def test__verify_not_aligned(self):
import bezier
edge0 = bezier.Curve(np.asfortranarray([[0.0], [0.0]]), 1)
edge1 = bezier.Curve(self.NODES1, 2)
with self.assertRaises(ValueError):
self._make_one(edge0, edge1)
def test_convergence(self):
import bezier
nodes1 = np.asfortranarray(
[[0.0, 0.25, 0.5, 0.75, 1.0], [0.0, 1.0, -0.75, 1.0, 0.0]]
)
curve1 = bezier.Curve(nodes1, degree=4)
# Vertical line forces a unique solution.
nodes2 = np.asfortranarray([[0.5, 0.5], [0.0, 1.0]])
curve2 = bezier.Curve(nodes2, degree=1)
num_guess = 4
parameters = np.zeros((2, num_guess), order="F")
# NOTE: This means our "first" guess is (s, t) = (0, 0).
for guess in range(1, num_guess):
prev_s, prev_t = parameters[:, guess - 1]
parameters[:, guess] = self._call_function_under_test(
prev_s, nodes1, prev_t, nodes2
)
expected = np.asfortranarray(
[[0.0, 0.5, 0.5, 0.5], [0.0, 2.0, 0.21875, 0.21875]]
)
self.assertEqual(parameters, expected)
# Make sure that we've actually converged.
exact_s, exact_t = parameters[:, -1]
self.assertEqual(curve1.evaluate(exact_s), curve2.evaluate(exact_t))
def drawPath(map1, G, points):
#compute shortest paths for all points
path = []
for i in range(0, len(points) - 1):
path.append(
nx.shortest_path(G,
source=len(map1[0]) * points[i][0] + points[i][1],
target=len(map1[0]) * points[i + 1][0] +
points[i + 1][1]))
paths_draw = []
for i in range(0, len(path)):
paths_draw.append(np.reshape(map1[:, :, 0],
(len(map1) * len(map1[1]))))
paths_draw[i][path[i]] = 150
paths_draw[i] = np.reshape(paths_draw[i], (len(map1), len(map1[1])))
plt.ioff()
plt.figure(figsize=(10, 10))
nodes = np.asfortranarray([
[0.0],
[0.0],
])
curve = bezier.Curve(nodes, degree=2)
ax = curve.plot(num_pts=256)
#Draw all bezier curves one by one on the same plot
for i in range(0, len(path)):
controlX = np.zeros(len(path[i]))
controlY = np.zeros(len(path[i]))
for j in range(0, len(path[i])):
controlY[j] = len(map1) - path[i][j] / len(map1[0])
controlX[j] = path[i][j] % len(map1[0])
nodes = np.asfortranarray([
controlX,
controlY,
])
curve = bezier.Curve(nodes, degree=2)
normalizedCurve = curve.nodes
normalizedCurve[0] = normalizedCurve[0] / len(map1[0])
normalizedCurve[1] = normalizedCurve[1] / len(map1)
#color of path
c0 = (255 - 244) * i / len(path) + 244
c1 = (237 - 160) * i / len(path) + 160
c2 = (160 - 101) * i / len(path) + 101
#curves on same plot
bezier.Curve(normalizedCurve, degree=10).plot(
num_pts=256, ax=ax, color=[c0 / 255.0, c1 / 255.0, c2 / 255.0])
#Save the image
plt.axis(xmin=0, ymin=0, xmax=1, ymax=1)
ax.set_axis_off()
plt.savefig("./flaskr/map/sPath.jpg", frameon=True, bbox_inches='tight')
def image1():
figure = plt.figure()
ax = figure.gca()
curve1 = bezier.Curve(COEFFS1, degree=2, _copy=False)
curve2 = bezier.Curve(COEFFS2, degree=2, _copy=False)
curve1.plot(256, ax=ax, color=plot_utils.BLUE)
ax.lines[-1].set_label("$b_0(s)$")
curve2.plot(256, ax=ax, color=plot_utils.GREEN)
ax.lines[-1].set_label("$b_1(t)$")
ax.plot(
[0.0],
[1.0],
marker="o",
markersize=4.0,
color="black",
linestyle="none",
)
ax.legend(fontsize=plot_utils.TEXT_SIZE)
ax.tick_params(labelsize=plot_utils.TICK_SIZE)
ax.axis("scaled")
figure.set_size_inches(5.4, 1.6)
figure.subplots_adjust(
left=0.05, bottom=0.09, right=0.99, top=0.99, wspace=0.2, hspace=0.2
)
filename = "tangent_intersection.pdf"
path = plot_utils.get_path("slides", filename)
figure.savefig(path)
print("Saved {}".format(filename))
plt.close(figure)
def extend_curve(curve_point_list, base_value, x_or_y, apply_extend=True):
""" Extends the curve to the given value.
Args:
curve_point_list:: [RPoint, RPoint, RPoint, RPoint]
4 RPoint objects forming a cubic bezier curve. The order is
[(start point), (control point1), (control point2), (end point)].
The extension works from the end point.
base_value:: int
The coordinate value of how far you want to extend. The curve
will extend to this value.
x_or_y:: str
If base_value is an x coordinate value, type 'x'.
If it is an y coordinate value, type 'y'.
apply_extend:: bool (default is True)
If it is True, the change is applied. Input False if you
do not want to apply the changes.
Returns:
nodes:: 2x4 numpy.ndarray (float)
The coordinate values of the result of the extension. The rows
represent the coordinates(x, y) and the columns represent 4 points
that form a cubic bezier curve. For example:
[[start_point_x, control_point_1_x, control_point_2_x, end_point_x]
[start_point_y, control_point_1_y, control_point_2_y, end_point_y]]
"""
if len(curve_point_list) != 4:
raise _InputError('curve_point_list: ' + str(curve_point_list), \
"The number of data is not correct. Need 4 RPoint objects in the list")
curve_x = [float(point.x) for point in curve_point_list]
curve_y = [float(point.y) for point in curve_point_list]
base_value = float(base_value)
nodes = np.asfortranarray([curve_x, curve_y])
curve = bezier.Curve(nodes, degree=3)
new_curve = curve.specialize(0, 2.5)
x_or_y = _make_lower_string(x_or_y)
if x_or_y == 'y':
nodes = np.asfortranarray([[0., 1000.], [base_value, base_value]])
elif x_or_y == 'x':
nodes = np.asfortranarray([[base_value, base_value], [0., 1000.]])
else:
raise _InputError("x_or_y: " + x_or_y, "Put 'x' or 'y'")
line = bezier.Curve(nodes, degree=1)
s_vals = new_curve.intersect(line)[0, :]
point = new_curve.evaluate(s_vals[0])
rate = new_curve.locate(point)
result_curve = new_curve.specialize(0, rate)
if apply_extend:
for i in range(4):
curve_point_list[i].position = (result_curve.nodes[0, i],
result_curve.nodes[1, i])
return result_curve.nodes
def _get_quadratics():
import bezier
nodes1 = np.asfortranarray([[0.0, 0.5, 1.0], [0.0, 1.0, 0.0]])
nodes2 = np.asfortranarray([[1.0, 0.5, 0.0], [0.75, -0.25, 0.75]])
curve1 = bezier.Curve(nodes1, degree=2)
curve2 = bezier.Curve(nodes2, degree=2)
return curve1, curve2
def test__verify_bad_dimension(self):
import bezier
nodes0 = np.asfortranarray([[1.0, 2.0], [1.0, 2.0]])
edge0 = bezier.Curve(nodes0, 1)
edge1 = bezier.Curve(self.NODES1, 2)
with self.assertRaises(ValueError):
self._make_one(edge0, edge1)
def test_constructor(self):
import bezier
edge0 = bezier.Curve(self.NODES0, 2)
edge1 = bezier.Curve(self.NODES1, 2)
curved_poly = self._make_one(edge0, edge1)
self.assertEqual(curved_poly._edges, (edge0, edge1))
self.assertEqual(curved_poly._num_sides, 2)
def test_constructor_with_metadata(self):
import bezier
edge0 = bezier.Curve(self.NODES0, 2)
edge1 = bezier.Curve(self.NODES1, 2)
metadata = ((0, 0.0, 0.5), (4, 0.5, 1.0))
curved_poly = self._make_one(edge0, edge1, metadata=metadata)
self.assertEqual(curved_poly._edges, (edge0, edge1))
self.assertEqual(curved_poly._num_sides, 2)
self.assertEqual(curved_poly._metadata, metadata)
def get_curve_scribble(region, min_srb=2, max_srb=4, sort=True):
# Draw random curves
num_lines = np.random.randint(min_srb, max_srb)
scribbles = []
lengths = []
eval_pts = np.linspace(0.0, 1.0, 1024)
if sort:
# Generate more anyway, pick the best k at last
num_gen = 10
else:
num_gen = num_lines
for _ in range(num_gen):
region_indices = np.argwhere(region)
include_idx = np.random.choice(region_indices.shape[0],
size=3,
replace=False)
y_nodes = np.asfortranarray([
[0.0, 0.5, 1.0],
region_indices[include_idx, 0],
])
x_nodes = np.asfortranarray([
[0.0, 0.5, 1.0],
region_indices[include_idx, 1],
])
x_curve = bezier.Curve(x_nodes, degree=2)
y_curve = bezier.Curve(y_nodes, degree=2)
x_pts = x_curve.evaluate_multi(eval_pts)
y_pts = y_curve.evaluate_multi(eval_pts)
this_scribble = np.zeros_like(region)
pts = np.stack([x_pts[1, :], y_pts[1, :]], 1)
pts = pts.reshape((-1, 1, 2)).astype(np.int32)
this_scribble = cv2.polylines(this_scribble, [pts],
isClosed=False,
color=(1),
thickness=3)
# Mask away path outside the allowed region, allow some error in labeling
allowed_error = np.random.randint(3, 7)
allowed_region = cv2.dilate(region, disk_kernel(allowed_error))
this_scribble = this_scribble * allowed_region
scribbles.append(this_scribble)
lengths.append(this_scribble.sum())
# Sort according to length, we want the long lines
scribbles = [
x for _, x in sorted(
zip(lengths, scribbles), key=lambda pair: pair[0], reverse=True)
]
scribble = sum(scribbles[:num_lines])
return (scribble > 0.5).astype(np.uint8)
def get_envelope(t_note_length,
sample_rate,
audio_length,
attack_percent=1.0,
attack_slope=0.5,
release_percent=25.0,
release_slope=0.5):
"""Create an attack sustain release amplitude envelope."""
i_attack = int(sample_rate * audio_length * (attack_percent / 100))
i_release = int(sample_rate * audio_length * (release_percent / 100))
i_tot = int(sample_rate * audio_length)
envelope = np.ones(i_tot)
def expand_slope(slope):
if (slope <= 0.5):
slope = ((slope * 2)**2) / 2
else:
slope = 1 - ((((1 - slope) * 2)**2) / 2)
return slope
# Bezier curve attack
a_slope = expand_slope(float(attack_slope))
a_curve_point = 1 - a_slope
a_nodes = np.asfortranarray([[0.0, a_curve_point, 1.0],
[0.0, a_slope, 1.0]])
a_curve = bezier.Curve(a_nodes, degree=2)
a_samples = np.linspace(0.0, 1.0, i_attack)
envelope[:i_attack] = a_curve.evaluate_multi(a_samples)[1]
# Bezier curve release
release_slope = 1 - release_slope
r_slope = expand_slope(float(release_slope))
r_curve_point = r_slope
r_nodes = np.asfortranarray([[0.0, r_curve_point, 1.0],
[1.0, r_slope, 0.0]])
r_curve = bezier.Curve(r_nodes, degree=2)
r_samples = np.linspace(0.0, 1.0, i_release)
envelope[-i_release:i_tot] = r_curve.evaluate_multi(r_samples)[1]
"""# Linear attack
envelope[:i_attack] = np.linspace(0.0, 1.0, i_attack)
# Linear release
envelope[-i_release:i_tot] = np.linspace(1.0, 0.0, i_release)"""
envelope = np.expand_dims(envelope, axis=1)
envelope = np.concatenate((envelope, envelope), axis=1)
return envelope
def image4():
figure, all_axes = plt.subplots(2, 7)
all_axes = all_axes.flatten()
nodes15 = np.asfortranarray([[0.25, 0.625, 1.0], [0.625, 0.25, 1.0]])
curve15 = bezier.Curve(nodes15, degree=2)
nodes25 = np.asfortranarray([[0.0, 0.25, 0.75, 1.0], [0.5, 1.0, 1.5, 0.5]])
curve25 = bezier.Curve(nodes25, degree=3)
color1 = plot_utils.BLUE
curve15.plot(256, ax=all_axes[0], color=color1)
color2 = plot_utils.GREEN
curve25.plot(256, ax=all_axes[0], color=color2)
choices1 = [1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1]
choices2 = [1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1]
first = curve15
second = curve25
for i in range(13):
ax = all_axes[i + 1]
index1 = choices1[i]
index2 = choices2[i]
first = first.subdivide()[index1]
second = second.subdivide()[index2]
first.plot(256, ax=ax, color=color1)
second.plot(256, ax=ax, color=color2)
# After splitting, put the bounding box on the previous axis.
prev_ax = all_axes[i]
add_patch(first, prev_ax, color1)
add_patch(second, prev_ax, color2)
for ax in all_axes:
ax.axis("equal")
ax.set_xticklabels([])
ax.set_yticklabels([])
figure.set_size_inches(6.4, 2.4)
figure.subplots_adjust(left=0.01,
bottom=0.01,
right=0.99,
top=0.99,
wspace=0.06,
hspace=0.04)
filename = "subdivision_linearized.pdf"
path = plot_utils.get_path("bezier-intersection", filename)
figure.savefig(path)
print("Saved {}".format(filename))
plt.close(figure)
def get_bezier(self, pnts):
try:
import bezier as bz
except:
print('To run this function, \'bezier\' sould be installed.')
return
#to well-bended curve
v1=(pnts[1]-pnts[0])/np.linalg.norm(pnts[1]-pnts[0])
v2=(pnts[2]-pnts[3])/np.linalg.norm(pnts[2]-pnts[3])
pnts[1]=pnts[1]+self.bending_factor*v1
pnts[2]=pnts[2]+self.bending_factor*v2
x=pnts[:,0].tolist(); y=pnts[:,1].tolist(); z=pnts[:,2].tolist();
nodes = np.asfortranarray([x,y,z])
curve = bz.Curve(nodes, degree=2)
stp=self.connect_step
steps=np.arange(0+stp, 1-stp, stp)
new_pnts=[]
for i in steps:
new_pnts.append(np.ravel(curve.evaluate(i)))
return np.array(new_pnts)
def LineString_to_jittered_bezier(ls,
n_midpoints=1,
xbias=0.,
xstd=0.,
ybias=0.,
ystd=0.,
normalized=True,
n_eval_points=50):
if normalized == True:
xbias = xbias * ls.length
xstd = xstd * ls.length
ybias = ybias * ls.length
ystd = ystd * ls.length
jitter_ls = add_jittered_midpoints(
ls,
n_midpoints=n_midpoints,
xbias=xbias,
xstd=xstd,
ybias=ybias,
ystd=ystd,
)
curve1 = bezier.Curve(np.asfortranarray(jitter_ls).T,
degree=n_midpoints + 1)
bez = curve1.evaluate_multi(np.linspace(0., 1., n_eval_points))
return sg.asLineString(bez.T)
def __calcBezier(self):
for i in range(int(self._endIdx / self._degree)):
if self._endList[i * self._degree][2] < 0:
self._endList[i * self._degree][2] += 2 * pi
for j in range(1, self._degree + 1):
delta = self._endList[i * self._degree +
j][2] - self._endList[i * self._degree +
j - 1][2]
if fabs(delta) > fabs(delta + 2 * pi):
self._endList[i * self._degree + j][2] += 2 * pi
curve = bezier.Curve(
self._endList[i * self._degree:(i + 1) * self._degree + 1, :],
degree=self._degree)
s_vals = np.linspace(0.0, 1.0, self._sampling)
if i == 0:
self._bezierList = curve.evaluate_multi(s_vals)
else:
self._bezierList = np.concatenate(
(self._bezierList, curve.evaluate_multi(s_vals)))
for j in range(self._degree + 1):
if self._endList[i * self._degree + j][2] >= pi:
self._endList[i * self._degree + j][2] -= 2 * pi
for j in range(self._sampling):
if self._bezierList[i * self._sampling + j][2] >= pi:
self._bezierList[i * self._sampling + j][2] -= 2 * pi
def layer2curves(self, layer, contours=None):
if contours is None:
contours = []
for path in layer.paths:
contour = []
for segment in path.segments:
pts = []
degree = 3
if len(segment.points) <= 1:
continue
if segment.type == "line":
pt0 = self.double((segment.points[0].x, segment.points[0].y))
pt1 = self.double((segment.points[1].x, segment.points[1].y))
pts = [pt0, pt0, pt1, pt1]
elif segment.type == "qcurve":
pts = [self.double((point.x, point.y)) for point in segment.points]
degree = 2
elif segment.type == "curve":
pts = [self.double((point.x, point.y)) for point in segment.points]
else:
continue
nodes = np.asfortranarray(pts)
curve = bezier.Curve(nodes, degree=degree)
contour.append(curve)
contours.append(contour)
for component in layer.components:
contours = self.layer2curves(Glyphs.font.glyphs[component.componentName].layers[0], contours)
return contours
def bezier_trajectory(start,
end,
dt,
max_v=0.4,
end_derivative_scale=0.5,
ramp=3):
"""
Computes a bezier fit to the start and end conditions, and returns a
sequence of points that smoothly coneys the robot to the desired target
configuration.
"""
x0, y0, th0 = start
x1, y1, th1 = end
r = end_derivative_scale
qs = np.array(
[
[x0, y0],
[x0 + r * np.cos(th0), y0 + r * np.sin(th0)],
[x1 - r * np.cos(th1), y1 - r * np.sin(th1)],
[x1, y1],
],
dtype=np.float64,
)
bezier_curve = bezier.Curve(qs.T, degree=3)
T = int(np.ceil(bezier_curve.length / dt / max_v))
s = get_ramp(ramp, T)
pts = bezier_curve.evaluate_multi(s).T
return s, pts, bezier_curve
def intersect_by_x(curve, xs: np.ndarray):
ys = []
for x in xs:
# 交点を求める為のX線上の直線
line1 = bezier.Curve(np.asfortranarray([[x, x], [-9999999999, 9999999999]]), degree=1)
try:
# 交点を求める（高精度は求めない）
intersections = curve.intersect(line1, _verify=False)
# tからyを求め直す
s_vals = np.asfortranarray(intersections[0, :])
# 評価する
es = curve.evaluate_multi(s_vals)
# 値が取れている場合、その値を設定する
if es.shape == (2, 1):
ys.append(es[1][0])
# 取れていない場合、無視
else:
ys.append(0)
except:
# エラーが起きた場合、無視
ys.append(0)
return np.array(ys, dtype=np.float)
def drawCurve(beg, ctrl, end, step):
turtle.penup()
turtle.goto(*beg)
turtle.pendown()
nodes = [
[beg[0], ctrl[0], end[0]],
[beg[1], ctrl[1], end[1]],
]
curve = bezier.Curve(nodes, degree=2)
interval = 1.0 / step
progress = interval
for i in range(step):
arr = curve.evaluate(progress)
pt = (arr[0][0], arr[1][0])
turtle.goto(*pt)
progress += interval
turtle.penup()
for pt in (beg, ctrl, end):
print(pt)
turtle.goto(*pt)
turtle.stamp()
turtle.pendown()
def plot_binvals(bin_centerpoints,
bin_vals,
tumor_short,
label,
vert_line_at_x=None):
curve, xnorm = binvals_fit(bin_centerpoints, bin_vals)
xvals = [c / xnorm for c in bin_centerpoints]
plt.scatter(xvals, bin_vals, marker="x", alpha=0.5)
plt.title("{} - {}".format(tumor_short, label))
plt.ylabel('fraction of donors with mutation in sample')
plt.xlabel('cdna length')
ax = plt.gca()
curve.plot(num_pts=256, ax=ax, color='red')
if vert_line_at_x:
x = vert_line_at_x / xnorm
plt.ylim([0.0, 0.3])
vertical_line = bezier.Curve(np.asfortranarray([[float(x),
float(x)],
[0.0, 0.75]]),
degree=1)
vertical_line.plot(num_pts=25, ax=ax, color='red')
plt.show()
def curveTo(self, *points):
pts = [self.double(self.__currentPoint)]
pts.extend([self.double(pt) for pt in points])
nodes = np.asfortranarray(pts)
curve = bezier.Curve(nodes, degree=self.degree)
self.current_contour.append(curve)
self.__currentPoint = points[-1]
def _calc_curve_override(self, curve: Curve):
if self.side_offset is None:
self.curve_override = None
else:
nodes = curve.curve.nodes
nodes[:, 0] = list(self.position)
self.curve_override = bezier.Curve(nodes, degree=2)
def plot_line(points):
points = np.array(points, dtype=int).T
curve = bezier.Curve(points, degree=points.shape[1] - 1)
s_vals = np.linspace(0.0, 1.0, 100) # 100 is the num of pionts
data = curve.evaluate_multi(s_vals)
data = tuple(data.T)
return data
def _qCurveToOne(self, pt1, pt2):
pts = [self.double(self.__currentPoint)]
pts.append(self.double(pt1))
pts.append(self.double(pt2))
nodes = np.asfortranarray(pts)
curve = bezier.Curve(nodes, degree=self.degree)
self.current_contour.append(curve)
def _get_bezier_curve(x1, x2): pi, ei = x1 pf, ef = x2 p1 = pi + D_1 * ei p2 = pf - D_1 * ef nodes = np.concatenate([pi, p1, p2, pf], axis=1) return bezier.Curve(nodes, degree=3)
def plot_glif(glyph_path, show_points=True):
""" Plotting .glif XML format file in UFO font data.
Args:
glyph_path:: str
"""
class _Point:
def __init__(self, x, y, type_):
self.x = x
self.y = y
self.type = type_
# subplot = plt.subplot(xlim=(0, xml_glyph.find('advance').attrib['width']),
# ylim=(0, 1000)) # TODO: Needs modify
xml_glyph = et.parse(glyph_path).getroot()
contours = xml_glyph.find('outline').getchildren()
curve_points = [_Point(p.attrib['x'], p.attrib['y'], p.attrib.get('type')) \
for p in contours[0].getchildren()[:4]]
nodes = np.asfortranarray([
[float(p.x) for p in curve_points],
[float(p.y) for p in curve_points]])
subplot = bezier.Curve(nodes, degree=3).plot(100) # TODO: width
for contour in contours:
points = [_Point(p.attrib['x'], p.attrib['y'], p.attrib.get('type')) \
for p in contour.getchildren()]
for idx, point in enumerate(points):
if point.type == 'line':
plot_line(subplot, [points[idx+i] for i in range(-1, 1)], show_points)
elif point.type == 'curve':
plot_curve(subplot, [points[idx+i] for i in range(-3, 1)], show_points)
else:
continue
plt.show()
def compute_edge_shape(location_nextlocs, location_prototype):
fmov = list()
weight = list()
for lid1 in location_nextlocs:
for lid2 in location_nextlocs[lid1]:
s = location_prototype[lid1]
e = location_prototype[lid2]
gap = 0.05 * abs(e[1] - s[1]) / 0.05
nodes = np.asfortranarray([
[
s[1], (s[1] + e[1]) / 2 + np.random.choice([gap, -gap]),
e[1]
],
[
s[0], (s[0] + e[0]) / 2 + np.random.choice([gap, -gap]),
e[0]
],
])
curve = bezier.Curve(nodes, degree=2)
val = curve.evaluate_multi(np.linspace(0.0, 1.0, 10))
x_val = val[0]
y_val = val[1]
mov = list()
for xv, yv in zip(x_val, y_val):
mov.append([xv, yv])
fmov.append(mov)
weight.append(np.log(location_nextlocs[lid1][lid2] * 10))
return fmov, weight
def curve_value_at_x(curve, x):
# strategy = bezier.curve.IntersectionStrategy.ALGEBRAIC fails with
# The only degrees supported at this time are 0, 1, 2, 3 and 4 (degree=11)
# crashing on arbitrarty intersection points - never figured out why
# File "src/bezier/_speedup.pyx", line 485, in bezier._speedup.curve_intersections
# ValueError: Curve intersection failed to converge to approximately linear subdivisions after 20 iterations.
# solved by renormalizing the x-range to [0, 1.0] interval
strategy = bezier.curve.IntersectionStrategy.GEOMETRIC
vertical_line = bezier.Curve(np.asfortranarray([[float(x),
float(x)], [-0.75,
0.75]]),
degree=1)
intersections = curve.intersect(
vertical_line,
strategy=strategy) # why is this plural? why two parameters?
s_vals = np.asfortranarray(intersections[0, :])
point = curve.evaluate_multi(s_vals)
# point is given as [[x],[y]]
if point.size == 2:
return point[1][0]
else:
return None
def binvals_fit(bin_centerpoints, bin_vals):
# decimation - Bezier chokes on too many points
superbin_size = int(len(bin_centerpoints) / 20)
x = [0]
y = [0]
for i in range(0, len(bin_centerpoints), superbin_size):
n = len(bin_centerpoints[i:i + superbin_size])
x.append(sum(bin_centerpoints[i:i + superbin_size]) / n)
y.append(sum(bin_vals[i:i + superbin_size]) / n)
xnorm = x[
-1] # bezier apparently does not like really big numbers (as in 10^5)
x = [e / xnorm for e in x]
nodes = np.asfortranarray([x, y])
curve = bezier.Curve(nodes, degree=2)
# plt.scatter(x, y)
# plt.title("test")
# plt.ylabel('fraction of donors with mutation in sample')
# plt.xlabel('cdna length')
# ax = plt.gca()
# curve.plot(num_pts=256, ax=ax, color = 'red')
# plt.ylim([0.0, 0.32])
# p = [float(x[-2]/2), float(161745)/norm]
# vertical_line = bezier.Curve(np.asfortranarray([[float(p[0]), float(p[0])],[0.0, 0.75]]), degree=1)
# vertical_line.plot(num_pts=25, ax=ax, color = 'red')
# vertical_line = bezier.Curve(np.asfortranarray([[float(p[1]), float(p[1])],[0.0, 0.75]]), degree=1)
# vertical_line.plot(num_pts=25, ax=ax, color = 'blue')
# plt.show()
# print(" %d %.3f" % (p[0]*norm, curve_value_at_x (curve, p[0])) )
# print(" %d %.3f" % (p[1]*norm, curve_value_at_x (curve, p[1])) )
# exit()
return curve, xnorm
def main():
# x = [0.0, 1.0, 2.0, 3.0]
# y = [0.0, 1.0, 2.0, 3.0]
# ps = [1.0, 2.0]
# this will crash with
# File "src/bezier/_speedup.pyx", line 485, in bezier._speedup.curve_intersections
# ValueError: Curve intersection failed to converge to approximately linear subdivisions after 20 iterations.
x = [0.0, 69708.0, 204470.0, 339500.0]
y = [0.000, 0.052, 0.141, 0.214]
ps = [237685.0, 161745.0]
# this, however, works
norm = x[-1]
x = [e / norm for e in x]
ps = [p / norm for p in ps]
nodes = np.asfortranarray([x, y])
curve = bezier.Curve(nodes, degree=2)
plt.scatter(x, y)
plt.title("test")
plt.ylabel('x')
plt.xlabel('y')
ax = plt.gca()
curve.plot(num_pts=256, ax=ax, color='red')
plt.ylim([0.0, y[-1] * 1.1])
vertical_lines = []
for p in ps:
vertical_lines.append(
bezier.Curve(np.asfortranarray([[float(p), float(p)], [0.0, 5.0]]),
degree=1))
for vl in vertical_lines:
vl.plot(num_pts=25, ax=ax, color='red')
plt.show()
for vl in vertical_lines:
intersections = curve.intersect(vl)
s_vals = np.asfortranarray(intersections[0, :])
point = curve.evaluate_multi(s_vals)
if point.size == 2:
print(" >> ", point[1][0])
else:
print(" >> ", "no return")
