Commit a5cb2b75 authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

updated doc

parent 87e3854a
......@@ -9,15 +9,15 @@
<title>404 Page not found</title>
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......
......@@ -12,20 +12,20 @@
<title>Capabilities :: Documentation for Hugo Learn Theme</title>
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<script src="/js/jquery-3.3.1.min.js?1622743956"></script>
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<style>
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1622743956"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622743956"></script>
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......@@ -3646,19 +3646,19 @@
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<script src="/js/perfect-scrollbar.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622743956"></script>
<script src="/js/jquery.sticky.js?1622743956"></script>
<script src="/js/featherlight.min.js?1622743956"></script>
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<script src="/js/clipboard.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622746701"></script>
<script src="/js/jquery.sticky.js?1622746701"></script>
<script src="/js/featherlight.min.js?1622746701"></script>
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mermaid.initialize({ startOnLoad: true });
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......
......@@ -12,20 +12,20 @@
<title>Categories :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1622743956" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622743956" rel="stylesheet">
<link href="/css/hybrid.css?1622743956" rel="stylesheet">
<link href="/css/featherlight.min.css?1622743956" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622743956" rel="stylesheet">
<link href="/css/auto-complete.css?1622743956" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622743956" rel="stylesheet">
<link href="/css/theme.css?1622743956" rel="stylesheet">
<link href="/css/hugo-theme.css?1622743956" rel="stylesheet">
<link href="/css/nucleus.css?1622746701" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622746701" rel="stylesheet">
<link href="/css/hybrid.css?1622746701" rel="stylesheet">
<link href="/css/featherlight.min.css?1622746701" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622746701" rel="stylesheet">
<link href="/css/auto-complete.css?1622746701" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622746701" rel="stylesheet">
<link href="/css/theme.css?1622746701" rel="stylesheet">
<link href="/css/hugo-theme.css?1622746701" rel="stylesheet">
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<script src="/js/jquery-3.3.1.min.js?1622743956"></script>
<script src="/js/jquery-3.3.1.min.js?1622746701"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1622743956"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622743956"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622746701"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622746701"></script>
<script type="text/javascript">
var baseurl = "";
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<script type="text/javascript" src="/js/search.js?1622746701"></script>
</div>
......@@ -3601,19 +3601,19 @@
<div style="left: -1000px; overflow: scroll; position: absolute; top: -1000px; border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;">
<div style="border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;"></div>
</div>
<script src="/js/clipboard.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622743956"></script>
<script src="/js/jquery.sticky.js?1622743956"></script>
<script src="/js/featherlight.min.js?1622743956"></script>
<script src="/js/highlight.pack.js?1622743956"></script>
<script src="/js/clipboard.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622746701"></script>
<script src="/js/jquery.sticky.js?1622746701"></script>
<script src="/js/featherlight.min.js?1622746701"></script>
<script src="/js/highlight.pack.js?1622746701"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1622743956"></script>
<script src="/js/learn.js?1622743956"></script>
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<script src="/mermaid/mermaid.js?1622746701"></script>
<script>
mermaid.initialize({ startOnLoad: true });
</script>
......
......@@ -12,20 +12,20 @@
<title>Contacts :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1622743956" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622743956" rel="stylesheet">
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<link href="/css/perfect-scrollbar.min.css?1622743956" rel="stylesheet">
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<link href="/css/atom-one-dark-reasonable.css?1622743956" rel="stylesheet">
<link href="/css/theme.css?1622743956" rel="stylesheet">
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<link href="/css/nucleus.css?1622746701" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622746701" rel="stylesheet">
<link href="/css/hybrid.css?1622746701" rel="stylesheet">
<link href="/css/featherlight.min.css?1622746701" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622746701" rel="stylesheet">
<link href="/css/auto-complete.css?1622746701" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622746701" rel="stylesheet">
<link href="/css/theme.css?1622746701" rel="stylesheet">
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<script src="/js/jquery-3.3.1.min.js?1622743956"></script>
<script src="/js/jquery-3.3.1.min.js?1622746701"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1622743956"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622743956"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622746701"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622746701"></script>
<script type="text/javascript">
var baseurl = "";
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<script type="text/javascript" src="/js/search.js?1622743956"></script>
<script type="text/javascript" src="/js/search.js?1622746701"></script>
</div>
......@@ -3679,19 +3679,19 @@
<div style="left: -1000px; overflow: scroll; position: absolute; top: -1000px; border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;">
<div style="border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;"></div>
</div>
<script src="/js/clipboard.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622743956"></script>
<script src="/js/jquery.sticky.js?1622743956"></script>
<script src="/js/featherlight.min.js?1622743956"></script>
<script src="/js/highlight.pack.js?1622743956"></script>
<script src="/js/clipboard.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622746701"></script>
<script src="/js/jquery.sticky.js?1622746701"></script>
<script src="/js/featherlight.min.js?1622746701"></script>
<script src="/js/highlight.pack.js?1622746701"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1622743956"></script>
<script src="/js/learn.js?1622743956"></script>
<script src="/js/hugo-learn.js?1622743956"></script>
<script src="/js/modernizr.custom-3.6.0.js?1622746701"></script>
<script src="/js/learn.js?1622746701"></script>
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<script src="/mermaid/mermaid.js?1622746701"></script>
<script>
mermaid.initialize({ startOnLoad: true });
</script>
......
......@@ -12,20 +12,20 @@
<title>Frequently Asked Questions :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1622743956" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622743956" rel="stylesheet">
<link href="/css/hybrid.css?1622743956" rel="stylesheet">
<link href="/css/featherlight.min.css?1622743956" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622743956" rel="stylesheet">
<link href="/css/auto-complete.css?1622743956" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622743956" rel="stylesheet">
<link href="/css/theme.css?1622743956" rel="stylesheet">
<link href="/css/hugo-theme.css?1622743956" rel="stylesheet">
<link href="/css/nucleus.css?1622746701" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622746701" rel="stylesheet">
<link href="/css/hybrid.css?1622746701" rel="stylesheet">
<link href="/css/featherlight.min.css?1622746701" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622746701" rel="stylesheet">
<link href="/css/auto-complete.css?1622746701" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622746701" rel="stylesheet">
<link href="/css/theme.css?1622746701" rel="stylesheet">
<link href="/css/hugo-theme.css?1622746701" rel="stylesheet">
<link href="/css/theme-blue.css?1622743956" rel="stylesheet">
<link href="/css/theme-blue.css?1622746701" rel="stylesheet">
<script src="/js/jquery-3.3.1.min.js?1622743956"></script>
<script src="/js/jquery-3.3.1.min.js?1622746701"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1622743956"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622743956"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622746701"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622746701"></script>
<script type="text/javascript">
var baseurl = "";
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<script type="text/javascript" src="/js/search.js?1622743956"></script>
<script type="text/javascript" src="/js/search.js?1622746701"></script>
</div>
......@@ -4030,19 +4030,19 @@ TIFF Directory at offset 0x800008 (8388616)
<div style="left: -1000px; overflow: scroll; position: absolute; top: -1000px; border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;">
<div style="border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;"></div>
</div>
<script src="/js/clipboard.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622743956"></script>
<script src="/js/jquery.sticky.js?1622743956"></script>
<script src="/js/featherlight.min.js?1622743956"></script>
<script src="/js/highlight.pack.js?1622743956"></script>
<script src="/js/clipboard.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622746701"></script>
<script src="/js/jquery.sticky.js?1622746701"></script>
<script src="/js/featherlight.min.js?1622746701"></script>
<script src="/js/highlight.pack.js?1622746701"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1622743956"></script>
<script src="/js/learn.js?1622743956"></script>
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<script src="/js/modernizr.custom-3.6.0.js?1622746701"></script>
<script src="/js/learn.js?1622746701"></script>
<script src="/js/hugo-learn.js?1622746701"></script>
<link href="/mermaid/mermaid.css?1622743956" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1622743956"></script>
<link href="/mermaid/mermaid.css?1622746701" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1622746701"></script>
<script>
mermaid.initialize({ startOnLoad: true });
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......
......@@ -12,20 +12,20 @@
<title>Github Repositories :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1622743956" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622743956" rel="stylesheet">
<link href="/css/hybrid.css?1622743956" rel="stylesheet">
<link href="/css/featherlight.min.css?1622743956" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622743956" rel="stylesheet">
<link href="/css/auto-complete.css?1622743956" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622743956" rel="stylesheet">
<link href="/css/theme.css?1622743956" rel="stylesheet">
<link href="/css/hugo-theme.css?1622743956" rel="stylesheet">
<link href="/css/nucleus.css?1622746701" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1622746701" rel="stylesheet">
<link href="/css/hybrid.css?1622746701" rel="stylesheet">
<link href="/css/featherlight.min.css?1622746701" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1622746701" rel="stylesheet">
<link href="/css/auto-complete.css?1622746701" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1622746701" rel="stylesheet">
<link href="/css/theme.css?1622746701" rel="stylesheet">
<link href="/css/hugo-theme.css?1622746701" rel="stylesheet">
<link href="/css/theme-blue.css?1622743956" rel="stylesheet">
<link href="/css/theme-blue.css?1622746701" rel="stylesheet">
<script src="/js/jquery-3.3.1.min.js?1622743956"></script>
<script src="/js/jquery-3.3.1.min.js?1622746701"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1622743956"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622743956"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622746701"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622746701"></script>
<script type="text/javascript">
var baseurl = "";
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<script type="text/javascript" src="/js/search.js?1622746701"></script>
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......@@ -3607,19 +3607,19 @@ repositories hosting our programs</p>
<div style="left: -1000px; overflow: scroll; position: absolute; top: -1000px; border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;">
<div style="border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;"></div>
</div>
<script src="/js/clipboard.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.min.js?1622743956"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622743956"></script>
<script src="/js/jquery.sticky.js?1622743956"></script>
<script src="/js/featherlight.min.js?1622743956"></script>
<script src="/js/highlight.pack.js?1622743956"></script>
<script src="/js/clipboard.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.min.js?1622746701"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1622746701"></script>
<script src="/js/jquery.sticky.js?1622746701"></script>
<script src="/js/featherlight.min.js?1622746701"></script>
<script src="/js/highlight.pack.js?1622746701"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1622743956"></script>
<script src="/js/learn.js?1622743956"></script>
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<script src="/js/modernizr.custom-3.6.0.js?1622746701"></script>
<script src="/js/learn.js?1622746701"></script>
<script src="/js/hugo-learn.js?1622746701"></script>
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"title": "How to use the notebooks locally on your computer",
"tags": [],
"description": "",
"content": " When working with your data files we recommend\nusing the notebooks from the analysis machine but we also want to provide the flexibility of using the notebooks from your own computer, especially if you want to modify or implement new notebooks.\nWe describe here the procedure to follow to bring those notebooks from our repository to your computer and how to set up your python environment to get all the right libraries.\nInstructions We provide here two ways to install the notebooks on your computer. The easy way using Anaconda Navigator, and the hard way using command line and terminal, in case you don\u0026rsquo;t want to use anaconda.\n Easy way - Anaconda Navigator Geeky/hard/fancy way - Command line \n Easy way - Anaconda Step 1 - Download and install Anaconda Navigator Download and install the Anaconda Navigator by selecting the right version according to your operating system (OS) and following the instructions found in their web page.\nStep2 - Download the notebooks Go to the GitHub page (https://github.com/neutronimaging/python_notebooks) and click the green switch called Code and select Download ZIP\nOnce the download is done, navigate to the folder where the zip file has been created and simply double click to unzip the file. From there feel free to move that folder to its final location on your hard drive. For example, in my case, I moved it to /Users/j35/git/.\nStep 3 - Create conda environment Start the Anaconda Navigator application. From there, navigate to Environments This is where you will import the environment.yml file from the python notebook folder you just downloaded and unzipped.\n Click Import enter any string in the field Name (this won\u0026rsquo;t be used) Click the folder icon and navigate to the python notebooks folder and select the file environment.yml.\n The following animation shows you those steps\nStep 4 - Select the environment The new environment created, named neutron-imaging, should be selected by default. If not, activate it by clicking it.\nStep5 - Run the notebooks All you have to do then is launch the jupyter notebook engine. Go to the Home page and click the LAUNCH button in the jupyter notebook box.\nA browser window will show up with a list of all your files and folders. Navigate to the jupyter notebook folder you downloaded and unzip from github and go in the notebooks folder. From there, feel free to start any of the notebook!\n\n Geeky/hard/fancy way - Command line for Mac/Linux for Windows \n for Mac Step 1 - Download or clone the notebooks Select either one of the two ways to bring the notebooks to your computer\nDownload\nWe recommend using the latest tag (stable) version of the notebooks. Click either the zip or the tar.gz link.\nGo to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nClone\nOpen a terminal, move to the location where you want to clone (import) the notebooks and then type the clone command\n$ cd ~/git $ git clone https://github.com/neutronimaging/python_notebooks.git Go to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nStep 2 - Install Anaconda on your computer Anaconda is a free program that will make the installation and management of the python libraries very easy. You can install either Anaconda (the full package) or just the light version called miniconda3\nStep 3 - Create a virtual python environment A virtual python environment is like a python version running on your machine but being isolated from the rest of the system. This way anything you will do in this environment, like installing new libraries, will not affect the rest of your computer.\nIn the following example we chose neutron_imaging as the name of our virtual environment. Feel free to replace it with whatever name makes more sense to you.\nTo do so, simply type the following command on your terminal\n$ conda create -n neutron_imaging python=3 Now let\u0026rsquo;s switch to that environment\n$ conda activate neutron_imaging Step 4 - Set up environment Final step, we need to install all the librairies used by the notebooks. To do so, in your terminal, navigate to the notebooks folder your downloaded (tag version)\ncd ~/git/python_notebooks-0.1.0 and execute the installation script config_conda_env.sh\n$ bash config_conda_env.sh This will take a while!\nStep 5 - launch the notebooks Last step, start the notebooks\n$ jupyter notebook Your favorite browser will show up with the notebooks. Enjoy!\n\n for Windows Step 1 - Install Anaconda First thing to do will be do download and install anaconda. To do so, go to the anaconda download page.\nClick the Download button.\nClick the 64-Bit or 32-Bit version according to your machine.\nIf you don\u0026rsquo;t know, there is a higher chance that you are on a 64-Bit machine so give it a try. If you did not use wisely, the installation will fail and you will need to try the other version.\n Once the download of the program finished, go to your download folder and run the installer by double clicking it.\nKeep the default settings all the way by clicking next.\nStep 1 - Create conda environment Once the installation is done you will have a set of new tools in the Anaconda menu. Launch the tool called Anaconda Powershell Prompt\nThis is where we are going to import the imaging notebooks and installed the python libraries you will need to run the notebooks.\nOnce the terminal comes to life, we are going to create a folder that will contain the code to import. Let\u0026rsquo;s say we will call it git in your home folder\n$ cd ~/ $ mkdir ~/git $ cd git Now we are going to create a special python environment that will allow us to stay away from the native python of the system, this is a recommended way to work with python packages.\n$ conda create -y -n neutron_imaging python=3.7 The name of our environment is called neutron_imaging and we are telling the system to install python version 3.7\nJust let the terminal install the libraries.\nOnce the installation is done, we need to activate that environment.\n$ conda activate neutron_imaging Step 3 - Import or Clone Notebooks Select either one of the two ways to bring the notebooks to your computer\nDownload\nWe recommend using the latest tag (stable) version of the notebooks. Click either the zip or the tar.gz link.\nGo to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nClone\nOpen a terminal, move to the location where you want to clone (import) the notebooks and then type the clone command\n$ cd ~/git $ git clone https://github.com/neutronimaging/python_notebooks.git Go to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nStep 4 - Import all libraries Now in the anaconda power shell terminal, import all the librairies by typing\n$ conda update -y -n base -c defaults conda $ conda install -y requests requests-oauthlib numpy scipy pandas scikit-image matplotlib plotly $ conda install -y nodejs qtpy pyqtgraph astropy $ conda install -y -c conda-forge ipywe lmfit $ pip install neutronbraggedge NeuNorm sectorizedradialprofile inflect ImagingReso ipywidgets $ pip install https://oncat.ornl.gov/packages/pyoncat-1.4.1-py3-none-any.whl $ jupyter labextension install @jupyter-widgets/jupyterlab-manager $ jupyter nbextension enable --py widgetsnbextension $ jupyter lab build You can now launch the Anaconda Navigator and select the environment you created and called neutron_imaging.\nNow you can go back to the HOME menu within the Anaconda Navigator and launch the Jupyter notebooks.\nFrom there, navigate to the folder ~/git/python_notebooks/notebooks/ to get access to all the notebooks!\n"
"content": " When working with your data files we recommend\nusing the notebooks from the analysis machine but we also want to provide the flexibility of using the notebooks from your own computer, especially if you want to modify or implement new notebooks.\nWe describe here the procedure to follow to bring those notebooks from our repository to your computer and how to set up your python environment to get all the right libraries.\nInstructions We provide here two ways to install the notebooks on your computer. The easy way using Anaconda Navigator, and the hard way using command line and terminal, in case you don\u0026rsquo;t want to use anaconda.\n Easy way - Anaconda Navigator Geeky/hard/fancy way - Command line \n Easy way - Anaconda Step 1 - Download and install Anaconda Navigator Download and install the Anaconda Navigator by selecting the right version according to your operating system (OS) and following the instructions found in their web page.\nStep2 - Download the notebooks Go to the GitHub page (https://github.com/neutronimaging/python_notebooks) and click the green switch called Code and select Download ZIP\nOnce the download is done, navigate to the folder where the zip file has been created and simply double click to unzip the file. From there feel free to move that folder to its final location on your hard drive. For example, in my case, I moved it to /Users/j35/git/.\nStep 3 - Create conda environment Start the Anaconda Navigator application. From there, navigate to Environments This is where you will import the environment.yml file from the python notebook folder you just downloaded and unzipped.\n Click Import No need to enter any text in the name field. This field will be populated automatically once you have selected the file (see next line). Click the folder icon and navigate to the python notebooks folder and select the file environment.yml.\n The following animation shows you those steps\nStep 4 - Select the environment The new environment created, named neutron-imaging, should be selected by default. If not, activate it by clicking it.\nStep5 - Run the notebooks All you have to do then is launch the jupyter notebook engine. Go to the Home page and click the LAUNCH button in the jupyter notebook box.\nA browser window will show up with a list of all your files and folders. Navigate to the jupyter notebook folder you downloaded and unzip from github and go in the notebooks folder. From there, feel free to start any of the notebook!\n\n Geeky/hard/fancy way - Command line for Mac/Linux for Windows \n for Mac Step 1 - Download or clone the notebooks Select either one of the two ways to bring the notebooks to your computer\nDownload\nWe recommend using the latest tag (stable) version of the notebooks. Click either the zip or the tar.gz link.\nGo to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nClone\nOpen a terminal, move to the location where you want to clone (import) the notebooks and then type the clone command\n$ cd ~/git $ git clone https://github.com/neutronimaging/python_notebooks.git Go to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nStep 2 - Install Anaconda on your computer Anaconda is a free program that will make the installation and management of the python libraries very easy. You can install either Anaconda (the full package) or just the light version called miniconda3\nStep 3 - Create a virtual python environment A virtual python environment is like a python version running on your machine but being isolated from the rest of the system. This way anything you will do in this environment, like installing new libraries, will not affect the rest of your computer.\nIn the following example we chose neutron_imaging as the name of our virtual environment. Feel free to replace it with whatever name makes more sense to you.\nTo do so, simply type the following command on your terminal\n$ conda create -n neutron_imaging python=3 Now let\u0026rsquo;s switch to that environment\n$ conda activate neutron_imaging Step 4 - Set up environment Final step, we need to install all the libraries used by the notebooks. To do so, in your terminal, navigate to the notebooks folder your downloaded (tag version)\ncd ~/git/python_notebooks-0.1.0 and execute the installation script config_conda_env.sh\n$ bash config_conda_env.sh This will take a while!\nStep 5 - launch the notebooks Last step, start the notebooks\n$ jupyter notebook Your favorite browser will show up with the notebooks. Enjoy!\n\n for Windows Step 1 - Install Anaconda First thing to do will be do download and install anaconda. To do so, go to the anaconda download page.\nClick the Download button.\nClick the 64-Bit or 32-Bit version according to your machine.\nIf you don\u0026rsquo;t know, there is a higher chance that you are on a 64-Bit machine so give it a try. If you did not use wisely, the installation will fail and you will need to try the other version.\n Once the download of the program finished, go to your download folder and run the installer by double clicking it.\nKeep the default settings all the way by clicking next.\nStep 1 - Create conda environment Once the installation is done you will have a set of new tools in the Anaconda menu. Launch the tool called Anaconda Powershell Prompt\nThis is where we are going to import the imaging notebooks and installed the python libraries you will need to run the notebooks.\nOnce the terminal comes to life, we are going to create a folder that will contain the code to import. Let\u0026rsquo;s say we will call it git in your home folder\n$ cd ~/ $ mkdir ~/git $ cd git Now we are going to create a special python environment that will allow us to stay away from the native python of the system, this is a recommended way to work with python packages.\n$ conda create -y -n neutron_imaging python=3.7 The name of our environment is called neutron_imaging and we are telling the system to install python version 3.7\nJust let the terminal install the libraries.\nOnce the installation is done, we need to activate that environment.\n$ conda activate neutron_imaging Step 3 - Import or Clone Notebooks Select either one of the two ways to bring the notebooks to your computer\nDownload\nWe recommend using the latest tag (stable) version of the notebooks. Click either the zip or the tar.gz link.\nGo to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nClone\nOpen a terminal, move to the location where you want to clone (import) the notebooks and then type the clone command\n$ cd ~/git $ git clone https://github.com/neutronimaging/python_notebooks.git Go to your download folder and double click the file you just downloaded. Move this folder to your location of choice on your computer (for example, I used ~/git/ on my computer)\nStep 4 - Import all libraries Now in the anaconda power shell terminal, import all the librairies by typing\n$ conda update -y -n base -c defaults conda $ conda install -y requests requests-oauthlib numpy scipy pandas scikit-image matplotlib plotly $ conda install -y nodejs qtpy pyqtgraph astropy $ conda install -y -c conda-forge ipywe lmfit $ pip install neutronbraggedge NeuNorm sectorizedradialprofile inflect ImagingReso ipywidgets $ pip install https://oncat.ornl.gov/packages/pyoncat-1.4.1-py3-none-any.whl $ jupyter labextension install @jupyter-widgets/jupyterlab-manager $ jupyter nbextension enable --py widgetsnbextension $ jupyter lab build You can now launch the Anaconda Navigator and select the environment you created and called neutron_imaging.\nNow you can go back to the HOME menu within the Anaconda Navigator and launch the Jupyter notebooks.\nFrom there, navigate to the folder ~/git/python_notebooks/notebooks/ to get access to all the notebooks!\n"
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