/rawPy

Tool to analyze raw data from the biaxial apparatus BRAVA

Primary LanguageJupyter Notebook

rawPy

Release notes
version Beta_0_0 11/04/2020
note: the name has been given by my wife Allie (supposed to be a joke for raw pie)
version Beta_0_1 03/05/2020
contributors:

This verison includes:

  • Addition to the utilities of rawPy

    • Remove average slope (derivative)
    • Take slope and polynominal fit
    • Correction for geometrical thinning (rgt)
    • Smoothing data using a low pass filter

  • Additon of Rate- and State Friction tool to model velocity steps

Scope:
This program has been created to build a tool for reproducible data analysis of raw data collected with the biaxial rock deformation apparatus BRAVA.
It allows to import the raw data and produce an output file with elaborated quantities.
It takes inspiration from the program xlook developed by Chris Marone et al. for the Penn State Biax and the module biaxtools developed by John Leeman.

Installation

In later version I will package everything and allow for installation on a conda channel. FOr now you have to follow these instructions.

  • Download Anaconda package manager Python version 3.7
  • create a directory called PythonModules
  • download the rawPy folder in the PythonModules directory
  • Add the PythonModules folder to the PYTHONPATH. This allows to import the rawPy as a module.
    • To add the directory to the PYTHONPATH execute this command in the anaconda prompt for windows user (access it by going on search and type the name) or a terminal for mac users.
      conda-develop /path/to/PythonModules
    • If this does not work open the Spyder IDE by typing in the anaconda prompt/terminal spyder.
      Open the Python path manager and add to the PYTHONPATH the the choosen directory.

Usage

  • Open Anaconda prompt/Terminal and type jupyter lab.
  • A local server will be initialized and you will be brought to the jupyter lab environment in a new browser window.
  • On the left side, open the navigation panel and navigate to the directory where you have saved the file rawPy_reduction.ipynb.
  • Open the rawPy_reduction.ipynb. To use the functions provided with this tool you will notice at the beginning the call:
from rawPy import rawPy as rp
  • To analyze the data follow the instruction given in that notebook.
    p.s. as a first try please follow the example given with the data provided in the example directory.

For routine operational usage you will save the file rawPy_reduction.ipynb in the same directory of the experimental data and experimental sheet. You may want to rename the file as bxxx_r.ipynb.

All the details about the different functions can be found in the manual.ipynb.

PyRSF

This is a web based GUI (Graphical User Interface) that allow to perform inversion models of experimental velocity steps based on the structure used in xlook. It uses as base algorithm the Py-RSF developed by Martijn Van Den Ende. The GUI is designed to allow for data loading, plotting and inversion.

Installation

Some steps must be taken to install all the packages that allow to use the tool. I assume that you have installed Anaconda.

  • First, add to the PYTHONPATH the Py-RSF directory (same procedure as above)
  • Install ipywidgets:
    • Open anaconda prompt (a terminal for mac users) and copy and paste the commands highlighted below
    • install nodejs conda install nodejs
    • install ipympl conda install ipympl
    • install jupyter extensions:
      • jupyter labextension install @jupyter-widgets/jupyterlab-manager
      • jupyter labextension install jupyter-matplotlib
      • jupyter nbextension enable --py widgetsnbextension

If you find any problems please try to resolve yourself and don't give up. This is the only way to learn !!
Some useful resources can be found at:
- Official documentation
- Stackoverflow
- Stackoverflow
and if you don't find the answer here, internet is a beautiful place to find answers.

  • install bqplot as the widget plotting library
    • conda install -c conda-forge bqplot
    • jupyter labextension install bqplot
  • install voila that is used to render the web application
    • conda install -c conda-forge voila
    • jupyter labextension install @jupyter-voila/jupyterlab-preview

Usage

If everything is installed properly, open an anaconda prompt and navigate to directory where the inversion_rsf_master.ipynb is placed. Once there type voila inversion_mater.ipynb and a web page should open in you browser where you can use the RSF tool. If you have any problems:

  1. Open the notebook and execute the different cells and see what is the error
  2. Contact me at marco.scuderi@uniroma1.it

Author comments

There is still a very long to do list !!
Some of the things I will add soonish are:

  • non linear elastic correction
  • package the installation (not in the near future)
  • More functions depending on users input

Something that is unlikely to happen any time soon:

  • put toghether a GUI

For any comment/complain/suggestion email me at: marco.scuderi@uniroma1.it