Chunkflow

Breaking Changes

Deprecations

Features
- replace pillow with [pypng](https://github.com/seung-lab/chunkflow/pull/267) for faster IO of png files.
Bug Fixes

Improved Documentation

Breaking Changes

Deprecations

Features

Bug Fixes

Improved Documentation

Breaking Changes

Deprecations

Features
- add operator skip-none
- add operator read-npy
- add support to visualize points in neuroglancer
- make read-json work with bbox in task
- add operator load-synapses
- add new class of Synapses. This class will handle all the synapse operations.
Bug Fixes
- fix thresholding threshold type

Improved Documentation

Breaking Changes
- neuroglancer operator input changed from `chunk_names` to `inputs` to be consistent with other layers.
- move agglomerate operator to a plugin to remove dependency of waterz. Waterz is not easy to install in MAC os and is not currently supported in python 3.9. After this change, we should be able to support python 3.9 now.
- replaced evaluate code from waterz to gala. The evaluate code is copied from gala following the license permission. This was also got agreement from the package author [Juan](https://github.com/janelia-flyem/gala/issues/99#issuecomment-823767079)
- change default connectivity from 26 to 6 in connected-components operator
Deprecations

Features
- added synapse annotation visualization.
- add read-json operator
- The code of neuroglancer operator is splitted to functions and becomes more modular. The code is more readable and maintainable.
- add zero-filling option for load-h5 operator. If there is no such file, we fill it with zeros.
- add skip-task operator. if a result file already exists, we skip the task
- add skip-all-zero operator. if a chunk is all zero, we skip that task.
- add new patch inference backend: prebuilt. [PR](https://github.com/seung-lab/chunkflow/pull/250)
- add new operator read-json
Bug Fixes
- fix chunk transpose with None voxel size and voxel offset

Improved Documentation

Breaking Changes

Deprecations

Features
- write png files with Z corrdinate as file name
- aligned block size option for generating tasks. This is useful to force alignment of chunks, and is used to align segmentation chunks for DVID.
- add task number and current task index in global states. Thus, we know that a task could be the last one. This is useful to compute global statistics, such as maximum segmentation id in a segmentation and target indices of segmentation in DVID.
- new operators to read and write NRRD file
- add a plugin to cutout target chunk from DVID server.
Bug Fixes

Improved Documentation

Breaking Changes
- use python logging module instead of verbose parameter
- changed the `plugin` operator parameter input and output names. So it can accept both chunk and other data, such as bounding box.
- the default downsampling factor changes from (1,2,2) to (2,2,2)
- default input to plugin changed from chunk to None
Deprecations

Features
- quit neuroglancer by enter q and return.
- work with Flatiron disBatch.
- a new operator remap to renumber a serials of segmentation chunks.
- shard meshing. It is not validated yet. The data is written, but Neuroglancer is still not showing them. There is something like manifest missing.
- support downsample in Z
- support disbatch in manifest operator
- add voxel size of chunk
- automatically use chunk voxel size in neuroglancer operator
- mask out a chunk with smaller voxel size. The voxel size should be divisible though.
- plugin with bounding box and argument
- more options for generate-tasks operator
Bug Fixes
- fix manifest by updating cloud storage to CloudFiles
- fix load-h5 operator when only cutout size is provided
- fix grid size bug of generating tasks
Improved Documentation