Additional tools for particle accelerator data analysis and machine information

Related tags

Data Analysispythonanalysisacceleratoropticscernlhcomcpylhc
Overview

PyLHC Tools

Cron Testing Code Climate coverage Code Climate maintainability (percentage) GitHub last commit GitHub release

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

Documentation

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

    BPM Calibration

    opened by Mael-Le-Garrec 5
  • Properly organise extra dependencies for the CERN GPN

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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)

  • 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)

  • v0.0.1(Jun 21, 2019)

Owner
PyLHC
Organisation for the OMC Team at CERN
PyLHC
GitHub Repository https://pylhc.github.io/PyLHC/
Stochastic Gradient Trees implementation in Python

Stochastic Gradient Trees - Python Stochastic Gradient Trees1 by Henry Gouk, Bernhard Pfahringer, and Eibe Frank implementation in Python. Based on th

John Koumentis 2 Nov 18, 2022
Statistical Analysis 📈 focused on statistical analysis and exploration used on various data sets for personal and professional projects.

Statistical Analysis 📈 This repository focuses on statistical analysis and the exploration used on various data sets for personal and professional pr

Andy Pham 1 Sep 03, 2022
Analyzing Earth Observation (EO) data is complex and solutions often require custom tailored algorithms.

eo-grow Earth observation framework for scaled-up processing in Python. Analyzing Earth Observation (EO) data is complex and solutions often require c

Sentinel Hub 18 Dec 23, 2022
Clean and reusable data-sciency notebooks.

KPACUBO KPACUBO is a set Jupyter notebooks focused on the best practices in both software development and data science, namely, code reuse, explicit d

Matvey Morozov 1 Jan 28, 2022
Pandas and Spark DataFrame comparison for humans

DataComPy DataComPy is a package to compare two Pandas DataFrames. Originally started to be something of a replacement for SAS's PROC COMPARE for Pand

Capital One 259 Dec 24, 2022
Finding project directories in Python (data science) projects, just like there R rprojroot and here packages

Find relative paths from a project root directory Finding project directories in Python (data science) projects, just like there R here and rprojroot

Daniel Chen 102 Nov 16, 2022
A neural-based binary analysis tool

A neural-based binary analysis tool Introduction This directory contains the demo of a neural-based binary analysis tool. We test the framework using

Facebook Research 208 Dec 22, 2022
This creates a ohlc timeseries from downloaded CSV files from NSE India website and makes a SQLite database for your research.

NSE-timeseries-form-CSV-file-creator-and-SQL-appender- This creates a ohlc timeseries from downloaded CSV files from National Stock Exchange India (NS

PILLAI, Amal 1 Oct 02, 2022
Creating a statistical model to predict 10 year treasury yields

Predicting 10-Year Treasury Yields Intitially, I wanted to see if the volatility in the stock market, represented by the VIX index (data source), had

10 Oct 27, 2021
An ETL framework + Monitoring UI/API (experimental project for learning purposes)

Fastlane An ETL framework for building pipelines, and Flask based web API/UI for monitoring pipelines. Project structure fastlane |- fastlane: (ETL fr

Dan Katz 2 Jan 06, 2022
A program that uses an API and a AI model to get info of sotcks

Stock-Market-AI-Analysis I dont mind anyone using this code but please give me credit A program that uses an API and a AI model to get info of stocks

1 Dec 17, 2021
SparseLasso: Sparse Solutions for the Lasso

SparseLasso: Sparse Solutions for the Lasso Introduction SparseLasso provides a Scikit-Learn based estimation of the Lasso with cross-validation tunin

Gabriel Okasa 1 Nov 08, 2021
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano

PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) an

PyMC 7.2k Dec 30, 2022
PyPDC is a Python package for calculating asymptotic Partial Directed Coherence estimations for brain connectivity analysis.

Python asymptotic Partial Directed Coherence and Directed Coherence estimation package for brain connectivity analysis. Free software: MIT license Doc

Heitor Baldo 3 Nov 26, 2022
Methylation/modified base calling separated from basecalling.

Remora Methylation/modified base calling separated from basecalling. Remora primarily provides an API to call modified bases for basecaller programs s

Oxford Nanopore Technologies 72 Jan 05, 2023
Mortgage-loan-prediction - Show how to perform advanced Analytics and Machine Learning in Python using a full complement of PyData utilities

Mortgage-loan-prediction - Show how to perform advanced Analytics and Machine Learning in Python using a full complement of PyData utilities. This is aimed at those looking to get into the field of D

Joachim 1 Dec 26, 2021
PyStan, a Python interface to Stan, a platform for statistical modeling. Documentation: https://pystan.readthedocs.io

PyStan PyStan is a Python interface to Stan, a package for Bayesian inference. Stan® is a state-of-the-art platform for statistical modeling and high-

Stan 229 Dec 29, 2022
MetPy is a collection of tools in Python for reading, visualizing and performing calculations with weather data.

MetPy MetPy is a collection of tools in Python for reading, visualizing and performing calculations with weather data. MetPy follows semantic versioni

Unidata 971 Dec 25, 2022
Collections of pydantic models

pydantic-collections The pydantic-collections package provides BaseCollectionModel class that allows you to manipulate collections of pydantic models

Roman Snegirev 20 Dec 26, 2022
wikirepo is a Python package that provides a framework to easily source and leverage standardized Wikidata information

Python based Wikidata framework for easy dataframe extraction wikirepo is a Python package that provides a framework to easily source and leverage sta

Andrew Tavis McAllister 35 Jan 04, 2023