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	"uri": "/en/tutorial/how_to_access_data/",
	"title": "Access your data",
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	"content": "  This will require that you complete 2 steps:\n Step 1: request access to our computer Step 2: reach your data   Step 1. Request access to our computers 1. Create an XCAMS account\nIf you have not done so, please create an XCAMS account 2. Request access to HFIR data\nYou can request access to your data by visiting this page https://neutronsr.us/accounts/request.html TOP \n Step 2. Reach your data If the goal is to bring your data to your computer for local visualization and analysis -not recommended due to the size of the data and the tools we offer via our analysis computer - the easiest way is to use FileZilla.\n1. Install FileZilla.\n2 Create and configure a new bookmark\nEnter the information as followed:\n Host: analysis.sns.gov Port: 22 Protocol: Select SFTP - SSH File Transfer Protocol Logon Type: Normal User: \u0026lt;your xcams\u0026gt; Password: \u0026lt;your password\u0026gt;  Click Connect\nYou can now browse to your data by following the structure /HFIR/CG1D/IPTS-XXXX\nIf you get lost in the file system, here is a typical map of the file structure.\n\n"
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	"uri": "/en/prepare_venue/",
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	"title": "Before your Arrival",
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	"content": " Prepare your experiment In order to optimize your experiment time, we recommend you to go through the check lists from this Before your Arrival menu.\nFeel free to print out the pdf version and check out the items one by one.\n"
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	"uri": "/en/prepare_venue/proposal_confirmation/",
	"title": "Proposal Confirmation",
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	"content": "To be completed only by the Principal Investigator (PI) of the experiment at least 3 weeks before beam time.\n You can access your proposal using the IPTS page\n Confirmed samples (adding any new samples, and including composition)?\n Confirmed need for lab space?\n Confirmed experiment team that will be present at beam time (add any new members)?\n Confirmed experiment equipment and/or sample environment?\n"
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	"uri": "/en/tutorial/how_to_access_computer/",
	"title": "Connect to our computer",
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	"tags": [],
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	"content": " For any personal tutorial, demonstration or request, please contact Jean Bilheux.\nIn order to analyze or visualize your data, please follow the following recipe.\nConnect to our analysis computer Using your favorite browser, go to https://cg1d-analysis2.ornl.gov\nEnter your XCAMS and your password and hit Login\nThe first time you log in, you will be presented the following display\njust click OK to finish up logging in.\nAnd if it is not the first time, you will probably see a black screen. Just click anywhere within the window to activate the screensaver log in.\nEnter your password and click Unlock.\nYou are now connected to our analysis computer.\n"
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	"uri": "/en/prepare_venue/safety/",
	"title": "Engineering & Equipment Safety",
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	"content": "To be completed only by the Principal Investigator (PI) of the experiment\n  Provided all safety documentation for user provided equipment immediately?\n Shipped/delivered all user provided equipment at least 2 weeks prior to beam time for electrical and safety inspection?\n Answered all safety related questions through IPTS?\n Ensured that sample environment requested equipment is available and compatible with experiment/beam line?\n Written a Job Hazard Analysis (JHA) for hands on work at HFIR?\n"
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	"uri": "/en/tutorial/",
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	"title": "How To",
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	"tags": [],
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	"content": "You will find here various step by step tutorial showing you:\n how to access your data how to use our analysis computer how to run the analysis software etc.  "
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	"uri": "/en/prepare_venue/access/",
	"title": "Access",
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	"content": "This must be completed by all participants to the experiment before the first day of experiment.\n  Received training e-mail from user office (neutronusers@ornl.gov)?\n Completed online training if assigned? ORNL training website\n Scheduled onsite training and tour for HFIR access?\n Followed attached procedure to access CG-1D data?\n Followed attached procedure to access CG-1D analysis computer?\n"
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	"uri": "/en/tutorial/how_to_start_notebooks/",
	"title": "Start the python notebooks",
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	"content": "We provide a set of jupyter python notebooks. Those provide many advantages:\n rapid implementation for your special needs ease of use easy to modify if you need to use of python language (widely used in the scientific world) nothing to install for you as we take care of this for you when you use your analysis computer  To launch the jupyter notebooks, navigate to Applications \u0026gt; Analysis \u0026gt; Jupyter. Be patient as the python server starts a firefox browser with the right python environment and move to the right folder, for you!\nGetting the browser up and running with the notebooks page display takes around 10 to 20 seconds.\n To start a notebook, just click any of the .ipynb file (normalization.ipynb in this tutorial).\nFirst thing we recommend at this point is to make a copy of this notebook. This way, update of the notebooks will not overwrite your work.  "
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	"uri": "/en/tutorial/how_to_run_notebooks/",
	"title": "Run a jupyter notebook",
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	"content": "  Our jupyter python notebooks are very straighforward to use but there are just a few key points you need to know.\n notebook layout run the notebook modify the notebook  \n Notebook layout \n Run the notebook Execute cells The notebooks must be run from top to bottom. Place the cursor in the first cell and either click the  icon, or by using the keyboard shortcut SHIFT + ENTER.\nThis is showing a busy notebook with the background cell green and the full circle at the top right corner of the notebook.\nFolder Navigation At least one time per notebook, you will need to select a folder or one or more files. This widget will look like this The UI is pretty self explanatory but you just need to know that:\n In the file/folder listing widget\n . means refresh of the current location .. means moving up one directory, or folder.  The file or folder will be really selected only once you have clicked the Select button at the bottom right corner.\n To select more than one file (when this option is available), CLICK first file then SHIFT + CLICK the last one. Or ALT + CLICK to individually select each file.\n  Output and widgets The cell is then executed and depending on the contain of this one, you may see or not an output to the cell. The output is always displayed just below the cell ran. In some of our notebooks you will see widgets that you will need to interact with. Here are a few examples of widgets you may encounter in your notebook.\nIn some notebooks, the output may even show up in the back of the notebook (the default cell output will give you a message that let you know where to look). Those outside widgets are more complex user interface such as the one shown here.\n\n Modify the notebook "
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	"uri": "/en/prepare_venue/sample/",
	"title": "Sample Handling",
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	"tags": [],
	"description": "",
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	"content": " Sample Shipping and/or Handling at HFIR Your samples must be confirmed in IPTS before shipping.\nNeutron Sciences User Sample IPTS #XXXX Oak Ridge National Laboratory / HFIR Site Bldg 7972 DP1 Oak Ridge, TN, 37831 USA  If you prefer to bring your samples, please go first to the Sample Management Desk located in the Cold Guide Hall and work with Kristin Nevius to have all your samples labeled with an item Barcode before proceeding to the beamline.\n"
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{
	"uri": "/en/tutorial/how_to_run_imars3d/",
	"title": "Do a CT reconstruction",
	"tags": [],
	"description": "",
	"content": "This tutorial explains how to use SNS jupyter notebook site to perform CT reconstruction.\nYou will find this tutorial here\n"
},
{
	"uri": "/en/tutorial/how_to_other/",
	"title": "... More",
	"tags": [],
	"description": "",
	"content": "  How can I create a movie from a sequence of images?   Answer will go here.\n  "
},
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	"uri": "/en/faq/",
	"title": "Frequently Asked Questions",
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	"content": " Before Your Venue Proposal   How do I submit a proposal?   Answer will go here.\n    When will I know my proposal has been accepted?   Answer will go here.\n    My proposal has been rejected, what to do next?   Answer will go here.\n \nSamples   Can I bring my samples?   answer here\n    Can I leave with my samples?   answer here\n \nDuring your Experiment   Where can I stay?   A few options are available off-site and on-site. Check the neutron.ornl.gov users page for more infos.\n \nData Analysis   How can I get help analyzing my data?   Just contact Jean Bilheux to discuss your needs.\nBy going over your experiment together, Jean will show you how to run the current tools and will develop customed python notebooks if needed.\n    What are those \u0026#39;jupyter notebooks\u0026#39;?   The jupyter notebook developed by jupyter are an easy way to run python code using only a browser. By accessing our analysis computer, you won\u0026rsquo;t have anythign to install. Refer to our How To page to learn how to do that.\n    Where are my data and how can I access them?   The following tutorial will show you where are you data and how you can access them. Just go to How To \u0026gt; Access your data\n    I get a firefox error message when trying to start the jupyter notebooks on the analysis machine.   After double clicking the start jupyter icon, I get an Firefox error message telling me that I have another Firefox window opened.\nThe short way to fix that is by starting the Help me application.\nThen go to the Desperate Actions\nand click the Fix Firefox!\nThis should fix your issue and you should be able to start the jupyter notebooks now.\n    Where do I find ImageJ (or Fiji) on the analysis computer?   Just follow the following path to find and start ImageJ. If you need to learn how to use ImageJ, check their tutorial web site\n    How to cite our work?    Use of CG1D beam line iMars3D iBeatles   \n"
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{
	"uri": "/en/links/",
	"title": "Links",
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	"content": " Laboratory Utilities   ORNL User Program Guide   User Program Guide.     Neutron Imaging Facility Official Web Page   Neutron Imaging Facility Official Web Page.     Neutrons (SNS/HFIR) Web Page   https://neutrons.ornl.gov/     ORNL Web Page   https://www.ornl.gov/  \nAnalysis Tools   Calculate Transmission and Scattering Power   https://webapps.frm2.tum.de/intranet/neutroncalc/     Neutron Transmission Calculator   http://apps.jcns.fz-juelich.de/toolbox/nXsection.php     Neutron Scattering Lengths and Cross Sections   https://www.ncnr.nist.gov/resources/n-lengths/  \nReferences   Standard Guide for Thermal Neutron Radiography of Materials   ASTM Guide for Thermal Neutron Radiography.     International Society for Neutron Radiology (ISNR)   International Society for Neutron Radiology  \n"
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	"uri": "/en/categories/",
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	"title": "Categories",
	"tags": [],
	"description": "",
	"content": ""
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	"uri": "/en/credits/",
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	"title": "Contacts",
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	"content": "            Hassina Bilheux - Instrument ScientistExpertise: HFIR and SNS imaging beam lines bilheuxhn@ornl.gov (865) 384 - 9630 (865) 574 - 0241    Lou Santodonato - Instrument ScientistExpertise: HFIR imaging beam line santodonatol@ornl.gov (865) 719 - 0656 (865) 574 - 4641     Jean Bilheux - Computer ScientistExpertise: Python Notebooks and Data Analysis bilheuxjm@ornl.gov (865) 406 - 1704 (865) 574 - 4637 jbilheux.com jeanbilheux.pages.ornl.gov github.com/jeanbilheux      Jiao Lin - Computer ScientistExpertise: 3D Reconstruction and visualization linjiao@ornl.gov (626) 200 - 5247 (626) 200 - 5247     Yuxuan Zhang (Shawn) - PostdoctorateExpertise: Resonance Imaging zhangy6@ornl.gov    Paris Cornwell - Scientific Associate  cornwellpa@ornl.gov (865) 257 - 1127 (865) 574 - 2122    Brianne Beers - Graduate Student    Past Team Members  Gian Song Sophie Voisin Lakeisha Walker  "
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	"uri": "/en/github/",
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	"title": "Github Repositories",
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	"content": "Our gloal is to only develop open source tools. You will find here a list of the major repositories hosting our programs\n jupyter notebooks used in the analysis of the data python_notebooks python library used for normalization neunorm Imaging Resonance python library imagingReso iBeatles for Bragg Edge fitting iBeatles set of jupyter widgets ipywe Root analysis library RootPlantProcessing  "
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	"uri": "/en/",
	"title": "Neutron Imaging",
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	"content": " Neutron Imaging for Users Home Page  You are planning on submitting a proposal to our Neutron Imaging beam lines but do not know where to start. Your beam time has been granted but you do not know what to do next or who to contact. Your experiment beam time is over but do not know how to analyze the data, or even reach your data. If you have any doubt about what to do before, during and after your beam time, then you came to the right place!  This web site will answer any of the questions you may have. And if it does not, will let you know who to contact to get those answers.\nWelcome to our Imaging Web Page!\nWe recommend that you discuss your experiment with the instrument team as soon as you receive approval of your beam time.\n Main features  Prepare your venue: Everything you will need to do before coming to our laboratory. How to: short tutorials such as how to access your data, connect to the computers, etc. Frequently Asked Questions: answers to the most frequent questions we got from our users. Links: handy links.  We would like to thank the contribution from our users in the implementation of this web site, and always welcome your comments to make it even better (contact Jean Bilheux).\n   Credit for web site logo goes here\n"
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	"uri": "/en/tags/",
	"title": "Tags",
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	"tags": [],
	"description": "",
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	"content": ""
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	"uri": "/en/showcase/",
	"title": "What We Do",
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	"tags": [],
	"description": "",
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}]