I have two sets of data. One is nominal form. The other is actual form. The problem is that when I wish to calculate the form error alone. It's a big problem when the two sets of data isn't "on top of each other". That gives errors that also include positional error.
Both curves are read from a series of data. The nominal shape (black) is made up from many different size radius that are tangent to each other. Its the leading edge of an airfoil profile.
I have tried various methods of "Best-Fit" I've found both here and on where ever google took me. But the problem is that they all smooth my "actual" data. So it get modified and is not keeping it's actual form.
Is there any function in scipy or any other python lib that "simply" can fit my two curves together without altering the actual shape?
I wish for the green curve with red dots to lie as much as possible on top of the black.
Might it be possible to calculate the center of gravity of both curves and then move the actual curve in x and y depending on the value difference from the center point? It might not be the ultimate solution, but it would get closer?
Here is a solution assuming that the nominal form can be described as a conic, i.a as solution of the equation ax^2 + by^2 + cxy + dx + ey = 1. Then, a least square fit can be applied to find the coefficients (a, b, c, d, e).
import numpy as np
import matplotlib.pylab as plt
# Generate example data
t = np.linspace(-2, 2.5, 25)
e, theta = 0.5, 0.3 # ratio minor axis/major & orientation angle major axis
c, s = np.cos(theta), np.sin(theta)
x = c*np.cos(t) - s*e*np.sin(t)
y = s*np.cos(t) + c*e*np.sin(t)
# add noise:
xy = 4*np.vstack((x, y))
xy += .08 *np.random.randn(*xy.shape) + np.random.randn(2, 1)
# Least square fit by a generic conic equation
# a*x^2 + b*y^2 + c*x*y + d*x + e*y = 1
x, y = xy
x = x - x.mean()
y = y - y.mean()
M = np.vstack([x**2, y**2, x*y, x, y]).T
b = np.ones_like(x)
# solve M*w = b
w, res, rank, s = np.linalg.lstsq(M, b, rcond=None)
a, b, c, d, e = w
# Get x, y coordinates for the fitted ellipse:
# using polar coordinates
# x = r*cos(theta), y = r*sin(theta)
# for a given theta, the radius is obtained with the 2nd order eq.:
# (a*ct^2 + b*st^2 + c*cs*st)*r^2 + (d*ct + e*st)*r - 1 = 0
# with ct = cos(theta) and st = sin(theta)
theta = np.linspace(-np.pi, np.pi, 97)
ct, st = np.cos(theta), np.sin(theta)
A = a*ct**2 + b*st**2 + c*ct*st
B = d*ct + e*st
D = B**2 + 4*A
radius = (-B + np.sqrt(D))/2/A
# Graph
plt.plot(radius*ct, radius*st, '-k', label='fitted ellipse');
plt.plot(x, y, 'or', label='measured points');
plt.axis('equal'); plt.legend();
plt.xlabel('x'); plt.ylabel('y');
Related
I have a set of data ([x[0],x[1]],y), many points in 3D space
and use scikit-learn to fit a learn model.
How I can calculate the distance between all the points to the fitting plane?
Does sklearn provide such function? I mean perpendicular distance.
My code works but too manually.
I am looking for an existing quick function in a package like sklearn.
Thanks.
def Linfit3D(x,y):
# x is a 2D array, they should be location of each bump, x_loc and y_loc
# y is the CTV or BTV that need to be fit to the least square plane
# three value will be returned, a,b, and c, which indicate a + b*x1 + c*x2 =y
model = sklearn.linear_model.LinearRegression()
model.fit(x, y)
coefs = model.coef_
intercept = model.intercept_
print("Equation: y = {:.5f} + {:.5f}*x1 + {:.5f}*x2".format(intercept, coefs[0],coefs[1]))
a=coefs[0]
b=coefs[1]
c=-1
d=intercept
return a,b,c,d
def point_to_plane_dist(x,y, a, b, c, d):
# the plane equation is: a*x + b*y + c*z + d = 0, and typically c=-1
# so the plane equation typicall is z = a*x + b*y + d
# and output has concerned the positive/negtive of point on top/bottom of the plane
f = abs((a * x[0] + b * x[1] + c * y + d))
e = (math.sqrt(a * a + b * b + c * c))
zp=a*x[0]+b*x[1]+d
# print('y = %2f, zp = %2f' %(y,zp))
if y>=zp:
return f/e
elif y<zp:
return (f/e)*(-1)
I looked at this code:
import numpy as np
from matplotlib import pyplot as plt
def dipole(m, r, r0):
"""
Calculation of field B in point r. B is created by a dipole moment m located in r0.
"""
# R = r - r0 - subtraction of elements of vectors r and r0, transposition of array
R = np.subtract(np.transpose(r), r0).T
# Spatial components of r are the outermost axis
norm_R = np.sqrt(np.einsum("i...,i...", R, R)) # einsum - Einsteinova sumace
# Dot product of R and m
m_dot_R = np.tensordot(m, R, axes=1)
# Computation of B
B = 3 * m_dot_R * R / norm_R**5 - np.tensordot(m, 1 / norm_R**3, axes=0)
B *= 1e-7 # abbreviation for B = B * 1e-7, multiplication B of 1e-7, permeability of vacuum: 4\pi * 10^(-7)
# The result is the magnetic field B
return B
X = np.linspace(-1, 1)
Y = np.linspace(-1, 1)
Bx, By = dipole(m=[0, 1], r=np.meshgrid(X, Y), r0=[-0.2,0.8])
plt.figure(figsize=(8, 8))
plt.streamplot(X, Y, Bx, By)
plt.margins(0, 0)
plt.show()
It shows the following figure:
Is it possible to get coordinates of one line of force? I don't understand how it is plotted.
The streamplot returns a container object 'StreamplotSet' with two parts:
lines: a LineCollection of the streamlines
arrows: a PatchCollection containing FancyArrowPatch objects (these are the triangular arrows)
c.lines.get_paths() gives all the segments. Iterating through these segments, their vertices can be examined. When a segment starts where the previous ended, both belong to the same curve. Note that each segment is a short straight line; many segments are used together to form a streamline curve.
The code below demonstrates iterating through the segments. To show what's happening, each segment is converted to an array of 2D points suitable for plt.plot. Default, plt.plot colors each curve with a new color (repeating every 10). The dots show where each of the short straight segments are located.
To find one particular curve, you could hover with the mouse over the starting point, and note the x coordinate of that point. And then test for that coordinate in the code. As an example, the curve that starts near x=0.48 is drawn in a special way.
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import patches
def dipole(m, r, r0):
R = np.subtract(np.transpose(r), r0).T
norm_R = np.sqrt(np.einsum("i...,i...", R, R))
m_dot_R = np.tensordot(m, R, axes=1)
B = 3 * m_dot_R * R / norm_R**5 - np.tensordot(m, 1 / norm_R**3, axes=0)
B *= 1e-7
return B
X = np.linspace(-1, 1)
Y = np.linspace(-1, 1)
Bx, By = dipole(m=[0, 1], r=np.meshgrid(X, Y), r0=[-0.2,0.8])
plt.figure(figsize=(8, 8))
c = plt.streamplot(X, Y, Bx, By)
c.lines.set_visible(False)
paths = c.lines.get_paths()
prev_end = None
start_indices = []
for index, segment in enumerate(paths):
if not np.array_equal(prev_end, segment.vertices[0]): # new segment
start_indices.append(index)
prev_end = segment.vertices[-1]
for i0, i1 in zip(start_indices, start_indices[1:] + [len(paths)]):
# get all the points of the curve that starts at index i0
curve = np.array([paths[i].vertices[0] for i in range(i0, i1)] + [paths[i1 - 1].vertices[-1]])
special_x_coord = 0.48
for i0, i1 in zip(start_indices, start_indices[1:] + [len(paths)]):
# get all the points of the curve that starts at index i0
curve = np.array([paths[i].vertices[0] for i in range(i0, i1)] + [paths[i1 - 1].vertices[-1]])
if abs(curve[0,0] - special_x_coord) < 0.01: # draw one curve in a special way
plt.plot(curve[:, 0], curve[:, 1], '-', lw=10, alpha=0.3)
else:
plt.plot(curve[:, 0], curve[:, 1], '.', ls='-')
plt.margins(0, 0)
plt.show()
My aim is to make the image1 move along the ring from its current position upto 180 degree. I have been trying to do different things but nothing seem to work. My final aim is to move both the images along the ring in different directions and finally merge them to and make them disappear.I keep getting the error above.Can you please help? Also can you tell how I can go about this problem?
from visual import *
import numpy as np
x = 3
y = 0
z = 0
i = pi/3
c = 0.120239 # A.U/minute
r = 1
for theta in arange(0, 2*pi, 0.1): #range of theta values; 0 to
xunit = r * sin(theta)*cos(i) +x
yunit = r * sin(theta)*sin(i) +y
zunit = r*cos(theta) +z
ring = curve( color = color.white ) #creates a curve
for theta in arange(0, 2*pi, 0.01):
ring.append( pos=(sin(theta)*cos(i) +x,sin(theta)*sin(i) +y,cos(theta) +z) )
image1=sphere(pos=(2.5,-0.866,0),radius=0.02, color=color.yellow)
image2=sphere(pos=(2.5,-0.866,0),radius=0.02, color=color.yellow)
earth=sphere(pos=(-3,0,-0.4),color=color.yellow, radius =0.3,material=materials.earth) #creates the observer
d_c_p = pow((x-xunit)**2 + (y-yunit)**2 + (z-zunit)**2,0.5) #calculates the distance between the center and points on ring
d_n_p = abs(yunit + 0.4998112152755791) #calculates the distance to the nearest point
t1 = ( d_c_p+d_n_p)/c
t0=d_c_p/c
t=t1-t0 #calculates the time it takes from one point to another
theta = []
t = []
dtheta = np.diff(theta) #calculates the difference in theta
dt = np.diff(t) #calculates the difference in t
speed = r*dtheta/dt #hence this calculates the speed
deltat = 0.005
t2=0
while True:
rate(5)
image2.pos = image2.pos + speed*deltat #increments the position of the image1
t2 = t2 + deltat
Your problem is that image2.pos is a vector (that's the "3" in the error message) but speed*deltat is a scalar (that's the "0" in the error message). You can't add a vector and a scalar. Instead of a scalar "speed" you need a vector velocity. There seem to be some errors in indentation in the program you posted, so there is some possibility I've misinterpreted what you're trying to do.
For VPython questions it's better to post to the VPython forum, where there are many more VPython users who will see your question than if you post to stackoverflow:
https://groups.google.com/forum/?fromgroups&hl=en#!forum/vpython-users
I want to make a program which plots a Sierpinsky triangle (of any modulo). In order to do it I've used TkInter. The program generates the fractal by moving a point randomly, always keeping it in the sides. After repeating the process many times, the fractal appears.
However, there's a problem. I don't know how to plot points on a canvas in TkInter. The rest of the program is OK, but I had to "cheat" in order to plot the points by drawing small lines instead of points. It works more or less, but it doesn't have as much resolution as it could have.
Is there a function to plot points on a canvas, or another tool to do it (using Python)? Ideas for improving the rest of the program are also welcome.
Thanks. Here's what I have:
from tkinter import *
import random
import math
def plotpoint(x, y):
global canvas
point = canvas.create_line(x-1, y-1, x+1, y+1, fill = "#000000")
x = 0 #Initial coordinates
y = 0
#x and y will always be in the interval [0, 1]
mod = int(input("What is the modulo of the Sierpinsky triangle that you want to generate? "))
points = int(input("How many points do you want the triangle to have? "))
tkengine = Tk() #Window in which the triangle will be generated
window = Frame(tkengine)
window.pack()
canvas = Canvas(window, height = 700, width = 808, bg = "#FFFFFF") #The dimensions of the canvas make the triangle look equilateral
canvas.pack()
for t in range(points):
#Procedure for placing the points
while True:
#First, randomly choose one of the mod(mod+1)/2 triangles of the first step. a and b are two vectors which point to the chosen triangle. a goes one triangle to the right and b one up-right. The algorithm gives the same probability to every triangle, although it's not efficient.
a = random.randint(0,mod-1)
b = random.randint(0,mod-1)
if a + b < mod:
break
#The previous point is dilated towards the origin of coordinates so that the big triangle of step 0 becomes the small one at the bottom-left of step one (divide by modulus). Then the vectors are added in order to move the point to the same place in another triangle.
x = x / mod + a / mod + b / 2 / mod
y = y / mod + b / mod
#Coordinates [0,1] converted to pixels, for plotting in the canvas.
X = math.floor(x * 808)
Y = math.floor((1-y) * 700)
plotpoint(X, Y)
tkengine.mainloop()
If you are wanting to plot pixels, a canvas is probably the wrong choice. You can create a PhotoImage and modify individual pixels. It's a little slow if you plot each individual pixel, but you can get dramatic speedups if you only call the put method once for each row of the image.
Here's a complete example:
from tkinter import *
import random
import math
def plotpoint(x, y):
global the_image
the_image.put(('#000000',), to=(x,y))
x = 0
y = 0
mod = 3
points = 100000
tkengine = Tk() #Window in which the triangle will be generated
window = Frame(tkengine)
window.pack()
the_image = PhotoImage(width=809, height=700)
label = Label(window, image=the_image, borderwidth=2, relief="raised")
label.pack(fill="both", expand=True)
for t in range(points):
while True:
a = random.randint(0,mod-1)
b = random.randint(0,mod-1)
if a + b < mod:
break
x = x / mod + a / mod + b / 2 / mod
y = y / mod + b / mod
X = math.floor(x * 808)
Y = math.floor((1-y) * 700)
plotpoint(X, Y)
tkengine.mainloop()
You can use canvas.create_oval with the same coordinates for the two corners of the bounding box:
from tkinter import *
import random
import math
def plotpoint(x, y):
global canvas
# point = canvas.create_line(x-1, y-1, x+1, y+1, fill = "#000000")
point = canvas.create_oval(x, y, x, y, fill="#000000", outline="#000000")
x = 0 #Initial coordinates
y = 0
#x and y will always be in the interval [0, 1]
mod = int(input("What is the modulo of the Sierpinsky triangle that you want to generate? "))
points = int(input("How many points do you want the triangle to have? "))
tkengine = Tk() #Window in which the triangle will be generated
window = Frame(tkengine)
window.pack()
canvas = Canvas(window, height = 700, width = 808, bg = "#FFFFFF") #The dimensions of the canvas make the triangle look equilateral
canvas.pack()
for t in range(points):
#Procedure for placing the points
while True:
#First, randomly choose one of the mod(mod+1)/2 triangles of the first step. a and b are two vectors which point to the chosen triangle. a goes one triangle to the right and b one up-right. The algorithm gives the same probability to every triangle, although it's not efficient.
a = random.randint(0,mod-1)
b = random.randint(0,mod-1)
if a + b < mod:
break
#The previous point is dilated towards the origin of coordinates so that the big triangle of step 0 becomes the small one at the bottom-left of step one (divide by modulus). Then the vectors are added in order to move the point to the same place in another triangle.
x = x / mod + a / mod + b / 2 / mod
y = y / mod + b / mod
#Coordinates [0,1] converted to pixels, for plotting in the canvas.
X = math.floor(x * 808)
Y = math.floor((1-y) * 700)
plotpoint(X, Y)
tkengine.mainloop()
with a depth of 3 and 100,000 points, this gives:
Finally found a solution: if a 1x1 point is to be placed in pixel (x,y), a command which does it exactly is:
point = canvas.create_line(x, y, x+1, y+1, fill = "colour")
The oval is a good idea for 2x2 points.
Something remarkable about the original program is that it uses a lot of RAM if every point is treated as a separate object.
I have three coordinates (lat,lon) on a sphere. If you would rotate the whole sphere from coord1 to coord2, where will coord3 now be located?
I've been trying this out in Python using Great Circle (http://www.koders.com/python/fid0A930D7924AE856342437CA1F5A9A3EC0CAEACE2.aspx?s=coastline) but I create strange results as the newly calculated points all group together at the equator. That must have something to do with the azimuth calculation I assume?
Does anyone maybe know how to calculate this correctly?
Thanks in advance!
EDIT
I found the following: http://www.uwgb.edu/dutchs/mathalgo/sphere0.htm
I guess I now need to calculate the rotation axis and the rotation angle from the two points in cartesian coords (and 0,0,0)? I guess this must be very simple, something to do with defining a plane and determining the normal line? Does someone maybe know where I can find the needed equations?
EDIT 2
Coord1 and coord2 make a great circle. Is there an easy way to find the location of the great circle normal axis on the sphere?
EDIT 3
Looks like I was able to solve it ;)
http://articles.adsabs.harvard.edu//full/1953Metic...1...39L/0000039.000.html did the trick.
Ok I don't know the exactly formula, I believe it would be a simple matrix multiplication but here's how you can figure out without it.
Transform coordinates so that the poles of the rotation are at 90,0 and -90,0 respectively and so that the line along your rotation from coord1 to coord2 is then on the "equator" (this should be simply delta lat, delta long)
then the rotation is just change in longitude and you can apply the same delta long to any coord3, then simply transform back to the original coordinates (via negative delta lat and negative delta long)
1 & 2 are pretty much what your matrix would do - if you can figure out the matrices for each step, you can just multiply them and get the final matrix
Using Visual Python I think I now have solved it:
# Rotation first described for geo purposes: http://www.uwgb.edu/dutchs/mathalgo/sphere0.htm
# http://stackoverflow.com/questions/6802577/python-rotation-of-3d-vector
# http://vpython.org/
from visual import *
from math import *
import sys
def ll2cart(lon,lat):
# http://rbrundritt.wordpress.com/2008/10/14/conversion-between-spherical-and-cartesian-coordinates-systems/
x = cos(lat) * cos(lon)
y = cos(lat) * sin(lon)
z = sin(lat)
return x,y,z
def cart2ll(x,y,z):
# http://rbrundritt.wordpress.com/2008/10/14/conversion-between-spherical-and-cartesian-coordinates-systems/
r = sqrt((x**2) + (y**2) + (z**2))
lat = asin(z/r)
lon = atan2(y, x)
return lon, lat
def distance(lon1, lat1, lon2, lat2):
# http://code.activestate.com/recipes/576779-calculating-distance-between-two-geographic-points/
# http://en.wikipedia.org/wiki/Haversine_formula
dlat = lat2 - lat1
dlon = lon2 - lon1
q = sin(dlat/2)**2 + (cos(lat1) * cos(lat2) * (sin(dlon/2)**2))
return 2 * atan2(sqrt(q), sqrt(1-q))
if len(sys.argv) == 1:
sys.exit()
else:
csv = sys.argv[1]
# Points A and B defining the rotation:
LonA = radians(float(sys.argv[2]))
LatA = radians(float(sys.argv[3]))
LonB = radians(float(sys.argv[4]))
LatB = radians(float(sys.argv[5]))
# A and B are both vectors
# The crossproduct AxB is the rotation pole vector P:
Ax, Ay, Az = ll2cart(LonA, LatA)
Bx, By, Bz = ll2cart(LonB, LatB)
A = vector(Ax,Ay,Az)
B = vector(Bx,By,Bz)
P = cross(A,B)
Px,Py,Pz = P
LonP, LatP = cart2ll(Px,Py,Pz)
# The Rotation Angle in radians:
# http://code.activestate.com/recipes/576779-calculating-distance-between-two-geographic-points/
# http://en.wikipedia.org/wiki/Haversine_formula
RotAngle = distance(LonA,LatA,LonB,LatB)
f = open(csv,"r")
o = open(csv[:-4] + "_translated.csv","w")
o.write(f.readline())
for line in f:
(lon, lat) = line.strip().split(",")
# Point C which will be translated:
LonC = radians(float(lon))
LatC = radians(float(lat))
# Point C in Cartesian coordinates:
Cx,Cy,Cz = ll2cart(LonC,LatC)
C = vector(Cx,Cy,Cz)
# C rotated to D:
D = rotate(C,RotAngle,P)
Dx,Dy,Dz = D
LonD,LatD = cart2ll(Dx,Dy,Dz)
o.write(str(degrees(LonD)) + "," + str(degrees(LatD)) + "\n")