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Merged
merged 1 commit into from
Dec 23, 2024
Merged

Infreastructure: docker modifications #59

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16 changes: 12 additions & 4 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,21 @@ FROM python:3.12 AS app

ARG APP_FOLDER=/app

COPY . ${APP_FOLDER}
RUN pip install tensorflow totalsegmentator

RUN python `python -c "import os; import totalsegmentator; print(os.path.dirname(totalsegmentator.__file__))"`/download_pretrained_weights.py

# taken from TotalSegmentator Dockerfile
# https://github.com/wasserth/TotalSegmentator/blob/master/Dockerfile
RUN apt-get update && apt-get install ffmpeg libsm6 libxext6 xvfb -y
RUN pip install fury

WORKDIR ${APP_FOLDER}

RUN pip install tensorflow
RUN pip install -r requirements.txt
COPY . ${APP_FOLDER}

RUN pip install .

COPY --from=helper /app/weights.keras ${APP_FOLDER}/checkpoints/weights.keras

CMD ["python", "./src/pancreas_ai/bin/predict.py"]
CMD ["predict"]
2 changes: 1 addition & 1 deletion src/pancreas_ai/bin/predict.py
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Expand Up @@ -36,7 +36,7 @@ def is_ct_folder_exists(self):
return True

def segment(self):
segmentation = totalsegmentator(self.ct_folder, fastest=False)
segmentation = totalsegmentator(self.ct_folder, fastest=False, verbose=True)
nib.save(segmentation, self.mask_file)

def cancer_probability(self) -> np.array:
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