From d2fcff9b5f4eec71b6ed39c441fbe2e17e587ec1 Mon Sep 17 00:00:00 2001
From: "Woude, Auke van der" <auke.vanderwoude@wur.nl>
Date: Mon, 7 Nov 2022 16:53:51 +0100
Subject: [PATCH] Added functionality to write dictionaries to file; write GPP
and TER separately
---
da/preprocessing/classes.py | 33 +++++++++++++++++++++++++--------
da/preprocessing/upscale_bio.py | 11 +++++++++--
2 files changed, 34 insertions(+), 10 deletions(-)
diff --git a/da/preprocessing/classes.py b/da/preprocessing/classes.py
index d255fc28..c789b11b 100644
--- a/da/preprocessing/classes.py
+++ b/da/preprocessing/classes.py
@@ -35,9 +35,18 @@ class Regional(object):
self.name = 'Here goes the flux name' # Overwrite in the subclasses
- def create_filename(self):
+ def create_filename(self, change_name=None, outdir=None):
"""Create the filename for a regional file"""
- return '{0}/regional.{1}.nc'.format(self.dacycle['dir.output'], self.name)
+ # Add possibility to write to a different file than self.name
+ if change_name is None:
+ name = self.name
+ else:
+ name = change_name
+
+ if outdir is None:
+ outdir = self.dacycle['dir.output']
+
+ return '{0}/regional.{1}.nc'.format(outdir, name)
def get_filenames(self):
"""Get all filenames for the current month"""
@@ -125,9 +134,12 @@ class Regional(object):
A[iy, :] = Alat
return A # m2
- def write(self, values, varname=None):
+ def write(self, values, varname=None, filename=None, outdir=None):
# Write the biosphere fluxes to a file
- filename = self.create_filename()
+ if outdir is None:
+ outdir = self.dacycle['dir.output']
+ filename = self.create_filename(change_name=filename, outdir=outdir)
+
logging.debug('Writing fluxes to file {}'.format(filename))
if varname is None:
@@ -143,8 +155,8 @@ class Regional(object):
values = np.nan_to_num(values)
# Only make the file if this is the first variable to put there
if i == 0:
- if not os.path.exists(self.dacycle['dir.output']):
- os.mkdir(self.dacycle['dir.output'])
+ if not os.path.exists(outdir):
+ os.mkdir(outdir)
with io.CT_CDF(filename, method='create') as f:
dimtime, dimlat, dimlon = f.add_dimensions(self.times, self.lats, self.lons)
@@ -196,9 +208,14 @@ class Global(Regional):
dtstart=self.startdate, until=self.enddate)) # rrule includes until
self.times = times
- def create_filename(self):
+ def create_filename(self, change_name=None):
"""Create the filename for a regional file"""
- return '{0}/global.{1}_{2:%Y%m}.nc'.format(self.dacycle['dir.output'], self.name, self.dacycle['time.start'])
+ # Add possibility to write to a different file than self.name
+ if change_name is None:
+ name = self.name
+ else:
+ name = change_name
+ return '{0}/global.{1}_{2:%Y%m}.nc'.format(self.dacycle['dir.output'], name, self.dacycle['time.start'])
def combine_with_regional(self):
"""Combine the high resolution with global fluxes
diff --git a/da/preprocessing/upscale_bio.py b/da/preprocessing/upscale_bio.py
index 7a3d7190..a7726575 100644
--- a/da/preprocessing/upscale_bio.py
+++ b/da/preprocessing/upscale_bio.py
@@ -33,12 +33,17 @@ class SiBUpscaler(Regional):
self.sibfile = self.sibdir + sibfile
self.sibfile_avg = self.sibfile.replace('lu.qp3', 'g.qp2')
logging.debug('Reading SiB data from {}'.format(self.sibfile))
+ # Write GPP and TER
datadict = {}
- for v in ('nee', 'resp_tot', 'assim'):
+ for v in ('resp_tot', 'assim'):
logging.info(f'Getting high-res {v}')
data = self.load_biosphere_emissions(v)
datadict[v] = data
- outfile = self.write(datadict)
+ outfile = self.write(datadict, filename='bio')
+
+ # Write NEP seperately
+ data = self.load_biosphere_emissions('nee')
+ outfile = self.write(data)
return outfile, self.name
def load_biosphere_emissions(self, fluxname):
@@ -93,6 +98,8 @@ class SiBUpscaler(Regional):
fluxname = 'reco'
elif fluxname == 'assim':
fluxname = 'gpp'
+ elif fluxname == 'nee':
+ fluxname == 'nep'
nee_averaged = ds[fluxname]
nee_averaged = nee_averaged[startindex:stopindex, :].astype(np.float32)
nee_averaged = np.flip(st.convert_2d(nee_averaged, latsib, lonsib), axis=-2)
--
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