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#!/usr/bin/env python
import os.path as op
import functools as ft
import shutil
import pytest
nib = pytest.importorskip("nibabel")
import numpy as np
import indexed_gzip as igzip
from indexed_gzip.tests import tempdir
import platform
if platform.machine() == 'riscv64':
pytest.skip('nibabel fails on riscv64', allow_module_level=True)
pytestmark = pytest.mark.nibabel_test
@ft.total_ordering
class Version(object):
def __init__(self, vstr):
self.v = [int(v) for v in vstr.split('.')]
def __eq__(self, other):
return other.v == self.v
def __lt__(self, other):
for sv, ov in zip(self.v, other.v):
if sv > ov: return False
if sv < ov: return True
return False
nibver = Version(nib.__version__)
if nibver >= Version('2.1.0'):
from nibabel.filebasedimages import ImageFileError
else:
from nibabel.spatialimages import ImageFileError
def create_random_image(shape, fname):
data = np.random.random(shape).astype(np.float32)
aff = np.eye(4)
nib.Nifti1Image(data, aff, None).to_filename(fname)
return data
def load_image(fname):
basename = op.basename(fname)[:-7]
# nibabel pre-2.1 is not indexed_gzip-aware
if nibver <= Version('2.1.0'):
fobj = igzip.IndexedGzipFile(fname)
fmap = nib.Nifti1Image.make_file_map()
fmap[basename].fileobj = fobj
image = nib.Nifti1Image.from_file_map(fmap)
# nibabel 2.2.x, we have to set keep_file_open='auto'
# to get it to use indexed_gzip
elif Version('2.2.0') <= nibver < Version('2.3.0'):
image = nib.load(fname, keep_file_open='auto')
# nibabel >= 2.3.x uses indexed_gzip automatically
else:
image = nib.load(fname)
return image
def test_nibabel_integration():
with tempdir():
data = create_random_image((50, 50, 50, 50), 'image.nii.gz')
image = load_image('image.nii.gz')
idata = np.asanyarray(image.dataobj)
assert np.all(np.isclose(data, idata))
assert not image.in_memory
if nibver < Version('2.2.0'):
assert isinstance(image.file_map['image'].fileobj,
igzip.IndexedGzipFile)
else:
assert isinstance(image.dataobj._opener.fobj,
igzip.IndexedGzipFile)
# https://github.com/pauldmccarthy/indexed_gzip/issues/40
def test_readdata_twice():
with tempdir():
# the bug only occurs on relatively small images,
# where the full index comprises only one or two
# index points
data = create_random_image((10, 10, 10, 10), 'image.nii.gz')
image = load_image('image.nii.gz')
d1 = np.asanyarray(image.dataobj)
d2 = np.asanyarray(image.dataobj)
assert np.all(np.isclose(data, d1))
assert np.all(np.isclose(data, d2))
# https://github.com/pauldmccarthy/indexed_gzip/pull/45
def test_bad_image_error():
if nibver < Version('2.3.0'):
return
with tempdir():
create_random_image((10, 10, 10, 10), 'image.nii.gz')
shutil.move('image.nii.gz', 'image.nii')
with pytest.raises(ImageFileError):
nib.load('image.nii')
create_random_image((10, 10, 10, 10), 'image.nii')
shutil.move('image.nii', 'image.nii.gz')
with pytest.raises(ImageFileError):
nib.load('image.nii.gz')
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