Could Someone Help me with Script for Data Analysis in Mantid?

General
1

Hello there, :wave:

I am new to using Mantid and am currently trying to analyze some data for my research project. I have a specific task that I am hoping to accomplish using a script; but I am having trouble figuring out the right commands and workflow.

My dataset consists of neutron scattering data; and I need to perform some basic data reduction steps. Specifically; I would like to normalize the data; apply a background correction; and then visualize the results using a plot. I have read through the documentation and have found some examples; but I am struggling to piece everything together into a coherent script.

I have been using LoadNexus to import my .nxs files; but I am unsure if I need to set any specific parameters for my dataset.

Also, I have gone through this post; https://forum.mantidproject.org/t/outputcompositemembers-in-fit-with-histogram-evaluation-type-integration-error-mlops/ which definitely helped me out a lot.

I would appreciate any tips on applying background corrections effectively. Are there specific functions or methods in Mantid that are particularly useful for this? :thinking:

Thank you in advance for your help and assistance. :innocent:

2

Hi Robert,

Apologies for the delay in getting back to you, hopefully I’ll be more useful from now onwards. :innocent:

If you haven’t already, I would start by looking at this page on running algorithms in Python of our Python in Mantid course.

(I’ll post the rest of my answer below because there is a limit of two links for a new post)

3

The Mantid basic course might also contain some useful information, in particular this page, which shows how you can produce a script automatically to recreate your workflows.

From what you have mentioned, it looks like the script you are looking for might look like this:

# import mantid algorithms, numpy and matplotlib
from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy as np
from mantid.plots._compatability import plotSpectrum #import needed outside Workbench

'''Processing'''

# Load the spectral range of the interest of the data
ws=Load(Filename="GEM40979.raw", SpectrumMin=451, SpectrumMax=650)

# Create a workspace with Flat Background
wsFlat = CreateSampleWorkspace("Histogram","Flat background")
wsFlat = wsFlat * 10

# Remove Background
ws_no_bg = RemoveBackground(InputWorkspace=ws, BkgWorkspace=wsFlat)

# Convert to dSpacing
ws_norm=NormaliseSpectra(InputWorkspace=ws_no_bg)

'''Plotting'''

# Plot three spectra
plotSpectrum(ws_norm, [0,1,2])

# Get Figure and Axes for formatting
fig, axes = plt.gcf(), plt.gca()

# Alter the Y label
axes.set_ylabel('Neutron Counts ($\AA$)$^{-1}$')

# Optionally rename the curve titles
axes.legend(["bank2 sp-431", "bank2 sp-432", "bank2 sp-433", "bank2 sp-436"])

# Give the plot a title
plt.title("Example", fontsize=20)

Please keep in mind that I just put this together as an example, with disregard for physical correctness.

4

Using LoadNexus is fine, any parameters you set should not change the values of the data.

As for background corrections, from what I could find it looks like RemoveBackground could be quite useful?

If you need further assistance, could let me know which instrument nexus files are you loading into Mantid? I could get some members of my team from that particular science area to comment on this thread :relieved: