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MSlice Testing¶

Introduction ¶

MSlice is a tool for visualizing cuts and slices of inelastic neutron scattering data. This version uses Mantid to process the data and plots it using matplotlib. It includes both a GUI and a commandline interface with a script generator.

See here for the current MSlice documentation: http://mantidproject.github.io/mslice

Set Up ¶

Ensure you have the ISIS Sample Data available on your machine.
If you are using a conda install of Mantid Workbench, make sure to install MSlice by running mamba install -c mantid mslice inside your conda enviroment and restart the Mantid Workbench.
If you are using a standalone install of Mantid Workbench, MSlice should already be available within it.
Open Interfaces > Direct > MSlice
Go to the Data Loading tab and select MAR21335_Ei60meV.nxs from the sample data.
Click Load Data
This should open the Workspace Manager tab with a workspace called MAR21335_Ei60meV

Default Settings ¶

In the Options menu, change Default Energy Units from meV to cm-1 and Cut algorithm default from Rebin (Averages Counts) to Integration (Sum Counts).
The en setting on the Slice tab changes from meV to cm-1 and the values in the row labelled y change. Please note that the Slice and Cut tabs are not enabled before at least one data set has been loaded.
Navigate to the Cut tab
Verify that en is set to cm-1 and Cut Algorithm to Integration (Sum Counts)
Change both settings back to their original values, Default Energy Units to meV and Cut algorithm default to Rebin (Averages Counts).

Taking Slices ¶

1. Plotting a Slice ¶

In the Workspace Manager tab select the workspace MAR21335_Ei60meV
Click Display in the Slice tab without changing the default values
On the slice plot, click Keep

2. Modifying a Slice ¶

Modify the slice settings in the Slice tab, for instance the values for x for from to 1.5 and to to 5.5 , and click Display
A second slice plot should open with a plot reflecting your changes in the settings
The original slice plot should remain unchanged

3. The Plots Tab ¶

Navigate to the Plots tab of MSlice and check that there are entries for two plots
Open the Plots tab of Mantid and check that there are no entries for plots
Select one of the plots in the Plots tab of MSlice and click on Hide, the corresponding plot should disappear
Now click on Show for this plot and it should re-appear again
Double-click on elements of the original slice plot and modify settings, for instance the plot itself and the colorbar axes
Change the plot title and the y axis label to LaTeX, for instance $\mathrm{\AA}^{-1}$ , and ensure the text is displayed correctly (for $\mathrm{\AA}^{-1}$ it should be $\mathrm{\AA}^{-1}$)
Ensure that the slice plot changes accordingly
Click Make Current on the original slice plot
Modify the slice settings in the Slice tab again and click Display
This time the new slice plot overwrites the original slice plot

4. Overplot Recoil Lines and Bragg Peaks ¶

Navigate to the Information menu on the slice plot
Select Hydrogen from the submenu for Recoil lines. A blue line should appear on the slice plot.
Select two or three materials from the submenu for Bragg peaks and ensure that Bragg peaks in different colours per material are plotted on the slice plot.
Make sure that when deselecting one of the materials only the respective Bragg peaks are removed from the slice plot but the ones still selected remain.

5. Generate a Script ¶

Navigate to the File menu on the slice plot
Select Generate Script to Clipboard and paste the script into the Mantid editor. Please note that on Linux Ctrl + V might not work as expected. Use shift insert instead in this case.
Run the script and check that the same slice plot is displayed

Taking Cuts ¶

1. Plotting a Cut ¶

In the Workspace Manager tab select the workspace MAR21335_Ei60meV
Navigate to the Cut tab
In the row labelled along, set the from value to 0 and the to value to 10
In the row labelled over, set the from value to -5 and the to value to 5
Click Plot. A new window with a cut plot should open.

2. Changing the intensity of a Cut ¶

Navigate to the Intensity menu on the cut plot
Select Chi''(Q,E) and set a value of 100
The y axis of the cut plot should change to a higher maximal value

3. Modifying a Cut ¶

Check that the menu item Recoil lines is disabled within the menu item Information.
Modify the step size on the Cut tab to 0.02 and click Plot Over. A second cut should appear on the cut plot in a different colour.
Click on Plot Options on the cut plot and modify settings
Ensure that the cut plot changes accordingly
Click on Save to Workbench on the Cut tab and check that in Mantid a workspace with the name MAR21335_Ei60meV_cut(-5.000,5.000) appears. In case there are several cuts with the same parameter, these workspaces are differentiated by appending an index, so there might be a workspace named MAR21335_Ei60meV_cut(-5.000,5.000)_(2) instead.
In the row labelled over, set the from value to -1 and the to value to 1 and click Plot
Navigate to the tab MD Histo tab and check that there are at least two entries, MAR21335_Ei60meV_cut(-5.000,5.000) and MAR21335_Ei60meV_cut(-1.000,1.000). Please note that there might be more entries from the previous tests.
Select MAR21335_Ei60meV_cut(-1.000,1.000) and click Save to Workbench
Check that in Mantid a workspace with the name MAR21335_Ei60meV_cut(-1.000,1.000) appears
Navigate to the Cut tab
In the row labelled along, select DeltaE
In the row labelled over, select 2Theta
In the row labelled along, set the from value to -5 and the to value to 5
In the row labelled over, set the from value to 30 and the to value to 60
Click Plot
Depending on the cutting algorithm, the plot will look similar to the plot below when using the integration method

and similar to the plot below when using the rebin method.

4. Interactive Cuts ¶

Navigate to the Slice tab of the Workspace Manager tab
Click Display in the Slice tab without changing the default values
On the slice plot, select Interactive Cuts
Use the cursor to select a rectangular region in the slice plot. A second window with a cut plot should open.
Check that the menu item Intensity is disabled as well as the item Recoil lines within the menu item Information in the new plot window
Check that the File menu only has one menu item, Close
Change the rectangle by changing its size or dragging it to a different area of the slice plot. The cut plot should update accordingly.
Click on Save Cut to Workspace and check the MD Histo tab of the Workspace Manager to verify that the new workspace was added
Click on Flip Integration Axis. The x axis label changes from Energy Transfer (meV) to $|Q| (\mathrm{\AA}^{-1})$ or vice versa, depending on the initial label.

5. Overplot Bragg Peaks ¶

Navigate to the Information menu on the cut plot
Select Aluminium from the submenu for Bragg peaks. Green lines should appear on the cut plot with a respective legend entry.
Deselect Aluminium form the submenu for Bragg peaks. Both green lines and the respective legend entry should disappear.

6. Generate a Script ¶

Navigate to the Cut tab
In the row labelled along, select |Q| and set the from value to 0 and the to value to 10
In the row labelled over, set the from value to -5 and the to value to 5
Click Plot. A new window with a cut plot should open.
Navigate to the Information menu on the cut plot
Select Aluminium from the submenu for Bragg peaks. Green lines should appear on the cut plot with a respective legend entry.
Navigate to the File menu on a cut plot. Please note that this needs to be a cut plot created via the Cut tab and not an interactive cut.
Select Generate Script to Clipboard and paste the script into the Mantid editor. Please note that on Linux Ctrl + V might not work as expected. Use shift insert instead in this case.
Run the script and check that the same cut plot is displayed

The Command Line Interface ¶

1. Use the Mantid Editor ¶

Close all plots currently open but not the MSlice interface
Copy the following code into the Mantid editor. You might have to modify the file path for the Load command to the correct location of MAR21335_Ei60meV.nxs.

import mslice.cli as mc

ws = mc.Load('C:\\MAR21335_Ei60meV.nxs')
wsq = mc.Cut(ws, '|Q|', 'DeltaE, -1, 1')
mc.PlotCut(wsq)

ws2d = mc.Slice(ws, '|Q|, 0, 10, 0.01', 'DeltaE, -5, 55, 0.5')
mc.PlotSlice(ws2d)

2. Run an Example Script ¶

Run the script.
There should be two new windows with a slice plot and a cut plot

3. Use the Jupyter QtConsole ¶

Repeat the same test by copying the script into the Jupyter QtConsole of the MSlice interface

4. Run Another Example Script in the Mantid Editor ¶

Select the MAR21335_Ei60meV workspace in the Workspace Manager, click Compose and then Scale
Enter a scale factor of 1.0 and click Ok
Select the MAR21335_Ei60meV workspace again and click Subtract
Select the MAR21335_Ei60meV_scaled workspace and leave the self-shielding factor as 1.0, then click Ok
Select the MAR21335_Ei60meV_subtracted workspace and click Display in the Slice tab
Verify that all values are zeros
Navigate to the File menu on the slice plot, select Generate Script to Clipboard and paste the script into the Mantid editor
Close the slice plot with all zeros
Run the script in the Mantid editor and verify that a slice plot with all zeros is reproduced