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Feature 2388 update tci #2550

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3dcc2e6
Major refactor including elimination of unnecessary imports, only com…
DanielAdriaansen Oct 31, 2023
6d58b2c
Removes extraneous imports.
DanielAdriaansen Mar 4, 2024
841f664
Switches to function call for the coupling index.
DanielAdriaansen Mar 4, 2024
edcb4d9
Correct number of args in comment.
DanielAdriaansen Mar 4, 2024
cd9c2e2
Summation has to have a dimension supplied for the gridded data, but …
DanielAdriaansen Mar 12, 2024
c12c1c6
Adds static station lookup file for use with Python embedding for FLU…
DanielAdriaansen Apr 5, 2024
8b94a64
Major overhaul to forecast Python embedding script for the TCI use case.
DanielAdriaansen Apr 5, 2024
7d65a3c
Major overhaul to observation Python embedding script for the TCI use…
DanielAdriaansen Apr 5, 2024
6647c43
Updates documentation file for TCI use case.
DanielAdriaansen Apr 5, 2024
29c7ad7
Adds METcalcpy version number.
DanielAdriaansen Apr 5, 2024
4879955
Refactors wording and fixes typo.
DanielAdriaansen Apr 5, 2024
91faa59
Fixes RST formatting.
DanielAdriaansen Apr 5, 2024
0cf8f28
Finally fixed RST error.
DanielAdriaansen Apr 5, 2024
7cc809b
Adds support to remove leap days if requested.
DanielAdriaansen Apr 5, 2024
c5228f6
Updates command line args for Python embedding scripts.
DanielAdriaansen Apr 5, 2024
7a9fd24
Updated conf file for use case.
DanielAdriaansen Apr 9, 2024
e0642ba
Removes new TCI function because it is in METcalcpy now.
DanielAdriaansen Apr 9, 2024
7ead6f0
Removes old code, somsome reorganization and clarification and settin…
DanielAdriaansen Apr 9, 2024
06b7af5
Support for environment variables or default options for filtering an…
DanielAdriaansen Apr 10, 2024
d0e7db9
Makes DEBUG an env var for config via metplus wrappers.
DanielAdriaansen Apr 10, 2024
db877e0
Reorganization of config file, adds environment variables, and update…
DanielAdriaansen Apr 10, 2024
757f7a6
Updates to documentation.
DanielAdriaansen Apr 10, 2024
51d03fd
Fixes tables.
DanielAdriaansen Apr 10, 2024
e1a640c
Adds table of contents to the top for users to click on.
DanielAdriaansen Apr 10, 2024
0630880
Updates use case documentation file.
DanielAdriaansen Apr 10, 2024
d151586
Merge branch 'develop' into feature_2388_Update_TCI
DanielAdriaansen Apr 11, 2024
47cc8a0
Updated config file with obs and fcst subirectories in the path.
DanielAdriaansen Apr 11, 2024
b867dac
Switches to using metplotpy_env to get metcalcpy dependency.
DanielAdriaansen Apr 12, 2024
05dcedb
Adds filtering based on missing data values.
DanielAdriaansen Apr 15, 2024
6f74ea6
Finishing touches to debug statements for testing.
DanielAdriaansen Apr 15, 2024
7fc9b50
Fixing a few minor code smells from last week.
DanielAdriaansen Apr 15, 2024
c28f52d
Update docs/use_cases/model_applications/land_surface/PointStat_fcstC…
DanielAdriaansen Apr 16, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -5,50 +5,84 @@
model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI.conf

"""
##############################################################################
# .. contents::
# :depth: 1
# :local:
# :backlinks: none

##############################################################################
# Scientific Objective
# --------------------
# This use case ingests two CESM (CAM and CLM) files and a new FLUX2015 dataset (NETCDF) that Paul Dirmeyer, GMU prepared from FLUXNET2015 ASCII dataset.
# The use case will calculate Terrestrial Coupling Index (TCI) from CESM datasets.
# Utilizing Python embedding, this use case taps into a new vital observation dataset and compares it to CESM simulations TCI forecast.
# Finally, it will generate plots of model TCI and observed TCI.
# This use case ingests two CESM (CAM and CLM) files and raw FLUXNET2015 data.
# The use case calculates the Terrestrial Coupling Index (TCI) from the CESM forecasts and FLUXNET observations.
# Utilizing Python embedding, this use case taps into a new vital observation dataset and compares it to CESM forecasts of TCI.
# Finally, it will generate plots of model forecast TCI overlaid with TCI observations at FLUXNET sites.
#
# The reference for the Terrestrial Coupling Index calculation is as follows:
#
# Dirmeyer, P. A., 2011: The terrestrial segment of soil moisture-climate coupling. *Geophys. Res. Lett.*, **38**, L16702, doi: 10.1029/2011GL048268.
#

##############################################################################
# Datasets
# ---------------------
#
# | **Forecast:** CESM 1979-1983 Simulations a. Community Land Model (CLM) and b. Community Atmosphere Model (CAM)
#
# | **Observations:** FLUXNET2015 post processed and converted to NETCDF. This data includes data collected from multiple regional flux towers.
# | **Forecast:** CESM 1979-1983 Simulations
# | * Community Land Model (CLM) file
# | * Community Atmosphere Model (CAM) file
#
# | **Observations:** Raw FLUXNET2015 observations
#
# | **Location:** All of the input data required for this use case can be found in the met_test sample data tarball. Click here to the METplus releases page and download sample data for the appropriate release: https://github.com/dtcenter/METplus/releases
# | **Location:** All of the input data required for this use case can be found in the land_surface sample data tarball. Click here to the METplus releases page and download sample data for the appropriate release: https://github.com/dtcenter/METplus/releases
# | This tarball should be unpacked into the directory that you will set the value of INPUT_BASE. See `Running METplus`_ section for more information.
#
# | **Data Source:** CESM - CGD; FLUXNET2015 - Paul Dirmeyer
# | **Data Source:** CESM - NSF NCAR Climate & Global Dynamics (CGD); FLUXNET2015 "SUBSET" Data Product: https://fluxnet.org/data/fluxnet2015-dataset/subset-data-product/
#

##############################################################################
# Python Dependencies
# ---------------------
#
# This use case requires the following Python dependencies::
#
# * Xarray
# * Pandas
# * METcalcpy 3.0.0+
#

##############################################################################
# METplus Components
# ------------------
#
# This use case utilizes the METplus PyEmbedIngest to read the CESM files and calculate TCI using python embedding and a NETCDF file of the TCI is generated.
# The METplus PointStat processes the output of PyEmbedIngest and FLUXNET2015 dataset (using python embedding), and outputs the requested line types.
# Then METplus PlotPointObs tool reads the output of PyEmbedIngest and FLUXNET2015 dataset and produce plots of TCI from CESM and point observations.
# The METplus PointStat processes the output of PyEmbedIngest and FLUXNET2015 dataset (using Python embedding), and outputs the requested line types.
# Then the METplus PlotPointObs tool reads the output of PyEmbedIngest and FLUXNET2015 dataset and produce plots of TCI from CESM and point observations.
# A custom loop runs through all the pre-defined seasons (DJF, MAM, JJA, SON) and runs PyEmbedIngest, PointStat, and PlotPointObs.
#

##############################################################################
# METplus Workflow
# ----------------
#
# The PyEmbedIngest tool reads 2 CESM files containing Soil Moisture and Sensible Heat Flux, each composed of daily forecasts from
# 1979 to 1983 and calculates TCI and generates a NETCDF file of the TCI. One FLUXNET2015 NETCDF file containing station observations
# of several variables including Coupling Index of Soil Moisture and Sensible Heat Flux is read by Python Embedding.
#
# The PyEmbedIngest tool reads 2 CESM files containing Soil Moisture (CLM file) and Sensible Heat Flux (CAM file), each composed of daily forecasts from
# 1979 to 1983 and calculates TCI and generates a NETCDF file of the TCI. Raw CSV files containing FLUXNET station observations of latent heat flux (LE_F_MDS)
# and soil water content at the shallowest level (SWC_F_MDS_1) are read using Python embedding, and TCI is computed.
#
# | **Valid Beg:** 1979-01-01 at 00z
# | **Valid End:** 1979-01-01 at 00z
#
#
# PointStat is used to compare the two new fields (TCI calculated from CESM dataset and FLUXNET2015).
# Finally, PlotPointObs is run to plot the CESM TCI overlaying the FLUXNET2015 point observations.
# Finally, PlotPointObs is run to plot the CESM TCI overlaying the FLUXNET2015 point observations.
#
# .. note::
#
# The CESM forecasts cover a time period prior to the availability of FLUXNET observations. Thus,
# this use case should be considered a demonstration of the capability to read CESM forecast data,
# raw FLUXNET observation data, and compute TCI, rather than a bonafide scientific application.
# The use case is designed to enforce seasonal alignment, but it is not designed to enforce date/time alignment.
# In this case, the CESM data cover 1979-1983, whereas the sample FLUXNET observations cover varying time ranges depending on the site.
#

##############################################################################
# METplus Configuration
Expand Down Expand Up @@ -76,18 +110,107 @@
# Python Embedding
# ----------------
#
# This use case uses a Python embedding script to read input data
# This use case uses a Python embedding script to read both the forecast and observation data, in order to compute TCI,
# which is the diagnostic that is being verified by MET using PointStat. The CESM forecast data is read using:
#
# parm/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/cesm_tci.py
#
# .. highlight:: python
# .. literalinclude:: ../../../../parm/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/cesm_tci.py
#
# The user can control all arguments to this script via the METplus use case configuration file using the following config entries:
#
# .. glossary::
#
# CESM_CAM_VAR
# The CESM Community Atmosphere Model variable to use for computing TCI
#
# | *Default:* LHFLX
#
# CESM_CLM_VAR
# The CESM Community Land Model variable to use for computing TCI
#
# | *Default:* SOILWATER_10CM
#
# CESM_CAM_FILE_PATH
# The absolute path to the CESM Community Atmosphere Model netcdf file
#
# | *Default:*
#
# CESM_CLM_FILE_PATH
# The absolute path to the CESM Community Land Model netcdf file
#
# | *Default:*
#
# The raw FLUXNET2015 SUBSET data are read using:
#
# parm/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnet2015_tci.py
#
# .. highlight:: python
# .. literalinclude:: ../../../../parm/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnet2015_tci.py
#
# The user can control all command line arguments to this script via METplus config entries:
#
# .. glossary::
#
# FLUXNET_DATA_DIR
# The directory containing raw FLUXNET CSV files
#
# | *Default:*
#
# FLUXNET_LAT_HEAT_VAR
# The FLUXNET surface latent heat flux variable name to use for computing TCI
#
# | *Default:* LE_F_MDS
#
# FLUXNET_SOIL_MOIST_VAR
# The FLUXNET soil moisture variable name to use for computing TCI
#
# | *Default:* SWC_F_MDS_1
#
# FLUXNET_OBS_METADATA_FILE
# The absolute path to the fluxnetstations.csv metadata file included with the use case
#
# | *Default:*
#
# and for data filtering options, via METplus config entries:
#
# .. glossary::
#
# FLUXNET_SKIP_LEAP_DAYS
# Skip FLUXNET observations from 29 February days
#
# | *Default:* True
#
# FLUXNET_HIGHRES_QC_THRESH
# The fraction of higher temporal resolution FLUXNET data required to have
# passed quality control in order to use the daily data.
#
# | *Default:* 0.8
#
# FLUXNET_MIN_DAYS_PER_SEASON
# The minimum number of days to include in individual seasons at each site
#
# | *Default:* 1
#
# FLUXNET_MIN_DAYS_PER_SITE
# The minimum number of days for all seasons at each site
#
# | *Default:* 10
#
# FLUXNET_RAW_FILENAME_PATTERN
# A filename pattern matching the template of the raw FLUXNET CSV files
#
# | *Default:* FLX_*_DD_*.csv
#
# FLUXNET_DEBUG
# Turn on additional print statements from the Python embedding script
#
# | *Default:* False
#
# Both of the above Python embedding scripts compute TCI using the ``calc_tci()`` function in METcalcpy. See the METcalcpy
# documentation for more information: https://metcalcpy.readthedocs.io/en/latest/index.html.
#

##############################################################################
# Running METplus
Expand All @@ -99,6 +222,7 @@
# run_metplus.py /path/to/METplus/parm/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI.conf /path/to/user_system.conf
#
# See :ref:`running-metplus` for more information.
#

##############################################################################
# Expected Output
Expand Down
2 changes: 1 addition & 1 deletion internal/tests/use_cases/all_use_cases.txt
Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ Category: data_assimilation


Category: land_surface
0::PointStat_fcstCESM_obsFLUXNET2015_TCI:: model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI.conf:: py_embed
0::PointStat_fcstCESM_obsFLUXNET2015_TCI:: model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI.conf:: metplotpy_env, py_embed


Category: marine_and_cryosphere
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -40,107 +40,93 @@ CUSTOM_LOOP_LIST = DJF,MAM,JJA,SON
LOG_LEVEL=DEBUG

############################################################
# PyEmbedIngest Settings
# PyEmbedIngest Settings for CESM forecast data
# https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#pyembedingest
# User can modify which flux and soil variable is extracted from the CESM files
############################################################

CESM_CAM_VAR = LHFLX
CESM_CLM_VAR = SOILWATER_10CM
CESM_CAM_FILE_PATH = {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fcst/f.e21.FHIST.f09_f09_mg17.CESM2-CLM45physics.002.cam.h1.1979-83_CIvars.nc
CESM_CLM_FILE_PATH = {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fcst/f.e21.FHIST.f09_f09_mg17.CESM2-CLM45physics.002.clm2.h1.1979-83_SoilWater10cm.nc

PY_EMBED_INGEST_1_OUTPUT_DIR =
PY_EMBED_INGEST_1_OUTPUT_TEMPLATE = {OUTPUT_BASE}/regrid_data_plane_{custom}.nc

############################################################
# The last argument is the Latent Heat Flux.
# User can change it to use any other variable present in CESM files.
############################################################

PY_EMBED_INGEST_1_SCRIPT = {PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/cesm_tci.py {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/f.e21.FHIST.f09_f09_mg17.CESM2-CLM45physics.002.clm2.h1.1979-83_SoilWater10cm.nc {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/f.e21.FHIST.f09_f09_mg17.CESM2-CLM45physics.002.cam.h1.1979-83_CIvars.nc {custom} LHFLX
PY_EMBED_INGEST_1_SCRIPT = {PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/cesm_tci.py {CESM_CAM_FILE_PATH} {CESM_CAM_VAR} {CESM_CLM_FILE_PATH} {CESM_CLM_VAR} {custom}

PY_EMBED_INGEST_1_TYPE = NUMPY
#PY_EMBED_INGEST_1_OUTPUT_GRID = G129
PY_EMBED_INGEST_1_OUTPUT_GRID = "latlon 288 192 -90.0 -0.0 0.9375 1.25"

############################################################
# PointStat Settings
# https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#pointstat
# Python embedding settings for using FLUXNET2015 obs data with PointStat.
# User can change the variables used from FLUXNET here to compute TCI.
# The FLUXNET_* config items are also used for PlotPointObs below.
############################################################
FLUXNET_DATA_DIR = {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/obs
FLUXNET_LAT_HEAT_VAR = LE_F_MDS
FLUXNET_SOIL_MOIST_VAR = SWC_F_MDS_1
FLUXNET_OBS_METADATA_FILE={PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnetstations.csv

FCST_POINT_STAT_INPUT_TEMPLATE = PYTHON_NUMPY
OBS_POINT_STAT_INPUT_TEMPLATE = PYTHON_NUMPY={PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnet2015_tci.py {FLUXNET_DATA_DIR} {FLUXNET_LAT_HEAT_VAR} {FLUXNET_SOIL_MOIST_VAR} {custom} {FLUXNET_OBS_METADATA_FILE}

############################################################
# The default variables for the FLUXNET2015 observations id 10CM Soil Moisture
# and Latent Heat Flux. User can change them in the python Embedding script
# fluxnet_tci.py in the PointStat_fcstCESM_obsFLUXNET2015_TCI
# directory.
# PointStat Settings
# https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#pointstat
############################################################
OBS_POINT_STAT_INPUT_TEMPLATE = PYTHON_NUMPY={PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnet2015_tci.py {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/F2015_LoCo_AllChains_F2015.nc4 {custom}

POINT_STAT_OUTPUT_DIR = {OUTPUT_BASE}/PointStat

############################################################
# Field Info
# https://metplus.readthedocs.io/en/latest/Users_Guide/systemconfiguration.html#field-info
############################################################

POINT_STAT_ONCE_PER_FIELD = False

FCST_POINT_STAT_INPUT_DIR = {OUTPUT_BASE}/
FCST_POINT_STAT_INPUT_TEMPLATE = regrid_data_plane_{custom}.nc
FCST_POINT_STAT_VAR1_LEVELS =
OBS_POINT_STAT_VAR1_NAME = TCI
OBS_POINT_STAT_VAR1_LEVELS = L0
OBS_POINT_STAT_VAR1_LEVELS = L0
OBS_POINT_STAT_WINDOW_BEGIN = -1000000000
OBS_POINT_STAT_WINDOW_END = 2000000000

FCST_POINT_STAT_VAR1_NAME = TCI_10cm_soil_depth
FCST_POINT_STAT_VAR1_NAME = TCI_10cm_soil_depth
FCST_POINT_STAT_VAR1_LEVELS = Z10
BOTH_POINT_STAT_VAR1_THRESH =
FCST_POINT_STAT_INPUT_DIR = {OUTPUT_BASE}
FCST_POINT_STAT_INPUT_TEMPLATE = regrid_data_plane_{custom}.nc

############################################################
# PointStat Settings
# https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#pointstat
# General PointStat Settings
############################################################

LOG_POINT_STAT_VERBOSITY = 2

POINT_STAT_CONFIG_FILE ={PARM_BASE}/met_config/PointStatConfig_wrapped

POINT_STAT_CONFIG_FILE = {PARM_BASE}/met_config/PointStatConfig_wrapped
POINT_STAT_DESC = TCI
POINT_STAT_INTERP_TYPE_METHOD = NEAREST
POINT_STAT_INTERP_TYPE_WIDTH = 1

POINT_STAT_MASK_GRID = FULL
POINT_STAT_MASK_POLY =
POINT_STAT_MASK_SID =
POINT_STAT_MESSAGE_TYPE = ADPSFC
POINT_STAT_OBS_VALID_BEG = 19790101_000000
POINT_STAT_OBS_VALID_END = 20130101_000000
POINT_STAT_OFFSETS = 0
POINT_STAT_ONCE_PER_FIELD = False
POINT_STAT_OUTPUT_DIR = {OUTPUT_BASE}/PointStat
POINT_STAT_OUTPUT_FLAG_CTC = BOTH
POINT_STAT_OUTPUT_FLAG_MPR = BOTH
POINT_STAT_OUTPUT_FLAG_CNT = BOTH

OBS_POINT_STAT_WINDOW_BEGIN = -1000000000
OBS_POINT_STAT_WINDOW_END = 2000000000

POINT_STAT_OFFSETS = 0

MODEL = CESM

POINT_STAT_DESC = TCI
OBTYPE =

POINT_STAT_OUTPUT_PREFIX = {custom}
POINT_STAT_REGRID_TO_GRID = NONE
POINT_STAT_REGRID_METHOD = BILIN
POINT_STAT_REGRID_WIDTH = 2

POINT_STAT_OBS_VALID_BEG = 19790101_000000
POINT_STAT_OBS_VALID_END = 20130101_000000

POINT_STAT_MASK_GRID = FULL
POINT_STAT_MASK_POLY =
POINT_STAT_MASK_SID =

POINT_STAT_MESSAGE_TYPE = ADPSFC

POINT_STAT_OUTPUT_PREFIX = {custom}
LOG_POINT_STAT_VERBOSITY = 2
MODEL = CESM
OBTYPE = FLUXNET

############################################################
# PlotPointObs Settings
# https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#plotpointobs
############################################################

PLOT_POINT_OBS_INPUT_TEMPLATE =PYTHON_NUMPY={PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnet2015_tci.py {INPUT_BASE}/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/F2015_LoCo_AllChains_F2015.nc4 {custom}
PLOT_POINT_OBS_INPUT_TEMPLATE =PYTHON_NUMPY={PARM_BASE}/use_cases/model_applications/land_surface/PointStat_fcstCESM_obsFLUXNET2015_TCI/fluxnet2015_tci.py {FLUXNET_DATA_DIR} {FLUXNET_LAT_HEAT_VAR} {FLUXNET_SOIL_MOIST_VAR} {custom} {FLUXNET_OBS_METADATA_FILE}

PLOT_POINT_OBS_GRID_INPUT_DIR = {OUTPUT_BASE}/
PLOT_POINT_OBS_GRID_INPUT_DIR = {OUTPUT_BASE}
PLOT_POINT_OBS_GRID_INPUT_TEMPLATE = regrid_data_plane_{custom}.nc

PLOT_POINT_OBS_OUTPUT_DIR = {OUTPUT_BASE}/plot_point_obs
Expand Down Expand Up @@ -170,3 +156,13 @@ PLOT_POINT_OBS_POINT_DATA =
}
}

############################################################
# FLUXNET Python Embedding Script options
############################################################
[user_env_vars]
FLUXNET_SKIP_LEAP_DAYS=True
FLUXNET_HIGHRES_QC_THRESH=0.8
FLUXNET_MIN_DAYS_PER_SEASON=1
FLUXNET_MIN_DAYS_PER_SITE_ALL_SEASONS=10
FLUXNET_RAW_FILENAME_PATTERN=FLX_*_DD_*.csv
FLUXNET_DEBUG=False
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