def test_nonsparse_zvariable_blocking(self):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Block_Factor'] = 10000
data = np.linspace(0, 999999, num=1000000)
self.test_file.write_var(var_spec, var_data=data)
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
var = self.test_file_reader.varget("Variable1")
self.assertEqual(var[99999], 99999)
# Close the reading file
self.test_file_reader.close()
def test_sparse_zvariable_previous(self):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Sparse'] = 'prev_sparse'
data = [[200, 3000, 3100, 3500, 4000, 5000, 6000, 10000, 10001, 10002, 20000],
np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])]
self.test_file.write_var(var_spec, var_data=data)
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
varinq = self.test_file_reader.varinq("Variable1")
var = self.test_file_reader.varget("Variable1")
pad_num = varinq['Pad'][0]
self.assertEqual(var[100], pad_num)
self.assertEqual(var[6001], var[6000])
# Close the reading file
self.test_file_reader.close()
def cdf_to_ds(cdf_file, cdf_vars):
'''
Read variables from CDF files into an XArray DataSet
Parameters
----------
cdf_file : str
Name of the CDF file to read
cdf_vars : str or list
Names of the variables to read
Returns
-------
out : `xarray.DataSet`
The data.
'''
if not isinstance(cdf_file, str):
raise ValueError('cdf_file must be a string or path.')
if isinstance(cdf_vars, str):
cdf_vars = [cdf_vars]
cdf = cdfread.CDF(cdf_file)
ds = xr.Dataset()
variables = []
for varname in cdf_vars:
ds = ds.assign({varname: cdf_load_var(cdf, varname)})
return ds
def test_create_2d_rvariable_dimvary(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Var_Type'] = 'rvariable'
var_spec['Data_Type'] = 21
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Dim_Vary'] = [True, False]
tfile = cdf_create(fnbasic, {'rDim_sizes': [2, 20]})
tfile.write_var(var_spec,
var_data=np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8,
9]]))
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
varinfo = reader.varinq("Variable1")
assert varinfo['Data_Type'] == 21
var = reader.varget("Variable1")
for x in [0, 1, 2, 3, 4]:
assert var[x][0] == 2 * x
assert var[x][1] == 2 * x + 1
def test_checksum(cdf_create):
# Setup the test_file
tfile = cdf_create(fncsum, {'Checksum': True})
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 4
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
varatts = {}
varatts['Attribute1'] = 1
varatts['Attribute2'] = '500'
tfile.write_var(var_spec,
var_attrs=varatts,
var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
tfile.close()
# %% Open the file to read
reader = cdfread.CDF(fncsum, validate=True)
# Test CDF info
var = reader.varget("Variable1")
assert (var == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]).all()
def test_create_zvariables_then_attributes(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
tfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
tfile.write_var(var_spec,
var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
var_spec['Variable'] = 'Variable2'
tfile.write_var(var_spec,
var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
varatts = {}
varatts['Attribute1'] = {'Variable1': 1, 'Variable2': 2}
varatts['Attribute2'] = {0: '500', 1: '1000'}
tfile.write_variableattrs(varatts)
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
att = reader.attget("Attribute1", entry=0)
assert att['Data'] == [1]
att = reader.attget("Attribute2", entry=1)
att['Data'] == '1000'
def test_sparse_zvariable_blocking(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Block_Factor'] = 10000
var_spec['Sparse'] = 'pad_sparse'
data = np.linspace(0, 99999, num=100000)
physical_records1 = np.linspace(1, 10000, num=10000)
physical_records2 = np.linspace(20001, 30000, num=10000)
physical_records3 = np.linspace(50001, 60000, num=10000)
physical_records4 = np.linspace(70001, 140000, num=70000)
physical_records = np.concatenate(
(physical_records1, physical_records2, physical_records3,
physical_records4)).astype(int)
sparse_data = [physical_records, data]
tfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
tfile.write_var(var_spec, var_data=sparse_data)
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF infotfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
varinq = reader.varinq("Variable1")
var = reader.varget("Variable1")
pad_num = varinq['Pad'][0]
assert var[30001] == pad_num
assert var[70001] == 30000
def test_checksum_compressed(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 2
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
varatts = {}
varatts['Attribute1'] = 1
varatts['Attribute2'] = '500'
v = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
tfile = cdf_create(fncomp, {'Compressed': 6, 'Checksum': True})
tfile.write_var(var_spec, var_attrs=varatts, var_data=v)
tfile.close()
# %% Open the file to read
reader = cdfread.CDF(fncomp, validate=True)
var = reader.varget("Variable1")
assert (var == v).all()
att = reader.attget("Attribute1", entry=0)
assert att['Data'] == [1]
att = reader.attget("Attribute2", entry=0)
assert att['Data'] == '500'
def test_globalattrs(self):
# Setup the test_file
globalAttrs = {}
globalAttrs['Global1'] = {0: 'Global Value 1'}
globalAttrs['Global2'] = {0: 'Global Value 2'}
globalAttrs['Global3'] = {0: [12, 'cdf_int4']}
globalAttrs['Global4'] = {0: [12.34, 'cdf_double']}
globalAttrs['Global5'] = {0: [12.34, 21.43]}
GA6 = {}
GA6[0] = 'abcd'
GA6[1] = [12, 'cdf_int2']
GA6[2] = [12.5, 'cdf_float']
GA6[3] = [[0, 1, 2], 'cdf_int8']
globalAttrs['Global6'] = GA6
self.test_file.write_globalattrs(globalAttrs)
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
attrib = self.test_file_reader.attinq('Global2')
self.assertEqual(attrib['num_gr_entry'], 1)
attrib = self.test_file_reader.attinq('Global6')
self.assertEqual(attrib['num_gr_entry'], 4)
entry = self.test_file_reader.attget('Global6', 3)
self.assertEqual(entry['Data_Type'], 'CDF_INT8')
for x in [0, 1, 2]:
self.assertEqual(entry['Data'][x], x)
# Close the reading file
self.test_file_reader.close()
def test_create_zvariable(self):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 1
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Dim_Vary'] = True
self.test_file.write_var(var_spec, var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
varinfo = self.test_file_reader.varinq("Variable1")
self.assertEqual(varinfo['Data_Type'], 1)
var = self.test_file_reader.varget("Variable1")
for x in [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]:
self.assertEqual(var[x], x)
# Close the reading file
self.test_file_reader.close()
def test_sparse_zvariable_previous(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Sparse'] = 'prev_sparse'
data = [[
200, 3000, 3100, 3500, 4000, 5000, 6000, 10000, 10001, 10002, 20000
],
np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])]
tfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
tfile.write_var(var_spec, var_data=data)
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
varinq = reader.varinq("Variable1")
var = reader.varget("Variable1")
pad_num = varinq['Pad'][0]
assert var[100] == pad_num
assert var[6001] == var[6000]
def test_checksum_compressed(self):
# Setup the test_file
cdf_spec = {'Compressed': 6, 'Checksum': True}
self.checksum_test_file = cdfwrite.CDF(os.path.dirname(__file__) +
"/testfiles/testing_checksum.cdf",
cdf_spec=cdf_spec)
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
varatts = {}
varatts['Attribute1'] = 1
varatts['Attribute2'] = '500'
self.checksum_test_file.write_var(var_spec, var_attrs=varatts,
var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
# Close the file so we can read
self.checksum_test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing_checksum.cdf",
validate=True)
# Test CDF info
var = self.test_file_reader.varget("Variable1")
for x in [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]:
self.assertEqual(var[x], x)
# Close the reading file
self.test_file_reader.close()
def test_create_rvariable(cdf_create):
# Setup the test_file
vs = {}
vs['Variable'] = 'Variable1'
vs['Var_Type'] = 'rvariable'
vs['Data_Type'] = 12
vs['Num_Elements'] = 1
vs['Rec_Vary'] = True
vs['Dim_Sizes'] = []
vs['Dim_Vary'] = [True]
tfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
tfile.write_var(vs, var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
varinfo = reader.varinq("Variable1")
assert varinfo['Data_Type'] == 12
var = reader.varget("Variable1")
for x in [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]:
assert var[x] == x
def test_create_zvariables_then_attributes(self):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
self.test_file.write_var(var_spec, var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
var_spec['Variable'] = 'Variable2'
self.test_file.write_var(var_spec, var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
varatts = {}
varatts['Attribute1'] = {'Variable1': 1, 'Variable2': 2}
varatts['Attribute2'] = {0: '500', 1: '1000'}
self.test_file.write_variableattrs(varatts)
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
att = self.test_file_reader.attget("Attribute1", entry=0)
self.assertEqual(att['Data'], [1])
att = self.test_file_reader.attget("Attribute2", entry=1)
self.assertEqual(att['Data'], '1000')
# Close the reading file
self.test_file_reader.close()
def test_cdf_creation(cdf_create):
cdf_create(fnbasic, {'rDim_sizes': [1]}).close()
reader = cdfread.CDF(fnbasic)
# Test CDF info
info = reader.cdf_info()
assert info['Majority'] == 'Column_major'
def test_create_2d_r_and_z_variables(self):
# Create a new test_file
self.test_file.close()
os.remove(os.path.dirname(__file__)+"/testfiles/testing.cdf")
cdf_spec = {'rDim_sizes': [2, 20]}
self.test_file = cdfwrite.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf",
cdf_spec=cdf_spec)
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Var_Type'] = 'rvariable'
var_spec['Data_Type'] = 22
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Dim_Vary'] = [True, False]
self.test_file.write_var(var_spec, var_data=np.array([[0, 1],
[2, 3],
[4, 5],
[6, 7],
[8, 9]]))
var_spec['Variable'] = 'Variable2'
var_spec['Var_Type'] = 'zvariable'
varatts = {}
varatts['Attribute1'] = 2
varatts['Attribute2'] = '1000'
self.test_file.write_var(var_spec, var_attrs=varatts,
var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
varinfo = self.test_file_reader.varinq("Variable1")
self.assertEqual(varinfo['Data_Type'], 22)
var = self.test_file_reader.varget("Variable1")
for x in [0, 1, 2, 3, 4]:
self.assertEqual(var[x][0], 2*x)
self.assertEqual(var[x][1], 2*x+1)
var = self.test_file_reader.varget("Variable2")
for x in [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]:
self.assertEqual(var[x], x)
att = self.test_file_reader.attget("Attribute1", entry='Variable2')
self.assertEqual(att['Data'], [2])
att = self.test_file_reader.attget("Attribute2", entry='Variable2')
self.assertEqual(att['Data'], '1000')
# Close the reading file
self.test_file_reader.close()
def cdf_to_ds(filename, variables=None, varformat=None, data_vars=True):
'''
Read variables from CDF files into an XArray DataSet
Parameters
----------
filename : str
Name of the CDF file to read
variables : str or list
Names of the variables to read or a pattern by which to match
variable names. If not given, all variables will be read
varformat : str or list
Regular expression(s) used to match variable names. Mutually
exclusive with `variables`.
data_vars : bool
Read only those variables with VAR_TYPE of "data". Ignored if
`variables` is given.
Returns
-------
ds : `xarray.Dataset`
The data.
'''
if not isinstance(filename, str):
raise ValueError('cdf_file must be a string or path.')
if isinstance(variables, str):
variables = [variables]
if isinstance(varformat, str):
varformat = [varformat]
# Open the CDF file
cdf = cdfread.CDF(filename)
# Match regular expression(s)
if variables is not None:
varnames = variables
elif varformat is not None:
all_variables = cdf_varnames(cdf, data_vars=data_vars)
varnames = []
for fmt in varformat:
varnames =+ [v for v in all_variables if re.match(fmt, v)]
# Select all (data) variables
else:
varnames = cdf_varnames(cdf, data_vars=data_vars)
# Read the data
ds = xr.Dataset()
variables = []
for varname in varnames:
ds = ds.assign({varname: cdf_load_var(cdf, varname)})
# Grab the global attributes from the data file
ds.attrs['filename'] = filename
ds.attrs.update(cdf.globalattsget())
return ds
def cdf_to_ds(filename, variables=None, varformat=None, data_vars=True):
'''
Read variables from CDF files into an XArray DataSet
Parameters
----------
filename : str
Name of the CDF file to read
variables : str or list
Names of the variables to read or a pattern by which to match
variable names. If not given, all variables will be read
varformat : str or list
Regular expression(s) used to match variable names. Mutually
exclusive with `variables`.
data_vars : bool
Read only those variables with VAR_TYPE of "data". Ignored if
`variables` is given.
Returns
-------
ds : `xarray.Dataset`
The data.
'''
global cdf_vars_read
cdf_vars_read = {}
if not isinstance(filename, str):
raise ValueError('cdf_file must be a string or path.')
if isinstance(variables, str):
variables = [variables]
if isinstance(varformat, str):
varformat = [varformat]
# Open the CDF file
cdf = cdfread.CDF(filename)
varnames = check_variables(cdf, variables, varformat, data_vars)
# Read the data
for varname in varnames:
cdf_load_var(cdf, varname)
cdf.close()
# Create the dataset
ds = xr.Dataset(cdf_vars_read)
# Grab the global attributes from the data file
ds.attrs['filename'] = filename
ds.attrs.update(cdf.globalattsget())
return ds
def test_cdf_creation(self):
# Setup the test_file
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
test_file_info = self.test_file_reader.cdf_info()
self.assertEqual(test_file_info['Majority'], 'Column_major')
# Close the reading file
self.test_file_reader.close()
def test_create_2d_r_and_z_variables(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Var_Type'] = 'rvariable'
var_spec['Data_Type'] = 22
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Dim_Vary'] = [True, False]
tfile = cdf_create(fnbasic, {'rDim_sizes': [2, 20]})
tfile.write_var(var_spec,
var_data=np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8,
9]]))
var_spec['Variable'] = 'Variable2'
var_spec['Var_Type'] = 'zvariable'
varatts = {}
varatts['Attribute1'] = 2
varatts['Attribute2'] = '1000'
tfile.write_var(var_spec,
var_attrs=varatts,
var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
varinfo = reader.varinq("Variable1")
assert varinfo['Data_Type'] == 22
var = reader.varget("Variable1")
for x in [0, 1, 2, 3, 4]:
assert var[x][0] == 2 * x
assert var[x][1] == 2 * x + 1
var = reader.varget("Variable2")
assert (var == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]).all()
att = reader.attget("Attribute1", entry='Variable2')
assert att['Data'] == [2]
att = reader.attget("Attribute2", entry='Variable2')
assert att['Data'] == '1000'
def test_create_2d_rvariable(self):
# Create a new test_file
self.test_file.close()
os.remove(os.path.dirname(__file__)+"/testfiles/testing.cdf")
cdf_spec = {'rDim_sizes': [2, 2]}
self.test_file = cdfwrite.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf", cdf_spec=cdf_spec)
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Var_Type'] = 'rvariable'
var_spec['Data_Type'] = 14
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Dim_Vary'] = [True, True]
self.test_file.write_var(var_spec, var_data=np.array([[[0, 1], [1, 2]],
[[2, 3], [3, 4]],
[[4, 5], [5, 6]],
[[6, 7], [7, 8]],
[[8, 9], [9, 10]]]))
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
varinfo = self.test_file_reader.varinq("Variable1")
self.assertEqual(varinfo['Data_Type'], 14)
var = self.test_file_reader.varget("Variable1")
for x in [0, 1, 2, 3, 4]:
self.assertEqual(var[x][0][0], 2*x)
self.assertEqual(var[x][0][1], 2*x+1)
self.assertEqual(var[x][1][0], 2*x+1)
self.assertEqual(var[x][1][1], 2*x+2)
# Close the reading file
self.test_file_reader.close()
def test_nonsparse_zvariable_blocking(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Block_Factor'] = 10000
data = np.linspace(0, 999999, num=1000000)
tfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
tfile.write_var(var_spec, var_data=data)
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
var = reader.varget("Variable1")
assert var[99999] == 99999
def test_sparse_virtual_zvariable_blocking(self):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
var_spec['Block_Factor'] = 10000
var_spec['Sparse'] = 'pad_sparse'
data = np.linspace(0, 140000, num=140001)
physical_records1 = np.linspace(1, 10000, num=10000)
physical_records2 = np.linspace(20001, 30000, num=10000)
physical_records3 = np.linspace(50001, 60000, num=10000)
physical_records4 = np.linspace(70001, 140000, num=70000)
physical_records = np.concatenate((physical_records1,
physical_records2,
physical_records3,
physical_records4)).astype(int)
sparse_data = [physical_records, data]
self.test_file.write_var(var_spec, var_data=sparse_data)
# Close the file so we can read
self.test_file.close()
# Open the file to read
self.test_file_reader = cdfread.CDF(os.path.dirname(__file__) +
"/testfiles/testing.cdf")
# Test CDF info
varinq = self.test_file_reader.varinq("Variable1")
var = self.test_file_reader.varget("Variable1")
pad_num = varinq['Pad'][0]
self.assertEqual(var[30001], pad_num)
self.assertEqual(var[70001], 70001)
# Close the reading file
self.test_file_reader.close()
def test_create_zvariable_no_recvory(cdf_create):
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 8
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = False
var_spec['Dim_Sizes'] = []
var_spec['Dim_Vary'] = True
tfile = cdf_create(fnbasic, {'rDim_sizes': [1]})
tfile.write_var(var_spec, var_data=np.array([2]))
tfile.close()
# Open the file to read
reader = cdfread.CDF(fnbasic)
# Test CDF info
varinfo = reader.varinq("Variable1")
assert varinfo['Data_Type'] == 8
var = reader.varget("Variable1")
assert var == 2
def test_create_zvariable(cdf_create):
# Setup the test_file
vs = {}
vs['Variable'] = 'Variable1'
vs['Data_Type'] = 1
vs['Num_Elements'] = 1
vs['Rec_Vary'] = True
vs['Dim_Sizes'] = []
vs['Dim_Vary'] = True
tfile = cdf_create(fncsum, {'Checksum': True})
tfile.write_var(vs, var_data=np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]))
tfile.close()
# %% Open the file to read
reader = cdfread.CDF(fncsum)
# Test CDF info
varinfo = reader.varinq("Variable1")
assert varinfo['Data_Type'] == 1
var = reader.varget("Variable1")
assert (var == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]).all()
def test_file_compression():
# Setup the test_file
var_spec = {}
var_spec['Variable'] = 'Variable1'
var_spec['Data_Type'] = 2
var_spec['Num_Elements'] = 1
var_spec['Rec_Vary'] = True
var_spec['Dim_Sizes'] = []
varatts = {}
varatts['Attribute1'] = 1
varatts['Attribute2'] = '500'
v = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
tfile = cdf_create(fncomp, {'Compressed': 6, 'Checksum': True})
tfile.write_var(var_spec, var_attrs=varatts, var_data=v)
tfile.close()
# Open the file to read
reader = cdfread.CDF(fncomp)
# Test CDF info
var = reader.varget("Variable1")
assert (var == v).all()
def test_globalattrs(cdf_create):
# Setup the test_file
globalAttrs = {}
globalAttrs['Global1'] = {0: 'Global Value 1'}
globalAttrs['Global2'] = {0: 'Global Value 2'}
globalAttrs['Global3'] = {0: [12, 'cdf_int4']}
globalAttrs['Global4'] = {0: [12.34, 'cdf_double']}
globalAttrs['Global5'] = {0: [12.34, 21.43]}
GA6 = {}
GA6[0] = 'abcd'
GA6[1] = [12, 'cdf_int2']
GA6[2] = [12.5, 'cdf_float']
GA6[3] = [[0, 1, 2], 'cdf_int8']
globalAttrs['Global6'] = GA6
tfile = cdf_create(fncsum, {'Checksum': True})
tfile.write_globalattrs(globalAttrs)
tfile.close()
# %% Open the file to read
reader = cdfread.CDF(fncsum)
# Test CDF info
attrib = reader.attinq('Global2')
assert attrib['num_gr_entry'] == 1
attrib = reader.attinq('Global6')
assert attrib['num_gr_entry'] == 4
entry = reader.attget('Global6', 3)
assert entry['Data_Type'] == 'CDF_INT8'
for x in [0, 1, 2]:
assert entry['Data'][x] == x
def cdf_read(fn: Path, validate: bool = False):
return cdfread.CDF(fn, validate=validate)
def cdf_read(fn: Path, validate: bool = False):
# str(fn) is a Python==3.5 workaround
return cdfread.CDF(str(fn), validate=validate)
def cdf_to_df(cdf_files, cdf_vars, epoch='Epoch'):
'''
Read variables from CDF files into a dataframe
Parameters
----------
cdf_files : str or list
CDF files to be read
cdf_vars : str or list
Names of the variables to be read
epoch : str
Name of the time variable that serves as the data frame index
Returns
-------
out : `pandas.DataFrame`
The data. If a variable is 2D, "_#" is appended, where "#"
increases from 0 to var.shape[1]-1.
'''
tepoch = epochs.CDFepoch()
if isinstance(cdf_files, str):
cdf_files = [cdf_files]
if isinstance(cdf_vars, str):
cdf_vars = [cdf_vars]
if epoch not in cdf_vars:
cdf_vars.append(epoch)
out = []
for file in cdf_files:
file_df = pd.DataFrame()
cdf = cdfread.CDF(file)
for var_name in cdf_vars:
# Read the variable data
data = cdf.varget(var_name)
if var_name == epoch:
data = tepoch.to_datetime(data, to_np=True)
# Store as column in data frame
if data.ndim == 1:
file_df[var_name] = data
# 2D variables get "_#" appended to name for each column
elif data.ndim == 2:
for idx in range(data.shape[1]):
file_df['{0}_{1}'.format(var_name, idx)] = data[:, idx]
# 3D variables gets reshaped to 2D and treated as 2D
# This includes variables like the pressure and temperature tensors
elif data.ndim == 3:
dims = data.shape
data = data.reshape(dims[0], dims[1] * dims[2])
for idx in range(data.shape[1]):
file_df['{0}_{1}'.format(var_name, idx)] = data[:, idx]
else:
print('cdf_var.ndims > 3. Skipping. {0}'.format(var_name))
continue
# Close the file
cdf.close()
# Set the epoch variable as the index
file_df.set_index(epoch, inplace=True)
out.append(file_df)
# Concatenate all of the file data
out = pd.concat(out)
# Check that the index is unique
# Some contiguous low-level data files have data overlap at the edges of the files (e.g., AFG)
if not out.index.is_unique:
out['index'] = out.index
out.drop_duplicates(subset='index', inplace=True, keep='first')
out.drop(columns='index', inplace=True)
# File names are not always given in order, so sort the data
out.sort_index(inplace=True)
return out