Feature/b2i (#1275)

6 bufr to ioda converters this is second refactoring of the code. the variables are grouped into metadata, obs and additional ioda vars metadata is read from a yaml file (could also be a json file) additional variables now include ocean basin converters generate log files and have a command line option to test the log against a reference file Log files contain some human readable data, as well as cryptographic hash strings computed from the variables. Simple utilities to plot data are included. --------- Co-authored-by: Guillaume Vernieres <[email protected]>
NOAA-EMC · Sep 27, 2024 · 2be1fcd · 2be1fcd
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diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -146,3 +146,5 @@ add_subdirectory(atm)
 
 # gdas aerosol tests
 add_subdirectory(aero)
+
+add_subdirectory(marine)
diff --git a/test/marine/CMakeLists.txt b/test/marine/CMakeLists.txt
@@ -0,0 +1,161 @@
+# Copy the bkg files
+# ------------------
+set(TESTDATA ${PROJECT_BINARY_DIR}/test/testdata )
+
+
+# Symlink test input yaml files
+# -----------------------------
+# create testinput dir
+set (TESTINPUT_DIR ${PROJECT_BINARY_DIR}/test/marine/testinput)
+
+file(MAKE_DIRECTORY ${TESTINPUT_DIR})
+
+# symlink
+foreach(FILENAME ${test_input})
+	get_filename_component(filename ${FILENAME} NAME)
+	execute_process( COMMAND ${CMAKE_COMMAND} -E create_symlink
+		${FILENAME}
+		${TESTINPUT_DIR}
+	)
+endforeach(FILENAME)
+
+# install
+install(FILES ${test_input}
+        DESTINATION "test/testinput/")
+
+
+###########################################################################
+# bufr to ioda tests:
+###########################################################################
+
+# prepare a test.yaml file from test.yaml.in by replacing
+# placeholder patterns __BUFRINPUTDIR__ and __IODAOUTPUTDIR__ and __OCEANBASIN__
+# with actual directory paths
+function(CREATE_CONFIG_FILE 
+	test_config_in 
+	test_config_out 
+	bufr_input_dir 
+	ioda_output_dir
+	ocean_basin_file
+)
+	file(READ "${test_config_in}" file_content)
+	string(REPLACE "__BUFRINPUTDIR__" "\"${bufr_input_dir}\"" temp_content "${file_content}")
+	string(REPLACE "__IODAOUTPUTDIR__" "\"${ioda_output_dir}\"" temp_content2 "${temp_content}")
+	string(REPLACE "__OCEANBASIN__" "\"${ocean_basin_file}\"" temp_content3 "${temp_content2}")
+	file(WRITE "${test_config_out}" "${temp_content3}")
+endfunction()
+
+
+set(TEST_WORKING_DIR ${PROJECT_BINARY_DIR}/test/marine)
+
+set(MARINE_BUFR2IODA_DIR ${PROJECT_SOURCE_DIR}/ush/ioda/bufr2ioda/marine)
+set(MARINE_BUFR2IODA_DIR ${MARINE_BUFR2IODA_DIR}/b2i)
+set(CONFIG_DIR ${PROJECT_SOURCE_DIR}/test/marine/testinput)
+set(TESTREF_DIR ${PROJECT_SOURCE_DIR}/test/marine/testref)
+
+
+function(CHECK_AND_SET_PATH PATH1 PATH2 RESULT_VAR)
+    # Check if PATH1 exists
+    if(EXISTS ${PATH1})
+        set(${RESULT_VAR} ${PATH1} PARENT_SCOPE)
+        set(${RESULT_VAR}_EXISTS TRUE PARENT_SCOPE)
+        return()
+    endif()
+
+    # Check if PATH2 exists
+    if(EXISTS ${PATH2})
+        set(${RESULT_VAR} ${PATH2} PARENT_SCOPE)
+        set(${RESULT_VAR}_EXISTS TRUE PARENT_SCOPE)
+        return()
+    endif()
+
+    # If neither path exists
+    set(${RESULT_VAR} "" PARENT_SCOPE)
+    set(${RESULT_VAR}_EXISTS FALSE PARENT_SCOPE)
+endfunction()
+
+
+# find the input files
+set(BUFR_TEST_DIR_ORION
+	"/work/noaa/da/marineda/gfs-marine/data/obs/ci/bufr"
+)
+set(BUFR_TEST_DIR_HERA
+	"/scratch1/NCEPDEV/da/common/ci/bufr"
+)
+CHECK_AND_SET_PATH(
+	${BUFR_TEST_DIR_ORION} 
+	${BUFR_TEST_DIR_HERA} 
+	BUFR_TEST_DIR
+)
+if (NOT BUFR_TEST_DIR_EXISTS)
+	message(STATUS "BUFR test file directory not found -- bufr to ioda tests not generted.")
+	set(GENERATE_BUFR2IODA_TESTS FALSE)
+else()
+    # message(STATUS "Found bufr test directory: ${BUFR_TEST_DIR}")
+
+	set(OCEAN_BASIN_FILE_HERA
+		"/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/common/RECCAP2_region_masks_all_v20221025.nc"
+	)
+	set(OCEAN_BASIN_FILE_ORION
+		"/work/noaa/global/glopara/fix/gdas/soca/20240802/common/RECCAP2_region_masks_all_v20221025.nc"
+	)
+	CHECK_AND_SET_PATH(
+		${OCEAN_BASIN_FILE_ORION} 
+		${OCEAN_BASIN_FILE_HERA} 
+		OCEAN_BASIN_FILE
+	)
+	if (NOT OCEAN_BASIN_FILE_EXISTS)
+		message("Ocean basin data file not found -- bufr to ioda tests not generated.")
+		set(GENERATE_BUFR2IODA_TESTS FALSE)
+	endif()
+	# message(STATUS "Found ocean basin data in ${OCEAN_BASIN_FILE}")
+	set(GENERATE_BUFR2IODA_TESTS TRUE)
+endif()
+
+
+function(ADD_INSITU_TEST testname testbufr)
+	# set(CONFIG_TYPE "json")
+	set(CONFIG_TYPE "yaml")
+	set(DATE "2021063006")
+	set(TEST "bufr2ioda_insitu_${testname}")
+
+	set(TESTREF_FILE "${TEST}_${DATE}.ref")
+
+	# stage the input file to directory ${BUFR_INPUT_DIR}
+	set(BUFR_INPUT_DIR ${TEST_WORKING_DIR})
+	set(BUFR_TEST_FILE "${DATE}-gdas.t06z.${testbufr}.tm00.bufr_d")
+	set(BUFR_FILE "${BUFR_TEST_DIR}/${BUFR_TEST_FILE}")
+	if (NOT EXISTS ${BUFR_FILE})
+		message(FATAL_ERROR "BUFR file ${BUFR_FILE} not found")
+	endif()
+	file(COPY ${BUFR_FILE} DESTINATION ${BUFR_INPUT_DIR})
+
+	# stage the config file
+	set(CONFIG_FILE_NAME ${TEST}_${DATE}.${CONFIG_TYPE})
+	set(CONFIG_FILE_IN "${CONFIG_DIR}/${CONFIG_FILE_NAME}.in")
+	set(CONFIG_FILE "${TEST_WORKING_DIR}/${CONFIG_FILE_NAME}")
+	set(IODA_OUTPUT_DIR ${TEST_WORKING_DIR})
+	CREATE_CONFIG_FILE(
+		${CONFIG_FILE_IN}
+		${CONFIG_FILE}
+		${BUFR_INPUT_DIR}
+		${IODA_OUTPUT_DIR}
+		${OCEAN_BASIN_FILE}
+	)
+
+	add_test(
+		NAME test_${TEST}
+		COMMAND ${MARINE_BUFR2IODA_DIR}/${TEST}.py -c ${CONFIG_FILE} -t ${TESTREF_DIR}/${TESTREF_FILE}
+		WORKING_DIRECTORY ${TEST_WORKING_DIR}
+	)
+endfunction()
+
+
+if (GENERATE_BUFR2IODA_TESTS)
+	ADD_INSITU_TEST("profile_argo" "subpfl")
+	ADD_INSITU_TEST("profile_bathy" "bathy")
+	ADD_INSITU_TEST("profile_glider" "subpfl")
+	ADD_INSITU_TEST("profile_tesac" "tesac")
+	ADD_INSITU_TEST("profile_xbtctd" "xbtctd")
+	ADD_INSITU_TEST("surface_trkob" "trkob")
+endif()
diff --git a/test/marine/testinput/bufr2ioda_insitu_profile_argo_2021063006.yaml.in b/test/marine/testinput/bufr2ioda_insitu_profile_argo_2021063006.yaml.in
@@ -0,0 +1,13 @@
+---
+data_format: subpfl
+subsets: SUBPFL
+source: NCEP data tank
+data_type: argo
+cycle_type: gdas
+cycle_datetime: '2021063006'
+dump_directory: __BUFRINPUTDIR__
+ioda_directory: __IODAOUTPUTDIR__
+ocean_basin: __OCEANBASIN__
+data_description: 6-hrly in situ ARGO profiles
+data_provider: U.S. NOAA
+
diff --git a/test/marine/testinput/bufr2ioda_insitu_profile_bathy_2021063006.yaml.in b/test/marine/testinput/bufr2ioda_insitu_profile_bathy_2021063006.yaml.in
@@ -0,0 +1,13 @@
+---
+data_format: bathy
+subsets: BATHY
+source: NCEP data tank
+data_type: bathy
+cycle_type: gdas
+cycle_datetime: '2021063006'
+dump_directory: __BUFRINPUTDIR__
+ioda_directory: __IODAOUTPUTDIR__
+ocean_basin: __OCEANBASIN__
+data_description: 6-hrly in situ Bathythermal profiles
+data_provider: U.S. NOAA
+
diff --git a/test/marine/testinput/bufr2ioda_insitu_profile_glider_2021063006.yaml.in b/test/marine/testinput/bufr2ioda_insitu_profile_glider_2021063006.yaml.in
@@ -0,0 +1,13 @@
+---
+data_format: subpfl
+subsets: SUBPFL
+source: NCEP data tank
+data_type: glider
+cycle_type: gdas
+cycle_datetime: '2021063006'
+dump_directory: __BUFRINPUTDIR__
+ioda_directory: __IODAOUTPUTDIR__
+ocean_basin: __OCEANBASIN__
+data_description: 6-hrly in situ GLIDER profiles
+data_provider: U.S. NOAA
+
diff --git a/test/marine/testinput/bufr2ioda_insitu_profile_tesac_2021063006.yaml.in b/test/marine/testinput/bufr2ioda_insitu_profile_tesac_2021063006.yaml.in
@@ -0,0 +1,13 @@
+---
+data_format: tesac
+subsets: TESAC
+source: NCEP data tank
+data_type: tesac
+cycle_type: gdas
+cycle_datetime: '2021063006'
+dump_directory: __BUFRINPUTDIR__
+ioda_directory: __IODAOUTPUTDIR__
+ocean_basin: __OCEANBASIN__
+data_description: 6-hrly in situ TESAC profiles
+data_provider: U.S. NOAA
+
diff --git a/test/marine/testinput/bufr2ioda_insitu_profile_xbtctd_2021063006.yaml.in b/test/marine/testinput/bufr2ioda_insitu_profile_xbtctd_2021063006.yaml.in
@@ -0,0 +1,13 @@
+---
+data_format: xbtctd
+subsets: XBTCTD
+source: NCEP data tank
+data_type: xbtctd
+cycle_type: gdas
+cycle_datetime: '2021063006'
+dump_directory: __BUFRINPUTDIR__
+ioda_directory: __IODAOUTPUTDIR__
+ocean_basin: __OCEANBASIN__
+data_description: 6-hrly in situ XBT/XCTD profiles
+data_provider: U.S. NOAA
+
diff --git a/test/marine/testinput/bufr2ioda_insitu_surface_trkob_2021063006.yaml.in b/test/marine/testinput/bufr2ioda_insitu_surface_trkob_2021063006.yaml.in
@@ -0,0 +1,13 @@
+---
+data_format: trkob
+subsets: TRACKOB
+source: NCEP data tank
+data_type: trackob
+cycle_type: gdas
+cycle_datetime: '2021063006'
+dump_directory: __BUFRINPUTDIR__
+ioda_directory: __IODAOUTPUTDIR__
+ocean_basin: __OCEANBASIN__
+data_description: 6-hrly in situ TRACKOB surface
+data_provider: U.S. NOAA
+
diff --git a/test/marine/testref/bufr2ioda_insitu_profile_argo_2021063006.ref b/test/marine/testref/bufr2ioda_insitu_profile_argo_2021063006.ref
@@ -0,0 +1,23 @@
+dateTime: 97150, int64    min, max = 1625022120, 1625047140
+dateTime hash = efcd92a143d8589288563e635318f2705900b0970e68a193eeffca3526cb4824
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+lon: 97150, float32    min, max = -174.8090057373047, 170.48915100097656
+lon hash = e79a198bd3a8d0e72c3749ee84db8f5d6b6499a6c231540117c1270abff515ea
+lat: 97150, float32    min, max = -59.77299880981445, 76.25086212158203
+lat hash = be568a690e0f32204326993b16d4f7863b4f77db6cbe5febf30523098c9186b3
+depth: 97150, float32    min, max = 0.0, 5700.7001953125
+depth hash = 805664f9daa328e4dce41c33fdadfdf026908d7f6f044b3079bde03f343fe79a
+stationID: 97150, <U11
+stationID hash = 85faa16d0fc1e02d2fb4da51dea715732088589a45233b81a1f9f65932df6df5
+temp: 97150, float32    min, max = -1.817999243736267, 31.73198890686035
+temp hash = 674e8493b492fb7ac91207f706e79f94056009c61d16a7c657bfab391b4745af
+saln: 97150, float32    min, max = 3.305000066757202, 42.47999954223633
+saln hash = 57e87adc01b398c3e40b2d23c929aae3613f9811580bb4cffb18408a3c953584
+seqNum: 97150, int32    min, max = 0, 155
+seqNum hash = 91c64cfe2001beb9608338e86485d622485f9b9117c477d1ea64ccb01c32cbde
+PreQC: 97150, int32    min, max = 0, 0
+ObsError_temp: 97150, float32    min, max = 0.019999999552965164, 0.019999999552965164
+ObsError_saln: 97150, float32    min, max = 0.009999999776482582, 0.009999999776482582
+OceanBasin: 97150, int32    min, max = 0, 5
+OceanBasin hash = f3a46a8533511f5885db7ff9623707a36b4a7135643041e9878c327e4378e42d
diff --git a/test/marine/testref/bufr2ioda_insitu_profile_bathy_2021063006.ref b/test/marine/testref/bufr2ioda_insitu_profile_bathy_2021063006.ref
@@ -0,0 +1,20 @@
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+lon: 1751, float32    min, max = -79.9000015258789, 13.020000457763672
+lon hash = eb89f459093a674845f3de8277409658090f0c2e9a4af84367d0dcb4598fea39
+lat: 1751, float32    min, max = -27.549999237060547, 29.93000030517578
+lat hash = cc86ce703edb7b8b32dac497fd28576c77527ba168348af785315ce02f8cbfb7
+depth: 1751, float32    min, max = 2.0, 1298.0
+depth hash = 7fde28c9dae36779d0ad21459946791cc6cd3a461a6b5d544399c2bf22eb3d04
+stationID: 1751, <U6
+stationID hash = 41e65ec9607faf118615a8d9ce2bfabbbe6b6e835520cd35e9ed30abdc26c2f3
+temp: 1751, float32    min, max = 3.5999999046325684, 29.100000381469727
+temp hash = c00bbe5d969f8de8232ae22cd0948621e6b3e326e4931cdcfa2f7dd4d2509879
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+seqNum hash = 7429963169776e1dc0d26732c5053c7e81131cc66654c23aa6393258e9b5b9ae
+PreQC: 1751, int32    min, max = 0, 0
+ObsError_temp: 1751, float32    min, max = 0.23999999463558197, 0.23999999463558197
+OceanBasin: 1751, int32    min, max = 1, 1
+OceanBasin hash = 7de61dfe030e0fabc021c5e1c509cbd2f01afba06ac93959f94c5726d513937f
diff --git a/test/marine/testref/bufr2ioda_insitu_profile_glider_2021063006.ref b/test/marine/testref/bufr2ioda_insitu_profile_glider_2021063006.ref
@@ -0,0 +1,23 @@
+dateTime: 27280, int64    min, max = 1625022060, 1625046720
+dateTime hash = 2761399c297bbda0b22acbe64f47b86f677e32ebf495a3cb8b7800ad84f25f75
+rcptdateTime: 27280, int64    min, max = 1625030220, 1625580780
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+lon hash = 6367f3579cd1641387a49a60d766d3dc4a1352f760e7c6851469e2b6d5be9aa5
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+lat hash = ae48a82fc017206b16d4db9efdc63813763b131ebb0d47e81cbf90feea1d0d1f
+depth: 27280, float32    min, max = 0.0, 1007.0
+depth hash = 93d7c59fb8cf0cdcee45a96263515281be53b4557dcca9b86af9a9785728dcdc
+stationID: 27280, <U11
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+temp hash = b1f6cc4411776b9f2315a6f945c38a520bb6199a9da544ece2ca2f772520634e
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+seqNum: 27280, int32    min, max = 0, 140
+seqNum hash = eed58b20f19414e540dcf6e32a0c7ef9beaf3906045bd05279caa326e7a8e106
+PreQC: 27280, int32    min, max = 0, 0
+ObsError_temp: 27280, float32    min, max = 0.019999999552965164, 0.019999999552965164
+ObsError_saln: 27280, float32    min, max = 0.009999999776482582, 0.009999999776482582
+OceanBasin: 27280, int32    min, max = 0, 2
+OceanBasin hash = 85f985fd1d0c5596e07c480680abd31277664a7bc61ae466f9cf733626a2ac46
diff --git a/test/marine/testref/bufr2ioda_insitu_profile_tesac_2021063006.ref b/test/marine/testref/bufr2ioda_insitu_profile_tesac_2021063006.ref
@@ -0,0 +1,23 @@
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+ObsError_temp: 5487, float32    min, max = 0.019999999552965164, 0.019999999552965164
+ObsError_saln: 5487, float32    min, max = 0.009999999776482582, 0.009999999776482582
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diff --git a/test/marine/testref/bufr2ioda_insitu_profile_xbtctd_2021063006.ref b/test/marine/testref/bufr2ioda_insitu_profile_xbtctd_2021063006.ref
@@ -0,0 +1,23 @@
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+PreQC: 109, int32    min, max = 0, 0
+ObsError_temp: 109, float32    min, max = 0.11999999731779099, 0.11999999731779099
+ObsError_saln: 109, float32    min, max = 1.0, 1.0
+OceanBasin: 109, int32    min, max = 0, 2
+OceanBasin hash = db7f48faf153ae3f838436037b5a2d64e4be9368d5c8d1f9d3701d4c6802779b
diff --git a/test/marine/testref/bufr2ioda_insitu_surface_trkob_2021063006.ref b/test/marine/testref/bufr2ioda_insitu_surface_trkob_2021063006.ref
@@ -0,0 +1,19 @@
+dateTime: 929, int64    min, max = 1625011200, 1625043540
+dateTime hash = fe44939ae1f54dbee46edec3c024dc1298017a51cf85fcfff2c261aeec886a3c
+rcptdateTime: 929, int64    min, max = 1625088960, 1625175540
+rcptdateTime hash = a08519e6ebdefd8b7946c32a557273d81608837a615965528c933996d4e444bf
+lon: 929, float32    min, max = -4.429999828338623, 152.17999267578125
+lon hash = 985190343e99bbbf3979e7285e8e276148b9291ad04f8e5ca5cdbb6ffe34010b
+lat: 929, float32    min, max = -23.479999542236328, 48.91999816894531
+lat hash = 4293df46db1a98b72f455c8682a9fbc9b655e3898f4f20912b49147539de5479
+stationID: 929, <U4
+stationID hash = b168519bf422422975e2f63be7bac9e8de9613e071534def510bfb9e2d01ff7c
+temp: 929, float32    min, max = 13.600000381469727, 27.9999942779541
+temp hash = 8cc9791112272e02bdf6b0b2c4a936a690efd00a311e81b49d9df8ba3a4b77a6
+saln: 929, float32    min, max = 33.75, 37.58000183105469
+saln hash = 3bc415581fbe183e324449621debeb359ed1599335a2ce70b98258e6811c1dca
+PreQC: 929, int32    min, max = 0, 0
+ObsError_temp: 929, float32    min, max = 0.30000001192092896, 0.30000001192092896
+ObsError_saln: 929, float32    min, max = 1.0, 1.0
+OceanBasin: 929, int32    min, max = 0, 2
+OceanBasin hash = cd8318dfcc18b3c9fbcd8264ec98c4db6e1551185282e2cd08a499a2f26682d8