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CliMA / GriddingMachine.jl

Functions to read gridded data so as to feed Clima Land model
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Datasets #62

Open Yujie-W opened 2 years ago

Yujie-W commented 2 years ago

This issue page is meant for contributing new datasets and documenting existing datasets, for the bibtex information, please visit https://clima.github.io/GriddingMachine.jl/stable/API/#Collector.

Change logs

  1. Add uncertainty (filled with NaN)
  2. Make the map to global scale (fill with NaN)
  3. Reformatted from GeoTIFF or binary to NetCDF
  4. Latitude and Longitude re-oriented to from South to North and from West to East
  5. Data scaling removed (from log(x), exp(x), or kx+b to x)
  6. Data regridded to coarser resolution by averaging all data falling into the new grid
  7. Unit standardization
  8. Reorder the dimensions to (lon, lat, ind)
  9. Unrealistic values to NaN

The datasets that are not supposed to be updated:

Dataset type LABEL EXTRALABEL IX JT YEAR VK Reference Change logs
Biomass BIOMASS ROOT 120X 1Y - V1 Huang et al. (2021) 1,2
BIOMASS SHOOT 120X 1Y - V2 Santoro et al. (2021) 1,2
Canopy height CH - 20X 1Y - V1 Simrad et al. (2021) 1
CH - 2X 2Y - V2 Boonman et al. (2020) 1,3,4,5
Clumping Index CI - 240X 1Y - V1 He et al. (2012) 1,3,4
CI - 2X 1Y - V1 He et al. (2012) 1,3,4,6
CI - 2X 1Y - V2 Braghiere et al. (2019) 1
CI - 20X 1M - V3 Wei et al. (2019) 1,3,4
CI - 2X 1M - V3 Wei et al. (2019) 1,3,4,6
Elevation ELEV - 4X 1Y - V1 Yamazaki et al. (2017) 1,4
Land mask LM - 4X 1Y - V1 ERA5 1
Leaf nitrogen content LNC - 2X 1Y - V1 Butler et al. (2017)
LNC - 2X 1Y - V2 Boonman et al. (2020) 1,3,4,5
Leaf phosphorus content LPC - 2X 1Y - V1 Butler et al. (2017)
Plant functional type PFT - 2X 1Y - V1 Lawrence and Chase (2007) 1,4,7
Solar induced luminescence SIL - 20X 1Y - V1 Köhler et al. (2021) 1,3,4
Specific leaf area SLA - 2X 1Y - V1 Butler et al. (2017)
SLA - 2X 1Y - V2 Boonman et al. (2020) 1,3,4,5
Soil color SC - 2X 1Y - V1 Lawrence and Chase (2007) 1,4,6
Soil hydraulic parameters SOIL SWCR 12X 1Y - V1 Dai et al. (2019) 1,3,6
SOIL SWCR 120X 1Y - V1 Dai et al. (2019) 1,3
SOIL SWCS 12X 1Y - V1 Dai et al. (2019) 1,3,6
SOIL SWCS 120X 1Y - V1 Dai et al. (2019) 1,3
SOIL VGA 12X 1Y - V1 Dai et al. (2019) 1,3,6
SOIL VGA 120X 1Y - V1 Dai et al. (2019) 1,3
SOIL VGN 12X 1Y - V1 Dai et al. (2019) 1,3,5,6
SOIL VGN 120X 1Y - V1 Dai et al. (2019) 1,3,5
SOIL KSAT 100X 1Y - V2 Gupta et al. (2021) 1,2,3,4,5
Surface area SA - 1X 1Y - V1 Lawrence and Chase (2007) 1,4,6
SA - 2X 1Y - V1 Lawrence and Chase (2007) 1,4
Tree density TD - 2X 1Y - V1 Crowther et al. (2017) 1,3,4,6
TD - 120X 1Y - V1 Crowther et al. (2017) 1,3,4
Maximum carboxylation rate VCMAX - 2X 1Y - V1 Smith et al. (2019) 1,2,4
VCMAX - 2X 1Y - V2 Luo et al. (2019) 1,8
Wood density WD - 2X 1Y - V1 Boonman et al. (2020) 1,3,4,7
Yujie-W commented 2 years ago

These datasets are supposed to be updated on annually basis:

Dataset type LABEL EXTRALABEL IX JT YEAR VK Reference Change logs
Gross primary productivity GPP MPI_RS 2X 1M, 8D 2001-2019 V1 Tramontana et al. (2016) 4,9
GPP VPM 5X, 12X 8D 2000-2019 V2 Zhang et al. (2017) 1,4
Leaf area index LAI MODIS 2X, 10X, 20X 1M, 8D 2000-2020 V1 Yuan et al. (2011) 1,4,9
Latent heat flux LE MPI_RS 2X 1M, 8D 2001-2015 V1 Jung et al. (2019) 4,9
Solar induced chlorophyll fluorescence SIF TROPOMI_683, TROPOMI_683DC 1X, 2X, 4X, 5X, 12X 1M, 8D 2018-2020 V2 Köhler et al. (2020) 1,8
SIF TROPOMI_740, TROPOMI_740DC 1X, 2X, 4X, 5X, 12X 1M, 8D 2018-2021 V1 Köhler et al. (2018) 1,8
SIF OCO2_757, OCO2_757DC, OCO2_771, OCO2_771DC 5X 1M 2014-2020 V3 Sun et al. (2017) 1,8
Vegetation cover fraction VCF MODIS_MOD44B 2X 1Y 2000-2021 V1 DiMiceli et al. (2022 7,9
Yujie-W commented 2 years ago

Example of contributing data via tagging an issue.

NOTICE: By submitting the issue, you authorize us to share your data to the public!

Fields Please fill in this form
Data URL (A public url to download the data)
Publication DOI (DOI to the publication)
Propsed TAG (A unique tag for the data, e.g., VCMAX_1X_1Y_V3)
Description of the Data (breifly describe the data so we know how to deal with it)
drnimbusrain commented 1 year ago

@Yujie-W Thank you for these amazing datasets! Can you tell me if GriddingMachine also will have a global gridded forest cover fraction (FCF) dataset available soon (e.g., from MODIS)? Thank you!

Yujie-W commented 1 year ago

@Yujie-W Thank you for these amazing datasets! Can you tell me if GriddingMachine also will have a global gridded forest cover fraction (FCF) dataset available soon (e.g., from MODIS)? Thank you!

Does this data work for you? If so, we can download and reprocess it to meet the requirements. It may take a few days. https://icdc.cen.uni-hamburg.de/thredds/catalog/ftpthredds/modis_vcf/global_0.5deg/catalog.html

drnimbusrain commented 1 year ago

That would be great, thanks Yujie!!

On Mon, Feb 6, 2023, 6:32 PM Yujie Wang @.***> wrote:

@Yujie-W https://github.com/Yujie-W Thank you for these amazing datasets! Can you tell me if GriddingMachine also will have a global gridded forest cover fraction (FCF) dataset available soon (e.g., from MODIS)? Thank you!

Does this data work for you? If so, we can download and reprocess it to meet the requirements. It may take a few days. https://icdc.cen.uni-hamburg.de/thredds/catalog/ftpthredds/modis_vcf/global_0.5deg/catalog.html

— Reply to this email directly, view it on GitHub https://github.com/CliMA/GriddingMachine.jl/issues/62#issuecomment-1419936579, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGLFYNR3TC3LIO7FU7ZQ3Y3WWGCXLANCNFSM5GC37U7A . You are receiving this because you commented.Message ID: @.***>

drnimbusrain commented 1 year ago

@Yujie-W Hi, just checking in to see if/when the MODIS FCF dataset will be available from GriddingMachine. Thank you!

drnimbusrain commented 1 year ago

@Yujie-W Also, a suggestion. For your forest canopy height (CH) datasets, you could add the GEDI (Global Ecosystem Dynamics Investigation) LIDAR observations too. While GEDI itself is limited in expanse globally, there is some work from UMD that combines GEDI and Landsat ARD:

https://glad.earthengine.app/view/global-forest-canopy-height-2019 https://glad.umd.edu/dataset/gedi/ https://daac.ornl.gov/cgi-bin/dataset_lister.pl?p=40

P. Potapov, X. Li, A. Hernandez-Serna, A. Tyukavina, M.C. Hansen, A. Kommareddy, A. Pickens, S. Turubanova, H. Tang, C. E. Silva, J. Armston, R. Dubayah, J. B. Blair, M. Hofton (2020). https://doi.org/10.1016/j.rse.2020.112165

Yujie-W commented 1 year ago

@Yujie-W Hi, just checking in to see if/when the MODIS FCF dataset will be available from GriddingMachine. Thank you!

You may find the data with the lasted version, see changes in #77

Thanks for the suggestions of the datasets, we will add the data in the next round after we finish a general template to process the data