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 f.close() def tearDown(self): # Remove the temporary files 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') 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(':') # 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()