General Tools

General Tools#

abs_pre_calc

Routine for the pre-calculation of absorption correction and autoreduction configuration for NOMAD and POWGEN. For the evaluation of the absorption, once the sample information is ready, it can already be done even before the experiment data are ready. So, the idea here is to use this routine to collect the sample information (via talking to the ITEMS database where the sample information will be stored), perform the absorption calculation and cache the result for later reduction use. In the documentation page for NOMAD autoreduction, detailed introduction and instructions for the routine are available – see here. Regarding the autoreduction setup, we also need to populate the characterization runs information to specify those characterization runs to be used for the reduction, including the empty container run(s), empty instrument run(s), vanadium run(s) and the calibration diamond run. With the current routine, one can do (on Analysis cluster, from the command line),
```
abs_pre_calc -c
```
to directly open the central characterization table file for editing, skipping the sample information collection and the absorption calculation steps. Or, one can do,
```
abs_pre_calc <instrument_name> <IPTS>
```
e.g., abs_pre_calc NOM 28922, to run the full process. First, the routine will talk to the ITEMS database to fetch the sample information (ID, composition ,etc.). The information will then be populated into a CSV file which will be opened automatically right after the information is collected and populated into the file. Now, at this stage, it is our chance to correct whatever incorrect information there and fill in whatever is missing. Refer to the link here for more details. The absorption calculation will be kicked off right next and the calculated absorption spectra will be saved into the experiment-specific directory so that later reduction with MantidTotalScattering (MTS) can find and use the cached absorption calculation. In MTS, path to the central configuration file containing instrument-specific configurations is hard coded (see the documentation here). In the central configuration, the absorption save location for the absorption cache files should be specified. In the case for NOMAD, it is,
```
/SNS/NOM/shared/autoreduce/abs_ms
```
For POWGEN, it is,
```
/SNS/PG3/shared/autoreduce/mts_abs_ms
```
Once the absorption calculation and caching is finished, the program will prompt users with the question whether to bring up the central characterization file for editing. If yes, the characterization file will be brought up and one can fill in the characterization runs as needed.
mts

The local version of MantidTotalScattering (MTS) on Analysis. This local version is using the local conda environment under the name of Dr. Yuanpeng Zhang on Analysis cluster.
mts_data

Routine for extracting data from the reduced \(S(Q)\) data from the MTS running. In a terminal on Analysis cluster, just execute this command followed by the name of the NeXus file we want to extract.

This routine only works with the non-debugging mode, where only one workspace will be generated to host the finally reduced data. If the DebugMode is set to true in MTS (see the instructions here), this routine is not applicable. Normally, the debug mode is more for developers anyways.
mantidl

Run a local version of Mantid Workbench on Analysis. This local version is using the local conda environment under the name of Dr. Yuanpeng Zhang on Analysis cluster.
pystog_cli

Run a local version of pystog_cli on Analysis. This local version is using the local conda environment under the name of Dr. Yuanpeng Zhang on Analysis cluster. Refer to the following links for further information about pystog,