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tst_atts.py
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tst_atts.py
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import math
import subprocess
import sys
import unittest
import os
import tempfile
import warnings
import numpy as NP
from numpy.random.mtrand import uniform
import netCDF4
try:
from collections import OrderedDict
except ImportError: # or else use drop-in substitute
from ordereddict import OrderedDict
# test attribute creation.
FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
VAR_NAME="dummy_var"
GROUP_NAME = "dummy_group"
DIM1_NAME="x"
DIM1_LEN=2
DIM2_NAME="y"
DIM2_LEN=3
DIM3_NAME="z"
DIM3_LEN=25
STRATT = 'string attribute'
EMPTYSTRATT = ''
INTATT = 1
FLOATATT = math.pi
SEQATT = NP.arange(10)
STRINGSEQATT = ['mary ','','had ','a ','little ','lamb',]
#ATTDICT = {'stratt':STRATT,'floatatt':FLOATATT,'seqatt':SEQATT,
# 'stringseqatt':''.join(STRINGSEQATT), # changed in issue #770
# 'emptystratt':EMPTYSTRATT,'intatt':INTATT}
ATTDICT = {'stratt':STRATT,'floatatt':FLOATATT,'seqatt':SEQATT,
'stringseqatt':STRINGSEQATT,
'emptystratt':EMPTYSTRATT,'intatt':INTATT}
class VariablesTestCase(unittest.TestCase):
def setUp(self):
self.file = FILE_NAME
f = netCDF4.Dataset(self.file,'w')
# try to set a dataset attribute with one of the reserved names.
f.setncattr('file_format','netcdf4_format')
# test attribute renameing
f.stratt_tmp = STRATT
f.renameAttribute('stratt_tmp','stratt')
f.emptystratt = EMPTYSTRATT
f.intatt = INTATT
f.floatatt = FLOATATT
f.seqatt = SEQATT
# sequences of strings converted to a single string.
f.stringseqatt = STRINGSEQATT
f.setncattr_string('stringseqatt_array',STRINGSEQATT) # array of NC_STRING
g = f.createGroup(GROUP_NAME)
f.createDimension(DIM1_NAME, DIM1_LEN)
f.createDimension(DIM2_NAME, DIM2_LEN)
f.createDimension(DIM3_NAME, DIM3_LEN)
g.createDimension(DIM1_NAME, DIM1_LEN)
g.createDimension(DIM2_NAME, DIM2_LEN)
g.createDimension(DIM3_NAME, DIM3_LEN)
g.stratt_tmp = STRATT
g.renameAttribute('stratt_tmp','stratt')
g.emptystratt = EMPTYSTRATT
g.intatt = INTATT
g.floatatt = FLOATATT
g.seqatt = SEQATT
g.stringseqatt = STRINGSEQATT
if netCDF4.__version__ > "1.4.2":
with self.assertRaises(ValueError):
g.arrayatt = [[1, 2], [3, 4]] # issue #841
g.setncattr_string('stringseqatt_array',STRINGSEQATT) # array of NC_STRING
v = f.createVariable(VAR_NAME, 'f8',(DIM1_NAME,DIM2_NAME,DIM3_NAME))
# try to set a variable attribute with one of the reserved names.
v.setncattr('ndim','three')
v.setncatts({'foo': 1})
v.setncatts(OrderedDict(bar=2))
v.stratt_tmp = STRATT
v.renameAttribute('stratt_tmp','stratt')
v.emptystratt = EMPTYSTRATT
v.intatt = INTATT
v.floatatt = FLOATATT
v.seqatt = SEQATT
v.stringseqatt = STRINGSEQATT
v.setncattr_string('stringseqatt_array',STRINGSEQATT) # array of NC_STRING
v1 = g.createVariable(VAR_NAME, 'f8',(DIM1_NAME,DIM2_NAME,DIM3_NAME))
v1.stratt = STRATT
v1.emptystratt = EMPTYSTRATT
v1.intatt = INTATT
v1.floatatt = FLOATATT
v1.seqatt = SEQATT
v1.stringseqatt = STRINGSEQATT
v1.setncattr_string('stringseqatt_array',STRINGSEQATT) # array of NC_STRING
# issue #485 (triggers segfault in C lib
# with version 1.2.1 without pull request #486)
f.foo = NP.array('bar','S')
f.foo = NP.array('bar','U')
# issue #529 write string attribute as NC_CHAR unless
# it can't be decoded to ascii. Add setncattr_string
# method to force NC_STRING.
f.charatt = u'foo' # will be written as NC_CHAR
f.setncattr_string('stringatt','bar') # NC_STRING
f.cafe = u'caf\xe9' # NC_STRING
f.batt = u'caf\xe9'.encode('utf-8') #NC_CHAR
v.setncattr_string('stringatt','bar') # NC_STRING
# issue #882 - provide an option to always string attribute
# as NC_STRINGs. Testing various approaches to setting text attributes...
f.set_ncstring_attrs(True)
f.stringatt_ncstr = u'foo' # will now be written as NC_STRING
f.setncattr_string('stringatt_ncstr','bar') # NC_STRING anyway
f.caf_ncstr = u'caf\xe9' # NC_STRING anyway
f.bat_ncstr = u'caf\xe9'.encode('utf-8') # now NC_STRING
g.stratt_ncstr = STRATT # now NC_STRING
#g.renameAttribute('stratt_tmp','stratt_ncstr')
v.setncattr_string('stringatt_ncstr','bar') # NC_STRING anyway
v.stratt_ncstr = STRATT
v1.emptystratt_ncstr = EMPTYSTRATT
f.close()
def tearDown(self):
# Remove the temporary files
#pass
os.remove(self.file)
def runTest(self):
"""testing attributes"""
f = netCDF4.Dataset(self.file, 'r')
v = f.variables[VAR_NAME]
g = f.groups[GROUP_NAME]
v1 = g.variables[VAR_NAME]
# check attributes in root group.
# global attributes.
# check __dict__ method for accessing all netCDF attributes.
for key,val in ATTDICT.items():
if type(val) == NP.ndarray:
assert f.__dict__[key].tolist() == val.tolist()
else:
assert f.__dict__[key] == val
# check accessing individual attributes.
assert f.intatt == INTATT
assert f.floatatt == FLOATATT
assert f.stratt == STRATT
assert f.emptystratt == EMPTYSTRATT
assert f.seqatt.tolist() == SEQATT.tolist()
#assert f.stringseqatt == ''.join(STRINGSEQATT) # issue 770
assert f.stringseqatt == STRINGSEQATT
assert f.stringseqatt_array == STRINGSEQATT
assert f.getncattr('file_format') == 'netcdf4_format'
# variable attributes.
# check __dict__ method for accessing all netCDF attributes.
for key,val in ATTDICT.items():
if type(val) == NP.ndarray:
assert v.__dict__[key].tolist() == val.tolist()
else:
assert v.__dict__[key] == val
# check accessing individual attributes.
assert v.intatt == INTATT
assert v.floatatt == FLOATATT
assert v.stratt == STRATT
assert v.seqatt.tolist() == SEQATT.tolist()
#assert v.stringseqatt == ''.join(STRINGSEQATT) # issue 770
assert v.stringseqatt == STRINGSEQATT
assert v.stringseqatt_array == STRINGSEQATT
assert v.getncattr('ndim') == 'three'
assert v.getncattr('foo') == 1
assert v.getncattr('bar') == 2
# check type of attributes using ncdump (issue #529)
try: # ncdump may not be on the system PATH
nc_proc = subprocess.Popen(
['ncdump', '-h', FILE_NAME], stdout=subprocess.PIPE)
except OSError:
warnings.warn('"ncdump" not on system path; cannot test '
'read of some attributes')
pass
else: # We do have ncdump output
dep = nc_proc.communicate()[0]
try: # python 2
ncdump_output = dep.split('\n')
except TypeError: # python 3
ncdump_output = str(dep,encoding='utf-8').split('\n')
for line in ncdump_output:
line = line.strip('\t\n\r')
line = line.strip()# Must be done another time for group variables
if "stringatt" in line: assert line.startswith('string')
if "charatt" in line: assert line.startswith(':')
if "cafe" in line: assert line.startswith('string')
if "batt" in line: assert line.startswith(':')
if "_ncstr" in line: assert line.startswith('string')
# check attributes in subgroup.
# global attributes.
for key,val in ATTDICT.items():
if type(val) == NP.ndarray:
assert g.__dict__[key].tolist() == val.tolist()
else:
assert g.__dict__[key] == val
assert g.intatt == INTATT
assert g.floatatt == FLOATATT
assert g.stratt == STRATT
assert g.emptystratt == EMPTYSTRATT
assert g.seqatt.tolist() == SEQATT.tolist()
#assert g.stringseqatt == ''.join(STRINGSEQATT) # issue 770
assert g.stringseqatt == STRINGSEQATT
assert g.stringseqatt_array == STRINGSEQATT
for key,val in ATTDICT.items():
if type(val) == NP.ndarray:
assert v1.__dict__[key].tolist() == val.tolist()
else:
assert v1.__dict__[key] == val
assert v1.intatt == INTATT
assert v1.floatatt == FLOATATT
assert v1.stratt == STRATT
assert v1.emptystratt == EMPTYSTRATT
assert v1.seqatt.tolist() == SEQATT.tolist()
#assert v1.stringseqatt == ''.join(STRINGSEQATT) # issue 770
assert v1.stringseqatt == STRINGSEQATT
assert v1.stringseqatt_array == STRINGSEQATT
assert getattr(v1,'nonexistantatt',None) == None
f.close()
if __name__ == '__main__':
unittest.main()