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Merge pull request #212 from alan-turing-institute/add-nb-circ23-team7
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Notebook - CIRC23  Variational data assimilation with deep prior
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acocac authored Sep 19, 2023
2 parents a9ed065 + bebe294 commit 6ef7d4b
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6 changes: 5 additions & 1 deletion .gitmodules
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[submodule "book/notebooks/gallery/93463cac-471a-469d-ad52-0514fd9b67f2"]
path = book/notebooks/gallery/93463cac-471a-469d-ad52-0514fd9b67f2
url = https://github.com/eds-book-gallery/93463cac-471a-469d-ad52-0514fd9b67f2.git
branch = render
branch = render
[submodule "book/notebooks/gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3"]
path = book/notebooks/gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3
url = https://github.com/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3.git
branch = render
15 changes: 14 additions & 1 deletion book/_bibliography/references.bib
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Expand Up @@ -407,4 +407,17 @@ @article{Richardson_2018
year = {2018},
bdsk-url-1 = {https://dx.doi.org/10.1088/1748-9326/aab305},
topic = {93463cac-471a-469d-ad52-0514fd9b67f2_dataset}
}
}

### 39d9c177-11da-41b2-9b64-63f4c1c834b3
@article{filoche_2023,
title={Deep prior in variational assimilation to estimate an ocean circulation without explicit regularization},
volume={2},
DOI={10.1017/eds.2022.31},
journal={Environmental Data Science},
author={Filoche, Arthur and Béréziat, Dominique and Charantonis, Anastase},
year={2023},
pages={e2},
topic = {39d9c177-11da-41b2-9b64-63f4c1c834b3}
}
2 changes: 2 additions & 0 deletions book/_toc.yml
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Expand Up @@ -23,6 +23,8 @@ parts:
- file: notebooks/gallery
title: Gallery
sections:
- file: notebooks/gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/notebook
title: Variational data assimilation with deep prior (CIRC23)
- file: notebooks/gallery/93463cac-471a-469d-ad52-0514fd9b67f2/notebook
title: Deep learning and variational inversion for climate science (CIRC23)
- file: notebooks/gallery/3286b92f-4fae-4cc6-a29e-e408bc844542/notebook
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36 changes: 36 additions & 0 deletions book/notebooks/gallery.md
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::::{grid} 1 3 3 3
:gutter: 2

:::{grid-item-card} Variational data assimilation with deep prior (CIRC23)
:margin: 3 0 0 0
:link: ./gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/notebook.html
:link-type: url
:text-align: center
:shadow: md

{bdg-primary}`Ocean`
{bdg-secondary}`Modelling`
<br>
{bdg-warning}`Special Issue`
{bdg-info}`Python`
^^^

<img src="https://github.com/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/assets/13321552/22a8817b-27ed-4dac-af7a-580dbce2e607?raw=True"/>

+++
Pahari *et al.* (2023)

<p align="center">
<a href="https://github.com/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/blob/main/LICENSE">
<img alt="license" src="https://img.shields.io/badge/license-MIT-yellow.svg">
</a>
<a href="http://mybinder.org/v2/gh/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/main?labpath=notebook.ipynb">
<img alt="binder" src="https://mybinder.org/badge_logo.svg">
</a>
<a href="https://github.com/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/actions/workflows/render.yaml">
<img alt="render" src="https://github.com/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/actions/workflows/render.yaml/badge.svg">
</a>
<a href="https://zenodo.org/badge/latestdoi/643572395">
<img alt="doi" src="https://zenodo.org/badge/643572395.svg">
</a>
<br/>
</p>
:::

:::{grid-item-card} Deep learning and variational inversion for climate science (CIRC23)
:margin: 3 0 0 0
:link: ./gallery/93463cac-471a-469d-ad52-0514fd9b67f2/notebook.html
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71 changes: 33 additions & 38 deletions misc/rohub/register.py
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# metadata
metadata_contribution = {
'environment': 'general',
'environment': 'ocean',
'topic': 'modelling',
'reponame': '93463cac-471a-469d-ad52-0514fd9b67f2',
'title': "Deep learning and variational inversion to quantify and attribute climate change (CIRC23)",
'inputs': {'input1':{'name':'Input dataset for paper',
'url':'https://gitlab.com/ConstantinBone/detection-and-attribution-of-climate-change-a-deep-learning-and-variational-approach/-/raw/main/data_pre_ind_2.zip'},
'reponame': '39d9c177-11da-41b2-9b64-63f4c1c834b3',
'title': "Variational data assimilation with deep prior (CIRC23)",
'inputs': {'input1':{'name':'Codebase of the reproduced paper',
'url':'https://github.com/ArFiloche/Deepprior4DVar_CI22'},
},
'outputs': {'content': 'figures, models and results',
'url': "https://doi.org/10.5281/zenodo.8279574"},
'url': "https://doi.org/10.5281/zenodo.8338556"},
'author_GHuser': 'eds-book-gallery',
'references':{'ref1':{'name':'Detection and attribution of climate change: A deep learning and variational approach','url':"http://doi.org/10.1017/eds.2022.17"}},
'sketch': {'title':'Image showing mean and standard deviation of the simulations of 12 climate models',
'path':'_temp/rohub/93463cac-471a-469d-ad52-0514fd9b67f2/plot.png'}
'references':{'ref1':{'name':'Deep prior in variational assimilation to estimate an ocean circulation without explicit regularization',
'url':"http://doi.org/10.1017/eds.2022.31"}},
'sketch': {'title':'Image showing an example of the estimated motion fields with various algorithms',
'path':'_temp/rohub/39d9c177-11da-41b2-9b64-63f4c1c834b3/plot.png'}
}

title_nb = metadata_contribution['title']

metadata_rohub = {
'title': f'{title_nb} (Jupyter Notebook) published in the Environmental Data Science book',
'research_areas': ['Environmental research', 'Climate science', 'Deep learning'],
'research_areas': ['Environmental research', 'Oceanography', 'Deep learning'],
'description': f'The research object refers to the {title_nb} notebook published in the Environmental Data Science book.',
'ros_type': 'Executable Research Object',
'ros_template': 'Executable Research Object folders structure',
Expand All @@ -47,46 +48,40 @@
# edition
authors=[
{"agent_type": "user",
"display_name": "Viktor Domazetoski",
"name": "Viktor Domazetoski",
"orcid_id": "0000-0001-9830-7032",
"email": "[email protected]",
"affiliation": "University of Göttingen"},
{"agent_type": "user",
"display_name": "Andrés Zúñiga-González ",
"name": "Andrés Zúñiga-González ",
"email": "[email protected]",
"display_name": "Mukulika Pahari",
"name": "Mukulika Pahari",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "University of Cambridge"},
"affiliation": "University of Mumbai"},
{"agent_type": "user",
"display_name": "Owen Allemang",
"name": "Owen Allemang",
"email": "[email protected]",
"display_name": "Rutika Bhoir",
"name": "Rutika Bhoir",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "University of Cambridge"}
"affiliation": "University of Mumbai"},
]

ro.set_authors(agents=authors)

reviewers=[
{"agent_type": "user",
"display_name": "Meghna Asthana",
"name": "Meghna Asthana",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "The Alan Turing Institute"},
"display_name": "Tina Odaka",
"name": "Tina Odaka",
"email": "[email protected]",
"orcid_id": "0000-0002-1500-0156",
"affiliation": "Ifremer"},
{"agent_type": "user",
"display_name": "Nick Homer",
"name": "Nick Homer",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "The University of Edinburgh"},
"display_name": "Caroline Arnold",
"name": "Caroline Arnold",
"email": "[email protected]",
"orcid_id": "0000-0002-9458-1517",
"affiliation": "German Climate Computing Center"},
{"agent_type": "user",
"display_name": "Devanjan Bhattacharya",
"name": "Devanjan Bhattacharya",
"email": "[email protected]",
"display_name": "Paolo Pelucchi",
"name": "Paolo Pelucchi",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "The University of Edinburgh"},
"affiliation": "Universitat de València"},
]

ro.set_contributors(agents=reviewers)
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