v0.2.52

Bump cluster-tools from 1.46 to 1.48 (#194)

Bumps [cluster-tools](https://github.com/scalableminds/cluster_tools) from 1.46 to 1.48.
- [Release notes](https://github.com/scalableminds/cluster_tools/releases)
- [Commits](https://github.com/scalableminds/cluster_tools/compare/v1.46...v1.48)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>

Co-authored-by: dependabot-preview[bot] <27856297+dependabot-preview[bot]@users.noreply.github.com>

v0.2.51

Bounding Box from checkpoint name (#191)

* add from_checkpoint_name constructor

* format

v0.2.50

use the implementation of the most recent commit from voxelytics (#190)

v0.2.49: High level dataset api chunking (#184)

* only log downsampling for each MB ob precessed data

* log every gigabyte instead of every megabyte

* implement PR feedback

* WIP: implement high level dataset api

* WIP: implement TiffMag

* implement test for dataset api

* refactor high level dataset api

* add test data for WKDataset

* improve high level dataset api and add more tests

* use seed in tests to achieve deterministic behaviour

* implement a test for writing out of bounds with a wk_slice

* add possibility to define pattern for TiffDatasets

* implement tiled tiff

* improve quality of dataset tests

* make naming schema of test files consistent

* implement PR feedback

* rename tiffs in testdata

* Improve error message and reformat code

* add type annotation

* rename Slice to View

* remove comments and reformat code

* add scikit-image (which is needed for skimage) as dependency

* update version of scikit-image

* fix relative paths in tests

* add possibility to get data of specific tile

* reformat code

* add test for png images

* reformat code

* make TiledTiffDataset a seperate class

* add support for opening datasets which do not have num_channels in properties.json

* add test for advanced pattern

* use more efficient method to detect tile_ranges

* rename file path of test case

* support largestSegmentationId in properties

* restructure properties

* add dataType attribute to properties

* WIP: implement chunking

* implement PR feedback

* remove comment

* fix relative paths

* fix writing data to an unopened dataset and support different orders of the dimensions with patterns

* Adjust docstring of method

Co-Authored-By: Philipp Otto <philippotto@users.noreply.github.com>

* use type to call subclass constructor

* reformat code

* Support tiled tiffs in high level dataset API (#178)

* add possibility to define pattern for TiffDatasets

* implement tiled tiff

* add possibility to get data of specific tile

* add test for png images

* reformat code

* make TiledTiffDataset a seperate class

* add support for opening datasets which do not have num_channels in properties.json

* add test for advanced pattern

* use more efficient method to detect tile_ranges

* rename file path of test case

* support largestSegmentationId in properties

* restructure properties

* add dataType attribute to properties

* implement PR feedback

* fix writing data to an unopened dataset and support different orders of the dimensions with patterns

* Adjust docstring of method

Co-Authored-By: Philipp Otto <philippotto@users.noreply.github.com>

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

* implement get_view for a View; fix check_chunk_size for WKView

* reformat code

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

v0.2.48: Support tiled tiffs in high level dataset API (#185)

* only log downsampling for each MB ob precessed data

* log every gigabyte instead of every megabyte

* implement PR feedback

* WIP: implement high level dataset api

* WIP: implement TiffMag

* implement test for dataset api

* refactor high level dataset api

* add test data for WKDataset

* improve high level dataset api and add more tests

* use seed in tests to achieve deterministic behaviour

* implement a test for writing out of bounds with a wk_slice

* add possibility to define pattern for TiffDatasets

* implement tiled tiff

* improve quality of dataset tests

* make naming schema of test files consistent

* implement PR feedback

* rename tiffs in testdata

* Improve error message and reformat code

* add type annotation

* rename Slice to View

* remove comments and reformat code

* add scikit-image (which is needed for skimage) as dependency

* update version of scikit-image

* fix relative paths in tests

* add possibility to get data of specific tile

* reformat code

* add test for png images

* reformat code

* make TiledTiffDataset a seperate class

* add support for opening datasets which do not have num_channels in properties.json

* add test for advanced pattern

* use more efficient method to detect tile_ranges

* rename file path of test case

* support largestSegmentationId in properties

* restructure properties

* add dataType attribute to properties

* implement PR feedback

* fix writing data to an unopened dataset and support different orders of the dimensions with patterns

* Adjust docstring of method

Co-Authored-By: Philipp Otto <philippotto@users.noreply.github.com>

* Support tiled tiffs in high level dataset API (#178)

* add possibility to define pattern for TiffDatasets

* implement tiled tiff

* add possibility to get data of specific tile

* add test for png images

* reformat code

* make TiledTiffDataset a seperate class

* add support for opening datasets which do not have num_channels in properties.json

* add test for advanced pattern

* use more efficient method to detect tile_ranges

* rename file path of test case

* support largestSegmentationId in properties

* restructure properties

* add dataType attribute to properties

* implement PR feedback

* fix writing data to an unopened dataset and support different orders of the dimensions with patterns

* Adjust docstring of method

Co-Authored-By: Philipp Otto <philippotto@users.noreply.github.com>

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

v0.2.47: Enable Compression for NIFTI Conversion Script (#182)

Enabled wkw compression when converting NIFTI files

v0.2.46

fix edge case in get_next_anisotropic_mag (fixes #176) (#179)

Co-authored-by: Norman Rzepka <code@normanrz.com>

v0.2.45

Fix nifti file conversion (#180)

* use comparisons with absolute path only

* change used datatype for segmentation layer when converting from nifti files to uint8, so that max value will not cause overflow in voxelytics pipeline.

* Reformat

v0.2.44

This release includes a new high-level dataset API. See https://github.com/scalableminds/webknossos-cuber/wiki/High-level-dataset-API-overview for details.

v0.2.43: Poetry (#175)

* use poetry instead of pip/setup.py
* install poetry
* docker
* mention setuptools-scm
* test publish
* ci
* ci
* Update main.yml
* ci
* Merge branch 'poetry' of github.com:scalableminds/webknossos-cuber into poetry
* publish