Feature 2136 cross spectra (#2208)

.github/parm/use_case_groups.json

@@ -137,7 +137,7 @@
   {
     "category": "s2s",
     "index_list": "3",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",

docs/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.py → docs/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.py

@@ -1,46 +1,48 @@
 """
-UserScript: Make a Cross Spectra plot 
+UserScript: Compue Cross Spectra and make a plot 
 ========================================================================
 
 model_applications/
 s2s/
-UserScript_obsPrecip_obsOnly_CrossSpectraPlot.py
+UserScript_fcstS2S_obsERAI_CrossSpectra.py
 
 """
 
 #################################################################################
 # Scientific Objective
 # --------------------
 #
-# This use case calls the METplotpy space time plot to create a sample cross 
-# spectra diagram
-# using sample data created by METcalcpy cross spectra functions
+# This use case calls the METcalcpy cross spectra function and then the METplotpy 
+# space time plot to compute cross-spectra and create a sample cross spectra 
+# diagram using sample data.
 #
 # The space time plot and cross spectra calculations were created by Maria Gehne 
-# at the 
-# Physical Sciences Labratory in NOAA 
+# at the Physical Sciences Labratory in NOAA. 
 
 #################################################################################
 # Datasets
 # --------
 #
+#  * Forecast dataset: UFS Prototype 7
+#  * Observation dataset: ERAI
+#
 
 ##############################################################################
 # METplus Components
 # ------------------
 #
-# This use case runs the UserScript wrapper tool to run a user provided script,
-# in this case, cross_spectra_plot.py.
+# This use case runs the UserScript wrapper tool to run a user provided script, 
+# in this case, cross_spectra.py and cross_spectra_plot.py.
 #
 
 ##############################################################################
 # METplus Workflow
 # ----------------
 #
-# This use case does not loop but plots the entire time period of data
-# 
-# UserScript
-#
+# This use case computes spectra and plots for the entire time period of data. 
+# The use case loops over two processes, computing and plotting the 
+# cross-spectra. The user is able to edit the process list to turn off the 
+# computation part if only plotting is desired, or vice versa.
 #
 
 ##############################################################################
@@ -49,10 +51,10 @@
 #
 # METplus first loads all of the configuration files found in parm/metplus_config,
 # then it loads any configuration files passed to METplus via the command line
-# with the -c option, i.e. -c parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf
+# with the -c option, i.e. -c parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
 #
 # .. highlight:: bash
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
 #
 
 #############################################################################
@@ -76,7 +78,7 @@
 # This use case uses a Python script to perform plotting
 #
 # .. highlight:: python
-# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot/cross_spectra_plot.py
+# .. literalinclude:: ../../../../parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/cross_spectra_plot.py
 #
 
 ##############################################################################
@@ -85,14 +87,14 @@
 #
 # This use case can be run two ways:
 #
-# 1) Passing in UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf, 
+# 1) Passing in UserScript_fcstS2S_obsERAI_CrossSpectra.conf, 
 # then a user-specific system configuration file::
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf -c /path/to/user_system.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf -c /path/to/user_system.conf
 #
-# 2) Modifying the configurations in parm/metplus_config, then passing in UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf::
+# 2) Modifying the configurations in parm/metplus_config, then passing in UserScript_fcstS2S_obsERAI_CrossSpectra.conf::
 #
-#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf
+#        run_metplus.py -c /path/to/METplus/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf
 #
 # The former method is recommended. Whether you add them to a user-specific configuration file or modify the metplus_config files, the following variables must be set correctly:
 #
@@ -143,4 +145,4 @@
 #
 #
 #
-# sphinx_gallery_thumbnail_path = '_static/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.png'
+# sphinx_gallery_thumbnail_path = '_static/s2s-UserScript_fcstS2S_obsERAI_CrossSpectra.png'

internal/tests/use_cases/all_use_cases.txt

@@ -129,7 +129,7 @@ Category: s2s
 0::GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast:: model_applications/s2s/GridStat_SeriesAnalysis_fcstNMME_obsCPC_seasonal_forecast.conf:: netcdf4_env
 1::TCGen_fcstGFSO_obsBDECKS_GDF_TDF:: model_applications/s2s/TCGen_fcstGFSO_obsBDECKS_GDF_TDF.conf:: metplotpy_env,cartopy,metplus
 2::UserScript_obsPrecip_obsOnly_Hovmoeller:: model_applications/s2s/UserScript_obsPrecip_obsOnly_Hovmoeller.conf:: metplotpy_env,cartopy
-3:: UserScript_obsPrecip_obsOnly_CrossSpectraPlot:: model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot.conf:: spacetime_env
+3:: UserScript_fcstS2S_obsERAI_CrossSpectra:: model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf:: spacetime_env
 4:: UserScript_obsERA_obsOnly_Stratosphere:: model_applications/s2s/UserScript_obsERA_obsOnly_Stratosphere.conf:: metplotpy_env,metdataio
 5::SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool:: model_applications/s2s/SeriesAnalysis_fcstCFSv2_obsGHCNCAMS_climoStandardized_MultiStatisticTool.conf:: netcdf4_env
 6::GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile:: model_applications/s2s/GridStat_fcstCFSv2_obsGHCNCAMS_MultiTercile.conf:: netcdf4_env

parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra.conf

@@ -0,0 +1,45 @@
+[config]
+
+PROCESS_LIST = UserScript(comp_spectra), UserScript(plot_spectra)
+
+# Note: time looping is not used in this use case
+LOOP_BY = REALTIME
+VALID_TIME_FMT = %Y
+VALID_BEG = 2014
+
+USER_SCRIPT_RUNTIME_FREQ = RUN_ONCE
+
+[user_env_vars]
+# Make output base avabilable to the script
+COMP_SPECTRA_SCRIPT_OUTPUT_DIR = {OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output
+
+# YAML configuration file for the cross spectra calculation
+COMP_SPECTRA_YAML_CONFIG_NAME = {METPLUS_BASE}/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/spectra_comp.yaml
+
+# Input files for the cross spectra calculation
+COMP_SPECTRA_INPUT_FILE_NAMES = {INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/precip.erai.sfc.1p0.2x.2014-2016.nc,{INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/prate_avg_ufs_p7_2014040100.nc,{INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/u850_ufs_p7_2014040100.nc,{INPUT_BASE}/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/data/u200_ufs_p7_2014040100.nc
+
+PLOT_SPECTRA_INPUT_FILE_NAMES = {OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output/SpaceTimeSpectra_ufs_p7_P_D850_symm_4spd.nc,{OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output/SpaceTimeSpectra_ufs_p7_P_D200_symm_4spd.nc,{OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/output/SpaceTimeSpectra_ufs_p7_P_D200_symm_4spd.nc
+
+PLOT_SPECTRA_YAML_CONFIG_NAME = {METPLUS_BASE}/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/spectra_plot.yaml
+
+PLOT_SPECTRA_OUTPUT_DIR = {OUTPUT_BASE}/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/plots/
+
+
+[comp_spectra]
+# Settings for computing the cross-spectra
+USER_SCRIPT_COMMAND = python {METCALCPY_BASE}/metcalcpy/contributed/spacetime/cross_spectra.py
+
+LOG_FILE = "cross_spectra.log"
+LOG_LEVEL = "DEBUG"
+
+METCALCPY_BASE = {METPLUS_BASE}/../METcalcpy
+
+
+[plot_spectra]
+# settings for plotting the cross-spectra
+
+USER_SCRIPT_COMMAND = python {METPLUS_BASE}/parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/cross_spectra_plot.py
+
+LOG_FILE = "cross_spectra_plot.log"
+LOG_LEVEL = "INFO"

parm/use_cases/model_applications/s2s/UserScript_obsPrecip_obsOnly_CrossSpectraPlot/cross_spectra_plot.py → parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/cross_spectra_plot.py

@@ -18,7 +18,7 @@
 # user can use their own, if none specified at the command line,
 # use the "default" example YAML config file, spectra_plot_coh2.py
 # Using a custom YAML reader so we can use environment variables
-plot_config_file = os.getenv("YAML_CONFIG_NAME","spectra_plot.yaml")
+plot_config_file = os.getenv("PLOT_SPECTRA_YAML_CONFIG_NAME","spectra_plot.yaml")
 
 config_dict = readconfig.parse_config(plot_config_file)
 
@@ -27,6 +27,9 @@
 #pathdata = config_dict['pathdata'][0]
 plotpath = config_dict['plotpath'][0]
 print("Output path ",plotpath)
+model = config_dict['model']
+var2 = config_dict['var2']
+var3 = config_dict['var3']
 
 # plot layout parameters
 flim = 0.5  # maximum frequency in cpd for plotting
@@ -36,17 +39,18 @@
 contourspace = 0.1  # contour spacing
 N = [1, 2]  # wave modes for plotting
 source = ""
-spd = 2
+spd = 4
 
 symmetry = "symm"      #("symm", "asymm", "latband")
-filenames = os.environ.get("INPUT_FILE_NAMES","ERAI_TRMM_P_symn,ERAI_P_D850_symn,ERAI_P_D200_symn").split(",")
-#filenames = ['ERAI_TRMM_P_symm_'+str(spd)+'spd',
-#             'ERAI_P_D850_symm_'+str(spd)+'spd',
-#             'ERAI_P_D200_symm_'+str(spd)+'spd']
-vars1 = ['ERAI P', 'ERAI P', 'ERAI P']
-vars2 = ['TRMM', 'ERAI D850', 'ERAI D200']
+#filenames = os.environ.get("INPUT_FILE_NAMES","ERAI_TRMM_P_symn,ERAI_P_D850_symn,ERAI_P_D200_symn").split(",")
+#vars1 = ['ERAI P', 'ERAI P', 'ERAI P']
+#vars2 = ['TRMM', 'ERAI D850', 'ERAI D200']
+filenames = os.environ.get("PLOT_SPECTRA_INPUT_FILE_NAMES","ERAI_P_D850_symn,ERAI_P_D200_symn,ERAI_P_D200_symn").split(",")
+vars1 = [model+' P',model+' P',model+' P']
+vars2 = [model+' '+var2,model+' '+var3,model+' '+var3]
 nplot = len(vars1)
 
+npanel =3
 for pp in np.arange(0, nplot, 1):
 
     # read data from file
@@ -58,8 +62,8 @@
     wnum = fin['wnum']
     freq = fin['freq']
 
-    ifreq = np.where((freq[:] >= 0) & (freq[:] <= flim))
-    iwave = np.where(abs(wnum[:]) <= nWavePlt)
+    #ifreq = np.where((freq[:] >= 0) & (freq[:] <= flim))
+    #iwave = np.where(abs(wnum[:]) <= nWavePlt)
 
     STC[:, freq[:] == 0, :] = 0.
     STC = STC.sel(wnum=slice(-nWavePlt, nWavePlt))
@@ -75,11 +79,13 @@
     pow2.where(pow2 <= 0, drop=True)
 
     if pp == 0:
-        Coh2 = np.empty([nplot, len(freq[ifreq]), len(wnum[iwave])])
-        Phs1 = np.empty([nplot, len(freq[ifreq]), len(wnum[iwave])])
-        Phs2 = np.empty([nplot, len(freq[ifreq]), len(wnum[iwave])])
-        Pow1 = np.empty([nplot, len(freq[ifreq]), len(wnum[iwave])])
-        Pow2 = np.empty([nplot, len(freq[ifreq]), len(wnum[iwave])])
+        ifreq = np.where((freq[:] >= 0) & (freq[:] <= flim))
+        iwave = np.where(abs(wnum[:]) <= nWavePlt)
+        Coh2 = np.full([npanel, len(freq[ifreq]), len(wnum[iwave])], np.nan)
+        Phs1 = np.full([npanel, len(freq[ifreq]), len(wnum[iwave])], np.nan)
+        Phs2 = np.full([npanel, len(freq[ifreq]), len(wnum[iwave])], np.nan)
+        Pow1 = np.full([npanel, len(freq[ifreq]), len(wnum[iwave])], np.nan)
+        Pow2 = np.full([npanel, len(freq[ifreq]), len(wnum[iwave])], np.nan)
         k = wnum[iwave]
         w = freq[ifreq]
 
@@ -103,7 +109,7 @@
 
 # plot coherence
 stp.plot_coherence(Coh2, Phs1, Phs2, symmetry, source, vars1, vars2, plotpath, flim, 20, contourmin, contourmax,
-                   contourspace, nplot, N)
+                   contourspace, npanel, N)
 
 # check if output file exists since plotting function
 # doesn't return an error code on failure

parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/spectra_comp.yaml

@@ -0,0 +1,12 @@
+pathout:
+- !ENV '${COMP_SPECTRA_SCRIPT_OUTPUT_DIR}' 
+
+model: 'ufs_p7'
+spd : 4
+nperseg : 15 # in days
+segOverLap : -5 # in days
+Symmetry : 'symm'
+latMin : -15.
+latMax : 15.
+datestrt : '2014-04-01T06:00:00'  # start date, format: yyyy-mm-ddTHH:MM:ss
+datelast : '2014-05-04T18:00:00'  # end date, format: yyyy-mm-ddTHH:MM:ss

parm/use_cases/model_applications/s2s/UserScript_fcstS2S_obsERAI_CrossSpectra/spectra_plot.yaml

@@ -0,0 +1,5 @@
+plotpath: 
+- !ENV '${PLOT_SPECTRA_OUTPUT_DIR}'
+model: 'ufs_p7'
+var2: 'u850'
+var3: 'u200'