def test_richardson_lucy_deprecated_iterations_kwarg():
psf = np.ones((5, 5)) / 25
data = convolve2d(test_img, psf, 'same')
np.random.seed(0)
data += 0.1 * data.std() * np.random.standard_normal(data.shape)
with expected_warnings(["`iterations` is a deprecated argument"]):
restoration.richardson_lucy(data, psf, iterations=5)
def dogonvole(image, psf, gpu_algorithm, kernel=(2., 2., 0.), blur=(0.9, 0.9, 0.), niter=10, use_gpu=1):
"""
Perform deconvolution and difference of gaussian processing.
Parameters
----------
image : ndarray
psf : ndarray
kernel : tuple
blur : tuple
niter : int
Returns
-------
image : ndarray
Processed image same shape as image input.
"""
global hot_pixels
if not psf.sum() == 1.:
raise ValueError("psf must be normalized so it sums to 1")
image = image.astype('float32')
imin = image.min()
border =1
for y, x in hot_pixels:
y_min = y-border
x_min = x-border
y_max = y+border
x_max = x+border
if y-1<=border:
y_min=0
if x-1<=border:
x_min=0
if y+1>=2048-border:
y_max=2048
if x+1>=2048-border:
x_max=2048
image[y, x] = np.average(image[y_min:y_max, x_min:x_max]);
img_bg = gaussian(image, kernel[:len(image.shape)], preserve_range=True)
image = numpy.subtract(image, img_bg)
numpy.place(image, image<0, 1./2**16)
image = image.astype('uint16')
if len(image.shape)==3:
for i in range(image.shape[2]):
if use_gpu==1:
image[:,:,i] = gpu_algorithm.run(fd_data.Acquisition(data=image[:,:,i], kernel=psf), niter=niter).data
else:
image[:,:,i] = restoration.richardson_lucy(image[:,:,i], psf,niter, clip=False)
elif len(image.shape)==2:
if use_gpu==1:
image = gpu_algorithm.run(fd_data.Acquisition(data=image, kernel=psf), niter=niter).data
else:
image = restoration.richardson_lucy(image, psf, niter, clip=False)
else:
raise ValueError('image is not a supported dimensionality.')
image = gaussian(image, blur[:len(image.shape)], preserve_range=True)
return image
def dogonvole(image, psf, kernel=(2., 2., 0.), blur=(1.2, 1.2, 0.), niter=20):
"""
Perform deconvolution and difference of gaussian processing.
Parameters
----------
image : ndarray
psf : ndarray
kernel : tuple
blur : tuple
niter : int
Returns
-------
image : ndarray
Processed image same shape as image input.
"""
global hot_pixels, use_gpu, gpu_algorithm
if not psf.sum() == 1.:
raise ValueError("psf must be normalized so it sums to 1")
image = image.astype('float32')
imin = image.min()
for y, x in hot_pixels:
image[y, x] = imin
img_bg = ndimage.gaussian_filter(image, kernel[:len(image.shape)])
image = numpy.subtract(image, img_bg)
numpy.place(image, image < 0, 1. / 2**16)
image = image.astype('uint16')
if len(image.shape) == 3:
for i in range(image.shape[2]):
if use_gpu == 1:
image[:, :,
i] = gpu_algorithm.run(fd_data.Acquisition(data=image,
kernel=psf),
niter=niter).data
else:
image[:, :, i] = restoration.richardson_lucy(image[:, :, i],
psf,
niter,
clip=False)
elif len(image.shape) == 2:
if use_gpu == 1:
image = gpu_algorithm.run(fd_data.Acquisition(data=image,
kernel=psf),
niter=niter).data
else:
image = restoration.richardson_lucy(image, psf, niter, clip=False)
else:
raise ValueError('image is not a supported dimensionality.')
image = ndimage.gaussian_filter(image, blur[:len(image.shape)])
return image
def deconvolve_psf(self, method='WH'):
self.full_map.meta['lvl_num'] = 1.4
if method == 'WH':
self.full_map.data = restoration.unsupervised_wiener(self.full_map.data.astype('float64'), self.psf.astype('float64'), clip=False)[0]
if method == 'RL_SSW':
# should be equivalent to the IDL AIA_DECONVOLVE_RICHARDSONLUCY() routine but it isn't
# Not working...
image = self.full_map.data.astype(np.float)
im_deconv = np.copy(self.full_map.data.astype(np.float))
psf = self.psf.astype(np.float)
psf_mirror = psf[::-1, ::-1] # to make the correlation easier
psfnorm = fftconvolve(psf, np.ones_like(psf), 'same')
for _ in range(25):
relative_blur = image / fftconvolve(psf, im_deconv, 'same')
im_deconv *= fftconvolve(relative_blur, psf_mirror, 'same')/psfnorm
self.full_map.data=np.abs(im_deconv)
if method == 'RL':
# Not working...
self.full_map.data = restoration.richardson_lucy(self.full_map.data.astype('float64'), self.psf.astype('float64'), iterations=25, clip=False)
def preprocess(self, image):
# convert to gray scale at first
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
# compute the Laplacian of the image and then return the focus
# measure, which is simply the variance of the Laplacian
fm = cv2.Laplacian(gray, cv2.CV_64F).var()
if fm < self.thres:
self.blurred = True
# if blurred, remove blurry via Wiener filter
if self.blurred:
from scipy.signal import convolve2d
from skimage import color, data, restoration
img = color.rgb2gray(image)
psf = np.ones((5, 5)) / 25
img = convolve2d(gray, psf, 'same')
img += 0.1 * img.std() * np.random.standard_normal(img.shape)
deconvolved_img = restoration.richardson_lucy(img,
psf,
5,
clip=False)
# #deconvolved_img = restoration.wiener(img, psf, 50, clip=False)
# deconvolved_img, _ = restoration.unsupervised_wiener(img, psf,
# clip=False)
#
# print(deconvolved_img)
return deconvolved_img
else:
return image
def deconvolve(self, psf, iterations):
'''
Method for deconvolution of convolved 2d data by using Richardson-Lucy algorithm
:param psf: tuple(float(Gaussian kernel length), float(Gaussian kernel sigma))
2d array, point spread function
:param iterations: int, number of iterations
:return: 2d array, convolved data
'''
def gkern(kernlen=psf[0], nsig=psf[1]):
"""Returns a 2D Gaussian kernel array."""
interval = (2 * nsig + 1.) / (kernlen)
x = np.linspace(-nsig - interval / 2., nsig + interval / 2.,
kernlen + 1)
kern1d = np.diff(st.norm.cdf(x))
kernel_raw = np.sqrt(np.outer(kern1d, kern1d))
kernel = kernel_raw / kernel_raw.sum()
return kernel
if type(psf) == tuple:
current_psf = gkern()
else:
current_psf = psf
self.dehazed_image = restoration.richardson_lucy(self.dehazed_image,
current_psf,
iterations=iterations,
clip=False)
def psfmatch(psf_sharp, psf_broad, kernelname, method='fft', window=window_default, iterations=30):
"""Derive the kernel that matches psf_sharp to psf_broad"""
psf1 = fits.getdata(psf_sharp)
psf2 = fits.getdata(psf_broad)
assert psf1.shape[0] % 2 == 1
assert psf2.shape[0] % 2 == 1
assert psf1.shape[0] == psf1.shape[1]
assert psf2.shape[0] == psf2.shape[1]
psf1 = psf1 / psf1.sum()
psf2 = psf2 / psf2.sum()
if psf1.shape[0] > psf2.shape[0]:
pad = (psf1.shape[0] - psf2.shape[0]) / 2
psf1 = psf1[pad:-pad, pad:-pad]
elif psf2.shape[0] > psf1.shape[0]:
pad = (psf2.shape[0] - psf1.shape[0]) / 2
psf2 = psf2[pad:-pad, pad:-pad]
if method == 'RL':
kernel = richardson_lucy(psf2, psf1, iterations=iterations)
elif method == 'fft':
kernel = create_matching_kernel(psf1, psf2, window=window)
# normalize the kernel
kernel = kernel / kernel.sum()
hdr2 = fits.getheader(psf_sharp)
if os.path.exists(kernelname):
os.remove(kernelname)
fits.append(kernelname, kernel, hdr2)
return kernel
def psfmatch_RL(psf_ref, psf_input, kernelname, iterations=30):
"""
Derive the kernel that matches psf_2match to psf_ref, so that psf_2match,
when convolved with the kernel, gives psf_ref.
Make sure that both PSF images have the same pixel scales, are centered,
and have the same image size.
USE THE RICHARDSON-LUCY DECONVOLUTION ALGORITHM.
"""
psf1 = fits.getdata(psf_ref)
psf2 = fits.getdata(psf_input)
assert psf1.shape[0] % 2 == 1
assert psf2.shape[0] % 2 == 1
assert psf1.shape[0] == psf1.shape[1]
assert psf2.shape[0] == psf2.shape[1]
psf1 = psf1 / psf1.sum()
psf2 = psf2 / psf2.sum()
if psf1.shape[0] > psf2.shape[0]:
pad = (psf1.shape[0] - psf2.shape[0]) / 2
psf1 = psf1[pad:-pad, pad:-pad]
elif psf2.shape[0] > psf1.shape[0]:
pad = (psf2.shape[0] - psf1.shape[0]) / 2
psf2 = psf2[pad:-pad, pad:-pad]
kernel = richardson_lucy(psf1, psf2)
# normalize the kernel
kernel = kernel / kernel.sum()
hdr2 = fits.getheader(psf_input)
if os.path.exists(kernelname):
os.remove(kernelname)
fits.append(kernelname, kernel, hdr2)
return kernel
def richardson_lucy_deconv(img: np.ndarray, num_iter: int, psf: np.ndarray, clip: bool=False) -> np.ndarray:
"""
Deconvolves input image with a specified point spread function. This simply calls
skimage.restoration.richardson_lucy
Parameters
----------
img : np.ndarray
Image to filter.
num_iter : int
Number of iterations to run algorithm
psf :
Point spread function
clip : bool (default = False)
If true, pixel value of the result above 1 or under -1 are thresholded for skimage pipeline compatibility.
Returns
-------
np.ndarray :
Deconvolved image, same shape as input
"""
# TODO ambrosejcarr: the restoration function is producing the following warning:
# /usr/local/lib/python3.6/site-packages/skimage/restoration/deconvolution.py:389: RuntimeWarning: invalid value
# encountered in true_divide:
# relative_blur = image / convolve_method(im_deconv, psf, 'same')
img_deconv: np.ndarray = restoration.richardson_lucy(img, psf, iterations=num_iter, clip=clip)
# here be dragons. img_deconv is a float. this should not work, but the result looks nice
# modulo boundary values? wtf indeed.
img_deconv = img_deconv.astype(np.uint16)
return img_deconv
def richardson_lucy(img, psf=np.ones((5, 5)) / 25, iterations=30):
"""
Richardson-Lucy deconvolution
"""
deconv = restoration.richardson_lucy(img.copy(),
psf,
iterations=iterations)
return deconv
def loop(imgFiles,rank):
for f in imgFiles:
img = img_as_float(data.load(os.path.join(noisyDir,f)))
psf = np.ones((5, 5)) / 25
startTime = time.time()
img = richardson_lucy(img, psf, iterations=30)
io.imsave(os.path.join(denoisedDir,f), img)
print ("Process %d: Took %f seconds for %s" %(rank, time.time() - startTime, f))
def deconvolvePSF(image_path, psf, iterations):
img = io.imread(image_path)
img = img_as_float(img)
img += np.amax(img) * 1E-5
# Restore Image using Richardson-Lucy algorithm
deconvolved_RL = restoration.richardson_lucy(img, psf, iterations)
# deconvolved_RL = img_as_int(deconvolved_RL)
return deconvolved_RL
def deconvolve(self, image, iterations):
## Code for deconvolution
psf = ai.airy_psf(self.window, self.psf_radius)
image = np.pad(image, int(psf.shape[0] / 2), mode="reflect")
deconvolved = restoration.richardson_lucy(image, psf, iterations,
False)
deconvolved = util.crop(deconvolved, int(psf.shape[0] / 2))
return deconvolved
def processedImage(image, final_size, show=False, save=True):
"""
Converts image into silhouette with proper size for final cube
Input: image name or location of image [String contatining a .jpg/.png/etc]
Output: silhouette [2D array]
"""
# load image, resize, convert to array, and make grayscale
img0 = color.rgb2gray(
np.asarray(Image.open(image).resize((final_size, final_size))))
# [using method from skimage restoration]
# sharpen image after rescaling
psf = np.ones((5, 5)) / 25
img0 = conv2(img0, psf, 'same')
img_noisy = img0.copy()
img_noisy += (np.random.poisson(lam=25, size=img0.shape) - 10) / 255.
deconvolved_RL = restoration.richardson_lucy(img_noisy, psf, iterations=30)
# [combining skimage functions]
# use chan_vese to separate into distinct shades
float_deconv = img_as_float(deconvolved_RL)
cv = chan_vese(float_deconv,
mu=0.25,
lambda1=1,
lambda2=1,
tol=1e-3,
max_iter=200,
dt=0.5,
init_level_set="checkerboard",
extended_output=True)
# make ~silhouette by taking the hard edge between contrasting colors
edge = roberts(cv[0])
# debugging/visual confirmation [toggle-able]
if show:
plt.plot()
plt.gray()
plt.imshow(edge)
plt.show()
if save:
if not os.path.exists(imageFolder):
os.makedirs(imageFolder)
image = os.path.splitext(image)[0]
with cd(imageFolder):
np.save(image + '_{}'.format(final_size), edge)
return edge
def test_richardson_lucy():
psf = np.ones((5, 5)) / 25
data = convolve2d(test_img, psf, "same")
np.random.seed(0)
data += 0.1 * data.std() * np.random.standard_normal(data.shape)
deconvolved = restoration.richardson_lucy(data, psf, 5)
path = pjoin(dirname(abspath(__file__)), "camera_rl.npy")
np.testing.assert_allclose(deconvolved, np.load(path), rtol=1e-3)
def perform_richardson_lucy_deconv(bandpass_data, bandpass_wvl, LSA_wvl,
LSA_data, save_dir, wavelen_val):
""" Function to perform the spectral deconvolution of Laser Linewidth from
the spectral bandpass data
"""
#print(LSA_wvl.shape)
#print(LSA_data.shape)
# print(bandpass_data.shape)
for i in range(1000, 1001): #np.shape(bandpass_data)[1]):
normalized_data = bandpass_data[:, i] / np.max(bandpass_data[:, i])
wavelength = bandpass_wvl[:, i]
bp_data = np.array([wavelength, normalized_data]).T
bp_data = bp_data[bp_data[:, 0].argsort()]
wavelength = bp_data[:, 0]
normalized_data = bp_data[:, 1]
#LSA_data = LSA_data[max_loc-480 :max_loc+480]
if len(LSA_data) > len(normalized_data):
factor = len(LSA_data) / len(normalized_data)
wvl_LSA = LSA_wvl[:, i]
LSA_data = LSA_data[::int(factor) + 1]
wvl_LSA = wvl_LSA[::int(factor) + 1]
#LSA_data = LSA_data-0.010
LSA_data = LSA_data / np.max(LSA_data)
CW = np.where(LSA_data == max(LSA_data))[0]
val = int(25)
wvl_LSA = wvl_LSA[int(CW) - val:int(CW) + val]
LSA_data = LSA_data[int(CW) - val:int(CW) + val] - 0.01
LSA_data = LSA_data / np.max(LSA_data)
# plt.figure(); plt.plot(wvl_LSA, LSA_data,'r')
# plt.plot(wavelength, normalized_data,'b.')
# plt.grid(True, linestyle=':')
# plt.show()
normalized_data1 = conv2(normalized_data, LSA_data, mode='same')
normalized_data1 = normalized_data1 / np.max(normalized_data1)
deconvolved_RL = restoration.richardson_lucy(np.array(
[normalized_data]),
np.array([LSA_data]),
iterations=2)
deconvolved_RL = deconvolved_RL.T
deconvolved_RL = deconvolved_RL.real
print(deconvolved_RL / np.max(deconvolved_RL))
# cc
plt.figure()
np.savetxt(r"C:\Users\nmishra\Desktop\spectral_deconv\foo.csv",
deconvolved_RL,
delimiter=",")
plt.plot(wavelength, normalized_data, 'b')
plt.plot(wavelength, deconvolved_RL, 'r')
plt.plot(wvl_LSA, LSA_data, 'go--')
plt.show()
cc
def _map_function(defl, *args, **kwargs):
"""
:param defl:
:type defl:
:param args:
:type args:
:param kwargs:
:type kwargs:
:returns: List [inst_freq, amplitude, phase, tfp, shift, pwr_diss]
WHERE
[type] inst_freq is...
[type] amplitude is...
[type] phase is...
[type] tfp is...
[type] shift is...
[type] pwr_diss is...
"""
parm_dict = args[0]
pixel_params = args[1]
impulse = args[2]
pix = Pixel(defl, parm_dict, **pixel_params)
if parm_dict['if_only']:
inst_freq, _, _ = pix.generate_inst_freq()
tfp = 0
shift = 0
amplitude = 0
phase = 0
pwr_diss = 0
elif parm_dict['deconvolve']:
iterations = parm_dict['conv_iterations']
impulse = impulse[
parm_dict['impulse_window'][0]:parm_dict['impulse_window'][1]]
inst_freq, amplitude, phase = pix.generate_inst_freq()
conv = restoration.richardson_lucy(inst_freq,
impulse,
clip=False,
num_iter=iterations)
pix.inst_freq = conv
pix.find_tfp()
tfp = pix.tfp
shift = pix.shift
pix.calculate_power_dissipation()
pwr_diss = pix.power_dissipated
else:
tfp, shift, inst_freq = pix.analyze()
pix.calculate_power_dissipation()
amplitude = pix.amplitude
phase = pix.phase
pwr_diss = pix.power_dissipated
return [inst_freq, amplitude, phase, tfp, shift, pwr_diss]
def test_richardson_lucy():
psf = np.ones((5, 5)) / 25
data = convolve2d(test_img, psf, 'same')
np.random.seed(0)
data += 0.1 * data.std() * np.random.standard_normal(data.shape)
deconvolved = restoration.richardson_lucy(data, psf, 5)
path = fetch('restoration/tests/camera_rl.npy')
np.testing.assert_allclose(deconvolved, np.load(path), rtol=1e-3)
def deconvolve(self):
self.load_psf()
stk = self.stk.astype('float64')
stk = stk - stk.min()
stk = stk / stk.max()
if self.verbose:
iterable = tqdm(range(int(round(self.deconvolution_batches / 2))),
desc='Deconvolving Stack')
else:
iterable = range(int(round(self.deconvolution_batches / 2)))
step = int(stk.shape[0] / (self.deconvolution_batches / 2))
if self.gpu:
if self.deconvolution_batches > 1:
for i in iterable:
i0 = int(step * i)
for j in iterable:
j0 = int(step * j)
temp = stk[i0:i0 + step, j0:j0 + step, :]
if self.gpu:
stk[i0:i0 + step,
j0:j0 + step, :] = self.gpu_algorithm.run(
fd_data.Acquisition(data=temp,
kernel=self.psf),
niter=self.deconvolution_niterations).data
else:
stk[i0:i0 + step,
j0:j0 + step, :] = restoration.richardson_lucy(
temp,
self.psf,
self.deconvolution_niterations,
clip=False)
else:
stk = self.gpu_algorithm.run(
fd_data.Acquisition(data=stk, kernel=self.psf),
niter=self.deconvolution_niterations).data
else:
stk = restoration.richardson_lucy(stk,
self.psf,
self.deconvolution_niterations,
clip=False)
self.stk = stk
del self.gpu_algorithm
def rl_dec(array, coupling):
kernal = np.zeros((3, 3))
coupling = coupling * .01
kernal[0, 1] = coupling
kernal[1, 0] = coupling
kernal[1, 2] = coupling
kernal[2, 1] = coupling
kernal[1, 1] = 1 - 4 * coupling
psf = np.asarray(kernal)
print psf
return restoration.richardson_lucy(array, psf, iterations=30, clip=False)
def rlDeconvolve(img_data,
psfFunction,
psfParam,
psfWidth=16,
iterations=30,
newWidth=0.5):
# skimage.restoration.richardson_lucy accepts float64 as input
img_data_64 = convertTo(img_data, np.float64)
# Set up PSF
xx = np.linspace(-psfWidth, psfWidth, 2 * psfWidth + 1, dtype=np.float32)
X, Y = np.meshgrid(xx, xx)
pos = np.array([X.ravel(), Y.ravel()]).T
psf = psfFunction(pos, 1.0, 0.0, 0.0, psfParam[0], psfParam[1],
psfParam[2], psfParam[3],
0.0).reshape(2 * psfWidth + 1, 2 * psfWidth + 1)
# PSF for the deconvoluted image
psf_new = psfFunction(pos, 1.0, 0.0, 0.0,
newWidth * newWidth * psfParam[0],
newWidth * newWidth * psfParam[1],
newWidth * newWidth * psfParam[2],
newWidth * newWidth * psfParam[3],
0.0).reshape(2 * psfWidth + 1, 2 * psfWidth + 1)
# The PSF for deconvolution
psf_deconv = restoration.richardson_lucy(psf,
psf_new,
iterations=iterations)
# Deconvolve
if img_data_64.ndim != 3:
img_deconv = restoration.richardson_lucy(img_data_64,
psf_deconv,
iterations=iterations)
else:
img_deconv = np.empty(img_data_64.shape)
for i in range(img_data_64.shape[-1]):
img_deconv[:, :,
i] = restoration.richardson_lucy(img_data_64[:, :, i],
psf_deconv,
iterations=iterations)
return img_deconv
def richardsonLucy():
camera = color.rgb2gray(data.camera())
imgO = camera.copy()
psf = np.ones((5, 5)) / 25
camera = convolve2d(camera, psf, 'same')
camera += 0.5 * camera.std() * np.random.standard_normal(camera.shape)
imgN = camera.copy()
deconvolved = restoration.richardson_lucy(camera, psf, 5)
imgR = deconvolved
return [imgO, imgN, imgR]
def deBlur(img): # unused return img ## print "Deblurring" image_gray = img psf = np.ones((3,3)) /9 image_gray = conv2(image_gray, psf, 'same') # Restore Image using Richardson-Lucy algorithm deconvolved_RL = restoration.richardson_lucy(image_gray, psf, iterations=10) return img
def deconvolve(roi):
"""Deconvolves the image.
Args:
roi: ROI given as a (z, y, x) subset of image5d.
Returns:
The ROI deconvolved.
"""
# currently very simple with a generic point spread function
psf = np.ones((5, 5, 5)) / 125
roi_deconvolved = restoration.richardson_lucy(roi, psf, iterations=30)
#roi_deconvolved = restoration.unsupervised_wiener(roi, psf)
return roi_deconvolved
def test_richardson_lucy_filtered():
test_img_astro = rgb2gray(astronaut())
psf = np.ones((5, 5)) / 25
data = convolve2d(test_img_astro, psf, 'same')
deconvolved = restoration.richardson_lucy(data,
psf,
5,
filter_epsilon=1e-6)
path = image_fetcher.fetch('restoration/tests/astronaut_rl.npy')
np.testing.assert_allclose(deconvolved,
np.load(path),
rtol=1e-3,
atol=1e-8)
def frame_deconvolution(array, psf, n_it=30):
"""
Iterative image deconvolution following the scikit-image implementation
of the Richardson-Lucy algorithm.
Considering an image that has been convolved by the point spread function
of an instrument, the algorithm will sharpen the blurred
image through a user-defined number of iterations, which changes the
regularisation.
Reference: William Hadley Richardson, “Bayesian-Based Iterative Method of
Image Restoration”, J. Opt. Soc. Am. A 27, 1593-1607 (1972),
DOI:10.1364/JOSA.62.000055
See also description at:
https://en.wikipedia.org/wiki/Richardson%E2%80%93Lucy_deconvolution
Parameters
----------
array : numpy ndarray
Input image, 2d frame.
psf : numpy ndarray
Input psf, 2d frame.
n_it : int, optional
Number of iterations.
Returns
-------
deconv : numpy ndarray
Deconvolved image.
"""
if array.ndim != 2:
raise TypeError('Input array is not a frame or 2d array.')
if psf.ndim != 2:
raise TypeError('Input psf is not a frame or 2d array.')
max_I = np.amax(array)
min_I = np.amin(array)
drange = max_I-min_I
deconv = richardson_lucy((array-min_I)/drange, psf, iterations=n_it)
deconv*=drange
deconv+=min_I
return deconv
def deconv_RL(f_tpl, w_tpl, bb=4):
# Deconvolution of f_tpl using Richardson Lucy algorithm
# needed for CRIRES data
psf = np.ones((1, bb)) / bb
f2 = f_tpl + 0.
f_tpl1 = np.reshape(f_tpl, (1, -1))
deconv_RL = restoration.richardson_lucy(f_tpl1 / np.max(f_tpl1) / 2.,
psf,
iterations=30)[0]
f_tpl = deconv_RL * np.max(f_tpl1) * 2
rv, ccc = pyasl.crosscorrRV(w_tpl[200:-200],
f_tpl[200:-200],
w_tpl[200:-200],
f2[200:-200],
-10.,
10.,
0.01,
skipedge=20)
pol = (np.poly1d(np.polyfit(rv, ccc, 15)))(rv)
shift = rv[np.argmax(pol)]
print('shift RL: ', shift, rv[np.argmax(ccc)])
# there seems to appear a shift in the spectra after the deconvolution
# why ???
# correction ???
# more testing needed, or another way of deconvolution
plot_RL = 0
if plot_RL:
gplot(rv, ccc, 'w l,', rv, pol, 'w l')
# gplot(w_tpl, f2, 'w l,', w_tpl /(1+shift/3e5),f_tpl,'w l')
pause()
# w_tpl /= (1+shift/3e5)
'''
bo = 10
f_tpl = f_tpl[bo:-bo]
w_tpl = w_tpl[bo:-bo]
f_ok = f_ok[bo:-bo]
w_ok = w_ok[bo:-bo]
x_ok = x_ok[bo:-bo]
'''
return f_tpl, w_tpl
def nick():
file_path = 's3://sofroniewn/image-data/smFISH/raw.zarr'
raw = da.from_zarr(file_path)
blurred = gaussian_filter(raw, (0, 2, 2))
x, y = np.meshgrid(np.linspace(-1, 1, 6), np.linspace(-1, 1, 6))
d = np.sqrt(x * x + y * y)
sigma, mu = 2.0, 0.0
psf = np.expand_dims(np.exp(-((d - mu) ** 2 / (2.0 * sigma ** 2))), axis=0)
deconvolved = blurred.map_blocks(
lambda block: richardson_lucy(block, psf, clip=False)
)
viewer = napari.Viewer()
viewer.add_image(raw, contrast_limits=(140.0, 1200.0))
viewer.add_image(blurred, contrast_limits=(140.0, 1200.0))
viewer.add_image(deconvolved, contrast_limits=(140.0, 1200.0))
def frame_deblur(raw_frame, sig = 4., Nit = 21, padding = ((10,10), (10,10))):
'''
raw_frame: a single frame of image
sig: the width of gaussian filter
'''
print("Initial size:",raw_frame.shape)
psf = build_psf(sig)
img = np.pad(raw_frame, padding, mode = 'constant')
img = blank_refill(img, cutoff=180, mode = 'peak')
dc_image = restoration.richardson_lucy(img, psf, iterations = Nit, clip = False)
ci, cf = padding
yi, xi = ci
yf, xf = cf
recrop = dc_image[yi:-yf, xi:-xf]
print("Final size:", recrop.shape)
return blank_refill(recrop, mode = 'peak')
def loop(imgFiles):
for f in imgFiles:
img = data.load(os.path.join(originalDir, f))
bwimg = color.rgb2gray(img)
# print(type(img))
psf = np.ones((5, 5)) / 25
img = conv2(bwimg, psf, 'same')
# Add Noise to Image
img = img.copy()
img += (np.random.poisson(lam=25, size=img.shape) - 10) / 255.
# io.imsave(os.path.join(noisyDir,f), img)
scipy.misc.imsave(os.path.join(noisyDir, f), img)
startTime = time.time()
img = richardson_lucy(img, psf, iterations=30, clip=True)
io.imsave(os.path.join(denoisedDir, f), img)
print("Took %f seconds for %s" % (time.time() - startTime, f))
def test_richardson_lucy_filtered(dtype_image, dtype_psf):
if dtype_image == np.float64:
atol = 1e-8
else:
atol = 1e-5
test_img_astro = rgb2gray(astronaut())
psf = np.ones((5, 5), dtype=dtype_psf) / 25
data = convolve2d(test_img_astro, psf, 'same')
data = data.astype(dtype_image, copy=False)
deconvolved = restoration.richardson_lucy(data, psf, 5,
filter_epsilon=1e-6)
assert deconvolved.dtype == data.dtype
path = fetch('restoration/tests/astronaut_rl.npy')
np.testing.assert_allclose(deconvolved, np.load(path), rtol=1e-3,
atol=atol)
def get_trap_positions(self, frame):
self.frame = frame
inverted_image = np.max(frame) - frame
edgemap = canny(inverted_image,
sigma=2.2,
low_threshold=self.low_threshold,
high_threshold=self.high_threshold)
dilated_edges = binary_dilation(edgemap,
selem=np.ones_like(frame[:3, :2]))
edges = sobel(dilated_edges)
deconvolved_image = richardson_lucy(edges, self.kernel, 6, clip=False)
self.trap_positions = np.array(
peak_local_max(deconvolved_image,
threshold_rel=self.point_intensity_limit))
def weiner_filter(img,psf):
astro = color.rgb2gray(data.astronaut())
print "running Weiner for a channel"
out = np.ndarray(shape=img.shape, dtype=np.float64) # redifine to correct type
out = np.copy(img)
min_intensity = np.amin(img)
out = out - min_intensity
max_intensity = np.amax(out)
out = out * (1.0 / max_intensity)
img = out
#psf = np.ones((5, 5)) / 25.0
astro = conv2(astro, psf, 'same')
astro += 0.22 * astro.std() * np.random.standard_normal(astro.shape)
#deconvolved, _ = restoration.unsupervised_wiener(img, psf)
#deconvolved = restoration.wiener(img, psf, 500)
deconvolved = restoration.richardson_lucy(img, psf, 200)
return deconvolved
img_eq = exposure.equalize_hist(log_img)
img_adapteq = exposure.equalize_adapthist(img, clip_limit=0.5,kernel_size=(4,4))
#img_adapteq3 = img - np.min(img)
img_adapteq3 = exposure.equalize_adapthist(log_img, clip_limit=0.5,kernel_size=(4,4))
img_adapteq4 = exposure.equalize_adapthist(log_img, clip_limit=0.01,kernel_size=(2,2),nbins=12)
#denois_img = img - np.min(img)
denois_img = img_adapteq - np.min(img_adapteq)
denois_img /= np.max(denois_img)
denois_img = np.uint8(denois_img*255)
tv_coins = restoration.richardson_lucy(log_img,)
better_contrast = exposure.rescale_intensity(denois_img)
dst = cv2.fastNlMeansDenoising(better_contrast)
dst2 = cv2.fastNlMeansDenoising(denois_img)
im_med = median_filter(img, 5)
#sift = cv2.Feat .SIFT_create()
print hog(img)
#print des.shape
plt.subplot(131),plt.imshow(real)
plt.subplot(132),plt.imshow(tv_coins )
plt.subplot(133),plt.imshow( img_adapteq4)
#%%Reconstruct t2ds.lam=40 t2ds.calibrate() noise=trainingnoise ssdh12= addNoise2D(t2ds.calcSignal(testsmp),noise) srdh12= t2ds.reconstruct(ssdh12) Ddcnv=srdh12 #%% Deconvolve with found convolution Sig = ssdh12 Sig+=Sig.min() esf=Sig.max() #psf=t2ds.sweetSpot sigclip=2*(Sig/esf) Rdcnv = restoration.richardson_lucy(sigclip,psf) Wdcnv=restoration.wiener(sigclip,psf,balance=500,clip=False) #Wdcnv+=1.0 Wdcnv*=esf/2 Rdcnv+=1 Rdcnv*=esf #%%Division in fourier space #Calculate F(testsignal) FS=fft.fft2(Sig) FSlev=np.percentile(np.abs(FS),80) threshFS=np.where(np.abs(FS)<FSlev,0,FS) #Calculate F(sweetspot), (have to pad to correct size for signal) padpsf=np.zeros_like(FS) halfFS=FS.shape[0]/2 halfpsf=iFSS.shape[0]/2
import numpy as np
from skimage import color, data, restoration
import numpy as np
import numpy.random as npr
from scipy.signal import convolve2d
import helper
camera = color.rgb2gray(data.camera())
camera = helper.get_image('cameraman')
from scipy.signal import convolve2d
psf = np.ones((5, 5)) / 25
camera = convolve2d(camera, psf, 'same')
camera += 0.1 * camera.std() * np.random.standard_normal(camera.shape)
deconvolved = restoration.richardson_lucy(camera, psf, 5)
helper.show_images({'deconv':deconvolved})
def deconv_scikit(d,h):
return restoration.richardson_lucy(d, h, 10, clip = False)
import matplotlib.pyplot as plt
from scipy.signal import convolve2d as conv2
from skimage import color, data, restoration
astro = color.rgb2gray(data.astronaut())
psf = np.ones((5, 5)) / 25
astro = conv2(astro, psf, 'same')
# Add Noise to Image
astro_noisy = astro.copy()
astro_noisy += (np.random.poisson(lam=25, size=astro.shape) - 10) / 255.
# Restore Image using Richardson-Lucy algorithm
deconvolved_RL = restoration.richardson_lucy(astro_noisy, psf, iterations=30)
fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(8, 5))
plt.gray()
for a in (ax[0], ax[1], ax[2]):
a.axis('off')
ax[0].imshow(astro)
ax[0].set_title('Original Data')
ax[1].imshow(astro_noisy)
ax[1].set_title('Noisy data')
ax[2].imshow(deconvolved_RL, vmin=astro_noisy.min(), vmax=astro_noisy.max())
ax[2].set_title('Restoration using\nRichardson-Lucy')