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+
+
+
+ 20240629144538-bcf99736c334c47c45cfd5ff5eeee532da4e6f08
+ 20240629144538
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 06
+ 2024
+
+
+ 9
+
+ 98
+
+
+
+ xCDAT: A Python Package for Simple and Robust Analysis
+of Climate Data
+
+
+
+ Tom
+ Vo
+ https://orcid.org/0000-0002-2461-0191
+
+
+ Stephen
+ Po-Chedley
+ https://orcid.org/0000-0002-0390-238X
+
+
+ Jason
+ Boutte
+ https://orcid.org/0009-0009-3996-3772
+
+
+ Jiwoo
+ Lee
+ https://orcid.org/0000-0002-0016-7199
+
+
+ Chengzhu
+ Zhang
+ https://orcid.org/0000-0002-9632-0716
+
+
+
+ 06
+ 29
+ 2024
+
+
+ 6426
+
+
+ 10.21105/joss.06426
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.12522560
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/6426
+
+
+
+ 10.21105/joss.06426
+ https://joss.theoj.org/papers/10.21105/joss.06426
+
+
+ https://joss.theoj.org/papers/10.21105/joss.06426.pdf
+
+
+
+
+
+ The DOE E3SM model version 2: Overview of the
+physical model and initial model evaluation
+ Golaz
+ Journal of Advances in Modeling Earth
+Systems
+ 12
+ 14
+ 10.1029/2022MS003156
+ 2022
+ Golaz, J.-C., Van Roekel, L. P.,
+Zheng, X., Roberts, A. F., Wolfe, J. D., Lin, W., Bradley, A. M., Tang,
+Q., Maltrud, M. E., Forsyth, R. M., Zhang, C., Zhou, T., Zhang, K.,
+Zender, C. S., Wu, M., Wang, H., Turner, A. K., Singh, B., Richter, J.
+H., … Bader, D. C. (2022). The DOE E3SM model version 2: Overview of the
+physical model and initial model evaluation. Journal of Advances in
+Modeling Earth Systems, 14(12), e2022MS003156.
+https://doi.org/10.1029/2022MS003156
+
+
+ A data model of the climate and forecast
+metadata conventions (CF-1.6) with a software implementation (cf-python
+v2.1)
+ Hassell
+ Geoscientific Model
+Development
+ 12
+ 10
+ 10.5194/gmd-10-4619-2017
+ 2017
+ Hassell, D., Gregory, J., Blower, J.,
+Lawrence, B. N., & Taylor, K. E. (2017). A data model of the climate
+and forecast metadata conventions (CF-1.6) with a software
+implementation (cf-python v2.1). Geoscientific Model Development,
+10(12), 4619–4646.
+https://doi.org/10.5194/gmd-10-4619-2017
+
+
+ Xarray: N-D labeled Arrays and Datasets in
+Python
+ Hoyer
+ Journal of Open Research
+Software
+ 5
+ 10.5334/jors.148
+ 2049-9647
+ 2017
+ Hoyer, S., & Hamman, J. J.
+(2017). Xarray: N-D labeled Arrays and Datasets in Python. Journal of
+Open Research Software, 5, 10.
+https://doi.org/10.5334/jors.148
+
+
+ Objective evaluation of earth system models:
+PCMDI metrics package (PMP) version 3
+ Lee
+ EGUsphere
+ 2023
+ 10.5194/egusphere-2023-2720
+ 2023
+ Lee, J., Gleckler, P. J., Ahn, M.-S.,
+Ordonez, A., Ullrich, P. A., Sperber, K. R., Taylor, K. E., Planton, Y.
+Y., Guilyardi, E., Durack, P., Bonfils, C., Zelinka, M. D., Chao, L.-W.,
+Dong, B., Doutriaux, C., Zhang, C., Vo, T., Boutte, J., Wehner, M. F., …
+Krasting, J. (2023). Objective evaluation of earth system models: PCMDI
+metrics package (PMP) version 3. EGUsphere, 2023, 1–48.
+https://doi.org/10.5194/egusphere-2023-2720
+
+
+ Internal variability and forcing influence
+model–satellite differences in the rate of tropical tropospheric
+warming
+ Po-Chedley
+ Proceedings of the National Academy of
+Sciences
+ 47
+ 119
+ 10.1073/pnas.2209431119
+ 2022
+ Po-Chedley, S., Fasullo, J. T.,
+Siler, N., Labe, Z. M., Barnes, E. A., Bonfils, C. J. W., & Santer,
+B. D. (2022). Internal variability and forcing influence model–satellite
+differences in the rate of tropical tropospheric warming. Proceedings of
+the National Academy of Sciences, 119(47), e2209431119.
+https://doi.org/10.1073/pnas.2209431119
+
+
+ The flexible climate data analysis tools
+(CDAT) for multi-model climate simulation data
+ Williams
+ 10.1109/ICDMW.2009.64
+ 2009
+ Williams, D. N., Doutriaux, C. M.,
+Drach, R. S., & Mccoy, R. B. (2009). The flexible climate data
+analysis tools (CDAT) for multi-model climate simulation data. 254–261.
+https://doi.org/10.1109/ICDMW.2009.64
+
+
+ Visualization and analysis tools for
+ultrascale climate data
+ Williams
+ Advanced Earth and Space
+Sciences
+ 42
+ 95
+ 10.1002/2014EO420002
+ 2014
+ Williams, D. N. (2014). Visualization
+and analysis tools for ultrascale climate data. Advanced Earth and Space
+Sciences, 95(42), 377–378.
+https://doi.org/10.1002/2014EO420002
+
+
+ The E3SM diagnostics package (E3SM diags
+v2.7): A python-based diagnostics package for earth system model
+evaluation
+ Zhang
+ Geoscientific Model
+Development
+ 24
+ 15
+ 10.5194/gmd-15-9031-2022
+ 2022
+ Zhang, C., Golaz, J.-C., Forsyth, R.,
+Vo, T., Xie, S., Shaheen, Z., Potter, G. L., Asay-Davis, X. S., Zender,
+C. S., Lin, W., Chen, C.-C., Terai, C. R., Mahajan, S., Zhou, T.,
+Balaguru, K., Tang, Q., Tao, C., Zhang, Y., Emmenegger, T., … Ullrich,
+P. A. (2022). The E3SM diagnostics package (E3SM diags v2.7): A
+python-based diagnostics package for earth system model evaluation.
+Geoscientific Model Development, 15(24), 9031–9056.
+https://doi.org/10.5194/gmd-15-9031-2022
+
+
+ Dask: Library for dynamic task
+scheduling
+ Dask-Development-Team
+ 2016
+ Dask-Development-Team. (2016). Dask:
+Library for dynamic task scheduling.
+https://dask.org
+
+
+ CDAT/cdat: CDAT 8.1
+ Doutriaux
+ 10.5281/zenodo.2586088
+ 2019
+ Doutriaux, C., Nadeau, D.,
+Wittenburg, S., Lipsa, D., Muryanto, L., Chaudhary, A., & Williams,
+D. N. (2019). CDAT/cdat: CDAT 8.1 (Version v8.1). Zenodo.
+https://doi.org/10.5281/zenodo.2586088
+
+
+ Cf_xarray
+ Cherian
+ 10.5281/zenodo.10038784
+ 2023
+ Cherian, D., Almansi, M., Bourgault,
+P., Thyng, K., Thielen, J., Magin, J., Aoun, A., Buntemeyer, L.,
+Caneill, R., Davis, L., Fernandes, F., Hauser, M., Heerdegen, A., Kent,
+J., Mankoff, K., Müller, S., Schupfner, M., Vo, T., & Haëck, C.
+(2023). Cf_xarray (Version v0.8.5). Zenodo.
+https://doi.org/10.5281/zenodo.10038784
+
+
+ E3SM-project/e3sm_diags:
+v2.9.0
+ Zhang
+ 10.5281/zenodo.8339034
+ 2023
+ Zhang, J. C., Shaheen, Z., Vo, T.,
+Forsyth, R., Golaz, Asay-Davis, X., Mahfouz, N., Bradley, A. M., &
+Doutriaux, C. (2023). E3SM-project/e3sm_diags: v2.9.0 (Version v2.9.0).
+Zenodo. https://doi.org/10.5281/zenodo.8339034
+
+
+ E3SM-unified: A metapackage for a unified
+anaconda environment for analyzing results from the energy exascale
+earth system model (E3SM)
+ Asay-Davis
+ 2023
+ Asay-Davis, X. (2023). E3SM-unified:
+A metapackage for a unified anaconda environment for analyzing results
+from the energy exascale earth system model (E3SM) (Version v1.9.1).
+GitHub.
+https://github.com/E3SM-Project/e3sm-unified
+
+
+ PCMDI/pcmdi_metrics: PMP version
+3.1.2
+ Lee
+ 10.5281/zenodo.10236521
+ 2023
+ Lee, J., Gleckler, P., Ordonez, A.,
+Ahn, M.-S., Ullrich, P., Vo, T., Boutte, J., Doutriaux, C., Durack, P.,
+Shaheen, Z., Muryanto, L., Painter, J., & Krasting, J. (2023).
+PCMDI/pcmdi_metrics: PMP version 3.1.2 (Version v3.1.2). Zenodo.
+https://doi.org/10.5281/zenodo.10236521
+
+
+ Pangeo-data/xESMF: v0.8.2
+ Zhuang
+ 10.5281/zenodo.8356796
+ 2023
+ Zhuang, J., Dussin, R., Huard, D.,
+Bourgault, P., Banihirwe, A., Raynaud, S., Malevich, B., Schupfner, M.,
+Filipe, Levang, S., Gauthier, C., Jüling, A., Almansi, M.,
+Richardscottoz, Rondeaug, Rasp, S., Smith, T. J., Stachelek, J., Plough,
+M., … Li, X. (2023). Pangeo-data/xESMF: v0.8.2 (Version v0.8.2). Zenodo.
+https://doi.org/10.5281/zenodo.8356796
+
+
+ Xgcm
+ Abernathey
+ 10.5281/zenodo.7348619
+ 2022
+ Abernathey, R. P., Busecke, J. J. M.,
+Smith, T. A., Deauna, J. D., Banihirwe, A., Nicholas, T., Fernandes, F.,
+James, B., Dussin, R., Cherian, D. A., Caneill, R., Sinha, A., Uieda,
+L., Rath, W., Balwada, D., Constantinou, N. C., Ponte, A., Zhou, Y.,
+Uchida, T., & Thielen, J. (2022). Xgcm (Version v0.8.1). Zenodo.
+https://doi.org/10.5281/zenodo.7348619
+
+
+
+
+
+
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+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+6426
+10.21105/joss.06426
+
+xCDAT: A Python Package for Simple and Robust Analysis of
+Climate Data
+
+
+
+https://orcid.org/0000-0002-2461-0191
+
+Vo
+Tom
+
+
+
+
+https://orcid.org/0000-0002-0390-238X
+
+Po-Chedley
+Stephen
+
+
+
+
+https://orcid.org/0009-0009-3996-3772
+
+Boutte
+Jason
+
+
+
+
+https://orcid.org/0000-0002-0016-7199
+
+Lee
+Jiwoo
+
+
+
+
+https://orcid.org/0000-0002-9632-0716
+
+Zhang
+Chengzhu
+
+
+
+
+
+Lawrence Livermore National Lab, Livermore,
+USA
+
+
+
+
+24
+6
+2024
+
+9
+98
+6426
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+Python
+python
+xarray
+climate science
+climate research
+climate data
+climate data analysis
+
+
+
+
+
+ Summary
+
xCDAT (Xarray Climate Data Analysis Tools) is an open-source Python
+ package that extends Xarray
+ (Hoyer
+ & Hamman, 2017) for climate data analysis on structured
+ grids. xCDAT streamlines analysis of climate data by exposing common
+ climate analysis operations through a set of straightforward APIs.
+ Some of xCDAT’s key features include spatial averaging, temporal
+ averaging, and regridding. These features are inspired by the
+ Community Data Analysis Tools
+ (CDAT)
+ library
+ (Dean
+ N. Williams et al., 2009)
+ (D.
+ N. Williams, 2014)
+ (Doutriaux
+ et al., 2019) and leverage powerful packages in the
+ Xarray
+ ecosystem including
+ xESMF
+ (Zhuang
+ et al., 2023),
+ xgcm
+ (Abernathey
+ et al., 2022), and
+ CF
+ xarray
+ (Cherian
+ et al., 2023). To ensure general compatibility across various
+ climate models, xCDAT operates on datasets that are compliant with the
+ Climate and Forecast (CF) metadata conventions
+ (Hassell
+ et al., 2017).
+
+
+ Statement of Need
+
Analysis of climate data frequently requires a number of core
+ operations, including reading and writing of netCDF files, horizontal
+ and vertical regridding, and spatial and temporal averaging. While
+ many individual software packages address these needs in a variety of
+ computational languages, CDAT stands out because it provides these
+ essential operations via open-source, interoperable Python packages.
+ Since CDAT’s inception, the volume of climate data has grown
+ substantially as a result of both a larger pool of data products and
+ increasing spatiotemporal resolution of model and observational data.
+ Larger data stores are important for advancing geoscientific
+ understanding, but also require increasingly performant software and
+ hardware. These factors have sparked a need for new analysis software
+ that offers core geospatial analysis functionalities capable of
+ efficiently handling large datasets while using modern technologies
+ and standardized software engineering principles.
+
xCDAT addresses this need by combining the power of Xarray with
+ meticulously developed geospatial analysis features inspired by CDAT.
+ Xarray is the foundation of xCDAT because of its widespread adoption,
+ technological maturity, and ability to handle large datasets with
+ parallel computing via Dask. Xarray is also interoperable with the
+ scientific Python ecosystem (e.g.,
+ NumPy,
+ pandas,
+ Matplotlib),
+ which greatly benefits users who need to use additional analysis
+ tools. Since Xarray is designed as a general-purpose library, xCDAT
+ fills in domain specific gaps by providing features to serve the
+ climate science community (refer to
+ Key
+ Features).
+
Performance is one fundamental driver in how xCDAT is designed,
+ especially with large datasets. xCDAT conveniently inherits Xarray’s
+ support for parallel computing with Dask
+ (Dask-Development-Team,
+ 2016). Parallel computing with Dask enables users to take
+ advantage of compute resources through multithreading or
+ multiprocessing. To use Dask’s default multithreading scheduler, users
+ only need to open and chunk datasets in Xarray before calling xCDAT
+ APIs. xCDAT’s seamless support for parallel computing enables users to
+ run large-scale computations with minimal effort. If users require
+ more resources, they can also configure and use a local Dask cluster
+ to meet resource-intensive computational needs. Figure 1 shows xCDAT’s
+ significant performance advantage over CDAT for global spatial
+ averaging on datasets of varying sizes.
+
+
A performance benchmark for global spatial averaging
+ computations using CDAT (serial only) and xCDAT (serial and parallel
+ with Dask distributed scheduler). xCDAT outperforms CDAT by a wide
+ margin for the 7 GB and 12 GB datasets. Runtimes could not be
+ captured for CDAT with datasets >= 22 GB and xCDAT serial for the
+ 105 GB dataset due to memory allocation errors. The performance
+ benchmark setup and scripts are available in the
+ xcdat-validation
+ repo. Disclaimer: Performance will vary depending
+ on hardware, dataset shapes/sizes, and how Dask and chunking schemes
+ are configured. There are also some cases where selecting a regional
+ averaging domain (e.g., Niño 3.4) can lead to CDAT outperforming
+ xCDAT.
+
+
+
+
xCDAT’s intentional design emphasizes software sustainability and
+ reproducible science. It aims to make analysis code reusable,
+ readable, and less-error prone by abstracting common Xarray
+ boilerplate logic into simple and configurable APIs. xCDAT extends
+ Xarray by using
+ accessor
+ classes that operate directly on Xarray Dataset objects.
+ xCDAT is rigorously tested using real-world datasets and maintains
+ 100% unit test coverage (at the time this paper was written). To
+ demonstrate the value in xCDAT’s API design, Figure 2 compares code to
+ calculate annual averages for global climatological anomalies using
+ Xarray against xCDAT. xCDAT requires fewer lines of code and supports
+ further user options (e.g., regional or seasonal averages, not shown).
+ Figure 2 shows the plots for the results produced by xCDAT.
+
+
A comparison of the code to calculate annual averages
+ for global climatological anomalies in A) Xarray and B) xCDAT. xCDAT
+ abstracts most of the Xarray boilerplate logic for calculating
+ weights and grouping data by specific time frequencies, leading to
+ code that is more readable, maintainable, and flexible. The results
+ from both sets of code are within machine precision.
+
+
+
+
+
A) Monthly surface skin temperature anomalies for
+ September 1850. B) Monthly (gray) and annual (black) global mean
+ surface skin temperature anomaly values. Temperature data is from an
+ E3SMv2 climate model
+ (Golaz
+ et al., 2022) simulation over the historical period (1850 –
+ 2014).
+
+
+
+
xCDAT’s mission is to provide a maintainable and extensible package
+ that serves the needs of the climate community in the long-term. xCDAT
+ is a community-driven project and the development team encourages all
+ who are interested to get involved through the
+ GitHub
+ repository.
+
+
+ Key Features
+
+ Extension of xarray.open_dataset() and
+ xarray.open_mfdataset() with post-processing
+ options
+
xCDAT extends xarray.open_dataset() and
+ xarray.open_mfdataset() with additional
+ post-processing operations to support climate data analysis. These
+ APIs can generate missing coordinate bounds for the X, Y, T, and/or
+ Z axes and lazily decode time coordinates represented by
+ cftime
+ (more
+ info). Other functionality includes re-centering time
+ coordinates between time bounds and converting the longitudinal axis
+ orientation between [0, 360) and [-180, 180).
+
+
+ Robust interpretation of CF metadata
+
xCDAT uses
+ CF
+ xarray to interpret CF metadata present in datasets,
+ enabling xCDAT to operate generally across model and observational
+ datasets that are CF-compliant. This feature enables xCDAT to
+ generate missing coordinate bounds, recognize the coordinates and
+ coordinate bounds to use for computational operations, and lazily
+ decode time coordinates based on the CF calendar attribute.
+
+
+ Temporal averaging
+
xCDAT’s temporal averaging API utilizes Xarray and Pandas. It
+ includes features for calculating time series averages
+ (single-snapshot), grouped time series averages (e.g., seasonal or
+ annual averages), climatologies, and departures. Averages can be
+ weighted (default) or unweighted. There are optional configurations
+ for seasonal grouping including how to group the month of December
+ (DJF or JFD) and defining custom seasons to group by.
+
+
+ Geospatial weighted averaging
+
xCDAT’s geospatial weighted averaging supports rectilinear grids
+ with an option to compute averages over a regional domain (e.g.,
+ tropical region, Niño 3.4 region).
+
+
+ Horizontal structured regridding
+
xCDAT makes use of
+ xESMF
+ for horizontal regridding capabilities. It simplifies and extends
+ the xESMF horizontal regridding API by generating missing bounds and
+ ensuring bounds and metadata are preserved in the output dataset.
+ xCDAT also offers a Python implementation of
+ regrid2
+ for handling cartesian latitude by longitude grids.
+
+
+ Vertical structured regridding
+
xCDAT makes use of
+ xgcm
+ for vertical regridding capabilities. It simplifies and extends the
+ xgcm vertical regridding API by automatically attempting to
+ determine the grid point position relative to the bounds,
+ transposing the output data to match the dimensional order of the
+ input data, and ensuring bounds and metadata are preserved in the
+ output dataset.
+
+
+
+ Documentation & Case Studies
+
The xCDAT
+ documentation
+ includes the
+ public
+ API list and a Jupyter Notebook
+ Gallery
+ that demonstrates real-world applications of xCDAT:
+
+
+
A
+ Gentle Introduction to xCDAT (Xarray Climate Data Analysis
+ Tools)
+
+
+
General
+ Dataset Utilities
+
+
+
Calculate
+ Geospatial Weighted Averages from Monthly Time
+ Series
+
+
+
Calculate
+ Time Averages from Time Series Data
+
+
+
Calculating
+ Climatology and Departures from Time Series Data
+
+
+
Horizontal
+ Regridding
+
+
+
Vertical
+ Regridding
+
+
+
+
+ Distribution
+
xCDAT is available for Linux, MacOS, and Windows via the
+ conda-forge channel on
+ Anaconda.
+ The
+ GitHub
+ Repository is where we host all development activity. xCDAT
+ is released under the Apache 2-0 license.
+
+
+ Projects using xCDAT
+
xCDAT is actively being integrated as a core component of the
+ Program
+ for Climate Model Diagnosis and Intercomparison (PCMDI) Metrics
+ Package
+ (Jiwoo
+ Lee et al., 2023)
+ (J.
+ Lee et al., 2023) and the
+ Energy
+ Exascale Earth System Model (E3SM) Diagnostics Package
+ (C.
+ Zhang et al., 2022)
+ (J.
+ C. Zhang et al., 2023). xCDAT is also included in the
+ E3SM
+ Unified Anaconda Environment
+ (Asay-Davis,
+ 2023) deployed on numerous U.S Department of Energy
+ supercomputers to run E3SM software tools. Members of the development
+ team are also active users of xCDAT and apply the software to advance
+ their own climate research
+ (Po-Chedley
+ et al., 2022).
+
+
+ Acknowledgements
+
xCDAT is jointly developed by scientists and developers at Lawrence
+ Livermore National Laboratory
+ (LLNL)
+ from the Energy Exascale Earth System Model
+ (E3SM)
+ Project and Program for Climate Model Diagnosis and Intercomparison
+ (PCMDI).
+ The work is performed for the E3SM project, which is sponsored by
+ Earth System Model Development
+ (ESMD)
+ program, and the Simplifying ESM Analysis Through Standards
+ (SEATS)
+ project, which is sponsored by the Regional and Global Model Analysis
+ (RGMA)
+ program. ESMD and RGMA are programs for the Earth and Environmental
+ Systems Sciences Division
+ (EESSD)
+ in the Office of Biological and Environmental Research
+ (BER)
+ within the
+ Department
+ of Energy’s
+ Office
+ of Science. This work is performed under the auspices of
+ the U.S. Department of Energy by LLNL under Contract
+ No. DE-AC52-07NA27344.
+
Thank you to all of the xCDAT contributors and users including Rob
+ Jacob, Ana Ordonez, Mark Zelinka, Christopher Terai, Min-Seop Ahn,
+ Celine Bonfils, Jean-Yves Peterschmitt, Olivier Marti, Andrew
+ Manaster, and Andrew Friedman. We also give a special thanks to Karl
+ Taylor, Peter Gleckler, Paul Durack, and Chris Golaz who all have
+ provided valuable knowledge and guidance throughout the course of this
+ project.
+
+
+
+
+
+
+
+
+ GolazJean-Christophe
+ Van RoekelLuke P.
+ ZhengXue
+ RobertsAndrew F.
+ WolfeJonathan D.
+ LinWuyin
+ BradleyAndrew M.
+ TangQi
+ MaltrudMathew E.
+ ForsythRyan M.
+ ZhangChengzhu
+ ZhouTian
+ ZhangKai
+ ZenderCharles S.
+ WuMingxuan
+ WangHailong
+ TurnerAdrian K.
+ SinghBalwinder
+ RichterJadwiga H.
+ QinYi
+ PetersenMark R.
+ MametjanovAzamat
+ MaPo-Lun
+ LarsonVincent E.
+ KrishnaJayesh
+ KeenNoel D.
+ JefferyNicole
+ HunkeElizabeth C.
+ HannahWalter M.
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