def test_denoise_bilateral_multidimensional():
img = np.ones((10, 10, 10, 10))
with pytest.raises(ValueError):
restoration.denoise_bilateral(img, multichannel=False)
with pytest.raises(ValueError):
restoration.denoise_bilateral(
img, multichannel=True)
def denoising(astro):
noisy = astro + 0.6 * astro.std() * np.random.random(astro.shape)
noisy = np.clip(noisy, 0, 1)
fig, ax = plt.subplots(nrows=2, ncols=3, figsize=(8, 5), sharex=True,
sharey=True, subplot_kw={'adjustable': 'box-forced'})
plt.gray()
ax[0, 0].imshow(noisy)
ax[0, 0].axis('off')
ax[0, 0].set_title('noisy')
ax[0, 1].imshow(denoise_tv_chambolle(noisy, weight=0.1, multichannel=True))
ax[0, 1].axis('off')
ax[0, 1].set_title('TV')
ax[0, 2].imshow(denoise_bilateral(noisy, sigma_range=0.05, sigma_spatial=15))
ax[0, 2].axis('off')
ax[0, 2].set_title('Bilateral')
ax[1, 0].imshow(denoise_tv_chambolle(noisy, weight=0.2, multichannel=True))
ax[1, 0].axis('off')
ax[1, 0].set_title('(more) TV')
ax[1, 1].imshow(denoise_bilateral(noisy, sigma_range=0.1, sigma_spatial=15))
ax[1, 1].axis('off')
ax[1, 1].set_title('(more) Bilateral')
ax[1, 2].imshow(astro)
ax[1, 2].axis('off')
ax[1, 2].set_title('original')
fig.tight_layout()
plt.show()
def getSubImages(img, pixels, size):
subImages = []
originals = []
for i in range(len(img)):
subImageRow = []
originalRow = []
for j in range(len(img[i])):
if i % pixels == 0 and j % pixels == 0 and i+size-1 < len(img) and j+size-1 < len(img[i]):
subImage = []
for k in range(i, i+size, int(size/20)):
line = []
for l in range(j, j+size, int(size/20)):
line.append(img[k][l])
subImage.append(line)
originalRow.append(subImage)
if preprocess == preprocessing.SOBEL:
subImage = denoise_bilateral(subImage, sigma_range=0.1, sigma_spatial=15)
subImage = sobel(subImage)
elif preprocess == preprocessing.HOG:
subImage = useHoG(subImage)
else:
subImage = denoise_bilateral(subImage, sigma_range=0.1, sigma_spatial=15)
subImage = sobel(subImage)
subImage = useHoG(subImage)
subImageRow.append(subImage)
if len(subImageRow) > 0:
subImages.append(subImageRow)
originals.append(originalRow)
return subImages, originals
def test_denoise_bilateral_3d():
img = lena
# add some random noise
img += 0.5 * img.std() * np.random.random(img.shape)
img = np.clip(img, 0, 1)
out1 = restoration.denoise_bilateral(img, sigma_range=0.1, sigma_spatial=20)
out2 = restoration.denoise_bilateral(img, sigma_range=0.2, sigma_spatial=30)
# make sure noise is reduced
assert img.std() > out1.std()
assert out1.std() > out2.std()
def test_denoise_sigma_range_and_sigma_color():
img = checkerboard_gray.copy()[:50,:50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
out1 = restoration.denoise_bilateral(img, sigma_color=0.1,
sigma_spatial=10, multichannel=False)
with expected_warnings('`sigma_range` has been deprecated in favor of `sigma_color`. '
'The `sigma_range` keyword argument will be removed in v0.14'):
out2 = restoration.denoise_bilateral(img, sigma_color=0.2, sigma_range=0.1,
sigma_spatial=10, multichannel=False)
assert_equal(out1, out2)
def test_denoise_bilateral_color():
img = checkerboard.copy()
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
out1 = restoration.denoise_bilateral(img, sigma_range=0.1, sigma_spatial=20)
out2 = restoration.denoise_bilateral(img, sigma_range=0.2, sigma_spatial=30)
# make sure noise is reduced in the checkerboard cells
assert img[30:45, 5:15].std() > out1[30:45, 5:15].std()
assert out1[30:45, 5:15].std() > out2[30:45, 5:15].std()
def test_denoise_bilateral_color():
img = checkerboard.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
out1 = restoration.denoise_bilateral(img, sigma_color=0.1,
sigma_spatial=10, multichannel=True)
out2 = restoration.denoise_bilateral(img, sigma_color=0.2,
sigma_spatial=20, multichannel=True)
# make sure noise is reduced in the checkerboard cells
assert_(img[30:45, 5:15].std() > out1[30:45, 5:15].std())
assert_(out1[30:45, 5:15].std() > out2[30:45, 5:15].std())
def denoise_image(data, type=None):
from skimage.restoration import denoise_tv_chambolle, denoise_bilateral
if type == "tv":
return denoise_tv_chambolle(data, weight=0.2, multichannel=True)
return denoise_bilateral(data, sigma_range=0.1, sigma_spatial=15)
def crop_resize_other(img, pixelspacing ):
print("image shape {}".format(np.array(img).shape))
xmeanspacing = float(1.25826490244)
ymeanspacing = float(1.25826490244)
xscale = float(pixelspacing) / xmeanspacing
yscale = float(pixelspacing) / ymeanspacing
xnewdim = round( xscale * np.array(img).shape[0])
ynewdim = round( yscale * np.array(img).shape[1])
img = transform.resize(img, (xnewdim, ynewdim))
#img = cv2.normalize(img, None, 0, 255, cv2.NORM_MINMAX)
#img = auto_canny(img)
img = denoise_bilateral(img, sigma_range=0.05, sigma_spatial=15)
#im = cv2.normalize(im, None, 0, 255, cv2.NORM_MINMAX)
#img = img.Canny(im,128,128)
"""crop center and resize"""
if img.shape[0] < img.shape[1]:
img = img.T
# we crop image from center
short_egde = min(img.shape[:2])
yy = int((img.shape[0] - short_egde) / 2)
xx = int((img.shape[1] - short_egde) / 2)
crop_img = img[yy : yy + short_egde, xx : xx + short_egde]
crop_img *= 255
return crop_img.astype("uint8")
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 test_denoise_bilateral_nan():
img = np.full((50, 50), np.NaN)
# This is in fact an optional warning for our test suite.
# Python 3.5 will not trigger a warning.
with expected_warnings([r'invalid|\A\Z']):
out = restoration.denoise_bilateral(img, multichannel=False)
assert_equal(img, out)
def denoise_image(self):
"""
Abstracted version of denoise_bilateral function. Runs function on raw image using given constants
"""
return restoration.denoise_bilateral(
self.im,
sigma_color=self.C['BILATERAL_SIGMA_COLOR'],
sigma_spatial=self.C['BILATERAL_SIGMA_SPATIAL'],
multichannel=False)
def test_denoise_sigma_range_and_sigma_color():
img = checkerboard_gray.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
out1 = restoration.denoise_bilateral(img,
sigma_color=0.1,
sigma_spatial=10,
multichannel=False)
with expected_warnings(
'`sigma_range` has been deprecated in favor of `sigma_color`. '
'The `sigma_range` keyword argument will be removed in v0.14'):
out2 = restoration.denoise_bilateral(img,
sigma_color=0.2,
sigma_range=0.1,
sigma_spatial=10,
multichannel=False)
assert_equal(out1, out2)
def test_denoise_bilateral_3d_multichannel():
img = np.ones((50, 50, 50))
with expected_warnings(["grayscale"]):
result = restoration.denoise_bilateral(img)
expected = np.empty_like(img)
expected.fill(np.nan)
assert_equal(result, expected)
def test_denoise_bilateral_3d_multichannel():
img = np.ones((50, 50, 50))
with expected_warnings(["grayscale"]):
result = restoration.denoise_bilateral(img)
expected = np.empty_like(img)
expected.fill(np.nan)
assert_equal(result, expected)
def test_denoise_bilateral_nan():
import sys
img = np.full((50, 50), np.NaN)
# TODO: This warning is not optional in python3. This should be
# made a strict warning when we get to 0.15
with expected_warnings(['invalid|\A\Z']):
out = restoration.denoise_bilateral(img, multichannel=False)
assert_equal(img, out)
def test_denoise_bilateral_multichannel_deprecation():
img = checkerboard.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
with expected_warnings(["`multichannel` is a deprecated argument"]):
out1 = restoration.denoise_bilateral(img, sigma_color=0.1,
sigma_spatial=10,
multichannel=True)
with expected_warnings(["`multichannel` is a deprecated argument"]):
out2 = restoration.denoise_bilateral(img, sigma_color=0.2,
sigma_spatial=20,
multichannel=True)
# make sure noise is reduced in the checkerboard cells
assert img[30:45, 5:15].std() > out1[30:45, 5:15].std()
assert out1[30:45, 5:15].std() > out2[30:45, 5:15].std()
def test_denoise_bilateral_color():
img = checkerboard.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
out1 = restoration.denoise_bilateral(img,
sigma_color=0.1,
sigma_spatial=10,
multichannel=True)
out2 = restoration.denoise_bilateral(img,
sigma_color=0.2,
sigma_spatial=20,
multichannel=True)
# make sure noise is reduced in the checkerboard cells
assert_(img[30:45, 5:15].std() > out1[30:45, 5:15].std())
assert_(out1[30:45, 5:15].std() > out2[30:45, 5:15].std())
def test_denoise_bilateral_types(dtype):
img = checkerboard_gray.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
# check that we can process multiple float types
out = restoration.denoise_bilateral(img, sigma_color=0.1,
sigma_spatial=10, multichannel=False)
def thresh_norm_filt(image,thresh=0,norm=1):
from skimage.restoration import denoise_bilateral
'''Thresholds image to >0 to get rid of dark current,
applies a simple denoise filter, and threshes and renormalizes again
Returns the normalized image
'''
normed=thresh_norm(image,thresh=thresh,norm=norm, copy=True)
filt=denoise_bilateral(normed,multichannel=False)
norm=thresh_norm(filt,norm=norm,copy=False)
return norm
def test_denoise_bilateral_pad():
"""This test checks if the bilateral filter is returning an image
correctly padded."""
img = img_as_float(data.chelsea())[100:200, 100:200]
img_bil = restoration.denoise_bilateral(img,
sigma_color=0.1,
sigma_spatial=10,
multichannel=True)
condition_padding = np.count_nonzero(np.isclose(img_bil, 0, atol=0.001))
assert_equal(condition_padding, 0)
def loop(imgFiles):
for f in imgFiles:
img = img_as_float(data.load(os.path.join(noisyDir, f)))
startTime = time.time()
img = denoise_bilateral(img,
sigma_color=0.1,
sigma_spatial=3,
multichannel=True)
skimage.io.imsave(os.path.join(denoisedDir, f), img)
print("Took %f seconds for %s" % (time.time() - startTime, f))
def bilateral(imagePath, outputPath):
warnings.filterwarnings("ignore")
imagePath = "" + imagePath
color = io.imread(imagePath)
img = rgb2gray(color)
image = img_as_ubyte(img)
cleaned = denoise_bilateral(image, mode='edge')
cleaned_uint8 = img_as_ubyte(cleaned)
imsave('' + outputPath, cleaned_uint8)
cleaned_uint8
def image_features_hog3(img, num_features,orientation,maxcell,maxPixel):
image=denoise_bilateral(img, win_size=5, sigma_range=None, sigma_spatial=1, bins=10000, mode='constant', cval=0)
thresh = threshold_otsu(image)
binary = image > thresh
im = resize(binary, (maxPixel, maxPixel))
##hog scikit transform
return image_features_hog_fd(im)
def preprocess_image(self, imagefilename):
rgb_image = img_as_ubyte(io.imread(imagefilename))
rgb_image = restoration.denoise_bilateral(rgb_image, multichannel=True)
if rgb_image.shape[2] == 3:
alpha_channel = np.ones(rgb_image.shape[:-1])
rgba_image = np.dstack((rgb_image, alpha_channel))
else:
rgba_image = rgb_image
io.imsave(filenames.preprocessed_file(imagefilename), rgba_image)
def image_features_hog3(img, num_features,orientation,maxcell,maxPixel):
image=denoise_bilateral(img, win_size=5, sigma_range=None, sigma_spatial=1, bins=10000, mode='constant', cval=0)
thresh = threshold_otsu(image)
binary = image > thresh
im = resize(binary, (maxPixel, maxPixel))
##hog scikit transform
fd= hog(im, orientations=orientation, pixels_per_cell=(maxcell, maxcell),
cells_per_block=(1, 1), visualise=False,normalise=True)
return fd
def Bilateral_proj(S, image_size, lambda_this):
"""
This function does the Non local mean projection
"""
S1 = np.reshape(S[0, :], image_size)
S2 = np.reshape(S[1, :], image_size)
sm1 = S1.min() + 0.5
sm2 = S2.min() + 0.5
S1 = S1 + sm1
S2 = S2 + sm2
# Nonlocal mean denoising
S1 = denoise_bilateral(S1, sigma_spatial=lambda_this, multichannel=False)
S2 = denoise_bilateral(S2, sigma_spatial=lambda_this, multichannel=False)
S[0, :] = np.reshape(S1, (1, image_size[0] * image_size[1])) - sm1
S[1, :] = np.reshape(S2, (1, image_size[0] * image_size[1])) - sm2
return S
def test_denoise_bilateral_types(dtype):
img = checkerboard_gray.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1).astype(dtype)
# check that we can process multiple float types
out = restoration.denoise_bilateral(img,
sigma_color=0.1,
sigma_spatial=10,
multichannel=False)
def test_denoise_bilateral_color(channel_axis):
img = checkerboard.copy()[:50, :50]
# add some random noise
img += 0.5 * img.std() * np.random.rand(*img.shape)
img = np.clip(img, 0, 1)
img = np.moveaxis(img, -1, channel_axis)
out1 = restoration.denoise_bilateral(img, sigma_color=0.1,
sigma_spatial=10,
channel_axis=channel_axis)
out2 = restoration.denoise_bilateral(img, sigma_color=0.2,
sigma_spatial=20,
channel_axis=channel_axis)
img = np.moveaxis(img, channel_axis, -1)
out1 = np.moveaxis(out1, channel_axis, -1)
out2 = np.moveaxis(out2, channel_axis, -1)
# make sure noise is reduced in the checkerboard cells
assert img[30:45, 5:15].std() > out1[30:45, 5:15].std()
assert out1[30:45, 5:15].std() > out2[30:45, 5:15].std()
def BF_proc(newimg, backimg, FilterSts, FilterOrder, FilterSelect, back_sbs):
if back_sbs == 2 and FilterSts == 2:
if FilterSelect == 'Median':
ImageFinal = ndimage.median_filter(np.subtract(newimg, backimg),
FilterOrder)
elif FilterSelect == 'Gaussian':
ImageFinal = ndimage.gaussian_filter(np.subtract(newimg, backimg),
FilterOrder)
elif FilterSelect == 'Uniform':
ImageFinal = ndimage.uniform_filter(np.subtract(newimg, backimg),
FilterOrder)
elif FilterSelect == 'Denoise TV':
ImageFinal = denoise_tv_chambolle(np.subtract(newimg, backimg),
weight=FilterOrder,
multichannel=True)
elif FilterSelect == 'Bilateral':
ImageFinal = denoise_bilateral(np.subtract(newimg, backimg),
sigma_range=FilterOrder,
sigma_spatial=15)
elif back_sbs == 2 and FilterSts == 0:
ImageFinal = np.subtract(newimg, backimg)
elif back_sbs == 0 and FilterSts == 2:
if FilterSelect == 'Median':
ImageFinal = ndimage.median_filter(newimg, FilterOrder)
elif FilterSelect == 'Gaussian':
ImageFinal = ndimage.gaussian_filter(newimg, FilterOrder)
elif FilterSelect == 'Uniform':
ImageFinal = ndimage.uniform_filter(newimg, FilterOrder)
elif FilterSelect == 'Denoise TV':
ImageFinal = denoise_tv_chambolle(newimg,
weight=FilterOrder,
multichannel=True)
elif FilterSelect == 'Bilateral':
ImageFinal = denoise_bilateral(newimg,
sigma_range=FilterOrder,
sigma_spatial=15)
elif back_sbs == 0 and FilterSts == 0:
ImageFinal = newimg
return ImageFinal
def denoiseBilateral(imagen,multichannel):
"""
-Reemplaza el valor de cada pixel en funcion de la proximidad espacial y radiometrica
medida por la funcion Gaussiana de la distancia euclidiana entre dos pixels y con
cierta desviacion estandar.
-False si la imagen es una escala de grises, sino True
"""
noisy = img_as_float(imagen)
denoise = denoise_bilateral(noisy, 7, 9, 0.08,multichannel)
return denoise
def _filter_depth(self, depth):
temp = self._fill_in_nans(depth)
if temp.max() > 1.0:
factor = temp.max()
temp /= factor
else:
factor = 1.0
temp_denoised = \
denoise_bilateral(temp, sigma_range=30, sigma_spatial=4.5)
temp_denoised[np.isnan(depth)] = np.nan
temp_denoised *= factor
return temp_denoised
def findmembranes(arr_raw):
'''Morphological operations to find cell membranes from dystrophin channel, or similar'''
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5, 5))
kernelsm = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3))
# Need to check here that the values in arr lie between 0 and 255!
arr = np.array(arr_raw, dtype=np.uint8)
recipe = [
(cv2.dilate, kernelsm),
(cv2.dilate, kernelsm),
(cv2.dilate, kernelsm),
#(cv2.dilate,kernel),
#(cv2.dilate,kernel),
#(cv2.erode,kernel),
(cv2.erode, kernelsm),
(cv2.erode, kernelsm),
(cv2.erode, kernelsm)
]
#arrf = ndimage.gaussian_filter(arr,0.3)
#arrf = cv2.GaussianBlur(arr, ksize=(3,3),sigmaX=0,sigmaY=0)
#arrf = cv2.medianBlur(arr,3)
#arrf = cv2.bilateralFilter(arr,d=9,sigmaColor=1555,sigmaSpace=1555)
#ret,thresh = cv2.threshold(arrf.astype(np.uint8),1,255,cv2.THRESH_BINARY)
arrf = restoration.denoise_bilateral(arr,
11,
sigma_color=3,
sigma_spatial=3,
multichannel=False)
Image.fromarray(makepseudo(arrf)).show()
#glob_thresh = filters.threshold_otsu(arrf)
#thresh = np.array(255*(arrf > glob_thresh/2.0),dtype=np.uint8)
locthresh = filters.threshold_local(arrf, block_size=21, offset=0)
thresh = arrf > (locthresh)
Image.fromarray(makepseudo(255 * thresh)).show()
threshclean = morphology.remove_small_objects(thresh, 600)
Image.fromarray(makepseudo(255 * threshclean)).show()
#thresh = morphology.skeletonize(thresh)
#Image.fromarray(makepseudo(255*thresh)).show()
#thresh = morphology.binary_dilation(thresh)
#Image.fromarray(makepseudo(255*thresh)).show()
thresh = np.array(255 * thresh, dtype=np.uint8)
comb0 = threshorig(arr, thresh)
for func, kern in recipe:
thresh = func(thresh, kern)
Image.fromarray(makepseudo(thresh)).show()
ithresh = cv2.bitwise_not(thresh)
return ((ithresh, comb0, threshorig(arr, thresh)))
def imageDenoise(self, denoise_method='TV'):
if denoise_method == 'TV':
return denoise_tv_chambolle(self.altered_image)
elif denoise_method == 'bilateral':
return denoise_bilateral(self.altered_image,
sigma_color=0.05,
sigma_spatial=15,
multichannel=True)
elif denoise_method == 'wavelet':
return denoise_wavelet(self.altered_image, multichannel=True)
else:
print denoise_method, ' is not a valid denoising method choice.'
def bilateral_filter(noisy_images: np.ndarray,
noise_std_dev: float,
show_progress: bool = False) -> np.ndarray:
"""
Params:
noisy_images: receive noisy_images with shape (IMG, M, N, C),
where IMG is the quantity of noisy images
with dimensions MxN and
C represents the color dimensions, i.e. if the images are colored,
C = 3 (RGB), otherwise if C = 1, is grayscale.
noise_std_dev: the standart deviation from noise.
"""
validate_array_input(noisy_images)
validate_if_noise_std_dev_is_a_float(noise_std_dev)
filtered_images = []
if show_progress:
for i in tqdm(range(noisy_images.shape[0])):
filtered_images.append(
denoise_bilateral(noisy_images[i, :, :, 0],
win_size=(3, 3),
sigma_color=noise_std_dev,
sigma_spatial=noise_std_dev,
multichannel=False))
else:
for i in range(noisy_images.shape[0]):
filtered_images.append(
denoise_bilateral(noisy_images[i, :, :, 0],
win_size=(3, 3),
sigma_color=noise_std_dev,
sigma_spatial=noise_std_dev,
multichannel=False))
filtered_images = np.array(filtered_images)
return filtered_images
def depthFilter(disp):
# Filter the depth
noisy = disp
result = denoise_bilateral(noisy,
sigma_color=0.5,
sigma_spatial=4,
win_size=7,
multichannel=False)
b = np.percentile(noisy, list(range(100)))
a = np.percentile(result, list(range(100)))
x = estimate_coef(a, b)
result = (result * x[1] + x[0])
return result
def nlm(self):
# print('Entrou no non local means')
# estimate the noise standard deviation from the noisy image
sigma_est = np.mean(estimate_sigma(self.environment, multichannel=False))
# print(f"Estimated noise standard deviation = {sigma_est}")
# slow algorithm
# denoise = denoise_nl_means(self.environment, h=1.15 * sigma_est, fast_mode=False)
denoise = denoise_bilateral(self.environment, win_size=3, sigma_spatial=sigma_est,
multichannel=False)
denoise = np.reshape(denoise, self.environment.shape)
return scale(denoise)
def bilateral_2d_filter(image):
""" TODO
"""
return restoration.denoise_bilateral(
image,
win_size=None,
sigma_color=None,
sigma_spatial=1,
bins=10000,
mode="constant",
cval=0,
multichannel=False,
)
def image_features_resize_thres(img, maxPixel, num_features,imageSize):
# X is the feature vector with one row of features per image
# consisting of the pixel values a, num_featuresnd our metric
X=np.zeros(num_features, dtype=float)
image=denoise_bilateral(img, win_size=5, sigma_range=None, sigma_spatial=1, bins=10000, mode='constant', cval=0)
thresh = threshold_otsu(image)
binary = image > thresh
im = resize(binary, (maxPixel, maxPixel))
# Store the rescaled image pixels
X[0:imageSize] = np.reshape(im,(1, imageSize))
return X
def register_image_pair(idx, path_img_target, path_img_source, path_out):
""" register two images together
:param int idx: empty parameter for using the function in parallel
:param str path_img_target: path to the target image
:param str path_img_source: path to the source image
:param str path_out: path for exporting the output
:return (str, float):
"""
start = time.time()
# load and denoise reference image
img_target = io.imread(path_img_target)
img_target = denoise_wavelet(img_target,
wavelet_levels=7,
multichannel=True)
img_target_gray = rgb2gray(img_target)
# load and denoise moving image
img_source = io.imread(path_img_source)
img_source = denoise_bilateral(img_source,
sigma_color=0.05,
sigma_spatial=2,
multichannel=True)
img_source_gray = rgb2gray(img_source)
# detect ORB features on both images
detector_target = ORB(n_keypoints=150)
detector_source = ORB(n_keypoints=150)
detector_target.detect_and_extract(img_target_gray)
detector_source.detect_and_extract(img_source_gray)
matches = match_descriptors(detector_target.descriptors,
detector_source.descriptors)
# robustly estimate affine transform model with RANSAC
model, _ = ransac((detector_target.keypoints[matches[:, 0]],
detector_source.keypoints[matches[:, 1]]),
AffineTransform,
min_samples=25,
max_trials=500,
residual_threshold=0.95)
# warping source image with estimated transformations
img_warped = warp(img_target,
model.inverse,
output_shape=img_target.shape[:2])
path_img_warped = os.path.join(path_out, NAME_IMAGE_WARPED % idx)
io.imsave(path_img_warped, img_warped)
# summarise experiment
execution_time = time.time() - start
return path_img_warped, execution_time
def _filter(photo, parameter):
# scale is 1/8 of the maximum image size
scale = max(photo.shape[:2]) / (8 * max(photo.shape[:2]))
# parameters have to do with pixel diameter for filter,
# and color space smoothing
new_pic = denoise_bilateral(photo,
int(32 * scale),
50,
10 * scale,
multichannel=True)
edited = photo + (photo - new_pic) * parameter
edited = np.clip(edited, 0, 1)
return edited
def deoniseBilateral():
astro = img_as_float(data.astronaut())
astro = astro[220:300, 220:320]
imgO = astro.copy()
noisy = astro + 0.6 * astro.std() * np.random.random(astro.shape)
noisy = np.clip(noisy, 0, 1)
imgN = noisy.copy()
denoised = denoise_bilateral(noisy,
sigma_color=0.05,
sigma_spatial=15,
multichannel=True)
imgR = denoised.copy()
return [imgO, imgN, imgR]
def autoenhancing():
global panelA,panelB
path = tkFileDialog.askopenfilename()
print("AUTO ENHANCE")
astro = cv2.imread(path)
astro = cv2.cvtColor(astro, cv2.COLOR_BGR2GRAY)
img=astro
p2, p98 = np.percentile(img, (2, 98))
img_rescale = exposure.rescale_intensity(img, in_range=(p2, p98))
img=img_rescale
adapteq = exposure.equalize_adapthist(img, clip_limit=0.03)
img=adapteq
denoised = denoise_bilateral(img, sigma_color=0.1,sigma_spatial=15, multichannel=False)
img=denoised
for i in range(len(img)):
for j in range(len(img[0])):
img[i][j]=255*img[i][j]
# convert the images to PIL format...
pic1 = Image.fromarray(astro)
pic = Image.fromarray(img)
# ...and then to ImageTk format
image = ImageTk.PhotoImage(pic1)
edged = ImageTk.PhotoImage(pic)
if panelA is None or panelB is None:
# the first panel will store our original image
panelA = Label(image=image)
panelA.image = image
panelA.pack(side="left", padx=10, pady=10)
# while the second panel will store the edge map
panelB = Label(image=edged)
panelB.image = edged
panelB.pack(side="right", padx=10, pady=10)
# otherwise, update the image panels
else:
# update the pannels
panelA.configure(image=image)
panelB.configure(image=edged)
panelA.image = image
panelB.image = edged
def nldenoise(X):
"""
Pre-process images that are fed to neural network.
:param X: X
"""
print('Denoising images...')
progbar = Progbar(X.shape[0]) # progress bar for pre-processing status tracking
for i in range(X.shape[0]):
X[i] = denoise_bilateral(X[i], sigma_range=0.05, sigma_spatial=4)
progbar.add(1)
return X
def image_features_resize_thres(img, maxPixel, num_features,imageSize):
# X is the feature vector with one row of features per image
# consisting of the pixel values a, num_featuresnd our metric
X=np.zeros(num_features, dtype=float)
image=denoise_bilateral(img, win_size=5, sigma_range=None, sigma_spatial=1, bins=10000, mode='constant', cval=0)
thresh = threshold_otsu(image)
binary = image > thresh
im = resize(binary, (maxPixel, maxPixel))
# Store the rescaled image pixels
X[0:imageSize] = np.reshape(im,(1, imageSize))
return X
def apply_bilateral_filtering(img, d=15, sigmacolor=75, sigmacoordinate=75):
# Retain original data type
orig_dtype = img.pixel_array.dtype
# Convert from [0; max] to [0; 1] as it is required by denoise_nl_means
upper_bound = np.max(img.pixel_array)
img_as_float = img.pixel_array / upper_bound
new_img = denoise_bilateral(img_as_float, win_size=d, sigma_color=sigmacolor, sigma_spatial=sigmacoordinate)
# Convert back to [0; max]
new_img *= upper_bound
return new_img.astype(orig_dtype)
def watershed(image):
""" the watershed algorithm """
if len(image.shape) != 2:
raise TypeError("The input image must be gray-scale ")
h, w = image.shape
image = cv2.equalizeHist(image)
image = denoise_bilateral(image, sigma_range=0.1, sigma_spatial=10)
image = rescale_intensity(image)
image = img_as_ubyte(image)
image = rescale_intensity(image)
# com.debug_im(image)
_, thres = cv2.threshold(image, 80, 255, cv2.THRESH_BINARY_INV)
distance = ndi.distance_transform_edt(thres)
local_maxi = peak_local_max(distance, indices=False,
labels=thres,
min_distance=5)
# com.debug_im(thres)
# implt = plt.imshow(-distance, cmap=plt.cm.jet, interpolation='nearest')
# plt.show()
markers = ndi.label(local_maxi, np.ones((3, 3)))[0]
labels = ws(-distance, markers, mask=thres)
labels = np.uint8(labels)
# result = np.round(255.0 / np.amax(labels) * labels).astype(np.uint8)
# com.debug_im(result)
segments = []
for idx in range(1, np.amax(labels) + 1):
indices = np.where(labels == idx)
left = np.amin(indices[1])
right = np.amax(indices[1])
top = np.amin(indices[0])
down = np.amax(indices[0])
# region = labels[top:down, left:right]
# m = (region > 0) & (region != idx)
# region[m] = 0
# region[region >= 1] = 1
region = image[top:down, left:right]
cont = Contour(mask=region)
cont.lt = [left, top]
cont.rb = [right, down]
segments.append(cont)
return segments
def get_regions(img):
denoised=restoration.denoise_bilateral(img.astype('uint16'),
# sigma_range=0.01,
sigma_spatial=15,
multichannel=False)
smoothened = filters.median(denoised,np.ones((4,4)))
markers = np.zeros(smoothened.shape, dtype=np.uint)
# otsu works only for only for multi-channel images
# markers[smoothened < filters.threshold_otsu(smoothened)] = 1
# markers[smoothened > filters.threshold_otsu(smoothened)] = 2
markers[smoothened < filters.median(smoothened)] = 1
markers[smoothened > filters.median(smoothened)] = 2
labels = random_walker(smoothened, markers, beta=10, mode='bf')
regions= measure.label(labels)
return regions, denoised, smoothened,markers
def localToneMap(img,dR=4,filt="bilateral",sigma=6, sr=0.05, ss=15): r = img[:,:,0] g = img[:,:,1] b = img[:,:,2] pixList = [r,g,b] (width,height,_) = img.shape # Intensity -- consider using weighted average?? I = np.mean(pixList, axis=0) # Chrominance Channels chromeChannels = map(lambda x:x/I, pixList) # Log Intensity L = np.log2(I) # bilateral filter if filt == "gaussian": B = ndimage.filters.gaussian_filter(L,sigma) else: B = denoise_bilateral(L,sigma_range=sr, sigma_spatial=ss) # Compute the detail layer: D = L - B offset = np.amax(B) scale = dR / (offset - np.amin(B)) B_Prime = (B - offset*np.ones((width,height))) * scale # Reconstruct the log intensity: O = 2^(B' + D) reconLogIntens = map(lambda x: 2**x, B_Prime + D) # New Colors R',G',B' = O * (R/I, G/I, B/I) newColors = map(lambda x: x * reconLogIntens, chromeChannels) # Gamma Compression/correction newColors = map(gammaCorrect, newColors) img[:,:,0] = newColors[0] img[:,:,1] = newColors[1] img[:,:,2] = newColors[2] return img
def _get_processed_image(self):
# read image
image = mpimg.imread(self.image_path)
mask = image[:,:,1] > 150.
image[mask] = 255.
#plt.imshow(image)
#plt.show()
# convert to grayscale
image = self.rgb2gray(image)
# crop image
image = image[100:1000,200:1100]
mask = mask[100:1000,200:1100]
image = image - np.min(image)
image[mask] *= 255. / np.max(image[mask])
if self.filter == True:
image = denoise_bilateral(image, sigma_spatial=self.denoise_spatial)
if self.denoise == True:
image = threshold_adaptive(image, self.block_size, offset=self.offset)
return image, mask
def crop_resize(img, pixelspacing, center, size):
print("image shape {}".format(np.array(img).shape))
xmeanspacing = float(1.25826490244)
ymeanspacing = float(1.25826490244)
xscale = float(pixelspacing) / xmeanspacing
yscale = float(pixelspacing) / ymeanspacing
xnewdim = round( xscale * np.array(img).shape[0])
ynewdim = round( yscale * np.array(img).shape[1])
img = transform.resize(img, (xnewdim, ynewdim))
img = np.uint8(img * 255)
#img = cv2.normalize(img, None, 0, 255, cv2.NORM_MINMAX)
#img = auto_canny(img)
img = denoise_bilateral(img, sigma_range=0.05, sigma_spatial=15)
#im = cv2.normalize(im, None, 0, 255, cv2.NORM_MINMAX)
#img = img.Canny(im,128,128)
"""crop center and resize"""
if img.shape[0] < img.shape[1]:
img = img.T
# we crop image from center
short_egde = min(img.shape[:2])
#yy = int((img.shape[0] - short_egde) / 2)
#xx = int((img.shape[1] - short_egde) / 2)
#crop_img = img[yy : yy + short_egde, xx : xx + short_egde]
# resize to 64, 64
resized_img = None
yy = int(center[1] - 64)
xx = int(center[0] - 64)
if yy > 0 and xx > 0 and (yy+128) < img.shape[0] and xx + 128 < img.shape[1]:
resized_img = img[yy : yy + 128, xx : xx + 128]
else:
yy = int((img.shape[0] - short_egde) / 2)
xx = int((img.shape[1] - short_egde) / 2)
resized_img = img[yy : yy + 128, xx : xx + 128]
resized_img *= 255
return resized_img.astype("uint8")
def _smooth_image(self):
from skimage import restoration
self._image = restoration.denoise_bilateral(self.image)
def smoothen(img):
denoised=restoration.denoise_bilateral(img.astype('uint16'), sigma_range=0.01, sigma_spatial=15)
smoothened = filters.median(denoised,np.ones((4,4)))
return smoothened
noisy = np.clip(noisy, 0, 1)
fig, ax = plt.subplots(nrows=2, ncols=3, figsize=(8, 5))
fig.suptitle('George O. Barros - Noisy redution (scikit-image)')
plt.gray()
ax[0, 0].imshow(noisy)
ax[0, 0].axis('off')
ax[0, 0].set_title('noisy')
ax[0, 1].imshow(denoise_tv_chambolle(noisy, weight=0.1, multichannel=True))
ax[0, 1].axis('off')
ax[0, 1].set_title('TV')
ax[0, 2].imshow(denoise_bilateral(noisy, sigma_range=0.05, sigma_spatial=15))
ax[0, 2].axis('off')
ax[0, 2].set_title('Bilateral')
ax[1, 0].imshow(denoise_tv_chambolle(noisy, weight=0.2, multichannel=True))
ax[1, 0].axis('off')
ax[1, 0].set_title('(more) TV')
ax[1, 1].imshow(denoise_bilateral(noisy, sigma_range=0.1, sigma_spatial=15))
ax[1, 1].axis('off')
ax[1, 1].set_title('(more) Bilateral')
ax[1, 2].imshow(lena)
ax[1, 2].axis('off')
ax[1, 2].set_title('original')
def save_roc_curve(actual_pixel_labels, predicted_pixel_labels):
y_actual = actual_pixel_labels.flatten()
y_predicted = predicted_pixel_labels.flatten()
auc = roc_auc_score(y_actual, y_predicted)
fpr, tpr, thresholds = roc_curve(y_actual, y_predicted)
plt.figure(figsize=(12, 7))
plt.plot(fpr, tpr, label='ROC curve (area = %0.2f)' % auc)
plt.plot([0, 1], [0, 1], 'k--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.0])
plt.xlabel('False Positive Rate', fontsize="xx-large")
plt.ylabel('True Positive Rate', fontsize="xx-large")
plt.title('Receiver Operating Characteristic', fontsize="xx-large")
plt.legend(loc="lower right")
plt.savefig("results/roc_curve.png")
plt.show()
return True
BILATERAL_FILTERING = False
folder = sys.argv[1]
actual_pixel_labels, predicted_pixel_labels = np.load("results/" + folder + "/y.npy"), np.load("results/" + folder + "/output.npy")
if BILATERAL_FILTERING:
predicted_pixel_labels = np.array([denoise_bilateral(im) for im in predicted_pixel_labels])
save_random_images(actual_pixel_labels, predicted_pixel_labels, 3)
output_stats(actual_pixel_labels, predicted_pixel_labels)
#save_roc_curve(actual_pixel_labels, predicted_pixel_labels)
def test_denoise_bilateral_nan():
img = np.NaN + np.empty((50, 50))
out = restoration.denoise_bilateral(img, multichannel=False)
assert_equal(img, out)
def test_denoise_bilateral_zeros():
img = np.zeros((10, 10))
assert_equal(img, restoration.denoise_bilateral(img, multichannel=False))
def test_denoise_bilateral_3d_multichannel():
img = np.ones((50, 50, 50))
with expected_warnings(["grayscale"]):
result = restoration.denoise_bilateral(img, multichannel=True)
assert_equal(result, img)
def test_denoise_bilateral_3d_grayscale():
img = np.ones((50, 50, 3))
with testing.raises(ValueError):
restoration.denoise_bilateral(img, multichannel=False)
def test_denoise_bilateral_constant():
img = np.ones((10, 10)) * 5
assert_equal(img, restoration.denoise_bilateral(img, multichannel=False))
