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
Breaking Changes
Added
Changed
- Upgrades
black
,mypy
,pylint
,pytest
. #873
Fixed
0.12.3 - 2023-02-22
0.12.2 - 2023-02-20
Fixed
- Fixed Docker container startup, by adding version information during build time. #872
0.12.1 - 2023-02-16
0.12.0 - 2023-02-10
Breaking Changes
- Dropped support for Python 3.7. #833
Added
- Added support for Python 3.10. #833
0.11.4 - 2023-02-09
0.11.3 - 2023-02-06
Fixed
- Fixed a bug where converting coarse-mag Knossos data would crash with an assertion error. #857
0.11.2 - 2023-01-18
0.11.1 - 2023-01-05
Changed
- Improved perfomance of
wkcuber.tile_cubing
and making it more robust. #840
0.11.0 - 2022-12-09
0.10.27 - 2022-12-07
0.10.26 - 2022-12-05
0.10.25 - 2022-11-29
0.10.24 - 2022-11-09
Changed
- Updated cattrs dependency to 22.2.0. #819
0.10.23 - 2022-11-01
0.10.22 - 2022-10-27
0.10.21 - 2022-10-26
0.10.20 - 2022-10-20
0.10.19 - 2022-10-18
Changed
- Some methods now take and
executor
argument instead ofargs
orexecutor_args
. This does not affect the CLI arguments. #805
0.10.18 - 2022-09-29
0.10.17 - 2022-09-26
0.10.16 - 2022-09-13
Added
- The modules
wkcuber
andwkcuber.converter' also accept
--pad` as a CLI argument to allow converting image data with differing image extents. #796
0.10.14 - 2022-08-30
0.10.13 - 2022-08-22
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
0.10.11 - 2022-08-03
0.10.10 - 2022-07-26
0.10.9 - 2022-07-22
0.10.8 - 2022-07-15
0.10.7 - 2022-07-14
Changed
- Made the dataset upload more robust against network errors. #757
0.10.6 - 2022-06-27
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
0.10.4 - 2022-06-15
0.10.3 - 2022-06-03
Fixed
- Fixed a bug where nifti datasets would not be converted if called from the CLI. #733
0.10.2 - 2022-05-20
Changed
- Added Python 3.9 support to wkcuber #716
0.10.1 - 2022-05-10
0.10.0 - 2022-05-09
0.9.24 - 2022-05-03
0.9.23 - 2022-05-03
0.9.22 - 2022-05-02
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
0.9.20 - 2022-04-20
Breaking Changes
- Deprecated
--wkw_file_len
flags in favor of--chunks_per_shard
. #679 - Deprecated
wkcuber.api
in favor of the high-levelwebknososs.Dataset
API. #679 - Deprecated external use of
wkcuber.utils
. #679 - Remove the deprecated modules
wkcuber.downsampling_utils
andwkcuber.upsampling_utils
. Use the high-levelLayer.downsample
andLayer.upsample
methods in thewebknossos
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
, andwkcuber.recubing
. These commands now take a--data_format
flag that can either bewkw
orzarr
. 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
Added
- Added support for converting
.bmp
image files. #689
0.9.18 - 2022-04-06
0.9.17 - 2022-04-05
0.9.16 - 2022-03-31
0.9.15 - 2022-03-31
0.9.14 - 2022-03-24
0.9.13 - 2022-03-24
Fixed
- Fixed that wkcuber.downsampling didn't support anisotropic downsampling for some downsampling modes like
nearest
. #643
0.9.12 - 2022-03-18
Added
- Added logging to file in
./logs
directory. #641
0.9.11 - 2022-03-16
0.9.10 - 2022-03-15
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
0.9.8 - 2022-02-28
0.9.7 - 2022-02-28
0.9.6 - 2022-02-15
0.9.5 - 2022-02-10
0.9.4 - 2022-02-09
0.9.3 - 2022-02-07
0.9.2 - 2022-02-03
0.9.1 - 2022-01-31
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
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
0.8.30 - 2021-12-27
0.8.29 - 2021-12-14
0.8.28 - 2021-12-09
Changed
- Improved the performance of cubing and tile-cubing and integrated the dataset API into tile-cubing. #480
0.8.27 - 2021-12-09
Added
- Added importable
cube_with_args
function to main module of wkcuber. #507
v0.8.25 - 2021-12-07
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
Fixed
- Fixed
--version
CLI argument. #493
v0.8.23 - 2021-11-29
Added
- Added the flag
--version
towkcuber
. #471
v0.8.20 - 2021-10-28
v0.8.19 - 2021-10-21
Fixed
- Fixed two bugs in
cubing
(regardingstart_z
andpad
). As a result, the ImageConverters do no longer cache metadata. #460
v0.8.18 - 2021-10-18
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
andCZI
reader to work with a wider variety of formats. The moduleconvert_image_stack_to_wkw
is now capable of making the result webKnossos compatible. #335
Fixed
0.8.16 - 2021-09-01
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
toanisotropic
. #391 - Make parameter
executor
optional forView.for_each_chunk
andView.for_zipped_chunks
. #404 - Add option to rename foreign layer with add_{symlink,copy}_layer. #419
Fixed
- Reverted that
dataset.add_symlink_layer
anddataset.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
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 ofLayer.name
. - The functions
Layer.get_view_configuration
andLayer.set_view_conficuration
are replaced by the propertyLayer.default_view_configuration
. (Same applies toDataset.get_view_configuration
andDataset.set_view_configuration
) - Moved
LayerViewConfiguration
andDatasetViewConfiguration
intoproperties.py
- Removed
Layer.set_bounding_box_offset
andLayer.set_bounding_box_size
. - Renamed
Layer.get_bounding_box()
to the propertyLayer.bounding_box
. The methodLayer.set_bounding_box
is replaced with the setter of the propertyLayer.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
Breaking Changes in Config & CLI
Added
Changed
- Rollback
scikit-image
version from0.18.0
to0.16.2
because the newer version cause problems in voxelytics. #390
Fixed
0.8.11 - 2021-08-19
Breaking Changes in Config & CLI
Added
dataset.add_symlink_layer
anddataset.add_copy_layer
can now handleLayer
arguments as well. The parameterforeign_layer_path
was renamed toforeign_layer
. #389
Changed
Fixed
0.8.10 - 2021-08-19
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
Breaking Changes in Config & CLI
Added
Changed
- Bump scipy to
1.6.0
andscikit-image
to0.18.0
while keepingnumpy
to under1.20.0
#372
Fixed
- Fixes a bug where modifications to an existing dataset with floats as dtype failed. #375
0.8.8 - 2021-08-06
Breaking Changes in Config & CLI
Added
Changed
- Bump cluster-tools from 1.59 to 1.60. #373
Fixed
0.8.7 - 2021-08-04
Breaking Changes in Config & CLI
Added
Changed
- Bump cluster-tools from 1.58 to 1.59. #371
Fixed
0.8.6 - 2021-07-29
Breaking Changes in Config & CLI
Added
- Implement descriptive string representations for
Dataset
,Layer
,MagView
andView
. #369 - Added option to rename a layer. #368
Changed
Fixed
0.8.5 - 2021-07-29
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
andwkcuber.api.layer.Layer
to set and get the view configuration. #344 - Added functions to add mags of a foreign dataset (
Layer.add_symlink_mag
andLayer.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
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
Breaking Changes in Config & CLI
Added
Changed
- Updated
cluster-tools
to1.58
#361
Fixed
0.8.2 - 2021-07-26
Breaking Changes in Config & CLI
Added
- Added option
make_relative: bool
towkcuber.api.dataset.Dataset.add_symlink_layer
to make the symlink relative. #360
Changed
Fixed
0.8.1 - 2021-07-22
Breaking Changes in Config & CLI
Added
- Added
add_copy_layer()
towkcuber.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
Breaking Changes in Config & CLI
- Some breaking changes in the dataset API: #339
- The interfaces of the methods
Layer.add_mag
andLayer.get_or_add_mag
have changed: the parameterblock_type
is now replaced withcompress
. - Previously
Layer.mags
was of typeDict[str, MagView]
. This was now changed toDict[Mag, MagView]
. - Renamed
LayerTypes
toLayerCategories
.
Added
- Added multiple small features: #339
- Names of datasets can now be passed optionally when creating a dataset.
- The
Layer
does now expose thelargest_segment_id
. - Add methods to get category specific layers for a given dataset.
0.7.0 - 2021-07-08
Breaking Changes in Config & CLI
- Refactoring of the dataset API: #331
- Tiff-support is now dropped (
TiffDataset
andTiledTiffDataset
are now removed (alongside their correspondingLayer
andMagDataset
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
andLayer.SEGMENTATION
) are now moved into their own classwkcuber.api.layer.LayerTypes
. View
(in particularget_view()
) is refactored to be safer (this is also a breaking change).- The attribute
path_to_mag_dataset
was renamed topath_to_mag_view
- Changes for
View.get_view()
(these changes also apply forMagView.get_view()
(previouslyMagDataset.get_view()
)):- The parameter
relative_offset
was renamed tooffset
. - The parameter
is_bounded
was dropped (View
s are now always bounded). - The order of the parameters
size
andoffset
was changed, so thatoffset
is now the first parameter.
- The parameter
- The shorthand
wkcuber.api.dataset.Dataset.get_view()
was removed. - The flag
--write_tiff
ofconvert_nifti
was removed.
- Tiff-support is now dropped (
Added
Changed
Fixed
- Use an os independent path separator for regexes. #334
0.6.8 - 2021-06-18
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 todocs/api
by invokingdocs/api.sh --persist
. #322
Changed
Fixed
0.6.7 - 2021-05-28
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
toBoundingBoxNamedTuple
. #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
Fixed
- After downsampling data, the bounding box gets saved correctly to the
datasource-properties.json
. #320
0.6.5 - 2021-05-12
Breaking Changes in Config & CLI
- The interface for
downsampling
was completely reworked. The flagsanisotropic_target_mag
andisotropic
are now deprecated. Usemax
andsampling_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
Fixed
- Fixed PEP 561 compatibility for type support
0.6.3 - 2021-05-12
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). Thedatasource-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
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 likenp.uint8
. #308 - In a previous PR we switched from
str
toPath
for paths. This PR allows both for the top-level methods in the Dataset API. #307 - Bump wkw from
0.1.4
to1.1.9
. #309 - Bump cluster-tools from 1.54 to 1.56 #315
Fixed
- Re-export WKDataset. #312
0.6.1 - 2021-04-29
This is the latest release at the time of creating this changelog.