[develop] Add verification of snowfall accumulation #853

willmayfield · 2023-07-06T18:57:21Z

DESCRIPTION OF CHANGES:

This PR completes the final deliverable of the DTC UFS SRW project to include verification support of new variables in the workflow via MET. This PR adds relevant METplus configuration files and modifies various scripts to allow for verification via the NOHRSC gridded accumulated snowfall product. The forecast variable created by post is 'TSNOWP' for 6-and 24-hour snowfall accumulation with a fixed density, which will be verified on a 6- and 12-hour cadence, respectively. When the GSL variable-density snowfall product is included in post in the future, the variable in the METplus configuration files may be changed to 'ASNOW'.

Currently this addition does not turn on accumulated snowfall verification by default. This is because NOHRSC observations were not located on NOAA HPSS previous to March 2020, as well as the idea that many non-winter cases likely will not desire to run the additional verification tasks. This PR achieves removal of snowfall verification tasks by omitting it by default from the VX_FIELDS variable. Therefore, to turn on snowfall verification, users may simply include VX_FIELDS in their configuration with "ASNOW" added.

This PR also turns off all “ncpairs” file creation in METplus configuration files. These files represent the majority of the filespace footprint for METplus outputs, and are not necessary to produce verification statistical output.

Type of change

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

TESTS CONDUCTED:

MET_verification and MET_ensemble_verification tests were run without error. Note that features were not tested as a part of these because the new "ASNOW" tasks are not run by default, as noted above. A winter case (20220202) was run for a 36 hour ensemble forecast that included "ASNOW" in VX_FIELDS. The experiment directory on hera is in /scratch2/BMC/fv3lam/mayfield/srw_vx/snowfall_vx/expt_dirs/test_community_nohrsc. METplus stat files were reviewed for meaningful statistics, and “ncpairs” files were turned on and reviewed to show that both observations and forecasts as processed by METplus are verifiable.

DEPENDENCIES:

None

DOCUMENTATION:

Documentation was updated to include additional information about NOHRSC observation data in verification sections.

ISSUE:

None

CHECKLIST

My code follows the style guidelines in the Contributor's Guide
My changes need updates to the documentation. I have made corresponding changes to the documentation
My changes generate no new warnings
New and existing tests pass with my changes

REQUEST SPECIFIC REVIEWERS:

@gsketefian @mkavulich

…ombine

…d snowfall

…/ufs-srweather-app into feature/snowfall_vx

MichaelLueken

@willmayfield I have gone over your changes in this PR and overall everything looks pretty good. I have noted a few spelling/grammatical issues and had a question regarding the NOHRSC_OBS_DIR path in RunSRW.rst, but otherwise, everything else looks okay.

I was able to successfully run all of the verification WE2E tests on Hera, as well as the fundamental WE2E tests. I was even able to test the newly added ASNOW option. I do have a question regarding this.

The metatask_PcpCombine_fcst_APCP_all_accums_all_mems entry correctly sets ACCUM_HH to 01, 03, and 06 for FCST_LEN_HRS = 6. I noted that the only way that I could get metatask_PcpCombine_fcst_ASNOW_all_accums_all_mems to set ACCUM_HH to 06 was by setting FCST_LEN_HRS to a value of 24 or greater. Is this correct, or should I be able to set FCST_LEN_HRS = 6 and still have ACCUM_HH set to 06? If this is what is supposed to happen, would you mind running a test with FCST_LEN_HRS = 6 and seeing whether ACCUM_HH is properly set?

Once the above question has been answered, I think I can move forward with approving these changes.

docs/UsersGuide/source/RunSRW.rst

scripts/exregional_get_obs_nohrsc.sh

willmayfield · 2023-07-12T22:55:37Z

@MichaelLueken Thank you for your review. I fixed the typos and another duplicate line I noticed in default_workflow.yaml.

Good catch for the issue when forecast length is less than 24h. It seems when only one element of the verification.VX_ASNOW_ACCUMS_HRS list is used, it propagates ACCUM_HH without the 2-digit formatting, but I have no idea why, as it should happen in the loop in verify_pre.yaml:
ACCUM_HH: '{% for ah in verification.VX_ASNOW_ACCUMS_HRS %}{% if workflow.FCST_LEN_HRS >= ah %}{{ "%02d " % ah }}{% endif %}{% endfor %}'
I also checked that for a 2 hour forecast length, the APCP tasks also fail for the same reason. Checking FV3LAM_wflow.xml, I see the following:
For a 5 hour forecast length:

<metatask name="PcpCombine_fcst_APCP_all_accums_all_mems" >
  <var name="ACCUM_HH">01 03 </var>

For a 2 hour forecast length:

<metatask name="PcpCombine_fcst_APCP_all_accums_all_mems" >
  <var name="ACCUM_HH">1</var>

(the workflow also fails because the ACCUM_HH var is empty for PcpCombine_fcst_ASNOW_all_accums_all_mems, so I will try to find a way to handle that as well, probably by removing those tasks with some logic in setup.py)

Maybe @gsketefian or @mkavulich can offer any ideas of why it isn't doing the 2-digit formatting?

gsketefian · 2023-07-14T19:12:27Z

docs/UsersGuide/source/ConfigWorkflow.rst

@@ -151,23 +151,31 @@ METplus Parameters
      * ``SS`` refers to the two-digit valid seconds of the hour

 ``CCPA_OBS_DIR``: (Default: "")
-   User-specified location of top-level directory where CCPA hourly precipitation files used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_CCPA`` task. (This task is activated in the workflow by using the taskgroup file ``parm/wflow/verify.yaml``).
+   User-specified location of top-level directory where CCPA hourly precipitation files used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_CCPA`` task. (This task is activated in the workflow by using the taskgroup file ``parm/wflow/verify_pre.yaml``).


Change the task name to lowercase, i.e. GET_OBS_CCPA --> get_obs_ccpa.

gsketefian · 2023-07-14T19:13:00Z

docs/UsersGuide/source/ConfigWorkflow.rst

 ``MRMS_OBS_DIR``: (Default: "")
-   User-specified location of top-level directory where MRMS composite reflectivity files used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_MRMS`` task (activated in the workflow automatically when using the taskgroup file ``parm/wflow/verify.yaml``). When pulling observations directly from NOAA HPSS, the data retrieved will be placed in this directory. Please note, this path must be defind as ``/<full-path-to-obs>/mrms/proc``. 
+   User-specified location of top-level directory where MRMS composite reflectivity files used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_MRMS`` task (activated in the workflow automatically when using the taskgroup file ``parm/wflow/verify_pre.yaml``). When pulling observations directly from NOAA HPSS, the data retrieved will be placed in this directory. Please note, this path must be defind as ``/<full-path-to-obs>/mrms/proc``. 


Change the task name to lowercase, i.e. GET_OBS_MRMS --> get_obs_mrms.

gsketefian · 2023-07-14T19:13:35Z

docs/UsersGuide/source/ConfigWorkflow.rst


   METplus configuration files require the use of a predetermined directory structure and file names. Therefore, if the MRMS files are user-provided, they need to follow the anticipated naming structure: ``{YYYYMMDD}/MergedReflectivityQCComposite_00.50_{YYYYMMDD}-{HH}{mm}{SS}.grib2``, where YYYYMMDD and {HH}{mm}{SS} are as described in the note :ref:`above <METParamNote>`. 

 .. note::
   METplus is configured to look for a MRMS composite reflectivity file for the valid time of the forecast being verified; since MRMS composite reflectivity files do not always exactly match the valid time, a script (within the main script that retrieves MRMS data from the NOAA HPSS) is used to identify and rename the MRMS composite reflectivity file to match the valid time of the forecast. The script to pull the MRMS data from the NOAA HPSS has an example of the expected file-naming structure: ``scripts/exregional_get_obs_mrms.sh``. This script calls the script used to identify the MRMS file closest to the valid time: ``ush/mrms_pull_topofhour.py``.

 ``NDAS_OBS_DIR``: (Default: "")
-   User-specified location of the top-level directory where NDAS prepbufr files used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_NDAS`` task (activated in the workflow automatically when using the taskgroup file ``parm/wflow/verify.yaml``). When pulling observations directly from NOAA HPSS, the data retrieved will be placed in this directory. Please note, this path must be defined as ``/<full-path-to-obs>/ndas/proc``. METplus is configured to verify near-surface variables hourly and upper-air variables at 00 and 12 UTC with NDAS prepbufr files. 
+   User-specified location of the top-level directory where NDAS prepbufr files used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_NDAS`` task (activated in the workflow automatically when using the taskgroup file ``parm/wflow/verify_pre.yaml``). When pulling observations directly from NOAA HPSS, the data retrieved will be placed in this directory. Please note, this path must be defined as ``/<full-path-to-obs>/ndas/proc``. METplus is configured to verify near-surface variables hourly and upper-air variables at 00 and 12 UTC with NDAS prepbufr files. 


Change the task name to lowercase, i.e. GET_OBS_NDAS --> get_obs_ndas.

gsketefian · 2023-07-14T19:14:58Z

docs/UsersGuide/source/ConfigWorkflow.rst


   METplus configuration files require the use of a predetermined directory structure and file names. If the CCPA files are user-provided, they need to follow the anticipated naming structure: ``{YYYYMMDD}/ccpa.t{HH}z.01h.hrap.conus.gb2``, where YYYYMMDD and HH are as described in the note :ref:`above <METParamNote>`. When pulling observations from NOAA HPSS, the data retrieved will be placed in the ``CCPA_OBS_DIR`` directory. This path must be defind as ``/<full-path-to-obs>/ccpa/proc``. METplus is configured to verify 01-, 03-, 06-, and 24-h accumulated precipitation using hourly CCPA files.    

   .. note::
      There is a problem with the valid time in the metadata for files valid from 19 - 00 UTC (i.e., files under the "00" directory). The script to pull the CCPA data from the NOAA HPSS (``scripts/exregional_get_obs_ccpa.sh``) has an example of how to account for this and organize the data into a more intuitive format. When a fix is provided, it will be accounted for in the ``exregional_get_obs_ccpa.sh`` script.

+``NOHRSC_OBS_DIR``: (Default: "")
+   User-specified location of top-level directory where NOHRSC 06- and 24-hour snowfall accumulation files (available every 6 and 12 hours respectively) used by METplus are located. This parameter needs to be set for both user-provided observations and for observations that are retrieved from the NOAA :term:`HPSS` (if the user has access) via the ``GET_OBS_NOHRSC`` task. (This task is activated in the workflow by using the taskgroup file ``parm/wflow/verify_pre.yaml``).


Change the task name to lowercase, i.e. GET_OBS_NOHRSC --> get_obs_nohrsc.

gsketefian · 2023-07-14T19:21:41Z

docs/UsersGuide/source/RunSRW.rst

@@ -827,18 +831,24 @@ In addition to the baseline tasks described in :numref:`Table %s <WorkflowTasksT
   | **Workflow Task**     | **Task Description**                                       |
   +=======================+============================================================+
   | GET_OBS_CCPA          | Retrieves and organizes hourly :term:`CCPA` data from NOAA |


@willmayfield @gspetro This is not directly related to this PR, but we will have to update the names of the vx and related tasks in this table, e.g. GET_OBS_CCPA becomes get_obs_ccpa, etc. I think I'll do that as part of Issue #630.

@gsketefian I'm actually working on updates now! The code is in my text/ug-updates branch.
RTD version here: https://srw-ug.readthedocs.io/en/text-ug-updates/BuildingRunningTesting/RunSRW.html#vxworkflowtaskstable
I'm generally not touching much of the VX stuff, but since I'm updating the run chapter, I did get update some of the info there.

One thing I was trying to decide was whether to name the (meta)tasks based on what is in the YAML config file or based on what the Rocoto/log output is. I went with what is in the YAML because that is the name users may actually add/change/remove in their config file.

gsketefian · 2023-07-14T19:33:40Z

parm/metplus/GridStat_APCP01h.conf

@@ -246,13 +246,13 @@ GRID_STAT_OUTPUT_FLAG_NBRCNT = STAT

 # NetCDF matched pairs output file
 #GRID_STAT_NC_PAIRS_VAR_NAME =
-GRID_STAT_NC_PAIRS_FLAG_LATLON = TRUE
-GRID_STAT_NC_PAIRS_FLAG_RAW = TRUE
+GRID_STAT_NC_PAIRS_FLAG_LATLON = FALSE


Just curious why we're turning off GRID_STAT_NC_PAIRS_FLAG_LATLON, GRID_STAT_NC_PAIRS_FLAG_RAW, and GRID_STAT_NC_PAIRS_FLAG_NBRHD. See here for descriptions of these options (or their conterparts in MET).

@gsketefian I discussed this with @michelleharrold and we decided it would be best to have these turned off by default. The ncpairs files are useful for checking that verification fields are created correctly, but the files are not needed in order to create the verification statistics. They can be rather large files as well, so it will help with reducing the footprint of the verification WE2E tests.

gsketefian · 2023-07-14T19:45:54Z

scripts/exregional_get_obs_nohrsc.sh

+#-----------------------------------------------------------------------
+#
+
+set -x


Probably should remove this set -x since it adds a lot of clutter to the log file. User can add it when debugging (or you can put this in an if-statement on the DEBUG or similar flag; or maybe that already exists in $USHdir/preamble.sh).

gsketefian · 2023-07-14T20:24:44Z

scripts/exregional_run_met_genensprod_or_ensemblestat.sh

+        FCST_INPUT_DIR="${vx_fcst_input_basedir}"
+        ;;
+      "ASNOW")
+        OBS_INPUT_FN_TEMPLATE="${OBS_NOHRSC_ASNOW_FN_TEMPLATE}"


@willmayfield I will try to run this PR myself to understand better what's going on, but can you say why FCST_INPUT_DIR for ASNOW is set to vx_output_basedir? Is there a vx pre-processing task (like PCP_COMBINE for APCPgt01h) that first needs to run and that places output in vx_output_basedir?

@gsketefian Yes, pcpcombine_fcst runs for ASNOW prior to this task.

Oh, just saw that the answer to my question is "yes"!

So what do the PCP_COMBINE tasks do exactly for ASNOW? Are the hours in the obs every 6 hours, and those get combined to 12, (not 18?), 24, (not 30?), 36, etc? And same for forecasts?

The obs are available as 6- and 24-hour accumulations in grib2 format from nohrsc on HPSS (and those are the accumulations recommended to be verified in the Metrics Spreadsheet). Therefore those are simply retrieved and pcp_bombine_obs is not needed. Note that the 6-h accumulations are available every 6 hours and the 24-h accumulations are available every 12 hours, so I am verifying them at that pace.

The forecasts, on the other hand, are hourly 1-h accumulations output in post. So they are run with pcp_combine_fcst to combine them into the 6- and 24-h accumulations to match the obs.

MichaelLueken · 2023-07-14T21:06:26Z

@willmayfield I've some some additional testing today and it looks like incorporating some of @danielabdi-noaa's changes from PR #701 will allow both ASNOW to properly work with FCST_LEN_HRS of 6 and APCP to work with FCST_LEN_HRS of 1 and 2. Specifically, the changes made to ush/python_utils/environment.py on lines 82 through 86 will allow the tests to verification tasks to properly set ACCUM_HH. The verification WE2E tests were ran, along with the coverage tests for Hera Intel and GNU, and all tests passed. Additional testing using the MET_verification test and setting FCST_LEN_HRS to 1 and 2 passed; setting FCST_LEN_HRS to 6 and adding ASNOW to the MET_verification test also passed.

…ing shorter forecast lengths with 2-digit ACCUM_HH..

…/ufs-srweather-app into feature/snowfall_vx

willmayfield · 2023-07-16T01:26:40Z

@MichaelLueken @gsketefian @gspetro-NOAA thank you for your feedback. I fixed the typos/task names in the documentation, and incorporated the changes to ush/python_utils/environment.py that Michael suggested to solve the issue with ACCUM_HH. I also needed to add the line from ush/set_FV3nml_ens_stoch_seeds.py that is a part of @danielabdi-noaa's PR #701, in order for stochastic physics to run. With these changes the case I ran with ASNOW turned on for a 6 hour forecast was successful.

mkavulich

I tested these changes as part of my PR #864 and confirmed the snow accumulation verification gives the expected output for a winter case (2023021700).

MichaelLueken

@willmayfield Thanks for working with me to apply several of @danielabdi-noaa's bug fixes from PR #701 into this work! Testing the current verification WE2E tests have passed, as well as testing ASNOW with a 6 hour forecast. Approving now.

I'll go ahead and launch the automated Jenkins tests now.

Since @gsketefian noted that he is wrapping up his review of these changes, I hold off merging this PR until he has given his approval.

MichaelLueken · 2023-07-21T21:04:42Z

The Cheyenne Intel tests successfully passed on Hera:

----------------------------------------------------------------------------------------------------
Experiment name                                                  | Status    | Core hours used 
----------------------------------------------------------------------------------------------------
custom_GFDLgrid__GFDLgrid_USE_NUM_CELLS_IN_FILENAMES_eq_FALSE      COMPLETE              13.81
grid_RRFS_CONUS_13km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16_plot     COMPLETE              32.38
grid_RRFS_CONUS_25km_ics_NAM_lbcs_NAM_suite_GFS_v16                COMPLETE              20.12
grid_RRFS_CONUScompact_13km_ics_HRRR_lbcs_RAP_suite_HRRR           COMPLETE              25.68
grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta    COMPLETE               8.84
grid_SUBCONUS_Ind_3km_ics_HRRR_lbcs_HRRR_suite_HRRR                COMPLETE              16.40
pregen_grid_orog_sfc_climo                                         COMPLETE              10.12
specify_template_filenames                                         COMPLETE               9.34
----------------------------------------------------------------------------------------------------
Total                                                              COMPLETE             136.69

Will manually run the Cheyenne GNU tests first thing on Monday, then get this PR merged.

MichaelLueken · 2023-07-24T14:57:25Z

The Cheyenne GNU tests were ran on Hera using the GNU compiler. All tests successfully passed:

----------------------------------------------------------------------------------------------------
Experiment name                                                  | Status    | Core hours used 
----------------------------------------------------------------------------------------------------
grid_CONUS_25km_GFDLgrid_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16      COMPLETE              22.86
grid_RRFS_CONUS_13km_ics_FV3GFS_lbcs_FV3GFS_suite_RRFS_v1beta      COMPLETE             236.47
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_2017_gfdlmp  COMPLETE             115.17
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v17_p8_plot  COMPLETE              29.21
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_HRRR             COMPLETE              39.48
grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16   COMPLETE              25.17
grid_RRFS_NA_13km_ics_FV3GFS_lbcs_FV3GFS_suite_RAP                 COMPLETE             328.18
grid_SUBCONUS_Ind_3km_ics_NAM_lbcs_NAM_suite_GFS_v16               COMPLETE              51.57
specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS                              COMPLETE              10.73
----------------------------------------------------------------------------------------------------
Total                                                              COMPLETE             858.84

Following either an approval or comment saying that @gsketefian is okay with the changes, this work can get merged.

gsketefian

Glad @MichaelLueken and @willmayfield figured out the ACCUM_HH bug. Looks good to me and I'm approving. I just have one suggestion. It would be a good idea to either modify one of the WE2E tests to include snowfall accum vx or to add a new one that does this. I've now learned to add tests consistently for features I know at least I (or projects I'm involved with) will use often.

willmayfield added 20 commits June 23, 2023 03:17

Initial work to add NOHRSC snowfall accumulation obs pulling and pcpc…

cb3a355

…ombine

new files for snowfall accumulation obs pulling and pcpcombine

338dbdf

metplus conf files for pcp_combine and gridstat related to accumulate…

6ea427b

…d snowfall

GridStat vx for snowfall accumulation

94fabfd

Changes for ensemble verification of snowfall accumulation

412dd33

documentation and cleanup for snowfall vx

6385801

documentation formatting

53ad792

clean whitespace

cb2fe28

documentation updates and code cleanup

1d80d7b

Resolve conflicts

b7c3f2e

new files for snowfall accumulation obs pulling and pcpcombine

951137c

metplus conf files for pcp_combine and gridstat related to accumulate…

dda8aea

…d snowfall

GridStat vx for snowfall accumulation

c64a051

Changes for ensemble verification of snowfall accumulation

e35769f

documentation and cleanup for snowfall vx

8409c61

documentation formatting

fc1d90b

clean whitespace

25446be

documentation updates and code cleanup

edf6e3e

Merge branch 'feature/snowfall_vx' of https://github.com/willmayfield…

e6a906a

…/ufs-srweather-app into feature/snowfall_vx

Remove ncpairs output turned on by default

a23b55e

willmayfield requested review from mkavulich, gsketefian, JeffBeck-NOAA, RatkoVasic-NOAA, BenjaminBlake-NOAA, ywangwof, chan-hoo, panll, christinaholtNOAA and christopherwharrop-noaa as code owners July 6, 2023 18:57

willmayfield requested review from gspetro-NOAA, natalie-perlin, EdwardSnyder-NOAA and MichaelLueken as code owners July 6, 2023 18:57

MichaelLueken changed the title ~~Add verification of snowfall accumulation~~ [develop] Add verification of snowfall accumulation Jul 6, 2023

MichaelLueken reviewed Jul 12, 2023

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docs/UsersGuide/source/RunSRW.rst Outdated Show resolved Hide resolved

scripts/exregional_get_obs_nohrsc.sh Outdated Show resolved Hide resolved

fix typos and duplicated line

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gsketefian reviewed Jul 14, 2023

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willmayfield added 2 commits July 16, 2023 01:21

Corrected names of tasks for vx docs, and incorporated fixes for runn…

6557a3f

…ing shorter forecast lengths with 2-digit ACCUM_HH..

Merge branch 'feature/snowfall_vx' of https://github.com/willmayfield…

666fbe9

…/ufs-srweather-app into feature/snowfall_vx

mkavulich mentioned this pull request Jul 19, 2023

[develop] Consolidate verification tasks using retrieve_data.py #864

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mkavulich approved these changes Jul 21, 2023

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MichaelLueken approved these changes Jul 21, 2023

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MichaelLueken added the run_we2e_coverage_tests Run the coverage set of SRW end-to-end tests label Jul 21, 2023

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MichaelLueken mentioned this pull request Jul 24, 2023

[develop] Bug fix for Issue #851 (renaming NET to NET_default) #868

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[develop] bug fix for processing radar reflectivity task #849

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DESCRIPTION OF CHANGES:

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TESTS CONDUCTED:

DEPENDENCIES:

DOCUMENTATION:

ISSUE:

CHECKLIST

REQUEST SPECIFIC REVIEWERS:

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