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and Ice Sheets","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"[[https://www.gnu.org/licenses/gpl-3.0][https://img.shields.io/badge/License-GPLv3-blue.svg]]\n[[https://github.com/GEUS-SICE/SICE/actions][file:https://github.com/GEUS-SICE/SICE/workflows/CI/badge.svg]]\n\n* Table of Contents                               :toc_2:noexport:\n- [[#sentinel-3-s3-albedo-processing-pipeline][Sentinel-3 (S3) Albedo Processing Pipeline]]\n  - [[#fetch-s3-olci--slstr-products][Fetch S3 OLCI \u0026 SLSTR products]]\n  - [[#process-with-snap][Process with SNAP]]\n  - [[#pysice][pySICE]]\n  - [[#mosaic][Mosaic]]\n  - [[#outputs][Outputs]]\n- [[#debugging--testing][Debugging \u0026 Testing]]\n- [[#development-environment][Development Environment]]\n  - [[#bash][Bash]]\n  - [[#python][Python]]\n  - [[#parallel][Parallel]]\n  - [[#grass][GRASS]]\n  - [[#gpt][GPT]]\n  - [[#snap][SNAP]]\n- [[#misc-notes--code-snippets][Misc Notes \u0026 Code Snippets]]\n  - [[#generate-ice-mask][Generate ice mask]]\n  - [[#footprint][Footprint]]\n  - [[#regional-masks][Regional masks]]\n- [[#post-processing-analysis-and-visualisation][Post-processing, analysis and visualisation]]\n\n* Sentinel-3 (S3) Albedo Processing Pipeline\n\n1. Fetch S3 OLCI \u0026 SLSTR products\n2. Process OLCI \u0026 SLSTR using SNAP GPT\n3. Process using pySICE\n4. Build daily mosaic\n\nThe steps above are encapsulated in [[./S3_wrapper.sh]].\n\nIn more detail:\n\n** Fetch S3 OLCI \u0026 SLSTR products\n\n+ Download OLCI EFR and SLSTR RBT products for a specified day with [[./dhusget_wrapper.sh]].\n\n** Process with SNAP\n\n+ This step is a combination of running GPT on [[./S3.xml]] with [[./S3_proc.sh]].\n+ Inputs: OLCI and SLSTR scenes\n+ Outputs: A folder OLCI timestamp\n\n** pySICE\n\n+ Run [[./sice.py]] passing in one of the folders generated in the previous step.\n+ *WARNING*: This step is slow, and may take \u003e 24 hours.\n\n** Mosaic\n\n+ As implemented in [[./dm.sh]] and [[./dm.grass.sh]], for each day\n  + Combine all the files from to form a mosaic\n  + Mask out clouds, then...\n  + When scenes overlap, use minimum SZA\n\n** Outputs\n| File Name                     | Description                                                            | Units       |\n|-------------------------------+------------------------------------------------------------------------+-------------|\n| grain_diameter                |                                                                        | mm          |\n| snow_specific_surface_area    |                                                                        | m^{2}kg^{-1}|\n| ndsi                          | normalized difference snow index                                       |             |\n| ndbi                          | normalized difference blue ice index                                   |             |\n| auto_cloud                    | in development                                                         |             |\n| sza                           | sun zenith angle                                                       |             |\n| vza                           | viewing zenith angle                                                   |             |\n| saa                           | sun azimuth angle                                                      |             |\n| vaa                           | viewing azimuth angle                                                  |             |\n| albedo_bb_planar_nir          | near infrared broadband planar albedo                                  | 700-2400 nm |\n| albedo_bb_planar_sw           | shortwave broadband planar albedo                                      | 300-2400 nm |\n| albedo_bb_planar_vis          | visible broadband planar albedo                                        | 300-700 nm  |\n| albedo_bb_spherical_nir       | near infrared broadband spherical albedo                               | 700-2400 nm |\n| albedo_bb_spherical_sw        | shortwave broadband spherical albedo                                   | 300-2400 nm |\n| albedo_bb_spherical_vis       | visible broadband spherical albedo                                     | 300-700 nm  |\n| Oa01..21_reflectance          | top of the atmosphere reflectance (OLCI bands 1 through 21)            |             |\n| rBRR_01..21                   | bottom of the atmosphere surface reflectance (OLCI bands 1 through 21) |             |\n| albedo_spectral_planar_01..21 | spectral planar albedo (OLCI bands 1 through 21)                       |             |\n| diagnostic_retrieval          | See next table.                                                        |             |\n\n\n| Diagnostic Code | Description                                                                                   |\n|-----------------+-----------------------------------------------------------------------------------------------|\n|               0 | clean snow                                                                                    |\n|               1 | polluted snow                                                                                 |\n|               6 | polluted snow for which r0 was calculated and not derived from observations                   |\n|               7 | polluted snow of calculated spherical albedo in bands 1 and 2 \u003e0.98 reprocessed as clean snow |\n|             100 | sza\u003e75, no retrival                                                                           |\n|             102 | TOA reflectance at band 21 \u003c 0.1, no retrieval                                                |\n|             104 | grain_diameter \u003c 0.1, no retrieval, potential cloud flag                                      |\n|              -n | impossible to solve polluted snow albedo equation at band n                                   |\n\n* Debugging \u0026 Testing\n\nChange the year and day for loops in [[./S3_wrapper.sh]] to one year and one day. E.g.\n\n#+BEGIN_SRC bash :results verbatim\nfor year in 2017; do # one year\n  for doy in 227 180; do # two example days\n  # loop contents\n  done\ndone\n#+END_SRC\n\n#+RESULTS:\n\n* Development Environment\n:PROPERTIES:\n:header-args:bash+: :eval no-export\n:END:\n\nThis work is developed with the following software versions\n\n** Bash\n#+BEGIN_SRC bash :results verbatim :exports both\nbash --version\n#+END_SRC\n\n#+RESULTS:\n: GNU bash, version 4.4.20(1)-release (x86_64-pc-linux-gnu)\n: Copyright (C) 2016 Free Software Foundation, Inc.\n: License GPLv3+: GNU GPL version 3 or later \u003chttp://gnu.org/licenses/gpl.html\u003e\n: \n: This is free software; you are free to change and redistribute it.\n: There is NO WARRANTY, to the extent permitted by law.\n\n** Python\n\nRun the following using [[./SICE.yml]] in order to set up an identical Anaconda Python environment.\n\n#+BEGIN_SRC bash :results verbatim\nconda env create -f SICE.yml\n#+END_SRC\n\nAnd then run =conda activate SICE= to activate the SICE environment.\n\n=ResolvePackageNotFound= error can be raised. In that case, run =conda env export --no-builds \u003e environment.yml= instead. \n\n\n** Parallel\n\n#+BEGIN_SRC bash :results verbatim :exports both\nparallel --version\n#+END_SRC\n\n#+RESULTS:\n#+begin_example\nGNU parallel 20161222\nCopyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016\nOle Tange and Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later \u003chttp://gnu.org/licenses/gpl.html\u003e\nThis is free software: you are free to change and redistribute it.\nGNU parallel comes with no warranty.\n\nWeb site: http://www.gnu.org/software/parallel\n\nWhen using programs that use GNU Parallel to process data for publication\nplease cite as described in 'parallel --citation'.\n#+end_example\n\n** GRASS\n#+BEGIN_SRC bash :results verbatim :exports both\ngrass --version 2\u003e\u00261\n#+END_SRC\n\n#+RESULTS:\n#+begin_example\nGRASS GIS 7.4.0\n\nGeographic Resources Analysis Support System (GRASS) is Copyright,\n1999-2018 by the GRASS Development Team, and licensed under terms of the\nGNU General Public License (GPL) version \u003e=2.\n \nThis GRASS GIS 7.4.0 release is coordinated and produced by\nthe GRASS Development Team with contributions from all over the world.\n\nThis program is distributed in the hope that it will be useful, but\nWITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\nGeneral Public License for more details.\n\n#+end_example\n\n** GPT\n\n#+BEGIN_SRC sh :results verbatim :exports both\n~/local/snap/bin/gpt --diag\n#+END_SRC\n\n#+RESULTS:\n#+begin_example\nSNAP Release version 7.0\nSNAP home: /home/kdm/local/snap/bin//..\nSNAP debug: null\nSNAP log level: null\nJava home: /home/kdm/local/snap/jre\nJava version: 1.8.0_202\nProcessors: 8\nMax memory: 18.7 GB\nCache size: 1024.0 MB\nTile parallelism: 8\nTile size: 512 x 512 pixels\n\nTo configure your gpt memory usage:\nEdit snap/bin/gpt.vmoptions\n\nTo configure your gpt cache size and parallelism:\nEdit .snap/etc/snap.properties or gpt -c ${cachesize-in-GB}G -q ${parallelism} \n#+end_example\n\n** SNAP\n\nSNAP extensions used in this toolchain are listed in [[SNAP_extensions.txt]].\n\n* Misc Notes \u0026 Code Snippets\n:PROPERTIES:\n:header-args:bash+: :eval no\n:END:\n\n** Generate ice mask\n \n+ Use the icemask from BedMachine v3\n\n#+BEGIN_SRC bash :results verbatim :eval no\ngrass72 -c EPSG:3413 ./Gtmp\nr.in.gdal input=NetCDF:~/data/Greenland/Morlighem_2017/BedMachineGreenland-2017-09-20.nc:mask output=icemask\n\ng.region raster=icemask\ng.region res=500 -ap\ng.region zoom=icemask\n\nd.mon start=wx0\nd.erase\nd.rast icemask\n\nr.mapcalc \"mask = if(icemask == 4, null(), icemask)\" --o\nd.rast mask\ng.region zoom=mask\n\nr.out.gdal -c -m input=mask output=mask.tif type=Byte createopt=COMPRESS=DEFLATE --o\nexit\ntrash Gtmp\n#+END_SRC\n*** Buffered ice mask\n#+BEGIN_SRC bash :results verbatim\ngrass -c mask.tif ./Gtmp\nr.in.gdal input=mask.tif output=mask\n# 50 cells = 25 km @ 500 m\nr.mapcalc \"ice = if(mask == 2, 1, null())\"\nr.grow input=ice output=ice_grow radius=50 new=1\n\nr.null ice_grow null=100\nr.clump input=ice_grow output=clumps\nr.stats -c clumps sort=asc\nfor ID in $(r.stats -c clumps sort=asc | head -n7 | cut -d\" \" -f1); do\n  r.mapcalc \"ice_grow = if(clumps == ${ID}, 1, ice_grow)\" --o\ndone\nr.null ice_grow setnull=100\n\nr.out.gdal input=ice_grow output=ice_mask_buffer.tif format=GTiff type=Byte createopt=\"COMPRESS=DEFLATE\"\nexit\ntrash Gtmp\n#+END_SRC\n\n\n** Footprint\n\nGet GL outline by drawing in Google Earth, export KML, then:\n\n#+BEGIN_SRC bash :results verbatim :eval no-export\nogrinfo -al GL_outline.kml  | grep LINESTRING | sed s/\\ 0//g\n#+END_SRC\n\n** Regional masks\n\nRegional masks stored in the [[https://github.com/GEUS-SICE/SICE/tree/master/masks][masks]] folder are clips from the \n[[https://www.esa-landcover-cci.org/?q=node/197][ESA global Land Cover products]] (download [[https://cds.climate.copernicus.eu/cdsapp#!/dataset/satellite-land-cover?tab=form][here]]). Masks were downloaded for 2018 and are available\nat 300m and 1km resolutions ({region}_300m.tif and {region}_1km.tif, respectively). A description of the 22 [[https://www.esa-landcover-cci.org/?q=node/197][ESA global Land Cover products]] can be found [[https://www.esa-landcover-cci.org/?q=webfm_send/84][here]].\n\n* Post-processing, analysis and visualisation\n\n  Post-processing, analysis and visualisation tools have been implemented in the [[https://github.com/GEUS-SICE/SICE-toolbox][SICE toolbox]].\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["greenland","weather","weather-station"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/140244","html_url":"https://ost.ecosyste.ms/projects/140244"}