Adds user guide for terminal, plot and controls windows

doc/source/user/control.rst

@@ -1,2 +1,57 @@
 Controls Window
 ===============
+The fitting controls window allows the user select and configure a fit procedure, start/stop a fit, and view
+the final chi-squared from a fit.
+
+.. image:: ../images/controls_window.png
+   :scale: 80
+   :alt: Fitting Controls Window
+   :align: center
+
+RasCAL-2 exposes different fit procedures from the Reflectivity Algorithm Toolbox (RAT), a different procedure can
+be selected in the procedure dropdown box. When the procedure is changed, the options on the right side of the window
+will be updated to match the selected procedure. RAT has |general options| which are available for all procedures and
+unique options for each procedure:
+
+1. |simplex|
+2. |de|
+3. |ns|
+4. |dream|
+
+After selecting and configuring a procedure, a fit can be started by clicking the **Run** button, starting a fit will
+disable the **Run** button and enable the **Stop** button, to stop a fit simply click the **Stop** button, stopping a
+fit will disable the **Stop** button and enable the **Run** button. The **Run** button will be re-enabled if the fit
+finishes without being stopped.
+
+.. note:: A calculation cannot be started while editing the project, the control window will be
+   disabled until the project is saved.
+
+.. image:: ../images/controls_window_running.png
+   :scale: 80
+   :alt: Fitting Controls Window with Active Run
+   :align: center
+
+If the selected procedure is Simplex or DE, stopping a fit before completion will return the current best result, the
+current chi-squared textbox will show the best value during the fit. For the remaining procedures, stopping a fit will
+not return a result and the current chi-squared textbox is only updated on fit completion.
+
+
+.. |general options| raw:: html
+
+   <a href="https://rascalsoftware.github.io/RAT-Docs/1.0/tutorial/controls.html#general-parameters-for-the-controls-class/" target="_blank">general options</a>
+
+.. |simplex| raw:: html
+
+   <a href="https://rascalsoftware.github.io/RAT-Docs/1.0/algorithms/simplex.html" target="_blank">Simplex</a>
+
+.. |de| raw:: html
+
+   <a href="https://rascalsoftware.github.io/RAT-Docs/1.0/algorithms/DE.html" target="_blank">Differential Evolution (de)</a>
+
+.. |ns| raw:: html
+
+   <a href="https://rascalsoftware.github.io/RAT-Docs/1.0/algorithms/nestedSampling.html" target="_blank">Nested Sampler (ns)</a>
+
+.. |dream| raw:: html
+
+   <a href="https://rascalsoftware.github.io/RAT-Docs/1.0/algorithms/DREAM.html" target="_blank">DREAM</a>

doc/source/user/plot.rst

@@ -1,2 +1,120 @@
 Plot Window
 ===========
+The plot window displays plots of the reflectivity curve and SLD profile. The plots are automatically updated
+whenever the results are updated.
+
+Overview
+--------
+The plot window provides a pan and zoom tool for interacting with the plots. Clicking on the |pan| button will enable
+panning and the plots can be panned around by clicking and dragging with the left mouse button. Click the
+|pan| button again to disable panning. Clicking on the |zoom| button will enable zooming and the plots can be zoomed
+into by clicking and dragging with the left mouse button to select a region. Click the |zoom| button again to disable
+zooming. After panning or zooming, the plots can be reset by clicking the |reset| button. Without a reset, the plot
+will keep any zoom or pan until it is updated.
+
+The spacing between reflectivity curves in the plot can be adjusted using the slider on the left of the plots, simply
+drag and release the slider to change the spacing. The maximum spacing is achieved when the slider is dragged to the
+bottom of the window.
+
+.. image:: ../images/plots_window.png
+   :scale: 80
+   :alt: Plots Window
+   :align: center
+
+The plot window provides more options for customising the plots in a side panel, the |options| button toggles the
+visibility of the side panel which can be hidden to amke the plots slightly bigger. The side panel contains the
+following options:
+
+1. **X-Axis**: sets the X-Axis of the reflectivity curve to linear or log scale.
+2. **Y-Axis**: sets the Y-Axis of the reflectivity curve to show ref or Q^4.
+3. **Show Error Bars**: toggle the error bars in the reflectivity curve plot.
+4. **Show Grid**: toggles a grid in both plots.
+5. **Show Legend**: toggles the legend in both plots.
+
+.. image:: ../images/plots_window_settings.png
+   :scale: 80
+   :alt: Plots Window Settings
+   :align: center
+
+Bayesian Plots
+--------------
+After running a Bayesian fit, click the **View Bayes Plots** button in the top right of the plot window to view and
+customize plots from the Bayesian analysis. This will open the **Bayes Results** dialog which contains the following
+sections:
+
+.. note:: The **View Bayes Plots** button will only be visible after a Bayesian fit is completed, it will be hidden
+   for non-Bayesian fits.
+
+1. **Shaded Plot**: This displays a shaded plot with a 65% or 95% confidence interval for the Bayesian analysis. The
+confidence interval can be changed using the dropdown in the left side panel.
+
+.. image:: ../images/bayes_results_shaded_plot.png
+   :scale: 60
+   :alt: Bayes Results Dialog showing Shaded Plot
+   :align: center
+
+2. **Posteriors**: This displays the marginalised posteriors for selected parameters from the Bayesian analysis. In the
+left side panel, the desired parameters to plot can be selected, plot smoothing can be applied or removed, and estimated
+density can be plotted using 3 different methods (normal, log-normal, and KDE).
+
+.. image:: ../images/bayes_results_posteriors.png
+   :scale: 60
+   :alt: Bayes Results Dialog showing Parameter Values
+   :align: center
+
+3. **Diagnostics**: This displays the MCMC chain for selected parameters from the Bayesian analysis. In the left side
+panel, the desired parameters to plot can be selected, and the maximum number of points to plot can also be adjusted.
+
+.. image:: ../images/bayes_results_diagnostics.png
+   :scale: 60
+   :alt: Bayes Results Dialog showing Parameter Values
+   :align: center
+
+4. **Corner Plot**: This displays the corner plot for selected parameters from the Bayesian analysis. To improve
+responsiveness, the corner plot is not drawn immediately, the **Update Plot** button in the left side panel can be
+used to draw the plot as needed. Clicking the **Update Plot** button will start rendering the plots in the background,
+the button text will show render progress, and the plots will be displayed when rendering is completed. The desired
+parameters to plot can also be selected in the side panel, and plot smoothing can be applied or removed.
+
+.. image:: ../images/bayes_results_corner_plot_empty.png
+   :scale: 60
+   :alt: Bayes Results Dialog showing Parameter Values
+   :align: center
+
+.. image:: ../images/bayes_results_corner_plot.png
+   :scale: 60
+   :alt: Bayes Results Dialog showing Parameter Values
+   :align: center
+
+
+5. **Parameter Values**: This displays the mean, 65% and 95% confidence interval values for the fitted parameters in
+the Bayesian analysis.
+
+.. image:: ../images/bayes_results_parameter_values.png
+   :scale: 60
+   :alt: Bayes Results Dialog showing Parameter Values
+   :align: center
+
+Exporting a Plot
+----------------
+To export any given plot as an image:
+
+1. Click the **Export Plot** button at the bottom of the left side panel.
+2. Navigate to the desired save location in the file dialog
+3. Enter a name for the file and press the **Save** button.
+
+The plot will be saved as png file with a white background by default, the background can be made transparent
+by changing the **Export Background Colour** option to **none** in Settings dialog
+
+
+.. |options| image:: ../images/settings.png
+            :scale: 10
+
+.. |reset| image:: ../images/refresh.png
+            :scale: 10
+
+.. |pan| image:: ../images/pan.png
+            :scale: 10
+
+.. |zoom| image:: ../images/zoom.png
+            :scale: 10

doc/source/user/terminal.rst

@@ -1,2 +1,34 @@
 Terminal Window
 ===============
+The terminal window displays fit status, error messages and other information to the user. Messages could
+be displayed when modifying a project, running a fit, or when an unexpected issue is encountered. The text
+in the terminal cannot be modified but can be selected and copied, the text will be cleared automatically when a
+new fit is started but can be cleared manually by clicking *Tools > Clear Terminal* in the menu.
+
+.. image:: ../images/terminal_window.png
+   :scale: 80
+   :alt: Terminal Window
+   :align: center
+
+During a fit, the window will inform the user when the run is started, finished, or stopped by user. It will
+also show the progress of the fit, the format of the progress information will vary with the procedure e.g. Most
+procedures will print a new line of information text as the fit is progressing, but the DREAM procedure will print
+a setting summary and show the progress of the fit in a progress bar at the bottom of the window.
+
+.. note::
+  The amount of information printed during a fit can be customised using the  `display` or `updateFreq` options
+  in the controls window.
+
+.. image:: ../images/terminal_window_run_info.png
+   :scale: 80
+   :alt: Terminal Window showing Run Information
+   :align: center
+
+If an error occurs during project validation or a fit, an error message would be displayed with red text,
+sometimes the message could contain extra debug information which shows the line of code where the error occurred,
+this debug information is useful for finding problems with custom files.
+
+.. image:: ../images/terminal_window_error.png
+   :scale: 80
+   :alt: Terminal Window showing Error Message
+   :align: center

rascal2/widgets/plot.py

@@ -40,7 +40,7 @@ def __init__(self, parent):
         layout.setContentsMargins(0, 5, 0, 5)
         self.setLayout(layout)
 
-        self.bayes_plots_button = QtWidgets.QPushButton("View Bayes plots", objectName="InteractButton")
+        self.bayes_plots_button = QtWidgets.QPushButton("View Bayes Plots", objectName="InteractButton")
         self.bayes_plots_button.setVisible(False)
         self.bayes_plots_button.pressed.connect(self.show_bayes_plots)
         self.reflectivity_plot.interaction_layout.addWidget(self.bayes_plots_button)
@@ -84,7 +84,7 @@ def __init__(self, parent, initial_plot_settings: list):
         self.plot_tabs = QtWidgets.QTabWidget()
 
         plots = {
-            "Shaded plot": ShadedPlotWidget,
+            "Shaded Plot": ShadedPlotWidget,
             "Posteriors": HistPlotWidget,
             "Diagnostics": ChainPlotWidget,
             "Corner Plot": CornerPlotWidget,

rascal2/widgets/project/project.py

@@ -117,7 +117,7 @@ def create_project_view(self) -> QtWidgets.QWidget:
         main_layout = QtWidgets.QVBoxLayout()
         main_layout.setSpacing(20)
 
-        show_sliders_button = QtWidgets.QPushButton("Show sliders")
+        show_sliders_button = QtWidgets.QPushButton("Show Sliders")
         show_sliders_button.clicked.connect(self.parent.toggle_sliders)
 
         self.edit_project_button = QtWidgets.QPushButton("Edit Project", icon=QtGui.QIcon(IconEngine("edit-light.png")))