hotfix checkpoint download in docker

Merge pull request #326 from Deep-MI/hotfix/Dockerfiles_segonly_ckpt_download
Added CerebNet, removed copying empty dir and corrected ckpt downloaddir

Author: m-reuter

Docker/Dockerfile_FastSurferCNN

@@ -63,13 +63,13 @@ SHELL ["/bin/bash", "--login", "-c"]
 # Copy venv and FastSurferCNN 
 COPY --from=build /venv /venv
 COPY ./FastSurferCNN /fastsurfer/FastSurferCNN/
-COPY ./checkpoints /fastsurfer/FastSurferCNN/checkpoints/
+COPY ./CerebNet /fastsurfer/CerebNet
 COPY ./Docker/entrypoint.sh /fastsurfer/Docker/entrypoint.sh
 
 # Download all remote network checkpoints already
 ENV PYTHONPATH=/fastsurfer:$PYTHONPATH \
     MPLCONFIGDIR=/tmp
-RUN python3 /fastsurfer/FastSurferCNN/download_checkpoints.py --all; chmod +r -R /fastsurfer/FastSurferCNN/checkpoints
+RUN python3 /fastsurfer/FastSurferCNN/download_checkpoints.py --all
 
 # Set FastSurfer workdir and entrypoint
 #  the script entrypoint ensures that our conda env is active

Docker/Dockerfile_FastSurferCNN_AMD

@@ -20,13 +20,14 @@ RUN pip3 install \
 
 
 # Copy FastSurferCNN 
-COPY ./FastSurferCNN /FastSurferCNN/
+COPY ./FastSurferCNN /fastsurfer/FastSurferCNN/
+COPY ./CerebNet /fastsurfer/CerebNet
 
 # Download all remote network checkpoints already
-RUN cd /FastSurferCNN/ ; python3 download_checkpoints.py --all --vinn
+RUN python3 /fastsurfer/FastSurferCNN/download_checkpoints.py --all
 
 # Set FastSurferCNN workdir and entrypoint
 #  the script entrypoint ensures that our conda env is active
-WORKDIR "/FastSurferCNN"
-ENTRYPOINT ["python3.7", "run_prediction.py"]
+WORKDIR "/fastsurfer"
+ENTRYPOINT ["python3.7", "./FastSurferCNN/run_prediction.py"]
 CMD ["--help"]

Docker/Dockerfile_FastSurferCNN_CPU

@@ -63,13 +63,13 @@ SHELL ["/bin/bash", "--login", "-c"]
 # Copy venv and FastSurferCNN 
 COPY --from=build /venv /venv
 COPY ./FastSurferCNN /fastsurfer/FastSurferCNN/
-COPY ./checkpoints /fastsurfer/FastSurferCNN/checkpoints/
+COPY ./CerebNet /fastsurfer/CerebNet
 COPY ./Docker/entrypoint.sh /fastsurfer/Docker/entrypoint.sh
 
 # Download all remote network checkpoints already
 ENV PYTHONPATH=/fastsurfer:$PYTHONPATH \
     MPLCONFIGDIR=/tmp
-RUN python3 /fastsurfer/FastSurferCNN/download_checkpoints.py --all; chmod +r -R /fastsurfer/FastSurferCNN/checkpoints
+RUN python3 /fastsurfer/FastSurferCNN/download_checkpoints.py --all
 
 # Set FastSurfer workdir and entrypoint
 #  the script entrypoint ensures that our conda env is active