Additional tools for particle accelerator data analysis and machine information

Last update: Apr 13, 2022

Overview

PyLHC Tools

This package is a collection of useful scripts and tools for the Optics Measurements and Corrections group (OMC) at CERN.

Documentation

Autogenerated docs via Sphinx can be found at https://pylhc.github.io/PyLHC/.
General documentation of the OMC-Team is located at https://pylhc.github.io/

Getting Started

This package is Python 3.7+ compatible, and can be installed through pip:

pip install pylhc

One can also install from VCS:

git clone https://github.com/pylhc/PyLHC
pip install /path/to/PyLHC

Or simply from the online master branch, which is stable:

pip install git+https://github.com/pylhc/PyLHC.git#egg=pylhc

After installing, scripts can be run with either python -m pylhc.SCRIPT --FLAG ARGUMENT or by calling the .py files directly.

Note: some scripts access functionality only available on the CERN Technical Network. To use those, you should make sure to install the relevant extra dependencies with pip install path/to/Pylhc[cern].

Description

This package provides tools for particle accelerator data analysis, simulations management and machine information extraction; complementing the optics measurement analysis tools of the omc3 package.

Functionality

Forced DA Analysis - Script to analyse forced DA. (forced_da_analysis.py)
Machine Settings Info - Prints an overview over the machine settings at a given time. (machine_settings_info.py)
BSRT Logger and BSRT Analysis - Saves data coming straight from LHC BSRT FESA class and allows subsequent analysis. (bsrt_logger.py & bsrt_analysis.py )
BPM Calibration Factors - Compute the BPM calibration factors using ballistic optics. Two methods are available: using the beta function and using the dispersion. (bpm_calibration.py)

Quality checks

Unit and accuracy tests are run automatically through CI Github Actions. See our workflows in this readme.
Additional checks for code-complexity, design-rules, test-coverage and duplication are made through CodeClimate.
Pull requests implementing functionality or fixes are merged into the master branch after passing CI, and getting a reviewer's approval.

Changelog

See the CHANGELOG file.

Hints for Developers

In case you want to contribute to PyLHC's development, you should install it in editable mode:

git clone https://github.com/pylhc/PyLHC
pip install --editable PyLHC

You can install extra dependencies (as defined in setup.py) suited to your use case with the following commands:

pip install --editable PyLHC[cern]
pip install --editable PyLHC[test]
pip install --editable PyLHC[test,doc]
pip install --editable PyLHC[all]

Open an issue, make your changes in a branch and submit a pull request.

Authors

pyLHC/OMC-Team - Working Group - pyLHC

License

This project is licensed under the GNU GPLv3 License - see the LICENSE file for details.

Comments

BPM Calibration
Script to compute the calibration factors using several methods:

β from phase and its fit

Dispersion and its fit

This code is based on get_ballistic_calibration.py and get_dispersion_calibration.py

Fixes #27
opened by Mael-Le-Garrec 5
Properly organise extra dependencies for the CERN GPN

This is essentially https://github.com/pylhc/omc3/issues/272 applied to this package. I will also rename the extra from tech to cern as agreed in https://github.com/pylhc/omc3/pull/273.
Enhancement Feature Release

opened by fsoubelet 2
Refactor for consistency

Refactor for consistency with other pylhc packages, which should close #41

There's some imports changes in there from Pycharm's optimize imports, but the important changes are in setup.py and conf.py. Includes dependencies version updates.

Important change regarding pyjapc, which is not kept up-to-date on PyPI (and installing from master can mess things up badly in builds): it is now declared as an extra dependency ([tech]) as we discussed on Mattermost, but this can still change. Tbd in this PR.

Moving to GA will be in another issue / PR.

opened by fsoubelet 2
Update setup for consistency with pylhc packages

Would also be a good time to think about the dependencies' versions.

Since we're all fine with pandas 1.x in other packages, we probably shouldn't require 0.25.x here.
Enhancement

opened by fsoubelet 2
SDDS update for llong

Hi,

The new format for sdds files often uses llong format. I was able to use your code with the following modifications : classes.py, line 17-19 : add llong format (>i8, 8, int) reader.py line 139 : convert num_dims to int -> int(num_dims)

Thank you for the good work! Is there any plan to add ascii compatibility?

opened by pbelange 2
LSA knob to MAD-X script converter

Adds a script which can take an LSA knob and an optics it is defined for to create both a definition TFS file and a MAD-X script which will reproduce the knob in simulations.

The script can also be fed a text file with many knobs definitions as well as their trim values, and run for all of these knobs. See examples in the module docstring.

opened by fsoubelet 1
Remove submitter scripts
Closes #71

Removed:

Entrypoint scripts for job_submitter and autosix

The htc and sixdesk_tools modules

Tests for the above

Documentation files for the modules and the entrypoints

Mentions in the README

Release Request
opened by fsoubelet 1

Import ABCs from the proper modules

Current job_submitter raises the following:

DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
  from collections import OrderedDict, Iterable

Should be a very quick change to become compliant (the warning is for Iterable only though).

Enhancement

opened by fsoubelet 1

Fix lsa to madx writer
LSA to MADX sign convention

Better trim naming

check madx names for allowed characters

option to init all variables

machine settings info takes ISO time
opened by JoschD 0
CI Updates
Update to the CI workflows making use of the newer versions of certain official worflows.

Caching and cache management left to the setup-python action

Properly call pip as module everywhere

Do not run the build (and build check) twice in the publish repo

CI/CD
opened by fsoubelet 0
Rewrite Forced_DA to da_analysis
Allow input of measurements from blown-up beams, (single) kicked beams and excited beams (forced da) via switches.

add missing formulas

input to be checked for heated (no kick)

input also nominal emittance (HL-LHC)
opened by JoschD 0
add script to calculate RDT from tracking data

complementary to metaclass/opticsclass, create script which takes PTC trackone data and returns processed RDTs

compared to omc3 RDT reconstruction, no px reconstruction necessary
Enhancement

opened by mihofer 3

Releases(0.7.4)

0.7.4(Oct 19, 2022)
Path release 0.7.4:

Changes in Machine Settings Info

Default behaviour for no knobs given(no --knobs or knobs=None): extract None.

Old behaviour of extracting all restored by giving knobs = ["all"] (CLI: --knobs all)

Option ["default"] available for default knobs as used in OMC3. (CLI: --knobs default)

Additional debug logging

What's Changed

Machine settings debug logging and knobs by @JoschD in https://github.com/pylhc/PyLHC/pull/105

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.7.3...0.7.4
Source code(tar.gz)
Source code(zip)
0.7.3(Oct 11, 2022)
Release 0.7.3 is a patch release which fixes:

LSA to MADX sign convention

Better trim naming

check madx names for allowed characters

option to init all variables

machine settings info takes ISO time

What's Changed

CI Updates by @fsoubelet in https://github.com/pylhc/PyLHC/pull/103

Fix lsa to madx writer by @JoschD in https://github.com/pylhc/PyLHC/pull/104

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.7.2...0.7.3
Source code(tar.gz)
Source code(zip)
0.7.2(May 31, 2022)
Release 0.7.2 brings a fix to the lsa_to_madx module, ensuring it does not make the user run into a MAD-X bug later on when using the created knobs.

Fixed:

Trim variables generated in the MAD-X script will make sure not to be longer than 47 characters (hard MAD-X limit), nor start with an underscore or a digit.

What's Changed

Fix: MAD-X Variable Name Length Limit by @fsoubelet in https://github.com/pylhc/PyLHC/pull/102

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.7.1...0.7.2
Source code(tar.gz)
Source code(zip)
0.7.1(May 23, 2022)
Release 0.7.1 brings a fix to the lsa_to_madx module.

Fixed:

Will not attempt to write to disk knobs that were not found by LSA in the provided optics.

What's Changed

Fix: Do not attempt to write when knob isn't found in LSA optics by @fsoubelet in https://github.com/pylhc/PyLHC/pull/101

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.7.0...0.7.1
Source code(tar.gz)
Source code(zip)
0.7.0(May 23, 2022)
Release 0.7.0 contains the following changes:

Added:

Added a new module, pylhc.lsa_to_madx, with functionality to parse LSA knobs from the command line or a text file, retrieve relevant information from LSA and create MAD-X files with the commands necessary to reproduce these knobs in simulations. This is of particular use when trying to reproduce a specific machine configuration in simulations.

What's Changed

LSA knob to MAD-X script converter by @fsoubelet in https://github.com/pylhc/PyLHC/pull/100

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.6.2...0.7.0
Source code(tar.gz)
Source code(zip)
0.6.2(Apr 23, 2022)
Release 0.6.2 adds a flag to the info functionality of pylhc.kickgroups to display a copy-pastable list of kick files once can use in the GUI to load them all at once.

What's Changed

Kickgroups file list by @JoschD and @fsoubelet in https://github.com/pylhc/PyLHC/pull/99

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.6.1...0.6.2
Source code(tar.gz)
Source code(zip)
0.6.1(Apr 22, 2022)
Release 0.6.1 brings a fix to the kickgroups module.

Fixed:

Correctly detect the plane of the excitationSettings being read.

Better handling of kickgroups with no kickfiles.

Changed:

The command-line commands have been renamed to list and info.

What's Changed

fix by @JoschD in https://github.com/pylhc/PyLHC/pull/98

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.6.0...0.6.1
Source code(tar.gz)
Source code(zip)
0.6.0(Apr 22, 2022)
Release 0.6.0 contains the following changes:

Added:

Added a new module, pylhc.kickgroups, with functionality to query available kickgroup files from a location, retrieve information of a given kickgroup, and retrieve relevant information for all kicks in a kickgroup. It can be called as a script (python -m pylhc.kickgroups) to printout copy-pastable information to put in the OMC logbook.

What's Changed

Added KickGroup Infos by @JoschD and @fsoubelet in https://github.com/pylhc/PyLHC/pull/97

Full Changelog: https://github.com/pylhc/PyLHC/compare/v0.5.0...0.6.0
Source code(tar.gz)
Source code(zip)
v0.5.0(Apr 20, 2022)
What's Changed

Cron workflow fix by @fsoubelet in https://github.com/pylhc/PyLHC/pull/95

Removed IRNL RDT Correction by @JoschD in https://github.com/pylhc/PyLHC/pull/96 which can now be found as its own package in https://github.com/pylhc/irnl_rdt_correction

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.4.2...v0.5.0
Source code(tar.gz)
Source code(zip)
0.4.2(Mar 31, 2022)
Minor bugfixes in machine_settings_info.

Fixed:

The knob finding function needed some fixes after updates in pjlsa.

Source code(tar.gz)
Source code(zip)
v0.4.1(Feb 20, 2022)
Minor bugfixes in machine_settings_info.

Added:

time and start_time can now be given as AccDatetime-objects.

Fixed:

trims variable is initialized as None. Was not initialized if no trims were found, but used later on.

Source code(tar.gz)
Source code(zip)
v0.4.0(Feb 16, 2022)
What's Changed

Add Zenodo DOI to README by @fsoubelet in https://github.com/pylhc/PyLHC/pull/89

Adds check for non-existing knobs by @JoschD in https://github.com/pylhc/PyLHC/pull/90

Update CI by @fsoubelet in https://github.com/pylhc/PyLHC/pull/91

Lsa with timerange by @JoschD in https://github.com/pylhc/PyLHC/pull/92

Release 0.4.0 brings the trim-history option to the machine-info extractor. To enable this, one needs to provide a start_time. The return values are now organized into a dictionary.

Full Changelog: https://github.com/pylhc/PyLHC/compare/0.3.0...v0.4.0
Source code(tar.gz)
Source code(zip)
0.3.0(Nov 16, 2021)
Release 0.3.0 brings the following:

Added:

Non-linear correction script for the (HL)LHC Insertion Regions Resonance Driving Terms, including feed-down effects.

Changed:

The package's license has been moved from GPLv3 to MIT.

Note: if one wishes to extend the IRNL correction script to a different accelerator, there are valuable pointers in the following PR comment.
Source code(tar.gz)
Source code(zip)
0.2.0(Nov 3, 2021)
This is the first release of pylhc since its omc3 dependency is available on PyPI.

Added:

BPM calibration script to get calibration factors from different BPMs

Proper mocking of CERN TN packages (functionality imported from omc3)

Changed:

Minimum required tfs-pandas version is now 3.0.2

Minimum required generic-parser version is now 1.0.8

Minimum required omc3 version is now 0.2.0

Extras related to the CERN TN are now installed with python -m pip install pylhc[cern]

Removed:

The HTCondor and AutoSix functionality have been removed and extracted to another package at https://github.com/pylhc/submitter

Source code(tar.gz)
Source code(zip)
0.1.0(Dec 11, 2020)
Added:

Job submitter script to easily generate and schedule jobs through HTCondor.

Autosix script to easily generate and submit parametric SixDesk studies through HTCondor.

Script to analyse forced dynamic aperture data.

Scripts for logging and analysis of LHC BSRT data.

Utility modules supporting functionality for the above scripts.

Changed:

License moved to GNU GPLv3 to comply with the use of the omc3 package.

Miscellaneous:

Introduced extra dependencies tailored to different use cases of the package.

Reworked package organisation for consistency.

Set minimum requirements versions.

Moved CI/CD setup to Github Actions.

Improved testing and test coverage.

Source code(tar.gz)
Source code(zip)
v0.0.2(Jun 24, 2019)

Source code(tar.gz)
Source code(zip)
v0.0.1(Jun 21, 2019)

Source code(tar.gz)
Source code(zip)

Owner

PyLHC

Organisation for the OMC Team at CERN

GitHub Repository https://pylhc.github.io/PyLHC/

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Additional tools for particle accelerator data analysis and machine information

Related tags

Overview

PyLHC Tools

Documentation

Getting Started

Description

Functionality

Quality checks

Changelog

Hints for Developers

Authors

License

Comments

Releases(0.7.4)

0.7.4(Oct 19, 2022)

What's Changed

0.7.3(Oct 11, 2022)

What's Changed

0.7.2(May 31, 2022)

What's Changed

0.7.1(May 23, 2022)

What's Changed

0.7.0(May 23, 2022)

What's Changed

0.6.2(Apr 23, 2022)

What's Changed

0.6.1(Apr 22, 2022)

What's Changed

0.6.0(Apr 22, 2022)

What's Changed

v0.5.0(Apr 20, 2022)

What's Changed

0.4.2(Mar 31, 2022)

v0.4.1(Feb 20, 2022)

v0.4.0(Feb 16, 2022)

What's Changed

0.3.0(Nov 16, 2021)

0.2.0(Nov 3, 2021)

0.1.0(Dec 11, 2020)

v0.0.2(Jun 24, 2019)

v0.0.1(Jun 21, 2019)

Owner

PyLHC

MIR Cheatsheet - Survival Guidebook for MIR Researchers in the Lab

ToeholdTools is a Python package and desktop app designed to facilitate analyzing and designing toehold switches, created as part of the 2021 iGEM competition.

GWpy is a collaboration-driven Python package providing tools for studying data from ground-based gravitational-wave detectors

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