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detecting if the input is empty early on! #611

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Merged
merged 10 commits into from
Mar 22, 2018
Merged

detecting if the input is empty early on! #611

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e06ed5e
first implementation of aseg stats reader
raamana Aug 2, 2017
83b55a2
Merge branch 'master' of github.com:nipy/nibabel
raamana Nov 28, 2017
870bb1d
updating docs and improving implementation
raamana Nov 28, 2017
e4825f4
first stab at a simple test
raamana Nov 28, 2017
af4e046
basic implementation of aparc.stats reader (returning everything)
raamana Feb 11, 2018
a4f8c3c
detecting if the input is empty early on! Apparently no one needed it ;)
raamana Mar 19, 2018
a01855b
merging with upstream master to undo changes not ready to PR/merge
raamana Mar 19, 2018
3e3fe30
removing unnecessary space that nibabel checks dont like
raamana Mar 19, 2018
d207360
Using another existing exception, and shorter message
raamana Mar 19, 2018
a974b70
better file checks - path.exists is try/except for os.stat anyways!
raamana Mar 20, 2018
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10 changes: 7 additions & 3 deletions nibabel/loadsave.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
# module imports
""" Utilities to load and save image objects """

import os.path as op
import os
import numpy as np

from .filename_parser import splitext_addext
Expand All @@ -36,8 +36,12 @@ def load(filename, **kwargs):
img : ``SpatialImage``
Image of guessed type
'''
if not op.exists(filename):
raise FileNotFoundError("No such file: '%s'" % filename)
try:
stat_result = os.stat(filename)
except OSError:
raise FileNotFoundError("No such file or no access: '%s'" % filename)
if stat_result.st_size <= 0:
raise ImageFileError("Empty file: '%s'" % filename)
sniff = None
for image_klass in all_image_classes:
is_valid, sniff = image_klass.path_maybe_image(filename, sniff)
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8 changes: 8 additions & 0 deletions nibabel/tests/test_loadsave.py
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Expand Up @@ -58,6 +58,14 @@ def test_file_not_found():
assert_raises(FileNotFoundError, load, 'does_not_exist.nii.gz')


def test_load_empty_image():
with InTemporaryDirectory():
open('empty.nii', 'w').close()
with assert_raises(ImageFileError) as err:
load('empty.nii')
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I'm surprised this works on Python 3 - I thought that the err variable went out of scope.

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It seems to work - didn’t dig into why

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From the docs:

Signature: unittest.TestCase.assertRaises(self, expected_exception, *args, **kwargs)
Docstring:
Fail unless an exception of class expected_exception is raised
by the callable when invoked with specified positional and
keyword arguments. If a different type of exception is
raised, it will not be caught, and the test case will be
deemed to have suffered an error, exactly as for an
unexpected exception.

If called with the callable and arguments omitted, will return a
context object used like this::

     with self.assertRaises(SomeException):
         do_something()

An optional keyword argument 'msg' can be provided when assertRaises
is used as a context object.

The context manager keeps a reference to the exception as
the 'exception' attribute. This allows you to inspect the
exception after the assertion::

    with self.assertRaises(SomeException) as cm:
        do_something()
    the_exception = cm.exception
    self.assertEqual(the_exception.error_code, 3)
File:      /anaconda3/lib/python3.6/unittest/case.py
Type:      function

assert_true(err.exception.args[0].startswith('Empty file: '))


def test_read_img_data_nifti():
shape = (2, 3, 4)
data = np.random.normal(size=shape)
Expand Down