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))
import copy
deep_si = copy.deepcopy(si)
np.testing.assert_array_equal(si, deep_si)
si.sort_on = imagedata.formats.SORT_ON_SLICE
# si.sort_on = imagedata.formats.SORT_ON_TAG
log.debug("test_write_4d_itk: si.sort_on {}".format(
imagedata.formats.sort_on_to_str(si.sort_on)))
si.output_dir = 'single'
# si.output_dir = 'multi'
with tempfile.TemporaryDirectory() as d:
si.write(d, formats=['itk'], opts=self.opts)
np.testing.assert_array_equal(si, deep_si)
# Read back the DICOM data and verify the header
si2 = Series(
d,
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si.shape, si2.shape)
compare_headers(self, si, si2, uid=False)
np.testing.assert_array_almost_equal(si, si2, decimal=4)
def test_write_4d_nifti(self):
si1 = Series(
os.path.join('data', 'dicom', 'time'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
si1.sort_on = imagedata.formats.SORT_ON_SLICE
logging.debug("test_write_4d_nifti: si1.sort_on {}".format(
imagedata.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,
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
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)
