def try_stirtonifti():
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Starting STIR to Nifti test...\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'
)
time.sleep(0.5)
import pSTIR
# Input filenames
nifti_filename = SIRF_PATH + '/data/examples/Registration/test2.nii.gz'
# Load the image as a NiftiImageData3D
image_nifti = pReg.NiftiImageData3D(nifti_filename)
# Read as STIRImageData, convert to NiftiImageData3D and save to file
image_stir = pSTIR.ImageData(nifti_filename)
image_nifti_from_stir = pReg.NiftiImageData3D(image_stir)
image_nifti_from_stir.write('results/stir_to_nifti.nii',
image_nifti.get_original_datatype())
# Compare the two
if image_nifti != image_nifti_from_stir:
raise AssertionError("Conversion from STIR to Nifti failed.")
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Finished STIR to Nifti test.\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'
)
time.sleep(0.5)
def try_niftiimage():
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Starting NiftiImageData test...\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'
)
time.sleep(0.5)
# default constructor
a = pReg.NiftiImageData()
if a.handle is None:
raise AssertionError()
# Read from file
b = pReg.NiftiImageData(ref_aladin_filename)
# Save to file
b.write(save_nifti_image)
# Fill
b.fill(100)
# Get max
if b.get_max() != 100:
raise AssertionError('NiftiImageData fill()/get_max() failed.')
# Get min
if b.get_min() != 100:
raise AssertionError('NiftiImageData fill()/get_min() failed.')
# Deep copy
d = b.deep_copy()
if d.handle == b.handle:
raise AssertionError('NiftiImageData deep_copy failed.')
if d != b:
raise AssertionError("NiftiImageData deep_copy failed.")
# Addition
e = d + d
if abs(e.get_max() - 2 * d.get_max()) > 0.0001:
raise AssertionError('NiftiImageData __add__/get_max() failed.')
# Subtraction
e = d - d
if abs(e.get_max()) > 0.0001:
raise AssertionError('NiftiImageData __sub__ failed.')
# Sum
if abs(e.get_sum()) > 0.0001:
raise AssertionError('NiftiImageData get_sum() failed.')
# Add num to image
q = e + 1
if q.get_max() != e.get_max() + 1:
raise AssertionError('NiftiImageData __add__ val failed.')
# Subtract num from image
r = e - 1
if r.get_max() != e.get_max() - 1:
raise AssertionError('NiftiImageData __sub__ val failed.')
# Multiply image by num
s = e * 10
if s.get_max() != e.get_max() * 10:
raise AssertionError('NiftiImageData __mul__ val failed.')
# Dimensions
f = e.get_dimensions()
if not np.array_equal(f, [3, 64, 64, 64, 1, 1, 1, 1]):
raise AssertionError('NiftiImageData get_dimensions() failed.')
# Get as array
arr = d.as_array()
if arr.max() != 100:
raise AssertionError('NiftiImageData as_array().max() failed.')
if arr.ndim != 3:
raise AssertionError('NiftiImageData as_array() ndims failed.')
if arr.shape != (64, 64, 64):
raise AssertionError('NiftiImageData as_array().shape failed.')
# Test saving to datatype
ref_aladin.write(output_float, 16) # float
ref_aladin_float = pReg.NiftiImageData3D(output_float)
arr1 = ref_aladin.as_array()
arr2 = ref_aladin_float.as_array()
if not np.array_equal(arr1, arr2):
raise AssertionError(
"NiftiImageData::write()/change_datatype() failed.")
# Test print methods
q.print_header()
pReg.NiftiImageData.print_headers([q, s])
# Crop image
min_ = []
max_ = []
for i in range(0, 7):
min_.append(0)
max_.append(f[i + 1] - 1)
max_[2] = 62
s = e
s.crop(min_, max_)
if s.as_array().shape != (64, 64, 63):
raise AssertionError("NiftiImageData crop() failed.")
# Get voxel sizes
s = b.get_voxel_sizes()
if not all(
numpy.equal(s, numpy.array([0, 4.0625, 4.0625, 4.0625, 0, 0, 0, 0
]))):
raise AssertionError("NiftiImageData get_voxel_sizes() failed.")
# Check upsampling/downsampling
u = pReg.NiftiImageData(ref_aladin_filename)
original_spacing = u.get_voxel_sizes()
original_spacing = original_spacing[1:4]
upsampled_spacing = [
original_spacing[0] / 2, original_spacing[1] / 4, original_spacing[2]
]
downsampled_spacing = [
original_spacing[0] * 2, original_spacing[1] * 4, original_spacing[2]
]
# Downsample
v = u.deep_copy()
v.set_voxel_spacing(downsampled_spacing, 3)
v.write(save_nifti_image_downsample)
# Upsample then downsample, check nothing has changed
w = u.deep_copy()
w.set_voxel_spacing(upsampled_spacing, 0)
w.write(save_nifti_image_upsample)
x = w.deep_copy()
x.set_voxel_spacing(original_spacing, 0)
x.write(save_nifti_image_up_downsample)
pReg.NiftiImageData.print_headers([u, v, w, x])
if x != u:
raise AssertionError('NiftiImageData::upsample()/downsample() failed.')
# Check get_contains_nans
x_arr = x.as_array()
x_arr.fill(0)
x.fill(x_arr)
if x.get_contains_nans():
raise AssertionError('NiftiImageData::get_contains_nans() 1 failed.')
x_arr[1] = np.nan
x.fill(x_arr)
if not x.get_contains_nans():
raise AssertionError('NiftiImageData::get_contains_nans() 2 failed.')
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Finished NiftiImageData test.\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'
)
time.sleep(0.5)
def try_niftiimage3d():
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Starting NiftiImageData3D test...\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'
)
time.sleep(0.5)
# default constructor
a = pReg.NiftiImageData3D()
if a.handle is None:
raise AssertionError()
# Read from file
b = pReg.NiftiImageData3D(ref_aladin_filename)
# Save to file
b.write(save_nifti_image_3d)
# Fill
b.fill(100)
# Get max
if b.get_max() != 100:
raise AssertionError('NiftiImageData3D fill()/get_max() failed.')
# Get min
if b.get_min() != 100:
raise AssertionError('NiftiImageData3D fill()/get_min() failed.')
# Deep copy
d = b.deep_copy()
if d.handle == b.handle:
raise AssertionError('NiftiImageData3D deep_copy failed.')
if d != b:
raise AssertionError("NiftiImageData3D deep_copy failed.")
# Addition
e = d + d
if abs(e.get_max() - 2 * d.get_max()) > 0.0001:
raise AssertionError('NiftiImageData3D __add__/get_max() failed.')
# Subtraction
e = d - d
if abs(e.get_max()) > 0.0001:
raise AssertionError('NiftiImageData3D __sub__ failed.')
# Sum
if abs(e.get_sum()) > 0.0001:
raise AssertionError('NiftiImageData3D get_sum() failed.')
# Dimensions
f = e.get_dimensions()
if not np.array_equal(f, [3, 64, 64, 64, 1, 1, 1, 1]):
raise AssertionError('NiftiImageData3D get_dimensions() failed.')
# Get as array
arr = d.as_array()
if arr.max() != 100:
raise AssertionError('NiftiImageData3D as_array().max() failed.')
if arr.ndim != 3:
raise AssertionError('NiftiImageData3D as_array() ndims failed.')
if arr.shape != (64, 64, 64):
raise AssertionError('NiftiImageData3D as_array().shape failed.')
# try linear algebra
h = d / 10000
if abs(h.get_max() - d.get_max() / 10000) > 1e-4:
raise AssertionError('NiftiImageData3D linear algebra failed.')
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Finished NiftiImageData3D test.\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'
)
time.sleep(0.5)
aladin_def_inverse = output_prefix + "aladin_def_inverse_%s.nii"
aladin_disp_forward = output_prefix + "aladin_disp_forward.nii"
aladin_disp_inverse = output_prefix + "aladin_disp_inverse_%s.nii"
f3d_def_forward = output_prefix + "f3d_disp_forward.nii"
f3d_def_inverse = output_prefix + "f3d_disp_inverse_%s.nii"
f3d_disp_forward = output_prefix + "f3d_disp_forward.nii"
f3d_disp_inverse = output_prefix + "f3d_disp_inverse_%s.nii"
rigid_resample = output_prefix + "rigid_resample.nii"
nonrigid_resample_disp = output_prefix + "nonrigid_resample_disp.nii"
nonrigid_resample_def = output_prefix + "nonrigid_resample_def.nii"
output_weighted_mean = output_prefix + "weighted_mean.nii"
output_weighted_mean_def = output_prefix + "weighted_mean_def.nii"
output_float = output_prefix + "reg_aladin_float.nii"
ref_aladin = pReg.NiftiImageData3D(ref_aladin_filename)
flo_aladin = pReg.NiftiImageData3D(flo_aladin_filename)
ref_f3d = pReg.NiftiImageData3D(ref_f3d_filename)
flo_f3d = pReg.NiftiImageData3D(flo_f3d_filename)
# NiftiImageData
def try_niftiimage():
time.sleep(0.5)
sys.stderr.write(
'\n# --------------------------------------------------------------------------------- #\n'
)
sys.stderr.write(
'# Starting NiftiImageData test...\n')
sys.stderr.write(
'# --------------------------------------------------------------------------------- #\n'