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Python package for digitizing pollen diagrams

Project description

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STRADITIZE (Stratigraphic Diagram Digitizer) is an open-source program that allows stratigraphic figures to be digitized in a single semi-automated operation. It is designed to detect multiple plots of variables analyzed along the same vertical axis, whether this is a sediment core or any similar depth/time series.

Usually, in an age of digital data analysis, gaining access to data from the pre-digital era – or any data that is only available as a figure on a page – remains a problem and an under-utilized scientific resource.

This program tackles this problem by providing a python package to digitize especially pollen diagrams, but also any other type of stratigraphic diagram.

Straditize is written in python and supports mixtures of many different diagram types, such as bar plots, line plots, as well as shaded, stacked, and filled area plots. The package provides an extensively documented graphical user interface for a point-and-click handling of the semi-automatic process, but can also be scripted or used from the command line. Other features of STRADITIZE include text recognition to interpret the names of the different plotted variables, the automatic and semi-automatic recognition of picture artifacts, as well an automatic measurement finder to exactly reproduce the data that has been used to create the diagram.

Installation

We highly recommend to use anaconda and install straditize into its own environment:

conda create -n straditize -c conda-forge straditize
conda activate straditize

or install it from the source files via:

git clone https://github.com/Chilipp/straditize.git
cd straditize
pip install .  # or python setup.py install, but pip is recommended

It can then be started from the command line via:

straditize

A more detailed description is provided in the docs.

License

straditize is published under the GNU General Public License v3.0 under the copyright of Philipp S. Sommer, 2018-2019

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