Metadata-Version: 1.0
Name: magnetmatter
Version: 0.2.7
Summary: Visualization of FullProf-refined neutron and X-ray powder diffraction data
Home-page: https://github.com/pgarbus/magnetmatter
Author: Pelle Garbus
Author-email: garbus@inano.au.dk
License: MIT
Description: INTRODUCTION
        ============
        
        Materials science research visualization of FullProf-refined neutron (DMC::SINQ::PSI) and X-ray powder diffraction data.
        FullProf .prf, .out and .pcr files are read and informations on:
        
        *  refined parameters,
        *  phases,
        *  apparent crystalline sizes,
        *  phase fractions
        
        are hardcoded next to the graph of "Yobs", "Ycal" and "Yobs-Ycal".
        Two images are saved:
        
        * Truncated graph enhanced with refined parameters.
        * Full graph without distractions.
        * Both graphs are displayed in reciprocal space.
        
        .. image:: https://github.com/pgarbus/magnetmatter/blob/master/magnetmatter/plot_prf_examples/8nm_plain.png?raw=true
        
        .. image:: https://github.com/pgarbus/magnetmatter/blob/master/magnetmatter/plot_prf_examples/8nm.png?raw=true
        
        see section `HOW SHOULD FILES BE ORGANIZED`_ to understand how your files should be organized. The example folders shown are possible to download.
        
        TOC:
        
        * `INSTALLATION`_
        * `HOW TO USE`_
        * `HOW SHOULD FILES BE ORGANIZED`_
        * `NEW FORMAT OF PCR FILE`_
        * `LaTeX FORMAT OF PHASENAMES`_
        * `REPOSITORY`_
        * `TODO`_
        
        
        ============
        INSTALLATION
        ============
        
        This installation assumes that you have access to python3 (version > 3.6).
        If 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.
        
        Before installing, try
        
        ::
        
           $ pip search magnetmatter
        
        and you should see
        
        * "magnetmatter (?.?.?)  - Visualization of FullProf-refined neutron and X-ray powder diffraction data"
        
        now go ahead with the installation
        
        ::
        
           $ pip install magnetmatter
        
        now be patient while "magnetmatter" is installed.
        Installation may be longer because dependencies such as
        
        * "numpy", "pandas", "matplotlib"
        
        are installed if missing.
        
        
        ==========
        HOW TO USE
        ==========
        
        Initiate python in a terminal or use your favorite editor. Then type
        
        ::
        
            >>> import magnetmatter as mm
        
        Type now
        
        ::
        
           >>> path = r"C:\give\a\valid\path\to\folder\with\datasubfolders\"  # Windows
           >>> path = r"C:/give/a/valid/path/to/folder/with/datasubfolders/"  # Linux
           >>> mm.plot_prf(path)
        
        By default printsize = "two_in_docx" and xlim = (2.8,3.6).
        The xlim parameter (values in reciprocal space) truncates the enhanced graph.
        The default printed size is approximately 8 cm (two plots fit into a docx document).
        Other options include:
        
        ::
        
        	>>> mm.plot_prf(path, xlim = (2.8,3.6)) # default!
        	>>> mm.plot_prf(path, xlim = (1.0,2.0)) # show 1 to 2 invers Ã… in enhanced graph
        	>>> mm.plot_prf(path, xlim = None) # Enhanced graph is not truncated
        	>>> mm.plot_prf(path, printsize = "one_in_docx") # 15 cm wide
        	>>> mm.plot_prf(path, printsize = "two_in_ppt")  # 17 cm wide
        	>>> mm.plot_prf(path, printsize = "one_in_ppt")  # 32 cm wide
        
        The files are saved as .png in the "path" folder.
        
        =============================
        HOW SHOULD FILES BE ORGANIZED
        =============================
        
        The script goes into each subfolder and looks for an .out, a .pcr and a .prf file.
        If no such files are found (or if indeed multiple files are found), the script will skip the respective folder.
        Note the "backup" folder is not mandatory. I like to keep a copy of an uncorrupted .pcr at hand.
        
        The below examples can be downloaded from `here <https://github.com/pgarbus/magnetmatter/tree/master/magnetmatter/plot_prf_examples>`_.
        
        ::
        
         |./
         |   CoKa_BB_ISx.irf
         |   CoKa_PB_ISxmm.irf
         |   17nm.png
         |   8nm.png
         |
         |---17nm
         |   |   size_bigger_10nm.dat
         |   |   size_bigger_10nm.ras
         |   |   size_bigger_10nm_Theta_2-Theta.asc
         |   |   size_bigger_10nm_Theta_2-Theta.raw
         |   |   _gFe2O3_Fe3O4_.out
         |   |   _gFe2O3_Fe3O4_.pcr
         |   |   _gFe2O3_Fe3O4_.prf
         |   |   _gFe2O3_Fe3O4_.sum
         |   |   _gFe2O3_Fe3O4_1.fst
         |   |   _gFe2O3_Fe3O4_1.mic
         |   |   _gFe2O3_Fe3O4_2.fst
         |   |   _gFe2O3_Fe3O4_2.mic
         |   |
         |   `---backup
         |           _gFe2O3_Fe3O4_.pcr
         |
         `---8nm
             |   size_smaller_10nm.dat
             |   size_smaller_10nm.ras
             |   size_smaller_10nm_Theta_2-Theta.asc
             |   size_smaller_10nm_Theta_2-Theta.raw
             |   _gFe2O3_Fe3O4_.out
             |   _gFe2O3_Fe3O4_.pcr
             |   _gFe2O3_Fe3O4_.prf
             |   _gFe2O3_Fe3O4_.sum
             |   _gFe2O3_Fe3O4_1.fst
             |   _gFe2O3_Fe3O4_1.mic
             |   _gFe2O3_Fe3O4_2.fst
             |   _gFe2O3_Fe3O4_2.mic
             |
             `---backup
                     _gFe2O3_Fe3O4_.pcr
        
        ======================
        NEW FORMAT OF PCR FILE
        ======================
        
        The new FullProf .pcr format is expected.
        Make sure that you have this format by using the FullProf toolbar:
        
        * click "EdPCR"
        * click "output"
        * unclick "Classical Output Format for a Single Pattern in PCR".
        
        ==========================
        LaTeX FORMAT OF PHASENAMES
        ==========================
        
        Below is a phase-example from a .pcr file. Note that the phasename is given by "$\gamma$-Fe$_2$O$_3$".
        The dollarsigns indicate that LaTeX format should be used for the from dollarsigns-inclosed characters.
        
        ::
        
         !-------------------------------------------------------------------------------
         !  Data for PHASE number:   1  ==> Current R_Bragg for Pattern#  1:     3.75
         !-------------------------------------------------------------------------------
         $\gamma$-Fe$_2$O$_3$
         !
         !Nat Dis Ang Jbt Isy Str Furth        ATZ     Nvk More
           8   0   0   0   0   0   0       1703.3091   0   0
         !Contributions (0/1) of this phase to the  1 patterns
         1
         !Irf Npr Jtyp  Nsp_Ref Ph_Shift for Pattern#  1
           0   7    0      0      0
         ! Pr1    Pr2    Pr3   Brind.   Rmua   Rmub   Rmuc     for Pattern#  1
          0.000  0.000  1.000  1.000  0.000  0.000  0.000
         !
         !
         P 43 21 2                <--Space group symbol
         !Atom   Typ       X        Y        Z     Biso       Occ     In Fin N_t Spc /Codes
         Fe1    Fe      0.74400  0.99600  0.12000  0.10000   1.00000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         Fe2    Fe      0.62000  0.62000  0.00000  0.10000   0.50000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         Fe3    Fe      0.36400  0.86700 -0.01600  0.10000   1.00000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         Fe4    Fe      0.14000  0.14000  0.00000  0.10000   0.16650   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         O1     O       0.61500  0.86900 -0.01400  0.10000   1.00000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         O2     O       0.11900  0.37700 -0.00500  0.10000   1.00000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         O3     O       0.13700  0.86100  0.00700  0.10000   1.00000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         O4     O       0.38300  0.63100 -0.00300  0.10000   1.00000   0   0   0    0
               0.00       0.00     0.00     0.00     0.00
         !-------> Profile Parameters for Pattern #  1
         !  Scale        Shape1      Bov      Str1      Str2      Str3   Strain-Model
           0.90441E-03   0.00000   2.25111   0.00000   0.00000   0.00000       0
           111.00000     0.000   151.000     0.000     0.000     0.000
         !       U         V          W           X          Y        GauSiz   LorSiz Size-Model
           0.000000   0.000000   0.000000   0.00000     0.380097    0.00000   0.0000     0
           0.000000   0.000000   0.000000   0.00000   131.000       0.00000   0.0000
         !     a          b         c        alpha      beta       gamma      #Cell Info
           8.362284   8.362284   8.319425  90.000000  90.000000  90.000000
           11.00000   11.00000   61.00000    0.00000    0.00000    0.00000
         !  Pref1    Pref2      Asy1     Asy2     Asy3     Asy4      S_L      D_L
           0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.02957  0.02957
           0.00     0.00     0.00     0.00     0.00     0.00     0.00     0.00
        
        ==========
        REPOSITORY
        ==========
        
        The source code and examples can be found at `GitHub <https://github.com/pgarbus/magnetmatter/>`_.
        
        ====
        TODO
        ====
        
        * make plot of .dat/.xye file if plot_prf fails to finish.
        
Platform: UNKNOWN
