Add docker and solution to vectorfield error #7
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| # Registrationtools docker | ||
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| The dockerfile makes an image that contains a set of relevant packages for image registration in python. | ||
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| The relevant packages for image registration that contains are: | ||
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| - [`registrationtools`](https://github.com/GuignardLab/registration-tools): This package | ||
| - [`vt-python`](https://gitlab.inria.fr/morpheme/vt-python): Original package over which this package makes a wrapper. | ||
| - [`SimpelITK`](https://simpleitk.org/): Classical package for image registration, wrapper over the ITK package. | ||
| - [`skimage`](https://scikit-image.org/): Well-stablished package for image manipulation in python based on numpy. | ||
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| In addition to these packages, other packages are installed (e.g. numpy, matplotlib...). A list can be seen in environment.yaml. | ||
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| Constructed images are already deposited in [dsblab/registrationtools](https://hub.docker.com/repository/docker/dsblab/registrationtools), so there is not need of building the image except if you want to extend further capabilities. | ||
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| # Running the image | ||
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| ## Interactive Shell | ||
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| Start the container in interactive format. | ||
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| ```shell | ||
| docker run -it \ | ||
| --mount type=bind,source="$(pwd)",target=/home \ | ||
| dsblab/registrationtools:v0.1 | ||
| ``` | ||
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| Activate the conda image. | ||
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| ```shell | ||
| source activate registration | ||
| cd home | ||
| ``` | ||
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| And now all the packages and modules will be loaded. You can start a python shell: | ||
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| ```shell | ||
| python | ||
| ``` | ||
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| or execute packages installed from the command line (e.g. blockmatching) | ||
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| ```shell | ||
| blockmatching -h | ||
| ``` | ||
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| ## Script | ||
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| To execute directly a bash script simply | ||
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| ```shell | ||
| docker run \ | ||
| --mount type=bind,source="$(pwd)",target=/home \ | ||
| dsblab/registrationtools:v0.1 /bin/bash -c "source activate registration: cd home; <bash_script.sh>" | ||
| ``` | ||
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| and a python script | ||
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| ```shell | ||
| docker run \ | ||
| --mount type=bind,source="$(pwd)",target=/home \ | ||
| dsblab/registrationtools:v0.1 /bin/bash -c "source activate registration; cd home; python <python_script.py>" | ||
| ``` | ||
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| ## Jupyter lab | ||
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| If you want to work interactively with a jupyter notebook. | ||
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| ```shell | ||
| docker run -it \ | ||
| -p 8888:8888 \ | ||
| --mount type=bind,source="$(pwd)",target=/home \ | ||
| dsblab/registrationtools:v0.1 /bin/bash -c "jupyter lab --notebook-dir=/home --ip='*' --port=8888 --allow-root" | ||
| ``` | ||
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| You can then view the Jupyter Notebook by opening http://localhost:8888 in your browser, or http://<DOCKER-MACHINE-IP>:8888 if you are using a Docker. |
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| #!/bin/bash | ||
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| version=v0.1 | ||
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| docker build . -t dsblab/registrationtools:$version | ||
| docker push dsblab/registrationtools:$version |
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| FROM continuumio/miniconda3:4.12.0 | ||
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| RUN apt-get update | ||
| COPY environment.yaml . | ||
| RUN conda install cmake make | ||
| RUN apt-get install g++ gcc -y | ||
| RUN conda env create -f environment.yaml | ||
| RUN pip install git+https://github.com/GuignardLab/registration-tools |
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| name: registration | ||
| channels: | ||
| - morpheme | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=conda_forge | ||
| - _openmp_mutex=4.5=2_gnu | ||
| - ca-certificates=2024.6.2=hbcca054_0 | ||
| - ld_impl_linux-64=2.38=h1181459_1 | ||
| - libblas=3.9.0=22_linux64_openblas | ||
| - libcblas=3.9.0=22_linux64_openblas | ||
| - libffi=3.4.4=h6a678d5_1 | ||
| - libgcc=7.2.0=h69d50b8_2 | ||
| - libgcc-ng=13.2.0=h77fa898_13 | ||
| - libgfortran-ng=13.2.0=h69a702a_13 | ||
| - libgfortran5=13.2.0=h3d2ce59_13 | ||
| - libgomp=13.2.0=h77fa898_13 | ||
| - liblapack=3.9.0=22_linux64_openblas | ||
| - libopenblas=0.3.27=pthreads_h413a1c8_0 | ||
| - libstdcxx-ng=13.2.0=hc0a3c3a_13 | ||
| - libzlib=1.2.13=h4ab18f5_6 | ||
| - ncurses=6.4=h6a678d5_0 | ||
| - openssl=3.3.1=h4ab18f5_1 | ||
| - pip=24.0=py39h06a4308_0 | ||
| - pybind11=2.9.2=py39hf939315_1 | ||
| - pybind11-global=2.9.2=py39hf939315_1 | ||
| - python=3.9.19=h955ad1f_1 | ||
| - python_abi=3.9=2_cp39 | ||
| - readline=8.2=h5eee18b_0 | ||
| - setuptools=69.5.1=py39h06a4308_0 | ||
| - sqlite=3.45.3=h5eee18b_0 | ||
| - tk=8.6.14=h39e8969_0 | ||
| - vt=1.0.0=h3fd9d12_0 | ||
| - wheel=0.43.0=py39h06a4308_0 | ||
| - xtensor=0.24.0=h4bd325d_0 | ||
| - xtensor-python=0.26.0=py39h5472131_1 | ||
| - xtl=0.7.4=h4bd325d_0 | ||
| - xz=5.4.6=h5eee18b_1 | ||
| - zlib=1.2.13=h4ab18f5_6 | ||
| - pip: | ||
| - 3d-registration @ git+https://github.com/GuignardLab/registration-tools | ||
| - anyio==4.4.0 | ||
| - argon2-cffi==23.1.0 | ||
| - argon2-cffi-bindings==21.2.0 | ||
| - arrow==1.3.0 | ||
| - asttokens==2.4.1 | ||
| - async-lru==2.0.4 | ||
| - attrs==23.2.0 | ||
| - babel==2.15.0 | ||
| - beautifulsoup4==4.12.3 | ||
| - bleach==6.1.0 | ||
| - certifi==2024.6.2 | ||
| - cffi==1.16.0 | ||
| - charset-normalizer==3.3.2 | ||
| - comm==0.2.2 | ||
| - contourpy==1.2.1 | ||
| - cycler==0.12.1 | ||
| - debugpy==1.8.2 | ||
| - decorator==5.1.1 | ||
| - defusedxml==0.7.1 | ||
| - ensure==1.0.4 | ||
| - exceptiongroup==1.2.1 | ||
| - executing==2.0.1 | ||
| - fastjsonschema==2.20.0 | ||
| - fonttools==4.53.0 | ||
| - fqdn==1.5.1 | ||
| - h11==0.14.0 | ||
| - h5py==3.11.0 | ||
| - httpcore==1.0.5 | ||
| - httpx==0.27.0 | ||
| - idna==3.7 | ||
| - imageio==2.34.2 | ||
| - importlib-metadata==8.0.0 | ||
| - importlib-resources==6.4.0 | ||
| - ipykernel==6.29.4 | ||
| - ipython==8.18.1 | ||
| - ipywidgets==8.1.3 | ||
| - isoduration==20.11.0 | ||
| - jedi==0.19.1 | ||
| - jinja2==3.1.4 | ||
| - json5==0.9.25 | ||
| - jsonpointer==3.0.0 | ||
| - jsonschema==4.22.0 | ||
| - jsonschema-specifications==2023.12.1 | ||
| - jupyter==1.0.0 | ||
| - jupyter-client==8.6.2 | ||
| - jupyter-console==6.6.3 | ||
| - jupyter-core==5.7.2 | ||
| - jupyter-events==0.10.0 | ||
| - jupyter-lsp==2.2.5 | ||
| - jupyter-server==2.14.1 | ||
| - jupyter-server-terminals==0.5.3 | ||
| - jupyterlab==4.2.3 | ||
| - jupyterlab-pygments==0.3.0 | ||
| - jupyterlab-server==2.27.2 | ||
| - jupyterlab-widgets==3.0.11 | ||
| - kiwisolver==1.4.5 | ||
| - lab==8.2 | ||
| - lazy-loader==0.4 | ||
| - markupsafe==2.1.5 | ||
| - matplotlib==3.9.0 | ||
| - matplotlib-inline==0.1.7 | ||
| - mistune==3.0.2 | ||
| - nbclient==0.10.0 | ||
| - nbconvert==7.16.4 | ||
| - nbformat==5.10.4 | ||
| - nest-asyncio==1.6.0 | ||
| - networkx==3.2.1 | ||
| - notebook==7.2.1 | ||
| - notebook-shim==0.2.4 | ||
| - numpy==1.23.0 | ||
| - overrides==7.7.0 | ||
| - packaging==24.1 | ||
| - pandas==2.2.2 | ||
| - pandocfilters==1.5.1 | ||
| - parso==0.8.4 | ||
| - patsy==0.5.6 | ||
| - pexpect==4.9.0 | ||
| - pillow==10.3.0 | ||
| - platformdirs==4.2.2 | ||
| - prometheus-client==0.20.0 | ||
| - prompt-toolkit==3.0.47 | ||
| - psutil==6.0.0 | ||
| - ptyprocess==0.7.0 | ||
| - pure-eval==0.2.2 | ||
| - pycparser==2.22 | ||
| - pygments==2.18.0 | ||
| - pyparsing==3.1.2 | ||
| - python-dateutil==2.9.0.post0 | ||
| - python-json-logger==2.0.7 | ||
| - pytz==2024.1 | ||
| - pyyaml==6.0.1 | ||
| - pyzmq==26.0.3 | ||
| - qtconsole==5.5.2 | ||
| - qtpy==2.4.1 | ||
| - referencing==0.35.1 | ||
| - requests==2.32.3 | ||
| - rfc3339-validator==0.1.4 | ||
| - rfc3986-validator==0.1.1 | ||
| - rpds-py==0.18.1 | ||
| - scikit-image==0.24.0 | ||
| - scipy==1.13.1 | ||
| - send2trash==1.8.3 | ||
| - simpleitk==2.3.1 | ||
| - simplejson==3.19.2 | ||
| - six==1.16.0 | ||
| - sniffio==1.3.1 | ||
| - soupsieve==2.5 | ||
| - stack-data==0.6.3 | ||
| - statsmodels==0.14.2 | ||
| - terminado==0.18.1 | ||
| - tifffile==2024.6.18 | ||
| - tinycss2==1.3.0 | ||
| - tomli==2.0.1 | ||
| - tornado==6.4.1 | ||
| - traitlets==5.14.3 | ||
| - transforms3d==0.4.2 | ||
| - txt2tags==3.9 | ||
| - types-python-dateutil==2.9.0.20240316 | ||
| - typing-extensions==4.12.2 | ||
| - tzdata==2024.1 | ||
| - uri-template==1.3.0 | ||
| - urllib3==2.2.2 | ||
| - vtpython @ git+https://gitlab.inria.fr/morpheme/vt-python@122be17b2a25641a982649d54c17434e46989706 | ||
| - wcwidth==0.2.13 | ||
| - webcolors==24.6.0 | ||
| - webencodings==0.5.1 | ||
| - websocket-client==1.8.0 | ||
| - widgetsnbextension==4.0.11 | ||
| - zipp==3.19.2 |
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| name: registrationtools | ||
| channels: | ||
| - morpheme | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=conda_forge | ||
| - _openmp_mutex=4.5=2_gnu | ||
| - bzip2=1.0.8=hd590300_5 | ||
| - ca-certificates=2024.2.2=hbcca054_0 | ||
| - ld_impl_linux-64=2.40=h41732ed_0 | ||
| - libblas=3.9.0=22_linux64_openblas | ||
| - libcblas=3.9.0=22_linux64_openblas | ||
| - libffi=3.4.2=h7f98852_5 | ||
| - libgcc-ng=13.2.0=h807b86a_5 | ||
| - libgfortran-ng=13.2.0=h69a702a_5 | ||
| - libgfortran5=13.2.0=ha4646dd_5 | ||
| - libgomp=13.2.0=h807b86a_5 | ||
| - liblapack=3.9.0=22_linux64_openblas | ||
| - libnsl=2.0.1=hd590300_0 | ||
| - libopenblas=0.3.27=pthreads_h413a1c8_0 | ||
| - libsqlite=3.45.3=h2797004_0 | ||
| - libstdcxx-ng=13.2.0=h7e041cc_5 | ||
| - libuuid=2.38.1=h0b41bf4_0 | ||
| - libxcrypt=4.4.36=hd590300_1 | ||
| - libzlib=1.2.13=hd590300_5 | ||
| - ncurses=6.4.20240210=h59595ed_0 | ||
| - numpy=1.26.4=py39h474f0d3_0 | ||
| - openssl=3.2.1=hd590300_1 | ||
| - pip=24.0=pyhd8ed1ab_0 | ||
| - pybind11=2.12.0=py39h7633fee_0 | ||
| - pybind11-global=2.12.0=py39h7633fee_0 | ||
| - python=3.9.19=h0755675_0_cpython | ||
| - python_abi=3.9=4_cp39 | ||
| - readline=8.2=h8228510_1 | ||
| - setuptools=69.5.1=pyhd8ed1ab_0 | ||
| - tk=8.6.13=noxft_h4845f30_101 | ||
| - vt=1.0.0=h3fd9d12_0 | ||
| - vt-python=1.1.0=py39h3fd9d12_5 | ||
| - wheel=0.43.0=pyhd8ed1ab_1 | ||
| - xtensor=0.24.0=h4bd325d_0 | ||
| - xtensor-python=0.26.0=py39h5472131_1 | ||
| - xtl=0.7.4=h4bd325d_0 | ||
| - xz=5.2.6=h166bdaf_0 | ||
| - zlib=1.2.13=hd590300_5 | ||
| - pip: | ||
| - 3d-registration==0.5.2 | ||
| - contourpy==1.2.1 | ||
| - cycler==0.12.1 | ||
| - ensure==1.0.4 | ||
| - fonttools==4.51.0 | ||
| - h5py==3.11.0 | ||
| - imageio==2.34.0 | ||
| - importlib-resources==6.4.0 | ||
| - kiwisolver==1.4.5 | ||
| - lazy-loader==0.4 | ||
| - matplotlib==3.8.4 | ||
| - networkx==3.2.1 | ||
| - packaging==24.0 | ||
| - pandas==2.2.2 | ||
| - patsy==0.5.6 | ||
| - pillow==10.3.0 | ||
| - pyparsing==3.1.2 | ||
| - python-dateutil==2.9.0.post0 | ||
| - pytz==2024.1 | ||
| - scikit-image==0.22.0 | ||
| - scipy==1.13.0 | ||
| - simpleitk==2.3.1 | ||
| - six==1.16.0 | ||
| - statsmodels==0.14.2 | ||
| - tifffile==2024.4.18 | ||
| - transforms3d==0.4.1 | ||
| - tzdata==2024.1 | ||
| - zipp==3.18.1 |
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Not that it's necessary wrong but it looks like a very long list of dependencies like for example is
networkxreally necessary?But anyway, since it's already built it does not matter too much.
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This is just because
skimageis installed.I added some aditional basic packages to help visualizing the results and working around with the data (
matplotlib,scikitimage), an those installed all the rest (networkxfor example is a installed byscikitimage)With the docker is the same, I even installed SimpleITK to rich set os tools without having to install anything else.
Do you think a more minimalistec version with just
registrationtoolswill be better?There was a problem hiding this comment.
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Hi, yes I think that if there is no direct use of a library it's better to leave it out.
That being said, I am not super familiar with docker builds and I might be wrong