Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/weiji14/deepbedmap

Going beyond BEDMAP2 using a super resolution deep neural network. Also a convenient flat file data repository for high resolution bed elevation datasets around Antarctica.
https://github.com/weiji14/deepbedmap

antarctica bedmap binder chainer data-science deep-neural-network digital-elevation-model flat-file-db generative-adversarial-network glaciology jupyter-notebook optuna pangeo remote-sensing super-resolution

Last synced: 26 days ago
JSON representation

Going beyond BEDMAP2 using a super resolution deep neural network. Also a convenient flat file data repository for high resolution bed elevation datasets around Antarctica.

Awesome Lists containing this project

README 

        
# DeepBedMap  [[paper]](https://doi.org/10.5194/tc-14-3687-2020) [[poster]](https://github.com/weiji14/deepbedmap/issues/133) [[presentation]](https://hackmd.io/@weiji14/2022ML4Polar)



Going beyond BEDMAP2 using a super resolution deep neural network.

Also a convenient [flat file](https://en.wikipedia.org/wiki/Flat-file_database) data repository for high resolution bed elevation datasets around Antarctica.



[![DOI](https://zenodo.org/badge/147595013.svg)](https://zenodo.org/badge/latestdoi/147595013)

![GitHub top language](https://img.shields.io/github/languages/top/weiji14/deepbedmap.svg)

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)

[![Comet.ML: experiments](https://img.shields.io/badge/Comet.ml-experiments-orange.svg?logo=data:image/png;base64,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)](https://www.comet.ml/weiji14/deepbedmap/)

[![Github Actions Build Status](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fweiji14%2Fdeepbedmap%2Fbadge&style=flat)](https://github.com/weiji14/deepbedmap/actions)

[![Dependabot Status](https://api.dependabot.com/badges/status?host=github&repo=weiji14/deepbedmap)](https://dependabot.com)



![DeepBedMap DEM over entire Antarctic continent, EPSG:3031 projection](https://user-images.githubusercontent.com/23487320/94385232-16dee180-01a1-11eb-83ce-8793709079ff.png)



![DeepBedMap Pipeline](https://yuml.me/diagram/scruffy;dir:LR/class/[Data|Highres/Lowres/Misc]->[Preprocessing|data_prep.ipynb],[Preprocessing]->[Model-Training|srgan_train.ipynb],[Model-Training]->[Inference|deepbedmap.ipynb])



Directory structure



```

  deepbedmap/

    ├── features/ (files describing the high level behaviour of various features)

    │    ├── *.feature... (easily understandable specifications written using the Given-When-Then gherkin language)

    │    └── README.md (markdown information on the feature files)

    ├── highres/ (contains high resolution localized DEMs)

    │    ├── *.txt/csv/grd/xyz... (input vector file containing the point-based bed elevation data)

    │    ├── *.json (the pipeline file used to process the xyz point data)

    │    ├── *.nc (output raster netcdf files)

    │    └── README.md (markdown information on highres data sources)

    ├── lowres/ (contains low resolution whole-continent DEMs)

    │    ├── bedmap2_bed.tif (the low resolution DEM!)

    │    └── README.md (markdown information on lowres data sources)

    ├── misc/ (miscellaneous raster datasets)

    │    ├── *.tif (Surface DEMs, Ice Flow Velocity, etc. See list in Issue #9)

    │    └── README.md (markdown information on miscellaneous data sources)

    ├── model/ (*hidden in git, neural network model related files)

    │    ├── train/ (a place to store the raster tile bounds and model training data)

    │    └── weights/ (contains the neural network model's architecture and weights)

    ├── .env (environment variable config file used by pipenv)

    ├── .ignore (files ignored by a particular piece of software)

    ├── . (stuff to make the code in this repo look and run nicely e.g. linters, CI/CD config files, etc)

    ├── Dockerfile (set of commands to fully reproduce the software stack here into a docker image, used by binder)

    ├── LICENSE.md (the license covering this repository)

    ├── Pipfile (what you want, the summary list of core python dependencies)

    ├── Pipfile.lock (what you need, all the pinned python dependencies for full reproducibility)

    ├── README.md (the markdown file you're reading now)

    ├── data_list.yml (human and machine readable list of the datasets and their metadata)

    ├── data_prep.ipynb/py (paired jupyter notebook/python script that prepares the data)

    ├── deepbedmap.ipynb/py (paired jupyter notebook/python script that predicts an Antarctic bed digital elevation model)

    ├── environment.yml (conda binary packages to install)

    ├── paper_figures.ipynb/py (paired jupyter notebook/python script to produce figures for DeepBedMap paper

    ├── srgan_train.ipynb/py (paired jupyter notebook/python script that trains the ESRGAN neural network model)

    └── test_ipynb.ipynb/py (paired jupyter notebook/python script that runs doctests in the other jupyter notebooks!)

```



# Getting started



## Quickstart



Launch in [Binder](https://mybinder.readthedocs.io) (Interactive jupyter notebook/lab environment in the cloud).



[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/weiji14/deepbedmap/master)

[![Open All Collab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/weiji14/deepbedmap)



## Installation



![Installation steps](https://yuml.me/diagram/scruffy/class/[Git|clone-repo]->[Conda|install-binaries-and-pipenv],[Conda]->[Pipenv|install-python-libs])



Start by cloning this [repo-url](/../../)



    git clone 



Then I recommend [using conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) to install the non-python binaries (e.g. GMT, CUDA, etc).

The conda virtual environment will also be created with Python and [pipenv](https://pipenv.readthedocs.io) installed.



    cd deepbedmap

    conda env create -f environment.yml



Activate the conda environment first.



    conda activate deepbedmap



Then set some environment variables **before** using pipenv to install the necessary python libraries,

otherwise you may encounter some problems (see Common problems below).

You may want to ensure that `which pipenv` returns something similar to ~/.conda/envs/deepbedmap/bin/pipenv.



    export HDF5_DIR=$CONDA_PREFIX/

    export LD_LIBRARY_PATH=$CONDA_PREFIX/lib/

    pipenv install --python $CONDA_PREFIX/bin/python --dev

    #or just

    HDF5_DIR=$CONDA_PREFIX/ LD_LIBRARY_PATH=$CONDA_PREFIX/lib/ pipenv install --python $CONDA_PREFIX/bin/python --dev



Finally, double-check that the libraries have been installed.



    pipenv graph



### Syncing/Updating to new dependencies



    conda env update -f environment.yml

    pipenv sync --dev



### Common problems



Note that the [.env](https://pipenv.readthedocs.io/en/latest/advanced/#configuration-with-environment-variables) file stores some environment variables.

So if you run `conda activate deepbedmap` followed by some other command and get an `...error while loading shared libraries: libpython3.7m.so.1.0...`,

you may need to run `pipenv shell` or do `pipenv run ` to have those environment variables registered properly.

Or just run this first:



    export LD_LIBRARY_PATH=$CONDA_PREFIX/lib/



Also, if you get a problem when using `pipenv` to install [netcdf4](https://github.com/Unidata/netcdf4-python), make sure you have done:



    export HDF5_DIR=$CONDA_PREFIX/



and then you can try using `pipenv install` or `pipenv sync` again.

See also this [issue](https://github.com/pydata/xarray/issues/3185#issuecomment-520693149) for more information.



## Running jupyter lab



    conda activate deepbedmap

    pipenv shell



    python -m ipykernel install --user --name deepbedmap  #to install conda env properly

    jupyter kernelspec list --json                        #see if kernel is installed

    jupyter lab &



## Citing



The paper is published at [The Cryosphere](https://www.the-cryosphere.net) and can be referred to using the following BibTeX code:



    @Article{tc-14-3687-2020,

        AUTHOR = {Leong, W. J. and Horgan, H. J.},

        TITLE = {DeepBedMap: a deep neural network for resolving the bed topography of Antarctica},

        JOURNAL = {The Cryosphere},

        VOLUME = {14},

        YEAR = {2020},

        NUMBER = {11},

        PAGES = {3687--3705},

        URL = {https://tc.copernicus.org/articles/14/3687/2020/},

        DOI = {10.5194/tc-14-3687-2020}

    }



The DeepBedMap_DEM v1.1.0 dataset is available from Zenodo at https://doi.org/10.5281/zenodo.4054246.

Neural network model training experiment runs are also recorded at https://www.comet.ml/weiji14/deepbedmap.

Python code for the DeepBedMap model here on Github is also mirrored on Zenodo at https://doi.org/10.5281/zenodo.3752613.