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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
Add comments
jiaruidong2017 Nov 15, 2024
db46314
Merge branch 'develop' into feature/snow-sogr
jiaruidong2017 Nov 22, 2024
91f160e
Update the missing value for elevation from bufr file.
jiaruidong2017 Nov 22, 2024
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31 changes: 31 additions & 0 deletions parm/snow/ioda_bufr_python_encoder.py
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@jiaruidong2017 move this to https://github.com/NOAA-EMC/GDASApp/tree/develop/ush/ioda/bufr2ioda but change its name to something more descriptive/specific until we can move things to SPOC

Original file line number Diff line number Diff line change
@@ -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):
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Some comments here would be helpful to explain what we're doing - specifically what snogr is, and why we're selecting out the values that we are.

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Excellent suggestions. I will add the comments here later. Thanks.

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Add the comments to explain the steps.

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
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Without having seen the data, I think there should be an if statement here - so that we only replace the snod when it was undefined / missing.

i.e., if snod > 0. (or some, slighty higher threshold), and sogr indictaes no snow cover, I assume we would want to use the snod value, not 0.

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Above (with an if statement) is all consistent with how the PR description.

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Good suggestions. I will investigate this.

@rmclaren Do you have any suggestions?

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Thanks again for the good findings. I modified to only replace the filled/missing snod.

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()))
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Could be 1 liner data = next(iter(Encoder(YAML_PATH).encode(masked_container).values())). Up to you :)

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Thanks @rmclaren for your suggestions. Will change it.


return data
17 changes: 10 additions & 7 deletions parm/snow/obs/config/bufr_sfcsno_mapping.yaml
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Original file line number Diff line number Diff line change
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"

6 changes: 4 additions & 2 deletions parm/snow/obs/config/sfcsno_snow.yaml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,11 @@
halo size: 250e3
obsdatain:
engine:
type: bufr
type: script
script file: "{{ PARMgfs }}/gdas/snow/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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