def setUp(self):
self.data1 = egads.EgadsData(value=[0.5, 2.3, 6.2, 8.1, 4.],
units='mm',
long_name='a common data',
scale_factor=1.,
_FillValue=-999)
self.data2 = egads.EgadsData(value=[0., 1., 2., 3., 4.],
units='days since 20170101 00:00:00Z',
long_name='a common time vector',
scale_factor=1.,
_FillValue=-999)
self.ncfilename = tempfile.mktemp('.nc')
self.nafilename = tempfile.mktemp('.na')
self.csvfilename = tempfile.mktemp('.csv')
f = einput.EgadsNetCdf(self.ncfilename, 'w')
f.add_attribute('Conventions', 'CF-1.0')
f.add_attribute('history', 'the netcdf file has been created by EGADS')
f.add_attribute('comments', 'no comments on the netcdf file')
f.add_attribute('institution', 'EUFAR')
f.add_attribute('source', 'computer')
f.add_attribute('title', 'a test file')
f.add_attribute('authors', 'John Doe ([email protected])')
f.add_dim('time', len(self.data2))
f.write_variable(self.data2, 'time', ('time', ), 'double')
f.write_variable(self.data1, 'data', ('time', ), 'double')
f.add_attribute('long_name', self.data1.metadata['long_name'], 'data')
f.add_attribute('units', self.data1.metadata['units'], 'data')
f.add_attribute('scale_factor', self.data1.metadata['scale_factor'],
'data')
f.add_attribute('units', self.data2.metadata['units'], 'time')
f.add_attribute('long_name', self.data2.metadata['long_name'], 'time')
f.add_attribute('scale_factor', self.data2.metadata['scale_factor'],
'time')
f.close()
def test_convert_na_to_nc(self):
""" Test conversion of NASA Ames to NetCDF"""
f = einput.NasaAmes(self.na_filename)
f.convert_to_netcdf(self.nc_filename)
g = einput.EgadsNetCdf(self.nc_filename, 'r')
author = g.get_attribute_value('authors')
special_com = g.get_attribute_value('special_comments')
time = g.read_variable('Time_np')
self.assertEqual(self.authors, author,
'Originator values do not match')
self.assertEqual(self.special_com, special_com,
'Special comments do not match')
self.assertListEqual(time.value.tolist(), time.value.tolist(),
'both time values do not match')
def test_convert_nc_to_na_egadsnetcdf(self):
""" Test conversion of NetCDF to NASA Ames, using the EgadsNetCdf class """
f = einput.EgadsNetCdf(self.ncfilename)
f.convert_to_nasa_ames(self.nafilename)
f.close()
g = einput.NasaAmes(self.nafilename)
self.assertEqual('John Doe ([email protected])',
g.file_metadata['Originator'],
'Originator values do not match')
self.assertEqual('computer', g.file_metadata['Source'],
'Source values do not match')
data = g.read_variable('data')
self.assertListEqual(self.data1.value.tolist(), data.value.tolist(),
'data and data1 values do not match')
g.close()
def test_read_n6sp_data(self):
""" Test reading in data using N6SP formatted NetCDF """
infile = einput.EgadsNetCdf(self.file)
self.assertEqual(infile.file_metadata['title'], TITLE,
'NetCDF title attribute doesnt match')
data = infile.read_variable(VAR_NAME)
assert_array_equal(data.value, random_data)
self.assertEqual(data.units, VAR_UNITS,
'EgadsData units attribute doesnt match')
self.assertEqual(data.metadata['units'], VAR_UNITS,
'EgadsData units attribute doesnt match')
self.assertEqual(data.metadata['long_name'], VAR_LONG_NAME,
'EgadsData long name attribute doesnt match')
self.assertEqual(data.metadata['standard_name'], VAR_STD_NAME,
'EgadsData standard name attribute doesnt match')
infile.close()
def test_egadsnetcdf_instance_creation(self):
""" Test creation of a netcdf file via the EgadsNetCdf class """
filename = tempfile.mktemp('.nc')
g = einput.EgadsNetCdf(filename, 'w')
g.add_dim('time', len(self.data2))
g.write_variable(self.data2, 'time', ('time', ), 'double')
g.write_variable(self.data1, 'data', ('time', ), 'double')
g.close()
f = netCDF4.Dataset(filename, 'r') # @UndefinedVariable
varin = f.variables['data']
self.assertEqual(varin.shape[0], len(self.data2),
'Variable dimensions dont match')
self.assertEqual(varin.scale_factor, 1.0,
'Variable scale factor dont match')
self.assertEqual(varin.long_name, 'a common data',
'Variable long name dont match')
f.close()
def netcdf_reading(self):
logging.debug(
'gui - reading_functions.py - netcdf_reading: open_file_name ' +
str(self.open_file_name))
clear_gui(self)
self.opened_file = input.EgadsNetCdf(self.open_file_name, 'a')
list_of_variables = sorted(self.opened_file.get_variable_list())
self.list_of_global_attributes = self.opened_file.get_attribute_list()
self.list_of_dimensions = self.opened_file.get_dimension_list()
add_global_attributes_to_buttons(self)
for var in list_of_variables:
dimensions = self.opened_file.get_dimension_list(str(var))
list_of_var_attributes = self.opened_file.get_attribute_list(str(var))
list_of_var_attributes['var_name'] = str(var)
list_of_var_attributes = add_correct_units(self,
list_of_var_attributes)
try:
egads_instance = self.opened_file.read_variable(var)
self.list_of_variables_and_attributes[var] = [
var, list_of_var_attributes, dimensions, egads_instance
]
except Exception:
self.list_of_unread_variables.append(var)
logging.exception(
'gui - reading_functions.py - : an error occured during the re'
+ 'ading of a variable, variable ' + str(var))
update_compatibility_label(self)
out_file_base, out_file_ext = ntpath.splitext(
ntpath.basename(self.open_file_name))
read_set_attribute_gui(self, self.gm_filename_ln,
out_file_base + out_file_ext)
update_global_attribute_gui(self, 'NetCDF')
self.listWidget.addItems(list_of_variables)
self.listWidget.itemClicked.connect(lambda: var_reading(self))
self.tabWidget.currentChanged.connect(lambda: update_icons_state(self))
all_buttons = self.tabWidget.findChildren(QtWidgets.QToolButton)
for widget in all_buttons:
if widget.objectName() != '' and widget.objectName() != 'gm_button_7':
widget.clicked.connect(lambda: modify_attribute_gui(self, 'left'))
widget.rightClick.connect(
lambda: modify_attribute_gui(self, 'right'))
logging.debug(
'gui - reading_functions.py - netcdf_reading: netcdf file loaded')
def test_convert_nc_to_csv_egadsnetcdf(self):
""" Test conversion of NetCDF to Nasa/Ames CSV, using the EgadsNetCdf class """
f = einput.EgadsNetCdf(self.ncfilename)
f.convert_to_csv(self.csvfilename)
f.close()
g = einput.EgadsCsv()
g.open(self.csvfilename, 'r')
lines = g.read()
author = lines[1][0]
computer = lines[3][0]
raw = lines[-5:]
time = []
data = []
for i in raw:
time.append(float(i[0]))
data.append(float(i[1]))
self.assertEqual('John Doe ([email protected])', author,
'Originator values do not match')
self.assertEqual('computer', computer, 'Source values do not match')
self.assertListEqual(self.data1.value.tolist(), data,
'data and data1 values do not match')
self.assertListEqual(self.data2.value.tolist(), time,
'time and data2 values do not match')