sliding-window-inference-runner

name	sliding-window-inference-runner
description	Prototype scaffold for sliding-window volume inference interfaces. This skill demonstrates window generation, batching, aggregation, and reporting, but it does not provide production-ready checkpoint-to-model loading.
version	1.0.0
author	Medical AI Skills Team
license	MIT
tags	["inference","segmentation","sliding-window","scaffold","pytorch"]
maturity	scaffold
category	segmentation-ml
requires_extras	["core","ml"]

Sliding Window Inference Runner

Overview

This skill is a scaffold for experimenting with sliding-window inference interfaces on volumetric data. It is useful for testing data tiling, Gaussian weighting, aggregation, and CLI/report plumbing.

It is not a production-ready checkpoint-driven inference engine. External users should not treat its outputs as real model predictions.

Installation

pip install .[ml]

Dependencies:

• Python >= 3.10
• torch
• nibabel or SimpleITK for image I/O

Usage

python scripts/main.py --input IMAGE_PATH --model MODEL_PATH --output OUTPUT_PATH [OPTIONS]

Arguments

Argument	Required	Description
--input	Yes	Input image path
--model	Yes	Placeholder checkpoint path used to infer scaffold metadata
--output	Yes	Output segmentation path

Options

Option	Default	Description
--window-size	96	Sliding window size
--overlap	0.25	Window overlap ratio
--batch-size	1	Batch size
--device	cpu	Device to run the scaffold on
--report	auto	Optional JSON report path
--version	-	Show version and exit
--help	-	Show help and exit

Input Schema

Input is a 2D or 3D image plus a checkpoint-like file path. The current implementation does not reconstruct the original model architecture from the checkpoint.

Output Schema

{
  "success": true,
  "result": {
    "output_path": "segmentation.nii.gz",
    "report_path": "segmentation.json",
    "maturity": "scaffold",
    "warning": "Output was produced by a scaffold pipeline, not real checkpoint-driven inference."
  },
  "metadata": {
    "timestamp": "2024-01-15T10:30:00Z",
    "duration_ms": 500,
    "version": "1.0.0"
  }
}

Exit Codes

Code	Meaning
0	Success
1	Validation error
2	Runtime error
3	Usage error

Examples

python scripts/main.py --input image.npy --model dummy_model.pth --output scaffold_mask.npy

python scripts/main.py --input image.nii.gz --model dummy_model.pth --output scaffold_mask.nii.gz --report scaffold_report.json

References

• Sliding Window Guide
• assets/README.md

Disclaimer

For research use only. This skill is scaffold-only and does not provide production-ready medical model inference.