[develop] Add IMS snow cover obs

.gitmodules

@@ -23,3 +23,7 @@
 	url = https://github.com/NOAA-EMC/jcb-algorithms.git
         ignore = dirty
 
+[submodule "sorc/IMS_proc"]
+        path = sorc/IMS_proc
+        url = https://github.com/NOAA-PSL/land-SCF_proc.git
+        ignore = dirty

parm/jedi/IMS.yaml

@@ -0,0 +1,53 @@
+  - obs space:
+      name: SnowDepthIMS
+      distribution:
+         name: Halo
+         halo size: 250e3
+      simulated variables: [totalSnowDepth]
+      observed variables: [totalSnowDepth]
+      obsdatain:
+        engine:
+          type: H5File
+          obsfile: ioda.IMSscf.{{ yyyymmddhh }}.{{ tstub }}.nc
+      obsdataout:
+        engine:
+          type: H5File
+          obsfile: output/DA/hofx/letkf_hofx_ims_{{ yyyymmddhh }}.nc
+    obs operator:
+      name: Identity
+    obs error:
+      covariance model: diagonal
+    obs localizations:
+    - localization method: Horizontal SOAR
+      lengthscale: 250e3
+      soar horizontal decay: 0.000021
+      max nobs: 1
+    obs filters:
+    - filter: Perform Action
+      filter variables:
+      - name: totalSnowDepth
+      action:
+        name: assign error
+        error parameter: 40.0
+    - filter: Bounds Check # negative / missing snow
+      filter variables:
+      - name: totalSnowDepth
+      minvalue: 0.0
+    - 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: Background Check # gross error check
+      filter variables:
+      - name: totalSnowDepth
+      threshold: 6.25
+      action:
+        name: reject

parm/setup_wflow_env.py

@@ -229,7 +229,7 @@ def set_default_parm():
         "nprocs_analysis": 6,
         "nprocs_fcst_ic": 36,
         "obsdir": "",
-        "obs_ghcn": "YES",
+        "obs_type": "GHCN",
         "output_fh": "1 -1",
         "res": 96,
         "restart_interval": "12 -1",

parm/templates/template.land_analysis.yaml

@@ -58,7 +58,7 @@ workflow:
     NPROCS_FORECAST_LND: "{{ nprocs_forecast_lnd }}"
     NPROCS_PER_NODE: "{{ nprocs_per_node }}"
     OBSDIR: "{{ obsdir }}"
-    OBS_GHCN: "{{ obs_ghcn }}"
+    OBS_TYPE: "{{ obs_type }}"
     OUTPUT_FH: "{{ output_fh }}"
     RES: "{{ res }}"
     RESTART_INTERVAL: "{{ restart_interval }}"
@@ -133,7 +133,7 @@ workflow:
         MACHINE: "&MACHINE;"
         model_ver: "&model_ver;"
         OBSDIR: "&OBSDIR;"
-        OBS_GHCN: "&OBS_GHCN;"
+        OBS_TYPE: "&OBS_TYPE;"
         PDY: "&PDY;"
         SCHED: "&SCHED;"
       account: "&ACCOUNT;"
@@ -238,7 +238,7 @@ workflow:
         MACHINE: "&MACHINE;"
         model_ver: "&model_ver;"
         NPROCS_ANALYSIS: "&NPROCS_ANALYSIS;"
-        OBS_GHCN: "&OBS_GHCN;"
+        OBS_TYPE: "&OBS_TYPE;"
         PDY: "&PDY;"
         RES: "&RES;"
         SCHED: "&SCHED;"

scripts/exlandda_analysis.sh

@@ -52,7 +52,14 @@ do
   cp -p ${sfc_fn} "${sfc_fn}_ini"
 done
 # Copy obserbation file to work directory
-ln -nsf ${COMIN}/obs/GHCN_${YYYY}${MM}${DD}${HH}.nc .
+# TODO: Figure out if this var can be passed in through the yaml file
+# TODO: same with this var at line 141 
+TSTUB=C96.mx100_oro_data # oro_C96.mx100
+if [ "${OBS_TYPE}" = "GHCN" ]; then
+  ln -nsf ${COMIN}/obs/GHCN_${YYYY}${MM}${DD}${HH}.nc .
+elif [ "${OBS_TYPE}" = "IMS" ]; then
+  ln -nsf ${COMIN}/obs/ioda.IMSscf.${YYYY}${MM}${DD}.${TSTUB}.nc .
+fi
 
 # update coupler.res file
 settings="\
@@ -108,8 +115,10 @@ RESP1=$((RES+1))
 mkdir -p output/DA/hofx
 
 cp "${PARMlandda}/jedi/letkfoi_snow.yaml" "${DATA}/letkf_land.yaml"
-if [ "${OBS_GHCN}" = "YES" ]; then
+if [ "${OBS_TYPE}" = "GHCN" ]; then
   cat ${PARMlandda}/jedi/GHCN.yaml >> letkf_land.yaml
+elif [ "${OBS_TYPE}" = "IMS" ]; then
+  cat ${PARMlandda}/jedi/IMS.yaml >> letkf_land.yaml
 fi
 
 # update jedi yaml file
@@ -129,6 +138,7 @@ settings="\
   'res': ${RES}
   'resp1': ${RESP1}
   'driver_obs_only': false
+  'tstub': C96.mx100_oro_data
 " # End of settings variable
 
 fp_template="${DATA}/letkf_land.yaml"

scripts/exlandda_prep_obs.sh

@@ -13,12 +13,102 @@ YYYP=${PTIME:0:4}
 MP=${PTIME:4:2}
 DP=${PTIME:6:2}
 HP=${PTIME:8:2}
+echo "ptime=$PTIME"
+echo "pdy=$PDY"
 
 OBSDIR="${OBSDIR:-${FIXlandda}/DA_obs}"
 DATA_GHCN_RAW="${DATA_GHCN_RAW:-${FIXlandda}/DATA_ghcn}"
 
+
+#TODO: figure out if spack-stack can build this
+# set pythonpath for ioda converters
+PYTHONPATH=$PYTHONPATH:/scratch2/NCEPDEV/land/data/DA/GDASApp/sorc/iodaconv/src/:/scratch2/NCEPDEV/land/data/DA/GDASApp/build/lib/python3.10
+
+# IMS snow cover data
+if [ "${OBS_TYPE}" == "IMS" ]; then
+  # TODO: figure out if these variables can be sourced
+  RES=96 #FV3 resolution
+  TSTUB=C96.mx100_oro_data #oro_C96.mx100
+  DOY=$(date -d "${YYYY}-${MM}-${DD}" +%j)
+  echo "DOY is ${DOY}"
+  # TODO: the date seems to be for the next day. Need to figure out if this impacts the ghcn case
+
+  if [[ ${PDY}${cyc} -gt 2014120200 ]]; then
+    ims_vsn=1.3
+    imsformat=2 # nc
+    imsres="4km"
+    fsuf="nc"
+    ascii=""
+  elif [[ ${PDY}${cyc} -gt 2004022400 ]]; then
+    ims_vsn=1.2
+    imsformat=2 # nc
+    imsres="4km"
+    fsuf="nc"
+    ascii=""
+  else # TODO: switch back when we get obs data for 2000 or use a new case
+    ims_vsn=1.3 #1.1
+    imsformat=2 #1 # asc
+    imsres="4km" #"24km"
+    fsuf="nc" #"asc"
+    ascii="" #"ascii"
+  fi
+
+  obs_fn="ims${YYYY}${DOY}_${imsres}_v${ims_vsn}.${fsuf}"
+  # TODO: figure out which data is needed and stage them
+  #obs_fp="${OBSDIR}/snow_ice_cover/IMS/${YYYY}"
+  obs_fp="/scratch1/NCEPDEV/stmp4/Edward.Snyder/IMS_snowcover_obs/git-repo/ims_case_data/"
+  out_fn="ioda.IMSscf.${YYYY}${MM}${DD}.${TSTUB}.nc"
+
+   # check obs is available
+  if [ -f "${obs_fp}" ]; then
+    echo "IMS observation file: ${obs_fp}"
+    cp -p "${obs_fp}" .
+    cp -p "${obs_fp}" "${COMOUTobs}/${out_fn}"
+  fi
+
+  # pre-process and call IODA converter for IMS obs
+  if [[ -f fims.nml ]]; then
+        rm -rf fims.nml
+  fi
+# TODO: update fcst_path when we find the right case data
+cat >> fims.nml << EOF
+ &fIMS_nml
+  idim=$RES, jdim=$RES,
+  otype=${TSTUB},
+  jdate=${YYYY}${DOY},
+  yyyymmddhh=${YYYY}${MM}${DD}.${HH},
+  fcst_path="/scratch1/NCEPDEV/stmp4/Edward.Snyder/IMS_snowcover_obs/land-DA_update/jedi/restarts/",
+  imsformat=${imsformat},
+  imsversion=${ims_vsn},
+  imsres=${imsres},
+  IMS_OBS_PATH="${obs_fp}/",
+  IMS_IND_PATH="${obs_fp}/",
+  /
+EOF
+  echo "calling fIMS"
+
+  # TODO: Do we need to run with mpiexec?
+  ${EXEClandda}/calcfIMS.exe
+  if [[ $? != 0 ]]; then
+    echo "fIMS failed"
+    exit 10
+  fi
+
+  #IMS_IODA=imsfv3_scf2iodaTemp.py # 2024-07-12 temporary until GDASApp ioda converter updated.
+  #cp ${LANDDADIR}/jedi/ioda/${IMS_IODA} $JEDIWORKDIR
+
+  echo "calling ioda converter"
+  # TODO: create input_fn var
+  ${USHlandda}/imsfv3_scf2iodaTemp.py -i IMSscf.${YYYY}${MM}${DD}.${TSTUB}.nc -o ${out_fn}
+  if [[ $? != 0 ]]; then
+    echo "IMS IODA converter failed"
+    exit 10
+  fi
+  cp -p "${out_fn}" "${COMOUTobs}/${out_fn}"
+fi
+
 # GHCN snow depth data
-if [ "${OBS_GHCN}" = "YES" ]; then
+if [ "${OBS_TYPE}" = "GHCN" ]; then
   # GHCN are time-stamped at 18. If assimilating at 00, need to use previous day's obs, 
   # so that obs are within DA window.
   obs_fn="ghcn_snwd_ioda_${YYYP}${MP}${DP}${HP}.nc"

sorc/CMakeLists.txt

@@ -135,6 +135,20 @@ ExternalProject_Add(tile2tile_converter.fd
   STEP_TARGETS build
   )
 
+# IMS Snow cover obs
+list(APPEND IMS_PROC_ARGS
+  "-DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}"
+)
+list(APPEND TARGET LIST IMS_proc)
+ExternalProject_Add(IMS_proc
+  PREFIX ${CMAKE_CURRENT_BINARY_DIR}/IMS_proc
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/IMS_proc
+  INSTALL_DIR ${CMAKE_INSTALL_PREFIX}
+  CMAKE_ARGS ${IMS_PROC_ARGS}
+  BUILD_ALWAYS TRUE
+  STEP_TARGETS build
+  )
+
 # C-Test
 add_subdirectory(test)
 

sorc/app_build.sh

@@ -203,6 +203,10 @@ if [ "${REMOVE}" = true ]; then
     printf "... Remove UFS_UTILS.fd ...\n"
     rm -rf "${SORC_DIR}/UFS_UTILS.fd"
   fi
+  if [ -d "${SORC_DIR}/IMS_proc" ]; then
+    printf "... Remove IMS_proc ...\n"
+    rm -rf "${SORC_DIR}/IMS_proc"
+  fi
 
   cd "${HOME_DIR}"
   git submodule update --init --recursive