From f860a98f8d27400509e0e038e8dcc1e8fc28f907 Mon Sep 17 00:00:00 2001 From: trchudley Date: Thu, 24 Oct 2024 10:17:16 +0100 Subject: [PATCH] add JOSS citation to docs --- CITATION.cff | 38 +++++++++++++++++++++++++++ README.md | 27 +++++++++++-------- docs/appendix/faq.md | 0 docs/conf.py | 11 ++++++-- docs/getting_started/cite.md | 18 ++++++++++--- docs/getting_started/why_pdemtools.md | 6 ++--- docs/index.rst | 20 +++++++++++--- 7 files changed, 96 insertions(+), 24 deletions(-) create mode 100644 CITATION.cff mode change 100755 => 100644 docs/appendix/faq.md mode change 100755 => 100644 docs/getting_started/why_pdemtools.md diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..030c240 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,38 @@ +cff-version: "1.2.0" +authors: +- family-names: Chudley + given-names: Thomas R. + orcid: "https://orcid.org/0000-0001-8547-1132" +- family-names: Howat + given-names: Ian M. + orcid: "https://orcid.org/0000-0002-8072-6260" +contact: +- family-names: Chudley + given-names: Thomas R. + orcid: "https://orcid.org/0000-0001-8547-1132" +doi: 10.5281/zenodo.13936813 +message: If you use this software, please cite our article in the + Journal of Open Source Software. +preferred-citation: + authors: + - family-names: Chudley + given-names: Thomas R. + orcid: "https://orcid.org/0000-0001-8547-1132" + - family-names: Howat + given-names: Ian M. + orcid: "https://orcid.org/0000-0002-8072-6260" + date-published: 2024-10-23 + doi: 10.21105/joss.07149 + issn: 2475-9066 + issue: 102 + journal: Journal of Open Source Software + publisher: + name: Open Journals + start: 7149 + title: "pDEMtools: conveniently search, download, and process + ArcticDEM and REMA products" + type: article + url: "https://joss.theoj.org/papers/10.21105/joss.07149" + volume: 9 +title: "pDEMtools: conveniently search, download, and process ArcticDEM + and REMA products" diff --git a/README.md b/README.md index d329e7c..dac6c28 100644 --- a/README.md +++ b/README.md @@ -3,10 +3,9 @@ __Conveniently search, download, and process ArcticDEM and REMA products__ -[![conda-forge version](https://anaconda.org/conda-forge/pdemtools/badges/version.svg)](https://anaconda.org/conda-forge/pdemtools) [![PyPI version](https://badge.fury.io/py/pdemtools.svg)](https://pypi.org/project/pdemtools/) [![Documentation Status](https://readthedocs.org/projects/pdemtools/badge/?version=latest)](https://pdemtools.readthedocs.io/en/latest/?badge=latest) [![Unit Tests](https://github.com/trchudley/pdemtools/actions/workflows/unit_test.yml/badge.svg)](https://github.com/trchudley/pdemtools/actions/workflows/unit_test.yml) [![JOSS paper](https://joss.theoj.org/papers/2a10e67d2709a6cfb672538b4a21726e/status.svg)](https://joss.theoj.org/papers/2a10e67d2709a6cfb672538b4a21726e) +[![conda-forge version](https://anaconda.org/conda-forge/pdemtools/badges/version.svg)](https://anaconda.org/conda-forge/pdemtools) [![PyPI version](https://badge.fury.io/py/pdemtools.svg)](https://pypi.org/project/pdemtools/) [![Documentation Status](https://readthedocs.org/projects/pdemtools/badge/?version=latest)](https://pdemtools.readthedocs.io/en/latest/?badge=latest) [![Unit Tests](https://github.com/trchudley/pdemtools/actions/workflows/unit_test.yml/badge.svg)](https://github.com/trchudley/pdemtools/actions/workflows/unit_test.yml) [![JOSS paper](https://joss.theoj.org/papers/10.21105/joss.07149/status.svg)](https://doi.org/10.21105/joss.07149) - -pDEMtool provides a convenient set of functions to explore, download, and preprocess high-resolution DEMs of the polar regions from the ArcticDEM (Porter _et al._ 2022; 2023) and Reference Elevation Model of Antarctica (REMA; Howat _et al._ 2022a, b) products, courtesy of the Polar Geospatial Center (PGC). +pDEMtools provides a convenient set of functions to explore, download, and preprocess high-resolution DEMs of the polar regions from the ArcticDEM (Porter _et al._ 2022; 2023) and Reference Elevation Model of Antarctica (REMA; Howat _et al._ 2022a, b) products, courtesy of the Polar Geospatial Center (PGC). The first aim of pDEMtools is to enable access to ArcticDEM and REMA mosaics and multitemporal strips using the `search()` function and `load` module: @@ -36,19 +35,25 @@ Please visit the [pDEMtools readthedocs](https://pdemtools.readthedocs.io/) for ## Cite - - -A software paper is being prepared for the [Journal of Open Source Software](https://joss.theoj.org/). In the meantime, the use of the pDEMtools package can be cited as follows: +A software paper for `pdemtools` is published in the [Journal of Open Source Software](https://joss.theoj.org/), and can be cited as follows: -> Chudley, T. R. and Howat, I. M. (2024) pDEMtools: conveniently search, download, and process ArcticDEM and REMA products (vX.X.X). GitHub. https://github.com/trchudley/pDEMtools +> Chudley, T. R., and Howat, I. M. (2024). pDEMtools: conveniently search, download, and process ArcticDEM and REMA products. _Journal of Open Source Software_, _9_(102), 7149, doi.org/10.21105/joss.07149 or by using `bibtex`: ``` -@software{pDEMtools - author = {Chudley, Thomas R. and Howat, Ian M.}, title = {pDEMtools: conveniently search, download, and process ArcticDEM and REMA products}, year = 2024, publisher = {GitHub}, version = {X.X.X}, url = {https://github.com/trchudley/pDEMtools} +@article{Chudley2024, + title = {pDEMtools: conveniently search, download, and process ArcticDEM and REMA products}, + volume = {9}, + ISSN = {2475-9066}, + url = {http://dx.doi.org/10.21105/joss.07149}, + DOI = {10.21105/joss.07149}, + number = {102}, + journal = {Journal of Open Source Software}, + publisher = {The Open Journal}, + author = {Chudley, Thomas R. and Howat, Ian M.}, + year = {2024}, + pages = {7149} } ``` diff --git a/docs/appendix/faq.md b/docs/appendix/faq.md old mode 100755 new mode 100644 diff --git a/docs/conf.py b/docs/conf.py index 3d20e75..ac341a2 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -6,8 +6,12 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information +import datetime + +year = datetime.date.today().year + project = "pdemtools" -# copyright = "2024, Tom Chudley" +copyright = "2023-{}, The pdemtools Development Team".format(year) author = "Tom Chudley" # release = "0.6" @@ -55,8 +59,10 @@ # Book theme options html_theme_options = { "repository_url": "https://github.com/trchudley/pdemtools", + "home_page_in_toc": False, "use_repository_button": True, - "home_page_in_toc": True, + "use_source_button": True, + "use_issues_button": True # "logo": { # "image_light": "_static/logo-light.png", # "image_dark": "_static/logo-dark.png", @@ -66,3 +72,4 @@ # Site-wide logo! html_logo = "_static/pdemtools_logo_1600px.png" + diff --git a/docs/getting_started/cite.md b/docs/getting_started/cite.md index 93177a8..b9ed701 100644 --- a/docs/getting_started/cite.md +++ b/docs/getting_started/cite.md @@ -1,14 +1,24 @@ # Cite -A software paper is being prepared for the [Journal of Open Source Software](https://joss.theoj.org/). In the meantime, the use of the pDEMtools package can be cited as follows: +A software paper for `pdemtools` is published in the [Journal of Open Source Software](https://joss.theoj.org/), and can be cited as follows: -> Chudley, T. R. and Howat, I. M. (2024) pDEMtools: conveniently search, download, and process ArcticDEM and REMA products (vX.X.X). GitHub. https://github.com/trchudley/pDEMtools +> Chudley, T. R., and Howat, I. M. (2024). pDEMtools: conveniently search, download, and process ArcticDEM and REMA products. _Journal of Open Source Software_, _9_(102), 7149, doi.org/10.21105/joss.07149 or by using `bibtex`: ``` -@software{pDEMtools - author = {Chudley, Thomas R. and Howat, Ian M.}, title = {pDEMtools: conveniently search, download, and process ArcticDEM and REMA products}, year = 2024, publisher = {GitHub}, version = {X.X.X}, url = {https://github.com/trchudley/pDEMtools} +@article{Chudley2024, + title = {pDEMtools: conveniently search, download, and process ArcticDEM and REMA products}, + volume = {9}, + ISSN = {2475-9066}, + url = {http://dx.doi.org/10.21105/joss.07149}, + DOI = {10.21105/joss.07149}, + number = {102}, + journal = {Journal of Open Source Software}, + publisher = {The Open Journal}, + author = {Chudley, Thomas R. and Howat, Ian M.}, + year = {2024}, + pages = {7149} } ``` diff --git a/docs/getting_started/why_pdemtools.md b/docs/getting_started/why_pdemtools.md old mode 100755 new mode 100644 index 3f4d76a..bfaaa66 --- a/docs/getting_started/why_pdemtools.md +++ b/docs/getting_started/why_pdemtools.md @@ -1,13 +1,13 @@ # Why pDEMtools? -> This page reproduces the 'Statement of Need' of the [_Journal of Open Source Software_ manuscript](https://joss.theoj.org/papers/2a10e67d2709a6cfb672538b4a21726e) for `pdemtools`. +> This page reproduces the 'Statement of Need' of the [_Journal of Open Source Software_ manuscript](http://dx.doi.org/10.21105/joss.07149) for `pdemtools`. [ArcticDEM](https://www.pgc.umn.edu/data/arcticdem/) and [REMA](https://www.pgc.umn.edu/data/rema/) are high-resolution, time-stamped 2-metre-resolution DEMs of the polar regions provided by the Polar Geospatial Center (PGC). They are extracted by applying stereo auto-correlation techniques ([Noh & Howat, 2017](https://doi.org/10.1016/j.isprsjprs.2017.04.019)) to pairs of submetre Maxar satellite imagery. The data includes Worldview-1, Worldview-2, Worldview-3, and GeoEye-1, beginning in 2007 (ArcticDEM) or 2009 (REMA) and ongoing to the present day. Products are available as tens of thousands of time-stamped 'strips' ([Porter _et al._ 2022](ttps://doi.org/10.7910/DVN/OHHUKH); [Howat _et al._ 2022a](https://doi.org/10.7910/DVN/X7NDNY)) constructed from individual scene pairs, or as a single mosaic ([Porter _et al._ 2023](https://doi.org/10.7910/DVN/3VDC4W); [Howat _et al._ 2022a](https://doi.org/10.7910/DVN/EBW8UC)) compiled from the combined stack of strips. Strips allow users to perform change detection by comparing data from different seasons or years, whilst mosaics provide a consistent and comprehensive product over the entire polar regions. -As Earth Science has moved into the 'big data' era, increasing amounts of Arctic- and Antarctic-focused resources are available as public, cloud-optimised datasets. New approaches are providing Python tools to act as combined API and processing tools, such as [`icepyx`](https://icepyx.readthedocs.io) ([Scheick _et al._ 2023](https://doi.org/10.21105/joss.04912)) or [`pypromice`](https://pypromice.readthedocs.io) ([How _et al._ 2023](https://doi.org/10.21105/joss.05298)). From 2022 (ArcticDEM v4.1 and REMA v2), the PGC DEM products are [hosted](https://polargeospatialcenter.github.io/stac-browser/#/external/pgc-opendata-dems.s3.us-west-2.amazonaws.com/pgc-data-stac.json) as Cloud Optimised GeoTIFFs (CoGs) in a SpatioTemporal Asset Catalog (STAC), a standardised structure for cataloguing spatiotemporal data. However, the PGC STAC is currently a 'static' rather than 'dynamic' STAC, which means there is no convenient Application Programming Interface (API) for searching the datasets in response to user queries. This limits the ability of users to programmatically interact with ArcticDEM and REMA data in a quick and efficient manner. The `pdemtools` package has two aims: the first is to provide a Python-focussed alternative for searching and downloading ArcticDEM and REMA data, emulating dynamic STAC query tools such as [`pystac`](https://pystac.readthedocs.io); whilst the second is to provide commonly used processing functions specific to the needs of ArcticDEM and REMA users (a focus on ice sheet and cryosphere work), as well as the particular strengths of the ArcticDEM and REMA datasets (high-resolution and multitemporal). +As Earth Science has moved into the 'big data' era, increasing amounts of Arctic- and Antarctic-focused resources are available as public, cloud-optimised datasets. New approaches are providing Python tools to act as combined Application Programming Interface (API) and processing tools, such as [`icepyx`](https://icepyx.readthedocs.io) ([Scheick _et al._ 2023](https://doi.org/10.21105/joss.04912)) or [`pypromice`](https://pypromice.readthedocs.io) ([How _et al._ 2023](https://doi.org/10.21105/joss.05298)). From 2022 (ArcticDEM v4.1 and REMA v2), the PGC DEM products are [hosted](https://polargeospatialcenter.github.io/stac-browser/#/external/pgc-opendata-dems.s3.us-west-2.amazonaws.com/pgc-data-stac.json) as Cloud Optimised GeoTIFFs (CoGs) in a SpatioTemporal Asset Catalog (STAC), a standardised structure for cataloguing spatiotemporal data. However, the PGC STAC is currently a 'static' rather than 'dynamic' STAC, which means there is no convenient API for searching the datasets in response to user queries. This limits the ability of users to programmatically interact with ArcticDEM and REMA data in a quick and efficient manner. The `pdemtools` package has two aims: the first is to provide a Python-focussed alternative for searching and downloading ArcticDEM and REMA data, emulating dynamic STAC query tools such as [`pystac`](https://pystac.readthedocs.io); whilst the second is to provide commonly used processing functions specific to the needs of ArcticDEM and REMA users (a focus on ice sheet and cryosphere work), as well as the particular strengths of the ArcticDEM and REMA datasets (high-resolution and multitemporal). The `pdemtools` `search()` tool and `load` module allow for convenient access to the ArcticDEM and REMA datasets. Mosaics can be downloaded from a one-line `load.mosaic()` function, whilst the `search()` function allows for convenient filtering of a locally downloading ArcticDEM/REMA strip index according to variables such as date, region of interest, spatial coverage, temporal baseline, source sensors, accuracy, and cross-track data. The results of searches are returned as a [`geopandas`](https://geopandas.org) dataframe, and can be downloaded using the `load.from_search()` function. Elevation models are returned as [`xarray`](https://docs.xarray.dev) DataArrays [Hoyer _et al. 2017](https://doi.org/10.5334/jors.148) with geospatial metadata via the [`rioxarray`](https://corteva.github.io) extension - a standard format for storing and processing n-dimensional geospatial data within the geospatial Python community. By utilising standardised formats, the aim is to allow the user to quickly move beyond `pdemtools` into their own analysis in whatever format they desire, be that `xarray`, `numpy` or `dask` datasets, DEM analysis Python packages such as [`xdem`](https://xdem.readthedocs.io/) for advanced coregistration or [`richdem`](https://richdem.readthedocs.io) for flow analysis, or exporting to geospatial file formats for analysis beyond Python. After download, there exist a number of (pre-)processing steps that are near universally common in topographic analyses. These include geoid-correction, co-registration of time-series data, and/or the construction of terrain parameters such as hillshade, slope, aspect, and curvature. `pdemtools` contains pre-built functions to perform these processing steps, as well as further functionality specific to ArcticDEM and REMA use cases. For instance, we include functions to quickly extract the EIGEN-6C4 geoid [Foerste _et al._ 2014](https://doi.org/10.5880/icgem.2015.1) and Greenland/Antarctic bedrock masks directly from local versions of the Greenland and Antarctic BedMachine datasets (Morlighem _et al_, [2022a](https://doi.org/10.5067/GMEVBWFLWA7X), [2022b](https://doi.org/10.5067/FPSU0V1MWUB6)), reprojecting and resampling the data to match the target DEM. Options for ingesting user-provided mask and geoid data are also provided. Additionally, partial derivatives of the surface used to calculate terrain parameters (∂z/∂x, ∂z/∂y, ∂2z/∂x2, ∂2z/∂y2, ∂2z/∂x∂y) are calculated following [Florinsky (2009)](https://doi.org/10.1080/13658810802527499), as opposed to more common methods such as [Zevenbergen and Thorne (1987)](https://doi.org/10.1002/esp.3290120107). The newer approach computes partial derivatives of elevation based on fitting a third-order polynomial, by the least-squares approach, to a 5 $\times$ 5 window as opposed to the more common 3 $\times$ 3 window. This is more appropriate for high-resolution DEMs: curvature over a 10 m window for the 2 m resolution ArcticDEM/REMA strips will lead to a local denoising effect that limits the impact of noise common in high-resolution photogrammetric products. These methods are also adapted into a co-registration routine, which otherwise follows the commonly used approach of [Nuth & Kääb (2011)](https://doi.org/10.5194/tc-5-271-2011). -We aim to grow `pdemtools` by implementing new methods developed by the ArcticDEM and REMA research community. For instance, we currently include sea-level-filtering and iceberg detection routines outlined by @shiggins_automated_2023, and invite community contributions or requests of other routines that will be of use to users of `pdemtools`. Ongoing research projects making use of `pdemtools` are applying ArcticDEM and REMA data to the mapping of crevasses, ice cliff heights, and subglacial lakes, as well as the initiation of ice sheet models. It has also been used within training exercises at the 2024 Polar Geospatial Center Data Workshop, contributing to a growing international network of `pdemtools` users. \ No newline at end of file +We aim to grow `pdemtools` by implementing new methods developed by the ArcticDEM and REMA research community. For instance, we currently include sea-level-filtering and iceberg detection routines outlined by Shiggins _et al._ (2023), and invite community contributions or requests of other routines that will be of use to users of `pdemtools`. Ongoing research projects making use of `pdemtools` are applying ArcticDEM and REMA data to the mapping of crevasses, ice cliff heights, and subglacial lakes, as well as the initiation of ice sheet models. It has also been used within training exercises at the 2024 Polar Geospatial Center Data Workshop, contributing to a growing international network of `pdemtools` users. \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 2431eec..7bccd95 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,8 +3,16 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -pDEMtools -========= +.. |version badge| image:: https://badge.fury.io/py/pdemtools.svg + :alt: PyPi package link and version + :target: https://pypi.org/project/pdemtools/ + +.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.07149/status.svg + :alt: JOSS publication link and DOI + :target: https://doi.org/10.21105/joss.07149 + +pDEMtools |version badge| |JOSS| +===================================== .. .. image:: _static/pdemtools_logo_1600px.png .. :align: center @@ -38,8 +46,11 @@ Rather than introducing custom classes, pDEMtools will always try and return DEM **Contact me:** Tom Chudley, thomas.r.chudley@durham.ac.uk +**Cite pDEMtools:** Chudley, T. R., and Howat, I. M. (2024). pDEMtools: conveniently search, download, and process ArcticDEM and REMA products. *Journal of Open Source Software*, *9*(102), 7149, doi.org/10.21105/joss.07149 + .. toctree:: :maxdepth: 2 + :hidden: :caption: Getting Started: getting_started/why_pdemtools.md @@ -49,6 +60,7 @@ Rather than introducing custom classes, pDEMtools will always try and return DEM .. toctree:: :maxdepth: 2 + :hidden: :caption: Examples: examples/mosaic_and_terrain @@ -58,7 +70,7 @@ Rather than introducing custom classes, pDEMtools will always try and return DEM .. toctree:: :maxdepth: 3 - :glob: + :hidden: :caption: API reference: api/search.rst @@ -68,7 +80,7 @@ Rather than introducing custom classes, pDEMtools will always try and return DEM .. toctree:: :maxdepth: 2 - :glob: + :hidden: :caption: Appendix: appendix/faq.md