def test_circle_model_residuals():
model = CircleModel()
model.params = (0, 0, 5)
assert_almost_equal(abs(model.residuals(np.array([[5, 0]]))), 0)
assert_almost_equal(abs(model.residuals(np.array([[6, 6]]))),
np.sqrt(2 * 6**2) - 5)
assert_almost_equal(abs(model.residuals(np.array([[10, 0]]))), 5)
def test_circle_model_residuals():
model = CircleModel()
model.params = (0, 0, 5)
assert_almost_equal(abs(model.residuals(np.array([[5, 0]]))), 0)
assert_almost_equal(abs(model.residuals(np.array([[6, 6]]))),
np.sqrt(2 * 6**2) - 5)
assert_almost_equal(abs(model.residuals(np.array([[10, 0]]))), 5)
class RadiusEstimator(RadialFinder):
'''Estimate vessel radius by fitting a circle'''
def __init__(self, img, threshold=0.2):
# The main idea of the algo is based on assumed radiual "symmetry"
# of the result. So when we fit the circle we don't want to work with
# all the pixels by just the "rim" ones for each angle
super(RadiusEstimator, self).__init__(
f=lambda x: x,
# For each ray, how do you find a rim?
reduction=lambda x: reduce_last(x, threshold * np.max(x)),
img=img)
# And we will be fitting a circle
self.model = CircleModel()
def __call__(self, img):
'''Estimate for the given image'''
x_, y_ = self.collect(img)
ii, = np.where(
np.logical_and(np.logical_and(x_ > 10, x_ < 80),
np.logical_and(y_ > 10, y_ < 80)))
x_, y_ = x_[ii], y_[ii]
self.model.estimate(np.c_[x_, y_])
# Give back the circle parameters
return self.model.params
def test_circle_model_predict():
model = CircleModel()
r = 5
model.params = (0, 0, r)
t = np.arange(0, 2 * np.pi, np.pi / 2)
xy = np.array(((5, 0), (0, 5), (-5, 0), (0, -5)))
assert_almost_equal(xy, model.predict_xy(t))
def test_circle_model_int_overflow():
xy = np.array([[1, 0], [0, 1], [-1, 0], [0, -1]], dtype=np.int32)
xy += 500
model = CircleModel()
model.estimate(xy)
assert_almost_equal(model.params, [500, 500, 1])
def test_circle_model_predict():
model = CircleModel()
r = 5
model.params = (0, 0, r)
t = np.arange(0, 2 * np.pi, np.pi / 2)
xy = np.array(((5, 0), (0, 5), (-5, 0), (0, -5)))
assert_almost_equal(xy, model.predict_xy(t))
def __init__(self, img, threshold=0.2):
# The main idea of the algo is based on assumed radiual "symmetry"
# of the result. So when we fit the circle we don't want to work with
# all the pixels by just the "rim" ones for each angle
super(RadiusEstimator, self).__init__(
f=lambda x: x,
# For each ray, how do you find a rim?
reduction=lambda x: reduce_last(x, threshold * np.max(x)),
img=img)
# And we will be fitting a circle
self.model = CircleModel()
def test_circle_model_insufficient_data():
model = CircleModel()
with expected_warnings(["Input data does not contain enough significant"]):
model.estimate(np.array([[1, 2], [3, 4]]))
with expected_warnings(["Input data does not contain enough significant"]):
model.estimate(np.ones((6, 2)))
with expected_warnings(["Input data does not contain enough significant"]):
model.estimate(np.array([[0, 0], [1, 1], [2, 2]]))
def fit(self, image):
B = image > 0.5 * np.max(image) #+3*np.std(image)
circle = CircleModel()
# Need a better model here
hull = array_convex_hull(B)
x_, y_ = hull.T
x_ = np.r_[x_, x_[0]]
y_ = np.r_[y_, y_[0]]
circle.estimate(np.c_[x_, y_])
# Plot ellipse
XC, YC, R = circle.params
x = XC + R * np.sin(self.thetas)
y = YC + R * np.cos(self.thetas)
self.params = (XC, YC, R)
return B, np.c_[x, y]
def test_ransac_shape():
# generate original data without noise
model0 = CircleModel()
model0.params = (10, 12, 3)
t = np.linspace(0, 2 * np.pi, 1000)
data0 = model0.predict_xy(t)
# add some faulty data
outliers = (10, 30, 200)
data0[outliers[0], :] = (1000, 1000)
data0[outliers[1], :] = (-50, 50)
data0[outliers[2], :] = (-100, -10)
# estimate parameters of corrupted data
model_est, inliers = ransac(data0, CircleModel, 3, 5, random_state=1)
# test whether estimated parameters equal original parameters
assert_almost_equal(model0.params, model_est.params)
for outlier in outliers:
assert outlier not in inliers
def test_ransac_shape():
# generate original data without noise
model0 = CircleModel()
model0.params = (10, 12, 3)
t = np.linspace(0, 2 * np.pi, 1000)
data0 = model0.predict_xy(t)
# add some faulty data
outliers = (10, 30, 200)
data0[outliers[0], :] = (1000, 1000)
data0[outliers[1], :] = (-50, 50)
data0[outliers[2], :] = (-100, -10)
# estimate parameters of corrupted data
model_est, inliers = ransac(data0, CircleModel, 3, 5,
random_state=1)
# test whether estimated parameters equal original parameters
assert_equal(model0.params, model_est.params)
for outlier in outliers:
assert outlier not in inliers
def fit(self, image):
B = np.zeros_like(image)
# Radial sample for maximum
x_, y_ = self.m.collect(image)
# We are only after points that are not too far
ii, = np.where(
np.logical_and(np.logical_and(x_ > 10, x_ < 80),
np.logical_and(y_ > 10, y_ < 80)))
x_ = x_[ii]
y_ = y_[ii]
B[x_, y_] = 1
circle = CircleModel()
circle.estimate(np.c_[x_, y_])
XC, YC, R = circle.params
x = XC + R * np.sin(self.thetas)
y = YC + R * np.cos(self.thetas)
self.params = (XC, YC, R)
return B, np.c_[x, y]
def test_circle_model_estimate():
# generate original data without noise
model0 = CircleModel()
model0.params = (10, 12, 3)
t = np.linspace(0, 2 * np.pi, 1000)
data0 = model0.predict_xy(t)
# add gaussian noise to data
random_state = np.random.RandomState(1234)
data = data0 + random_state.normal(size=data0.shape)
# estimate parameters of noisy data
model_est = CircleModel()
model_est.estimate(data)
# test whether estimated parameters almost equal original parameters
assert_almost_equal(model0.params, model_est.params, 0)
def test_circle_model_estimate():
# generate original data without noise
model0 = CircleModel()
model0.params = (10, 12, 3)
t = np.linspace(0, 2 * np.pi, 1000)
data0 = model0.predict_xy(t)
# add gaussian noise to data
random_state = np.random.RandomState(1234)
data = data0 + random_state.normal(size=data0.shape)
# estimate parameters of noisy data
model_est = CircleModel()
model_est.estimate(data)
# test whether estimated parameters almost equal original parameters
assert_almost_equal(model0.params, model_est.params, 1)
def fit_objects(image, fit_obj='circle'):
"""Fits objects in each region of the input image, returning the
parameters of each object.
Parameters
----------
image : (N, M) ndarray
Binary input image.
fit_obj : string, optional (default : 'circle')
Object to be fitted on the regions. Accepts the strings 'circle'
and 'ellipse'.
Returns
-------
image_fit : (N, M, 3) ndarray
An image with objects in green representing the fitted objects
labeling each region.
data_fit : array
The parameters for each object fitted. Each row corresponds to
a region present on the input image. Each column represents one
parameter of the fitted object. For fit_obj='circle', they are
the coordinates for the center of the circle, and the radius
(x_center, y_center, radius); for fit_obj='ellipse', they are
the coordinates for the center of the ellipse, the major and
minor axis and the orientation (x_center, y_center, minor_axis,
major_axis, theta).
Examples
--------
>>> from skcv.draw import draw_synthetic_circles
>>> from skimage import img_as_bool
>>> image = draw_synthetic_circles((512, 512), quant=20, shades=1,
seed=0)
>>> image_fit, data_fit = fit_objects(img_as_bool(image),
fit_obj='circle')
>>> from skcv.draw import draw_synthetic_ellipses
>>> from skimage import img_as_bool
>>> image = draw_synthetic_ellipses((512, 512), quant=20, shades=1,
seed=0)
>>> image_fit, data_fit = fit_objects(img_as_bool(image),
fit_obj='ellipse')
"""
image_fit = gray2rgb(image)
# checking labels.
img_label, num_objects = label(image, return_num=True)
if fit_obj == 'circle':
obj = CircleModel()
data_fit = np.zeros((num_objects, 3))
elif fit_obj == 'ellipse':
obj = EllipseModel()
data_fit = np.zeros((num_objects, 5))
for num in range(num_objects):
# finding the contour.
obj_contour = find_contours(img_label == num+1,
fully_connected='high',
level=0)
try:
# modelling image using obtained points.
obj.estimate(obj_contour[0])
data_fit[num] = obj.params
aux_fit = data_fit[num].astype(int)
if fit_obj == 'circle':
# drawing circle.
rows, cols = circle(aux_fit[0], aux_fit[1], aux_fit[2],
shape=image_fit.shape)
image_fit[rows, cols] = [False, True, False]
elif fit_obj == 'ellipse':
# drawing ellipse.
rows, cols = ellipse_perimeter(aux_fit[0], aux_fit[1],
aux_fit[2], aux_fit[3],
aux_fit[4],
shape=image_fit.shape)
image_fit[rows, cols] = [False, True, False]
except TypeError:
print('No sufficient points on region #', num)
return image_fit, data_fit
hsv = rgb2hsv(small)
deviations = []
for color in (0, 1, 2):
masked = ma.array(hsv[:, :, color], mask=~canvas.astype(np.bool))
deviations.append(masked.std())
mole.h = deviations[0]
mole.s = deviations[1]
mole.v = deviations[2]
# In[104]:
from skimage.measure import CircleModel
circle_model = CircleModel()
circle_model.estimate(contours[0])
symmetry = circle_model.residuals(contours[0]).mean()
mole.symmetry = symmetry
# In[125]:
diameter = (19.05 / coin_radius) * (circle_model.params[2])
mole.diameter = diameter
mole.status = 100
db.session.merge(mole)
db.session.commit()
def test_circle_model_invalid_input():
with testing.raises(ValueError):
CircleModel().estimate(np.empty((5, 3)))
max_ = np.argmax(vals)
first = (i[:c][max_], j[:c][max_], vals[max_])
vals = line_values[c:]
max_ = np.argmax(vals)
second = (i[c:][max_], j[c:][max_], vals[max_])
return first, second
# --------------------------------------------------------------------
if __name__ == '__main__':
from skimage.measure import EllipseModel, CircleModel
ellipse, circle = EllipseModel(), CircleModel()
from filters import normalize
import matplotlib
#matplotlib.use('AGG')
import matplotlib.pyplot as plt
import skimage.io as io
rpath = '/home/mirok/Downloads/MIRO_TSeries-01302019-0918-028_cycle_001_ch02_short_video-1.tif'
red_seq = io.imread(rpath)
red_nseq = normalize(red_seq)
gpath = '/home/mirok/Downloads/MIRO_TSeries-01302019-0918-028_cycle_001_ch01_short_video-1.tif'
green_seq = io.imread(gpath)
def grid_field_props(
A, maxima='centroid', allProps=True,
**kwargs):
"""
Extracts various measures from a spatial autocorrelogram
Parameters
----------
A : array_like
The spatial autocorrelogram (SAC)
maxima : str, optional
The method used to detect the peaks in the SAC.
Legal values are 'single' and 'centroid'. Default 'centroid'
allProps : bool, optional
Whether to return a dictionary that contains the attempt to fit an
ellipse around the edges of the central size peaks. See below
Default True
Returns
-------
props : dict
A dictionary containing measures of the SAC. Keys include:
* gridness score
* scale
* orientation
* coordinates of the peaks (nominally 6) closest to SAC centre
* a binary mask around the extent of the 6 central fields
* values of the rotation procedure used to calculate gridness
* ellipse axes and angle (if allProps is True and the it worked)
Notes
-----
The output from this method can be used as input to the show() method
of this class.
When it is the plot produced will display a lot more informative.
See Also
--------
ephysiopy.common.binning.autoCorr2D()
"""
A_tmp = A.copy()
A_tmp[~np.isfinite(A)] = -1
A_tmp[A_tmp <= 0] = -1
A_sz = np.array(np.shape(A))
# [STAGE 1] find peaks & identify 7 closest to centre
if 'min_distance' in kwargs:
min_distance = kwargs.pop('min_distance')
else:
min_distance = np.ceil(np.min(A_sz / 2) / 8.).astype(int)
peak_idx, field_labels = _get_field_labels(
A_tmp, neighbours=7, **kwargs)
# a fcn for the labeled_comprehension function that returns
# linear indices in A where the values in A for each label are
# greater than half the max in that labeled region
def fn(val, pos):
return pos[val > (np.max(val)/2)]
nLbls = np.max(field_labels)
indices = ndimage.labeled_comprehension(
A_tmp, field_labels, np.arange(0, nLbls), fn, np.ndarray, 0, True)
# turn linear indices into coordinates
coords = [np.unravel_index(i, np.shape(A)) for i in indices]
half_peak_labels = np.zeros_like(A)
for peak_id, coord in enumerate(coords):
xc, yc = coord
half_peak_labels[xc, yc] = peak_id
# Get some statistics about the labeled regions
# fieldPerim = bwperim(half_peak_labels)
lbl_range = np.arange(0, nLbls)
# meanRInLabel = ndimage.mean(A, half_peak_labels, lbl_range)
# nPixelsInLabel = np.bincount(np.ravel(half_peak_labels.astype(int)))
# sumRInLabel = ndimage.sum_labels(A, half_peak_labels, lbl_range)
# maxRInLabel = ndimage.maximum(A, half_peak_labels, lbl_range)
peak_coords = ndimage.maximum_position(
A, half_peak_labels, lbl_range)
# Get some distance and morphology measures
centre = np.floor(np.array(np.shape(A))/2)
centred_peak_coords = peak_coords - centre
peak_dist_to_centre = np.hypot(
centred_peak_coords.T[0],
centred_peak_coords.T[1]
)
closest_peak_idx = np.argsort(peak_dist_to_centre)
central_peak_label = closest_peak_idx[0]
closest_peak_idx = closest_peak_idx[1:np.min((7, len(closest_peak_idx)-1))]
# closest_peak_idx should now the indices of the labeled 6 peaks
# surrounding the central peak at the image centre
scale = np.median(peak_dist_to_centre[closest_peak_idx])
orientation = np.nan
orientation = grid_orientation(
centred_peak_coords, closest_peak_idx)
central_pt = peak_coords[central_peak_label]
x = np.linspace(-central_pt[0], central_pt[0], A_sz[0])
y = np.linspace(-central_pt[1], central_pt[1], A_sz[1])
xv, yv = np.meshgrid(x, y, indexing='ij')
dist_to_centre = np.hypot(xv, yv)
# get the max distance of the half-peak width labeled fields
# from the centre of the image
max_dist_from_centre = 0
for peak_id, _coords in enumerate(coords):
if peak_id in closest_peak_idx:
xc, yc = _coords
if np.any(xc) and np.any(yc):
xc = xc - np.floor(A_sz[0]/2)
yc = yc - np.floor(A_sz[1]/2)
d = np.max(np.hypot(xc, yc))
if d > max_dist_from_centre:
max_dist_from_centre = d
# Set the outer bits and the central region of the SAC to nans
# getting ready for the correlation procedure
dist_to_centre[np.abs(dist_to_centre) > max_dist_from_centre] = 0
dist_to_centre[half_peak_labels == central_peak_label] = 0
dist_to_centre[dist_to_centre != 0] = 1
dist_to_centre = dist_to_centre.astype(bool)
sac_middle = A.copy()
sac_middle[~dist_to_centre] = np.nan
if 'step' in kwargs.keys():
step = kwargs.pop('step')
else:
step = 30
try:
gridscore, rotationCorrVals, rotationArr = gridness(
sac_middle, step=step)
except Exception:
gridscore, rotationCorrVals, rotationArr = np.nan, np.nan, np.nan
im_centre = central_pt
if allProps:
# attempt to fit an ellipse around the outer edges of the nearest
# peaks to the centre of the SAC. First find the outer edges for
# the closest peaks using a ndimages labeled_comprehension
try:
def fn2(val, pos):
xc, yc = np.unravel_index(pos, A_sz)
xc = xc - np.floor(A_sz[0]/2)
yc = yc - np.floor(A_sz[1]/2)
idx = np.argmax(np.hypot(xc, yc))
return xc[idx], yc[idx]
ellipse_coords = ndimage.labeled_comprehension(
A, half_peak_labels, closest_peak_idx, fn2, tuple, 0, True)
ellipse_fit_coords = np.array([(x, y) for x, y in ellipse_coords])
from skimage.measure import EllipseModel
E = EllipseModel()
E.estimate(ellipse_fit_coords)
im_centre = E.params[0:2]
ellipse_axes = E.params[2:4]
ellipse_angle = E.params[-1]
ellipseXY = E.predict_xy(np.linspace(0, 2*np.pi, 50), E.params)
# get the min containing circle given the eliipse minor axis
from skimage.measure import CircleModel
_params = im_centre
_params.append(np.min(ellipse_axes))
circleXY = CircleModel().predict_xy(
np.linspace(0, 2*np.pi, 50), params=_params)
except (TypeError, ValueError): # non-iterable x and y i.e. ellipse coords fail
ellipse_axes = None
ellipse_angle = (None, None)
ellipseXY = None
circleXY = None
# collect all the following keywords into a dict for output
closest_peak_coords = np.array(peak_coords)[closest_peak_idx]
dictKeys = (
'gridscore', 'scale', 'orientation', 'closest_peak_coords',
'dist_to_centre', 'ellipse_axes',
'ellipse_angle', 'ellipseXY', 'circleXY', 'im_centre',
'rotationArr', 'rotationCorrVals')
outDict = dict.fromkeys(dictKeys, np.nan)
for thiskey in outDict.keys():
outDict[thiskey] = locals()[thiskey]
# neat trick: locals is a dict holding all locally scoped variables
return outDict
def test_circle_model_invalid_input():
assert_raises(ValueError, CircleModel().estimate, np.empty((5, 3)))
time_idx = np.arange(len(time))
my_times = split_jobs(comm, time_idx)
results = []
fig, ax = plt.subplots(1, 3, figsize=(20, 14))
for i in tqdm.tqdm(my_times):
ax[1].set_title('Time {} s'.format(i * 0.33))
image = red_nseq[i]
#hist, hist_centers = histogram(image, nbins=10)
#plt.figure()
#plt.plot(hist_centers, hist)
B = image > 0.5 * np.max(image) #+3*np.std(image)
ellipse, circle = EllipseModel(), CircleModel()
hull = array_convex_hull(B)
x_, y_ = hull.T
x_ = np.r_[x_, x_[0]]
y_ = np.r_[y_, y_[0]]
ellipse.estimate(np.c_[x_, y_])
circle.estimate(np.c_[x_, y_])
# Plot original
ax[0].imshow(red_nseq_bk[i])
# Auxiliary
ax[1].imshow(B)
blue = np.zeros_like(image)
ax[2].imshow(np.stack([red_nseq_bk[i], green_nseq[i], blue], axis=2))