Commit 5ac233ce authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

UPdated doc.

parent bdad9db3
......@@ -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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......@@ -61,14 +61,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
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......@@ -3941,19 +3941,19 @@
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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?1651164722" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651164722" rel="stylesheet">
<link href="/css/hybrid.css?1651164722" rel="stylesheet">
<link href="/css/featherlight.min.css?1651164722" rel="stylesheet">
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<link href="/css/auto-complete.css?1651164722" rel="stylesheet">
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<link href="/css/nucleus.css?1651693154" rel="stylesheet">
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<link href="/css/hybrid.css?1651693154" rel="stylesheet">
<link href="/css/featherlight.min.css?1651693154" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1651693154" rel="stylesheet">
<link href="/css/auto-complete.css?1651693154" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1651693154" rel="stylesheet">
<link href="/css/theme.css?1651693154" rel="stylesheet">
<link href="/css/hugo-theme.css?1651693154" rel="stylesheet">
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<script src="/js/jquery-3.3.1.min.js?1651164722"></script>
<script src="/js/jquery-3.3.1.min.js?1651693154"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -61,14 +61,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1651164722"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651164722"></script>
<script type="text/javascript" src="/js/lunr.min.js?1651693154"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651693154"></script>
<script type="text/javascript">
var baseurl = "";
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......@@ -3896,19 +3896,19 @@
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<script src="/js/clipboard.min.js?1651164722"></script>
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<script>hljs.initHighlightingOnLoad();</script>
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<script src="/mermaid/mermaid.js?1651693154"></script>
<script>
mermaid.initialize({ startOnLoad: true });
</script>
......
......@@ -12,20 +12,20 @@
<title>Contacts :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1651164722" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651164722" rel="stylesheet">
<link href="/css/hybrid.css?1651164722" rel="stylesheet">
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<script src="/js/jquery-3.3.1.min.js?1651164722"></script>
<script src="/js/jquery-3.3.1.min.js?1651693154"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -61,14 +61,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1651164722"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651164722"></script>
<script type="text/javascript" src="/js/lunr.min.js?1651693154"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651693154"></script>
<script type="text/javascript">
var baseurl = "";
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......@@ -3974,19 +3974,19 @@
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<div style="border: none; box-sizing: content-box; height: 200px; margin: 0px; padding: 0px; width: 200px;"></div>
</div>
<script src="/js/clipboard.min.js?1651164722"></script>
<script src="/js/perfect-scrollbar.min.js?1651164722"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1651164722"></script>
<script src="/js/jquery.sticky.js?1651164722"></script>
<script src="/js/featherlight.min.js?1651164722"></script>
<script src="/js/highlight.pack.js?1651164722"></script>
<script src="/js/clipboard.min.js?1651693154"></script>
<script src="/js/perfect-scrollbar.min.js?1651693154"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1651693154"></script>
<script src="/js/jquery.sticky.js?1651693154"></script>
<script src="/js/featherlight.min.js?1651693154"></script>
<script src="/js/highlight.pack.js?1651693154"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1651164722"></script>
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<script src="/mermaid/mermaid.js?1651693154"></script>
<script>
mermaid.initialize({ startOnLoad: true });
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......
......@@ -12,20 +12,20 @@
<title>Frequently Asked Questions :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1651164722" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651164722" rel="stylesheet">
<link href="/css/hybrid.css?1651164722" rel="stylesheet">
<link href="/css/featherlight.min.css?1651164722" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1651164722" rel="stylesheet">
<link href="/css/auto-complete.css?1651164722" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1651164722" rel="stylesheet">
<link href="/css/theme.css?1651164722" rel="stylesheet">
<link href="/css/hugo-theme.css?1651164722" rel="stylesheet">
<link href="/css/nucleus.css?1651693154" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651693154" rel="stylesheet">
<link href="/css/hybrid.css?1651693154" rel="stylesheet">
<link href="/css/featherlight.min.css?1651693154" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1651693154" rel="stylesheet">
<link href="/css/auto-complete.css?1651693154" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1651693154" rel="stylesheet">
<link href="/css/theme.css?1651693154" rel="stylesheet">
<link href="/css/hugo-theme.css?1651693154" rel="stylesheet">
<link href="/css/theme-blue.css?1651164722" rel="stylesheet">
<link href="/css/theme-blue.css?1651693154" rel="stylesheet">
<script src="/js/jquery-3.3.1.min.js?1651164722"></script>
<script src="/js/jquery-3.3.1.min.js?1651693154"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -61,14 +61,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1651164722"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651164722"></script>
<script type="text/javascript" src="/js/lunr.min.js?1651693154"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651693154"></script>
<script type="text/javascript">
var baseurl = "";
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......@@ -4325,19 +4325,19 @@ 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?1651164722"></script>
<script src="/js/perfect-scrollbar.min.js?1651164722"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1651164722"></script>
<script src="/js/jquery.sticky.js?1651164722"></script>
<script src="/js/featherlight.min.js?1651164722"></script>
<script src="/js/highlight.pack.js?1651164722"></script>
<script src="/js/clipboard.min.js?1651693154"></script>
<script src="/js/perfect-scrollbar.min.js?1651693154"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1651693154"></script>
<script src="/js/jquery.sticky.js?1651693154"></script>
<script src="/js/featherlight.min.js?1651693154"></script>
<script src="/js/highlight.pack.js?1651693154"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1651164722"></script>
<script src="/js/learn.js?1651164722"></script>
<script src="/js/hugo-learn.js?1651164722"></script>
<script src="/js/modernizr.custom-3.6.0.js?1651693154"></script>
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<script src="/js/hugo-learn.js?1651693154"></script>
<link href="/mermaid/mermaid.css?1651164722" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1651164722"></script>
<link href="/mermaid/mermaid.css?1651693154" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1651693154"></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?1651164722" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651164722" rel="stylesheet">
<link href="/css/hybrid.css?1651164722" rel="stylesheet">
<link href="/css/featherlight.min.css?1651164722" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1651164722" rel="stylesheet">
<link href="/css/auto-complete.css?1651164722" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1651164722" rel="stylesheet">
<link href="/css/theme.css?1651164722" rel="stylesheet">
<link href="/css/hugo-theme.css?1651164722" rel="stylesheet">
<link href="/css/nucleus.css?1651693154" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651693154" rel="stylesheet">
<link href="/css/hybrid.css?1651693154" rel="stylesheet">
<link href="/css/featherlight.min.css?1651693154" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1651693154" rel="stylesheet">
<link href="/css/auto-complete.css?1651693154" rel="stylesheet">
<link href="/css/atom-one-dark-reasonable.css?1651693154" rel="stylesheet">
<link href="/css/theme.css?1651693154" rel="stylesheet">
<link href="/css/hugo-theme.css?1651693154" rel="stylesheet">
<link href="/css/theme-blue.css?1651164722" rel="stylesheet">
<link href="/css/theme-blue.css?1651693154" rel="stylesheet">
<script src="/js/jquery-3.3.1.min.js?1651164722"></script>
<script src="/js/jquery-3.3.1.min.js?1651693154"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -61,14 +61,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
</div>
<script type="text/javascript" src="/js/lunr.min.js?1651164722"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651164722"></script>
<script type="text/javascript" src="/js/lunr.min.js?1651693154"></script>
<script type="text/javascript" src="/js/auto-complete.js?1651693154"></script>
<script type="text/javascript">
var baseurl = "";
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......@@ -3902,19 +3902,19 @@ 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>
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<script src="/js/clipboard.min.js?1651164722"></script>
<script src="/js/perfect-scrollbar.min.js?1651164722"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1651164722"></script>
<script src="/js/jquery.sticky.js?1651164722"></script>
<script src="/js/featherlight.min.js?1651164722"></script>
<script src="/js/highlight.pack.js?1651164722"></script>
<script src="/js/clipboard.min.js?1651693154"></script>
<script src="/js/perfect-scrollbar.min.js?1651693154"></script>
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<script src="/js/featherlight.min.js?1651693154"></script>
<script src="/js/highlight.pack.js?1651693154"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1651164722"></script>
<script src="/js/learn.js?1651164722"></script>
<script src="/js/hugo-learn.js?1651164722"></script>
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<link href="/mermaid/mermaid.css?1651693154" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1651693154"></script>
<script>
mermaid.initialize({ startOnLoad: true });
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......
......@@ -12,20 +12,20 @@
<title>Neutron Imaging :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1651164722" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1651164722" rel="stylesheet">
<link href="/css/hybrid.css?1651164722" rel="stylesheet">
<link href="/css/featherlight.min.css?1651164722" rel="stylesheet">
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"title": "Group Images by Cycle for Grating Experiment",
"tags": [],
"description": "",
"content": " Notebook name: group_images_by_cycle_for_grating_experiment.ipynb\nDescription Grating experiment in CT mode collect a multitude of data files, all created in the same folder. Those data must be sorted using first the rotation value and then the G0 value. Then\nThe following notebook will automatically sort the data by group using two metadata. By default those are the G0 and rotation angle, but any other metadata found in the tiff file can be used. Once sorted, the files are renamed to be processed by Angel and the configuration file, excel file, used by Angel is generated to speed up the input required by the user.\nTutorial Select your IPTS Need help using the IPTS selector?\n Select data to sort Using the folder selection tool, select the folder containing the data to process, and then select all the images to work with. The selection of files instead of the entire data in the folder, allows you to have sample and ob within the same folder without compromising the sorting.\nSelect Metadata to use for sorting This is where you can specify how the images will be sorted. The left column will be used as the outer loop parameter and the right column the inner loop parameter. A Search tool is available at the top to allow you to quickly narrow down the list by entering a few keystrokes. The button labeled X to the right of the search fields reset the search criteria.\nGrouping Using the list of files you defined, and the metadata criteria, the files are sorted and the resulting grouping is displayed when running this cell.\nThe left column displays the name of the group, i.e., the outer loop. The second column, the original name of the images and just to its right, the new name that will be used.\nIn the case where more than 1 image have the same inner and outer metadadata values, the images are then combined using a median algorithm.\n In the far right column is displayed the corresponding metadata values of the image selected.\nUnder the table a label reminds the user of the folder name where these images are coming from.\nSelect Output Folder Select where you want the new images to be created. Once selected, the notebook will automatically trigger the renaming and grouping of those files. A couple of progress bars will allow you to follow the progress of the process.\nGenerate Angel Configuration File (Excel) This step is optional but will surely simplify your life if you need to normalize the data using Angel.\nThe first cell (%gui qt) is necessary to bring to life the user interface in the next cell.\nRunning the second cell will give you a few options\n did you sort the sample or the ob data? This is required to be able to populate the right columns in the excel document\n do you want to create a new excel document or do you want to load a previously created excel?\n Create new Excel If you select this option, a new excel will be created and the sample or ob columns will be filled with the files from this notebook. Default values for all the other fields are provided.\nAny cell in red is an indication that this excel will not work in Angel in the current state.\nEditing the table\nYou can manually edit all the cells, except the rotation column. Once the cell has been edited, click the button below the table labeled Checking if current table can be loaded in Angel to check the status of the excel document.\nOnce you modified any of the widget found inside the cell, a pop up window asks you if you want to duplicate that change to all the other widgets of the same column, or not.\nRight clicking inside the table\nSome of the cells, such as the one requesting a file or a folder, allows you, by right clicking inside the cell to bring a file dialog.\nYou can either\n browse for a file and replace the content of the current cell browse for a file and replace the content of all the cells of this column A right click inside any of the cell also allows you to remove the current row or to duplicate that row to the bottom of the table.\nSave as \u0026hellip;\nClick that button, placed at the bottom right of the user interface, to export that table into an excel document.\nSome of the cells can not be modified, such as all the cells in the the rotation column. The last 3 columns, sample_information, used_environment and osc_pixel are not used in Angel.\n Open existing excel In this case, a file dialog will ask you to select the excel file to use and will bring the same user interface. Refer to the section Create new excel to learn how the UI works.\n"
"content": " Notebook name: group_images_by_cycle_for_grating_experiment.ipynb\nDescription Grating experiment in CT mode collect a multitude of data files, all created in the same folder. Those data must be sorted using first the rotation value and then the G0 value. Then\nThe following notebook will automatically sort the data by group using two metadata. By default those are the G0 and rotation angle, but any other metadata found in the tiff file can be used. Once sorted, the files are renamed to be processed by Angel and the configuration file, excel file, used by Angel is generated to speed up the input required by the user.\nTutorial Select your IPTS Need help using the IPTS selector?\n Select data to sort Using the folder selection tool, select the folder containing the data to process, and then select all the images to work with. The selection of files instead of the entire data in the folder, allows you to have sample and ob within the same folder without compromising the sorting.\nSelect the type of data to sort Are you working with sample data or with open beam (ob) data? The choice of the data type will allow the notebook to define the output folder name, and to figure out the right columns to fill up in the excel document.\nSelect Metadata to use for sorting This is where you can specify how the images will be sorted. The left column will be used as the outer loop parameter and the right column the inner loop parameter. A Search tool is available at the top to allow you to quickly narrow down the list by entering a few keystrokes. The button labeled X to the right of the search fields reset the search criteria.\nGrouping Using the list of files you defined, and the metadata criteria, the files are sorted and the resulting grouping is displayed when running this cell.\nThe left column displays the name of the group, i.e., the outer loop. The second column, the original name of the images and just to its right, the new name that will be used.\nIn the case where more than 1 image have the same inner and outer metadadata values, the images are then combined using a median algorithm.\n In the far right column is displayed the corresponding metadata values of the image selected.\nUnder the table a label reminds the user of the folder name where these images are coming from.\nSelect Output Folder Select where you want the new images to be created. Once selected, the notebook will automatically trigger the renaming and grouping of those files. A couple of progress bars will allow you to follow the progress of the process.\nGenerate Angel Configuration File (Excel) This step is optional but will surely simplify your life if you need to normalize the data using Angel.\nThe first cell (%gui qt) is necessary to bring to life the user interface in the next cell.\nDo you want to create a new excel document or do you want to load a previously created excel?\nCreate new Excel If you select this option, a new excel will be created and the sample or ob columns will be filled with the files from this notebook. Default values for all the other fields are provided.\nAny cell in red is an indication that this excel will not work in Angel in the current state.\nEditing the table\nYou can manually edit all the cells, except the rotation column. Once the cell has been edited, click the button below the table labeled Checking if current table can be loaded in Angel to check the status of the excel document.\nOnce you modified any of the widget found inside the cell, a pop up window asks you if you want to duplicate that change to all the other widgets of the same column, or not.\nRight clicking inside the table\nSome of the cells, such as the one requesting a file or a folder, allows you, by right clicking inside the cell to bring a file dialog.\nYou can either\n browse for a file and replace the content of the current cell browse for a file and replace the content of all the cells of this column A right click inside any of the cell also allows you to remove the current row or to duplicate that row to the bottom of the table.\nSave as \u0026hellip;\nClick that button, placed at the bottom right of the user interface, to export that table into an excel document.\nSome of the cells can not be modified, such as all the cells in the the rotation column. The last 3 columns, sample_information, used_environment and osc_pixel are not used in Angel.\n Open existing excel In this case, a file dialog will ask you to select the excel file to use and will bring the same user interface. Refer to the section Create new excel to learn how the UI works.\n"
},
{
"uri": "/tutorial/notebooks/group_images_by_cycle_for_panoramic_stitching/",
......@@ -501,7 +501,7 @@
"title": "Neutron Imaging",
"tags": [],
"description": "",
"content": " User Home Page Welcome to the ORNL Neutron Imaging Website! This site is designed to help you with the preparation of your experiment and subsequent data processing and analysis. If you are not familiar with neutron imaging and may be interested in collaborating with us, visit the publications page to review the science we do.\nFor industrial applications, please contact Hassina Bilheux or Yuxuan Zhang.\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 arrival: Everything you will need to do before coming to our laboratory. Capabilities: list of imaging instruments available. 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 the research community in the implementation of this web site, and always welcome your comments to improve it (contact Jean Bilheux).\n latest updated pages:\n combine_images_n_by_n Normalization Normalization with simplify selection outliers_filtering_tool table_of_contents Last updated: April 8th, 2022\n"
"content": " User Home Page Welcome to the ORNL Neutron Imaging Website! This site is designed to help you with the preparation of your experiment and subsequent data processing and analysis. If you are not familiar with neutron imaging and may be interested in collaborating with us, visit the publications page to review the science we do.\nFor industrial applications, please contact Hassina Bilheux or Yuxuan Zhang.\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 arrival: Everything you will need to do before coming to our laboratory. Capabilities: list of imaging instruments available. 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 the research community in the implementation of this web site, and always welcome your comments to improve it (contact Jean Bilheux).\n latest updated pages:\n combine_images_n_by_n Normalization Normalization with simplify selection outliers_filtering_tool table_of_contents Last updated: May 4th, 2022\n"
},
{
"uri": "/tutorial/notebooks/normalization/",
......
......@@ -12,20 +12,20 @@
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