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Add the "state of ground" to bring in the extra snow depth reports #1368

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Add the "state of ground" to bring in the extra snow depth reports #1368

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1c8096f
Add state of ground to increase the snow depth reports.
jiaruidong2017 Nov 9, 2024
365675d
Update the defined index with zero snow depth.
jiaruidong2017 Nov 13, 2024
aee4dc2
Merge branch 'develop' into feature/snow-sogr
jiaruidong2017 Nov 13, 2024
0c02522
Move python code to parm/gdas/snow/ directory to aviod extra copy.
jiaruidong2017 Nov 13, 2024
e57ac67
Modif to only replace the missing/filled snod values.
jiaruidong2017 Nov 13, 2024
4376049
Merge branch 'develop' into feature/snow-sogr
jiaruidong2017 Nov 13, 2024
244693c
Address reviewer's comments.
jiaruidong2017 Nov 14, 2024
76a5e94
Fix py norms error.
jiaruidong2017 Nov 14, 2024
2a72e4d
Add the mapping_path indicating the script backend requirements.
jiaruidong2017 Nov 15, 2024
a2d87fd
Merge branch 'develop' into feature/snow-sogr
jiaruidong2017 Nov 15, 2024
fbd1bb9
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jiaruidong2017 Nov 15, 2024
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1 change: 1 addition & 0 deletions parm/snow/obs/config/bufr2ioda_mapping.yaml.j2
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Expand Up @@ -2,3 +2,4 @@ mkdir:
- '{{ DATA }}/obs'
copy:
- ['{{PARMgfs}}/gdas/snow/obs/config/bufr_sfcsno_mapping.yaml', '{{ DATA }}/obs/']
- ['{{PARMgfs}}/gdas/snow/obs/config/ioda_bufr_python_encoder.py', '{{ DATA }}']
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does the python script need copied? and should it go here? we might need to talk to @emilyhcliu about the progress of SPOC

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Thanks @CoryMartin-NOAA for your suggestions. Do you agree if I put this python code to sorc/gdas.cd/parm/snow/, so that this code can be used directly?
@emilyhcliu Any suggestions?

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I moved this py code to the parm/gdas/snow/ directory for a temporary solution. @emilyhcliu Please let me know if you have any other suggestions. Thanks.

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Scripts shouldn't be in parm/, until we move to SPOC, it should probably go here: https://github.com/NOAA-EMC/GDASApp/tree/develop/ush/ioda/bufr2ioda

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Understood. Wait for @emilyhcliu suggestions.

17 changes: 10 additions & 7 deletions parm/snow/obs/config/bufr_sfcsno_mapping.yaml
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Expand Up @@ -17,7 +17,6 @@ bufr:
query: "[*/CLON, */CLONH]"
stationIdentification:
query: "*/RPID"

stationElevation:
query: "[*/SELV, */HSMSL]"

Expand All @@ -26,11 +25,8 @@ bufr:
query: "[*/SNWSQ1/TOSD, */MTRMSC/TOSD, */STGDSNDM/TOSD]"
transforms:
- scale: 1000.0
filters:
- bounding:
variable: totalSnowDepth
lowerBound: 0
upperBound: 10000000
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For my understanding:

  • is this introducing a 10 m limit on snow depth obs?
  • if they are above 10 m, are they discarded, or set to 10.?

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I previously put this large number (10000m) here for removing the missing values. Here, we don't need this any more because we need to set the missing snod values to 0 when sogr satisfies the defined conditions.

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We might still have missing values though wouldn't we?

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The missing values will be removed after applying sogr conditions.

groundState:
query: "[*/GRDSQ1/SOGR, */STGDSNDM/SOGR]"

encoder:
variables:
Expand Down Expand Up @@ -65,11 +61,18 @@ encoder:
coordinates: "longitude latitude"
source: variables/stationIdentification
longName: "Identification of Observing Location"
units: "m"
units: "index"

# ObsValue
- name: "ObsValue/totalSnowDepth"
coordinates: "longitude latitude"
source: variables/totalSnowDepth
longName: "Total Snow Depth"
units: "mm"

- name: "ObsValue/groundState"
coordinates: "longitude latitude"
source: variables/groundState
longName: "STATE OF THE GROUND"
units: "index"

31 changes: 31 additions & 0 deletions parm/snow/obs/config/ioda_bufr_python_encoder.py
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@@ -0,0 +1,31 @@
import numpy as np
import bufr
from pyioda.ioda.Engines.Bufr import Encoder


def mask_container(container, mask):
new_container = bufr.DataContainer()
for var_name in container.list():
print(f" ... variable name: {var_name} ...")
var = container.get(var_name)
paths = container.get_paths(var_name)
new_container.add(var_name, var[mask], paths)

return new_container

def create_obs_group(input_path):
YAML_PATH = "./obs/bufr_sfcsno_mapping.yaml"
container = bufr.Parser(input_path, YAML_PATH).parse()

sogr = container.get('variables/groundState')
snod = container.get('variables/totalSnowDepth')
snod[(sogr <= 11.0) | (sogr == 15.0)] = 0.0
container.replace('variables/totalSnowDepth', snod)

print(f" ... Remove filled/missing snow values ...")
masked_container = mask_container(container, (~snod.mask))

encoder = Encoder(YAML_PATH)
data = next(iter(encoder.encode(masked_container).values()))

return data
6 changes: 4 additions & 2 deletions parm/snow/obs/config/sfcsno_snow.yaml.j2
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Expand Up @@ -5,9 +5,11 @@
halo size: 250e3
obsdatain:
engine:
type: bufr
type: script
script file: "{{ DATA }}/ioda_bufr_python_encoder.py"
args:
input_path: '{{ DATA }}/obs/{{ OPREFIX }}sfcsno.tm00.bufr_d'
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Suggestion:
Make the mapping file as input to the Python script for create_obs_group

args:
 input_path:  '{{ DATA }}/obs/{{ OPREFIX }}sfcsno.tm00.bufr_d'
 mapping_path: = "./obs/bufr_sfcsno_mapping.yaml"

This will make it clear that the script backend requires two inputs: bufr file and the mapping file

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Thanks @emilyhcliu for the suggestions. I made the changes as suggested.

obsfile: '{{ DATA }}/obs/{{ OPREFIX }}sfcsno.tm00.bufr_d'
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Don't forget to add an issue so they do not assume the formatting of the YAML file (obsfile variable shoould not be necessary). Reading the backend engines YAML breaks encapsulation (external modules should not be dependent on the private configuration for a backend type. Some backends may not have any kind of file associated with them (like a db...).

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yes thanks @rmclaren I'm aware of that issue, I/we/others need to figure out how best to handle it on the workflow side.

mapping file: '{{ DATA }}/obs/bufr_sfcsno_mapping.yaml'
obsdataout:
engine:
type: H5File
Expand Down
2 changes: 1 addition & 1 deletion sorc/bufr-query
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Submodule bufr-query updated 36 files
+4 −2 CMakeLists.txt
+5 −5 cmake/Targets.cmake
+4 −2 core/CMakeLists.txt
+8 −0 core/include/bufr/BufrParser.h
+25 −2 core/include/bufr/DataContainer.h
+523 −1 core/include/bufr/DataObject.h
+5 −7 core/include/bufr/DataProvider.h
+8 −3 core/include/bufr/File.h
+3 −0 core/include/bufr/NcepDataProvider.h
+3 −0 core/include/bufr/WmoDataProvider.h
+66 −1 core/src/bufr/BufrReader/BufrParser.cpp
+51 −11 core/src/bufr/BufrReader/Query/DataProvider/DataProvider.cpp
+8 −0 core/src/bufr/BufrReader/Query/DataProvider/NcepDataProvider.cpp
+7 −0 core/src/bufr/BufrReader/Query/DataProvider/WmoDataProvider.cpp
+12 −5 core/src/bufr/BufrReader/Query/File.cpp
+56 −0 core/src/bufr/DataContainer.cpp
+11 −2 core/src/encoders/netcdf/Encoder.cpp
+31 −0 docs/python_api.rst
+1 −0 docs/uml/BUFR_BigPicture.puml
+25 −28 python/CMakeLists.txt
+17 −10 python/DataObjectFunctions.cpp
+4 −4 python/DataObjectFunctions.h
+4 −0 python/py_bufr.cpp
+17 −1 python/py_data_container.cpp
+2 −1 python/py_file.cpp
+49 −0 python/py_mpi.cpp
+23 −0 python/py_mpi.h
+15 −2 python/py_parser.cpp
+12 −8 test/CMakeLists.txt
+2 −2 test/testinput/bufrtest_fieldname_validation.py
+88 −0 test/testinput/bufrtest_python_mpi_test.py
+21 −12 test/testinput/bufrtest_python_test.py
+3 −0 tools/bufr2netcdf/CMakeLists.txt
+140 −44 tools/bufr2netcdf/bufr2netcdf.cpp
+1 −1 tools/build_scripts/bufr_query_cpp_lint.py
+11 −3 tools/show_queries/QueryPrinter.cpp
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