Commit dda8103a authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
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Updated raw_sample_and_powder notebook

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"title": "Bragg Edge Raw Sample and Powder",
"tags": [],
"description": "",
"content": " Notebook name: bragg_edge_raw_sample_and_powder.ipynb\nDescription 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\nSelect Raw Data Input Folder Select the folder containing the full sample tof data. The program will automatically try to locate the time spectra file in this folder. If not found, you will need to locate it next.\nSelect Open Beam Input Folder Just like it was done for the sample data, select the open beam folder. The notebook will let you know if the sample and ob folders have the same number of files.\nSelect ROI of sample You need to define the position of the sample in the view.\nSelect how many random files to use to select sample position The first widget allows you to select how many images to use (those will be summed into a single view) to define that region of interest. The higher the number of images used, the longer the next user interface will take to show up. Usually the default value is a good compromise and is high enough to get a good idea of the position of the sample.\nSelect location of sample in integrated image Check the ROI selection tool tutorial to learn how to use that tool.\nNormalize Data The program will use the sample and ob loaded to normalized the data.\nPowder element This is where you can define one, or more element to use to compare the Bragg edges with.\nYou can choose any element from the following list:\n\u0026lsquo;C (diamond)\u0026rsquo; \u0026lsquo;C (graphite)\u0026rsquo; \u0026lsquo;Si\u0026rsquo; \u0026lsquo;Ge\u0026rsquo; \u0026lsquo;AlAs\u0026rsquo; \u0026lsquo;AlP\u0026rsquo; \u0026lsquo;AlSb\u0026rsquo; \u0026lsquo;GaP\u0026rsquo; \u0026lsquo;GaAs\u0026rsquo; \u0026lsquo;GaSb\u0026rsquo; \u0026lsquo;inconel\u0026rsquo; \u0026lsquo;InP\u0026rsquo; \u0026lsquo;InAs\u0026rsquo; \u0026lsquo;InSb\u0026rsquo; \u0026lsquo;MgO\u0026rsquo; \u0026lsquo;SiC\u0026rsquo; \u0026lsquo;CdS\u0026rsquo; \u0026lsquo;CdSe\u0026rsquo; \u0026lsquo;CdTe\u0026rsquo; \u0026lsquo;ZnO\u0026rsquo; \u0026lsquo;ZnS\u0026rsquo; \u0026lsquo;PbS\u0026rsquo; \u0026lsquo;PbTe\u0026rsquo; \u0026lsquo;BN\u0026rsquo; \u0026lsquo;BP\u0026rsquo; \u0026lsquo;CdS\u0026rsquo; \u0026lsquo;ZnS\u0026rsquo; \u0026lsquo;AlN\u0026rsquo; \u0026lsquo;GaN\u0026rsquo; \u0026lsquo;InN\u0026rsquo; \u0026lsquo;LiF\u0026rsquo; \u0026lsquo;LiCl\u0026rsquo; \u0026lsquo;LiBr\u0026rsquo; \u0026lsquo;LiI\u0026rsquo; \u0026lsquo;NaF\u0026rsquo; \u0026lsquo;NaCl\u0026rsquo; \u0026lsquo;NaBr\u0026rsquo; \u0026lsquo;NaI\u0026rsquo; \u0026lsquo;KF\u0026rsquo; \u0026lsquo;KCl\u0026rsquo; \u0026lsquo;KBr\u0026rsquo; \u0026lsquo;KI\u0026rsquo; \u0026lsquo;RbF\u0026rsquo; \u0026lsquo;RbCl\u0026rsquo; \u0026lsquo;RbBr\u0026rsquo; \u0026lsquo;RbI\u0026rsquo; \u0026lsquo;CsF\u0026rsquo; \u0026lsquo;CsCl\u0026rsquo; \u0026lsquo;CsI\u0026rsquo; \u0026lsquo;Al\u0026rsquo; \u0026lsquo;Fe\u0026rsquo; \u0026lsquo;Ni\u0026rsquo; \u0026lsquo;Cu\u0026rsquo; \u0026lsquo;Mo\u0026rsquo; \u0026lsquo;Pd\u0026rsquo; \u0026lsquo;Ag\u0026rsquo; \u0026lsquo;W\u0026rsquo; \u0026lsquo;Pt\u0026rsquo; \u0026lsquo;Au\u0026rsquo; \u0026lsquo;Pb\u0026rsquo; \u0026lsquo;TiN\u0026rsquo; \u0026lsquo;ZrN\u0026rsquo; \u0026lsquo;HfN\u0026rsquo; \u0026lsquo;VN\u0026rsquo; \u0026lsquo;CrN\u0026rsquo; \u0026lsquo;NbN\u0026rsquo; \u0026lsquo;TiC\u0026rsquo; \u0026lsquo;ZrC0.97\u0026rsquo; \u0026lsquo;HfC0.99\u0026rsquo; \u0026lsquo;VC0.97\u0026rsquo; \u0026lsquo;NC0.99\u0026rsquo; \u0026lsquo;TaC0.99\u0026rsquo; \u0026lsquo;Cr3C2\u0026rsquo; \u0026lsquo;WC\u0026rsquo; \u0026lsquo;ScN\u0026rsquo; \u0026lsquo;LiNbO3\u0026rsquo; \u0026lsquo;KTaO3\u0026rsquo; \u0026lsquo;BaTiO3\u0026rsquo; \u0026lsquo;SrTiO3\u0026rsquo; \u0026lsquo;CaTiO3\u0026rsquo; \u0026lsquo;PbTiO3\u0026rsquo; \u0026lsquo;EuTiO3\u0026rsquo; \u0026lsquo;SrVO3\u0026rsquo; \u0026lsquo;CaVO3\u0026rsquo; \u0026lsquo;BaMnO3\u0026rsquo; \u0026lsquo;CaMnO3\u0026rsquo; \u0026lsquo;SrRuO3\u0026rsquo; \u0026lsquo;YAlO3\u0026rsquo;\nThis is based on a library we developped called BraggEdge.\nTo enter more than 1 element, use a colon to separate them. Run the next cell to check if the element is part of the list.\nDefine Experiment Setup Those information will be needed to convert the time of flight values into lambda.\nCalculate Bragg Edge Data Just run this cell to let the notebook convert TOF information into lambda and prepare the data to compare them with the unstrained, powder, Bragg edges.\nDisplay Bragg Edges vs Signal Sample signal and unstrained Bragg edges of elements selected will be displayed on the same plot.\nFeel free to play with the iPlot widgets (above the plot) to zoom, pan, \u0026hellip; etc\n"
"content": " Notebook name: bragg_edge_raw_sample_and_powder.ipynb\nDescription 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\nSelect Raw Data Input Folder Select the folder containing the full sample tof data. The program will automatically try to locate the time spectra file in this folder. If not found, you will need to locate it next.\nSelect Open Beam Input Folder Just like it was done for the sample data, select the open beam folder. The notebook will let you know if the sample and ob folders have the same number of files.\nSelect Background Region In order to improve the normalization, you have the option to select a region of interest (ROI) in the radiographs of the sample. Make sure that if you select a region, this region is away from the sample, and only contain the background.\nSelect how many random files to use to select ROI The first widget allows you to select how many images to use (those will be summed into a single view) to define that region of interest. The higher the number of images used, the longer the next user interface will take to show up. Usually the default value is a good compromise and is high enough to get a good idea of the position of the sample.\nSelect background region in integrated image Check the ROI selection tool tutorial to learn how to use that tool.\nNormalize Data The program will use the sample and ob loaded, and the optional background ROI, to normalized the data.\nPowder element(s) to use to compare the Bragg edges This is where you can define one, or more element to use to compare the Bragg edges with.\nYou can choose any element from the following list:\n\u0026lsquo;C (diamond)\u0026rsquo; \u0026lsquo;C (graphite)\u0026rsquo; \u0026lsquo;Si\u0026rsquo; \u0026lsquo;Ge\u0026rsquo; \u0026lsquo;AlAs\u0026rsquo; \u0026lsquo;AlP\u0026rsquo; \u0026lsquo;AlSb\u0026rsquo; \u0026lsquo;GaP\u0026rsquo; \u0026lsquo;GaAs\u0026rsquo; \u0026lsquo;GaSb\u0026rsquo; \u0026lsquo;inconel\u0026rsquo; \u0026lsquo;InP\u0026rsquo; \u0026lsquo;InAs\u0026rsquo; \u0026lsquo;InSb\u0026rsquo; \u0026lsquo;MgO\u0026rsquo; \u0026lsquo;SiC\u0026rsquo; \u0026lsquo;CdS\u0026rsquo; \u0026lsquo;CdSe\u0026rsquo; \u0026lsquo;CdTe\u0026rsquo; \u0026lsquo;ZnO\u0026rsquo; \u0026lsquo;ZnS\u0026rsquo; \u0026lsquo;PbS\u0026rsquo; \u0026lsquo;PbTe\u0026rsquo; \u0026lsquo;BN\u0026rsquo; \u0026lsquo;BP\u0026rsquo; \u0026lsquo;CdS\u0026rsquo; \u0026lsquo;ZnS\u0026rsquo; \u0026lsquo;AlN\u0026rsquo; \u0026lsquo;GaN\u0026rsquo; \u0026lsquo;InN\u0026rsquo; \u0026lsquo;LiF\u0026rsquo; \u0026lsquo;LiCl\u0026rsquo; \u0026lsquo;LiBr\u0026rsquo; \u0026lsquo;LiI\u0026rsquo; \u0026lsquo;NaF\u0026rsquo; \u0026lsquo;NaCl\u0026rsquo; \u0026lsquo;NaBr\u0026rsquo; \u0026lsquo;NaI\u0026rsquo; \u0026lsquo;KF\u0026rsquo; \u0026lsquo;KCl\u0026rsquo; \u0026lsquo;KBr\u0026rsquo; \u0026lsquo;KI\u0026rsquo; \u0026lsquo;RbF\u0026rsquo; \u0026lsquo;RbCl\u0026rsquo; \u0026lsquo;RbBr\u0026rsquo; \u0026lsquo;RbI\u0026rsquo; \u0026lsquo;CsF\u0026rsquo; \u0026lsquo;CsCl\u0026rsquo; \u0026lsquo;CsI\u0026rsquo; \u0026lsquo;Al\u0026rsquo; \u0026lsquo;Fe\u0026rsquo; \u0026lsquo;Ni\u0026rsquo; \u0026lsquo;Cu\u0026rsquo; \u0026lsquo;Mo\u0026rsquo; \u0026lsquo;Pd\u0026rsquo; \u0026lsquo;Ag\u0026rsquo; \u0026lsquo;W\u0026rsquo; \u0026lsquo;Pt\u0026rsquo; \u0026lsquo;Au\u0026rsquo; \u0026lsquo;Pb\u0026rsquo; \u0026lsquo;TiN\u0026rsquo; \u0026lsquo;ZrN\u0026rsquo; \u0026lsquo;HfN\u0026rsquo; \u0026lsquo;VN\u0026rsquo; \u0026lsquo;CrN\u0026rsquo; \u0026lsquo;NbN\u0026rsquo; \u0026lsquo;TiC\u0026rsquo; \u0026lsquo;ZrC0.97\u0026rsquo; \u0026lsquo;HfC0.99\u0026rsquo; \u0026lsquo;VC0.97\u0026rsquo; \u0026lsquo;NC0.99\u0026rsquo; \u0026lsquo;TaC0.99\u0026rsquo; \u0026lsquo;Cr3C2\u0026rsquo; \u0026lsquo;WC\u0026rsquo; \u0026lsquo;ScN\u0026rsquo; \u0026lsquo;LiNbO3\u0026rsquo; \u0026lsquo;KTaO3\u0026rsquo; \u0026lsquo;BaTiO3\u0026rsquo; \u0026lsquo;SrTiO3\u0026rsquo; \u0026lsquo;CaTiO3\u0026rsquo; \u0026lsquo;PbTiO3\u0026rsquo; \u0026lsquo;EuTiO3\u0026rsquo; \u0026lsquo;SrVO3\u0026rsquo; \u0026lsquo;CaVO3\u0026rsquo; \u0026lsquo;BaMnO3\u0026rsquo; \u0026lsquo;CaMnO3\u0026rsquo; \u0026lsquo;SrRuO3\u0026rsquo; \u0026lsquo;YAlO3\u0026rsquo;\nThis is based on a library we developed called BraggEdge.\nTo enter more than 1 element, use a colon to separate them. Run the next cell to check if the element is part of the list.\nSelect Sample ROI This is where you define the position (ROI) of your sample on the radiographs. Only the counts within that region will be used in the rest of the notebook.\nCheck the ROI selection tool tutorial to learn how to use that tool.\nDefine Experiment Setup Those information will be needed to convert the time of flight values into lambda. Make sure you used the right units\n dSD (distance source detector) in meters detector offset in micro seconds Calculate Bragg Edge Data Just run this cell to let the notebook convert TOF information into lambda and prepare the data to compare them with the un-strained, powder, Bragg edges.\nDisplay Bragg Edges vs Signal Sample signal and un-strained Bragg edges of elements selected will be displayed on the same plot.\nFeel free to play with the iPlot widgets (above the plot) to zoom, pan, \u0026hellip; etc\nExport Data Transmission versus Lambda You can now export into an ascii file the average transmission vs Lambda (and tof) The ascii file created will have the following format\n# input sample folder # list of region of interest used to define sample position # list of region of interest used to define background position # # tof (micros), lambda (Angstroms), Average transmission # all data in 3 columns format Power Bragg edge table You can also export the Bragg edges values of the various elements you selected\n"
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......
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