Changeset 78f02c3 in sasview

Timestamp:

Feb 14, 2015 10:12:40 AM (10 years ago)

Author:

smk78

Branches:

master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, release_4.0.1, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

898a8b9

Parents:

3e2ebbb

Message:

Level 1 sphinx-ready commit of remaining help files

Location:

src/sas

Files:

• calculator/media/density_calculator_help.rst (modified) (1 diff)
• calculator/media/kiessig_calculator_help.rst (modified) (1 diff)
• calculator/media/resolution_calculator_help.rst (modified) (1 diff)
• calculator/media/sas_calculator_help.rst (modified) (1 diff)
• calculator/media/sld_calculator_help.rst (modified) (1 diff)
• calculator/media/slit_calculator_help.rst (modified) (1 diff)
• data_util/media/data_operator_help.rst (modified) (1 diff)
• fit/media/fitting_help.rst (modified) (1 diff)
• guiframe/media/data_explorer_help.rst (modified) (1 diff)
• guiframe/media/graph_help.rst (modified) (1 diff)
• invariant/media/invariant_help.rst (modified) (1 diff)
• invariant/media/pr_help.rst (modified) (1 diff)
• perspectives/calculator/media/image_viewer_help.rst (modified) (1 diff)
• perspectives/calculator/media/python_shell_help.rst (modified) (1 diff)

src/sas/calculator/media/density_calculator_help.rst

@@ -1 +1 @@
 ..density_calculator_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.
 
 Density/Volume Calculator Tool
 ==============================
 
-Placeholder for density calculator help
+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 +1 @@
 ..kiessig_calculator_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.
 
 Kiessig Thickness Calculator Tool
 =================================
 
-Placeholder for Kiessig calculator help
+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 +1 @@
 ..resolution_calculator_help.rst
 
-Resolution Calculator
-=====================
+.. 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.
 
-Placeholder for resolution calculator help
+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 +1 @@
 ..sas_calculator_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
+.. |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
 ==================================
 
-Placeholder for generic SAS calculator help
+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/sld_calculator_help.rst

@@ -1 +1 @@
 ..sld_calculator_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.
 
 SLD Calculator Tool
 ===================
 
-Placeholder for SLD calculator help
+Description
+-----------
+
+The neutron scattering length density is defined as
+
+SLD = (b_c1 +b_c2+...+b_cn )/Vm
+
+where 
+
+b_ci is the bound coherent scattering length of ith of n atoms in a molecule 
+with the molecular volume Vm
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+How to Format the Compound Name
+-------------------------------
+
+To calculate scattering length densities enter a compound and a mass density 
+and click "Calculate". Entering a wavelength value is optional (a default 
+value of 6.0 Angstroms will be used).
+
+* Formula strings consist of counts and atoms such as "CaCO3+6H2O".
+
+* Groups can be separated by *'+'* or *space*, so "CaCO3 6H2O" works as well.
+
+* Groups and be defined using parentheses, such as "CaCO3(H2O)6".
+
+* Parentheses can be nested, such as "(CaCO3(H2O)6)1".
+
+* Isotopes are represented by their index, e.g., "CaCO[18]3+6H2O", H[1], or 
+H[2].
+
+* Counts can be integer or decimal, e.g. "CaCO3+(3HO0.5)2".
+
+* Other compositions can be calculated as well, for example, for a 70-30 
+mixture of H2O/D2O write *H14O7+ D6O3* or more simply *H7D3O5* (i.e. this says 
+7 hydrogens, 3 deuteriums, and 5 oxygens) and the mass density calculated 
+based on the percentages of H and D.
+
+* Type *C[13]6 H[2]12 O[18]6* for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12 
+deuterium atoms, and 6 Oxygen-18 atoms)

src/sas/calculator/media/slit_calculator_help.rst

@@ -1 +1 @@
 ..slit_calculator_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.
 
 Slit Size Calculator Tool
 =========================
 
-Placeholder for slit calculator help
+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 +1 @@
 ..data_operator_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.
 
 Data Operations Tool
 ====================
 
-Placeholder for data operator help
+Description
+-----------
+This dialog panel provides arithmetic operations between two data sets (the 
+last data set could be a number).
+
+When the 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: The 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 +1 @@
 ..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
 ===================
 
-Placeholder for fitting help
+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(s)_ 
+
+.. _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(s):
+
+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:: img/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:: img/pd_image002.png
+
+The PD (polydispersity) is
+
+.. image:: img/pd_image003.png
+
+.. image:: img/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:: img/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:: img/pd_image003.png
+
+.. image:: img/pd_image006.jpg
+
+.. _Lognormal_Distribution:
+
+Lognormal Distribution
+----------------------
+
+.. image:: img/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:: img/pd_image008.png
+
+For the angular distribution
+
+.. image:: img/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:: img/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:: img/pd_image011.png
+
+The xmeanis 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:: img/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:: img/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:: img/sm_image002.gif
+
+where Norm =
+
+.. image:: img/sm_image003.gif
+
+Equation 1
+
+The functions .. image:: img/sm_image004.gif and .. image:: img/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:: img/sm_image006.gif
+
+Equation 2
+
+and
+
+.. image:: img/sm_image007.gif
+
+Equation 3
+
+so that .. image:: img/sm_image008.gif .. image::img/sm_image009.gif for 
+.. image:: img/sm_image010.gif and u.
+
+The .. image::img/sm_image011.gif and .. image::img/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:: img/sm_image013.gif
+
+Equation 4
+
+Numerical Implementation of Equation 4
+--------------------------------------
+
+Case 1
+------
+
+For .. image:: img/sm_image012.gif = 0 and .. image:: img/sm_image011.gif = 
+constant.
+
+.. image:: img/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:: img/sm_image011.gif the smeared 
+intensity can be calculated approximately
+
+.. image:: img/sm_image017.gif
+
+Equation 5
+
+.. image:: img/sm_image018.gif = 0 for *Is* in *j* < *i* or *j* > N-1*.
+
+Case 2
+------
+
+For .. image:: img/sm_image012.gif = constant and 
+.. image:: img/sm_image011.gif = 0.
+
+Similarly to Case 1, we get
+
+.. image:: img/sm_image019.gif for qp= qi-.. image:: img/sm_image012.gif 
+and qN= qi+.. image:: img/sm_image012.gif. .. image:: img/sm_image018.gif = 0 
+for *Is* in *j* < *p* or *j* > *N-1*.
+
+Case 3
+------
+
+For .. image:: img/sm_image011.gif = constant and 
+.. image:: img/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:: img/sm_image020.gif
+
+Equation 7
+
+for qp= qi-.. image:: img/sm_image012.gif and 
+qN= qi+.. image:: img/sm_image012.gif. .. image:: img/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:: img/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:: img/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:: img/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:: img/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:: img/sm_image025.gif
+
+Equation 11
+
+where
+
+.. image:: img/sm_image026.gif
+
+while for the x-y symmetric smear
+
+.. image:: img/sm_image027.gif
+
+Equation 12
+
+where
+
+.. image:: img/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:: img/mag_vector.bmp
+
+The magnetic scattering length density is then
+
+.. image:: img/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:: img/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:: img/sld1.gif
+
+for spin-flips
+
+.. image:: img/sld2.gif
+
+where
+
+.. image:: img/mxp.gif
+
+.. image:: img/myp.gif
+
+.. image:: img/mzp.gif
+
+.. image:: img/mqx.gif
+
+.. image:: img/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:: img/m0x_eq.gif
+
+.. image:: img/m0y_eq.gif
+
+.. image:: img/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(SciPy)_
+
+.. _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(SciPy): 
+
+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 +1 @@
 .. _data_explorer_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.
 
 Loading Data
 ============
 
-Introduction_ 
-Load data_
-Handy menu_
-Activate data_
-Remove data_
-Append plot to graph_
-Create new plot_
-Freeze theory_
-Send data to applications_
+1. Introduction_ 
+2. Load Data_
+3. Handy Menu_
+4. Activate Data_
+5. Remove Data_
+6. Append Plot to Graph_
+7. Create New Plot_
+8. Freeze Theory_
+9. Send Data to Applications_
 
-.. _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* .
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 
-*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.
+.. _Introduction:
 
-.. _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.
+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* .
 
-.. _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.
+*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 : 
--------------------
-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.
+.. _Activate Data:
 
-There is a combo box labeled *Selection Options*  that allows to activate or select multiple data simultaneously.
+Activate Data
+-------------
 
-.. _Remove 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.
 
-.. _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 : 
----------------------
-Click on *New Plot*  button to create a new plot panel where selected data will be plotted.
+.. _Append Plot to Graph:
 
-.. _Freeze theory : 
+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 to application:
+
+Send to Application
 -------------------
-*Freeze Theory*  button generate Data from selected theory. This operation can only be performed when theory labels are selected.
 
-.. _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.
-
+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 +1 @@
 ..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
 ====================
 
-Placeholder for graph help
+1. Graph Menu_
+2. 2D Data Averaging_
+3. 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: 
+
+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: 
+
+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: 
+
+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.
+
+.. _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.*
+
+.. _Data Info: 
+
+From the context menu, select 'Data Info' to see the data information dialog 
+panel.
+
+.. _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: 
+
+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.
+
+.. _Remove data from plot: 
+
+Highlight the plot and the context menu appears.Select *remove [file name]*. 
+The plot selected will disappear.
+
+.. _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 combination_ help for 
+details).
+
+.. _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.
+
+.. _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.
+
+.. _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. 
+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 statusbar.
+
+.. image:: guinier_fit.png
+
+.. _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_
+Perform Circular Average_ 
+Masked Circular Average_ 
+Sector [Q view]_ 
+Annulus [Phi view]_ 
+Box Sum_ 
+Box Averaging in Qx_ 
+Box Averaging in Qy_ 
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _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 
+
+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:
+
+???
+
+.. _Perform Circular Average: 
+
+It will perform and average in constant q-rings around the (x,y) pixel 
+location of the beam center.
+
+.. _Masked Circular Average: 
+
+This operation is same as 'Perform Circular Average' except that the masked 
+region is excluded if masked.
+
+.. _Sector [Q view]: 
+
+It averages in constant q-arcs. The width of the sector is specified in 
+degrees (+/- delta phi) each direction from the central angle (phi).
+
+.. _Annulus [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: 
+
+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: 
+
+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: 
+
+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 combination
+
+Key Combination
+---------------
+
+Floating Panel_ 
+Graph Context Menu_ 
+Zoom In and Out_ 
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. _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: 
+
+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 In and 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 +1 @@
 ..invariant_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.
 
 Invariant Calculation Perspective
 =================================
 
-Placeholder for invariant help
+1. Scattering Invariant_
+2. Volume Fraction_
+3. Specific Surface Area_
+4. Definitions_
+5. Reference_
+6. 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 data’s 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/ <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 +1 @@
 ..pr_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.
 
 P(r) Inversion Perspective
 ==========================
 
-Placeholder for P(r) help
+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**2P(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.

src/sas/perspectives/calculator/media/image_viewer_help.rst

@@ -1 +1 @@
 ..image_viewer_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.
 
 Image Viewer Tool
 =================
 
-Placeholder for image viewer help
+Description
+-----------
+
+This tool loads image files and displays them as 2D (x-y coordinate against 
+counts per pixel). The plot can then can be saved, printed, and copied. The 
+plot can also be resized by dragging the corner of the panel.
+
+Supported image formats are png, bmp, gif, or jpg. (There is currently a bug in 
+the tif loader)
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+How To
+------
+
+1. Select 'Image Viewer' under the 'Tool' menu in the menubar.
+
+2. Select a file type from the drop-box at the bottom of the file dialog panel, 
+choose a file of interest, and then click the 'Open' button (see the 
+picture below).
+
+.. image:: load_image.bmp
+
+3. If the loading is successful, the image will be displayed. The file name 
+will be shown in the title bar (see the picture below).
+
+4. Some options such as saving, printing, and copying are available from the 
+menubar, or in the context-menu (by right-clicking anywhere in the plot).
+
+.. image:: pic_plot.bmp
+
+5. If the image is taken from a 2D detector, it can be converted into 2D data 
+where the z values are computed as 
+
+z = (0.299 x R) + (0.587 x G) + (0.114 x B)
+
+unless the picture file is formatted as 8-bit grey-scale tif.
+
+In the "Convert to Data" dialog, set the parameters relevant to your data and 
+then click the OK button.
+
+.. image:: pic_convert.bmp

src/sas/perspectives/calculator/media/python_shell_help.rst

@@ -1 +1 @@
 ..python_shell_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.
 
 Python Shell Tool
 =================
 
-Placeholder for python shell help
+Description 
+-----------
+
+This is a Python shell (PyCrust) provided with WxPython. An editing notebook 
+will show up when a Python file is loaded from the 'New' or 'Open' menu. 
+
+The 'Run' menu is added for the editor to be able to compile and run the Python 
+code.
+
+For the details about the Python, visit the website 
+http://docs.python.org/tutorial/
+
+The numpy, scipy, matplotlib, etc, libraries are shipped with SasView. However, 
+some functionalities of those packages may or may not work.
+
+PyCrust includes its own Help menu in the shell window.
+
+Note: Help() and Credits() do not work on Macs.
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+Example
+-------
+
+An example from the matplotlib gallery:
+
+.. image:: pycrust_example.bmp