We Keep Coding

Change in coordinate density for np.meshgrid() in matplotlib

I am plotting a vector field using the numpy function quiver() and it works. But I would like to emphasize the cowlick in the following plot:
I am not sure how to go about it, but increasing the density of arrows in the center could possibly do the trick. To do so, I would like to resort to some option within np.meshgrid() that would allow me to get more tightly packed x,y coordinate points in the center. A linear, quadratic or other specification does not seem to be built in. I am not sure if sparse can be modified to this end.
The code:
lim = 10
int = 0.22 *lim
x,y = np.meshgrid(np.arange(-lim, lim, int), np.arange(-lim, lim, int))
u = 3 * np.cos(np.arctan2(y,x)) - np.sqrt(x**2+y**2) * np.sin(np.arctan2(y,x))
v = 3 * np.sin(np.arctan2(y,x)) + np.sqrt(x**2+y**2) * np.cos(np.arctan2(y,x))
color = x**2 + y**2
plt.rcParams["image.cmap"] = "Greys_r"
mult = 1
plt.figure(figsize=(mult*lim, mult*lim))
plt.quiver(x,y,u,v,color, linewidths=.006, lw=.1)
plt.show()
Closing the loop on this, thanks to the accepted answer I was able to finally strike a balance between the density of the mesh as I learned from to do from #flwr and keeping the "cowlick" structure of the vector field conspicuous (avoiding the radial structure around the origin as much as possible):

You can construct the points whereever you want to calculate your field on and quivers will be happy about it. The code below uses polar coordinates and stretches the radial coordinate non-linearly.
import numpy as np
import matplotlib.pyplot as plt
lim = 10
N = 10
theta = np.linspace(0.1, 2*np.pi, N*2)
stretcher_factor = 2
r = np.linspace(0.3, lim**(1/stretcher_factor), N)**stretcher_factor
R, THETA = np.meshgrid(r, theta)
x = R * np.cos(THETA)
y = R * np.sin(THETA)
# x,y = np.meshgrid(x, y)
r = x**2 + y**2
u = 3 * np.cos(THETA) - np.sqrt(r) * np.sin(THETA)
v = 3 * np.sin(THETA) + np.sqrt(r) * np.cos(THETA)
plt.rcParams["image.cmap"] = "Greys_r"
mult = 1
plt.figure(figsize=(mult*lim, mult*lim))
plt.quiver(x,y,u,v,r, linewidths=.006, lw=.1)
Edit: Bug taking meshgrid twice

np.meshgrid just makes a grid of the vectors you provide.
What you could do is contract this regular grid in the center to have more points in the center (best visible with more points), e.g. like so:
# contract in the center
a = 0.5 # how far to contract
b = 0.8 # how strongly to contract
c = 1 - b*np.exp(-((x/lim)**2 + (y/lim)**2)/a**2)
x, y = c*x, c*y
plt.plot(x,y,'.k')
plt.show()
Alternatively you can x,y cooridnates that are not dependent on a grid at all:
x = np.random.randn(500)
y = np.random.randn(500)
plt.plot(x,y,'.k')
plt.show()
But I think you'd prefer a slightly more regular patterns you could look into poisson disk sampling with adaptive distances or something like that, but the key point here is that for using quiver, you can use ANY set of coordinates, they do not have to be in a regular grid.

Generate profiles through a 2D array at an angle without altering pixels

I'd like to plot two profiles through the highest intensity point in a 2D numpy array, which is an image of a blob (i.e. a line through the semi-major axis, and another line through the semi-minor axis). The blob is rotated at an angle theta counterclockwise from the standard x-axis and is asymmetric.
It is a 600x600 array with a max intensity of 1 (at only one pixel) that is located right at the center at (300, 300). The angle rotation from the x-axis (which then gives the location of the semi-major axis when rotated by that angle) is theta = 89.54 degrees. I do not want to use scipy.ndimage.rotate because it uses spline interpolation, and I do not want to change any of my pixel values. But I suppose a nearest-neighbor interpolation method would be okay.
I tried generating lines corresponding to the major and minor axes across the image, but the result was not right at all (the peak was far less than 1), so maybe I did something wrong. The code for this is below:
import numpy as np
import matplotlib.pyplot as plt
from scipy import ndimage
def profiles_at_angle(image, axis, theta):
theta = np.deg2rad(theta)
if axis == 'major':
x_0, y_0 = 0, 300-300*np.tan(theta)
x_1, y_1 = 599, 300+300*np.tan(theta)
elif axis=='minor':
x_0, y_0 = 300-300*np.tan(theta), 599
x_1, y_1 = 300+300*np.tan(theta), -599
num = 600
x, y = np.linspace(x_0, x_1, num), np.linspace(y_0, y_1, num)
z = ndimage.map_coordinates(image, np.vstack((x,y)))
fig, axes = plt.subplots(nrows=2)
axes[0].imshow(image, cmap='gray')
axes[0].axis('image')
axes[1].plot(z)
plt.xlim(250,350)
plt.show()
profiles_at_angle(image, 'major', theta)
Did I do something obviously wrong in my code above? Or how else can I accomplish this? Thank you.
Edit: Here are some example images. Sorry for the bad quality; my browser crashed every time I tried uploading them anywhere so I had to take photos of the screen.
Figure 1: This is the result of my code above, which is clearly wrong since the peak should be at 1. I'm not sure what I did wrong though.
Figure 2: I made this plot below by just taking the profiles through the standard x and y axes, ignoring any rotation (this only looks good coincidentally because the real angle of rotation is so close to 90 degrees, so I was able to just switch the labels and get this). I want my result to look something like this, but taking the correction rotation angle into account.
Edit: It could be useful to run tests on this method using data very much like my own (it's a 2D Gaussian with nearly the same parameters):
image = np.random.random((600,600))
def generate(data_set):
xvec = np.arange(0, np.shape(data_set)[1], 1)
yvec = np.arange(0, np.shape(data_set)[0], 1)
X, Y = np.meshgrid(xvec, yvec)
return X, Y
def gaussian_func(xy, x0, y0, sigma_x, sigma_y, amp, theta, offset):
x, y = xy
a = (np.cos(theta))**2/(2*sigma_x**2) + (np.sin(theta))**2/(2*sigma_y**2)
b = -np.sin(2*theta)/(4*sigma_x**2) + np.sin(2*theta)/(4*sigma_y**2)
c = (np.sin(theta))**2/(2*sigma_x**2) + (np.cos(theta))**2/(2*sigma_y**2)
inner = a * (x-x0)**2
inner += 2*b*(x-x0)*(y-y0)
inner += c * (y-y0)**2
return (offset + amp * np.exp(-inner)).ravel()
xx, yy = generate(image)
image = gaussian_func((xx.ravel(), yy.ravel()), 300, 300, 5, 4, 1, 1.56, 0)
image = np.reshape(image, (600, 600))

This should do it for you. You just did not properly compute your lines.
theta = 65
peak = np.argwhere(image==1)[0]
x = np.linspace(peak[0]-100,peak[0]+100,1000)
y = lambda x: (x-peak[1])*np.tan(np.deg2rad(theta))+peak[0]
y_maj = np.linspace(y(peak[1]-100),y(peak[1]+100),1000)
y = lambda x: -(x-peak[1])/np.tan(np.deg2rad(theta))+peak[0]
y_min = np.linspace(y(peak[1]-100),y(peak[1]+100),1000)
del y
z_min = scipy.ndimage.map_coordinates(image, np.vstack((x,y_min)))
z_maj = scipy.ndimage.map_coordinates(image, np.vstack((x,y_maj)))
fig, axes = plt.subplots(nrows=2)
axes[0].imshow(image)
axes[0].plot(x,y_maj)
axes[0].plot(x,y_min)
axes[0].axis('image')
axes[1].plot(z_min)
axes[1].plot(z_maj)
plt.show()

How to make a fittable Ring Gaussian model in python?

The purpose of my experiment is to fit a ring gaussian model to image data and find out the parameters of elliptical or ring Gaussian object in an image.
I've tried Astropy to make a Ring Gaussian model for simplicity and trial. Unfortunately, it's completely different from my artificial data.
from astropy.modeling import Fittable2DModel, Parameter, fitting
import matplotlib.pyplot as plt
import numpy as np
class ringGaussian(Fittable2DModel):
background = Parameter(default=5.)
amplitude = Parameter(default=1500.)
x0 = Parameter(default=15.)
y0 = Parameter(default=15.)
radius = Parameter(default=2.)
width = Parameter(default=1.)
#staticmethod
def evaluate(x, y, background, amplitude, x0, y0, radius, width):
z = background + amplitude * np.exp( -((np.sqrt((x-x0)**2. + (y-y0)**2.) - radius) / width)**2 )
return z
Then I made some artificial data (initial parameters) to test the fitting function of ring gaussian class.
back = 10 # background
amp = 2000 # highest value of the Gaussian
x0 = 10 # x coordinate of center
y0 = 10 # y coordinate of center
radius = 3
width = 1
xx, yy = np.mgrid[:30, :30]
z = back + amp * np.exp( -((np.sqrt((xx-x0)**2. + (yy-y0)**2.) - radius) / width)**2 )
I plotted xx, yy and z using contourf:
fig = plt.subplots(figsize=(7,7))
plt.contourf(xx,yy,z)
plt.show()
It is what I got:
enter image description here
Then I tried to fit the z using my fittable class:
p_init = ringGaussian() #bounds={"x0":[0., 20.], "y0":[0., 20.]}
fit_p = fitting.LevMarLSQFitter()
p = fit_p(p_init, xx, yy, z)
# It is the parameter I got:
<ringGaussian(background=133.0085329497139, amplitude=-155.53652181827655, x0=25.573499373946227, y0=25.25813520725603, radius=8.184302497405568, width=-7.273935403490675)>
I plotted the model:
fig = plt.subplots(figsize=(7,7))
plt.contourf(xx,yy,p(xx,yy))
plt.show()
It is what I got:
enter image description here
Originally, I also tried to include the derivative in my class:
#staticmethod
def fit_deriv(x, y, background, amplitude, x0, y0, radius, width):
g = (np.sqrt((x-x0)**2. + (y-y0)**2.) - radius) / width
z = amplitude * np.exp( -g**2 )
dg_dx0 = - (x-x0)/np.sqrt((x-x0)**2. + (y-y0)**2.)
dg_dy0 = - (y-y0)/np.sqrt((x-x0)**2. + (y-y0)**2.)
dg_dr0 = - 1/width
dg_dw0 = g * -1/width
dz_dB = 1.
dz_dA = z / amplitude
dz_dx0 = -2 * z * g**3 * dg_dx0
dz_dy0 = -2 * z * g**3 * dg_dy0
dz_dr0 = -2 * z * g**3 * dg_dr0
dz_dw0 = -2 * z * g**3 * dg_dw0
return [dz_dB, dz_dA, dz_dx0, dz_dy0, dz_dr0, dz_dw0]
But it returned "ValueError: setting an array element with a sequence."
I'm quite desperate now. Can anyone suggest some possible solutions? or alternative ways to implement the ring gaussian fit in python?
Many many thanks~~~

Your implementation is OK (I did not try or check your fit_deriv implementation).
The issue is just that your fit doesn't converge because the initial model parameters are too far from the true values, so the optimiser fails. When I run your code, I get this warning:
WARNING: The fit may be unsuccessful; check fit_info['message'] for more information. [astropy.modeling.fitting]
If you change to model parameters so that your model roughly matches the data, the fit succeeds:
p_init = ringGaussian(x0=11, y0=11)
To check how your model compares with the data, you can use imshow to display data and model images (or also e.g. residual images):
plt.imshow(z)
plt.imshow(p_init(xx,yy))
plt.imshow(p(xx,yy))

Fitting 2D sum of gaussians, scipy.optimise.leastsq (Ans: Use curve_fit!)

I want to fit an 2D sum of gaussians to this data:
After failing at fitting a sum to this initially I instead sampled each peak separately (image) and returned a fit by find it's moments (essentially using this code).
Unfortunately, this results in an incorrect peak position measurement, due to the overlapping signal of the neighbouring peaks. Below is a plot of the sum of the separate fits. Obviously their peak all lean toward the centre. I need to account for this in order to return the correct peak position.
I've got working code which plots a 2D gaussian envelope function (twoD_Gaussian()), and I parse this through optimize.leastsq as a 1D array using numpy.ravel and an appropriate error function, however this results in a nonsense output.
I tried fitting a single peak within the sum and get the following erroneous output:
I'd appreciate any advice on what i could try to make this work, or alternative approaches if this isn't appropriate. All input welcomed of course!
Code below:
from scipy.optimize import leastsq
import numpy as np
import matplotlib.pyplot as plt
def twoD_Gaussian(amp0, x0, y0, amp1=13721, x1=356, y1=247, amp2=14753, x2=291, y2=339, sigma=40):
x0 = float(x0)
y0 = float(y0)
x1 = float(x1)
y1 = float(y1)
x2 = float(x2)
y2 = float(y2)
return lambda x, y: (amp0*np.exp(-(((x0-x)/sigma)**2+((y0-y)/sigma)**2)/2))+(
amp1*np.exp(-(((x1-x)/sigma)**2+((y1-y)/sigma)**2)/2))+(
amp2*np.exp(-(((x2-x)/sigma)**2+((y2-y)/sigma)**2)/2))
def fitgaussian2D(x, y, data, params):
"""Returns (height, x, y, width_x, width_y)
the gaussian parameters of a 2D distribution found by a fit"""
errorfunction = lambda p: np.ravel(twoD_Gaussian(*p)(*np.indices(np.shape(data))) - data)
p, success = optimize.leastsq(errorfunction, params)
return p
# Create data indices
I = image # Red channel of a scanned image, equivalent to the 1st image displayed in this post.
p = np.asarray(I).astype('float')
w,h = np.shape(I)
x, y = np.mgrid[0:h, 0:w]
xy = (x,y)
# scanned at 150 dpi = 5.91 dots per mm
dpmm = 5.905511811
plot_width = 40*dpmm
# create function indices
fdims = np.round(plot_width/2)
xdims = (RC[0] - fdims, RC[0] + fdims)
ydims = (RC[1] - fdims, RC[1] + fdims)
fx = np.linspace(xdims[0], xdims[1], np.round(plot_width))
fy = np.linspace(ydims[0], ydims[1], np.round(plot_width))
fx,fy = np.meshgrid(fx,fy)
#Crop image for display
crp_data = image[xdims[0]:xdims[1], ydims[0]:ydims[1]]
z = crp_data
# Parameters obtained from separate fits
Amplitudes = (13245, 13721, 15374)
px = (410, 356, 290)
py = (350, 247, 339)
initial_guess_sum = (Amp[0], px[0], py[0], Amp[1], px[1], py[1], Amp[2], px[2], py[2])
initial_guess_peak3 = (Amp[0], px[0], py[0]) # Try fitting single peak within sum
fitted_pars = fitgaussian2D(x, y, z, initial_guess_sum)
#fitted_pars = fitgaussian2D(x, y, z, initial_guess_peak3)
data_fitted= twoD_Gaussian(*fitted_pars)(fx,fy)
#data_fitted= twoD_Gaussian(*initial_guess_sum)(fx,fy)
fig = plt.figure(figsize=(10, 30))
ax = fig.add_subplot(111, aspect="equal")
#fig, ax = plt.subplots(1)
cb = ax.imshow(p, cmap=plt.cm.jet, origin='bottom',
extent=(x.min(), x.max(), y.min(), y.max()))
ax.contour(fx, fy, data_fitted.reshape(fx.shape[0], fy.shape[1]), 4, colors='w')
ax.set_xlim(np.int(RC[0])-135, np.int(RC[0])+135)
ax.set_ylim(np.int(RC[1])+135, np.int(RC[1])-135)
#plt.colorbar(cb)
plt.show()

I tried any number of other things before giving up and trying curve_fit again, albeit with more knowledge of parsing lambda functions. It worked. Example output and code below (still with redundancies) for the sake of posterity.
def twoD_Gaussian(amp0, x0, y0, amp1=13721, x1=356, y1=247, amp2=14753, x2=291, y2=339, sigma=40):
x0 = float(x0)
y0 = float(y0)
x1 = float(x1)
y1 = float(y1)
x2 = float(x2)
y2 = float(y2)
return lambda x, y: (amp0*np.exp(-(((x0-x)/sigma)**2+((y0-y)/sigma)**2)/2))+(
amp1*np.exp(-(((x1-x)/sigma)**2+((y1-y)/sigma)**2)/2))+(
amp2*np.exp(-(((x2-x)/sigma)**2+((y2-y)/sigma)**2)/2))
def twoD_GaussianCF(xy, amp0, x0, y0, amp1=13721, amp2=14753, x1=356, y1=247, x2=291, y2=339, sigma_x=12, sigma_y=12):
x0 = float(x0)
y0 = float(y0)
x1 = float(x1)
y1 = float(y1)
x2 = float(x2)
y2 = float(y2)
g = (amp0*np.exp(-(((x0-x)/sigma_x)**2+((y0-y)/sigma_y)**2)/2))+(
amp1*np.exp(-(((x1-x)/sigma_x)**2+((y1-y)/sigma_y)**2)/2))+(
amp2*np.exp(-(((x2-x)/sigma_x)**2+((y2-y)/sigma_y)**2)/2))
return g.ravel()
# Create data indices
I = image # Red channel of a scanned image, equivalent to the 1st image displayed in this post.
p = np.asarray(I).astype('float')
w,h = np.shape(I)
x, y = np.mgrid[0:h, 0:w]
xy = (x,y)
N_points = 3
display_width = 80
initial_guess_sum = (Amp[0], px[0], py[0], Amp[1], px[1], py[1], Amp[2], px[2], py[2])
popt, pcov = opt.curve_fit(twoD_GaussianCF, xy, np.ravel(p), p0=initial_guess_sum)
data_fitted= twoD_Gaussian(*popt)(x,y)
peaks = [(popt[1],popt[2]), (popt[5],popt[6]), (popt[7],popt[8])]
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, aspect="equal")
cb = ax.imshow(p, cmap=plt.cm.jet, origin='bottom',
extent=(x.min(), x.max(), y.min(), y.max()))
ax.contour(x, y, data_fitted.reshape(x.shape[0], y.shape[1]), 20, colors='w')
ax.set_xlim(np.int(RC[0])-135, np.int(RC[0])+135)
ax.set_ylim(np.int(RC[1])+135, np.int(RC[1])-135)
for k in range(0,N_points):
plt.plot(peaks[k][0],peaks[k][1],'bo',markersize=7)
plt.show()

If all you care about is the centroid of each gaussian, I would just go with scipy.optimize.minimize. Multiply your data by -1 and then do some coarse sampling to find minima. The height of each peak will be offset by the neighboring gaussians but the positions are unchanged, so if you find a local extreme value then that must be the centroid of a gaussian.
If you need the other parameters, it might make sense to find the centroids as I suggest and then use leastsq to find the amplitudes and widths. It might add a lot of overhead if you're running these fits many times, but it would significantly reduce the number of free parameters in the least squares fit.

Buggy behavior in matplotlib pcolormesh with FFT arrays?

I am trying to reproduce the example of the Gabor transform that it is in his wikipedia entry, and I do not know if it is a bug or I am missing something. The example is the calculate the Gabor transform of a sinusoidal signal:
To plot the frequencies sorted, I create an unsorted axis. Then I use mesh grid to create 2D axes and plot with pcolormesh. Here is the piece of the code:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridsp
dt = 0.05
x = np.arange(-50.0,50.0,dt)
y = np.sin(2.0 * np.pi * x)
Nx = len(x)
w = np.fft.fftfreq(Nx,dt)
sigma = 1.0 / 3.0
neg = np.where (x <= 0.0)
pos = np.where (x > 0.0)
T,W = np.meshgrid(x,w)
func = np.zeros(Nx)
tmp = np.zeros(Nx,dtype='complex64')
gabor = np.zeros((Nx,Nx))
func[neg] = np.sin(2.0 * np.pi * x[neg])
func[pos] = np.sin(4.0 * np.pi * x[pos])
for it in range(Nx):
tmp[:] = np.fft.fft(func[:] * np.exp( - ( x[it] - x[:] ) * ( x[it] - x[:] ) / 2.0 / sigma / sigma ) )
gabor[:,it] = np.real(np.conj(tmp) * tmp)
fig = plt.figure(figsize=(20,10),facecolor='white')
gs = gridsp.GridSpec(2, 1)
ax1 = plt.subplot(gs[0,0])
ax1.plot(x,func,'r',linewidth=2)
ax1.axis('tight')
ax1.set_xticks(np.arange(min(x),max(x),1.) )
ax1.set_xlabel('time',fontsize=20)
ax1.set_ylabel(r'$\sin{time}$',fontsize=20)
ax1.set_xlim([-6.0,6.0])
ax2 = plt.subplot(gs[1,0])
surf1 = ax2.pcolormesh(T,W,gabor,shading='gouraud')
ax2.axis('tight')
ax2.set_xticks(np.arange(min(x),max(x),2.) )
ax2.set_yticks(np.arange(min(w),max(w),2.) )
ax2.set_xlabel('time',fontsize=20)
ax2.set_ylabel('frequency',fontsize=20)
ax2.set_xlim([-6.0,6.0])
ax2.set_ylim([-4.0,4.0])
gs.tight_layout(fig)
plt.show()
Here is the figure I get,
It seems that the upper part of the plot is reduced to zero. If I try it using fftshift when I create the transform and the axis,
for it in range(Nx):
tmp[:] = np.fft.fftshift(np.fft.fft(func[:] * np.exp( - ( x[it] - x[:] ) * ( x[it] - x[:] ) / 2.0 / sigma / sigma ) ) )
gabor[:,it] = np.real(np.conj(tmp) * tmp)
T,W = np.meshgrid(x,np.fft.fftshift(w))
Then I get this figure:
!
It seems that pcolormesh routine can not flip upside down the array as it is usually done in 1D plots. does anybody know exactly why it is doing this?
Thanks,
Alex

The problem lies in W. Or actually in w. When w is plotted:
Thus pcolormesh receives non-monotonic Y coordinates and gets confused. If you look at the description of pcolor or pcolormesh it is clear they cannot do anything reasonable with non-monotonic data.
So, your gabor is fine:
ax.imshow(gabor)
as you can see:
There are several possibilities how to fix this. One of them is to feed both W and gabor to fftshift that way the frequencies will roll back to monotonic. Or - if you want to have the figure as above (negative frequencies on the top), just add the maximum frequency to all negative values of W.
It might also be cleaner to supply pcolormesh with x and w instead of T and W.
If you want performance, you might be better of with imshow (it can be used when the data is equispaced in both dimensions. The only slight problem is the calculation of extents (which actually may be slightly off even in the question). The extents tell the outer limets of the highest, lowest, leftmost and rightmost pixels. However, the pixel vectors only tell the centers of the pixels.
We need to know the following:
number of points in X direction (num_x)
number of points in Y direction (num_y)
value of the first and last x sample (x0, x1)
value of the first and last y sample (y0, y1)
After that we can use imshow to show the data with correct scaling:
dx = 1. * (x1 - x0) / (num_x-1)
dy = 1. * (y1 - y0) / (num_y-1)
ax.imshow(img, extent=[x0 - dx/2, x1 + dx/2, y0 - dy/2, y1 + dy/2], origin='lower', interpolation='nearest')
So, applied to the question's data:
gabor_shifted = np.fft.fftshift(gabor, axes=0)
w_shifted = np.fft.fftshift(w)
x0 = x[0]
x1 = x[-1]
w0 = w_shifted[0]
w1 = w_shifted[-1]
dx = 1.*(x1-x0) / (len(x) - 1)
dw = 1.*(w1-w0) / (len(w) - 1)
ax2.imshow(gabor_shifted, extent=[x0-dx/2, x1+dx/2, w0-dw/2, w1+dw/2], interpolation='nearest', origin='lower', aspect='auto')
ax2.grid('on', color='w')
ax2.ylim(-4,4)
which gives: