import unittest
import os.path
import tempfile
import numpy as np
import logging
import argparse
import nibabel
import imagedata.cmdline as cmdline
import imagedata.formats as formats
from imagedata.series import Series
from imagedata.collection import Cohort
from imagedata.apps.diffusion import read_b_value_file, read_b_vector_file
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class TestWriteNIfTIPlugin(unittest.TestCase):
def _compare_nifti_data(self, img1, img2, descr1='img1', descr2='img2', verify_zooms=True):
hdr1, hdr2 = img1.header, img2.header
self.assertEqual(hdr1.get_data_shape(), hdr2.get_data_shape(), "get_data_shape")
self.assertEqual(hdr1.get_dim_info(), hdr2.get_dim_info(), "get_dim_info")
self.assertEqual(hdr1.get_xyzt_units(), hdr2.get_xyzt_units(), "get_xyzt_units")
if verify_zooms:
np.testing.assert_array_almost_equal(hdr1.get_zooms(), hdr2.get_zooms(), decimal=4, err_msg="get_zooms")
sform1, sform2 = hdr1.get_sform(coded=True)[0], hdr2.get_sform(coded=True)[0]
np.testing.assert_array_almost_equal(sform1, sform2, decimal=4)
qform1, qform2 = hdr1.get_qform(coded=True)[0], hdr2.get_qform(coded=True)[0]
if qform1 is not None:
self.assertIsNotNone(qform2)
np.testing.assert_array_almost_equal(qform1, qform2, decimal=4)
si1, si2 = np.asarray(img1.dataobj), np.asarray(img2.dataobj)
np.testing.assert_array_equal(si1, si2)
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def test_tra_rl(self):
dcm = Series(os.path.join('data', 'dicom', 'tra_rl.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'tra_rl.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
diff = Series(nii.dataobj) - Series(check.dataobj)
# diff.write(d, formats=['dicom'])
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_tra_oblique(self):
dcm = Series(os.path.join('data', 'dicom', 'tra_oblique.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'tra_oblique.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_cor_hf(self):
dcm = Series(os.path.join('data', 'dicom', 'cor_hf.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'cor_hf.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_cor_oblique(self):
dcm = Series(os.path.join('data', 'dicom', 'cor_oblique.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'cor_oblique.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_cor_rl(self):
dcm = Series(os.path.join('data', 'dicom', 'cor_rl.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'cor_rl.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_sag_ap(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_ap.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'sag_ap.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_sag_hf(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_hf.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'sag_hf.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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def test_sag_oblique(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_oblique.zip'), input_format='dicom')
nii = nibabel.load(
os.path.join('data', 'nifti', 'sag_oblique.nii.gz')
)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
for entry in os.scandir(path=d):
filename = entry.path
check = nibabel.load(filename)
self._compare_nifti_data(nii, check, 'dcm2niix', 'niftiplugin')
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class TestReadWriteNIfTIPlugin(unittest.TestCase):
def _compare_dicom_data(self, dcm, nifti, verify_spacing=True):
self.assertEqual('dicom', dcm.input_format, "dicom input_format")
self.assertEqual(dcm.shape, nifti.shape, "shape")
self.assertEqual(dcm.slices, nifti.slices, "slices")
if verify_spacing:
np.testing.assert_allclose(nifti.spacing, dcm.spacing,
atol=1e-4, err_msg="nifti vs dicom spacing")
for s in range(dcm.slices):
np.testing.assert_allclose(nifti.imagePositions[s].reshape(3), dcm.imagePositions[s].reshape(3),
atol=1e-3, err_msg="imagePositions[{}]".format(s))
np.testing.assert_allclose(nifti.orientation, dcm.orientation,
atol=1e-6, err_msg="orientation")
np.testing.assert_allclose(nifti.transformationMatrix, dcm.transformationMatrix,
atol=1e-2, err_msg="transformationMatrix")
np.testing.assert_array_equal(nifti, dcm, err_msg="voxel values")
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def test_compare_sag_ap(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_ap.zip'), input_format='dicom')
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
nifti = Series(d, input_format='nifti')
self._compare_dicom_data(dcm, nifti)
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class TestReadNIfTIPlugin(unittest.TestCase):
def _compare_dicom_data(self, dcm, nifti, verify_spacing=True):
self.assertEqual('dicom', dcm.input_format, "dicom input_format")
self.assertEqual(dcm.shape, nifti.shape, "shape")
self.assertEqual(dcm.slices, nifti.slices, "slices")
if verify_spacing:
np.testing.assert_allclose(nifti.spacing, dcm.spacing,
atol=1e-4, err_msg="nifti vs dicom spacing")
for s in range(dcm.slices):
np.testing.assert_allclose(
np.sort(nifti.imagePositions[s]),
np.sort(dcm.imagePositions[s]),
atol=1e-3, err_msg="imagePositions[{}]".format(s))
np.testing.assert_allclose(nifti.orientation, dcm.orientation,
atol=1e-6, err_msg="orientation")
np.testing.assert_allclose(nifti.transformationMatrix, dcm.transformationMatrix,
atol=1e-2, err_msg="transformationMatrix")
np.testing.assert_array_equal(nifti, dcm, err_msg="voxel values")
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def test_compare_sag_ap(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_ap.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'sag_ap.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti)
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def test_compare_sag_hf(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_hf.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'sag_hf.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti)
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def test_compare_sag_oblique(self):
dcm = Series(os.path.join('data', 'dicom', 'sag_oblique.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'sag_oblique.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti, verify_spacing=False)
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def test_compare_cor_hf(self):
dcm = Series(os.path.join('data', 'dicom', 'cor_hf.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'cor_hf.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti)
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def test_compare_cor_oblique(self):
dcm = Series(os.path.join('data', 'dicom', 'cor_oblique.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'cor_oblique.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti, verify_spacing=False)
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def test_compare_cor_rl(self):
dcm = Series(os.path.join('data', 'dicom', 'cor_rl.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'cor_rl.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti)
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def test_compare_tra_oblique(self):
dcm = Series(os.path.join('data', 'dicom', 'tra_oblique.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'tra_oblique.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti, verify_spacing=False)
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def test_compare_tra_rl(self):
dcm = Series(os.path.join('data', 'dicom', 'tra_rl.zip'), input_format='dicom')
nifti = Series(os.path.join('data', 'nifti', 'tra_rl.nii.gz'), input_format='nifti')
self._compare_dicom_data(dcm, nifti)
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class Test2DNIfTIPlugin(unittest.TestCase):
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def test_read_single_slice(self):
dcm = Series(os.path.join('data', 'dicom', 'time', 'time00', 'Image_00020.dcm'), input_format='dicom')
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
_ = Series(d, input_format='nifti')
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class Test3DNIfTIPlugin(unittest.TestCase):
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def setUp(self):
parser = argparse.ArgumentParser()
cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'nifti', '--serdes', '1'])
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def test_nifti_plugin(self):
plugins = formats.get_plugins_list()
self.nifti_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'nifti':
self.nifti_plugin = pclass
self.assertIsNotNone(self.nifti_plugin)
# @unittest.skip("skipping test_read_single_file")
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def test_read_single_file(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'none',
input_format='nifti')
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
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def test_dtype_int64(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'none',
dtype=int,
input_format='nifti')
self.assertEqual(si1.dtype, np.int64)
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def test_dtype_float(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'none',
dtype=float,
input_format='nifti')
self.assertEqual(si1.dtype, np.float64)
# @unittest.skip("skipping test_qform_3D")
# @unittest.skip("skipping test_compare_qform_to_dicom")
# @unittest.skip("skipping test_read_two_files")
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def test_read_two_files(self):
si1 = Series(
[
os.path.join('data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
os.path.join('data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz')
],
formats.INPUT_ORDER_TIME,
input_format='nifti')
self.assertEqual(np.int16, si1.dtype)
self.assertEqual((3, 3, 192, 152), si1.shape)
# @unittest.skip("skipping test_zipread_single_file")
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def test_zipread_single_file(self):
si1 = Series(
os.path.join(
'data',
'nifti',
'time_all.zip?time/time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'none',
input_format='nifti')
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_single_directory")
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def test_zipread_single_directory(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all.zip?time'),
formats.INPUT_ORDER_TIME,
input_format='nifti')
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_all_files")
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def test_zipread_all_files(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all.zip'),
formats.INPUT_ORDER_TIME,
input_format='nifti')
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
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def test_write_ndarray(self):
with tempfile.TemporaryDirectory() as d:
Series(np.eye(128)).write(d, formats=['nifti'])
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def test_write_single_file_not_directory(self):
a = Series(np.eye(128))
with tempfile.TemporaryDirectory() as d:
filename = os.path.join(d, 'test.nii.gz')
a.write(
filename,
formats=['nifti']
)
if not os.path.isfile(filename):
raise AssertionError('File does not exist: {}'.format(filename))
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def test_write_single_file_in_directory(self):
a = Series(np.eye(128))
with tempfile.TemporaryDirectory() as d:
a.write(
d,
formats=['nifti']
)
expect_filename = os.path.join(d, 'Image.nii.gz')
if not os.path.isfile(expect_filename):
raise AssertionError('File does not exist: {}'.format(expect_filename))
# @unittest.skip("skipping test_read_3d_nifti_no_opt")
# noinspection PyArgumentList
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def test_read_3d_nifti_no_opt(self):
si1 = Series(os.path.join(
'data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
input_format='nifti')
logging.debug('test_read_3d_nifti_no_opt: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_read_3d_nifti_no_opt: si1.slices {}'.format(si1.slices))
# @unittest.skip("skipping test_write_3d_nifti_no_opt")
# noinspection PyArgumentList
[docs]
def test_write_3d_nifti_no_opt(self):
si1 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
logging.debug('test_write_3d_nifti_no_opt: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_write_3d_nifti_no_opt: si1.slices {}'.format(si1.slices))
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['nifti'])
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class Test4DNIfTIPlugin(unittest.TestCase):
[docs]
def setUp(self):
parser = argparse.ArgumentParser()
cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'nifti', '--input_shape', '8x30'])
plugins = formats.get_plugins_list()
self.nifti_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'nifti':
self.nifti_plugin = pclass
self.assertIsNotNone(self.nifti_plugin)
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def test_write_4d_nifti_time(self):
si1 = Series(
os.path.join('data', 'dicom', 'time'),
formats.INPUT_ORDER_TIME,
input_format='dicom')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
si1.sort_on = formats.SORT_ON_SLICE
logging.debug("test_write_4d_nifti: si1.sort_on {}".format(
formats.sort_on_to_str(si1.sort_on)))
si1.output_dir = 'single'
# si1.output_dir = 'multi'
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['nifti'], opts=self.opts)
# Read back the NIfTI data and verify that the header was modified
si2 = Series(
d,
formats.INPUT_ORDER_TIME,
input_format='nifti')
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
[docs]
def test_write_4d_nifti_dwi(self):
si1 = Series(
os.path.join('data', 'dicom', 'dwi'),
formats.INPUT_ORDER_B,
input_format='dicom'
)
self.assertEqual(si1.shape, (3, 30, 384, 312))
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['nifti'], opts=self.opts)
# Read back the NIfTI data and verify
si2 = Series(d,
formats.INPUT_ORDER_B,
input_format='nifti')
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_almost_equal(si1.spacing, si2.spacing)
np.testing.assert_array_equal(si1, si2)
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def test_write_4d_nifti_dti(self):
si = Series(
os.path.join('data', 'dicom', 'ep2d_RSI_b0_500_1500_6dir.zip'),
'dti',
accept_duplicate_tag=True,
input_format='dicom'
)
with tempfile.TemporaryDirectory() as d:
si.write(d, formats=['nifti'])
nii_bval = read_b_value_file(os.path.join(d, 'Image.bval'))
self.assertEqual(
[0.0, 500.0, 500.0, 500.0, 500.0, 500.0, 500.0, 1500.0, 1500.0, 1500.0, 1500.0, 1500.0, 1500.0],
nii_bval)
nii_bvec = read_b_vector_file(os.path.join(d, 'Image.bvec'))
a = np.array([[0., 0., 0.],
[0., -0.70640218, -0.7078107],
[-0.70640218, 0., -0.7078107],
[0.70640218, 0., -0.7078107],
[-0.70710397, -0.70710385, -0.00282839],
[0.70710397, -0.70710385, -0.00282839],
[0., -0.70781636, 0.70639646],
[0., -0.70663589, -0.70757741],
[7.0663589e-01, -6.0000000e-08, -7.0757729e-01],
[-7.0663589e-01, 6.0000000e-08, -7.0757729e-01],
[-0.70710641, -0.70710647, -0.00094281],[0.70710641, -0.70710647, -0.00094281],
[0., -0.70757866, 0.70663464]
])
np.testing.assert_array_equal(a, nii_bvec)
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class Test5DNIfTIPlugin(unittest.TestCase):
[docs]
def test_write_5d_nifti_rsi(self):
si = Series(
os.path.join('data', 'dicom', 'ep2d_RSI_b0_500_1500_6dir.zip'),
'b,bvector',
accept_duplicate_tag=True,
input_format='dicom'
)
with tempfile.TemporaryDirectory() as d:
si.write(d, formats=['nifti'])
nii_bval = read_b_value_file(os.path.join(d, 'Image.bval'))
self.assertEqual(
[0.0, 500.0, 1500.0],
nii_bval)
nii_bvec = read_b_vector_file(os.path.join(d, 'Image.bvec'))
a = np.array([[0., 0., 0.],
[0., -0.70640218, -0.7078107],
[-0.70640218, 0., -0.7078107],
[0.70640218, 0., -0.7078107],
[-0.70710397, -0.70710385, -0.00282839],
[0.70710397, -0.70710385, -0.00282839],
[0., -0.70781636, 0.70639646]
])
np.testing.assert_array_equal(a, nii_bvec)
[docs]
class TestNIfTIPluginWrite(unittest.TestCase):
[docs]
def test_write_dicom(self):
si1 = Series(
# os.path.join('data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
os.path.join('data', 'nifti', 'cor_rl.nii.gz'),
'time',
input_format='nifti')
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (3, 320, 220))
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['dicom'])
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def test_write_cohort(self):
cohort = Cohort('data/dicom/cohort.zip', input_format='dicom')
with tempfile.TemporaryDirectory() as d:
cohort.write(d, formats=['nifti'])
if __name__ == '__main__':
unittest.main()