Reupload exported editable mapping annotation zip #8969
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -21,9 +21,17 @@ import play.api.i18n.MessagesProvider | |
|
|
||
| import scala.concurrent.{ExecutionContext, Future} | ||
|
|
||
| case class UploadedVolumeLayer(tracing: VolumeTracing, | ||
| dataZipLocation: String, | ||
| name: Option[String], | ||
| editedMappingEdgesLocation: Option[String], | ||
| editedMappingBaseMappingName: Option[String]) { | ||
| def getDataZipFrom(otherFiles: Map[String, File]): Option[File] = | ||
| otherFiles.get(dataZipLocation) | ||
|
|
||
| def getEditableMappingEdgesZipFrom(otherFiles: Map[String, File]): Option[File] = | ||
| editedMappingEdgesLocation.flatMap(otherFiles.get) | ||
|
|
||
| } | ||
|
|
||
| case class SharedParsingParameters(useZipName: Boolean, | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -249,6 +249,23 @@ class WKRemoteTracingStoreClient( | |
| } yield () | ||
| } | ||
|
|
||
| def saveEditableMappingIfPresent(annotationId: ObjectId, | ||
| newTracingId: String, | ||
| editedMappingEdgesZip: Option[File], | ||
| editedMappingBaseMappingName: Option[String], | ||
| startVersion: Long): Fox[Long] = | ||
| (editedMappingEdgesZip, editedMappingBaseMappingName) match { | ||
| case (Some(zipfile), Some(baseMappingName)) => | ||
| rpc(s"${tracingStore.url}/tracings/mapping/$newTracingId/save") | ||
| .addQueryString("token" -> RpcTokenHolder.webknossosToken) | ||
| .addQueryString("annotationId" -> annotationId.toString) | ||
| .addQueryString("baseMappingName" -> baseMappingName) | ||
| .addQueryString("startVersion" -> startVersion.toString) | ||
| .postFileWithJsonResponse[Long](zipfile) | ||
| case (None, None) => Fox.successful(0L) | ||
| case _ => Fox.failure("annotation.upload.editableMappingIncompleteInformation") | ||
| } | ||
|
|
||
| def getVolumeTracing(annotationId: ObjectId, | ||
| annotationLayer: AnnotationLayer, | ||
| version: Option[Long], | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -91,10 +91,13 @@ class NmlParser @Inject()(datasetDAO: DatasetDAO) | |
| segmentGroups = v.segmentGroups, | ||
| hasSegmentIndex = None, // Note: this property may be adapted later in adaptPropertiesToFallbackLayer | ||
| editPositionAdditionalCoordinates = nmlParams.editPositionAdditionalCoordinates, | ||
| additionalAxes = nmlParams.additionalAxisProtos, | ||
| hasEditableMapping = if (v.editedMappingEdgesLocation.isDefined) Some(true) else None | ||
| ), | ||
| basePath.getOrElse("") + v.dataZipPath, | ||
| v.name, | ||
| v.editedMappingEdgesLocation.map(location => basePath.getOrElse("") + location), | ||
|
There was a problem hiding this comment. Shouldn't this preferably use UPath or so to use a |
||
| v.editedMappingBaseMappingName | ||
| ) | ||
| } | ||
| skeletonTracing: SkeletonTracing = SkeletonTracing( | ||
|
|
@@ -220,7 +223,9 @@ class NmlParser @Inject()(datasetDAO: DatasetDAO) | |
| getSingleAttributeOpt(node, "name"), | ||
| parseVolumeSegmentMetadata(node \ "segments" \ "segment"), | ||
| getSingleAttributeOpt(node, "largestSegmentId").flatMap(_.toLongOpt), | ||
| extractSegmentGroups(node \ "groups").getOrElse(List()), | ||
| getSingleAttributeOpt(node, "editedMappingEdgesLocation"), | ||
| getSingleAttributeOpt(node, "editedMappingBaseMappingName") | ||
| ) | ||
| } | ||
| ) | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,4 +9,6 @@ case class NmlVolumeTag(dataZipPath: String, | |
| name: Option[String], | ||
| segments: Seq[Segment], | ||
| largestSegmentId: Option[Long], | ||
| segmentGroups: Seq[SegmentGroup], | ||
| editedMappingEdgesLocation: Option[String], | ||
| editedMappingBaseMappingName: Option[String]) | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -200,6 +200,7 @@ tracingstore { | |
| address = "localhost" | ||
| port = 6379 | ||
| } | ||
| cache.chunkCacheMaxSizeBytes = 2000000000 # 2 GB | ||
| } | ||
|
|
||
| # Serve image data. Only active if the corresponding play module is enabled | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -267,6 +267,7 @@ annotation.idForTracing.failed=Could not find the annotation id for this tracing | |
| annotation.editableMapping.getAgglomerateGraph.failed=Could not look up an agglomerate graph for requested agglomerate. | ||
| annotation.editableMapping.getAgglomerateIdsForSegments.failed=Could not look up agglomerate ids for requested segments. | ||
| annotation.duplicate.failed=Failed to duplicate annotation | ||
| annotation.upload.editableMappingIncompleteInformation=Could not store editable mapping, either file or baseMappingName is missing. | ||
|
|
||
| mesh.file.listChunks.failed=Failed to load chunk list for segment {0} from mesh file “{1}” | ||
| mesh.file.loadChunk.failed=Failed to load mesh chunk for segment | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -167,7 +167,7 @@ const descriptionFns: Record< | |
| ? `at position ${action.value.segmentPosition1}` | ||
| : (action.value.segmentId1 ?? "unknown"); | ||
| const segment2Description = | ||
| action.value.segmentPosition2 ?? action.value.segmentId2 ?? "unknown"; | ||
|
There was a problem hiding this comment. uff xD, thanks for fixing this |
||
| const description = `Split agglomerate ${action.value.agglomerateId} by separating the segments ${segment1Description} and ${segment2Description}.`; | ||
| return { | ||
| description, | ||
|
|
@@ -180,7 +180,7 @@ const descriptionFns: Record< | |
| ? `at position ${action.value.segmentPosition1}` | ||
| : (action.value.segmentId1 ?? "unknown"); | ||
| const segment2Description = | ||
| action.value.segmentPosition2 ?? action.value.segmentId2 ?? "unknown"; | ||
| const description = `Merged agglomerates ${action.value.agglomerateId1} and ${action.value.agglomerateId2} by combining the segments ${segment1Description} and ${segment2Description}.`; | ||
| return { | ||
| description, | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| ### Added | ||
| - Editable mapping (aka proofreading) annotations can now be downloaded as zipfile and re-uploaded. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -61,7 +61,7 @@ class DataStoreModule extends AbstractModule { | |
| bind(classOf[Hdf5ConnectomeFileService]).asEagerSingleton() | ||
| bind(classOf[NeuroglancerPrecomputedMeshFileService]).asEagerSingleton() | ||
| bind(classOf[RemoteSourceDescriptorService]).asEagerSingleton() | ||
| bind(classOf[DSChunkCacheService]).asEagerSingleton() | ||
| bind(classOf[DatasetCache]).asEagerSingleton() | ||
| } | ||
| } | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -4,62 +4,66 @@ import com.scalableminds.util.enumeration.ExtendedEnumeration | |
|
|
||
| object ArrayDataType extends ExtendedEnumeration { | ||
| type ArrayDataType = Value | ||
| val f8, f4, i8, u8, i4, u4, i2, u2, i1, u1, bool = Value | ||
|
|
||
| def bytesPerElement(dataType: ArrayDataType): Int = | ||
| dataType match { | ||
| case ArrayDataType.f8 => 8 | ||
| case ArrayDataType.f4 => 4 | ||
| case ArrayDataType.i8 => 8 | ||
| case ArrayDataType.u8 => 8 | ||
| case ArrayDataType.i4 => 4 | ||
| case ArrayDataType.u4 => 4 | ||
| case ArrayDataType.i2 => 2 | ||
| case ArrayDataType.u2 => 2 | ||
| case ArrayDataType.i1 => 1 | ||
| case ArrayDataType.u1 => 1 | ||
| case ArrayDataType.bool => 1 | ||
| } | ||
|
|
||
| def maxValue(dataType: ArrayDataType): Number = | ||
| dataType match { | ||
| case ArrayDataType.f8 => Double.MaxValue | ||
| case ArrayDataType.f4 => Float.MaxValue | ||
| case ArrayDataType.i8 => Long.MaxValue | ||
| case ArrayDataType.u8 => Long.MaxValue // Max value for primitive datatypes | ||
| case ArrayDataType.i4 => Int.MaxValue | ||
| case ArrayDataType.u4 => Math.pow(2, 4 * 8).toLong - 1 | ||
| case ArrayDataType.i2 => Char.MaxValue | ||
| case ArrayDataType.u2 => Math.pow(2, 2 * 8).toLong - 1 | ||
| case ArrayDataType.i1 => Byte.MaxValue | ||
| case ArrayDataType.u1 => Math.pow(2, 1 * 8).toLong - 1 | ||
| case ArrayDataType.bool => 1 | ||
| } | ||
|
|
||
| def minValue(dataType: ArrayDataType): Number = | ||
| dataType match { | ||
| case ArrayDataType.f8 => Double.MinValue | ||
| case ArrayDataType.f4 => Float.MinValue | ||
| case ArrayDataType.i8 => Long.MinValue | ||
| case ArrayDataType.u8 => 0 | ||
| case ArrayDataType.i4 => Int.MinValue | ||
| case ArrayDataType.u4 => 0 | ||
| case ArrayDataType.i2 => Char.MinValue | ||
| case ArrayDataType.u2 => 0 | ||
| case ArrayDataType.i1 => Byte.MinValue | ||
| case ArrayDataType.u1 => 0 | ||
| case ArrayDataType.bool => 0 | ||
| } | ||
|
|
||
| def toWKWId(dataType: ArrayDataType): Int = | ||
| dataType match { | ||
| case ArrayDataType.u1 => 1 | ||
| case ArrayDataType.u2 => 2 | ||
| case ArrayDataType.u4 => 3 | ||
| case ArrayDataType.u8 => 4 | ||
| case ArrayDataType.f4 => 5 | ||
| case ArrayDataType.f8 => 6 | ||
| case ArrayDataType.i1 => 7 | ||
| case ArrayDataType.i2 => 8 | ||
| case ArrayDataType.i4 => 9 | ||
| case ArrayDataType.i8 => 10 | ||
| case ArrayDataType.bool => ??? | ||
| } | ||
fm3 marked this conversation as resolved.
Show resolved
Hide resolved
|
||
|
|
||
| def fromWKWTypeId(wkwVoxelTypeId: Int): ArrayDataType.Value = | ||
|
|
||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I think this assertion here is not correct. What if I upload an annotation with 2 "custom" volume layers where each has no fallback layer? In that case this assertion would fail but the annotation should be correct 🤔