From 71bb209a43deb8942c0aca0c5272d02fbf573e67 Mon Sep 17 00:00:00 2001
From: thopri <thopri@noc.ac.uk>
Date: Wed, 18 Mar 2020 14:38:08 +0000
Subject: [PATCH] added salinity check
---
pynemo/profile.py | 3 ++-
unit_tests/gen_tools.py | 12 ++++++------
unit_tests/test_gen.py | 4 +++-
unit_tests/unit_test.py | 20 ++++++++++----------
4 files changed, 21 insertions(+), 18 deletions(-)
diff --git a/pynemo/profile.py b/pynemo/profile.py
index 7931c68..9110828 100644
--- a/pynemo/profile.py
+++ b/pynemo/profile.py
@@ -505,7 +505,8 @@ def process_bdy(setup_filepath=0, mask_gui=False):
if settings['use_cmems'] == True:
logger.info('using CMEMS variable names......')
if ln_tra:
- var_in['t'].extend(['thetao']) # ,'so'])
+ var_in['t'].extend(['thetao'])
+ var_in['t'].extend(['so'])
if ln_dyn2d or ln_dyn3d:
var_in['u'].extend(['uo'])
diff --git a/unit_tests/gen_tools.py b/unit_tests/gen_tools.py
index b7ed9b9..6dddbf9 100644
--- a/unit_tests/gen_tools.py
+++ b/unit_tests/gen_tools.py
@@ -557,7 +557,6 @@ def write_parameter(fileout, grid_h,grid_z,params):
dataset.createDimension('z', nz)
dataset.createDimension('time', nt)
-
# Create Variables
longitude = dataset.createVariable('longitude', np.float32, ('y', 'x'))
latitude = dataset.createVariable('latitude', np.float32, ('y', 'x'))
@@ -577,11 +576,12 @@ def write_parameter(fileout, grid_h,grid_z,params):
latitude[:, :] = grid_h['latt'].T
depth[:] = grid_z['dept_1d']
time_counter[:] = np.linspace(587340.00,588060.00,31)
- parameter = dataset.createVariable(str(params['name']), np.float64, ('time','z', 'y', 'x'))
- parameter.units, parameter.long_name = str(params['units']), str(params['longname'])
- value_fill = np.ones(np.shape(grid_z['e3t']))
- value_fill = value_fill*params['const_value']
- parameter[:, :, :] = value_fill.T
+ for key in params:
+ parameter = dataset.createVariable(str(params[key]['name']), np.float64, ('time','z', 'y', 'x'))
+ parameter.units, parameter.long_name = str(params[key]['units']), str(params[key]['longname'])
+ value_fill = np.ones(np.shape(grid_z['e3t']))
+ value_fill = value_fill*params[key]['const_value']
+ parameter[:, :, :] = value_fill.T
# Close off pointer
dataset.close()
diff --git a/unit_tests/test_gen.py b/unit_tests/test_gen.py
index 8e8cd19..f7825cf 100644
--- a/unit_tests/test_gen.py
+++ b/unit_tests/test_gen.py
@@ -105,7 +105,9 @@ def _main():
# write boundary files (constant parameters)
out_fname = 'unit_tests/test_data/output_boundary_T.nc'
- params = {'name':'thetao','const_value':15.0,'longname':'temperature','units':'degreesC'}
+ params = {'param1': {'name':'thetao','const_value':15.0,'longname':'temperature','units':'degreesC'},
+ 'param2': {'name':'so','const_value':35.0,'longname':'salinity','units':'PSU'}
+ }
boundary = gt.write_parameter(out_fname,grid_h1,grid_z1,params)
if boundary == 0:
print('Success!')
diff --git a/unit_tests/unit_test.py b/unit_tests/unit_test.py
index c5d6784..7757c48 100644
--- a/unit_tests/unit_test.py
+++ b/unit_tests/unit_test.py
@@ -33,16 +33,16 @@ def test_temp():
assert abs(temp_[temp_ != 0.0].max() - 15) <= 0.001
assert abs(temp_[temp_ != 0.0].min() - 15) <= 0.001
-#def test_salinty():
-# test_files = glob.glob('unit_tests/test_outputs/unit_test*')
-# for t in test_files:
-# results = Dataset(t) # open results
-# sal = results['so'][:]
-# results.close()
-# sal_ = np.ma.masked_array(sal,sal == -32767.0)
-# assert abs(sal_[sal_!=0.0].mean() - 35) <= 0.001
-# assert abs(sal_[sal_ != 0.0].max() - 35) <= 0.001
-# assert abs(sal_[sal_ != 0.0].min() - 35) <= 0.001
+def test_salinty():
+ test_files = glob.glob('unit_tests/test_outputs/unit_test*')
+ for t in test_files:
+ results = Dataset(t) # open results
+ sal = results['so'][:]
+ results.close()
+ sal_ = np.ma.masked_array(sal,sal == -32767.0)
+ assert abs(sal_[sal_!=0.0].mean() - 35) <= 0.001
+ assert abs(sal_[sal_ != 0.0].max() - 35) <= 0.001
+ assert abs(sal_[sal_ != 0.0].min() - 35) <= 0.001
# clean up test I/O
files = glob.glob('unit_tests/test_outputs/*')
--
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