Adds getting started to README and conda environment

README.md

@@ -51,4 +51,14 @@ The main folder of this repository also contains a few helper files, for example
 
 ## Data set
 
-The data set of this project is not publicly available as it contains privacy-sensitive information.
+The data set of this project is not publicly available as it contains privacy-sensitive information.
+
+## Getting started
+
+How to get the notebooks running? Assuming the raw data set and metadata is available.
+
+1. Install all Python packages required, using conda and the environment.yml file.
+2. Update the config_template.py file and rename to config.py.
+3. Use the preprocessing notebooks to process the raw data to usable data for either the ML or DL models (separate notebooks).
+4. The 'model training' notebooks can be used the train and save models.
+5. The 'model validation' notebooks can be used to assess the performance of the models.

environment.yml

@@ -0,0 +1,285 @@
+name: mne
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - appnope=0.1.0=py38h50d1736_1002
+  - apptools=4.5.0=pyh9f0ad1d_1
+  - argon2-cffi=20.1.0=py38h7e3306e_2
+  - asciitree=0.3.3=py_2
+  - async_generator=1.10=py_0
+  - attrs=20.3.0=pyhd3deb0d_0
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.6.1=py_0
+  - bleach=3.2.1=pyh9f0ad1d_0
+  - blosc=1.20.1=hb1e8313_0
+  - brotli=1.0.9=hb1e8313_3
+  - brotlipy=0.7.0=py38h94c058a_1001
+  - brunsli=0.1=hb1e8313_0
+  - bzip2=1.0.8=haf1e3a3_3
+  - c-ares=1.17.1=hc929b4f_0
+  - ca-certificates=2020.12.5=h033912b_0
+  - cached-property=1.5.1=py_0
+  - certifi=2020.12.5=py38h50d1736_1
+  - cffi=1.14.4=py38h6afc60c_0
+  - cftime=1.3.0=py38hfb243c8_0
+  - chardet=3.0.4=py38h5347e94_1008
+  - charls=2.1.0=h4a8c4bd_2
+  - cloudpickle=1.6.0=py_0
+  - configobj=5.0.6=py_0
+  - cryptography=3.2.1=py38h5c1d3f9_0
+  - curl=7.71.1=hcb81553_8
+  - cvxpy=1.1.7=py38h11c0d25_0
+  - cvxpy-base=1.1.7=py38h6be0db6_0
+  - cycler=0.10.0=py_2
+  - cytoolz=0.11.0=py38h4d0b108_1
+  - dask-core=2.30.0=py_0
+  - dbus=1.13.6=h0c50699_1
+  - decorator=4.4.2=py_0
+  - defusedxml=0.6.0=py_0
+  - dipy=1.3.0=py38hf3d72b9_1
+  - double-conversion=3.1.5=h4a8c4bd_2
+  - ecos=2.0.7.post1=py38hf3d72b9_3
+  - eigen=3.3.8=h6516342_0
+  - entrypoints=0.3=pyhd8ed1ab_1003
+  - envisage=4.9.2=pyh9f0ad1d_1
+  - expat=2.2.9=hb1e8313_2
+  - fasteners=0.14.1=py_3
+  - ffmpeg=4.3.1=he496704_1
+  - freetype=2.10.4=h3f75d11_0
+  - future=0.18.2=py38h50d1736_2
+  - gettext=0.19.8.1=haf92f58_1004
+  - giflib=5.2.1=hbcb3906_2
+  - gl2ps=1.4.2=ha233b18_0
+  - glew=2.1.0=h4a8c4bd_0
+  - glib=2.66.3=h519c658_0
+  - gmp=6.2.1=h2e338ed_0
+  - gnutls=3.6.13=h756fd2b_1
+  - hdf4=4.2.13=h84186c3_1003
+  - hdf5=1.10.6=nompi_h4444151_1111
+  - icu=67.1=hb1e8313_0
+  - idna=2.10=pyh9f0ad1d_0
+  - imagecodecs=2020.5.30=py38h5c28ed5_4
+  - imageio=2.9.0=py_0
+  - imageio-ffmpeg=0.4.2=py_0
+  - importlib-metadata=3.1.0=pyhd8ed1ab_0
+  - importlib_metadata=3.1.0=hd8ed1ab_0
+  - ipykernel=5.3.4=py38h9bb44b7_1
+  - ipython=7.19.0=py38h9bb44b7_0
+  - ipython_genutils=0.2.0=py_1
+  - ipywidgets=7.5.1=pyh9f0ad1d_1
+  - jedi=0.17.2=py38h50d1736_1
+  - jinja2=2.11.2=pyh9f0ad1d_0
+  - joblib=0.17.0=py_0
+  - jpeg=9d=hbcb3906_0
+  - jsoncpp=1.8.4=ha1b3eb9_1002
+  - jsonschema=3.2.0=py_2
+  - jupyter=1.0.0=py_2
+  - jupyter_client=6.1.7=py_0
+  - jupyter_console=6.2.0=py_0
+  - jupyter_contrib_core=0.3.3=py_2
+  - jupyter_core=4.7.0=py38h50d1736_0
+  - jupyter_nbextensions_configurator=0.4.1=py38h50d1736_2
+  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
+  - jxrlib=1.1=h0b31af3_2
+  - kiwisolver=1.3.1=py38h9250c2b_0
+  - krb5=1.17.2=h60d9502_0
+  - lame=3.100=h1de35cc_1001
+  - lcms2=2.11=h11f7e16_1
+  - lerc=2.2=hb1e8313_0
+  - libaec=1.0.4=h4a8c4bd_1
+  - libblas=3.9.0=3_openblas
+  - libcblas=3.9.0=3_openblas
+  - libclang=10.0.1=default_hf57f61e_1
+  - libcurl=7.71.1=h9bf37e3_8
+  - libcxx=11.0.0=h4c3b8ed_1
+  - libedit=3.1.20191231=h0678c8f_2
+  - libev=4.33=haf1e3a3_1
+  - libffi=3.2.1=hb1e8313_1007
+  - libgfortran=5.0.0=h7cc5361_13
+  - libgfortran5=9.3.0=h7cc5361_13
+  - libglib=2.66.3=h2575888_0
+  - libiconv=1.16=haf1e3a3_0
+  - liblapack=3.9.0=3_openblas
+  - libllvm10=10.0.1=h009f743_3
+  - libnetcdf=4.7.4=nompi_h4844aed_106
+  - libnghttp2=1.41.0=h7580e61_2
+  - libogg=1.3.2=h0b31af3_1002
+  - libopenblas=0.3.12=openmp_h54245bb_1
+  - libpng=1.6.37=h7cec526_2
+  - libpq=12.3=haa216e0_2
+  - libsodium=1.0.18=hbcb3906_1
+  - libssh2=1.9.0=h8a08a2b_5
+  - libtheora=1.1.1=haf1e3a3_1004
+  - libtiff=4.1.0=hca7d577_6
+  - libvorbis=1.3.7=h4a8c4bd_0
+  - libwebp-base=1.1.0=hbcb3906_3
+  - libxml2=2.9.10=h2c6e4a5_2
+  - libzopfli=1.0.3=h4a8c4bd_0
+  - llvm-openmp=11.0.0=h73239a0_1
+  - llvmlite=0.34.0=py38h3707e27_2
+  - loguru=0.5.3=py38h32f6830_2
+  - lz4-c=1.9.2=hb1e8313_3
+  - markupsafe=1.1.1=py38h94c058a_2
+  - matplotlib=3.3.3=py38h50d1736_0
+  - matplotlib-base=3.3.3=py38h9bfd75d_0
+  - mayavi=4.7.2=py38haf0748e_4
+  - meshio=4.3.5=pyhd8ed1ab_0
+  - mffpy=0.5.8=pyhd8ed1ab_0
+  - mistune=0.8.4=py38h7e3306e_1002
+  - mne=0.21.2=py38h50d1736_0
+  - mock=4.0.2=py38h32f6830_1
+  - monotonic=1.5=py_0
+  - msgpack-python=1.0.2=py38hd9c93a9_1
+  - mysql-common=8.0.21=2
+  - mysql-libs=8.0.21=hfb8f7af_2
+  - nbclient=0.5.1=py_0
+  - nbconvert=6.0.7=py38h50d1736_3
+  - nbformat=5.0.8=py_0
+  - ncurses=6.2=h2e338ed_4
+  - nest-asyncio=1.4.3=pyhd8ed1ab_0
+  - netcdf4=1.5.4=nompi_py38he235a2f_103
+  - nettle=3.6=hedd7734_0
+  - networkx=2.5=py_0
+  - nibabel=3.2.0=py_0
+  - nilearn=0.7.0=pyhd8ed1ab_0
+  - notebook=6.1.5=py38h50d1736_0
+  - nspr=4.29=hb1e8313_1
+  - nss=3.47=hc0980d9_0
+  - numba=0.51.2=py38h6be0db6_0
+  - numcodecs=0.7.3=py38h23ab428_0
+  - numexpr=2.7.1=py38h6be0db6_3
+  - olefile=0.46=pyh9f0ad1d_1
+  - openh264=2.1.1=hd174df1_0
+  - openjpeg=2.3.1=h254dc36_3
+  - openssl=1.1.1k=h0d85af4_0
+  - osqp=0.6.1=py38h5fc983b_2
+  - packaging=20.4=pyh9f0ad1d_0
+  - pandas=1.1.4=py38hcf432d8_0
+  - pandoc=2.11.2=hc929b4f_0
+  - pandocfilters=1.4.2=py_1
+  - parso=0.7.1=pyh9f0ad1d_0
+  - patsy=0.5.1=py_0
+  - pcre=8.44=hb1e8313_0
+  - pexpect=4.8.0=pyh9f0ad1d_2
+  - pickleshare=0.7.5=py_1003
+  - pillow=8.0.1=py38h565d989_0
+  - proj=7.1.1=h45baca5_3
+  - prometheus_client=0.9.0=pyhd3deb0d_0
+  - prompt-toolkit=3.0.8=pyha770c72_0
+  - prompt_toolkit=3.0.8=hd8ed1ab_0
+  - psutil=5.7.3=py38h94c058a_0
+  - ptyprocess=0.6.0=py_1001
+  - pugixml=1.10=hb1e8313_1
+  - pycparser=2.20=pyh9f0ad1d_2
+  - pydicom=2.1.0=pyhd3deb0d_0
+  - pyface=7.1.0=pyh9f0ad1d_0
+  - pygments=2.7.2=py_0
+  - pyopenssl=19.1.0=py_1
+  - pyparsing=2.4.7=pyh9f0ad1d_0
+  - pyqt=5.12.3=py38hca2ab18_4
+  - pyrsistent=0.17.3=py38h7e3306e_1
+  - pysocks=1.7.1=py38h5347e94_2
+  - pysurfer=0.11.0=py_0
+  - pytables=3.6.1=py38h4e4ac5c_3
+  - python=3.8.6=hcfdab8c_0_cpython
+  - python-dateutil=2.8.1=py_0
+  - python-picard=0.4=pyh5ca1d4c_1
+  - python_abi=3.8=1_cp38
+  - pytz=2020.4=pyhd8ed1ab_0
+  - pyvista=0.27.2=pyhd8ed1ab_0
+  - pyvistaqt=0.2.0=py_0
+  - pywavelets=1.1.1=py38h174b24a_3
+  - pyyaml=5.3.1=py38h94c058a_1
+  - pyzmq=20.0.0=py38h9b3f83f_1
+  - qt=5.12.9=h717870c_0
+  - qtconsole=5.0.1=pyhd8ed1ab_0
+  - qtpy=1.9.0=py_0
+  - readline=8.0=h0678c8f_2
+  - requests=2.25.0=pyhd3deb0d_0
+  - scikit-image=0.17.2=py38hcf432d8_4
+  - scikit-learn=0.23.2=py38h740a60c_3
+  - scipy=1.5.3=py38hb6cd474_0
+  - scooby=0.5.6=pyh9f0ad1d_0
+  - scs=2.1.2=py38hd88393d_2
+  - seaborn=0.11.1=pyhd3eb1b0_0
+  - send2trash=1.5.0=py_0
+  - setuptools=49.6.0=py38h5347e94_2
+  - six=1.15.0=pyh9f0ad1d_0
+  - snappy=1.1.8=hb1e8313_3
+  - spyder-kernels=1.10.0=py38h50d1736_0
+  - sqlite=3.33.0=h960bd1c_1
+  - statsmodels=0.12.1=py38hfb243c8_1
+  - tbb=2019.9=ha1b3eb9_1
+  - tbb-devel=2019.9=ha1b3eb9_1
+  - terminado=0.9.1=py38h50d1736_1
+  - testpath=0.4.4=py_0
+  - threadpoolctl=2.1.0=pyh5ca1d4c_0
+  - tifffile=2020.11.18=pyhd8ed1ab_0
+  - tk=8.6.10=hb0a8c7a_1
+  - toolz=0.11.1=py_0
+  - tornado=6.1=py38h7e3306e_0
+  - tqdm=4.53.0=pyhd8ed1ab_1
+  - traitlets=5.0.5=py_0
+  - traits=6.1.1=py38h7e3306e_0
+  - traitsui=7.1.0=pyh9f0ad1d_0
+  - urllib3=1.25.11=py_0
+  - utfcpp=3.1.2=0
+  - vtk=9.0.1=no_osmesa_py38h523a0c9_102
+  - wcwidth=0.2.5=pyh9f0ad1d_2
+  - webencodings=0.5.1=py_1
+  - wheel=0.35.1=pyh9f0ad1d_0
+  - widgetsnbextension=3.5.1=py38h50d1736_4
+  - wurlitzer=2.0.0=py38h32f6830_2
+  - x264=1!152.20180806=h1de35cc_0
+  - xlrd=1.2.0=pyh9f0ad1d_1
+  - xz=5.2.5=haf1e3a3_1
+  - yaml=0.2.5=haf1e3a3_0
+  - zarr=2.7.0=pyhd8ed1ab_0
+  - zeromq=4.3.3=h74dc148_3
+  - zfp=0.5.5=hb1e8313_4
+  - zipp=3.4.0=py_0
+  - zlib=1.2.11=h7795811_1010
+  - zstd=1.4.5=h289c70a_2
+  - pip:
+    - absl-py==0.11.0
+    - astunparse==1.6.3
+    - autoreject==0.2.2
+    - cachetools==4.1.1
+    - flatbuffers==1.12
+    - gast==0.3.3
+    - google-auth==1.23.0
+    - google-auth-oauthlib==0.4.2
+    - google-pasta==0.2.0
+    - grpcio==1.32.0
+    - h5py==2.10.0
+    - keras-preprocessing==1.1.2
+    - markdown==3.3.3
+    - mne-features==0.1
+    - numpy==1.19.5
+    - oauthlib==3.1.0
+    - opt-einsum==3.3.0
+    - pip==21.0.1
+    - protobuf==3.14.0
+    - pyasn1==0.4.8
+    - pyasn1-modules==0.2.8
+    - pyqt5-sip==4.19.18
+    - pyqtchart==5.12
+    - pyqtwebengine==5.12.1
+    - requests-oauthlib==1.3.0
+    - rsa==4.6
+    - scikit-rvm==0.1.0a1
+    - sklearn-rvm==0.1.1
+    - tensorboard==2.4.1
+    - tensorboard-plugin-wit==1.7.0
+    - tensorflow==2.4.1
+    - tensorflow-addons==0.11.2
+    - tensorflow-estimator==2.4.0
+    - termcolor==1.1.0
+    - tf-estimator-nightly==2.5.0.dev2020123101
+    - typeguard==2.10.0
+    - typing-extensions==3.7.4.3
+    - werkzeug==1.0.1
+    - wrapt==1.12.1