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Changelog

All notable changes to webknossos-cuber are documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning MAJOR.MINOR.PATCH. For upgrade instructions, please check the respective Breaking Changes sections.

Unreleased

Commits

Breaking Changes

Added

Changed

  • Upgrades black, mypy, pylint, pytest. #873

Fixed

0.12.3 - 2023-02-22

Commits

0.12.2 - 2023-02-20

Commits

Fixed

  • Fixed Docker container startup, by adding version information during build time. #872

0.12.1 - 2023-02-16

Commits

0.12.0 - 2023-02-10

Commits

Breaking Changes

  • Dropped support for Python 3.7. #833

Added

  • Added support for Python 3.10. #833

0.11.4 - 2023-02-09

Commits

0.11.3 - 2023-02-06

Commits

Fixed

  • Fixed a bug where converting coarse-mag Knossos data would crash with an assertion error. #857

0.11.2 - 2023-01-18

Commits

0.11.1 - 2023-01-05

Commits

Changed

  • Improved perfomance of wkcuber.tile_cubing and making it more robust. #840

0.11.0 - 2022-12-09

Commits

0.10.27 - 2022-12-07

Commits

0.10.26 - 2022-12-05

Commits

0.10.25 - 2022-11-29

Commits

0.10.24 - 2022-11-09

Commits

Changed

  • Updated cattrs dependency to 22.2.0. #819

0.10.23 - 2022-11-01

Commits

0.10.22 - 2022-10-27

Commits

0.10.21 - 2022-10-26

Commits

0.10.20 - 2022-10-20

Commits

0.10.19 - 2022-10-18

Commits

Changed

  • Some methods now take and executor argument instead of args or executor_args. This does not affect the CLI arguments. #805

0.10.18 - 2022-09-29

Commits

0.10.17 - 2022-09-26

Commits

0.10.16 - 2022-09-13

Commits

Added

  • The modules wkcuber and wkcuber.converter' also accept--pad` as a CLI argument to allow converting image data with differing image extents. #796

0.10.14 - 2022-08-30

Commits

0.10.13 - 2022-08-22

Commits

Breaking Changes

  • Deprecated --chunk_size in favor of --chunk_shape. #706

Added

  • Added support for WebDAV storage for remote Zarr-based datasets. #706

0.10.12 - 2022-08-15

Commits

0.10.11 - 2022-08-03

Commits

0.10.10 - 2022-07-26

Commits

0.10.9 - 2022-07-22

Commits

0.10.8 - 2022-07-15

Commits

0.10.7 - 2022-07-14

Commits

Changed

  • Made the dataset upload more robust against network errors. #757

0.10.6 - 2022-06-27

Commits

Changed

  • Make KNOSSOS conversion compatible with mag-prefixed mag folders. #756
  • When using multiprocessing, warning filters are set up to behave as in the spawning context. #741

Fixed

  • Fixed broken KNOSSOS to wkw conversion. #756

0.10.5 - 2022-06-15

Commits

0.10.4 - 2022-06-15

Commits

0.10.3 - 2022-06-03

Commits

Fixed

  • Fixed a bug where nifti datasets would not be converted if called from the CLI. #733

0.10.2 - 2022-05-20

Commits

Changed

  • Added Python 3.9 support to wkcuber #716

0.10.1 - 2022-05-10

Commits

0.10.0 - 2022-05-09

Commits

0.9.24 - 2022-05-03

Commits

0.9.23 - 2022-05-03

Commits

0.9.22 - 2022-05-02

Commits

Breaking Changes

  • Deprecated --scale in favor of --voxel_size. #704

Fixed

  • Fixed a bug where upper-case file extensions would lead to errors during channel count detection. #709

0.9.21 - 2022-04-20

Commits

0.9.20 - 2022-04-20

Commits

Breaking Changes

  • Deprecated --wkw_file_len flags in favor of --chunks_per_shard. #679
  • Deprecated wkcuber.api in favor of the high-level webknososs.Dataset API. #679
  • Deprecated external use of wkcuber.utils. #679
  • Remove the deprecated modules wkcuber.downsampling_utils and wkcuber.upsampling_utils. Use the high-level Layer.downsample and Layer.upsample methods in the webknossos package instead. #679

Added

  • Added Zarr support for wkcuber, wkcuber.cubing, wkcuber.converter, wkcuber.convert_knossos, wkcuber.convert_image_stack_to_wkw, wkcuber.convert_nifti, wkcuber.convert_raw, wkcuber.convert_zarr, and wkcuber.recubing. These commands now take a --data_format flag that can either be wkw or zarr. Additionally, --chunk_size and --chunks_per_shard flag are available and take either a single number or a 3-tuple (e.g. 32,32,32). #689

0.9.19 - 2022-04-11

Commits

Added

  • Added support for converting .bmp image files. #689

0.9.18 - 2022-04-06

Commits

0.9.17 - 2022-04-05

Commits

0.9.16 - 2022-03-31

Commits

0.9.15 - 2022-03-31

Commits

0.9.14 - 2022-03-24

Commits

0.9.13 - 2022-03-24

Commits

Fixed

  • Fixed that wkcuber.downsampling didn't support anisotropic downsampling for some downsampling modes like nearest. #643

0.9.12 - 2022-03-18

Commits

Added

  • Added logging to file in ./logs directory. #641

0.9.11 - 2022-03-16

Commits

0.9.10 - 2022-03-15

Commits

Fixed

  • Fixed that wkcuber.downsampling didn't support an anisotropic mag for --from. #638
  • Fixed that wkcuber.downsampling didn't provide a meaningful error message when trying to do downsampling with an unsupported interpolation mode. #619

0.9.9 - 2022-03-03

Commits

0.9.8 - 2022-02-28

Commits

0.9.7 - 2022-02-28

Commits

0.9.6 - 2022-02-15

Commits

0.9.5 - 2022-02-10

Commits

0.9.4 - 2022-02-09

Commits

0.9.3 - 2022-02-07

Commits

0.9.2 - 2022-02-03

Commits

0.9.1 - 2022-01-31

Commits

Added

  • Added wkcuber.convert_zarr tool to convert zarr files to wkw datasets. #549

Fixed

  • Fixed automatic conversion of 3D tiff files which only have a single page. #575

0.9.0 - 2022-01-19

Commits

Added

  • wkcuber.upload for uploading local datasets to webKnossos. #544

Changed

  • Logging is now set to log level INFO by default. DEBUG logging can be enabled with the --verbose flag. Consequently, the --silent flag has been removed. #544

0.8.31 - 2022-01-07

Commits

0.8.30 - 2021-12-27

Commits

0.8.29 - 2021-12-14

Commits

0.8.28 - 2021-12-09

Commits

Changed

  • Improved the performance of cubing and tile-cubing and integrated the dataset API into tile-cubing. #480

0.8.27 - 2021-12-09

Commits

Added

  • Added importable cube_with_args function to main module of wkcuber. #507

v0.8.25 - 2021-12-07

Commits

Added

  • wkcuber.convert_raw conversion tool for raw binary data files. #498
  • Added the wkcuber executable that is installed when the package is installed. #495

v0.8.24 - 2021-11-30

Commits

Fixed

  • Fixed --version CLI argument. #493

v0.8.23 - 2021-11-29

Commits

Added

  • Added the flag --version to wkcuber. #471

v0.8.20 - 2021-10-28

Commits

v0.8.19 - 2021-10-21

Commits

Fixed

  • Fixed two bugs in cubing (regarding start_z and pad). As a result, the ImageConverters do no longer cache metadata. #460

v0.8.18 - 2021-10-18

Commits

Breaking Changes in Config & CLI

  • Use Dataset API inside cubing to automatically write metadata. Cubing does now require a scale. #418

Added

Changed

  • Updated scikit-image dependency to 0.18.3. #435
  • Improved the TIFF and CZI reader to work with a wider variety of formats. The module convert_image_stack_to_wkw is now capable of making the result webKnossos compatible. #335

Fixed

0.8.16 - 2021-09-01

Commits

Breaking Changes in Config & CLI

Added

  • Add jp2 support. #428

Changed

  • Adjust downsampling scheme to always try to minimize the scaled difference between the different dimensions of a mag and renamed the sampling mode auto to anisotropic. #391
  • Make parameter executor optional for View.for_each_chunk and View.for_zipped_chunks. #404
  • Add option to rename foreign layer with add_{symlink,copy}_layer. #419

Fixed

  • Reverted that dataset.add_symlink_layer and dataset.add_copy_layer resolved the layer path if it was a symlink. #408
  • Fixed the string translation for signed int layer. #428

0.8.13 - 2021-09-01

Commits

Breaking Changes in Config & CLI

  • Replaced the old properties classes of the Dataset API with attr-classes.
  • The Layer.rename() function is now replaced with the setter of Layer.name.
  • The functions Layer.get_view_configuration and Layer.set_view_conficuration are replaced by the property Layer.default_view_configuration. (Same applies to Dataset.get_view_configuration and Dataset.set_view_configuration)
  • Moved LayerViewConfiguration and DatasetViewConfiguration into properties.py
  • Removed Layer.set_bounding_box_offset and Layer.set_bounding_box_size.
  • Renamed Layer.get_bounding_box() to the property Layer.bounding_box. The method Layer.set_bounding_box is replaced with the setter of the property Layer.bounding_box.

Added

  • The API documentation is now hosted on a publicwebpage. #392

Changed

  • Uses the new webknossos package. All classes and functions are re-exported under the same names. #398

Fixed

  • Fixes support for Windows. #394

0.8.12 - 2021-08-19

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Rollback scikit-image version from 0.18.0 to 0.16.2 because the newer version cause problems in voxelytics. #390

Fixed

0.8.11 - 2021-08-19

Commits

Breaking Changes in Config & CLI

Added

  • dataset.add_symlink_layer and dataset.add_copy_layer can now handle Layer arguments as well. The parameter foreign_layer_path was renamed to foreign_layer. #389

Changed

Fixed

0.8.10 - 2021-08-19

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Avoid warnings for compressed/unaligned data, if the data is directly at the border of the bounding box. #378

Fixed

0.8.9 - 2021-08-12

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Bump scipy to 1.6.0 and scikit-image to 0.18.0 while keeping numpy to under 1.20.0 #372

Fixed

  • Fixes a bug where modifications to an existing dataset with floats as dtype failed. #375

0.8.8 - 2021-08-06

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Bump cluster-tools from 1.59 to 1.60. #373

Fixed

0.8.7 - 2021-08-04

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Bump cluster-tools from 1.58 to 1.59. #371

Fixed

0.8.6 - 2021-07-29

Commits

Breaking Changes in Config & CLI

Added

  • Implement descriptive string representations for Dataset, Layer, MagView and View. #369
  • Added option to rename a layer. #368

Changed

Fixed

0.8.5 - 2021-07-29

Commits

Breaking Changes in Config & CLI

  • The parameter allow_compressed_write from View.write() is now removed. Writing to compressed magnifications is now always allowed. If the user decides to write unaligned data, a warning about a possible performance impact is displayed once. #356

Added

  • Added functions to wkcuber.api.dataset.Dataset and wkcuber.api.layer.Layer to set and get the view configuration. #344
  • Added functions to add mags of a foreign dataset (Layer.add_symlink_mag and Layer.add_copy_mag) #367

Changed

Fixed

  • Fixed a bug where Dataset.add_symlink_layer(make_relative=True) failed to look up dataset properties. #365

0.8.4 - 2021-07-26

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Datasets with a missing largestSegmentId can now be loaded with a default of -1. #362

Fixed

0.8.3 - 2021-07-26

Commits

Breaking Changes in Config & CLI

Added

Changed

  • Updated cluster-tools to 1.58 #361

Fixed

0.8.2 - 2021-07-26

Commits

Breaking Changes in Config & CLI

Added

  • Added option make_relative: bool to wkcuber.api.dataset.Dataset.add_symlink_layer to make the symlink relative. #360

Changed

Fixed

0.8.1 - 2021-07-22

Commits

Breaking Changes in Config & CLI

Added

  • Added add_copy_layer() to wkcuber.api.dataset.Dataset to copy the layer of a different dataset. #345
  • Added View.read_bbox() which takes only a single bounding box as parameter (instead of an offset and size). #347

Changed

Fixed

0.8.0 - 2021-07-16

Commits

Breaking Changes in Config & CLI

  • Some breaking changes in the dataset API: #339
  • The interfaces of the methods Layer.add_mag and Layer.get_or_add_mag have changed: the parameter block_type is now replaced with compress.
  • Previously Layer.mags was of type Dict[str, MagView]. This was now changed to Dict[Mag, MagView].
  • Renamed LayerTypes to LayerCategories.

Added

  • Added multiple small features: #339
  • Names of datasets can now be passed optionally when creating a dataset.
  • The Layer does now expose the largest_segment_id.
  • Add methods to get category specific layers for a given dataset.

0.7.0 - 2021-07-08

Commits

Breaking Changes in Config & CLI

  • Refactoring of the dataset API: #331
    • Tiff-support is now dropped (TiffDataset and TiledTiffDataset are now removed (alongside their corresponding Layer and MagDataset classes))
    • Module names are now lowercase (previously: wkcuber.api.Dataset, wkcuber.api.Layer, wkcuber.api.View, wkcuber.api.properties.DatasetProperties, wkcuber.api.properties.LayerProperties, wkcuber.api.properties.ResolutionProperties)
    • Some classes are renamed (WKDataset -> Dataset, WKMagDataset -> MagView)
    • The "Layer types" (previously Layer.COLOR and Layer.SEGMENTATION) are now moved into their own class wkcuber.api.layer.LayerTypes.
    • View (in particular get_view()) is refactored to be safer (this is also a breaking change).
    • The attribute path_to_mag_dataset was renamed to path_to_mag_view
    • Changes for View.get_view() (these changes also apply for MagView.get_view() (previously MagDataset.get_view())):
      • The parameter relative_offset was renamed to offset.
      • The parameter is_bounded was dropped (Views are now always bounded).
      • The order of the parameters size and offset was changed, so that offset is now the first parameter.
    • The shorthand wkcuber.api.dataset.Dataset.get_view() was removed.
    • The flag --write_tiff of convert_nifti was removed.

Added

Changed

Fixed

  • Use an os independent path separator for regexes. #334

0.6.8 - 2021-06-18

Commits

Breaking Changes in Config & CLI

Added

  • Added docs/api.sh which opens a server displaying the docs. It can also be used to persist the html to docs/api by invoking docs/api.sh --persist. #322

Changed

Fixed

0.6.7 - 2021-05-28

Commits

Breaking Changes in Config & CLI

Added

  • Added distribution flags to wkcuber in order to limit the parallel jobs or use a cluster scheduler. #323
  • Added a function for converting BoundingBox to BoundingBoxNamedTuple. #324

Changed

Fixed

  • Fixed a bug for writing compressed data. This previously caused an error when downsampling certain datasets. #326

0.6.6 - 2021-05-14

Commits

Fixed

  • After downsampling data, the bounding box gets saved correctly to the datasource-properties.json. #320

0.6.5 - 2021-05-12

Commits

Breaking Changes in Config & CLI

  • The interface for downsampling was completely reworked. The flags anisotropic_target_mag and isotropic are now deprecated. Use max and sampling_mode instead. #304

Changed

  • Relaxes the constraint that all input files need to have the same type when auto-converting. #317

0.6.4 - 2021-05-12

Commits

Fixed

  • Fixed PEP 561 compatibility for type support

0.6.3 - 2021-05-12

Commits

Breaking Changes in Config & CLI

  • The dataset API now interprets float as 32bit. double can be passed as a string to use a floatingpoint with 64bit as dtype (specifying the dtype explicitly, e.g. np.float64, still works). The datasource-properties.json stores 32bit floats as "float" and 64bit floats as "double". #316

Added

  • Added py.typed to conform PEP 561 for type support

0.6.2 - 2021-05-10

Commits

Breaking Changes in Config & CLI

Added

  • Added method to Dataset API to compress WKMagDatasets. #296
  • This PR allows the auto-conversion to select one channel at a time for conversion to create multiple layer. Thus, more channel formats are supported. #291

Changed

  • Previously Dataset.get_or_add_layer did not support dtypes like np.uint8. #308
  • In a previous PR we switched from str to Path for paths. This PR allows both for the top-level methods in the Dataset API. #307
  • Bump wkw from 0.1.4 to 1.1.9. #309
  • Bump cluster-tools from 1.54 to 1.56 #315

Fixed

  • Re-export WKDataset. #312

0.6.1 - 2021-04-29

Commits

This is the latest release at the time of creating this changelog.