def chunk_lcn(chunk, sigma_mean, sigma_std, std_bias=0.0, rescale=1.0):
"""
based on matlab code by Guanglei Xiong, see http://www.mathworks.com/matlabcentral/fileexchange/8303-local-normalization
assuming chunk.shape == (num_examples, x, y, channels)
'rescale' is an additional rescaling constant to get the variance of the result in the 'right' range.
"""
means = np.zeros(chunk.shape, dtype=chunk.dtype)
for k in xrange(len(chunk)):
means[k] = filters.gaussian_filter(chunk[k],
sigma_mean,
multichannel=True)
chunk = chunk - means # centering
del means # keep memory usage in check
variances = np.zeros(chunk.shape, dtype=chunk.dtype)
chunk_squared = chunk**2
for k in xrange(len(chunk)):
variances[k] = filters.gaussian_filter(chunk_squared[k],
sigma_std,
multichannel=True)
chunk = chunk / np.sqrt(variances + std_bias)
return chunk / rescale
def filter(data, filtType, par):
if filtType == "sobel":
filt_data = sobel(data)
elif filtType == "roberts":
filt_data = roberts(data)
elif filtType == "canny":
filt_data = canny(data)
elif filtType == "lowpass_avg":
from scipy import ndimage
p = int(par)
kernel = np.ones((p, p), np.float32) / (p * p)
filt_data = ndimage.convolve(data, kernel)
elif filtType == "lowpass_gaussian":
s = float(par)
filt_data = gaussian_filter(data, sigma=s)
elif filtType == "highpass_gaussian":
s = float(par)
lp_data = gaussian_filter(data, sigma=s)
filt_data = data - lp_data
elif filtType == "highpass_avg":
from scipy import ndimage
p = int(par)
kernel = np.ones((p, p), np.float32) / (p * p)
lp_data = ndimage.convolve(data, kernel)
filt_data = data - lp_data
#elif filtType == "gradient":
return filt_data
def hybrid():
# Read Images
input_image_1 = skio.imread(INPUT_IMAGES_NAME[0])
input_image_2 = skio.imread(INPUT_IMAGES_NAME[1])
#----------------------------------------------------------------------
# Transform to float
image_1 = img_as_float(input_image_1)
image_2 = img_as_float(input_image_2)
#----------------------------------------------------------------------
# Align images using provided functiom
image_aligned_1, image_aligned_2 = align_images(image_1, image_2)
#----------------------------------------------------------------------
# Divide image in color channels
color_channels_1 = np.array([
image_aligned_1[:, :, 0], image_aligned_1[:, :, 1],
image_aligned_1[:, :, 2]
])
color_channels_2 = np.array([
image_aligned_2[:, :, 0], image_aligned_2[:, :, 1],
image_aligned_2[:, :, 2]
])
# Use color channels to compose an unique gray scale image
# http://stackoverflow.com/questions/12201577/how-can-i-convert-an-rgb-image-into-grayscale-in-python
image_1_grayscale = np.clip(
color_channels_1[0] * 0.299 + color_channels_1[1] * 0.587 +
color_channels_1[2] * 0.114, 0.0, 1.0)
image_2_grayscale = np.clip(
color_channels_2[0] * 0.299 + color_channels_2[1] * 0.587 +
color_channels_2[2] * 0.114, 0.0, 1.0)
#----------------------------------------------------------------------
# Apply the Laplacian Filter (high pass filter) to the first image by subtracting the Gaussian Filtered Image from the original
low_frequency_image_1 = filter.gaussian_filter(image_1_grayscale,
HIGH_FREQUENCY_BLUR_RATIO)
high_frequency_image_1 = image_1_grayscale - low_frequency_image_1
# Apply the Gaussian Filter (low pass filter) to the second image
low_frequency_image_2 = filter.gaussian_filter(image_2_grayscale,
LOW_FREQUENCY_BLUR_RATIO)
#----------------------------------------------------------------------
# Add pictures together
output_image = np.clip(high_frequency_image_1 + low_frequency_image_2, 0.0,
1.0)
#----------------------------------------------------------------------
# Show final image
skio.imshow(output_image)
skio.show()
def test_several_gaussian_filter():
'''result:these are almost the same'''
a = np.zeros((5, 5),np.float32)
a[2, 2] = 1
import vigra
from skimage.filter import gaussian_filter
print gaussian_filter(a,1)
print vigra.gaussianSmoothing(a, 1)
print ndimage.gaussian_filter(a, 1)
def smoothing_gauss(data, sigma=1, pseudo_3D='True', sliceId=2):
if data.ndim == 3 and pseudo_3D:
if sliceId == 2:
for idx in range(data.shape[2]):
temp = skifil.gaussian_filter(data[:, :, idx], sigma=sigma)
data[:, :, idx] = (255 * temp).astype(np.uint8)
elif sliceId == 0:
for idx in range(data.shape[0]):
temp = skifil.gaussian_filter(data[idx, :, :], sigma=sigma)
data[idx, :, :] = (255 * temp).astype(np.uint8)
else:
data = skifil.gaussian_filter(data, sigma=sigma)
data = (255 * data).astype(np.uint8)
return data
def smoothing(self, sigma_zero):
"""
:param sigma_zero: initial sigma as a first smoothing
:return:void (images are saved at disc space in path+ '/npy_arrays_3DGaussianFiltering'
"""
path_to_save = '/3DGaussianSmoothing/'
sigmas_x = (self.k ** self.powers) * sigma_zero
sigmas_y = (self.k ** self.powers) * sigma_zero
sigmas_z = ((self.k ** self.powers) * sigma_zero) / (self.spacing[2] / self.spacing[0])
print(sigmas_x, sigmas_z)
saving = SaveImage(self.path + path_to_save)
for sigma_x, sigma_y, sigma_z in zip(sigmas_x, sigmas_y, sigmas_z):
im = self.image.Image3D
image = normalize(im, [np.min(im), np.max(im)], [-1.0, 1.0])
print('befor ', np.min(image), np.max(image))
smoothed_image = gaussian_filter(image, (sigma_x, sigma_y, sigma_z))
smoothed_image = smoothed_image.astype(dtype=np.float32)
smoothed_image = normalize(smoothed_image, [-1.0, 1.0], [0.0, 1.0])
temp_image = deepcopy(self.image)
temp_image.Image3D = smoothed_image
temp_image.sigma = sigma_x
saving.saveImage(temp_image)
def smoothing(self, sigma_zero):
"""
:param sigma_zero: initial sigma as a first smoothing
:return:void (images are saved at disc space in path+ '/npy_arrays_2DGaussianFiltering'
"""
path_to_save = '/2DGaussianSmoothing/'
sigmas_x = (self.k ** self.powers) * sigma_zero / self.spacing[0]
sigmas_y = (self.k ** self.powers) * sigma_zero / self.spacing[1]
# make directory
im = self.image.Image3D[:, :, 20]
saving = SaveImage(self.path + path_to_save)
for sigma_x, sigma_y in zip(sigmas_x, sigmas_y):
image = normalize(im, [np.min(im), np.max(im)], [-1.0, 1.0])
smoothed_image = gaussian_filter(image, (sigma_x, sigma_y))
print(np.min(smoothed_image), np.max(smoothed_image))
smoothed_image = normalize(smoothed_image, [-1.0, 1.0], [0.0, 1.0])
temp_image = deepcopy(self.image)
temp_image.Image3D = smoothed_image
temp_image.sigma = sigma_x
saving.saveImage(temp_image)
def impyramid_next_level(_img, filter='burt_adelson'):
"""
IMPYRAMID_NEXT_LEVEL: computes the next level in a Gaussian pyramidal
decomposition.
:param _img: numpy.ndarray
A grey-level image (_img.ndim == 2)
:param filter: string
Which filter to use in removing high frequencies:
- burt_adelson: [-0.125, 0.250, 0.375, 0.250, -0.125]
- custom1: [0.125, 0.275, 0.375, 0.125] (Gaussian, sigma=0.866)
:return: numpy.ndarray
The new level in the pyramid, an image half the size of the original.
"""
assert (_img.ndim == 2)
# classical low-pass filter, with the kernel from Burt & Adelson (1983):
if filter == 'burt_adelson':
a = 0.375
krn = [1/4 - a/2, 1/4, a, 1/4, 1/4 - a/2]
res = (_img - sepfir2d(_img, krn, krn))[::2, ::2]
elif filter == 'custom1':
res = gaussian_filter(_img, sigma=0.866)[::2, ::2]
return res
def gradient_field(im):
im = skimage_filter.gaussian_filter(im, 1.0)
gradx = np.hstack([im[:, 1:], im[:, -2:-1]]) - np.hstack(
[im[:, 0:1], im[:, :-1]])
grady = np.vstack([im[1:, :], im[-2:-1, :]]) - np.vstack(
[im[0:1, :], im[:-1, :]])
return gradx, grady
def label_nuclei(binary, min_size):
'''Label, watershed and remove small objects'''
distance = medial_axis(binary, return_distance=True)[1]
distance_blured = gaussian_filter(distance, 5)
local_maxi = peak_local_max(distance_blured,
indices=False,
labels=binary,
min_distance=30)
markers = measure_label(local_maxi)
# markers[~binary] = -1
# labels_rw = segmentation.random_walker(binary, markers)
# labels_rw[labels_rw == -1] = 0
# labels_rw = segmentation.relabel_sequential(labels_rw)
labels_ws = watershed(-distance, markers, mask=binary)
labels_large = remove_small_objects(labels_ws, min_size)
labels_clean_border = clear_border(labels_large)
labels_from_one = relabel_sequential(labels_clean_border)
# plt.imshow(ndimage.morphology.binary_dilation(markers))
# plt.show()
return labels_from_one[0]
def label_nuclei(binary, min_size):
'''Label, watershed and remove small objects'''
distance = medial_axis(binary, return_distance=True)[1]
distance_blured = gaussian_filter(distance, 5)
local_maxi = peak_local_max(distance_blured, indices=False, labels=binary, min_distance = 30)
markers = measure_label(local_maxi)
# markers[~binary] = -1
# labels_rw = segmentation.random_walker(binary, markers)
# labels_rw[labels_rw == -1] = 0
# labels_rw = segmentation.relabel_sequential(labels_rw)
labels_ws = watershed(-distance, markers, mask=binary)
labels_large = remove_small_objects(labels_ws,min_size)
labels_clean_border = clear_border(labels_large)
labels_from_one = relabel_sequential(labels_clean_border)
# plt.imshow(ndimage.morphology.binary_dilation(markers))
# plt.show()
return labels_from_one[0]
def preprocess_image(filename, simple_ds=4., mask_strength=None, nside_out=50):
from PIL import Image
from skimage.filter import gaussian_filter
# open file
x = np.array(Image.open(filename), dtype=np.float)
if ((simple_ds > 1) & (simple_ds != None)):
# Gaussian smooth with FWHM = "simple_ds" pixels.
for i in range(3):
x[:, :, i] = gaussian_filter(x[:, :, i], 1. * simple_ds / 2.355)
# subsample by simple_ds.
x = x[0::int(simple_ds), 0::int(simple_ds), :]
# take inner nside_out x nside_out.
ntmp = x.shape[0] - nside_out
if (ntmp % 2) == 0:
nside = ntmp / 2
x = x[nside:-nside, nside:-nside, :]
else:
nside = (ntmp - 1) / 2
x = x[nside + 1:-nside, nside + 1:-nside, :]
# If desired, apply mask.
if (mask_strength == None) | (mask_strength == 'none'):
return x
else:
if (mask_strength == 'weak'): mask_thresh = 15.
if (mask_strength == 'strong'): mask_thresh = 30.
avg = np.mean(x, axis=-1)
mask = get_mask(avg, thresh=mask_thresh)
x *= mask[:, :, np.newaxis]
return x
def train(self, _dataSet):
'''
Trains Model for given dataset (ImageDataSet)
'''
sys.stderr.write("Got " + str(len(_dataSet.get_inputs())) + " images\n")
for im in _dataSet.get_inputs():
self.filtered.append(filter.gaussian_filter(im, self.sigma, multichannel=False))
def impyramid_next_level(_img, filter='burt_adelson'):
"""
IMPYRAMID_NEXT_LEVEL: computes the next level in a Gaussian pyramidal
decomposition.
:param _img: numpy.ndarray
A grey-level image (_img.ndim == 2)
:param filter: string
Which filter to use in removing high frequencies:
- burt_adelson: [-0.125, 0.250, 0.375, 0.250, -0.125]
- custom1: [0.125, 0.275, 0.375, 0.125] (Gaussian, sigma=0.866)
:return: numpy.ndarray
The new level in the pyramid, an image half the size of the original.
"""
assert (_img.ndim == 2)
# classical low-pass filter, with the kernel from Burt & Adelson (1983):
if filter == 'burt_adelson':
a = 0.375
krn = [1 / 4 - a / 2, 1 / 4, a, 1 / 4, 1 / 4 - a / 2]
res = (_img - sepfir2d(_img, krn, krn))[::2, ::2]
elif filter == 'custom1':
res = gaussian_filter(_img, sigma=0.866)[::2, ::2]
return res
def FH_Seg(filename,labelMask,minSize,c):
rgbImg = io.imread(filename)
width=rgbImg.shape[1]
height=rgbImg.shape[0]
labImg = color.rgb2lab(rgbImg)
smooth_img=filter.gaussian_filter(labImg,sigma=0.8,multichannel=True)
labelList=unique(labelMask)
numSeg=len(labelList)
pixelSet=UnionSet(width*height)
threshold=[1.0/c]*(width*height)
for currLabel in labelList:
edgeList=creatEdgeList(smooth_img,labelMask,currLabel)
segment_graph(edgeList,pixelSet,threshold,c,minSize)
"""
现在已经有了pixelSet，接下来把每个labelMask标记成root的index，之后，用uniqueList找到对应的独立
item，然后再用item的index（0：segNum）代替label中的不规则编号
"""
segNum=pixelSet.setNum()
mySegNum=0
for i in range(width*height):
if i==pixelSet.find(i):
pixelSet.setNodeLabel(i,mySegNum)
mySegNum+=1
FH_Label=numpy.zeros((height,width))
for y in range(height):
for x in range(width):
index=y*width+x
FH_Label[y,x]=pixelSet.segLabel(index)
return FH_Label
def smoothing(self, sigma_zero):
"""
:param sigma_zero: initial sigma as a first smoothing
:return:void (images are saved at disc space in path+ '/npy_arrays_3DGaussianFiltering'
"""
path_to_save = '/3DGaussianSmoothing/'
sigmas_x = (self.k**self.powers) * sigma_zero
sigmas_y = (self.k**self.powers) * sigma_zero
sigmas_z = ((self.k**self.powers) * sigma_zero) / (self.spacing[2] /
self.spacing[0])
print(sigmas_x, sigmas_z)
saving = SaveImage(self.path + path_to_save)
for sigma_x, sigma_y, sigma_z in zip(sigmas_x, sigmas_y, sigmas_z):
im = self.image.Image3D
image = normalize(im, [np.min(im), np.max(im)], [-1.0, 1.0])
print('befor ', np.min(image), np.max(image))
smoothed_image = gaussian_filter(image,
(sigma_x, sigma_y, sigma_z))
smoothed_image = smoothed_image.astype(dtype=np.float32)
smoothed_image = normalize(smoothed_image, [-1.0, 1.0], [0.0, 1.0])
temp_image = deepcopy(self.image)
temp_image.Image3D = smoothed_image
temp_image.sigma = sigma_x
saving.saveImage(temp_image)
def smoothing(self, sigma_zero):
"""
:param sigma_zero: initial sigma as a first smoothing
:return:void (images are saved at disc space in path+ '/npy_arrays_2DGaussianFiltering'
"""
path_to_save = '/2DGaussianSmoothing/'
sigmas_x = (self.k**self.powers) * sigma_zero / self.spacing[0]
sigmas_y = (self.k**self.powers) * sigma_zero / self.spacing[1]
# make directory
im = self.image.Image3D[:, :, 20]
saving = SaveImage(self.path + path_to_save)
for sigma_x, sigma_y in zip(sigmas_x, sigmas_y):
image = normalize(im, [np.min(im), np.max(im)], [-1.0, 1.0])
smoothed_image = gaussian_filter(image, (sigma_x, sigma_y))
print(np.min(smoothed_image), np.max(smoothed_image))
smoothed_image = normalize(smoothed_image, [-1.0, 1.0], [0.0, 1.0])
temp_image = deepcopy(self.image)
temp_image.Image3D = smoothed_image
temp_image.sigma = sigma_x
saving.saveImage(temp_image)
def get_background_markers(image_gray):
'''
Finds the pixels that definitely belong in background regions.
Parameters
-----------
image_gray : 2-D numpy array
A grayscale image.
Returns
-----------
markers_background : 2-D Boolean numpy array
An array with the same shape as image_gray, where the seeds of
the background regions are True.
'''
dark_threshold = threshold_by_blocks(image_gray, 20, background_intensity)
dark_pixels = image_gray <= dark_threshold
image_smooth = gaussian_filter(image_gray, 1)
otsu = image_gray > threshold_otsu(image_gray)
#minima = local_min(image_smooth) & np.logical_not(otsu)
#minima = local_min(image_gray) & (~ otsu)
minima = local_min(image_gray)
markers_background = dark_pixels | minima
return markers_background
def applyProgressiveGaussian(im, dof, filterLevel):
#take the top dof pixels
top, bottom = np.vsplit(im, [dof])
#leave top, blur bottom
newbot = skfilter.gaussian_filter(bottom, filterLevel)
if (newbot.shape[0] > dof*2):
newbot = applyProgressiveGaussian(newbot, dof, filterLevel*1.1)
return np.vstack((top, newbot))
def energyFunctionChannel(channel):
# The energy function of a single-scaled image (channel)
# is the absolute and normalized value of the
# image after an laplacian filter
# (The energy function will be higher on edges)
blurred_channel = filter.gaussian_filter(channel, 2)
high_freq = channel - blurred_channel
absol = absolutize(high_freq)
return absol
def train(self, _dataSet):
'''
Trains Model for given dataset (ImageDataSet)
'''
sys.stderr.write("Got " + str(len(_dataSet.get_inputs())) +
" images\n")
for im in _dataSet.get_inputs():
self.filtered.append(
filter.gaussian_filter(im, self.sigma, multichannel=False))
def create_external_edge_force_gradients_from_img( img, sigma=30. ):
"""
Given an image, returns 2 functions, fx & fy, that compute
the gradient of the external edge force in the x and y directions.
img: ndarray
The image.
"""
# Gaussian smoothing.
smoothed = filt.gaussian_filter( (img-img.min()) / (img.max()-img.min()), sigma )
# Gradient of the image in x and y directions.
giy, gix = np.gradient( smoothed )
# Gradient magnitude of the image.
gmi = (gix**2 + giy**2)**(0.5)
# Normalize. This is crucial (empirical observation).
gmi = (gmi - gmi.min()) / (gmi.max() - gmi.min())
# Gradient of gradient magnitude of the image in x and y directions.
ggmiy, ggmix = np.gradient( gmi )
def fx(x, y):
"""
Return external edge force in the x direction.
x: ndarray
numpy array of floats.
y: ndarray:
numpy array of floats.
"""
# Check bounds.
x[ x < 0 ] = 0.
y[ y < 0 ] = 0.
x[ x > img.shape[1]-1 ] = img.shape[1]-1
y[ y > img.shape[0]-1 ] = img.shape[0]-1
return ggmix[ (y.round().astype(int), x.round().astype(int)) ]
def fy(x, y):
"""
Return external edge force in the y direction.
x: ndarray
numpy array of floats.
y: ndarray:
numpy array of floats.
"""
# Check bounds.
x[ x < 0 ] = 0.
y[ y < 0 ] = 0.
x[ x > img.shape[1]-1 ] = img.shape[1]-1
y[ y > img.shape[0]-1 ] = img.shape[0]-1
return ggmiy[ (y.round().astype(int), x.round().astype(int)) ]
return fx, fy
def CompareExampleToTraining(bwImg, preProcessedModel, getCandidates=False):
bwImg = filt.gaussian_filter(bwImg, 2.)
bwImg = bwImg[20:-20, :]
bwImg = bwImg[:, 20:-20]
charScores = []
for ch in preProcessedModel:
examples = preProcessedModel[ch]
for example, sourceObjId in examples:
#Tight crop
example = filt.gaussian_filter(example, 2.)
example = example[20:-20, :]
example = example[:, 20:-20]
flatExample = example.reshape(example.size)
flatBwImg = bwImg.reshape(bwImg.size)
if 0:
den = np.abs(flatExample - flatBwImg).mean()
if den > 0.:
score = 1. / den
else:
score = 100.
if 1:
score = np.corrcoef(flatExample, flatBwImg)[0, 1]
charScores.append((score, ch, example, sourceObjId))
charScores.sort(reverse=True)
#for score, ch, example, sourceObjId in charScores[:5]:
# #annot = GetAnnotForObjId(plates, sourceObjId)
# print ch, score, sourceObjId#, annot['reg']
mergeImg = None
if getCandidates:
mergeImg = bwImg.copy()
for score, ch, example, sourceObjId in charScores[:10]:
mergeImg = np.hstack((mergeImg, example))
#misc.imshow(mergeImg)
return charScores, mergeImg
def CompareExampleToTraining(bwImg, preProcessedModel, getCandidates = False): bwImg = filt.gaussian_filter(bwImg, 2.) bwImg = bwImg[20:-20,:] bwImg = bwImg[:,20:-20] charScores = [] for ch in preProcessedModel: examples = preProcessedModel[ch] for example, sourceObjId in examples: #Tight crop example = filt.gaussian_filter(example, 2.) example = example[20:-20,:] example = example[:,20:-20] flatExample = example.reshape(example.size) flatBwImg = bwImg.reshape(bwImg.size) if 0: den = np.abs(flatExample-flatBwImg).mean() if den > 0.: score = 1. / den else: score = 100. if 1: score = np.corrcoef(flatExample, flatBwImg)[0,1] charScores.append((score, ch, example, sourceObjId)) charScores.sort(reverse=True) #for score, ch, example, sourceObjId in charScores[:5]: # #annot = GetAnnotForObjId(plates, sourceObjId) # print ch, score, sourceObjId#, annot['reg'] mergeImg = None if getCandidates: mergeImg = bwImg.copy() for score, ch, example, sourceObjId in charScores[:10]: mergeImg = np.hstack((mergeImg, example)) #misc.imshow(mergeImg) return charScores, mergeImg
def highpass(stack, smth_width=100):
'''
Simulates a high pass filter in Fourier space by
substracting a smoothed version of the input image.
'''
stack = img_as_float(stack/stack.max())
lowpass = filter.gaussian_filter(stack, smth_width)
f_stack = stack - lowpass
f_stack -= f_stack.min()
return f_stack
def ssr(img, sig): img = img.astype(float) limg = gaussian_filter(img, sigma = sig) limg = limg + (limg == 0) img = img + (img == 0) img = (255*(log(img) - log(limg)) + 127) tmp = ones((img.shape[0], img.shape[1]), dtype = float)*255 tmp = (img > 255) * tmp img = ((img >= 0)*(img <= 255)*img + tmp).astype(uint8) return img
def get_labels(binary):
'''Return image with labeled cells'''
distance = distance_transform_edt(binary)
distance_blured = gaussian_filter(distance, 8)
local_maxi = peak_local_max(distance_blured, indices=False, labels=binary, min_distance = 10)
markers = label(local_maxi)
labels = watershed(-distance, markers, mask=binary)
labels = remove_small_objects(labels, 4000)
labels = clear_border(labels)
return labels
def get_mask(small, thresh=25):
# add color cut in here?
from skimage.filter import gaussian_filter
from scipy import ndimage
(nx, ny) = small.shape
sm = gaussian_filter(small, 4.0)
#sm = gaussian_filter(small, 3.0)
notdark = sm > thresh
label_objects, nb_labels = ndimage.label(notdark)
mask = label_objects == label_objects[np.round(nx / 2.), np.round(ny / 2.)]
return mask
def getImage(self,params): sigma = float(params['sigma']) r = float(params['red']) g = float(params['green']) b = float(params['blue']) image = data.coffee() new_image = filter.gaussian_filter(image, sigma=sigma, multichannel=True) new_image[:,:,0] = r*new_image[:,:,0] new_image[:,:,1] = g*new_image[:,:,1] new_image[:,:,2] = b*new_image[:,:,2] return new_image
def sim_wire(angle, gaussian_sigma=1, noise_level=0, L=100):
"Draw a wire with blur and optional noise."
# Noise level should be from 0 to 1. 0.02 is reasonable.
shape = (L, L)
a = np.zeros(shape, dtype=np.uint8)
a[draw.ellipse(L//2, L//2, L//24, L//4)] = 100 # horizontal ellipse
a = filter.gaussian_filter(a, gaussian_sigma)
b = transform.rotate(a, angle)
b += noise_level*np.random.randn(*shape)
return b
def apply_gaussian_filter(sigma, prob_map, relative_location_matrix_shape):
cprime_labels = prob_map.keys()
c_labels = next(prob_map.itervalues()).keys()
norm_prob_map = init_prob_map(cprime_labels, c_labels, relative_location_matrix_shape)
filtered_prob_map = init_prob_map(cprime_labels, c_labels, relative_location_matrix_shape)
for cprime, prob_map_c_given_cprime in prob_map.iteritems():
for c,relative_location_mat in prob_map_c_given_cprime.iteritems():
filtered_relative_location_mat = gaussian_filter(relative_location_mat, sigma=sigma, multichannel=True)
filtered_prob_map[cprime][c] = filtered_relative_location_mat
return filtered_prob_map
def generateGaussianPyramids(image, levels):
color_channels = [image[:, :, 0], image[:, :, 1], image[:, :, 2]]
gaussian_pyramids = []
for level in range(levels):
level_image_channels = []
for channel in color_channels:
blurred_channel = filter.gaussian_filter(channel, 2**level)
level_image_channels.append(blurred_channel)
gaussian_pyramids.append(level_image_channels)
return gaussian_pyramids
def apply_gaussian_filter(sigma, prob_map, relative_location_matrix_shape):
cprime_labels = prob_map.keys()
c_labels = next(prob_map.itervalues()).keys()
norm_prob_map = init_prob_map(cprime_labels, c_labels, relative_location_matrix_shape)
filtered_prob_map = init_prob_map(cprime_labels, c_labels, relative_location_matrix_shape)
for cprime, prob_map_c_given_cprime in prob_map.iteritems():
for c,relative_location_mat in prob_map_c_given_cprime.iteritems():
filtered_relative_location_mat = gaussian_filter(relative_location_mat, sigma=sigma, multichannel=True)
filtered_prob_map[cprime][c] = filtered_relative_location_mat
return filtered_prob_map
def structure_reliability(img, gamma=1):
""" Calculates the flow structure reliability
Parameters
----------
img: numpy array
Image to compute the structure
gamma: float, optional
Soft threshold
Return
------
reliability map (0 less reliable, 1 reliable)
"""
#compute gradient of the image in the three channels
#kernel for blurring
st = np.zeros((img.shape[0], img.shape[1]))
eps = 1e-6
for k in np.arange(img.shape[-1]):
grad = np.gradient(img[:, :, k])
#compute components of the structure tensor
wxx = filter.gaussian_filter(grad[0] ** 2, 1)
wxy = filter.gaussian_filter(grad[0] * grad[1], 1)
wyy = filter.gaussian_filter(grad[1] ** 2, 1)
#determinant and trace
wdet = wxx * wyy - wxy ** 2
wtr = wxx + wyy
st += wdet / (wtr + eps)
avg = st.mean()
return 1 - np.exp(-st / (0.7 * avg * gamma))
def get_markers(foci_pic, nucleus, peak_min_val_perc = 60):
'''Return foci markers'''
# foci_pic_blured = img_as_ubyte(gaussian_filter(foci_pic, 1))
foci_pic_blured = np.floor(gaussian_filter(foci_pic, 1)*255).astype(np.uint8)
foci_values = np.extract(nucleus, foci_pic)
min_peak_val = np.percentile(foci_values, (peak_min_val_perc))
local_maxi = peak_local_max(foci_pic_blured, min_distance=5, threshold_abs=min_peak_val, indices=False, labels=nucleus)
return measure_label(local_maxi)
def smooth_data(self, data):
if data is not None:
# smoothing data
print 'smoothing data...'
if self.params['smoothing'] == 1:
data = skifil.gaussian_filter(self.data, sigma=self.params['sigma'])
elif self.params['smoothing'] == 2:
data = tools.smoothing_bilateral(data, sigma_space=self.params['sigma_spatial'], sigma_color=self.params['sigma_range'], sliceId=0)
elif self.params['smoothing'] == 3:
data = tools.smoothing_tv(data, weight=self.params['weight'], sliceId=0)
else:
print '\tcurrently switched off'
return data
def fit(self, image):
if image.ndim > 2:
raise TypeError('only single channel images allowed')
# smooth image
im = gaussian_filter(image, self.sigma)
# gradients and grad. magnitude
im_x, im_y = self.__gradient(im)
im_r = np.sqrt(im_x * im_x + im_y * im_y)
# log gradients
log_im = np.log(im + self.__eps)
log_im_x, log_im_y = self.__gradient(log_im)
log_im_x = log_im_x.ravel()
log_im_y = log_im_y.ravel()
# compute weights
weights = np.exp(-im_r / (self.mu ** 2))
weights = weights.ravel()
# (x,y) coordinates
ny, nx = im.shape
x, y = np.meshgrid(range(nx), range(ny), indexing='xy')
x = x.ravel() - 0.5 * nx
y = y.ravel() - 0.5 * ny
# model (gradient) matrix
M = self.__M(x, y)
# observed (smoothed) gradient
g = np.row_stack((log_im_x, log_im_y))
g.shape = (g.size, 1)
# diag(weights) * M
weights.shape = (weights.size, 1)
WM = M * np.vstack((weights, weights))
# solve for gamma
_g = np.asmatrix(g)
_M = np.asmatrix(M)
_WM = np.asmatrix(WM)
gamma = np.linalg.inv(_WM.T * _M) * _WM.T * _g
# compute illumination profile
S = self.__S(x, y)
I = np.asarray(np.asmatrix(S) * gamma)
self.profile = np.exp(I - I.max())
self.profile = self.profile.reshape(im.shape)
def createHSVColourValues(imageRGB):
totalPixels = np.shape(imageRGB)[0] * np.shape(imageRGB)[1]
hsvSourceImage = color.rgb2hsv(imageRGB)
# Rather than just taking the pixel value, which might be noisy, average locally.
hsvSourceImage = filter.gaussian_filter( hsvSourceImage, sigma=1.0, multichannel=True )
allHuePixels = np.reshape(hsvSourceImage[:,:,0] , (totalPixels, 1) )
allSaturationPixels = np.reshape(hsvSourceImage[:,:,1] , (totalPixels, 1) )
allValueBrightPixels = np.reshape(hsvSourceImage[:,:,2] , (totalPixels, 1) )
hsvColourValueFeature = np.hstack( ( allHuePixels, allSaturationPixels, allValueBrightPixels ) )
return hsvColourValueFeature
def filter(data, filtType, par):
if filtType == "sobel":
filt_data = sobel(data)
elif filtType == "roberts":
filt_data = roberts(data)
elif filtType == "canny":
filt_data = canny(data)
elif filtType == "lowpass_avg":
from scipy import ndimage
p = int(par)
kernel = np.ones((p, p), np.float32) / (p * p)
filt_data = ndimage.convolve(data, kernel)
elif filtType == "lowpass_gaussian":
s = float(par)
filt_data = gaussian_filter(data, sigma=s)
elif filtType == "highpass_gaussian":
s = float(par)
lp_data = gaussian_filter(data, sigma=s)
filt_data = data - lp_data
elif filtType == "highpass_avg":
from scipy import ndimage
p = int(par)
kernel = np.ones((p, p), np.float32) / (p * p)
lp_data = ndimage.convolve(data, kernel)
filt_data = data - lp_data
# elif filtType == "gradient":
return filt_data
def impyramid_next_level_rgb(_img):
"""
IMPYRAMID_NEXT_LEVEL_RGB: computes the next level in a Gaussian
pyramidal decomposition, for color images (RGB, or any 3-channel
image).
:param _img: numpy.ndarray
A grey-level image (_img.ndim == 2)
:return: numpy.ndarray
The new level in the pyramid, an image half the size of the original.
"""
res = gaussian_filter(_img, sigma=0.866, multichannel=True)
return res[::2, ::2, :]
def impyramid_next_level_rgb(_img):
"""
IMPYRAMID_NEXT_LEVEL_RGB: computes the next level in a Gaussian
pyramidal decomposition, for color images (RGB, or any 3-channel
image).
:param _img: numpy.ndarray
A grey-level image (_img.ndim == 2)
:return: numpy.ndarray
The new level in the pyramid, an image half the size of the original.
"""
res = gaussian_filter(_img, sigma=0.866, multichannel=True)
return res[::2, ::2, :]
def main():
plt.figure(figsize=(15, 14))
planes = ['samolot01.jpg', 'samolot09.jpg', 'samolot05.jpg', 'samolot00.jpg', 'samolot07.jpg', 'samolot13.jpg']
i = 0
for file in planes:
img = data.imread(file, as_grey=True)
ax = plt.subplot(3, 2, i)
ax.axis('off')
#img = filter.sobel(img)
img **= 0.4
img = filter.canny(img, sigma=3.0)
img = morphology.dilation(img, morphology.disk(2))
img = filter.gaussian_filter(img, sigma=1.0)
ax.imshow(img, cmap=plt.cm.gray, aspect='auto')
i += 1
plt.savefig('zad1.pdf')
def get_markers(foci_pic, nucleus, peak_min_val_perc=60):
'''Return foci markers'''
# foci_pic_blured = img_as_ubyte(gaussian_filter(foci_pic, 1))
foci_pic_blured = np.floor(gaussian_filter(foci_pic, 1) * 255).astype(
np.uint8)
foci_values = np.extract(nucleus, foci_pic)
min_peak_val = np.percentile(foci_values, (peak_min_val_perc))
local_maxi = peak_local_max(foci_pic_blured,
min_distance=5,
threshold_abs=min_peak_val,
indices=False,
labels=nucleus)
return measure_label(local_maxi)
def createHSVColourValues(imageRGB):
totalPixels = np.shape(imageRGB)[0] * np.shape(imageRGB)[1]
hsvSourceImage = color.rgb2hsv(imageRGB)
# Rather than just taking the pixel value, which might be noisy, average locally.
hsvSourceImage = filter.gaussian_filter(hsvSourceImage,
sigma=1.0,
multichannel=True)
allHuePixels = np.reshape(hsvSourceImage[:, :, 0], (totalPixels, 1))
allSaturationPixels = np.reshape(hsvSourceImage[:, :, 1], (totalPixels, 1))
allValueBrightPixels = np.reshape(hsvSourceImage[:, :, 2],
(totalPixels, 1))
hsvColourValueFeature = np.hstack(
(allHuePixels, allSaturationPixels, allValueBrightPixels))
return hsvColourValueFeature
def showAttMap(
img,
attMaps,
tagName,
overlap=True,
cmap='autumn',
blur=False,
save=False,
):
pylab.rcParams['figure.figsize'] = (12.0, 12.0)
f, ax = plt.subplots(int(len(tagName) / 2 + 1), 2)
ax[0, 0].imshow(img)
if len(img.shape) == 2 or img.shape[2] == 1:
img = color.gray2rgb(img)
for i in range(len(tagName)):
attMap = attMaps[i].copy()
attMap -= attMap.min()
if attMap.max() > 0:
attMap /= attMap.max()
attMap = transform.resize(attMap, (img.shape[:2]),
order=3,
mode='nearest')
if blur:
attMap = filter.gaussian_filter(attMap, 0.02 * max(img.shape[:2]))
attMap -= attMap.min()
attMap /= attMap.max()
cmap = plt.get_cmap(cmap)
attMapV = cmap(attMap)
attMapV = np.delete(attMapV, 3, 2)
if overlap:
attMap = 1 * (1 - attMap**0.8).reshape(attMap.shape + (
1, )) * img + (attMap**0.8).reshape(attMap.shape +
(1, )) * attMapV
current_subplot_axes = ax[int((i + 1) / 2), int((i + 1) % 2)]
attention_map_subplot = current_subplot_axes.imshow(
attMap, interpolation='bicubic', cmap=cmap)
plt.colorbar(attention_map_subplot, ax=current_subplot_axes)
current_subplot_axes.set_title(tagName[i])
if save:
f.savefig("attentionmaps.jpg")
def get_binary(cells):
'''Returns binary image with cells'''
if (len(cells.shape) == 3):
cells = np.max(cells, 2)
blured = gaussian_filter(cells,8)
highpass = cells - 0.8*blured
sharp = highpass + cells
sharp = np.floor(sharp).astype(np.uint8)
diamond = np.array([0,1,0,1,1,1,0,1,0], dtype=bool).reshape((3,3))
edges = canny(sharp, sigma = 1, high_threshold = 35., low_threshold = 14.)
edges = double_dilation(edges, diamond)
binary = fill_holes(edges)
binary = double_erosion(binary, diamond)
return binary
def compute_features(filtered, frequencies,
proportion=0.5,
alpha=0.25):
"""Compute features for each filtered image.
``frequencies[i]`` is the center frequency of the Gabor filter
that generated ``filtered[i]``.
"""
# TODO: is this really what the paper means in formula 6?
nonlinear = np.tanh(alpha * filtered)
ncols = filtered.shape[1]
# paper says proportion * n_cols / frequency, but remember that
# their frequency is in cycles per image width. our frequency is
# in cycles per pixel, so we just need to take the inverse.
sigmas = proportion * (1.0 / np.array(frequencies))
features = np.dstack(gaussian_filter(nonlinear[:, :, i], sigmas[i])
for i in range(len(sigmas)))
return features
def record_mouse(event):
"""
Save a mouse action
"""
global counter
global session
if event.buttons != 1:
return
h, w, _, _, _ = session.console.display.get_screen_resolution(0)
png = session.console.display.take_screen_shot_png_to_array(0, h, w)
with open('screenshot.png', 'wb') as f:
f.write(png)
IMAGE_FILE_PATH = "screenshot.png"
FILE_TO_SAVE = "%s%s.png" % (SAVE_FOLDER, counter)
# load image
image = data.imread(IMAGE_FILE_PATH)
image = rgb2gray(image)
# edges
image = sobel(image)
# blur
image = gaussian_filter(image, sigma=10)
mpimg.imsave("output.png", image)
img = Image("output.png")
img_original = Image(IMAGE_FILE_PATH)
image = Image(IMAGE_FILE_PATH)
blobs = img.findBlobs(threshval = -1, minsize=10, maxsize=0, threshblocksize=0, threshconstant=5, appx_level=3)
if blobs:
blobs.draw(width=10)
img.save(FILE_TO_SAVE)
img_original.save(FILE_TO_SAVE+"_original.png")
counter += 1
def test():
'''
test function classifyIm with given tree and parameter vector A and B
'''
import sys
from skimage import io, color, filter
sys.path.append('/home/jo/Dropbox/FaceRegion') # navigate to the folder that contains
# A, B and tree
A = np.genfromtxt('A.csv', dtype = float, delimiter = ',')
B = np.genfromtxt('B.csv', dtype = float, delimiter = ',')
A = np.array(A, dtype = int8)
B = np.array(B, dtype = int8)
m = 9
pathData = '/host/Research Project/Data/Rdata' + str(m) + '.jpg';
tree = grabTree('myTree1.txt')
image = io.imread(pathData)
image = color.rgb2gray(image)
image = filter.gaussian_filter(image, sigma = 0.8)
classifyIm(tree, image)
def segment_texture(image, n_clusters=15, init=None):
# blur and take local maxima
blur_image = gaussian_filter(image, sigma=8)
blur_image = ndi.maximum_filter(blur_image, size=3)
# get texture features
feats = lbp(blur_image, n=5, method="uniform")
feats_r = feats.reshape(-1, 1)
# cluster the texture features, reusing initialised centres if already calculated
params = {"n_clusters": n_clusters, "batch_size": 500}
if init is not None:
params.update({"init": init})
km = k_means(**params)
clus = km.fit(feats_r)
# copy relevant attributes
labels = clus.labels_
clusters = clus.cluster_centers_
# reshape label arrays
labels = labels.reshape(blur_image.shape[0], blur_image.shape[1])
return (image, blur_image, labels, clusters)
ext_s_min[out_min_min] = 0
ext_s_max[out_max_min] = 0
# clamp the max to image bounds across each dimension
for i in xrange(image.n_dims):
ext_s_max[out_max_max[:, i], i] = image_size[i] - 1
ext_s_min[out_min_max[:, i], i] = image_size[i] - 1
# 3. Build the insertion slices
ins_s_min = ext_s_min - c_min
ins_s_max = np.maximum(ext_s_max - c_max + parts_shape, (0, 0))
for i, (e_a, e_b, i_a, i_b) in enumerate(zip(ext_s_min, ext_s_max,
ins_s_min, ins_s_max)):
# build a list of insertion slices and extraction slices
i_slices = [slice(a, b) for a, b in zip(i_a, i_b)]
e_slices = [slice(a, b) for a, b in zip(e_a, e_b)]
# get a view onto the parts we are on
part = parts[..., i, :]
# apply the slices to map
part[i_slices] = image.pixels[e_slices]
# build and return parts image
return Image(parts)
def flatten_out(list_of_lists):
return [i for l in list_of_lists for i in l]
fsmooth = lambda x, sigma: gaussian_filter(x, sigma, mode='constant')
################################################################################ from skimage.exposure import rescale_intensity rescaled_nuclei = rescale_intensity(nuclei, in_range=(np.min(nuclei),np.max(nuclei))) plt.imshow(rescaled_nuclei) new_range = tuple(np.percentile(nuclei,(2,98))) rescaled_nuclei = rescale_intensity(nuclei, in_range=new_range) plt.imshow(rescaled_nuclei) ################################################################################ ################################################################################ #### Применение фильтров, создание рисунка с повышенной чёткостью границ #### ################################################################################ from skimage.filter import gaussian_filter blured = gaussian_filter(nuclei,8) plt.imshow(blured) highpass = nuclei - 0.8*blured sharp = highpass + nuclei sharp = np.floor(sharp).astype(np.uint8) fig, ax = plt.subplots(1,2) plt.gray() ax[0].imshow(nuclei) ax[1].imshow(sharp) ################################################################################ ################################################################################ #### Бинаризация изображений (белые клетки, чёрный фон) ####
import skimage.io as io
from skimage.filter import gaussian_filter
import matplotlib.pyplot as plt
import numpy as np
img = io.imread('sobel.png')
def show_images(images, titles=None):
"""Display a list of images"""
n_ims = len(images)
if titles is None: titles = ['(%d)' % i for i in range(1, n_ims + 1)]
fig = plt.figure()
n = 1
for image, title in zip(images, titles):
a = fig.add_subplot(1, n_ims, n) # Make subplot
if image.ndim == 2: # Is image grayscale?
plt.gray(
) # Only place in this blog you can't replace 'gray' with 'grey'
plt.imshow(image)
a.set_title(title)
n += 1
fig.set_size_inches(np.array(fig.get_size_inches()) * n_ims)
plt.show()
blurred_image = gaussian_filter(img, sigma=3)
really_blurred_image = gaussian_filter(img, sigma=6)
show_images(images=[img, blurred_image, really_blurred_image],
titles=["Equalized", "3 Sigma Blur", "6 Sigma Blur"])
from skimage import measure, filter
from scipy import ndimage
from matplotlib import animation
import matplotlib.pyplot as plt
from matplotlib.patches import Ellipse
from glob import glob
reload(trackblobs)
files = glob('/Users/ethan/insight/nexrad/data/kmlb_grid/firstn/*.png')
frames = []
storm_list = []
for f in files:
im = Image.open(f)
z = np.flipud(np.array(im)) * 75.0 / 255.0
z1 = filter.gaussian_filter(1 * z, sigma=1.1)
im.close()
frames.append(z1)
storms = trackblobs.find_storms(z1)
storm_list.append(storms)
fig = plt.figure(figsize=(5, 5))
ax = fig.add_axes([0, 0, 1, 1])
axim = ax.imshow(z1, origin='lower')
def init():
pass
def animate(i):
def segment_image(prefix, filename, min_area, blur):
#import resource ; r = resource.getrusage(resource.RUSAGE_SELF)
#print 'maxrss start', r.ru_maxrss
image = images.load(filename)
height = image.shape[0]
width = image.shape[1]
print prefix, 'FG/BG'
blurred = filter.gaussian_filter(image, blur, multichannel=True)
image_raveled = numpy.reshape(blurred, (height * width, 3))
del blurred
# Allow for non-uniform lighting over image using a linear model
#pred = [ ]
#order = 2
#for i in xrange(order):
# for j in xrange(order):
# pred.append((
# numpy.cos(numpy.linspace(0,numpy.pi*i, width)).astype('float32')[None,:] *
# numpy.cos(numpy.linspace(0,numpy.pi*j, height)).astype('float32')[:,None] ).ravel())
#pred = numpy.transpose(pred)
#one = numpy.ones((height,width), dtype='float32').ravel()
#x = numpy.empty((height,width), dtype='float32')
#x[:,:] = numpy.linspace(0.0, 1.0, width)[None,:]
#x = x.ravel()
#y = numpy.empty((height,width), dtype='float32')
#y[:,:] = numpy.linspace(0.0, 1.0, height)[:,None]
#y = y.ravel()
#pred = numpy.array((
# one,
# #x,
# #y,
# #x*x,
# #y*y,
# #x*y,
# #x*x*x,
# #y*y*y,
# #x*x*y,
# #y*y*x,
# )).transpose()
#del one,x,y
#
#def fit(mask):
# result = numpy.zeros((height*width,3), dtype='float32')
# for i in xrange(3):
# model = linalg.lstsq(pred[mask],image_raveled[mask,i])[0]
# for j in xrange(pred.shape[1]):
# result[:,i] += pred[:,j] * model[j]
# return result
average = numpy.mean(image_raveled, axis=0)
# Initial guess
color_bg = (average * 1.5) #[None,:]
color_fg = (average * 0.5) #[None,:]
#offsets = image_raveled - average
#icovar_fg = icovar_bg = stats.inverse_covariance(offsets)
#mv_fg = mv_bg = stats.estimate_multivar(offsets)
#mv = stats.estimate_indivar(offsets)
#del offsets
#p_fg = 0.5
i = 0
while True:
#d_bg = a_raveled-color_bg[None,:]
#d_bg *= d_bg
#d_bg = numpy.sum(d_bg,1)
#d_fg = a_raveled-color_fg[None,:]
#d_fg *= d_fg
#d_fg = numpy.sum(d_fg,1)
#fg = d_fg*Background_weight < d_bg
#color_fg = numpy.median(a_raveled[fg,:],axis=0)
#color_bg = numpy.median(a_raveled[~fg,:],axis=0)
#d_bg = stats.length2s(icovar_bg, image_raveled - color_bg[None,:])
#d_fg = stats.length2s(icovar_fg, image_raveled - color_fg[None,:])
#fg = d_fg < d_bg
#logp_bg = mv.logps(image_raveled - color_bg) #+ numpy.log(1.0-p_fg)
#logp_fg = mv.logps(image_raveled - color_fg) #+ numpy.log(p_fg)
#fg = logp_fg > logp_bg
#del logp_bg, logp_fg
mid = (color_bg + color_fg) * 0.5
proj = (color_fg - color_bg)
fg = numpy.sum(image_raveled * proj[None, :], axis=1) > numpy.sum(
mid * proj)
#p_fg = numpy.mean(fg)
#p_fg = max(0.05,min(0.95,p_fg))
#print logp_bg[:10]
#print logp_fg[:10]
#print p_fg
if i >= 5: break
color_fg = numpy.mean(image_raveled[fg, :], axis=0)
color_bg = numpy.mean(image_raveled[~fg, :], axis=0)
#color_fg = fit(fg)
#color_bg = fit(~fg)
#offsets = image_raveled.copy()
#offsets[fg,:] -= color_fg #[fg,:]
#offsets[~fg,:] -= color_bg #[~fg,:]
#mv = stats.estimate_indivar(offsets)
#del offsets
#mv_fg = mv_bg = stats.estimate_multivar(offsets)
#icovar = stats.inverse_covariance(offsets)
#icovar_fg = stats.inverse_covariance(image_raveled[fg,:] - color_fg[None,:])
#icovar_bg = stats.inverse_covariance(image_raveled[~fg,:] - color_bg[None,:])
# mv_fg = stats.estimate_multivar(image_raveled[fg,:] - color_fg[fg,:])
# mv_bg = stats.estimate_multivar(image_raveled[~fg,:] - color_bg[~fg,:])
i += 1
fg = numpy.reshape(fg, (height, width))
pred = None
del color_fg, color_bg
print prefix, 'Detect size'
sizer = 1.0
n1 = numpy.sum(fg)
while True:
n2 = numpy.sum(images.erode(fg, sizer))
if n2 < n1 * 0.3: break
sizer += 0.1
print prefix, 'Size', sizer
print prefix, 'Cleave'
cores = images.cleave(fg, sizer)
print prefix, 'Segment'
core_labels, num_features = ndimage.label(cores)
#dist = ndimage.distance_transform_edt(~cores)
#dist = -ndimage.distance_transform_edt(fg)
dist = images.hessian(ndimage.gaussian_filter(fg.astype('float64'),
sizer)).i1
labels = morphology.watershed(dist, core_labels, mask=fg)
#===
#Remap labels to eliminate border cells and small cells
bad_labels = set()
for x in xrange(width):
bad_labels.add(labels[0, x])
bad_labels.add(labels[height - 1, x])
for y in xrange(height):
bad_labels.add(labels[y, 0])
bad_labels.add(labels[y, width - 1])
threshold = sizer * sizer * min_area
print prefix, 'Min cell area', threshold
areas = numpy.zeros(num_features + 1, 'int32')
for i in numpy.ravel(labels):
areas[i] += 1
for i in xrange(1, num_features + 1):
if areas[i] < threshold:
bad_labels.add(i)
mapping = numpy.zeros(num_features + 1, 'int32')
j = 1
for i in xrange(1, num_features + 1):
if i not in bad_labels:
mapping[i] = j
j += 1
labels = mapping[labels]
bounds = [
images.Rect(item[1].start, item[0].start, item[1].stop - item[1].start,
item[0].stop - item[0].start)
for item in ndimage.find_objects(labels)
]
labels -= 1 #Labels start from zero, index into bounds
print prefix, 'Saving'
#test = color.label2rgb(labels-1, image)
border = ndimage.maximum_filter(
labels, size=(3, 3)) != ndimage.minimum_filter(labels, size=(3, 3))
test = image.copy()
test[border, :] = 0.0
test[cores, :] *= 0.5
test[cores, :] += 0.5
#test[~fg,1] = 1.0
#test[cores,2] = 1.0
#test[:,:,1] = hatmax * 10.0
#test[good,1] = hatmax
#test[bounds[0]][:,:,1] = 1.0
#test[labels == 0,2] = 1.0
images.save(prefix + '-debug.png', test)
#test2 = image.copy()
#test2 /= numpy.reshape(color_fg, (height,width,3))
#images.save(prefix+'-corrected.png', test2)
images.save(prefix + '.png', image)
result = Segmentation()
result.n_cells = len(bounds)
result.sizer = sizer
result.labels = labels
result.bounds = bounds
util.save(prefix + '-segmentation.pgz', result)
util.clear(prefix + '-measure.pgz')
util.clear(prefix + '-classification.pgz')
util.save(prefix + '-labels.pgz', [None] * result.n_cells)
print prefix, 'Done'
def gradient_field(im):
im = skimage_filter.gaussian_filter(im, 1.0)
gradx = np.hstack([im[:, 1:], im[:, -2:-1]]) - np.hstack([im[:, 0:1], im[:, :-1]])
grady = np.vstack([im[1:, :], im[-2:-1, :]]) - np.vstack([im[0:1, :], im[:-1, :]])
return gradx, grady