Merge pull request #803 from EC-Earth/798-no-NEMO-dependency

798 no nemo dependency

ece2cmor3/lpjg2cmor.py

@@ -245,13 +245,6 @@ def execute(tasks):
                             % (getattr(task, cmor_task.output_path_key), task.source.variable()))
                     break
 
-                # special treatment of fco2nat=fco2nat_lpjg+fgco2_nemo
-                if outname=="fco2nat" and freq=="mon" and table=="Amon" and (cmor.get_cur_dataset_attribute("source_id") == "EC-Earth3-CC"):
-                    if not add_nemo_variable(task, ncfile, "fgco2", "1m"):
-                        log.error("There was a problem adding nemo variable %s to %s in table %s... "
-                                  "exiting ece2cmor3" % ("fgco2", task.target.variable, task.target.table))
-                        exit(-1)
-
                 dataset = netCDF4.Dataset(ncfile, 'r')
                 # Create the grid, need to do only once as all LPJG variables will be on same grid
                 # Currently create_grid just creates latitude and longitude axis since that should be all that is needed
@@ -527,102 +520,6 @@ def create_lpjg_netcdf(freq, inputfile, outname, outdims):
 
     return ncfile
 
-
-# finds the nemo output containing varname at nemo_freq
-# this uses code in nemo2cmor.py, which could be moved to cmor_utils
-def find_nemo_file(varname, nemo_freq):
-    # find the nemo output folder for this leg (assumes it is in the runtime/output/nemo/??? folder)
-    path_output_lpjg, leg_no = os.path.split(lpjg_path_)
-    path_output = os.path.split(path_output_lpjg)
-    nemo_path = os.path.join(path_output[0],'nemo',leg_no)
-    # get the file which contains fgco2
-    try:
-        nemo_files = cmor_utils.find_nemo_output(nemo_path, exp_name_)
-    except OSError:
-        log.error("Cannot find any nemo output files in %s"
-                  % (nemo_path))
-        return ""
-    print((str(nemo_files)))
-    file_candidates = [f for f in nemo_files if cmor_utils.get_nemo_frequency(f, exp_name_) == nemo_freq]
-    results = []
-    for ncfile in file_candidates:
-        ds = netCDF4.Dataset(ncfile)
-        if varname in ds.variables:
-            results.append(ncfile)
-        ds.close()
-    # simplified error reporting
-    if len(results) !=1:
-        log.error("Cannot find any suitable nemo output files in %s"
-                  % (nemo_path))
-        return ""
-    return results[0]
-
-# this function builds upon a combination of _get and save_nc functions from the out2nc.py tool originally by Michael
-#  Mischurow
-def add_nemo_variable(task, ncfile, nemo_var_name, nemo_var_freq):
-    # find nemo raw output file
-    nemo_ifile = find_nemo_file(nemo_var_name, nemo_var_freq)
-    if nemo_ifile == "":
-        log.error("NEMO variable %s needed for target %s in table %s was not found in nemo output... "
-                  % (nemo_var_name, task.target.variable, task.target.table))
-        return False
-
-    # define auxiliary and temp. files
-    nemo_maskfile = os.path.join(os.path.dirname(__file__), "resources", "nemo-mask-ece.nc")
-    nemo_ofile = os.path.join(ncpath_, "tmp_nemo.nc")
-    interm_file = os.path.join(ncpath_, "intermediate.nc")
-    if os.path.exists(nemo_ofile):
-        os.remove(nemo_ofile)
-    if os.path.exists(interm_file):
-        os.remove(interm_file)
-
-    # make sure the mask and input file have same dimensions
-    ds_maskfile = netCDF4.Dataset(nemo_maskfile, 'r')
-    ds_ifile = netCDF4.Dataset(nemo_ifile, 'r')
-    dims_maskfile = ds_maskfile.dimensions
-    dims_ofile = ds_ifile.dimensions
-    if dims_maskfile['x'].size != dims_ofile['x'].size or dims_maskfile['y'].size != dims_ofile['y'].size:
-            log.error("NEMO mask and output file, required for NEMO variable %s needed for target %s in table %s do not have same dimensions... "
-                      % (nemo_var_name, task.target.variable, task.target.table))
-            return False
-    ds_maskfile.close()
-    ds_ifile.close()
-
-    # perform the conservative remapping using cdo
-    #cdo -L selvar,${varname} ${ifile} tmp1.nc
-    #CDO_REMAP_NORM=destarea cdo -L invertlat -setmisstoc,0 -remapycon,n128 -selindexbox,2,361,2,292 -mul tmp1.nc $mask $ofile
-    log.info("Using the following cdo version for conservative remapping")
-    os.system("cdo -V")
-    os.system("cdo -L selvar,"+nemo_var_name+" "+nemo_ifile+" "+interm_file)
-    if target_grid_ == "T159":
-        remap_grid='n80'
-    elif target_grid_ == "T255":
-        remap_grid='n128'
-    else:
-        log.error("WRONG GRID %s in function add_nemo_variable in lpjg2cmor.py!" % target_grid_)
-        exit(-1)
-    os.system("CDO_REMAP_NORM=destarea cdo -L invertlat -setmisstoc,0 -remapycon,"+remap_grid+" -selindexbox,2,361,2,292 -mul "+interm_file+" "+nemo_maskfile+" "+nemo_ofile)
-
-    if not os.path.exists(nemo_ofile):
-        log.error("There was a problem remapping %s variable in nemo output file %s needed for %s in table %s... "
-                  % (nemo_var_name, nemo_ifile, task.target.variable, task.target.table))
-        return False
-
-    # add the nemo output to the lpjg output
-    if os.path.exists(interm_file):
-        os.remove(interm_file)
-    os.system("cdo -L add -selvar,"+task.target.variable+" "+ncfile+" "+nemo_ofile+" "+interm_file)
-    if not os.path.exists(interm_file):
-        log.error("There was a problem adding remapped %s variable from nemo output file %s to %s in table %s... "
-                  % (nemo_var_name, nemo_ifile, task.target.variable, task.target.table))
-        return False
-
-    # overwrite final ncfile and cleanup
-    os.remove(nemo_ofile)
-    shutil.move(interm_file, ncfile)
-
-    return True
-
 # Extracts single column from the .out-file
 def get_lpjg_datacolumn(df, freq, colname, months_as_cols):
     if freq == "day":