################################################ ######### WhatEELS beta 1.0 ######### ################################################ The current version requires the GOS databases from the GATAN digital micrograph tool These files should be locallized in a directory called: C:\Program Files (x86)\Gatan\DigitalMicrograph\EELS Reference Data\H-S GOS Tables Otherwise, WhatEELS cannot be run. ################################################################################################### DISCLAIMER This is a beta version distributed for free. There are still some stability issues that hopefully will be addressed in later versions. Feel free to contact us at jblanco@ub.edu and we will try to aid you as soon as possible ################################################################################################### The files in this folder contain all the required scripts to run the whatEELS tool in the current stable version (beta1.0) This version contains: 1- GOS surface visualization (experimental parameters effects over the GOS surface of any of the available materials) 2- Beta version of the clustering analysis tool. Only K-Means and Agglomerative (hierarchical) clustering are available. 3- NLLS tools 3.1 - Model creator (without the extra component addition) 3.2 - Results analysis The current verion (beta 1.0) does not allow (future updates will correct the known issues with this features): a - Extra components addition in the NLLS model creator (unstable for K-edges) b - Pre-analysis tools (unstable) c - Model expansion tools (unstable) d - Power-law background components (Slow and unstable. Background removal before the first elemental edge is recomended) e - Default functions for the continuum fitting (integrated X-sections functions) The current version relies on the GOS database from the GATAN Digital Micrograph ################################################################################################### Check that the following folder and files scheme is respected within the directory where the whatEELS library is stored, otherwise the program won't be able to run properly. \whatEELS | |__whatEELS_loader.py | |__\Library | |__clustering_panel_Spectrum_images.py |__clustering_panel_Spectrum_lines.py |__gos_surfaces.py |__initialization_panel.py |__interactive_NLLS_SImages.py |__interactive_NLLS_SLines.py |__main_app.py |__nlls_functions.py |__quantification_tool.py |__results_app.py |__saving_routines.py |__visual_displays.py |__\cross_sections | | | |__bethe_surface_caluclations.py | |__geometric_X_correlation_Correction_function.py | |__gos_loader.py | |__\css | |_css_styling.css | |__\icons |__database-settings.svg |__folder-download.svg |__folder-line.svg |__folder-upload.svg |__gear.svg |__Holoviews_Bokeh_logo.svg |__Holoviews_Plotly_logo.svg |__text-document-remove.svg |__unknown-file.svg #########################################################################################3 In order to use whatEELS, follow the instructions described bellow ################### Installation Guide. ################### WhatEELS is an interactive tool based on Panel, Holoviews, Bokeh .... In order to function properly, it relies in a jupyter notebook and a python kernel running on the background. The following lines may serve the user to get whatEELS working properly in any machine. 1- Download files. The specific files for the WhatEELS library are located in the compressed Code folder. In principle, this compressed file should have a .zip format (Code.zip). If any other format is provided, we recommend the WinRAR tool to decompres them (free). 2- Setting up the Anaconda enviroment (Anaconda is recomended to manage installation of the required libraries) WhatEELS cannot be accessed through the anaconda repository of libraries. Instead, the user will be required to set up an anaconda enviroment, and them copy the downloaded whatEELS folder in that anaconda enviroment. To create and set-up the enviroment, we recommend the use of the included .yml file (whatEELS.yml) 2.1 Download Anaconda from: https://www.anaconda.com/products/individual Remember the path to the installation folder, as it will be needed to configure the enviroment examples D:\Anaconda3\ C:\Users\yourusername\Anaconda3\ 2.2 Modifying the .yml: The yml will allow anaconda to take care of the enviroment setup, but some minor changes are required to ensure a successful installation Open the whatEELS.yml file using a text editor (Sublime Text, Visual Studio Code, Atom ...) At the end of the file, localize - prefix: D:\Anaconda3\envs\whatEELS_env Change the line, so the directory where anaconda was installed is now in the prefix examples C:\Users\YourUserName\Anaconda3\envs\whatEELS_env D:\Anaconda3\envs\whatEELS_env ######################### The enviroment created will be independent from any possible previous enviroment already in your system. I you already have a pre-existing Anaconda installation, use it as the base for the enviroment creation. In principle, the changes installed by the enviroment creator will not affect the preexisting enviroments, or the base installation. This is, if you already had installed Anaconda, locate its installation folder, and use that directory as the base for the WhatEELS enviroment. Hence, modify the .yml accordingly ...\PasteYourPreviousDirectoryPath\Anaconda3\env\whatEELS_env ########################### 2.3 Enviroment creation: a - Open the anaconda prompt (In windows, write in the search bar - anaconda prompt) c - Navigate to the directory where the whatEELS.yml file is stored - Let us suppose that the .yml file is stored in C:/Users/YourUserName/Desktop/whatEELS_Files - To navigate in the Anaconda prompt (in windows also), use the following commands cd C:/Users/YourUserName/Desktop/whatEELS_Files - Then, the line in the prompt should read as (base) C:/Users/YourUserName/Desktop/whatEELS_Files> - To check if the whatEELS.yml is in fact in this directory, write the following In windows dir In Ubuntu ls and the file should then be listed bellow b- Once inside the folder containing the whatEELS.yml, and having modified that file as indicated in 2.2, to create the enviroment write conda env create -f whatEELS.yml This step may take some time, so be patient. Once completed, the enviroment is setup to support the use of WhatEELS 2.4 Copy the downloaded whatEELS folder (inside the code folder) into the enviroment created Typically, the enviroment will be stored in the env folder, inside the directory where anaconda was installed examples D:\Anaconda3\envs\whatEELS_env C:\Users\username\Anaconda3\envs\whatEELS_env Inside that folder, localize the folder called Lib examples D:\Anaconda3\envs\whatEELS_env\Lib C:\Users\username\Anaconda3\envs\whatEELS_env\Lib Paste the whatEELS folder inside this directory, and now whatEELS should work in your machine. Remember, this whatEELS folder has to be decompressed from the Code.zip file (step 1). 3 - Testing installation 3.0 Access the enviroment The library will only work in the envirment created. To lauch such enviroment, write conda activate whatEELS_env If it fails to load the enviroment, check the previous steps (something went wrong in the installation) Else, the line should now read something like (the directory may be different, depending on the Anaconda installation) (whatEELS_env) C:\Users\YourUserName> The parenthesis indicate the current enviroment activated. 3.1 Launch a jupyter notebook (from the anaconda prompt, write - jupyter notebook - or - jupyter lab -, without the hyphens) a - We recomend jupyter lab, but sometimes the notebook may be useful ... 3.2 Access the notebook provided with the rest of the libraries - WhatEELS_test_setup.ipynb 3.3 Run the notebook. The app is automatically launched when importing whatEELS from a notebook. 3.4 Test functionalities with the test_EELS-SI_CGPO.hspy file included.