VPRM inputs cleaning and doc

pycif/plugins/datastreams/fluxes/VPRM_nc/__init__.py

 """
-Write here the README about the plugin.
-Example of relevant information: type of files treated, including format of names and shape of data, time resolution, and any specific treatment that prevents the plugin from working with another type of files.
 
-Use rst syntax since this README will be automatically displayed in the documentation
+This module read VPRM netcdf daily files at hourly resolution
+It need corner file in the same directory as the flux files
 
 """
 
@@ -21,4 +20,13 @@ input_arguments = {
        "default": "let's say it's not mandatory",
        "accepted": str
     },
+    "corners_file": {
+       "doc": ""
+              "file of the corner coordinates"
+              "assumed in the same directory as data"
+              "",
+       "accepted": str,
+       "default": 'corners_5km'
+    }
+
 }

pycif/plugins/datastreams/fluxes/VPRM_nc/fetch.py

@@ -36,9 +36,6 @@ def fetch(ref_dir, ref_file, input_dates, target_dir, tracer=None, **kwargs):
 
         if os.path.isfile(files_3d[0]):
             list_dates[dd] = [[dd, dd + datetime.timedelta(hours=1)]]
-            #list_dates[dd] = [[dd + i*datetime.timedelta(hours=1) for i in range(24)]]
-            #list_files[dd]=[files_3d]*len(list_dates[dd])
-            #list_dates[dd] = [dates_3d]
             list_files[dd] = [files_3d]
 
             # the  to fetch is a forecast
@@ -47,6 +44,4 @@ def fetch(ref_dir, ref_file, input_dates, target_dir, tracer=None, **kwargs):
             path.link(files_3d[0], target_file)
             local_files.append(target_file)
 
-    info(list_files) 
-    info(list_dates)
     return list_files, list_dates

pycif/plugins/datastreams/fluxes/VPRM_nc/get_domain.py

@@ -20,7 +20,6 @@ def get_domain(ref_dir, ref_file, input_dates, target_dir, tracer=None):
 #---------
 # setup of the domain in section "Initializes domain"
 
-    print('Here, read the horizontal grid e.g. longitudes and latitudes')
     # Looking for a reference file to read lon/lat in
     list_file = glob.glob("{}/*nc".format(ref_dir))
 
@@ -45,8 +44,7 @@ def get_domain(ref_dir, ref_file, input_dates, target_dir, tracer=None):
         raise Exception(
             "VPRM domain could not be initialized as no file was found"
         )
-    print('Domain file for template fluxes:',domain_file)
-    print('Order the centers and corners latitudes and longitudes increasing order')
+    print('Domain file for VPRM fluxes:',domain_file)
 
     # Read lon/lat in
     nc = xr.open_dataset(domain_file, decode_times=False)
@@ -62,18 +60,13 @@ def get_domain(ref_dir, ref_file, input_dates, target_dir, tracer=None):
 
     nlon = lon.shape[1]
     nlat = lat.shape[0]
-    info("nlon : {}".format(nlon)) 
-    corner_file = "{}/{}".format(ref_dir, 'corners_5km.nc')
-    info(corner_file)
+    cornersf = tracer.corners_file
+    corner_file = "{}/{}".format(ref_dir, cornersf)
+    info('corner_file: {}'.format(corner_file))
     # Read lon/lat in corner_file
     nc = xr.open_dataset(corner_file, decode_times=False)
     lonc = nc["XLONG_C"].values[0,:,:]
     latc = nc["XLAT_C"].values[0,:,:]
-    info("nlonc : {}".format(lonc.shape[0]))
-    #print('Here, read the vertical information, from the same file as the horizontal information or from another')
-    #print('Get the number of vertical levels')
-    #print('Get or deduce the coefficients XXX et si on n\'est pas en sigma??XXX from bottom to top.')
-    #print('If no vetical dimension for emissions, provide dummy vertical')
     punit = "Pa"
     nlevs = 1
     sigma_a = np.array([0])
@@ -103,15 +96,12 @@ def get_domain(ref_dir, ref_file, input_dates, target_dir, tracer=None):
         }
     )
 
-    info('setup')
     Setup.load_setup(setup, level=1)
-    info('setup')
     # if lon and lat are vectors, convert into a grid with
     # zlon, zlat = np.meshgrid(lon, lat)
     setup.domain.zlon = lon   # longitudes of centers
     setup.domain.zlat = lat   # latitudes of centers
     setup.domain.zlonc = lonc # longitudes of corners
     setup.domain.zlatc = latc # latitudes of corners
-    info('endsetup')
 
     return setup.domain

pycif/plugins/datastreams/fluxes/VPRM_nc/read.py

@@ -6,7 +6,6 @@ import xarray as xr
 from netCDF4 import Dataset
 
 from .....utils.netcdf import readnc
-from logging import info
 
 def read(
         self,
@@ -19,32 +18,25 @@ def read(
         tracer=None,
         **kwargs
 ):
-    """Get fluxes from raw files and load them into a pyCIF
+    """Get fluxes from VPRM files and load them into a pyCIF
     variables
 
     """
     # list of the various fields read:
     data = []
-    info(dates)
-    info(files)
     outdate = []
     for dd, ff in zip(dates, files):
-        print('Here put the reading of ', [varnames],' in ',ff,' for ',dd)
+        print('Reading of ', [varnames],' in ',ff,' for ',dd)
         nc = xr.open_dataset(ff[0], decode_times=False) 
         read_field = nc[varnames][dd[0].hour].values
-        print('e.g. get a 3d array read_field')
         data.append(read_field)
         outdate.append(dd[0])
-    info("check")
-    info(dates)
-    info(len(data[0]))
-    info(np.array(data).shape)
+
     # if only one level for emissions, create the axis:
     xmod = xr.DataArray(
         np.array(data)[:, np.newaxis, ...],
         coords={"time": outdate},
         dims=("time", "lev", "lat", "lon"),
     )
-    info(xmod.shape)
 
     return xmod