Changes in / [48153283:5dfdfa7] in sasview


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  • docs/sphinx-docs/source/user/user.rst

    r64c8fc1 ref325c7  
    1212   Plotting Data/Models <guiframe/graph_help> 
    1313    
    14    Fitting Perspective <fit/fitting_help> 
     14   Fitting Perspective <fitting/fitting_help> 
    1515    
    1616   P(r) Inversion Perspective <invariant/pr_help> 
    … …  
    3333   Generic Scattering Calculator Tool <calculator/sas_calculator_help> 
    3434    
    35    Python Shell Tool <perspectives/calculator/python_shell_help> 
     35   Python Shell Tool 
    3636    
    37    Image Viewer Tool <perspectives/calculator/image_viewer_help> 
     37   Image Viewer Tool 

  • src/sas/calculator/media/density_calculator_help.rst

    r920928f r0d66541  
    1 .. density_calculator_help.rst 
     1..density_calculator_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Density/Volume Calculator Tool 
    7 ============================== 
    8  
    9 Description 
    10 ----------- 
    11  
    12 This tool is to calculate the mass density from the molar volume or vice  
    13 versa. To calculate the mass density, the chemical formula and molar volume  
    14 should be provided. 
    15  
    16 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    17  
    18 How To 
    19 ------ 
    20  
    21 1. Molecular Formula: The chemical formula of ONE molecule or ONE atom. For  
    22 mixtures, the ratio of the each molecules should be used; for example,  
    23 (H2O)0.5(D2O)0.5. 
    24  
    25 2. Select input (molar volume or mass density) from combobox. Then type in the  
    26 input value. 
    27  
    28 3. Click the 'Calculate' button to perform the calculation. 
    29  
    30 4. Outputs also include the molar mass (weight) that depends only on the  
    31 chemical formula 
    32  
    33 .. image:: density_tutor.gif 
     3Placeholder for density calculator help 

  • src/sas/calculator/media/kiessig_calculator_help.rst

    r920928f r0d66541  
    1 .. kiessig_calculator_help.rst 
     1..kiessig_calculator_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Kiessig Thickness Calculator Tool 
    7 ================================= 
    8  
    9 Description 
    10 ----------- 
    11  
    12 This tool is to approximately estimate the thickness of a layer or the  
    13 diameter of particles from the Kiessig fringe in SAS/NR data, and using the  
    14 Kiessig relation 
    15  
    16 thickness = 2*Pi/fringe_width. 
    17    
    18 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    19  
    20  
    21 How To 
    22 ------ 
    23  
    24 To get a rough thickness or particle size, just type the Kiessig fringe width  
    25 (in units of 1/Angstrom) and click on the 'Compute' button. Then the output  
    26 value will be show up in the 'Thickness' text box. 
     3Placeholder for Kiessig calculator help 

  • src/sas/calculator/media/resolution_calculator_help.rst

    r920928f r0d66541  
    1 .. resolution_calculator_help.rst 
     1..resolution_calculator_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Q Resolution Estimator 
    7 ====================== 
    8  
    9 Description 
    10 ----------- 
    11  
    12 This tool is to approximately estimate the resolution of Q based on the SAS  
    13 instrumental parameter values assuming that the detector is flat and vertical  
    14 to the incident beam direction. 
    15  
    16 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    17  
    18 How To 
    19 ------ 
    20  
    21 1. Select the source and source type (Monochromatic or TOF). Note that the  
    22 computational difference between the sources is only the gravitational  
    23 contribution due to the mass. 
    24  
    25 2. Change the default values of the instrumental parameters as desired. 
    26  
    27 3. The input formats of wavelength and its spread (=FWHM/wavelength) depend on  
    28 the source type.For monochromatic wave, the inputs are just one values as shown  
    29 with the defaults.For TOF, the min and max values should be separated by "-"  
    30 to describe the wavelength band range. Optionally, the input of the wavelength  
    31 (NOT of the wavelength spread) could be extended by adding "; --" where the --  
    32 is the number of the bins for the numerical integration. Otherwise, the  
    33 default value "10" bins will be used. The same number of bins will be used  
    34 for the corresponding wavelength spread in either cases. 
    35  
    36 4. For TOF, the default wavelength spectrum is flat. The custom spectrum file  
    37 (with 2 column text: wavelength(A) vs. intensity) can also be loaded by  
    38 selecting "Add new" in the combobox. 
    39  
    40 5. Once set all the input values, click the compute button. Depending on  
    41 computation loads the calculation time will vary. 
    42  
    43 6. 1D and 2D dQ will be displayed in the text-box at the bottom of the panel.  
    44 Two dimensional resolution weight distribution (2D elliptical Gaussian  
    45 function) will also be displayed in the plot panel even if the Q inputs are  
    46 outside of the detector limit. The red lines indicate the limits of the  
    47 detector (if a green lines appear (for TOF), it indicates the limits of the  
    48 maximum q range for the largest wavelength due to the size of the detector).  
    49 Note that the effect from the beam block is ignored, so in the small q region  
    50 near the beam block  
    51  
    52 [ie., q<2*pi*(beam block diameter) / (sample to detector distance) / lamda_min]  
    53  
    54 the variance is slightly under estimated. 
    55  
    56 7. The summary can be accessed by clicking the 'light-bulb' icon at the bottom  
    57 of the SasView main window. 
    58  
    59 .. image:: resolution_tutor.gif 
    60  
    61 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    62  
    63 Theory 
    64 ------ 
    65  
    66 The scattering wave transfer vector is by definition 
    67  
    68 .. image:: q.gif 
    69  
    70 In the limit of the small angle, the variance of q in the first order  
    71 approximation is 
    72  
    73 .. image:: sigma_q.gif 
    74  
    75 In summary, the geometric and gravitational contributions depending on the  
    76 shape of each factors can be expressed as shown the table. 
    77  
    78 .. image:: sigma_table.gif 
    79  
    80 Finally, we use a Gaussian function to describe the 2D weighting distribution  
    81 of the uncertainty in q. 
    82  
    83 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    84  
    85 References 
    86 ---------- 
    87 D.F.R. Mildner and J.M. Carpenter, J. Appl. Cryst. 17, 249-256 (1984) 
    88  
    89 D.F.R. Mildner, J.M. Carpenter and D.L. Worcester, J. Appl. Cryst. 19, 311-319  
    90 (1986) 
     3Placeholder for resolution calculator help 

  • src/sas/calculator/media/sas_calculator_help.rst

    r920928f r0d66541  
    1 .. sas_calculator_help.rst 
     1..sas_calculator_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 .. |beta| unicode:: U+03B2 
    7 .. |gamma| unicode:: U+03B3 
    8 .. |theta| unicode:: U+03B8 
    9 .. |mu| unicode:: U+03BC 
    10 .. |sigma| unicode:: U+03C3 
    11 .. |phi| unicode:: U+03C6 
    12  
    13 .. |equiv| unicode:: U+2261 
    14 .. |noteql| unicode:: U+2260 
    15  
    16 Generic Scattering Calculator Tool 
    17 ================================== 
    18  
    19 Polarization and Magnetic Scattering 
    20  
    21 Theory_  
    22 GUI_  
    23 PDB_Data_  
    24  
    25 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    26  
    27 .. _Theory: 
    28  
    29 Theory 
    30 ------ 
    31  
    32 In general, a particle with a volume V can be described by an ensemble  
    33 containing N 3-dimensional rectangular pixels where each pixels are much  
    34 smaller than V. Assuming that all the pixel sizes are same, the elastic  
    35 scattering intensity by the particle 
    36  
    37 .. image:: gen_i.gif 
    38  
    39 where /beta/jand rj are the scattering length density and the position of the  
    40 j'th pixel respectively. And the total volume 
    41  
    42 .. image:: v_j.gif 
    43  
    44 for /beta/j/noteql/0 where vj is the volume of the j'th pixel (or the j'th  
    45 natural atomic volume (= atomic mass/natural molar density/Avogadro number) for  
    46 the atomic structures). The total volume V can be corrected by users. This  
    47 correction is useful especially for an atomic structure (taken from a pdb file)  
    48 to get the right normalization. Note that the /beta/j displayed in GUI may be  
    49 incorrect but will not affect the scattering computation if the correction of  
    50 the total volume is made. The scattering length density (SLD) of each pixel  
    51 where the SLD is uniform, is a combination of the nuclear and magnetic SLDs and  
    52 depends on the spin states of the neutrons as follows:For magnetic scattering,  
    53 only the magnetization component, *M*perp, perpendicular to the scattering  
    54 vector *Q* contributes to the the magnetic scattering length. (Figure below). 
    55  
    56 .. image:: mag_vector.bmp 
    57  
    58 The magnetic scattering length density is then 
    59  
    60 .. image:: dm_eq.gif 
    61  
    62 where /gamma/= -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0 is  
    63 the classical radius of electron, and */sigma/* is the Pauli spin. 
    64  
    65 For polarized neutron, the magnetic scattering is depending on the spin states. 
    66  
    67 Let's consider that the incident neutrons are polarised parallel (+)/  
    68 anti-parallel (-) to the x' axis (See both Figures above). The possible  
    69 out-coming states then are + and - states for both incident states, where  
    70  
    71 - Non-spin flips: (+ +) and (- -) 
    72 - Spin flips:     (+ -) and (- +) 
    73  
    74 .. image:: gen_mag_pic.bmp 
    75  
    76 Now, let's assume that the angles of the *Q*  vector and the spin-axis (x')  
    77 from x-axis are /phi/ and /theta/up respectively (See Figure above). Then,  
    78 depending upon the polarization (spin) state of neutrons, the scattering  
    79 length densities, including the nuclear scattering length density (/beta/N)  
    80 are given as, for non-spin-flips 
    81  
    82 .. image:: sld1.gif 
    83  
    84 and for spin-flips 
    85  
    86 .. image:: sld2.gif 
    87  
    88 where 
    89  
    90 .. image:: mxp.gif 
    91  
    92 .. image:: myp.gif 
    93  
    94 .. image:: mzp.gif 
    95  
    96 .. image:: mqx.gif 
    97  
    98 .. image:: mqy.gif 
    99  
    100 Here, the M0x, M0yand M0zare the x, y and z components of the magnetisation  
    101 vector given in the xyz lab frame.  
    102  
    103 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    104  
    105 .. _GUI: 
    106  
    107 GUI 
    108 --- 
    109  
    110 .. image:: gen_gui_help.bmp 
    111  
    112 After the computation, the result will be listed in the 'Theory' box in the  
    113 data explorer panel on the main window.The 'Up_frac_in' and 'Up_frac_out' are  
    114 the ratio, (spin up) /(spin up + spin down) neutrons before the sample and at  
    115 the analyzer, respectively. 
    116  
    117 *Note I: The values of 'Up_frac_in' and 'Up_frac_out' must be in the range  
    118 between 0 and 1. For example, both values are 0.5 for unpolarized neutrons.* 
    119  
    120 *Note II: This computation is totally based on the pixel (or atomic) data  
    121 fixed in the xyz coordinates. Thus no angular orientational averaging is  
    122 considered.* 
    123  
    124 *Note III: For the nuclear scattering length density, only the real component  
    125 is taken account.* 
    126  
    127 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    128  
    129 .. _PDB_Data: 
    130  
    131 PDB Data 
    132 -------- 
    133  
    134 This Generic scattering calculator also supports some pdb files without  
    135 considering polarized/magnetic scattering so that the related parameters  
    136 such as Up_*** will be ignored (see the Picture below). The calculation for  
    137 fixed orientation uses (the first) Equation above resulting in a 2D output,  
    138 whileas the scattering calculation averaged over all the orientations uses  
    139 the Debye equation providing a 1D output 
    140  
    141 .. image:: gen_debye_eq.gif 
    142  
    143 where vj /beta/j /equiv/ bj the scattering length of the j'th atom. The resultant outputs  
    144 will be displayed in the DataExplorer for further uses. 
    145  
    146 .. image:: pdb_combo.jpg 
     3Placeholder for generic SAS calculator help 

  • src/sas/calculator/media/slit_calculator_help.rst

    r920928f r0d66541  
    1 .. slit_calculator_help.rst 
     1..slit_calculator_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Slit Size Calculator Tool 
    7 ========================= 
    8  
    9 Description 
    10 ----------- 
    11 This tool is for X-ray users to calculate the slit size (FWHM/2) for smearing  
    12 based on their half beam profile data (SAXSess). 
    13  
    14 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    15  
    16 How To 
    17 ------- 
    18 To calculate the slit size (FWHM/2), just load the beam profile data using the  
    19 browse button. 
    20  
    21 Once a data is loaded, the slit size will be computed and show up in the text  
    22 box. 
    23  
    24 Because the unit is not specified in the data file, we do not convert it into  
    25 1/Angstrom so  users are responsible for converting the units of their data. 
    26  
    27 Note: This slit size calculator only works for beam profile data produced by  
    28 'SAXSess'. 
    29  
    30 To see the file format, check the file, 'beam profile.DAT', in the 'test'  
    31 folder of SasView. 
     3Placeholder for slit calculator help 

  • src/sas/data_util/media/data_operator_help.rst

    r920928f r0d66541  
    1 .. data_operator_help.rst 
     1..data_operator_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Data Operations Tool 
    7 ==================== 
    8  
    9 Description 
    10 ----------- 
    11 This dialog panel provides arithmetic operations between two data sets (the  
    12 last data set could be a number). 
    13  
    14 When data1 and data2 are selected, their x (or qx and qy for 2D) value(s) 
    15 must match with each other. 
    16  
    17 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    18  
    19 How To 
    20 ------ 
    21 1. Type the data name resulted from an operation. 
    22  
    23 2) Select a data/theory in the drop down menus. When data2 is set to number,  
    24    type a number in the text control box. 
    25  
    26 3) Select an arithmetic operator symbol; + (for addition), - (for subtraction),  
    27    * (for multiplication), / (for division), and | (for combination of two data 
    28    sets). 
    29  
    30    If two data sets do not match, the operation will fail and the background color 
    31    of the combo box items will turn to red (WIN only). 
    32  
    33 4) If the operation is successful, hit the Apply button to make the new data. 
    34    Then the data name will be shown up in the data box in the data explorer. 
    35  
    36 Note: Any errors and warnings will be displayed at the bottom of the SasView 
    37 window. 
    38  
    39 .. image:: data_oper_pic.png 
     3Placeholder for data operator help 

  • src/sas/fit/media/fitting_help.rst

    r920928f r0d66541  
    1 .. fitting_help.rst 
     1..fitting_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 .. |beta| unicode:: U+03B2 
    7 .. |gamma| unicode:: U+03B3 
    8 .. |mu| unicode:: U+03BC 
    9 .. |sigma| unicode:: U+03C3 
    10 .. |phi| unicode:: U+03C6 
    11 .. |theta| unicode:: U+03B8 
    12  
    13 Fitting Perspective 
    14 =================== 
    15  
    16 Load_a_File_ 
    17  
    18 Single_Fit_ 
    19  
    20 Simultaneous_Fitting_ 
    21  
    22 Batch_Fitting_ 
    23  
    24 Model_Selection_ 
    25  
    26 Model_Category_Manager_ 
    27  
    28 Model_Functions_ 
    29  
    30 Custom_Model_Editor_ 
    31  
    32 Polydispersity_Distributions_ 
    33  
    34 Smearing_Computation_ 
    35  
    36 Polarisation_Magnetic_Scattering_ 
    37  
    38 Key_Combinations_ 
    39  
    40 Status_Bar_Help_ 
    41  
    42 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    43  
    44 ..  _Load_a_File: 
    45  
    46 Load a File 
    47 ----------- 
    48  
    49 From Menu go to *Data* -> *Load Data File(or Folder)* . Select a file/folder  
    50 from the menu bar and click on Open button. Data contained in the file will be  
    51 displayed. To cancel the loading click on *cancel* . In case a file can not be  
    52 loaded, an error message will be displayed on the statusbar. 
    53  
    54 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    55  
    56 .. _Single_Fit: 
    57  
    58 Single Fit 
    59 ---------- 
    60  
    61 One of two fit-engines can be chosen from the Fitting menu bar. The Simple Fit- 
    62 engine uses Scipy's leasqr and the Complex Fit-Engine is a custom optimizer  
    63 that provides a better chance to find the global minimum of the chi2 but that  
    64 requires longer computation time. In order to set a data to a control panel  
    65 (FitPage), see the "DataLoader Help". Once a data set to the FiPage, select a  
    66 model from the combo box. The default parameters of the model will be display.  
    67 Set initial parameters if need. Check and uncheck parameters to fit/fix. Click  
    68 the *'Fit'*  button. When the fitting is finished, the resultant parameter  
    69 values will be displayed with the errors. If a error is missing, it generally  
    70 means that the corresponding parameter is not very depending on the model. The  
    71 chisq/Npt_fit and the plot associated with the fit operation will be also  
    72 updated. 
    73  
    74 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    75  
    76 ..  _Simultaneous_Fitting: 
    77  
    78 Simultaneous Fitting 
    79 -------------------- 
    80  
    81 This fitting option enables to set a number of the constraints between the  
    82 parameters of fitting(s). It requires one or more FitPages with a data and a  
    83 model set for the fitting, and performs multiple fittings given by the  
    84 FitPage(s). The Complex (ParkMC) FitEngine will be used automatically. 
    85  
    86 Simultaneous Fit without Constraint 
    87  
    88 Assuming some FitPages are already set up, check the checkboxes of the  
    89 model_data rows to fit. And click the 'Fit' button. The results will return to  
    90 each FitPages. 
    91  
    92 Note that the chi2/Npts returned is the sum of the chi2/Npts of each fits. If  
    93 one needs the chi2 value only for a page, click the 'Compute' button in the  
    94 FitPage to recalculate. 
    95  
    96 Simultaneous Fit with Constraint 
    97  
    98 Enter constraint in the text control next to *constraint fit*  button.  
    99 Constraint should be of type model1 parameter name = f(model2 parameter name)  
    100 for example, M0.radius=2*M1.radius. Many constraints can be entered for a  
    101 single fit. Each of them should be separated by a newline charater or ";"  
    102 The easy setup can generate many constraint inputs easily when the selected  
    103 two models are the same type. 
    104  
    105 Note that the chi2/Npts returned is the sum of the chi2/Npts of each fits.  
    106 If one needs the chi2 value only for one fit, click the 'Compute' button in  
    107 the FitPage to recalculate. 
    108  
    109 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    110  
    111 ..  _Batch_Fitting: 
    112  
    113 Batch Fitting 
    114 ------------- 
    115  
    116 Batch_Fit_ 
    117  
    118 Batch_Window_ 
    119  
    120 Edit_Grid_ 
    121  
    122 Save_Grid_ 
    123  
    124 Open_Batch_Results_ 
    125  
    126 Plot_ 
    127  
    128 View_Column_Cell_ 
    129  
    130 .. _Batch_Fit: 
    131  
    132 Batch Fit 
    133 ---------  
    134  
    135 Create a *Batch Page* by selecting the *Batch* radio button on the DataExplorer 
    136 (see figure below) and for a new control page select 'New FitPage' in the  
    137 Fitting menubar. 
    138  
    139 .. image:: batch_button_area.bmp 
    140  
    141 Figure 1: MenuBar:  
    142  
    143 Load Data to the DataExplorer if not already loaded. 
    144  
    145 Select one or more data sets by checking the check boxes, and then make sure  
    146 that "Fitting" is selected in the dropdown menu next to the "Send To" button.  
    147 Once ready, click the 'Send To' button to set data to a BatchPage. If already  
    148 an empty batch page exists, it will be set there. Otherwise it will create a  
    149 new Batch Page. Set up the model and the parameter values as same as a single  
    150 fitting (see Single Fit help) <Single_Fit_>. Then use 'Fit' button to  
    151 perform the fitting. 
    152  
    153 Unlike a single fit, the results of the fittings will not return to the  
    154 BatchPage'. Instead, a Grid window will be provided once the fitting is  
    155 completed. The Grid window is also accessible from the 'View' menu  
    156 (see Figure 2). 
    157  
    158 Note that only one model is used for all the data. The initial parameter  
    159 values given in the control page will be used all the data fittings. If one  
    160 wants the FitEngine to use the initial values from the results of the  
    161 previous data fitting (if any), choose the 'Chain Fitting' option in the  
    162 Fitting menubar, which will speed up the fitting especially when you have  
    163 lots of, and similar, data sets. 
    164  
    165 .. _Batch_Window: 
    166  
    167 Batch Window 
    168 ------------ 
    169 Batch Window provides an easy way to view the fit results, i.e., plot data,  
    170 fits, and residuals. Batch window will be automatically shown after a batch  
    171 fit is finished. 
    172  
    173 Once closed, it can be opened anytime from the "View" menubar item (see  
    174 Figure 2). 
    175  
    176 .. image:: restore_batch_window.bmp 
    177  
    178 Figure 2: Edit Menu:  
    179  
    180 .. _Edit_Grid: 
    181  
    182 Edit Grid 
    183 --------- 
    184  
    185 Once a batch fit is completed, all fitted and fixed model parameters are  
    186 displayed to the current sheet of the batch window except the errors of the  
    187 parameters. To view the errors, click on a given column then under *Edit*   
    188 menubar item, and insert the desired parameter by selecting a menu item with  
    189 the appropriated label. Empty column can be inserted in the same way. A  
    190 column value can be customized by editing an existing empty column. 
    191  
    192 To Remove column from the grid, select it, choose edit menu, and click the  
    193 *'remove'*  menu item. Any removed column should reinserted whenever needed. 
    194  
    195 All above options are also available when right clicking on a given column  
    196 label(see Figure 3). 
    197  
    198 *Note:*  A column always needs to be selected in order to remove or insert a  
    199 column in the grid. 
    200  
    201 .. image:: edit_menu.bmp 
    202  
    203 Figure 3: Edit Menu: 
    204  
    205 .. _Save_Grid: 
    206  
    207 Save Grid 
    208 --------- 
    209 To save the current page on the batch window, select the *'File'*  menubar  
    210 item(see Figure 4), then choose the *'Save as'*  menu item to save it as a  
    211 .csv file. 
    212  
    213 *Note:* The grid doesn't save the data array, fits, and the array residuals. 
    214 As a result, the 'View (fit) Results' functionality will be lost when 
    215 reloading the saved file. 
    216  
    217 Warning! To ensure accuracy of saved fit results, it is recommended to save  
    218 the current grid before modifying it . 
    219  
    220 .. _Open_Batch_Results: 
    221  
    222 Open Batch Results  
    223 ------------------ 
    224  
    225 Any *csv*  file can be opened in the grid by selecting the *'Open'*  under  
    226 the *'File'*  menu in the Grid Window(see Figure 4). All columns in the file  
    227 will be displayed but insertion will not available. Insertion will be  
    228 available only when at least one column will be removed from the grid. 
    229  
    230 .. image:: file_menu.bmp 
    231  
    232 Figure 4: MenuBar: 
    233  
    234 .. _Plot: 
    235  
    236 Plot 
    237 ---- 
    238  
    239 To *plot*  a column versus another, select one column at the time, click the  
    240 *'Add'*  button next to the text control of X/Y -axis *Selection Range*  to  
    241 plot the value of this column on the X/Y axis. Alternatively, all available  
    242 range can be selected by clicking the column letter (eg. B). Repeat the same  
    243 procedure the next axis. Finally, click the *'Plot'*  button. When clicking  
    244 on *Add*  button, the grid will automatically fill the axis label, but  
    245 different labels and units can be entered in the correct controls before  
    246 clicking on the plot button. 
    247  
    248 *X/Y -Axis Selection Range* can be edited manually. These text controls 
    249 allow the following types of expression (operation can be + - * /, or pow) 
    250   
    251 1) if the current axis label range is a function of 1 or more columns, write  
    252 this type of expression 
    253  
    254 constant1  * column_name1 [minimum row index :  maximum  row index] operator  
    255 constant2 * column_name2 [minimum row index :  maximum  row index]  
    256  
    257 Example: radius [2 : 5] -3 * scale [2 : 5]  
    258  
    259 2) if only some values of a given column are need but the range between the  
    260 first row and the last row used is not continuous, write the following  
    261 expression in the text control 
    262  
    263 column_name1 [minimum row index1 :  maximum  row index1] , column_name1  
    264 [minimum row index2 :  maximum  row index2]  
    265  
    266 Example : radius [2 : 5] , radius [10 : 25]  
    267  
    268 Note: Both text controls ( X and Y-axis Selection Ranges) need to be filled  
    269 with valid entries for plotting to work. The dY-bar is optional (see Figure 5). 
    270  
    271 .. image:: plot_button.bmp 
    272  
    273 Figure 5: Plotting 
    274  
    275 .. _View_Column_Cell: 
    276  
    277 View Column/Cell(s) 
    278 ------------------- 
    279  
    280 Select 1 or more cells from the same column, click the 'View Fits' button to  
    281 display available curves.  
    282  
    283 For example, select the cells of the  'Chi2'  column, then click the  'View Fits'   
    284 button. The plots generates will represent the residuals  plots.  
    285   
    286 If you select any cells of the 'Data' column and click the 'View Fits' button.  
    287 It generates both  data and fits in the graph (see Figure 6).  
    288  
    289 Alternatively, just click the column letter (eg. B) to choose all the  
    290 available data sets, then simply click the 'View Fits' button to plot the  
    291 data and fits.  
    292  
    293 .. image:: view_button.bmp 
    294  
    295 Figure 6: View Fits 
    296  
    297 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    298  
    299 ..  _Model_Selection: 
    300  
    301 Model_Type_  
    302  
    303 Change_Model_Parameters_ 
    304  
    305 Write_your_Own_Model_ 
    306  
    307 .. _Model_Type: 
    308  
    309 Model Type 
    310 ---------- 
    311  
    312 Models are grouped into three classes 
    313  
    314 *  *Shapes*  
    315 *  *Shape-Independent*  
    316 *  *Uncategorised* 
    317 *  *Customized Models*  
    318 *  *Structure Factor* 
    319  
    320 .. _Change_Model_Parameters: 
    321  
    322 Change Model Parameters 
    323 ----------------------- 
    324  
    325 To visualize model in a different window, from menu click on *Model*. Select  
    326 a type of model and then the name of your model.A new window will appear with  
    327 the plot of your model with default values. Change model's parameters on  
    328 *model view*  tab and view the plotted model with its new parameters. 
    329  
    330 .. _Write_your_Own_Model: 
    331  
    332 Write your Own Model 
    333 -------------------- 
    334  
    335 The custom model editors are provided from 'Fitting' menu in the menu bar.  
    336 See 'Custom model editor' in the side menu on left. Advanced users can write  
    337 your own model and save it (in .py format) into *plugin_models*  directory in  
    338 .sasview of your home directory (eg., username\.sasview>\plugin_models). Your  
    339 plugin model will be added into "<>Customized Models" on the next model  
    340 selection. 
    341  
    342 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    343  
    344 ..  _Model_Category_Manager: 
    345  
    346 Model Category Manager 
    347 ---------------------- 
    348  
    349 Our SAS models are, by default, classified into 5 categories; shapes,  
    350 shape-independent, structure factor, and customized models, where these  
    351 categories (except the customized models) can be reassigned, added, and  
    352 removed using 'Category Manager'. Each models can also be enabled(shown)/ 
    353 disabled(hidden) from the category that they belong. The Category Manager  
    354 panel is accessible from the model category 'Modify' button in the fitting  
    355 panel or the 'View/Category Manager' menu in the menu bar (Fig. 1). 
    356  
    357 1) Enable/Disable models: Check/uncheck the check boxes to enable/disable the  
    358 models (Fig. 2). 
    359  
    360 2) Change category: Highlight a model in the list by left-clicking and click  
    361 the 'Modify' button. In the 'Change Category' panel, one can create/use a  
    362 category for the model, then click the 'Add' button. In order to delete a  
    363 category, select a category name and click the 'Remove Selected' button  
    364 (Fig. 3). 
    365  
    366 3) To apply the changes made, hit the OK button. Otherwise, click the 'Cancel'  
    367 button (Fig. 2). 
    368  
    369 .. image:: cat_fig0.bmp 
    370  
    371 Fig.1 
    372  
    373 .. image:: cat_fig1.bmp 
    374  
    375 Fig.2 
    376  
    377 .. image:: cat_fig2.bmp 
    378  
    379 Fig.3 
    380  
    381 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    382  
    383 ..  _Model_Functions: 
    384  
    385 Model Functions 
    386 --------------- 
    387  
    388 Model Documentation <models/model_functions> 
    389  
    390 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    391  
    392 ..  _Custom_Model_Editor: 
    393  
    394 Custom Model Editor 
    395 ------------------- 
    396  
    397 Description_  
    398  
    399 New_ 
    400  
    401 Sum_Multi_p1_p2_ 
    402  
    403 Advanced_ 
    404  
    405 Delete_ 
    406  
    407 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    408  
    409 .. _Description: 
    410  
    411 Description 
    412 ----------- 
    413  
    414 This menu (Fitting/Edit Custom Model in the menu bar) interface is to provide  
    415 you an easy way to write your own custom models. The changes in a model  
    416 function are effective after it is re-selected from the combo-box menu. 
    417  
    418 .. image:: edit_model_menu.bmp 
    419  
    420 .. _New: 
    421  
    422 New 
    423 --- 
    424  
    425 This option is used to make a new model. A model code generated by this option  
    426 can be viewed and further modified by the 'Advanced' option below. 
    427  
    428 .. image:: new_model.bmp 
    429  
    430 .. _Sum_Multi_p1_p2: 
    431  
    432 Sum|Multi(p1,p2) 
    433 ---------------- 
    434  
    435 This option create a new sum (or multiplication) model. Fill up the (sum  
    436 model function) name and the description. The description will show up on  
    437 details button in the application. Then select the p1 or p2 model for the  
    438 sum/multi model, select an operator as necessary and click the Apply button  
    439 for activation. Hit the 'Close' button when it's done. 
    440  
    441 .. image:: sum_model.bmp 
    442  
    443 .. _Advanced: 
    444  
    445 Advanced 
    446 -------- 
    447  
    448 The menu option shows all the files in the plugin_models folder. You can edit,  
    449 modify, and save it. It is recommended to modify only the lines with arrow  
    450 (-------). In the end of edit, 'Compile' and 'Run' from the menu bar to 
    451 activate or to see the model working properly. 
    452  
    453 .. _Delete: 
    454  
    455 Delete 
    456 ------ 
    457  
    458 The menu option is to delete the custom models. Just select the file name to  
    459 delete. 
    460  
    461 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    462  
    463 ..  _Polydispersity_Distributions: 
    464  
    465 Polydispersity Distributions 
    466 ---------------------------- 
    467  
    468 Calculates the form factor for a polydisperse and/or angular population of  
    469 particles with uniform scattering length density. The resultant form factor  
    470 is normalized by the average particle volume such that  
    471  
    472 P(q) = scale*\<F*F\>/Vol + bkg 
    473  
    474 where F is the scattering amplitude and the\<\>denote an average over the size  
    475 distribution.  Users should use PD (polydispersity: this definition is  
    476 different from the typical definition in polymer science) for a size  
    477 distribution and Sigma for an angular distribution (see below). 
    478  
    479 Note that this computation is very time intensive thus applying polydispersion/ 
    480 angular distrubtion for more than one paramters or increasing Npts values  
    481 might need extensive patience to complete the computation. Also note that  
    482 even though it is time consuming, it is safer to have larger values of Npts  
    483 and Nsigmas. 
    484  
    485 The following five distribution functions are provided 
    486  
    487 *  *Rectangular_Distribution_* 
    488 *  *Array_Distribution_* 
    489 *  *Gaussian_Distribution_* 
    490 *  *Lognormal_Distribution_* 
    491 *  *Schulz_Distribution_* 
    492  
    493 .. _Rectangular_Distribution: 
    494  
    495 Rectangular Distribution 
    496 ------------------------ 
    497  
    498 .. image:: pd_image001.png 
    499  
    500 The xmean is the mean of the distribution, w is the half-width, and Norm is a  
    501 normalization factor which is determined during the numerical calculation.  
    502 Note that the Sigma and the half width *w*  are different. 
    503  
    504 The standard deviation is 
    505  
    506 .. image:: pd_image002.png 
    507  
    508 The PD (polydispersity) is 
    509  
    510 .. image:: pd_image003.png 
    511  
    512 .. image:: pd_image004.jpg 
    513  
    514 .. _Array_Distribution: 
    515  
    516 Array Distribution 
    517 ------------------ 
    518  
    519 This distribution is to be given by users as a txt file where the array  
    520 should be defined by two columns in the order of x and f(x) values. The f(x)  
    521 will be normalized by SasView during the computation. 
    522  
    523 Example of an array in the file 
    524  
    525 30        0.1 
    526 32        0.3 
    527 35        0.4 
    528 36        0.5 
    529 37        0.6 
    530 39        0.7 
    531 41        0.9 
    532  
    533 We use only these array values in the computation, therefore the mean value  
    534 given in the control panel, for example ‘radius = 60’, will be ignored. 
    535  
    536 .. _Gaussian_Distribution: 
    537  
    538 Gaussian Distribution 
    539 --------------------- 
    540  
    541 .. image:: pd_image005.png 
    542  
    543 The xmean is the mean of the distribution and Norm is a normalization factor  
    544 which is determined during the numerical calculation. 
    545  
    546 The PD (polydispersity) is 
    547  
    548 .. image:: pd_image003.png 
    549  
    550 .. image:: pd_image006.jpg 
    551  
    552 .. _Lognormal_Distribution: 
    553  
    554 Lognormal Distribution 
    555 ---------------------- 
    556  
    557 .. image:: pd_image007.png 
    558  
    559 The /mu/=ln(xmed), xmed is the median value of the distribution, and Norm is a  
    560 normalization factor which will be determined during the numerical calculation.  
    561 The median value is the value given in the size parameter in the control panel,  
    562 for example, “radius = 60”. 
    563  
    564 The PD (polydispersity) is given by /sigma/ 
    565  
    566 .. image:: pd_image008.png 
    567  
    568 For the angular distribution 
    569  
    570 .. image:: pd_image009.png 
    571  
    572 The mean value is given by xmean=exp(/mu/+p2/2). The peak value is given by  
    573 xpeak=exp(/mu/-p2). 
    574  
    575 .. image:: pd_image010.jpg 
    576  
    577 This distribution function spreads more and the peak shifts to the left as the  
    578 p increases, requiring higher values of Nsigmas and Npts. 
    579  
    580 .. _Schulz_Distribution: 
    581  
    582 Schulz Distribution 
    583 ------------------- 
    584  
    585 .. image:: pd_image011.png 
    586  
    587 The xmean is the mean of the distribution and Norm is a normalization factor 
    588 which is determined during the numerical calculation. 
    589  
    590 The z = 1/p2– 1. 
    591  
    592 The PD (polydispersity) is 
    593  
    594 .. image:: pd_image012.png 
    595  
    596 Note that the higher PD (polydispersity) might need higher values of Npts and  
    597 Nsigmas. For example, at PD = 0.7 and radisus = 60 A, Npts >= 160, and  
    598 Nsigmas >= 15 at least. 
    599  
    600 .. image:: pd_image013.jpg 
    601  
    602 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    603  
    604 .. _Smearing_Computation: 
    605  
    606 Smearing Computation 
    607 -------------------- 
    608  
    609 Slit_Smearing_  
    610  
    611 Pinhole_Smearing_ 
    612  
    613 2D_Smearing_ 
    614  
    615 .. _Slit_Smearing: 
    616  
    617 Slit Smearing 
    618 ------------- 
    619  
    620 The sit smeared scattering intensity for SAS is defined by 
    621  
    622 .. image:: sm_image002.gif 
    623  
    624 where Norm = 
    625  
    626 .. image:: sm_image003.gif 
    627  
    628 Equation 1 
    629  
    630 The functions .. image:: sm_image004.gif and .. image:: sm_image005.gif 
    631 refer to the slit width weighting function and the slit height weighting  
    632 determined at the q point, respectively. Here, we assumes that the weighting  
    633 function is described by a rectangular function, i.e., 
    634  
    635 .. image:: sm_image006.gif 
    636  
    637 Equation 2 
    638  
    639 and 
    640  
    641 .. image:: sm_image007.gif 
    642  
    643 Equation 3 
    644  
    645 so that .. image:: sm_image008.gif .. image:: sm_image009.gif for 
    646 .. image:: sm_image010.gif and u. 
    647  
    648 The .. image:: sm_image011.gif and .. image:: sm_image012.gif stand for 
    649 the slit height (FWHM/2) and the slit width (FWHM/2) in the q space. Now the  
    650 integral of Equation 1 is simplified to 
    651  
    652 .. image:: sm_image013.gif 
    653  
    654 Equation 4 
    655  
    656 Numerical Implementation of Equation 4 
    657 -------------------------------------- 
    658  
    659 Case 1 
    660 ------ 
    661  
    662 For .. image:: sm_image012.gif = 0 and .. image:: sm_image011.gif =  
    663 constant. 
    664  
    665 .. image:: sm_image016.gif 
    666  
    667 For discrete q values, at the q values from the data points and at the q  
    668 values extended up to qN= qi + .. image:: sm_image011.gif the smeared  
    669 intensity can be calculated approximately 
    670  
    671 .. image:: sm_image017.gif 
    672  
    673 Equation 5 
    674  
    675 .. image:: sm_image018.gif = 0 for *Is* in *j* < *i* or *j* > N-1*. 
    676  
    677 Case 2 
    678 ------ 
    679  
    680 For .. image:: sm_image012.gif = constant and  
    681 .. image:: sm_image011.gif = 0. 
    682  
    683 Similarly to Case 1, we get 
    684  
    685 .. image:: sm_image019.gif for qp= qi- .. image:: sm_image012.gif 
    686  
    687 and qN= qi+ .. image:: sm_image012.gif. .. image:: sm_image018.gif = 0 
    688 for *Is* in *j* < *p* or *j* > *N-1*. 
    689  
    690 Case 3 
    691 ------ 
    692  
    693 For .. image:: sm_image011.gif = constant and  
    694 .. image:: sm_image011.gif = constant. 
    695  
    696 In this case, the best way is to perform the integration, Equation 1,  
    697 numerically for both slit height and width. However, the numerical integration  
    698 is not correct enough unless given a large number of iteration, say at least  
    699 10000 by 10000 for each element of the matrix, W, which will take minutes and  
    700 minutes to finish the calculation for a set of typical SAS data. An  
    701 alternative way which is correct for slit width << slit hight, is used in  
    702 SasView. This method is a mixed method that combines method 1 with the  
    703 numerical integration for the slit width. 
    704  
    705 .. image:: sm_image020.gif 
    706  
    707 Equation 7 
    708  
    709 for qp= qi- .. image:: sm_image012.gif and 
    710 qN= qi+ .. image:: sm_image012.gif. .. image:: sm_image018.gif = 0 for 
    711 *Is* in *j* < *p* or *j* > *N-1*. 
    712  
    713 .. _Pinhole_Smearing: 
    714  
    715 Pinhole Smearing 
    716 ---------------- 
    717  
    718 The pinhole smearing computation is done similar to the case above except  
    719 that the weight function used is the Gaussian function, so that the Equation 6  
    720 for this case becomes 
    721  
    722 .. image:: sm_image021.gif 
    723  
    724 Equation 8 
    725  
    726 For all the cases above, the weighting matrix *W* is calculated when the  
    727 smearing is called at the first time, and it includes the ~ 60 q values  
    728 (finely binned evenly) below (\>0) and above the q range of data in order  
    729 to cover all data points of the smearing computation for a given model and  
    730 for a given slit size. The *Norm*  factor is found numerically with the  
    731 weighting matrix, and considered on *Is* computation. 
    732  
    733 .. _2D_Smearing: 
    734  
    735 2D Smearing 
    736 -----------  
    737  
    738 The 2D smearing computation is done similar to the 1D pinhole smearing above  
    739 except that the weight function used was the 2D elliptical Gaussian function 
    740  
    741 .. image:: sm_image022.gif 
    742  
    743 Equation 9 
    744  
    745 In Equation 9, x0 = qcos/theta/ and y0 = qsin/theta/, and the primed axes  
    746 are in the coordinate rotated by an angle /theta/ around the z-axis (below)  
    747 so that x’0= x0cos/theta/+y0sin/theta/ and y’0= -x0sin/theta/+y0cos/theta/. 
    748  
    749 Note that the rotation angle is zero for x-y symmetric elliptical Gaussian  
    750 distribution. The A is a normalization factor. 
    751  
    752 .. image:: sm_image023.gif 
    753  
    754 Now we consider a numerical integration where each bins in /theta/ and R are  
    755 *evenly* (this is to simplify the equation below) distributed by /delta//theta/  
    756 and /delta/R, respectively, and it is assumed that I(x’, y’) is constant  
    757 within the bins which in turn becomes 
    758  
    759 .. image:: sm_image024.gif 
    760  
    761 Equation 10 
    762  
    763 Since we have found the weighting factor on each bin points, it is convenient  
    764 to transform x’-y’ back to x-y coordinate (rotating it by -/theta/ around z  
    765 axis). Then, for the polar symmetric smear 
    766  
    767 .. image:: sm_image025.gif 
    768  
    769 Equation 11 
    770  
    771 where 
    772  
    773 .. image:: sm_image026.gif 
    774  
    775 while for the x-y symmetric smear 
    776  
    777 .. image:: sm_image027.gif 
    778  
    779 Equation 12 
    780  
    781 where 
    782  
    783 .. image:: sm_image028.gif 
    784  
    785 Here, the current version of the SasView uses Equation 11 for 2D smearing  
    786 assuming that all the Gaussian weighting functions are aligned in the polar  
    787 coordinate. 
    788  
    789 In the control panel, the higher accuracy indicates more and finer binnng  
    790 points so that it costs more in time. 
    791  
    792 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    793  
    794 .. _Polarisation_Magnetic_Scattering: 
    795  
    796 Polarisation/Magnetic Scattering 
    797 -------------------------------- 
    798  
    799 Magnetic scattering is implemented in five (2D) models  
    800  
    801 *  *SphereModel* 
    802 *  *CoreShellModel* 
    803 *  *CoreMultiShellModel* 
    804 *  *CylinderModel* 
    805 *  *ParallelepipedModel* 
    806  
    807 In general, the scattering length density (SLD) in each regions where the  
    808 SLD (=/beta/) is uniform, is a combination of the nuclear and magnetic SLDs and  
    809 depends on the spin states of the neutrons as follows. For magnetic scattering,  
    810 only the magnetization component, *M*perp, perpendicular to the scattering  
    811 vector *Q* contributes to the the magnetic scattering length. 
    812  
    813 .. image:: mag_vector.bmp 
    814  
    815 The magnetic scattering length density is then 
    816  
    817 .. image:: dm_eq.gif 
    818  
    819 where /gamma/ = -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0  
    820 is the classical radius of electron, and */sigma/* is the Pauli spin. For  
    821 polarised neutron, the magnetic scattering is depending on the spin states.  
    822  
    823 Let's consider that the incident neutrons are polarized parallel (+)/ 
    824 anti-parallel (-) to the x' axis (See both Figures above). The possible  
    825 out-coming states then are + and - states for both incident states 
    826  
    827 Non-spin flips: (+ +) and (- -) 
    828 Spin flips:     (+ -) and (- +) 
    829  
    830 .. image:: M_angles_pic.bmp 
    831  
    832 Now, let's assume that the angles of the *Q*  vector and the spin-axis (x')  
    833 against x-axis are /phi/ and /theta/up, respectively (See Figure above). Then,  
    834 depending upon the polarisation (spin) state of neutrons, the scattering length  
    835 densities, including the nuclear scattering length density (/beta/N) are given  
    836 as, for non-spin-flips 
    837  
    838 .. image:: sld1.gif 
    839  
    840 for spin-flips 
    841  
    842 .. image:: sld2.gif 
    843  
    844 where 
    845  
    846 .. image:: mxp.gif 
    847  
    848 .. image:: myp.gif 
    849  
    850 .. image:: mzp.gif 
    851  
    852 .. image:: mqx.gif 
    853  
    854 .. image:: mqy.gif 
    855  
    856 Here, the M0x, M0y and M0z are the x, y and z components of the magnetization  
    857 vector given in the xyz lab frame. The angles of the magnetization, /theta/M  
    858 and /phi/M as defined in the Figure (above) 
    859  
    860 .. image:: m0x_eq.gif 
    861  
    862 .. image:: m0y_eq.gif 
    863  
    864 .. image:: m0z_eq.gif 
    865  
    866 The user input parameters are M0_sld = DMM0, Up_theta = /theta/up,  
    867 M_theta = /theta/M, and M_phi = /phi/M. The 'Up_frac_i' and 'Up_frac_f' are  
    868 the ratio 
    869  
    870 (spin up)/(spin up + spin down) 
    871  
    872 neutrons before the sample and at the analyzer, respectively. 
    873  
    874 *Note:* The values of the 'Up_frac_i' and 'Up_frac_f' must be in the range 
    875 between 0 and 1. 
    876  
    877 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    878  
    879 .. _Key_Combinations: 
    880  
    881 Key Combinations 
    882 ---------------- 
    883  
    884 Copy_Paste_ 
    885  
    886 Bookmark_ 
    887  
    888 Graph_Context_Menu_ 
    889  
    890 FTolerance_ 
    891  
    892 .. _Copy_Paste: 
    893  
    894 Copy & Paste 
    895 ------------ 
    896  
    897 To copy the parameter values in a Fit(Model) panel to the clipboard: 
    898  
    899 *Ctrl(Cmd on MAC) + Left(Mouse)Click*  on the panel. 
    900  
    901 To paste the parameter values to a Fit(Model)panel from the clipboard: 
    902  
    903 *Ctrl(Cmd on MAC) + Shift + Left(Mouse)Click*  on the panel. 
    904  
    905 If this operation is successful, it will say so in the info line at the  
    906 bottom of the SasView window. 
    907  
    908 .. _Bookmark: 
    909  
    910 Bookmark 
    911 -------- 
    912  
    913 Bookmark of a fit-panel or model-panel status: 
    914  
    915 *(Mouse)Right-Click*  and select the bookmark in the popup list. 
    916  
    917 .. _Graph_Context_Menu: 
    918  
    919 Graph Context Menu 
    920 ------------------ 
    921  
    922 To get the graph context menu to print, copy, save data, (2D)average, etc.: 
    923  
    924 *Locate the mouse point on the plot to highlight and *(Mouse) Right Click*  
    925 to bring up the full menu. 
    926  
    927 .. _FTolerance:  
    928  
    929 FTolerance (SciPy) 
    930 ------------------ 
    931  
    932 To change the ftol value of the Scipy FitEngine (leastsq): 
    933  
    934 First, make sure that the Fit panel has data and a model selected. 
    935  
    936 *Ctrl(Cmd on MAC) + Shift + Alt + Right(Mouse)Click*  on the panel. 
    937  
    938 Then, set up the value in the dialog panel. 
    939  
    940 If this operation is successful, the new ftol value will be displayed in the  
    941 info line at the bottom of the SV window.Note that increasing the ftol value  
    942 may cause for the fitting to terminate with higher chisq. 
    943  
    944 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    945  
    946 .. _Status_Bar_Help: 
    947  
    948 Status Bar Help 
    949 --------------- 
    950  
    951 Message_Warning_Hint_  
    952  
    953 Console_ 
    954  
    955 .. _Message_Warning_Hint: 
    956  
    957 Message/Warning/Hint 
    958 -------------------- 
    959  
    960 The status bar located at the bottom of the application frame, displays  
    961 messages, hints, warnings and errors. 
    962  
    963 .. _Console: 
    964  
    965 Console 
    966 ------- 
    967  
    968 Select *light bulb/info icon*  button in the status bar at the bottom of the  
    969 application window to display available history. During a long task, the  
    970 console can also help users to understand the status in progressing. 
     3Placeholder for fitting help 

  • src/sas/guiframe/media/data_explorer_help.rst

    r23a9beb r0d66541  
    1 .. data_explorer_help.rst 
     1..data_explorer_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Loading Data 
    7 ============ 
    8  
    9 Introduction_ 
    10  
    11 Load_Data_ 
    12  
    13 Handy_Menu_ 
    14  
    15 Activate_Data_ 
    16  
    17 Remove_Data_ 
    18  
    19 Append_Plot_to_Graph_ 
    20  
    21 Create_New_Plot_ 
    22  
    23 Freeze_Theory_ 
    24  
    25 Send_Data_to_Applications_ 
    26  
    27 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    28  
    29 .. _Introduction: 
    30  
    31 Introduction 
    32 ------------ 
    33  
    34 *Data Explorer* is a panel that allows the user more interactions with data.  
    35 Some functionalities provided by the Data Explorer are also available through  
    36 the context menu of plot panels or other menus of the applications.Under menu  
    37 *View*  of the menubar, Data explorer can be toggled between Show and Hide by  
    38 clicking the menu *Show/Hide Data Explorer* . 
    39  
    40 *IMPORTANT!*  When Data explorer is hidden, all the data loaded will be sent  
    41 directly to the current active application, if possible. When data Explorer is  
    42 shown data go first to the Data Explorer for the user to handle them later. 
    43  
    44 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    45  
    46 .. _Load_Data: 
    47  
    48 Load Data 
    49 --------- 
    50  
    51 To Load data, click the button *Load Data* , then select one or more (holding  
    52 Ctrl key) files to load into the application. In the list, the *Data*  will be  
    53 displayed as the name of each selected file. Expending this data by clicking  
    54 the *+*  symbol will display available information about the data such as data  
    55 title if exists. 
    56  
    57 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    58  
    59 .. _Handy_Menu: 
    60  
    61 Handy Menu 
    62 ---------- 
    63  
    64 For a quick Data-info/Save/Plot/3d-plot(2d only)/Edit-mask(2d only),  
    65 high-light the data/theory, right-click, and select a proper item from the  
    66 context menu. 
    67  
    68 .. image:: hand_menu.png 
    69  
    70 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    71  
    72 .. _Activate_Data: 
    73  
    74 Activate Data 
    75 ------------- 
    76  
    77 To interact with data, check a data label and click on a button. Checking Data  
    78 make them active for the button operation. Unchecking Data labels will  
    79 deactivate them. 
    80  
    81 There is a combo box labeled *Selection Options*  that allows to activate or  
    82 select multiple data simultaneously. 
    83  
    84 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    85  
    86 .. _Remove_Data: 
    87  
    88 Remove Data 
    89 ----------- 
    90  
    91 Remove data button remove all reference of this data into the application. 
    92  
    93 *WARNING!* Remove data will stop any jobs currently using the selected data. 
    94  
    95 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    96  
    97 .. _Append_Plot_to_Graph: 
    98  
    99 Append Plot to Graph 
    100 -------------------- 
    101  
    102 Click on the button *Append To*  to append selected Data to a plot panel on  
    103 focus. Next to this button is a combo box containing available panels names.  
    104 Selecting a name from this combo box will set the corresponding lot panel on  
    105 focus. If not plot panel is available, the combo box and button will be  
    106 disable. 2D Data cannot be appended to any plot panels . This operation can  
    107 only be performed on 1D data and plot panels currently containing 1D data. 
    108  
    109 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    110  
    111 .. _Create_New_Plot: 
    112  
    113 Create New Plot 
    114 --------------- 
    115  
    116 Click on *New Plot*  button to create a new plot panel where selected data  
    117 will be plotted. 
    118  
    119 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    120  
    121 .. _Freeze_Theory: 
    122  
    123 Freeze Theory 
    124 ------------- 
    125  
    126 *Freeze Theory*  button generate Data from selected theory. This operation can  
    127 only be performed when theory labels are selected. 
    128  
    129 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    130  
    131 .. _Send_Data_to_Applications: 
    132  
    133 Send to Application 
    134 ------------------- 
    135  
    136 Click on the button *Send To*  to send Data to the current active control  
    137 page. One of the single/batch mode can be selected only for Fitting. The batch  
    138 mode provides serial (batch) fitting with one model, i.e., fitting one data by  
    139 another data. Note that only the Fitting allows more that one data to be sent. 
     3Placeholder for data explorer help 

  • src/sas/guiframe/media/graph_help.rst

    r23a9beb r0d66541  
    1 .. graph_help.rst 
     1..graph_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Plotting Data/Models 
    7 ==================== 
    8  
    9 Graph_Menu_ 
    10  
    11 2D_Data_Averaging_ 
    12  
    13 Key_Combinations_ 
    14  
    15 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    16  
    17 .. _Graph_Menu: 
    18  
    19 Graph Menu 
    20 ---------- 
    21  
    22 Introduction_ 
    23  
    24 Reset_Graph_ 
    25  
    26 Hide_Show_Delete_Graph_ 
    27  
    28 Data_Info_ 
    29  
    30 Save_Plot_Image_ 
    31  
    32 Save_Data_ 
    33  
    34 Drag_Plot_ 
    35  
    36 Zoom_In_Out_ 
    37  
    38 Remove_Data_ 
    39  
    40 Change_Scale_ 
    41  
    42 Linear_Fit_ 
    43  
    44 Other_Graph_Modifications_ 
    45  
    46 .. _Introduction: 
    47  
    48 Introduction 
    49 ------------ 
    50  
    51 Locating the pointer and right-clicking on a data/theory plot will bring a  
    52 context menu. On the menu, select a menu item. 
    53  
    54 .. _Reset_Graph: 
    55  
    56 Reset Graph 
    57 ----------- 
    58  
    59 To reset the graph's axis range, right click on the plot and the context menu  
    60 pops-up. Select *Reset Graph*  and the plot will take its initial range. Also  
    61 the 'home' icon in tool bar will do the same. 
    62  
    63 .. _Hide_Show_Delete_Graph: 
    64  
    65 Hide/Show/Delete Graph 
    66 ---------------------- 
    67  
    68 To Hide, click the Hide (bar) button in the tool bar.To Show, select the the  
    69 'Show' menu item in the 'Graph' menu in the menu bar.To Delete, click the 'x'  
    70 button in the title bar. 
    71  
    72 Note: If a residuals graph (in Fitting) is hidden, it will not show up after  
    73 computation. 
    74  
    75 .. _Data_Info: 
    76  
    77 Data Info 
    78 --------- 
    79  
    80 From the context menu, select 'Data Info' to see the data information dialog 
    81 panel. 
    82  
    83 .. _Save_Plot_Image: 
    84  
    85 Save Plot Image 
    86 --------------- 
    87  
    88 Right click on plot. Context menu will pop-up select save image [file name]. 
    89 A dialog window opens and write a the name of the file to save and click on  
    90 *Save Image.* 
    91  
    92 .. _Save_Data: 
    93  
    94 Save Data 
    95 --------- 
    96  
    97 From the context menu, select 'Save points as a file' for 1D, or 'Save as a  
    98 file(DAT)' for 2D. Note that two formats, txt and xml, are available in 1D  
    99 saving. 
    100  
    101 .. _Drag_Plot: 
    102  
    103 Drag Plot 
    104 --------- 
    105  
    106 Select the *crossed arrows*  button on the plot panel *toolbar*  to drag the  
    107 plot. To disable dragging mode, unselect the same button on the toolbar. 
    108  
    109 .. _Zoom_In_Out: 
    110  
    111 Zoom In/Out 
    112 ----------- 
    113  
    114 Select the *rectangle*  button on the plot panel *toolbar*  to zoom in a 
    115 region of the plot. 
    116  
    117 To disable zoom mode, unselect the same button on the toolbar. After zoom in 
    118 a region, select *left arrow*  or *right arrow*  button on the toolbar to set 
    119 the graph the the previous size. If a mouse wheel button is available, 
    120 *zoom in/out*  by scrolling the mouse wheel (see Key_Combinations_ help for 
    121 details). 
    122  
    123 .. _Remove_Data: 
    124  
    125 Remove Data from Plot 
    126 --------------------- 
    127  
    128 Highlight the plot and the context menu appears.Select *remove [file name]*. 
    129 The plot selected will disappear. 
    130  
    131 .. _Change_Scale: 
    132  
    133 Change Scale 
    134 ------------ 
    135  
    136 If the loaded data is a 1-D data changing scale or data representation will  
    137 work as follows. *Right click* on the plot window. A context menu pops-up and  
    138 select *Change Scale* . A dialog window titled *select the scale of the graph*  
    139 will pop-up then change the *x* , the *y*  and the *view*  values as wish. 
    140  
    141 The 'view' option includes the axis scale short-cuts such as Linear, Guinier,  
    142 Cross-sectional (XC) Guinier, and Porod plot scale. For a proper data set,  
    143 these axis scales can be used to estimate Rg, Rod diameter, or Background of  
    144 neutron scattering data respectively (via 'Linear Fit'; see below). For a 2D  
    145 image, *Right click*  on the image to pop-up the context menu. Select to  
    146 switch from linear to log scale. The scale selected is printed on the status  
    147 bar. 
    148  
    149 If the loaded data is an image. *Right click*  on the image to pop-up the 
    150 context menu. Select to switch from linear to log scale. The scale selected is 
    151 printed on the status bar. 
    152  
    153 .. _Linear_Fit: 
    154  
    155 Linear Fit 
    156 ---------- 
    157  
    158 Linear fit is to perform a line model fitting keeping the scale of the plot. 
    159 Highlight data to fit. From the context menu select *Linear Fit* . A dialog 
    160 window appears. Change model initial parameters, data limits and hit *fit* 
    161 button. New parameters values are displayed and the line with the new 
    162 parameters is added to the plot. Especially for Guinier, XC Guinier, and 
    163 Porod plot scale, this 'Linear Fit' will provides Rg, Rod diameter, and 
    164 background, respectively. The following figure shows an example for the 
    165 Guinier scale. 
    166  
    167 .. image:: guinier_fit.png 
    168  
    169 .. _Other_Graph_Modifications: 
    170  
    171 Other Graph Modifications 
    172 ------------------------- 
    173  
    174 Some custom modifications of the symbols, text, axis, etc of the graph are  
    175 provided. 
    176  
    177 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    178  
    179 .. _2D_Data_Averaging: 
    180  
    181 2D Data Averaging 
    182 ----------------- 
    183  
    184 Description_ 
    185  
    186 How_to_Average_ 
    187  
    188 Available_Averagings_ 
    189  
    190 Unmasked_Circular_Average_ 
    191  
    192 Masked_Circular_Average_ 
    193  
    194 Sector_Average_ 
    195  
    196 Annular_Average_ 
    197  
    198 Box_Sum_ 
    199  
    200 Box_Averaging_in_Qx_ 
    201  
    202 Box_Averaging_in_Qy_ 
    203  
    204 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    205  
    206 .. _Description:  
    207  
    208 Description 
    209 ----------- 
    210  
    211 This feature allows you to perform different types of averages on your data,  
    212 and allows you to see what regions of the detector will contribute to the  
    213 average. The region to be averaged will be drown and can be modified by  
    214 dragging the lines around. 
    215  
    216 .. _How_to_Average: 
    217  
    218 How to Average 
    219 -------------- 
    220  
    221 Right click on 2D data for the context menu to appear. Select one type of  
    222 averages among *"sector [Q view]", "Annulus [Phi view]", "Box sum", "Box  
    223 averaging in Qx ", "box averaging on Qy","Perform circular Average".* 
    224  
    225 A slicer will appear except for *"Perform circular Average"*  that you can  
    226 drag by clicking on a slicer 's marker. When the marker is highlighted in red,  
    227 it means that the slicer can change size.You can also move some of the slicer  
    228 by simply drag its side when highlighted in red. the slicer size will be reset  
    229 to its previous size if the user try to select a region greater than the size  
    230 of the data. 
    231  
    232 The user can also select a region to average when a slicer has been selected  
    233 already by *right clicking*  on the context menu and selecting *Edit Slicer  
    234 Parameters* . The dialog window will appears and the user can enter values to  
    235 selected a region or selected numbers of points to plot *nbins* . 
    236  
    237 For *Box sum* , when the user selects this option, a new panel is created  
    238 containing the result of average of the sum of every pixels contains on that  
    239 data.The user can also enter values to select a region. 
    240  
    241 .. _Available_Averagings: 
    242  
    243 Available Averagings 
    244 -------------------- 
    245  
    246 Some different types of averaging are provided for. 
    247  
    248 .. _Unmasked_Circular_Average: 
    249  
    250 Unmasked Circular Average 
    251 ------------------------- 
    252  
    253 This operation will perform and average in constant q-rings around the (x,y) pixel 
    254 location of the beam center. 
    255  
    256 .. _Masked_Circular_Average: 
    257  
    258 Masked Circular Average 
    259 ----------------------- 
    260  
    261 This operation is same as 'Masked Circular Average' except that the masked 
    262 region is excluded if masked. 
    263  
    264 .. _Sector_Average: 
    265  
    266 Sector Average [Q View] 
    267 ----------------------- 
    268  
    269 This operation averages in constant q-arcs. The width of the sector is specified in 
    270 degrees (+/- delta phi) each side of the central angle (phi). 
    271  
    272 .. _Annular_Average: 
    273  
    274 Annular Average [Phi View] 
    275 -------------------------- 
    276  
    277 It performs an average between two q-values centered in (0,0), and averaged  
    278 over a width of a specified number of pixels. The data is returned as a  
    279 function of angle (phi) in degrees. Moving one circle of this slicer to  
    280 radius of zero corresponding to a circular averaging on radius qmax , the  
    281 outer circle. The angle zero starts from the positive x-axis direction. 
    282  
    283 .. _Box_Sum: 
    284  
    285 Box Sum 
    286 ------- 
    287  
    288 Perform the sum of counts in a 2D region of interest.When editing the slicer,  
    289 the user can enter the length and the width the rectangle slicer and the  
    290 coordinates of the center of this rectangle. 
    291  
    292 .. _Box_Averaging_in_Qx: 
    293  
    294 Box Averaging in Qx 
    295 ------------------- 
    296  
    297 Computes average I(Qx) for a region of interest. When editing the slicer, the  
    298 user can control the length and the width the rectangle slicer. The averaged  
    299 output is calculated from the constant bins with rectangular shape. The  
    300 resultant q values are nominal values, i.e., the central values of each bins  
    301 on the x-axis. 
    302  
    303 .. _Box_Averaging_in_Qy: 
    304  
    305 Box Averaging in Qy 
    306 ------------------- 
    307  
    308 Computes average I(Qy) for a region of interest.When editing the slicer, the  
    309 user can control the length and the width the rectangle slicer. The averaged  
    310 output is calculated from the constant bins with rectangular shape. The  
    311 resultant q values are nominal values, i.e., the central values of each bins  
    312 on the y-axis. 
    313  
    314 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    315  
    316 .. _Key_Combinations: 
    317  
    318 Key Combination 
    319 --------------- 
    320  
    321 Floating_Panel_ 
    322  
    323 Graph_Context_Menu_ 
    324  
    325 Zoom_ 
    326  
    327 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    328  
    329 .. _Floating_Panel: 
    330  
    331 Floating Panel 
    332 -------------- 
    333  
    334 For a graph panel to float on the top of the SV window: 
    335  
    336 Press the *Ctrl(Cmd on MAC) key*  on dragging and placing a panel. Or if you  
    337 want to make all plot panels float, select 'Float' from Graph/Preperences in  
    338 the menu bar. Otherwise choose 'Dock'. 
    339  
    340 .. _Graph_Context_Menu: 
    341  
    342 Graph Context Menu 
    343 ------------------ 
    344  
    345 To get the graph context menu to print, copy, save data, (2D)average, etc,  
    346 *locate the mouse point on the plot to highlight and *(Mouse) Right Click*  
    347 to bring up the full menu. 
    348  
    349 .. _Zoom: 
    350  
    351 Zoom In/Out 
    352 ----------- 
    353  
    354 To Zoom in or out the full plot, *locate the mouse point inside the graph  
    355 which will be the center of the zooming, then *rotate MouseWheel*. 
    356  
    357 *To Zoom in or out the plot in x or y direction, *locate (and click) the  
    358 mouse point near x (or y) axis just outside of the graph and then *rotate  
    359 MouseWheel* .* Note that this works only on the 1D plots. 
     3Placeholder for graph help 

  • src/sas/invariant/media/invariant_help.rst

    r23a9beb r0d66541  
    1 .. invariant_help.rst 
     1..invariant_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 Invariant Calculation Perspective 
    7 ================================= 
    8  
    9 Scattering_Invariant_ 
    10  
    11 Volume_Fraction_ 
    12  
    13 Specific_Surface_Area_ 
    14  
    15 Definitions_ 
    16  
    17 Reference_ 
    18  
    19 How_to_Use_ 
    20  
    21 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    22  
    23 .. _Scattering_Invariant: 
    24  
    25 Scattering Invariant 
    26 -------------------- 
    27  
    28 The scattering invariant (Q*) is a model-independent quantity that can be  
    29 easily calculated from scattering data. 
    30  
    31 For two phase systems, the scattering invariant, Q*, is defined as the  
    32 integral of the square of the wave transfer (q) multiplied by the scattering  
    33 cross section over the full range of q. 
    34  
    35 Q* is given by the following equation 
    36  
    37 .. image:: image001.gif 
    38  
    39 This model independent quantity (Q*) is calculated from the scattering data  
    40 that can be used to determine the volume fraction and the specific area of the  
    41 sample under consideration. 
    42  
    43 These quantities are useful in their own right and can be used in further  
    44 analysis. With this scattering invariant module users will also be able to  
    45 determine the consistency of those properties between data. There is no real  
    46 data defined from zero to infinity, there usually have limited range. 
    47  
    48 Q* is not really computed from zero to infinity. Our maximum q range is  
    49 1e-5 ~ 10 (1/Angstrom). The lower and/or higher q range than data given can be  
    50 extrapolated by fitting some data nearby. 
    51  
    52 The scattering invariant is computed as follows 
    53  
    54 *I(q)* = *I(q)*  w/o background : If the data includes a background, user sets  
    55 the value to subtract the background for the Q* computation. 
    56  
    57 Reset *I(q)* = *I(q)* scaling factor* , delta *I(q) =*  delta *I(q)*scaling  
    58 factor* : If non-zero scaling factor is given, it will be considered. 
    59  
    60 Invariant 
    61  
    62 .. image:: image001.gif 
    63  
    64 where *g =q*  for the pinhole geometry and *g =qv*  (the slit height) for the  
    65 slit geometry which can be given in data or as a value. 
    66  
    67 Higher q-region (\>= qmax in data) 
    68  
    69 Power law (w/o background term) function = C/q4will be used 
    70  
    71 where the constant C(=2pi(delta(rho))Sv) is to be found by fitting part of  
    72 data with the range of qN-mto qN(m\<N). 
    73  
    74 Lower q-region (\<= qmin in data): 
    75  
    76 Guinier function = *I0exp(-Rg2q2/3)*  where I0and Rgare obtained by fitting, 
    77  
    78 similarly to the high q region above. 
    79  
    80 Power law can also be used. 
    81  
    82 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    83  
    84 .. _Volume_Fraction: 
    85  
    86 Volume Fraction 
    87 --------------- 
    88  
    89 .. image:: image002.gif 
    90  
    91 where delta(rho) is the SLD contrast of which value is given by users. 
    92  
    93 .. image:: image003.gif 
    94  
    95 Thus 
    96  
    97 where 0 =\< *A*  =\<1/4 in order for these values to be physically valid. 
    98  
    99 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    100  
    101 .. _Specific_Surface_Area: 
    102  
    103 Specific Surface Area 
    104 --------------------- 
    105  
    106 .. image:: image004.gif 
    107  
    108 where *A*  and *Q**  are obtained from previous sections, and the Porod  
    109 constant *Cp*  is given by users. 
    110  
    111 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    112  
    113 .. _Definitions: 
    114  
    115 Definitions 
    116 ----------- 
    117  
    118 Q: the magnitude of neutron (or X-ray) momentum transfer vector. 
    119  
    120 I(Q): the scattering intensity as a function of the momentum transfer Q. 
    121  
    122 Invariant total is the sum of the invariant calculated from datas q range and 
    123 the invariant resulting from extrapolation at low q range and at high q range  
    124 if considered. 
    125  
    126 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    127  
    128 .. _Reference: 
    129  
    130 References 
    131 ---------- 
    132  
    133 Chapter 2 in O. Glatter and O. Kratky, "Small Angle X-Ray Scattering", Academic  
    134 Press, New York, 1982 
    135  
    136 http://physchem.kfunigraz.ac.at/sm/ 
    137  
    138 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    139  
    140 .. _How_to_Use: 
    141  
    142 How to Use 
    143 ---------- 
    144  
    145 1. Loading data to the panel: Open the data file from File in the menu bar.  
    146 Select loaded data from a plot panel by highlighting that it until its color  
    147 turns yellow. Then right click on that the data and selects the option Compute  
    148 Invariant. The application automatically computes the invariant value if the  
    149 data loaded is valid. 
    150  
    151 2. To subtract a background or/and to rescale the data, type the values in  
    152 Customized Input box. 
    153  
    154 3. If you want to calculate the volume fraction and the specific surface  
    155 area, type the optional inputs in the customized input box, and then press  
    156 'Compute' button. 
    157  
    158 4. The invariant can also be calculated including the outside of the data Q  
    159 range:  To include the lower Q and/or the higher Q range, check in the enable  
    160 extrapolation check box in 'Extrapolation' box. If the power low is chosen, 
    161 the power (exponent) can be either held or fitted by checking the  
    162 corresponding radio button.  The Npts that is being used for the extrapolation  
    163 can be specified. 
    164  
    165 5. If the invariant calculated from the extrapolated region is too large, it  
    166 will be warn in red at the top of the panel, which means that your data is not  
    167 proper to calculate the invariant. 
    168  
    169 6. The details of the calculation is available by clicking the 'Details' 
    170 button in the middle of the panel. 
    171  
    172 .. image:: image005.gif 
     3Placeholder for invariant help 

  • src/sas/invariant/media/pr_help.rst

    r23a9beb r0d66541  
    1 .. pr_help.rst 
     1..pr_help.rst 
    22 
    3 .. This is a port of the original SasView html help file to ReSTructured text 
    4 .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
    5  
    6 .. |pi| unicode:: U+03C0 
    7 .. |chi| unicode:: U+03C7 
    8  
    9 P(r) Inversion Perspective 
    10 ========================== 
    11  
    12 The inversion approach is based on Moore, J. Appl. Cryst., (1980) 13, 168-175. 
    13  
    14 P(r) is set to be equal to an expansion of base functions of the type 
    15 phi_n(r) = 2 * r * sin(|pi| * n * r / D_max). 
    16  
    17 The coefficient of each base function in the expansion is found by performing  
    18 a least square fit with the following fit function: 
    19  
    20 |chi| ^2 = sum_i[ I_meas(q_i) - I_th(q_i) ]^2 / error^2 + Reg_term 
    21  
    22 where I_meas(q) is the measured scattering intensity and I_th(q) is the  
    23 prediction from the Fourier transform of the P(r) expansion.  
    24  
    25 The Reg_term term is a regularization term set to the second derivative  
    26 d^2 P(r) / dr^2 integrated over r. It is used to produce a smooth P(r) output. 
    27  
    28 The following are user inputs: 
    29  
    30 *  Number of terms: the number of base functions in the P(r) expansion. 
    31     
    32 *  Regularization constant: a multiplicative constant to set the size of 
    33    the regularization term. 
    34  
    35 *  Maximum distance: the maximum distance between any two points in the 
    36    system. 
     3Placeholder for P(r) help 
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