From b98703db8797e9024dfa193cc76ff07b4e4e4784 Mon Sep 17 00:00:00 2001
From: Roelofsen <hans.roelofsen@wur.nl>
Date: Mon, 5 Oct 2020 10:48:52 +0200
Subject: [PATCH] testing funtion to doren main class
---
doren_batch.sh | 2 +-
run_species.py | 1 +
utils/doren_classes.py | 22 +++++++++++++---------
3 files changed, 15 insertions(+), 10 deletions(-)
diff --git a/doren_batch.sh b/doren_batch.sh
index 03985e1..3f7e599 100644
--- a/doren_batch.sh
+++ b/doren_batch.sh
@@ -20,4 +20,4 @@ echo $SLURM_ARRAY_TASK_ID
# Run
cd /home/WUR/roelo008/projs/doren_2019
-python run_species.py $SLURM_ARRAY_TASK_ID 50 doren_20201001.pkl
\ No newline at end of file
+python run_species.py $SLURM_ARRAY_TASK_ID 50 doren_20201005.pkl
\ No newline at end of file
diff --git a/run_species.py b/run_species.py
index c8e7bc9..f660213 100644
--- a/run_species.py
+++ b/run_species.py
@@ -20,6 +20,7 @@ n_batches = int(args.n_batches)
# Recover the Pickled doren object
pkl_src = os.path.join('./pkl_src/', args.pkl)
+pkl_src = r'c:\Users\roelo008\OneDrive - WageningenUR\a_projects\DOREN\b_compiled_data\a_pkl\doren_20201001.pkl'
with open(pkl_src, 'rb') as handle:
doren = pickle.load(handle)
diff --git a/utils/doren_classes.py b/utils/doren_classes.py
index f4c50d5..6667e5d 100644
--- a/utils/doren_classes.py
+++ b/utils/doren_classes.py
@@ -310,7 +310,7 @@ class Doren:
self.eva['totN_kg_ha'] = self.eva.loc[:, 'totN_mg_m2'].divide(100)
self.eva['totN_mol_ha'] = self.eva.loc[:, 'totN_kg_ha'].divide(14)
- self.update_status()
+ self.update_status(covar=['totN_mg_m2', 'totN_kg_ha', 'totN_mol_ha'])
self.report += 'Added NDep from POSCH: {0} rows remaining.\n'.format(self.eva.shape[0])
def add_covar(self, covar_dir, covar_src, covar_name, nominal=False, keep_all=False, raster=True, **kwargs):
@@ -716,7 +716,11 @@ class Doren:
self.species = set(self.spec.species_name_hdr)
self.status.update(n_plots=self.eva.shape[0], columns=self.eva.columns.tolist(), n_species=len(self.species))
if covar:
- self.status['covars'] += covar
+ if not isinstance(covar, list):
+ covar_lst = [covar]
+ else:
+ covar_lst = covar
+ self.status['covars'] += covar_lst
def reset_species_sel(self):
# reset self.positive_plots and self.negative_plots
@@ -742,26 +746,26 @@ class Doren:
self.report += 'Testing dataset integrity\n'
# Check for NAs
- for check_col in self.status['covars'] + ['plot_id', 'country', 'year', 'veg_type', 'plot_coordinates_wgs84']:
+ for check_col in self.status['covars'] + ['plot_id', 'year', 'veg_type', 'plot_coordinates_wgs84']:
nas = self.eva.loc[:, check_col].isna()
if any(nas):
- msg = '{0} NA values found for {1} (index: {2})\n'.format(len(nas), check_col, self.eva.loc[nas].index)
+ msg = '{0} -- {1} NA values found (index: {2})\n'.format(check_col, sum(nas), self.eva.loc[nas].index)
else:
msg = '{0} -- no missing data\n'.format(check_col)
self.report += msg
-
# Check for invalid vals
earliest_yr, latest_yr = self.eva.year.min(), self.eva.year.max()
self.report += 'Plot years are between {0}-{1}\n'.format(earliest_yr, latest_yr)
- for check_col in [x for x in self.status['covars'] if not x.endswith('precip')]:
+ for check_col in [x for x in self.status['covars'] if not (x.endswith('precip') or
+ self.eva.loc[:, x].dtype.name == 'object')]:
sub_zeros = self.eva.loc[:, check_col] < 0
if any(sub_zeros):
- msg = '{0} NA values found for {1} (index: {2})\n'.format(len(sub_zeros), check_col,
- self.eva.loc[sub_zeros].index)
+ msg = '{0} values below 0 found for {1} (index: {2})\n'.format(sum(sub_zeros), check_col,
+ self.eva.loc[sub_zeros].index)
else:
- msg = '{0} -- all values > 0\n'
+ msg = '{0} -- all values > 0\n'.format(check_col)
self.report += msg
if self.eva.index.difference(set(self.spec.plot_obs_id)).empty:
--
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