TensorSwitch

This package provides a unified entry point and organized task modules for managing N5/Zarr dataset conversions and downsampling. It centralizes your workflow into a single pipeline to reduce manual work and errors.

Folder Structure

tensorswitch/
├── pixi.lock
├── pyproject.toml
├── README.md
├── src
│   └── tensorswitch
│       ├── __init__.py
│       ├── __main__.py # Main dispatcher script
│       ├── tasks
│       │   ├── __init__.py
│       │   ├── downsample_shard_zarr3.py # Downsample using shards
│       │   ├── n5_to_n5.py # N5 to N5 conversion logic
│       │   ├── n5_to_zarr2.py # N5 to Zarr V2 conversion logic
│       └── utils.py # Common utilities (chunk domain calculation)
└── tests
    ├── test_n5_to_n5.py
    ├── test_n5_to_zarr2.py
    ├── test_n5_to_zarr3_downsample_shard.py
    ├── test_zarr3_to_downsample_noshard_zarr3.py
    └── test_zarr3_to_downsample_shard_zarr3.py

Installation

Pip

pip install git+https://github.com/JaneliaSciComp/tensorswitch

Pixi

pixi add python
pixi add --pypi "tensorswitch @ git+https://github.com/JaneliaSciComp/tensorswitch"

How to Use

1. Run the Main Pipeline

Use the python -m tensorswitch as the entry point. Example:

python -m tensorswitch --task n5_to_zarr2     --base_path /path/to/n5     --output_path /path/to/zarr2     --level 0

2. Supported Tasks

Task Name	Description
n5_to_zarr2	Convert N5 to Zarr V2
n5_to_n5	Convert N5 to N5 (new chunking)
downsample_zarr	Downsample existing Zarr dataset
submit_downsample	Submit downsampling jobs to the cluster
submit_n5_zarr	Submit N5 to Zarr jobs to the cluster
submit_n5_n5	Submit N5 to N5 jobs to the cluster

3. Example Commands

Convert N5 to Zarr V2 locally

python -m tensorswitch --task n5_to_zarr2     --base_path /path/to/n5     --output_path /path/to/zarr2     --level 0

Downsample Zarr locally

python -m tensorswitch  --task downsample_zarr     --base_path /path/to/zarr     --level 1     --use_shard 1

Submit N5 to Zarr jobs to cluster

python -m tensorswitch --task submit_n5_zarr

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Requirements

• Python 3.10+
• TensorStore
• NumPy
• psutil
• requests (for N5 over HTTP)

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Support

If you need more enhancements (like adding logging or progress tracking), feel free to extend the tasks modules.

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