Index: docs/pre-sphinx-docs/Graph_help_v0.html
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-<html>
-<body>
-
-<h4>Graph Menu</h4>
-<ul>
-<li><a href="#intro">Introduction</a></li>
-<li><a href="#reset">Reset Graph</a></li>
-<li><a href="#hide">Hide/Show/Delete Graph</a></li>
-<li><a href="#info">Data Info</a></li>
-<li><a href="#save">Save plot Image</a></li>
-<li><a href="#savedata">Save Data</a></li>
-<li><a href="#drag">Drag plot</a></li>
-<li><a href="#zoom">Zoom In/Out</a></li>
-<li><a href="#remove">Remove Data</a></li>
-<li><a href="#scale">Change Scale</a></li>
-<li><a href="#linearfit">Linear Fit</a></li>
-<li><a href="#modify">Other Graph Modifications</a></li>
-</ul>
-
-<h5><a name="intro">Introduction</a></h5>
-<p> 
-	Locating the pointer and right-clicking on a data/theory plot will bring a context menu.
-	On the menu, select a menu item. 
-</p>
-
-<h5><a name="reset">Reset Graph</a></h5>
-<p>
-	To reset the graph's axis range, right click on the plot and the context menu pops-up.
-	Select <b>Reset Graph</b> and the plot will take its initial range. 
-	Also the 'home' icon in tool bar will do the same.
-</p>
-
-<h5><a name="hide">Hide/Show/Delete Graph</a></h5>
-<p>
-	To Hide, click the Hide (bar) button in the tool bar.<br>
-	To Show, select the the 'Show' menuitem in the 'Graph' menu in the menu bar.<br>
-	To Delete, click the 'x' button in the title bar.<br>
-	Note: If a residuals graph (in Fitting) is hidden, it will not show up after computation.
-</p>
-
-<h5><a name="save"> Save Plot Image</a></h5>
-<p>
-	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 <b>Save Image.</b>
-</p>
-
-<h5><a name="info"> Data Info</a></h5>
-<p>
-	From the context menu, select 'Data Info' to see the data information dialog panel.
-</p>
-
-<h5><a name="savedata"> Save Data</a></h5>
-<p>
-	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.
-</p>
-
-
-<h5><a name="drag"> Drag Plot</a></h5>
-<p>
-Select the <b>crossed arrows</b>  button on the plot panel <b>toolbar </b> to drag the plot.
-To disable dragging mode, unselect the same button on the toolbar.
-</p>
-
-<h5><a name="remove">Remove data from plot</a></h5>
-<p>
-	Highlight the plot and the context menu appears.Select <b>remove [file name]</b>.
-	The plot selected will disappear.
-</p>
-
-<h5><a name="zoom">Zoom In/Out</a></h5>
-<p>
- Select the <b>rectangle</b>  button on the plot panel <b>toolbar </b> to zoom in
- a region of the plot.
-</p>
-<p>
-To disable zoom mode, unselect the same button on the toolbar. 
-After zoom in a region, select <b>left arrow</b> or <b>right arrow</b>button on the toolbar
-to set the graph the the previous size.
-If a mouse wheel button is available, <b>zoom in/out</b> by scrolling the mouse wheel
- ( see 'Key combination' help for details).
-</p>
-<h5><a name="scale">Change Scale</a></h5>
-<p>
-	If the loaded data is a 1-D data.Changing scale or Data Representation will work as
-	followed:<b>right click</b> on the plot window.
-	A context menu pops-up  and select <b>Change Scale</b>. A dialog window titled<b>
-	select the scale of the graph</b> will pop-up then change the <b>x</b>, the <b>y</b>
-	and the <b>view </b> 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 Backgroud of neutron scattering data respectively (via 'Linear Fit'; see below).
-	<br>
-	For a 2D image, <b>Right click</b> on the image to pop-up the context
-	menu. Select <Toggle linear/Log scale> to switch from linear to log scale. The scale 
-	selected is printed on the statusbar.
-	
-</p>
-
-<h5><a name="linearfit">Linear Fit</a></h5>
-<p>
-	Linear fit is to perform a line model fitting keeping the scale of the plot. 
-	Highlight data to fit. 
-	From the context menu
-	select <b> Linear Fit</b>.A dialog window appears.
-	Change model initial parameters, data limits
-	and hit <b> fit</b> 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. 
-	</p>
-	<br>
-	<img src="guinier_fit.png" /><br>
-	<br>
-
-<h5><a name="modify">Other Graph Modifications</a></h5>
-<p>
-	Some custom modifications of the symbols, text, axis, etc of the graph are provided
-</p>
-</body>
-</html>
Index: docs/pre-sphinx-docs/README-OLD-DOCS.TXT
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-Files *_v0.html are help files distributed with SasView v2.2.1.
-
-NIST_IGOR_SANS_Model_Docs_v4.10.pdf should be used as the primary reference 
-for queries about the model descriptions, NOT model_functions_v0.html.
-
-Steve King
-Feb 2015
Index: docs/pre-sphinx-docs/averaging_help_v0.html
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-<html>
-<body>
-
-<h4>2D Data Averaging</h4>
-<ul>
-<li><a href="#Description">Description</a></li>
-<li><a href="#How to use">How to Average? </a></li>
-<p> Available averagings: </p>
-<li><a href="#Circular Average">Perform Circular Average</a></li>
-<li><a href="#Masked Average">Masked Circular Average</a></li>
-<li><a href="#Sector"> Sector [Q view]</a></li>
-<li><a href="#Annulus"> Annulus [Phi view]</a></li>
-<li><a href="#Box sum"> Box sum</a></li>
-<li><a href="#Box averaging in Qx"> Box averaging in Qx</a></li>
-<li><a href="#Box averaging in Qy"> Box averaging in Qy</a></li>
-
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
- 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. 
-</p>
-
-
-<h5><a name="How to use">How to Average?</a></h5>
-<p>
-Right click on 2D data for the context menu to appear. Select one type of averages
-among <b>"sector [Q view]", "Annulus [Phi view]", "Box sum", "Box averaging in Qx ",
-"box averaging on Qy","Perform circular Average".</b>
-</p> 
-<p>
-A slicer will appear except for <b> "Perform circular Average"</b>
-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.
- 
-</p>
- <p>The user can also select a region to average when a slicer has been selected already by <b>right 
- clicking </b> on the context menu and selecting <b>Edit Slicer Parameters</b>. The dialog window 
- will appears and the user can enter values to selected a region or selected numbers of points to 
- plot <b>nbins</b>.
-</p>
- 
-<p>
- For <b>Box sum</b> , 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.
-</p>
-
-<h5><a name="Circular Average">Perform Circular Average</a></h5>
-<p>
-It will perform and average in constant q-rings around the (x,y)
- pixel location of the beam center. 
-</p>
-
-
-<h5><a name="Masked Average">Masked Circular Average</a></h5>
-<p>
-This operation is same as 'Perform Circular Average' except that the masked region is excluded if masked.
-</p>
-
-<h5><a name="Sector">Sector [Q view]</a></h5>
-<p>
-It averages in constant q-arcs. The width of the sector
- is specified in degrees (+/- delta phi) each direction from the central angle (phi).
-</p>
-
-<h5><a name="Annulus"> Annulus [Phi view]</a></h5>
-<p>
-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.
-</p>
-
-<h5><a name="Box sum"> Box sum</a></h5>
-<p>
-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. 
-</p>
-<h5><a name="Box averaging in Qx"> Box averaging in Qx</a></h5>
-<p>
-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.
-
-</p>
-<h5><a name="Box averaging in Qy"> Box averaging in Qy</a></h5>
-<p>
- 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.
-</p>
-
-</body>
-</html>
-
Index: docs/pre-sphinx-docs/batch_help_v0.html
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-<html>
-<head>
-</head>
-
-
-<body>
-<h4> Batch Fit </h4>
-
-<ul>
-<li><a href="#fitpage">Batch Fit</a></li>
-<li><a href="#batchwindow">Batch Window</a></li>
-</ul>
-
-<h5><font color="blue"><a name="fitpage">Batch Fit</a></font></h5>
-<p>
-Create <b>Batch Page </b> by selecting <b>Batch </b> radio button on 
-Data Explorer<font color="blue"><a href="#batch_button">(see figure below)</a></font>
-and for a new control page select 'New FitPage' in the 'Fitting' menubar.<br />
-</p>
-<br /><img src="batch_button_area.bmp" /><br /><br />
-<a name="figure1"><u>Figure 1: MenuBar</u></a><br />
-<br />
-Load Data to Data Explorer if not loaded. <br/>
-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 <font color="blue"><a href="single_fit_help.html">(see single fit help)</a></font>.
-The use 'Fit' button to perform the fitting.
-<br />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 <font color="blue"><a href="#figure2">(see Figure 2)</a></font>. 
-<br /> 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' in the Fitting menubar, which will speed up the fitting 
-especially when you have lots of, and similar, data sets.
-</p>
-
-<h5><font color="blue"><a name="batchwindow">Batch Window</a></font></h5>
-<p>
-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. <br />
-Once closed, 
-it can be opened anytime from the "View" menubar item <font color="blue"><a href="#figure2">(see Figure 2)</a></font>.<br />
-</p>
-<br /><br /><img src="restore_batch_window.bmp" /><br /><br />
-<a name="#figure2"><u>Figure 2: Edit Menu</u></a><br />
-<br />
-  <ul>
-	<li> <a href="#edit_grid"> Edit Grid </a></li>
-	<li><a href="#save_grid"> Save Grid </a></li>
-	<li><a href="#load_batch"> Open Batch Results </a></li>
-	<li><a href="#plot"> Plot </a></li>
-	<li><a href="#view"> View Column/Cell(s) </a></li>
-   </ul>
-
-
-
-<h5><font color="blue"><a name="edit_grid"> Edit Grid </a></font></h5>
-<p>
-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 <b> Edit </b> 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.<br />
-To Remove column from the grid, select it, choose edit menu, and click the <b> 'remove' </b>  menu item.
-Any removed column should reinserted whenever needed.<br />
-All above options are also available when right clicking on a given column label 
-<font color="blue"><a href="#figure3">(see Figure 3)</a></font>.
-<b>Note:</b> A column always needs to be selected in order to remove or insert a column in the grid.<br /><br />
-
-<img src="edit_menu.bmp" /><br /><br />
-<a name="figure3"><u>Figure 3: Edit Menu</u></a><br />
-</p>
-
-
-<h5><font color="blue"><a name="save_grid"> Save Grid </a></font></h5>
-<p>
-To save the current page on the batch window, select the <b> 'File' </b> menubar item 
-<font color="blue"><a href="#figure4">(see Figure 4)</a></font>, then choose the <b> 'Save as' </b>
-menu item to save it as a .csv file. <br />
-<b>Note: </b> 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.<br />
-
-<font color="red">Warning! To ensure accuracy of saved fit results, It is recommended to save the current grid 
-before modifying it . </font>
-</p>
-
-
-<h5><font color="blue"><a name="load_batch"> Open Batch Results </a></font></h5>
-<p>
-Any <b> csv </b> file can be opened in the grid by selecting the <b> 'Open' </b> 
-under the <b> 'File' </b> menu in the Grid Window <font color="blue"><a href="#figure4">(see Figure 4)</a></font>. 
-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.
-
-<br /><img src="file_menu.bmp" /><br /><br />
-<a name="figure4"><u>Figure 4: MenuBar</u></a><br />
-</p>
-
-
-<h5><font color="blue"><a name="plot"> Plot </a></font></h5>
-<p>
-To <b> plot </b> a column versus another,
-select one column at the time, click the <b> 'Add' </b> button next to the text control
- of X/Y -axis <b> Selection Range </b>
-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 <b> 'Plot' </b> button. 
-When clicking on <b> Add </b> 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.<br />
-<b>X/Y -Axis Selection Range </b> can be edited manually. These text controls 
-allows the following types of expression:<br />
-
-operation can be <font color="#00CC33"><b>+</b></font>,<font color="#00CC33">
-<b> -</b></font>, <font color="#00CC33"><b>*</b></font>, 
-<font color="#00CC33"><b>/</b></font>, or <font color="#00CC33">pow</font>.<br /> <br />
-
-1) if the current axis label range is a function of 1 or more columns,
- write this type of expression: <br />
-constant1  * <font color="#CC9933">column_name1</font>
-<font color="blue">[minimum row index :  maximum  row index]</font> 
-<font color="#00CC33">operator</font>  constant2 <font color="#00CC33">
-<b>*</b></font> <font color="#CC9933">column_name2</font>
-<font color="blue">[minimum row index :  maximum  row index]</font> <br />
-Example : <font color="#CC9933">radius</font>[2 : 5]<font color="#00CC33"><big><
-b> -</b></big></font> 3 <font color="#00CC33"><b>*</b></font>
- <font color="#CC9933">scale</font>[2 : 5] <br /><br />
-
-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,<br />write
-the following expression in the text control: <br />
-<font color="#CC9933">column_name1</font>
-<font color="blue">[minimum row index1 :  maximum  row index1]</font>
-<font color="#00CC33"><big><b> , </b></big></font> 
-<font color="#CC9933">column_name1</font>
-<font color="blue">[minimum row index2 :  maximum  row index2]</font> <br />
-Example : <font color="#CC9933">radius </font><font color="blue"> [2 : 5] </font>
-<font color="#00CC33"><big><b> , </b></big></font><font color="#CC9933">radius </font>
- <font color="blue">[10 : 25] </font><br /><br />
-
-
-<b>Note: </b>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) 
-<font color="blue"><a href="#figure5">(see Figure 5)</a></font>.
-
-<br /><br /><img src="plot_button.bmp" /><br /><br />
-<a name="figure5"><u>Figure 5: Plotting</u></a><br />
-
-</p>
-
-
-<h5><font color="blue"><a name="view"> View Column/Cell(s) </a></font></h5>
-<p>
-Select 1 or more cells from the same column, click the <b> 'View Fits' </b>
-button  to display available curves. <br />
-
-For example, select the cells of the <b> 'Chi2' </b> column, then click the <b> 'View Fits' </b> 
-button. The plots generates will represent the <b>residuals </b> plots. <br />
- 
-
-If you select any cells of the <b> 'Data' </b> column and click the
-<b> 'View Fits' </b> button. It generates both
-<b> data and fits</b> in the graph <font color="blue"><a href="#figure6">(see Figure 6)</a></font>. <br />
-
-<b>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. 
-</b>
-<br />
-<br /><br /><img src="view_button.bmp" /><br /><br />
-<a name="figure6"><u>Figure 6: View Fits</u></a><br /><br />
-</p>
-
-
-</body>
-</html>
Index: docs/pre-sphinx-docs/category_manager_help_v0.html
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-<html>
-<body>
-<h4>Model Category Manager</h4>
-<ul>
-<li><a href="#description">Description</a></li>
-
-</ul>
-<h5><a name="description">Description</a></h5>
-<p>
-
-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).
-<br>
-1) Enable/Disable models: Check/uncheck the check boxes to enable/disable the models (Fig. 2).
-<br>
-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). 
-<br>
-3) To apply the changes made, hit the OK button. Otherwise, click the 'Cancel' button (Fig. 2).
-</p>
-<br>
-<img src="cat_fig0.bmp"/>
-<br>
-Fig.1
-<br>
-<br>
-<img src="cat_fig1.bmp"/>
-<br>
-Fig.2
-<br>
-<br>
-<img src="cat_fig2.bmp"/>
-<br>
-Fig.3
-<br>
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/change_scale_help_v0.html
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-<html>
-<body>
-<h4>Change scale</h4>
-<p>
-	If the loaded data is a 1-D data.Changing scale or Data Representation will work as
-	followed:<b>right click</b> on the plot window.
-	A context menu pops-up  and select <b>Change Scale</b>. A dialog window titled<b>
-	select the scale of the graph</b> will pop-up then change the <b>x</b>, the <b>y</b>
-	and the <b>view </b> values as wish.
-	If the loaded data  is an image.<b>Right click</b> on the image to pop-up the context
-	menu. Select <Toggle linear/Log scale> to switch from linear to log scale. The scale 
-	selected is printed on the statusbar.
-	
-</p>
-</body>
-</html>
Index: docs/pre-sphinx-docs/data_explorer_help_v0.html
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-<html>
-<body>
-
-<h4>Data Explorer Options</h4>
-<ul>
-<li><a href="#intro">Introduction</a></li>
-<li><a href="#load">Load data</a></li>
-<li><a href="#handy">Handy menu</a></li>
-<li><a href="#active">Activate data</a></li>
-<li><a href="#remove">Remove data</a></li>
-<li><a href="#append">Append plot to graph</a></li>
-<li><a href="#new">Create new plot</a></li>
-<li><a href="#freeze">Freeze theory</a></li>
-<li><a href="#send">Send data to applications</a></li>
-</ul>
-
-<h5><a name="intro"><font color="blue">Introduction</font></a></h5>
-<p> 
-<b>Data Explorer</b> 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 <b>View</b> of the menubar, Data explorer can be toggled between Show and Hide 
-by clicking the menu <b>Show/Hide Data Explorer</b>. 
-</p>
-<p><b><font size=2>IMPORTANT!</font></b> 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.
-</p>
-
-<h5><a name="load"><font color="blue">Load data</font></a></h5>
-<p>
-To Load data, click the button <b>Load Data</b>, then select one or more (holding Ctrl key)
-files to load into the application. In
-the list, the <b>Data</b> will be displayed as the name
-of each selected file.
- Expending this data by clicking the <b>+</b> symbol
-will display available information about the data such as data title if exists.
-</p>
-
-
-<h5><a name="handy"><font color="blue">Handy menu</font></a></h5>
-<p>
-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.
- <br>
-<img src="hand_menu.png"/>
-</p>
-
-<h5><a name="active"><font color="blue">Activate data</font></a></h5>
-<p>
-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.
-</p>
-<p>
-There is a combo box labeled <b> Selection Options</b> that allows to activate 
-or select multiple data simultaneously. 
-</p>
-
-<h5><a name="remove"><font color="blue">Remove data</font></a></h5>
-<p>
-Remove data button  remove all reference of this data into the application.
-</p>
-<p>
-<font size=2><b>WARNING!</b></font> Remove data will stop any jobs 
-currently using the selected data.
-</p>
-
-<h5><a name="append"><font color="blue">Append plot to graph</font></a></h5>
-<p>
-Click on the button <b>Append To</b> 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.
-</p>
-
-<h5><a name="new"><font color="blue">Create new plot</font></a></h5>
-<p>
-Click on <b>New Plot</b> button to create a new plot panel where selected data 
-will be plotted.
-</p>
-
-<h5><a name="freeze"><font color="blue">Freeze theory</font></a></h5>
-<p>
-<b>Freeze Theory</b> button generate Data from selected theory. This operation 
-can only be performed when theory labels are selected. 
-</p>
-
-<h5><a name="send"><font color="blue">Send to application</font></a></h5>
-<p>
-Click on the button <b>Send To</b> 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.
-
-</p>
-
-</body>
-</html>
Index: docs/pre-sphinx-docs/data_operator_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/data_operator_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,35 +1,0 @@
-<html>
-<body>
-<h4>Data Operator</h4>
-<ul>
-<li><a href="#Description">Description</a></li>
-<li><a href="#Howto">Howto?</a></li>
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
-This dialog panel provides arithmetic operations between two data sets (the last data set could be a number): <br> 
-When the data1 and data2 are selected, their x (or qx and qy for 2D) values must match with each other.
-</p>
-
-<h5><a name="Howto">Howto?</a></h5>
-<p>
-1) Type the data name resulted from an operation.<br>
-2) Select a data/theory in the drop down menus. When the data2 is set to number,
- type a number in the text control box. <br>
-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 are not match, the operation will fail and the background 
-color of the combo box items will turn to red (WIN only).<br>
-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.<br>
-Note: The errors and warnings will be displayed at the bottom of the SasView window. 
-</p> 
-<p>
-<img src="data_oper_pic.png">
-<br>
-Data operation dialog
-</p>
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/density_calculator_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/density_calculator_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,33 +1,0 @@
-<html>
-<body>
-<h4>Mass Density Calculator</h4>
-<ul>
-<li><a href="#Description">Description</a></li>
-<li><a href="#HowTo">HowTo?</a></li>
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
-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.
-</p>
-
-
-<h5><a name="HowTo">HowTo?</a></h5>
-<p>
-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.
-</p>
-<p>
-2. Select input (molar volume or mass density) from combobox. Then type in the input value.</p>
-<p>
-3. Click the 'Calculate' button to perform the calculation.
-</p>
-<p>
-4. Outputs also include the molar mass (weight) that depends only on the chemical formula
-</p>
-<p><img src="density_tutor.gif">
-</p>
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/fitting_help_v0.html
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-<div class="document" id="fitting-perspective">
-<h1 class="title">Fitting Perspective</h1>
-
-<!-- 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. -->
-<p><a class="reference internal" href="#load-a-file">Load_a_File</a></p>
-<p><a class="reference internal" href="#single-fit">Single_Fit</a></p>
-<p><a class="reference internal" href="#simultaneous-fitting">Simultaneous_Fitting</a></p>
-<p><a class="reference internal" href="#batch-fitting">Batch_Fitting</a></p>
-<p><a class="reference internal" href="#model-selection">Model_Selection</a></p>
-<p><a class="reference internal" href="#model-category-manager">Model_Category_Manager</a></p>
-<p><a class="reference internal" href="#model-functions">Model_Functions</a></p>
-<p><a class="reference internal" href="#custom-model-editor">Custom_Model_Editor</a></p>
-<p><a class="reference internal" href="#polydispersity-distributions">Polydispersity_Distributions</a></p>
-<p><a class="reference internal" href="#smearing-computation">Smearing_Computation</a></p>
-<p><a class="reference internal" href="#polarisation-magnetic-scattering">Polarisation_Magnetic_Scattering</a></p>
-<p><a class="reference internal" href="#key-combinations">Key_Combinations</a></p>
-<p><a class="reference internal" href="#status-bar-help">Status_Bar_Help</a></p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-<div class="section" id="id1">
-<span id="load-a-file"></span><h1>Load a File</h1>
-<p>From Menu go to <em>Data</em> -&gt; <em>Load Data File(or Folder)</em> . 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 <em>cancel</em> . In case a file can not be
-loaded, an error message will be displayed on the statusbar.</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id2">
-<span id="single-fit"></span><h1>Single Fit</h1>
-<p>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 <a href="#id3"><span class="problematic" id="id4">|</span></a>chi|2 but that
-requires longer computation time. In order to set a data to a control panel
-(FitPage), see the &quot;DataLoader Help&quot;. 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 <em>'Fit'</em>  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.</p>
-<div class="system-message" id="id3">
-<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">C:/Code/Eclipse_workspace/SasViewTrunk/src/sas/perspectives/fitting/media/fitting_help.rst</tt>, line 73); <em><a href="#id4">backlink</a></em></p>
-Inline substitution_reference start-string without end-string.</div>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id5">
-<span id="simultaneous-fitting"></span><h1>Simultaneous Fitting</h1>
-<p>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.</p>
-<p>Simultaneous Fit without Constraint</p>
-<p>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.</p>
-<p>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.</p>
-<p>Simultaneous Fit with Constraint</p>
-<p>Enter constraint in the text control next to <em>constraint fit</em>  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 &quot;;&quot;
-The easy setup can generate many constraint inputs easily when the selected
-two models are the same type.</p>
-<p>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.</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id6">
-<span id="batch-fitting"></span><h1>Batch Fitting</h1>
-<p><a class="reference internal" href="#batch-fit">Batch_Fit</a></p>
-<p><a class="reference internal" href="#batch-window">Batch_Window</a></p>
-<p><a class="reference internal" href="#edit-grid">Edit_Grid</a></p>
-<p><a class="reference internal" href="#save-grid">Save_Grid</a></p>
-<p><a class="reference internal" href="#open-batch-results">Open_Batch_Results</a></p>
-<p><a class="reference internal" href="#plot">Plot</a></p>
-<p><a class="reference internal" href="#view-column-cell">View_Column_Cell</a></p>
-</div>
-<div class="section" id="id7">
-<span id="batch-fit"></span><h1>Batch Fit</h1>
-<p>Create a <em>Batch Page</em> by selecting the <em>Batch</em> radio button on the DataExplorer
-(see figure below) and for a new control page select 'New FitPage' in the
-Fitting menubar.</p>
-<img alt="batch_button_area.bmp" src="batch_button_area.bmp" />
-<p>Figure 1: MenuBar:</p>
-<p>Load Data to the DataExplorer if not already loaded.</p>
-<p>Select one or more data sets by checking the check boxes, and then make sure
-that &quot;Fitting&quot; is selected in the dropdown menu next to the &quot;Send To&quot; 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) &lt;<a class="reference internal" href="#single-fit">Single_Fit</a>&gt;. Then use 'Fit' button to
-perform the fitting.</p>
-<p>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).</p>
-<p>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.</p>
-</div>
-<div class="section" id="id8">
-<span id="batch-window"></span><h1>Batch Window</h1>
-<p>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.</p>
-<p>Once closed, it can be opened anytime from the &quot;View&quot; menubar item (see
-Figure 2).</p>
-<img alt="restore_batch_window.bmp" src="restore_batch_window.bmp" />
-<p>Figure 2: Edit Menu:</p>
-</div>
-<div class="section" id="id9">
-<span id="edit-grid"></span><h1>Edit Grid</h1>
-<p>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 <em>Edit</em>
-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.</p>
-<p>To Remove column from the grid, select it, choose edit menu, and click the
-<em>'remove'</em>  menu item. Any removed column should reinserted whenever needed.</p>
-<p>All above options are also available when right clicking on a given column
-label(see Figure 3).</p>
-<p><em>Note:</em>  A column always needs to be selected in order to remove or insert a
-column in the grid.</p>
-<img alt="edit_menu.bmp" src="edit_menu.bmp" />
-<p>Figure 3: Edit Menu:</p>
-</div>
-<div class="section" id="id10">
-<span id="save-grid"></span><h1>Save Grid</h1>
-<p>To save the current page on the batch window, select the <em>'File'</em>  menubar
-item(see Figure 4), then choose the <em>'Save as'</em>  menu item to save it as a
-.csv file.</p>
-<p><em>Note:</em> 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.</p>
-<p>Warning! To ensure accuracy of saved fit results, it is recommended to save
-the current grid before modifying it .</p>
-</div>
-<div class="section" id="id11">
-<span id="open-batch-results"></span><h1>Open Batch Results</h1>
-<p>Any <em>csv</em>  file can be opened in the grid by selecting the <em>'Open'</em>  under
-the <em>'File'</em>  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.</p>
-<img alt="file_menu.bmp" src="file_menu.bmp" />
-<p>Figure 4: MenuBar:</p>
-</div>
-<div class="section" id="id12">
-<span id="plot"></span><h1>Plot</h1>
-<p>To <em>plot</em>  a column versus another, select one column at the time, click the
-<em>'Add'</em>  button next to the text control of X/Y -axis <em>Selection Range</em>  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 <em>'Plot'</em>  button. When clicking
-on <em>Add</em>  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.</p>
-<p><em>X/Y -Axis Selection Range</em> can be edited manually. These text controls
-allow the following types of expression (operation can be + - * /, or pow)</p>
-<p>1) if the current axis label range is a function of 1 or more columns, write
-this type of expression</p>
-<p>constant1  * column_name1 [minimum row index :  maximum  row index] operator
-constant2 * column_name2 [minimum row index :  maximum  row index]</p>
-<p>Example: radius [2 : 5] -3 * scale [2 : 5]</p>
-<p>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</p>
-<p>column_name1 [minimum row index1 :  maximum  row index1] , column_name1
-[minimum row index2 :  maximum  row index2]</p>
-<p>Example : radius [2 : 5] , radius [10 : 25]</p>
-<p>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).</p>
-<img alt="plot_button.bmp" src="plot_button.bmp" />
-<p>Figure 5: Plotting</p>
-</div>
-<div class="section" id="view-column-cell-s">
-<span id="view-column-cell"></span><h1>View Column/Cell(s)</h1>
-<p>Select 1 or more cells from the same column, click the 'View Fits' button to
-display available curves.</p>
-<p>For example, select the cells of the  'Chi2'  column, then click the  'View Fits'
-button. The plots generates will represent the residuals  plots.</p>
-<p>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).</p>
-<p>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.</p>
-<img alt="view_button.bmp" src="view_button.bmp" />
-<p>Figure 6: View Fits</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-<p id="model-selection"><a class="reference internal" href="#model-type">Model_Type</a></p>
-<p><a class="reference internal" href="#change-model-parameters">Change_Model_Parameters</a></p>
-<p><a class="reference internal" href="#write-your-own-model">Write_your_Own_Model</a></p>
-</div>
-<div class="section" id="id13">
-<span id="model-type"></span><h1>Model Type</h1>
-<p>Models are grouped into three classes</p>
-<ul class="simple">
-<li><em>Shapes</em></li>
-<li><em>Shape-Independent</em></li>
-<li><em>Uncategorised</em></li>
-<li><em>Customized Models</em></li>
-<li><em>Structure Factor</em></li>
-</ul>
-</div>
-<div class="section" id="id14">
-<span id="change-model-parameters"></span><h1>Change Model Parameters</h1>
-<p>To visualize model in a different window, from menu click on <em>Model</em>. 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
-<em>model view</em>  tab and view the plotted model with its new parameters.</p>
-</div>
-<div class="section" id="id15">
-<span id="write-your-own-model"></span><h1>Write your Own Model</h1>
-<p>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 <em>plugin_models</em>  directory in
-.sasview of your home directory (eg., username.sasview&gt;plugin_models). Your
-plugin model will be added into &quot;&lt;&gt;Customized Models&quot; on the next model
-selection.</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id16">
-<span id="model-category-manager"></span><h1>Model Category Manager</h1>
-<p>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).</p>
-<p>1) Enable/Disable models: Check/uncheck the check boxes to enable/disable the
-models (Fig. 2).</p>
-<p>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).</p>
-<p>3) To apply the changes made, hit the OK button. Otherwise, click the 'Cancel'
-button (Fig. 2).</p>
-<img alt="cat_fig0.bmp" src="cat_fig0.bmp" />
-<p>Fig.1</p>
-<img alt="cat_fig1.bmp" src="cat_fig1.bmp" />
-<p>Fig.2</p>
-<img alt="cat_fig2.bmp" src="cat_fig2.bmp" />
-<p>Fig.3</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id17">
-<span id="model-functions"></span><h1>Model Functions</h1>
-<p>Model Documentation &lt;models/model_functions&gt;</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id18">
-<span id="custom-model-editor"></span><h1>Custom Model Editor</h1>
-<p><a class="reference internal" href="#description">Description</a></p>
-<p><a class="reference internal" href="#new">New</a></p>
-<p><a class="reference internal" href="#sum-multi-p1-p2">Sum_Multi_p1_p2</a></p>
-<p><a class="reference internal" href="#advanced">Advanced</a></p>
-<p><a class="reference internal" href="#delete">Delete</a></p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id19">
-<span id="description"></span><h1>Description</h1>
-<p>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.</p>
-<img alt="edit_model_menu.bmp" src="edit_model_menu.bmp" />
-</div>
-<div class="section" id="id20">
-<span id="new"></span><h1>New</h1>
-<p>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.</p>
-<img alt="new_model.bmp" src="new_model.bmp" />
-</div>
-<div class="section" id="id21">
-<span id="sum-multi-p1-p2"></span><h1>Sum|Multi(p1,p2)</h1>
-<p>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.</p>
-<img alt="sum_model.bmp" src="sum_model.bmp" />
-</div>
-<div class="section" id="id22">
-<span id="advanced"></span><h1>Advanced</h1>
-<p>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.</p>
-</div>
-<div class="section" id="id23">
-<span id="delete"></span><h1>Delete</h1>
-<p>The menu option is to delete the custom models. Just select the file name to
-delete.</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id24">
-<span id="polydispersity-distributions"></span><h1>Polydispersity Distributions</h1>
-<p>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>
-<p>P(q) = scale*&lt;F*F&gt;/Vol + bkg</p>
-<p>where F is the scattering amplitude and the&lt;&gt;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).</p>
-<p>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.</p>
-<p>The following five distribution functions are provided</p>
-<ul class="simple">
-<li><em>Rectangular_Distribution_</em></li>
-<li><em>Array_Distribution_</em></li>
-<li><em>Gaussian_Distribution_</em></li>
-<li><em>Lognormal_Distribution_</em></li>
-<li><em>Schulz_Distribution_</em></li>
-</ul>
-</div>
-<div class="section" id="id25">
-<span id="rectangular-distribution"></span><h1>Rectangular Distribution</h1>
-<img alt="pd_image001.png" src="pd_image001.png" />
-<p>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 <em>w</em>  are different.</p>
-<p>The standard deviation is</p>
-<img alt="pd_image002.png" src="pd_image002.png" />
-<p>The PD (polydispersity) is</p>
-<img alt="pd_image003.png" src="pd_image003.png" />
-<img alt="pd_image004.jpg" src="pd_image004.jpg" />
-</div>
-<div class="section" id="id26">
-<span id="array-distribution"></span><h1>Array Distribution</h1>
-<p>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.</p>
-<p>Example of an array in the file</p>
-<p>30        0.1
-32        0.3
-35        0.4
-36        0.5
-37        0.6
-39        0.7
-41        0.9</p>
-<p>We use only these array values in the computation, therefore the mean value
-given in the control panel, for example Ã¢â¬Ëradius = 60Ã¢â¬â¢, will be ignored.</p>
-</div>
-<div class="section" id="id27">
-<span id="gaussian-distribution"></span><h1>Gaussian Distribution</h1>
-<img alt="pd_image005.png" src="pd_image005.png" />
-<p>The xmean is the mean of the distribution and Norm is a normalization factor
-which is determined during the numerical calculation.</p>
-<p>The PD (polydispersity) is</p>
-<img alt="pd_image003.png" src="pd_image003.png" />
-<img alt="pd_image006.jpg" src="pd_image006.jpg" />
-</div>
-<div class="section" id="id28">
-<span id="lognormal-distribution"></span><h1>Lognormal Distribution</h1>
-<img alt="pd_image007.png" src="pd_image007.png" />
-<p>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, Ã¢â¬Åradius = 60Ã¢â¬ï¿œ.</p>
-<p>The PD (polydispersity) is given by /sigma/</p>
-<img alt="pd_image008.png" src="pd_image008.png" />
-<p>For the angular distribution</p>
-<img alt="pd_image009.png" src="pd_image009.png" />
-<p>The mean value is given by xmean=exp(/mu/+p2/2). The peak value is given by
-xpeak=exp(/mu/-p2).</p>
-<img alt="pd_image010.jpg" src="pd_image010.jpg" />
-<p>This distribution function spreads more and the peak shifts to the left as the
-p increases, requiring higher values of Nsigmas and Npts.</p>
-</div>
-<div class="section" id="id29">
-<span id="schulz-distribution"></span><h1>Schulz Distribution</h1>
-<img alt="pd_image011.png" src="pd_image011.png" />
-<p>The xmean is the mean of the distribution and Norm is a normalization factor
-which is determined during the numerical calculation.</p>
-<p>The z = 1/p2Ã¢â¬â 1.</p>
-<p>The PD (polydispersity) is</p>
-<img alt="pd_image012.png" src="pd_image012.png" />
-<p>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 &gt;= 160, and
-Nsigmas &gt;= 15 at least.</p>
-<img alt="pd_image013.jpg" src="pd_image013.jpg" />
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id30">
-<span id="smearing-computation"></span><h1>Smearing Computation</h1>
-<p><a class="reference internal" href="#slit-smearing">Slit_Smearing</a></p>
-<p><a class="reference internal" href="#pinhole-smearing">Pinhole_Smearing</a></p>
-<p><a class="reference internal" href="#d-smearing">2D_Smearing</a></p>
-</div>
-<div class="section" id="id31">
-<span id="slit-smearing"></span><h1>Slit Smearing</h1>
-<p>The sit smeared scattering intensity for SAS is defined by</p>
-<img alt="sm_image002.gif" src="sm_image002.gif" />
-<p>where Norm =</p>
-<img alt="sm_image003.gif" src="sm_image003.gif" />
-<p>Equation 1</p>
-<p>The functions <img alt="inlineimage004" src="sm_image004.gif" /> and <img alt="inlineimage005" src="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.,</p>
-<img alt="sm_image006.gif" src="sm_image006.gif" />
-<p>Equation 2</p>
-<p>and</p>
-<img alt="sm_image007.gif" src="sm_image007.gif" />
-<p>Equation 3</p>
-<p>so that <img alt="inlineimage008" src="sm_image008.gif" /> <img alt="inlineimage009" src="sm_image009.gif" /> for <img alt="inlineimage010" src="sm_image010.gif" /> and u.</p>
-<p>The <img alt="inlineimage011" src="sm_image011.gif" /> and <img alt="inlineimage012" src="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</p>
-<img alt="sm_image013.gif" src="sm_image013.gif" />
-<p>Equation 4</p>
-</div>
-<div class="section" id="numerical-implementation-of-equation-4">
-<h1>Numerical Implementation of Equation 4</h1>
-</div>
-<div class="section" id="case-1">
-<h1>Case 1</h1>
-<p>For <img alt="inlineimage012" src="sm_image012.gif" /> = 0 and <img alt="inlineimage011" src="sm_image011.gif" /> = constant.</p>
-<img alt="sm_image016.gif" src="sm_image016.gif" />
-<p>For discrete q values, at the q values from the data points and at the q
-values extended up to qN= qi + <img alt="inlineimage011" src="sm_image011.gif" /> the smeared
-intensity can be calculated approximately</p>
-<img alt="sm_image017.gif" src="sm_image017.gif" />
-<p>Equation 5</p>
-<p><img alt="inlineimage018" src="sm_image018.gif" /> = 0 for <em>Is</em> in <em>j</em> &lt; <em>i</em> or <em>j</em> &gt; N-1*.</p>
-</div>
-<div class="section" id="case-2">
-<h1>Case 2</h1>
-<p>For <img alt="inlineimage012" src="sm_image012.gif" /> = constant and <img alt="inlineimage011" src="sm_image011.gif" /> = 0.</p>
-<p>Similarly to Case 1, we get</p>
-<p><img alt="inlineimage019" src="sm_image019.gif" /> for qp= qi- <img alt="inlineimage012" src="sm_image012.gif" /> and qN= qi+ <img alt="inlineimage012" src="sm_image012.gif" />. <img alt="inlineimage018" src="sm_image018.gif" /> = 0
-for <em>Is</em> in <em>j</em> &lt; <em>p</em> or <em>j</em> &gt; <em>N-1</em>.</p>
-</div>
-<div class="section" id="case-3">
-<h1>Case 3</h1>
-<p>For <img alt="inlineimage011" src="sm_image011.gif" /> = constant and
-<img alt="inlineimage011" src="sm_image011.gif" /> = constant.</p>
-<p>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 &lt;&lt; slit hight, is used in
-SasView. This method is a mixed method that combines method 1 with the
-numerical integration for the slit width.</p>
-<img alt="sm_image020.gif" src="sm_image020.gif" />
-<p>Equation 7</p>
-<p>for qp= qi- <img alt="inlineimage012" src="sm_image012.gif" /> and
-qN= qi+ <img alt="inlineimage012" src="sm_image012.gif" />. <img alt="inlineimage018" src="sm_image018.gif" /> = 0 for
-<em>Is</em> in <em>j</em> &lt; <em>p</em> or <em>j</em> &gt; <em>N-1</em>.</p>
-</div>
-<div class="section" id="id32">
-<span id="pinhole-smearing"></span><h1>Pinhole Smearing</h1>
-<p>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</p>
-<img alt="sm_image021.gif" src="sm_image021.gif" />
-<p>Equation 8</p>
-<p>For all the cases above, the weighting matrix <em>W</em> is calculated when the
-smearing is called at the first time, and it includes the ~ 60 q values
-(finely binned evenly) below (&gt;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 <em>Norm</em>  factor is found numerically with the
-weighting matrix, and considered on <em>Is</em> computation.</p>
-</div>
-<div class="section" id="id33">
-<span id="d-smearing"></span><h1>2D Smearing</h1>
-<p>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</p>
-<img alt="sm_image022.gif" src="sm_image022.gif" />
-<p>Equation 9</p>
-<p>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 xÃ¢â¬â¢0= x0cos/theta/+y0sin/theta/ and yÃ¢â¬â¢0= -x0sin/theta/+y0cos/theta/.</p>
-<p>Note that the rotation angle is zero for x-y symmetric elliptical Gaussian
-distribution. The A is a normalization factor.</p>
-<img alt="sm_image023.gif" src="sm_image023.gif" />
-<p>Now we consider a numerical integration where each bins in /theta/ and R are
-<em>evenly</em> (this is to simplify the equation below) distributed by /delta//theta/
-and /delta/R, respectively, and it is assumed that I(xÃ¢â¬â¢, yÃ¢â¬â¢) is constant
-within the bins which in turn becomes</p>
-<img alt="sm_image024.gif" src="sm_image024.gif" />
-<p>Equation 10</p>
-<p>Since we have found the weighting factor on each bin points, it is convenient
-to transform xÃ¢â¬â¢-yÃ¢â¬â¢ back to x-y coordinate (rotating it by -/theta/ around z
-axis). Then, for the polar symmetric smear</p>
-<img alt="sm_image025.gif" src="sm_image025.gif" />
-<p>Equation 11</p>
-<p>where</p>
-<img alt="sm_image026.gif" src="sm_image026.gif" />
-<p>while for the x-y symmetric smear</p>
-<img alt="sm_image027.gif" src="sm_image027.gif" />
-<p>Equation 12</p>
-<p>where</p>
-<img alt="sm_image028.gif" src="sm_image028.gif" />
-<p>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.</p>
-<p>In the control panel, the higher accuracy indicates more and finer binnng
-points so that it costs more in time.</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id34">
-<span id="polarisation-magnetic-scattering"></span><h1>Polarisation/Magnetic Scattering</h1>
-<p>Magnetic scattering is implemented in five (2D) models</p>
-<ul class="simple">
-<li><em>SphereModel</em></li>
-<li><em>CoreShellModel</em></li>
-<li><em>CoreMultiShellModel</em></li>
-<li><em>CylinderModel</em></li>
-<li><em>ParallelepipedModel</em></li>
-</ul>
-<p>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, <em>M*perp, perpendicular to the scattering
-vector *Q</em> contributes to the the magnetic scattering length.</p>
-<img alt="mag_vector.bmp" src="mag_vector.bmp" />
-<p>The magnetic scattering length density is then</p>
-<img alt="dm_eq.gif" src="dm_eq.gif" />
-<p>where /gamma/ = -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0
-is the classical radius of electron, and <em>/sigma/</em> is the Pauli spin. For
-polarised neutron, the magnetic scattering is depending on the spin states.</p>
-<p>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</p>
-<p>Non-spin flips: (+ +) and (- -)
-Spin flips:     (+ -) and (- +)</p>
-<img alt="M_angles_pic.bmp" src="M_angles_pic.bmp" />
-<p>Now, let's assume that the angles of the <em>Q</em>  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</p>
-<img alt="sld1.gif" src="sld1.gif" />
-<p>for spin-flips</p>
-<img alt="sld2.gif" src="sld2.gif" />
-<p>where</p>
-<img alt="mxp.gif" src="mxp.gif" />
-<img alt="myp.gif" src="myp.gif" />
-<img alt="mzp.gif" src="mzp.gif" />
-<img alt="mqx.gif" src="mqx.gif" />
-<img alt="mqy.gif" src="mqy.gif" />
-<p>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)</p>
-<img alt="m0x_eq.gif" src="m0x_eq.gif" />
-<img alt="m0y_eq.gif" src="m0y_eq.gif" />
-<img alt="m0z_eq.gif" src="m0z_eq.gif" />
-<p>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</p>
-<p>(spin up)/(spin up + spin down)</p>
-<p>neutrons before the sample and at the analyzer, respectively.</p>
-<p><em>Note:</em> The values of the 'Up_frac_i' and 'Up_frac_f' must be in the range
-between 0 and 1.</p>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id35">
-<span id="key-combinations"></span><h1>Key Combinations</h1>
-<p><a class="reference internal" href="#copy-paste">Copy_Paste</a></p>
-<p><a class="reference internal" href="#bookmark">Bookmark</a></p>
-<p><a class="reference internal" href="#graph-context-menu">Graph_Context_Menu</a></p>
-<p><a class="reference internal" href="#ftolerance">FTolerance</a></p>
-</div>
-<div class="section" id="id36">
-<span id="copy-paste"></span><h1>Copy &amp; Paste</h1>
-<p>To copy the parameter values in a Fit(Model) panel to the clipboard:</p>
-<p><em>Ctrl(Cmd on MAC) + Left(Mouse)Click</em>  on the panel.</p>
-<p>To paste the parameter values to a Fit(Model)panel from the clipboard:</p>
-<p><em>Ctrl(Cmd on MAC) + Shift + Left(Mouse)Click</em>  on the panel.</p>
-<p>If this operation is successful, it will say so in the info line at the
-bottom of the SasView window.</p>
-</div>
-<div class="section" id="id37">
-<span id="bookmark"></span><h1>Bookmark</h1>
-<p>Bookmark of a fit-panel or model-panel status:</p>
-<p><em>(Mouse)Right-Click</em>  and select the bookmark in the popup list.</p>
-</div>
-<div class="section" id="id38">
-<span id="graph-context-menu"></span><h1>Graph Context Menu</h1>
-<p>To get the graph context menu to print, copy, save data, (2D)average, etc.:</p>
-<p><em>Locate the mouse point on the plot to highlight and *(Mouse) Right Click</em>
-to bring up the full menu.</p>
-</div>
-<div class="section" id="ftolerance-scipy">
-<span id="ftolerance"></span><h1>FTolerance (SciPy)</h1>
-<p>To change the ftol value of the Scipy FitEngine (leastsq):</p>
-<p>First, make sure that the Fit panel has data and a model selected.</p>
-<p><em>Ctrl(Cmd on MAC) + Shift + Alt + Right(Mouse)Click</em>  on the panel.</p>
-<p>Then, set up the value in the dialog panel.</p>
-<p>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 <a href="#id39"><span class="problematic" id="id40">|</span></a>chi|sq.</p>
-<div class="system-message" id="id39">
-<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">C:/Code/Eclipse_workspace/SasViewTrunk/src/sas/perspectives/fitting/media/fitting_help.rst</tt>, line 947); <em><a href="#id40">backlink</a></em></p>
-Inline substitution_reference start-string without end-string.</div>
-<!-- ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ -->
-</div>
-<div class="section" id="id41">
-<span id="status-bar-help"></span><h1>Status Bar Help</h1>
-<p><a class="reference internal" href="#message-warning-hint">Message_Warning_Hint</a></p>
-<p><a class="reference internal" href="#console">Console</a></p>
-</div>
-<div class="section" id="id42">
-<span id="message-warning-hint"></span><h1>Message/Warning/Hint</h1>
-<p>The status bar located at the bottom of the application frame, displays
-messages, hints, warnings and errors.</p>
-</div>
-<div class="section" id="id43">
-<span id="console"></span><h1>Console</h1>
-<p>Select <em>light bulb/info icon</em>  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.</p>
-</div>
-</div>
-</body>
-</html>
Index: docs/pre-sphinx-docs/fitting_key_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/fitting_key_help_v0.html	(revision 476d4e306e96c71a9f3ada8af7ef235e85d9b59c)
+++ 	(revision )
@@ -1,35 +1,0 @@
-<html>
-<body>
-
-<h4>Key Combination</h4>
-<ul>
-<li><a href="#Copy">Copy & Paste</a></li>
-<li><a href="#Bookmark">Bookmark</a></li>
-</ul>
-<h5><a name="Copy">Copy & Paste</a></h5>
-<p>
-<h6>To copy the parameter values in a Fit(Model)panel to the clipboard:</h6></p>
-<p> <b>Ctrl(Cmd on MAC) + Left(Mouse)Click</b> on the panel.</p>
-<p>
-<h6>To paste the parameter values to a Fit(Model)panel from the clipboard:</h6></p>
-<p> <b>Ctrl(Cmd on MAC) + Shift + Left(Mouse)Click</b> on the panel.</p>
-<p> If this operation is successful, it will say so in the info line 
-at the bottom of the SV window.<p>
-<p>
-
-<p>
-<h5><a name="Bookmark">Bookmark</a></h5>
-<p>
-<h6>Bookmark of a fit-panel or model-panel status:</h6></p>
-<p> <b>(Mouse)Right-Click</b> and select the bookmark in the popup list.</p>
-
-<p>
-<h5><a name="GraphMenu">Graph Context Menu</a></h5>
-<p>
-<h6>To get the graph context menu to print, copy, save data, (2D)average, etc.:</h6></p>
-<p> <b>Locate the mouse point on the plot to highlight and 
-<b>(Mouse) Right Click</b> to bring up the full menu.</p>
-
-</body>
-</html>
-
Index: docs/pre-sphinx-docs/glossaryhelp_v0.html
===================================================================
--- docs/pre-sphinx-docs/glossaryhelp_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,19 +1,0 @@
-<html>
-
-<body bgcolor="#ffffff">
-<h4>Table of Contents</h4>
-
-<ul>
-<li><a href="load_data_help.html">Load a File</a></li>
-<li><a href="single_fit_help.html">Single fit</a></li>
-<li><a href="simultaneous_fit_help.html">Simultaneous fit</a></li>
-<li><a href="change_scale_help.html">Change scale</a></li>
-<li><a href="reset_Graph_help.html">Reset graph</a></li>
-<li><a href="save_data_help.html">Save data</a></li>
-<li><a href="model_use_help.html">visualize model</a></li>
-<li><a href="sld_calculator_help.html">SLD Calculator</a></li>
-<li><a href ="doc/averaging_help.html">Data Averaging</a><br></li>
-</ul>
-
-</body>
-</html>
Index: docs/pre-sphinx-docs/graph_key_help_v0.html
===================================================================
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+++ 	(revision )
@@ -1,40 +1,0 @@
-<html>
-<body>
-
-<h4>Key Combination</h4>
-<ul>
-<li><a href="#Float">Floating Panel</a></li>
-<li><a href="#GraphMenu">Graph Context Menu</a></li>
-<li><a href="#Zoom">Zoom In & Out</a></li>
-</ul>
-
-<h5><a name="Float">Floating Panel</a></h5>
-<p>
-<h6>For a graph panel to float on the top of the SV window:</h6></p>
-<p> Press the <b>Ctrl(Cmd on MAC) key</b> 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'.</p>
-
-<p>
-<h5><a name="GraphMenu">Graph Context Menu</a></h5>
-<p>
-<h6>To get the graph context menu to print, copy, save data, (2D)average, etc.:</h6></p>
-<p> <b>Locate the mouse point on the plot to highlight and 
-<b>(Mouse) Right Click</b> to bring up the full menu.</p>
-
-<p>
-<h5><a name="Zoom">Zoom In and Out</a></h5>
-<p>
-<h6>To Zoom in or out the full plot:</h6></p>
-<p> <b>Locate the mouse point inside the graph which will be the center of the zooming,
-then <b>rotate MouseWheel</b>.</p>
-<p>
-<h6>To Zoom in or out the plot in x or y direction:</h6></p>
-<p> <b>Locate (and click) the mouse point near x (or y) axis just outside of the graph 
-and then <b>rotate MouseWheel</b>.</p>
-<p> Note that this works only on the 1D plots.</p>
-
-
-</body>
-</html>
-
Index: docs/pre-sphinx-docs/help_v0.html
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+++ 	(revision )
@@ -1,11 +1,0 @@
-<html>
-
-<frameset cols="120,*">
-
-<frame src="model_use_help.html">
-<frame src="load_data_help.html" name="showframe">
-
-</frameset>
-
-</html>
-
Index: docs/pre-sphinx-docs/invariant_help_v0.html
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+++ 	(revision )
@@ -1,395 +1,0 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 12 (filtered)">
-<style>
-<!--
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-
-<div class=Section1>
-
-<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;line-height:normal'><span
-style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><b><span style='font-family:"Times New Roman","serif"'><a
-href="#invariant">Scattering Invariant</a></span></b></p>
-
-<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;line-height:normal'><span
-style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><a href="#volume"><b><span style='font-family:"Times New Roman","serif"'>Volume
-Fraction</span></b></a></p>
-
-<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;line-height:normal'><span
-style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><a href="#surface"><b><span style='font-family:"Times New Roman","serif"'>Specific
-Surface Area</span></b></a></p>
-
-<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;line-height:normal'><span
-style='font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><a href="#howto"><b><span style='font-family:"Times New Roman","serif"'>How
-to Compute</span></b></a></p>
-
-<p class=MsoNormal style='line-height:normal'><b><span style='font-family:"Times New Roman","serif"'>The
-scattering <a name=invariant>invariant</a> (Q*)</span></b><span
-style='font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>The
-scattering invariant (Q*) is a model-independent quantity that can be easily
-calculated from </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>scattering
-data. For two phase systems, the scattering invariant, Q*, is defined as the
-integral of</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'> the
-square of the wave transfer (q) multiplied by the scattering cross section over
-the full range of q. </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>Q*
-is given by the following equation, </span></p>
-
-<p class=MsoNormal style='line-height:normal'>
-
-<table cellpadding=0 cellspacing=0 align=left>
- <tr>
-  <td width=2 height=4></td>
- </tr>
- <tr>
-  <td></td>
-  <td><img width=127 height=35 src="image001.gif"></td>
- </tr>
-</table>
-
-<span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:150%'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<br clear=ALL>
-
-<p class=MsoNormal style='line-height:150%'><span style='font-family:"Times New Roman","serif"'>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. &nbsp;These quantities&nbsp;are useful in their own right
-and can be used in&nbsp;further analysis. With this scattering invariant module
-users will also be able to determine the consistency of those properties
-between data.&nbsp; 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/A). The lower and/or higher q range than
-data given can be extrapolated by fitting some data nearby.</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>The
-scattering invariant is computed as follow:</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;line-height:normal'><span
-style='font-family:"Arial","sans-serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><i><span style='font-family:"Times New Roman","serif"'>I(q)</span></i><span
-style='font-family:"Times New Roman","serif"'> =  <i>I(q)</i> w/o background :
-If the data includes a background, user sets the value to subtract the background
-for the Q* computation.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;line-height:normal'><span
-style='font-family:"Arial","sans-serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>Reset<i>
-I(q)  </i></span><span style='font-family:"Times New Roman","serif"'>= <i>I(q)*
-scaling factor </i>, delta<i>I(q) =  </i>delta<i>I(q)*scaling factor</i> : If
-non-zero scaling factor is given, it will be considered.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;line-height:normal'><span
-style='font-family:"Arial","sans-serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'> Invariant:</span></p>
-
-<p class=MsoNormal style='margin-left:.25in;line-height:normal'>
-
-<table cellpadding=0 cellspacing=0 align=left>
- <tr>
-  <td width=45 height=12></td>
- </tr>
- <tr>
-  <td></td>
-  <td><img width=127 height=35 src="image001.gif"></td>
- </tr>
-</table>
-
-<span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<br clear=ALL>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'>            where, <i>g =q</i>
-for the pinhole geometry and <i>g =<sub> </sub>q<sub>v</sub></i>(the slit
-height) for the slit geometry which can be given in data or as a value.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;line-height:normal'><span
-style='font-family:"Arial","sans-serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>&nbsp;Higher
-q-region (&gt;= qmax in data): </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>            Power
-law (w/o background term) function = C/q<sup>4</sup> will be used </span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'>            where the constant
-C(=2pi(delta(rho))S<sub>v</sub>) is to be found by fitting part of data with
-the range of q<sub>N-m</sub>  to q<sub>N</sub> (m&lt;N).</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;line-height:normal'><span
-style='font-family:"Arial","sans-serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'> Lower
-q-region (&lt;= qmin in data): </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>            Guinier
-function = <i>I<sub>0</sub>exp(-R<sub>g</sub><sup>2</sup>q<sup>2</sup>/3)</i>
-where I<sub>0</sub> and R<sub>g</sub> are obtained by fitting, </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>            similarly
-to the high q region above.</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>            Power
-law can also be used.</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>&nbsp;</span><b>The
-<a name=volume>volume </a>fraction</b>: </p>
-
-<p class=MsoNormal style='line-height:normal'><span style='position:absolute;
-z-index:3;margin-left:1px;margin-top:9px;width:161px;height:47px'><img
-width=161 height=47 src="image002.gif"></span><span
-style='font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>where
-delta(rho) is the SLD contrast of which value is given by users.</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='position:absolute;
-z-index:4;margin-left:1px;margin-top:29px;width:101px;height:45px'><img
-width=101 height=45 src="image003.gif"></span><span
-style='font-family:"Times New Roman","serif"'>Thus,  </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'> where
-0 =&lt; <i>A</i> =&lt;1/4 in order for these values to be physically valid.</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:normal'><b><span style='font-family:"Times New Roman","serif"'>The
-<a name=surface>specific surface area </a>:</span></b></p>
-
-<p class=MsoNormal style='line-height:normal'>
-
-<table cellpadding=0 cellspacing=0 align=left>
- <tr>
-  <td width=1 height=3></td>
- </tr>
- <tr>
-  <td></td>
-  <td><img width=184 height=47 src="image004.gif"></td>
- </tr>
-</table>
-
-<b><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></b></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<br clear=ALL>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'> where
-<i>A</i> and <i>Q<sup>*</sup></i> are obtained from previous sections, and the
-Porod constant <i>C<sub>p</sub></i> is given by users. </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:normal'><b><span style='font-family:"Times New Roman","serif"'>Definitions:</span></b><span
-style='font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>Q&nbsp;:
-the magnitude of neutron (or X-ray) momentum transfer vector.</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>I(Q):
-the scattering intensity as a function of the momentum transfer Q.</span></p>
-
-<p class=MsoNormal style='line-height:150%'><span style='font-family:"Times New Roman","serif"'>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.</span></p>
-
-<p class=MsoNormal style='line-height:150%'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal style='line-height:normal'><a name=reference><b><span
-style='font-family:"Times New Roman","serif"'>Reference</span></b></a><b><span
-style='font-family:"Times New Roman","serif"'>: </span></b></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>Porod's
-chapter (2) from  O. Glatter and O. Kratky, &quot;Small Angle X-Ray
-Scattering&quot;, Academic Press, New York, 1982</span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>Otto's
-web page: </span><a href="http://physchem.kfunigraz.ac.at/sm/"><span
-style='font-family:"Times New Roman","serif"'>http://physchem.kfunigraz.ac.at/sm/</span></a><span
-style='font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNormal style='line-height:normal'><a name=howto><b><span
-style='font-family:"Times New Roman","serif"'>HowTo</span></b></a><b><span
-style='font-family:"Times New Roman","serif"'>:</span></b></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>i)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>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.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>ii)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>To subtract a
-background or/and to rescale the data, type the values in Customized Input
-box.  </span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
-</span>iii)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>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.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
-</span>iv)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>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.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>v)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>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.</span></p>
-
-<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
-</span>vi)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>The details
-of the calculation is available by clicking the Details button in the middle
-of the panel. </span></p>
-
-<p class=MsoNormal align=center style='text-align:center;line-height:normal'><span
-style='font-family:"Times New Roman","serif"'><img border=0 width=572
-height=449 id="Object 4" src="image005.gif"></span></p>
-
-<p class=MsoNormal style='line-height:normal'><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-</div>
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/kiessig_calculator_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/kiessig_calculator_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,27 +1,0 @@
-<html>
-<body>
-<h4>Kiessig Thickness Calculator</h4>
-<ul>
-<li><a href="#Description">Description:</a></li>
-<li><a href="#HowTo">HowTo?</a></li>
-
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
-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 uses the Kiessig relation;
- thickness = 2*Pi/fringe_width.
-  
-</p>
-
-
-<h5><a name="HowTo">HowTo?</a></h5>
-<p>
-To get a rough thickness or particle size, just type the Kiessig fringe width (in the 1/A unit)
- and click on the 'Compute' button. Then the output value will be show up in the 'Thickness' text box.</p>
-
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/load_data_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/load_data_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,13 +1,0 @@
-<html>
-<body>
-
-<p>
-<h4>Loading Data File/Folder</h4>
-From Menu go to <b>Data</b> -><b>Load Data File(or Folder)</b>. 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 <b>cancel</b>.
-In case a file can not be loaded, an error message will be displayed on the statusbar.
-</p>
-
-</body>
-</html>
Index: docs/pre-sphinx-docs/load_image_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/load_image_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,48 +1,0 @@
-<body>
-<h4>Image Viewer</h4>
-<ul>
-<li><a href="#Description">Description</a></li>
-<li><a href="#HowTo">HowTo?</a></li>
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
-This tool is to load image files (in the format of png, bmp, gif, jpg, or tif) 
-and to display it in the x-y coordinate (against the pixel number). The displayed plot then
- can be saved, printed, and copied. 
- The plot can also be resized by dragging the corner of the panel. 
-</p>
-
-
-<h5><a name="HowTo">HowTo?</a></h5>
-<p>
-1. Select 'Image Viewer' under 'Tool' menu in the menubar.
-</p>
-<p>
-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 Picture below).</p>
-<p>
-<img src="load_image.bmp">
-</p>
-<p>
-3. If the loading is successful, the image will be displayed in the x-y coordinate. 
-The file name will be shown in the title bar (See Picture below). 
-</p>
-<p>
-4. Some options such as Saving, printing, and copying are available from the menubar, 
-or in the popup-menu by right-mouse-clicking anywhere in the plot (See Picture below).
-</p>
-<p><img src="pic_plot.bmp">
-</p>
-<p>
-5. If the image is taken from a 2D detector, it can be converted to our 2D data where 
-the z values are computed by the Eq. z = 0.299R + 0.587G + 0.114B unless the picture file
-is formatted in an 8 bit Grey-Scale tif. In the "Convert to Data" dialog, users set 
-the proper values in the text boxes and then click the OK button to close and to send the data generated to the Data
- Explorer in the SasView main window. The "Cancel" button will just close the dialog 
- (See Picture below).
-</p>
-
-<p><img src="pic_convert.bmp">
-</p>
-<br>
-</body>
Index: docs/pre-sphinx-docs/model_editor_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/model_editor_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,58 +1,0 @@
-<html>
-<body>
-<h4>Edit Custom Model</h4>
-<ul>
-<li><a href="#description">Description</a></li>
-<li><a href="#new">New</a></li>
-<li><a href="#sum">Sum|Multi(p1,p2)</a></li>
-<li><a href="#advanced">Advanced</a></li>
-<li><a href="#delete">Delete</a></li>
-
-</ul>
-<h5><a name="description">Description</a></h5>
-<p>
-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. 
-</p>
-<br/>
-<img src="edit_model_menu.bmp"/>
-<br/>
-<br/>
-<h5><a name="new">New</a></h5>
-<p>
-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.
-</p>
-<br/>
-<img src="new_model.bmp"/>
-<br/>
-<br/>
-<h5><a name="sum">Sum|Multi(p1,p2)</a></h5>
-<p>
-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.
-</p>
-<br/>
-<img src="sum_model.bmp"/>
-<br/>
-<br/>
-<h5><a name="advanced">Advanced</a></h5>
-<p>
-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 (## &#60-----). 
-In the end of edit, 'Compile' and 'Run' from the menu bar to activate or to see the model working properly.
-</p>
-
-
-<h5><a name="delete">Delete</a></h5>
-<p>
-The menu option is to delete the custom models. Just select the file name to delete.
-</p>
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/model_use_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/model_use_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,37 +1,0 @@
-<html>
-<body>
-
-<h4>Model Selection</h4>
-<ul>
-<li><a href="#Model type">Model type</a></li>
-<li><a href="#Visualize">Change Model's parameters</a></li>
-<li><a href="#Plugin"> Write your own model</a></li>
-</ul>
-
-<h5><a name="Model types">Model type</a></h5>
-<p> Models are grouped into three classes:
-	<ul>
-	<li><b> Shapes</b>: Regular  geometric shapes</li>
-	<li><b> Shape- Independent</b></li>
-	<li><b> Customized Models</b> : models written by the user</li>
-	<li><b> Structure Factor</b> </li>
-	</ul>
-</p>
-
-<h5><a name="Visualize">Change Model's parameters</a></h5>
-<p>
-	To visualize model in a different window, from menu click on <b>Model</b>.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 <b> model view</b> tab
-	and view the plotted model with its new parameters. 
-</p>
-
-<h5><a name="Plugin"> Write your own model</a></h5>
-<p>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 <b>plugin_models</b> directory
-	in .sasview of your home directory (eg., username\.sasview>\plugin_models). You plugin
-	model will be added into "<>Customized Models</>"  on the next model selection.
-</p>
-</body>
-</html>
Index: docs/pre-sphinx-docs/pd_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/pd_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,182 +1,0 @@
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 12 (filtered)">
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-<p class=MsoNormal><h3><span style='font-family:"Times New Roman","serif"'>Polydisperisty
-and Angular Distributions</span></h3></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>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*&lt;F*F&gt;/Vol + bkg, where
-F is the scattering amplitude and the &lt; &gt; 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).</span></p>
-<p> 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.</p>
-
-<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span
-style='font-family:"Times New Roman","serif"'>The following five distribution
-functions are provided;</span></p>
-<ul>
-<li><a href="#Rectangular">Rectangular distribution</a></li>
-<li><a href="#Array">Array distribution</a></li>
-<li><a href="#Gaussian">Gaussian distribution</a></li>
-<li><a href="#Lognormal">Lognormal distribution</a></li>
-<li><a href="#Schulz">Schulz distribution</a></li>
-</ul>
-<p>&nbsp;</p>
-<p><a name="Rectangular"><h4>Rectangular distribution</a></h4></p>
-<p><img src="img/pd_image001.png"></p>
-<p>&nbsp;</p>
-<p>The x<sub>mean</sub> 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 <i>w</i> are different.</p>
-<p>The standard deviation is </p>
-<p><img src="img/pd_image002.png"></p>
-<p>&nbsp;</p>
-<p>The PD (polydispersity) is </p>
-<p><img src="img/pd_image003.png"></p>
-<p>&nbsp;</p>
-<p><img width=511 height=270
-id="Picture 1" src="img/pd_image004.jpg" alt=flat.gif></p>
-<p>&nbsp;</p>
-<p>&nbsp;</p>
-<p><a name="Array"><h4>Array distribution</h4></a></p>
-
-<p>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.</p>
-
-<p>Example of an array in the file;</p>
-
-<p>30        0.1</p>
-
-<p>32        0.3</p>
-
-<p>35        0.4</p>
-
-<p>36        0.5</p>
-
-<p>37        0.6</p>
-
-<p>39        0.7</p>
-
-<p>41        0.9</p>
-
-<p'>&nbsp;</p>
-
-<p>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.</p>
-<p>&nbsp;</p>
-
-
-<p><a name="Gaussian"><h4>Gaussian distribution</h4></a></p>
-<p>&nbsp;</p>
-
-<p><img src="img/pd_image005.png"></p>
-
-<p>&nbsp;</p>
-
-<p>The x<sub>mean</sub> is the mean
-of the distribution and Norm is a normalization factor which is determined
-during the numerical calculation.</p>
-
-<p>&nbsp;</p>
-
-<p>The PD (polydispersity) is </p>
-
-<p><img src="img/pd_image003.png"></p>
-
-<p>&nbsp;</p>
-
-<p><img width=518 height=275
-id="Picture 2" src="img/pd_image006.jpg" alt=gauss.gif></p>
-
-<p>&nbsp;</p>
-
-<p><a name="Lognormal"><h4>Lognormal distribution</h4></a></p>
-
-<p>&nbsp;</p>
-
-<p><img src="img/pd_image007.png"></p>
-
-<p>&nbsp;</p>
-
-<p>The &#956; = ln(x<sub>med</sub>),  x<sub>med</sub>
-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.</p>
-
-<p >&nbsp;</p>
-
-<p>The PD (polydispersity) is given
-by &#963;,</p>
-
-<p><img src="img/pd_image008.png"></p>
-
-<p>&nbsp;</p>
-
-<p>For the angular distribution,</p>
-
-<p><img src="img/pd_image009.png"></p>
-
-<p>&nbsp;</p>
-
-<p>The mean value is given by x<sub>mean</sub>
-=exp(&#956;+p<sup>2</sup>/2).</p>
-
-<p>The peak value is given by x<sub>peak</sub>=exp(&#956;-p<sup>2</sup>).</span></p>
-
-<p>&nbsp;</p>
-
-<p><img width=450 height=239
-id="Picture 7" src="img/pd_image010.jpg" alt=lognormal.gif></p>
-
-<p>&nbsp;</p>
-
-<p>This distribution function
-spreads more and the peak shifts to the left as the p increases, requiring
-higher values of Nsigmas and Npts.</p>
-
-<p>&nbsp;</p>
-
-<p><a name="Schulz"><h4>Schulz distribution</h4></a></p>
-
-<p>&nbsp;</p>
-
-<p><img src="img/pd_image011.png"></p>
-
-<p>&nbsp;</p>
-
-<p>The x<sub>mean</sub> is the mean
-of the distribution and Norm is a normalization factor which is determined
-during the numerical calculation. </p>
-
-<p>The z = 1/p<sup>2</sup>  1.</p>
-<p>&nbsp;</p>
-
-<p>The PD (polydispersity) is </p>
-<p'><img src="img/pd_image012.png"></p>
-<p>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.</p>
- <p/>
-<p><img width=438 height=232
-id="Picture 4" src="img/pd_image013.jpg" alt=schulz.gif></p>
-
-</div>
-<br>
-</body>
Index: docs/pre-sphinx-docs/polar_mag_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/polar_mag_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,102 +1,0 @@
-<body>
-<br>
-<p><a name="magnetic"></a><strong><span style="font-size: 14pt;"> Polarization and Magnetic Scattering</span></strong></p>
-<br>
-<br>
-The magnetic scattering is implemented in five (2D) models, SphereModel, CoreShellModel, 
-CoreMultiShellModel, CylinderModel, and ParallelepipedModel. 
-In general, the scattering length density (SLD) in each regions where the SLD (=&#946;)
- is uniform, is a combination of the nuclear and magnetic SLDs 
-and depends on the spin states of the neutrons as follows:
-<br>
-<br>
-For magnetic scattering, only the magnetization component, <b>M</b><sub>perp</sub>, 
-perpendicular to the scattering vector <b>Q</b> contributes to the the magnetic 
-scattering length. (Figure below).
-<p>
-<img src="img/mag_vector.bmp"/>
-</p>
-<br>
-The magnetic scattering length density is then
-<p>
-<img src="img/dm_eq.gif"/>
-</p>
-<br>
-where &#947; = -1.913 the gyromagnetic ratio,  	&#956;<sub>B</sub> is the Bohr magneton, 
-r<sub>0</sub> is the classical radius of electron, 
-and <b>&#963;</b> is the Pauli spin.
-<br>
-For polarized neutron, the magnetic scattering is depending on the spin states.
-Let's consider that the incident neutrons are polarized parallel (+)/anti-parallel 
-(&#8211;) to the x' axis (See both Figures above).
-The possible out-coming states then are + and - states for both incident states.
-<br>
- - Non-spin-flips:  	(+ +) and  	(- -)
-<br>
- - Spin-flips:  	(+ -) and  	(- +)
-<br>
-<p>
-<img src="img/M_angles_pic.bmp"/>
-</p>
-<br>
-<br>
-Now, let's assume that the angles of the <b>Q</b> vector and the spin-axis (x') against x-axis 
-are &#966; and  &#952;<sub>up</sub>, respectively (See Figure above).
-Then, depending upon the polarization (spin) state of neutrons, the scattering length
-densities , including the nuclear scattering length density (&#946; <sub>N</sub>) are given as, for non-spin-flips,
-<p>
-<img src="img/sld1.gif"/>
-</p>
-<br>
-<br>
-for spin-flips,
-<p>
-<img src="img/sld2.gif"/>
-</p>
-<br>
-<br>
-where
-<p>
-<img src="img/mxp.gif"/>
-</p>
-<p>
-<img src="img/myp.gif"/>
-</p>
-<p>
-<img src="img/mzp.gif"/>
-</p>
-<p>
-<img src="img/mqx.gif"/>
-</p>
-<p>
-<img src="img/mqy.gif"/>
-</p>
-<br>
-<br>
-Here, the M<sub>0x</sub>, M<sub>0y</sub> and M<sub>0z</sub> are the x, y and z 
-components of the magnetization vector given in the xyz lab frame. 
-The angles of the magnetization, &#952;<sub>M</sub> and &#966;<sub>M</sub> as defined in the 
-Figure (above),
-<p>
-<img src="img/m0x_eq.gif"/>
-</p>
-<p>
-<img src="img/m0y_eq.gif"/>
-</p>
-<p>
-<img src="img/m0z_eq.gif"/>
-</p>
-<br>
-<p>
-The user input parameters are M0_sld = D<sub>M</sub>M<sub>0</sub>, Up_theta = &#952;<sub>up</sub>, 
-M_theta = &#952;<sub>M</sub>, and M_phi = &#966;<sub>M</sub>.
-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.
-</p>
-<br>
-*Note: The values of the 'Up_frac_i' and 'Up_frac_f' must be in the range between 0 and 1.
-</body>
-
-
-
-
Index: docs/pre-sphinx-docs/pycrust_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/pycrust_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,36 +1,0 @@
-<html>
-<body>
-<h4>Python (PyCrust) Shell</h4>
-<ul>
-<li><a href="#description">Description</a></li>
-<li><a href="#example">Example</a></li>
-</ul>
-<h5><a name="description">Description</a></h5>
-<p>
-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. 
-</p>
-<br/>
-For the details about the Python, visit the website, http://docs.python.org/tutorial/.
-<br/>
-The numpy, scipy, matplotlib, etc. are shipped with the SanView. 
-<br/>
-However, some functionalities of those packages may or may not work. 
-<br/>
-The PyCrust includes its own Help menu in the shell window.
-<br/>
-Note: Help(), Credits(), ... do not work on MAC.
-<br/>
-
-<p>
-<h5><a name="example">Example</a></h5>
-</p>
-<p>
-An example from the matplotlib gallery: 
-</p> 
-<img src="pycrust_example.bmp"/>
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/report_template_v0.html
===================================================================
--- docs/pre-sphinx-docs/report_template_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,201 +1,0 @@
-<html>
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator >
-</head>
-<body lang=EN-US>
-<div class=WordSection1>
-<font size='4'>
-<p class=MsoNormal><b><span >%s</span></b></p>
-<p class=MsoNormal><span >%s</span></p>
-</font>
-<font size='3'>
-<p class=MsoNormal><b><span > Input
-parameters</span></b></p>
-<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0>
- <tr>
-  <td width=170 valign=top>
-  <p class=MsoNormal > Parameter</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > Value</p>
-  </td>
-  <td width=170 valign=top >
-  <p class=MsoNormal > Unit</p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top >
-  <p class=MsoNormal > scale</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top >&nbsp;</p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top >
-  <p class=MsoNormal > porod constant</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top >&nbsp;</p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top>
-  <p class=MsoNormal > background</p>
-  </td>
-  <td width=170 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top ><span > cm<sup>-1</sup></span></p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top >
-  <p class=MsoNormal > contrast</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top >
-  <p class=MsoNormal ><span > A<sup>-2</sup></span></p>
-  </td>
- </tr>
-</table>
-<p class=MsoNormal><b><span > Extrapolation</span></b></p>
-<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0>
- <tr>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
- </tr>
- <tr>
-  <td width=213 valign=top >
-  <p class=MsoNormal > npts low = %s</p>
-  </td>
-  <td width=213 valign=top > npts high = %s</p>
-  </td>
- </tr>
- <tr>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
- </tr>
-</table>
-<p class=MsoNormal><b><span > Outputs</span></b></p>
-<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0>
- <tr>
-  <td width=110 valign=top >
-  <p class=MsoNormal s> Parameter</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
-  <td width=255 valign=top >
-  <p class=MsoNormal > Value</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > Unit</p>
-  </td>
- </tr>
- <tr>
-  <td width=110 rowspan=4 >
-  <p class=MsoNormal > invariant (Q<sup>*</sup>)</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal > low Q extrapolation</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=150 valign=top >
-  <p class=MsoNormal > data</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=150 valign=top >
-  <p class=MsoNormal > high Q extrapolation</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=150 valign=top >
-  <p class=MsoNormal > total</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=110 valign=top >
-  <p class=MsoNormal > volume fraction</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
- </tr>
- <tr>
-  <td width=110 valign=top >
-  <p class=MsoNormal > specific surface</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
- </tr>
-</table>
-</font>
-<p class=MsoNormal>&nbsp;</p>
-<font size=4>
-<br><b><span > Plot</span></b>
-<center>
-<br>Invariant Computation
-<br>Data: "%s"
-<img src="%s" height=400 width=550>
-</center>
-</font>
-</div>
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/resolution_calculator_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/resolution_calculator_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,83 +1,0 @@
-<html>
-<body>
-<h4>SAS Q Resolution Estimator</h4>
-<ul>
-<li><a href="#Description">Description</a></li>
-<li><a href="#HowTo">HowTo?</a></li>
-<li><a href="#Theory">Theory</a></li>
-<li><a href="#References">References</a></li>
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
-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.
-</p>
-
-
-<h5><a name="HowTo">HowTo?</a></h5>
-<p>
-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.</p>
-<p>
-2. Change the default values of the instrumental parameters as desired.</p>
-<p>
-3. The input formats of wavelength and its spread (=FWHM/wavelength) depend on the source type.
-<li>For monochromatic wave, the inputs are just one values as shown with the defaults.</li>
-<li>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.</li>
-</p>
-<p>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.</p>
-<p>
-5. Once set all the input values, click the compute button. 
-Depending on computation loads the calculation time will vary.
-</p>
-<p> 
-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.</p>
-<p>7. The summary can be accessed by clicking the 'light-bulb' icon 
-at the bottom of the SasView main window.
-</p>
-<p><img src="resolution_tutor.gif">
-</p>
-<h5><a name="Theory">Theory</a></h5>
-<p>
-The scattering wave transfer vector is by definition,
-<img src="q.gif">
-</p>
-<p>In the limit of the small angle, the variance of q in the first order approximation is</p>
-<p>
-<img src="sigma_q.gif">
-</p>
-In summary, the geometric and gravitational contributions depending on the shape of each factors can be expressed  
-as shown the table.</p>
-<p>
-<img src="sigma_table.gif">
-</p>
-<p>
-Finally, we use a Gaussian function to describe the 2D weighting distribution of the uncertainty in q.
-</p>
-<p/>
-<h5><a name="References">References</a></h5>
-<p>
-D.F.R. Mildner and J.M. Carpenter, J. Appl. Cryst. 17, 249-256 (1984).</p>
-<p>
-D.F.R. Mildner, J.M. Carpenter and D.L. Worcester, J. Appl. Cryst. 19, 311-319 (1986).</p>
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/simultaneous_fit_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/simultaneous_fit_help_v0.html	(revision 386ffe12ba023b3eab0fbbb16a6f958ed7c099a3)
+++ 	(revision )
@@ -1,37 +1,0 @@
-<html>
-<body>
-
-<h4>Simultaneous Fit</h4>
-<p>
-	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).
-</p>
-<ul>
-<li><a href="#noconstraint">Simultaneous Fit without constraint</a></li>
-<li><a href="#constraint">Simultaneous Fit with constraint</a></li>
-</ul>
-
-<h5><a name="noconstraint">Simultaneous Fit without constraint</a></h5>
-<p> 
-	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. 
-	<br/>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.
-	
-</p>
-
-<h5><a name="constraint">Simultaneous Fit with constraint</a></h5>
-<p>
-	Enter constraint in the text control next to  <b>constraint fit</b> 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.
-	<br/>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.
-</p>
-
-</body>
-</html>
Index: docs/pre-sphinx-docs/single_fit_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/single_fit_help_v0.html	(revision 476d4e306e96c71a9f3ada8af7ef235e85d9b59c)
+++ 	(revision )
@@ -1,24 +1,0 @@
-<html>
-<body>
-
-<h4>Single Fit</h4>
-<ul>
-<li><a href="#fitpage">Single Fit</a></li>
-
-</ul>
-
-<h5><a name="fitpage">Single Fit</a></h5>
-<p> 
-	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 <b> 'Fit'</b> 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.
-	
-</p>
-
-
-</body>
-</html>
Index: docs/pre-sphinx-docs/sld_calculator_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/sld_calculator_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,42 +1,0 @@
-<html>
-<body>
-<h4>Scattering Length Density (SLD) Calculator</h4>
-<ul>
-<li><a href="#SLD_calculator">Description</a></li>
-<li><a href="#How to use">How to format the compound name?</a></li>
-</ul>
-<h5><a name="SLD_calculator">Description</a></h5>
-<p>
-The neutron scattering length density is defined as: <br> 
-SLD = (b_c1 +b_c2+...+b_cn )/Vm  <br> where b_ci is the bound coherent scattering length of ith of 
-n atoms in a molecule with the molecular volume Vm
-</p>
-
-
-<h5><a name="How to use">How to format the compound name?</a></h5>
-<p>
-To calculate scattering length densities enter a compound and
-a mass density and click "Calculate". Enter a wavelength value is optional and its default 
-value will be 6.0A.
-</p> 
-<p>
-<ul>
-<li>Formula strings consist of counts and atoms such as "CaCO3+6H2O".</li>
-<li>Groups can be separated by <b>'+'</b> or <b>space</b>, so "CaCO3 6H2O" works as well.</li>
-<li>Groups and be defined using parentheses, such as "CaCO3(H2O)6".</li>
-<li>Parentheses can nest: "(CaCO3(H2O)6)1".</li>
-<li>Isotopes are represented by index, e.g., "CaCO[18]3+6H2O".</li>
-More examples: H[1], H[2].
-<li>Counts can be integer or decimal, e.g. "CaCO3+(3HO0.5)2".</li>
-Other compositions can be calculated as well,<br>
-for example a 70-30 mixture of H2O/D2O can be written as <b>H14O7+ D6O3</b><br>
-or more simply <b>H7D3O5 <\b>(i.e. 7 hydrogens, 3 deuteriums, and 5 oxygens)<br>
-and the mass density calculated based on the percentages of H and D. 
-Type for example "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) 
-
-</ul>
-</p>
-
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/slit_calculator_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/slit_calculator_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,33 +1,0 @@
-<html>
-<body>
-<h4>Slit Size Calculator</h4>
-<ul>
-<li><a href="#Description">Description:</a></li>
-<li><a href="#HowTo">HowTo?</a></li>
-<li><a href="#Note">Note</a></li>
-</ul>
-<h5><a name="Description">Description</a></h5>
-<p>
-This tool is for X-ray users to calculate the slit size (FWHM/2) 
-for smearing  based on their half beam profile data (SAXSess). 
-</p>
-
-
-<h5><a name="HowTo">HowTo?</a></h5>
-<p>
-To calculate the slit size (FWHM/2), just load the beam profile data using the browse button. </p>
-<p>
-Once a data is loaded, the slit size will be computed and show up in the text box. </p>
-<p>
-Because the unit is not specified in the data file, we do not convert it into 1/A so that users are responsible for converting the unit.
-</p>
-
-<h5><a name="Note">Note: </a></h5>
-This slit size calculator is working only for a beam profile data produced by 'SAXSess'. 
-
-<p>
-To see the file format, check the file, 'beam profile.DAT', in the 'test' folder of SasView. 
-</p>
-</body>
-
-</html>
Index: docs/pre-sphinx-docs/smear_computation_v0.html
===================================================================
--- docs/pre-sphinx-docs/smear_computation_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,283 +1,0 @@
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 12 (filtered)">
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-<p class=MsoNormal><span style='font-size:16.0pt;line-height:115%;font-family:
-"Times New Roman","serif"'><h4>Smear Computation </h4></span></p>
-
-
-<ul style='margin-top:0in' type=disc>
- <li class=MsoNormal style='line-height:115%'><a href="#Slit Smear"><b>Slit Smear</b></a>
-     </li>
- <li class=MsoNormal style='line-height:115%'><a href="#Pinhole Smear"><b>Pinhole Smear</b></a>
-	</li>
- <li class=MsoNormal style='line-height:115%'><a href="#2D Smear"><b>2D Smear</b></a> 
-	</li>
-</ul>
-
-<p class=MsoListParagraph><span style='font-size:14.0pt;line-height:115%;
-font-family:"Times New Roman","serif"'><h5><a name="Slit Smear">Slit Smear</a></h5></span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>The sit
-smeared scattering intensity for SAS is defined by</span></p>
-
-<p class=MsoNormal><img 
-src="img/sm_image002.gif" align=left hspace=12></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>           
-                                 ---- 1)</span><br clear=all>
-<span style='font-family:"Times New Roman","serif"'>where Norm = <span
-style='position:relative;top:15.0pt'><img 
-src="img/sm_image003.gif"></span>.</span></p>
-<br>
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>The
-functions <span style='position:relative;top:6.0pt'><img 
-src="img/sm_image004.gif"></span> and <span style='position:
-relative;top:6.0pt'><img 
-src="img/sm_image005.gif"></span> 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.,</span></p>
-
-<p class=MsoNormal><span style='position:relative;top:7.0pt'><img 
- src="img/sm_image006.gif">                                                                                                       
-  </span><span style='font-family:"Times New Roman","serif";position:relative;
-top:7.0pt'> ---- 2)</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>and </span></p>
-
-<p class=MsoNormal><span style='position:relative;top:7.0pt'><img 
- src="img/sm_image007.gif"></span>,                                                                              
-                         <span style='font-family:"Times New Roman","serif"'> ---- 3)</span></p>
-
-<p>so that <img 
-src="img/sm_image008.gif"> <img src="img/sm_image009.gif">  for <img 
-src="img/sm_image010.gif"> and <i>u</i>. The <img src="img/sm_image011.gif"> 
- and <img src="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 Eq. (1) is simplified to</span></p>
-
-<p class=MsoNormal><img 
-src="img/sm_image013.gif" align=left hspace=12><span
-style='font-family:"Times New Roman","serif"'>                                                  
-          ---- 4)</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif";
-position:relative;top:20.0pt'>&nbsp;</span></p>
-
-<p class=MsoListParagraphCxSpFirst style='margin-left:0in'><b><span
-style='font-family:"Times New Roman","serif"'>Numerical Implementation of Eq.
-(4) </span></b></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;text-indent:-.25in'><span
-style='font-family:"Times New Roman","serif"'>1)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>For </span><span
-style='position:relative;top:6.0pt'><img 
-src="img/sm_image012.gif"></span>= 0  <span style='font-family:
-"Times New Roman","serif"'>and </span><span style='position:relative;
-top:6.0pt'><img src="img/sm_image011.gif"></span> =
-<span style='font-family:"Times New Roman","serif"'>constant:</span></p>
-
-<p>
-<img src="img/sm_image016.gif"></p>
-
-<p> For discrete q values, at the q
-values from the data points and at the q values extended up to  q<sub>N</sub>=
-q<sub>i</sub> +  <img src="img/sm_image011.gif"> , the smeared intensity can be
-calculated approximately, </p>
-
-<p><img 
-src="img/sm_image017.gif">.                                                           
- ---- 5)</p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='position:relative;top:7.0pt'><img 
-src="img/sm_image018.gif"></span> <span style='font-family:
-"Times New Roman","serif"'>= 0 for <i>I<sub>s</sub></i> in</span> <i><span
-style='font-family:"Times New Roman","serif"'>j &lt; i</span></i><span
-style='font-family:"Times New Roman","serif"'> or<i> j&gt;N-1</i>.</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;text-indent:-.25in'><span
-style='font-family:"Times New Roman","serif"'>2)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>For  </span><span
-style='position:relative;top:6.0pt'><img 
-src="img/sm_image012.gif"></span>= <span style='font-family:
-"Times New Roman","serif"'>constant </span> <span style='font-family:"Times New Roman","serif"'>and
-</span><span style='position:relative;top:6.0pt'><img 
-src="img/sm_image011.gif"></span> = <span style='font-family:
-"Times New Roman","serif"'>0:</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>Similarly to 1), we get</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'>
-<img src="img/sm_image019.gif">                                                                                        
-<span style='font-family:"Times New Roman","serif"'> ---- 6)</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>for  q<sub>p</sub> = q<sub>i</sub>
-- </span><span style='position:relative;top:6.0pt'><img 
-src="img/sm_image012.gif"></span><span style='font-family:
-"Times New Roman","serif"'> and</span> <span style='font-family:"Times New Roman","serif"'>q<sub>N</sub>
-= q<sub>i</sub> + </span><span style='position:relative;top:6.0pt'><img
- src="img/sm_image012.gif"></span>.  <span
-style='position:relative;top:7.0pt'><img 
-src="img/sm_image018.gif"></span> <span style='font-family:
-"Times New Roman","serif"'>= 0 for <i>I<sub>s</sub></i> in</span> <i><span
-style='font-family:"Times New Roman","serif"'>j &lt; p</span></i><span
-style='font-family:"Times New Roman","serif"'> or<i> j&gt;N-1</i>.</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'>&nbsp;</p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in;text-indent:-.25in'><span
-style='font-family:"Times New Roman","serif"'>3)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span><span style='font-family:"Times New Roman","serif"'>For  </span><span
-style='position:relative;top:6.0pt'><img 
-src="img/sm_image011.gif"></span>= <span style='font-family:
-"Times New Roman","serif"'>constant </span> <span style='font-family:"Times New Roman","serif"'>and
-</span><span style='position:relative;top:6.0pt'><img 
-src="img/sm_image011.gif"></span> = <span style='font-family:
-"Times New Roman","serif"'>constant:</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>This case, the best way is to
-perform the integration, Eq. (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 &lt;&lt;
-slit hight, is used in the SASView:  This method is a mixed method that
-combines the method 1) with the numerical integration for the slit width.</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'>
-</p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'>
-<img src="img/sm_image020.gif">    <span style='font-family:
-"Times New Roman","serif"'> ---- (7)</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>for  q<sub>p</sub> = q<sub>i</sub>
-- </span><span style='position:relative;top:6.0pt'><img 
-src="img/sm_image012.gif"></span><span style='font-family:
-"Times New Roman","serif"'> and</span> <span style='font-family:"Times New Roman","serif"'>q<sub>N</sub>
-= q<sub>i</sub> + </span><span style='position:relative;top:6.0pt'><img
- src="img/sm_image012.gif"></span>.  <span
-style='position:relative;top:7.0pt'><img 
-src="img/sm_image018.gif"></span> <span style='font-family:
-"Times New Roman","serif"'>= 0 for <i>I<sub>s</sub></i> in</span> <i><span
-style='font-family:"Times New Roman","serif"'>j &lt; p</span></i><span
-style='font-family:"Times New Roman","serif"'> or<i> j&gt;N-1</i>. </span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoListParagraphCxSpLast><span style='font-size:14.0pt;line-height:
-115%;font-family:"Times New Roman","serif"'><h5><a name="Pinhole Smear">Pinhole Smear</a></h5></span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>The
-pinhole smearing computation is done similar to the Case 2) above except that
-the weight function used was the Gaussian function, so that the Eq. 6) for this
-case becomes</span></p>
-
-<p class=MsoNormal><img src="img/sm_image021.gif"><span
-style='font-family:"Times New Roman","serif"'>   ---- (8)</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>For all
-the cases above, the weighting matrix <i>W</i> is calculated when the smearing
-is called at the first time, and it includes the ~ 60 q values (finely binned
-evenly) below (&gt;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 <i>Norm</i> factor is found numerically with the weighting matrix, and
-considered on <i>I<sub>s</sub></i> computation.</span></p>
-
-<p class=MsoListParagraphCxSpFirst style='margin-left:.25in'><span
-style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoListParagraphCxSpLast><span style='font-size:14.0pt;line-height:
-115%;font-family:"Times New Roman","serif"'><h5><a name="2D Smear">2D Smear</a></h5></span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>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</span></p>
-
-<p class=MsoNormal><img src="img/sm_image022.gif"><span
-style='font-family:"Times New Roman","serif"'>     ---- (9)</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>In Eq
-(9), x<sub>0</sub> = qcos&#952;</span><span
-style='font-family:"Times New Roman","serif"'> and y<sub>0</sub> = qsin&#952;</span><span style='font-family:"Times New Roman","serif"'>
-, and the primed axes are in the coordinate rotated by an angle &#952;</span><span style='font-family:"Times New Roman","serif"'>
-around z-axis (below) so that x<sub>0</sub> =  x<sub>0</sub>cos&#952; + </span><span style='font-family:"Times New Roman","serif"'>y<sub>0</sub>
-sin&#952;  </span><span style='font-family:
-"Times New Roman","serif"'>and y<sub>0</sub> =  -x<sub>0</sub>sin&#952; + </span><span style='font-family:"Times New Roman","serif"'>y<sub>0</sub>
-cos&#952;.</span><span style='font-family:
-"Times New Roman","serif"'> Note that the rotation angle is zero for x-y
-symmetric elliptical Gaussian distribution</span>.
-<span style='font-family:"Times New Roman","serif"'>The  A is a
-normalization factor.</span></p>
-
-<p class=MsoNormal align=center style='text-align:center'><span
-style='font-family:"Times New Roman","serif"'><img 
-id="Object 1" src="img/sm_image023.gif"></span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>&nbsp;</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>Now we
-consider a numerical integration where each bins in </span> &#920; </span><span style='font-family:"Times New Roman","serif"'>
-and R are <b>evenly </b>(this is to simplify the equation below) distributed by
-</span>&#916;&#920; </span><span style='font-family:
-"Times New Roman","serif"'>and </span> &#916;</span><span
-style='font-family:"Times New Roman","serif"'>R, respectively, and it is
-assumed that I(x, y) is constant within the bins which in turn becomes</span></p>
-
-<p class=MsoNormal><img src="img/sm_image024.gif"></p>
-
-<p class=MsoNormal>                                                                                                                                                                                <span
-style='font-family:"Times New Roman","serif"'> ---- (10)</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>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 -&#952;</span><span style='font-family:"Times New Roman","serif"'>
-around z axis).  Then, for the polar symmetric smear,</span></p>
-
-<p class=MsoNormal><img src="img/sm_image025.gif"><span
-style='position:relative;top:35.0pt'>      </span> ---- (11)</p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>where,</span></p>
-
-<p class=MsoNormal><img src="img/sm_image026.gif">,</p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>while
-for the x-y symmetric smear,</span></p>
-
-<p class=MsoNormal><img src="img/sm_image027.gif"><span
-style='font-family:"Times New Roman","serif"'>  ---- (12)</span></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>where,</span></p>
-
-<p class=MsoNormal><img src="img/sm_image028.gif"></p>
-
-<p class=MsoNormal><span style='font-family:"Times New Roman","serif"'>Here, the
-current version of the SASVIEW uses the Eq. (11) for 2D smearing assuming that
-all the Gaussian weighting functions are aligned in the polar coordinate. </span></p>
-<p> In the control panel, the higher accuracy indicates more and finer binnng points 
-so that it costs more in time. </p>
-
-
-</div>
-
-</body>
-
Index: docs/pre-sphinx-docs/status_bar_help_v0.html
===================================================================
--- docs/pre-sphinx-docs/status_bar_help_v0.html	(revision 54b9ad250e663e6be56b32ad102c67ec8f762b14)
+++ 	(revision )
@@ -1,25 +1,0 @@
-<html>
-<body>
-
-<h4>Status Bar Help</h4>
-<ul>
-<li><a href="#message">Message, Warning, Hint</a></li>
-<li><a href="#console">Console</a></li>
-</ul>
-
-<h5><a name="message">Message, Warning, Hint</a></h5>
-<p> 
-The status bar located at the bottom of the application frame, displays messages,
-hints, warnings and errors.
-</p>
-
-<h5><a name="console">Console</a></h5>
-<p>
-Select <b> light bulb/info icon </b> 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.
-</p>
-
-
-</body>
-</html>
