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#!/usr/bin/env python
"""DeepISLES adapter script for subprocess invocation.
This script runs inside the isles_ensemble conda environment (Python 3.8)
and is called by our Gradio app (Python 3.10+) via subprocess.
Usage:
conda run -n isles_ensemble python scripts/deepisles_adapter.py \
--dwi /path/to/dwi.nii.gz \
--adc /path/to/adc.nii.gz \
--output /path/to/output \
[--flair /path/to/flair.nii.gz] \
[--fast]
Note: This script intentionally uses Python 3.8 compatible syntax and
os.path functions (not pathlib) for compatibility with DeepISLES environment.
"""
import argparse
import os
import sys
# Add DeepISLES to path
sys.path.insert(0, "/app")
from src.isles22_ensemble import IslesEnsemble
def main() -> None:
"""Run DeepISLES inference with command-line arguments."""
parser = argparse.ArgumentParser(description="DeepISLES inference adapter")
parser.add_argument("--dwi", required=True, help="Path to DWI NIfTI file")
parser.add_argument("--adc", required=True, help="Path to ADC NIfTI file")
parser.add_argument("--output", required=True, help="Output directory")
parser.add_argument("--flair", default=None, help="Path to FLAIR NIfTI file")
parser.add_argument("--fast", action="store_true", help="Fast mode (SEALS only)")
parser.add_argument("--ensemble-path", default="/app", help="Path to DeepISLES repo")
args = parser.parse_args()
# Validate inputs exist (using os.path for Py3.8 compatibility)
if not os.path.exists(args.dwi): # noqa: PTH110
print(f"ERROR: DWI file not found: {args.dwi}", file=sys.stderr)
sys.exit(1)
if not os.path.exists(args.adc): # noqa: PTH110
print(f"ERROR: ADC file not found: {args.adc}", file=sys.stderr)
sys.exit(1)
if args.flair and not os.path.exists(args.flair): # noqa: PTH110
print(f"ERROR: FLAIR file not found: {args.flair}", file=sys.stderr)
sys.exit(1)
# Create output directory (using os.makedirs for Py3.8 compatibility)
os.makedirs(args.output, exist_ok=True) # noqa: PTH103
# Run inference
print("Running DeepISLES inference...")
print(f" DWI: {args.dwi}")
print(f" ADC: {args.adc}")
print(f" FLAIR: {args.flair}")
print(f" Output: {args.output}")
print(f" Fast mode: {args.fast}")
stroke_segm = IslesEnsemble()
stroke_segm.predict_ensemble(
ensemble_path=args.ensemble_path,
input_dwi_path=args.dwi,
input_adc_path=args.adc,
input_flair_path=args.flair,
output_path=args.output,
fast=args.fast,
skull_strip=False,
save_team_outputs=False,
results_mni=False,
parallelize=True,
)
print(f"DeepISLES inference complete. Output: {args.output}")
if __name__ == "__main__":
main()
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