Add precipitable clouds in microwave all-sky assimilations (#63)

Add rain, snow, and graupel clouds for CRTM inputs. Add a prior filter to zero clouds over non-water surfaces. Add an option of clouds in the Hydrometeo check. Add gross error check threshold for precipition impacted channels. Add cold-air-outbreak filters. Read cloud fraction from GeoVals. Render list of not-bias corrected channels from JCB tables. Add configurations for atms_n21.
NOAA-EMC · Jan 16, 2025 · 875fb3c · 875fb3c
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diff --git a/observation_chronicle/atmosphere/atms_n21.yaml b/observation_chronicle/atmosphere/atms_n21.yaml
@@ -0,0 +1,43 @@
+# Instrument metadata
+# -------------------
+commissioned: 2023-05-01T12:00:00
+
+observer_type: satellite  # Type of chronicle to use
+
+# Instrument initial configuration
+# --------------------------------
+channel_variables:
+  simulated: min
+  active: min
+  biascorrtd: min
+  error: max
+  error_cld: max
+  ermax: max
+  var_b: min
+  var_pg: min
+  icld_det: min
+  icloud: min
+  iaerosol: min
+channel_values:
+  1:  [  1,  1,  1,  4.50, 20.00,  4.50, 10.00,  0.00, -2,  1, -1 ]
+  2:  [  1,  1,  1,  4.50, 25.00,  4.50, 10.00,  0.00, -2,  1, -1 ]
+  3:  [  1,  1,  1,  4.50, 12.00,  3.00, 10.00,  0.00, -2,  1, -1 ]
+  4:  [  1,  1,  1,  2.50,  7.00,  3.00, 10.00,  0.00, -2,  1, -1 ]
+  5:  [  1,  1,  1,  0.55,  3.50,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  6:  [  1,  1,  1,  0.30,  3.00,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  7:  [  1,  1,  1,  0.30,  0.80,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  8:  [  1,  1,  1,  0.40,  0.40,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  9:  [  1,  1,  1,  0.40,  0.40,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  10: [  1,  1,  1,  0.40,  0.40,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  11: [  1,  1,  1,  0.45,  0.45,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  12: [  1,  1,  1,  0.45,  0.45,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  13: [  1,  1,  1,  0.55,  0.55,  1.00, 10.00,  0.00, -2,  1, -1 ]
+  14: [  1,  1,  1,  0.80,  0.80,  2.00, 10.00,  0.00, -2,  1, -1 ]
+  15: [  1,  1,  0,  4.00,  4.00,  4.50, 10.00,  0.00, -2,  1, -1 ]
+  16: [  1,  1,  1,  4.00, 19.00,  4.50, 10.00,  0.00, -2,  1, -1 ]
+  17: [  1,  1,  1,  4.00, 30.00,  2.00, 10.00,  0.00, -2,  1, -1 ]
+  18: [  1,  1,  1,  3.50, 25.00,  2.00, 10.00,  0.00, -2,  1, -1 ]
+  19: [  1,  1,  1,  3.00, 16.50,  2.00, 10.00,  0.00, -2,  1, -1 ]
+  20: [  1,  1,  1,  3.00, 12.00,  2.00, 10.00,  0.00, -2,  1, -1 ]
+  21: [  1,  1,  1,  3.00,  9.00,  2.00, 10.00,  0.00, -2,  1, -1 ]
+  22: [  1,  1,  1,  3.00,  6.50,  2.00, 10.00,  0.00, -2,  1, -1 ]
diff --git a/observations/atmosphere/amsua_n19.yaml.j2 b/observations/atmosphere/amsua_n19.yaml.j2
@@ -21,9 +21,10 @@
   # --------------------
   obs operator:
     name: CRTM
-    Absorbers: [H2O, O3]
-    Clouds: [Water, Ice]
-    Cloud_Fraction: 1.0
+    Absorbers: [H2O, O3, CO2]
+    Clouds: &{{observation_from_jcb}}_clouds [Water, Ice, Rain, Snow, Graupel]
+#   Cloud_Fraction: 1.0
+    Cloud_Seeding: true
     obs options:
       Sensor_ID: &{{observation_from_jcb}}_sensor_id amsua_n19
       EndianType: little_endian
@@ -34,6 +35,8 @@
   obs bias:
     input file: "{{atmosphere_obsbiasin_path}}/{{atmosphere_obsbiasin_prefix}}{{observation_from_jcb}}{{atmosphere_obsbiasin_suffix}}"
     output file: "{{atmosphere_obsbiasout_path}}/{{atmosphere_obsbiasout_prefix}}{{observation_from_jcb}}{{atmosphere_obsbiasout_suffix}}"
+    variables without bc: [brightnessTemperature]
+    channels: {{ get_satellite_variable(observation_from_jcb, "not_biascorrtd") }}
     variational bc:
       predictors:
       - name: constant
@@ -64,7 +67,25 @@
 
   # Observation Filters (QC)
   # ------------------------
-  obs filters:
+  obs prior filters:
+  # Zero Atmospheric clouds in CRTM where water_area_fraction < 0.99
+  - filter: Variable Assignment
+    assignments:
+    - name: MetaData/zeroCloudInCRTM
+      type: int
+      function:
+        name: ObsFunction/Conditional
+        options:
+#         firstmatchingcase: false
+          defaultvalue: 0 # Will not zero clouds by default
+          cases:
+          - where:
+            - variable:
+                name: GeoVaLs/water_area_fraction
+              maxvalue: 0.99
+            value: 1 # Will zero clouds by default
+
+  obs post filters:
   - filter: BlackList
     filter variables:
     - name: brightnessTemperature
@@ -124,6 +145,7 @@
       channels: *{{observation_from_jcb}}_simulated_channels
       options:
         channels: *{{observation_from_jcb}}_simulated_channels
+        Clouds: *{{observation_from_jcb}}_clouds
         obserr_clearsky: *{{observation_from_jcb}}_err0
         clwret_function:
           name: ObsFunction/CLWRetMW
@@ -301,6 +323,8 @@
             x1: *{{observation_from_jcb}}_x1
             err0: *{{observation_from_jcb}}_err0
             err1: *{{observation_from_jcb}}_err1
+        threshold: 3
+        threshold_precip: 2.5
         obserr_bound_max: [{{ get_satellite_variable(observation_from_jcb, "ermax") }}]
     action:
       name: reject
@@ -334,8 +358,116 @@
     minvalue: 1.0e-12
     action:
       name: reject
+# Column liquid cloud
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/ColumnLiquidCloud
+      type: float
+      function:
+        name: TotalColumnCloudGuess@ObsFunction
+        options:
+          cloud_content: mass_content_of_cloud_liquid_water_in_atmosphere_layer
+# Column ice cloud
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/ColumnIceCloud
+      type: float
+      function:
+        name: TotalColumnCloudGuess@ObsFunction
+        options:
+          cloud_content: mass_content_of_cloud_ice_in_atmosphere_layer
+# Combined ColumnLiquidCloud + ColumnIceCloud
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/ColumnLiquidIceCloud
+      type: float
+      function:
+        name: ObsFunction/Arithmetic
+        options:
+          variables:
+          - name: DerivedMetaData/ColumnLiquidCloud
+          - name: DerivedMetaData/ColumnIceCloud
+          coefs: [1, 1]
+# replace zero by 1e-7 in DerivedMetaData/ColumnLiquidIceCloud
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/ColumnLiquidIceCloud
+      type: float
+      value: 1.0e-7
+    where:
+    - variable:
+        name: DerivedMetaData/ColumnLiquidIceCloud
+      maxvalue: 1.0e-8
 
-
+# ratio of liquid /(Liquid+Ice)
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/ColumnRatioLiquidCloud
+      type: float
+      function:
+        name: ObsFunction/ElementMultiply
+        options:
+          variables:
+          - name: DerivedMetaData/ColumnLiquidCloud
+          - name: DerivedMetaData/ColumnLiquidIceCloud
+          exponents: [1,-1]
+# TotalColumnVaporGuess
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/TotalColumnVaporGuess
+      type: float
+      function:
+        name: ObsFunction/TotalColumnVaporGuess
+# potentialTemperature at surface
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/PotentialTemperatureSurface
+      type: float
+      function:
+        name: PotentialTemperatureGuess2D@ObsFunction
+        options:
+          approximate pressure: surface_pressure
+# potentialTemperature near 700 hPa
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/PotentialTemperatureAt700hPa
+      type: float
+      function:
+        name: PotentialTemperatureGuess2D@ObsFunction
+        options:
+          approximate pressure: 70000.0
+# stability = Difference between PotentialTemperatur values
+  - filter: Variable Assignment
+    assignments:
+    - name: DerivedMetaData/PotentialTemperatureDiff
+      type: float
+      function:
+        name: ObsFunction/Arithmetic
+        options:
+          variables:
+          - name: DerivedMetaData/PotentialTemperatureAt700hPa
+          - name: DerivedMetaData/PotentialTemperatureSurface
+          coefs: [1, -1]
+## cao_check
+  - filter: BlackList
+    filter variables:
+    - name: brightnessTemperature
+      channels: 1-6, 15
+    where:
+    - variable:
+        name: ObsFunction/TotalColumnVaporGuess
+      maxvalue: 8.0
+    - variable:
+        name: DerivedMetaData/ColumnRatioLiquidCloud
+      maxvalue: 0.5
+    - variable:
+        name: DerivedMetaData/ColumnLiquidIceCloud
+      minvalue: 1.0e-6
+    - variable:
+        name: DerivedMetaData/PotentialTemperatureDiff
+      maxvalue: 12.0
+    action:
+      name: reject
   # GeoVaLs for Driving Observation Operators (testing mode)
   # --------------------------------------------------------
   geovals: