Skip to main content

Analysis tools for paleo/rock magnetic data

Project description

## What is it

PmagPy is a comprehensive set of tools for analyzing paleomagnetic data. It facilitates interpretation of demagnetization data, Thellier-type experimental data and data from other types of rock magnetic experiments. PmagPy can be used to create a wide variety of useful plots. It is designed to work with the MagIC database (https://earthref.org/MagIC), allowing manipulation of downloaded data sets as well as preparation of new contributions for uploading to the MagIC database. It also supports the use of IPython/Jupyter notebooks for fully documented and nicely illustrated data analysis.

## Main features

PmagPy is comprised of:
  • GUI programs for getting data into MagIC database format (pmag_gui), analyzing demagnetization data (demag_gui) and analyzing paleointensity data (thellier_gui). These GUIs are also availible for download as executable programs outside of this repository: - [Mac PmagPy Executable Application](https://github.com/PmagPy/PmagPy-Standalone-OSX/releases/latest) - [Windows PmagPy Executable Application](https://github.com/PmagPy/PmagPy-Standalone-Windows/releases/latest) - [Linux PmagPy Executable Application](https://github.com/PmagPy/PmagPy-Standalone-Linux/releases)

  • Command line programs for all sorts of paleomagnetic data analysis and wrangling (contained within the programs folder of the repository and pip installed as pmagpy-cli).

  • The pmagpy function module for paleomagnetic data analysis (pmagpy.pmag) and plotting (pmagpy.pmagplotlib) as well as a function module that further enables paleomagnetic data analysis within interactive computing environments such as the Jupyter notebook (pmagpy.ipmag). The functions within these modules are at the heart of the GUI and command line programs. With pmagpy in the python path (which is accomplished using pip, see below), these modules are can be imported (e.g. `import pmagpy.ipmag as ipmag`).

  • Example data files that are used in the examples provided in the PmagPy cookbook http://earthref.org/PmagPy/cookbook

Use of all these features is described in the cookbook and the underlying science behind the data and code can be explored in the book Essentials of Paleomagnetism: Third Web Edition (http://earthref.org/MagIC/books/Tauxe/Essentials/).

## How to get it

Much more complete documentation for PmagPy installation and use is available in the PmagPy cookbook: http://earthref.org/PmagPy/cookbook

### Stand alone applications If you do not need the full PmagPy functionality, and you only want to use Pmag GUI, MagIC GUI, Thellier GUI, and Demag GUI, there a standalone download for which Python does not need to be installed.

#### OSX Standalone download

To get started, download the zip file and put the resulting folder on your desktop. Inside the PmagPy-Standalone folder you will have one folder each for Pmag GUI and MagIC GUI. Open the appropriate folder and double click the icon (depending on your security settings, you may have to right click the icon and then select “ok” the first time you open it). You’ll find the latest stable release at: https://github.com/PmagPy/PmagPy-Standalone-OSX/releases/latest

#### Windows Standalone download

Get started by downloading the zip file (see links below) and putting the resulting folder wherever you wish. You’ll need to “extract all” files. Inside the PmagPy-Standalone folder you will find icons for Pmag GUI and MagIC GUI. You’ll find the latest stable release at: https://github.com/PmagPy/PmagPy-Standalone-Windows/releases/latest

#### Linux Standalone download

This binary has only been tested on a Ubuntu 14.04 (Trusty) distribution and might experience problems on other distributions. You can simply clone the standalone repository or download and unzip. The GUIs should run when you double click the executable, but will take time to start up (anywhere from 5 to 30 seconds) please be patient. You’ll find the latest stable release at: https://github.com/PmagPy/PmagPy-Standalone-Linux/releases

### Full PmagPy install

To get the full use of PmagPy functionality, you will first have to have a Python installation with some standard scientific modules. You can follow instructions to do so [here](https://earthref.org/PmagPy/cookbook/#x1-60001.2). Once you have Python installed:

  • Find and open your command line (for help finding your command prompt, see the [documentation](http://earthref.org/PmagPy/#command_line))

  • Update pip: type on the command line: `pip install --upgrade pip`

  • Install or update pmagpy: use the command: `pip install --upgrade pmagpy`

  • Install or update pmagpy-cli, use the command: `pip install --upgrade pmagpy-cli`

  • To uninstall, use the commands: `pip uninstall pmagpy` and `pip uninstall pmagpy-cli`

  • If you run into trouble, use pip to uninstall both pmagpy and pmagpy-cli, then try again to install first pmagpy and then pmagpy-cli

If you want access to the master branch rather than the latest release you can: - either clone the repository or download the latest release and then add the directory of the main repository folder (and the program directory for access to the command line programs) to their path. On a Mac or other Unix machine, this can be done by adding these lines to the bash_profile (edited as necessary for where the PmagPy directory is on your local machine): `export PATH=~/PmagPy:./:$PATH`; `export PATH=~/PmagPy/programs:./:$PATH`

  • Alternatively if you want simply to install the latest under development version without messing with environment variables you can download or clone the repository and run python setup.py install and it will use setup tools to install PmagPy somewhere where it is accessible to python and in your path. This, however, does not update your in path version of the library when you update using git pull origin master but rather you must update using setup tools manually.

## Background and support

The code base for the PmagPy project has been built up over many years by Lisa Tauxe (Distinguished Professor of Geophysics at the Scripps Institution of Oceanography) supported by grants from the National Science Foundation. Ron Shaar (Senior Lecturer at the Hebrew University of Jerusalem), Lori Jonestrask and Nick Swanson-Hysell (Assistant Professor at UC Berkeley) have also made substantial contributions to the project.

## Contributing

If you want to get involved with the project - whether that means reporting a bug, requesting a feature, or adding significant code - please check out our [Contribution guidelines](https://github.com/PmagPy/PmagPy/blob/master/CONTRIBUTING.md).

## More information

This code and the PmagPy cookbook (http://earthref.org/PmagPy/cookbook) are companions to the the book Essentials of Paleomagnetism: Third Web Edition (http://earthref.org/MagIC/books/Tauxe/Essentials/) written by Lisa Tauxe with contributions from Subir K. Banerjee, Robert F. Butler and Rob van der Voo. The printed version of the book came out in January, 2010 from University of California Press (http://www.ucpress.edu/book.php?isbn=9780520260313).

## Licensing

This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/ltauxe/PmagPy/blob/master/license.txt) for details.

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pmagpy-cli-3.8.5.tar.gz (926.6 kB view details)

Uploaded Source

Built Distribution

pmagpy_cli-3.8.5-py2-none-any.whl (923.6 kB view details)

Uploaded Python 2

File details

Details for the file pmagpy-cli-3.8.5.tar.gz.

File metadata

  • Download URL: pmagpy-cli-3.8.5.tar.gz
  • Upload date:
  • Size: 926.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No

File hashes

Hashes for pmagpy-cli-3.8.5.tar.gz
Algorithm Hash digest
SHA256 5fb6d7110fe3989a7bb1518e6d8e4ceea581ab4196ff35e035fc5160568a5141
MD5 016463a8ea3a15ee8c1dc63218a79090
BLAKE2b-256 a27c5224b227fa0f34a010022d024b99f955aa73c1d8349041427554b6e33f8d

See more details on using hashes here.

File details

Details for the file pmagpy_cli-3.8.5-py2-none-any.whl.

File metadata

File hashes

Hashes for pmagpy_cli-3.8.5-py2-none-any.whl
Algorithm Hash digest
SHA256 e8814fa8730764aeef189682786a18fd4fac624b4762cd4632a9bded7211c434
MD5 d9d009fb17838d377d73e504b86ff4d4
BLAKE2b-256 8ad0b38442bc3a74bcc217030ea55f4a1f017b8ff393dfc5fd9423501842e3d1

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page