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orbit2png.py
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orbit2png.py
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#!/usr/bin/python
import sys
import numpy as np
from math import pi
from numpy import arange, array, where, append, linspace
from ovf import readOvf
import colorsys
import matplotlib.pyplot as plt
from matplotlib.colors import to_rgba
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure(figsize=(12, 12), tight_layout=True)
ax = fig.add_subplot(1, 1, 1, projection='3d')
ax.set_aspect('equal','box')
ax.set_frame_on(True)
ax.set_axis_on()
ax.set_autoscale_on(False)
ax.set_xbound(0, 50)
ax.set_ybound(0, 50)
ax.set_zbound(0, 50)
ax.set_xlabel('x (nm)')
ax.set_ylabel('y (nm)')
ax.set_zlabel('z (nm)')
def drawVectorFieldWithTrajectories(trajectories, scatterpoints, m, corner_start=[0, 0, 0], corner_end=[-1, -1, -1], stepsize=[1, 1, 1], base=[0, 0, 0]):
sx = m[:, :, :, 0]
sy = m[:, :, :, 1]
sz = m[:, :, :, 2]
z0, y0, x0 = corner_start
z1, y1, x1 = corner_end
znodes, ynodes, xnodes, temp = m.shape
x0 = xnodes + x0 + 1 if x0 < 0 else x0
y0 = ynodes + y0 + 1 if y0 < 0 else y0
z0 = znodes + z0 + 1 if z0 < 0 else z0
x1 = xnodes + x1 + 1 if x1 < 0 else x1
y1 = ynodes + y1 + 1 if y1 < 0 else y1
z1 = znodes + z1 + 1 if z1 < 0 else z1
# position
y = np.arange(y0, y1) * stepsize[1] + base[1]
z = np.arange(z0, z1) * stepsize[2] + base[2]
x = np.arange(x0, x1) * stepsize[0] + base[0]
y, z, x = np.meshgrid(y, z, x)
x = x.flatten() / 1e-9
y = y.flatten() / 1e-9
z = z.flatten() / 1e-9
nspins = x.size
# color
sx, sy, sz = sx[z0:z1, y0:y1, x0:x1], sy[z0:z1, y0:y1, x0:x1], sz[z0:z1, y0:y1, x0:x1]
sx = sx.flatten()
sy = sy.flatten()
sz = sz.flatten()
mag = np.sqrt(sx*sx + sy*sy + sz*sz)
maxmag = np.max(mag)
sx = sx / maxmag
sy = sy / maxmag
sz = sz / maxmag
hue = np.arctan2(sy, sx) / (pi * 2) % 1.0
lightness = np.clip(sz * 0.5 + 0.5, 0, 1)
saturation = np.sqrt(sx*sx + sy*sy)
alpha = np.clip(mag / maxmag * 2, 0, 1)
rgba = np.zeros(hue.shape + (4,))
for i, hue1 in enumerate(hue):
rgba[i] = to_rgba(colorsys.hls_to_rgb(hue[i], lightness[i], 1), alpha[i])
rgba[i] = to_rgba(colorsys.hls_to_rgb(0.6, alpha[i], 1), alpha[i])
rgba[i] = to_rgba(colorsys.hls_to_rgb(hue[i], lightness[i], saturation[i]), alpha[i])
rgba = array(rgba)
# scale
s = np.ones(nspins) * 50
# position
ntracepoints = trajectories.size / 3
nsections = trajectories.shape[0]
trajectories = trajectories.reshape([nsections, -1, 3])
ntrajectories = trajectories.shape[1]
x2 = y2 = z2 = array([])
for i in range(ntrajectories):
x2 = np.concatenate((x2, trajectories[:, i, 0]))
y2 = np.concatenate((y2, trajectories[:, i, 1]))
z2 = np.concatenate((z2, trajectories[:, i, 2]))
# color
#rgba2 = np.clip(1 - arange(ntracepoints)[::-1] * 1.0 / decay, 0, 1)
rgba2 = np.ones(ntracepoints)
rgba2 = array([ to_rgba('k', alpha) for alpha in rgba2 ])
# scale
s2 = np.ones(ntracepoints) * 8
# position
nscatterpoints = scatterpoints.shape[0]
x3 = scatterpoints[:, 0]
y3 = scatterpoints[:, 1]
z3 = scatterpoints[:, 2]
# color
rgba_scatterpoints = np.ones(nscatterpoints)
rgba3 = array([ to_rgba(colorsys.hls_to_rgb(0, 0.2, 1), i) for i in rgba_scatterpoints ])
rgba4 = array([ to_rgba(colorsys.hls_to_rgb(0, 0.5, 1), i) for i in rgba_scatterpoints ])
rgba5 = array([ to_rgba(colorsys.hls_to_rgb(0, 0.7, 1), i) for i in rgba_scatterpoints ])
rgba6 = array([ to_rgba(colorsys.hls_to_rgb(0, 1.0, 1), i) for i in rgba_scatterpoints ])
# scale
s3 = s4 = s5 = s6 = np.ones(nscatterpoints)
s3 = s3 * 100
s4 = s4 * 80
s5 = s5 * 40
s6 = s6 * 7
# merge
x = np.concatenate((x, x2, x3, x3+1e-12, x3+2e-12, x3+3e-12))
y = np.concatenate((y, y2, y3, y3+1e-10, y3+1.2e-10, y3+1.4e-10))
z = np.concatenate((z, z2, z3, z3+1e-10, z3+1.2e-10, z3+1.4e-10))
rgba = np.concatenate((rgba, rgba2, rgba3, rgba4, rgba5, rgba6))
rgba = rgba.reshape([-1, 4])
s = np.concatenate((s, s2, s3, s4, s5, s6))
ind = np.lexsort((s,x,y,z))
xall = array([ x[i] for i in ind ])
yall = array([ y[i] for i in ind ])
zall = array([ z[i] for i in ind ])
call = array([ rgba[i, :] for i in ind ])
sall = array([ s[i] for i in ind ])
ax.scatter(xall, yall, zall, c=call, s=sall, marker='.', edgecolors='none')
def main(argv):
ovf1 = readOvf(argv[1])
config = ovf1['config']
m1 = ovf1['data']
# unzip the configuration
xnodes, ynodes, znodes = config['xnodes'], config['ynodes'], config['znodes']
stepsize = xstepsize, ystepsize, zstepsize = config['xstepsize'], config['ystepsize'], config['zstepsize']
base = xbase, ybase, zbase = config['xbase'], config['ybase'], config['zbase']
# read the trajectories from file
trace = np.zeros([1000, 2*13*3+1]) # ad hoc configured
ftrace = open(argv[2], 'r')
lines = ftrace.readlines()
for iline, line in enumerate(lines):
trace[iline, :] = [ float(term) for term in line.split(',') ]
trace = trace + 25
nsections = int(argv[3]) + 1
trace = trace[:nsections, 13*3+1:] # ad hoc configured
ntrajectories = 13
# the number of points are cut by half
reducingfactor = int(argv[4])
trace = trace[::reducingfactor, :]
nsections = trace.shape[0]
# the trajectories are reconstructed by interpolation
toriginal = linspace(0, 1, nsections)
tinterp = linspace(0, 1, (nsections-1)*reducingfactor*5+1)
trajectories = np.zeros([(nsections-1)*reducingfactor*5+1, ntrajectories * 3])
for i in range(ntrajectories * 3):
trajectories[:, i] = np.interp(tinterp, toriginal, trace[:, i].flatten())
# the scatter points on each trajectory are picked out
scatterpoints = trace[-1:, :].reshape([-1, 3])
drawVectorFieldWithTrajectories(trajectories, scatterpoints, m1, [25, 25, 25], [75, 75, 75], stepsize=stepsize, base=base)
print(nsections)
ax.view_init(elev=30, azim=100 + nsections*0.5)
plt.savefig('vf-1.png')
# plt.savefig('vf-' + num_vector_figures.__repr__() + '.png', dpi=300)
if __name__ == "__main__":
main(sys.argv)