*********************************** This file contains a jupyter notebook with all the steps taken for EELS dataset clustering and dimensionality reduction techniques showcased in : Strategies for EELS data analysis. Dimensionality reduction and clustering analysis. Introducing UMAP and HDBSCAN. Authors: Javier Blanco-Portals ,Francesca Peiró and Sònia Estradé ************************************ The following libraries of python will be required (as well as an anaconda enviroment) # Name Version Build Channel algopy 0.5.7 py_0 conda-forge appdirs 1.4.3 py_1 conda-forge asciitree 0.3.3 py_2 conda-forge asteval 0.9.16 pyh5ca1d4c_0 conda-forge astroid 2.4.2 py38_0 anaconda attrs 19.3.0 py_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge blas 1.0 mkl conda-forge bleach 3.1.5 pyh9f0ad1d_0 conda-forge blosc 1.19.0 ha925a31_0 conda-forge bokeh 2.0.2 py38h32f6830_0 conda-forge brotlipy 0.7.0 py38h1e8a9f7_1000 conda-forge bzip2 1.0.8 hfa6e2cd_2 conda-forge ca-certificates 2021.5.25 haa95532_1 certifi 2021.5.30 py38haa95532_0 cffi 1.14.0 py38ha419a9e_0 conda-forge cftime 1.1.3 py38h40bdaab_0 conda-forge chardet 3.0.4 py38h32f6830_1006 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge cloudpickle 1.4.1 py_0 conda-forge colorama 0.4.3 py_0 conda-forge colorcet 2.0.1 py_0 pyviz cryptography 2.9.2 py38hba49e27_0 conda-forge curl 7.69.1 h1dcc11c_0 conda-forge cycler 0.10.0 py_2 conda-forge cython 0.29.21 py38ha925a31_0 anaconda cytoolz 0.10.1 py38hfa6e2cd_0 conda-forge dask 2.17.2 py_0 conda-forge dask-core 2.17.2 py_0 conda-forge datashader 0.11.1 pypi_0 pypi datashape 0.5.4 py_1 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge dill 0.3.2 pyh9f0ad1d_0 conda-forge distributed 2.18.0 py38h32f6830_0 conda-forge entrypoints 0.3 py38h32f6830_1001 conda-forge et_xmlfile 1.0.1 py_1001 anaconda expat 2.2.9 he025d50_2 conda-forge fastcache 1.1.0 py38h9de7a3e_1 conda-forge fasteners 0.14.1 py_3 conda-forge fastparquet 0.4.0 py38h40bdaab_0 pyviz firefox 86.0 h0e60522_0 conda-forge freetype 2.10.2 hd328e21_0 conda-forge fsspec 0.7.4 py_0 conda-forge future 0.18.2 py38h32f6830_1 conda-forge geckodriver 0.29.0 hdb13177_0 conda-forge h5py 2.10.0 nompi_py38h422b98e_102 conda-forge hdbscan 0.8.27 py38h347fdf6_0 conda-forge hdf4 4.2.13 hf8e6fe8_1003 conda-forge hdf5 1.10.5 nompi_ha405e13_1104 conda-forge heapdict 1.0.1 py_0 conda-forge holoviews 1.13.2 pyh9f0ad1d_0 conda-forge holoviz 0.11.6 pypi_0 pypi hvplot 0.6.0 pyh9f0ad1d_0 conda-forge hyperspy 1.5.2 py38h32f6830_2 conda-forge hyperspy-base 1.5.2 py38h1e8a9f7_2 conda-forge hyperspy-gui-ipywidgets 1.2 py_2 conda-forge hyperspy-gui-traitsui 1.2 py_0 conda-forge icc_rt 2019.0.0 h0cc432a_1 icu 64.2 he025d50_1 conda-forge idna 2.9 py_1 conda-forge imageio 2.8.0 py_0 conda-forge importlib-metadata 1.6.1 py38h32f6830_0 conda-forge importlib_metadata 1.6.1 0 conda-forge intel-openmp 2019.4 245 ipykernel 5.3.0 py38h5ca1d4c_0 conda-forge ipyparallel 6.3.0 py38h32f6830_0 conda-forge ipython 7.15.0 py38h32f6830_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.5.1 py_0 conda-forge isort 5.6.1 py38_0 anaconda jdcal 1.4.1 py_0 anaconda jedi 0.17.0 py38h32f6830_0 conda-forge jinja2 2.11.2 pyh9f0ad1d_0 conda-forge joblib 1.0.0 pypi_0 pypi jpeg 9d he774522_0 conda-forge json5 0.9.4 pyh9f0ad1d_0 conda-forge jsoncpp 1.8.4 h1ad3211_1002 conda-forge jsonschema 3.2.0 py38h32f6830_1 conda-forge jupyter_client 6.1.3 py_0 conda-forge jupyter_core 4.6.3 py38h32f6830_1 conda-forge jupyterlab 2.1.4 py_1 conda-forge jupyterlab_server 1.1.5 py_0 conda-forge kiwisolver 1.2.0 py38heaebd3c_0 conda-forge krb5 1.17.1 hdd46e55_0 conda-forge lazy-object-proxy 1.4.3 py38he774522_0 anaconda libblas 3.8.0 14_mkl conda-forge libcblas 3.8.0 14_mkl conda-forge libclang 9.0.1 default_hf44288c_0 conda-forge libcurl 7.69.1 h1dcc11c_0 conda-forge libiconv 1.15 hfa6e2cd_1006 conda-forge liblapack 3.8.0 14_mkl conda-forge libnetcdf 4.7.4 nompi_hc957ea6_101 conda-forge libpng 1.6.37 hfe6a214_1 conda-forge libsodium 1.0.17 h2fa13f4_0 conda-forge libssh2 1.9.0 h3235a2c_2 conda-forge libtiff 4.1.0 h885aae3_6 conda-forge libxml2 2.9.10 h5d81f1c_1 conda-forge link-traits 1.0.3 py38h32f6830_0 conda-forge llvmdev 10.0.1 2 numba llvmlite 0.34.0 pypi_0 pypi lmfit 1.0.0 py_0 conda-forge locket 0.2.0 py_2 conda-forge lz4-c 1.9.2 h62dcd97_1 conda-forge m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gmp 6.1.0 2 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 markdown 3.2.2 py_0 conda-forge markupsafe 1.1.1 py38h9de7a3e_1 conda-forge matplotlib 3.1.3 py38_0 matplotlib-base 3.1.3 py38h64f37c6_0 mccabe 0.6.1 py38_1 anaconda meshio 4.0.15 py_0 conda-forge mistune 0.8.4 py38h9de7a3e_1001 conda-forge mkl 2019.4 245 mkl-service 2.3.0 py38hfa6e2cd_0 conda-forge mkl_fft 1.1.0 py38hc8d92b1_1 conda-forge mkl_random 1.1.0 py38hf9181ef_0 monotonic 1.5 py_0 conda-forge mpmath 1.1.0 py_0 conda-forge mrcz 0.5.6 pyh9f0ad1d_1 conda-forge msgpack-python 1.0.0 py38heaebd3c_1 conda-forge msys2-conda-epoch 20160418 1 multipledispatch 0.6.0 py_0 conda-forge multiprocess 0.70.11.1 py38h294d835_1 conda-forge natsort 7.0.1 py_0 conda-forge nbconvert 5.6.1 py38h32f6830_1 conda-forge nbformat 5.0.6 py_0 conda-forge netcdf4 1.5.3 nompi_py38h5d7d79e_103 conda-forge networkx 2.4 py_1 conda-forge nodejs 14.4.0 0 conda-forge notebook 6.0.3 py38h32f6830_0 conda-forge numba 0.50.0 pypi_0 pypi numcodecs 0.7.2 py38h7ae7562_1 conda-forge numdifftools 0.9.39 py_0 conda-forge numexpr 2.7.1 py38h7ae7562_1 conda-forge numpy 1.18.1 pypi_0 pypi numpy-base 1.18.1 py38hc3f5095_1 olefile 0.46 py_0 conda-forge openpyxl 3.0.5 py_0 anaconda openssl 1.1.1k h2bbff1b_0 packaging 20.4 pyh9f0ad1d_0 conda-forge pandas 1.0.3 py38h47e9c7a_0 pandoc 2.9.2.1 0 conda-forge pandocfilters 1.4.2 py_1 conda-forge panel 0.10.0a6 py_0 pyviz/label/dev param 1.9.3 py_0 pyviz parso 0.7.0 pyh9f0ad1d_0 conda-forge partd 1.1.0 py_0 conda-forge pathos 0.2.7 pyhd3deb0d_0 conda-forge patsy 0.5.1 py_0 conda-forge pickleshare 0.7.5 py38h32f6830_1001 conda-forge pillow 7.1.2 py38h7011068_0 conda-forge pint 0.9 py38_2 conda-forge pip 20.1.1 py_1 conda-forge plotly 4.14.3 py_0 plotly pox 0.2.9 pyhd3deb0d_0 conda-forge ppft 1.6.6.3 pyhd3deb0d_0 conda-forge prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge prompt-toolkit 3.0.5 py_0 conda-forge pscript 0.7.4 pyh9f0ad1d_0 conda-forge psutil 5.7.0 py38h9de7a3e_1 conda-forge ptable 0.9.2 py_0 conda-forge pycparser 2.20 py_0 conda-forge pyct 0.4.6 py_0 pyviz pyct-core 0.4.6 py_0 pyviz pyface 7.0.0 pyh9f0ad1d_1 conda-forge pygments 2.6.1 py_0 conda-forge pylint 2.6.0 py38_0 anaconda pynndescent 0.5.2 pyh44b312d_0 conda-forge pyopenssl 19.1.0 py_1 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py38h7ae7562_3 conda-forge pyqt5-sip 4.19.18 pypi_0 pypi pyqtchart 5.12 pypi_0 pypi pyqtwebengine 5.12.1 pypi_0 pypi pyreadline 2.1 py38_1001 conda-forge pyrsistent 0.16.0 py38h9de7a3e_0 conda-forge pysocks 1.7.1 py38h32f6830_1 conda-forge python 3.8.3 cpython_h5fd99cc_0 conda-forge python-blosc 1.9.1 py38hccd8c24_0 conda-forge python-dateutil 2.8.1 py_0 conda-forge python-snappy 0.5.4 py38h9a6de72_1 conda-forge python_abi 3.8 1_cp38 conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge pyvista 0.25.3 py_0 conda-forge pyviz_comms 0.7.5 pyh9f0ad1d_0 conda-forge pywavelets 1.1.1 py38h40bdaab_1 conda-forge pywin32 227 py38hfa6e2cd_0 conda-forge pywinpty 0.5.7 py38_0 conda-forge pyyaml 5.3.1 py38h9de7a3e_0 conda-forge pyzmq 19.0.1 py38h77b9d75_0 conda-forge qt 5.12.5 h7ef1ec2_0 conda-forge requests 2.23.0 pyh8c360ce_2 conda-forge retrying 1.3.3 py_2 rise 5.6.1 py38_0 conda-forge scikit-image 0.16.2 py38he350917_0 conda-forge scikit-learn 0.23.1 py38ha1d60b4_0 conda-forge scipy 1.3.2 py38h582fac2_0 conda-forge scooby 0.5.5 pyh9f0ad1d_0 conda-forge seaborn 0.10.1 py_0 anaconda selenium 3.141.0 py38he774522_1000 send2trash 1.5.0 py_0 conda-forge setuptools 57.0.0 pypi_0 pypi six 1.15.0 pyh9f0ad1d_0 conda-forge snappy 1.1.8 ha925a31_2 conda-forge sortedcontainers 2.2.2 pyh9f0ad1d_0 conda-forge sparse 0.9.1 py_0 conda-forge sqlite 3.30.1 hfa6e2cd_0 conda-forge statsmodels 0.11.1 py38h1e8a9f7_2 conda-forge sympy 1.4 py38_0 conda-forge tbb 2020.1 he980bc4_0 conda-forge tblib 1.6.0 py_0 conda-forge terminado 0.8.3 py38h32f6830_1 conda-forge testpath 0.4.4 py_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge thrift 0.11.0 py38h6538335_1001 conda-forge tk 8.6.10 hfa6e2cd_0 conda-forge toml 0.10.1 py_0 anaconda toolz 0.10.0 py_0 conda-forge tornado 6.0.4 py38hfa6e2cd_0 conda-forge tqdm 4.46.1 pyh9f0ad1d_0 conda-forge traitlets 4.3.3 py38h32f6830_1 conda-forge traits 6.1.0 py38h1e8a9f7_0 conda-forge traitsui 7.0.0 pyh9f0ad1d_1 conda-forge typing_extensions 3.7.4.2 py_0 conda-forge uncertainties 3.1.4 py_0 conda-forge urllib3 1.25.9 py_0 conda-forge vc 14.1 h869be7e_1 conda-forge vs2015_runtime 14.16.27012 h30e32a0_2 conda-forge vtk 8.2.0 py38h64fe603_214 conda-forge wcwidth 0.2.4 pyh9f0ad1d_0 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.34.2 py_1 conda-forge widgetsnbextension 3.5.1 py38_0 conda-forge win_inet_pton 1.1.0 py38_0 conda-forge wincertstore 0.2 py38_1003 conda-forge winpty 0.4.3 4 conda-forge wrapt 1.11.2 py38he774522_0 anaconda xarray 0.15.1 py_0 conda-forge xlsxwriter 1.3.9 pyhd8ed1ab_0 conda-forge xz 5.2.5 h2fa13f4_0 conda-forge yaml 0.2.5 he774522_0 conda-forge zarr 2.5.0 py_0 conda-forge zeromq 4.3.2 h6538335_2 conda-forge zict 2.0.0 py_0 conda-forge zipp 3.1.0 py_0 conda-forge zlib 1.2.11 h2fa13f4_1006 conda-forge zstd 1.4.4 h9f78265_3 conda-forge umap