Rename Resolution to Mag (#8111)

* start to replace term resolution * rename resolution to mag in backend where possible * rename resolution restrictions * rename resolution info to mag info * rename in dataset accessor, a.o. * rename in frontend code * rename in docs * rename node resolution to mag * adjust mag slider * fix tests * add explaining sentences * refresh snapshots * improve explanation in info tab and status bar * adapt param name * remove application conf edits * lint * rename columns + table in sql, add migration * adapt test db after schema change * changelog * slightly adjust changelog entry to lower expectations * adjust docs and revert some changes * adjust neuroglancer docs * Update webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingDownsampling.scala Co-authored-by: MichaelBuessemeyer <[email protected]> * address review * fix previous version in db evolution * adjust version in schema.sql * also adapt schema version in reversion * adjust form names * adjust get params for /createExplorational * remove unused messages --------- Co-authored-by: Florian M <[email protected]> Co-authored-by: Florian M <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Tom Herold <[email protected]>
scalableminds · Oct 21, 2024 · 60f77ac · 60f77ac
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -211,25 +211,3 @@ workflows:
           filters:
             tags:
               only: /.*/
-  circleci_nightly:
-    jobs:
-      - nightly
-    triggers:
-      - schedule:
-          # 02:15 AM UTC
-          cron: "15 2 * * *"
-          filters:
-            branches:
-              only:
-                - master
-  circleci_wkorg_nightly:
-    jobs:
-      - wkorg_nightly
-    triggers:
-      - schedule:
-          # 03:15 AM UTC
-          cron: "15 3 * * *"
-          filters:
-            branches:
-              only:
-                - master
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -16,6 +16,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Most sliders have been improved: Wheeling above a slider now changes its value and double-clicking its knob resets it to its default value. [#8095](https://github.com/scalableminds/webknossos/pull/8095)
 - It is now possible to search for unnamed segments with the full default name instead of only their id. [#8133](https://github.com/scalableminds/webknossos/pull/8133)
 - Increased loading speed for precomputed meshes. [#8110](https://github.com/scalableminds/webknossos/pull/8110)
+- Unified wording in UI and code: “Magnification”/“mag” is now used in place of “Resolution“ most of the time, compare [https://docs.webknossos.org/webknossos/terminology.html](terminology document). [#8111](https://github.com/scalableminds/webknossos/pull/8111)
 
 ### Changed
 - Some mesh-related actions were disabled in proofreading-mode when using meshfiles that were created for a mapping rather than an oversegmentation. [#8091](https://github.com/scalableminds/webknossos/pull/8091)

diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md
@@ -11,3 +11,4 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 ### Postgres Evolutions:
 
 - [121-worker-name.sql](conf/evolutions/121-worker-name.sql)
+- [122-resolution-to-mag.sql](conf/evolutions/122-resolution-to-mag.sql)
diff --git a/app/controllers/AnnotationController.scala b/app/controllers/AnnotationController.scala
@@ -14,7 +14,7 @@ import com.scalableminds.webknossos.datastore.models.annotation.{
 }
 import com.scalableminds.webknossos.datastore.models.datasource.AdditionalAxis
 import com.scalableminds.webknossos.datastore.rpc.RPC
-import com.scalableminds.webknossos.tracingstore.tracings.volume.ResolutionRestrictions
+import com.scalableminds.webknossos.tracingstore.tracings.volume.MagRestrictions
 import com.scalableminds.webknossos.tracingstore.tracings.{TracingIds, TracingType}
 import mail.{MailchimpClient, MailchimpTag}
 import models.analytics.{AnalyticsService, CreateAnnotationEvent, OpenAnnotationEvent}
@@ -44,7 +44,7 @@ case class AnnotationLayerParameters(typ: AnnotationLayerType,
                                      fallbackLayerName: Option[String],
                                      autoFallbackLayer: Boolean = false,
                                      mappingName: Option[String] = None,
-                                     resolutionRestrictions: Option[ResolutionRestrictions],
+                                     magRestrictions: Option[MagRestrictions],
                                      name: Option[String],
                                      additionalAxes: Option[Seq[AdditionalAxis]])
 object AnnotationLayerParameters {

diff --git a/app/controllers/AnnotationIOController.scala b/app/controllers/AnnotationIOController.scala
@@ -335,7 +335,7 @@ class AnnotationIOController @Inject()(
         largestSegmentId =
           annotationService.combineLargestSegmentIdsByPrecedence(volumeTracing.largestSegmentId,
                                                                  fallbackLayerOpt.map(_.largestSegmentId)),
-        resolutions = VolumeTracingDownsampling.magsForVolumeTracing(dataSource, fallbackLayerOpt).map(vec3IntToProto),
+        mags = VolumeTracingDownsampling.magsForVolumeTracing(dataSource, fallbackLayerOpt).map(vec3IntToProto),
         hasSegmentIndex = Some(tracingCanHaveSegmentIndex)
       )
   }

diff --git a/app/controllers/LegacyApiController.scala b/app/controllers/LegacyApiController.scala
@@ -5,7 +5,7 @@ import play.silhouette.api.actions.SecuredRequest
 import com.scalableminds.util.tools.Fox
 import com.scalableminds.webknossos.datastore.models.VoxelSize
 import com.scalableminds.webknossos.datastore.models.annotation.{AnnotationLayer, AnnotationLayerType}
-import com.scalableminds.webknossos.tracingstore.tracings.volume.ResolutionRestrictions
+import com.scalableminds.webknossos.tracingstore.tracings.volume.MagRestrictions
 import models.dataset.DatasetService
 import models.organization.OrganizationDAO
 
@@ -24,7 +24,7 @@ import scala.concurrent.ExecutionContext
 
 case class LegacyCreateExplorationalParameters(typ: String,
                                                fallbackLayerName: Option[String],
-                                               resolutionRestrictions: Option[ResolutionRestrictions])
+                                               resolutionRestrictions: Option[MagRestrictions])
 object LegacyCreateExplorationalParameters {
   implicit val jsonFormat: OFormat[LegacyCreateExplorationalParameters] =
     Json.format[LegacyCreateExplorationalParameters]

diff --git a/app/controllers/TaskTypeController.scala b/app/controllers/TaskTypeController.scala
@@ -69,7 +69,7 @@ class TaskTypeController @Inject()(taskTypeDAO: TaskTypeDAO,
         taskTypeIdValidated <- ObjectId.fromString(taskTypeId) ?~> "taskType.id.invalid"
         taskType <- taskTypeDAO.findOne(taskTypeIdValidated) ?~> "taskType.notFound" ~> NOT_FOUND
         _ <- bool2Fox(taskTypeFromForm.tracingType == taskType.tracingType) ?~> "taskType.tracingTypeImmutable"
-        _ <- bool2Fox(taskTypeFromForm.settings.resolutionRestrictions == taskType.settings.resolutionRestrictions) ?~> "taskType.resolutionRestrictionsImmutable"
+        _ <- bool2Fox(taskTypeFromForm.settings.magRestrictions == taskType.settings.magRestrictions) ?~> "taskType.magRestrictionsImmutable"
         updatedTaskType = taskTypeFromForm.copy(_id = taskType._id)
         _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(request.identity, taskType._team)) ?~> "notAllowed" ~> FORBIDDEN
         _ <- Fox

diff --git a/app/models/annotation/AnnotationService.scala b/app/models/annotation/AnnotationService.scala
@@ -35,7 +35,7 @@ import com.scalableminds.webknossos.datastore.rpc.RPC
 import com.scalableminds.webknossos.tracingstore.tracings._
 import com.scalableminds.webknossos.tracingstore.tracings.volume.VolumeDataZipFormat.VolumeDataZipFormat
 import com.scalableminds.webknossos.tracingstore.tracings.volume.{
-  ResolutionRestrictions,
+  MagRestrictions,
   VolumeDataZipFormat,
   VolumeTracingDefaults,
   VolumeTracingDownsampling
@@ -144,15 +144,15 @@ class AnnotationService @Inject()(
       boundingBox: Option[BoundingBox] = None,
       startPosition: Option[Vec3Int] = None,
       startRotation: Option[Vec3Double] = None,
-      resolutionRestrictions: ResolutionRestrictions,
+      magRestrictions: MagRestrictions,
       mappingName: Option[String]
   ): Fox[VolumeTracing] = {
-    val resolutions = VolumeTracingDownsampling.magsForVolumeTracing(dataSource, fallbackLayer)
-    val resolutionsRestricted = resolutionRestrictions.filterAllowed(resolutions)
+    val mags = VolumeTracingDownsampling.magsForVolumeTracing(dataSource, fallbackLayer)
+    val magsRestricted = magRestrictions.filterAllowed(mags)
     val additionalAxes =
       fallbackLayer.map(_.additionalAxes).getOrElse(dataSource.additionalAxesUnion)
     for {
-      _ <- bool2Fox(resolutionsRestricted.nonEmpty) ?~> "annotation.volume.resolutionRestrictionsTooTight"
+      _ <- bool2Fox(magsRestricted.nonEmpty) ?~> "annotation.volume.magRestrictionsTooTight"
       remoteDatastoreClient = new WKRemoteDataStoreClient(datasetDataStore, rpc)
       fallbackLayerHasSegmentIndex <- fallbackLayer match {
         case Some(layer) =>
@@ -175,7 +175,7 @@ class AnnotationService @Inject()(
         VolumeTracingDefaults.zoomLevel,
         organizationId = Some(datasetOrganizationId),
         mappingName = mappingName,
-        resolutions = resolutionsRestricted.map(vec3IntToProto),
+        mags = magsRestricted.map(vec3IntToProto),
         hasSegmentIndex = Some(fallbackLayer.isEmpty || fallbackLayerHasSegmentIndex),
         additionalAxes = AdditionalAxis.toProto(additionalAxes)
       )
@@ -286,8 +286,7 @@ class AnnotationService @Inject()(
                 datasetOrganizationId,
                 dataStore,
                 fallbackLayer,
-                resolutionRestrictions =
-                  annotationLayerParameters.resolutionRestrictions.getOrElse(ResolutionRestrictions.empty),
+                magRestrictions = annotationLayerParameters.magRestrictions.getOrElse(MagRestrictions.empty),
                 mappingName = annotationLayerParameters.mappingName
               )
               volumeTracingAdapted = oldPrecedenceLayerProperties.map { p =>
@@ -417,7 +416,7 @@ class AnnotationService @Inject()(
         usedFallbackLayerName,
         autoFallbackLayer = false,
         None,
-        Some(ResolutionRestrictions.empty),
+        Some(MagRestrictions.empty),
         Some(AnnotationLayer.defaultNameForType(newAnnotationLayerType)),
         None
       )
@@ -551,14 +550,14 @@ class AnnotationService @Inject()(
     )
   }
 
-  def createVolumeTracingBase(datasetName: String,
-                              organizationId: String,
-                              boundingBox: Option[BoundingBox],
-                              startPosition: Vec3Int,
-                              startRotation: Vec3Double,
-                              volumeShowFallbackLayer: Boolean,
-                              resolutionRestrictions: ResolutionRestrictions)(implicit ctx: DBAccessContext,
-                                                                              m: MessagesProvider): Fox[VolumeTracing] =
+  def createVolumeTracingBase(
+      datasetName: String,
+      organizationId: String,
+      boundingBox: Option[BoundingBox],
+      startPosition: Vec3Int,
+      startRotation: Vec3Double,
+      volumeShowFallbackLayer: Boolean,
+      magRestrictions: MagRestrictions)(implicit ctx: DBAccessContext, m: MessagesProvider): Fox[VolumeTracing] =
     for {
       organization <- organizationDAO.findOne(organizationId)
       dataset <- datasetDAO.findOneByNameAndOrganization(datasetName, organizationId) ?~> Messages("dataset.notFound",
@@ -583,7 +582,7 @@ class AnnotationService @Inject()(
         },
         startPosition = Some(startPosition),
         startRotation = Some(startRotation),
-        resolutionRestrictions = resolutionRestrictions,
+        magRestrictions = magRestrictions,
         mappingName = None
       )
     } yield volumeTracing

diff --git a/app/models/annotation/AnnotationSettings.scala b/app/models/annotation/AnnotationSettings.scala
@@ -3,7 +3,7 @@ package models.annotation
 import com.scalableminds.util.enumeration.ExtendedEnumeration
 import com.scalableminds.webknossos.tracingstore.tracings.TracingType
 import com.scalableminds.webknossos.tracingstore.tracings.TracingType.TracingType
-import com.scalableminds.webknossos.tracingstore.tracings.volume.ResolutionRestrictions
+import com.scalableminds.webknossos.tracingstore.tracings.volume.MagRestrictions
 import play.api.libs.json._
 
 object TracingMode extends ExtendedEnumeration {
@@ -18,7 +18,7 @@ case class AnnotationSettings(
     somaClickingAllowed: Boolean = true,
     volumeInterpolationAllowed: Boolean = true,
     mergerMode: Boolean = false,
-    resolutionRestrictions: ResolutionRestrictions = ResolutionRestrictions.empty
+    magRestrictions: MagRestrictions = MagRestrictions.empty
 )
 
 object AnnotationSettings {

diff --git a/app/models/annotation/WKRemoteTracingStoreClient.scala b/app/models/annotation/WKRemoteTracingStoreClient.scala
@@ -17,7 +17,7 @@ import com.scalableminds.webknossos.datastore.models.annotation.{
 import com.scalableminds.webknossos.datastore.models.datasource.DataSourceLike
 import com.scalableminds.webknossos.datastore.rpc.RPC
 import com.scalableminds.webknossos.tracingstore.tracings.TracingSelector
-import com.scalableminds.webknossos.tracingstore.tracings.volume.ResolutionRestrictions
+import com.scalableminds.webknossos.tracingstore.tracings.volume.MagRestrictions
 import com.scalableminds.webknossos.tracingstore.tracings.volume.VolumeDataZipFormat.VolumeDataZipFormat
 import com.typesafe.scalalogging.LazyLogging
 import controllers.RpcTokenHolder
@@ -100,7 +100,7 @@ class WKRemoteTracingStoreClient(
   def duplicateVolumeTracing(volumeTracingId: String,
                              isFromTask: Boolean = false,
                              datasetBoundingBox: Option[BoundingBox] = None,
-                             resolutionRestrictions: ResolutionRestrictions = ResolutionRestrictions.empty,
+                             magRestrictions: MagRestrictions = MagRestrictions.empty,
                              downsample: Boolean = false,
                              editPosition: Option[Vec3Int] = None,
                              editRotation: Option[Vec3Double] = None,
@@ -109,8 +109,8 @@ class WKRemoteTracingStoreClient(
     rpc(s"${tracingStore.url}/tracings/volume/$volumeTracingId/duplicate").withLongTimeout
       .addQueryString("token" -> RpcTokenHolder.webknossosToken)
       .addQueryString("fromTask" -> isFromTask.toString)
-      .addQueryStringOptional("minResolution", resolutionRestrictions.minStr)
-      .addQueryStringOptional("maxResolution", resolutionRestrictions.maxStr)
+      .addQueryStringOptional("minMag", magRestrictions.minStr)
+      .addQueryStringOptional("maxMag", magRestrictions.maxStr)
       .addQueryStringOptional("editPosition", editPosition.map(_.toUriLiteral))
       .addQueryStringOptional("editRotation", editRotation.map(_.toUriLiteral))
       .addQueryStringOptional("boundingBox", boundingBox.map(_.toLiteral))
@@ -173,7 +173,7 @@ class WKRemoteTracingStoreClient(
 
   def saveVolumeTracing(tracing: VolumeTracing,
                         initialData: Option[File] = None,
-                        resolutionRestrictions: ResolutionRestrictions = ResolutionRestrictions.empty,
+                        magRestrictions: MagRestrictions = MagRestrictions.empty,
                         dataSource: Option[DataSourceLike] = None): Fox[String] = {
     logger.debug("Called to create VolumeTracing." + baseInfo)
     for {
@@ -185,8 +185,8 @@ class WKRemoteTracingStoreClient(
         case Some(file) =>
           rpc(s"${tracingStore.url}/tracings/volume/$tracingId/initialData").withLongTimeout
             .addQueryString("token" -> RpcTokenHolder.webknossosToken)
-            .addQueryStringOptional("minResolution", resolutionRestrictions.minStr)
-            .addQueryStringOptional("maxResolution", resolutionRestrictions.maxStr)
+            .addQueryStringOptional("minMag", magRestrictions.minStr)
+            .addQueryStringOptional("maxMag", magRestrictions.maxStr)
             .post(file)
         case _ =>
           Fox.successful(())

diff --git a/app/models/annotation/nml/NmlParser.scala b/app/models/annotation/nml/NmlParser.scala
@@ -33,7 +33,7 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
 
   private val DEFAULT_TIME = 0L
   private val DEFAULT_VIEWPORT = 0
-  private val DEFAULT_RESOLUTION = 0
+  private val DEFAULT_MAG = 0
   private val DEFAULT_BITDEPTH = 0
   private val DEFAULT_DESCRIPTION = ""
   private val DEFAULT_INTERPOLATION = false
@@ -519,8 +519,8 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
   private def parseViewport(node: XMLNode) =
     getSingleAttribute(node, "inVp").toIntOpt.getOrElse(DEFAULT_VIEWPORT)
 
-  private def parseResolution(node: XMLNode) =
-    getSingleAttribute(node, "inMag").toIntOpt.getOrElse(DEFAULT_RESOLUTION)
+  private def parseMag(node: XMLNode) =
+    getSingleAttribute(node, "inMag").toIntOpt.getOrElse(DEFAULT_MAG)
 
   private def parseBitDepth(node: XMLNode) =
     getSingleAttribute(node, "bitDepth").toIntOpt.getOrElse(DEFAULT_BITDEPTH)
@@ -540,21 +540,12 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
       position <- parseVec3Int(node) ?~ Messages("nml.node.attribute.invalid", "position", id)
     } yield {
       val viewport = parseViewport(node)
-      val resolution = parseResolution(node)
+      val mag = parseMag(node)
       val timestamp = parseTimestamp(node)
       val bitDepth = parseBitDepth(node)
       val interpolation = parseInterpolation(node)
       val rotation = parseRotationForNode(node).getOrElse(NodeDefaults.rotation)
-      Node(id,
-           position,
-           rotation,
-           radius,
-           viewport,
-           resolution,
-           bitDepth,
-           interpolation,
-           timestamp,
-           additionalCoordinates)
+      Node(id, position, rotation, radius, viewport, mag, bitDepth, interpolation, timestamp, additionalCoordinates)
     }
   }
 

diff --git a/app/models/annotation/nml/NmlWriter.scala b/app/models/annotation/nml/NmlWriter.scala
@@ -359,7 +359,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
         writer.writeAttribute("rotY", n.rotation.y.toString)
         writer.writeAttribute("rotZ", n.rotation.z.toString)
         writer.writeAttribute("inVp", n.viewport.toString)
-        writer.writeAttribute("inMag", n.resolution.toString)
+        writer.writeAttribute("inMag", n.mag.toString)
         writer.writeAttribute("bitDepth", n.bitDepth.toString)
         writer.writeAttribute("interpolation", n.interpolation.toString)
         writer.writeAttribute("time", n.createdTimestamp.toString)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,3 +11,4 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
		### Postgres Evolutions:

		- [121-worker-name.sql](conf/evolutions/121-worker-name.sql)
		- [122-resolution-to-mag.sql](conf/evolutions/122-resolution-to-mag.sql)