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Add metadata for BIOS ancillaries #3

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7981fef
Remove TODO
SeanBryan51 Oct 21, 2024
eea8da2
Add comment and references for BIOS soil parameters
SeanBryan51 Oct 21, 2024
813e66f
Set units and long_name attributes for BIOS variables
SeanBryan51 Oct 21, 2024
e8764c0
Set sfc units to 1
SeanBryan51 Oct 22, 2024
98eeacb
Use upper case for long_name description
SeanBryan51 Oct 22, 2024
855970f
Add comment and references to mvg
SeanBryan51 Oct 22, 2024
aad786c
Set c4frac references attribute
SeanBryan51 Nov 19, 2024
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242 changes: 240 additions & 2 deletions regrid_aus_05x05_to_005x005.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -120,8 +120,6 @@ modification_attr="${script_name}: Update soil parameter values with fields as u
echo "Add modification note to global attributes"
ncatted -h -a modification,global,p,c,"${modification_attr}" ${output_file}

# TODO(Sean): check unit, standard name, long name attributes for appended variables

silt_file=${BIOS_PARAM_DIR}/siltfrac1.nc
echo "silt_file: ${silt_file}"

Expand All @@ -145,6 +143,22 @@ ncks --overwrite --no-alphabetize -x -v silt \
echo "Append silt variable to output file"
ncks -A -v silt silt.nc ${output_file}

echo "Set silt units attribute"
att_nm='units'
var_nm='silt'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set silt long_name attribute"
att_nm='long_name'
var_nm='silt'
mode='o'
att_type='c'
att_val='UM SOIL TEXTURE - SILT FRACTION'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

clay_file=${BIOS_PARAM_DIR}/clayfrac1.nc
echo "clay_file: ${clay_file}"

Expand All @@ -168,6 +182,22 @@ ncks --overwrite --no-alphabetize -x -v clay \
echo "Append clay variable to output file"
ncks -A -v clay clay.nc ${output_file}

echo "Set clay units attribute"
att_nm='units'
var_nm='clay'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set clay long_name attribute"
att_nm='long_name'
var_nm='clay'
mode='o'
att_type='c'
att_val='UM SOIL TEXTURE - CLAY FRACTION'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Create sand file"
ncks --overwrite --no-alphabetize silt.nc sand.nc
ncks -A -v clay clay.nc sand.nc
Expand All @@ -183,6 +213,22 @@ ncks --overwrite --no-alphabetize -x -v sand \
echo "Append sand variable to output file"
ncks -A -v sand sand.nc ${output_file}

echo "Set sand units attribute"
att_nm='units'
var_nm='sand'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set sand long_name attribute"
att_nm='long_name'
var_nm='sand'
mode='o'
att_type='c'
att_val='UM SOIL TEXTURE - SAND FRACTION'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

css_file=${BIOS_PARAM_DIR}/csoil1.nc
echo "css_file: ${css_file}"

Expand All @@ -206,6 +252,22 @@ ncks --overwrite --no-alphabetize -x -v css \
echo "Append css variable to output file"
ncks -A -v css css.nc ${output_file}

echo "Set css units attribute"
att_nm='units'
var_nm='css'
mode='o'
att_type='c'
att_val='J/kg/K'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set css long_name attribute"
att_nm='long_name'
var_nm='css'
mode='o'
att_type='c'
att_val='SOIL SPECIFIC HEAT CAPACITY'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

sfc_file=${BIOS_PARAM_DIR}/wvol1fc_m3m3.nc
echo "sfc_file: ${sfc_file}"

Expand All @@ -229,6 +291,22 @@ ncks --overwrite --no-alphabetize -x -v sfc \
echo "Append sfc variable to output file"
ncks -A -v sfc sfc.nc ${output_file}

echo "Set sfc units attribute"
att_nm='units'
var_nm='sfc'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set sfc long_name attribute"
att_nm='long_name'
var_nm='sfc'
mode='o'
att_type='c'
att_val='VOL SMC AT CRIT PT'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

rhosoil_file=${BIOS_PARAM_DIR}/bulkdens1_kgm3.nc
echo "rhosoil_file: ${rhosoil_file}"

Expand All @@ -252,6 +330,22 @@ ncks --overwrite --no-alphabetize -x -v rhosoil \
echo "Append rhosoil variable to output file"
ncks -A -v rhosoil rhosoil.nc ${output_file}

echo "Set rhosoil units attribute"
att_nm='units'
var_nm='rhosoil'
mode='o'
att_type='c'
att_val='kg/m^3'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set rhosoil long_name attribute"
att_nm='long_name'
var_nm='rhosoil'
mode='o'
att_type='c'
att_val='SOIL BULK DENSITY'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

bch_file=${BIOS_PARAM_DIR}/b1.nc
echo "bch_file: ${bch_file}"

Expand Down Expand Up @@ -280,6 +374,22 @@ ncks --overwrite --no-alphabetize -x -v bch \
echo "Append bch variable to output file"
ncks -A -v bch bch.nc ${output_file}

echo "Set bch units attribute"
att_nm='units'
var_nm='bch'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set bch long_name attribute"
att_nm='long_name'
var_nm='bch'
mode='o'
att_type='c'
att_val='CLAPP-HORNBERGER B COEFFICIENT'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

hyds_file=${BIOS_PARAM_DIR}/hyk1sat_ms.nc
echo "hyds_file: ${hyds_file}"

Expand Down Expand Up @@ -308,6 +418,22 @@ ncks --overwrite --no-alphabetize -x -v hyds \
echo "Append hyds variable to output file"
ncks -A -v hyds hyds.nc ${output_file}

echo "Set hyds units attribute"
att_nm='units'
var_nm='hyds'
mode='o'
att_type='c'
att_val='m/s'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set hyds long_name attribute"
att_nm='long_name'
var_nm='hyds'
mode='o'
att_type='c'
att_val='SAT SOIL CONDUCTIVITY'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

ssat_file=${BIOS_PARAM_DIR}/wvol1sat_m3m3.nc
echo "ssat_file: ${ssat_file}"

Expand Down Expand Up @@ -336,6 +462,22 @@ ncks --overwrite --no-alphabetize -x -v ssat \
echo "Append ssat variable to output file"
ncks -A -v ssat ssat.nc ${output_file}

echo "Set ssat units attribute"
att_nm='units'
var_nm='ssat'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set ssat long_name attribute"
att_nm='long_name'
var_nm='ssat'
mode='o'
att_type='c'
att_val='VOL SMC AT SATURATION'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

swilt_file=${BIOS_PARAM_DIR}/wvol1w_m3m3.nc
echo "swilt_file: ${swilt_file}"

Expand Down Expand Up @@ -364,6 +506,22 @@ ncks --overwrite --no-alphabetize -x -v swilt \
echo "Append swilt variable to output file"
ncks -A -v swilt swilt.nc ${output_file}

echo "Set swilt units attribute"
att_nm='units'
var_nm='swilt'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set swilt long_name attribute"
att_nm='long_name'
var_nm='swilt'
mode='o'
att_type='c'
att_val='VOL SMC AT WILTING'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

sucs_file=${BIOS_PARAM_DIR}/psie1_m.nc
echo "sucs_file: ${sucs_file}"

Expand Down Expand Up @@ -397,6 +555,22 @@ ncks --overwrite --no-alphabetize -x -v sucs \
echo "Append sucs variable to output file"
ncks -A -v sucs sucs.nc ${output_file}

echo "Set sucs units attribute"
att_nm='units'
var_nm='sucs'
mode='o'
att_type='c'
att_val='m'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set sucs long_name attribute"
att_nm='long_name'
var_nm='sucs'
mode='o'
att_type='c'
att_val='SATURATED SOIL WATER SUCTION'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

mvg_file=${BIOS_PARAM_DIR}/nvis5pre1750grp.nc
echo "mvg_file: ${mvg_file}"

Expand All @@ -423,6 +597,30 @@ ncks --overwrite --no-alphabetize -x -v mvg \
echo "Append mvg variable to output file"
ncks -A -v mvg mvg.nc ${output_file}

echo "Set mvg long_name attribute"
att_nm='long_name'
var_nm='mvg'
mode='o'
att_type='c'
att_val='NVIS MAJOR VEGETATION GROUP (V5.0)'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set mvg comment attribute"
att_nm='comment'
var_nm='mvg'
mode='o'
att_type='c'
att_val='Data provided from National Vegetation Information System (NVIS)'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set mvg references attribute"
att_nm='references'
var_nm='mvg'
mode='o'
att_type='c'
att_val='https://www.dcceew.gov.au/environment/land/native-vegetation/national-vegetation-information-system/data-products#mvg5'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

c4frac_file=${BIOS_PARAM_DIR}/c4_grass_frac_cov.nc
echo "c4frac_file: ${c4frac_file}"

Expand All @@ -446,6 +644,46 @@ ncks --overwrite --no-alphabetize -x -v c4frac \
echo "Append c4frac variable to output file"
ncks -A -v c4frac c4frac.nc ${output_file}

echo "Set c4frac units attribute"
att_nm='units'
var_nm='c4frac'
mode='o'
att_type='c'
att_val='1'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set c4frac long_name attribute"
att_nm='long_name'
var_nm='c4frac'
mode='o'
att_type='c'
att_val='FRACTIONAL COVER OF C4 GRASS'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Set c4frac references attribute"
att_nm='references'
var_nm='c4frac'
mode='o'
att_type='c'
att_val='https://doi.org/10.5194/bg-10-2011-2013 following https://doi.org/10.1007/BF00379569'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

bios_soil_vars_regex='^clay$|^sand$|^ssat$|^bch$|^css$|^hyds$|^sfc$|^sucs$|^rhosoil$|^silt$|^swilt$'

echo "Add provenance information to BIOS soil parameters"
att_nm='comment'
var_nm=${bios_soil_vars_regex}
mode='o'
att_type='c'
att_val='Data provided from the Atlas of Australian Soils (digital)'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
att_nm='references'
var_nm=${bios_soil_vars_regex}
mode='o'
att_type='c'
att_val='https://doi.org/10.25919/5df03e991672d and https://publications.csiro.au/publications/publication/PIlegacy:889'
ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}

echo "Clean up"
rm clay.nc sand.nc ssat.nc bch.nc css.nc hyds.nc mvg.nc sfc.nc sucs.nc c4frac.nc rhosoil.nc silt.nc swilt.nc