def test_hessian_matrix(dtype):
square = np.zeros((5, 5), dtype=dtype)
square[2, 2] = 4
Hrr, Hrc, Hcc = hessian_matrix(square,
sigma=0.1,
order='rc',
use_gaussian_derivatives=False)
out_dtype = _supported_float_type(dtype)
assert all(a.dtype == out_dtype for a in (Hrr, Hrc, Hcc))
assert_almost_equal(
Hrr,
np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [2, 0, -2, 0, 2],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
assert_almost_equal(
Hrc,
np.array([[0, 0, 0, 0, 0], [0, 1, 0, -1, 0], [0, 0, 0, 0, 0],
[0, -1, 0, 1, 0], [0, 0, 0, 0, 0]]))
assert_almost_equal(
Hcc,
np.array([[0, 0, 2, 0, 0], [0, 0, 0, 0, 0], [0, 0, -2, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 2, 0, 0]]))
with expected_warnings(["use_gaussian_derivatives currently defaults"]):
# FutureWarning warning when use_gaussian_derivatives is not
# specified.
hessian_matrix(square, sigma=0.1, order='rc')
def apply_filters(images, sigmas):
""" Apply multiple filters to 'images'
"""
filtered_images = []
for img in images:
filtered = []
for sigma in sigmas:
for conv_filter in [
gaussian_filter, gaussian_laplace,
gaussian_gradient_magnitude
]:
filtered.append(conv_filter(img, sigma))
# *_eigenvals has changed from version 0.13 to 0.14.
try:
# v. 0.14
eigs_struc = structure_tensor_eigvals(
*structure_tensor(img, sigma=sigma))
eigs_hess = hessian_matrix_eigvals(
hessian_matrix(img, sigma=sigma, order="xy"))
except TypeError as e:
# v. 0.13
eigs_struc = structure_tensor_eigvals(
*structure_tensor(img, sigma=sigma))
eigs_hess = hessian_matrix_eigvals(
*hessian_matrix(img, sigma=sigma, order="xy"))
for eig_h, eig_s in zip(eigs_struc, eigs_hess):
filtered.append(eig_h)
filtered.append(eig_s)
filtered.append(equalize_hist(img))
#selem = disk(30)
#filtered.append(equalize(img, selem=selem))
filtered_images.append(filtered)
return np.array(filtered_images)
def ridge_filter_hessian(img, sigma=3):
""" Apply Hessian filtering to enhance vessel-like structures
Parameters
----------
img : numpy array
(n_rows, n_cols) grayscale input image
sigma : int
width of the Gaussian used for smoothing gradients
Returns
-------
i2 : numpy array
image same size image showing enhanced ridge like structures
"""
from skimage.feature import hessian_matrix, hessian_matrix_eigvals
from skimage.filters import threshold_otsu
from skimage.morphology import skeletonize
hxx, hxy, hyy = hessian_matrix(img, sigma=sigma)
i1, i2 = hessian_matrix_eigvals(hxx, hxy, hyy)
i2 = i2 <= threshold_otsu(i2)
i2 = skeletonize(i2)
return i2
def remove_ridges(image, width=6, threshold=160, dilation=1,
return_mask=False):
"""Detect ridges of width pixels using the highest eigenvector of the
Hessian matrix, then create a binarized mask with threshold and remove
it from image (set to black). Default values are optimized for text
detection and removal.
A dilation radius in pixels can be passed in to thicken the mask prior
to being applied."""
gray_image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
# The value of sigma is calculated according to Steger's work:
# An Unbiased Detector of Curvilinear Structures,
# IEEE Transactions on Pattern Analysis and Machine Intelligence,
# Vol. 20, No. 2, Feb 1998
# http://ieeexplore.ieee.org/document/659930/
sigma = (width / 2) / np.sqrt(3)
hxx, hxy, hyy = feature.hessian_matrix(gray_image, sigma=sigma, order='xy')
large_eigenvalues, _ = feature.hessian_matrix_eigvals(hxx, hxy, hyy)
mask = convert(large_eigenvalues)
mask = binarize_image(mask, method='boolean', threshold=threshold)
if dilation:
dilation = (2 * dilation) + 1
dilation_kernel = np.ones((dilation, dilation), np.uint8)
mask = cv2.dilate(mask, dilation_kernel)
return image, 255 - mask
def enhance_ridges(frame):
"""A ridge detection filter (larger hessian eigenvalue)"""
blurred = filters.gaussian(frame, 2)
sigma = 4.5
Hxx, Hxy, Hyy = feature.hessian_matrix(blurred, sigma=sigma, mode='nearest', order='xy')
ridges = feature.hessian_matrix_eigvals(Hxx, Hxy, Hyy)[1]
return np.abs(ridges)
def enhance_ridges(frame, mask=None):
"""Detect ridges (larger hessian eigenvalue)"""
blurred = filters.gaussian_filter(frame, 2)
Hxx, Hxy, Hyy = feature.hessian_matrix(blurred, sigma=4.5, mode="nearest")
ridges = feature.hessian_matrix_eigvals(Hxx, Hxy, Hyy)[0]
return np.abs(ridges)
def meijering(image, sigma, black_ridges=False):
# sigma equals the radius of the ridge being emphasized
print "Applying meijering filter ..."
image = image.astype(np.float64)
if black_ridges: image = -image
value = np.zeros(image.shape)
Hxx, Hxy, Hyy = hessian_matrix(image, sigma=sigma, order="rc")
b1 = Hxx + Hyy
b2 = Hxx - Hyy
d = np.sqrt(4 * Hxy * Hxy + b2 * b2)
L1 = (b1 + 2 * d) / 3.0
L2 = (b1 - 2 * d) / 3.0
vect1x = b2 + d
vect2x = b2 - d
vecty = 2 * Hxy
vectx = np.array([vect1x, vect2x])
sortedL, sortedvectx = sortbyabs(np.array([L1, L2]), auxiliary=vectx)
L = sortedL[1]
vectx = sortedvectx[0]
vectlen = np.sqrt(vectx**2 + vecty**2)
vectx /= vectlen
vecty /= vectlen
valL = np.where(L > 0, 0, L)
mask = np.abs(vecty) < np.cos(
np.deg2rad(ALLOWED_ANGLE)
) # make sure to remove unnecessary signals oriented close to the y-axis
valL[mask] = 0
valL = divide_nonzero(valL, np.min(valL))
vect = np.array([vectx, vecty])
print " -> complete!"
return valL, vect
def enhance_ridges(frame, mask=None):
"""Detect ridges (larger hessian eigenvalue)"""
blurred = filters.gaussian_filter(frame, 2)
Hxx, Hxy, Hyy = feature.hessian_matrix(blurred, sigma=4.5, mode='nearest')
ridges = feature.hessian_matrix_eigvals(Hxx, Hxy, Hyy)[0]
return np.abs(ridges)
def detect_ridges(gray, sigma=3.0):
# https://stackoverflow.com/questions/48727914/how-to-use-ridge-detection-filter-in-opencv
hxx, hxy, hyy = hessian_matrix(gray, sigma)
i1, i2 = hessian_matrix_eigvals(hxx, hxy, hyy)
maxima_ridges = i1
minima_ridges = i2
return maxima_ridges, minima_ridges
def detect_ridges_concurrent(data, logging=True):
"""Detects sulcus-like "ravines" from 3d image using modified hessian ridge detection
Args:
data (ndarray): 3-dimensional image data array.
logging (bool, optional): Process execution logging. Defaults to True.
"""
(xMax, _, _) = data.shape
P_COUNT = 4
H_elems = hessian_matrix(data, sigma=1)
with Pool(P_COUNT) as pool:
width = math.ceil(xMax / P_COUNT)
multi_res = [
pool.apply_async(p_main,
(width * i, min(width *
(i + 1), xMax), H_elems, logging))
for i in range(P_COUNT)
]
results = [res.get(timeout=300) for res in multi_res]
output_data = np.zeros(data.shape)
for i in range(P_COUNT):
output_data += results[i]
if logging:
print("\nall processes completed")
return (output_data)
def meijering(image, black_ridges=True):
# sigma equals the radius of the ridge being emphasized
sigma = (FILAMENT_DIAMETER - FILAMENT_INNER_DIAMETER) / APIX / BIN / 2
image = image.astype(np.float64)
if black_ridges: image = -image
value = np.zeros(image.shape)
Hxx, Hxy, Hyy = hessian_matrix(image, sigma=sigma, order="rc")
b1 = Hxx + Hyy
b2 = Hxx - Hyy
d = np.sqrt(4 * Hxy * Hxy + b2 * b2)
L1 = (b1 + 2 * d) / 3.0
L2 = (b1 - 2 * d) / 3.0
vect1x = b2 + d
vect2x = b2 - d
vecty = 2 * Hxy
vectx = np.array([vect1x, vect2x])
sortedL, sortedvectx = sortbyabs(np.array([L1, L2]), auxiliary=vectx)
L = sortedL[1]
vectx = sortedvectx[0]
vectlen = np.sqrt(vectx**2 + vecty**2)
vectx /= vectlen
vecty /= vectlen
valL = np.where(L > 0, 0, L)
valL = divide_nonzero(valL, np.min(valL))
vect = np.array([vectx, vecty])
return valL, vect
def enhance_ridges(frame):
"""A ridge detection filter (larger hessian eigenvalue)"""
blurred = filters.gaussian_filter(frame, 2)
sigma = 4.5
Hxx, Hxy, Hyy = feature.hessian_matrix(blurred, sigma=sigma, mode='nearest')
ridges = feature.hessian_matrix_eigvals(Hxx, Hxy, Hyy)[0]
return np.abs(ridges)
def preprocess_image(image, out_skeleton=False, out_branching_image=False):
"""
Performs preprocessing of keratin images.
Returns:
- normalized ridges;
- branchings potential;
- branchings forces;
"""
# 1) Compute hessian matrix and find its eigen values
hxx, hxy, hyy = hessian_matrix(image, sigma=1.5)
eigenval_large = hessian_matrix_eigvals(hxx, hxy, hyy)[1]
# 2) Take largest eigenvalue and detect ridges
ridges = 1.0 - exposure.rescale_intensity(eigenval_large)
# 3) Normalize ridges
# 3.1) Calculate intensity histogram
hvals, hticks = exposure.histogram(ridges)
th0 = hticks[np.argmax(hvals)]
# 3.2) Rescale based on the peek-internsity (assumed to be background)
ridges_rescale = (ridges - th0) * INTENSITY_SCALE
# 3.3) Apply double-side thresholding
ridges_norm = double_threshold(ridges_rescale, INTENSITY_THRESHOLD_MIN,
INTENSITY_THRESHOLD_MAX)
# 4) Calculate and process binary mask
mask = ridges_norm > 0.1 # cv2.adaptiveThreshold(255 - (255 * ridges).astype(np.uint8), 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY, 11, 2) == 0
mask_denoised = remove_small_objects(mask, 50)
mask_connected = remove_small_holes(mask_denoised, 3)
# 5) Build skeleton
skeleton = skeletonize(mask_connected)
# skeleton = pruning(skeleton_raw, 15) # skeleton pruning
# 6) Find branching points
branching_points = np.logical_or(
branchedPoints(skeleton) > 0,
endPoints(skeleton) > 0)
branching_props = measure.regionprops(measure.label(branching_points),
cache=False)
branching_coords = np.array([prop.centroid
for prop in branching_props])[:, [1, 0]]
# branching_indices = np.where(branching_points)
# branching_coords = np.hstack([branching_indices[1].reshape(-1, 1), branching_indices[0].reshape(-1, 1)])
results = [ridges_norm, branching_coords, mask_connected]
if out_skeleton:
results.append(skeleton)
if out_branching_image:
results.append(branching_points)
# Return results
return tuple(results)
def track(self, frame1_grayscale_mat, frame2_grayscale_mat,
pos1_rotation_mat, pos1_translation):
print('track frame started')
octaves = SiftTrackerVadimFarutin.generate_differences_of_gaussians(
frame2_grayscale_mat)
extrema = []
for octave in octaves:
height, width = octave[0].shape
scale_x = self.frame_size[0] / width
scale_y = self.frame_size[1] / height
for i in range(1, len(octave) - 1):
Hxx, Hxy, Hyy = hessian_matrix(octave[i], order='rc')
histograms = SiftTrackerVadimFarutin.histograms(octave[i])
for x in range(1, width - 1):
for y in range(1, height - 1):
hessian = [Hxx[y][x], Hxy[y][x], Hyy[y][x]]
is_keypoint = SiftTrackerVadimFarutin.is_keypoint(
octave[i - 1], octave[i], octave[i + 1], x, y,
hessian)
if is_keypoint:
histogram = histograms[y][x][0][0]
orientation = np.argmax(histogram)
descriptor = SiftTrackerVadimFarutin.generate_descriptor(
octave[i], x, y)
extrema.append([
x * scale_x, y * scale_y, scale_x, scale_y,
orientation, descriptor
])
# Keypoint localization, find subpixel extrema
# Keypoint descriptor
# Match features
# keypoint_image = cv2.cvtColor(frame2_grayscale_mat, cv2.COLOR_GRAY2BGR)
# for keypoint in extrema:
# cv2.circle(keypoint_image,
# (int(keypoint[0]), int(keypoint[1])),
# 1, (0, 0, 255), 1)
# while True:
# cv2.imshow('keypoints', keypoint_image)
# if cv2.waitKey(1) & 0xFF == ord('q'):
# cv2.destroyAllWindows()
# break
pos2_rotation_mat = pos1_rotation_mat
pos2_translation = pos1_translation
print('track frame finished')
return pos2_rotation_mat, pos2_translation
def _frangi_hessian_common_filter(idx, image, sigmas, beta1, beta2):
"""
See skimage implementation and documentation.
Modified from skimage to facilitate intermediary caching
and the exponential scale to improve performance of frangi
when same images are being used multiple times.
(As is the case when using CMA-ES optimisations).
"""
# pylint: disable=too-many-locals
if np.any(np.asarray(sigmas) < 0.0):
raise ValueError("Sigma values less than zero are not valid")
beta1 = 2 * beta1**2
beta2 = 2 * beta2**2
filtered_array = np.zeros(sigmas.shape + image.shape)
lambdas_array = np.zeros(sigmas.shape + image.shape)
use_cache = idx is not None
if use_cache:
ensure_cache_dir_exists()
# Disable naming warnings as this is skimage code that I don't have time to rewrite.
# pylint: disable=invalid-name
# Filtering for all sigmas
for i, sigma in enumerate(sigmas):
key = str(idx) + ':' + str(sigma)
# idx of None implies do not use key
if use_cache and is_in_lambda_cache(key):
lambda1, rb, s2 = load_from_cache(key)
else:
# Make 2D hessian
D = hessian_matrix(image, sigma, order='rc')
# Correct for scale
D = np.array(D) * (sigma**2)
# Calculate (abs sorted) eigenvalues and vectors
lambda1, lambda2 = hessian_matrix_eigvals(D)
# Compute some similarity measures
lambda1[lambda1 == 0] = 1e-10
rb = (lambda2 / lambda1)**2
s2 = lambda1**2 + lambda2**2
if use_cache:
save_to_cache(key, (lambda1, rb, s2))
# Compute the output image
filtered = np.exp(
-rb / beta1) * (np.ones(np.shape(image)) - np.exp(-s2 / beta2))
# Store the results in 3D matrices
filtered_array[i] = filtered
lambdas_array[i] = lambda1
# pylint: enable=invalid-name
# pylint: enable=too-many-locals
return filtered_array, lambdas_array
def principal_directions(img, sigma, H=None):
"""
will ignore calculation of principal directions of masked areas
despite the name, this function actually returns the theta corresponding to
leading and trailing principal directions, i.e. angle w / x axis
"""
if H is None:
H = hessian_matrix(img, sigma)
Hxx, Hxy, Hyy = H
# check if input image is masked
try:
mask = img.mask
except AttributeError:
masked = False
else:
masked = True
dims = img.shape
# where to store
trailing_thetas = np.zeros_like(img)
leading_thetas = np.zeros_like(img)
# maybe implement a small angle correction
for i, (xx, xy, yy) in enumerate(np.nditer([Hxx, Hxy, Hyy])):
# grab the (x,y) coordinate of the hxx, hxy, hyy you're using
subs = np.unravel_index(i, dims)
# ignore masked areas (if masked array)
if masked and img.mask[subs]:
continue
h = np.array([[xx, xy], [xy, yy]]) # per-pixel hessian
l, v = eig(h) # eigenvectors as columns
# reorder eigenvectors by (increasing) magnitude of eigenvalues
v = v[:,np.argsort(np.abs(l))]
# angle between each eigenvector and positive x-axis
# arccos of first element (dot product with (1,0) and eigvec is already
# normalized)
trailing_thetas[subs] = np.arccos(v[0,0]) # first component of each
leading_thetas[subs] = np.arccos(v[0,1]) # first component of each
if masked:
leading_thetas = ma.masked_array(leading_thetas, mask)
trailing_thetas = ma.masked_array(trailing_thetas, mask)
return trailing_thetas, leading_thetas
def multiscale_seed_sequence(prob, l1_threshold=0, grid_density=10):
npoints = ((prob.shape[1] // grid_density) *
(prob.shape[2] // grid_density))
seeds = np.zeros(prob.shape, dtype=int)
for seed, p in zip(seeds, prob):
hm = feature.hessian_matrix(p, sigma=3)
l1, l2 = feature.hessian_matrix_eigvals(*hm)
curvy = (l1 > l1_threshold)
seed[:] = multiscale_regular_seeds(curvy, npoints)
return seeds
def detect_ridges(self, image, sigma=3.0):
pad = round(sigma * 3)
padded = np.pad(image, pad, 'edge')
hessian = hessian_matrix(padded, sigma, order="rc")
hessian[0] = np.zeros(hessian[0].shape)
hessian[1] = np.zeros(hessian[1].shape)
i1, i2 = hessian_matrix_eigvals(hessian)
i1 = i1[pad:image.shape[0] + pad, pad:image.shape[1] + pad]
i2 = i2[pad:image.shape[0] + pad, pad:image.shape[1] + pad]
return i1, i2
def test_hessian_matrix_3d():
cube = np.zeros((5, 5, 5))
cube[2, 2, 2] = 4
Hs = hessian_matrix(cube, sigma=0.1, order='rc')
assert len(Hs) == 6, ("incorrect number of Hessian images (%i) for 3D" %
len(Hs))
assert_almost_equal(
Hs[2][:, 2, :],
np.array([[0, 0, 0, 0, 0], [0, 1, 0, -1, 0], [0, 0, 0, 0, 0],
[0, -1, 0, 1, 0], [0, 0, 0, 0, 0]]))
def multiscale_seed_sequence(prob, l1_threshold=0, grid_density=10):
npoints = ((prob.shape[1] // grid_density) *
(prob.shape[2] // grid_density))
seeds = np.zeros(prob.shape, dtype=int)
for seed, p in zip(seeds, prob):
hm = feature.hessian_matrix(p, sigma=3)
l1, l2 = feature.hessian_matrix_eigvals(*hm)
curvy = (l1 > l1_threshold)
seed[:] = multiscale_regular_seeds(curvy, npoints)
return seeds
def derivatives(img, sigma):
# ALL RETURN VALUES ARE ARRAYS SAME SIZE AS img
# convolve with 0th derivative along axis 0 and 1st derivative along axis 1 gives us x-gradient
# x is axis 1, y is axis 0
rx = gaussian_filter(img.astype(np.float64), sigma = sigma, order = (0,1))
# vice versa
ry = gaussian_filter(img.astype(np.float64), sigma = sigma, order = (1,0))
# mode constant: used to handle image edges
rxx, rxy, ryy = hessian_matrix(img, sigma = sigma, mode = 'constant', cval = 0)
return rx, ry, rxx, rxy, ryy
def test_hessian_matrix_3d():
cube = np.zeros((5, 5, 5))
cube[2, 2, 2] = 4
Hs = hessian_matrix(cube, sigma=0.1, order='rc')
assert len(Hs) == 6, ("incorrect number of Hessian images (%i) for 3D" %
len(Hs))
assert_almost_equal(Hs[2][:, 2, :], np.array([[0, 0, 0, 0, 0],
[0, 1, 0, -1, 0],
[0, 0, 0, 0, 0],
[0, -1, 0, 1, 0],
[0, 0, 0, 0, 0]]))
def test_hessian_matrix_eigvals():
square = np.zeros((5, 5))
square[2, 2] = 1
Hxx, Hxy, Hyy = hessian_matrix(square, sigma=0.1)
l1, l2 = hessian_matrix_eigvals(Hxx, Hxy, Hyy)
assert_array_equal(
l1, np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]])
)
assert_array_equal(
l2, np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]])
)
def apply_filters(imDsets, lblDsets, sigma, gauss, gaussLaplace,
gaussGradientMagnitude, structTensor, hessEigenvalues):
for i in range(3):
for j in range(len(sigma)):
gauss.append(ndi.gaussian_filter(imDsets[i], sigma[j]))
gaussLaplace.append(ndi.gaussian_laplace(imDsets[i], sigma[j]))
gaussGradientMagnitude.append(
ndi.gaussian_gradient_magnitude(imDsets[i], sigma[j]))
structTensor.append(feat.structure_tensor(imDsets[i], sigma[j]))
hessianMat = feat.hessian_matrix(imDsets[i], sigma[j])
def hessian_and_theta(data, margin_cut=1):
# compute hessian matrices on the image
Hxx, Hxy, Hyy = hessian_matrix(data, sigma=3, order='xy')
lambda_plus = 0.5 * ((Hxx + Hyy) + np.sqrt((Hxx - Hyy)**2 + 4 * Hxy * Hxy))
lambda_minus = 0.5 * (
(Hxx + Hyy) - np.sqrt((Hxx - Hyy)**2 + 4 * Hxy * Hxy))
theta = 0.5 * np.arctan2(2 * Hxy, Hyy - Hxx) * 180 / np.pi
# remove the margins
lambda_minus = lambda_minus[margin_cut:-margin_cut, margin_cut:-margin_cut]
lambda_plus = lambda_plus[margin_cut:-margin_cut, margin_cut:-margin_cut]
theta = theta[margin_cut:-margin_cut, margin_cut:-margin_cut]
return lambda_plus, lambda_minus, theta
def ridge_filter_3D(im, sigma=3):
#crop = gaussian(crop, sigma=1)
H_elems = hessian_matrix(im, sigma=sigma)
#i1, i2 = hessian_matrix_eigvals(hxx, hxy, hyy)
eigs = hessian_matrix_eigvals(H_elems)
LambdaAbs1=abs(eigs[0]);
LambdaAbs2=abs(eigs[1]);
LambdaAbs3=abs(eigs[2]);
return LambdaAbs1, LambdaAbs2, LambdaAbs3
def hessian_response(im, sigma=3, threshold=0.05):
# # derivative in x direction of the image
# imx = np.zeros(im.shape)
# imxx = np.zeros(im.shape)
# filters.gaussian_filter(im, (sigma, sigma), (0, 1), imx)
# filters.gaussian_filter(imx, (sigma, sigma), (0, 1), imxx)
#
# # derivative in y direction of the image
# imy = np.zeros(im.shape)
# imyy = np.zeros(im.shape)
# filters.gaussian_filter(im, (sigma, sigma), (1, 0), imy)
# filters.gaussian_filter(imy, (sigma, sigma), (1, 0), imyy)
#
# imxy = np.zeros(im.shape)
# filters.gaussian_filter(imx, (sigma, sigma), (1, 0), imxy)
#
# Wxx = filters.gaussian_filter(imxx, sigma)
# Wxy = filters.gaussian_filter(imxy, sigma)
# Wyy = filters.gaussian_filter(imyy, sigma)
#
# H = np.array([[Wxx, Wxy],
# [Wxy, Wyy]])
#
from numpy import linalg as LA
from skimage.feature import hessian_matrix, hessian_matrix_eigvals
Hxx, Hxy, Hyy = hessian_matrix(im, sigma=0.1)
e_big, e_small = hessian_matrix_eigvals(Hxx, Hxy, Hyy)
#eiglast = 0.5 * (Wxx + Wyy + np.sqrt(Wxx**2 + 4*Wxy**2 - 2*Wxx*Wyy + Wyy**2 ))
# det_hes = Wxx * Wyy - Wxy ** 2
eiglast = e_big
# get maxima of the determinant
# det_thresh = eiglast.max() * threshold
# det_bin = (eiglast >= det_thresh) * 1
#
# coordinates = np.array(det_bin.nonzero()).T
x = [p[0] for p in coordinates]
y = [p[1] for p in coordinates]
edges = np.zeros(im.shape)
edges[x, y] = 1
pl.imshow(edges)
pl.gray()
pl.show()
return
def hessian(img): scales = [] s = 2 k = math.pow(2,0.25) for i in range(12): image = hessian_matrix_det(img, sigma=1.2*i) # image = hessian_matrix_det(img, sigma=math.pow(k,i)*s) Hrr, Hrc, Hcc = hessian_matrix(integral_image(img), sigma=math.pow(k,i)*s, order='rc') det = Hrr*Hcc - np.power((0.9*Hrc),2) scales.append(image) keypts = keypt(scales) return keypts
def test_hessian_matrix_eigvals():
square = np.zeros((5, 5))
square[2, 2] = 4
H = hessian_matrix(square, sigma=0.1, order='rc')
l1, l2 = hessian_matrix_eigvals(H)
assert_almost_equal(
l1,
np.array([[0, 0, 2, 0, 0], [0, 1, 0, 1, 0], [2, 0, -2, 0, 2],
[0, 1, 0, 1, 0], [0, 0, 2, 0, 0]]))
assert_almost_equal(
l2,
np.array([[0, 0, 0, 0, 0], [0, -1, 0, -1, 0], [0, 0, -2, 0, 0],
[0, -1, 0, -1, 0], [0, 0, 0, 0, 0]]))
def test_hessian_matrix():
square = np.zeros((5, 5))
square[2, 2] = 1
Hxx, Hxy, Hyy = hessian_matrix(square, sigma=0.1)
assert_array_equal(
Hxx, np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]])
)
assert_array_equal(
Hxy, np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]])
)
assert_array_equal(
Hyy, np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]])
)
def test_hessian_matrix_eigvals():
square = np.zeros((5, 5))
square[2, 2] = 1
Hxx, Hxy, Hyy = hessian_matrix(square, sigma=0.1)
l1, l2 = hessian_matrix_eigvals(Hxx, Hxy, Hyy)
assert_array_equal(
l1,
np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
assert_array_equal(
l2,
np.array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
def pre_process_image(self):
## self.image = cv.split(self.image)
## self.image = self.image[1]
self.image = filters.median(self.image, disk(self.median_value))
self.image = filters.gaussian(self.image, sigma=self.gaussian_sigma)
## self.image = morphology.erosion(self.image, disk(4))
## self.image = morphology.dilation(self.image, disk(2))
min = self.image.min()
max = self.image.max()
self.image = (self.image - min) / (max - min) * 255
self.image = self.image.astype(np.uint8)
self.image = self.image.astype(np.uint8)
hxx, hyy, hxy = hessian_matrix(self.image, 4.0, order="xy")
i1, i2 = hessian_matrix_eigvals(hxx, hxy, hyy)
i1 = self.normalize(i1)
i2 = self.normalize(i2)
i3 = i1 + self.invert_image(i2)
i3 = self.normalize(i3)
i3 = self.to_binary_image(i3, 0.3)
self.expert_image = self.normalize(self.expert_image)
self.expert_image = self.to_binary_image(self.expert_image, 0.5)
result_matrix = self.compare_images(i3, self.expert_image)
accuracy = self.get_accuracy(result_matrix)
sensitivity = self.get_sensitivity(result_matrix)
specificity = self.get_specificity(result_matrix)
# i1 = self.to_binary_image(i1, 0.5)
# i2 = self.to_binary_image(i2, 0.5)
# i3 = self.to_binary_image(i3, 0.3)
cv.imshow("i1", i1)
cv.waitKey(0)
cv.imshow("i2", i2)
cv.waitKey(0)
# i3 = morphology.dilation(i3, disk(self.dilation_value))
# i3 = morphology.erosion(i3, disk(self.erosion_value))
cv.imshow("i3", i3)
cv.waitKey(0)
cv.imshow("expert", self.expert_image)
cv.waitKey(0)
def hessian_eigvals_abs_sorted(volume):
N = volume.ndim
H = hessian_matrix(volume)
L = hessian_matrix_eigvals(H)
sorting = np.argsort(np.abs(L), axis=0)
res = []
for i in range(N):
newL = np.zeros_like(L[0])
for j in range(N):
newL[sorting[i, :] == j] = L[j, sorting[i, :] == j]
res.append(newL)
return res
def ridge_filter_hessian(img, sigma=3):
from skimage.feature import hessian_matrix, hessian_matrix_eigvals
from skimage.filters import threshold_otsu
from skimage.morphology import skeletonize
#assume you have an image img
hxx, hxy, hyy = hessian_matrix(img, sigma=sigma)
i1, i2 = hessian_matrix_eigvals(hxx, hxy, hyy)
i2 = i2 <= threshold_otsu(i2)
i2 = skeletonize(i2)
return i2
def test_hessian_matrix_eigvals(dtype):
square = np.zeros((5, 5), dtype=dtype)
square[2, 2] = 4
H = hessian_matrix(square, sigma=0.1, order='rc')
l1, l2 = hessian_matrix_eigvals(H)
out_dtype = _supported_float_type(dtype)
assert all(a.dtype == out_dtype for a in (l1, l2))
assert_almost_equal(
l1,
np.array([[0, 0, 2, 0, 0], [0, 1, 0, 1, 0], [2, 0, -2, 0, 2],
[0, 1, 0, 1, 0], [0, 0, 2, 0, 0]]))
assert_almost_equal(
l2,
np.array([[0, 0, 0, 0, 0], [0, -1, 0, -1, 0], [0, 0, -2, 0, 0],
[0, -1, 0, -1, 0], [0, 0, 0, 0, 0]]))
def read_image(self, image_name, size=None):
options = self.get_options()
if size:
im = np.array(Image.open(image_name).convert("L").resize(size))
else:
im = np.array(Image.open(image_name).convert("L"))
options["image"] = im
H_elems = hessian_matrix(**options)
feature = hessian_matrix_eigvals(H_elems)[0]
# plt.imshow(feature)
# plt.show()
return feature.reshape((1, feature.shape[0] * feature.shape[1]))[0]
def test_hessian_matrix_eigvals():
square = np.zeros((5, 5))
square[2, 2] = 4
Hrr, Hrc, Hcc = hessian_matrix(square, sigma=0.1, order='rc')
l1, l2 = hessian_matrix_eigvals(Hrr, Hrc, Hcc)
assert_almost_equal(l1, np.array([[0, 0, 2, 0, 0],
[0, 1, 0, 1, 0],
[2, 0, -2, 0, 2],
[0, 1, 0, 1, 0],
[0, 0, 2, 0, 0]]))
assert_almost_equal(l2, np.array([[0, 0, 0, 0, 0],
[0, -1, 0, -1, 0],
[0, 0, -2, 0, 0],
[0, -1, 0, -1, 0],
[0, 0, 0, 0, 0]]))
def _get_hessian_matrix_features(im, features_window_size, sigma_hm):
features_arr = np.empty(0)
center = im_center(im)
Hxx, Hxy, Hyy = feature.hessian_matrix(im, sigma=sigma_hm)
h1, h2 = feature.hessian_matrix_eigvals(Hxx, Hxy, Hyy)
h1 = utils.extract_pad_image(input_img=h1,
pt=center,
window_size=features_window_size)
h2 = utils.extract_pad_image(input_img=h2,
pt=center,
window_size=features_window_size)
h1 = arr_to_vec(h1)
h2 = arr_to_vec(h2)
features_arr = np.append(features_arr, h1)
features_arr = np.append(features_arr, h2)
return features_arr
def principal_directions(img, sigma, H=None):
"""2D only, handles masked arrays"""
if H is None:
Hxx, Hxy, Hyy = hessian_matrix(img, sigma)
try:
mask = img.mask
except AttributeError:
masked = False
else:
masked = True
dims = img.shape
# where to store
trailing_thetas = np.zeros_like(img)
leading_thetas = np.zeros_like(img)
# maybe implement a small angle correction
for i, (xx, xy, yy) in enumerate(np.nditer([Hxx, Hxy, Hyy])):
subs = np.unravel_index(i, dims)
# ignore masked areas (if masked array)
if masked and img.mask[subs]:
continue
h = np.array([[xx, xy], [xy, yy]]) # per-pixel hessian
l, v = eig(h) # eigenvectors as columns
# reorder eigenvectors by (increasing) magnitude of eigenvalues
v = v[:,np.argsort(np.abs(l))]
# angle between each eigenvector and positive x-axis
# arccos of first element (dot product with (1,0) and eigvec is already
# normalized)
trailing_thetas[subs] = np.arccos(v[0,0]) # first component of each
leading_thetas[subs] = np.arccos(v[0,1]) # first component of each
if masked:
leading_thetas = ma.masked_array(leading_thetas, img.mask)
trailing_thetas = ma.masked_array(trailing_thetas, img.mask)
return trailing_thetas, leading_thetas
def __init__(self, img=None, path=None, block_size=5):
if path and not img:
img = cv2.imread(path)
#img = Preprocess().blur_image(img)
self.block_size = block_size
self.img_rgb = img.copy()
self.img_hsv = cv2.cvtColor(img, cv2.COLOR_RGB2HSV)
#self.img_ycbcr = cv2.cvtColor(img, cv2.COLOR_RGB2YCrCb)
self.img_gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
self.height, self.width, _ = img.shape
self.Hxx, self.Hxy, self.Hyy = hessian_matrix(self.img_gray)
#vector, self.hog = hog(self.img_gray, orientations=8, pixels_per_cell=(3, 3),
# cells_per_block=(1, 1), visualise=True)
neighours = disk(25)
self.entropy = entropy(self.img_gray, neighours)
def test_hessian_matrix_eigvals_3d(im3d):
H = hessian_matrix(im3d)
E = hessian_matrix_eigvals(H)
# test descending order:
e0, e1, e2 = E
assert np.all(e0 >= e1) and np.all(e1 >= e2)
E0, E1, E2 = E[:, E.shape[1] // 2] # cross section
row_center, col_center = np.array(E0.shape) // 2
circles = [draw.circle_perimeter(row_center, col_center, radius,
shape=E0.shape)
for radius in range(1, E0.shape[1] // 2 - 1)]
response0 = np.array([np.mean(E0[c]) for c in circles])
response2 = np.array([np.mean(E2[c]) for c in circles])
# eigenvalues are negative just inside the sphere, positive just outside
assert np.argmin(response2) < np.argmax(response0)
assert np.min(response2) < 0
assert np.max(response0) > 0
def find_blobs_hessian(img):
size = 20
img0 = np.zeros((img.shape[0]+ 2*size, img.shape[1]+ 2*size))
img0[size:size+img.shape[0], size:size+img.shape[1]] = img
blobs = blob_doh(img0, max_sigma=10, num_sigma=10)
true_blobs = []
for y0, x0, b0 in blobs:
p0 = util.neighbour(img0, y0, x0, 1)
y, x = np.unravel_index(p0.argmax(), p0.shape)
y0 += y - 1
x0 += x - 1
p0 = util.neighbour(img0, y0, x0, 2*b0)
if True:
# method 1 (hessian diagonal)
hs0, hs1, hs2 = hessian_matrix(p0, 0.5*b0)
q0 = 0.5 *(hs0 + hs2)
if b0 >= 2 \
and b0 <= 8 \
and q0[2*b0,2*b0] > 0.95*util.neighbour(q0,2*b0,2*b0,b0).max():
true_blobs.append([y0,x0,b0])
else:
# method 2 (hessian determinant)
q0 = hessian_matrix_det(p0, b0)
print b0, q0[2*b0, 2*b0], util.neighbour(q0, 2*b0,2*b0,b0).max()
if b0 >= 2 \
and b0 <= 8 \
and q0[2*b0,2*b0] > 0.8*util.neighbour(q0,2*b0,2*b0,b0).max():
true_blobs.append([y0, x0, b0])
if len(true_blobs) > 0:
true_blobs = np.array(true_blobs) - [size, size, 0]
if len(blobs) > 0:
blobs = blobs - [size, size, 0]
return true_blobs, blobs
def test_hessian_matrix():
square = np.zeros((5, 5))
square[2, 2] = 4
Hrr, Hrc, Hcc = hessian_matrix(square, sigma=0.1, order='rc')
assert_almost_equal(Hrr, np.array([[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[2, 0, -2, 0, 2],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]]))
assert_almost_equal(Hrc, np.array([[0, 0, 0, 0, 0],
[0, 1, 0, -1, 0],
[0, 0, 0, 0, 0],
[0, -1, 0, 1, 0],
[0, 0, 0, 0, 0]]))
assert_almost_equal(Hcc, np.array([[0, 0, 2, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, -2, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 2, 0, 0]]))
matrix2d = np.random.rand(3, 3)
assert_warns(UserWarning, hessian_matrix, matrix2d, sigma=0.1)
#cv2.imshow('dst',img)
plt.figure(1); plt.clf();
plt.subplot(1,2,1)
plt.imshow(img);
plt.subplot(1,2,2)
plt.imshow(dst)
#if cv2.waitKey(0) & 0xff == 27:
# cv2.destroyAllWindows()
hess= ftr.hessian_matrix(img)
plt.figure(100); plt.clf();
for i in range(len(hess)):
plt.subplot(1,len(hess), i +1);
plt.imshow(hess[i]);
import imageprocessing.active_worm as aw;
img = exp.load_img(t = 500000)
img = cv2.GaussianBlur(img, (5,5), 1);
wm = aw.WormModel();
wm.from_image(img);
from skimage import io from skimage.feature import hessian_matrix, hessian_matrix_eigvals, hessian_matrix_det from skimage.filters import gaussian_filter from skimage.morphology import watershed, closing, opening from scipy.stats import logistic filename = "skeletons & matching cropped pics/cropped pics/v018-penn.9-1uB2D2-cropm.png" img = io.imread(filename) img = (img - np.mean(img)) / np.std(img) sigma = .75 Hxx, Hxy, Hyy = hessian_matrix(img, sigma=sigma, mode="wrap") e1, e2 = hessian_matrix_eigvals(Hxx, Hxy, Hyy) # How much bigger is the first eigenvalue's magnitude # compared with the second? log_condition = np.log(abs(e1/e2)) log_condition = log_condition / np.std(log_condition) out = logistic.cdf(log_condition) markers = np.zeros_like(out) markers[out < 0] = 1 markers[out > np.percentile(out, 90)] = 2
b = partial(plt.imshow, cmap=plt.cm.Blues)
sp = partial(plt.imshow, cmap=plt.cm.spectral)
s = plt.show
import time
img = get_preprocessed(mode='G')
for sigma in [0.5, 1, 2, 3, 5, 10]:
print('-'*80)
print('σ=',sigma)
print('calculating hessian H')
tic = time.time()
H = hessian_matrix(img, sigma=sigma)
toc = time.time()
print('time elapsed: ', toc - tic)
tic = time.time()
print('calculating hessian via FFT (F)')
h = fft_hessian(img, sigma)
toc = time.time()
print('time elapsed: ', toc - tic)
tic = time.time()
print('calculating principal curvatures for σ={}'.format(sigma))
K1,K2 = principal_curvatures(img, sigma=sigma, H=H)
toc = time.time()
print('time elapsed: ', toc - tic)
tic = time.time()
def principal_curvatures(img, sigma=1.0, H=None):
"""
Return the principal curvatures {κ1, κ2} of an image, that is, the
eigenvalues of the Hessian at each point (x,y). The output is arranged such
that |κ1| <= |κ2|.
Input:
img: An ndarray representing a 2D or multichannel image. If the image
is multichannel (e.g. RGB), then each channel will be proccessed
individually. Additionally, the input image may be a masked
array-- in which case the output will preserve this mask
identically.
PLEASE ADD SOME INFO HERE ABOUT WHAT SORT OF DTYPES ARE
EXPECTED/REQUIRED, IF ANY
sigma: (optional) The scale at which the Hessian is calculated.
H: (optional) provide sigma (else it will be calculated)
Output:
(K1, K2): A tuple where K1, K2 each are the exact dimension of the
input image, ordered in magnitude such that |κ1| <= |κ2|
in all locations. If *signed* option is used, then elements
of K1, K2 may be negative.
Example:
>>> K1, K2 = principal_curvatures(img)
>>> K1.shape == img.shape
True
>>> (K1 <= K2).all()
True
>> K1.mask == img.mask
True
"""
# determine if multichannel
multichannel = (img.ndim == 3)
if not multichannel:
# add a trivial dimension
img = img[:,:,np.newaxis]
K1 = np.zeros_like(img, dtype='float64')
K2 = np.zeros_like(img, dtype='float64')
for ic in range(img.shape[2]):
channel = img[:,:,ic]
# returns the tuple (Hxx, Hxy, Hyy)
if H is None:
H = hessian_matrix(channel, sigma=sigma)
# returns tuple (l1,l2) where l1 >= l2 but this *includes sign*
L = hessian_matrix_eigvals(*H)
L = np.dstack(L)
mag = np.argsort(abs(L), axis=-1)
# just some slice nonsense
ix = np.ogrid[0:L.shape[0], 0:L.shape[1], 0:L.shape[2]]
L = L[ix[0], ix[1], mag]
# now k2 is larger in absolute value, as consistent with Frangi paper
K1[:,:,ic] = L[:,:,0]
K2[:,:,ic] = L[:,:,1]
try:
mask = img.mask
except AttributeError:
pass
else:
K1 = ma.masked_array(K1, mask=mask)
K2 = ma.masked_array(K2, mask=mask)
# now undo the trivial dimension
if not multichannel:
K1 = np.squeeze(K1)
K2 = np.squeeze(K2)
return K1, K2