Added calibrated transmission documentation

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Calibrated Transmission <i class='fa fa-battery-empty'></i>
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">
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Calibrated Transmission <i class='fa fa-battery-empty'></i>
Calibrated Transmission <i class='fa fa-battery-full'></i>
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">
<a href="/en/tutorial/notebooks/calibrated_transmission/">
Calibrated Transmission <i class='fa fa-battery-empty'></i>
Calibrated Transmission <i class='fa fa-battery-full'></i>
<i class="fa fa-check read-icon"></i>
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......@@ -88,7 +88,7 @@
"title": "Notebooks Tutorials",
"tags": [],
"description": "",
"content": " bin_images calculate_water_intake_profile calibrated_transmission combine_folders combine_images create_list_of_file_name_vs_time_stamp deal_files display_and_export_images_with_metadata_profile display_and_export_images_with_timestamp display_counts_of_region_vs_stack display_integrated_stack_of_images file_name_and_metadata_vs_time_stamp fix_images fix_images_with_negative_pixels format_filename_index frederick_ipts from_dsc_time_info_to_ascii_file_vs_time ipts_18813 gamma_filtering_tool linear_profile list_tiff_metadata locate_pixels normalization_live normalization_batch profile_vs_file_index radial_profile registration resonance_imaging_experiment_vs_theory rotate_and_crop_images template_ui topaz_config_generator water_intake_profile_calculator \nTools File Selector Select IPTS \n Recently updated\n"
"content": " bin_images calculate_water_intake_profile calibrated_transmission combine_folders combine_images create_list_of_file_name_vs_time_stamp deal_files display_and_export_images_with_metadata_profile display_and_export_images_with_timestamp display_counts_of_region_vs_stack display_integrated_stack_of_images file_name_and_metadata_vs_time_stamp fix_images fix_images_with_negative_pixels format_filename_index frederick_ipts from_dsc_time_info_to_ascii_file_vs_time ipts_18813 gamma_filtering_tool linear_profile list_tiff_metadata locate_pixels normalization_live normalization_batch profile_vs_file_index radial_profile registration resonance_imaging_experiment_vs_theory rotate_and_crop_images template_ui topaz_config_generator water_intake_profile_calculator \nTools File Selector Select IPTS \n Recently updated\n"
},
{
"uri": "/en/tutorial/how_to_other/",
......@@ -123,7 +123,7 @@
"title": "Calibrated Transmission",
"tags": [],
"description": "",
"content": "Notebook name: calibrated_transmission.ipynb\n"
"content": " Notebook name: calibrated_transmission.ipynb\nDescription The goal of this notebook is to display the average counts of region selected for each file. It\u0026rsquo;s possible to calibrate up to 2 regions by giving them a value. If a region with a mean counts of 100 is calibrated to 1 for example, all the other value displayed will use this new scaled defined. That means, if for a file the mean counts of a region is 200, the program will display 2. When 2 calibrated region are defined, a linear interpolation is used to dislay the mean counts of the region selected. When no calibrated region have been defined, the true (raw) mean counts are displayed.\nStart the notebook If you need help accessing this notebook, check the How To \u0026gt; Start the python notebooks tutorial.\nSelect your IPTS Need help using the IPTS selector?\n Select Images to Process Select the images you want to process using the File Selector. Once you click the Select button, the time stamp and the images will be automatically loaded. Wait for the progress bar to be done.\nNeed help using the File Selector?\n Calibrated Transmission UI Presentation How Does it Work ? Define the Calibration Regions Activate or deactivate the calibration region you want/do not want. Define the position and size of the region (using mouse in the image viewer, or by manual input) Select the value corresponding to this region Select the file to use corresponding to that region Define the Measurement Regions Go the Measurement Regions tab Add new regions by clicking the + button at the bottom right Change the position (using mouse in image viewer or by manual input in the table) Remove regions using the - button Summary Tab The Summary tab display the list of files, time stamp, relative time (using the first file as reference or time 0), and mean counts calibrated for each measurement regions.\nExport Calibrated Transmission You can now export the calibrated transmission signal for each file by clicking the Export Calibrated Transmission button. Just select the output location. The file name created will be based on the input data folder and will look like this.\nIf input data file is light_loop1_flow2, the output file will be named light_loop1_flow2_calibrated_transmission.txt\n"
},
{
"uri": "/en/categories/",
......
......@@ -13,19 +13,19 @@
<title>Links :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1525292826" rel="stylesheet">
<link href="/css/font-awesome.min.css?1525292826" rel="stylesheet">
<link href="/css/hybrid.css?1525292826" rel="stylesheet">
<link href="/css/featherlight.min.css?1525292826" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1525292826" rel="stylesheet">
<link href="/css/auto-complete.css?1525292826" rel="stylesheet">
<link href="/css/theme.css?1525292826" rel="stylesheet">
<link href="/css/hugo-theme.css?1525292826" rel="stylesheet">
<link href="/css/nucleus.css?1525972153" rel="stylesheet">
<link href="/css/font-awesome.min.css?1525972153" rel="stylesheet">
<link href="/css/hybrid.css?1525972153" rel="stylesheet">
<link href="/css/featherlight.min.css?1525972153" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1525972153" rel="stylesheet">
<link href="/css/auto-complete.css?1525972153" rel="stylesheet">
<link href="/css/theme.css?1525972153" rel="stylesheet">
<link href="/css/hugo-theme.css?1525972153" rel="stylesheet">
<link href="/css/theme-blue.css?1525292826" rel="stylesheet">
<link href="/css/theme-blue.css?1525972153" rel="stylesheet">
<script src="/js/jquery-2.x.min.js?1525292826"></script>
<script src="/js/jquery-2.x.min.js?1525972153"></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?1525292826"></script>
<script type="text/javascript" src="/js/auto-complete.js?1525292826"></script>
<script type="text/javascript" src="/js/lunr.min.js?1525972153"></script>
<script type="text/javascript" src="/js/auto-complete.js?1525972153"></script>
<script type="text/javascript">
var baseurl = "\/en";
</script>
<script type="text/javascript" src="/js/search.js?1525292826"></script>
<script type="text/javascript" src="/js/search.js?1525972153"></script>
</div>
......@@ -467,7 +467,7 @@
">
<a href="/en/tutorial/notebooks/calibrated_transmission/">
Calibrated Transmission <i class='fa fa-battery-empty'></i>
Calibrated Transmission <i class='fa fa-battery-full'></i>
<i class="fa fa-check read-icon"></i>
......@@ -2610,20 +2610,20 @@
<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?1525292826"></script>
<script src="/js/perfect-scrollbar.min.js?1525292826"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1525292826"></script>
<script src="/js/jquery.sticky.js?1525292826"></script>
<script src="/js/featherlight.min.js?1525292826"></script>
<script src="/js/html5shiv-printshiv.min.js?1525292826"></script>
<script src="/js/highlight.pack.js?1525292826"></script>
<script src="/js/clipboard.min.js?1525972153"></script>
<script src="/js/perfect-scrollbar.min.js?1525972153"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1525972153"></script>
<script src="/js/jquery.sticky.js?1525972153"></script>
<script src="/js/featherlight.min.js?1525972153"></script>
<script src="/js/html5shiv-printshiv.min.js?1525972153"></script>
<script src="/js/highlight.pack.js?1525972153"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom.71422.js?1525292826"></script>
<script src="/js/learn.js?1525292826"></script>
<script src="/js/hugo-learn.js?1525292826"></script>
<script src="/js/modernizr.custom.71422.js?1525972153"></script>
<script src="/js/learn.js?1525972153"></script>
<script src="/js/hugo-learn.js?1525972153"></script>
<link href="/mermaid/mermaid.css?1525292826" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1525292826"></script>
<link href="/mermaid/mermaid.css?1525972153" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1525972153"></script>
<script>
mermaid.initialize({ startOnLoad: true });
</script>
......
......@@ -13,19 +13,19 @@
<title>Access :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1525292826" rel="stylesheet">
<link href="/css/font-awesome.min.css?1525292826" rel="stylesheet">
<link href="/css/hybrid.css?1525292826" rel="stylesheet">
<link href="/css/featherlight.min.css?1525292826" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1525292826" rel="stylesheet">
<link href="/css/auto-complete.css?1525292826" rel="stylesheet">
<link href="/css/theme.css?1525292826" rel="stylesheet">
<link href="/css/hugo-theme.css?1525292826" rel="stylesheet">
<link href="/css/nucleus.css?1525972153" rel="stylesheet">
<link href="/css/font-awesome.min.css?1525972153" rel="stylesheet">
<link href="/css/hybrid.css?1525972153" rel="stylesheet">
<link href="/css/featherlight.min.css?1525972153" rel="stylesheet">
<link href="/css/perfect-scrollbar.min.css?1525972153" rel="stylesheet">
<link href="/css/auto-complete.css?1525972153" rel="stylesheet">
<link href="/css/theme.css?1525972153" rel="stylesheet">
<link href="/css/hugo-theme.css?1525972153" rel="stylesheet">
<link href="/css/theme-blue.css?1525292826" rel="stylesheet">
<link href="/css/theme-blue.css?1525972153" rel="stylesheet">
<script src="/js/jquery-2.x.min.js?1525292826"></script>
<script src="/js/jquery-2.x.min.js?1525972153"></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?1525292826"></script>
<script type="text/javascript" src="/js/auto-complete.js?1525292826"></script>
<script type="text/javascript" src="/js/lunr.min.js?1525972153"></script>
<script type="text/javascript" src="/js/auto-complete.js?1525972153"></script>
<script type="text/javascript">
var baseurl = "\/en";
</script>
<script type="text/javascript" src="/js/search.js?1525292826"></script>
<script type="text/javascript" src="/js/search.js?1525972153"></script>
</div>
......@@ -467,7 +467,7 @@
">
<a href="/en/tutorial/notebooks/calibrated_transmission/">
Calibrated Transmission <i class='fa fa-battery-empty'></i>
Calibrated Transmission <i class='fa fa-battery-full'></i>
<i class="fa fa-check read-icon"></i>
......@@ -2389,20 +2389,20 @@
<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?1525292826"></script>
<script src="/js/perfect-scrollbar.min.js?1525292826"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1525292826"></script>
<script src="/js/jquery.sticky.js?1525292826"></script>
<script src="/js/featherlight.min.js?1525292826"></script>
<script src="/js/html5shiv-printshiv.min.js?1525292826"></script>
<script src="/js/highlight.pack.js?1525292826"></script>
<script src="/js/clipboard.min.js?1525972153"></script>
<script src="/js/perfect-scrollbar.min.js?1525972153"></script>
<script src="/js/perfect-scrollbar.jquery.min.js?1525972153"></script>
<script src="/js/jquery.sticky.js?1525972153"></script>
<script src="/js/featherlight.min.js?1525972153"></script>
<script src="/js/html5shiv-printshiv.min.js?1525972153"></script>
<script src="/js/highlight.pack.js?1525972153"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom.71422.js?1525292826"></script>
<script src="/js/learn.js?1525292826"></script>
<script src="/js/hugo-learn.js?1525292826"></script>
<script src="/js/modernizr.custom.71422.js?1525972153"></script>
<script src="/js/learn.js?1525972153"></script>
<script src="/js/hugo-learn.js?1525972153"></script>
<link href="/mermaid/mermaid.css?1525292826" type="text/css" rel="stylesheet" />
<script src="/mermaid/mermaid.js?1525292826"></script>
<link href="/mermaid/mermaid.css?1525972153"