def test_dicom():
i = ndar.Image('test_data/NDAR_INVXT425UFT_image03_1357865972017.zip')
dicom_file = i.path(i.files['DICOM'][0])
assert os.path.exists(dicom_file)
i.clean()
assert not os.path.exists(dicom_file)
assert os.path.exists(i.path(i.files['DICOM'][0]))
def test_clean():
i = ndar.Image('test_data/06025B_mprage.nii.gz')
tempdir = i._tempdir
assert os.path.exists(tempdir)
i.clean()
assert not os.path.exists(tempdir)
assert os.path.exists(i._tempdir)
def test_dicom_2():
i = ndar.Image('test_data/s1615890.zip')
assert len(i.files['DICOM']) == 166
for (k, v) in i.files.iteritems():
if k != 'DICOM':
assert not v
assert os.path.exists(i.path('i1616037.MRDC.160'))
def test_dicom():
i = ndar.Image('test_data/NDAR_INVXT425UFT_image03_1357865972017.zip')
assert i.files['DICOM'] == ['0001.dcm']
for (k, v) in i.files.iteritems():
if k != 'DICOM':
assert not v
assert os.path.exists(i.path('0001.dcm'))
def test_nifti_1():
i = ndar.Image('test_data/06025B_mprage.nii.gz')
assert i.files['NIfTI-1'] == ['06025B_mprage.nii.gz']
for (k, v) in i.files.iteritems():
if k != 'NIfTI-1':
assert not v
assert os.path.exists(i.path('06025B_mprage.nii.gz'))
def test_tempdir_noremove():
i = ndar.Image('test_data/06025B_mprage.nii.gz')
tempdir = i._tempdir
i._clean_on_del = False
del i
assert os.path.exists(tempdir)
shutil.rmtree(tempdir)
def test_nifti_1():
i = ndar.Image('test_data/06025B_mprage.nii.gz')
nifti_1_file = i.path(i.files['NIfTI-1'][0])
assert os.path.exists(nifti_1_file)
i.clean()
assert not os.path.exists(nifti_1_file)
assert os.path.exists(i.path(i.files['NIfTI-1'][0]))
def test_thumbnail():
i = ndar.Image('test_data/06025B_mprage.nii.gz')
thumbnail = i.thumbnail
assert os.path.exists(thumbnail)
i.clean()
assert not os.path.exists(thumbnail)
assert os.path.exists(i.thumbnail)
def test_nifti_nonnifti():
"""image is not a NIfTI-1 file"""
i = ndar.Image('test_data/NDAR_INVZU049GXV_image03_1326225820791.zip')
nifti_1_file = i.nifti_1
assert os.path.exists(nifti_1_file)
i.clean()
assert not os.path.exists(nifti_1_file)
assert os.path.exists(i.nifti_1)
def test_nifti_nifti():
"""image is already a NIfTI-1 file"""
i = ndar.Image('test_data/06025B_mprage.nii.gz')
nifti_1_file = i.nifti_1
assert os.path.exists(nifti_1_file)
i.clean()
assert not os.path.exists(nifti_1_file)
assert os.path.exists(i.nifti_1)
def test_brik():
i = ndar.Image('test_data/NDAR_INVZU049GXV_image03_1326225820791.zip')
assert i.files['AFNI'] == ['20783.spgr_at+tlrc']
for (k, v) in i.files.iteritems():
if k != 'AFNI':
assert not v
assert os.path.exists(i.path(i.files['AFNI'][0] + '.HEAD'))
assert os.path.exists(i.path(i.files['AFNI'][0] + '.BRIK'))
assert not os.path.exists(i.path(i.files['AFNI'][0]))
def test_nifti_mcfail():
"""mri_convert failure (by way of a bad image)"""
im = ndar.Image('test_data/bogus.mnc')
nose.tools.assert_raises(AttributeError, lambda: im.nifti_1)
def test_nifti_nonnifti():
"""image is not a NIfTI-1 file"""
im = ndar.Image('test_data/NDAR_INVZU049GXV_image03_1326225820791.zip')
assert os.path.exists(im.nifti_1)
def test_nifti_unzipped_nifti():
"""image is already an uncompressed NIfTI-1 file"""
im = ndar.Image('test_data/a.nii')
assert im.nifti_1 == im.path(im.files['NIfTI-1'][0])
def test_afni_dicom():
"""image is DICOM"""
im = ndar.Image('test_data/s1615890.zip')
assert os.path.exists('%s.BRIK' % im.afni)
assert os.path.exists('%s.HEAD' % im.afni)
def test_afni_minc():
"""image is a MINC file"""
im = ndar.Image('test_data/a.mnc')
assert os.path.exists('%s.BRIK' % im.afni)
assert os.path.exists('%s.HEAD' % im.afni)
def test_thumbnail_slicerfail():
"""slicer failure (by way of a bad image)"""
im = ndar.Image('test_data/bogus.nii.gz')
nose.tools.assert_raises(AttributeError, lambda: im.thumbnail)
def test_nifti_nifti():
"""image is already a NIfTI-1 file"""
im = ndar.Image('test_data/06025B_mprage.nii.gz')
assert im.nifti_1 == im.path(im.files['NIfTI-1'][0])
def test_afni_fail():
"""conversion failure (by way of a bad image)"""
im = ndar.Image('test_data/bogus.mnc')
nose.tools.assert_raises(AttributeError, lambda: im.afni)
def test_tempdir_remove():
i = ndar.Image('test_data/06025B_mprage.nii.gz')
tempdir = i._tempdir
del i
assert not os.path.exists(tempdir)
def test_nrrd_dicom():
"""image is DICOM"""
im = ndar.Image('test_data/s1615890.zip')
assert os.path.exists(im.nrrd)
def test_bad_file():
nose.tools.assert_raises(
Exception, lambda: ndar.Image('test_data/bogus', check_existence=True))
i = ndar.Image('test_data/bogus')
assert not i.exists()
nose.tools.assert_raises(Exception, lambda: i.files)
def test_nifti_nifti_gz():
"""image is a gzipped NIfTI-1 file"""
im = ndar.Image('test_data/06025B_mprage.nii.gz')
assert im.nifti_1_gz == im.path(im.files['NIfTI-1'][0])
def test_afni_afni():
"""image is already an AFNI file"""
im = ndar.Image('test_data/NDAR_INVZU049GXV_image03_1326225820791.zip')
assert im.afni == im.path(im.files['AFNI'][0])
def test_nifti_unzipped_nifti_gz():
"""image is an unzipped NIfTI-1 file"""
im = ndar.Image('test_data/a.nii')
assert im.nifti_1_gz != im.path(im.files['NIfTI-1'][0])
assert im.nifti_1_gz.endswith('.nii.gz')
assert os.path.exists(im.nifti_1_gz)
def test_afni_nifti():
"""image is a NIfTI-1 file"""
im = ndar.Image('test_data/06025B_mprage.nii.gz')
assert os.path.exists('%s.BRIK' % im.afni)
assert os.path.exists('%s.HEAD' % im.afni)
def test_nrrd_nrrd():
"""image is already a NRRD file"""
im = ndar.Image('test_data/002-12AU_t1w.nrrd')
assert im.nrrd == im.path(im.files['NRRD'][0])
def test_thumbnail():
im = ndar.Image('test_data/06025B_mprage.nii.gz')
assert os.path.exists(im.thumbnail)
def test_nrrd_nonvolume():
"""image is not a volume"""
im = ndar.Image('test_data/10_425-02_li1_146.png')
nose.tools.assert_raises(AttributeError, lambda: im.nrrd)
def test_no_attributes():
im = ndar.Image('test_data/s1615890.zip')
nose.tools.assert_raises(AttributeError, lambda: im.acquisition_matrix)
