| Current File : //usr/lib64/python2.7/site-packages/numpy/lib/tests/test_io.py |
import sys
import gzip
import os
import threading
from tempfile import mkstemp, NamedTemporaryFile
import time
from datetime import datetime
import warnings
import gc
from numpy.testing.utils import WarningManager
import numpy as np
import numpy.ma as ma
from numpy.lib._iotools import ConverterError, ConverterLockError, \
ConversionWarning
from numpy.compat import asbytes, asbytes_nested, bytes
from nose import SkipTest
from numpy.ma.testutils import (TestCase, assert_equal, assert_array_equal,
assert_raises, run_module_suite)
from numpy.testing import assert_warns, assert_, build_err_msg
if sys.version_info[0] >= 3:
from io import BytesIO
def StringIO(s=""):
return BytesIO(asbytes(s))
else:
from StringIO import StringIO
BytesIO = StringIO
MAJVER, MINVER = sys.version_info[:2]
def strptime(s, fmt=None):
"""This function is available in the datetime module only
from Python >= 2.5.
"""
if sys.version_info[0] >= 3:
return datetime(*time.strptime(s.decode('latin1'), fmt)[:3])
else:
return datetime(*time.strptime(s, fmt)[:3])
class RoundtripTest(object):
def roundtrip(self, save_func, *args, **kwargs):
"""
save_func : callable
Function used to save arrays to file.
file_on_disk : bool
If true, store the file on disk, instead of in a
string buffer.
save_kwds : dict
Parameters passed to `save_func`.
load_kwds : dict
Parameters passed to `numpy.load`.
args : tuple of arrays
Arrays stored to file.
"""
save_kwds = kwargs.get('save_kwds', {})
load_kwds = kwargs.get('load_kwds', {})
file_on_disk = kwargs.get('file_on_disk', False)
if file_on_disk:
# Do not delete the file on windows, because we can't
# reopen an already opened file on that platform, so we
# need to close the file and reopen it, implying no
# automatic deletion.
if sys.platform == 'win32' and MAJVER >= 2 and MINVER >= 6:
target_file = NamedTemporaryFile(delete=False)
else:
target_file = NamedTemporaryFile()
load_file = target_file.name
else:
target_file = StringIO()
load_file = target_file
arr = args
save_func(target_file, *arr, **save_kwds)
target_file.flush()
target_file.seek(0)
if sys.platform == 'win32' and not isinstance(target_file, BytesIO):
target_file.close()
arr_reloaded = np.load(load_file, **load_kwds)
self.arr = arr
self.arr_reloaded = arr_reloaded
def test_array(self):
a = np.array([[1, 2], [3, 4]], float)
self.roundtrip(a)
a = np.array([[1, 2], [3, 4]], int)
self.roundtrip(a)
a = np.array([[1 + 5j, 2 + 6j], [3 + 7j, 4 + 8j]], dtype=np.csingle)
self.roundtrip(a)
a = np.array([[1 + 5j, 2 + 6j], [3 + 7j, 4 + 8j]], dtype=np.cdouble)
self.roundtrip(a)
def test_1D(self):
a = np.array([1, 2, 3, 4], int)
self.roundtrip(a)
@np.testing.dec.knownfailureif(sys.platform == 'win32', "Fail on Win32")
def test_mmap(self):
a = np.array([[1, 2.5], [4, 7.3]])
self.roundtrip(a, file_on_disk=True, load_kwds={'mmap_mode': 'r'})
def test_record(self):
a = np.array([(1, 2), (3, 4)], dtype=[('x', 'i4'), ('y', 'i4')])
self.roundtrip(a)
class TestSaveLoad(RoundtripTest, TestCase):
def roundtrip(self, *args, **kwargs):
RoundtripTest.roundtrip(self, np.save, *args, **kwargs)
assert_equal(self.arr[0], self.arr_reloaded)
class TestSavezLoad(RoundtripTest, TestCase):
def roundtrip(self, *args, **kwargs):
RoundtripTest.roundtrip(self, np.savez, *args, **kwargs)
for n, arr in enumerate(self.arr):
assert_equal(arr, self.arr_reloaded['arr_%d' % n])
def test_multiple_arrays(self):
a = np.array([[1, 2], [3, 4]], float)
b = np.array([[1 + 2j, 2 + 7j], [3 - 6j, 4 + 12j]], complex)
self.roundtrip(a, b)
def test_named_arrays(self):
a = np.array([[1, 2], [3, 4]], float)
b = np.array([[1 + 2j, 2 + 7j], [3 - 6j, 4 + 12j]], complex)
c = StringIO()
np.savez(c, file_a=a, file_b=b)
c.seek(0)
l = np.load(c)
assert_equal(a, l['file_a'])
assert_equal(b, l['file_b'])
def test_savez_filename_clashes(self):
# Test that issue #852 is fixed
# and savez functions in multithreaded environment
def writer(error_list):
fd, tmp = mkstemp(suffix='.npz')
os.close(fd)
try:
arr = np.random.randn(500, 500)
try:
np.savez(tmp, arr=arr)
except OSError, err:
error_list.append(err)
finally:
os.remove(tmp)
errors = []
threads = [threading.Thread(target=writer, args=(errors,))
for j in xrange(3)]
for t in threads:
t.start()
for t in threads:
t.join()
if errors:
raise AssertionError(errors)
def test_not_closing_opened_fid(self):
# Test that issue #2178 is fixed:
# verify could seek on 'loaded' file
fd, tmp = mkstemp(suffix='.npz')
os.close(fd)
try:
fp = open(tmp, 'wb')
np.savez(fp, data='LOVELY LOAD')
fp.close()
fp = open(tmp, 'rb', 10000)
fp.seek(0)
assert_(not fp.closed)
_ = np.load(fp)['data']
assert_(not fp.closed) # must not get closed by .load(opened fp)
fp.seek(0)
assert_(not fp.closed)
finally:
fp.close()
os.remove(tmp)
def test_closing_fid(self):
# Test that issue #1517 (too many opened files) remains closed
# It might be a "week" test since failed to get triggered on
# e.g. Debian sid of 2012 Jul 05 but was reported to
# trigger the failure on Ubuntu 10.04:
# http://projects.scipy.org/numpy/ticket/1517#comment:2
fd, tmp = mkstemp(suffix='.npz')
os.close(fd)
try:
fp = open(tmp, 'wb')
np.savez(fp, data='LOVELY LOAD')
fp.close()
for i in range(1, 1025):
try:
np.load(tmp)["data"]
except Exception, e:
raise AssertionError("Failed to load data from a file: %s" % e)
finally:
os.remove(tmp)
class TestSaveTxt(TestCase):
def test_array(self):
a = np.array([[1, 2], [3, 4]], float)
fmt = "%.18e"
c = StringIO()
np.savetxt(c, a, fmt=fmt)
c.seek(0)
assert_equal(c.readlines(),
asbytes_nested(
[(fmt + ' ' + fmt + '\n') % (1, 2),
(fmt + ' ' + fmt + '\n') % (3, 4)]))
a = np.array([[1, 2], [3, 4]], int)
c = StringIO()
np.savetxt(c, a, fmt='%d')
c.seek(0)
assert_equal(c.readlines(), asbytes_nested(['1 2\n', '3 4\n']))
def test_1D(self):
a = np.array([1, 2, 3, 4], int)
c = StringIO()
np.savetxt(c, a, fmt='%d')
c.seek(0)
lines = c.readlines()
assert_equal(lines, asbytes_nested(['1\n', '2\n', '3\n', '4\n']))
def test_record(self):
a = np.array([(1, 2), (3, 4)], dtype=[('x', 'i4'), ('y', 'i4')])
c = StringIO()
np.savetxt(c, a, fmt='%d')
c.seek(0)
assert_equal(c.readlines(), asbytes_nested(['1 2\n', '3 4\n']))
def test_delimiter(self):
a = np.array([[1., 2.], [3., 4.]])
c = StringIO()
np.savetxt(c, a, delimiter=asbytes(','), fmt='%d')
c.seek(0)
assert_equal(c.readlines(), asbytes_nested(['1,2\n', '3,4\n']))
def test_format(self):
a = np.array([(1, 2), (3, 4)])
c = StringIO()
# Sequence of formats
np.savetxt(c, a, fmt=['%02d', '%3.1f'])
c.seek(0)
assert_equal(c.readlines(), asbytes_nested(['01 2.0\n', '03 4.0\n']))
# A single multiformat string
c = StringIO()
np.savetxt(c, a, fmt='%02d : %3.1f')
c.seek(0)
lines = c.readlines()
assert_equal(lines, asbytes_nested(['01 : 2.0\n', '03 : 4.0\n']))
# Specify delimiter, should be overiden
c = StringIO()
np.savetxt(c, a, fmt='%02d : %3.1f', delimiter=',')
c.seek(0)
lines = c.readlines()
assert_equal(lines, asbytes_nested(['01 : 2.0\n', '03 : 4.0\n']))
def test_header_footer(self):
"""
Test the functionality of the header and footer keyword argument.
"""
c = StringIO()
a = np.array([(1, 2), (3, 4)], dtype=np.int)
test_header_footer = 'Test header / footer'
# Test the header keyword argument
np.savetxt(c, a, fmt='%1d', header=test_header_footer)
c.seek(0)
assert_equal(c.read(),
asbytes('# ' + test_header_footer +'\n1 2\n3 4\n' ))
# Test the footer keyword argument
c = StringIO()
np.savetxt(c, a, fmt='%1d', footer=test_header_footer)
c.seek(0)
assert_equal(c.read(),
asbytes('1 2\n3 4\n# ' + test_header_footer + '\n'))
# Test the commentstr keyword argument used on the header
c = StringIO()
commentstr = '% '
np.savetxt(c, a, fmt='%1d', header=test_header_footer,
comments=commentstr)
c.seek(0)
assert_equal(c.read(),
asbytes(commentstr + test_header_footer + '\n' + '1 2\n3 4\n'))
# Test the commentstr keyword argument used on the footer
c = StringIO()
commentstr = '% '
np.savetxt(c, a, fmt='%1d', footer=test_header_footer,
comments=commentstr)
c.seek(0)
assert_equal(c.read(),
asbytes('1 2\n3 4\n' + commentstr + test_header_footer + '\n'))
def test_file_roundtrip(self):
f, name = mkstemp()
os.close(f)
try:
a = np.array([(1, 2), (3, 4)])
np.savetxt(name, a)
b = np.loadtxt(name)
assert_array_equal(a, b)
finally:
os.unlink(name)
def test_complex_arrays(self):
ncols = 2
nrows = 2
a = np.zeros((ncols, nrows), dtype=np.complex128)
re = np.pi
im = np.e
a[:] = re + 1.0j * im
# One format only
c = StringIO()
np.savetxt(c, a, fmt=' %+.3e')
c.seek(0)
lines = c.readlines()
_assert_floatstr_lines_equal(lines, asbytes_nested([
' ( +3.142e+00+ +2.718e+00j) ( +3.142e+00+ +2.718e+00j)\n',
' ( +3.142e+00+ +2.718e+00j) ( +3.142e+00+ +2.718e+00j)\n']))
# One format for each real and imaginary part
c = StringIO()
np.savetxt(c, a, fmt=' %+.3e' * 2 * ncols)
c.seek(0)
lines = c.readlines()
_assert_floatstr_lines_equal(lines, asbytes_nested([
' +3.142e+00 +2.718e+00 +3.142e+00 +2.718e+00\n',
' +3.142e+00 +2.718e+00 +3.142e+00 +2.718e+00\n']))
# One format for each complex number
c = StringIO()
np.savetxt(c, a, fmt=['(%.3e%+.3ej)'] * ncols)
c.seek(0)
lines = c.readlines()
_assert_floatstr_lines_equal(lines, asbytes_nested([
'(3.142e+00+2.718e+00j) (3.142e+00+2.718e+00j)\n',
'(3.142e+00+2.718e+00j) (3.142e+00+2.718e+00j)\n']))
def _assert_floatstr_lines_equal(actual_lines, expected_lines):
"""A string comparison function that also works on Windows + Python 2.5.
This is necessary because Python 2.5 on Windows inserts an extra 0 in
the exponent of the string representation of floating point numbers.
Only used in TestSaveTxt.test_complex_arrays, no attempt made to make this
more generic.
Once Python 2.5 compatibility is dropped, simply use `assert_equal` instead
of this function.
"""
for actual, expected in zip(actual_lines, expected_lines):
if actual != expected:
expected_win25 = expected.replace("e+00", "e+000")
if actual != expected_win25:
msg = build_err_msg([actual, expected], '', verbose=True)
raise AssertionError(msg)
class TestLoadTxt(TestCase):
def test_record(self):
c = StringIO()
c.write(asbytes('1 2\n3 4'))
c.seek(0)
x = np.loadtxt(c, dtype=[('x', np.int32), ('y', np.int32)])
a = np.array([(1, 2), (3, 4)], dtype=[('x', 'i4'), ('y', 'i4')])
assert_array_equal(x, a)
d = StringIO()
d.write(asbytes('M 64.0 75.0\nF 25.0 60.0'))
d.seek(0)
mydescriptor = {'names': ('gender', 'age', 'weight'),
'formats': ('S1',
'i4', 'f4')}
b = np.array([('M', 64.0, 75.0),
('F', 25.0, 60.0)], dtype=mydescriptor)
y = np.loadtxt(d, dtype=mydescriptor)
assert_array_equal(y, b)
def test_array(self):
c = StringIO()
c.write(asbytes('1 2\n3 4'))
c.seek(0)
x = np.loadtxt(c, dtype=int)
a = np.array([[1, 2], [3, 4]], int)
assert_array_equal(x, a)
c.seek(0)
x = np.loadtxt(c, dtype=float)
a = np.array([[1, 2], [3, 4]], float)
assert_array_equal(x, a)
def test_1D(self):
c = StringIO()
c.write(asbytes('1\n2\n3\n4\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int)
a = np.array([1, 2, 3, 4], int)
assert_array_equal(x, a)
c = StringIO()
c.write(asbytes('1,2,3,4\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',')
a = np.array([1, 2, 3, 4], int)
assert_array_equal(x, a)
def test_missing(self):
c = StringIO()
c.write(asbytes('1,2,3,,5\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',', \
converters={3:lambda s: int(s or - 999)})
a = np.array([1, 2, 3, -999, 5], int)
assert_array_equal(x, a)
def test_converters_with_usecols(self):
c = StringIO()
c.write(asbytes('1,2,3,,5\n6,7,8,9,10\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',', \
converters={3:lambda s: int(s or - 999)}, \
usecols=(1, 3,))
a = np.array([[2, -999], [7, 9]], int)
assert_array_equal(x, a)
def test_comments(self):
c = StringIO()
c.write(asbytes('# comment\n1,2,3,5\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',', \
comments='#')
a = np.array([1, 2, 3, 5], int)
assert_array_equal(x, a)
def test_skiprows(self):
c = StringIO()
c.write(asbytes('comment\n1,2,3,5\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',', \
skiprows=1)
a = np.array([1, 2, 3, 5], int)
assert_array_equal(x, a)
c = StringIO()
c.write(asbytes('# comment\n1,2,3,5\n'))
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',', \
skiprows=1)
a = np.array([1, 2, 3, 5], int)
assert_array_equal(x, a)
def test_usecols(self):
a = np.array([[1, 2], [3, 4]], float)
c = StringIO()
np.savetxt(c, a)
c.seek(0)
x = np.loadtxt(c, dtype=float, usecols=(1,))
assert_array_equal(x, a[:, 1])
a = np.array([[1, 2, 3], [3, 4, 5]], float)
c = StringIO()
np.savetxt(c, a)
c.seek(0)
x = np.loadtxt(c, dtype=float, usecols=(1, 2))
assert_array_equal(x, a[:, 1:])
# Testing with arrays instead of tuples.
c.seek(0)
x = np.loadtxt(c, dtype=float, usecols=np.array([1, 2]))
assert_array_equal(x, a[:, 1:])
# Checking with dtypes defined converters.
data = '''JOE 70.1 25.3
BOB 60.5 27.9
'''
c = StringIO(data)
names = ['stid', 'temp']
dtypes = ['S4', 'f8']
arr = np.loadtxt(c, usecols=(0, 2), dtype=zip(names, dtypes))
assert_equal(arr['stid'], asbytes_nested(["JOE", "BOB"]))
assert_equal(arr['temp'], [25.3, 27.9])
def test_fancy_dtype(self):
c = StringIO()
c.write(asbytes('1,2,3.0\n4,5,6.0\n'))
c.seek(0)
dt = np.dtype([('x', int), ('y', [('t', int), ('s', float)])])
x = np.loadtxt(c, dtype=dt, delimiter=',')
a = np.array([(1, (2, 3.0)), (4, (5, 6.0))], dt)
assert_array_equal(x, a)
def test_shaped_dtype(self):
c = StringIO("aaaa 1.0 8.0 1 2 3 4 5 6")
dt = np.dtype([('name', 'S4'), ('x', float), ('y', float),
('block', int, (2, 3))])
x = np.loadtxt(c, dtype=dt)
a = np.array([('aaaa', 1.0, 8.0, [[1, 2, 3], [4, 5, 6]])],
dtype=dt)
assert_array_equal(x, a)
def test_3d_shaped_dtype(self):
c = StringIO("aaaa 1.0 8.0 1 2 3 4 5 6 7 8 9 10 11 12")
dt = np.dtype([('name', 'S4'), ('x', float), ('y', float),
('block', int, (2, 2, 3))])
x = np.loadtxt(c, dtype=dt)
a = np.array([('aaaa', 1.0, 8.0, [[[1, 2, 3], [4, 5, 6]],[[7, 8, 9], [10, 11, 12]]])],
dtype=dt)
assert_array_equal(x, a)
def test_empty_file(self):
warn_ctx = WarningManager()
warn_ctx.__enter__()
try:
warnings.filterwarnings("ignore",
message="loadtxt: Empty input file:")
c = StringIO()
x = np.loadtxt(c)
assert_equal(x.shape, (0,))
x = np.loadtxt(c, dtype=np.int64)
assert_equal(x.shape, (0,))
assert_(x.dtype == np.int64)
finally:
warn_ctx.__exit__()
def test_unused_converter(self):
c = StringIO()
c.writelines([asbytes('1 21\n'), asbytes('3 42\n')])
c.seek(0)
data = np.loadtxt(c, usecols=(1,),
converters={0: lambda s: int(s, 16)})
assert_array_equal(data, [21, 42])
c.seek(0)
data = np.loadtxt(c, usecols=(1,),
converters={1: lambda s: int(s, 16)})
assert_array_equal(data, [33, 66])
def test_dtype_with_object(self):
"Test using an explicit dtype with an object"
from datetime import date
import time
data = asbytes(""" 1; 2001-01-01
2; 2002-01-31 """)
ndtype = [('idx', int), ('code', np.object)]
func = lambda s: strptime(s.strip(), "%Y-%m-%d")
converters = {1: func}
test = np.loadtxt(StringIO(data), delimiter=";", dtype=ndtype,
converters=converters)
control = np.array([(1, datetime(2001, 1, 1)), (2, datetime(2002, 1, 31))],
dtype=ndtype)
assert_equal(test, control)
def test_uint64_type(self):
tgt = (9223372043271415339, 9223372043271415853)
c = StringIO()
c.write(asbytes("%s %s" % tgt))
c.seek(0)
res = np.loadtxt(c, dtype=np.uint64)
assert_equal(res, tgt)
def test_int64_type(self):
tgt = (-9223372036854775807, 9223372036854775807)
c = StringIO()
c.write(asbytes("%s %s" % tgt))
c.seek(0)
res = np.loadtxt(c, dtype=np.int64)
assert_equal(res, tgt)
def test_universal_newline(self):
f, name = mkstemp()
os.write(f, asbytes('1 21\r3 42\r'))
os.close(f)
try:
data = np.loadtxt(name)
assert_array_equal(data, [[1, 21], [3, 42]])
finally:
os.unlink(name)
def test_empty_field_after_tab(self):
c = StringIO()
c.write(asbytes('1 \t2 \t3\tstart \n4\t5\t6\t \n7\t8\t9.5\t'))
c.seek(0)
dt = { 'names': ('x', 'y', 'z', 'comment'),
'formats': ('<i4', '<i4', '<f4', '|S8')}
x = np.loadtxt(c, dtype=dt, delimiter='\t')
a = np.array([asbytes('start '), asbytes(' '), asbytes('')])
assert_array_equal(x['comment'], a)
def test_structure_unpack(self):
txt = StringIO(asbytes("M 21 72\nF 35 58"))
dt = { 'names': ('a', 'b', 'c'), 'formats': ('|S1', '<i4', '<f4')}
a, b, c = np.loadtxt(txt, dtype=dt, unpack=True)
assert_(a.dtype.str == '|S1')
assert_(b.dtype.str == '<i4')
assert_(c.dtype.str == '<f4')
assert_array_equal(a, np.array([asbytes('M'), asbytes('F')]))
assert_array_equal(b, np.array([21, 35]))
assert_array_equal(c, np.array([ 72., 58.]))
def test_ndmin_keyword(self):
c = StringIO()
c.write(asbytes('1,2,3\n4,5,6'))
c.seek(0)
assert_raises(ValueError, np.loadtxt, c, ndmin=3)
c.seek(0)
assert_raises(ValueError, np.loadtxt, c, ndmin=1.5)
c.seek(0)
x = np.loadtxt(c, dtype=int, delimiter=',', ndmin=1)
a = np.array([[1, 2, 3], [4, 5, 6]])
assert_array_equal(x, a)
d = StringIO()
d.write(asbytes('0,1,2'))
d.seek(0)
x = np.loadtxt(d, dtype=int, delimiter=',', ndmin=2)
assert_(x.shape == (1, 3))
d.seek(0)
x = np.loadtxt(d, dtype=int, delimiter=',', ndmin=1)
assert_(x.shape == (3,))
d.seek(0)
x = np.loadtxt(d, dtype=int, delimiter=',', ndmin=0)
assert_(x.shape == (3,))
e = StringIO()
e.write(asbytes('0\n1\n2'))
e.seek(0)
x = np.loadtxt(e, dtype=int, delimiter=',', ndmin=2)
assert_(x.shape == (3, 1))
e.seek(0)
x = np.loadtxt(e, dtype=int, delimiter=',', ndmin=1)
assert_(x.shape == (3,))
e.seek(0)
x = np.loadtxt(e, dtype=int, delimiter=',', ndmin=0)
assert_(x.shape == (3,))
# Test ndmin kw with empty file.
warn_ctx = WarningManager()
warn_ctx.__enter__()
try:
warnings.filterwarnings("ignore",
message="loadtxt: Empty input file:")
f = StringIO()
assert_(np.loadtxt(f, ndmin=2).shape == (0, 1,))
assert_(np.loadtxt(f, ndmin=1).shape == (0,))
finally:
warn_ctx.__exit__()
def test_generator_source(self):
def count():
for i in range(10):
yield asbytes("%d" % i)
res = np.loadtxt(count())
assert_array_equal(res, np.arange(10))
class Testfromregex(TestCase):
def test_record(self):
c = StringIO()
c.write(asbytes('1.312 foo\n1.534 bar\n4.444 qux'))
c.seek(0)
dt = [('num', np.float64), ('val', 'S3')]
x = np.fromregex(c, r"([0-9.]+)\s+(...)", dt)
a = np.array([(1.312, 'foo'), (1.534, 'bar'), (4.444, 'qux')],
dtype=dt)
assert_array_equal(x, a)
def test_record_2(self):
c = StringIO()
c.write(asbytes('1312 foo\n1534 bar\n4444 qux'))
c.seek(0)
dt = [('num', np.int32), ('val', 'S3')]
x = np.fromregex(c, r"(\d+)\s+(...)", dt)
a = np.array([(1312, 'foo'), (1534, 'bar'), (4444, 'qux')],
dtype=dt)
assert_array_equal(x, a)
def test_record_3(self):
c = StringIO()
c.write(asbytes('1312 foo\n1534 bar\n4444 qux'))
c.seek(0)
dt = [('num', np.float64)]
x = np.fromregex(c, r"(\d+)\s+...", dt)
a = np.array([(1312,), (1534,), (4444,)], dtype=dt)
assert_array_equal(x, a)
#####--------------------------------------------------------------------------
class TestFromTxt(TestCase):
#
def test_record(self):
"Test w/ explicit dtype"
data = StringIO(asbytes('1 2\n3 4'))
# data.seek(0)
test = np.ndfromtxt(data, dtype=[('x', np.int32), ('y', np.int32)])
control = np.array([(1, 2), (3, 4)], dtype=[('x', 'i4'), ('y', 'i4')])
assert_equal(test, control)
#
data = StringIO('M 64.0 75.0\nF 25.0 60.0')
# data.seek(0)
descriptor = {'names': ('gender', 'age', 'weight'),
'formats': ('S1', 'i4', 'f4')}
control = np.array([('M', 64.0, 75.0), ('F', 25.0, 60.0)],
dtype=descriptor)
test = np.ndfromtxt(data, dtype=descriptor)
assert_equal(test, control)
def test_array(self):
"Test outputing a standard ndarray"
data = StringIO('1 2\n3 4')
control = np.array([[1, 2], [3, 4]], dtype=int)
test = np.ndfromtxt(data, dtype=int)
assert_array_equal(test, control)
#
data.seek(0)
control = np.array([[1, 2], [3, 4]], dtype=float)
test = np.loadtxt(data, dtype=float)
assert_array_equal(test, control)
def test_1D(self):
"Test squeezing to 1D"
control = np.array([1, 2, 3, 4], int)
#
data = StringIO('1\n2\n3\n4\n')
test = np.ndfromtxt(data, dtype=int)
assert_array_equal(test, control)
#
data = StringIO('1,2,3,4\n')
test = np.ndfromtxt(data, dtype=int, delimiter=asbytes(','))
assert_array_equal(test, control)
def test_comments(self):
"Test the stripping of comments"
control = np.array([1, 2, 3, 5], int)
# Comment on its own line
data = StringIO('# comment\n1,2,3,5\n')
test = np.ndfromtxt(data, dtype=int, delimiter=asbytes(','), comments=asbytes('#'))
assert_equal(test, control)
# Comment at the end of a line
data = StringIO('1,2,3,5# comment\n')
test = np.ndfromtxt(data, dtype=int, delimiter=asbytes(','), comments=asbytes('#'))
assert_equal(test, control)
def test_skiprows(self):
"Test row skipping"
control = np.array([1, 2, 3, 5], int)
kwargs = dict(dtype=int, delimiter=asbytes(','))
#
data = StringIO('comment\n1,2,3,5\n')
test = np.ndfromtxt(data, skip_header=1, **kwargs)
assert_equal(test, control)
#
data = StringIO('# comment\n1,2,3,5\n')
test = np.loadtxt(data, skiprows=1, **kwargs)
assert_equal(test, control)
def test_skip_footer(self):
data = ["# %i" % i for i in range(1, 6)]
data.append("A, B, C")
data.extend(["%i,%3.1f,%03s" % (i, i, i) for i in range(51)])
data[-1] = "99,99"
kwargs = dict(delimiter=",", names=True, skip_header=5, skip_footer=10)
test = np.genfromtxt(StringIO(asbytes("\n".join(data))), **kwargs)
ctrl = np.array([("%f" % i, "%f" % i, "%f" % i) for i in range(41)],
dtype=[(_, float) for _ in "ABC"])
assert_equal(test, ctrl)
def test_skip_footer_with_invalid(self):
warn_ctx = WarningManager()
warn_ctx.__enter__()
try:
basestr = '1 1\n2 2\n3 3\n4 4\n5 \n6 \n7 \n'
warnings.filterwarnings("ignore")
# Footer too small to get rid of all invalid values
assert_raises(ValueError, np.genfromtxt,
StringIO(basestr), skip_footer=1)
# except ValueError:
# pass
a = np.genfromtxt(StringIO(basestr), skip_footer=1, invalid_raise=False)
assert_equal(a, np.array([[1., 1.], [2., 2.], [3., 3.], [4., 4.]]))
#
a = np.genfromtxt(StringIO(basestr), skip_footer=3)
assert_equal(a, np.array([[1., 1.], [2., 2.], [3., 3.], [4., 4.]]))
#
basestr = '1 1\n2 \n3 3\n4 4\n5 \n6 6\n7 7\n'
a = np.genfromtxt(StringIO(basestr), skip_footer=1, invalid_raise=False)
assert_equal(a, np.array([[1., 1.], [3., 3.], [4., 4.], [6., 6.]]))
a = np.genfromtxt(StringIO(basestr), skip_footer=3, invalid_raise=False)
assert_equal(a, np.array([[1., 1.], [3., 3.], [4., 4.]]))
finally:
warn_ctx.__exit__()
def test_header(self):
"Test retrieving a header"
data = StringIO('gender age weight\nM 64.0 75.0\nF 25.0 60.0')
test = np.ndfromtxt(data, dtype=None, names=True)
control = {'gender': np.array(asbytes_nested(['M', 'F'])),
'age': np.array([64.0, 25.0]),
'weight': np.array([75.0, 60.0])}
assert_equal(test['gender'], control['gender'])
assert_equal(test['age'], control['age'])
assert_equal(test['weight'], control['weight'])
def test_auto_dtype(self):
"Test the automatic definition of the output dtype"
data = StringIO('A 64 75.0 3+4j True\nBCD 25 60.0 5+6j False')
test = np.ndfromtxt(data, dtype=None)
control = [np.array(asbytes_nested(['A', 'BCD'])),
np.array([64, 25]),
np.array([75.0, 60.0]),
np.array([3 + 4j, 5 + 6j]),
np.array([True, False]), ]
assert_equal(test.dtype.names, ['f0', 'f1', 'f2', 'f3', 'f4'])
for (i, ctrl) in enumerate(control):
assert_equal(test['f%i' % i], ctrl)
def test_auto_dtype_uniform(self):
"Tests whether the output dtype can be uniformized"
data = StringIO('1 2 3 4\n5 6 7 8\n')
test = np.ndfromtxt(data, dtype=None)
control = np.array([[1, 2, 3, 4], [5, 6, 7, 8]])
assert_equal(test, control)
def test_fancy_dtype(self):
"Check that a nested dtype isn't MIA"
data = StringIO('1,2,3.0\n4,5,6.0\n')
fancydtype = np.dtype([('x', int), ('y', [('t', int), ('s', float)])])
test = np.ndfromtxt(data, dtype=fancydtype, delimiter=',')
control = np.array([(1, (2, 3.0)), (4, (5, 6.0))], dtype=fancydtype)
assert_equal(test, control)
def test_names_overwrite(self):
"Test overwriting the names of the dtype"
descriptor = {'names': ('g', 'a', 'w'),
'formats': ('S1', 'i4', 'f4')}
data = StringIO('M 64.0 75.0\nF 25.0 60.0')
names = ('gender', 'age', 'weight')
test = np.ndfromtxt(data, dtype=descriptor, names=names)
descriptor['names'] = names
control = np.array([('M', 64.0, 75.0),
('F', 25.0, 60.0)], dtype=descriptor)
assert_equal(test, control)
def test_commented_header(self):
"Check that names can be retrieved even if the line is commented out."
data = StringIO("""
#gender age weight
M 21 72.100000
F 35 58.330000
M 33 21.99
""")
# The # is part of the first name and should be deleted automatically.
test = np.genfromtxt(data, names=True, dtype=None)
ctrl = np.array([('M', 21, 72.1), ('F', 35, 58.33), ('M', 33, 21.99)],
dtype=[('gender', '|S1'), ('age', int), ('weight', float)])
assert_equal(test, ctrl)
# Ditto, but we should get rid of the first element
data = StringIO("""
# gender age weight
M 21 72.100000
F 35 58.330000
M 33 21.99
""")
test = np.genfromtxt(data, names=True, dtype=None)
assert_equal(test, ctrl)
def test_autonames_and_usecols(self):
"Tests names and usecols"
data = StringIO('A B C D\n aaaa 121 45 9.1')
test = np.ndfromtxt(data, usecols=('A', 'C', 'D'),
names=True, dtype=None)
control = np.array(('aaaa', 45, 9.1),
dtype=[('A', '|S4'), ('C', int), ('D', float)])
assert_equal(test, control)
def test_converters_with_usecols(self):
"Test the combination user-defined converters and usecol"
data = StringIO('1,2,3,,5\n6,7,8,9,10\n')
test = np.ndfromtxt(data, dtype=int, delimiter=',',
converters={3:lambda s: int(s or - 999)},
usecols=(1, 3,))
control = np.array([[2, -999], [7, 9]], int)
assert_equal(test, control)
def test_converters_with_usecols_and_names(self):
"Tests names and usecols"
data = StringIO('A B C D\n aaaa 121 45 9.1')
test = np.ndfromtxt(data, usecols=('A', 'C', 'D'), names=True,
dtype=None, converters={'C':lambda s: 2 * int(s)})
control = np.array(('aaaa', 90, 9.1),
dtype=[('A', '|S4'), ('C', int), ('D', float)])
assert_equal(test, control)
def test_converters_cornercases(self):
"Test the conversion to datetime."
converter = {'date': lambda s: strptime(s, '%Y-%m-%d %H:%M:%SZ')}
data = StringIO('2009-02-03 12:00:00Z, 72214.0')
test = np.ndfromtxt(data, delimiter=',', dtype=None,
names=['date', 'stid'], converters=converter)
control = np.array((datetime(2009, 02, 03), 72214.),
dtype=[('date', np.object_), ('stid', float)])
assert_equal(test, control)
def test_converters_cornercases2(self):
"Test the conversion to datetime64."
converter = {'date': lambda s: np.datetime64(strptime(s, '%Y-%m-%d %H:%M:%SZ'))}
data = StringIO('2009-02-03 12:00:00Z, 72214.0')
test = np.ndfromtxt(data, delimiter=',', dtype=None,
names=['date', 'stid'], converters=converter)
control = np.array((datetime(2009, 02, 03), 72214.),
dtype=[('date', 'datetime64[us]'), ('stid', float)])
assert_equal(test, control)
def test_unused_converter(self):
"Test whether unused converters are forgotten"
data = StringIO("1 21\n 3 42\n")
test = np.ndfromtxt(data, usecols=(1,),
converters={0: lambda s: int(s, 16)})
assert_equal(test, [21, 42])
#
data.seek(0)
test = np.ndfromtxt(data, usecols=(1,),
converters={1: lambda s: int(s, 16)})
assert_equal(test, [33, 66])
def test_invalid_converter(self):
strip_rand = lambda x : float((asbytes('r') in x.lower() and x.split()[-1]) or
(not asbytes('r') in x.lower() and x.strip() or 0.0))
strip_per = lambda x : float((asbytes('%') in x.lower() and x.split()[0]) or
(not asbytes('%') in x.lower() and x.strip() or 0.0))
s = StringIO("D01N01,10/1/2003 ,1 %,R 75,400,600\r\n" \
"L24U05,12/5/2003, 2 %,1,300, 150.5\r\n"
"D02N03,10/10/2004,R 1,,7,145.55")
kwargs = dict(converters={2 : strip_per, 3 : strip_rand}, delimiter=",",
dtype=None)
assert_raises(ConverterError, np.genfromtxt, s, **kwargs)
def test_tricky_converter_bug1666(self):
"Test some corner case"
s = StringIO('q1,2\nq3,4')
cnv = lambda s:float(s[1:])
test = np.genfromtxt(s, delimiter=',', converters={0:cnv})
control = np.array([[1., 2.], [3., 4.]])
assert_equal(test, control)
def test_dtype_with_converters(self):
dstr = "2009; 23; 46"
test = np.ndfromtxt(StringIO(dstr,),
delimiter=";", dtype=float, converters={0:bytes})
control = np.array([('2009', 23., 46)],
dtype=[('f0', '|S4'), ('f1', float), ('f2', float)])
assert_equal(test, control)
test = np.ndfromtxt(StringIO(dstr,),
delimiter=";", dtype=float, converters={0:float})
control = np.array([2009., 23., 46],)
assert_equal(test, control)
def test_dtype_with_object(self):
"Test using an explicit dtype with an object"
from datetime import date
import time
data = asbytes(""" 1; 2001-01-01
2; 2002-01-31 """)
ndtype = [('idx', int), ('code', np.object)]
func = lambda s: strptime(s.strip(), "%Y-%m-%d")
converters = {1: func}
test = np.genfromtxt(StringIO(data), delimiter=";", dtype=ndtype,
converters=converters)
control = np.array([(1, datetime(2001, 1, 1)), (2, datetime(2002, 1, 31))],
dtype=ndtype)
assert_equal(test, control)
#
ndtype = [('nest', [('idx', int), ('code', np.object)])]
try:
test = np.genfromtxt(StringIO(data), delimiter=";",
dtype=ndtype, converters=converters)
except NotImplementedError:
pass
else:
errmsg = "Nested dtype involving objects should be supported."
raise AssertionError(errmsg)
def test_userconverters_with_explicit_dtype(self):
"Test user_converters w/ explicit (standard) dtype"
data = StringIO('skip,skip,2001-01-01,1.0,skip')
test = np.genfromtxt(data, delimiter=",", names=None, dtype=float,
usecols=(2, 3), converters={2: bytes})
control = np.array([('2001-01-01', 1.)],
dtype=[('', '|S10'), ('', float)])
assert_equal(test, control)
def test_spacedelimiter(self):
"Test space delimiter"
data = StringIO("1 2 3 4 5\n6 7 8 9 10")
test = np.ndfromtxt(data)
control = np.array([[ 1., 2., 3., 4., 5.],
[ 6., 7., 8., 9., 10.]])
assert_equal(test, control)
def test_integer_delimiter(self):
"Test using an integer for delimiter"
data = " 1 2 3\n 4 5 67\n890123 4"
test = np.genfromtxt(StringIO(data), delimiter=3)
control = np.array([[1, 2, 3], [4, 5, 67], [890, 123, 4]])
assert_equal(test, control)
def test_missing(self):
data = StringIO('1,2,3,,5\n')
test = np.ndfromtxt(data, dtype=int, delimiter=',', \
converters={3:lambda s: int(s or - 999)})
control = np.array([1, 2, 3, -999, 5], int)
assert_equal(test, control)
def test_missing_with_tabs(self):
"Test w/ a delimiter tab"
txt = "1\t2\t3\n\t2\t\n1\t\t3"
test = np.genfromtxt(StringIO(txt), delimiter="\t",
usemask=True,)
ctrl_d = np.array([(1, 2, 3), (np.nan, 2, np.nan), (1, np.nan, 3)],)
ctrl_m = np.array([(0, 0, 0), (1, 0, 1), (0, 1, 0)], dtype=bool)
assert_equal(test.data, ctrl_d)
assert_equal(test.mask, ctrl_m)
def test_usecols(self):
"Test the selection of columns"
# Select 1 column
control = np.array([[1, 2], [3, 4]], float)
data = StringIO()
np.savetxt(data, control)
data.seek(0)
test = np.ndfromtxt(data, dtype=float, usecols=(1,))
assert_equal(test, control[:, 1])
#
control = np.array([[1, 2, 3], [3, 4, 5]], float)
data = StringIO()
np.savetxt(data, control)
data.seek(0)
test = np.ndfromtxt(data, dtype=float, usecols=(1, 2))
assert_equal(test, control[:, 1:])
# Testing with arrays instead of tuples.
data.seek(0)
test = np.ndfromtxt(data, dtype=float, usecols=np.array([1, 2]))
assert_equal(test, control[:, 1:])
def test_usecols_as_css(self):
"Test giving usecols with a comma-separated string"
data = "1 2 3\n4 5 6"
test = np.genfromtxt(StringIO(data),
names="a, b, c", usecols="a, c")
ctrl = np.array([(1, 3), (4, 6)], dtype=[(_, float) for _ in "ac"])
assert_equal(test, ctrl)
def test_usecols_with_structured_dtype(self):
"Test usecols with an explicit structured dtype"
data = StringIO("""JOE 70.1 25.3\nBOB 60.5 27.9""")
names = ['stid', 'temp']
dtypes = ['S4', 'f8']
test = np.ndfromtxt(data, usecols=(0, 2), dtype=zip(names, dtypes))
assert_equal(test['stid'], asbytes_nested(["JOE", "BOB"]))
assert_equal(test['temp'], [25.3, 27.9])
def test_usecols_with_integer(self):
"Test usecols with an integer"
test = np.genfromtxt(StringIO("1 2 3\n4 5 6"), usecols=0)
assert_equal(test, np.array([1., 4.]))
def test_usecols_with_named_columns(self):
"Test usecols with named columns"
ctrl = np.array([(1, 3), (4, 6)], dtype=[('a', float), ('c', float)])
data = "1 2 3\n4 5 6"
kwargs = dict(names="a, b, c")
test = np.genfromtxt(StringIO(data), usecols=(0, -1), **kwargs)
assert_equal(test, ctrl)
test = np.genfromtxt(StringIO(data),
usecols=('a', 'c'), **kwargs)
assert_equal(test, ctrl)
def test_empty_file(self):
"Test that an empty file raises the proper warning."
warn_ctx = WarningManager()
warn_ctx.__enter__()
try:
warnings.filterwarnings("ignore", message="genfromtxt: Empty input file:")
data = StringIO()
test = np.genfromtxt(data)
assert_equal(test, np.array([]))
finally:
warn_ctx.__exit__()
def test_fancy_dtype_alt(self):
"Check that a nested dtype isn't MIA"
data = StringIO('1,2,3.0\n4,5,6.0\n')
fancydtype = np.dtype([('x', int), ('y', [('t', int), ('s', float)])])
test = np.mafromtxt(data, dtype=fancydtype, delimiter=',')
control = ma.array([(1, (2, 3.0)), (4, (5, 6.0))], dtype=fancydtype)
assert_equal(test, control)
def test_shaped_dtype(self):
c = StringIO("aaaa 1.0 8.0 1 2 3 4 5 6")
dt = np.dtype([('name', 'S4'), ('x', float), ('y', float),
('block', int, (2, 3))])
x = np.ndfromtxt(c, dtype=dt)
a = np.array([('aaaa', 1.0, 8.0, [[1, 2, 3], [4, 5, 6]])],
dtype=dt)
assert_array_equal(x, a)
def test_withmissing(self):
data = StringIO('A,B\n0,1\n2,N/A')
kwargs = dict(delimiter=",", missing_values="N/A", names=True)
test = np.mafromtxt(data, dtype=None, **kwargs)
control = ma.array([(0, 1), (2, -1)],
mask=[(False, False), (False, True)],
dtype=[('A', np.int), ('B', np.int)])
assert_equal(test, control)
assert_equal(test.mask, control.mask)
#
data.seek(0)
test = np.mafromtxt(data, **kwargs)
control = ma.array([(0, 1), (2, -1)],
mask=[(False, False), (False, True)],
dtype=[('A', np.float), ('B', np.float)])
assert_equal(test, control)
assert_equal(test.mask, control.mask)
def test_user_missing_values(self):
data = "A, B, C\n0, 0., 0j\n1, N/A, 1j\n-9, 2.2, N/A\n3, -99, 3j"
basekwargs = dict(dtype=None, delimiter=",", names=True,)
mdtype = [('A', int), ('B', float), ('C', complex)]
#
test = np.mafromtxt(StringIO(data), missing_values="N/A",
**basekwargs)
control = ma.array([(0, 0.0, 0j), (1, -999, 1j),
(-9, 2.2, -999j), (3, -99, 3j)],
mask=[(0, 0, 0), (0, 1, 0), (0, 0, 1), (0, 0, 0)],
dtype=mdtype)
assert_equal(test, control)
#
basekwargs['dtype'] = mdtype
test = np.mafromtxt(StringIO(data),
missing_values={0:-9, 1:-99, 2:-999j}, **basekwargs)
control = ma.array([(0, 0.0, 0j), (1, -999, 1j),
(-9, 2.2, -999j), (3, -99, 3j)],
mask=[(0, 0, 0), (0, 1, 0), (1, 0, 1), (0, 1, 0)],
dtype=mdtype)
assert_equal(test, control)
#
test = np.mafromtxt(StringIO(data),
missing_values={0:-9, 'B':-99, 'C':-999j},
**basekwargs)
control = ma.array([(0, 0.0, 0j), (1, -999, 1j),
(-9, 2.2, -999j), (3, -99, 3j)],
mask=[(0, 0, 0), (0, 1, 0), (1, 0, 1), (0, 1, 0)],
dtype=mdtype)
assert_equal(test, control)
def test_user_filling_values(self):
"Test with missing and filling values"
ctrl = np.array([(0, 3), (4, -999)], dtype=[('a', int), ('b', int)])
data = "N/A, 2, 3\n4, ,???"
kwargs = dict(delimiter=",",
dtype=int,
names="a,b,c",
missing_values={0:"N/A", 'b':" ", 2:"???"},
filling_values={0:0, 'b':0, 2:-999})
test = np.genfromtxt(StringIO(data), **kwargs)
ctrl = np.array([(0, 2, 3), (4, 0, -999)],
dtype=[(_, int) for _ in "abc"])
assert_equal(test, ctrl)
#
test = np.genfromtxt(StringIO(data), usecols=(0, -1), **kwargs)
ctrl = np.array([(0, 3), (4, -999)], dtype=[(_, int) for _ in "ac"])
assert_equal(test, ctrl)
def test_withmissing_float(self):
data = StringIO('A,B\n0,1.5\n2,-999.00')
test = np.mafromtxt(data, dtype=None, delimiter=',',
missing_values='-999.0', names=True,)
control = ma.array([(0, 1.5), (2, -1.)],
mask=[(False, False), (False, True)],
dtype=[('A', np.int), ('B', np.float)])
assert_equal(test, control)
assert_equal(test.mask, control.mask)
def test_with_masked_column_uniform(self):
"Test masked column"
data = StringIO('1 2 3\n4 5 6\n')
test = np.genfromtxt(data, dtype=None,
missing_values='2,5', usemask=True)
control = ma.array([[1, 2, 3], [4, 5, 6]], mask=[[0, 1, 0], [0, 1, 0]])
assert_equal(test, control)
def test_with_masked_column_various(self):
"Test masked column"
data = StringIO('True 2 3\nFalse 5 6\n')
test = np.genfromtxt(data, dtype=None,
missing_values='2,5', usemask=True)
control = ma.array([(1, 2, 3), (0, 5, 6)],
mask=[(0, 1, 0), (0, 1, 0)],
dtype=[('f0', bool), ('f1', bool), ('f2', int)])
assert_equal(test, control)
def test_invalid_raise(self):
"Test invalid raise"
data = ["1, 1, 1, 1, 1"] * 50
for i in range(5):
data[10 * i] = "2, 2, 2, 2 2"
data.insert(0, "a, b, c, d, e")
mdata = StringIO("\n".join(data))
#
kwargs = dict(delimiter=",", dtype=None, names=True)
# XXX: is there a better way to get the return value of the callable in
# assert_warns ?
ret = {}
def f(_ret={}):
_ret['mtest'] = np.ndfromtxt(mdata, invalid_raise=False, **kwargs)
assert_warns(ConversionWarning, f, _ret=ret)
mtest = ret['mtest']
assert_equal(len(mtest), 45)
assert_equal(mtest, np.ones(45, dtype=[(_, int) for _ in 'abcde']))
#
mdata.seek(0)
assert_raises(ValueError, np.ndfromtxt, mdata,
delimiter=",", names=True)
def test_invalid_raise_with_usecols(self):
"Test invalid_raise with usecols"
data = ["1, 1, 1, 1, 1"] * 50
for i in range(5):
data[10 * i] = "2, 2, 2, 2 2"
data.insert(0, "a, b, c, d, e")
mdata = StringIO("\n".join(data))
kwargs = dict(delimiter=",", dtype=None, names=True,
invalid_raise=False)
# XXX: is there a better way to get the return value of the callable in
# assert_warns ?
ret = {}
def f(_ret={}):
_ret['mtest'] = np.ndfromtxt(mdata, usecols=(0, 4), **kwargs)
assert_warns(ConversionWarning, f, _ret=ret)
mtest = ret['mtest']
assert_equal(len(mtest), 45)
assert_equal(mtest, np.ones(45, dtype=[(_, int) for _ in 'ae']))
#
mdata.seek(0)
mtest = np.ndfromtxt(mdata, usecols=(0, 1), **kwargs)
assert_equal(len(mtest), 50)
control = np.ones(50, dtype=[(_, int) for _ in 'ab'])
control[[10 * _ for _ in range(5)]] = (2, 2)
assert_equal(mtest, control)
def test_inconsistent_dtype(self):
"Test inconsistent dtype"
data = ["1, 1, 1, 1, -1.1"] * 50
mdata = StringIO("\n".join(data))
converters = {4: lambda x:"(%s)" % x}
kwargs = dict(delimiter=",", converters=converters,
dtype=[(_, int) for _ in 'abcde'],)
assert_raises(ValueError, np.genfromtxt, mdata, **kwargs)
def test_default_field_format(self):
"Test default format"
data = "0, 1, 2.3\n4, 5, 6.7"
mtest = np.ndfromtxt(StringIO(data),
delimiter=",", dtype=None, defaultfmt="f%02i")
ctrl = np.array([(0, 1, 2.3), (4, 5, 6.7)],
dtype=[("f00", int), ("f01", int), ("f02", float)])
assert_equal(mtest, ctrl)
def test_single_dtype_wo_names(self):
"Test single dtype w/o names"
data = "0, 1, 2.3\n4, 5, 6.7"
mtest = np.ndfromtxt(StringIO(data),
delimiter=",", dtype=float, defaultfmt="f%02i")
ctrl = np.array([[0., 1., 2.3], [4., 5., 6.7]], dtype=float)
assert_equal(mtest, ctrl)
def test_single_dtype_w_explicit_names(self):
"Test single dtype w explicit names"
data = "0, 1, 2.3\n4, 5, 6.7"
mtest = np.ndfromtxt(StringIO(data),
delimiter=",", dtype=float, names="a, b, c")
ctrl = np.array([(0., 1., 2.3), (4., 5., 6.7)],
dtype=[(_, float) for _ in "abc"])
assert_equal(mtest, ctrl)
def test_single_dtype_w_implicit_names(self):
"Test single dtype w implicit names"
data = "a, b, c\n0, 1, 2.3\n4, 5, 6.7"
mtest = np.ndfromtxt(StringIO(data),
delimiter=",", dtype=float, names=True)
ctrl = np.array([(0., 1., 2.3), (4., 5., 6.7)],
dtype=[(_, float) for _ in "abc"])
assert_equal(mtest, ctrl)
def test_easy_structured_dtype(self):
"Test easy structured dtype"
data = "0, 1, 2.3\n4, 5, 6.7"
mtest = np.ndfromtxt(StringIO(data), delimiter=",",
dtype=(int, float, float), defaultfmt="f_%02i")
ctrl = np.array([(0, 1., 2.3), (4, 5., 6.7)],
dtype=[("f_00", int), ("f_01", float), ("f_02", float)])
assert_equal(mtest, ctrl)
def test_autostrip(self):
"Test autostrip"
data = "01/01/2003 , 1.3, abcde"
kwargs = dict(delimiter=",", dtype=None)
mtest = np.ndfromtxt(StringIO(data), **kwargs)
ctrl = np.array([('01/01/2003 ', 1.3, ' abcde')],
dtype=[('f0', '|S12'), ('f1', float), ('f2', '|S8')])
assert_equal(mtest, ctrl)
mtest = np.ndfromtxt(StringIO(data), autostrip=True, **kwargs)
ctrl = np.array([('01/01/2003', 1.3, 'abcde')],
dtype=[('f0', '|S10'), ('f1', float), ('f2', '|S5')])
assert_equal(mtest, ctrl)
def test_replace_space(self):
"Test the 'replace_space' option"
txt = "A.A, B (B), C:C\n1, 2, 3.14"
# Test default: replace ' ' by '_' and delete non-alphanum chars
test = np.genfromtxt(StringIO(txt),
delimiter=",", names=True, dtype=None)
ctrl_dtype = [("AA", int), ("B_B", int), ("CC", float)]
ctrl = np.array((1, 2, 3.14), dtype=ctrl_dtype)
assert_equal(test, ctrl)
# Test: no replace, no delete
test = np.genfromtxt(StringIO(txt),
delimiter=",", names=True, dtype=None,
replace_space='', deletechars='')
ctrl_dtype = [("A.A", int), ("B (B)", int), ("C:C", float)]
ctrl = np.array((1, 2, 3.14), dtype=ctrl_dtype)
assert_equal(test, ctrl)
# Test: no delete (spaces are replaced by _)
test = np.genfromtxt(StringIO(txt),
delimiter=",", names=True, dtype=None,
deletechars='')
ctrl_dtype = [("A.A", int), ("B_(B)", int), ("C:C", float)]
ctrl = np.array((1, 2, 3.14), dtype=ctrl_dtype)
assert_equal(test, ctrl)
def test_incomplete_names(self):
"Test w/ incomplete names"
data = "A,,C\n0,1,2\n3,4,5"
kwargs = dict(delimiter=",", names=True)
# w/ dtype=None
ctrl = np.array([(0, 1, 2), (3, 4, 5)],
dtype=[(_, int) for _ in ('A', 'f0', 'C')])
test = np.ndfromtxt(StringIO(data), dtype=None, **kwargs)
assert_equal(test, ctrl)
# w/ default dtype
ctrl = np.array([(0, 1, 2), (3, 4, 5)],
dtype=[(_, float) for _ in ('A', 'f0', 'C')])
test = np.ndfromtxt(StringIO(data), **kwargs)
def test_names_auto_completion(self):
"Make sure that names are properly completed"
data = "1 2 3\n 4 5 6"
test = np.genfromtxt(StringIO(data),
dtype=(int, float, int), names="a")
ctrl = np.array([(1, 2, 3), (4, 5, 6)],
dtype=[('a', int), ('f0', float), ('f1', int)])
assert_equal(test, ctrl)
def test_names_with_usecols_bug1636(self):
"Make sure we pick up the right names w/ usecols"
data = "A,B,C,D,E\n0,1,2,3,4\n0,1,2,3,4\n0,1,2,3,4"
ctrl_names = ("A", "C", "E")
test = np.genfromtxt(StringIO(data),
dtype=(int, int, int), delimiter=",",
usecols=(0, 2, 4), names=True)
assert_equal(test.dtype.names, ctrl_names)
#
test = np.genfromtxt(StringIO(data),
dtype=(int, int, int), delimiter=",",
usecols=("A", "C", "E"), names=True)
assert_equal(test.dtype.names, ctrl_names)
#
test = np.genfromtxt(StringIO(data),
dtype=int, delimiter=",",
usecols=("A", "C", "E"), names=True)
assert_equal(test.dtype.names, ctrl_names)
def test_fixed_width_names(self):
"Test fix-width w/ names"
data = " A B C\n 0 1 2.3\n 45 67 9."
kwargs = dict(delimiter=(5, 5, 4), names=True, dtype=None)
ctrl = np.array([(0, 1, 2.3), (45, 67, 9.)],
dtype=[('A', int), ('B', int), ('C', float)])
test = np.ndfromtxt(StringIO(data), **kwargs)
assert_equal(test, ctrl)
#
kwargs = dict(delimiter=5, names=True, dtype=None)
ctrl = np.array([(0, 1, 2.3), (45, 67, 9.)],
dtype=[('A', int), ('B', int), ('C', float)])
test = np.ndfromtxt(StringIO(data), **kwargs)
assert_equal(test, ctrl)
def test_filling_values(self):
"Test missing values"
data = "1, 2, 3\n1, , 5\n0, 6, \n"
kwargs = dict(delimiter=",", dtype=None, filling_values= -999)
ctrl = np.array([[1, 2, 3], [1, -999, 5], [0, 6, -999]], dtype=int)
test = np.ndfromtxt(StringIO(data), **kwargs)
assert_equal(test, ctrl)
def test_comments_is_none(self):
# Github issue 329 (None was previously being converted to 'None').
test = np.genfromtxt(StringIO("test1,testNonetherestofthedata"),
dtype=None, comments=None, delimiter=',')
assert_equal(test[1], asbytes('testNonetherestofthedata'))
test = np.genfromtxt(StringIO("test1, testNonetherestofthedata"),
dtype=None, comments=None, delimiter=',')
assert_equal(test[1], asbytes(' testNonetherestofthedata'))
def test_recfromtxt(self):
#
data = StringIO('A,B\n0,1\n2,3')
kwargs = dict(delimiter=",", missing_values="N/A", names=True)
test = np.recfromtxt(data, **kwargs)
control = np.array([(0, 1), (2, 3)],
dtype=[('A', np.int), ('B', np.int)])
self.assertTrue(isinstance(test, np.recarray))
assert_equal(test, control)
#
data = StringIO('A,B\n0,1\n2,N/A')
test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
control = ma.array([(0, 1), (2, -1)],
mask=[(False, False), (False, True)],
dtype=[('A', np.int), ('B', np.int)])
assert_equal(test, control)
assert_equal(test.mask, control.mask)
assert_equal(test.A, [0, 2])
def test_recfromcsv(self):
#
data = StringIO('A,B\n0,1\n2,3')
kwargs = dict(missing_values="N/A", names=True, case_sensitive=True)
test = np.recfromcsv(data, dtype=None, **kwargs)
control = np.array([(0, 1), (2, 3)],
dtype=[('A', np.int), ('B', np.int)])
self.assertTrue(isinstance(test, np.recarray))
assert_equal(test, control)
#
data = StringIO('A,B\n0,1\n2,N/A')
test = np.recfromcsv(data, dtype=None, usemask=True, **kwargs)
control = ma.array([(0, 1), (2, -1)],
mask=[(False, False), (False, True)],
dtype=[('A', np.int), ('B', np.int)])
assert_equal(test, control)
assert_equal(test.mask, control.mask)
assert_equal(test.A, [0, 2])
#
data = StringIO('A,B\n0,1\n2,3')
test = np.recfromcsv(data, missing_values='N/A',)
control = np.array([(0, 1), (2, 3)],
dtype=[('a', np.int), ('b', np.int)])
self.assertTrue(isinstance(test, np.recarray))
assert_equal(test, control)
def test_gft_using_filename(self):
# Test that we can load data from a filename as well as a file object
wanted = np.arange(6).reshape((2,3))
if sys.version_info[0] >= 3:
# python 3k is known to fail for '\r'
linesep = ('\n', '\r\n')
else:
linesep = ('\n', '\r\n', '\r')
for sep in linesep:
data = '0 1 2' + sep + '3 4 5'
f, name = mkstemp()
# We can't use NamedTemporaryFile on windows, because we cannot
# reopen the file.
try:
os.write(f, asbytes(data))
assert_array_equal(np.genfromtxt(name), wanted)
finally:
os.close(f)
os.unlink(name)
def test_gft_using_generator(self):
def count():
for i in range(10):
yield asbytes("%d" % i)
res = np.genfromtxt(count())
assert_array_equal(res, np.arange(10))
def test_gzip_load():
a = np.random.random((5, 5))
s = StringIO()
f = gzip.GzipFile(fileobj=s, mode="w")
np.save(f, a)
f.close()
s.seek(0)
f = gzip.GzipFile(fileobj=s, mode="r")
assert_array_equal(np.load(f), a)
def test_gzip_loadtxt():
# Thanks to another windows brokeness, we can't use
# NamedTemporaryFile: a file created from this function cannot be
# reopened by another open call. So we first put the gzipped string
# of the test reference array, write it to a securely opened file,
# which is then read from by the loadtxt function
s = StringIO()
g = gzip.GzipFile(fileobj=s, mode='w')
g.write(asbytes('1 2 3\n'))
g.close()
s.seek(0)
f, name = mkstemp(suffix='.gz')
try:
os.write(f, s.read())
s.close()
assert_array_equal(np.loadtxt(name), [1, 2, 3])
finally:
os.close(f)
os.unlink(name)
def test_gzip_loadtxt_from_string():
s = StringIO()
f = gzip.GzipFile(fileobj=s, mode="w")
f.write(asbytes('1 2 3\n'))
f.close()
s.seek(0)
f = gzip.GzipFile(fileobj=s, mode="r")
assert_array_equal(np.loadtxt(f), [1, 2, 3])
def test_npzfile_dict():
s = StringIO()
x = np.zeros((3, 3))
y = np.zeros((3, 3))
np.savez(s, x=x, y=y)
s.seek(0)
z = np.load(s)
assert_('x' in z)
assert_('y' in z)
assert_('x' in z.keys())
assert_('y' in z.keys())
for f, a in z.iteritems():
assert_(f in ['x', 'y'])
assert_equal(a.shape, (3, 3))
assert_(len(z.items()) == 2)
for f in z:
assert_(f in ['x', 'y'])
assert_('x' in list(z.iterkeys()))
def test_load_refcount():
# Check that objects returned by np.load are directly freed based on
# their refcount, rather than needing the gc to collect them.
f = StringIO()
np.savez(f, [1, 2, 3])
f.seek(0)
gc.collect()
n_before = len(gc.get_objects())
np.load(f)
n_after = len(gc.get_objects())
assert_equal(n_before, n_after)
if __name__ == "__main__":
run_module_suite()