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Notebook","category":"Cryosphere","sub_category":"Glacier and Ice Sheets","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# DeepIceDrain [[poster]](https://github.com/weiji14/nzasc2021)\n\nMapping and monitoring deep subglacial water activity\nin Antarctica using remote sensing and machine learning.\n\n[![Zenodo Digital Object Identifier](https://zenodo.org/badge/DOI/10.5281/zenodo.4071235.svg)](https://doi.org/10.5281/zenodo.4071235)\n![GitHub top language](https://img.shields.io/github/languages/top/weiji14/deepicedrain.svg)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)\n[![Test DeepIceDrain package](https://github.com/weiji14/deepicedrain/actions/workflows/python-app.yml/badge.svg)](https://github.com/weiji14/deepicedrain/actions/workflows/python-app.yml)\n[![Dependabot Status](https://api.dependabot.com/badges/status?host=github\u0026repo=weiji14/deepicedrain)](https://dependabot.com)\n![License](https://img.shields.io/github/license/weiji14/deepicedrain)\n\n| Ice Surface Elevation trends over Antactica | Active Subglacial Lake fill-drain event |\n|---|---|\n| ![ICESat-2 ATL11 rate of height change over time in Antarctica 2019-03-29 to 2020-12-24](https://user-images.githubusercontent.com/23487320/123902132-65cfd680-d9c0-11eb-88d6-4e0e8c5abc47.png) | ![dsm_whillans_ix_cycles_3-9.gif](https://user-images.githubusercontent.com/23487320/124219379-5ed7ce00-db50-11eb-95d0-f1f660d4d688.gif) |\n\n![DeepIceDrain Pipeline Part 1 Exploratory Data Analysis](https://yuml.me/diagram/scruffy;dir:LR/class/[Land-Ice-Elevation|atl06_play.ipynb]-\u003e[Convert|atl06_to_atl11.ipynb],[Convert]-\u003e[Land-Ice-Height-time-series|atl11_play.ipynb])\n![DeepIceDrain Pipeline Part 2 Subglacial Lake Analysis](https://yuml.me/diagram/scruffy;dir:LR/class/[Height-Change-over-Time-(dhdt)|atlxi_dhdt.ipynb],[Height-Change-over-Time-(dhdt)]-\u003e[Subglacial-Lake-Finder|atlxi_lake.ipynb],[Subglacial-Lake-Finder]-\u003e[Crossover-Analysis|atlxi_xover.ipynb])\n\n| Along track view of an ATL11 Ground Track | Elevation time-series at Crossover Points |\n|---|---|\n| ![alongtrack_whillans_ix_1080_pt3](https://user-images.githubusercontent.com/23487320/124219416-744cf800-db50-11eb-83a1-45e1e1159ba6.png) | ![crossover_anomaly_whillans_ix_2019-03-29_2020-12-24](https://user-images.githubusercontent.com/23487320/124219432-7a42d900-db50-11eb-92b4-c83728b8dc1c.png) |\n\n\n\n# Getting started\n\n## Quickstart\n\nLaunch in [Binder](https://mybinder.readthedocs.io) (Interactive jupyter lab environment in the cloud).\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/weiji14/deepicedrain/main)\n\nAlternative [Pangeo BinderHub](https://pangeo-binder.readthedocs.io) link.\nRequires a GitHub account and you'll have to install your own computing environment,\nbut it runs on AWS uswest2 which allows for\n[cloud access to ICESat-2](https://nsidc.org/data/user-resources/data-announcements/data-set-updates-new-earthdata-cloud-access-option-icesat-2-and-icesat-data-sets)!\n\n[![Pangeo BinderHub](https://aws-uswest2-binder.pangeo.io/badge_logo.svg)](https://hub.aws-uswest2-binder.pangeo.io/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fweiji14%2Fdeepicedrain\u0026urlpath=lab%2Ftree%2Fdeepicedrain%2F\u0026branch=main)\n\n\n## Usage\n\nOnce you've properly installed the [`deepicedrain` package](deepicedrain)\n(see installation instructions further below), you'll have access to a\n[wide range of tools](https://github.com/weiji14/deepicedrain/tree/main/deepicedrain)\nfor downloading and performing quick calculations on ICESat-2 datasets.\nThe example below shows how to calculate ice surface elevation change\non a sample ATL11 dataset between ICESat's Cycle 3 and Cycle 4.\n\n    import deepicedrain\n    import xarray as xr\n\n    # Loads a sample ATL11 file from the intake catalog into xarray\n    atl11_dataset: xr.Dataset = deepicedrain.catalog.test_data.atl11_test_case.read()\n\n    # Calculate elevation change in metres from ICESat-2 Cycle 3 to Cycle 4\n    delta_height: xr.DataArray = deepicedrain.calculate_delta(\n          dataset=atl11_dataset, oldcyclenum=3, newcyclenum=4, variable=\"h_corr\"\n    )\n\n    # Quick plot of delta_height along the ICESat-2 track\n    delta_height.plot()\n\n![ATL11 delta_height along ref_pt track](https://user-images.githubusercontent.com/23487320/83319030-bf7e4280-a28e-11ea-9bed-331e35dbc266.png)\n\n\n\n## Installation\n\n### Basic\n\nTo just try out the scripts, download the `environment.yml` file from the repository and run the commands below:\n\n    cd deepicedrain\n    mamba env create --name deepicedrain --file environment.yml\n    pip install git+https://github.com/weiji14/deepicedrain.git\n\n### Intermediate\n\nTo help out with development, start by cloning this [repo-url](/../../)\n\n    git clone \u003crepo-url\u003e\n\nThen I recommend [using mamba](https://mamba.readthedocs.io/en/latest/installation.html)\nto install the non-python binaries.\nA virtual environment will also be created with Python and\n[poetry](https://github.com/python-poetry/poetry) installed.\n\n    cd deepicedrain\n    mamba env create --file environment.yml\n\nActivate the virtual environment first.\n\n    mamba activate deepicedrain\n\nThen install the python libraries listed in the `pyproject.toml`/`poetry.lock` file.\n\n    poetry install\n\nFinally, double-check that the libraries have been installed.\n\n    poetry show\n\n### Advanced\n\nThis is for those who want full reproducibility of the virtual environment,\nand more computing power by using Graphical Processing Units (GPU).\n\nMaking an explicit [conda-lock](https://github.com/conda-incubator/conda-lock) file\n(only needed if creating a new virtual environment/refreshing an existing one).\n\n    mamba env create -f environment.yml\n    mamba list --explicit \u003e environment-linux-64.lock\n\nCreating/Installing a virtual environment from a conda lock file.\nSee also https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments.\n\n    mamba create --name deepicedrain --file environment-linux-64.lock\n    mamba install --name deepicedrain --file environment-linux-64.lock\n\nIf you have a [CUDA](https://en.wikipedia.org/wiki/CUDA)-capable GPU,\nyou can also install the optional \"cuda\" packages to accelerate some calculations.\n\n    poetry install --extras cuda\n\n\n## Running jupyter lab\n\n    mamba activate deepicedrain\n    python -m ipykernel install --user --name deepicedrain  # to install virtual env properly\n    jupyter kernelspec list --json                          # see if kernel is installed\n    jupyter lab \u0026\n\n\n## Related Projects\n\nThis work would not be possible without inspiration\nfrom the following cool open source projects!\nGo check them out if you have time.\n\n- [ATL11](https://github.com/suzanne64/ATL11)\n- [ICESAT-2 HackWeek](https://github.com/ICESAT-2HackWeek)\n- [icepyx](https://github.com/icesat2py/icepyx)\n\n\n## Citing\n\nThe work in this repository has not been peer-reviewed, but if you do want to\ncite it for some reason, use the following BibLaTeX code from this conference\nproceedings ([poster presentation](https://github.com/weiji14/nzasc2021)):\n\n    @inproceedings{LeongSpatiotemporalvariabilityactive2021,\n      title = {{Spatiotemporal Variability of Active Subglacial Lakes in Antarctica from 2018-2020 Using ICESat-2 Laser Altimetry}},\n      author = {Leong, W. J. and Horgan, H. J.},\n      date = {2021-02-10},\n      publisher = {{Unpublished}},\n      location = {{Christchurch, New Zealand}},\n      doi = {10.13140/RG.2.2.27952.07680},\n      eventtitle = {{New Zealand Antarctic Science Conference}}},\n      langid = {english}\n    }\n\nPython code for the DeepIceDrain package here on Github is also mirrored on Zenodo at https://doi.org/10.5281/zenodo.4071235.\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.4071235"],"works":{"https://doi.org/10.5281/zenodo.4071235":null},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["transformations","measuring","compose","archives","reporter","optimize","observation","annotation","animations","numeric"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/680","html_url":"https://ost.ecosyste.ms/projects/680"}