Context: I'm trying to display the gradients as fixed-length lines on a plot of gradient noise. Each "gradient" can be seen as a tangent on a given point. The issue is, even if I make sure the lines have the same length, the aspect ratio stretches them:
The complete code to generate this:
from math import sqrt, floor, modf, sin
import matplotlib.pyplot as plt
mix = lambda a, b, x: a*(1-x) + b*x
interpolant = lambda t: ((6*t - 15)*t + 10)*t*t*t
rng01 = lambda x: modf(sin(x) * 43758.5453123)[0]
def _gradient_noise(t):
i = floor(t)
f = t - i
s0 = rng01(i) * 2 - 1
s1 = rng01(i + 1) * 2 - 1
v0 = s0 * f;
v1 = s1 * (f - 1);
return mix(v0, v1, interpolant(f))
def _plot_noise(n, interp_npoints=100):
xdata = [i/interp_npoints for i in range(n * interp_npoints)]
gnoise = [_gradient_noise(x) for x in xdata]
plt.plot(xdata, gnoise, label='gradient noise')
plt.xlabel('t')
plt.ylabel('amplitude')
plt.grid(linestyle=':')
plt.legend()
for i in range(n + 1):
a = rng01(i) * 2 - 1 # gradient slope
norm = sqrt(1 + a**2)
norm *= 4 # 1/4 length
vnx, vny = 1/norm, a/norm
x = (i-vnx/2, i+vnx/2)
y = (-vny/2, vny/2)
plt.plot(x, y, 'r-')
plt.show()
if __name__ == '__main__':
_plot_noise(15)
The red-lines drawing is located in the for-loop.
hypot(x[1]-x[0], y[1]-y[0]) gives me a constant .25 for every vector, which corresponds to my target length (¼). Which means my segments are actually in the correct length for the given aspect. This can also be "verified" with .set_aspect(1):
I've tried several things, such as translating the coordinates into display coordinates (plt.gca().transData.transform(...)), scale them, then back again (plt.gca().transData.inverted().transform(...)), without success (as if the aspect was applied on top of the display coordinates). Doing that would probably also actually change the angles as well anyway.
So to sum up: I'm looking for a way to display lines with a fixed length (expressed in the x data coordinates system), and oriented (rotated) in the xy data coordinates system.
Welcome to SO. What a well asked first question. It made me question my sanity for a hot second once I reproduced the plot and the math checked out...
However, you identified the core problem yourself: the issue is that in your code the length of the gradient lines is determined in data coordinates, when it should be dependent on the aspect ratio of the plot.
So, if you want the gradient lines to be of uniform length in display space then you need to rescale the either the dx or the dy component by the aspect ratio of the plot (or its inverse, respectively) when computing then norm:
import matplotlib.pyplot as plt
from math import sqrt, floor
mix = lambda a, b, x: a*(1-x) + b*x
interpolant = lambda t: ((6*t - 15)*t + 10)*t*t*t
rng01 = lambda x: ((1103515245*x + 12345) % 2**32) / 2**32
def _gradient_noise(t):
i = floor(t)
f = t - i
s0 = rng01(i) * 2 - 1
s1 = rng01(i + 1) * 2 - 1
v0 = s0 * f;
v1 = s1 * (f - 1);
return mix(v0, v1, interpolant(f))
def _plot_noise(n, interp_npoints=100):
xdata = [i/interp_npoints for i in range(n * interp_npoints)]
gnoise = [_gradient_noise(x) for x in xdata]
fig, ax = plt.subplots()
ax.plot(xdata, gnoise, label='gradient noise')
ax.set_xlabel('t')
ax.set_ylabel('amplitude')
ax.grid(linestyle=':')
ax.legend(loc=1)
x0, x1, y0, y1 = ax.axis()
aspect = (y1 - y0) / (x1 - x0)
for i in range(n + 1):
dy = rng01(i) * 2 - 1 # gradient slope
dx = 1
norm = sqrt(dx**2 + (dy / aspect)**2)
# norm *= 4 # 1/4 length
vnx, vny = dx/norm, dy/norm
x = (i-vnx/2, i+vnx/2)
y = (-vny/2, vny/2)
ax.plot(x, y, 'r-')
plt.show()
if __name__ == '__main__':
_plot_noise(15)
Final code with proper aspect ratio and resize event handled:
import matplotlib.pyplot as plt
from matplotlib.patches import Ellipse
from math import hypot, floor, modf, sin
mix = lambda a, b, x: a*(1-x) + b*x
interpolant = lambda t: ((6*t - 15)*t + 10)*t*t*t
rng01 = lambda x: modf(sin(x) * 43758.5453123)[0]
def _gradient_noise(t):
i = floor(t)
f = t - i
s0 = rng01(i) * 2 - 1
s1 = rng01(i + 1) * 2 - 1
v0 = s0 * f;
v1 = s1 * (f - 1);
return mix(v0, v1, interpolant(f))
def _get_ar(ax):
fs = ax.figure.get_size_inches()
pos = ax.get_position(original=False)
return 1 / (ax.get_data_ratio() * (fs[0] * pos.width) / (fs[1] * pos.height))
def _get_line_coords(aspect, i):
dx, dy = 1, rng01(i) * 2 - 1 # gradient slope
norm = hypot(dx, dy * aspect)
vnx, vny = dx/norm, dy/norm
x = (i-vnx/2, i+vnx/2)
y = (-vny/2, vny/2)
return x, y
def _plot_noise(n, interp_npoints=100):
xdata = [i/interp_npoints for i in range(n * interp_npoints)]
gnoise = [_gradient_noise(x) for x in xdata]
fig, ax = plt.subplots()
ax.plot(xdata, gnoise, label='gradient noise')
ax.set_xlabel('t')
ax.set_ylabel('amplitude')
ax.grid(linestyle=':')
ax.legend(loc=1)
xlim = ax.get_xlim()
ylim = ax.get_ylim()
aspect = _get_ar(ax)
resize_objects = []
for i in range(n + 1):
lx, ly = _get_line_coords(aspect, i)
line = ax.plot(lx, ly, 'r-')[0]
ellipse = Ellipse(xy=(i, 0), width=1, height=1/aspect, fill=False, linestyle=':')
ax.add_patch(ellipse)
resize_objects.append((line, ellipse))
def _onresize(event):
ar = _get_ar(ax)
for i, (line, ellipse) in enumerate(resize_objects):
ellipse.set_height(1 / ar)
lx, ly = _get_line_coords(ar, i)
line.set_xdata(lx)
line.set_ydata(ly)
ax.figure.canvas.mpl_connect('resize_event', _onresize)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
plt.show()
if __name__ == '__main__':
_plot_noise(10)
Some notes:
the same question was asked on matplotlib discourse, where jklymak provided the correct answer for the ratio computation: https://discourse.matplotlib.org/t/drawing-segments-tangents-of-fixed-lengths-preserving-the-aspect-angles-with-matplotlib/21844/14
the ax.get_{x,y}lim() → ax.set_{x,y}lim() roundtrip seems necessary because the aspect is computed based on the initial axis, which changes when plotting the lines/ellipses
the resize events is not necessary in case of export
Related
I made this code as a CFD of sorts for fun, and I want to add a color bar to show the velocity of the fluid in different places. Unfortunately, every time it plots a new frame it also plots a new colorbar rather than refreshing the old one. I'd like to get it to refresh rather than draw a new one entirely. Any help would be appreciated. Plotting Begins on line 70
import numpy as np
from matplotlib import pyplot
plot_every = 100
def distance(x1,y1,x2,y2):
return np.sqrt((x2-x1)**2 + (y2-y1)**2)
def main():
Nx = 400 #Cells Across x direction
Ny = 100 #Cells Across y direction
#CELL <> NODE
tau = .53 #kinimatic viscosity
tymestep = tau
Nt = 30000 #total iterations
#Lattice Speeds and Velcoties
NL = 9 #There are 9 differnct velocites, (up, down, left, right, up-left diag, up-right diag, down-left diag, down-right diag, and zero)
#NL would be 27 in 3D flow
cxs = np.array([0,0,1,1,1,0,-1,-1,-1]) #I don't know what this is
cys = np.array([0,1,1,0,-1,-1,-1,0,1]) #I don't know what this is
weights = np.array([4/9,1/9,1/36,1/9,1/36,1/9,1/36,1/9,1/36])
#COMPLETELY DIFFERNT WEIGTS FOR 2D AND 3D FLOW
#Initial Conditions
F = np.ones((Ny,Nx,NL)) + 0.01*np.random.randn(Ny,Nx,NL)
F[:,:,3] = 2.3 #Assigning an inital speed in x direction with right as posative
#Drawing Our cylinder
cylinder = np.full((Ny,Nx), False)
radius = 13
for y in range(0,Ny):
for x in range(0,Nx):
if (distance(Nx//4,Ny//2,x,y) < radius):
cylinder[y][x] = True
#main loop
for it in range(Nt):
#print(it)
F[:,-1, [6,7,8]] = F[:,-2, [6,7,8]] #without this, fluid will bounce off of outside walls (you may want this to happen)
F[:,0, [2,3,4]] = F[:,1, [2,3,4]] #without this, fluid will bounce off of outside walls (you may want this to happen)
for i, cx, cy in zip(range(NL),cxs, cys): #this line is sligtly differnt than his because I think he made a typo
F[:,:,i] = np.roll(F[:,:,i], cx, axis = 1)
F[:,:,i] = np.roll(F[:,:,i], cy, axis = 0)
bndryF = F[cylinder,:]
bndryF = bndryF[:, [0,5,6,7,8,1,2,3,4]] #defines what happens in a colsion (reverse the velocity). This works by setting the up vel to down vel etc
#Fluid Variables
rho = np.sum(F,2) #density
ux = np.sum(F * cxs, 2)/rho #x velocity (momentum/mass)
uy = np.sum(F * cys, 2)/rho #y velocity
F[cylinder,: ] = bndryF
ux[cylinder] = 0 #set all velocities in cylinder = 0
uy[cylinder] = 0 #set all velocities in cylinder = 0
#collisions
Feq = np.zeros(F.shape)
for i, cx, cy, w in zip(range(NL), cxs, cys, weights):
Feq[:, :, i] = rho * w * (
1 + 3*(cx*ux + cy*uy) + 9*(cx*ux + cy*uy)**2/2 - 3*(ux**2 + uy**2)/2
)
F += -1/tau * (F-Feq)
if(it%plot_every == 0):
dfydx = ux[2:, 1:-1] - ux[0:-2, 1: -1]
dfxdy = uy[1: -1, 2:] - uy[1: -1, 0: -2]
curl = dfydx - dfxdy
pyplot.imshow(np.sqrt(ux**2+uy**2),cmap = "bwr")
#pyplot.imshow(curl, cmap = "bwr")
pyplot.colorbar(label="Velocity", orientation="horizontal")
pyplot.pause(0.01)
pyplot.cla()
if __name__ == "__main__":
main()
In your code you are adding a new colorbar at every iteration.
As far as I know, it is impossible to update a colorbar. The workaround is to delete the colorbar of the previous time step, and replace it with a new one.
This is achieved by the update_colorbar function in the code below.
import numpy as np
from matplotlib import pyplot
from matplotlib.cm import ScalarMappable
from matplotlib.colors import Normalize
plot_every = 100
def distance(x1,y1,x2,y2):
return np.sqrt((x2-x1)**2 + (y2-y1)**2)
def update_colorbar(fig, cmap, param, norm=None):
"""The name is misleading: here we create a new colorbar which will be
placed on the same colorbar axis as the original.
"""
# colorbar axes
cax = None
if len(fig.axes) > 1:
cax = fig.axes[-1]
# remove the previous colorbar, if present
if cax is not None:
cax.clear()
if norm is None:
norm = Normalize(vmin=np.amin(param), vmax=np.amax(param))
mappable = ScalarMappable(cmap=cmap, norm=norm)
fig.colorbar(mappable, orientation="horizontal", label="Velocity", cax=cax)
def main():
Nx = 400 #Cells Across x direction
Ny = 100 #Cells Across y direction
#CELL <> NODE
tau = .53 #kinimatic viscosity
tymestep = tau
Nt = 30000 #total iterations
#Lattice Speeds and Velcoties
NL = 9 #There are 9 differnct velocites, (up, down, left, right, up-left diag, up-right diag, down-left diag, down-right diag, and zero)
#NL would be 27 in 3D flow
cxs = np.array([0,0,1,1,1,0,-1,-1,-1]) #I don't know what this is
cys = np.array([0,1,1,0,-1,-1,-1,0,1]) #I don't know what this is
weights = np.array([4/9,1/9,1/36,1/9,1/36,1/9,1/36,1/9,1/36])
#COMPLETELY DIFFERNT WEIGTS FOR 2D AND 3D FLOW
#Initial Conditions
F = np.ones((Ny,Nx,NL)) + 0.01*np.random.randn(Ny,Nx,NL)
F[:,:,3] = 2.3 #Assigning an inital speed in x direction with right as posative
#Drawing Our cylinder
cylinder = np.full((Ny,Nx), False)
radius = 13
for y in range(0,Ny):
for x in range(0,Nx):
if (distance(Nx//4,Ny//2,x,y) < radius):
cylinder[y][x] = True
fig, ax = pyplot.subplots()
cmap = "bwr"
#main loop
for it in range(Nt):
# clear previous images
ax.images.clear()
#print(it)
F[:,-1, [6,7,8]] = F[:,-2, [6,7,8]] #without this, fluid will bounce off of outside walls (you may want this to happen)
F[:,0, [2,3,4]] = F[:,1, [2,3,4]] #without this, fluid will bounce off of outside walls (you may want this to happen)
for i, cx, cy in zip(range(NL),cxs, cys): #this line is sligtly differnt than his because I think he made a typo
F[:,:,i] = np.roll(F[:,:,i], cx, axis = 1)
F[:,:,i] = np.roll(F[:,:,i], cy, axis = 0)
bndryF = F[cylinder,:]
bndryF = bndryF[:, [0,5,6,7,8,1,2,3,4]] #defines what happens in a colsion (reverse the velocity). This works by setting the up vel to down vel etc
#Fluid Variables
rho = np.sum(F,2) #density
ux = np.sum(F * cxs, 2)/rho #x velocity (momentum/mass)
uy = np.sum(F * cys, 2)/rho #y velocity
F[cylinder,: ] = bndryF
ux[cylinder] = 0 #set all velocities in cylinder = 0
uy[cylinder] = 0 #set all velocities in cylinder = 0
#collisions
Feq = np.zeros(F.shape)
for i, cx, cy, w in zip(range(NL), cxs, cys, weights):
Feq[:, :, i] = rho * w * (
1 + 3*(cx*ux + cy*uy) + 9*(cx*ux + cy*uy)**2/2 - 3*(ux**2 + uy**2)/2
)
F += -1/tau * (F-Feq)
if(it%plot_every == 0):
dfydx = ux[2:, 1:-1] - ux[0:-2, 1: -1]
dfxdy = uy[1: -1, 2:] - uy[1: -1, 0: -2]
curl = dfydx - dfxdy
img = np.sqrt(ux**2+uy**2)
ax.imshow(img ,cmap = cmap)
#pyplot.imshow(curl, cmap = "bwr")
update_colorbar(fig, cmap, param=img)
pyplot.pause(0.01)
if __name__ == "__main__":
main()
One thing you can definitely improve is the following line of code, which defines the values visible in the colorbar:
norm = Normalize(vmin=np.amin(param), vmax=np.amax(param))
Specifically, you'd have to choose a wise (conservative) value for vmax=. Currently, vmax=np.amax(param), but the maximum is going to change at every iteration. If I were you, I would chose a value big enough such that np.amax(param) < your_value, in order to ensure consistent colors for each time step.
I need an tensorflow alternative of a PILLOW ImageDraw.Polygon as a part of tensorflow graph ( gradients are not needed). I have corners of a parallelogram and need to use this parallelogram as a binary mask to fill with zeroes anything except the area inside the parallelogram. Coping between gpu and cpu to use the pillow is extremely slow. Any way to draw it with tensorflow? Or on gpu? Any lib?
def fill(A, B, fill_below_or_right=True, resolution = (800, 480), meshGrid = None, tfMode = False):
xs, ys = resolution
if (tfMode):
# select whether, >=0 is True, or, <=0 is True, to determine whether to
# fill above or below the line
op = tf.math.greater_equal if fill_below_or_right else tf.math.less_equal
op_rev = tf.math.less_equal if fill_below_or_right else tf.math.greater_equal
close_op = tf.experimental.numpy.allclose
else:
op = np.greater_equal if fill_below_or_right else np.less_equal
close_op = np.allclose
if(meshGrid is None):
Y, X = np.mgrid[0:ys, 0:xs]
if (tfMode): # Just cache X, Y tuple and pass as a meshGrid to make is fast
Y = cast_f32(tf.convert_to_tensor(Y))
X = cast_f32(tf.convert_to_tensor(X))
else:
Y, X = meshGrid
if(close_op(B[0], A[0])): #X = A
a = B[0]
return op(X, a)
elif(close_op(B[1], A[1])): #Y = A
a = B[1]
return op(Y, a)
else:
m = (B[1]-A[1])/(B[0]-A[0]) # m = (y2 - y1)/(x2 - x1) = slope
# the equation for a line is y = m*x + b, so calculate
# m and b from the two points on the line
b = A[1] - m*A[0] # b = y1 - m*x1 = y intercept
# for each points of the grid, calculate whether it's above, below, or on
# the line. Since y = m*x + b, calculating m*x + b - y will give
# 0 when on the line, <0 when above, and >0 when below
L = m*X + b - Y
if m < 1.0:
return op_rev(L, 0.0)
else:
return op(L, 0.0)
def draw_quad(pts, resolution = (800, 480), meshGrid = None, tfMode = False):
pts = [cast_f32(item) for item in pts]
x0, y0, x1, y1, x2, y2, x3, y3 = pts
r = fill((x0, y0), (x1, y1), True, resolution, meshGrid, tfMode) & \
fill((x1, y1), (x2, y2), False, resolution, meshGrid, tfMode) & \
fill((x2, y2), (x3, y3), False, resolution, meshGrid, tfMode) & \
fill((x3, y3), (x0, y0), True, resolution, meshGrid, tfMode)
return r
I would like to rotate only the positive value pixels in my 2d array some degree about the center point. The data represents aerosol concentrations from a plume dispersion model, and the chimney position is the origin of rotation.
I would like to rotate this dispersion pattern given the wind direction.
The concentrations are first calculated for a wind direction along the x-axis and then translated to their rotated position using a 2d linear rotation about the center point of my array (the chimney position) for all points whose concentration is > 0.
The input X,Y to the rotation formula are pixel indexes.
My problem is that the output is aliased since integers become floats. In order to obtain integers, I rounded up or down the output. However, this creates null cells which become increasingly numerous as the angle increases.
Can anyone help me find a solution to my problem? I would like to fix this problem if possible using numpy, or a minimum of packages...
The part of my script that deals with computing the concentrations and rotating the pixel by 50°N is the following. Thank you for your help.
def linear2D_rotation(xcoord,ycoord,azimuth_degrees):
radians = (90 - azimuth_degrees) * (np.pi / 180) # in radians
xcoord_rotated = (xcoord * np.cos(radians)) - (ycoord * np.sin(radians))
ycoord_rotated = (xcoord * np.sin(radians)) + (ycoord * np.cos(radians))
return xcoord_rotated,ycoord_rotated
u_orient = 50 # wind orientation in degres from North
kernel = np.zeros((NpixelY, NpixelX)) # initialize matrix
Yc = int((NpixelY - 1) / 2) # position of central pixel
Xc = int((NpixelX - 1) / 2) # position of central pixel
nk = 0
for Y in list(range(0,NpixelX)):
for X in list(range(0,NpixelY)):
# compute concentrations only in positive x-direction
if (X-Xc)>0:
# nnumber of pixels to origin point (chimney)
dx = ((X-Xc)+1)
dy = ((Y-Yc)+1)
# distance of point to origin (chimney)
DX = dx*pixel_size_X
DY = dy*pixel_size_Y
# compute diffusivity coefficients
Sy, Sz = calcul_diffusivity_coeff(DX, stability_class)
# concentration at ground level below the centerline of the plume
C = (Q / (2 * np.pi * u * Sy * Sz)) * \
np.exp(-(DY / (2 * Sy)) ** 2) * \
(np.exp(-((Z - H) / (2 * Sz)) ** 2) + np.exp(-((Z + H) / (2 * Sz)) ** 2)) # at point away from center line
C = C * 1e9 # convert MBq to Bq
# rotate only if concentration value at pixel is positive
if C > 1e-12:
X_rot, Y_rot = linear2D_rotation(xcoord=dx, ycoord=dy,azimuth_degrees=u_orient)
X2 = int(round(Xc+X_rot))
Y2 = int(round(Yc-Y_rot)) # Y increases downwards
# pixels that fall out of bounds -> ignore
if (X2 > (NpixelX - 1)) or (X2 < 0) or (Y2 > (NpixelY - 1)):
continue
else:
# replace new pixel position in kernel array
kernel[Y2, X2] = C
The original array to be rotated
The rotated array by 40°N showing the data loss
Your problem description is not 100% clear, but here are a few recommendations:
1.) Don't reinvent the wheel. There are standard solutions for things like rotating pixels. Use them! In this case
scipy.ndimage.affine_transform for performing the rotation
a homogeneous coordinate matrix for specifying the rotation
nearest neighbor interpolation (parameter order=0 in code below).
2.) Don't loop where not necessary. The speed you gain by not processing non-positive pixels is nothing against the speed you lose by looping. Compiled functions can ferry around a lot of redundant zeros before hand-written python code catches up with them.
3.) Don't expect a solution that maps pixels one-to-one because it is a fact that there will be points that are no ones nearest neighbor and points that are nearest neighbor to multiple other points. With that in mind, you may want to consider a higher order, smoother interpolation.
Comparing your solution to the standard tools solution we find that the latter
gives a comparable result much faster and without those hole artifacts.
Code (without plotting). Please note that I had to transpose and flipud to align the results :
import numpy as np
from scipy import ndimage as sim
from scipy import stats
def mock_data(n, Theta=50, put_neg=True):
y, x = np.ogrid[-20:20:1j*n, -9:3:1j*n, ]
raster = stats.norm.pdf(y)*stats.norm.pdf(x)
if put_neg:
y, x = np.ogrid[-5:5:1j*n, -3:9:1j*n, ]
raster -= stats.norm.pdf(y)*stats.norm.pdf(x)
raster -= (stats.norm.pdf(y)*stats.norm.pdf(x)).T
return {'C': raster * 1e-9, 'Theta': Theta}
def rotmat(Theta, offset=None):
theta = np.radians(Theta)
c, s = np.cos(theta), np.sin(theta)
if offset is None:
return np.array([[c, -s] [s, c]])
R = np.array([[c, -s, 0], [s, c,0], [0,0,1]])
to, fro = np.identity(3), np.identity(3)
offset = np.asanyarray(offset)
to[:2, 2] = offset
fro[:2, 2] = -offset
return to # R # fro
def f_pp(C, Theta):
m, n = C.shape
clipped = np.maximum(0, 1e9 * data['C'])
clipped[:, :n//2] = 0
M = rotmat(Theta, ((m-1)/2, (n-1)/2))
return sim.affine_transform(clipped, M, order = 0)
def linear2D_rotation(xcoord,ycoord,azimuth_degrees):
radians = (90 - azimuth_degrees) * (np.pi / 180) # in radians
xcoord_rotated = (xcoord * np.cos(radians)) - (ycoord * np.sin(radians))
ycoord_rotated = (xcoord * np.sin(radians)) + (ycoord * np.cos(radians))
return xcoord_rotated,ycoord_rotated
def f_OP(C, Theta):
kernel = np.zeros_like(C)
m, n = C.shape
for Y in range(m):
for X in range(n):
if X > n//2:
c = C[Y, X] * 1e9
if c > 1e-12:
dx = X - n//2 + 1
dy = Y - m//2 + 1
X_rot, Y_rot = linear2D_rotation(xcoord=dx, ycoord=dy,azimuth_degrees=Theta)
X2 = int(round(n//2+X_rot))
Y2 = int(round(m//2-Y_rot)) # Y increases downwards
# pixels that fall out of bounds -> ignore
if (X2 > (n - 1)) or (X2 < 0) or (Y2 > (m - 1)):
continue
else:
# replace new pixel position in kernel array
kernel[Y2, X2] = c
return kernel
n = 100
data = mock_data(n, 70)
I am trying to train the MNIST data (which I downloaded from Kaggle) with simple multi-class logistic regression, but the scipy.optimize functions hang.
Here's the code:
import csv
from math import exp
from numpy import *
from scipy.optimize import fmin, fmin_cg, fmin_powell, fmin_bfgs
# Prepare the data
def getIiter(ifname):
"""
Get the iterator from a csv file with filename ifname
"""
ifile = open(ifname, 'r')
iiter = csv.reader(ifile)
iiter.__next__()
return iiter
def parseRow(s):
y = [int(x) for x in s]
lab = y[0]
z = y[1:]
return (lab, z)
def getAllRows(ifname):
iiter = getIiter(ifname)
x = []
l = []
for row in iiter:
lab, z = parseRow(row)
x.append(z)
l.append(lab)
return x, l
def cutData(x, y):
"""
70% training
30% testing
"""
m = len(x)
t = int(m * .7)
return [(x[:t], y[:t]), (x[t:], y[t:])]
def num2IndMat(l):
t = array(l)
tt = [vectorize(int)((t == i)) for i in range(10)]
return array(tt).T
def readData(ifname):
x, l = getAllRows(ifname)
t = [[1] + y for y in x]
return array(t), num2IndMat(l)
#Calculate the cost function
def sigmoid(x):
return 1 / (1 + exp(-x))
vSigmoid = vectorize(sigmoid)
vLog = vectorize(log)
def costFunction(theta, x, y):
sigxt = vSigmoid(dot(x, theta))
cm = (- y * vLog(sigxt) - (1 - y) * vLog(1 - sigxt)) / m / N
return sum(cm)
def unflatten(flatTheta):
return [flatTheta[i * N : (i + 1) * N] for i in range(n + 1)]
def costFunctionFlatTheta(flatTheta):
return costFunction(unflatten(flatTheta), trainX, trainY)
def costFunctionFlatTheta1(flatTheta):
return costFunction(flatTheta.reshape(785, 10), trainX, trainY)
x, y = readData('train.csv')
[(trainX, trainY), (testX, testY)] = cutData(x, y)
m = len(trainX)
n = len(trainX[0]) - 1
N = len(trainY[0])
initTheta = zeros(((n + 1), N))
flatInitTheta = ndarray.flatten(initTheta)
flatInitTheta1 = initTheta.reshape(1, -1)
In the last two lines we flatten initTheta because the fmin{,_cg,_bfgs,_powell} functions seem to only take vectors as the initial value argument x0. I also flatten initTheta using reshape in hope this answer can be of help.
There is no problem computing the cost function which takes up less than 2 seconds on my computer:
print(costFunctionFlatTheta(flatInitTheta), costFunctionFlatTheta1(flatInitTheta1))
# 0.69314718056 0.69314718056
But all the fmin functions hang, even if I set maxiter=0.
e.g.
newFlatTheta = fmin(costFunctionFlatTheta, flatInitTheta, maxiter=0)
or
newFlatTheta1 = fmin(costFunctionFlatTheta1, flatInitTheta1, maxiter=0)
When I interrupt the program, it seems to me it all hangs at lines in optimize.py calling the cost functions, lines like this:
return function(*(wrapper_args + args))
For example, if I use fmin_cg, this would be line 292 in optimize.py (Version 0.5).
How do I solve this problem?
OK I found a way to stop fmin_cg from hanging.
Basically I just need to write a function that computes the gradient of the cost function, and pass it to the fprime parameter of fmin_cg.
def gradient(theta, x, y):
return dot(x.T, vSigmoid(dot(x, theta)) - y) / m / N
def gradientFlatTheta(flatTheta):
return ndarray.flatten(gradient(flatTheta.reshape(785, 10), trainX, trainY))
Then
newFlatTheta = fmin_cg(costFunctionFlatTheta, flatInitTheta, fprime=gradientFlatTheta, maxiter=0)
terminates within seconds, and setting maxiter to a higher number (say 100) one can train the model within reasonable amount of time.
The documentation of fmin_cg says the gradient would be numerically computed if no fprime is given, which is what I suspect caused the hanging.
Thanks to this notebook by zgo2016#Kaggle which helped me find the solution.
In other words, I want to make a heatmap (or surface plot) where the color varies as a function of 2 variables. (Specifically, luminance = magnitude and hue = phase.) Is there any native way to do this?
Some examples of similar plots:
Several good examples of exactly(?) what I want to do.
More examples from astronomy, but with non-perceptual hue
Edit: This is what I did with it: https://github.com/endolith/complex_colormap
imshow can take an array of [r, g, b] entries. So you can convert the absolute values to intensities and phases - to hues.
I will use as an example complex numbers, because for it it makes the most sense. If needed, you can always add numpy arrays Z = X + 1j * Y.
So for your data Z you can use e.g.
imshow(complex_array_to_rgb(Z))
where (EDIT: made it quicker and nicer thanks to this suggestion)
def complex_array_to_rgb(X, theme='dark', rmax=None):
'''Takes an array of complex number and converts it to an array of [r, g, b],
where phase gives hue and saturaton/value are given by the absolute value.
Especially for use with imshow for complex plots.'''
absmax = rmax or np.abs(X).max()
Y = np.zeros(X.shape + (3,), dtype='float')
Y[..., 0] = np.angle(X) / (2 * pi) % 1
if theme == 'light':
Y[..., 1] = np.clip(np.abs(X) / absmax, 0, 1)
Y[..., 2] = 1
elif theme == 'dark':
Y[..., 1] = 1
Y[..., 2] = np.clip(np.abs(X) / absmax, 0, 1)
Y = matplotlib.colors.hsv_to_rgb(Y)
return Y
So, for example:
Z = np.array([[3*(x + 1j*y)**3 + 1/(x + 1j*y)**2
for x in arange(-1,1,0.05)] for y in arange(-1,1,0.05)])
imshow(complex_array_to_rgb(Z, rmax=5), extent=(-1,1,-1,1))
imshow(complex_array_to_rgb(Z, rmax=5, theme='light'), extent=(-1,1,-1,1))
imshow will take an NxMx3 (rbg) or NxMx4 (grba) array so you can do your color mapping 'by hand'.
You might be able to get a bit of traction by sub-classing Normalize to map your vector to a scaler and laying out a custom color map very cleverly (but I think this will end up having to bin one of your dimensions).
I have done something like this (pdf link, see figure on page 24), but the code is in MATLAB (and buried someplace in my archives).
I agree a bi-variate color map would be useful (primarily for representing very dense vector fields where your kinda up the creek no matter what you do).
I think the obvious extension is to let color maps take complex arguments. It would require specialized sub-classes of Normalize and Colormap and I am going back and forth on if I think it would be a lot of work to implement. I suspect if you get it working by hand it will just be a matter of api wrangling.
I created an easy to use 2D colormap class, that takes 2 NumPy arrays and maps them to an RGB image, based on a reference image.
I used #GjjvdBurg's answer as a starting point. With a bit of work, this could still be improved, and possibly turned into a proper Python module - if you want, feel free to do so, I grant you all credits.
TL;DR:
# read reference image
cmap_2d = ColorMap2D('const_chroma.jpeg', reverse_x=True) # , xclip=(0,0.9))
# map the data x and y to the RGB space, defined by the image
rgb = cmap_2d(data_x, data_y)
# generate a colorbar image
cbar_rgb = cmap_2d.generate_cbar()
The ColorMap2D class:
class ColorMap2D:
def __init__(self, filename: str, transpose=False, reverse_x=False, reverse_y=False, xclip=None, yclip=None):
"""
Maps two 2D array to an RGB color space based on a given reference image.
Args:
filename (str): reference image to read the x-y colors from
rotate (bool): if True, transpose the reference image (swap x and y axes)
reverse_x (bool): if True, reverse the x scale on the reference
reverse_y (bool): if True, reverse the y scale on the reference
xclip (tuple): clip the image to this portion on the x scale; (0,1) is the whole image
yclip (tuple): clip the image to this portion on the y scale; (0,1) is the whole image
"""
self._colormap_file = filename or COLORMAP_FILE
self._img = plt.imread(self._colormap_file)
if transpose:
self._img = self._img.transpose()
if reverse_x:
self._img = self._img[::-1,:,:]
if reverse_y:
self._img = self._img[:,::-1,:]
if xclip is not None:
imin, imax = map(lambda x: int(self._img.shape[0] * x), xclip)
self._img = self._img[imin:imax,:,:]
if yclip is not None:
imin, imax = map(lambda x: int(self._img.shape[1] * x), yclip)
self._img = self._img[:,imin:imax,:]
if issubclass(self._img.dtype.type, np.integer):
self._img = self._img / 255.0
self._width = len(self._img)
self._height = len(self._img[0])
self._range_x = (0, 1)
self._range_y = (0, 1)
#staticmethod
def _scale_to_range(u: np.ndarray, u_min: float, u_max: float) -> np.ndarray:
return (u - u_min) / (u_max - u_min)
def _map_to_x(self, val: np.ndarray) -> np.ndarray:
xmin, xmax = self._range_x
val = self._scale_to_range(val, xmin, xmax)
rescaled = (val * (self._width - 1))
return rescaled.astype(int)
def _map_to_y(self, val: np.ndarray) -> np.ndarray:
ymin, ymax = self._range_y
val = self._scale_to_range(val, ymin, ymax)
rescaled = (val * (self._height - 1))
return rescaled.astype(int)
def __call__(self, val_x, val_y):
"""
Take val_x and val_y, and associate the RGB values
from the reference picture to each item. val_x and val_y
must have the same shape.
"""
if val_x.shape != val_y.shape:
raise ValueError(f'x and y array must have the same shape, but have {val_x.shape} and {val_y.shape}.')
self._range_x = (np.amin(val_x), np.amax(val_x))
self._range_y = (np.amin(val_y), np.amax(val_y))
x_indices = self._map_to_x(val_x)
y_indices = self._map_to_y(val_y)
i_xy = np.stack((x_indices, y_indices), axis=-1)
rgb = np.zeros((*val_x.shape, 3))
for indices in np.ndindex(val_x.shape):
img_indices = tuple(i_xy[indices])
rgb[indices] = self._img[img_indices]
return rgb
def generate_cbar(self, nx=100, ny=100):
"generate an image that can be used as a 2D colorbar"
x = np.linspace(0, 1, nx)
y = np.linspace(0, 1, ny)
return self.__call__(*np.meshgrid(x, y))
Usage:
Full example, using the constant chroma reference taken from here as a screenshot:
# generate data
x = y = np.linspace(-2, 2, 300)
xx, yy = np.meshgrid(x, y)
ampl = np.exp(-(xx ** 2 + yy ** 2))
phase = (xx ** 2 - yy ** 2) * 6 * np.pi
data = ampl * np.exp(1j * phase)
data_x, data_y = np.abs(data), np.angle(data)
# Here is the 2D colormap part
cmap_2d = ColorMap2D('const_chroma.jpeg', reverse_x=True) # , xclip=(0,0.9))
rgb = cmap_2d(data_x, data_y)
cbar_rgb = cmap_2d.generate_cbar()
# plot the data
fig, plot_ax = plt.subplots(figsize=(8, 6))
plot_extent = (x.min(), x.max(), y.min(), y.max())
plot_ax.imshow(rgb, aspect='auto', extent=plot_extent, origin='lower')
plot_ax.set_xlabel('x')
plot_ax.set_ylabel('y')
plot_ax.set_title('data')
# create a 2D colorbar and make it fancy
plt.subplots_adjust(left=0.1, right=0.65)
bar_ax = fig.add_axes([0.68, 0.15, 0.15, 0.3])
cmap_extent = (data_x.min(), data_x.max(), data_y.min(), data_y.max())
bar_ax.imshow(cbar_rgb, extent=cmap_extent, aspect='auto', origin='lower',)
bar_ax.set_xlabel('amplitude')
bar_ax.set_ylabel('phase')
bar_ax.yaxis.tick_right()
bar_ax.yaxis.set_label_position('right')
for item in ([bar_ax.title, bar_ax.xaxis.label, bar_ax.yaxis.label] +
bar_ax.get_xticklabels() + bar_ax.get_yticklabels()):
item.set_fontsize(7)
plt.show()
I know this is an old post, but want to help out others that may arrive late. Below is a python function to implement complex_to_rgb from sage. Note: This implementation isn't optimal, but it is readable. See links: (examples)(source code)
Code:
import numpy as np
def complex_to_rgb(z_values):
width = z_values.shape[0]
height = z_values.shape[1]
rgb = np.zeros(shape=(width, height, 3))
for i in range(width):
row = z_values[i]
for j in range(height):
# define value, real(value), imag(value)
zz = row[j]
x = np.real(zz)
y = np.imag(zz)
# define magnitued and argument
magnitude = np.hypot(x, y)
arg = np.arctan2(y, x)
# define lighness
lightness = np.arctan(np.log(np.sqrt(magnitude) + 1)) * (4 / np.pi) - 1
if lightness < 0:
bot = 0
top = 1 + lightness
else:
bot = lightness
top = 1
# define hue
hue = 3 * arg / np.pi
if hue < 0:
hue += 6
# set ihue and use it to define rgb values based on cases
ihue = int(hue)
# case 1
if ihue == 0:
r = top
g = bot + hue * (top - bot)
b = bot
# case 2
elif ihue == 1:
r = bot + (2 - hue) * (top - bot)
g = top
b = bot
# case 3
elif ihue == 2:
r = bot
g = top
b = bot + (hue - 2) * (top - bot)
# case 4
elif ihue == 3:
r = bot
g = bot + (4 - hue) * (top - bot)
b = top
# case 5
elif ihue == 4:
r = bot + (hue - 4) * (top - bot)
g = bot
b = top
# case 6
else:
r = top
g = bot
b = bot + (6 - hue) * (top - bot)
# set rgb array values
rgb[i, j, 0] = r
rgb[i, j, 1] = g
rgb[i, j, 2] = b
return rgb