def test_wrong_mag_dimensions(self):
# Call prelude phase with wrong dimensions
mag_e1 = np.ones([4, 4, 4])
try:
prelude(self.phase_e1, self.affine_phase_e1, mag=mag_e1)
except RuntimeError:
# If an exception occurs, this is the desired behaviour
return 0
# If there isn't an error, then there is a problem
print('\nWrong dimensions for mag input')
assert False
def test_default_works(self):
"""
Runs prelude and check output integrity.
"""
# default prelude call
unwrapped_phase_e1 = prelude(self.phase_e1, self.affine_phase_e1)
assert (unwrapped_phase_e1.shape == self.phase_e1.shape)
def test_wrong_size_mask(self):
# Create mask with wrong dimensions
mask = np.ones([4, 4, 4])
# Call prelude with mask
try:
prelude(self.phase_e1,
self.affine_phase_e1,
mag=self.mag_e1,
mask=mask)
except RuntimeError:
# If an exception occurs, this is the desired behaviour since the mask is the wrong dimensions
return 0
# If there isn't an error, then there is a problem
print('\nWrong dimensions for mask does not throw an error')
assert False
def test_threshold(self):
"""
Call prelude with a threshold for masking
"""
unwrapped_phase_e1 = prelude(self.phase_e1,
self.affine_phase_e1,
mag=self.mag_e1,
threshold=200)
assert (unwrapped_phase_e1.shape == self.phase_e1.shape)
def test_phase_2d(self):
"""
Call prelude with a 2D phase and mag array
"""
# Get first slice
phase_e1_2d = self.phase_e1[:, :, 0]
mag_e1_2d = self.mag_e1[:, :, 0]
unwrapped_phase_e1 = prelude(phase_e1_2d,
self.affine_phase_e1,
mag=mag_e1_2d)
assert (unwrapped_phase_e1.shape == phase_e1_2d.shape)
def test_2nd_dim_singleton(self):
"""
Call prelude on data with a singleton on the 2nd dimension
"""
# Prepare singleton
phase_singleton = np.expand_dims(self.phase_e1[:, 0, 0], -1)
mag_singleton = np.expand_dims(self.mag_e1[:, 0, 0], -1)
unwrapped_phase_singleton = prelude(phase_singleton,
self.affine_phase_e1,
mag=mag_singleton)
assert unwrapped_phase_singleton.ndim == 2
def test_non_default_mask(self):
"""
Check prelude function with input binary mask.
"""
# Create mask with all ones
mask = np.ones(self.phase_e1.shape)
# Call prelude with mask (is_unwrapping_in_2d is also used because it is significantly faster)
unwrapped_phase_e1 = prelude(self.phase_e1,
self.affine_phase_e1,
mag=self.mag_e1,
mask=mask,
is_unwrapping_in_2d=True)
# Make sure the phase is not 0. When there isn't a mask, the phase is 0
assert (unwrapped_phase_e1[5, 5, 0] != 0)
def general_demo(path_output=os.path.join(os.path.curdir, 'output_dir')):
"""
Args:
path_output (str): Output directory to store data and results.
Returns:
str: File name and path of output figure
"""
logging.basicConfig(level='INFO')
# Download example data
path_testing_data = os.path.join(path_output, 'testing_data')
run_subprocess(f'st_download_data testing_data --output {path_testing_data}')
# Transfer from dicom to nifti
path_dicom_unsorted = os.path.join(path_testing_data, 'dicom_unsorted')
path_nifti = os.path.join(path_output, 'niftis')
dicom_to_nifti(path_dicom_unsorted, path_nifti, subject_id='sub-01')
# Open phase data
fname_phases = glob.glob(os.path.join(path_nifti, 'sub-01', 'fmap', '*phase*.nii.gz'))
nii_phase_e1 = nib.load(fname_phases[0])
nii_phase_e2 = nib.load(fname_phases[1])
# Scale phase to radians
phase_e1 = np.interp(nii_phase_e1.get_fdata(), [0, 4096], [-np.pi, np.pi])
phase_e2 = np.interp(nii_phase_e2.get_fdata(), [0, 4096], [-np.pi, np.pi])
# Open mag data
fname_mags = glob.glob(os.path.join(path_nifti, 'sub-01', 'fmap', '*magnitude*.nii.gz'))
nii_mag_e1 = nib.load(fname_mags[0])
nii_mag_e2 = nib.load(fname_mags[1])
# Call prelude to unwrap the phase
unwrapped_phase_e1 = prelude(phase_e1, nii_phase_e1.affine, mag=nii_mag_e1.get_fdata())
unwrapped_phase_e2 = prelude(phase_e2, nii_phase_e2.affine, mag=nii_mag_e2.get_fdata(), threshold=200)
# Plot results
fig = Figure(figsize=(10, 10))
# FigureCanvas(fig)
ax = fig.add_subplot(3, 2, 1)
im = ax.imshow(nii_mag_e1.get_fdata()[:-1, :-1, 0])
fig.colorbar(im)
ax.set_title("Mag e1")
ax = fig.add_subplot(3, 2, 2)
im = ax.imshow(nii_mag_e2.get_fdata()[:-1, :-1, 0])
fig.colorbar(im)
ax.set_title("Mag e2")
ax = fig.add_subplot(3, 2, 3)
im = ax.imshow(phase_e1[:-1, :-1, 0])
fig.colorbar(im)
ax.set_title("Wrapped e1")
ax = fig.add_subplot(3, 2, 4)
im = ax.imshow(phase_e2[:-1, :-1, 0])
fig.colorbar(im)
ax.set_title("Wrapped e2")
ax = fig.add_subplot(3, 2, 5)
im = ax.imshow(unwrapped_phase_e1[:-1, :-1, 0])
fig.colorbar(im)
ax.set_title("Unwrapped e1")
ax = fig.add_subplot(3, 2, 6)
im = ax.imshow(unwrapped_phase_e2[:-1, :-1, 0])
fig.colorbar(im)
ax.set_title("Unwrapped e2")
fname_figure = os.path.join(path_output, 'unwrap_phase_plot.png')
fig.savefig(fname_figure)
return fname_figure
