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resolve inconsistencies between bufr2ioda python converters and jcb templates #1241

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merged 10 commits into from
Aug 12, 2024
Merged

resolve inconsistencies between bufr2ioda python converters and jcb templates #1241

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26e4464
resolve inconsistencies between bufr2ioda python converters and jcb t…
RussTreadon-NOAA Jul 31, 2024
412307b
Merge branch 'develop' into feature/bufr2ioda
RussTreadon-NOAA Aug 4, 2024
d5ef559
Merge branch 'NOAA-EMC:develop' into feature/bufr2ioda
RussTreadon-NOAA Aug 7, 2024
1466e09
add tm00 to adp prepbufr bufr2ioda converters, use nc instead of nc4 …
RussTreadon-NOAA Aug 7, 2024
4e43edd
update parm/jcb-gdas hash (#1227)
RussTreadon-NOAA Aug 7, 2024
182086d
Merge branch 'develop' into feature/bufr2ioda
RussTreadon-NOAA Aug 8, 2024
7fef398
update jcb-gdas hash to point at authoritaive repo (#1227)
RussTreadon-NOAA Aug 8, 2024
6fc0341
remove bufr from gnssro bufr2ioda converter and json filenames (#1227)
RussTreadon-NOAA Aug 9, 2024
8d842b2
remove obsolete gpsro bufr2ioda converter and json files (#1227)
RussTreadon-NOAA Aug 9, 2024
f44cf3b
Merge branch 'develop' into feature/bufr2ioda
RussTreadon-NOAA Aug 10, 2024
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25 changes: 21 additions & 4 deletions parm/atm/jcb-prototype_3dvar.yaml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,27 @@ algorithm: 3dvar
# Observation things
# ------------------
observations:
- satwnd.abi_goes-16
# - ADPSFC
# - ADPUPA
# - SFCSHP
- aircraft
- ascatw.ascat_metop-b
#- conv_ps # Turned off until naming convention of obs files is resolved.
#- gnssro # Turned off until naming convention of obs files is resolved.
# - ascatw.ascat_metop-c
- atms_n20
- atms_npp
- conventional_ps
- gnssro
# - gpsro
# - mtiasi_metop-a
# - mtiasi_metop-b
# - ompsnp_n20
- ompsnp_npp
# - ompstc_n20
- ompstc_npp
- omi_aura
- satwnd.abi_goes-16
- satwnd.abi_goes-18
- satwnd.leogeo_multi
- satwnd.viirs_n20
- satwnd.viirs_npp
# - scatwind_ascat_metop-a
# - snowcvr
28 changes: 24 additions & 4 deletions parm/atm/jcb-prototype_lgetkf.yaml.j2
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@@ -1,7 +1,7 @@
# Use observations for lgetkf
# ---------------------------
app_path_observations: {{PARMgfs}}/gdas/jcb-gdas/observations/atmosphere-lgetkf
app_path_observation_chronicle: {{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/atmosphere-lgetkf
app_path_observation_chronicle: {{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/atmosphere

# Algorithm
# ---------
Expand All @@ -14,7 +14,27 @@ atmosphere_background_ensemble_path: ./bkg/mem%mem%
# Observation things
# ------------------
observations:
- satwnd.abi_goes-16
# - ADPSFC
# - ADPUPA
# - SFCSHP
- aircraft
- ascatw.ascat_metop-b
#- conv_ps # Turned off until naming convention of obs files is resolved.
#- gnssro # Turned off until naming convention of obs files is resolved.
# - ascatw.ascat_metop-c
- atms_n20
- atms_npp
- conventional_ps
- gnssro
# - gpsro
# - mtiasi_metop-a
# - mtiasi_metop-b
# - ompsnp_n20
- ompsnp_npp
# - ompstc_n20
- ompstc_npp
- satwnd.abi_goes-16
- satwnd.abi_goes-18
- satwnd.leogeo_multi
- satwnd.viirs_n20
- satwnd.viirs_npp
# - scatwind_ascat_metop-a
# - snowcvr
2 changes: 1 addition & 1 deletion parm/jcb-gdas
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Submodule jcb-gdas updated 24 files
+0 −0 observation_chronicle/atmosphere/mtiasi_metop-a.yaml
+0 −0 observation_chronicle/atmosphere/mtiasi_metop-b.yaml
+365 −0 observations/atmosphere-lgetkf/aircraft.yaml.j2
+546 −0 observations/atmosphere-lgetkf/atms_n20.yaml.j2
+564 −0 observations/atmosphere-lgetkf/atms_npp.yaml.j2
+373 −0 observations/atmosphere-lgetkf/conventional_ps.yaml.j2
+588 −0 observations/atmosphere-lgetkf/mtiasi_metop-a.yaml.j2
+588 −0 observations/atmosphere-lgetkf/mtiasi_metop-b.yaml.j2
+339 −0 observations/atmosphere-lgetkf/ompsnp_npp.yaml.j2
+144 −0 observations/atmosphere-lgetkf/ompstc_npp.yaml.j2
+610 −0 observations/atmosphere-lgetkf/satwnd.abi_goes-18.yaml.j2
+270 −0 observations/atmosphere-lgetkf/satwnd.leogeo_multi.yaml.j2
+298 −0 observations/atmosphere-lgetkf/satwnd.viirs_n20.yaml.j2
+298 −0 observations/atmosphere-lgetkf/satwnd.viirs_npp.yaml.j2
+7 −7 observations/atmosphere/atms_n20.yaml.j2
+7 −7 observations/atmosphere/atms_npp.yaml.j2
+0 −0 observations/atmosphere/conventional_ps.yaml.j2
+7 −7 observations/atmosphere/cris-fsr_n20.yaml.j2
+7 −7 observations/atmosphere/cris-fsr_npp.yaml.j2
+7 −7 observations/atmosphere/mtiasi_metop-a.yaml.j2
+7 −7 observations/atmosphere/mtiasi_metop-b.yaml.j2
+601 −0 observations/atmosphere/satwnd.abi_goes-18.yaml.j2
+7 −7 observations/atmosphere/ssmis_f17.yaml.j2
+7 −7 observations/atmosphere/ssmis_f18.yaml.j2
2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_acft_profiles_prepbufr.py
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Expand Up @@ -342,7 +342,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': np.arange(0, lat.shape[0])}

iodafile = f"{cycle_type}.t{hh}z.acft_profiles.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.acft_profiles.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_adpsfc_prepbufr.py
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Expand Up @@ -232,7 +232,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': np.arange(0, lat.shape[0])}

iodafile = f"{cycle_type}.t{hh}z.{data_type}.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_adpupa.py
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Expand Up @@ -300,7 +300,7 @@ def bufr_to_ioda(config, logger):
dims = {'Location': np.arange(0, clat.shape[0])}

# Create IODA ObsSpace
iodafile = f"{cycle_type}.t{hh}z.{data_type}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.info(f"Create output file: {OUTPUT_PATH}")
obsspace = ioda_ospace.ObsSpace(OUTPUT_PATH, mode='w', dim_dict=dims)
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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_adpupa_prepbufr.py
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Expand Up @@ -352,7 +352,7 @@ def bufr_to_ioda(config, logger):
dims = {'Location': np.arange(0, lat.shape[0])}

# Create IODA ObsSpace
iodafile = f"{cycle_type}.t{hh}z.{data_type}.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.info(f"Create output file: {OUTPUT_PATH}")
obsspace = ioda_ospace.ObsSpace(OUTPUT_PATH, mode='w', dim_dict=dims)
Expand Down
2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_conventional_prepbufr_ps.py
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Expand Up @@ -864,7 +864,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': np.arange(0, lat.shape[0])}

iodafile = f"{cycle_type}.t{hh}z.{data_description}.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_description}.tm00.nc"
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OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_gnssro_bufr.py
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Expand Up @@ -403,7 +403,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': np.arange(0, clath.shape[0])}

iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_gpsro_bufr_combined.py
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Expand Up @@ -343,7 +343,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': np.arange(0, clath.shape[0])}

iodafile = f"{cycle_type}.t{hh}z.{data_type}.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_sfcshp_prepbufr.py
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Expand Up @@ -265,7 +265,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': np.arange(0, lat.shape[0])}

iodafile = f"{cycle_type}.t{hh}z.{data_type}.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.tm00.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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2 changes: 1 addition & 1 deletion ush/ioda/bufr2ioda/bufr2ioda_snocvr_bufr.py
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Expand Up @@ -131,7 +131,7 @@ def bufr_to_ioda(config, logger):
# Create the dimensions
dims = {'Location': snod.shape[0]}

iodafile = f"{cycle_type}.t{hh}z.{data_type}.{data_format}.nc"
iodafile = f"{cycle_type}.t{hh}z.{data_type}.nc"
OUTPUT_PATH = os.path.join(ioda_dir, iodafile)
logger.debug(f" ... ... Create OUTPUT file: {OUTPUT_PATH}")

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4 changes: 2 additions & 2 deletions ush/run_satbias_conv.py
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Expand Up @@ -101,7 +101,7 @@ def run_satbias_conv(config):
f.write('output:\n')
for sat in satlist:
f.write(f'- sensor: {sat}\n')
f.write(f' output file: {sat}_satbias.nc4\n')
f.write(f' output file: {sat}_satbias.nc\n')
f.write(' predictors: *default_preds\n')
# run executable
runcmd = f'./satbias2ioda.x satbias_converter.yaml'
Expand All @@ -110,7 +110,7 @@ def run_satbias_conv(config):
# copy output files to output directory
outdir = os.path.join(ufo_bc_root, f'{cdump}.{pdy}', cyc, 'atmos')
os.makedirs(outdir, exist_ok=True)
ncfiles = glob.glob(os.path.join(workdir, '*.nc4'))
ncfiles = glob.glob(os.path.join(workdir, '*.nc'))
txtfiles = glob.glob(os.path.join(workdir, '*.txt'))
allfiles = ncfiles + txtfiles
for f in allfiles:
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