Commit dc1d4abe authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

Built new site

parent a1ab3705
......@@ -10,16 +10,16 @@
<title>404 Page not found</title>
<link href="/css/nucleus.css?1516812797" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516812797" rel="stylesheet">
<link href="/css/hybrid.css?1516812797" rel="stylesheet">
<link href="/css/featherlight.min.css?1516812797" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516812797" rel="stylesheet">
<link href="/css/horsey.css?1516812797" rel="stylesheet">
<link href="/css/theme.css?1516812797" rel="stylesheet">
<link href="/css/hugo-theme.css?1516812797" rel="stylesheet">
<link href="/css/nucleus.css?1516978306" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516978306" rel="stylesheet">
<link href="/css/hybrid.css?1516978306" rel="stylesheet">
<link href="/css/featherlight.min.css?1516978306" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516978306" rel="stylesheet">
<link href="/css/horsey.css?1516978306" rel="stylesheet">
<link href="/css/theme.css?1516978306" rel="stylesheet">
<link href="/css/hugo-theme.css?1516978306" rel="stylesheet">
<link href="/css/theme-blue.css?1516812797" rel="stylesheet">
<link href="/css/theme-blue.css?1516978306" rel="stylesheet">
<style type="text/css">
:root #header + #content > #left > #rlblock_left {
......@@ -61,3 +61,4 @@
</body>
</html>
......@@ -827,3 +827,5 @@ repositories hosting our programs</p>
......@@ -1662,3 +1662,5 @@ When you build the site with hugo server, hugo generates it internally and of co
......@@ -1711,3 +1711,5 @@ hugo new basics/second-content/_index.md
......@@ -13,19 +13,19 @@
<title>Capabilities :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1516812797" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516812797" rel="stylesheet">
<link href="/css/hybrid.css?1516812797" rel="stylesheet">
<link href="/css/featherlight.min.css?1516812797" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516812797" rel="stylesheet">
<link href="/css/auto-complete.css?1516812797" rel="stylesheet">
<link href="/css/theme.css?1516812797" rel="stylesheet">
<link href="/css/hugo-theme.css?1516812797" rel="stylesheet">
<link href="/css/nucleus.css?1516978306" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516978306" rel="stylesheet">
<link href="/css/hybrid.css?1516978306" rel="stylesheet">
<link href="/css/featherlight.min.css?1516978306" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516978306" rel="stylesheet">
<link href="/css/auto-complete.css?1516978306" rel="stylesheet">
<link href="/css/theme.css?1516978306" rel="stylesheet">
<link href="/css/hugo-theme.css?1516978306" rel="stylesheet">
<link href="/css/theme-blue.css?1516812797" rel="stylesheet">
<link href="/css/theme-blue.css?1516978306" rel="stylesheet">
<script src="/js/jquery-2.x.min.js?1516812797"></script>
<script src="/js/jquery-2.x.min.js?1516978306"></script>
<style type="text/css">
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fa fa-close"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1516812797"></script>
<script type="text/javascript" src="/js/auto-complete.js?1516812797"></script>
<script type="text/javascript" src="/js/lunr.min.js?1516978306"></script>
<script type="text/javascript" src="/js/auto-complete.js?1516978306"></script>
<script type="text/javascript">
var baseurl = "\/en";
</script>
<script type="text/javascript" src="/js/search.js?1516812797"></script>
<script type="text/javascript" src="/js/search.js?1516978306"></script>
</div>
......@@ -491,11 +491,11 @@
<ul>
<li class="" role="">
<a class="padding" href="en/github"><i class='fa fa-github'></i> Github Repos</a>
<a class="padding" href="/en/github"><i class='fa fa-github'></i> Github Repos</a>
</li>
<li class="" role="">
<a class="padding" href="en/showcase"><i class='fa fa-camera'></i> Photo Gallery</a>
<a class="padding" href="/en/showcase"><i class='fa fa-camera'></i> Photo Gallery</a>
</li>
<li class="" role="">
......@@ -503,7 +503,7 @@
</li>
<li class="" role="">
<a class="padding" href="en/credits"><i class='fa fa-user-circle'></i> Contacts</a>
<a class="padding" href="/en/credits"><i class='fa fa-user-circle'></i> Contacts</a>
</li>
</ul>
......@@ -966,20 +966,20 @@
<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?1516812797"></script>
<script src="/js/perfect-scrollbar.min.js?1516812797"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1516812797"></script>
<script src="/js/jquery.sticky.js?1516812797"></script>
<script src="/js/featherlight.min.js?1516812797"></script>
<script src="/js/html5shiv-printshiv.min.js?1516812797"></script>
<script src="/js/highlight.pack.js?1516812797"></script>
<script src="/js/clipboard.min.js?1516978306"></script>
<script src="/js/perfect-scrollbar.min.js?1516978306"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1516978306"></script>
<script src="/js/jquery.sticky.js?1516978306"></script>
<script src="/js/featherlight.min.js?1516978306"></script>
<script src="/js/html5shiv-printshiv.min.js?1516978306"></script>
<script src="/js/highlight.pack.js?1516978306"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom.71422.js?1516812797"></script>
<script src="/js/learn.js?1516812797"></script>
<script src="/js/hugo-learn.js?1516812797"></script>
<script src="/js/modernizr.custom.71422.js?1516978306"></script>
<script src="/js/learn.js?1516978306"></script>
<script src="/js/hugo-learn.js?1516978306"></script>
<link href="/mermaid/mermaid.css?1516812797" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1516812797"></script>
<link href="/mermaid/mermaid.css?1516978306" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1516978306"></script>
<script>
mermaid.initialize({ startOnLoad: true });
</script>
......@@ -1004,3 +1004,4 @@
</body>
</html>
......@@ -1667,3 +1667,5 @@ Lorem Ipsum.
......@@ -1698,3 +1698,5 @@ languageName = &quot;Français&quot;
......@@ -1597,3 +1597,5 @@
......@@ -2363,3 +2363,5 @@ Content for chapter one.
......@@ -1620,3 +1620,5 @@ weight = 30
......@@ -1674,3 +1674,5 @@ menuTitle = &quot;Linux&quot;
......@@ -13,19 +13,19 @@
<title>Contacts :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1516812797" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516812797" rel="stylesheet">
<link href="/css/hybrid.css?1516812797" rel="stylesheet">
<link href="/css/featherlight.min.css?1516812797" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516812797" rel="stylesheet">
<link href="/css/auto-complete.css?1516812797" rel="stylesheet">
<link href="/css/theme.css?1516812797" rel="stylesheet">
<link href="/css/hugo-theme.css?1516812797" rel="stylesheet">
<link href="/css/nucleus.css?1516978306" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516978306" rel="stylesheet">
<link href="/css/hybrid.css?1516978306" rel="stylesheet">
<link href="/css/featherlight.min.css?1516978306" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516978306" rel="stylesheet">
<link href="/css/auto-complete.css?1516978306" rel="stylesheet">
<link href="/css/theme.css?1516978306" rel="stylesheet">
<link href="/css/hugo-theme.css?1516978306" rel="stylesheet">
<link href="/css/theme-blue.css?1516812797" rel="stylesheet">
<link href="/css/theme-blue.css?1516978306" rel="stylesheet">
<script src="/js/jquery-2.x.min.js?1516812797"></script>
<script src="/js/jquery-2.x.min.js?1516978306"></script>
<style type="text/css">
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fa fa-close"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1516812797"></script>
<script type="text/javascript" src="/js/auto-complete.js?1516812797"></script>
<script type="text/javascript" src="/js/lunr.min.js?1516978306"></script>
<script type="text/javascript" src="/js/auto-complete.js?1516978306"></script>
<script type="text/javascript">
var baseurl = "\/en";
</script>
<script type="text/javascript" src="/js/search.js?1516812797"></script>
<script type="text/javascript" src="/js/search.js?1516978306"></script>
</div>
......@@ -491,11 +491,11 @@
<ul>
<li class="" role="">
<a class="padding" href="en/github"><i class='fa fa-github'></i> Github Repos</a>
<a class="padding" href="/en/github"><i class='fa fa-github'></i> Github Repos</a>
</li>
<li class="" role="">
<a class="padding" href="en/showcase"><i class='fa fa-camera'></i> Photo Gallery</a>
<a class="padding" href="/en/showcase"><i class='fa fa-camera'></i> Photo Gallery</a>
</li>
<li class="" role="">
......@@ -503,7 +503,7 @@
</li>
<li class="" role="">
<a class="padding" href="en/credits"><i class='fa fa-user-circle'></i> Contacts</a>
<a class="padding" href="/en/credits"><i class='fa fa-user-circle'></i> Contacts</a>
</li>
</ul>
......@@ -542,28 +542,28 @@
<option id="es" value="/es/credits/">Spanish</option>
<option id="fr" value="/fr/credits/">Français</option>
</select>
<svg version="1.1" id="Capa_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
......@@ -1028,20 +1028,20 @@
<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?1516812797"></script>
<script src="/js/perfect-scrollbar.min.js?1516812797"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1516812797"></script>
<script src="/js/jquery.sticky.js?1516812797"></script>
<script src="/js/featherlight.min.js?1516812797"></script>
<script src="/js/html5shiv-printshiv.min.js?1516812797"></script>
<script src="/js/highlight.pack.js?1516812797"></script>
<script src="/js/clipboard.min.js?1516978306"></script>
<script src="/js/perfect-scrollbar.min.js?1516978306"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1516978306"></script>
<script src="/js/jquery.sticky.js?1516978306"></script>
<script src="/js/featherlight.min.js?1516978306"></script>
<script src="/js/html5shiv-printshiv.min.js?1516978306"></script>
<script src="/js/highlight.pack.js?1516978306"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom.71422.js?1516812797"></script>
<script src="/js/learn.js?1516812797"></script>
<script src="/js/hugo-learn.js?1516812797"></script>
<script src="/js/modernizr.custom.71422.js?1516978306"></script>
<script src="/js/learn.js?1516978306"></script>
<script src="/js/hugo-learn.js?1516978306"></script>
<link href="/mermaid/mermaid.css?1516812797" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1516812797"></script>
<link href="/mermaid/mermaid.css?1516978306" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1516978306"></script>
<script>
mermaid.initialize({ startOnLoad: true });
</script>
......@@ -1067,3 +1067,4 @@
</body>
</html>
......@@ -13,19 +13,19 @@
<title>Frequently Asked Questions :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1516812797" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516812797" rel="stylesheet">
<link href="/css/hybrid.css?1516812797" rel="stylesheet">
<link href="/css/featherlight.min.css?1516812797" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516812797" rel="stylesheet">
<link href="/css/auto-complete.css?1516812797" rel="stylesheet">
<link href="/css/theme.css?1516812797" rel="stylesheet">
<link href="/css/hugo-theme.css?1516812797" rel="stylesheet">
<link href="/css/nucleus.css?1516978306" rel="stylesheet">
<link href="/css/font-awesome.min.css?1516978306" rel="stylesheet">
<link href="/css/hybrid.css?1516978306" rel="stylesheet">
<link href="/css/featherlight.min.css?1516978306" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1516978306" rel="stylesheet">
<link href="/css/auto-complete.css?1516978306" rel="stylesheet">
<link href="/css/theme.css?1516978306" rel="stylesheet">
<link href="/css/hugo-theme.css?1516978306" rel="stylesheet">
<link href="/css/theme-blue.css?1516812797" rel="stylesheet">
<link href="/css/theme-blue.css?1516978306" rel="stylesheet">
<script src="/js/jquery-2.x.min.js?1516812797"></script>
<script src="/js/jquery-2.x.min.js?1516978306"></script>
<style type="text/css">
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fa fa-close"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1516812797"></script>
<script type="text/javascript" src="/js/auto-complete.js?1516812797"></script>
<script type="text/javascript" src="/js/lunr.min.js?1516978306"></script>
<script type="text/javascript" src="/js/auto-complete.js?1516978306"></script>
<script type="text/javascript">
var baseurl = "\/en";
</script>
<script type="text/javascript" src="/js/search.js?1516812797"></script>
<script type="text/javascript" src="/js/search.js?1516978306"></script>
</div>
......@@ -491,11 +491,11 @@
<ul>
<li class="" role="">
<a class="padding" href="en/github"><i class='fa fa-github'></i> Github Repos</a>
<a class="padding" href="/en/github"><i class='fa fa-github'></i> Github Repos</a>
</li>
<li class="" role="">
<a class="padding" href="en/showcase"><i class='fa fa-camera'></i> Photo Gallery</a>
<a class="padding" href="/en/showcase"><i class='fa fa-camera'></i> Photo Gallery</a>
</li>
<li class="" role="">
......@@ -503,7 +503,7 @@
</li>
<li class="" role="">
<a class="padding" href="en/credits"><i class='fa fa-user-circle'></i> Contacts</a>
<a class="padding" href="/en/credits"><i class='fa fa-user-circle'></i> Contacts</a>
</li>
</ul>
......@@ -542,28 +542,28 @@
<option id="es" value="/es/faq/">Spanish</option>
<option id="fr" value="/fr/faq/">Français</option>
</select>
<svg version="1.1" id="Capa_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
......@@ -686,7 +686,10 @@
</span>
</div>
<div class="expand-content" style="display: none;">
<p>Answer will go here.</p>
<ul>
<li>To learn more about submitting a proposal for beam time, go to <a href='https://neutrons.ornl.gov/users'>neutrons.ornl.gov/users</a>.</li>
<li>To submit your proposal, go to the <a href='https://snsapp1.sns.ornl.gov/xprod/f?p=100'>proposal system</a>.</li>
</ul>
</div>
</div>
......@@ -781,6 +784,28 @@ neutron.ornl.gov users page</a> for more infos.</p>
<span>
How can I browse my data?
</span>
</div>
<div class="expand-content" style="display: none;">
<p>Using <a href='https://oncat.ornl.gov/#/'>ONCat</a>, you will be able to
<ul>
<li>view your data</li>
<li>view the metadata and get infos about such or such data set</li>
<li>find an experiment using keyword</li>
<li>More features coming soon</li>
</ul>
<img src='/faq/images/oncat.png' /></p>
</div>
</div>
<div class="expand">
<div class="expand-label" style="cursor: pointer;" onclick="$h = $(this);$h.next('div').slideToggle(100,function () {$h.children('i').attr('class',function () {return $h.next('div').is(':visible') ? 'fa fa-chevron-down' : 'fa fa-chevron-right';});});">
<i style="font-size:x-small;" class="fa fa-chevron-right"></i>
<span>
How can I get help analyzing my data?
</span>
......@@ -892,6 +917,176 @@ web site</a></p>
<li>iBeatles</li>
</ul>
</div>
</div>
<div class="expand">
<div class="expand-label" style="cursor: pointer;" onclick="$h = $(this);$h.next('div').slideToggle(100,function () {$h.children('i').attr('class',function () {return $h.next('div').is(':visible') ? 'fa fa-chevron-down' : 'fa fa-chevron-right';});});">
<i style="font-size:x-small;" class="fa fa-chevron-right"></i>
<span>
Metadata of the images and their meaning
</span>
</div>
<div class="expand-content" style="display: none;">
<p>You can retrieve the metadata of your TIFF images using:
<ul>
<li><a href='https://oncat.ornl.gov/#/'>ONCat</a></li>
<li>the jupyter notebook <strong>list_tiff_metadata.ipynb</strong>. Check <a href="/en/tutorial/how_to_start_notebooks">How To &gt; Start the python notebooks</a></li>
</ul></p>
<table>
<tr><td width="250"><strong>Tag Name</td><td><strong>Description</td></tr>
<tr><td>ImageWidth</td><td>The number of columns in the image</td></tr>
<tr><td>ImageHeight</td><td>The number of rows in the image</td></tr>
<tr><td>BitsPerSample</td><td>The number of bits per component (ie. 16-bits or 32-bits for each greyscale pixel in our case)</td></tr>
<tr><td>SampleFormat</td><td>Specifies how to interpret each data sample in a pixel (1 = unsigned integer)</td></tr>
<tr><td>SamplesPerPixel</td><td>The number of components per pixel (1 in our case, which is grey scale)</td></tr>
<tr><td>Compression</td><td>1 = None</td></tr>
<tr><td>PhotometricInterpretation</td><td>1 = Min is black</td></tr>
<tr><td>MakeStr</td><td>The detector manufacture (eg. 'Andor' or 'SBIG')</td></tr>
<tr><td>ModelStr</td><td>The detector model number</td></tr>
<tr><td>SoftwareStr</td><td>EPICS areaDetector</td></tr>
</table>
<p><br>
Tags 65000 to 650009 have no name and are used for timestamps and a unique ID</p>
<table>
<tr><td width="250"><strong>Tag Name</td><td><strong>Description</td></tr>
<tr><td>65000</td><td>EPICS timestamp. The timestamp is made when the image is read out from the camera. Format is seconds.nanoseconds since Jan 1st 00:00 1990.</td></tr>
<tr><td>65001</td><td>Unique ID for the image. Always 1 for single image acquisition, and incrementing up for camera and CT scans. Should always match the ImageCounter value.</td></tr>
<tr><td>65002</td><td>EPICS timestamp (seconds part only)</td></tr>
<tr><td>65003</td><td>EPICS timestamp (nanoseconds part only)</td></tr>
</table>
<h3 id="scan-information">Scan Information</h3>
<table>
<tr><td width="250"><strong>Tag Name</td><td><strong>Description</td></tr>
<tr><td>FileNameStr</td><td>The original file name part of the constructed file name (see below)</td></tr>
<tr><td>InstrumentStr</td><td>'CG1D' or 'VENUS'</td></tr>
<tr><td>IPTS</td><td>IPTS Number</td></tr>
<tr><td>ITEMS</td><td>ITEMS Number</td></tr>
<tr><td>SampleDescStr</td><td>Sample description (user entered)</td></tr>
<tr><td>NotesStr</td><td>User notes</td></tr>
<tr><td>DataSetStr</td><td>'2D' or '3D'</td></tr>
<tr><td>DataAcqModeStr</td><td>'White Beam', 'TOF-cold/thermal', 'Epithermal' or 'Monochromatic'</td></tr>
<tr><td>DataTypeStr</td><td>'OB', 'Raw' or 'DF'</td></tr>
</table>
<h3 id="camera-image-information">Camera/Image Information</h3>
<table>
<tr><td width="250"><strong>Tag Name</td><td><strong>Description</td></tr>
<tr><td>ExposureTime</td><td>Exposure time for the image (in seconds)</td></tr>
<tr><td>ExposurePeriod</td><td>Exposure period for the image (Exposure Time + Readout Time in seconds). Not relevant for single image exposures.</td></tr>
<tr><td>NumImages</td><td>1= single image exposure (our normal mode of operation)</td></tr>
<tr><td>ImageCounter</td><td>Always 1 for single image acquisition, and incrementing up for camera and CT scans.</td></tr>
<tr><td>MinX</td><td>Min X pixel (0 for full frame images)</td></tr>
<tr><td>MinY</td><td>Min Y pixel (0 for full frame images)</td></tr>
<tr><td>SizeX</td><td>Size of image in X dimension (should be equal to the ImageWidth value)</td></tr>
<tr><td>SizeY</td><td>Size of image in Y dimension (should be equal to the ImageLength value)</td></tr>
<tr><td>Temperature</td><td>The setpoint temperature (in C)</td></tr>
<tr><td>TemperatureActual</td><td>The actual temperature read from the detector (in C)</td></tr>
</table>
<h3 id="motor-position-scan-device">Motor Position &amp; Scan Device</h3>
<table>
<tr><td width="250"><strong>Tag Name</td><td><strong>Description</td></tr>
<tr><td>MotScanDeviceStr</td><td>'Small Rot' or 'Large Rot' used for this CT scan (if we are doing a camera scan or single image acquisition, this is not relevant)</td></tr>
<tr><td>RotationActual</td><td>Actual position of the rotation stage used in the CT scan (or the previous scan if we are doing a camera scan or single image acquisition)</td></tr>
<tr><td>MotRotTable.RBV</td><td>Large rotation table actual position</td></tr>
<tr><td>MotRotTable</td><td>Large rotation table setpoint</td></tr>
<tr><td>MotSmallRotTable.RBV</td><td>Small rotation table actual position</td></tr>
<tr><td>MotSmallRotTable</td><td>Small rotation table setpoint</td></tr>
<tr><td>MotLiftTable.RBV</td><td>Lift Table actual position</td></tr>
<tr><td>MotLiftTable</td><td>Lift table setpoint</td></tr>
<tr><td>MotShortAxis.RBV</td><td>Short axis actual posiiton</td></tr>
<tr><td>...</td><td></td></tr>
</table>
<h2 id="tiff-file-header-example">TIFF File Header Example</h2>
<pre>
TIFF Directory at offset 0x800008 (8388616)
Image Width: 2048 Image Length: 2048
Bits/Sample: 16
Sample Format: unsigned integer
Compression Scheme: None
Photometric Interpretation: min-is-black
Samples/Pixel: 1
Rows/Strip: 2048
Planar Configuration: single image plane
Make: Unknown
Model: Unknown
Software: EPICS areaDetector
Tag 65000: 837380408.136687
Tag 65001: 1
Tag 65002: 837380408
Tag 65003: 148080423