Merge branch 'NOAA-EMC:develop' into feature/hercules

RussTreadon-NOAA · Jan 9, 2024 · 23453d7 · 23453d7
2 parents 4bb1fbf + 69b1eb4
commit 23453d7
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Showing 11 changed files with 60 additions and 59 deletions.
diff --git a/parm/land/obs/config/adpsfc_snow.yaml b/parm/land/obs/config/adpsfc_snow.yaml
@@ -26,7 +26,22 @@ obs localizations:
     max nobs: 50
   - localization method: Vertical Brasnett
     vertical lengthscale: 700
-obs filters:
+obs pre filters:
+  - 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
+obs prior filters:
   - filter: Bounds Check
     filter variables:
     - name: totalSnowDepth
@@ -37,7 +52,7 @@ obs filters:
   - filter: Domain Check
     where:
     - variable:
-        name: MetaData/height
+        name: MetaData/stationElevation
       minvalue: -999.0
   - filter: Domain Check # land only
     where:
@@ -57,12 +72,18 @@ obs filters:
         name: MetaData/stationIdentification
       is_in: [71120,71397,71621,71727,71816]
       size where true: 5
+obs post filters:
   - filter: Background Check # gross error check
     filter variables:
     - name: totalSnowDepth
     threshold: 6.25
     action:
       name: reject
+  - filter: Temporal Thinning
+    min_spacing: '{{ LAND_WINDOW_LENGTH }}'
+    seed_time: '{{ current_cycle | to_isotime }}'
+    category_variable:
+      name: MetaData/stationIdentification
   - filter: Met Office Buddy Check
     filter variables:
     - name: totalSnowDepth
@@ -86,18 +107,4 @@ obs filters:
       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
 
diff --git a/parm/land/obs/config/snocvr_snow.yaml b/parm/land/obs/config/snocvr_snow.yaml
@@ -26,7 +26,22 @@ obs localizations:
     max nobs: 50
   - localization method: Vertical Brasnett
     vertical lengthscale: 700
-obs filters:
+obs pre filters:
+  - 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
+obs prior filters:
   - filter: Bounds Check
     filter variables:
     - name: totalSnowDepth
@@ -37,7 +52,7 @@ obs filters:
   - filter: Domain Check
     where:
     - variable:
-        name: MetaData/height
+        name: MetaData/stationElevation
       minvalue: -999.0
   - filter: Domain Check # land only
     where:
@@ -51,17 +66,18 @@ obs filters:
         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
+obs post filters:
   - filter: Background Check # gross error check
     filter variables:
     - name: totalSnowDepth
     threshold: 6.25
     action:
       name: reject
+  - filter: Temporal Thinning
+    min_spacing: '{{ LAND_WINDOW_LENGTH }}'
+    seed_time: '{{ current_cycle | to_isotime }}'
+    category_variable:
+      name: MetaData/stationIdentification
   - filter: Met Office Buddy Check
     filter variables:
     - name: totalSnowDepth
@@ -85,18 +101,3 @@ obs filters:
       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
-
diff --git a/parm/land/prep/prep_gts.yaml b/parm/land/prep/prep_gts.yaml
@@ -3,11 +3,8 @@ gtsbufr:
     - $(DATA)/obs
   copy:
     - [{{ COM_OBS }}/{{ OPREFIX }}adpsfc.tm00.bufr_d, {{ DATA }}/obs/]
-    - [{{ COM_OBS }}/{{ OPREFIX }}snocvr.tm00.bufr_d, {{ DATA }}/obs/]
 gtsioda:
   copy:
     - [{{ DATA }}/{{ OPREFIX }}adpsfc_snow.nc4, {{ COM_OBS }}/{{ OPREFIX }}adpsfc_snow.nc4]
-    - [{{ DATA }}/{{ OPREFIX }}snocvr_snow.nc4, {{ COM_OBS }}/{{ OPREFIX }}snocvr_snow.nc4]
 bufr2ioda:
      adpsfc: {{ HOMEgfs }}/sorc/gdas.cd/test/testinput/bufr_adpsfc_snow.yaml
-     snocvr: {{ HOMEgfs }}/sorc/gdas.cd/test/testinput/bufr_snocvr_snow.yaml
diff --git a/parm/land/prep/prep_ims.yaml b/parm/land/prep/prep_ims.yaml
@@ -6,5 +6,5 @@ calcfims:
     - [$(COM_OBS)/$(OPREFIX)IMS4km_to_FV3_mapping.$(CASE)_oro_data.nc, $(DATA)/obs/IMS4km_to_FV3_mapping.$(CASE)_oro_data.nc]
 ims2ioda:
   copy:
-    - [$(DATA)/ims_snow_{{ current_cycle | to_YMDH }}.nc4, $(COM_OBS)/$(OPREFIX)ims_snow.nc4]
+    - [$(DATA)/ims_snow_{{ current_cycle | to_YMDH }}.nc4, $(DATA)/obs/$(OPREFIX)ims_snow.nc4]
 
diff --git a/test/testinput/bufr_adpsfc_snow.yaml b/test/testinput/bufr_adpsfc_snow.yaml
@@ -24,7 +24,7 @@ observations:
           stationIdentification:
             query: "*/RPID"
 
-          height:
+          stationElevation:
             query: "[*/SELV, */HSMSL]"
 
           # ObsValue
@@ -64,9 +64,9 @@ observations:
           units: "degree_east"
           range: [-180, 180]
 
-        - name: "MetaData/height"
+        - name: "MetaData/stationElevation"
           coordinates: "longitude latitude"
-          source: variables/height
+          source: variables/stationElevation
           longName: "Height of Station"
 
         - name: "MetaData/stationIdentification"

diff --git a/test/testinput/bufr_snocvr_snow.yaml b/test/testinput/bufr_snocvr_snow.yaml
@@ -24,7 +24,7 @@ observations:
           stationIdentification:
             query: "*/WGOSLID"
 
-          height:
+          stationElevation:
             query: "[*/SELV, */HSMSL]"
 
           # ObsValue
@@ -64,9 +64,9 @@ observations:
           units: "degree_east"
           range: [-180, 180]
 
-        - name: "MetaData/height"
+        - name: "MetaData/stationElevation"
           coordinates: "longitude latitude"
-          source: variables/height
+          source: variables/stationElevation
           longName: "Height of Station"
 
         - name: "MetaData/stationIdentification"

diff --git a/ush/ioda/bufr2ioda/bufr2ioda_subpfl_argo_profiles.py b/ush/ioda/bufr2ioda/bufr2ioda_subpfl_argo_profiles.py
diff --git a/utils/obsproc/Ghrsst2Ioda.h b/utils/obsproc/Ghrsst2Ioda.h
@@ -36,10 +36,6 @@ namespace gdasapp {
       fullConfig_.get("bounds.min", sstMin);
       float sstMax;
       fullConfig_.get("bounds.max", sstMax);
-      if ( sstUnits == "C" ) {
-        sstMin += 273.15;
-        sstMax += 273.15;
-      }
 
       // Open the NetCDF file in read-only mode
       netCDF::NcFile ncFile(fileName, netCDF::NcFile::read);
@@ -135,9 +131,9 @@ namespace gdasapp {
           preqc[i][j] = 5 - static_cast<int>(sstPreQC[0][i][j]);
 
           // bias corrected sst, regressed to the drifter depth
-          sst[i][j] = static_cast<float>(sstObsVal[index]) * sstScaleFactor + sstOffSet
+          // Remove added sstOffSet for Celsius
+          sst[i][j] = static_cast<float>(sstObsVal[index]) * sstScaleFactor
                     - static_cast<float>(sstObsBias[index]) * biasScaleFactor;
-
           // mask
           if (sst[i][j] >= sstMin && sst[i][j] <= sstMax && preqc[i][j] ==0) {
             mask[i][j] = 1;

diff --git a/utils/obsproc/NetCDFToIodaConverter.h b/utils/obsproc/NetCDFToIodaConverter.h
@@ -120,7 +120,8 @@ namespace gdasapp {
         ioda::Variable iodaDatetime =
           ogrp.vars.createWithScales<int64_t>("MetaData/dateTime",
                                           {ogrp.vars["Location"]}, long_params);
-        iodaDatetime.atts.add<std::string>("units", {iodaVarsAll.referenceDate_}, {1});
+        // TODO(MD): Make sure units with iodaVarsAll when applying mpi
+        iodaDatetime.atts.add<std::string>("units", {iodaVars.referenceDate_}, {1});
         ioda::Variable iodaLat =
           ogrp.vars.createWithScales<float>("MetaData/latitude",
                                             {ogrp.vars["Location"]}, float_params);

diff --git a/utils/test/testinput/gdas_ghrsst2ioda.yaml b/utils/test/testinput/gdas_ghrsst2ioda.yaml
@@ -5,7 +5,6 @@ binning:
   stride: 2
   min number of obs: 1
 bounds:
-  units: C
   min: -3.0
   max: 50.0
 output file: ghrsst_sst_mb_20210701.ioda.nc

diff --git a/utils/test/testref/ghrsst2ioda.test b/utils/test/testref/ghrsst2ioda.test
@@ -1,9 +1,9 @@
 Reading: [ghrsst_sst_mb_202107010000.nc4,ghrsst_sst_mb_202107010100.nc4]
 seconds since 1981-01-01T00:00:00Z
 obsVal:
-    Min: 276.708
-    Max: 281.714
-    Sum: 10051.7
+    Min: 3.558
+    Max: 8.5635
+    Sum: 218.297
 obsError:
     Min: 0.32
     Max: 0.61