542 lines
19 KiB
Python
542 lines
19 KiB
Python
''' Tests for netcdf '''
|
|
import os
|
|
from os.path import join as pjoin, dirname
|
|
import shutil
|
|
import tempfile
|
|
import warnings
|
|
from io import BytesIO
|
|
from glob import glob
|
|
from contextlib import contextmanager
|
|
|
|
import numpy as np
|
|
from numpy.testing import (assert_, assert_allclose, assert_equal,
|
|
suppress_warnings)
|
|
from pytest import raises as assert_raises
|
|
|
|
from scipy.io.netcdf import netcdf_file, IS_PYPY
|
|
from scipy._lib._tmpdirs import in_tempdir
|
|
|
|
TEST_DATA_PATH = pjoin(dirname(__file__), 'data')
|
|
|
|
N_EG_ELS = 11 # number of elements for example variable
|
|
VARTYPE_EG = 'b' # var type for example variable
|
|
|
|
|
|
@contextmanager
|
|
def make_simple(*args, **kwargs):
|
|
f = netcdf_file(*args, **kwargs)
|
|
f.history = 'Created for a test'
|
|
f.createDimension('time', N_EG_ELS)
|
|
time = f.createVariable('time', VARTYPE_EG, ('time',))
|
|
time[:] = np.arange(N_EG_ELS)
|
|
time.units = 'days since 2008-01-01'
|
|
f.flush()
|
|
yield f
|
|
f.close()
|
|
|
|
|
|
def check_simple(ncfileobj):
|
|
'''Example fileobj tests '''
|
|
assert_equal(ncfileobj.history, b'Created for a test')
|
|
time = ncfileobj.variables['time']
|
|
assert_equal(time.units, b'days since 2008-01-01')
|
|
assert_equal(time.shape, (N_EG_ELS,))
|
|
assert_equal(time[-1], N_EG_ELS-1)
|
|
|
|
def assert_mask_matches(arr, expected_mask):
|
|
'''
|
|
Asserts that the mask of arr is effectively the same as expected_mask.
|
|
|
|
In contrast to numpy.ma.testutils.assert_mask_equal, this function allows
|
|
testing the 'mask' of a standard numpy array (the mask in this case is treated
|
|
as all False).
|
|
|
|
Parameters
|
|
----------
|
|
arr: ndarray or MaskedArray
|
|
Array to test.
|
|
expected_mask: array_like of booleans
|
|
A list giving the expected mask.
|
|
'''
|
|
|
|
mask = np.ma.getmaskarray(arr)
|
|
assert_equal(mask, expected_mask)
|
|
|
|
|
|
def test_read_write_files():
|
|
# test round trip for example file
|
|
cwd = os.getcwd()
|
|
try:
|
|
tmpdir = tempfile.mkdtemp()
|
|
os.chdir(tmpdir)
|
|
with make_simple('simple.nc', 'w') as f:
|
|
pass
|
|
# read the file we just created in 'a' mode
|
|
with netcdf_file('simple.nc', 'a') as f:
|
|
check_simple(f)
|
|
# add something
|
|
f._attributes['appendRan'] = 1
|
|
|
|
# To read the NetCDF file we just created::
|
|
with netcdf_file('simple.nc') as f:
|
|
# Using mmap is the default (but not on pypy)
|
|
assert_equal(f.use_mmap, not IS_PYPY)
|
|
check_simple(f)
|
|
assert_equal(f._attributes['appendRan'], 1)
|
|
|
|
# Read it in append (and check mmap is off)
|
|
with netcdf_file('simple.nc', 'a') as f:
|
|
assert_(not f.use_mmap)
|
|
check_simple(f)
|
|
assert_equal(f._attributes['appendRan'], 1)
|
|
|
|
# Now without mmap
|
|
with netcdf_file('simple.nc', mmap=False) as f:
|
|
# Using mmap is the default
|
|
assert_(not f.use_mmap)
|
|
check_simple(f)
|
|
|
|
# To read the NetCDF file we just created, as file object, no
|
|
# mmap. When n * n_bytes(var_type) is not divisible by 4, this
|
|
# raised an error in pupynere 1.0.12 and scipy rev 5893, because
|
|
# calculated vsize was rounding up in units of 4 - see
|
|
# https://www.unidata.ucar.edu/software/netcdf/guide_toc.html
|
|
with open('simple.nc', 'rb') as fobj:
|
|
with netcdf_file(fobj) as f:
|
|
# by default, don't use mmap for file-like
|
|
assert_(not f.use_mmap)
|
|
check_simple(f)
|
|
|
|
# Read file from fileobj, with mmap
|
|
with suppress_warnings() as sup:
|
|
if IS_PYPY:
|
|
sup.filter(RuntimeWarning,
|
|
"Cannot close a netcdf_file opened with mmap=True.*")
|
|
with open('simple.nc', 'rb') as fobj:
|
|
with netcdf_file(fobj, mmap=True) as f:
|
|
assert_(f.use_mmap)
|
|
check_simple(f)
|
|
|
|
# Again read it in append mode (adding another att)
|
|
with open('simple.nc', 'r+b') as fobj:
|
|
with netcdf_file(fobj, 'a') as f:
|
|
assert_(not f.use_mmap)
|
|
check_simple(f)
|
|
f.createDimension('app_dim', 1)
|
|
var = f.createVariable('app_var', 'i', ('app_dim',))
|
|
var[:] = 42
|
|
|
|
# And... check that app_var made it in...
|
|
with netcdf_file('simple.nc') as f:
|
|
check_simple(f)
|
|
assert_equal(f.variables['app_var'][:], 42)
|
|
|
|
except: # noqa: E722
|
|
os.chdir(cwd)
|
|
shutil.rmtree(tmpdir)
|
|
raise
|
|
os.chdir(cwd)
|
|
shutil.rmtree(tmpdir)
|
|
|
|
|
|
def test_read_write_sio():
|
|
eg_sio1 = BytesIO()
|
|
with make_simple(eg_sio1, 'w'):
|
|
str_val = eg_sio1.getvalue()
|
|
|
|
eg_sio2 = BytesIO(str_val)
|
|
with netcdf_file(eg_sio2) as f2:
|
|
check_simple(f2)
|
|
|
|
# Test that error is raised if attempting mmap for sio
|
|
eg_sio3 = BytesIO(str_val)
|
|
assert_raises(ValueError, netcdf_file, eg_sio3, 'r', True)
|
|
# Test 64-bit offset write / read
|
|
eg_sio_64 = BytesIO()
|
|
with make_simple(eg_sio_64, 'w', version=2) as f_64:
|
|
str_val = eg_sio_64.getvalue()
|
|
|
|
eg_sio_64 = BytesIO(str_val)
|
|
with netcdf_file(eg_sio_64) as f_64:
|
|
check_simple(f_64)
|
|
assert_equal(f_64.version_byte, 2)
|
|
# also when version 2 explicitly specified
|
|
eg_sio_64 = BytesIO(str_val)
|
|
with netcdf_file(eg_sio_64, version=2) as f_64:
|
|
check_simple(f_64)
|
|
assert_equal(f_64.version_byte, 2)
|
|
|
|
|
|
def test_bytes():
|
|
raw_file = BytesIO()
|
|
f = netcdf_file(raw_file, mode='w')
|
|
# Dataset only has a single variable, dimension and attribute to avoid
|
|
# any ambiguity related to order.
|
|
f.a = 'b'
|
|
f.createDimension('dim', 1)
|
|
var = f.createVariable('var', np.int16, ('dim',))
|
|
var[0] = -9999
|
|
var.c = 'd'
|
|
f.sync()
|
|
|
|
actual = raw_file.getvalue()
|
|
|
|
expected = (b'CDF\x01'
|
|
b'\x00\x00\x00\x00'
|
|
b'\x00\x00\x00\x0a'
|
|
b'\x00\x00\x00\x01'
|
|
b'\x00\x00\x00\x03'
|
|
b'dim\x00'
|
|
b'\x00\x00\x00\x01'
|
|
b'\x00\x00\x00\x0c'
|
|
b'\x00\x00\x00\x01'
|
|
b'\x00\x00\x00\x01'
|
|
b'a\x00\x00\x00'
|
|
b'\x00\x00\x00\x02'
|
|
b'\x00\x00\x00\x01'
|
|
b'b\x00\x00\x00'
|
|
b'\x00\x00\x00\x0b'
|
|
b'\x00\x00\x00\x01'
|
|
b'\x00\x00\x00\x03'
|
|
b'var\x00'
|
|
b'\x00\x00\x00\x01'
|
|
b'\x00\x00\x00\x00'
|
|
b'\x00\x00\x00\x0c'
|
|
b'\x00\x00\x00\x01'
|
|
b'\x00\x00\x00\x01'
|
|
b'c\x00\x00\x00'
|
|
b'\x00\x00\x00\x02'
|
|
b'\x00\x00\x00\x01'
|
|
b'd\x00\x00\x00'
|
|
b'\x00\x00\x00\x03'
|
|
b'\x00\x00\x00\x04'
|
|
b'\x00\x00\x00\x78'
|
|
b'\xd8\xf1\x80\x01')
|
|
|
|
assert_equal(actual, expected)
|
|
|
|
|
|
def test_encoded_fill_value():
|
|
with netcdf_file(BytesIO(), mode='w') as f:
|
|
f.createDimension('x', 1)
|
|
var = f.createVariable('var', 'S1', ('x',))
|
|
assert_equal(var._get_encoded_fill_value(), b'\x00')
|
|
var._FillValue = b'\x01'
|
|
assert_equal(var._get_encoded_fill_value(), b'\x01')
|
|
var._FillValue = b'\x00\x00' # invalid, wrong size
|
|
assert_equal(var._get_encoded_fill_value(), b'\x00')
|
|
|
|
|
|
def test_read_example_data():
|
|
# read any example data files
|
|
for fname in glob(pjoin(TEST_DATA_PATH, '*.nc')):
|
|
with netcdf_file(fname, 'r'):
|
|
pass
|
|
with netcdf_file(fname, 'r', mmap=False):
|
|
pass
|
|
|
|
|
|
def test_itemset_no_segfault_on_readonly():
|
|
# Regression test for ticket #1202.
|
|
# Open the test file in read-only mode.
|
|
|
|
filename = pjoin(TEST_DATA_PATH, 'example_1.nc')
|
|
with suppress_warnings() as sup:
|
|
sup.filter(RuntimeWarning,
|
|
"Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist")
|
|
with netcdf_file(filename, 'r', mmap=True) as f:
|
|
time_var = f.variables['time']
|
|
|
|
# time_var.assignValue(42) should raise a RuntimeError--not seg. fault!
|
|
assert_raises(RuntimeError, time_var.assignValue, 42)
|
|
|
|
|
|
def test_appending_issue_gh_8625():
|
|
stream = BytesIO()
|
|
|
|
with make_simple(stream, mode='w') as f:
|
|
f.createDimension('x', 2)
|
|
f.createVariable('x', float, ('x',))
|
|
f.variables['x'][...] = 1
|
|
f.flush()
|
|
contents = stream.getvalue()
|
|
|
|
stream = BytesIO(contents)
|
|
with netcdf_file(stream, mode='a') as f:
|
|
f.variables['x'][...] = 2
|
|
|
|
|
|
def test_write_invalid_dtype():
|
|
dtypes = ['int64', 'uint64']
|
|
if np.dtype('int').itemsize == 8: # 64-bit machines
|
|
dtypes.append('int')
|
|
if np.dtype('uint').itemsize == 8: # 64-bit machines
|
|
dtypes.append('uint')
|
|
|
|
with netcdf_file(BytesIO(), 'w') as f:
|
|
f.createDimension('time', N_EG_ELS)
|
|
for dt in dtypes:
|
|
assert_raises(ValueError, f.createVariable, 'time', dt, ('time',))
|
|
|
|
|
|
def test_flush_rewind():
|
|
stream = BytesIO()
|
|
with make_simple(stream, mode='w') as f:
|
|
x = f.createDimension('x',4) # x is used in createVariable
|
|
v = f.createVariable('v', 'i2', ['x'])
|
|
v[:] = 1
|
|
f.flush()
|
|
len_single = len(stream.getvalue())
|
|
f.flush()
|
|
len_double = len(stream.getvalue())
|
|
|
|
assert_(len_single == len_double)
|
|
|
|
|
|
def test_dtype_specifiers():
|
|
# Numpy 1.7.0-dev had a bug where 'i2' wouldn't work.
|
|
# Specifying np.int16 or similar only works from the same commit as this
|
|
# comment was made.
|
|
with make_simple(BytesIO(), mode='w') as f:
|
|
f.createDimension('x',4)
|
|
f.createVariable('v1', 'i2', ['x'])
|
|
f.createVariable('v2', np.int16, ['x'])
|
|
f.createVariable('v3', np.dtype(np.int16), ['x'])
|
|
|
|
|
|
def test_ticket_1720():
|
|
io = BytesIO()
|
|
|
|
items = [0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9]
|
|
|
|
with netcdf_file(io, 'w') as f:
|
|
f.history = 'Created for a test'
|
|
f.createDimension('float_var', 10)
|
|
float_var = f.createVariable('float_var', 'f', ('float_var',))
|
|
float_var[:] = items
|
|
float_var.units = 'metres'
|
|
f.flush()
|
|
contents = io.getvalue()
|
|
|
|
io = BytesIO(contents)
|
|
with netcdf_file(io, 'r') as f:
|
|
assert_equal(f.history, b'Created for a test')
|
|
float_var = f.variables['float_var']
|
|
assert_equal(float_var.units, b'metres')
|
|
assert_equal(float_var.shape, (10,))
|
|
assert_allclose(float_var[:], items)
|
|
|
|
|
|
def test_mmaps_segfault():
|
|
filename = pjoin(TEST_DATA_PATH, 'example_1.nc')
|
|
|
|
if not IS_PYPY:
|
|
with warnings.catch_warnings():
|
|
warnings.simplefilter("error")
|
|
with netcdf_file(filename, mmap=True) as f:
|
|
x = f.variables['lat'][:]
|
|
# should not raise warnings
|
|
del x
|
|
|
|
def doit():
|
|
with netcdf_file(filename, mmap=True) as f:
|
|
return f.variables['lat'][:]
|
|
|
|
# should not crash
|
|
with suppress_warnings() as sup:
|
|
sup.filter(RuntimeWarning,
|
|
"Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist")
|
|
x = doit()
|
|
x.sum()
|
|
|
|
|
|
def test_zero_dimensional_var():
|
|
io = BytesIO()
|
|
with make_simple(io, 'w') as f:
|
|
v = f.createVariable('zerodim', 'i2', [])
|
|
# This is checking that .isrec returns a boolean - don't simplify it
|
|
# to 'assert not ...'
|
|
assert v.isrec is False, v.isrec
|
|
f.flush()
|
|
|
|
|
|
def test_byte_gatts():
|
|
# Check that global "string" atts work like they did before py3k
|
|
# unicode and general bytes confusion
|
|
with in_tempdir():
|
|
filename = 'g_byte_atts.nc'
|
|
f = netcdf_file(filename, 'w')
|
|
f._attributes['holy'] = b'grail'
|
|
f._attributes['witch'] = 'floats'
|
|
f.close()
|
|
f = netcdf_file(filename, 'r')
|
|
assert_equal(f._attributes['holy'], b'grail')
|
|
assert_equal(f._attributes['witch'], b'floats')
|
|
f.close()
|
|
|
|
|
|
def test_open_append():
|
|
# open 'w' put one attr
|
|
with in_tempdir():
|
|
filename = 'append_dat.nc'
|
|
f = netcdf_file(filename, 'w')
|
|
f._attributes['Kilroy'] = 'was here'
|
|
f.close()
|
|
|
|
# open again in 'a', read the att and and a new one
|
|
f = netcdf_file(filename, 'a')
|
|
assert_equal(f._attributes['Kilroy'], b'was here')
|
|
f._attributes['naughty'] = b'Zoot'
|
|
f.close()
|
|
|
|
# open yet again in 'r' and check both atts
|
|
f = netcdf_file(filename, 'r')
|
|
assert_equal(f._attributes['Kilroy'], b'was here')
|
|
assert_equal(f._attributes['naughty'], b'Zoot')
|
|
f.close()
|
|
|
|
|
|
def test_append_recordDimension():
|
|
dataSize = 100
|
|
|
|
with in_tempdir():
|
|
# Create file with record time dimension
|
|
with netcdf_file('withRecordDimension.nc', 'w') as f:
|
|
f.createDimension('time', None)
|
|
f.createVariable('time', 'd', ('time',))
|
|
f.createDimension('x', dataSize)
|
|
x = f.createVariable('x', 'd', ('x',))
|
|
x[:] = np.array(range(dataSize))
|
|
f.createDimension('y', dataSize)
|
|
y = f.createVariable('y', 'd', ('y',))
|
|
y[:] = np.array(range(dataSize))
|
|
f.createVariable('testData', 'i', ('time', 'x', 'y'))
|
|
f.flush()
|
|
f.close()
|
|
|
|
for i in range(2):
|
|
# Open the file in append mode and add data
|
|
with netcdf_file('withRecordDimension.nc', 'a') as f:
|
|
f.variables['time'].data = np.append(f.variables["time"].data, i)
|
|
f.variables['testData'][i, :, :] = np.full((dataSize, dataSize), i)
|
|
f.flush()
|
|
|
|
# Read the file and check that append worked
|
|
with netcdf_file('withRecordDimension.nc') as f:
|
|
assert_equal(f.variables['time'][-1], i)
|
|
assert_equal(f.variables['testData'][-1, :, :].copy(), np.full((dataSize, dataSize), i))
|
|
assert_equal(f.variables['time'].data.shape[0], i+1)
|
|
assert_equal(f.variables['testData'].data.shape[0], i+1)
|
|
|
|
# Read the file and check that 'data' was not saved as user defined
|
|
# attribute of testData variable during append operation
|
|
with netcdf_file('withRecordDimension.nc') as f:
|
|
with assert_raises(KeyError) as ar:
|
|
f.variables['testData']._attributes['data']
|
|
ex = ar.value
|
|
assert_equal(ex.args[0], 'data')
|
|
|
|
def test_maskandscale():
|
|
t = np.linspace(20, 30, 15)
|
|
t[3] = 100
|
|
tm = np.ma.masked_greater(t, 99)
|
|
fname = pjoin(TEST_DATA_PATH, 'example_2.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
Temp = f.variables['Temperature']
|
|
assert_equal(Temp.missing_value, 9999)
|
|
assert_equal(Temp.add_offset, 20)
|
|
assert_equal(Temp.scale_factor, np.float32(0.01))
|
|
found = Temp[:].compressed()
|
|
del Temp # Remove ref to mmap, so file can be closed.
|
|
expected = np.round(tm.compressed(), 2)
|
|
assert_allclose(found, expected)
|
|
|
|
with in_tempdir():
|
|
newfname = 'ms.nc'
|
|
f = netcdf_file(newfname, 'w', maskandscale=True)
|
|
f.createDimension('Temperature', len(tm))
|
|
temp = f.createVariable('Temperature', 'i', ('Temperature',))
|
|
temp.missing_value = 9999
|
|
temp.scale_factor = 0.01
|
|
temp.add_offset = 20
|
|
temp[:] = tm
|
|
f.close()
|
|
|
|
with netcdf_file(newfname, maskandscale=True) as f:
|
|
Temp = f.variables['Temperature']
|
|
assert_equal(Temp.missing_value, 9999)
|
|
assert_equal(Temp.add_offset, 20)
|
|
assert_equal(Temp.scale_factor, np.float32(0.01))
|
|
expected = np.round(tm.compressed(), 2)
|
|
found = Temp[:].compressed()
|
|
del Temp
|
|
assert_allclose(found, expected)
|
|
|
|
|
|
# ------------------------------------------------------------------------
|
|
# Test reading with masked values (_FillValue / missing_value)
|
|
# ------------------------------------------------------------------------
|
|
|
|
def test_read_withValuesNearFillValue():
|
|
# Regression test for ticket #5626
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var1_fillval0'][:]
|
|
assert_mask_matches(vardata, [False, True, False])
|
|
|
|
def test_read_withNoFillValue():
|
|
# For a variable with no fill value, reading data with maskandscale=True
|
|
# should return unmasked data
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var2_noFillval'][:]
|
|
assert_mask_matches(vardata, [False, False, False])
|
|
assert_equal(vardata, [1,2,3])
|
|
|
|
def test_read_withFillValueAndMissingValue():
|
|
# For a variable with both _FillValue and missing_value, the _FillValue
|
|
# should be used
|
|
IRRELEVANT_VALUE = 9999
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var3_fillvalAndMissingValue'][:]
|
|
assert_mask_matches(vardata, [True, False, False])
|
|
assert_equal(vardata, [IRRELEVANT_VALUE, 2, 3])
|
|
|
|
def test_read_withMissingValue():
|
|
# For a variable with missing_value but not _FillValue, the missing_value
|
|
# should be used
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var4_missingValue'][:]
|
|
assert_mask_matches(vardata, [False, True, False])
|
|
|
|
def test_read_withFillValNaN():
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var5_fillvalNaN'][:]
|
|
assert_mask_matches(vardata, [False, True, False])
|
|
|
|
def test_read_withChar():
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var6_char'][:]
|
|
assert_mask_matches(vardata, [False, True, False])
|
|
|
|
def test_read_with2dVar():
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
|
vardata = f.variables['var7_2d'][:]
|
|
assert_mask_matches(vardata, [[True, False], [False, False], [False, True]])
|
|
|
|
def test_read_withMaskAndScaleFalse():
|
|
# If a variable has a _FillValue (or missing_value) attribute, but is read
|
|
# with maskandscale set to False, the result should be unmasked
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
|
# Open file with mmap=False to avoid problems with closing a mmap'ed file
|
|
# when arrays referring to its data still exist:
|
|
with netcdf_file(fname, maskandscale=False, mmap=False) as f:
|
|
vardata = f.variables['var3_fillvalAndMissingValue'][:]
|
|
assert_mask_matches(vardata, [False, False, False])
|
|
assert_equal(vardata, [1, 2, 3])
|