81d1c 100644
--- a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeUpdateActions.scala
+++ b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeUpdateActions.scala
@@ -373,7 +373,8 @@ object CompactVolumeUpdateAction {
"name" -> o.name,
"value" -> (Json.obj("actionTracingId" -> o.actionTracingId,
"actionTimestamp" -> o.actionTimestamp,
- "actionAuthorId" -> o.actionAuthorId) ++ o.value)
+ "actionAuthorId" -> o.actionAuthorId) ++ o.value),
+ "isCompacted" -> true
)
}
}
From 068112c65c1e9a946d5b3017c99e48b37aa61e00 Mon Sep 17 00:00:00 2001
From: Florian M <fm3@users.noreply.github.com>
Date: Thu, 30 Jan 2025 16:28:59 +0100
Subject: [PATCH 2/4] Update application.conf
---
conf/application.conf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/conf/application.conf b/conf/application.conf
index f62ca861b1b..a775b1ae0a3 100644
--- a/conf/application.conf
+++ b/conf/application.conf
@@ -161,7 +161,7 @@ features {
exportTiffMaxVolumeMVx = 1024
exportTiffMaxEdgeLengthVx = 8192
defaultToLegacyBindings = false
- editableMappingsEnabled = true
+ editableMappingsEnabled = false
# The only valid item value is currently "ConnectomeView":
optInTabs = []
openIdConnectEnabled = false
From 76f89bf33025a899e28a6f3f52d544c5cc79f270 Mon Sep 17 00:00:00 2001
From: Florian M <florian@scm.io>
Date: Thu, 30 Jan 2025 16:30:53 +0100
Subject: [PATCH 3/4] changelog
---
CHANGELOG.unreleased.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
index 9039e0c0d38..c3b778ae19e 100644
--- a/CHANGELOG.unreleased.md
+++ b/CHANGELOG.unreleased.md
@@ -19,6 +19,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
### Fixed
- Fixed a bug that lead to trees being dropped when merging to trees together. [#8359](https://github.com/scalableminds/webknossos/pull/8359)
+- Fixed a bug where merging edigable mapping (“proofreading”) annotations would sometimes fail. [#8367](https://github.com/scalableminds/webknossos/pull/8367)
### Removed
- Removed the feature to downsample existing volume annotations. All new volume annotations had a whole mag stack since [#4755](https://github.com/scalableminds/webknossos/pull/4755) (four years ago). [#7917](https://github.com/scalableminds/webknossos/pull/7917)
From ad11ca3f6cf40a43be0e97a6f80e8e08431f6154 Mon Sep 17 00:00:00 2001
From: Florian M <fm3@users.noreply.github.com>
Date: Thu, 30 Jan 2025 17:01:02 +0100
Subject: [PATCH 4/4] Apply suggestions from code review
Co-authored-by: MichaelBuessemeyer <39529669+MichaelBuessemeyer@users.noreply.github.com>
---
CHANGELOG.unreleased.md | 2 +-
.../tracings/editablemapping/EditableMappingUpdater.scala | 3 +--
2 files changed, 2 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
index c3b778ae19e..b1f4d521117 100644
--- a/CHANGELOG.unreleased.md
+++ b/CHANGELOG.unreleased.md
@@ -19,7 +19,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
### Fixed
- Fixed a bug that lead to trees being dropped when merging to trees together. [#8359](https://github.com/scalableminds/webknossos/pull/8359)
-- Fixed a bug where merging edigable mapping (“proofreading”) annotations would sometimes fail. [#8367](https://github.com/scalableminds/webknossos/pull/8367)
+- Fixed a bug where merging editable mapping (“proofreading”) annotations would sometimes fail. [#8367](https://github.com/scalableminds/webknossos/pull/8367)
### Removed
- Removed the feature to downsample existing volume annotations. All new volume annotations had a whole mag stack since [#4755](https://github.com/scalableminds/webknossos/pull/4755) (four years ago). [#7917](https://github.com/scalableminds/webknossos/pull/7917)
diff --git a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala
index 65419d8b75c..29d3af64380 100644
--- a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala
+++ b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingUpdater.scala
@@ -341,7 +341,7 @@ class EditableMappingUpdater(
_ <- updateSegmentToAgglomerate(agglomerateGraph2.segments, agglomerateId1) ?~> s"Failed to update segment to agglomerate buffer"
_ = updateAgglomerateGraph(agglomerateId1, mergedGraph)
_ = if (agglomerateId1 != agglomerateId2)
- // The second agglomerate vanishes, all its segments have been moved to agglomerateId1
+ // The second agglomerate vanishes, as all its segments have been moved to agglomerateId1
updateAgglomerateGraph(agglomerateId2, AgglomerateGraph(List.empty, List.empty, List.empty, List.empty))
} yield ()
}
@@ -355,7 +355,6 @@ class EditableMappingUpdater(
val newEdge = AgglomerateEdge(segmentId1, segmentId2)
if (agglomerateGraph1 == agglomerateGraph2) {
// Agglomerate is merged with itself. Insert new edge anyway, if it does not exist yet
- val newEdge = AgglomerateEdge(segmentId1, segmentId2)
if (agglomerateGraph1.edges.contains(newEdge)) {
Some(agglomerateGraph1)
} else {