\(\renewcommand\AA{\mathring{A}}\)

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

1. Ensure you have the ISIS Sample Data available on your machine.

2. Open Interfaces > Direct > MSlice

3. Go to the Data Loading tab and select MAR21335_Ei60meV.nxs from the sample data.

4. Click Load Data

5. This should open the Workspace Manager tab with a workspace called MAR21335_Ei60meV

Default Settings

1. 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).

2. The en setting on the Slice tab changes from meV to cm-1 and the values in the row labelled y change.

3. Navigate to the Cut tab

4. Verify that en is set to cm-1 and Cut Algorithm to Integration (Sum Counts)

5. 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

1. In the Workspace Manager tab select the workspace MAR21335_Ei60meV

2. Click Display in the Slice tab without changing the default values

3. On the slice plot, click Keep

2. Modifying a Slice

1. 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

2. A second slice plot should open with a plot reflecting your changes in the settings

3. The original slice plot should remain unchanged

3. The Plots Tab

1. Navigate to the Plots tab of MSlice and check that there are entries for two plots

2. Open the Plots tab of Mantid and check that there are no entries for plots

3. Select one of the plots in the Plots tab of MSlice and click on Hide, the corresponding plot should disappear

4. Now click on Show for this plot and it should re-appear again

5. Double-click on elements of the original slice plot and modify settings, for instance the plot itself and the colorbar axes

6. 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 \(\mathrm{\AA}^{-1}\))

7. Ensure that the slice plot changes accordingly

8. Click Make Current on the original slice plot

9. Modify the slice settings in the Slice tab again and click Display

10. This time the new slice plot overwrites the original slice plot

4. Overplot Recoil Lines and Bragg Peaks

1. Navigate to the Information menu on the slice plot

2. Select Hydrogen from the submenu for Recoil lines. A blue line should appear on the slice plot.

3. 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.

4. 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. The Plot Toolbar

1. In the plot window, check that the following buttons are working as expected: Zoom in, Zoom out, Legends (add a recoil line to display a legend first), Save, Copy, Print and Plot Options. Modify plot options and make sure that the plot changes accordingly.

6. Generate a Script

1. Navigate to the File menu on the slice plot

2. 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.

3. Run the script and check that the same slice plot is displayed

Taking Cuts

1. Plotting a Cut

1. In the Workspace Manager tab select the workspace MAR21335_Ei60meV

2. Navigate to the Cut tab

3. In the row labelled along, set the from value to 0 and the to value to 10

4. In the row labelled over, set the from value to -5 and the to value to 5

5. Click Plot. A new window with a cut plot should open.

2. Changing the intensity of a Cut

1. Navigate to the Intensity menu on the cut plot

2. Select Chi''(Q,E) and set a value of 100

3. The y axis of the cut plot should change to a higher maximal value

3. Modifying a Cut

1. Check that the menu item Recoil lines is disabled within the menu item Information.

2. 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.

3. Click on Plot Options on the cut plot and modify settings

4. Ensure that the cut plot changes accordingly

5. 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

6. In the row labelled over, set the from value to -1 and the to value to 1 and click Plot

7. 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.

8. Select MAR21335_Ei60meV_cut(-1.000,1.000) and click Save to Workbench

9. Check that in Mantid a workspace with the name MAR21335_Ei60meV_cut(-1.000,1.000) appears

10. Navigate to the Cut tab

11. In the row labelled along, select DeltaE

12. In the row labelled over, select 2Theta

13. In the row labelled along, set the from value to -5 and the to value to 5

14. In the row labelled over, set the from value to 30 and the to value to 60

15. Click Plot

4. Interactive Cuts

1. Navigate to the Slice tab of the Workspace Manager tab

2. Click Display in the Slice tab without changing the default values

3. On the slice plot, select Interactive Cuts

4. Use the cursor to select a rectangular region in the slice plot. A second window with a cut plot should open.

5. 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

6. Check that the File menu only has one menu item, Close

7. Change the rectangle by changing its size or dragging it to a different area of the slice plot. The cut plot should update accordingly.

8. Click on Save Cut to Workspace and check the MD Histo tab of the Workspace Manager to verify that the new workspace was added

9. Click on Flip Integration Axis. The y axis label changes from Energy Transfer (meV) to \(|Q| (\mathrm{\AA}^{-1})\) or vice versa, depending on the initial label.

5. Overplot Bragg Peaks

1. Navigate to the Information menu on the cut plot

2. Select Aluminium from the submenu for Bragg peaks. Green lines should appear on the cut plot with a respective legend entry.

3. Deselect Aluminium form the submenu for Bragg peaks. Both green lines and the respective legend entry should disappear.

6. Generate a Script

1. Navigate to the Cut tab

2. In the row labelled along, select |Q| and set the from value to 0 and the to value to 10

3. In the row labelled over, set the from value to -5 and the to value to 5

4. Click Plot. A new window with a cut plot should open.

5. Navigate to the Information menu on the cut plot

6. Select Aluminium from the submenu for Bragg peaks. Green lines should appear on the cut plot with a respective legend entry.

7. 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.

8. 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.

9. Run the script and check that the same cut plot is displayed

7. Waterfall Plots

1. Navigate to the Cut tab

2. In the row labelled along, set the from value to 0 and the to value to 10

3. In the row labelled over, set the from value to -5 and the to value to 5 as well as the width value to 2

4. Click Plot. A new window with a cut plot should open.

5. Click Waterfall and set the x value to 0.5, then hit enter. The cuts are now plotted with a 0.5 offset in direction of the x axis.

6. Set the y value to 2 and hit enter. The cuts are now plotted with an additional offset (2) in direction of the y axis.

The Command Line Interface

1. Use the Mantid Editor

1. Close all plots currently open but not the MSlice interface

2. 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

1. Run the script.

2. There should be two new windows with a slice plot and a cut plot

3. Use the Jupyter QtConsole

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

The Workspace Manager

1. Check Scale and Subtract

1. Select the MAR21335_Ei60meV workspace in the Workspace Manager, click on Save and select ASCII

2. A file dialog opens and allows entering a name for saving the file

3. Verify that a txt file with the selected name has been created and contains ASCII data (the first line should be # X , Y , E)

4. Select the MAR21335_Ei60meV workspace again, click on Rename and rename the workspace

5. In the Slice tab of the renamed workspace click on Display and verify that the original slice plot is displayed

6. Select the renamed workspace and click on Delete

7. The renamed workspace should disappear and the Workspace Manager should be empty

8. Go to the Data Loading tab and select MAR21335_Ei60meV.nxs from the sample data.

9. Click Load Data

10. Select the MAR21335_Ei60meV workspace again, click on Compose, select Scale and enter a scale factor of 2, then click Ok

11. A new workspace with the name MAR21335_Ei60meV_scaled appears

12. Select the MAR21335_Ei60meV_scaled workspace and click on Subtract. Select MAR21335_Ei60meV in the dialog that opens and click Ok.

13. A new workspace with the name MAR21335_Ei60meV_scaled_subtracted appears

14. In the Workspace Manager tab select the workspace MAR21335_Ei60meV

15. Navigate to the Cut tab

16. In the row labelled along, set the from value to 0 and the to value to 10

17. In the row labelled over, set the from value to -5 and the to value to 5

18. Click Plot.

19. Follow the same steps for the workspaces MAR21335_Ei60meV_scaled and MAR21335_Ei60meV_scaled_subtracted but click Plot Over for these two

20. The cut plot window should now contain three differently coloured lines with corresponding legends. The line for MAR21335_Ei60meV will be exactly covered by the line for MAR21335_Ei60meV_scaled_subtracted. The line for MAR21335_Ei60meV_scaled will be scaled by factor 2.0.

2. Check Delete and Sum

1. Delete all workspaces apart from the MAR21335_Ei60meV workspace

2. Scale the MAR21335_Ei60meV workspace with a factor of 1.0

3. A new workspace with the name MAR21335_Ei60meV_scaled appears

4. Select the MAR21335_Ei60meV workspace again, click on Add and select MAR21335_Ei60meV_scaled, then click Ok

5. A new workspace with the name MAR21335_Ei60meV_sum appears

6. Delete the workspace with the name MAR21335_Ei60meV_scaled

7. Scale the MAR21335_Ei60meV workspace with a factor of 2.0

8. A new workspace with the name MAR21335_Ei60meV_scaled appears

9. In the Workspace Manager tab select the workspace MAR21335_Ei60meV_scaled

10. Navigate to the Cut tab

11. In the row labelled along, set the from value to 0 and the to value to 10

12. In the row labelled over, set the from value to -5 and the to value to 5

13. Click Plot.

14. Follow the same steps for the workspace MAR21335_Ei60meV_sum but click Plot Over

15. There should be two differently coloured lines with corresponding legends that match exactly