Commit 8e09f9f9 authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

updated normalization_with_simplify_selection

parent 404d898c
......@@ -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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......@@ -3604,19 +3604,19 @@
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mermaid.initialize({ startOnLoad: true });
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......
......@@ -12,20 +12,20 @@
<title>Categories :: Documentation for Hugo Learn Theme</title>
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<link href="/css/fontawesome-all.min.css?1621434625" rel="stylesheet">
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<link href="/css/nucleus.css?1622032872" rel="stylesheet">
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<script src="/js/jquery-3.3.1.min.js?1622032872"></script>
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......@@ -60,14 +60,14 @@
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......@@ -3559,19 +3559,19 @@
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mermaid.initialize({ startOnLoad: true });
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......
......@@ -12,20 +12,20 @@
<title>Contacts :: Documentation for Hugo Learn Theme</title>
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<link href="/css/fontawesome-all.min.css?1621434625" rel="stylesheet">
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<script src="/js/jquery-3.3.1.min.js?1621434625"></script>
<script src="/js/jquery-3.3.1.min.js?1622032872"></script>
<style>
:root #header + #content > #left > #rlblock_left{
......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
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<script type="text/javascript" src="/js/lunr.min.js?1621434625"></script>
<script type="text/javascript" src="/js/auto-complete.js?1621434625"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622032872"></script>
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......@@ -3637,19 +3637,19 @@
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<script src="/js/perfect-scrollbar.min.js?1621434625"></script>
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......
......@@ -12,20 +12,20 @@
<title>Frequently Asked Questions :: Documentation for Hugo Learn Theme</title>
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<script src="/js/jquery-3.3.1.min.js?1621434625"></script>
<script src="/js/jquery-3.3.1.min.js?1622032872"></script>
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......@@ -60,14 +60,14 @@
<span data-search-clear=""><i class="fas fa-times"></i></span>
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<script type="text/javascript" src="/js/lunr.min.js?1621434625"></script>
<script type="text/javascript" src="/js/auto-complete.js?1621434625"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622032872"></script>
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......@@ -3988,19 +3988,19 @@ TIFF Directory at offset 0x800008 (8388616)
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<script src="/js/featherlight.min.js?1622032872"></script>
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<script>hljs.initHighlightingOnLoad();</script>
<script src="/js/modernizr.custom-3.6.0.js?1621434625"></script>
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<script>
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......@@ -12,20 +12,20 @@
<title>Github Repositories :: Documentation for Hugo Learn Theme</title>
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<script src="/js/jquery-3.3.1.min.js?1621434625"></script>
<script src="/js/jquery-3.3.1.min.js?1622032872"></script>
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......@@ -60,14 +60,14 @@
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<script type="text/javascript" src="/js/lunr.min.js?1621434625"></script>
<script type="text/javascript" src="/js/auto-complete.js?1621434625"></script>
<script type="text/javascript" src="/js/lunr.min.js?1622032872"></script>
<script type="text/javascript" src="/js/auto-complete.js?1622032872"></script>
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......@@ -3565,19 +3565,19 @@ repositories hosting our programs</p>
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......@@ -12,20 +12,20 @@
<title>Neutron Imaging :: Documentation for Hugo Learn Theme</title>
<link href="/css/nucleus.css?1621434625" rel="stylesheet">
<link href="/css/fontawesome-all.min.css?1621434625" rel="stylesheet">
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"title": "Notebooks Tutorials",
"tags": [],
"description": "",
"content": " A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z\nB bin_images bragg_edge_signal_vs_powder_peaks bragg_edge_normalization bragg_edge_profile \nC calibrated_transmission circular_profile_of_a_ring combine_folders combine_all_images_selected combine_images_n_by_n combine_images_without_outliers create_list_of_file_name_vs_time_stamp cylindrical_geometry_correction \nD deal_images display_and_export_images_with_metadata_profile display_and_export_images_with_timestamp display_counts_of_region_vs_stack display_file_names_vs_time_stamp display_integrated_stack_of_images dual_energy \nE extract_evenly_spaced_files extract_nexus_daslogs \nF file_name_and_metadata_vs_time_stamp fix_images frederick_ipts from_attenuation_to_concentration from_dsc_time_info_to_ascii_file_vs_time \nG gamma_filtering_tool group_images_by_cycle_for_panoramic_stitching \nH hfir_reactor_element_analysis \nI images_and_metadata_extrapolation_matcher integrated_roi_counts_vs_file_name_and_time_stamp \nL list_element_bragg_edges list_metadata_and_time_with_oncat list_tiff_metadata \nM mcp_chips_corrector metadata_ascii_parser metadata_overlapping_images \nN normalization normalization_with_simplify_selection \nO overlay_images \nP panoramic_stitching panoramic_stitching_for_tof profile \nR radial_profile registration rename_files resonance_imaging_experiment_vs_theory rotate_and_crop_images \nS sequential_combine_images_using_metadata \nT template_ui topaz_config_generator \nW water_intake_profile_calculator \nTools File Selector Select IPTS \nExtra extract_sans_reductionlog_metadata \n Recently updated\n Levels of documentation\n"
"content": " A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z\nB bin_images bragg_edge_signal_vs_powder_peaks bragg_edge_normalization bragg_edge_profile \nC calibrated_transmission circular_profile_of_a_ring combine_folders combine_all_images_selected combine_images_n_by_n combine_images_without_outliers create_list_of_file_name_vs_time_stamp cylindrical_geometry_correction \nD deal_images display_and_export_images_with_metadata_profile display_and_export_images_with_timestamp display_counts_of_region_vs_stack display_file_names_vs_time_stamp display_integrated_stack_of_images dual_energy \nE extract_evenly_spaced_files extract_nexus_daslogs \nF file_name_and_metadata_vs_time_stamp fix_images frederick_ipts from_attenuation_to_concentration from_dsc_time_info_to_ascii_file_vs_time \nG gamma_filtering_tool group_images_by_cycle_for_panoramic_stitching \nH hfir_reactor_element_analysis \nI images_and_metadata_extrapolation_matcher integrated_roi_counts_vs_file_name_and_time_stamp \nL list_element_bragg_edges list_metadata_and_time_with_oncat list_tiff_metadata \nM mcp_chips_corrector metadata_ascii_parser metadata_overlapping_images \nN normalization normalization_with_simplify_selection \nO overlay_images \nP panoramic_stitching panoramic_stitching_for_tof profile \nR radial_profile registration rename_files resonance_imaging_experiment_vs_theory rotate_and_crop_images \nS sequential_combine_images_using_metadata \nT template_ui topaz_config_generator \nW water_intake_profile_calculator \nTools File Selector Select IPTS \nExtra extract_sans_reductionlog_metadata \n Recently updated\n Levels of documentation\n"
},
{
"uri": "/tutorial/notebooks/bin_images/",
......@@ -487,7 +487,7 @@
"title": "Normalization with Simplify Selection",
"tags": [],
"description": "",
"content": " Notebook name: normalization_with_simplify_selection.ipynb\nDescription This notebook normalized the imaging data (tiff or fits) by removing the background and fixing the fluctuations of the neutron beam. You will need:\n select your sample images folder Keep default option of using all open beam (OB) and dark field (DF) images from the same IPTS or select a different time frame select output folder where the normalized images will be saved The big improvement of this notebook compared to the old normalization notebook is that now, the notebook will take care of finding all the OB and DF for you, and will match them to your sample data by making sure that:\n the slits have the same position the acquisition time is identical the detector type is identical Start the notebook If you need help accessing this notebook, check the How To \u0026gt; Start the python notebooks tutorial.\nHow to Use It? Select your IPTS Check the full tutorial here\nSelecting the Sample Images Simply navigate to the folder containing all the data your want to normalize. The program will then list the files with the most dominant extension, for example, if you have a folder with 10 tiff images and 2 fits, only the 10 tiff images will be used. All the sample images will be grouped according to the following criteria:\n acquisition time slits positions detector type The notebook will then retrieve all the OB and DF of the same IPTS by looking into the /raw/ob and /raw/df folders respectively of your IPTS folder. The OB and DF that match the sample criteria will then be associated to their sample data.\nNormalization workflow This table will summarizes the data reduction that is about to take place. If a config has no OB, the table will let you know that this config won\u0026rsquo;t be normalized unless you provide at least one OB.\nSelect Output Folder Select the output location where you want all the normalized folders to be created. Then a message will let you know when the normalization is done and the name of the files created.\nCheck the folder selection tool tutorial to learn how to use the folder selector tool. "
"content": " Notebook name: normalization_with_simplify_selection.ipynb\nDescription This notebook normalized the imaging data (tiff or fits) by removing the background and fixing the fluctuations of the neutron beam. You will need to follow these steps:\n select your sample images folder Select the OB from the list proposed select output folder where the normalized images will be saved The big improvement of this notebook compared to the old normalization notebook is that now, the notebook takes care of finding all the OB and DF for you, and matches them with your sample data by making sure that:\n the slits have the same position the acquisition time is identical the detector type is identical Start the notebook If you need help accessing this notebook, check the How To \u0026gt; Start the python notebooks tutorial.\nHow to Use It? Select your IPTS Check the full tutorial here\nSelecting the Sample Images Simply navigate to the folder containing all the data your want to normalize. The program will then list the files with the most dominant extension, for example, if you have a folder with 10 tiff images and 2 fits, only the 10 tiff images will be used. All the sample images will be grouped according to the following criteria:\n acquisition time slits positions detector type The notebook will then retrieve all the OB and DF of the same IPTS by looking into the /raw/ob and /raw/df folders respectively of your IPTS folder. The OB and DF that match the sample criteria will then be associated to their sample data.\nAt that point, you have the power to finalize the selection:\n For each configuration, you can reject it from normalization by turning off the switch named Normalize this configuration The list of OB proposed include ALL the OBs found with matching metadata (see above) in the corresponding IPTS, no matter how long before or after they were acquired. By default they are all selected in the list widget. Feel free to narrow down that selection by manually selecting them (see next animation). You can also narrow down that selection by setting up yourself a time range before and after the sample data runs (see the next animation) Normalization workflow This table will summarizes the data reduction that is about to take place. If a config has no OB, the table will let you know that this config won\u0026rsquo;t be normalized unless you provide at least one OB. Also, if you decided to turn off the normalization of any particular config, you will see it in that table.\nSelect Output Folder Select the output location where you want all the normalized folders to be created. Then a message will let you know when the normalization is done and the name of the files created.\nCheck the folder selection tool tutorial to learn how to use the folder selector tool. "
},
{
"uri": "/tutorial/notebooks/overlay_images/",
......
......@@ -12,20 +12,20 @@
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