def test_read_3d_nifti(self):
si1 = Series(
os.path.join(
'data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
si1 = si1[0]
logging.debug('test_read_3d_nifti: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_read_3d_nifti: si1.slices {}'.format(si1.slices))
si1.spacing = (5, 0.41015625, 0.41015625)
for slice in range(si1.shape[0]):
si1.imagePositions = {
slice:
np.array([slice, 1, 0])
}
si1.orientation = np.array([1, 0, 0, 0, 1, 0])
logging.debug('test_read_3d_nifti: si1.tags {}'.format(si1.tags))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'nifti?Image_%05d'), formats=['nifti'], opts=self.opts)
logging.debug('test_read_3d_nifti: si1 {} {} {}'.format(si1.dtype, si1.min(), si1.max()))
si2 = Series(
os.path.join(d, 'nifti', 'Image_00000.nii.gz'),
'none',
self.opts)
# noinspection PyArgumentList
logging.debug('test_read_3d_nifti: si2 {} {} {}'.format(si2.dtype, si2.min(), si2.max()))
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
logging.debug('test_read_3d_nifti: Get si1.slices {}'.format(si1.slices))
logging.debug('test_read_3d_nifti: Set s3')
s3 = si1.astype(np.float64)
logging.debug('test_read_3d_nifti: s3 {} {} {} {}'.format(type(s3),
issubclass(type(s3), Series), s3.dtype, s3.shape))
logging.debug('test_read_3d_nifti: s3 {} {} {}'.format(s3.dtype,
s3.min(), s3.max()))
logging.debug('test_read_3d_nifti: s3.slices {}'.format(s3.slices))
si3 = Series(s3)
np.testing.assert_array_almost_equal(si1, si3, decimal=4)
logging.debug('test_read_3d_nifti: si3.slices {}'.format(si3.slices))
logging.debug('test_read_3d_nifti: si3 {} {} {}'.format(type(si3), si3.dtype, si3.shape))
with tempfile.TemporaryDirectory() as d:
si3.write(os.path.join(d, 'n?Image_%05d'), formats=['nifti'], opts=self.opts)
s3 = si1 - si2
with tempfile.TemporaryDirectory() as d:
s3.write(os.path.join(d, 'diff?Image_%05d'), formats=['nifti'], opts=self.opts)
def test_write_3d_mat(self):
si1 = Series(os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none', self.opts)
logging.debug('test_write_3d_mat: si1 {} {} {} {}'.format(
type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_write_3d_mat: si1.shape {}, si1.slices {}'.format(
si1.shape, si1.slices))
logging.debug('test_write_3d_mat: si1.tags {}'.format(si1.tags))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'mat?Image_%05d'),
formats=['mat'],
opts=self.opts)
logging.debug('test_write_3d_mat: si1 {} {} {}'.format(
si1.dtype, si1.min(), si1.max()))
logging.debug(
'test_write_3d_mat: si1.shape {}, si1.slices {}'.format(
si1.shape, si1.slices))
si2 = Series(os.path.join(d, 'mat', 'Image_00000.mat'), 'none',
self.opts)
logging.debug('test_write_3d_mat: si2 {} {} {}'.format(
si2.dtype, si2.min(), si2.max()))
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
logging.debug('test_write_3d_mat: Get si1.slices {}'.format(
si1.slices))
logging.debug('test_write_3d_mat: Set s3')
s3 = si1.astype(np.float64)
logging.debug('test_write_3d_mat: s3 {} {} {} {}'.format(
type(s3), issubclass(type(s3), Series), s3.dtype, s3.shape))
logging.debug('test_write_3d_mat: s3 {} {} {}'.format(
s3.dtype, s3.min(), s3.max()))
logging.debug('test_write_3d_mat: s3.slices {}'.format(s3.slices))
si3 = Series(s3)
np.testing.assert_array_almost_equal(si1, si3, decimal=4)
logging.debug('test_write_3d_mat: si3.slices {}'.format(si3.slices))
logging.debug('test_write_3d_mat: si3 {} {} {}'.format(
type(si3), si3.dtype, si3.shape))
s3 = si1 - si2
with tempfile.TemporaryDirectory() as d:
s3.write(os.path.join(d, 'diff?Image_%05d.mat'),
formats=['mat'],
opts=self.opts)
