Merge pull request #79 from falconstryker/devel

Update help for testing round 2

Author: falconstryker

bin/MarsFiles.py

@@ -152,8 +152,8 @@ def parse_args(self, *args, **kwargs):
         f"  - ``diurn``  : 5-sol averages binned by time of day\n"
         f"  - ``average``: 5-sol averages\n"
         f"{Green}Example:\n"
-        f"> MarsFiles filename.nc -bin fixed\n"
-        f"> MarsFiles filename.nc -bin fixed diurn"
+        f"> MarsFiles fort.11_* -bin fixed daily diurn average\n"
+        f"> MarsFiles fort.11_* -bin fixed diurn"
         f"{Nclr}\n\n"
     )
 )
@@ -187,10 +187,10 @@ def parse_args(self, *args, **kwargs):
         f"-dim.\nIf a file contains multiple Mars Years of data, the "
         f"function splits the file in the first Mars Year.\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_average.nc --split 0 90"
-        f"> MarsFiles 00668.atmos_average.nc --split 270\n"
+        f"> MarsFiles 01336.atmos_average.nc --split 0 90"
+        f"> MarsFiles 01336.atmos_average.nc --split 270\n"
         f"{Yellow}Use -dim to specify the dimension:{Green}\n"
-        f"> MarsFiles 00668.atmos_average.nc --split 0 90 -dim lat"
+        f"> MarsFiles 01336.atmos_average.nc --split 0 90 -dim lat"
         f"{Nclr}\n\n"
     )
 )
@@ -206,9 +206,9 @@ def parse_args(self, *args, **kwargs):
         f"files.\n"
         f"{Yellow}Generates a new file ending in ``_T.nc``{Nclr}\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_diurn.nc -t"
+        f"> MarsFiles 01336.atmos_diurn.nc -t"
         f" {Blue}(outputs data for all 24 local times){Green}\n"
-        f"> MarsFiles 00668.atmos_diurn.nc -t '3 15'"
+        f"> MarsFiles 01336.atmos_diurn.nc -t '3 15'"
         f" {Blue}(outputs data for target local times only)"
         f"{Nclr}\n\n"
     )
@@ -224,8 +224,8 @@ def parse_args(self, *args, **kwargs):
         f"Requires input file to be in MGCM 'daily' format.\n"
         f"{Yellow}Generates a new file ending in ``_to_average.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -ba {Blue}(5-sol bin){Green}\n"
-        f"> MarsFiles 00668.atmos_daily_pstd.nc -ba 10 {Blue}(10-sol bin)"
+        f"> MarsFiles 01336.atmos_daily.nc -ba {Blue}(5-sol bin){Green}\n"
+        f"> MarsFiles 01336.atmos_daily_pstd.nc -ba 10 {Blue}(10-sol bin)"
         f"{Nclr}\n\n"
     )
 )
@@ -241,10 +241,10 @@ def parse_args(self, *args, **kwargs):
         f"Requires input file to be in MGCM 'daily' format.\n"
         f"{Yellow}Generates a new file ending in ``_to_diurn.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -bd {Blue}(5-sol bin){Green}\n"
-        f"> MarsFiles 00668.atmos_daily_pstd.nc -bd -ba 10 "
+        f"> MarsFiles 01336.atmos_daily.nc -bd {Blue}(5-sol bin){Green}\n"
+        f"> MarsFiles 01336.atmos_daily_pstd.nc -bd -ba 10 "
         f"{Blue}(10-sol bin){Green}\n"
-        f"> MarsFiles 00668.atmos_daily_pstd.nc -bd -ba 1 "
+        f"> MarsFiles 01336.atmos_daily_pstd.nc -bd -ba 1 "
         f"{Blue}(no binning, mimics raw Legacy output)"
         f"{Nclr}\n\n"
     )
@@ -262,7 +262,7 @@ def parse_args(self, *args, **kwargs):
         f"to add the original linear trend to the amplitudes \n"
         f"\n{Yellow}Generates a new file ending in ``_hpt.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -hpt 10.\n"
+        f"> MarsFiles 01336.atmos_daily.nc -hpt 10.\n"
         f"{Nclr}\n\n"
     )
 )
@@ -279,7 +279,7 @@ def parse_args(self, *args, **kwargs):
         f"to add the original linear trend to the amplitudes \n"
         f"\n{Yellow}Generates a new file ending in ``_lpt.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -lpt 0.5\n"
+        f"> MarsFiles 01336.atmos_daily.nc -lpt 0.5\n"
         f"{Nclr}\n\n"
     )
 )
@@ -296,7 +296,7 @@ def parse_args(self, *args, **kwargs):
         f"to add the original linear trend to the amplitudes \n"
         f"\n{Yellow}Generates a new file ending in ``bpt.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -hpt 0.5 10.\n"
+        f"> MarsFiles 01336.atmos_daily.nc -hpt 0.5 10.\n"
         f"{Nclr}\n\n"
     )
 )
@@ -312,7 +312,7 @@ def parse_args(self, *args, **kwargs):
         f"in Sols.\n"
         f"{Yellow}Generates a new file ending in ``_hps.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -hps 10 --add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -hps 10 --add_trend\n"
         f"{Nclr}\n\n"
     )
 )
@@ -327,7 +327,7 @@ def parse_args(self, *args, **kwargs):
         f"cutoff frequency in Sols.\n"
         f"{Yellow}Generates a new file ending in ``_lps.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -lps 20 --add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -lps 20 --add_trend\n"
         f"{Nclr}\n\n"
     )
 )
@@ -342,7 +342,7 @@ def parse_args(self, *args, **kwargs):
         f"cutoff frequency in Sols.\nData detrended before filtering.\n"
         f"{Yellow}Generates a new file ending in ``_bps.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -bps 10 20 --add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -bps 10 20 --add_trend\n"
         f"{Nclr}\n\n"
     )
 )
@@ -358,7 +358,7 @@ def parse_args(self, *args, **kwargs):
         f"N = 1 diurnal tide, N = 2 semi-diurnal, etc.\n"
         f"{Yellow}Generates a new file ending in ``_tide_decomp.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_diurn.nc -tide 2 -incl ps temp "
+        f"> MarsFiles 01336.atmos_diurn.nc -tide 2 -incl ps temp "
         f"{Blue}(extracts semi-diurnal tide component of ps and temp "
         f"variables; 2 harmonics)"
         f"{Nclr}\n\n"
@@ -376,8 +376,11 @@ def parse_args(self, *args, **kwargs):
         f"to the same standard grid [zstd, zagl, pstd, etc.].\n"
         f"{Yellow}Generates a new file ending in ``_regrid.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsInterp sim1/00668.atmos_average_pstd.nc -regrid "
-        f"sim2/00668.atmos_average_pstd.nc"
+        f"> MarsInterp 01336.atmos_average_pstd.nc -regrid "
+        f"01336.atmos_average_pstd_c48.nc"
+        f"{Yellow}NOTE: name of regridded file does not matter."
+        f"{Green}> MarsInterp sim1/01336.atmos_average_pstd.nc -regrid "
+        f"sim2/01336.atmos_average_pstd.nc"
         f"{Nclr}\n\n"
     )
 )
@@ -392,7 +395,7 @@ def parse_args(self, *args, **kwargs):
         f"length <= 1.\n"
         f"{Yellow}Generates a new file ending in ``_zavg.nc``\n"
         f"{Green}Example:\n"
-        "> MarsFiles 00668.atmos_diurn.nc -zavg"
+        "> MarsFiles 01336.atmos_diurn.nc -zavg"
         f"{Nclr}\n\n"
     )
 )
@@ -405,8 +408,8 @@ def parse_args(self, *args, **kwargs):
         f"dimension on which to trim the file.\nAcceptable values are "
         f"'areo', 'lev', 'lat', 'lon'. Default = 'areo'.\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_average.nc --split 0 90 -dim areo"
-        f"> MarsFiles 00668.atmos_average.nc --split -70 -dim lat"
+        f"> MarsFiles 01336.atmos_average.nc --split 0 90 -dim areo"
+        f"> MarsFiles 01336.atmos_average.nc --split -70 -dim lat"
         f"{Nclr}\n\n"
     )
 )
@@ -421,7 +424,7 @@ def parse_args(self, *args, **kwargs):
         f"N = 1 diurnal tide, N = 2 semi-diurnal, etc.\n"
         f"{Yellow}Generates a new file ending in ``_norm.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_diurn.nc -tide 6 -incl ps "
+        f"> MarsFiles 01336.atmos_diurn.nc -tide 6 -incl ps "
         f"-norm"
         f"{Nclr}\n\n"
     )
@@ -438,9 +441,9 @@ def parse_args(self, *args, **kwargs):
         f"``-hpt``, ``-bpt``).\n"
         f"{Yellow}Generates a new file ending in ``_trended.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -hpt 10. -add_trend\n"
-        f"> MarsFiles 00668.atmos_daily.nc -lpt 0.5 -add_trend\n"
-        f"> MarsFiles 00668.atmos_daily.nc -hpt 0.5 10. -add_trend"
+        f"> MarsFiles 01336.atmos_daily.nc -hpt 10. -add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -lpt 0.5 -add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -hpt 0.5 10. -add_trend"
         f"{Nclr}\n\n"
     )
 )
@@ -453,7 +456,7 @@ def parse_args(self, *args, **kwargs):
         f"Reconstructs the first N harmonics.\n"
         f"{Yellow}Generates a new file ending in ``_reconstruct.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_diurn.nc -tide 6 -incl ps temp "
+        f"> MarsFiles 01336.atmos_diurn.nc -tide 6 -incl ps temp "
         f"-recon"
         f"{Nclr}\n\n"
     )
@@ -467,7 +470,7 @@ def parse_args(self, *args, **kwargs):
         f"{Yellow}Overwrites existing target file. To override, use "
         f"-ext.{Nclr}\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_daily.nc -ba -incl ps temp ts"
+        f"> MarsFiles 01336.atmos_daily.nc -ba -incl ps temp ts"
         f"{Nclr}\n\n"
     )
 )
@@ -491,7 +494,7 @@ def parse_args(self, *args, **kwargs):
         f"Use with any other argument to pass all Python errors and\n"
         f"status messages to the screen when running CAP.\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00668.atmos_average.nc -t '3 15' --debug"
+        f"> MarsFiles 01336.atmos_average.nc -t '3 15' --debug"
         f"{Nclr}\n\n"
     )
  )

bin/MarsFormat.py

@@ -181,6 +181,7 @@ def main():
         #=================================================================
         if model_type == 'marswrf':
             # First save all variable descriptions in attrs longname
+            print(f"{Cyan}Current variables at top of marswrf processing:\n{list(DS.variables)}{Nclr}\n")
             for var_name in DS.data_vars:
                 var = DS[var_name]
                 if 'description' in var.attrs:
@@ -409,6 +410,7 @@ def main():
         # ==============================================================
         # check that vertical grid starts at toa with highest level at surface
         if DS[model.dim_pfull][0] != DS[model.dim_pfull].min(): # if toa, lev = 0 is surface then flip
+            print(f"{Cyan}Current variables at start of processing for all models:\n{list(DS.variables)}{Nclr}\n")
             DS = DS.isel(**{model.dim_pfull: slice(None, None, -1)})
             DS=DS.isel(**{model.dim_phalf: slice(None, None, -1)}) #Also flip phalf,ak, bk
             print(f"{Red}NOTE: all variables flipped along vertical dimension, so that the top of the atmosphere is now index 0")

bin/MarsInterp.py

@@ -78,8 +78,8 @@
     help=(
         f"Interpolation interp_: ``pstd``, ``zstd``, or ``zagl``.\n"
         f"{Green}Example:\n"
-        f"> MarsInterp 00668.atmos_average.nc\n"
-        f"> MarsInterp 00668.atmos_average.nc -t pstd"
+        f"> MarsInterp 01336.atmos_average.nc\n"
+        f"> MarsInterp 01336.atmos_average.nc -t pstd"
         f"{Nclr}\n\n"
     )
 )
@@ -93,7 +93,7 @@
         f"{Cyan}cp path/to/amesCAP/mars_templates/amescap_profile "
         f"~/.amescap_profile\n"
         f"{Green}Example:\n"
-        f"> MarsInterp 00668.atmos_average.nc -t zstd -v phalf_mb"
+        f"> MarsInterp 01336.atmos_average.nc -t zstd -v phalf_mb"
         f"{Nclr}\n\n"
     )
 )
@@ -103,7 +103,7 @@
         f"Only include the listed variables. Dimensions and 1D "
         f"variables are always included.\n"
         f"{Green}Example:\n"
-        f"> MarsInterp 00668.atmos_daily.nc -incl temp ps ts"
+        f"> MarsInterp 01336.atmos_daily.nc -incl temp ps ts"
         f"{Nclr}\n\n"
     )
 )
@@ -113,7 +113,7 @@
         f"Print the vertical grid to the screen. {Yellow}This does not "
         f"run the interpolation, it only prints grid information.\n"
         f"{Green}Example:\n"
-        f"> MarsInterp 00668.atmos_average.nc -t pstd -v p44 -print"
+        f"> MarsInterp 01336.atmos_average.nc -t pstd -v p44 -print"
         f"{Nclr}\n\n"
     )
 )
@@ -139,7 +139,7 @@
         f"Use with any other argument to pass all Python errors and\n"
         f"status messages to the screen when running CAP.\n"
         f"{Green}Example:\n"
-        f"> MarsInterp 00668.atmos_average.nc -t pstd --debug"
+        f"> MarsInterp 01336.atmos_average.nc -t pstd --debug"
         f"{Nclr}\n\n"
     )
  )

bin/MarsPlot.py

@@ -110,7 +110,7 @@
         f"Print the content of a netCDF file to the screen. This is a "
         f"ncdump-like feature. Variables are sorted by dimension.\n"
         f"{Green}Example:\n"
-        f"> MarsPlot -i 00668.atmos_daily.nc"
+        f"> MarsPlot -i 01336.atmos_daily.nc"
         f"{Nclr}\n\n"
     )
 )
@@ -130,7 +130,7 @@
     help=(
         f"Specify the file to use. Default is the last file created.\n"
         f"{Green}Example:\n"
-        f"> MarsPlot Custom.in -d 00668"
+        f"> MarsPlot Custom.in -d 01336"
         f"{Nclr}\n\n"
     )
 )
@@ -211,9 +211,9 @@
         f"For use with ``-i --inspect``: print the values of the "
         f"specified variable to the screen.\n"
         f"{Green}Example:\n"
-        f"> MarsPlot -i 00668.atmos_daily.nc -values temp\n"
+        f"> MarsPlot -i 01336.atmos_daily.nc -values temp\n"
         f"{Blue}(quotes '' req. for browsing dimensions){Green}\n"
-        f"> MarsPlot -i 00668.atmos_daily.nc -values 'temp[6,:,30,10]'"
+        f"> MarsPlot -i 01336.atmos_daily.nc -values 'temp[6,:,30,10]'"
         f"{Nclr}\n\n"
     )
 )
@@ -224,9 +224,9 @@
         f"For use with ``-i --inspect``: print the min, mean, and max "
         f"values of the specified variable to the screen.\n"
         f"{Green}Example:\n"
-        f"> MarsPlot -i 00668.atmos_daily.nc -stats temp\n"
+        f"> MarsPlot -i 01336.atmos_daily.nc -stats temp\n"
         f"{Blue}(quotes '' req. for browsing dimensions){Green}\n"
-        f"> MarsPlot -i 00668.atmos_daily.nc -stats 'temp[6,:,30,10]'"
+        f"> MarsPlot -i 01336.atmos_daily.nc -stats 'temp[6,:,30,10]'"
         f"{Nclr}\n\n"
     )
 )
@@ -259,7 +259,7 @@
                               args.generate_template is False and
                               args.inspect_file is None):
     parser.error(f"{Red}The -d argument requires a template file "
-                 f"like Custom.in (e.g., MarsPlot Custom.in -d 00668)"
+                 f"like Custom.in (e.g., MarsPlot Custom.in -d 01336)"
                  f"{Nclr}")
     exit()
 
@@ -292,13 +292,13 @@
 if args.statistics is not None and args.inspect_file is None:
     parser.error(f"{Red}The -stat argument requires a template "
                  f"file like Custom.in (e.g., MarsPlot -i "
-                 f"00668.atmos_daily.nc -stats temp{Nclr}")
+                 f"01336.atmos_daily.nc -stats temp{Nclr}")
     exit()
 
 if args.print_values is not None and args.inspect_file is None:
     parser.error(f"{Red}The -values argument requires a template "
                  f"file like Custom.in (e.g., MarsPlot -i "
-                 f"00668.atmos_daily.nc -values temp{Nclr}")
+                 f"01336.atmos_daily.nc -values temp{Nclr}")
     exit()
 
 if args.trim_text and (args.generate_template is False):
@@ -2073,7 +2073,7 @@ def prep_file(var_name, file_type, simuID, sol_array):
         file_has_sol_number = True
         if sol_array != [None]:
             # File number explicitly provided in varfull
-            # (e.g., 00668.atmos_average.nc)
+            # (e.g., 01336.atmos_average.nc)
             Sol_num_current = sol_array
         elif Ncdf_num is not None:
             # File number NOT provided in varfull
@@ -2701,8 +2701,8 @@ def get_topo_2D(self, varfull, plot_type):
         This function returns the longitude, latitude, and topography
         to overlay as contours in a ``2D_lon_lat`` plot. Because the
         main variable requested may be complex
-        (e.g., ``[00668.atmos_average_psdt2.temp]/1000.``), we will
-        ensure to load the matching topography (here ``00668.fixed.nc``
+        (e.g., ``[01336.atmos_average_psdt2.temp]/1000.``), we will
+        ensure to load the matching topography (here ``01336.fixed.nc``
         from the 2nd simulation). This function essentially does a
         simple task in a complicated way. Note that a great deal of
         the code is borrowed from the ``data_loader_2D()`` function.
@@ -2734,8 +2734,8 @@ def get_topo_2D(self, varfull, plot_type):
             f = get_list_varfull(varfull)
             sol_array, filetype, var, simuID = split_varfull(varfull_list[0])
 
-        # If requesting a lat-lon plot for 00668.atmos_average.nc,
-        # try to find matching 00668.fixed.nc
+        # If requesting a lat-lon plot for 01336.atmos_average.nc,
+        # try to find matching 01336.fixed.nc
         try:
             f, var_info, dim_info, dims = prep_file(
                 "zsurf", "fixed", simuID, sol_array)