def img_filt(fname):
# Load the thresholded CT
img = nib.load(fname)
# convert to nipy format for filtering
nipy_img = nipy.io.nifti_ref.nifti2nipy(img)
# build and apply gaussian filter
smoother = LinearFilter(nipy_img.coordmap, nipy_img.shape, 1)
smoothed_im = smoother.smooth(nipy_img)
# convert smoothed im back to nifti
nifti_img = nipy.io.nifti_ref.nipy2nifti(smoothed_im)
# get data array for saving
smoothed_CT = nifti_img.get_data()
smoothed_CT = np.array(smoothed_CT)
# save the smoothed thresholded ct
hdr = img.get_header()
affine = img.get_affine()
N = nib.Nifti1Image(smoothed_CT, affine, hdr)
new_fname = 'smoothed_' + fname
N.to_filename(new_fname)
def test_kernel():
# Verify the the convolution with a delta function
# gives the correct answer.
tol = 0.9999
sdtol = 1.0e-8
for x in range(6):
shape = randint(30,60,(3,))
ii, jj, kk = randint(11,17, (3,))
coordmap = Affine.from_start_step('ijk', 'xyz',
randint(5,20,(3,))*0.25,
randint(5,10,(3,))*0.5)
signal = np.zeros(shape)
signal[ii,jj,kk] = 1.
signal = Image(signal, coordmap=coordmap)
kernel = LinearFilter(coordmap, shape,
fwhm=randint(50,100)/10.)
ssignal = kernel.smooth(signal)
ssignal = np.asarray(ssignal)
ssignal[:] *= kernel.norms[kernel.normalization]
I = np.indices(ssignal.shape)
I.shape = (kernel.coordmap.ndim[0], np.product(shape))
i, j, k = I[:,np.argmax(ssignal[:].flat)]
yield assert_equal, (i,j,k), (ii,jj,kk)
Z = kernel.coordmap(I) - kernel.coordmap([i,j,k])
_k = kernel(Z)
_k.shape = ssignal.shape
yield assert_true, (np.corrcoef(_k[:].flat, ssignal[:].flat)[0,1] > tol)
yield assert_true, ((_k[:] - ssignal[:]).std() < sdtol)
def _indices(i,j,k,axis):
I = np.zeros((3,20))
I[0] += i
I[1] += j
I[2] += k
I[axis] += np.arange(-10,10)
return I
vx = ssignal[i,j,(k-10):(k+10)]
vvx = coordmap(_indices(i,j,k,2)) - coordmap([[i],[j],[k]])
yield assert_true, (np.corrcoef(vx, kernel(vvx))[0,1] > tol)
vy = ssignal[i,(j-10):(j+10),k]
vvy = coordmap(_indices(i,j,k,1)) - coordmap([[i],[j],[k]])
yield assert_true, (np.corrcoef(vy, kernel(vvy))[0,1] > tol)
vz = ssignal[(i-10):(i+10),j,k]
vvz = coordmap(_indices(i,j,k,0)) - coordmap([[i],[j],[k]])
yield assert_true, (np.corrcoef(vz, kernel(vvz))[0,1] > tol)
def test_kernel():
# Verify that convolution with a delta function gives the correct
# answer.
tol = 0.9999
sdtol = 1.0e-8
for x in range(6):
shape = randint(30,60,(3,))
# pos of delta
ii, jj, kk = randint(11,17, (3,))
# random affine coordmap (diagonal and translations)
coordmap = AffineTransform.from_start_step('ijk', 'xyz',
randint(5,20,(3,))*0.25,
randint(5,10,(3,))*0.5)
# delta function in 3D array
signal = np.zeros(shape)
signal[ii,jj,kk] = 1.
signal = Image(signal, coordmap=coordmap)
# A filter with coordmap, shape matched to image
kernel = LinearFilter(coordmap, shape,
fwhm=randint(50,100)/10.)
# smoothed normalized 3D array
ssignal = kernel.smooth(signal).get_data()
ssignal[:] *= kernel.norms[kernel.normalization]
# 3 points * signal.size array
I = np.indices(ssignal.shape)
I.shape = (kernel.coordmap.ndims[0], np.product(shape))
# location of maximum in smoothed array
i, j, k = I[:, np.argmax(ssignal[:].flat)]
# same place as we put it before smoothing?
assert_equal((i,j,k), (ii,jj,kk))
# get physical points position relative to position of delta
Z = kernel.coordmap(I.T) - kernel.coordmap([i,j,k])
_k = kernel(Z)
_k.shape = ssignal.shape
assert_true((np.corrcoef(_k[:].flat, ssignal[:].flat)[0,1] > tol))
assert_true(((_k[:] - ssignal[:]).std() < sdtol))
def _indices(i,j,k,axis):
I = np.zeros((3,20))
I[0] += i
I[1] += j
I[2] += k
I[axis] += np.arange(-10,10)
return I.T
vx = ssignal[i,j,(k-10):(k+10)]
xformed_ijk = coordmap([i, j, k])
vvx = coordmap(_indices(i,j,k,2)) - xformed_ijk
assert_true((np.corrcoef(vx, kernel(vvx))[0,1] > tol))
vy = ssignal[i,(j-10):(j+10),k]
vvy = coordmap(_indices(i,j,k,1)) - xformed_ijk
assert_true((np.corrcoef(vy, kernel(vvy))[0,1] > tol))
vz = ssignal[(i-10):(i+10),j,k]
vvz = coordmap(_indices(i,j,k,0)) - xformed_ijk
assert_true((np.corrcoef(vz, kernel(vvz))[0,1] > tol))
def smooth_volume(nifti_file, smoothmm):
"""
@param nifti_file: string
@param smoothmm: int
@return:
"""
try:
img = load_image(nifti_file)
except Exception as exc:
raise Exception('Error reading file {0}.'.format(nifti_file), exc_info=True) from exc
if smoothmm <= 0:
return img
filter = LinearFilter(img.coordmap, img.shape)
return filter.smooth(img)
def _smooth_img(nii_img, smooth_fwhm):
"""
Parameters
----------
nii_img: nipy.Image
smooth_fwhm: float
Returns
-------
smoothed nipy.Image
"""
# delayed import because could not install nipy on Python 3 on OSX
from nipy.algorithms.kernel_smooth import LinearFilter
if smooth_fwhm <= 0:
return nii_img
filter = LinearFilter(nii_img.coordmap, nii_img.shape)
return filter.smooth(nii_img)
def test_anat_smooth():
anat = load_image(anatfile)
smoother = LinearFilter(anat.coordmap, anat.shape)
sanat = smoother.smooth(anat)
