def test_subtract_series(self):
a = Series(np.eye(128))
b = Series(np.eye(128))
a.spacing = (1, 1, 1)
b.spacing = a.spacing
si = a - b
self.assertEqual(si.slices, 1)
np.testing.assert_array_equal(si.spacing, np.array((1, 1, 1)))
def test_assign_slice(self):
a = np.array(range(4 * 5 * 6), dtype=np.uint16)
a.shape = (4, 5, 6)
s = Series(a)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
n = np.zeros((2, 2, 2), dtype=np.uint16)
p = Series(n)
p.spacing = (1, 1, 1)
p.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, p.shape[0])
a[1:3, 2:4, 2:4] = n[:]
s[1:3, 2:4, 2:4] = p[:]
np.testing.assert_array_equal(a, s)
self.assertEqual(s.slices, 4)
def test_ellipsis_first(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a2 = np.vstack([a1, a1, a1])
a2.shape = (1, 3, 128, 128)
a = np.empty([4, 3, 128, 128])
for i in range(4):
a[i] = a2
# a = np.vstack([a2,a2,a2,a2])
s = Series(a, input_order=imagedata.formats.INPUT_ORDER_TIME)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('time', 0, s.shape[0])
s.axes[1] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[1])
tags = {}
k = 0
for i in range(s.slices):
tags[i] = np.arange(k, k + s.shape[0])
k += s.shape[0]
s.tags = tags
a_slice = a[..., 3:5]
s_slice = s[..., 3:5]
np.testing.assert_array_equal(a_slice, s_slice)
self.assertEqual(s_slice.slices, s.slices)
self.assertEqual(len(s_slice.tags[0]), len(s.tags[0]))
def test_copy_series2(self):
a = np.eye(128)
si1 = Series(a)
si1.spacing = (1, 1, 1)
si2 = si1.copy()
self.assertEqual(si2.slices, 1)
np.testing.assert_array_equal(si2.spacing, np.array((1, 1, 1)))
def test_assign_slice_x(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a = np.vstack([a1, a1, a1])
s = Series(a)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
n = np.ones_like(a) * 4
p = Series(n)
p.spacing = (1, 1, 1)
p.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, p.shape[0])
a[:, 3:5, ...] = n[:, 3:5, ...]
s[:, 3:5, ...] = p[:, 3:5, ...]
np.testing.assert_array_equal(a, s)
np.testing.assert_array_equal(s[:, 3:5, ...], p[:, 3:5, ...])
self.assertEqual(s.slices, 3)
def test_slicing_x(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a = np.vstack([a1, a1, a1])
s = Series(a)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
a_slice = a[:, 3:5, ...]
s_slice = s[:, 3:5, ...]
np.testing.assert_array_equal(a_slice, s_slice)
self.assertEqual(s_slice.slices, 3)
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_slicing_t_neg(self):
from numpy.random import default_rng
rng = default_rng()
s = Series(rng.standard_normal(192).reshape((3, 4, 4, 4)))
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('time', 0, s.shape[0])
s.axes[1] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[1])
np.testing.assert_array_equal(s[2], s[-1])
np.testing.assert_array_equal(s[1], s[-2])
np.testing.assert_array_equal(s[0], s[-3])
np.testing.assert_array_equal(s[1:2], s[1:-1])
np.testing.assert_array_equal(s[1:2, :, :], s[1:-1, :, :])
np.testing.assert_array_equal(s[0:1, :, :], s[0:-2, :, :])
def test_slicing_dim(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a = np.vstack([a1, a1, a1, a1, a1])
s = Series(a)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
s_slice = s[2]
self.assertEqual(s_slice.ndim, 2)
self.assertEqual(len(s_slice.axes), 2)
self.assertEqual(s_slice.axes[0].name, 'row')
self.assertEqual(s_slice.axes[1].name, 'column')
def test_slicing_x_neg(self):
from numpy.random import default_rng
rng = default_rng()
s = Series(rng.standard_normal(64).reshape((4, 4, 4)))
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
np.testing.assert_array_equal(s[:, :, 3], s[:, :, -1])
np.testing.assert_array_equal(s[:, :, 2], s[:, :, -2])
np.testing.assert_array_equal(s[:, :, 1], s[:, :, -3])
np.testing.assert_array_equal(s[:, :, 0], s[:, :, -4])
np.testing.assert_array_equal(s[:, :, 2:3], s[:, :, 2:-1])
np.testing.assert_array_equal(s[:, :, 1:2], s[:, :, 1:-2])
np.testing.assert_array_equal(s[:, :, 0:2], s[:, :, 0:-2])
def test_slicing_z_neg(self):
from numpy.random import default_rng
rng = default_rng()
s = Series(rng.standard_normal(64).reshape((4, 4, 4)))
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
np.testing.assert_array_equal(s[3, :, :], s[-1, :, :])
np.testing.assert_array_equal(s[2, :, :], s[-2, :, :])
np.testing.assert_array_equal(s[1, :, :], s[-3, :, :])
np.testing.assert_array_equal(s[0, :, :], s[-4, :, :])
np.testing.assert_array_equal(s[2:3], s[2:-1])
np.testing.assert_array_equal(s[2:3, :, :], s[2:-1, :, :])
np.testing.assert_array_equal(s[1:2, :, :], s[1:-2, :, :])
np.testing.assert_array_equal(s[0:2, :, :], s[0:-2, :, :])
def test_write_3d_itk(self):
log = logging.getLogger("TestWritePluginITK.test_write_3d_itk")
log.debug("test_write_3d_itk")
si = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
'none',
self.opts)
self.assertEqual(si.dtype, np.uint16)
self.assertEqual(si.shape, (40, 192, 152))
# log.debug("test_write_3d_itk: sliceLocations {}".format(
# si.sliceLocations))
log.debug("test_write_3d_itk: tags {}".format(si.tags))
log.debug("test_write_3d_itk: spacing {}".format(si.spacing))
log.debug("test_write_3d_itk: imagePositions {}".format(
si.imagePositions))
log.debug("test_write_3d_itk: orientation {}".format(si.orientation))
# Modify header
si.sliceLocations = [i for i in range(40)]
si.spacing = (3, 2, 1)
for slice in range(len(si.sliceLocations)):
si.imagePositions = {
slice:
np.array([slice, 1, 0])
}
for slice in range(si.shape[1]):
si.imagePositions = {
slice: si.getPositionForVoxel(np.array([slice, 0, 0]))
}
# Store image with modified header
with tempfile.TemporaryDirectory() as d:
si.write(d, self.opts)
# Read back the ITK data and verify that the header was modified
si2 = Series(
d,
'none',
self.opts)
self.assertEqual(si.shape, si2.shape)
np.testing.assert_array_equal(si, si2)
# np.testing.assert_array_equal(hdr.sliceLocations, hdr2.sliceLocations)
compare_headers(self, si, si2)
def test_multiple_ellipses(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a2 = np.vstack([a1, a1, a1])
a2.shape = (1, 3, 128, 128)
a = np.vstack([a2, a2, a2, a2])
s = Series(a, input_order=imagedata.formats.INPUT_ORDER_TIME)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('time', 0, s.shape[0])
s.axes[1] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[1])
tags = {}
k = 0
for i in range(s.slices):
tags[i] = np.arange(k, k + s.shape[0])
k += s.shape[0]
s.tags = tags
with self.assertRaises(IndexError):
s_slice = s[..., 1:3, ...]
def test_slicing_z(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a = np.vstack([a1, a1, a1])
s = Series(a)
s.spacing = (1, 1, 1)
s.sliceLocations = [3, 6, 9]
for slice in range(s.slices):
s.imagePositions = {slice: np.array([slice, 0, 0])}
s.axes[0] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[0])
a_slice = a[0:2, ...]
s_slice = s[0:2, ...]
np.testing.assert_array_equal(a_slice, s_slice)
self.assertEqual(s_slice.slices, 2)
np.testing.assert_array_equal(s_slice.sliceLocations, np.array([3, 6]))
# Compare imagePositions
ipp2 = {}
for slice in range(2):
ipp2[slice] = np.array([slice, 0, 0])
self.assertEqual(len(s_slice.imagePositions), len(ipp2))
for slice in range(2):
np.testing.assert_array_equal(s_slice.imagePositions[slice],
ipp2[slice])
def test_slicing_t(self):
a1 = np.eye(128)
a1.shape = (1, 128, 128)
a2 = np.vstack([a1, a1, a1])
a2.shape = (1, 3, 128, 128)
a = np.vstack([a2, a2, a2, a2])
s = Series(a, input_order=imagedata.formats.INPUT_ORDER_TIME)
s.spacing = (1, 1, 1)
s.axes[0] = imagedata.axis.UniformLengthAxis('time', 0, s.shape[0])
s.axes[1] = imagedata.axis.UniformLengthAxis('slice', 0, s.shape[1])
tags = {}
k = 0
for i in range(s.slices):
tags[i] = np.arange(k, k + s.shape[0])
k += s.shape[0]
s.tags = tags
a_slice = a[1:3, ...]
s_slice = s[1:3, ...]
np.testing.assert_array_equal(a_slice, s_slice)
self.assertEqual(s_slice.slices, 3)
self.assertEqual(len(s_slice.tags[0]), 2)
for s in range(s_slice.slices):
np.testing.assert_array_equal(s_slice.tags[s], tags[s][1:3])
def test_write_4d_itk(self):
log = logging.getLogger("TestWritePlugin.test_write_4d_itk")
log.debug("test_write_4d_itk")
si = Series(
[os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
os.path.join('data', 'itk', 'time', 'Image_00001.mha'),
os.path.join('data', 'itk', 'time', 'Image_00002.mha')],
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si.dtype, np.uint16)
self.assertEqual(si.shape, (3, 3, 192, 152))
# np.testing.assert_array_almost_equal(np.arange(0, 10*2.256, 2.256), hdr.getTimeline(), decimal=2)
# log.debug("test_write_4d_itk: sliceLocations", hdr.sliceLocations)
# log.debug("test_write_4d_itk: tags {}".format(hdr.tags))
# log.debug("test_write_4d_itk: spacing", hdr.spacing)
# log.debug("test_write_4d_itk: imagePositions", hdr.imagePositions)
# log.debug("test_write_4d_itk: orientation", hdr.orientation)
# Modify header
si.sliceLocations = (1, 2, 3)
si.spacing = (3, 2, 1)
for slice in range(si.shape[1]):
si.imagePositions = {
slice:
np.array([slice, 1, 0])
}
si.orientation = np.array([0, 0, 1, 0, 1, 0])
for slice in range(si.shape[1]):
si.imagePositions = {
slice: si.getPositionForVoxel(np.array([slice, 0, 0])).reshape((3, 1))
}
si.sort_on = imagedata.formats.SORT_ON_TAG
log.debug("test_write_4d_itk: hdr.sort_on {}".format(
imagedata.formats.sort_on_to_str(si.sort_on)))
si.output_dir = 'single'
with tempfile.TemporaryDirectory() as d:
si.write(d, self.opts)
# Read back the ITK data and verify that the header was modified
si2 = Series(
d,
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual((3, 3, 192, 152), si2.shape)
# np.testing.assert_array_equal(si, si2)
# np.testing.assert_array_equal(hdr.sliceLocations, hdr2.sliceLocations)
# log.debug("hdr2.tags.keys(): {}".format(hdr2.tags.keys()))
tags = {}
for slice in range(3):
tags[slice] = np.arange(3)
self.assertEqual(tags.keys(), si2.tags.keys())
for k in si2.tags.keys():
np.testing.assert_array_equal(tags[k], si2.tags[k])
np.testing.assert_array_equal(si.spacing, si2.spacing)
image_positions = {}
for slice in range(3):
image_positions[slice] = np.array([0, 1 + 3 * slice, 0])
self.assertEqual(image_positions.keys(),
si2.imagePositions.keys())
np.testing.assert_array_equal(si.orientation, si2.orientation)
def test_print_header(self):
a = np.eye(128)
si = Series(a)
si.spacing = (1, 1, 1)
self.assertEqual(si.slices, 1)
np.testing.assert_array_equal(si.spacing, np.array((1, 1, 1)))
