Python skimage.draw.ellipse() Examples
The following are 8
code examples of skimage.draw.ellipse().
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Example #1
| Source File: geometry.py From phidl with MIT License | 6 votes |
|
def _expand_raster(raster, distance = (4,2)):
try:
from skimage import draw, morphology
except:
raise ImportError("""
The fill function requires the module "scikit-image"
to operate. Please retry after installing scikit-image:
$ pip install --upgrade scikit-image """)
if distance[0] <= 0.5 and distance[1] <= 0.5: return raster
num_pixels = np.array(np.ceil(distance), dtype = int)
neighborhood = np.zeros((num_pixels[1]*2+1, num_pixels[0]*2+1), dtype=np.bool)
rr, cc = draw.ellipse(num_pixels[1], num_pixels[0], distance[1]+0.5, distance[0]+0.5)
neighborhood[rr, cc] = 1
return morphology.binary_dilation(image = raster, selem=neighborhood)
Example #2
| Source File: geometry.py From phidl with MIT License | 5 votes |
|
def ellipse(radii = (10,5), angle_resolution = 2.5, layer = 0):
"""Generate an ellipse geometry.
Parameters
----------
radii : tuple
Semimajor (x) and semiminor (y) axis lengths of the ellipse.
angle_resolution : float
Resolution of the curve of the ring (# of degrees per point).
layer : int, array-like[2], or set
Specific layer(s) to put polygon geometry on.
Returns
-------
A Device with an ellipse polygon in it
"""
D = Device(name = 'ellipse')
a = radii[0]
b = radii[1]
t = np.linspace(0, 360, int(np.ceil(360/angle_resolution) + 1))*pi/180
r = a*b/(sqrt((b*cos(t))**2 + (a*sin(t))**2))
xpts = r*cos(t)
ypts = r*sin(t)
D.add_polygon(points = (xpts,ypts), layer = layer)
return D
Example #3
| Source File: layer.py From uchroma with GNU Lesser General Public License v3.0 | 5 votes |
|
def ellipse(self, row: int, col: int, radius_r: float, radius_c: float,
color: ColorType, fill: bool=False, alpha: float=1.0) -> 'Layer':
"""
Draw an ellipse centered on the specified row and column,
with the given radiuses.
:param row: Center row of ellipse
:param col: Center column of ellipse
:param radius_r: Radius of ellipse on y axis
:param radius_c: Radius of ellipse on x axis
:param color: Color to draw with
:param fill: True if the circle should be filled
:return: This frame instance
"""
if fill:
rr, cc = draw.ellipse(row, col, math.floor(radius_r), math.floor(radius_c),
shape=self.matrix.shape)
self._draw(rr, cc, color, alpha)
else:
rr, cc = draw.ellipse_perimeter(row, col, math.floor(radius_r), math.floor(radius_c),
shape=self.matrix.shape)
self._draw(rr, cc, color, alpha)
return self
Example #4
| Source File: test_descriptors.py From pyImSegm with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
def test_ray_features_ellipse(self):
seg = np.ones((400, 600), dtype=bool)
x, y = draw.ellipse(200, 250, 120, 200, rotation=np.deg2rad(30),
shape=seg.shape)
seg[x, y] = False
points = [(200, 250), (150, 200), (250, 300)]
for i, point in enumerate(points):
ray_dist_raw = compute_ray_features_segm_2d(
seg, point, angle_step=ANGULAR_STEP)
# ray_dist, shift = seg_fts.shift_ray_features(ray_dist_raw)
points = reconstruct_ray_features_2d(point, ray_dist_raw)
p_fig = export_ray_results(seg, point, points, ray_dist_raw, [],
'ellipse-%i.png' % i)
self.assertTrue(os.path.exists(p_fig))
Example #5
| Source File: drawing.py From pyImSegm with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
def ellipse(r, c, r_radius, c_radius, orientation=0., shape=None):
""" temporary wrapper until release New version scikit-image v0.13
.. note:: Should be solved in skimage v0.13
:param int r: center position in rows
:param int c: center position in columns
:param int r_radius: ellipse diam in rows
:param int c_radius: ellipse diam in columns
:param float orientation: ellipse orientation
:param tuple(int,int) shape: size of output mask
:return tuple(list(int),list(int)): indexes of filled positions
>>> img = np.zeros((14, 20), dtype=int)
>>> rr, cc = ellipse(7, 10, 3, 9, np.deg2rad(30), img.shape)
>>> img[rr, cc] = 1
>>> img
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, 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, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
"""
rr, cc = draw.ellipse(r, c, r_radius, c_radius,
rotation=orientation, shape=shape)
# alternative version
# rr, cc = _ellipse(r, c, r_radius, c_radius, orientation, shape)
return rr, cc
Example #6
| Source File: drawing.py From pyImSegm with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
def ellipse_perimeter(r, c, r_radius, c_radius, orientation=0., shape=None):
""" see New version scikit-image v0.14
.. note:: Should be solved in skimage v0.14
:param int r: center position in rows
:param int c: center position in columns
:param int r_radius: ellipse diam in rows
:param int c_radius: ellipse diam in columns
:param float orientation: ellipse orientation
:param tuple(int,int) shape: size of output mask
:return tuple(list(int),list(int)): indexes of filled positions
>>> img = np.zeros((14, 20), dtype=int)
>>> rr, cc = ellipse_perimeter(7, 10, 3, 9, np.deg2rad(30), img.shape)
>>> img[rr, cc] = 1
>>> img
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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
"""
rr, cc = draw.ellipse_perimeter(r, c, r_radius, c_radius,
orientation=-orientation, shape=shape)
return rr, cc
Example #7
| Source File: drawing.py From pyImSegm with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
def figure_ellipse_fitting(img, seg, ellipses, centers, crits, fig_size=9):
""" show figure with result of the ellipse fitting
:param ndarray img: image
:param ndarray seg: segmentation
:param list(tuple(int,int,int,int,float)) ellipses: collection of ellipse parameters
ell. parameters: (x, y, height, width, orientation)
:param list(tuple(int,int)) centers: points
:param list(float) crits:
:param float fig_size: maximal figure size
:return Figure:
>>> img = np.random.random((100, 150, 3))
>>> seg = np.random.randint(0, 2, (100, 150))
>>> ells = np.random.random((3, 5)) * 25
>>> centers = np.random.random((3, 2)) * 25
>>> crits = np.random.random(3)
>>> fig = figure_ellipse_fitting(img[:, :, 0], seg, ells, centers, crits)
>>> isinstance(fig, matplotlib.figure.Figure)
True
"""
assert len(ellipses) == len(centers) == len(crits), \
'number of ellipses (%i) and centers (%i) and criteria (%i) ' \
'should match' % (len(ellipses), len(centers), len(crits))
fig, ax = create_figure_by_image(img.shape[:2], fig_size)
assert img.ndim == 2, \
'required image dimension is 2 to instead %r' % img.shape
ax.imshow(img, cmap=plt.cm.Greys_r)
for i, params in enumerate(ellipses):
c1, c2, h, w, phi = params
rr, cc = ellipse_perimeter(int(c1), int(c2), int(h), int(w), phi)
ax.plot(cc, rr, '.', color=COLORS[i % len(COLORS)],
label='#%i with crit=%d' % ((i + 1), int(crits[i])))
ax.legend(loc='lower right')
# plt.plot(centers[:, 1], centers[:, 0], 'ow')
for i in range(len(centers)):
ax.plot(centers[i, 1], centers[i, 0], 'o',
color=COLORS[i % len(COLORS)])
ax.set(xlim=[0, seg.shape[1]], ylim=[seg.shape[0], 0])
ax.axis('off')
fig.subplots_adjust(left=0, right=1, top=1, bottom=0)
return fig
Example #8
| Source File: drawing.py From pyImSegm with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
def draw_eggs_ellipse(mask_shape, pos_ant, pos_lat, pos_post,
threshold_overlap=0.6):
""" from given 3 point estimate the ellipse
:param tuple(int,int) mask_shape:
:param [tuple(int,int)] pos_ant: anterior
:param [tuple(int,int)] pos_lat: latitude
:param [tuple(int,int)] pos_post: postlude
:param float threshold_overlap:
:return ndarray:
>>> pos_ant, pos_lat, pos_post = [10, 10], [20, 20], [35, 20]
>>> points = np.array([pos_ant, pos_lat, pos_post])
>>> _= plt.plot(points[:, 0], points[:, 1], 'og')
>>> mask = draw_eggs_ellipse([30, 50], [pos_ant], [pos_lat], [pos_post])
>>> mask.shape
(30, 50)
>>> _= plt.imshow(mask, alpha=0.5, interpolation='nearest')
>>> _= plt.xlim([0, mask.shape[1]]), plt.ylim([0, mask.shape[0]]), plt.grid()
>>> # plt.show()
"""
mask_eggs = np.zeros(mask_shape)
for i, (ant, lat, post) in enumerate(zip(pos_ant, pos_lat, pos_post)):
ant, lat, post = map(np.array, [ant, lat, post])
center = ant + (post - ant) / 2.
lat_proj = closest_point_on_line(ant, post, lat)
# http://stackoverflow.com/questions/433371/ellipse-bounding-a-rectangle
radius_a = (np.linalg.norm(post - ant) / 2. / np.sqrt(2)) * 1.
radius_b = (np.linalg.norm(lat - lat_proj) / np.sqrt(2)) * 1.
angle = np.arctan2(*(post - ant))
rr, cc = ellipse(int(center[1]), int(center[0]),
int(radius_a), int(radius_b),
orientation=angle, shape=mask_eggs.shape)
mask = np.zeros(mask_shape)
mask[rr, cc] = True
# mask = ndimage.morphology.binary_fill_holes(mask)
# distance = ndimage.distance_transform_edt(mask)
# probab = distance / np.max(distance)
# mask = probab >= threshold_dist
m_overlap = np.sum(np.logical_and(mask > 0, mask_eggs > 0)) / float(np.sum(mask))
if m_overlap > threshold_overlap:
logging.debug('skip egg drawing while it overlap by %f', m_overlap)
continue
mask_eggs[mask.astype(bool)] = i + 1
return mask_eggs
