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Merged
AndrewVFranco merged 2 commits into from
Mar 27, 2026
Merged

Working branch #3

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11cc3ba
Add Dockerfile and dockerignore for inference service
AndrewVFranco Mar 27, 2026
32160d7
Update inference endpoint to accept .nii.gz uploads
AndrewVFranco Mar 27, 2026
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Binary file added .DS_Store
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Binary file added checkpoints/best_model.pth
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8 changes: 8 additions & 0 deletions docker/.dockerignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
.venv/
data/
checkpoints/
notebooks/
.git/
__pycache__/
*.pth
*.egg-info/
7 changes: 7 additions & 0 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
FROM python:3.11-slim
WORKDIR /app
COPY requirements.txt .
RUN pip install -r requirements.txt
COPY . .
EXPOSE 8000
CMD ["uvicorn", "src.inference.predict:app", "--host", "0.0.0.0", "--port", "8000"]
8 changes: 4 additions & 4 deletions src/inference/predict.py
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Expand Up @@ -40,19 +40,19 @@ async def segment(request: Request,
model = request.app.state.model
device = request.app.state.device

with tempfile.NamedTemporaryFile(suffix=".nii", delete=False) as tmp:
with tempfile.NamedTemporaryFile(suffix=".nii.gz", delete=False) as tmp:
tmp.write(await t1c.read())
t1c_path = tmp.name

with tempfile.NamedTemporaryFile(suffix=".nii", delete=False) as tmp:
with tempfile.NamedTemporaryFile(suffix=".nii.gz", delete=False) as tmp:
tmp.write(await t1n.read())
t1n_path = tmp.name

with tempfile.NamedTemporaryFile(suffix=".nii", delete=False) as tmp:
with tempfile.NamedTemporaryFile(suffix=".nii.gz", delete=False) as tmp:
tmp.write(await t2f.read())
t2f_path = tmp.name

with tempfile.NamedTemporaryFile(suffix=".nii", delete=False) as tmp:
with tempfile.NamedTemporaryFile(suffix=".nii.gz", delete=False) as tmp:
tmp.write(await t2w.read())
t2w_path = tmp.name

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