webknossos-libs

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## Detailed Description - Affected library: e.g. webknossos - The current default PIMS reader for tiff image files, does not provide all information about additional axes in the PIMS specific...

markbader

### Description: - abc ### Issues: - fixes #... ### Todos: Make sure to delete unnecessary points or to check all before merging: - [ ] Updated Changelog - [...

normanrz

wk.Annotation constructor should require organization name

2

When creating a new annotation via `a = wk.Annotation(name, dataset_name=dataset_name, voxel_size=voxel_size)` it should be required to pass an organization name for the specified dataset to avoid ambiguity. Otherwise during upload...

fm3

## Detailed Description - Affected library: webknossos - Functionality is currently implemented in the CLI merge_fallback.py file. It should be moved to a well fitting place within the libs.

markbader

Disable `boto` logging in tests

1

## Detailed Description - Affected library: e.g. webknossos The `boto` library spams our logs when running the tests. We should tune the logger to only include warnings/errors. Example: https://github.com/scalableminds/webknossos-libs/actions/runs/7917874379/job/21615004914

hotzenklotz

## Context - Affected library: webknossos python library I was trying to create a segmentation dataset from tiff images. For this, I created grayscale png files and converted them to...

frcroth

## Context - Affected library: webknossos When using the webknossos CLI to download an annotation, the download command is overloaded to take care of dataset downloads and annotation downloads. An...

markbader

Hi, I tried to upload annotations with a `fallback_layer` included: ```python # test.py import webknossos as wk fallback_layer = wk.Dataset\ .open_remote('https://webknossos.org/datasets/Demo_Organization/kasthuri2011')\ .get_segmentation_layers()[0] annotation = wk.Annotation( name="test_annotation", dataset_name = fallback_layer.dataset.name, voxel_size...

erjel

## Detailed Description At the moment, the BufferedSliceWriter has to be instantiated with a z offset which cannot be changed afterwards. Changing the z offset after instantiation should be possible,...

philippotto

docs imprecise: temporary_volume_layer_copy doesn't return an iterable

2

the documentation says it should return an iterable https://docs.webknossos.org/api/webknossos/annotation/annotation.html#Annotation.temporary_volume_layer_copy ``` print(hasattr(a.temporary_volume_layer_copy('Volume'),'__iter__')) -> False ```

boergens