Changes in / [5dfdfa7:48153283] in sasview

Files:

• docs/sphinx-docs/source/user/user.rst (modified) (2 diffs)
• src/sas/calculator/media/density_calculator_help.rst (modified) (1 diff)
• src/sas/calculator/media/kiessig_calculator_help.rst (modified) (1 diff)
• src/sas/calculator/media/resolution_calculator_help.rst (modified) (1 diff)
• src/sas/calculator/media/sas_calculator_help.rst (modified) (1 diff)
• src/sas/calculator/media/sld_calculator.rst (deleted)
• src/sas/calculator/media/sld_calculator_help.rst (added)
• src/sas/calculator/media/slit_calculator_help.rst (modified) (1 diff)
• src/sas/data_util/media/data_operator_help.rst (modified) (1 diff)
• src/sas/fit/media/fitting_help.rst (modified) (1 diff)
• src/sas/guiframe/media/data_explorer_help.rst (modified) (1 diff)
• src/sas/guiframe/media/graph_help.rst (modified) (1 diff)
• src/sas/invariant/media/invariant_help.rst (modified) (1 diff)
• src/sas/invariant/media/pr_help.rst (modified) (1 diff)
• src/sas/perspectives/calculator/media/image_viewer_help.rst (added)
• src/sas/perspectives/calculator/media/python_shell_help.rst (added)

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

@@ -12 +12 @@
    Plotting Data/Models <guiframe/graph_help>
    
-   Fitting Perspective <fitting/fitting_help>
+   Fitting Perspective <fit/fitting_help>
    
    P(r) Inversion Perspective <invariant/pr_help>
@@ -33 +33 @@
    Generic Scattering Calculator Tool <calculator/sas_calculator_help>
    
-   Python Shell Tool
+   Python Shell Tool <perspectives/calculator/python_shell_help>
    
-   Image Viewer Tool
+   Image Viewer Tool <perspectives/calculator/image_viewer_help>

src/sas/calculator/media/density_calculator_help.rst

@@ -1 @@
-..density_calculator_help.rst
+.. density_calculator_help.rst
 
-Placeholder for density calculator help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Density/Volume Calculator Tool
+==============================
+
+Description
+-----------
+
+This tool is to calculate the mass density from the molar volume or vice 
+versa. To calculate the mass density, the chemical formula and molar volume 
+should be provided.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+How To
+------
+
+1. Molecular Formula: The chemical formula of ONE molecule or ONE atom. For 
+mixtures, the ratio of the each molecules should be used; for example, 
+(H2O)0.5(D2O)0.5.
+
+2. Select input (molar volume or mass density) from combobox. Then type in the 
+input value.
+
+3. Click the 'Calculate' button to perform the calculation.
+
+4. Outputs also include the molar mass (weight) that depends only on the 
+chemical formula
+
+.. image:: density_tutor.gif

src/sas/calculator/media/kiessig_calculator_help.rst

@@ -1 @@
-..kiessig_calculator_help.rst
+.. kiessig_calculator_help.rst
 
-Placeholder for Kiessig calculator help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Kiessig Thickness Calculator Tool
+=================================
+
+Description
+-----------
+
+This tool is to approximately estimate the thickness of a layer or the 
+diameter of particles from the Kiessig fringe in SAS/NR data, and using the 
+Kiessig relation
+
+thickness = 2*Pi/fringe_width.
+  
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+
+How To
+------
+
+To get a rough thickness or particle size, just type the Kiessig fringe width 
+(in units of 1/Angstrom) and click on the 'Compute' button. Then the output 
+value will be show up in the 'Thickness' text box.

src/sas/calculator/media/resolution_calculator_help.rst

@@ -1 @@
-..resolution_calculator_help.rst
+.. resolution_calculator_help.rst
 
-Placeholder for resolution calculator help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Q Resolution Estimator
+======================
+
+Description
+-----------
+
+This tool is to approximately estimate the resolution of Q based on the SAS 
+instrumental parameter values assuming that the detector is flat and vertical 
+to the incident beam direction.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+How To
+------
+
+1. Select the source and source type (Monochromatic or TOF). Note that the 
+computational difference between the sources is only the gravitational 
+contribution due to the mass.
+
+2. Change the default values of the instrumental parameters as desired.
+
+3. The input formats of wavelength and its spread (=FWHM/wavelength) depend on 
+the source type.For monochromatic wave, the inputs are just one values as shown 
+with the defaults.For TOF, the min and max values should be separated by "-" 
+to describe the wavelength band range. Optionally, the input of the wavelength 
+(NOT of the wavelength spread) could be extended by adding "; --" where the -- 
+is the number of the bins for the numerical integration. Otherwise, the 
+default value "10" bins will be used. The same number of bins will be used 
+for the corresponding wavelength spread in either cases.
+
+4. For TOF, the default wavelength spectrum is flat. The custom spectrum file 
+(with 2 column text: wavelength(A) vs. intensity) can also be loaded by 
+selecting "Add new" in the combobox.
+
+5. Once set all the input values, click the compute button. Depending on 
+computation loads the calculation time will vary.
+
+6. 1D and 2D dQ will be displayed in the text-box at the bottom of the panel. 
+Two dimensional resolution weight distribution (2D elliptical Gaussian 
+function) will also be displayed in the plot panel even if the Q inputs are 
+outside of the detector limit. The red lines indicate the limits of the 
+detector (if a green lines appear (for TOF), it indicates the limits of the 
+maximum q range for the largest wavelength due to the size of the detector). 
+Note that the effect from the beam block is ignored, so in the small q region 
+near the beam block 
+
+[ie., q<2*pi*(beam block diameter) / (sample to detector distance) / lamda_min] 
+
+the variance is slightly under estimated.
+
+7. The summary can be accessed by clicking the 'light-bulb' icon at the bottom 
+of the SasView main window.
+
+.. image:: resolution_tutor.gif
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+Theory
+------
+
+The scattering wave transfer vector is by definition
+
+.. image:: q.gif
+
+In the limit of the small angle, the variance of q in the first order 
+approximation is
+
+.. image:: sigma_q.gif
+
+In summary, the geometric and gravitational contributions depending on the 
+shape of each factors can be expressed as shown the table.
+
+.. image:: sigma_table.gif
+
+Finally, we use a Gaussian function to describe the 2D weighting distribution 
+of the uncertainty in q.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+References
+----------
+D.F.R. Mildner and J.M. Carpenter, J. Appl. Cryst. 17, 249-256 (1984)
+
+D.F.R. Mildner, J.M. Carpenter and D.L. Worcester, J. Appl. Cryst. 19, 311-319 
+(1986)

src/sas/calculator/media/sas_calculator_help.rst

@@ -1 @@
-..sas_calculator_help.rst
+.. sas_calculator_help.rst
 
-Placeholder for generic SAS calculator help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+.. |beta| unicode:: U+03B2
+.. |gamma| unicode:: U+03B3
+.. |theta| unicode:: U+03B8
+.. |mu| unicode:: U+03BC
+.. |sigma| unicode:: U+03C3
+.. |phi| unicode:: U+03C6
+
+.. |equiv| unicode:: U+2261
+.. |noteql| unicode:: U+2260
+
+Generic Scattering Calculator Tool
+==================================
+
+Polarization and Magnetic Scattering
+
+Theory_ 
+GUI_ 
+PDB_Data_ 
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Theory:
+
+Theory
+------
+
+In general, a particle with a volume V can be described by an ensemble 
+containing N 3-dimensional rectangular pixels where each pixels are much 
+smaller than V. Assuming that all the pixel sizes are same, the elastic 
+scattering intensity by the particle
+
+.. image:: gen_i.gif
+
+where /beta/jand rj are the scattering length density and the position of the 
+j'th pixel respectively. And the total volume
+
+.. image:: v_j.gif
+
+for /beta/j/noteql/0 where vj is the volume of the j'th pixel (or the j'th 
+natural atomic volume (= atomic mass/natural molar density/Avogadro number) for 
+the atomic structures). The total volume V can be corrected by users. This 
+correction is useful especially for an atomic structure (taken from a pdb file) 
+to get the right normalization. Note that the /beta/j displayed in GUI may be 
+incorrect but will not affect the scattering computation if the correction of 
+the total volume is made. The scattering length density (SLD) of each pixel 
+where the SLD is uniform, is a combination of the nuclear and magnetic SLDs and 
+depends on the spin states of the neutrons as follows:For magnetic scattering, 
+only the magnetization component, *M*perp, perpendicular to the scattering 
+vector *Q* contributes to the the magnetic scattering length. (Figure below).
+
+.. image:: mag_vector.bmp
+
+The magnetic scattering length density is then
+
+.. image:: dm_eq.gif
+
+where /gamma/= -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0 is 
+the classical radius of electron, and */sigma/* is the Pauli spin.
+
+For polarized neutron, the magnetic scattering is depending on the spin states.
+
+Let's consider that the incident neutrons are polarised parallel (+)/ 
+anti-parallel (-) to the x' axis (See both Figures above). The possible 
+out-coming states then are + and - states for both incident states, where 
+
+- Non-spin flips: (+ +) and (- -)
+- Spin flips:     (+ -) and (- +)
+
+.. image:: gen_mag_pic.bmp
+
+Now, let's assume that the angles of the *Q*  vector and the spin-axis (x') 
+from x-axis are /phi/ and /theta/up respectively (See Figure above). Then, 
+depending upon the polarization (spin) state of neutrons, the scattering 
+length densities, including the nuclear scattering length density (/beta/N) 
+are given as, for non-spin-flips
+
+.. image:: sld1.gif
+
+and for spin-flips
+
+.. image:: sld2.gif
+
+where
+
+.. image:: mxp.gif
+
+.. image:: myp.gif
+
+.. image:: mzp.gif
+
+.. image:: mqx.gif
+
+.. image:: mqy.gif
+
+Here, the M0x, M0yand M0zare the x, y and z components of the magnetisation 
+vector given in the xyz lab frame. 
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _GUI:
+
+GUI
+---
+
+.. image:: gen_gui_help.bmp
+
+After the computation, the result will be listed in the 'Theory' box in the 
+data explorer panel on the main window.The 'Up_frac_in' and 'Up_frac_out' are 
+the ratio, (spin up) /(spin up + spin down) neutrons before the sample and at 
+the analyzer, respectively.
+
+*Note I: The values of 'Up_frac_in' and 'Up_frac_out' must be in the range 
+between 0 and 1. For example, both values are 0.5 for unpolarized neutrons.*
+
+*Note II: This computation is totally based on the pixel (or atomic) data 
+fixed in the xyz coordinates. Thus no angular orientational averaging is 
+considered.*
+
+*Note III: For the nuclear scattering length density, only the real component 
+is taken account.*
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _PDB_Data:
+
+PDB Data
+--------
+
+This Generic scattering calculator also supports some pdb files without 
+considering polarized/magnetic scattering so that the related parameters 
+such as Up_*** will be ignored (see the Picture below). The calculation for 
+fixed orientation uses (the first) Equation above resulting in a 2D output, 
+whileas the scattering calculation averaged over all the orientations uses 
+the Debye equation providing a 1D output
+
+.. image:: gen_debye_eq.gif
+
+where vj /beta/j /equiv/ bj the scattering length of the j'th atom. The resultant outputs 
+will be displayed in the DataExplorer for further uses.
+
+.. image:: pdb_combo.jpg

src/sas/calculator/media/slit_calculator_help.rst

@@ -1 @@
-..slit_calculator_help.rst
+.. slit_calculator_help.rst
 
-Placeholder for slit calculator help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Slit Size Calculator Tool
+=========================
+
+Description
+-----------
+This tool is for X-ray users to calculate the slit size (FWHM/2) for smearing 
+based on their half beam profile data (SAXSess).
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+How To
+-------
+To calculate the slit size (FWHM/2), just load the beam profile data using the 
+browse button.
+
+Once a data is loaded, the slit size will be computed and show up in the text 
+box.
+
+Because the unit is not specified in the data file, we do not convert it into 
+1/Angstrom so  users are responsible for converting the units of their data.
+
+Note: This slit size calculator only works for beam profile data produced by 
+'SAXSess'.
+
+To see the file format, check the file, 'beam profile.DAT', in the 'test' 
+folder of SasView.

src/sas/data_util/media/data_operator_help.rst

@@ -1 @@
-..data_operator_help.rst
+.. data_operator_help.rst
 
-Placeholder for data operator help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Data Operations Tool
+====================
+
+Description
+-----------
+This dialog panel provides arithmetic operations between two data sets (the 
+last data set could be a number).
+
+When data1 and data2 are selected, their x (or qx and qy for 2D) value(s)
+must match with each other.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+How To
+------
+1. Type the data name resulted from an operation.
+
+2) Select a data/theory in the drop down menus. When data2 is set to number, 
+   type a number in the text control box.
+
+3) Select an arithmetic operator symbol; + (for addition), - (for subtraction), 
+   * (for multiplication), / (for division), and | (for combination of two data
+   sets).
+
+   If two data sets do not match, the operation will fail and the background color
+   of the combo box items will turn to red (WIN only).
+
+4) If the operation is successful, hit the Apply button to make the new data.
+   Then the data name will be shown up in the data box in the data explorer.
+
+Note: Any errors and warnings will be displayed at the bottom of the SasView
+window.
+
+.. image:: data_oper_pic.png

src/sas/fit/media/fitting_help.rst

@@ -1 @@
-..fitting_help.rst
-
-Placeholder for fitting help
+.. fitting_help.rst
+
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+.. |beta| unicode:: U+03B2
+.. |gamma| unicode:: U+03B3
+.. |mu| unicode:: U+03BC
+.. |sigma| unicode:: U+03C3
+.. |phi| unicode:: U+03C6
+.. |theta| unicode:: U+03B8
+
+Fitting Perspective
+===================
+
+Load_a_File_
+
+Single_Fit_
+
+Simultaneous_Fitting_
+
+Batch_Fitting_
+
+Model_Selection_
+
+Model_Category_Manager_
+
+Model_Functions_
+
+Custom_Model_Editor_
+
+Polydispersity_Distributions_
+
+Smearing_Computation_
+
+Polarisation_Magnetic_Scattering_
+
+Key_Combinations_
+
+Status_Bar_Help_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Load_a_File:
+
+Load a File
+-----------
+
+From Menu go to *Data* -> *Load Data File(or Folder)* . Select a file/folder 
+from the menu bar and click on Open button. Data contained in the file will be 
+displayed. To cancel the loading click on *cancel* . In case a file can not be 
+loaded, an error message will be displayed on the statusbar.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Single_Fit:
+
+Single Fit
+----------
+
+One of two fit-engines can be chosen from the Fitting menu bar. The Simple Fit-
+engine uses Scipy's leasqr and the Complex Fit-Engine is a custom optimizer 
+that provides a better chance to find the global minimum of the chi2 but that 
+requires longer computation time. In order to set a data to a control panel 
+(FitPage), see the "DataLoader Help". Once a data set to the FiPage, select a 
+model from the combo box. The default parameters of the model will be display. 
+Set initial parameters if need. Check and uncheck parameters to fit/fix. Click 
+the *'Fit'*  button. When the fitting is finished, the resultant parameter 
+values will be displayed with the errors. If a error is missing, it generally 
+means that the corresponding parameter is not very depending on the model. The 
+chisq/Npt_fit and the plot associated with the fit operation will be also 
+updated.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Simultaneous_Fitting:
+
+Simultaneous Fitting
+--------------------
+
+This fitting option enables to set a number of the constraints between the 
+parameters of fitting(s). It requires one or more FitPages with a data and a 
+model set for the fitting, and performs multiple fittings given by the 
+FitPage(s). The Complex (ParkMC) FitEngine will be used automatically.
+
+Simultaneous Fit without Constraint
+
+Assuming some FitPages are already set up, check the checkboxes of the 
+model_data rows to fit. And click the 'Fit' button. The results will return to 
+each FitPages.
+
+Note that the chi2/Npts returned is the sum of the chi2/Npts of each fits. If 
+one needs the chi2 value only for a page, click the 'Compute' button in the 
+FitPage to recalculate.
+
+Simultaneous Fit with Constraint
+
+Enter constraint in the text control next to *constraint fit*  button. 
+Constraint should be of type model1 parameter name = f(model2 parameter name) 
+for example, M0.radius=2*M1.radius. Many constraints can be entered for a 
+single fit. Each of them should be separated by a newline charater or ";" 
+The easy setup can generate many constraint inputs easily when the selected 
+two models are the same type.
+
+Note that the chi2/Npts returned is the sum of the chi2/Npts of each fits. 
+If one needs the chi2 value only for one fit, click the 'Compute' button in 
+the FitPage to recalculate.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Batch_Fitting:
+
+Batch Fitting
+-------------
+
+Batch_Fit_
+
+Batch_Window_
+
+Edit_Grid_
+
+Save_Grid_
+
+Open_Batch_Results_
+
+Plot_
+
+View_Column_Cell_
+
+.. _Batch_Fit:
+
+Batch Fit
+--------- 
+
+Create a *Batch Page* by selecting the *Batch* radio button on the DataExplorer
+(see figure below) and for a new control page select 'New FitPage' in the 
+Fitting menubar.
+
+.. image:: batch_button_area.bmp
+
+Figure 1: MenuBar: 
+
+Load Data to the DataExplorer if not already loaded.
+
+Select one or more data sets by checking the check boxes, and then make sure 
+that "Fitting" is selected in the dropdown menu next to the "Send To" button. 
+Once ready, click the 'Send To' button to set data to a BatchPage. If already 
+an empty batch page exists, it will be set there. Otherwise it will create a 
+new Batch Page. Set up the model and the parameter values as same as a single 
+fitting (see Single Fit help) <Single_Fit_>. Then use 'Fit' button to 
+perform the fitting.
+
+Unlike a single fit, the results of the fittings will not return to the 
+BatchPage'. Instead, a Grid window will be provided once the fitting is 
+completed. The Grid window is also accessible from the 'View' menu 
+(see Figure 2).
+
+Note that only one model is used for all the data. The initial parameter 
+values given in the control page will be used all the data fittings. If one 
+wants the FitEngine to use the initial values from the results of the 
+previous data fitting (if any), choose the 'Chain Fitting' option in the 
+Fitting menubar, which will speed up the fitting especially when you have 
+lots of, and similar, data sets.
+
+.. _Batch_Window:
+
+Batch Window
+------------
+Batch Window provides an easy way to view the fit results, i.e., plot data, 
+fits, and residuals. Batch window will be automatically shown after a batch 
+fit is finished.
+
+Once closed, it can be opened anytime from the "View" menubar item (see 
+Figure 2).
+
+.. image:: restore_batch_window.bmp
+
+Figure 2: Edit Menu: 
+
+.. _Edit_Grid:
+
+Edit Grid
+---------
+
+Once a batch fit is completed, all fitted and fixed model parameters are 
+displayed to the current sheet of the batch window except the errors of the 
+parameters. To view the errors, click on a given column then under *Edit*  
+menubar item, and insert the desired parameter by selecting a menu item with 
+the appropriated label. Empty column can be inserted in the same way. A 
+column value can be customized by editing an existing empty column.
+
+To Remove column from the grid, select it, choose edit menu, and click the 
+*'remove'*  menu item. Any removed column should reinserted whenever needed.
+
+All above options are also available when right clicking on a given column 
+label(see Figure 3).
+
+*Note:*  A column always needs to be selected in order to remove or insert a 
+column in the grid.
+
+.. image:: edit_menu.bmp
+
+Figure 3: Edit Menu:
+
+.. _Save_Grid:
+
+Save Grid
+---------
+To save the current page on the batch window, select the *'File'*  menubar 
+item(see Figure 4), then choose the *'Save as'*  menu item to save it as a 
+.csv file.
+
+*Note:* The grid doesn't save the data array, fits, and the array residuals.
+As a result, the 'View (fit) Results' functionality will be lost when
+reloading the saved file.
+
+Warning! To ensure accuracy of saved fit results, it is recommended to save 
+the current grid before modifying it .
+
+.. _Open_Batch_Results:
+
+Open Batch Results 
+------------------
+
+Any *csv*  file can be opened in the grid by selecting the *'Open'*  under 
+the *'File'*  menu in the Grid Window(see Figure 4). All columns in the file 
+will be displayed but insertion will not available. Insertion will be 
+available only when at least one column will be removed from the grid.
+
+.. image:: file_menu.bmp
+
+Figure 4: MenuBar:
+
+.. _Plot:
+
+Plot
+----
+
+To *plot*  a column versus another, select one column at the time, click the 
+*'Add'*  button next to the text control of X/Y -axis *Selection Range*  to 
+plot the value of this column on the X/Y axis. Alternatively, all available 
+range can be selected by clicking the column letter (eg. B). Repeat the same 
+procedure the next axis. Finally, click the *'Plot'*  button. When clicking 
+on *Add*  button, the grid will automatically fill the axis label, but 
+different labels and units can be entered in the correct controls before 
+clicking on the plot button.
+
+*X/Y -Axis Selection Range* can be edited manually. These text controls
+allow the following types of expression (operation can be + - * /, or pow)
+ 
+1) if the current axis label range is a function of 1 or more columns, write 
+this type of expression
+
+constant1  * column_name1 [minimum row index :  maximum  row index] operator 
+constant2 * column_name2 [minimum row index :  maximum  row index] 
+
+Example: radius [2 : 5] -3 * scale [2 : 5] 
+
+2) if only some values of a given column are need but the range between the 
+first row and the last row used is not continuous, write the following 
+expression in the text control
+
+column_name1 [minimum row index1 :  maximum  row index1] , column_name1 
+[minimum row index2 :  maximum  row index2] 
+
+Example : radius [2 : 5] , radius [10 : 25] 
+
+Note: Both text controls ( X and Y-axis Selection Ranges) need to be filled 
+with valid entries for plotting to work. The dY-bar is optional (see Figure 5).
+
+.. image:: plot_button.bmp
+
+Figure 5: Plotting
+
+.. _View_Column_Cell:
+
+View Column/Cell(s)
+-------------------
+
+Select 1 or more cells from the same column, click the 'View Fits' button to 
+display available curves. 
+
+For example, select the cells of the  'Chi2'  column, then click the  'View Fits'  
+button. The plots generates will represent the residuals  plots. 
+ 
+If you select any cells of the 'Data' column and click the 'View Fits' button. 
+It generates both  data and fits in the graph (see Figure 6). 
+
+Alternatively, just click the column letter (eg. B) to choose all the 
+available data sets, then simply click the 'View Fits' button to plot the 
+data and fits. 
+
+.. image:: view_button.bmp
+
+Figure 6: View Fits
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Model_Selection:
+
+Model_Type_ 
+
+Change_Model_Parameters_
+
+Write_your_Own_Model_
+
+.. _Model_Type:
+
+Model Type
+----------
+
+Models are grouped into three classes
+
+*  *Shapes* 
+*  *Shape-Independent* 
+*  *Uncategorised*
+*  *Customized Models* 
+*  *Structure Factor*
+
+.. _Change_Model_Parameters:
+
+Change Model Parameters
+-----------------------
+
+To visualize model in a different window, from menu click on *Model*. Select 
+a type of model and then the name of your model.A new window will appear with 
+the plot of your model with default values. Change model's parameters on 
+*model view*  tab and view the plotted model with its new parameters.
+
+.. _Write_your_Own_Model:
+
+Write your Own Model
+--------------------
+
+The custom model editors are provided from 'Fitting' menu in the menu bar. 
+See 'Custom model editor' in the side menu on left. Advanced users can write 
+your own model and save it (in .py format) into *plugin_models*  directory in 
+.sasview of your home directory (eg., username\.sasview>\plugin_models). Your 
+plugin model will be added into "<>Customized Models" on the next model 
+selection.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Model_Category_Manager:
+
+Model Category Manager
+----------------------
+
+Our SAS models are, by default, classified into 5 categories; shapes, 
+shape-independent, structure factor, and customized models, where these 
+categories (except the customized models) can be reassigned, added, and 
+removed using 'Category Manager'. Each models can also be enabled(shown)/
+disabled(hidden) from the category that they belong. The Category Manager 
+panel is accessible from the model category 'Modify' button in the fitting 
+panel or the 'View/Category Manager' menu in the menu bar (Fig. 1).
+
+1) Enable/Disable models: Check/uncheck the check boxes to enable/disable the 
+models (Fig. 2).
+
+2) Change category: Highlight a model in the list by left-clicking and click 
+the 'Modify' button. In the 'Change Category' panel, one can create/use a 
+category for the model, then click the 'Add' button. In order to delete a 
+category, select a category name and click the 'Remove Selected' button 
+(Fig. 3).
+
+3) To apply the changes made, hit the OK button. Otherwise, click the 'Cancel' 
+button (Fig. 2).
+
+.. image:: cat_fig0.bmp
+
+Fig.1
+
+.. image:: cat_fig1.bmp
+
+Fig.2
+
+.. image:: cat_fig2.bmp
+
+Fig.3
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Model_Functions:
+
+Model Functions
+---------------
+
+Model Documentation <models/model_functions>
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Custom_Model_Editor:
+
+Custom Model Editor
+-------------------
+
+Description_ 
+
+New_
+
+Sum_Multi_p1_p2_
+
+Advanced_
+
+Delete_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Description:
+
+Description
+-----------
+
+This menu (Fitting/Edit Custom Model in the menu bar) interface is to provide 
+you an easy way to write your own custom models. The changes in a model 
+function are effective after it is re-selected from the combo-box menu.
+
+.. image:: edit_model_menu.bmp
+
+.. _New:
+
+New
+---
+
+This option is used to make a new model. A model code generated by this option 
+can be viewed and further modified by the 'Advanced' option below.
+
+.. image:: new_model.bmp
+
+.. _Sum_Multi_p1_p2:
+
+Sum|Multi(p1,p2)
+----------------
+
+This option create a new sum (or multiplication) model. Fill up the (sum 
+model function) name and the description. The description will show up on 
+details button in the application. Then select the p1 or p2 model for the 
+sum/multi model, select an operator as necessary and click the Apply button 
+for activation. Hit the 'Close' button when it's done.
+
+.. image:: sum_model.bmp
+
+.. _Advanced:
+
+Advanced
+--------
+
+The menu option shows all the files in the plugin_models folder. You can edit, 
+modify, and save it. It is recommended to modify only the lines with arrow 
+(-------). In the end of edit, 'Compile' and 'Run' from the menu bar to
+activate or to see the model working properly.
+
+.. _Delete:
+
+Delete
+------
+
+The menu option is to delete the custom models. Just select the file name to 
+delete.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+..  _Polydispersity_Distributions:
+
+Polydispersity Distributions
+----------------------------
+
+Calculates the form factor for a polydisperse and/or angular population of 
+particles with uniform scattering length density. The resultant form factor 
+is normalized by the average particle volume such that 
+
+P(q) = scale*\<F*F\>/Vol + bkg
+
+where F is the scattering amplitude and the\<\>denote an average over the size 
+distribution.  Users should use PD (polydispersity: this definition is 
+different from the typical definition in polymer science) for a size 
+distribution and Sigma for an angular distribution (see below).
+
+Note that this computation is very time intensive thus applying polydispersion/
+angular distrubtion for more than one paramters or increasing Npts values 
+might need extensive patience to complete the computation. Also note that 
+even though it is time consuming, it is safer to have larger values of Npts 
+and Nsigmas.
+
+The following five distribution functions are provided
+
+*  *Rectangular_Distribution_*
+*  *Array_Distribution_*
+*  *Gaussian_Distribution_*
+*  *Lognormal_Distribution_*
+*  *Schulz_Distribution_*
+
+.. _Rectangular_Distribution:
+
+Rectangular Distribution
+------------------------
+
+.. image:: pd_image001.png
+
+The xmean is the mean of the distribution, w is the half-width, and Norm is a 
+normalization factor which is determined during the numerical calculation. 
+Note that the Sigma and the half width *w*  are different.
+
+The standard deviation is
+
+.. image:: pd_image002.png
+
+The PD (polydispersity) is
+
+.. image:: pd_image003.png
+
+.. image:: pd_image004.jpg
+
+.. _Array_Distribution:
+
+Array Distribution
+------------------
+
+This distribution is to be given by users as a txt file where the array 
+should be defined by two columns in the order of x and f(x) values. The f(x) 
+will be normalized by SasView during the computation.
+
+Example of an array in the file
+
+30        0.1
+32        0.3
+35        0.4
+36        0.5
+37        0.6
+39        0.7
+41        0.9
+
+We use only these array values in the computation, therefore the mean value 
+given in the control panel, for example ‘radius = 60’, will be ignored.
+
+.. _Gaussian_Distribution:
+
+Gaussian Distribution
+---------------------
+
+.. image:: pd_image005.png
+
+The xmean is the mean of the distribution and Norm is a normalization factor 
+which is determined during the numerical calculation.
+
+The PD (polydispersity) is
+
+.. image:: pd_image003.png
+
+.. image:: pd_image006.jpg
+
+.. _Lognormal_Distribution:
+
+Lognormal Distribution
+----------------------
+
+.. image:: pd_image007.png
+
+The /mu/=ln(xmed), xmed is the median value of the distribution, and Norm is a 
+normalization factor which will be determined during the numerical calculation. 
+The median value is the value given in the size parameter in the control panel, 
+for example, “radius = 60”.
+
+The PD (polydispersity) is given by /sigma/
+
+.. image:: pd_image008.png
+
+For the angular distribution
+
+.. image:: pd_image009.png
+
+The mean value is given by xmean=exp(/mu/+p2/2). The peak value is given by 
+xpeak=exp(/mu/-p2).
+
+.. image:: pd_image010.jpg
+
+This distribution function spreads more and the peak shifts to the left as the 
+p increases, requiring higher values of Nsigmas and Npts.
+
+.. _Schulz_Distribution:
+
+Schulz Distribution
+-------------------
+
+.. image:: pd_image011.png
+
+The xmean is the mean of the distribution and Norm is a normalization factor
+which is determined during the numerical calculation.
+
+The z = 1/p2– 1.
+
+The PD (polydispersity) is
+
+.. image:: pd_image012.png
+
+Note that the higher PD (polydispersity) might need higher values of Npts and 
+Nsigmas. For example, at PD = 0.7 and radisus = 60 A, Npts >= 160, and 
+Nsigmas >= 15 at least.
+
+.. image:: pd_image013.jpg
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Smearing_Computation:
+
+Smearing Computation
+--------------------
+
+Slit_Smearing_ 
+
+Pinhole_Smearing_
+
+2D_Smearing_
+
+.. _Slit_Smearing:
+
+Slit Smearing
+-------------
+
+The sit smeared scattering intensity for SAS is defined by
+
+.. image:: sm_image002.gif
+
+where Norm =
+
+.. image:: sm_image003.gif
+
+Equation 1
+
+The functions .. image:: sm_image004.gif and .. image:: sm_image005.gif
+refer to the slit width weighting function and the slit height weighting 
+determined at the q point, respectively. Here, we assumes that the weighting 
+function is described by a rectangular function, i.e.,
+
+.. image:: sm_image006.gif
+
+Equation 2
+
+and
+
+.. image:: sm_image007.gif
+
+Equation 3
+
+so that .. image:: sm_image008.gif .. image:: sm_image009.gif for
+.. image:: sm_image010.gif and u.
+
+The .. image:: sm_image011.gif and .. image:: sm_image012.gif stand for
+the slit height (FWHM/2) and the slit width (FWHM/2) in the q space. Now the 
+integral of Equation 1 is simplified to
+
+.. image:: sm_image013.gif
+
+Equation 4
+
+Numerical Implementation of Equation 4
+--------------------------------------
+
+Case 1
+------
+
+For .. image:: sm_image012.gif = 0 and .. image:: sm_image011.gif = 
+constant.
+
+.. image:: sm_image016.gif
+
+For discrete q values, at the q values from the data points and at the q 
+values extended up to qN= qi + .. image:: sm_image011.gif the smeared 
+intensity can be calculated approximately
+
+.. image:: sm_image017.gif
+
+Equation 5
+
+.. image:: sm_image018.gif = 0 for *Is* in *j* < *i* or *j* > N-1*.
+
+Case 2
+------
+
+For .. image:: sm_image012.gif = constant and 
+.. image:: sm_image011.gif = 0.
+
+Similarly to Case 1, we get
+
+.. image:: sm_image019.gif for qp= qi- .. image:: sm_image012.gif
+
+and qN= qi+ .. image:: sm_image012.gif. .. image:: sm_image018.gif = 0
+for *Is* in *j* < *p* or *j* > *N-1*.
+
+Case 3
+------
+
+For .. image:: sm_image011.gif = constant and 
+.. image:: sm_image011.gif = constant.
+
+In this case, the best way is to perform the integration, Equation 1, 
+numerically for both slit height and width. However, the numerical integration 
+is not correct enough unless given a large number of iteration, say at least 
+10000 by 10000 for each element of the matrix, W, which will take minutes and 
+minutes to finish the calculation for a set of typical SAS data. An 
+alternative way which is correct for slit width << slit hight, is used in 
+SasView. This method is a mixed method that combines method 1 with the 
+numerical integration for the slit width.
+
+.. image:: sm_image020.gif
+
+Equation 7
+
+for qp= qi- .. image:: sm_image012.gif and
+qN= qi+ .. image:: sm_image012.gif. .. image:: sm_image018.gif = 0 for
+*Is* in *j* < *p* or *j* > *N-1*.
+
+.. _Pinhole_Smearing:
+
+Pinhole Smearing
+----------------
+
+The pinhole smearing computation is done similar to the case above except 
+that the weight function used is the Gaussian function, so that the Equation 6 
+for this case becomes
+
+.. image:: sm_image021.gif
+
+Equation 8
+
+For all the cases above, the weighting matrix *W* is calculated when the 
+smearing is called at the first time, and it includes the ~ 60 q values 
+(finely binned evenly) below (\>0) and above the q range of data in order 
+to cover all data points of the smearing computation for a given model and 
+for a given slit size. The *Norm*  factor is found numerically with the 
+weighting matrix, and considered on *Is* computation.
+
+.. _2D_Smearing:
+
+2D Smearing
+----------- 
+
+The 2D smearing computation is done similar to the 1D pinhole smearing above 
+except that the weight function used was the 2D elliptical Gaussian function
+
+.. image:: sm_image022.gif
+
+Equation 9
+
+In Equation 9, x0 = qcos/theta/ and y0 = qsin/theta/, and the primed axes 
+are in the coordinate rotated by an angle /theta/ around the z-axis (below) 
+so that x’0= x0cos/theta/+y0sin/theta/ and y’0= -x0sin/theta/+y0cos/theta/.
+
+Note that the rotation angle is zero for x-y symmetric elliptical Gaussian 
+distribution. The A is a normalization factor.
+
+.. image:: sm_image023.gif
+
+Now we consider a numerical integration where each bins in /theta/ and R are 
+*evenly* (this is to simplify the equation below) distributed by /delta//theta/ 
+and /delta/R, respectively, and it is assumed that I(x’, y’) is constant 
+within the bins which in turn becomes
+
+.. image:: sm_image024.gif
+
+Equation 10
+
+Since we have found the weighting factor on each bin points, it is convenient 
+to transform x’-y’ back to x-y coordinate (rotating it by -/theta/ around z 
+axis). Then, for the polar symmetric smear
+
+.. image:: sm_image025.gif
+
+Equation 11
+
+where
+
+.. image:: sm_image026.gif
+
+while for the x-y symmetric smear
+
+.. image:: sm_image027.gif
+
+Equation 12
+
+where
+
+.. image:: sm_image028.gif
+
+Here, the current version of the SasView uses Equation 11 for 2D smearing 
+assuming that all the Gaussian weighting functions are aligned in the polar 
+coordinate.
+
+In the control panel, the higher accuracy indicates more and finer binnng 
+points so that it costs more in time.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Polarisation_Magnetic_Scattering:
+
+Polarisation/Magnetic Scattering
+--------------------------------
+
+Magnetic scattering is implemented in five (2D) models 
+
+*  *SphereModel*
+*  *CoreShellModel*
+*  *CoreMultiShellModel*
+*  *CylinderModel*
+*  *ParallelepipedModel*
+
+In general, the scattering length density (SLD) in each regions where the 
+SLD (=/beta/) is uniform, is a combination of the nuclear and magnetic SLDs and 
+depends on the spin states of the neutrons as follows. For magnetic scattering, 
+only the magnetization component, *M*perp, perpendicular to the scattering 
+vector *Q* contributes to the the magnetic scattering length.
+
+.. image:: mag_vector.bmp
+
+The magnetic scattering length density is then
+
+.. image:: dm_eq.gif
+
+where /gamma/ = -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0 
+is the classical radius of electron, and */sigma/* is the Pauli spin. For 
+polarised neutron, the magnetic scattering is depending on the spin states. 
+
+Let's consider that the incident neutrons are polarized parallel (+)/
+anti-parallel (-) to the x' axis (See both Figures above). The possible 
+out-coming states then are + and - states for both incident states
+
+Non-spin flips: (+ +) and (- -)
+Spin flips:     (+ -) and (- +)
+
+.. image:: M_angles_pic.bmp
+
+Now, let's assume that the angles of the *Q*  vector and the spin-axis (x') 
+against x-axis are /phi/ and /theta/up, respectively (See Figure above). Then, 
+depending upon the polarisation (spin) state of neutrons, the scattering length 
+densities, including the nuclear scattering length density (/beta/N) are given 
+as, for non-spin-flips
+
+.. image:: sld1.gif
+
+for spin-flips
+
+.. image:: sld2.gif
+
+where
+
+.. image:: mxp.gif
+
+.. image:: myp.gif
+
+.. image:: mzp.gif
+
+.. image:: mqx.gif
+
+.. image:: mqy.gif
+
+Here, the M0x, M0y and M0z are the x, y and z components of the magnetization 
+vector given in the xyz lab frame. The angles of the magnetization, /theta/M 
+and /phi/M as defined in the Figure (above)
+
+.. image:: m0x_eq.gif
+
+.. image:: m0y_eq.gif
+
+.. image:: m0z_eq.gif
+
+The user input parameters are M0_sld = DMM0, Up_theta = /theta/up, 
+M_theta = /theta/M, and M_phi = /phi/M. The 'Up_frac_i' and 'Up_frac_f' are 
+the ratio
+
+(spin up)/(spin up + spin down)
+
+neutrons before the sample and at the analyzer, respectively.
+
+*Note:* The values of the 'Up_frac_i' and 'Up_frac_f' must be in the range
+between 0 and 1.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Key_Combinations:
+
+Key Combinations
+----------------
+
+Copy_Paste_
+
+Bookmark_
+
+Graph_Context_Menu_
+
+FTolerance_
+
+.. _Copy_Paste:
+
+Copy & Paste
+------------
+
+To copy the parameter values in a Fit(Model) panel to the clipboard:
+
+*Ctrl(Cmd on MAC) + Left(Mouse)Click*  on the panel.
+
+To paste the parameter values to a Fit(Model)panel from the clipboard:
+
+*Ctrl(Cmd on MAC) + Shift + Left(Mouse)Click*  on the panel.
+
+If this operation is successful, it will say so in the info line at the 
+bottom of the SasView window.
+
+.. _Bookmark:
+
+Bookmark
+--------
+
+Bookmark of a fit-panel or model-panel status:
+
+*(Mouse)Right-Click*  and select the bookmark in the popup list.
+
+.. _Graph_Context_Menu:
+
+Graph Context Menu
+------------------
+
+To get the graph context menu to print, copy, save data, (2D)average, etc.:
+
+*Locate the mouse point on the plot to highlight and *(Mouse) Right Click* 
+to bring up the full menu.
+
+.. _FTolerance: 
+
+FTolerance (SciPy)
+------------------
+
+To change the ftol value of the Scipy FitEngine (leastsq):
+
+First, make sure that the Fit panel has data and a model selected.
+
+*Ctrl(Cmd on MAC) + Shift + Alt + Right(Mouse)Click*  on the panel.
+
+Then, set up the value in the dialog panel.
+
+If this operation is successful, the new ftol value will be displayed in the 
+info line at the bottom of the SV window.Note that increasing the ftol value 
+may cause for the fitting to terminate with higher chisq.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Status_Bar_Help:
+
+Status Bar Help
+---------------
+
+Message_Warning_Hint_ 
+
+Console_
+
+.. _Message_Warning_Hint:
+
+Message/Warning/Hint
+--------------------
+
+The status bar located at the bottom of the application frame, displays 
+messages, hints, warnings and errors.
+
+.. _Console:
+
+Console
+-------
+
+Select *light bulb/info icon*  button in the status bar at the bottom of the 
+application window to display available history. During a long task, the 
+console can also help users to understand the status in progressing.

src/sas/guiframe/media/data_explorer_help.rst

@@ -1 @@
-..data_explorer_help.rst
+.. data_explorer_help.rst
 
-Placeholder for data explorer help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Loading Data
+============
+
+Introduction_
+
+Load_Data_
+
+Handy_Menu_
+
+Activate_Data_
+
+Remove_Data_
+
+Append_Plot_to_Graph_
+
+Create_New_Plot_
+
+Freeze_Theory_
+
+Send_Data_to_Applications_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Introduction:
+
+Introduction
+------------
+
+*Data Explorer* is a panel that allows the user more interactions with data. 
+Some functionalities provided by the Data Explorer are also available through 
+the context menu of plot panels or other menus of the applications.Under menu 
+*View*  of the menubar, Data explorer can be toggled between Show and Hide by 
+clicking the menu *Show/Hide Data Explorer* .
+
+*IMPORTANT!*  When Data explorer is hidden, all the data loaded will be sent 
+directly to the current active application, if possible. When data Explorer is 
+shown data go first to the Data Explorer for the user to handle them later.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Load_Data:
+
+Load Data
+---------
+
+To Load data, click the button *Load Data* , then select one or more (holding 
+Ctrl key) files to load into the application. In the list, the *Data*  will be 
+displayed as the name of each selected file. Expending this data by clicking 
+the *+*  symbol will display available information about the data such as data 
+title if exists.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Handy_Menu:
+
+Handy Menu
+----------
+
+For a quick Data-info/Save/Plot/3d-plot(2d only)/Edit-mask(2d only), 
+high-light the data/theory, right-click, and select a proper item from the 
+context menu.
+
+.. image:: hand_menu.png
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Activate_Data:
+
+Activate Data
+-------------
+
+To interact with data, check a data label and click on a button. Checking Data 
+make them active for the button operation. Unchecking Data labels will 
+deactivate them.
+
+There is a combo box labeled *Selection Options*  that allows to activate or 
+select multiple data simultaneously.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Remove_Data:
+
+Remove Data
+-----------
+
+Remove data button remove all reference of this data into the application.
+
+*WARNING!* Remove data will stop any jobs currently using the selected data.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Append_Plot_to_Graph:
+
+Append Plot to Graph
+--------------------
+
+Click on the button *Append To*  to append selected Data to a plot panel on 
+focus. Next to this button is a combo box containing available panels names. 
+Selecting a name from this combo box will set the corresponding lot panel on 
+focus. If not plot panel is available, the combo box and button will be 
+disable. 2D Data cannot be appended to any plot panels . This operation can 
+only be performed on 1D data and plot panels currently containing 1D data.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Create_New_Plot:
+
+Create New Plot
+---------------
+
+Click on *New Plot*  button to create a new plot panel where selected data 
+will be plotted.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Freeze_Theory:
+
+Freeze Theory
+-------------
+
+*Freeze Theory*  button generate Data from selected theory. This operation can 
+only be performed when theory labels are selected.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Send_Data_to_Applications:
+
+Send to Application
+-------------------
+
+Click on the button *Send To*  to send Data to the current active control 
+page. One of the single/batch mode can be selected only for Fitting. The batch 
+mode provides serial (batch) fitting with one model, i.e., fitting one data by 
+another data. Note that only the Fitting allows more that one data to be sent.

src/sas/guiframe/media/graph_help.rst

@@ -1 @@
-..graph_help.rst
-
-Placeholder for graph help
+.. graph_help.rst
+
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Plotting Data/Models
+====================
+
+Graph_Menu_
+
+2D_Data_Averaging_
+
+Key_Combinations_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Graph_Menu:
+
+Graph Menu
+----------
+
+Introduction_
+
+Reset_Graph_
+
+Hide_Show_Delete_Graph_
+
+Data_Info_
+
+Save_Plot_Image_
+
+Save_Data_
+
+Drag_Plot_
+
+Zoom_In_Out_
+
+Remove_Data_
+
+Change_Scale_
+
+Linear_Fit_
+
+Other_Graph_Modifications_
+
+.. _Introduction:
+
+Introduction
+------------
+
+Locating the pointer and right-clicking on a data/theory plot will bring a 
+context menu. On the menu, select a menu item.
+
+.. _Reset_Graph:
+
+Reset Graph
+-----------
+
+To reset the graph's axis range, right click on the plot and the context menu 
+pops-up. Select *Reset Graph*  and the plot will take its initial range. Also 
+the 'home' icon in tool bar will do the same.
+
+.. _Hide_Show_Delete_Graph:
+
+Hide/Show/Delete Graph
+----------------------
+
+To Hide, click the Hide (bar) button in the tool bar.To Show, select the the 
+'Show' menu item in the 'Graph' menu in the menu bar.To Delete, click the 'x' 
+button in the title bar.
+
+Note: If a residuals graph (in Fitting) is hidden, it will not show up after 
+computation.
+
+.. _Data_Info:
+
+Data Info
+---------
+
+From the context menu, select 'Data Info' to see the data information dialog
+panel.
+
+.. _Save_Plot_Image:
+
+Save Plot Image
+---------------
+
+Right click on plot. Context menu will pop-up select save image [file name].
+A dialog window opens and write a the name of the file to save and click on 
+*Save Image.*
+
+.. _Save_Data:
+
+Save Data
+---------
+
+From the context menu, select 'Save points as a file' for 1D, or 'Save as a 
+file(DAT)' for 2D. Note that two formats, txt and xml, are available in 1D 
+saving.
+
+.. _Drag_Plot:
+
+Drag Plot
+---------
+
+Select the *crossed arrows*  button on the plot panel *toolbar*  to drag the 
+plot. To disable dragging mode, unselect the same button on the toolbar.
+
+.. _Zoom_In_Out:
+
+Zoom In/Out
+-----------
+
+Select the *rectangle*  button on the plot panel *toolbar*  to zoom in a
+region of the plot.
+
+To disable zoom mode, unselect the same button on the toolbar. After zoom in
+a region, select *left arrow*  or *right arrow*  button on the toolbar to set
+the graph the the previous size. If a mouse wheel button is available,
+*zoom in/out*  by scrolling the mouse wheel (see Key_Combinations_ help for
+details).
+
+.. _Remove_Data:
+
+Remove Data from Plot
+---------------------
+
+Highlight the plot and the context menu appears.Select *remove [file name]*.
+The plot selected will disappear.
+
+.. _Change_Scale:
+
+Change Scale
+------------
+
+If the loaded data is a 1-D data changing scale or data representation will 
+work as follows. *Right click* on the plot window. A context menu pops-up and 
+select *Change Scale* . A dialog window titled *select the scale of the graph* 
+will pop-up then change the *x* , the *y*  and the *view*  values as wish.
+
+The 'view' option includes the axis scale short-cuts such as Linear, Guinier, 
+Cross-sectional (XC) Guinier, and Porod plot scale. For a proper data set, 
+these axis scales can be used to estimate Rg, Rod diameter, or Background of 
+neutron scattering data respectively (via 'Linear Fit'; see below). For a 2D 
+image, *Right click*  on the image to pop-up the context menu. Select to 
+switch from linear to log scale. The scale selected is printed on the status 
+bar.
+
+If the loaded data is an image. *Right click*  on the image to pop-up the
+context menu. Select to switch from linear to log scale. The scale selected is
+printed on the status bar.
+
+.. _Linear_Fit:
+
+Linear Fit
+----------
+
+Linear fit is to perform a line model fitting keeping the scale of the plot.
+Highlight data to fit. From the context menu select *Linear Fit* . A dialog
+window appears. Change model initial parameters, data limits and hit *fit*
+button. New parameters values are displayed and the line with the new
+parameters is added to the plot. Especially for Guinier, XC Guinier, and
+Porod plot scale, this 'Linear Fit' will provides Rg, Rod diameter, and
+background, respectively. The following figure shows an example for the
+Guinier scale.
+
+.. image:: guinier_fit.png
+
+.. _Other_Graph_Modifications:
+
+Other Graph Modifications
+-------------------------
+
+Some custom modifications of the symbols, text, axis, etc of the graph are 
+provided.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _2D_Data_Averaging:
+
+2D Data Averaging
+-----------------
+
+Description_
+
+How_to_Average_
+
+Available_Averagings_
+
+Unmasked_Circular_Average_
+
+Masked_Circular_Average_
+
+Sector_Average_
+
+Annular_Average_
+
+Box_Sum_
+
+Box_Averaging_in_Qx_
+
+Box_Averaging_in_Qy_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Description: 
+
+Description
+-----------
+
+This feature allows you to perform different types of averages on your data, 
+and allows you to see what regions of the detector will contribute to the 
+average. The region to be averaged will be drown and can be modified by 
+dragging the lines around.
+
+.. _How_to_Average:
+
+How to Average
+--------------
+
+Right click on 2D data for the context menu to appear. Select one type of 
+averages among *"sector [Q view]", "Annulus [Phi view]", "Box sum", "Box 
+averaging in Qx ", "box averaging on Qy","Perform circular Average".*
+
+A slicer will appear except for *"Perform circular Average"*  that you can 
+drag by clicking on a slicer 's marker. When the marker is highlighted in red, 
+it means that the slicer can change size.You can also move some of the slicer 
+by simply drag its side when highlighted in red. the slicer size will be reset 
+to its previous size if the user try to select a region greater than the size 
+of the data.
+
+The user can also select a region to average when a slicer has been selected 
+already by *right clicking*  on the context menu and selecting *Edit Slicer 
+Parameters* . The dialog window will appears and the user can enter values to 
+selected a region or selected numbers of points to plot *nbins* .
+
+For *Box sum* , when the user selects this option, a new panel is created 
+containing the result of average of the sum of every pixels contains on that 
+data.The user can also enter values to select a region.
+
+.. _Available_Averagings:
+
+Available Averagings
+--------------------
+
+Some different types of averaging are provided for.
+
+.. _Unmasked_Circular_Average:
+
+Unmasked Circular Average
+-------------------------
+
+This operation will perform and average in constant q-rings around the (x,y) pixel
+location of the beam center.
+
+.. _Masked_Circular_Average:
+
+Masked Circular Average
+-----------------------
+
+This operation is same as 'Masked Circular Average' except that the masked
+region is excluded if masked.
+
+.. _Sector_Average:
+
+Sector Average [Q View]
+-----------------------
+
+This operation averages in constant q-arcs. The width of the sector is specified in
+degrees (+/- delta phi) each side of the central angle (phi).
+
+.. _Annular_Average:
+
+Annular Average [Phi View]
+--------------------------
+
+It performs an average between two q-values centered in (0,0), and averaged 
+over a width of a specified number of pixels. The data is returned as a 
+function of angle (phi) in degrees. Moving one circle of this slicer to 
+radius of zero corresponding to a circular averaging on radius qmax , the 
+outer circle. The angle zero starts from the positive x-axis direction.
+
+.. _Box_Sum:
+
+Box Sum
+-------
+
+Perform the sum of counts in a 2D region of interest.When editing the slicer, 
+the user can enter the length and the width the rectangle slicer and the 
+coordinates of the center of this rectangle.
+
+.. _Box_Averaging_in_Qx:
+
+Box Averaging in Qx
+-------------------
+
+Computes average I(Qx) for a region of interest. When editing the slicer, the 
+user can control the length and the width the rectangle slicer. The averaged 
+output is calculated from the constant bins with rectangular shape. The 
+resultant q values are nominal values, i.e., the central values of each bins 
+on the x-axis.
+
+.. _Box_Averaging_in_Qy:
+
+Box Averaging in Qy
+-------------------
+
+Computes average I(Qy) for a region of interest.When editing the slicer, the 
+user can control the length and the width the rectangle slicer. The averaged 
+output is calculated from the constant bins with rectangular shape. The 
+resultant q values are nominal values, i.e., the central values of each bins 
+on the y-axis.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Key_Combinations:
+
+Key Combination
+---------------
+
+Floating_Panel_
+
+Graph_Context_Menu_
+
+Zoom_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Floating_Panel:
+
+Floating Panel
+--------------
+
+For a graph panel to float on the top of the SV window:
+
+Press the *Ctrl(Cmd on MAC) key*  on dragging and placing a panel. Or if you 
+want to make all plot panels float, select 'Float' from Graph/Preperences in 
+the menu bar. Otherwise choose 'Dock'.
+
+.. _Graph_Context_Menu:
+
+Graph Context Menu
+------------------
+
+To get the graph context menu to print, copy, save data, (2D)average, etc, 
+*locate the mouse point on the plot to highlight and *(Mouse) Right Click* 
+to bring up the full menu.
+
+.. _Zoom:
+
+Zoom In/Out
+-----------
+
+To Zoom in or out the full plot, *locate the mouse point inside the graph 
+which will be the center of the zooming, then *rotate MouseWheel*.
+
+*To Zoom in or out the plot in x or y direction, *locate (and click) the 
+mouse point near x (or y) axis just outside of the graph and then *rotate 
+MouseWheel* .* Note that this works only on the 1D plots.

src/sas/invariant/media/invariant_help.rst

@@ -1 @@
-..invariant_help.rst
+.. invariant_help.rst
 
-Placeholder for invariant help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+Invariant Calculation Perspective
+=================================
+
+Scattering_Invariant_
+
+Volume_Fraction_
+
+Specific_Surface_Area_
+
+Definitions_
+
+Reference_
+
+How_to_Use_
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Scattering_Invariant:
+
+Scattering Invariant
+--------------------
+
+The scattering invariant (Q*) is a model-independent quantity that can be 
+easily calculated from scattering data.
+
+For two phase systems, the scattering invariant, Q*, is defined as the 
+integral of the square of the wave transfer (q) multiplied by the scattering 
+cross section over the full range of q.
+
+Q* is given by the following equation
+
+.. image:: image001.gif
+
+This model independent quantity (Q*) is calculated from the scattering data 
+that can be used to determine the volume fraction and the specific area of the 
+sample under consideration.
+
+These quantities are useful in their own right and can be used in further 
+analysis. With this scattering invariant module users will also be able to 
+determine the consistency of those properties between data. There is no real 
+data defined from zero to infinity, there usually have limited range.
+
+Q* is not really computed from zero to infinity. Our maximum q range is 
+1e-5 ~ 10 (1/Angstrom). The lower and/or higher q range than data given can be 
+extrapolated by fitting some data nearby.
+
+The scattering invariant is computed as follows
+
+*I(q)* = *I(q)*  w/o background : If the data includes a background, user sets 
+the value to subtract the background for the Q* computation.
+
+Reset *I(q)* = *I(q)* scaling factor* , delta *I(q) =*  delta *I(q)*scaling 
+factor* : If non-zero scaling factor is given, it will be considered.
+
+Invariant
+
+.. image:: image001.gif
+
+where *g =q*  for the pinhole geometry and *g =qv*  (the slit height) for the 
+slit geometry which can be given in data or as a value.
+
+Higher q-region (\>= qmax in data)
+
+Power law (w/o background term) function = C/q4will be used
+
+where the constant C(=2pi(delta(rho))Sv) is to be found by fitting part of 
+data with the range of qN-mto qN(m\<N).
+
+Lower q-region (\<= qmin in data):
+
+Guinier function = *I0exp(-Rg2q2/3)*  where I0and Rgare obtained by fitting,
+
+similarly to the high q region above.
+
+Power law can also be used.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Volume_Fraction:
+
+Volume Fraction
+---------------
+
+.. image:: image002.gif
+
+where delta(rho) is the SLD contrast of which value is given by users.
+
+.. image:: image003.gif
+
+Thus
+
+where 0 =\< *A*  =\<1/4 in order for these values to be physically valid.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Specific_Surface_Area:
+
+Specific Surface Area
+---------------------
+
+.. image:: image004.gif
+
+where *A*  and *Q**  are obtained from previous sections, and the Porod 
+constant *Cp*  is given by users.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Definitions:
+
+Definitions
+-----------
+
+Q: the magnitude of neutron (or X-ray) momentum transfer vector.
+
+I(Q): the scattering intensity as a function of the momentum transfer Q.
+
+Invariant total is the sum of the invariant calculated from datas q range and
+the invariant resulting from extrapolation at low q range and at high q range 
+if considered.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _Reference:
+
+References
+----------
+
+Chapter 2 in O. Glatter and O. Kratky, "Small Angle X-Ray Scattering", Academic 
+Press, New York, 1982
+
+http://physchem.kfunigraz.ac.at/sm/
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _How_to_Use:
+
+How to Use
+----------
+
+1. Loading data to the panel: Open the data file from File in the menu bar. 
+Select loaded data from a plot panel by highlighting that it until its color 
+turns yellow. Then right click on that the data and selects the option Compute 
+Invariant. The application automatically computes the invariant value if the 
+data loaded is valid.
+
+2. To subtract a background or/and to rescale the data, type the values in 
+Customized Input box.
+
+3. If you want to calculate the volume fraction and the specific surface 
+area, type the optional inputs in the customized input box, and then press 
+'Compute' button.
+
+4. The invariant can also be calculated including the outside of the data Q 
+range:  To include the lower Q and/or the higher Q range, check in the enable 
+extrapolation check box in 'Extrapolation' box. If the power low is chosen,
+the power (exponent) can be either held or fitted by checking the 
+corresponding radio button.  The Npts that is being used for the extrapolation 
+can be specified.
+
+5. If the invariant calculated from the extrapolated region is too large, it 
+will be warn in red at the top of the panel, which means that your data is not 
+proper to calculate the invariant.
+
+6. The details of the calculation is available by clicking the 'Details'
+button in the middle of the panel.
+
+.. image:: image005.gif

src/sas/invariant/media/pr_help.rst

@@ -1 @@
-..pr_help.rst
+.. pr_help.rst
 
-Placeholder for P(r) help
+.. This is a port of the original SasView html help file to ReSTructured text
+.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.
+
+.. |pi| unicode:: U+03C0
+.. |chi| unicode:: U+03C7
+
+P(r) Inversion Perspective
+==========================
+
+The inversion approach is based on Moore, J. Appl. Cryst., (1980) 13, 168-175.
+
+P(r) is set to be equal to an expansion of base functions of the type
+phi_n(r) = 2 * r * sin(|pi| * n * r / D_max).
+
+The coefficient of each base function in the expansion is found by performing 
+a least square fit with the following fit function:
+
+|chi| ^2 = sum_i[ I_meas(q_i) - I_th(q_i) ]^2 / error^2 + Reg_term
+
+where I_meas(q) is the measured scattering intensity and I_th(q) is the 
+prediction from the Fourier transform of the P(r) expansion. 
+
+The Reg_term term is a regularization term set to the second derivative 
+d^2 P(r) / dr^2 integrated over r. It is used to produce a smooth P(r) output.
+
+The following are user inputs:
+
+*  Number of terms: the number of base functions in the P(r) expansion.
+   
+*  Regularization constant: a multiplicative constant to set the size of
+   the regularization term.
+
+*  Maximum distance: the maximum distance between any two points in the
+   system.