Commit cdaa254a authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

Added amira page and removed Lou from team members

parent cf376adf
......@@ -723,3 +723,4 @@
</html>
......@@ -688,3 +688,4 @@ liste des principaux outils que nous offrons.</p>
......@@ -693,3 +693,4 @@
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......@@ -794,3 +794,4 @@ hugo new basics/second-content/_index.md
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......@@ -670,3 +670,4 @@ trouverez dans les differents sous-menus de <strong>Preparer Votre Sejour</stron
</html>
......@@ -587,3 +587,4 @@ temps de faisceau.</p>
</html>
......@@ -704,3 +704,4 @@ and compatible with experiment/beam line?</p>
</html>
......@@ -747,3 +747,4 @@ Quand vous générez le site avec <code>hugo server</code>, Hugo génère le fic
</html>
......@@ -683,3 +683,4 @@
</body>
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......@@ -845,3 +845,4 @@ weight = 5
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......@@ -656,3 +656,4 @@
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......@@ -13,19 +13,19 @@
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......@@ -428,13 +428,13 @@
<li data-nav-id="/tutorial/how_to_run_imars3d/" title="Do a CT reconstruction" class="dd-item
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
">
<a href="/tutorial/how_to_run_imars3d/">
<b>e. </b>Do a CT reconstruction
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<i class="fa fa-check read-icon"></i>
......@@ -454,13 +454,13 @@
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
<li data-nav-id="/tutorial/how_to_run_mcp_detector_correction/" title="MCP Detector Correction" class="dd-item
">
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<a href="/tutorial/how_to_run_mcp_detector_correction/">
<b>g. </b>MCP Detector Correction
<i class="fa fa-check read-icon"></i>
......@@ -480,13 +480,13 @@
<li data-nav-id="/tutorial/how_to_run_mcp_detector_correction/" title="MCP Detector Correction" class="dd-item
<li data-nav-id="/tutorial/how_to_run_imars3d/" title="How to work with Amira" class="dd-item
">
<a href="/tutorial/how_to_run_mcp_detector_correction/">
<b>g. </b>MCP Detector Correction
<a href="/tutorial/how_to_run_imars3d/">
<b>h. </b>How to work with Amira
<i class="fa fa-check read-icon"></i>
......@@ -512,7 +512,7 @@
">
<a href="/tutorial/notebooks/">
<b>h. </b>Notebooks Tutorials
<b>i. </b>Notebooks Tutorials
<i class="fa fa-check read-icon"></i>
......@@ -1590,7 +1590,7 @@
">
<a href="/tutorial/how_to_other/">
<b>i. </b>More ...
<b>j. </b>More ...
<i class="fa fa-check read-icon"></i>
......@@ -2713,20 +2713,20 @@ repositories hosting our programs</p>
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:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fa fa-close"></i></span>
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<script type="text/javascript" src="/js/lunr.min.js?1540912316"></script>
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......@@ -428,13 +428,13 @@
<li data-nav-id="/tutorial/how_to_run_imars3d/" title="Do a CT reconstruction" class="dd-item
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
">
<a href="/tutorial/how_to_run_imars3d/">
<b>e. </b>Do a CT reconstruction
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<i class="fa fa-check read-icon"></i>
......@@ -454,13 +454,13 @@
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
<li data-nav-id="/tutorial/how_to_run_mcp_detector_correction/" title="MCP Detector Correction" class="dd-item
">
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<a href="/tutorial/how_to_run_mcp_detector_correction/">
<b>g. </b>MCP Detector Correction
<i class="fa fa-check read-icon"></i>
......@@ -480,13 +480,13 @@
<li data-nav-id="/tutorial/how_to_run_mcp_detector_correction/" title="MCP Detector Correction" class="dd-item
<li data-nav-id="/tutorial/how_to_run_imars3d/" title="How to work with Amira" class="dd-item
">
<a href="/tutorial/how_to_run_mcp_detector_correction/">
<b>g. </b>MCP Detector Correction
<a href="/tutorial/how_to_run_imars3d/">
<b>h. </b>How to work with Amira
<i class="fa fa-check read-icon"></i>
......@@ -512,7 +512,7 @@
">
<a href="/tutorial/notebooks/">
<b>h. </b>Notebooks Tutorials
<b>i. </b>Notebooks Tutorials
<i class="fa fa-check read-icon"></i>
......@@ -1590,7 +1590,7 @@
">
<a href="/tutorial/how_to_other/">
<b>i. </b>More ...
<b>j. </b>More ...
<i class="fa fa-check read-icon"></i>
......@@ -2701,20 +2701,20 @@ web site, and always <strong>welcome your comments</strong> to improve it (conta
<div style="left: -1000px; overflow: scroll; position: absolute; top: -1000px; border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;">
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......
......@@ -83,13 +83,6 @@
"description": "",
"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.\n\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 "
},
{
"uri": "/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": "/tutorial/",
"title": "Tutorials",
......@@ -111,6 +104,13 @@
"description": "",
"content": " The following tutorial will guide, step by step, in running the MCP correction program\nDescription Every single data acquired using the MCP detector needs to be corrected for detector efficiency.\nOld Way\nIn the past, one had to go through the following steps:\n start the windows command line tool locate the .exe script (using file browser) and drag and drop it into the command line window add a space in the command line locate the first image of the data set to correct Run the script and wait \u0026hellip; rename the folder correction created by the script grab this folder and move it to final location repeat for all other set of data New Way\n start MCPcorrection program select root folder containing all data set select output folder click correction button The parent folder must be the folder seating on top of the data folder! This looks confusing? Well just follow the following diagram. In such a case, you should select the first folder! Step by Step Select the parent folder Make sure the folder you select contains all the data folders. Any other folder selected (higher or lower in the hierarchy will crash the application)!\nSelect the data folder to correct In the table, simply select all the data folder you want to correct. If a row is highlighted, this folder will be corrected\nSelect the output folder The data corrected will be moved into this folder\nNaming convention\nEach data set corrected will be copied inside a folder based on the name of all the images and inside a folder of the data folder + \u0026ldquo;_corrected\u0026rdquo;.\nFull correction animation Configuration This is where you can define the starting default folder, default output folder and also the run correction time out. The script run in the back requires user input to finish it, because we wanted to allow you to run several job one after the other without your input, we, using the time out value, stop the process manually. During testing, we found that 35s is long enough to allow all the files to be translater. In case you find that the time out shows up too early, you may need to increase the time here.\n"
},
{
"uri": "/tutorial/how_to_run_imars3d/",
"title": "How to work with Amira",
"tags": [],
"description": "",
"content": " This tutorial will show you how to start and then do some of the most basics things with Amira\nConnect to the analysis computer You need first to connect to the analysis computer. To do so, just follow the step by step tutorial in the how to connect to the analysis computer \nStart Amira Start a terminal session (click small black icon at the top of the screen) and type\namira You should then see the Amira icon showing up\nIf this does not work for you, you can always type the long version of the command\n/usr/bin/vglrun /SNS/software/amira/latest/bin/Amira If you see this, contact your local contact Video Tutorials To get quickly started with Amira, here are a few YouTube videos that you may find interesting.\n Getting Started Tutorial Amira Basics Visualizing in 3D images Advanced Image Processing and Quantitative Analysis Measuring Diameter and Sphericity of Pores Getting Started with the Segmentation Editor Amira Image Segmentation Tutorial CLICK HERE: Getting Started Tutorial CLICK HERE: Amira Basics CLICK HERE: Visualizing 3D Images CLICK HERE: Advanced Image Processing and Quantitative Analysis CLICK HERE: Measuring Diameter and Sphericity of Pores CLICK HERE: Getting Started with the Segmentation Editor CLICK HERE: Amira Image Segmentation Tutorial "
},
{
"uri": "/tutorial/notebooks/",
"title": "Notebooks Tutorials",
......@@ -179,7 +179,7 @@
"title": "Contacts",
"tags": [],
"description": "",
"content": " Hassina Bilheux - Instrument ScientistExpertise: HFIR and SNS imaging beam lines Short Bio ... Dr. Hassina Bilheux obtained her Ph.D. in Physics at the Univ. of Versailles, France. Her work focused on plasma physics at the Oak Ridge National Laboratory’s Physics Division.\nShe has developed neutron imaging capabilities at ORNL’s High Flux Isotope Reactor CG-1D beamline and is prototyping neutron imaging at the Spallation Neutron Source. Her interests comprise the development of advanced neutron imaging techniques at the Spallation Neutron Source for material and biological applications. bilheuxhn@ornl.gov (865) 384 - 9630 (865) 574 - 0241 researchGate Scholar Google 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 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 Keita DeCarlo, Princeton Univ. Granger Endsley, Oak Ridge High School Vincenzo Finochiarro, Italy Susan Herringer, Brown Univ. Sarah Hammer, Virginia State Univ. Felix Kim, Univ. of TN-Knoxville Misun Kang, Univ. of TN-Knoxville Gian Song, Univ. of TN-Knoxville Sophie Voisin, Univ. of TN-Knoxville Lakeisha Walker, ORNL "
"content": " Hassina Bilheux - Instrument ScientistExpertise: HFIR and SNS imaging beam lines Short Bio ... Dr. Hassina Bilheux obtained her Ph.D. in Physics at the Univ. of Versailles, France. Her work focused on plasma physics at the Oak Ridge National Laboratory’s Physics Division.\nShe has developed neutron imaging capabilities at ORNL’s High Flux Isotope Reactor CG-1D beamline and is prototyping neutron imaging at the Spallation Neutron Source. Her interests comprise the development of advanced neutron imaging techniques at the Spallation Neutron Source for material and biological applications. bilheuxhn@ornl.gov (865) 384 - 9630 (865) 574 - 0241 researchGate Scholar Google Yuxuan Zhang (Shawn) - PostdoctorateExpertise: Resonance Imaging zhangy6@ornl.gov Jean Bilheux - Computer ScientistExpertise: Python Notebooks and Data Analysis bilheuxjm@ornl.gov (865) 406 - 1704 (865) 574 - 4637 jbilheux.com jeanbilheux.pages.ornl.gov Jiao Lin - Computer ScientistExpertise: 3D Reconstruction and visualization linjiao@ornl.gov (626) 200 - 5247 (626) 200 - 5247 Paris Cornwell - Scientific Associate cornwellpa@ornl.gov (865) 257 - 1127 (865) 574 - 2122 Brianne Beers - Graduate Student Past Team Members Lou Santodonato Keita DeCarlo, Princeton Univ. Granger Endsley, Oak Ridge High School Vincenzo Finochiarro, Italy Susan Herringer, Brown Univ. Sarah Hammer, Virginia State Univ. Felix Kim, Univ. of TN-Knoxville Misun Kang, Univ. of TN-Knoxville Gian Song, Univ. of TN-Knoxville Sophie Voisin, Univ. of TN-Knoxville Lakeisha Walker, ORNL "
},
{
"uri": "/tutorial/notebooks/create_list_of_file_name_vs_time_stamp/",
......
......@@ -13,19 +13,19 @@
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:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fa fa-close"></i></span>
</div>
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......@@ -428,13 +428,13 @@
<li data-nav-id="/tutorial/how_to_run_imars3d/" title="Do a CT reconstruction" class="dd-item
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
">
<a href="/tutorial/how_to_run_imars3d/">
<b>e. </b>Do a CT reconstruction
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<i class="fa fa-check read-icon"></i>
......@@ -454,13 +454,13 @@
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
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">
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<a href="/tutorial/how_to_run_mcp_detector_correction/">
<b>g. </b>MCP Detector Correction
<i class="fa fa-check read-icon"></i>
......@@ -480,13 +480,13 @@
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<a href="/tutorial/how_to_run_mcp_detector_correction/">
<b>g. </b>MCP Detector Correction
<a href="/tutorial/how_to_run_imars3d/">
<b>h. </b>How to work with Amira
<i class="fa fa-check read-icon"></i>
......@@ -512,7 +512,7 @@
">
<a href="/tutorial/notebooks/">
<b>h. </b>Notebooks Tutorials
<b>i. </b>Notebooks Tutorials
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......@@ -1590,7 +1590,7 @@
">
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<b>i. </b>More ...
<b>j. </b>More ...
<i class="fa fa-check read-icon"></i>
......@@ -2956,20 +2956,20 @@
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......
......@@ -13,19 +13,19 @@
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......@@ -428,13 +428,13 @@
<li data-nav-id="/tutorial/how_to_run_imars3d/" title="Do a CT reconstruction" class="dd-item
<li data-nav-id="/tutorial/how_to_do_bragg_edge_modeling/" title="Bragg Edge Modeling" class="dd-item
">
<a href="/tutorial/how_to_run_imars3d/">
<b>e. </b>Do a CT reconstruction
<a href="/tutorial/how_to_do_bragg_edge_modeling/">
<b>f. </b>Bragg Edge Modeling
<i class="fa fa-check read-icon"></i>
......@@ -454,13 +454,13 @@