D-Piper - A modified Piper diagram

Overview

D-Piper is a free source code developed in Python 3.7 that allows to represent large hydrochemical data sets throughout point density diagrams. Multiple methods of data distribution can be chosen for data visualization.

How to install

The program could be easily installed in a Windows system by:

• Download and unzip the repositoy zip file in your working directory.

or

• Cloning the repository using git*: git clone https://github.com/chesstor/D-Piper.git

D-Piper have been programmed using Python 3.7, and depends mainly on common Python packages.

For installing, running and managing Python packages, we recommend using Anaconda or Miniconda distribution. The latter is a lighter release of Anaconda.

For avoiding conflicts among the dependencies and Python versions while running D-Piper, it's recommended to create a new conda environment with the same Python and packages versions in which it was programmed. You can do this by:

• Option 1. Manually from the Anaconda Prompt by running:

  conda create --name dpiper python=3.7 numpy=1.17.4 pandas=1.1.3 matplotlib=3.2.2 jenkspy=0.2.0

or

• Option 2. From an yml file using the DPiper.yml file included in the repository. This option will create an environment with all the packages and its versions included in the file. The first line of the yml file sets the new environment's name. Be free to change it for other env name. Simply run the following line on the Anaconda Prompt from within the folder that holds the yml file:

  conda env create -f dpiper.yml

Dependecies:

The program relies on Python standard libraries. The library jenkspy is used when choosing Jenk's division method.

_ Numpy 1.17.4

_ Pandas 1.1.3

_ Matplotlib 3.2.2

_ Jenkspy 0.2.0

How does it work?

To make a D-Piper diagram just follow these steps:

1. Prepare the file structure:

Keep the file structure as shown in the figure:

• The input analytical data files must be saved in the Data folder. The sample files used in the article to make Figures 2, 3, 4 and 5 can be found in this folder.
• The D-Piper diagrams will be saved in the Graphics folder. It currently contains some example images.
• The file D_Piper_v1_options.txt contains the necessary instructions and explanations to build the desired D-Piper diagram.
• The file D_Piper_v1.py is the script that you have to run in Python to build a D-Piper diagram. The script is widely commented.
• The Tools.py file is an auxiliary Python code that act as a module and contains all the functions with which the D_Piper_v1.py file operates.

Do not delete or change any of the above files or folders. If necessary, you can add other folders or files. Note that automatically a pycache folder is created, requiered for an optimal execution of the program.

The script always reads the drawing options from the D_Piper_v1_options.txt file. If you want to save a set of options, you must do so by renaming the file or saving it to another location. For further use, you will have to name it as the original one (D_Piper_v1_options.txt) or update the new name in line 65 of the D_Piper_v1.py file.

2. Preparing the data file:

The data file must be in ASCII format and saved in the Data folder. The data file can have any name. The structure of the data file should be as follows:

• TAB-separated ASCII file
• It must contain ten columns:

Identifier: sample identification number.
Group: Each sample can belong to a different group. Up to nine groups can be differentiated. Although no error will be shown, setting more groups will create overlap problems.
Eight columns with analytical results. The ion content should be expressed in mg/L (milligrams per liter) or ppm (parts per million).

3. Preparing the Options file:

The D_Piper_v1_options.txt file must be in ASCII format, separated by semicolon (;) It is a self-explanatory file that shows all the options of the program. It is essential to comply with the file format to avoid execution errors.

The contents of this file are explained at the end of this document. Options that can be modified are shown in red, explanatory text and guidelines are shown in blue, and variable names in black.

4. Run the program:

The program simply works by running the D_Piper_v1.py script. This can be ahieved from the Anaconda prompt (with the correct env activated and python-path active) or from any development platform (Spyder, PYCharm...).

The execution from the Anaconda Prompt shell (or other shell) could be done by simply running:

>>> python D_Piper_v1.py

Get in Touch

• Questions or comments can be asked and answered on Github Discussions.
• Bugs, requests, installation problems and other improvements can be posted as Github Issues.

Authors

All authors belong to IGME Geological Survey of Spain. C/Ríos Rosas 23, 28003 Madrid, Spain

• M. González-Jiménez miguel.gj@ipna.csic.es

• L. Moreno Merino l.moreno@igme.es

• H. Aguilera Alonso h.aguilera@igme.es

• E. Díaz Losada elisabeth.diaz@igme.es

Paper

If you use the program in one of your studies, please cite this paper:

• Moreno Merino, L.; Aguilera, H.; González Jiménez, M.; Díaz Losada, E. 2021 D-Piper, a modified Piper diagram to represent big sets of hydrochemical analyses. Environmental Modelling and Software, 138.

  https://doi.org/10.1016/j.envsoft.2021.104979

Copyright

License: GPLv3