def test_write_4d_single_directory_explicit(self):
si1 = Series(
os.path.join('data', 'itk', 'time'),
'none',
self.opts)
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'Image%05d.mha'), formats=['itk'])
si2 = Series(d)
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
def test_dicom_template_prog(self):
# Read the DICOM empty header series,
# adding DICOM template in Series constructor
template = Series(os.path.join('data', 'dicom', 'time', 'time00'))
si1 = Series(os.path.join(self.emptydir.name, 'empty_header'),
template=template)
si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'))
# Compare constructed series si1 to original series si2
self.assertEqual(si1.dtype, si2.dtype)
np.testing.assert_array_equal(si1, si2)
compare_template_headers(self, si1, si2)
def test_write_single_file(self):
si1 = Series(
os.path.join(
'data', 'nifti',
'time_all.zip?time/time_all_fl3d_dynamic_20190207140517_14.nii.gz'
))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'nifti.zip'), formats=['nifti'])
si2 = Series(os.path.join(d, 'nifti.zip?Image.nii.gz'))
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
def test_write_single_file(self):
si1 = Series(
os.path.join('data', 'dicom',
'time.zip?time/time00/Image_00020.dcm'))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'dicom.zip'), formats=['dicom'])
si2 = Series(os.path.join(d, 'dicom.zip?Image_00000.dcm'))
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si2.dtype, np.uint16)
self.assertEqual(si1.shape, si2.shape)
self.assertEqual(si1.studyInstanceUID, si2.studyInstanceUID)
def test_qform_3D(self):
dcm = Series(os.path.join('data', 'dicom', 'time', 'time00'))
self.assertEqual('dicom', dcm.input_format)
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
n = Series(d)
self.assertEqual('nifti', n.input_format)
nt = n.transformationMatrix
self.assertEqual(dcm.shape, n.shape)
self.assertEqual(dcm.dtype, n.dtype)
np.testing.assert_allclose(n.transformationMatrix, dcm.transformationMatrix, rtol=1e-2)
def test_read_2D(self):
dcm = Series(os.path.join('data', 'dicom', 'time', 'time00'))
si2 = dcm[0, ...]
with tempfile.TemporaryDirectory() as d:
si2.write(d, formats=['nifti'])
si3 = Series(d, template=si2)
with tempfile.TemporaryDirectory() as d:
si3.write(d, formats=['dicom'])
self.assertEqual(si2.dtype, si3.dtype)
self.assertEqual(si2.shape, si3.shape)
np.testing.assert_array_equal(si2, si3)
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_2D(self):
si1 = Series(os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
imagedata.formats.INPUT_ORDER_TIME, self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
si2 = si1[0, 0, ...]
with tempfile.TemporaryDirectory() as d:
si2.write(d, formats=['mat'])
si3 = Series(d)
self.assertEqual(si2.dtype, si3.dtype)
self.assertEqual(si2.shape, si3.shape)
np.testing.assert_array_equal(si2, si3)
def test_copy_dicom_4D(self):
si = Series(
os.path.join('data', 'dicom', 'time'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
logging.debug("si.sliceLocations: {}".format(si.sliceLocations))
logging.debug("si.imagePositions.keys(): {}".format(si.imagePositions.keys()))
newsi = Series(si,
imagedata.formats.INPUT_ORDER_TIME)
compare_headers(self, si, newsi)
self.assertEqual(newsi.dtype, np.uint16)
self.assertEqual(newsi.shape, (3, 3, 192, 152))
def test_cross_talk(self):
si = Series('data/dicom/time/time00')
# print('si before', si.getDicomAttribute('SeriesInstanceUID'), si.seriesInstanceUID)
si1 = si[0]
si1.seriesNumber = si.seriesNumber + 10
self.assertNotEqual(si.seriesNumber, si1.seriesNumber)
# print('si after', si.getDicomAttribute('SeriesInstanceUID'), si.seriesInstanceUID)
# print('si1', si1.getDicomAttribute('SeriesInstanceUID'), si1.seriesInstanceUID)
self.assertNotEqual(si.seriesInstanceUID, si1.seriesInstanceUID)
si2 = Series('data/dicom/time/time00')
si2.seriesNumber += 10
self.assertNotEqual(si.seriesNumber, si2.seriesNumber)
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_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_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_set_axes(self):
si1 = Series('data/dicom/time/time00')
shape = si1.shape + (3, )
img = np.zeros(shape, dtype=np.uint8)
img[..., 0] = si1[:]
img[..., 1] = si1[:]
img[..., 2] = si1[:]
rgb = Series(img,
geometry=si1,
axes=si1.axes +
[imagedata.axis.VariableAxis('rgb', ['r', 'g', 'b'])])
def test_transport_single_image(self):
si1 = Series(
os.path.join('data', 'dicom', 'time', 'time00', 'Image_00020.dcm')
)
self.assertEqual((192, 152), si1.shape)
si1.write('dicom://localhost:11112/Temp', formats=['dicom'])
si2 = Series(
scpdir.name
)
# compare_headers(obj, si1, si2)
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
def test_write_single_file(self):
si1 = Series(
os.path.join(
'data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'time',
self.opts)
with tempfile.TemporaryDirectory() as d:
si1.write(d + '?Image%1d.nii.gz', formats=['nifti'])
si2 = Series(os.path.join(d, 'Image0.nii.gz'), 'time')
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
def test_compare_qform_to_dicom(self):
dcm = Series(
os.path.join('data', 'dicom', 'time'),
'time')
self.assertEqual('dicom', dcm.input_format)
dt = dcm.transformationMatrix
n = Series(
os.path.join('data', 'nifti', 'time', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'time')
self.assertEqual('nifti', n.input_format)
nt = n.transformationMatrix
self.assertEqual(dcm.shape, n.shape)
# obj.assertEqual(dcm.dtype, n.dtype)
np.testing.assert_allclose(n.transformationMatrix, dcm.transformationMatrix, rtol=1e-3)
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_read_2D(self):
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
'none',
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 192, 152))
si2 = si1[0, ...]
with tempfile.TemporaryDirectory() as d:
si2.write(os.path.join(d, '?Image.mha'), formats=['itk'])
si3 = Series(d)
self.assertEqual(si2.dtype, si3.dtype)
self.assertEqual(si2.shape, si3.shape)
np.testing.assert_array_equal(si2, si3)
def test_transport_cget_series(self):
patID = '123456'
stuInsUID = '1.2.3.4'
serInsUID = '1.2.3.4.5'
accno = '98765'
serNum = 4
si1 = Series('dicom://localhost:11112/Temp/{}/{}/{}'.format(
patID, stuInsUID, serInsUID
))
print(si1.shape, si1.spacing, si1.patientName, si1.accessionNumber, si1.seriesNumber)
si2 = Series('dicom://localhost:11112/Temp/{}/{}/{}'.format(
patID, accno, serNum
))
print(si2.shape, si2.spacing, si2.patientName, si2.accessionNumber, si2.seriesNumber)
def test_write_4d_mat(self):
si1 = Series(os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
imagedata.formats.INPUT_ORDER_TIME, self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'mat?Image_%05d'),
formats=['mat'],
opts=self.opts)
# Read back the MAT data and compare to original si1
si2 = Series(os.path.join(d, 'mat', 'Image_00000.mat'),
imagedata.formats.INPUT_ORDER_TIME, self.opts)
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
def test_read_single_directory(self):
si1 = Series(
os.path.join('data', 'dicom', 'time', 'time00'),
'none',
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 192, 152))
def test_read_all_files(self):
si1 = Series(
os.path.join('data', 'dicom', 'time.zip?time/'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
def test_read_two_files(self):
si1 = Series(
os.path.join('data', 'dicom', 'time.zip?time/time00/Image_0002[01].dcm'),
'none',
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (2, 192, 152))
def test_read_single_file_wildcard(self):
si1 = Series(
os.path.join('data', 'dicom', 'time.zip?*time00/Image_00020.dcm'),
'none',
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (192, 152))
def test_zipread_all_files(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all.zip'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
def test_read_two_files(self):
si1 = Series([
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
os.path.join('data', 'mat', 'time', 'Image_00000.mat')
], imagedata.formats.INPUT_ORDER_TIME, self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (2, 3, 3, 192, 152))
def test_read_two_files2(self):
si1 = Series(
os.path.join('data', 'dicom',
'time.zip?*0[01]/Image_0002[01].dcm'),
imagedata.formats.INPUT_ORDER_TIME, self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (2, 2, 192, 152))
def test_read_single_directory(self):
si1 = Series(
os.path.join('data', 'itk', 'time'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
def test_read_single_file(self):
si1 = Series(
os.path.join('data', 'dicom', 'time', 'time00', 'Image_00020.dcm'),
'none',
self.opts)
self.assertEqual(si1.input_format, 'dicom')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (192, 152))
