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v4.2.0

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@github-actions github-actions released this 05 Oct 15:40
· 33 commits to master since this release
v4.2.0
180bf4d

webknossos

Breaking Changes

  • The default transfer_mode of RemoteDataset.add_layer_as_copy, RemoteDataset.downsample, RemoteLayer.add_mag_as_copy, RemoteLayer.downsample, RemoteLayer.upsample and RemoteAttachments.add_attachment_as_copy is now TransferMode.HTTP instead of TransferMode.COPY, consistent with Dataset.upload. Pass transfer_mode=TransferMode.COPY explicitly to keep the previous behavior. #1554

Added

  • Layer.export.as_ozx, as_tiff_stack and as_ome_tiff take an access_mode to choose how a remote layer's data is read, instead of always using the dataset's access mode. as_ozx and as_ome_tiff take a downsample flag (default True); with downsample=False, only the requested mag is written, without coarser levels. #1558

Changed

  • Layer.export.as_ozx now reads only the requested mag and computes a fresh pyramid of coarser mags by downsampling the exported data (anisotropic sampling), instead of copying the layer's existing mags. All mags in the archive now cover the same region, also for bounding boxes that aren't aligned with the coarser mags. #1558
  • webknossos downsample and webknossos upsample no longer require --transfer-mode for remote datasets; it now defaults to http. #1554
  • Renamed RemoteMagView.paths to RemoteMagView.paths_by_access_mode, since it is a mapping from access mode to path rather than a sequence of paths. RemoteMagView.paths is kept as a deprecated alias. #1550
  • Layer.export.as_tiff_stack now names each slice by its absolute coordinates (z in Mag(1) coordinates, plus any additional axes) instead of numbering the slices from 0, zero-padded to the width of the layer's largest coordinate along each axis. A cutout starting at z=40 in mag 2 is written as 40.tiff, 42.tiff, …, and one starting at t=3 as t3_z….tiff. #1557

Fixed

  • Layer.add_mag_as_ref and Dataset.add_layer_as_ref no longer open the array of a RemoteMagView to validate its data format and dtype, but use the remote layer's properties instead. Referencing a remote mag via its direct path therefore works without credentials for the underlying storage. #1553
  • Volume layers without any voxel data (e.g. a fresh add_volume_layer with a fallback layer, used only to register segments) are now saved without a data zip, so uploading them to WEBKNOSSOS no longer fails with "Initializing without any mags". #1555
  • Annotation.add_volume_layer now accepts a RemoteLayer as fallback_layer instead of only accepting its string representation. #1559
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