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        "author": "Pelle Garbus",
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        "description": "INTRODUCTION\n============\n\nMaterials science research visualization of FullProf-refined neutron (DMC::SINQ::PSI) and X-ray powder diffraction data.\nFullProf .prf, .out and .pcr files are read and informations on:\n\n*  refined parameters,\n*  phases,\n*  apparent crystalline sizes,\n*  phase fractions\n\nare hardcoded next to the graph of \"Yobs\", \"Ycal\" and \"Yobs-Ycal\".\nTwo images are saved:\n\n* Truncated graph enhanced with refined parameters.\n* Full graph without distractions.\n* Both graphs are displayed in reciprocal space.\n\n.. image:: https://github.com/pgarbus/magnetmatter/blob/master/magnetmatter/plot_prf_examples/8nm_plain.png?raw=true\n\n.. image:: https://github.com/pgarbus/magnetmatter/blob/master/magnetmatter/plot_prf_examples/8nm.png?raw=true\n\nsee section `HOW SHOULD FILES BE ORGANIZED`_ to understand how your files should be organized. The example folders shown are possible to download.\n\nTOC:\n\n* `INSTALLATION`_\n* `HOW TO USE`_\n* `HOW SHOULD FILES BE ORGANIZED`_\n* `NEW FORMAT OF PCR FILE`_\n* `LaTeX FORMAT OF PHASENAMES`_\n* `REPOSITORY`_\n* `TODO`_\n\n\n============\nINSTALLATION\n============\n\nThis installation assumes that you have access to python3 (version > 3.6).\nIf on Ubuntu/MacTos, python 2.7 will be preinstalled. Then use \"python3\" and \"pip3\" for all purposes. Otherwise \"python\" and \"pip\" will be enough. Check version of python installation by typing \"python --version\" into command prompt or terminal.\n\nBefore installing, try\n\n::\n\n   $ pip search magnetmatter\n\nand you should see\n\n* \"magnetmatter (?.?.?)  - Visualization of FullProf-refined neutron and X-ray powder diffraction data\"\n\nnow go ahead with the installation\n\n::\n\n   $ pip install magnetmatter\n\nnow be patient while \"magnetmatter\" is installed.\nInstallation may be longer because dependencies such as\n\n* \"numpy\", \"pandas\", \"matplotlib\"\n\nare installed if missing.\n\n\n==========\nHOW TO USE\n==========\n\nInitiate python in a terminal or use your favorite editor. Then type\n\n::\n\n    >>> import magnetmatter as mm\n\nType now\n\n::\n\n   >>> path = r\"C:\\give\\a\\valid\\path\\to\\folder\\with\\datasubfolders\\\"  # Windows\n   >>> path = r\"C:/give/a/valid/path/to/folder/with/datasubfolders/\"  # Linux\n   >>> mm.plot_prf(path)\n\nBy default printsize = \"two_in_docx\" and xlim = (2.8,3.6).\nThe xlim parameter (values in reciprocal space) truncates the enhanced graph.\nThe default printed size is approximately 8 cm (two plots fit into a docx document).\nOther options include:\n\n::\n\n\t>>> mm.plot_prf(path, xlim = (2.8,3.6)) # default!\n\t>>> mm.plot_prf(path, xlim = (1.0,2.0)) # show 1 to 2 invers \u00c3\u2026 in enhanced graph\n\t>>> mm.plot_prf(path, xlim = None) # Enhanced graph is not truncated\n\t>>> mm.plot_prf(path, printsize = \"one_in_docx\") # 15 cm wide\n\t>>> mm.plot_prf(path, printsize = \"two_in_ppt\")  # 17 cm wide\n\t>>> mm.plot_prf(path, printsize = \"one_in_ppt\")  # 32 cm wide\n\nThe files are saved as .png in the \"path\" folder.\n\n=============================\nHOW SHOULD FILES BE ORGANIZED\n=============================\n\nThe script goes into each subfolder and looks for an .out, a .pcr and a .prf file.\nIf no such files are found (or if indeed multiple files are found), the script will skip the respective folder.\nNote the \"backup\" folder is not mandatory. I like to keep a copy of an uncorrupted .pcr at hand.\n\nThe below examples can be downloaded from `here <https://github.com/pgarbus/magnetmatter/tree/master/magnetmatter/plot_prf_examples>`_.\n\n::\n\n |./\n |   CoKa_BB_ISx.irf\n |   CoKa_PB_ISxmm.irf\n |   17nm.png\n |   8nm.png\n |\n |---17nm\n |   |   size_bigger_10nm.dat\n |   |   size_bigger_10nm.ras\n |   |   size_bigger_10nm_Theta_2-Theta.asc\n |   |   size_bigger_10nm_Theta_2-Theta.raw\n |   |   _gFe2O3_Fe3O4_.out\n |   |   _gFe2O3_Fe3O4_.pcr\n |   |   _gFe2O3_Fe3O4_.prf\n |   |   _gFe2O3_Fe3O4_.sum\n |   |   _gFe2O3_Fe3O4_1.fst\n |   |   _gFe2O3_Fe3O4_1.mic\n |   |   _gFe2O3_Fe3O4_2.fst\n |   |   _gFe2O3_Fe3O4_2.mic\n |   |\n |   `---backup\n |           _gFe2O3_Fe3O4_.pcr\n |\n `---8nm\n     |   size_smaller_10nm.dat\n     |   size_smaller_10nm.ras\n     |   size_smaller_10nm_Theta_2-Theta.asc\n     |   size_smaller_10nm_Theta_2-Theta.raw\n     |   _gFe2O3_Fe3O4_.out\n     |   _gFe2O3_Fe3O4_.pcr\n     |   _gFe2O3_Fe3O4_.prf\n     |   _gFe2O3_Fe3O4_.sum\n     |   _gFe2O3_Fe3O4_1.fst\n     |   _gFe2O3_Fe3O4_1.mic\n     |   _gFe2O3_Fe3O4_2.fst\n     |   _gFe2O3_Fe3O4_2.mic\n     |\n     `---backup\n             _gFe2O3_Fe3O4_.pcr\n\n======================\nNEW FORMAT OF PCR FILE\n======================\n\nThe new FullProf .pcr format is expected.\nMake sure that you have this format by using the FullProf toolbar:\n\n* click \"EdPCR\"\n* click \"output\"\n* unclick \"Classical Output Format for a Single Pattern in PCR\".\n\n==========================\nLaTeX FORMAT OF PHASENAMES\n==========================\n\nBelow is a phase-example from a .pcr file. Note that the phasename is given by \"$\\gamma$-Fe$_2$O$_3$\".\nThe dollarsigns indicate that LaTeX format should be used for the from dollarsigns-inclosed characters.\n\n::\n\n !-------------------------------------------------------------------------------\n !  Data for PHASE number:   1  ==> Current R_Bragg for Pattern#  1:     3.75\n !-------------------------------------------------------------------------------\n $\\gamma$-Fe$_2$O$_3$\n !\n !Nat Dis Ang Jbt Isy Str Furth        ATZ     Nvk More\n   8   0   0   0   0   0   0       1703.3091   0   0\n !Contributions (0/1) of this phase to the  1 patterns\n 1\n !Irf Npr Jtyp  Nsp_Ref Ph_Shift for Pattern#  1\n   0   7    0      0      0\n ! Pr1    Pr2    Pr3   Brind.   Rmua   Rmub   Rmuc     for Pattern#  1\n  0.000  0.000  1.000  1.000  0.000  0.000  0.000\n !\n !\n P 43 21 2                <--Space group symbol\n !Atom   Typ       X        Y        Z     Biso       Occ     In Fin N_t Spc /Codes\n Fe1    Fe      0.74400  0.99600  0.12000  0.10000   1.00000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n Fe2    Fe      0.62000  0.62000  0.00000  0.10000   0.50000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n Fe3    Fe      0.36400  0.86700 -0.01600  0.10000   1.00000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n Fe4    Fe      0.14000  0.14000  0.00000  0.10000   0.16650   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n O1     O       0.61500  0.86900 -0.01400  0.10000   1.00000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n O2     O       0.11900  0.37700 -0.00500  0.10000   1.00000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n O3     O       0.13700  0.86100  0.00700  0.10000   1.00000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n O4     O       0.38300  0.63100 -0.00300  0.10000   1.00000   0   0   0    0\n       0.00       0.00     0.00     0.00     0.00\n !-------> Profile Parameters for Pattern #  1\n !  Scale        Shape1      Bov      Str1      Str2      Str3   Strain-Model\n   0.90441E-03   0.00000   2.25111   0.00000   0.00000   0.00000       0\n   111.00000     0.000   151.000     0.000     0.000     0.000\n !       U         V          W           X          Y        GauSiz   LorSiz Size-Model\n   0.000000   0.000000   0.000000   0.00000     0.380097    0.00000   0.0000     0\n   0.000000   0.000000   0.000000   0.00000   131.000       0.00000   0.0000\n !     a          b         c        alpha      beta       gamma      #Cell Info\n   8.362284   8.362284   8.319425  90.000000  90.000000  90.000000\n   11.00000   11.00000   61.00000    0.00000    0.00000    0.00000\n !  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