Merge pull request #28190 from mantidproject/27839_Update_Muon_user_docs

Update Muon user documentation

docs/source/interfaces/Frequency Domain Analysis.rst

@@ -42,6 +42,7 @@ Tabs
 
 All these tabs can be dragged away from the interface into their own window.
 
+* :ref:`Plotting Window <muon_plotting_window-ref>`
 * :ref:`Home Tab <muon_home_tab-ref>`
 * :ref:`Grouping Tab <muon_grouping_tab-ref>`
 * :ref:`Phase Table Tab <muon_phase_table_tab-ref>`

docs/source/interfaces/Muon Analysis 2.rst

@@ -40,10 +40,12 @@ Tabs
 
 All these tabs can be dragged away from the interface into their own window.
 
+* :ref:`Plotting Window <muon_plotting_window-ref>`
 * :ref:`Home Tab <muon_home_tab-ref>`
 * :ref:`Grouping Tab <muon_grouping_tab-ref>`
 * :ref:`Phase Table Tab <muon_phase_table_tab-ref>`
 * :ref:`Fitting Tab <muon_fitting_tab-ref>`
+* :ref:`Sequential Fitting Tab <muon_sequential_fitting_tab-ref>`
 * :ref:`Results Table Tab <muon_results_tab-ref>`
 
 Feedback & Comments

docs/source/interfaces/muon_fitting_tab.rst

@@ -5,49 +5,22 @@ Fitting Tab
 
 .. image::  ../images/muon_interface_tab_fitting.png
    :align: right
-   :height: 500px
+   :height: 400px
 
-This tab is for performing fits on the data.
+This tab is used to evaluate a single fit object, which corresponds to a list of one or more input workspaces and a fit function.
 
-**Fit** Executes the chosen fit for the fitting functions to the selected data.
-
-**Single Fit** This option performs a fit for a single data set.
-
-**Sequential Fit** This option will perform multiple fits sequentially, using the output of the previous fit as the starting guess. 
+**Fit** Executes the specified fit.
 
 **Simultaneous Fit** This option will perform a fit for multiple data sets, which may share parameters. 
+The simultaneous fit can be performed over a selected run, or selected group/pair. 
 
-**Select data to fit** This launches a dialog box for selecting the data to be used in the fit.
-
-Data Selection
-^^^^^^^^^^^^^^
-
-.. image::  ../images/muon_interface_data_selection.png
-   :height: 250px
-
-**Search bar** The search bar can be used to find (Include) or filter out (Exclude) data sets by name.
-
-**Show Selected** If this option is checked the selection box will be limited to only the data sets that have already
-been selected to be output.
-
-**Selection Box** data sets are listed in this section, they can be selected individually by checking the boxes on the
-right side of the box.
-
-**Unselect/Select All** When clicked these buttons will automatically unselect or select all log values currently in the
-selection box
-
-**Run selection** Filter displayed data sets by run number
-
-**Group & Pair selection** filter by group or pair name.
-
-**Show PhaseQuad** If this option is checked the selection box will show any PhaseQuads that have been calculated for these runs.
-
+**Select Workspace** This drop-down list can be used select the workspace to perform a single fit over.
 
 Fit function browser
 ^^^^^^^^^^^^^^^^^^^^
 
 .. image::  ../images/muon_interface_tab_fitting_browser.png
-   :height: 250px
+   :height: 125px
 
 Right clicking in the central box will bring up a context menu for adding or removing functions.
 The fitting browser here is similar to that used in the :ref:`Multi-dataset Fitting Interface <Multi-dataset-Fitting-Interface>`.
@@ -55,11 +28,9 @@ The fitting browser here is similar to that used in the :ref:`Multi-dataset Fitt
 **Property** This is a list of property names, individual functions can be collapsed down for greater legibility.
 
 **Value** This lists the initial guesses for variables within fitting functions. Variables can be fixed for a given fit
-from the edit paramiter values dialog box (the ellipsis to the right of the value box)
-
-**Global** If multiple runs are being plotted then variables can be made identical for each run by checking the box next to it.
+from the edit paramiter values dialog box (the ellipsis to the right of the value box).
 
-All selected workspaces will share the same composite fitting function but can have different variables.
+**Global** If we are performing a simultaneous fit, parameters for each workspace in the fit can be tied by checking this box.
 
 Fit properties browser
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -73,8 +44,10 @@ If it is unchecked it will use the rebinned data as specified on the home tab.
 
 **Evaluate Function As** Select if to fit to histogram or point data.
 
+**TF Asymmetry Mode** Evaluate the fit in TF asymmetry mode, see :ref:`Calculate Muon Asymmetry <algm-CalculateMuonAsymmetry>`.
+
 Used By
 ^^^^^^^
 
-:ref:`Muon Analysis 2 <MuonAnalysis_2-ref>`
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`
 :ref:`Frequency Domain Analysis <Frequency_Domain_Analysis_2-ref>`

docs/source/interfaces/muon_grouping_tab.rst

@@ -5,20 +5,22 @@ Grouping Tab
 
 .. image::  ../images/muon_interface_tab_grouping.png
    :align: right
-   :height: 500px
+   :height: 400px
 
-**Load** Allows a grouping and pairing table xml file to be selected to load
+**Load** Allows a grouping and pairing table xml file to be selected to load.
 
-**Save** Saves the current grouping and pairing tables to an xml file
+**Save** Saves the current grouping and pairing tables to an xml file.
 
-**Clear** Clears all groups and pairs from the current tables
+**Clear** Clears all groups and pairs from the current tables.
 
-**Default** Loads in the default groups and pairs for the instrument
+**Default** Loads in the default groups and pairs for the instrument.
 
 Grouping Table
 ^^^^^^^^^^^^^^
 
-**Plus and Minus** Add or remove groups
+**Analyse (plot/fit)** Whether the selected group is included in the plot and fitting.
+
+**Plus and Minus** Add or remove groups.
 
 **Context Menu Pair Selection** Right clicking over the grouping table, when two groups are selected, allows a pair to be created with a specified name.
 
@@ -29,12 +31,20 @@ but may be overridden here if required.
 Pairing Table
 ^^^^^^^^^^^^^
 
-**Plus and Minus** Add or remove pairs
+**Analyse (plot/fit)** Whether the selected pair is included in the plot and fitting.
+
+**Plus and Minus** Add or remove pairs.
 
 **Guess Alpha** Estimates the alpha for the current pair and recalculates.
 
+Multi-Period Data
+^^^^^^^^^^^^^^^^^^^
+
+For multi period data, the summed and subratcted periods are specfied at the bottom of the tab. These periods will be used for all 
+the groups and pairs.
+
 Used By
 ^^^^^^^
 
-:ref:`Muon Analysis 2 <MuonAnalysis_2-ref>`,
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`,
 :ref:`Frequency Domain Analysis <Frequency_Domain_Analysis_2-ref>`
\ No newline at end of file

docs/source/interfaces/muon_home_tab.rst

@@ -5,12 +5,12 @@ Home Tab
 
 .. image::  ../images/muon_interface_tab_home.png
    :align: right
-   :height: 500px
+   :height: 400px
 
 Pre-processing parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-**Instrument** This selects the instrument used by the GUI
+**Instrument** This selects the instrument used by the GUI.
 
 **Time Zero** This is the time zero value used. By default the time zero is taken from the file but
 it can be specified here in which case the specified time zero is used for all calculations.
@@ -34,14 +34,8 @@ Rebin
 
 **Variable** Variable binning allows a string to be entered which specifies the required binning. The string is of the format used by the :ref:`Rebin <algm-Rebin>` algorithm.
 
-Groups and Pairs
-^^^^^^^^^^^^^^^^
-
-**Periods** For multi period data the Summed and Subracted periods may be specified here. These periods will then be used for
-all groups and pairs.
-
 Used By
 ^^^^^^^
 
-:ref:`Muon Analysis 2 <MuonAnalysis_2-ref>`,
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`,
 :ref:`Frequency Domain Analysis <Frequency_Domain_Analysis_2-ref>`

docs/source/interfaces/muon_phase_table_tab.rst

@@ -5,7 +5,7 @@ Phase Table Tab
 
 .. image::  ../images/muon_interface_tab_phase_table.png
    :align: right
-   :height: 500px
+   :height: 400px
 
 Phase Table Calculator
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -38,5 +38,5 @@ into a quadrature phase signal.
 Used By
 ^^^^^^^
 
-:ref:`Muon Analysis 2 <MuonAnalysis_2-ref>`,
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`,
 :ref:`Frequency Domain Analysis <Frequency_Domain_Analysis_2-ref>`
\ No newline at end of file

docs/source/interfaces/muon_plotting_window.rst

+.. _muon_plotting_window-ref:
+
+Plotting Window
+-----------------
+
+.. image::  ../images/muon_plotting_window.png
+   :align: right
+   :width: 350px
+
+
+The plotting window displays the data specified by the tabs within the interface. This data can be displayed as a single plot, 
+or as tiled plots, where each tile corresponds to either a Group/pair or a run.
+By default this plot window is docked to the right-hand side of the main interface window, but can be undocked by
+double-clicking on the title bar of the window. 
+
+Plotting Controls 
+^^^^^^^^^^^^^^^^^
+The plotting can be controlled through serveral options:
+
+**Plot type** Changes the plot type (e.g from asymmetry to counts). 
+
+**Tiled plotting** The 'tile plots by' checkbox enables tiled plotting, which can be performed over runs or Groups/pairs.
+
+**Plot raw** Plot raw controls whether the raw or rebinned workspaces are plotted. 
+
+.. image::  ../images/muon_plotting_window_tiled.png
+   :width: 350px
+   :align: right
+
+Plotting Options
+^^^^^^^^^^^^^^^^^
+.. image::  ../images/muon_plotting_window_options.png
+   :height: 40px
+
+**Subplot Selector** Which axis to change the options for. 
+
+**x-Range** Sets the x-limits for the selected axes.
+
+**Autoscale** Autoscales the y-axis based on the x-limits. 
+
+**y-Range**  Sets the y-limits for the selected axes.
+
+**Errors** Whether to display errors for the workspaces plotted on the selected axes. 
+
+
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`
+:ref:`Frequency Domain Analysis <Frequency_Domain_Analysis_2-ref>`

docs/source/interfaces/muon_results_tab.rst

@@ -5,7 +5,7 @@ Results Table Tab
 
 .. image::  ../images/muon_interface_tab_results.png
    :align: right
-   :height: 500px
+   :height: 400px
 
 The results table tab outputs the results from the fitting tab as well as the log values from selected runs into a
 tableworkspace.
@@ -55,5 +55,5 @@ Output
 Used By
 ^^^^^^^
 
-:ref:`Muon Analysis 2 <MuonAnalysis_2-ref>`
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`
 :ref:`Frequency Domain Analysis <Frequency_Domain_Analysis_2-ref>`

docs/source/interfaces/muon_sequential_fitting_tab.rst

+.. _muon_sequential_fitting_tab-ref:
+
+Sequential Fitting Tab
+------------------------
+
+.. image::  ../images/muon_interface_tab_sequential_fitting.png
+   :align: right
+   :height: 400px
+
+This tab allows the user to perform sequential fits. The sequential fits are based on the fit function specified in the fitting tab.
+The primary widget in this tab is the Fit Table, which is automatically generated based on the selected Groups/pairs and the fit function defined
+in the fitting tab.
+
+Sequential fitting options
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+**Sequentially Fit** Sequentiailly fits each of the fit objects specified in the fit table.
+
+**Fit selected** Performs a fit on the fit object selected in the table.
+
+**Plot fit results** Determines whether the results of the fit will be added to the plot window.
+
+**Parameters for previous fit** Uses the parameters from the previous fit calculation as initial values for the next fit. 
+
+**Initial parameters for each fit** Uses the initial values (as specified in the Fit Table) in each fit calculation.
+
+Fit Table
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Each entry of the Fit Table corresponds to a fit object, which comprises a list of input workspaces and a fit function. 
+
+**Run** The runs present in the fit object.
+
+**Groups/pairs** The groups/pairs present in the fit object.
+
+**Fit quality** The quality of the fit returned from the fitting algorithm.
+
+**List of fit parameters** The columns that proceed this correspond to the values of the fit parameters. The value of these
+parameters can be edited. 
+
+
+Used By
+^^^^^^^
+
+:ref:`Muon Analysis <MuonAnalysis_2-ref>`