diff --git a/.gitmodules b/.gitmodules index 65bc6cb0..0b6da147 100644 --- a/.gitmodules +++ b/.gitmodules @@ -54,3 +54,7 @@ path = book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b url = https://github.com/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b.git branch = render +[submodule "book/notebooks/gallery/95199651-9e81-4cae-a3a7-66398a9a5f62"] + path = book/notebooks/gallery/95199651-9e81-4cae-a3a7-66398a9a5f62 + url = https://github.com/eds-book-gallery/95199651-9e81-4cae-a3a7-66398a9a5f62 + branch = render diff --git a/book/_bibliography/references.bib b/book/_bibliography/references.bib index 678ebb93..6e1b1e6e 100644 --- a/book/_bibliography/references.bib +++ b/book/_bibliography/references.bib @@ -93,7 +93,7 @@ @article{Weinstein2020_MEE volume = {11}, url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13472}, year = {2020}, - topic = {15d986da-2d7c-44fb-af71-700494485def} + topic = {15d986da-2d7c-44fb-af71-700494485def, 95199651-9e81-4cae-a3a7-66398a9a5f62} } @article{Weinstein2020_EI, @@ -437,4 +437,17 @@ @misc{cocacastro2024_icenetnb doi = {10.5281/zenodo.10808514}, url = {https://doi.org/10.5281/zenodo.10808514}, topic = {67a1e320-7c47-4ea9-8df8-e868326bc90b} +} + +### 95199651-9e81-4cae-a3a7-66398a9a5f62 + +@misc{livestockdataset, + author = {G.J. Franke and Sander Mucher}, + publisher = {Harvard Dataverse}, + title = {{Annotated cows in aerial images for use in deep learning models}}, + year = {2021}, + version = {V1}, + doi = {10.7910/DVN/N7GJYU}, + url = {https://doi.org/10.7910/DVN/N7GJYU}, + topic = {95199651-9e81-4cae-a3a7-66398a9a5f62} } \ No newline at end of file diff --git a/book/_toc.yml b/book/_toc.yml index 75f58b45..a44f82e9 100644 --- a/book/_toc.yml +++ b/book/_toc.yml @@ -23,6 +23,8 @@ parts: - file: notebooks/gallery title: Gallery sections: + - file: notebooks/gallery/95199651-9e81-4cae-a3a7-66398a9a5f62/notebook + title: Livestock detection (DeepForest) - file: notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/notebook title: Daily sea ice forecasting (IceNet) - file: notebooks/gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/notebook diff --git a/book/notebooks/gallery.md b/book/notebooks/gallery.md index 5d091e2e..b48bdeae 100644 --- a/book/notebooks/gallery.md +++ b/book/notebooks/gallery.md @@ -5,6 +5,42 @@ ::::{grid} 1 3 3 3 :gutter: 2 +:::{grid-item-card} Livestock detection <br> (DeepForest) +:margin: 3 0 0 0 +:link: ./gallery/95199651-9e81-4cae-a3a7-66398a9a5f62/notebook.html +:link-type: url +:text-align: center +:shadow: md + +{bdg-primary}`Farming` +{bdg-secondary}`Modelling` +<br> +{bdg-warning}`Standard` +{bdg-info}`Python` +^^^ + +<img src="https://github.com/eds-book-gallery/95199651-9e81-4cae-a3a7-66398a9a5f62/blob/postprint/images/thumbnail.png?raw=True"/> + ++++ +Appel (2024) + +<p align="center"> + <a href="https://github.com/eds-book-gallery/95199651-9e81-4cae-a3a7-66398a9a5f62/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/95199651-9e81-4cae-a3a7-66398a9a5f62/main?labpath=notebook.ipynb"> + <img alt="binder" src="https://mybinder.org/badge_logo.svg"> + </a> + <a href="https://github.com/eds-book-gallery/95199651-9e81-4cae-a3a7-66398a9a5f62/actions/workflows/render.yaml"> + <img alt="render" src="https://github.com/eds-book-gallery/95199651-9e81-4cae-a3a7-66398a9a5f62/actions/workflows/render.yaml/badge.svg"> + </a> + <a href="https://zenodo.org/badge/latestdoi/880931043"> + <img alt="doi" src="https://zenodo.org/badge/880931043.svg"> + </a> + <br/> +</p> +::: + :::{grid-item-card} Daily sea ice forecasting <br> (IceNet library) :margin: 3 0 0 0 :link: ./gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/notebook.html diff --git a/book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b b/book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b index 6e38225e..50154723 160000 --- a/book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b +++ b/book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b @@ -1 +1 @@ -Subproject commit 6e38225e9abb162569ddfc01f3b9bd17da84b122 +Subproject commit 501547232a75237238f40fb5866c105a0209199e diff --git a/book/notebooks/gallery/95199651-9e81-4cae-a3a7-66398a9a5f62 b/book/notebooks/gallery/95199651-9e81-4cae-a3a7-66398a9a5f62 new file mode 160000 index 00000000..f834435f --- /dev/null +++ b/book/notebooks/gallery/95199651-9e81-4cae-a3a7-66398a9a5f62 @@ -0,0 +1 @@ +Subproject commit f834435f45fde0684f7490c7caf4bdd5787f7286 diff --git a/misc/rohub/register.py b/misc/rohub/register.py index c6d10dd6..40ef9380 100644 --- a/misc/rohub/register.py +++ b/misc/rohub/register.py @@ -10,27 +10,27 @@ # metadata metadata_contribution = { - 'environment': 'polar', + 'environment': 'farming', 'topic': 'modelling', - 'reponame': '67a1e320-7c47-4ea9-8df8-e868326bc90b', - 'title': "Sea ice forecasting using the IceNet library", - 'inputs': {'input1':{'name':'Codebase of the IceNet library', - 'url':'https://github.com/icenet-ai/icenet/'}, + 'reponame': '95199651-9e81-4cae-a3a7-66398a9a5f62', + 'title': "Livestock detection using DeepForest", + 'inputs': {'input1':{'name':'Input dataset for the fine-tuned model', + 'url':'https://doi.org/10.7910/DVN/N7GJYU'}, }, 'outputs': {'content': 'results', - 'url': "https://doi.org/10.5281/zenodo.12612126"}, + 'url': "https://doi.org/10.5281/zenodo.14279111"}, 'author_GHuser': 'eds-book-gallery', - 'references':{'ref1':{'name':'Seasonal Arctic sea ice forecasting with probabilistic deep learning', - 'url':"https://doi.org/10.1038/s41467-021-25257-4"}}, - 'sketch': {'title':'Image showing an example of the forecasted sea ice', - 'path':'_temp/rohub/67a1e320-7c47-4ea9-8df8-e868326bc90b/plot.png'} + 'references':{'ref1':{'name':'Deepforest: a python package for rgb deep learning tree crown delineation', + 'url':"https://doi.org/https://doi.org/10.1111/2041-210X.13472"}}, + 'sketch': {'title':'Image showing an example of the finetuned model predictions to detect livestock', + 'path':'_temp/rohub/95199651-9e81-4cae-a3a7-66398a9a5f62/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', 'Oceanography', 'Deep learning'], + 'research_areas': ['Environmental research', 'Agriculture', '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', @@ -48,34 +48,27 @@ # edition authors=[ {"agent_type": "user", - "display_name": "Bryn Noel Ubald", - "name": "Bryn Noel Ubald", - "email": "bryald@bas.ac.uk", - "orcid_id": "0000-0002-0206-7140", - "affiliation": "British Antarctic Survey"}, - {"agent_type": "user", - "display_name": "James Byrne", - "name": "James Byrne", - "email": "jambyr@bas.ac.uk", - "orcid_id": "0000-0003-3731-2377", - "affiliation": "British Antarctic Survey"}, + "display_name": "Cameron Appel", + "name": "Cameron Appel", + "email": "c.appel@qmul.ac.uk", + "affiliation": "Queen Mary University London"}, ] ro.set_authors(agents=authors) reviewers=[ {"agent_type": "user", - "display_name": "Wei Ji", - "name": "Wei Ji", - "email": "weiji@developmentseed.org", - "orcid_id": "0000-0003-2354-1988", - "affiliation": "Development Seed"}, + "display_name": "Ethan P. White", + "name": "Ethan P. White", + "email": "ethanwhite@ufl.edu", + "orcid_id": "0000-0001-6728-7745", + "affiliation": "University of Florida"}, {"agent_type": "user", - "display_name": "William Gregory", - "name": "William Gregory", - "email": "wg4031@princeton.edu", - "orcid_id": "0000-0001-8176-1642", - "affiliation": "Princeton University"}, + "display_name": "Louisa Van Zeeland", + "name": "Louisa Van Zeeland", + "email": "lvanzeeland@turing.ac.uk", + "orcid_id": "0009-0005-0392-4377", + "affiliation": "The Alan Turing Institute"}, ] ro.set_contributors(agents=reviewers) diff --git a/misc/uuid/gen_uuid.py b/misc/uuid/gen_uuid.py index b412b7ff..45da3882 100644 --- a/misc/uuid/gen_uuid.py +++ b/misc/uuid/gen_uuid.py @@ -205,6 +205,7 @@ def gen_new_uuid_edsbook(): 'ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef', '94486a7f-e046-461f-bbb9-334ec7b57040', 'bc30df18-fce2-42fa-aade-1ce5b7f3ca3c', '15d986da-2d7c-44fb-af71-700494485def', 'a2875cdc-ba6a-49dc-aab7-cdf7c4fc0fa8', '1b8921af-e77f-4ccf-ae38-4813cdceba0f', - 'b34facfa-cea8-48f5-89f6-f11ce00812a9', '93463cac-471a-469d-ad52-0514fd9b67f2'] + 'b34facfa-cea8-48f5-89f6-f11ce00812a9', '93463cac-471a-469d-ad52-0514fd9b67f2', + '67a1e320-7c47-4ea9-8df8-e868326bc90b', '95199651-9e81-4cae-a3a7-66398a9a5f62'] gen_new_uuid_edsbook()