Add the capability to assimilate the MADIS snow depth for global-work…

…flow (#602)


* Initialize the madis snow DA in GDASApp for Global-Workflow.

* Add temporal thinning filter for madis data

* Update the temporal thinning filter.

* Change '$(' to '{{' as suggested.

* Made changes from $() to {{ }}

parm/land/obs/config/snocvr_snow.yaml

@@ -0,0 +1,102 @@
+obs space:
+  name: snocvr_snow
+  distribution:
+    name: Halo
+    halo size: 250e3
+  obsdatain:
+    engine:
+      type: H5File
+      obsfile: '{{ DATA }}/obs/{{ OPREFIX }}snocvr_snow.nc4'
+  obsdataout:
+    engine:
+      type: H5File
+      obsfile: '{{ DATA }}/diags/diag_snocvr_snow.nc4'
+  simulated variables: [totalSnowDepth]
+obs operator:
+  name: Composite
+  components:
+  - name: Identity
+  - name: BackgroundErrorIdentity
+obs error:
+  covariance model: diagonal
+obs localizations:
+  - localization method: Horizontal SOAR
+    lengthscale: 250e3
+    soar horizontal decay: 0.000021
+    max nobs: 50
+  - localization method: Vertical Brasnett
+    vertical lengthscale: 700
+obs filters:
+  - filter: Bounds Check
+    filter variables:
+    - name: totalSnowDepth
+    minvalue: 0.0
+    maxvalue: 2000.0
+    action:
+      name: reject
+  - filter: Domain Check
+    where:
+    - variable:
+        name: MetaData/height
+      minvalue: -999.0
+  - filter: Domain Check # land only
+    where:
+    - variable:
+        name: GeoVaLs/slmsk
+      minvalue: 0.5
+      maxvalue: 1.5
+  - filter: RejectList  # no land-ice
+    where:
+    - variable:
+        name: GeoVaLs/vtype
+      minvalue: 14.5
+      maxvalue: 15.5
+  - filter: Temporal Thinning
+    min_spacing: '{{ LAND_WINDOW_LENGTH }}'
+    seed_time: '{{ current_cycle | to_isotime }}'
+    category_variable:
+      name: MetaData/stationIdentification
+  - filter: Background Check # gross error check
+    filter variables:
+    - name: totalSnowDepth
+    threshold: 6.25
+    action:
+      name: reject
+  - filter: Met Office Buddy Check
+    filter variables:
+    - name: totalSnowDepth
+      rejection_threshold: 0.5
+      traced_boxes: # trace all observations
+        min_latitude: -90
+        max_latitude:  90
+        min_longitude: -180
+        max_longitude:  180
+      search_radius: 150 # km
+      station_id_variable:
+        name: MetaData/stationIdentification
+      num_zonal_bands: 24
+      sort_by_pressure: false
+      max_total_num_buddies: 15
+      max_num_buddies_from_single_band: 10
+      max_num_buddies_with_same_station_id: 5
+      use_legacy_buddy_collector: false
+      horizontal_correlation_scale: { "-90": 150, "90": 150 }
+      temporal_correlation_scale: PT6H
+      damping_factor_1: 1.0
+      damping_factor_2: 1.0
+      background_error_group: BkgError
+  - filter: Perform Action
+    filter variables:
+    - name: totalSnowDepth
+    action:
+      name: assign error
+      error parameter: 40.0
+  - filter: Variable Assignment
+    assignments:
+    - name: GrossErrorProbability/totalSnowDepth
+      type: float
+      value: 0.02
+    - name: BkgError/totalSnowDepth_background_error
+      type: float
+      value: 30.0
+

parm/land/obs/lists/gdas_land_gts_only.yaml

@@ -0,0 +1,3 @@
+observers:
+- !INC ${OBS_YAML_DIR}/adpsfc_snow.yaml
+- !INC ${OBS_YAML_DIR}/snocvr_snow.yaml

parm/land/obs/lists/gdas_land_prototype.yaml

@@ -1,3 +1,4 @@
 observers:
 - !INC ${OBS_YAML_DIR}/adpsfc_snow.yaml
+- !INC ${OBS_YAML_DIR}/snocvr_snow.yaml
 - !INC ${OBS_YAML_DIR}/ims_snow.yaml

parm/land/prep/prep_gts.yaml

@@ -2,8 +2,12 @@ gtsbufr:
   mkdir:
     - $(DATA)/obs
   copy:
-    - [$(COM_OBS)/$(OPREFIX)adpsfc.tm00.bufr_d, $(DATA)/obs/]
+    - [{{ COM_OBS }}/{{ OPREFIX }}adpsfc.tm00.bufr_d, {{ DATA }}/obs/]
+    - [{{ COM_OBS }}/{{ OPREFIX }}snocvr.tm00.bufr_d, {{ DATA }}/obs/]
 gtsioda:
   copy:
-    - [$(DATA)/$(OPREFIX)adpsfc_snow.nc4, $(COM_OBS)/$(OPREFIX)adpsfc_snow.nc4]
-
+    - [{{ DATA }}/{{ OPREFIX }}adpsfc_snow.nc4, {{ COM_OBS }}/{{ OPREFIX }}adpsfc_snow.nc4]
+    - [{{ DATA }}/{{ OPREFIX }}snocvr_snow.nc4, {{ COM_OBS }}/{{ OPREFIX }}snocvr_snow.nc4]
+bufr2ioda:
+     adpsfc: {{ HOMEgfs }}/sorc/gdas.cd/test/testinput/bufr_adpsfc_snow.yaml
+     snocvr: {{ HOMEgfs }}/sorc/gdas.cd/test/testinput/bufr_snocvr_snow.yaml

test/testinput/bufr_adpsfc_snow.yaml

@@ -1,13 +1,11 @@
 # (C) Copyright 2021-2022 NOAA/NWS/NCEP/EMC
 #
-# This software is licensed under the terms of the Apache Licence Version 2.0
-# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
 
 observations:
   - obs space:
       name: bufr
 
-      obsdatain: $(DATA)/obs/$(OPREFIX)adpsfc.tm00.bufr_d
+      obsdatain: '{{ DATA }}/obs/{{ OPREFIX }}adpsfc.tm00.bufr_d'
 
       exports:
         variables:
@@ -41,7 +39,7 @@ observations:
 
     ioda:
       backend: netcdf
-      obsdataout: $(DATA)/$(OPREFIX)adpsfc_snow.nc4
+      obsdataout: '{{ DATA }}/{{ OPREFIX }}adpsfc_snow.nc4'
 
       variables:
 

test/testinput/bufr_snocvr_snow.yaml

@@ -0,0 +1,83 @@
+# (C) Copyright 2021-2022 NOAA/NWS/NCEP/EMC
+#
+
+observations:
+  - obs space:
+      name: bufr
+
+      obsdatain: '{{ DATA }}/obs/{{ OPREFIX }}snocvr.tm00.bufr_d'
+
+      exports:
+        variables:
+          # MetaData
+          timestamp:
+            datetime:
+              year: "*/YEAR[1]"
+              month: "*/MNTH[1]"
+              day: "*/DAYS[1]"
+              hour: "*/HOUR[1]"
+              minute: "*/MINU[1]"
+          latitude:
+            query: "[*/CLAT, */CLATH]"
+          longitude:
+            query: "[*/CLON, */CLONH]"
+          stationIdentification:
+            query: "*/WGOSLID"
+
+          height:
+            query: "[*/SELV, */HSMSL]"
+
+          # ObsValue
+          totalSnowDepth:
+            query: "*/TOSD"
+            transforms:
+              - scale: 1000.0
+        filters:
+          - bounding:
+              variable: totalSnowDepth
+              upperBound: 10000000
+
+    ioda:
+      backend: netcdf
+      obsdataout: '{{ DATA }}/{{ OPREFIX }}snocvr_snow.nc4'
+
+      variables:
+
+        # MetaData
+        - name: "MetaData/dateTime"
+          coordinates: "longitude latitude"
+          source: variables/timestamp
+          longName: "Datetime"
+          units: "seconds since 1970-01-01T00:00:00Z"
+
+        - name: "MetaData/latitude"
+          coordinates: "longitude latitude"
+          source: variables/latitude
+          longName: "Latitude"
+          units: "degree_north"
+          range: [-90, 90]
+
+        - name: "MetaData/longitude"
+          coordinates: "longitude latitude"
+          source: variables/longitude
+          longName: "Longitude"
+          units: "degree_east"
+          range: [-180, 180]
+
+        - name: "MetaData/height"
+          coordinates: "longitude latitude"
+          source: variables/height
+          longName: "Height of Station"
+
+        - name: "MetaData/stationIdentification"
+          coordinates: "longitude latitude"
+          source: variables/stationIdentification
+          longName: "Identification of Observing Location"
+          units: "m"
+
+        # ObsValue
+        - name: "ObsValue/totalSnowDepth"
+          coordinates: "longitude latitude"
+          source: variables/totalSnowDepth
+          longName: "Total Snow Depth"
+          units: "mm"