vis-workflow

Workflow visualiser: shows a bioimage workflow descriptor - Bilayers config.yaml, BIAFLOWS descriptor.json or biomero-schema JSON - as a Mermaid diagram of its inputs, parameters and outputs.

flowchart LR
  subgraph inputs["Inputs"]
    in_infolder[/"<b>Images and masks</b><br/>type: image<br/>formats: ometiff, omezarr<br/>files: multiple<br/>flag: --infolder"/]
  end
  tool[["<b>Measurements-CellProfiler</b><br/>container: cellularimagingcf/wb_measurements-cellprofiler:v2.0.0<br/>command: python /app/cellprofiler_run.py"]]
  subgraph parameters["Parameters"]
    direction LR
    param_nuclei_mask_suffix["<b>Suffix for Nuclei Mask</b><br/>_Nuclei_Mask"]
    param_cells_mask_suffix["<b>Suffix for Cells Mask</b><br/>_Cells_Mask"]
    param_aggregates_mask_suffix["<b>Suffix for Aggregates Mask</b><br/>_Aggregates_Mask"]
    param_metric_channels["<b>Channels to measure</b><br/>1,2,3"]
  end
  subgraph outputs["Outputs"]
    out_outfolder[/"<b>Measurement tables</b><br/>type: measurement<br/>formats: csv<br/>files: multiple<br/>flag: --outfolder"/]
  end
  in_infolder --> tool
  parameters -.-> tool
  tool --> out_outfolder

Loading

Web portal

Open a descriptor URL at https://nl-bioimaging.github.io/vis-workflow/?source=<url> - a file, or a GitHub repository or folder. It runs entirely in the browser (Pyodide + Mermaid); vis-workflow view <file> shows a local file in it.

Preview locally:

python web/build.py                       # wheels for Pyodide into web/wheels/
python -m http.server -d web 8001         # then open http://127.0.0.1:8001/?source=<url>
vis-workflow view config.yaml --portal http://127.0.0.1:8001/

Install

pip install -e .[test]

Usage

# SOURCE: a descriptor file, a directory/repository with descriptor.json, descriptor.yaml or config.yaml, or a URL
vis-workflow mermaid https://github.com/Cellular-Imaging-Amsterdam-UMC/cideconvolve
vis-workflow mermaid config.yaml --params all -o diagram.md   # .md gets a mermaid code block
vis-workflow convert config.yaml -o descriptor.json           # biomero-schema JSON
vis-workflow view config.yaml                                 # open in the web portal

From Python:

from vis_workflow import load_descriptor, to_mermaid

descriptor = load_descriptor(open("config.yaml", encoding="utf-8").read())
print(to_mermaid(descriptor, params="all"))

Parameter modes: all (default; Basic and Advanced boxes, each split by Bilayers section), beginner (advanced ones summarised in one node), grouped (by Bilayers section only), collapsed (one summary node), none.

Design and plans: notes/design.md, notes/todo_known_issues.md.