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Library to help write data analysis tools for experimental condensed matter physics.

Project description

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Introduction

The Stoner Python package is a set of utility classes for writing data analysis code. It was written within the Condensed Matter Physics group at the University of Leeds as a shared resource for quickly writing simple programs to do things like fitting functions to data, extract curve parameters, churn through large numbers of small text data files and work with certain types of scientific image files.

For a general introduction, users are referred to the Users Guide, which is part of the online documentation along with the API Reference guide. The github repository also contains some example scripts.

Getting this Code

Introduction and Installation Guide to Stoner Pythin Package

The Stoner package requires numpy >=1.8, scipy >=0.14, matplotlib >=1.5, h5py, lmfit,Pillow and has a number of optional dependencies on blist, filemagic, npTDMS, imreg_dft and numba.

Ananconda Python (and probably other scientific Python distributions) include nearly all of the dependencies, and the remaining dependencies are collected together in the phygbu repositry on anaconda cloud. The easiest way to install the Stoner package is, therefore, to install the most recent Anaconda Python distribution (Python 3.6, 3.5 or 2.7 should work) and then to install the Stoner package via:

conda install -c phygbu Stoner

If you are not using Anaconda python, then pip should also work:

pip install Stoner

This will install the Stoner package and any missing dependencies into your current Python environment. Since the package is under fairly constant updates, you might want to follow the development with git. The source code, along with example scripts and some sample data files can be obtained from the github repository: https://github.com/gb119/Stoner-PythonCode

The codebase is compatible with Python 2.7 and Python 3.5+, at present we still develop primarily in Python 3.6 but test with 2.7 as well.

Overview

The main part of the Stoner package provides two basic top-level classes that describe an individual file of experimental data and a list (such as a directory tree on disc) of many experimental files. For our research, a typical single experimental data file is essentially a single 2D table of floating point numbers with associated metadata, usually saved in some ASCII text format. This seems to cover most experiments in the physical sciences, but it you need a more complex format with more dimensions of data, we suggest you look elsewhere.

Data and Friends

Stoner.Core.DataFile is the base class for representing individual experimental data sets. It provides basic methods to examine and manipulate data, manage metadata and load and save data files. It has a large number of sub classes - most of these are in Stoner.FileFormats and are used to handle the loading of specific file formats.

There are also two mxin classes designed to work with DataFile to enable additional functionality for writing analysis programs.

  • Stoner.Analysis.AnalysisMixin provides additional methods for curve-fitting, differentiating, smoothing and carrying out basic calculations on data.
  • Stoner.plot.PlotMixin provides additional routines for plotting data on 2D or 3D plots.

For rapid development of small scripts, we would recommend the Stoner.Data class which is a superclass of the above, and provides a ‘kitchen-sink’ one stop shop for most of the package’s functionality.

DataFolder

Stoner.Folders.DataFolder is a class for assisting with the work of processing lots of files in a common directory structure. It provides methods to list. filter and group data according to filename patterns or metadata and then to execute a function on each file or group of files.

The Stoner.HDF5 module provides some experimental classes to manipulate DataFile and DataFolder objects within HDF5 format files. These are not a way to handle arbitary HDF5 files - the format is much to complex and flexible to make that an easy task, rather it is a way to work with large numbers of experimental sets using just a single file which may be less brutal to your computer’s OS than having directory trees with millions of individual files. The module also provides some classes to support loading some other HDF5 flavoured files into a DataFile.

The Stoner.Zip module provides a similar set of classes to Stoner.HDF5 but working with the ubiquitous zip compressed file format.

Image Subpackage

The Stoner.Image package is a new feature of recent versions of the package and provides dedicated classes for working with image data, and in particular for analysing Kerr Microscope image files. It provides an ImageFile class that is functionally similar to DataFile except that the numerical data is understood to represent image data and additional methods are incorporated to facilitate processing. The ImageFolder and ImageStack classes provide similar functionality to DataFolder but with additional methods specific to handling collections of images. ImageStack uses a 3D numpy array as it’s primary image store which permits faster access (at the expense of a larger memory footprint) than the lazy loading ordered dictionary of ImageFolder

Resources

Included in the github repository are a (small) collection of sample scripts for carrying out various operations and some sample data files for testing the loading and processing of data. There is also a User_Guide as part of this documentation, along with a doc(complete API reference <Stoner>)

Contact and Licensing

The lead developer for this code is Dr Gavin Burnell <g.burnell@leeds.ac.uk>, but many current and former members of the CM Physics group have contributed code, ideas and bug testing.

The User Guide gives the current list of other contributors to the project.

This code and the sample data are all (C) The University of Leeds 2008-2017 unless otherwise indficated in the source file. The contents of this package are licensed under the terms of the GNU Public License v3

Recent Changes

Current PyPi Version

The current version of the package on PyPi will be the stable branch until the development branch enters beta testing, when we start making beta packages available.

Development Version

The next development version will be on version 0.9. This will be started after the current 0.8 version is given a final release.

Online documentation for all versions can be found on the ReadTheDocs pages online documentation

Build Status

Version 0.7 onwards are tested using the Travis-CI services with unit test coverage assessed by Coveralls. We currently test against python 2.7 and 3.6 via Travis and internally test on Python 3.5 as well. Overall code quality is measured by landscape.io. The current status is shown at the top of this readme.

Citing the Stoner Package

We maintain a digital object identifier (doi) for this package (linked to on the status bar at the top of this readme) and encourage any users to cite this package via that doi.

Stable Versions

Version 0.8 is now in release-candidate phase. The main new features are

  • Reworking of the ImageArray, ImageFile and ImageFolder with many updates and new features.
  • New mixin based ImageStack2 that can manipulate a large number of images in a 3D numpy array
  • Continued re-factoring of DataFolder using the mixin approach
  • Further increases to unit-test coverage, bug fixes and refactoring of some parts of the code.
  • conda packages now being prepared as the preferred package format

After release 0.8 will continue to receive bug fixes and updates.

The current stable version is 0.7. Features of 0.7 include

  • Replace older AnalyseFile and PlotFile with mixin based versions AnalysisMixin and PlotMixin
  • Addition of Stoner.Image package to handle image analysis
  • Refactor DataFolder to use Mixin classes
  • DataFolder now defaults to using Stoner.Core.Data
  • DataFolder has an options to skip iterating over empty Data files
  • Further improvements to Stoner.Core.DataFile.setas handline.

0.7 will continue to have bug fix releases and back-ports of anything very useful until 0.8 is released.

The old stable version was 0.6. This features

  • Some major changes in the architecture,
  • Switching from a numpy MaskedArray as the main data store to a custom sub-class that contains most of the logic for indexing data by column name and designation.
  • The metadata storage has also been switched to using blist.sortteddict for a fast, alphabetically ordered dictionary storage.
  • Other underlying changes are a switch to using properties rather than straight attribute access.

0.6 now also makes use of filemagic to work out the mime type of files to be loaded to try and improve the resilience of the automatic file format detection on platforms where this is supported and adds some extra methods to AnalyseFile for extrapolation.

No further relases will be made to 0.6.

0.6 and 0.7 should work on Python 2.7 and 3.5

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