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APSG - structural geology module for Python

Project description

APSG - python package for structural geologists

GitHub version Build Status Documentation Status Anaconda-Server Badge DOI

APSG defines several new python classes to easily manage, analyze and visualize orientational structural geology data.

Installation

Using Conda

For Anaconda/Miniconda distributions you can install directly from my personal channel

conda install -c ondrolexa apsg

Using pip

You can install APSG from PyPI

pip install apsg

APSG requires dependencies which need to be installed (see Installing Python Scientific Packages).

Master version

To install most recent master version use

pip install https://github.com/ondrolexa/apsg/archive/master.zip

To upgrade to latest development version use

pip install --upgrade --upgrade-strategy only-if-needed \
  https://github.com/ondrolexa/apsg/archive/master.zip

Getting started

You can see APSG in action in accompanied Jupyter notebook http://nbviewer.jupyter.org/github/ondrolexa/apsg/blob/master/examples/apsg_tutorial.ipynb

And for fun check how simply you can animate stereonets http://nbviewer.jupyter.org/github/ondrolexa/apsg/blob/master/examples/animation_example.ipynb

Documentation

Explore the full features of APSG. You can find detailed documentation here.

Contributing

Most discussion happens on Github. Feel free to open an issue or comment on any open issue or pull request. Check CONTRIBUTING.md for more details.

Donate

APSG is an open-source project, available for you for free. It took a lot of time and resources to build this software. If you find this software useful and want to support its future development please consider donating me.

Donate via PayPal

License

APSG is free software: you can redistribute it and/or modify it under the terms of the MIT License. A copy of this license is provided in LICENSE file.

Changes

Master version

  • Stereogrid always use Euclidean norms as weights
  • DefGrad properties e1, e2, e3 (natural principal strains) added
  • DefGrad properties eoct, goct (octahedral strains) added
  • DefrGrad from_ratios class method added
  • DefGrad properties k, d, K, D (strain symmetries and intesities) added
  • New class Ellipsoid added to work with ellipsoids
  • FabricPLot renamed to VollmerPlot for consistency
  • RamsayPlot, FlinnPlot and HsuPlot implemented
  • All fabric plots have new path method accepting list of tensors

0.6.0 (07 Nov 2018)

  • Stress always gives eigenvalues sorted
  • Stress I1, I2, I3 properties for invariants implemented
  • Stress mean_stress property implemented
  • Stress hydrostatic and deviatoric properties implemented
  • precision added to settings to control numerical comparisms
  • figsize added to settings to control figure size across APSG
  • Animation examples fixed
  • rand class method implemented for Fol, Lin, Vec3 and Pair to generate random instance
  • Group to_csv and from_csv improved
  • SDB tags method works properly for multiple tags
  • SDB can modify database metadata
  • QGIS 3 plugin ReadSDB compatibility

0.5.4 (19 Oct 2018)

  • StereoNet has cbpad keyword for colorbar padding
  • FabricPlot bug introduced in 0.5.2 fixed.

0.5.3 (10 Oct 2018)

  • Bugfix release

0.5.2 (10 Oct 2018)

  • Fischer distribution sampling added
  • transform method has norm kwarg to normalize tranformed vectors
  • axisangle property to calculate axis and angle from rotation matrix
  • StereoNet arc method added
  • Vec3 and Group upper and flip properties implemented
  • DefGrad, VelGrad and Stress rotate method accepts also rotation matrix
  • velgrad method added to DefGrad to calculate matrix logarithm
  • StereoGrid has new methods max, min, max_at, min_at

0.5.1 (05 Dec 2017)

  • Kent distribution sampling added
  • Automatic kernel density estimate for contouring
  • UserWarnings fix

0.5.0 (19 Nov 2017)

  • bux fix minor release

0.4.4 (25 Mar 2017)

  • Group method centered improved
  • Group method halfspace added to reorient all vectors towards resultant halfspace

0.4.3 (25 Mar 2017)

  • Stress tensor with few basic methods implemented
  • StereoGrid keyword argument 'weighted' to control weighting
  • StereoNet kwargs are passed to underlying methods for immediate plots
  • StereoNet tensor method implemented (draw eigenlins or fols based on fol_plot settings)
  • Group totvar property and dot and proj methods implemented
  • Fol and Lin dot method returns absolute value of dot product
  • Vec3 H method implemented
  • StereoNet.contourf method draw contour lines as well by default. Option clines controls it.
  • centered bug fixed
  • StereoNet allows simple animations. Add animate=True kwarg to plotting method and finally call StereoNet animate method.

0.4.1-2 (04 Mar 2017)

  • bugfix

0.4.0 (04 Mar 2017)

  • Density class renamed to StereoGrid
  • Fault sense under rotation fixed
  • FaultSet example provided
  • Angelier-Mechler dihedra method implemented for FaultSet
  • StereoNet accepts StereoGrid and Ortensor as quick plot arguments
  • StereoNet instance has axtitle method to put text below stereonet

0.3.7 (05 Jan 2017)

  • conda build for all platforms
  • numpy, matplotlib and other helpres imported by default
  • ortensor is normed by default
  • ortensor MADp, MADo, MAD and kind properties added

0.3.6 (03 Jan 2017)

  • shell script iapsg opens interactive console

0.3.5 (12 Nov 2016)

  • Simple settings interface implemented in in apsg.core.seetings dictionary. To change settings use:
    from apsg.core import settings
    setting['name']=value
    
  • notation setting with values dd or rhr control how azimuth argument of Fol is represented.
  • vec2dd setting with values True or False control how Vec3 is represented.
  • Vec3 could be instantiated by one arument (vector like), 2 arguments (azimuth, inclination) or 3 arguments (azimuth, inclination, magnitude).
  • Group and FaultSet can return array or list of user-defined attributes of all elements

0.3.4 (20 Jun 2016)

  • RTD fix

0.3.3 (04 Jun 2016)

  • Added E1,E2,E3 properties and polar decomposition method to DefGrad object
  • StereoNet has vector method to mimics lower and upper hemisphere plotting of Lin and Vec3 objects as used in paleomagnetic plots
  • StereoNet could be initialized with subplots
  • rake method of Fol added to return vector defined by rake
  • Density could be initialized without data for user-defined calculations New method apply_func could be used to calculate density
  • Contour(f) methods accept Density object as argument
  • Added Group class methods to generate Spherical Fibonacci and Golden Section based uniform distributions of Vec3, Lin and Fol

0.3.2 (22 Feb 2016)

  • FabricPlot - triangular fabric plot added
  • .asvec3 property has .V alias
  • Resultant of Fol and Lin is calculated as vectorial in centered position
  • dv property of Fol added to return dip slip vector

0.3.1 (20 Nov 2015)

  • SDB class improved. Support basic filtering including tags
  • StereoNet has close method to close figure and new method to re-initialize figure when closed in interactive mode
  • iapsg shell script added to invoke apsg ipython shell

0.3.0 (09 Nov 2015)

  • Group fancy indexing implemented. Group could be indexed by sequences of indexes like list, tuple or array as well as sliced.
  • Cluster class with hierarchical clustering implemented
  • Group to_file and from_file methods implemented to store data in file
  • Group copy method for shallow copy implemented
  • StereoNet now accept Vec3 and Fault object as well for instant plotting.
  • Ortensor updated with new properties E1,E2,E3 and Vollmer(1989) indexes P,G,R and C. Bug in Woodcocks's shape and strength values fixed.
  • uniform_lin and uniform_fol improved.
  • asvec3 method implemented for Fol and Lin
  • fol_plot property of StereoNet allows choose poles or great circles for immediate plotting
  • bootstrap method of Group provide generator of random resampling with replacements.
  • Group examples method provide few well-known datasets.
  • Matplotlib deprecation warnings are ignored by default

0.2.3 (21 Oct 2015)

  • New Docstrings format
  • StereoNet.getfols method bug fixed.
  • Shell scripts to run interactive session improved.

0.2.2 (17 Apr 2015)

  • FaultSet class added. Fault and Hoeppner methods of StereoNet implemented
  • VelGrad and DefGrad classes used for transformations added
  • G class to quickly create groups from strings added.

0.2.1 (09 Dec 2014)

  • Quick plotting of groups fixed.

0.2.0 (09 Dec 2014)

  • new StereoNet class for Schmidt projection
  • Quick plot when data are passed as argument StereoNet class instantiation
  • mplstereonet dependency depreceated
  • new Pair and Fault classes to manipulate paired data (full support in future)
  • new uniform_lin and uniform_fol Group methods
  • abs for Group implemented to calculate euclidean norms
  • new Group method normalized
  • new Group properties and methods to calculate spherical statistics

0.1.0 (01 Nov 2014)

  • First release of APSG

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