diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md index 7c693819ae1..b9769572692 100644 --- a/CHANGELOG.unreleased.md +++ b/CHANGELOG.unreleased.md @@ -31,7 +31,8 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released - Updated antd UI library from version 4.24.8 to 4.24.15. [#7505](https://github.com/scalableminds/webknossos/pull/7505) - Changed the default dataset search mode to also search in subfolders. [#7539](https://github.com/scalableminds/webknossos/pull/7539) - When clicking a segment in the viewport, it is automatically focused in the segment list. A corresponding context menu entry was added as well. [#7512](https://github.com/scalableminds/webknossos/pull/7512) -- Updated the isValidName route in the API to return 200 for valid and invalid names. With this, the API version was bumped up to 6. [#7550](https://github.com/scalableminds/webknossos/pull/7550) +- Updated the isValidName route in the API to return 200 for valid and invalid names. With this, the API version was bumped up to 6. [#7550](https://github.com/scalableminds/webknossos/pull/7550) +- The metadata for ND datasets and their annotation has changed: upper bound of additionalAxes is now stored as an exclusive value, called "end" in the NML format. [#7547](https://github.com/scalableminds/webknossos/pull/7547) ### Fixed - Datasets with annotations can now be deleted. The concerning annotations can no longer be viewed but still be downloaded. [#7429](https://github.com/scalableminds/webknossos/pull/7429) @@ -49,6 +50,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released - Fixed regression in proofreading tool when automatic mesh loading was disabled and a merge/split operation was performed. [#7534](https://github.com/scalableminds/webknossos/pull/7534) - Fixed that last dimension value in ND dataset was not loaded. [#7535](https://github.com/scalableminds/webknossos/pull/7535) - Fixed the initialization of the mapping list for agglomerate views if json mappings are present. [#7537](https://github.com/scalableminds/webknossos/pull/7537) +- Fixed a bug where uploading ND volume annotations would lead to errors due to parsing of the chunk paths. [#7547](https://github.com/scalableminds/webknossos/pull/7547) ### Removed - Removed several unused frontend libraries. [#7521](https://github.com/scalableminds/webknossos/pull/7521) diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md index 8c46c6251e7..1cccde5d142 100644 --- a/MIGRATIONS.unreleased.md +++ b/MIGRATIONS.unreleased.md @@ -12,6 +12,7 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md). - If your setup contains webknossos-workers, postgres evolution 110 introduces the columns `maxParallelHighPriorityJobs` and `maxParallelLowPriorityJobs`. Make sure to set those values to match what you want for your deployment. [#7463](https://github.com/scalableminds/webknossos/pull/7463) - If your setup contains webknossos-workers, you may want to add the new available worker job `compute_segment_index_file` to the `supportedJobCommands` column of one or more of your workers. [#7493](https://github.com/scalableminds/webknossos/pull/7493) - The WEBKNOSSOS api version has changed to 6. The `isValidNewName` route for datasets now returns 200 regardless of whether the name is valid or not. The body contains a JSON object with the key "isValid". [#7550](https://github.com/scalableminds/webknossos/pull/7550) +- If your setup contains ND datasets, run the python3 script at `tools/migrate-axis-bounds/migration.py` on your datastores to update the datasource-properties.jsons of the ND datasets. ### Postgres Evolutions: diff --git a/app/models/annotation/nml/NmlParser.scala b/app/models/annotation/nml/NmlParser.scala index 452bfecc5b7..b830566c1dc 100755 --- a/app/models/annotation/nml/NmlParser.scala +++ b/app/models/annotation/nml/NmlParser.scala @@ -270,11 +270,11 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener name <- getSingleAttributeOpt(additionalAxisNode, "name") indexStr <- getSingleAttributeOpt(additionalAxisNode, "index") index <- indexStr.toIntOpt - minStr <- getSingleAttributeOpt(additionalAxisNode, "min") - min <- minStr.toIntOpt - maxStr <- getSingleAttributeOpt(additionalAxisNode, "max") - max <- maxStr.toIntOpt - } yield new AdditionalAxisProto(name, index, Vec2IntProto(min, max)) + startStr <- getSingleAttributeOpt(additionalAxisNode, "start") + start <- startStr.toIntOpt + endStr <- getSingleAttributeOpt(additionalAxisNode, "end") + end <- endStr.toIntOpt + } yield new AdditionalAxisProto(name, index, Vec2IntProto(start, end)) } ) ) diff --git a/app/models/annotation/nml/NmlWriter.scala b/app/models/annotation/nml/NmlWriter.scala index 3629cd21b2b..32648e605ce 100644 --- a/app/models/annotation/nml/NmlWriter.scala +++ b/app/models/annotation/nml/NmlWriter.scala @@ -234,8 +234,8 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits { Xml.withinElementSync("additionalAxis") { writer.writeAttribute("name", a.name) writer.writeAttribute("index", a.index.toString) - writer.writeAttribute("min", a.bounds.x.toString) - writer.writeAttribute("max", a.bounds.y.toString) + writer.writeAttribute("start", a.bounds.x.toString) + writer.writeAttribute("end", a.bounds.y.toString) } }) } diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index e16871e6495..32dfc98b292 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -232,7 +232,7 @@ class DataCube { for (const coord of coords || []) { if (coord.name in this.additionalAxes) { const { bounds } = this.additionalAxes[coord.name]; - if (coord.value < bounds[0] || coord.value > bounds[1]) { + if (coord.value < bounds[0] || coord.value >= bounds[1]) { return null; } } diff --git a/frontend/javascripts/oxalis/model/helpers/nml_helpers.ts b/frontend/javascripts/oxalis/model/helpers/nml_helpers.ts index 874068a06b0..73a491f3f43 100644 --- a/frontend/javascripts/oxalis/model/helpers/nml_helpers.ts +++ b/frontend/javascripts/oxalis/model/helpers/nml_helpers.ts @@ -273,14 +273,14 @@ function serializeParameters( ...(additionalAxes.length > 0 ? serializeTagWithChildren( - "additionalCoordinates", + "additionalAxes", {}, additionalAxes.map((coord) => - serializeTag("additionalCoordinate", { + serializeTag("additionalAxis", { name: coord.name, index: coord.index, - min: coord.bounds[0], - max: coord.bounds[1], + start: coord.bounds[0], + end: coord.bounds[1], }), ), ) diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index db2a07a6a6b..a8f66d92bec 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -110,7 +110,7 @@ function AdditionalCoordinatesInputView() { label={coord.name} key={coord.name} min={bounds[0]} - max={bounds[1]} + max={bounds[1] - 1} value={coord.value} spans={[2, 18, 4]} onChange={(newCoord) => { diff --git a/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.md b/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.md index 672b873ace1..ff8522951eb 100644 --- a/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.md +++ b/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.md @@ -82,9 +82,9 @@ Generated by [AVA](https://avajs.dev). ␊ ␊ ␊ - ␊ - ␊ - ␊ + ␊ + ␊ + ␊ ␊ ␊ ␊ diff --git a/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.snap b/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.snap index 94be274b569..046d13f7319 100644 Binary files a/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.snap and b/frontend/javascripts/test/snapshots/public-test/test-bundle/test/libs/nml.spec.js.snap differ diff --git a/tools/migrate-axis-bounds/migration.py b/tools/migrate-axis-bounds/migration.py new file mode 100644 index 00000000000..c3e6a0ddf4e --- /dev/null +++ b/tools/migrate-axis-bounds/migration.py @@ -0,0 +1,51 @@ +from pathlib import Path +import json +import shutil +import time +import argparse + +# Traverses a binaryData directory and changes all datasource-properties.jsons +# that include additionalAxes, increasing the upper bound by 1 +# This follows a change in the upper bound semantic to be exclusive + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument( + "--dry", + action="store_true", + ) + parser.add_argument("binary_data_dir", type=Path, help="WEBKNOSSOS binary data dir") + args = parser.parse_args() + dry = args.dry + binary_data_dir = args.binary_data_dir + + count = 0 + print(f"Traversing datasets at {binary_data_dir.resolve()} ...") + for orga_dir in [item for item in binary_data_dir.iterdir() if item.is_dir()]: + for dataset_dir in [item for item in orga_dir.iterdir() if item.is_dir()]: + json_path = dataset_dir / "datasource-properties.json" + if json_path.exists(): + changed = False + with open(json_path, 'r') as json_file: + content = json.load(json_file) + for layer in content.get("dataLayers", []): + for axis in layer.get("additionalAxes", []): + if "bounds" in axis: + bounds = axis["bounds"] + if len(bounds) >= 2: + bounds[1] = bounds[1] + 1 + changed = True + if changed: + print(f"Updating {json_path} (dry={dry})...") + count += 1 + backup_path = Path(f"{json_path}.{round(time.time() * 1000)}.bak") + + if not dry: + shutil.copyfile(json_path, backup_path) + with open(json_path, 'w') as json_outfile: + json.dump(content, json_outfile, indent=4) + + print(f"Updated {count} datasets (dry={dry})") + +if __name__ == '__main__': + main() diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorer.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorer.scala index 16192065d64..b12ef60a610 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorer.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorer.scala @@ -130,7 +130,7 @@ class NgffExplorer(implicit val ec: ExecutionContext) extends RemoteLayerExplore .filter(axis => !defaultAxes.contains(axis.name)) .zipWithIndex .map(axisAndIndex => - createAdditionalAxis(axisAndIndex._1.name, axisAndIndex._2, Array(0, shape(axisAndIndex._2) - 1)).toFox)) + createAdditionalAxis(axisAndIndex._1.name, axisAndIndex._2, Array(0, shape(axisAndIndex._2))).toFox)) duplicateNames = axes.map(_.name).diff(axes.map(_.name).distinct).distinct _ <- Fox.bool2Fox(duplicateNames.isEmpty) ?~> s"Additional axes names (${duplicateNames.mkString("", ", ", "")}) are not unique." } yield axes diff --git a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeDataZipHelper.scala b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeDataZipHelper.scala index eacaf413182..ab155c3162a 100644 --- a/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeDataZipHelper.scala +++ b/webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeDataZipHelper.scala @@ -85,7 +85,7 @@ trait VolumeDataZipHelper extends WKWDataFormatHelper with ByteUtils with BoxImp val additionalAxesNames: Seq[String] = dimensionNames.toSeq.drop(1).dropRight(3) // drop channel left, and xyz right // assume additionalAxes,x,y,z - val chunkPathRegex = s"(|.*/)(\\d+-\\d+-\\d+)/c\\.(.+)".r + val chunkPathRegex = s"(|.*/)(\\d+|\\d+-\\d+-\\d+)/c\\.(.+)".r path match { case chunkPathRegex(_, magStr, dimsStr) => @@ -99,7 +99,7 @@ trait VolumeDataZipHelper extends WKWDataFormatHelper with ByteUtils with BoxImp val bucketY = dims(dims.length - 2) val bucketZ = dims.last - Vec3Int.fromMagLiteral(magStr).map { mag => + Vec3Int.fromMagLiteral(magStr, allowScalar = true).map { mag => BucketPosition( bucketX.toInt * mag.x * DataLayer.bucketLength, bucketY.toInt * mag.y * DataLayer.bucketLength,