Difference between revisions of "Reduction scripts"
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Physically the '''Mantid script repository''' is located on [https://github.com/mantidproject/scriptrepository GitHub] and is normal Git repository, which is accessed through simplified Mantid GUI interface, but can also be operated by a person who has github account and is familiar with Git by accessing [https://github.com/mantidproject/scriptrepository GitScriptRepository] link and performing normal git operations. | Physically the '''Mantid script repository''' is located on [https://github.com/mantidproject/scriptrepository GitHub] and is normal Git repository, which is accessed through simplified Mantid GUI interface, but can also be operated by a person who has github account and is familiar with Git by accessing [https://github.com/mantidproject/scriptrepository GitScriptRepository] link and performing normal git operations. | ||
| − | [https:// | + | [https://isis.analysis.stfc.ac.uk/workspaces/ IDAaaS workspaces] have Git repository cloned at |
/opt/UserScripts/ | /opt/UserScripts/ | ||
Revision as of 16:16, 9 January 2023
Reduction scripts used to process the experimental results
ISIS reduction scripts contain number of interconnected scripts which are the part of Mantid and can be located in Mantid Installation Folder/scripts/Inelastic/Direct/ or see Mantid distribution on the web. These scripts set up and run various Mantid algorithms to process input data according to the instrument related settings defined in Instrument parameters files and the settings, specific to a particular experiment. The later settings have to be done by instrument scientist and user locally in special scripts, allowing user to make these settings and run Mantid to reduce their data. An instrument specific examples of such scripts are part of Mantid continuous integration system and can be accessed on the web: (see, e.g. MARI, MAPS, MERLIN and LET or their separate description within this wiki)
Instrument scientists modify these scripts according to the requests of a particular experiment and Mantid provides special way to share these scripts through Mantid script repository configured at
File->Script Repository
field of Mantid GUI (see field pointed at as 1 on the picture below):
The repository, installed locally according to the wizard invoked from this menu allows to download scripts located in the repository and share the changes made to these files with other users of this repository. In addition to data exchange, ScriptRepository wizard configures Python path, to make repository's scripts runnable from Mantid. When Mantid starts, it updates its local copy of the Mantid script repository from the web. The progress of this operations reported to the Mantid log window (shown as the background of the fig above) Default parameters of these scripts are part of Mantid and are described in Instrument Definition Files section of this Wiki.
Physically the Mantid script repository is located on GitHub and is normal Git repository, which is accessed through simplified Mantid GUI interface, but can also be operated by a person who has github account and is familiar with Git by accessing GitScriptRepository link and performing normal git operations.
IDAaaS workspaces have Git repository cloned at
/opt/UserScripts/
folder, where the folder:
/opt/UserScripts/direct_inelastic/[InstrumentName]
contains scripts, used by excitation group. Automatic user configuration scripts configure Mantid in user accounts to be able to run the scripts from this repository. In addition to that, configuration script processes special USER_Files_description.xml file, if one is found in particular instrument folder and copy all files, specified in this file to the RB folders, corresponding to the instrument.
To have write access to the repository through Mantid (and see what is actually there using Mantid GUI) users have to install Mantid script repository through Mantid (or Git) into their accounts.
Small configuration script runs on isiscompute every hour, and together with updating Instrument Parameters repository, updates git repository, so all files changed or added by instrument scientists become available on isiscompute within an hour. This script operations are logged to:
/var/log/UpdateSVN.log.
which is available on ndmlnx01 node only. Root can update the repository on request. See Automatic user configuration pages for detailed description of things, done to provide users with up-to-date data and parameters.
As Mantid script repository is a git repository, it has to obey the constrains imposed by GitHub. One of this constrains is the limitation on the size of the files allowed to be stored on GitHub. This does not allow to use Git repository for storing Instrument files, necessary for data analysis, so local svn repository, described in another chapter, has to be used instead.
MARI instrument scientists who use small instrument parameter files, were able to use Mantid script repository for instrument files, but even this does not work very well. Any other instrument just can not push sufficient size files to Git.
At the fall of 2015 GitHub introduced Large file storage so instrument files can be now stored in GitHub, though Mantid should be modified to use such possibility