Guide.md

Guide to Creating Scripts

Introduction

This project provides a unique opportunity for users to create their own scripts and plugins, granting additional functionality and flexibility.

Each script you create will be represented by two main files: app.py and manifest.json. app.py contains Python code that performs the task required. manifest.json is metadata describing the function, dependencies, and parameters of the script.

All scripts should be organized in their respective folders, matching the path specified in script_path.

Root manifest.json File

In the root folder of the project, there should be a manifest.json file that determines the order of script stages and their names.

Example:

{
  "name": "Segmentation",
  "description": "",
  "order": 1,
  "stages": [
    "Loading",
    "Preprocessing",
    "Cell segmentation",
    "Post processing",
    "Feature extraction"
  ]
}

Creating a Script

app.py File

The app.py file contains Python code that performs the script's functions. This file should include a run function, which takes arguments and returns a dictionary of results. The input arguments should match the parameters defined in the manifest.json file. Example of run function:

def run(**kwargs):
  # your code here
  return {'result': result}

manifest.json File

The manifest.json file describes the metadata of the script, including its function, dependencies, parameters, and returned values.

The main fields in the manifest.json file include:

• description: a brief description of the script's function.
• name: a unique name of the script.
• stage: grouping of scripts by stages (e.g., preprocessing, processing, post-processing).
• params: a dictionary of parameters that can be passed to the script. Each parameter has the following attributes:
  • name: the name of the parameter.
  • description: a description of the parameter.
  • type: the data type of the parameter.
  • hidden: if true, the parameter is hidden from the user.
  • default: the default value for the parameter.
  • required: if true, the parameter is mandatory.
• script_path: the relative path to the script directory.
• return: a dictionary of values returned by the script.
• depends_and_script: a list of scripts that must be executed before this script.
• depends_or_script: a list of scripts, one of which must be executed before this script.
• libs: a list of Python libraries required to execute the script.