Commit bcd4404b authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

ready to deploy new notebook about normalization with simplify selection

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......@@ -2425,7 +2425,8 @@ web site, and always <strong>welcome your comments</strong> to improve it (conta
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<p align="center">Last updated: March 24th, 2022</p>
<p><p align="center">Last updated: April 4th, 2022</p>
<p align="center">latest updated pages: <a href="/tutorial/notebooks/normalization_with_simplify_selection/#activate-search">Normalization with simplify selection</a></p>
......@@ -3843,19 +3844,19 @@ web site, and always <strong>welcome your comments</strong> to improve it (conta
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"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 Last updated: March 24th, 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 Last updated: April 4th, 2022\nlatest updated pages: Normalization with simplify selection\n"
},
{
"uri": "/tutorial/notebooks/normalization/",
......@@ -508,7 +508,7 @@
"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 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. "
"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) According to the number of sample and open beams loaded, you may have the option to combine the open beams or not, and to provide the algorithm to use to combine them. Here are the possible scenario:\n there is as many sample and ob data. You can either combine the OBs or not. If you choose not to combine them, each sample will use 1 OB.\n the number of sample and ob is different, you don\u0026rsquo;t have the choice to combine or not, but you can select how the OBs will be combine, either median and mean.\n A table below the DF list will summarize the state of that normalization.\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. 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/outliers_filtering_tool/",
......
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