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"""Direct DeepISLES invocation without Docker.
This module provides direct Python invocation of DeepISLES when running
inside the DeepISLES Docker image (e.g., on HF Spaces). This avoids
Docker-in-Docker which is not supported on HF Spaces.
Usage:
When running in HF Spaces, our container is based on isleschallenge/deepisles,
which has all DeepISLES dependencies pre-installed. This module imports
and calls DeepISLES directly.
See:
- https://github.com/ezequieldlrosa/DeepIsles
- docs/specs/07-hf-spaces-deployment.md
"""
from __future__ import annotations
import sys
import time
from dataclasses import dataclass
from pathlib import Path
from stroke_deepisles_demo.core.exceptions import DeepISLESError, MissingInputError
from stroke_deepisles_demo.core.logging import get_logger
from stroke_deepisles_demo.inference.deepisles import find_prediction_mask
logger = get_logger(__name__)
# Paths where DeepISLES source might be located in the Docker image
DEEPISLES_SEARCH_PATHS = [
"/app",
"/DeepIsles",
"/opt/deepisles",
"/home/user/DeepIsles",
]
@dataclass(frozen=True)
class DirectInvocationResult:
"""Result of direct DeepISLES invocation."""
prediction_path: Path
elapsed_seconds: float
def _ensure_deepisles_importable() -> str:
"""
Ensure DeepISLES modules are importable by adding to sys.path.
Returns:
Path where DeepISLES was found
Raises:
DeepISLESError: If DeepISLES cannot be found
"""
for path in DEEPISLES_SEARCH_PATHS:
if Path(path).exists():
if path not in sys.path:
sys.path.insert(0, path)
try:
# Test import (only available in DeepISLES Docker image)
from src.isles22_ensemble import IslesEnsemble # noqa: F401
logger.debug("Found DeepISLES at %s", path)
return path
except ImportError:
continue
raise DeepISLESError(
"DeepISLES modules not found. Direct invocation requires running "
"inside the DeepISLES Docker image. Searched paths: "
f"{DEEPISLES_SEARCH_PATHS}"
)
def validate_input_files(
dwi_path: Path,
adc_path: Path,
flair_path: Path | None = None,
) -> None:
"""
Validate that input files exist.
Args:
dwi_path: Path to DWI NIfTI file
adc_path: Path to ADC NIfTI file
flair_path: Optional path to FLAIR NIfTI file
Raises:
MissingInputError: If required files are missing
"""
if not dwi_path.exists():
raise MissingInputError(f"DWI file not found: {dwi_path}")
if not adc_path.exists():
raise MissingInputError(f"ADC file not found: {adc_path}")
if flair_path is not None and not flair_path.exists():
raise MissingInputError(f"FLAIR file not found: {flair_path}")
def run_deepisles_direct(
dwi_path: Path,
adc_path: Path,
output_dir: Path,
*,
flair_path: Path | None = None,
fast: bool = True,
skull_strip: bool = False,
parallelize: bool = True,
save_team_outputs: bool = False,
results_mni: bool = False,
) -> DirectInvocationResult:
"""
Run DeepISLES segmentation via direct Python invocation.
This function calls the DeepISLES IslesEnsemble.predict_ensemble() method
directly, bypassing Docker. It's used when running inside the DeepISLES
container on HF Spaces.
Args:
dwi_path: Path to DWI NIfTI file (b=1000)
adc_path: Path to ADC NIfTI file
output_dir: Directory for output files
flair_path: Optional path to FLAIR NIfTI file
fast: If True, use SEALS model only (faster, no FLAIR needed)
skull_strip: If True, perform skull stripping
parallelize: If True, run models in parallel
save_team_outputs: If True, save individual team outputs
results_mni: If True, output results in MNI space
Returns:
DirectInvocationResult with path to prediction mask
Raises:
DeepISLESError: If invocation fails
MissingInputError: If required input files are missing
Example:
>>> result = run_deepisles_direct(
... dwi_path=Path("/data/dwi.nii.gz"),
... adc_path=Path("/data/adc.nii.gz"),
... output_dir=Path("/data/output"),
... fast=True
... )
>>> print(result.prediction_path)
"""
start_time = time.time()
# Validate inputs
validate_input_files(dwi_path, adc_path, flair_path)
# Ensure DeepISLES is importable
deepisles_path = _ensure_deepisles_importable()
# Import DeepISLES (only available in DeepISLES Docker image)
try:
from src.isles22_ensemble import IslesEnsemble
except ImportError as e:
raise DeepISLESError(f"Failed to import DeepISLES: {e}") from e
# Create output directory
output_dir.mkdir(parents=True, exist_ok=True)
logger.info(
"Running DeepISLES direct invocation: dwi=%s, adc=%s, flair=%s, fast=%s",
dwi_path,
adc_path,
flair_path,
fast,
)
try:
# Initialize the ensemble
stroke_segm = IslesEnsemble()
# Run prediction
stroke_segm.predict_ensemble(
ensemble_path=deepisles_path,
input_dwi_path=str(dwi_path),
input_adc_path=str(adc_path),
input_flair_path=str(flair_path) if flair_path else None,
output_path=str(output_dir),
skull_strip=skull_strip,
fast=fast,
save_team_outputs=save_team_outputs,
results_mni=results_mni,
parallelize=parallelize,
)
except Exception as e:
logger.exception("DeepISLES inference failed")
raise DeepISLESError(f"DeepISLES inference failed: {e}") from e
# Find the prediction mask (using shared function from deepisles module)
prediction_path = find_prediction_mask(output_dir)
elapsed = time.time() - start_time
logger.info("DeepISLES direct invocation completed in %.2fs", elapsed)
return DirectInvocationResult(
prediction_path=prediction_path,
elapsed_seconds=elapsed,
)
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