def test_no_denoising_for_small_h():
img = np.zeros((40, 40))
img[10:-10, 10:-10] = 1.
img += 0.3 * np.random.randn(*img.shape)
# very small h should result in no averaging with other patches
denoised = restoration.nl_means_denoising(img, 7, 5, 0.01, fast_mode=True)
assert np.allclose(denoised, img)
denoised = restoration.nl_means_denoising(img, 7, 5, 0.01, fast_mode=False)
assert np.allclose(denoised, img)
def test_no_denoising_for_small_h():
img = np.zeros((40, 40))
img[10:-10, 10:-10] = 1.
img += 0.3*np.random.randn(*img.shape)
# very small h should result in no averaging with other patches
denoised = restoration.nl_means_denoising(img, 7, 5, 0.01, fast_mode=True)
assert np.allclose(denoised, img)
denoised = restoration.nl_means_denoising(img, 7, 5, 0.01, fast_mode=False)
assert np.allclose(denoised, img)
def test_nl_means_denoising_2d():
img = np.zeros((40, 40))
img[10:-10, 10:-10] = 1.
img += 0.3*np.random.randn(*img.shape)
denoised = restoration.nl_means_denoising(img, 7, 5, 0.2, fast_mode=True)
# make sure noise is reduced
assert img.std() > denoised.std()
denoised = restoration.nl_means_denoising(img, 7, 5, 0.2, fast_mode=False)
# make sure noise is reduced
assert img.std() > denoised.std()
def test_nl_means_denoising_2d():
img = np.zeros((40, 40))
img[10:-10, 10:-10] = 1.
img += 0.3 * np.random.randn(*img.shape)
denoised = restoration.nl_means_denoising(img, 7, 5, 0.2, fast_mode=True)
# make sure noise is reduced
assert img.std() > denoised.std()
denoised = restoration.nl_means_denoising(img, 7, 5, 0.2, fast_mode=False)
# make sure noise is reduced
assert img.std() > denoised.std()
def test_nl_means_denoising_multichannel():
img = np.zeros((21, 20, 10))
img[10, 9:11, 2:-2] = 1.
img += 0.3 * np.random.randn(*img.shape)
denoised_wrong_multichannel = restoration.nl_means_denoising(
img, 5, 4, 0.1, fast_mode=True, multichannel=True)
denoised_ok_multichannel = restoration.nl_means_denoising(
img, 5, 4, 0.1, fast_mode=True, multichannel=False)
snr_wrong = 10 * np.log10(1. /
((denoised_wrong_multichannel - img)**2).mean())
snr_ok = 10 * np.log10(1. / ((denoised_ok_multichannel - img)**2).mean())
assert snr_ok > snr_wrong
def test_nl_means_denoising_2drgb():
# reduce image size because nl means is very slow
img = np.copy(astro[:50, :50])
# add some random noise
img += 0.5 * img.std() * np.random.random(img.shape)
img = np.clip(img, 0, 1)
denoised = restoration.nl_means_denoising(img, 7, 9, 0.3, fast_mode=True)
# make sure noise is reduced
assert img.std() > denoised.std()
denoised = restoration.nl_means_denoising(img, 7, 9, 0.3, fast_mode=False)
# make sure noise is reduced
assert img.std() > denoised.std()
def test_nl_means_denoising_3d():
img = np.zeros((20, 20, 10))
img[5:-5, 5:-5, 3:-3] = 1.
img += 0.3*np.random.randn(*img.shape)
denoised = restoration.nl_means_denoising(img, 5, 4, 0.2, fast_mode=True,
multichannel=False)
# make sure noise is reduced
assert img.std() > denoised.std()
denoised = restoration.nl_means_denoising(img, 5, 4, 0.2, fast_mode=False,
multichannel=False)
# make sure noise is reduced
assert img.std() > denoised.std()
def test_nl_means_denoising_2drgb():
# reduce image size because nl means is very slow
img = np.copy(astro[:50, :50])
# add some random noise
img += 0.5 * img.std() * np.random.random(img.shape)
img = np.clip(img, 0, 1)
denoised = restoration.nl_means_denoising(img, 7, 9, 0.3, fast_mode=True)
# make sure noise is reduced
assert img.std() > denoised.std()
denoised = restoration.nl_means_denoising(img, 7, 9, 0.3, fast_mode=False)
# make sure noise is reduced
assert img.std() > denoised.std()
def test_nl_means_denoising_multichannel():
img = np.zeros((21, 20, 10))
img[10, 9:11, 2:-2] = 1.
img += 0.3*np.random.randn(*img.shape)
denoised_wrong_multichannel = restoration.nl_means_denoising(img,
5, 4, 0.1, fast_mode=True, multichannel=True)
denoised_ok_multichannel = restoration.nl_means_denoising(img,
5, 4, 0.1, fast_mode=True, multichannel=False)
snr_wrong = 10 * np.log10(1. /
((denoised_wrong_multichannel - img)**2).mean())
snr_ok = 10 * np.log10(1. /
((denoised_ok_multichannel - img)**2).mean())
assert snr_ok > snr_wrong
def crop_data(f,mask,t):
file_id = os.path.basename(f).split('.')[0]
img = irtk.imread( f, dtype='float32',force_neurological=True )
seg = mask.transform(t.invert(), target=img,interpolation='nearest')
x_min,y_min,z_min,x_max,y_max,z_max = seg.bbox()
seg = seg[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1]
img = img[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1].rescale(0,1000) + 1.0 # +1 to avoid zeros in the heart
img_file = output_dir + '/img_' + file_id + ".nii.gz"
irtk.imwrite( img_file, img )
for z in range(img.shape[0]):
scale = img[z].max()
img[z] = restoration.nl_means_denoising(img[z].rescale(0.0,1.0).view(np.ndarray),
fast_mode=False,
patch_size=5,
patch_distance=7,
h=0.05,
multichannel=False)
img[z] *= scale
img[seg==0] = 0
masked_file = output_dir + '/masked_' + file_id + ".nii.gz"
irtk.imwrite( masked_file, img )
def blur_predict(model, X, type="median", filter_size=3, sigma=1.0):
if type == "median":
blured_X = np.array(list(map(lambda x: ndimage.median_filter(x, filter_size),
X)))
elif type == "gaussian":
blured_X = np.array(list(map(lambda x: ndimage.gaussian_filter(x, filter_size),
X)))
elif type == "f_gaussian":
blured_X = np.array(list(map(lambda x: filters.gaussian_filter(x.reshape((28, 28)), sigma=sigma).reshape(784),
X)))
elif type == "tv_chambolle":
blured_X = np.array(list(map(lambda x: restoration.denoise_tv_chambolle(x.reshape((28, 28)), weight=0.2).reshape(784),
X)))
elif type == "tv_bregman":
blured_X = np.array(list(map(lambda x: restoration.denoise_tv_bregman(x.reshape((28, 28)), weight=5.0).reshape(784),
X)))
elif type == "bilateral":
blured_X = np.array(list(map(lambda x: restoration.denoise_bilateral(np.abs(x).reshape((28, 28))).reshape(784),
X)))
elif type == "nl_means":
blured_X = np.array(list(map(lambda x: restoration.nl_means_denoising(x.reshape((28, 28))).reshape(784),
X)))
elif type == "none":
blured_X = X
else:
raise ValueError("unsupported filter type", type)
return predict(model, blured_X)
def nl_means( noisy , patch_size=7 , patch_distance=11 , h=0.1 , multichannel=False ,
fast_mode=True ):
noisy[:] , m , delta = change_range( noisy )
denois = rst.nl_means_denoising( noisy , patch_size=patch_size ,
patch_distance=patch_distance ,
h=h , multichannel=multichannel ,
fast_mode=fast_mode )
denois[:] = restore_range( denois , m , delta )
return denois
def test_nl_means_denoising_3d():
img = np.zeros((20, 20, 10))
img[5:-5, 5:-5, 3:-3] = 1.
img += 0.3 * np.random.randn(*img.shape)
denoised = restoration.nl_means_denoising(img,
5,
4,
0.2,
fast_mode=True,
multichannel=False)
# make sure noise is reduced
assert img.std() > denoised.std()
denoised = restoration.nl_means_denoising(img,
5,
4,
0.2,
fast_mode=False,
multichannel=False)
# make sure noise is reduced
assert img.std() > denoised.std()
cameraman = sk.img_as_float(io.imread('../../cameraman.bmp'))
cameraman_uni = sk.img_as_float(io.imread('../../cameraman_uni.bmp'))
cameraman_nor = sk.img_as_float(io.imread('../../cameraman_nor.bmp'))
cameraman_ric = sk.img_as_float(io.imread('../../cameraman_ric.bmp'))
cameraman_sp = sk.img_as_float(io.imread('../../cameraman_sp.bmp'))
baboon = sk.img_as_float(io.imread('../../baboon.bmp'))
baboon_uni = sk.img_as_float(io.imread('../../baboon_uni.bmp'))
baboon_nor = sk.img_as_float(io.imread('../../baboon_nor.bmp'))
baboon_ric = sk.img_as_float(io.imread('../../baboon_ric.bmp'))
baboon_sp = sk.img_as_float(io.imread('../../baboon_sp.bmp'))
# Apply filters
lena_uni_f = sk.img_as_float(res.nl_means_denoising(lena_uni,patch_size=3))
lena_nor_f = sk.img_as_float(res.nl_means_denoising(lena_nor,patch_size=3))
lena_ric_f = sk.img_as_float(res.nl_means_denoising(lena_ric,patch_size=3))
lena_sp_f = sk.img_as_float(res.nl_means_denoising(lena_sp,patch_size=3))
cameraman_uni_f = sk.img_as_float(res.nl_means_denoising(cameraman_uni,patch_size=3))
cameraman_nor_f = sk.img_as_float(res.nl_means_denoising(cameraman_nor,patch_size=3))
cameraman_ric_f = sk.img_as_float(res.nl_means_denoising(cameraman_ric,patch_size=3))
cameraman_sp_f = sk.img_as_float(res.nl_means_denoising(cameraman_sp,patch_size=3))
baboon_uni_f = sk.img_as_float(res.nl_means_denoising(baboon_uni,patch_size=3))
baboon_nor_f = sk.img_as_float(res.nl_means_denoising(baboon_nor,patch_size=3))
baboon_ric_f = sk.img_as_float(res.nl_means_denoising(baboon_ric,patch_size=3))
baboon_sp_f = sk.img_as_float(res.nl_means_denoising(baboon_sp,patch_size=3))
# Calculate MSE
lena_sp = sk.img_as_float(io.imread('../../lena_sp.bmp'))
cameraman = sk.img_as_float(io.imread('../../cameraman.bmp'))
cameraman_uni = sk.img_as_float(io.imread('../../cameraman_uni.bmp'))
cameraman_nor = sk.img_as_float(io.imread('../../cameraman_nor.bmp'))
cameraman_ric = sk.img_as_float(io.imread('../../cameraman_ric.bmp'))
cameraman_sp = sk.img_as_float(io.imread('../../cameraman_sp.bmp'))
baboon = sk.img_as_float(io.imread('../../baboon.bmp'))
baboon_uni = sk.img_as_float(io.imread('../../baboon_uni.bmp'))
baboon_nor = sk.img_as_float(io.imread('../../baboon_nor.bmp'))
baboon_ric = sk.img_as_float(io.imread('../../baboon_ric.bmp'))
baboon_sp = sk.img_as_float(io.imread('../../baboon_sp.bmp'))
# Apply filters
lena_uni_f = sk.img_as_float(res.nl_means_denoising(lena_uni, patch_size=3))
lena_nor_f = sk.img_as_float(res.nl_means_denoising(lena_nor, patch_size=3))
lena_ric_f = sk.img_as_float(res.nl_means_denoising(lena_ric, patch_size=3))
lena_sp_f = sk.img_as_float(res.nl_means_denoising(lena_sp, patch_size=3))
cameraman_uni_f = sk.img_as_float(
res.nl_means_denoising(cameraman_uni, patch_size=3))
cameraman_nor_f = sk.img_as_float(
res.nl_means_denoising(cameraman_nor, patch_size=3))
cameraman_ric_f = sk.img_as_float(
res.nl_means_denoising(cameraman_ric, patch_size=3))
cameraman_sp_f = sk.img_as_float(
res.nl_means_denoising(cameraman_sp, patch_size=3))
baboon_uni_f = sk.img_as_float(res.nl_means_denoising(baboon_uni,
patch_size=3))
for ax in axes.flatten()]
for i, driver in enumerate(np.unique(drivers)[:5]):
for j, n in enumerate(range(3)):
#axes[i, j].imshow(denoise_bilateral(X[j*5+i,:,:,0], sigma_range=0.05, sigma_spatial=4), cmap='gray')
axes[i, j].imshow(exposure.equalize_hist(X[j * 5 + i, :, :, 0]),
cmap='gray')
axes[i, j].set_title(driver)
plt.show()
exit()
figs, axes = plt.subplots(5, 3, figsize=(10, 15))
[(ax.set_xticks([]), ax.set_yticks([]), ax.axis('off'))
for ax in axes.flatten()]
for i, driver in enumerate(np.unique(drivers)[:5]):
for j, n in enumerate(range(3)):
axes[i, j].imshow(nl_means_denoising(X[j * 5 + i, :, :, :], 3, 4,
0.08))
axes[i, j].set_title(driver)
plt.show()
exit()
# Compute the Canny filter for two values of sigma
edges1 = denoise_tv_chambolle(im, weight=0.1, multichannel=False)
ax1.imshow(im, cmap=plt.cm.gray)
ax1.axis('off')
ax1.set_title('Original image', fontsize=20)
ax2.imshow(edges1, cmap=plt.cm.gray)
ax2.axis('off')
ax2.set_title('Filtered' + str(j), fontsize=20)
blurred by other denoising algoritm.
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import data, img_as_float
from skimage.restoration import nl_means_denoising
astro = img_as_float(data.astronaut())
astro = astro[30:180, 150:300]
noisy = astro + 0.3 * np.random.random(astro.shape)
noisy = np.clip(noisy, 0, 1)
denoise = nl_means_denoising(noisy, 7, 9, 0.08)
fig, ax = plt.subplots(ncols=2, figsize=(8, 4))
ax[0].imshow(noisy)
ax[0].axis('off')
ax[0].set_title('noisy')
ax[1].imshow(denoise)
ax[1].axis('off')
ax[1].set_title('non-local means')
fig.subplots_adjust(wspace=0.02, hspace=0.2,
top=0.9, bottom=0.05, left=0, right=1)
plt.show()
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from skimage import io
im = io.imread('datasetpaper.jpg')
plt.imshow(im, cmap='gray')
from skimage import restoration
from skimage import img_as_float
im_float = img_as_float(im)
im_denoised = restoration.nl_means_denoising(im_float, h=0.05)
plt.imshow(im_denoised, cmap='gray')
ax = plt.axis('off')
plt.imshow(im_denoised, cmap='gray')
click_markers = plt.ginput(n=-1, timeout=-1)
x, y = np.load('indices_markers.npy').T
plt.imshow(im_denoised, cmap='gray')
plt.plot(y, x, 'or', ms=4)
from skimage import morphology
markers = np.zeros(im_denoised.shape, dtype=np.int)
markers[x.astype(np.int), y.astype(np.int)] = np.arange(len(x)) + 1
markers = morphology.dilation(markers, morphology.disk(7))
patch. As a result, this algorithm can restore well textures, that would be
blurred by other denoising algoritm.
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import data, img_as_float
from skimage.restoration import nl_means_denoising
astro = img_as_float(data.astronaut())
astro = astro[30:180, 150:300]
noisy = astro + 0.3 * np.random.random(astro.shape)
noisy = np.clip(noisy, 0, 1)
denoise = nl_means_denoising(noisy, 7, 9, 0.08)
fig, ax = plt.subplots(ncols=2, figsize=(8, 4))
ax[0].imshow(noisy)
ax[0].axis('off')
ax[0].set_title('noisy')
ax[1].imshow(denoise)
ax[1].axis('off')
ax[1].set_title('non-local means')
fig.subplots_adjust(wspace=0.02,
hspace=0.2,
top=0.9,
bottom=0.05,
left=0,