Repository for lsdtopytools, a python wrapper on LSDTopoTools. It binds c++ code from LSDTopoTools with lsdtt-xtensor and exposes it to python via numpy. It allows us to take advantage of both c++ speed and python flexibility. The lsdtopytools suite can be installed using conda, built in native linux or within a Docker container.
This repository hosts the static version of the code available for installation; it is updated at each release (usually when we are publishing a new manuscript utilising new features). Tutorials and example notebooks can be found in this dedicated repository.
- Raster i/o and basic operations
- Preprocessing depressions (carving, filling, nodata, ...)
- River extraction (drainage area threshold)
- ksn from segmented profiles (Mudd et al. 2014)
- concavity index (Mudd et al., 2018, Gailleton et al., 2021 (preprint))
- polyfit metrics
- ...
See https://github.com/LSDtopotools/lsdtt_pytools_docker for intructions on how to install the Docker container.
You need to first have a valid installation of anaconda on your computer. We suggest miniforge see readme here which guarantee a full open-source and open-license installation.
Installation from conda has been tested for windows10, MacOS and different linuxes (ubuntu, Debian, Redhat, WSL). Other OSes will need to build from source (explanation bellow).
First create a conda environment with python <= 3.8 (3.9 will come shortly) and activate it:
conda create -n lsdtopytools python=3.8
conda activate lsdtopytools
RECOMMENDED STEP IF YOU HAVE ANOTHER DISTRIBUTION THAN MINIFORGE: you need to fix an annoying tendency of gdal to rely on messed up dependencies:
conda config --prepend channels defaults
conda config --prepend channels conda-forge
conda config --set channel_priority strict
Then, you can install by simply running:
conda install lsdtopytools
If something went wrong, you need to check several things:
- You are on a previously created conda environment and trying to install lsdtt-xtensor-python in it, check that you DO have
python=3.7.X - You have a
32 bitOS/processor, You need to install from source (also it has been over 15 years since all the computers are 64 bit, this is the reason we do not guarentee compatibility) - You are on an antiquated computer unable to get recent
libc,libc++orlibstdc++, there is nothing we can do unfortunately although I'd be surprised if it happens. We needc++14forlsdtt-xtensorand that is a rigid dependency unfortunately.
You need to get the code (so far from the development repository under src/driver_analysis_BG/), and you need a c++14-ready compiler (tested with gcc 5+ and MSVS so far, should work with clang, theoretically icc as well). Make sure all the dependencies (see above) are installed, especially xtensor and xtensor-python. There are different ways to install a python package from source. From far the safest is to generate a wheel, i.e. a python binary.
For lsdtt-xtensor-python:
cd lsdtt-xtensor-python
python setup.py bdist_wheel
pip install dist/XXX.whl
where XXX is the name of the created wheel file.
Then for lsdtopytools:
cd ../lsdtopytools
pip install .
Done.
- [LINUX] GLIBC error: I am working on it, but basically your linux is older than the one with which I installed it and does not have as recent glibc. The good news is that there is a solution, bad news is that It will take me (BG) a bit of time to implement and you need to install from source. I need to build
manylinux2010wheels which involves using docker, which is not compatible with any of my hardware without accessing the BIOS and I cannot.
So far in early development stage, all of that code will evolve very rapidly and probably drastically. Contact boris.gailleton@gfz-potsdam.de for questions.