Related
Here I have some code that can vertically and horizontally shift images so that a specific feature can align (credits to https://stackoverflow.com/a/24769222/15016884):
def cross_image(im1, im2):
im1_gray = np.sum(im1.astype('float'), axis=2)
im2_gray = np.sum(im2.astype('float'), axis=2)
im1_gray -= np.mean(im1_gray)
im2_gray -= np.mean(im2_gray)
return signal.fftconvolve(im1_gray, im2_gray[::-1,::-1], mode='same')
corr_img_null = cross_image(cloud1,cloud1)
corr_img = cross_image(cloud1,cloud2)
y0, x0 = np.unravel_index(np.argmax(corr_img_null), corr_img_null.shape)
y, x = np.unravel_index(np.argmax(corr_img), corr_img.shape)
ver_shift = y0-y
hor_shift = x0-x
print('horizontally shifted', hor_shift)
print('vertically shifted', ver_shift)
#defining the bounds of the part of the images I'm actually analyzing
xstart = 100
xstop = 310
ystart = 50
ystop = 200
crop_cloud1 = cloud1[ystart:ystop, xstart:xstop]
crop_cloud2 = cloud2[ystart:ystop, xstart:xstop]
crop_cloud2_shift = cloud2[ystart+ver_shift:ystop+ver_shift, xstart+hor_shift:xstop+hor_shift]
plot_pos = plt.figure(5)
plt.title('image 1')
plt.imshow(crop_cloud1)
plot_pos = plt.figure(6)
plt.title('image 2')
plt.imshow(crop_cloud2)
plot_pos = plt.figure(7)
plt.title('Shifted image 2 to align with image 1')
plt.imshow(crop_cloud2_shift)
Here are the results:
Now, I want to work with the example shown below, where rotations in addition to translations will be needed to align the features in my image.
Here is my code for that: The idea is to convolve each possible configuration of image 2 for every angle from -45 to 45 (for my application, this angle is not likely to be exceeded) and find at which coordinates and rotation angle the convolution is maximized.
import cv2
def rotate(img, theta):
(rows, cols) = img.shape[:2]
M = cv2.getRotationMatrix2D((cols / 2, rows / 2), theta, 1)
res = cv2.warpAffine(img, M, (cols, rows))
return res
#testing all rotations of image 2
corr_bucket = []
for i in range(-45,45):
rot_img = rotate(bolt2,i)
corr_img = cross_image(bolt1,rot_img)
corr_bucket.append(corr_img)
corr_arr = np.asarray(corr_bucket)
corr_img_null = cross_image(bolt1,bolt1)
y0, x0 = np.unravel_index(np.argmax(corr_img_null), corr_img_null.shape)
r_index, y1, x1 = np.unravel_index(np.argmax(corr_arr), corr_arr.shape)
r = -45+r_index
ver_shift = y0-y
hor_shift = x0-x
ver_shift_r = y0-y1
hor_shift_r = x0-x1
#What parts of the image do you want to analyze
xstart = 200
xstop = 300
ystart = 100
ystop = 200
crop_bolt1 = bolt1[ystart:ystop, xstart:xstop]
crop_bolt2 = bolt2[ystart:ystop, xstart:xstop]
rot_bolt2 = rotate(bolt2,r)
shift_rot_bolt2 = rot_bolt2[ystart+ver_shift_r:ystop+ver_shift_r, xstart+hor_shift_r:xstop+hor_shift_r]
plot_1 = plt.figure(9)
plt.title('image 1')
plt.imshow(crop_bolt1)
plot_2 = plt.figure(10)
plt.title('image 2')
plt.imshow(crop_bolt2)
plot_3 = plt.figure(11)
plt.title('Shifted and rotated image 2 to align with image 1')
plt.imshow(shift_rot_bolt2)
Unfortunately, from the very last line, I get the error ValueError: zero-size array to reduction operation minimum which has no identity. I'm kind of new to python so I don't really know what this means or why my approach isn't working. I have a feeling that my error is somewhere in unraveling corr_arr because the x, y and r values it returns I can already see, just by estimating, would not make the lightning bolts align. Any advice?
The issue came from feeding in the entire rotated image into scipy.signal.fftconvolve. Crop a part of image2 after rotating to use as a "probe image" (crop your unrotated image 1 in the same way), and the code I have written in my question works fine.
I've been trying to create a 2D map of blobs of matter (Gaussian random field) using a variance I have calculated. This variance is a 2D array. I have tried using numpy.random.normal since it allows for a 2D input of the variance, but it doesn't really create a map with the trend I expect from the input parameters. One of the important input constants lambda_c should manifest itself as the physical size (diameter) of the blobs. However, when I change my lambda_c, the size of the blobs does not change if at all. For example, if I set lambda_c = 40 parsecs, the map needs blobs that are 40 parsecs in diameter. A MWE to produce the map using my variance:
import numpy as np
import random
import matplotlib.pyplot as plt
from matplotlib.pyplot import show, plot
import scipy.integrate as integrate
from scipy.interpolate import RectBivariateSpline
n = 300
c = 3e8
G = 6.67e-11
M_sun = 1.989e30
pc = 3.086e16 # parsec
Dds = 1097.07889283e6*pc
Ds = 1726.62069147e6*pc
Dd = 1259e6*pc
FOV_arcsec_original = 5.
FOV_arcmin = FOV_arcsec_original/60.
pix2rad = ((FOV_arcmin/60.)/float(n))*np.pi/180.
rad2pix = 1./pix2rad
x_pix = np.linspace(-FOV_arcsec_original/2/pix2rad/180.*np.pi/3600.,FOV_arcsec_original/2/pix2rad/180.*np.pi/3600.,n)
y_pix = np.linspace(-FOV_arcsec_original/2/pix2rad/180.*np.pi/3600.,FOV_arcsec_original/2/pix2rad/180.*np.pi/3600.,n)
X_pix,Y_pix = np.meshgrid(x_pix,y_pix)
conc = 10.
M = 1e13*M_sun
r_s = 18*1e3*pc
lambda_c = 40*pc ### The important parameter that doesn't seem to manifest itself in the map when changed
rho_s = M/((4*np.pi*r_s**3)*(np.log(1+conc) - (conc/(1+conc))))
sigma_crit = (c**2*Ds)/(4*np.pi*G*Dd*Dds)
k_s = rho_s*r_s/sigma_crit
theta_s = r_s/Dd
Renorm = (4*G/c**2)*(Dds/(Dd*Ds))
#### Here I just interpolate and zoom into my field of view to get better resolutions
A = np.sqrt(X_pix**2 + Y_pix**2)*pix2rad/theta_s
A_1 = A[100:200,0:100]
n_x = n_y = 100
FOV_arcsec_x = FOV_arcsec_original*(100./300)
FOV_arcmin_x = FOV_arcsec_x/60.
pix2rad_x = ((FOV_arcmin_x/60.)/float(n_x))*np.pi/180.
rad2pix_x = 1./pix2rad_x
FOV_arcsec_y = FOV_arcsec_original*(100./300)
FOV_arcmin_y = FOV_arcsec_y/60.
pix2rad_y = ((FOV_arcmin_y/60.)/float(n_y))*np.pi/180.
rad2pix_y = 1./pix2rad_y
x1 = np.linspace(-FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,n_x)
y1 = np.linspace(-FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,n_y)
X1,Y1 = np.meshgrid(x1,y1)
n_x_2 = 500
n_y_2 = 500
x2 = np.linspace(-FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,n_x_2)
y2 = np.linspace(-FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,n_y_2)
X2,Y2 = np.meshgrid(x2,y2)
interp_spline = RectBivariateSpline(y1,x1,A_1)
A_2 = interp_spline(y2,x2)
A_3 = A_2[50:450,0:400]
n_x_3 = n_y_3 = 400
FOV_arcsec_x = FOV_arcsec_original*(100./300)*400./500.
FOV_arcmin_x = FOV_arcsec_x/60.
pix2rad_x = ((FOV_arcmin_x/60.)/float(n_x_3))*np.pi/180.
rad2pix_x = 1./pix2rad_x
FOV_arcsec_y = FOV_arcsec_original*(100./300)*400./500.
FOV_arcmin_y = FOV_arcsec_y/60.
pix2rad_y = ((FOV_arcmin_y/60.)/float(n_y_3))*np.pi/180.
rad2pix_y = 1./pix2rad_y
x3 = np.linspace(-FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,n_x_3)
y3 = np.linspace(-FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,n_y_3)
X3,Y3 = np.meshgrid(x3,y3)
n_x_4 = 1000
n_y_4 = 1000
x4 = np.linspace(-FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,FOV_arcsec_x/2/pix2rad_x/180.*np.pi/3600.,n_x_4)
y4 = np.linspace(-FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,FOV_arcsec_y/2/pix2rad_y/180.*np.pi/3600.,n_y_4)
X4,Y4 = np.meshgrid(x4,y4)
interp_spline = RectBivariateSpline(y3,x3,A_3)
A_4 = interp_spline(y4,x4)
############### Function to calculate variance
variance = np.zeros((len(A_4),len(A_4)))
def variance_fluctuations(x):
for i in xrange(len(x)):
for j in xrange(len(x)):
if x[j][i] < 1.:
variance[j][i] = (k_s**2)*(lambda_c/r_s)*((np.pi/x[j][i]) - (1./(x[j][i]**2 -1)**3.)*(((6.*x[j][i]**4. - 17.*x[j][i]**2. + 26)/3.)+ (((2.*x[j][i]**6. - 7.*x[j][i]**4. + 8.*x[j][i]**2. - 8)*np.arccosh(1./x[j][i]))/(np.sqrt(1-x[j][i]**2.)))))
elif x[j][i] > 1.:
variance[j][i] = (k_s**2)*(lambda_c/r_s)*((np.pi/x[j][i]) - (1./(x[j][i]**2 -1)**3.)*(((6.*x[j][i]**4. - 17.*x[j][i]**2. + 26)/3.)+ (((2.*x[j][i]**6. - 7.*x[j][i]**4. + 8.*x[j][i]**2. - 8)*np.arccos(1./x[j][i]))/(np.sqrt(x[j][i]**2.-1)))))
variance_fluctuations(A_4)
#### Creating the map
mean = 0
delta_kappa = np.random.normal(0,variance,A_4.shape)
xfinal = np.linspace(-FOV_arcsec_x*np.pi/180./3600.*Dd/pc/2,FOV_arcsec_x*np.pi/180./3600.*Dd/pc/2,1000)
yfinal = np.linspace(-FOV_arcsec_x*np.pi/180./3600.*Dd/pc/2,FOV_arcsec_x*np.pi/180./3600.*Dd/pc/2,1000)
Xfinal, Yfinal = np.meshgrid(xfinal,yfinal)
plt.contourf(Xfinal,Yfinal,delta_kappa,100)
plt.show()
The map looks like this, with the density of blobs increasing towards the right. However, the size of the blobs don't change and the map looks virtually the same whether I use lambda_c = 40*pc or lambda_c = 400*pc.
I'm wondering if the np.random.normal function isn't really doing what I expect it to do? I feel like the pixel scale of the map and the way samples are drawn make no link to the size of the blobs. Maybe there is a better way to create the map using the variance, would appreciate any insight.
I expect the map to look something like this , the blob sizes change based on the input parameters for my variance :
This is quite a well visited problem in (surprise surprise) astronomy and cosmology.
You could use lenstool: https://lenstools.readthedocs.io/en/latest/examples/gaussian_random_field.html
You could also try here:
https://andrewwalker.github.io/statefultransitions/post/gaussian-fields
Not to mention:
https://github.com/bsciolla/gaussian-random-fields
I am not reproducing code here because all credit goes to the above authors. However, they did just all come right out a google search :/
Easiest of all is probably a python module FyeldGenerator, apparently designed for this exact purpose:
https://github.com/cphyc/FyeldGenerator
So (adapted from github example):
pip install FyeldGenerator
from FyeldGenerator import generate_field
from matplotlib import use
use('Agg')
import matplotlib.pyplot as plt
import numpy as np
plt.figure()
# Helper that generates power-law power spectrum
def Pkgen(n):
def Pk(k):
return np.power(k, -n)
return Pk
# Draw samples from a normal distribution
def distrib(shape):
a = np.random.normal(loc=0, scale=1, size=shape)
b = np.random.normal(loc=0, scale=1, size=shape)
return a + 1j * b
shape = (512, 512)
field = generate_field(distrib, Pkgen(2), shape)
plt.imshow(field, cmap='jet')
plt.savefig('field.png',dpi=400)
plt.close())
This gives:
Looks pretty straightforward to me :)
PS: FoV implied a telescope observation of the gaussian random field :)
A completely different and much quicker way may be just to blur the delta_kappa array with gaussian filter. Try adjusting sigma parameter to alter the blobs size.
from scipy.ndimage.filters import gaussian_filter
dk_gf = gaussian_filter(delta_kappa, sigma=20)
Xfinal, Yfinal = np.meshgrid(xfinal,yfinal)
plt.contourf(Xfinal,Yfinal,dk_ma,100, cmap='jet')
plt.show();
this is image with sigma=20
this is image with sigma=2.5
ThunderFlash, try this code to draw the map:
# function to produce blobs:
from scipy.stats import multivariate_normal
def blob (positions, mean=(0,0), var=1):
cov = [[var,0],[0,var]]
return multivariate_normal(mean, cov).pdf(positions)
"""
now prepare for blobs generation.
note that I use less dense grid to pick blobs centers (regulated by `step`)
this makes blobs more pronounced and saves calculation time.
use this part instead of your code section below comment #### Creating the map
"""
delta_kappa = np.random.normal(0,variance,A_4.shape) # same
step = 10 #
dk2 = delta_kappa[::step,::step] # taking every 10th element
x2, y2 = xfinal[::step],yfinal[::step]
field = np.dstack((Xfinal,Yfinal))
print (field.shape, dk2.shape, x2.shape, y2.shape)
>> (1000, 1000, 2), (100, 100), (100,), (100,)
result = np.zeros(field.shape[:2])
for x in range (len(x2)):
for y in range (len(y2)):
res2 = blob(field, mean = (x2[x], y2[y]), var=10000)*dk2[x,y]
result += res2
# the cycle above took over 20 minutes on Ryzen 2700X. It could be accelerated by vectorization presumably.
plt.contourf(Xfinal,Yfinal,result,100)
plt.show()
you may want to play with var parameter in blob() to smoothen the image and with step to make it more compressed.
Here is the image that I got using your code (somehow axes are flipped and more dense areas on the top):
I'm trying to interpolate between two images in Python.
Images are of shapes (188, 188)
I wish to interpolate the image 'in-between' these two images. Say Image_1 is at location z=0 and Image_2 is at location z=2. I want the interpolated image at location z=1.
I believe this answer (MATLAB) contains a similar problem and solution.
Creating intermediate slices in a 3D MRI volume with MATLAB
I've tried to convert this code to Python as follows:
from scipy.interpolate import interpn
from scipy.interpolate import griddata
# Construct 3D volume from images
# arr.shape = (2, 182, 182)
arr = np.r_['0,3', image_1, image_2]
slices,rows,cols = arr.shape
# Construct meshgrids
[X,Y,Z] = np.meshgrid(np.arange(cols), np.arange(rows), np.arange(slices));
[X2,Y2,Z2] = np.meshgrid(np.arange(cols), np.arange(rows), np.arange(slices*2));
# Run n-dim interpolation
Vi = interpn([X,Y,Z], arr, np.array([X1,Y1,Z1]).T)
However, this produces an error:
ValueError: The points in dimension 0 must be strictly ascending
I suspect I am not constructing my meshgrid(s) properly but am kind of lost on whether or not this approach is correct.
Any ideas?
---------- Edit -----------
Found some MATLAB code that appears to solve this problem:
Interpolating Between Two Planes in 3d space
I attempted to convert this to Python:
from scipy.ndimage.morphology import distance_transform_edt
from scipy.interpolate import interpn
def ndgrid(*args,**kwargs):
"""
Same as calling ``meshgrid`` with *indexing* = ``'ij'`` (see
``meshgrid`` for documentation).
"""
kwargs['indexing'] = 'ij'
return np.meshgrid(*args,**kwargs)
def bwperim(bw, n=4):
"""
perim = bwperim(bw, n=4)
Find the perimeter of objects in binary images.
A pixel is part of an object perimeter if its value is one and there
is at least one zero-valued pixel in its neighborhood.
By default the neighborhood of a pixel is 4 nearest pixels, but
if `n` is set to 8 the 8 nearest pixels will be considered.
Parameters
----------
bw : A black-and-white image
n : Connectivity. Must be 4 or 8 (default: 8)
Returns
-------
perim : A boolean image
From Mahotas: http://nullege.com/codes/search/mahotas.bwperim
"""
if n not in (4,8):
raise ValueError('mahotas.bwperim: n must be 4 or 8')
rows,cols = bw.shape
# Translate image by one pixel in all directions
north = np.zeros((rows,cols))
south = np.zeros((rows,cols))
west = np.zeros((rows,cols))
east = np.zeros((rows,cols))
north[:-1,:] = bw[1:,:]
south[1:,:] = bw[:-1,:]
west[:,:-1] = bw[:,1:]
east[:,1:] = bw[:,:-1]
idx = (north == bw) & \
(south == bw) & \
(west == bw) & \
(east == bw)
if n == 8:
north_east = np.zeros((rows, cols))
north_west = np.zeros((rows, cols))
south_east = np.zeros((rows, cols))
south_west = np.zeros((rows, cols))
north_east[:-1, 1:] = bw[1:, :-1]
north_west[:-1, :-1] = bw[1:, 1:]
south_east[1:, 1:] = bw[:-1, :-1]
south_west[1:, :-1] = bw[:-1, 1:]
idx &= (north_east == bw) & \
(south_east == bw) & \
(south_west == bw) & \
(north_west == bw)
return ~idx * bw
def signed_bwdist(im):
'''
Find perim and return masked image (signed/reversed)
'''
im = -bwdist(bwperim(im))*np.logical_not(im) + bwdist(bwperim(im))*im
return im
def bwdist(im):
'''
Find distance map of image
'''
dist_im = distance_transform_edt(1-im)
return dist_im
def interp_shape(top, bottom, num):
if num<0 and round(num) == num:
print("Error: number of slices to be interpolated must be integer>0")
top = signed_bwdist(top)
bottom = signed_bwdist(bottom)
r, c = top.shape
t = num+2
print("Rows - Cols - Slices")
print(r, c, t)
print("")
# rejoin top, bottom into a single array of shape (2, r, c)
# MATLAB: cat(3,bottom,top)
top_and_bottom = np.r_['0,3', top, bottom]
#top_and_bottom = np.rollaxis(top_and_bottom, 0, 3)
# create ndgrids
x,y,z = np.mgrid[0:r, 0:c, 0:t-1] # existing data
x1,y1,z1 = np.mgrid[0:r, 0:c, 0:t] # including new slice
print("Shape x y z:", x.shape, y.shape, z.shape)
print("Shape x1 y1 z1:", x1.shape, y1.shape, z1.shape)
print(top_and_bottom.shape, len(x), len(y), len(z))
# Do interpolation
out = interpn((x,y,z), top_and_bottom, (x1,y1,z1))
# MATLAB: out = out(:,:,2:end-1)>=0;
array_lim = out[-1]-1
out[out[:,:,2:out] >= 0] = 1
return out
I call this as follows:
new_image = interp_shape(image_1,image_2, 1)
Im pretty sure this is 80% of the way there but I still get this error when running:
ValueError: The points in dimension 0 must be strictly ascending
Again, I am probably not constructing my meshes correctly. I believe np.mgrid should produce the same result as MATLABs ndgrid though.
Is there a better way to construct the ndgrid equivalents?
I figured this out. Or at least a method that produces desirable results.
Based on: Interpolating Between Two Planes in 3d space
def signed_bwdist(im):
'''
Find perim and return masked image (signed/reversed)
'''
im = -bwdist(bwperim(im))*np.logical_not(im) + bwdist(bwperim(im))*im
return im
def bwdist(im):
'''
Find distance map of image
'''
dist_im = distance_transform_edt(1-im)
return dist_im
def interp_shape(top, bottom, precision):
'''
Interpolate between two contours
Input: top
[X,Y] - Image of top contour (mask)
bottom
[X,Y] - Image of bottom contour (mask)
precision
float - % between the images to interpolate
Ex: num=0.5 - Interpolate the middle image between top and bottom image
Output: out
[X,Y] - Interpolated image at num (%) between top and bottom
'''
if precision>2:
print("Error: Precision must be between 0 and 1 (float)")
top = signed_bwdist(top)
bottom = signed_bwdist(bottom)
# row,cols definition
r, c = top.shape
# Reverse % indexing
precision = 1+precision
# rejoin top, bottom into a single array of shape (2, r, c)
top_and_bottom = np.stack((top, bottom))
# create ndgrids
points = (np.r_[0, 2], np.arange(r), np.arange(c))
xi = np.rollaxis(np.mgrid[:r, :c], 0, 3).reshape((r**2, 2))
xi = np.c_[np.full((r**2),precision), xi]
# Interpolate for new plane
out = interpn(points, top_and_bottom, xi)
out = out.reshape((r, c))
# Threshold distmap to values above 0
out = out > 0
return out
# Run interpolation
out = interp_shape(image_1,image_2, 0.5)
Example output:
I came across a similar problem where I needed to interpolate the shift between frames where the change did not merely constitute a translation but also changes to the shape itself . I solved this problem by :
Using center_of_mass from scipy.ndimage.measurements to calculate the center of the object we want to move in each frame
Defining a continuous parameter t where t=0 first and t=1 last frame
Interpolate the motion between two nearest frames (with regard to a specific t value) by shifting the image back/forward via shift from scipy.ndimage.interpolation and overlaying them.
Here is the code:
def inter(images,t):
#input:
# images: list of arrays/frames ordered according to motion
# t: parameter ranging from 0 to 1 corresponding to first and last frame
#returns: interpolated image
#direction of movement, assumed to be approx. linear
a=np.array(center_of_mass(images[0]))
b=np.array(center_of_mass(images[-1]))
#find index of two nearest frames
arr=np.array([center_of_mass(images[i]) for i in range(len(images))])
v=a+t*(b-a) #convert t into vector
idx1 = (np.linalg.norm((arr - v),axis=1)).argmin()
arr[idx1]=np.array([0,0]) #this is sloppy, should be changed if relevant values are near [0,0]
idx2 = (np.linalg.norm((arr - v),axis=1)).argmin()
if idx1>idx2:
b=np.array(center_of_mass(images[idx1])) #center of mass of nearest contour
a=np.array(center_of_mass(images[idx2])) #center of mass of second nearest contour
tstar=np.linalg.norm(v-a)/np.linalg.norm(b-a) #define parameter ranging from 0 to 1 for interpolation between two nearest frames
im1_shift=shift(images[idx2],(b-a)*tstar) #shift frame 1
im2_shift=shift(images[idx1],-(b-a)*(1-tstar)) #shift frame 2
return im1_shift+im2_shift #return average
if idx1<idx2:
b=np.array(center_of_mass(images[idx2]))
a=np.array(center_of_mass(images[idx1]))
tstar=np.linalg.norm(v-a)/np.linalg.norm(b-a)
im1_shift=shift(images[idx2],-(b-a)*(1-tstar))
im2_shift=shift(images[idx1],(b-a)*(tstar))
return im1_shift+im2_shift
Result example
I don't know the solution to your problem, but I don't think it's possible to do this with interpn.
I corrected the code that you tried, and used the following input images:
But the result is:
Here's the corrected code:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from scipy import interpolate
n = 8
img1 = np.zeros((n, n))
img2 = np.zeros((n, n))
img1[2:4, 2:4] = 1
img2[4:6, 4:6] = 1
plt.figure()
plt.imshow(img1, cmap=cm.Greys)
plt.figure()
plt.imshow(img2, cmap=cm.Greys)
points = (np.r_[0, 2], np.arange(n), np.arange(n))
values = np.stack((img1, img2))
xi = np.rollaxis(np.mgrid[:n, :n], 0, 3).reshape((n**2, 2))
xi = np.c_[np.ones(n**2), xi]
values_x = interpolate.interpn(points, values, xi, method='linear')
values_x = values_x.reshape((n, n))
print(values_x)
plt.figure()
plt.imshow(values_x, cmap=cm.Greys)
plt.clim((0, 1))
plt.show()
I think the main difference between your code and mine is in the specification of xi. interpn tends to be somewhat confusing to use, and I've explained it in greater detail in an older answer. If you're curious about the mechanics of how I've specified xi, see this answer of mine explaining what I've done.
This result is not entirely surprising, because interpn just linearly interpolated between the two images: so the parts which had 1 in one image and 0 in the other simply became 0.5.
Over here, since one image is the translation of the other, it's clear that we want an image that's translated "in-between". But how would interpn interpolate two general images? If you had one small circle and one big circle, is it in any way clear that there should be a circle of intermediate size "between" them? What about interpolating between a dog and a cat? Or a dog and a building?
I think you are essentially trying to "draw lines" connecting the edges of the two images and then trying to figure out the image in between. This is similar to sampling a moving video at a half-frame. You might want to check out something like optical flow, which connects adjacent frames using vectors. I'm not aware if and what python packages/implementations are available though.
I would like to plot parallel lines with different colors. E.g. rather than a single red line of thickness 6, I would like to have two parallel lines of thickness 3, with one red and one blue.
Any thoughts would be appreciated.
Merci
Even with the smart offsetting (s. below), there is still an issue in a view that has sharp angles between consecutive points.
Zoomed view of smart offsetting:
Overlaying lines of varying thickness:
Plotting parallel lines is not an easy task. Using a simple uniform offset will of course not show the desired result. This is shown in the left picture below.
Such a simple offset can be produced in matplotlib as shown in the transformation tutorial.
Method1
A better solution may be to use the idea sketched on the right side. To calculate the offset of the nth point we can use the normal vector to the line between the n-1st and the n+1st point and use the same distance along this normal vector to calculate the offset point.
The advantage of this method is that we have the same number of points in the original line as in the offset line. The disadvantage is that it is not completely accurate, as can be see in the picture.
This method is implemented in the function offset in the code below.
In order to make this useful for a matplotlib plot, we need to consider that the linewidth should be independent of the data units. Linewidth is usually given in units of points, and the offset would best be given in the same unit, such that e.g. the requirement from the question ("two parallel lines of width 3") can be met.
The idea is therefore to transform the coordinates from data to display coordinates, using ax.transData.transform. Also the offset in points o can be transformed to the same units: Using the dpi and the standard of ppi=72, the offset in display coordinates is o*dpi/ppi. After the offset in display coordinates has been applied, the inverse transform (ax.transData.inverted().transform) allows a backtransformation.
Now there is another dimension of the problem: How to assure that the offset remains the same independent of the zoom and size of the figure?
This last point can be addressed by recalculating the offset each time a zooming of resizing event has taken place.
Here is how a rainbow curve would look like produced by this method.
And here is the code to produce the image.
import numpy as np
import matplotlib.pyplot as plt
dpi = 100
def offset(x,y, o):
""" Offset coordinates given by array x,y by o """
X = np.c_[x,y].T
m = np.array([[0,-1],[1,0]])
R = np.zeros_like(X)
S = X[:,2:]-X[:,:-2]
R[:,1:-1] = np.dot(m, S)
R[:,0] = np.dot(m, X[:,1]-X[:,0])
R[:,-1] = np.dot(m, X[:,-1]-X[:,-2])
On = R/np.sqrt(R[0,:]**2+R[1,:]**2)*o
Out = On+X
return Out[0,:], Out[1,:]
def offset_curve(ax, x,y, o):
""" Offset array x,y in data coordinates
by o in points """
trans = ax.transData.transform
inv = ax.transData.inverted().transform
X = np.c_[x,y]
Xt = trans(X)
xto, yto = offset(Xt[:,0],Xt[:,1],o*dpi/72. )
Xto = np.c_[xto, yto]
Xo = inv(Xto)
return Xo[:,0], Xo[:,1]
# some single points
y = np.array([1,2,2,3,3,0])
x = np.arange(len(y))
#or try a sinus
x = np.linspace(0,9)
y=np.sin(x)*x/3.
fig, ax=plt.subplots(figsize=(4,2.5), dpi=dpi)
cols = ["#fff40b", "#00e103", "#ff9921", "#3a00ef", "#ff2121", "#af00e7"]
lw = 2.
lines = []
for i in range(len(cols)):
l, = plt.plot(x,y, lw=lw, color=cols[i])
lines.append(l)
def plot_rainbow(event=None):
xr = range(6); yr = range(6);
xr[0],yr[0] = offset_curve(ax, x,y, lw/2.)
xr[1],yr[1] = offset_curve(ax, x,y, -lw/2.)
xr[2],yr[2] = offset_curve(ax, xr[0],yr[0], lw)
xr[3],yr[3] = offset_curve(ax, xr[1],yr[1], -lw)
xr[4],yr[4] = offset_curve(ax, xr[2],yr[2], lw)
xr[5],yr[5] = offset_curve(ax, xr[3],yr[3], -lw)
for i in range(6):
lines[i].set_data(xr[i], yr[i])
plot_rainbow()
fig.canvas.mpl_connect("resize_event", plot_rainbow)
fig.canvas.mpl_connect("button_release_event", plot_rainbow)
plt.savefig(__file__+".png", dpi=dpi)
plt.show()
Method2
To avoid overlapping lines, one has to use a more complicated solution.
One could first offset every point normal to the two line segments it is part of (green points in the picture below). Then calculate the line through those offset points and find their intersection.
A particular case would be when the slopes of two subsequent line segments equal. This has to be taken care of (eps in the code below).
from __future__ import division
import numpy as np
import matplotlib.pyplot as plt
dpi = 100
def intersect(p1, p2, q1, q2, eps=1.e-10):
""" given two lines, first through points pn, second through qn,
find the intersection """
x1 = p1[0]; y1 = p1[1]; x2 = p2[0]; y2 = p2[1]
x3 = q1[0]; y3 = q1[1]; x4 = q2[0]; y4 = q2[1]
nomX = ((x1*y2-y1*x2)*(x3-x4)- (x1-x2)*(x3*y4-y3*x4))
denom = float( (x1-x2)*(y3-y4) - (y1-y2)*(x3-x4) )
nomY = (x1*y2-y1*x2)*(y3-y4) - (y1-y2)*(x3*y4-y3*x4)
if np.abs(denom) < eps:
#print "intersection undefined", p1
return np.array( p1 )
else:
return np.array( [ nomX/denom , nomY/denom ])
def offset(x,y, o, eps=1.e-10):
""" Offset coordinates given by array x,y by o """
X = np.c_[x,y].T
m = np.array([[0,-1],[1,0]])
S = X[:,1:]-X[:,:-1]
R = np.dot(m, S)
norm = np.sqrt(R[0,:]**2+R[1,:]**2) / o
On = R/norm
Outa = On+X[:,1:]
Outb = On+X[:,:-1]
G = np.zeros_like(X)
for i in xrange(0, len(X[0,:])-2):
p = intersect(Outa[:,i], Outb[:,i], Outa[:,i+1], Outb[:,i+1], eps=eps)
G[:,i+1] = p
G[:,0] = Outb[:,0]
G[:,-1] = Outa[:,-1]
return G[0,:], G[1,:]
def offset_curve(ax, x,y, o, eps=1.e-10):
""" Offset array x,y in data coordinates
by o in points """
trans = ax.transData.transform
inv = ax.transData.inverted().transform
X = np.c_[x,y]
Xt = trans(X)
xto, yto = offset(Xt[:,0],Xt[:,1],o*dpi/72., eps=eps )
Xto = np.c_[xto, yto]
Xo = inv(Xto)
return Xo[:,0], Xo[:,1]
# some single points
y = np.array([1,1,2,0,3,2,1.,4,3]) *1.e9
x = np.arange(len(y))
x[3]=x[4]
#or try a sinus
#x = np.linspace(0,9)
#y=np.sin(x)*x/3.
fig, ax=plt.subplots(figsize=(4,2.5), dpi=dpi)
cols = ["r", "b"]
lw = 11.
lines = []
for i in range(len(cols)):
l, = plt.plot(x,y, lw=lw, color=cols[i], solid_joinstyle="miter")
lines.append(l)
def plot_rainbow(event=None):
xr = range(2); yr = range(2);
xr[0],yr[0] = offset_curve(ax, x,y, lw/2.)
xr[1],yr[1] = offset_curve(ax, x,y, -lw/2.)
for i in range(2):
lines[i].set_data(xr[i], yr[i])
plot_rainbow()
fig.canvas.mpl_connect("resize_event", plot_rainbow)
fig.canvas.mpl_connect("button_release_event", plot_rainbow)
plt.show()
Note that this method should work well as long as the offset between the lines is smaller then the distance between subsequent points on the line. Otherwise method 1 may be better suited.
The best that I can think of is to take your data, generate a series of small offsets, and use fill_between to make bands of whatever color you like.
I wrote a function to do this. I don't know what shape you're trying to plot, so this may or may not work for you. I tested it on a parabola and got decent results. You can also play around with the list of colors.
def rainbow_plot(x, y, spacing=0.1):
fig, ax = plt.subplots()
colors = ['red', 'yellow', 'green', 'cyan','blue']
top = max(y)
lines = []
for i in range(len(colors)+1):
newline_data = y - top*spacing*i
lines.append(newline_data)
for i, c in enumerate(colors):
ax.fill_between(x, lines[i], lines[i+1], facecolor=c)
return fig, ax
x = np.linspace(0,1,51)
y = 1-(x-0.5)**2
rainbow_plot(x,y)
In a project I'm doing, I have to take in a user input from a structured file (xml). The file contains road data of an area, which I have to plot on to the matplotlib canvas. The problem is that along with the road, I also have to render the road name, and most of the roads are curved. I know how to render text in an angle. But I was wondering whether it is possible to change the text angle midway through the string?
Something like this : Draw rotated text on curved path
But using matplotlib.
Here is my take on the problem:
In order to make the text robust to figure adjustments after drawing, I derive a child class, CurvedText, from matplotlib.text. The CurvedText object takes a string and a curve in the form of x- and y-value arrays. The text to be displayed itself is cut into separate characters, which each are added to the plot at the appropriate position. As matplotlib.text draws nothing if the string is empty, I replace all spaces by invisible 'a's. Upon figure adjustment, the overloaded draw() calls the update_positions() function, which takes care that the character positions and orientations stay correct. To assure the calling order (each character's draw() function will be called as well) the CurvedText object also takes care that the zorder of each character is higher than its own zorder. Following my example here, the text can have any alignment. If the text cannot be fit to the curve at the current resolution, the rest will be hidden, but will appear upon resizing. Below is the code with an example of application.
from matplotlib import pyplot as plt
from matplotlib import patches
from matplotlib import text as mtext
import numpy as np
import math
class CurvedText(mtext.Text):
"""
A text object that follows an arbitrary curve.
"""
def __init__(self, x, y, text, axes, **kwargs):
super(CurvedText, self).__init__(x[0],y[0],' ', **kwargs)
axes.add_artist(self)
##saving the curve:
self.__x = x
self.__y = y
self.__zorder = self.get_zorder()
##creating the text objects
self.__Characters = []
for c in text:
if c == ' ':
##make this an invisible 'a':
t = mtext.Text(0,0,'a')
t.set_alpha(0.0)
else:
t = mtext.Text(0,0,c, **kwargs)
#resetting unnecessary arguments
t.set_ha('center')
t.set_rotation(0)
t.set_zorder(self.__zorder +1)
self.__Characters.append((c,t))
axes.add_artist(t)
##overloading some member functions, to assure correct functionality
##on update
def set_zorder(self, zorder):
super(CurvedText, self).set_zorder(zorder)
self.__zorder = self.get_zorder()
for c,t in self.__Characters:
t.set_zorder(self.__zorder+1)
def draw(self, renderer, *args, **kwargs):
"""
Overload of the Text.draw() function. Do not do
do any drawing, but update the positions and rotation
angles of self.__Characters.
"""
self.update_positions(renderer)
def update_positions(self,renderer):
"""
Update positions and rotations of the individual text elements.
"""
#preparations
##determining the aspect ratio:
##from https://stackoverflow.com/a/42014041/2454357
##data limits
xlim = self.axes.get_xlim()
ylim = self.axes.get_ylim()
## Axis size on figure
figW, figH = self.axes.get_figure().get_size_inches()
## Ratio of display units
_, _, w, h = self.axes.get_position().bounds
##final aspect ratio
aspect = ((figW * w)/(figH * h))*(ylim[1]-ylim[0])/(xlim[1]-xlim[0])
#points of the curve in figure coordinates:
x_fig,y_fig = (
np.array(l) for l in zip(*self.axes.transData.transform([
(i,j) for i,j in zip(self.__x,self.__y)
]))
)
#point distances in figure coordinates
x_fig_dist = (x_fig[1:]-x_fig[:-1])
y_fig_dist = (y_fig[1:]-y_fig[:-1])
r_fig_dist = np.sqrt(x_fig_dist**2+y_fig_dist**2)
#arc length in figure coordinates
l_fig = np.insert(np.cumsum(r_fig_dist),0,0)
#angles in figure coordinates
rads = np.arctan2((y_fig[1:] - y_fig[:-1]),(x_fig[1:] - x_fig[:-1]))
degs = np.rad2deg(rads)
rel_pos = 10
for c,t in self.__Characters:
#finding the width of c:
t.set_rotation(0)
t.set_va('center')
bbox1 = t.get_window_extent(renderer=renderer)
w = bbox1.width
h = bbox1.height
#ignore all letters that don't fit:
if rel_pos+w/2 > l_fig[-1]:
t.set_alpha(0.0)
rel_pos += w
continue
elif c != ' ':
t.set_alpha(1.0)
#finding the two data points between which the horizontal
#center point of the character will be situated
#left and right indices:
il = np.where(rel_pos+w/2 >= l_fig)[0][-1]
ir = np.where(rel_pos+w/2 <= l_fig)[0][0]
#if we exactly hit a data point:
if ir == il:
ir += 1
#how much of the letter width was needed to find il:
used = l_fig[il]-rel_pos
rel_pos = l_fig[il]
#relative distance between il and ir where the center
#of the character will be
fraction = (w/2-used)/r_fig_dist[il]
##setting the character position in data coordinates:
##interpolate between the two points:
x = self.__x[il]+fraction*(self.__x[ir]-self.__x[il])
y = self.__y[il]+fraction*(self.__y[ir]-self.__y[il])
#getting the offset when setting correct vertical alignment
#in data coordinates
t.set_va(self.get_va())
bbox2 = t.get_window_extent(renderer=renderer)
bbox1d = self.axes.transData.inverted().transform(bbox1)
bbox2d = self.axes.transData.inverted().transform(bbox2)
dr = np.array(bbox2d[0]-bbox1d[0])
#the rotation/stretch matrix
rad = rads[il]
rot_mat = np.array([
[math.cos(rad), math.sin(rad)*aspect],
[-math.sin(rad)/aspect, math.cos(rad)]
])
##computing the offset vector of the rotated character
drp = np.dot(dr,rot_mat)
#setting final position and rotation:
t.set_position(np.array([x,y])+drp)
t.set_rotation(degs[il])
t.set_va('center')
t.set_ha('center')
#updating rel_pos to right edge of character
rel_pos += w-used
if __name__ == '__main__':
Figure, Axes = plt.subplots(2,2, figsize=(7,7), dpi=100)
N = 100
curves = [
[
np.linspace(0,1,N),
np.linspace(0,1,N),
],
[
np.linspace(0,2*np.pi,N),
np.sin(np.linspace(0,2*np.pi,N)),
],
[
-np.cos(np.linspace(0,2*np.pi,N)),
np.sin(np.linspace(0,2*np.pi,N)),
],
[
np.cos(np.linspace(0,2*np.pi,N)),
np.sin(np.linspace(0,2*np.pi,N)),
],
]
texts = [
'straight lines work the same as rotated text',
'wavy curves work well on the convex side',
'you even can annotate parametric curves',
'changing the plotting direction also changes text orientation',
]
for ax, curve, text in zip(Axes.reshape(-1), curves, texts):
#plotting the curve
ax.plot(*curve, color='b')
#adjusting plot limits
stretch = 0.2
xlim = ax.get_xlim()
w = xlim[1] - xlim[0]
ax.set_xlim([xlim[0]-stretch*w, xlim[1]+stretch*w])
ylim = ax.get_ylim()
h = ylim[1] - ylim[0]
ax.set_ylim([ylim[0]-stretch*h, ylim[1]+stretch*h])
#adding the text
text = CurvedText(
x = curve[0],
y = curve[1],
text=text,#'this this is a very, very long text',
va = 'bottom',
axes = ax, ##calls ax.add_artist in __init__
)
plt.show()
The result looks like this:
There are still some problems, when the text follows the concave side of a sharply bending curve. This is because the characters are 'stitched together' along the curve without accounting for overlap. If I have time, I'll try to improve on that. Any comments are very welcome.
Tested on python 3.5 and 2.7
I found your problem quite interesting, so I made something which comes pretty close using the matplotlib text tool:
from __future__ import division
import itertools
import matplotlib.pyplot as plt
import numpy as np
%matplotlib inline
# define figure and axes properties
fig, ax = plt.subplots(figsize=(8,6))
ax.set_xlim(left=0, right=10)
ax.set_ylim(bottom=-1.5, top=1.5)
(xmin, xmax), (ymin, ymax) = ax.get_xlim(), ax.get_ylim()
# calculate a shape factor, more explanation on usage further
# it is a representation of the distortion of the actual image compared to a
# cartesian space:
fshape = abs(fig.get_figwidth()*(xmax - xmin)/(ymax - ymin)/fig.get_figheight())
# the text you want to plot along your line
thetext = 'the text is flowing '
# generate a cycler, so that the string is cycled through
lettercycler = itertools.cycle(tuple(thetext))
# generate dummy river coordinates
xvals = np.linspace(1, 10, 300)
yvals = np.sin(xvals)**3
# every XX datapoints, a character is printed
markerevery = 10
# calculate the rotation angle for the labels (in degrees)
# the angle is calculated as the slope between two datapoints.
# it is then multiplied by a shape factor to get from the angles in a
# cartesian space to the angles in this figure
# first calculate the slope between two consecutive points, multiply with the
# shape factor, get the angle in radians with the arctangens functions, and
# convert to degrees
angles = np.rad2deg(np.arctan((yvals[1:]-yvals[:-1])/(xvals[1:]-xvals[:-1])*fshape))
# plot the 'river'
ax.plot(xvals, yvals, 'b', linewidth=3)
# loop over the data points, but only plot a character every XX steps
for counter in np.arange(0, len(xvals)-1, step=markerevery):
# plot the character in between two datapoints
xcoord = (xvals[counter] + xvals[counter+1])/2.
ycoord = (yvals[counter] + yvals[counter+1])/2.
# plot using the text method, set the rotation so it follows the line,
# aling in the center for a nicer look, optionally, a box can be drawn
# around the letter
ax.text(xcoord, ycoord, lettercycler.next(),
fontsize=25, rotation=angles[counter],
horizontalalignment='center', verticalalignment='center',
bbox=dict(facecolor='white', edgecolor='white', alpha=0.5))
The implementation is far from perfect, but it is a good starting point in my opinion.
Further, it seems that there is some development in matplotlib on having a scatterplot with rotation of the markers, which would be ideal for this case. However, my programming skills are nearly not as hardcore as they need to be to tackle this issue, so I cannot help here.
matplotlib on github: pull request
matplotlib on github: issue