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frame.py
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frame.py
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"""
Module frame renders images of the 2D system.
(modified from
https://github.com/yketa/active_particles/tree/master/analysis/frame.py)
"""
from coll_dyn_activem.init import get_env, mkdir
from coll_dyn_activem.read import Dat
from coll_dyn_activem.maths import normalise1D, amplogwidth, cooperativity,\
relative_positions, angle, wo_mean
from coll_dyn_activem.flow import Displacements, Velocities
from coll_dyn_activem.structure import Positions
from coll_dyn_activem.force import Force
from coll_dyn_activem.pycpp import pairIndex, invPairIndex
from coll_dyn_activem._pycpp import getBondsBrokenBonds, getBondsBrokenBondsBis
from os import getcwd, cpu_count
from os import environ as envvar
from os.path import join as joinpath
import sys
from math import ceil
import numpy as np
np.seterr(divide='ignore')
from scipy import sparse
import matplotlib as mpl
if get_env('NO_DISPLAY', default=False, vartype=bool): mpl.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.colors
from matplotlib.colors import Normalize as ColorsNormalise
from matplotlib.colors import BoundaryNorm, ListedColormap
from matplotlib.cm import ScalarMappable
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.lines import Line2D
from matplotlib.collections import PatchCollection
from matplotlib.patches import Polygon, FancyArrow
plt.rc('text', usetex=True)
plt.rc('text.latex', preamble=r'\usepackage{amsmath,amsfonts}')
from datetime import datetime
from collections import OrderedDict
from operator import itemgetter
import subprocess
from pathos.multiprocessing import ProcessingPool as Pool
# DEFAULT VARIABLES
_frame_per = 1 # default frame rendering period
_frame_max = 1000 # default maximum number of frames
_frame_ver = 12 # default vertical size of the frames (in inches)
_frame_hor = 16 # default horizontal size of the frames (in inches)
_frame_def = 80 # default definition of images (in dots per inches (dpi))
_arrow_width = 1e-3 # default width of the arrows
_arrow_head_width = _arrow_width*3e2 # default width of the arrows' head
_arrow_head_length = _arrow_head_width*1.5 # default length of the arrows' head
_font_size = 15 # font size
_colormap_label_pad = 30 # default separation between label and colormap
# FUNCTIONS AND CLASSES
class _Frame:
"""
This class is designed as the superclass of all other plotting classes
specific to each mode. It initialises the figure and provides methods to
plot circles representing particles and arrows at the particles' positions,
and to add a colorbar.
"""
def __init__(self, dat, frame, box_size, centre,
arrow_width=_arrow_width,
arrow_head_width=_arrow_head_width,
arrow_head_length=_arrow_head_length,
WCA_diameter=False, confinement=False, rasterized=False,
linewidth=1, colorbar_position='right', colorbar_label=None,
**kwargs):
"""
Initialises figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
arrow_width : float
Width of the arrows.
arrow_head_width : float
Width of the arrows' head.
arrow_head_length : float
Length of the arrows' head.
WCA_diameter : bool
Multiply diameters by 2^(1/6). (default: False)
confinement : bool
Draw circle of confinement, at centre (dat.L/2, dat.L/2), with
diameter dat.L - max(dat.diameters). (default: False)
rasterized : bool
Force rasterized (bitmap) drawing for vector graphics output.
(default: False)
linewidth : float or None
Linewidth of circles and arrows. (default: None)
colorbar_position : string
Position of the colorbar ('right' or 'top'). (default: 'right')
colorbar_label : string or None
Label of the colorbar. (default: None)
Optional keyword parameters
---------------------------
remove_cm : int or None
Remove centre of mass displacement from frame.
NOTE: if remove_cm == None, nothing is done.
"""
self.fig, self.ax = plt.subplots()
self.box_size = box_size
self.ax.set_xlim(np.array([-0.5, 0.5])*min(self.box_size, dat.Lxy[0]))
self.ax.set_ylim(np.array([-0.5, 0.5])*min(self.box_size, dat.Lxy[1]))
# self.ax.set_xlabel(r'$x$')
# self.ax.set_ylabel(r'$y$')
self.ax.set_aspect('equal')
self.ax.tick_params(axis='both', which='both', direction='in',
bottom=True, top=True, left=True, right=True)
self.dat = dat
self.frame = frame
self.centre = centre
self.positions = self.dat.getPositions(frame)
if 'remove_cm' in kwargs:
if kwargs['remove_cm'] != None:
self.remove_cm = kwargs['remove_cm']
# self.ax.set_xlabel(r'$\Delta^{\mathrm{CM}} x$')
# self.ax.set_ylabel(r'$\Delta^{\mathrm{CM}} y$')
self.positions -= self.dat.getDisplacements(
self.remove_cm, frame).mean(axis=0, keepdims=True)
self.positions -= (self.positions//self.dat.Lxy)*self.dat.Lxy
self.positions = relative_positions(self.positions, centre,
self.dat.Lxy) # particles' positions at frame frame with centre as centre of frame
self.diameters = self.dat.diameters*(2**(1./6.) if WCA_diameter else 1) # particles' diameters
if confinement:
self.ax.add_artist(
plt.Circle(
relative_positions(
(self.dat.L/2, self.dat.L/2), centre, self.dat.L),
radius=(self.dat.L - self.dat.diameters.max())/2,
ec='red', fc=(1, 1, 1, 0)))
self.particles = np.where(
(np.abs(self.positions) - self.diameters.reshape((self.dat.N, 1))/2
<= self.box_size/2).prod(axis=-1))[0] # particles inside box of centre centre and length box_size
# self.particles = [particle for particle in range(len(self.positions))
# if (np.abs(self.positions[particle]) <= self.box_size/2
# + self.diameters.reshape((self.dat.N, 1))/2).all()] # particles inside box of centre centre and length box_size
self.arrow_width = arrow_width
self.arrow_head_width = arrow_head_width
self.arrow_head_length = arrow_head_length
self.rasterized = rasterized
self.linewidth = linewidth
self.colorbar_position = colorbar_position
self.colorbar_label = colorbar_label
def __del__(self):
"""
Closes figure.
"""
plt.close(self.fig)
def draw_circle(self, particle, color='black', fill=False, alpha=1,
border=None, label=False):
"""
Draws circle at particle's position with particle's diameter.
Parameters
----------
particle : int
Particle index.
color : any matplotlib color
Circle color. (default: 'black')
fill : bool
Filling the circle with same color. (default: False)
alpha : float
Opacity. (default: 1)
border : string or None
Circle border color. (default: None)
NOTE: if border == None, do not add border.
label : bool
Write indexes of particles in circles. (default: False)
"""
def _draw_circle(position):
"""
Draw circle at position.
Parameters
----------
position : (2,) float array-like
Position of circle to draw.
"""
circle = plt.Circle(position,
self.diameters[particle]/2, color=color, fill=fill, alpha=alpha,
linewidth=self.linewidth,
zorder=0, rasterized=self.rasterized) # circle artist representing particle
self.ax.add_artist(circle)
if border != None: # add border
circleBorder = plt.Circle(position,
self.diameters[particle]/2, color=border, fill=False,
linewidth=self.linewidth,
zorder=1, rasterized=self.rasterized)
self.ax.add_artist(circleBorder)
_draw_circle(self.positions[particle])
# for dim in range(2):
# if (np.abs(self.positions[particle][dim]) >
# self.dat.Lxy[dim]/2 - self.diameters[particle]/2):
# newPosition = self.positions[particle].copy()
# newPosition[dim] -= (np.sign(self.positions[particle][dim])
# *self.dat.Lxy[dim])
# _draw_circle(newPosition)
# if (np.abs(self.positions[particle]) >
# self.dat.Lxy/2 - self.diameters[particle]/2).all():
# newPosition = self.positions[particle].copy()
# newPosition -= (np.sign(self.positions[particle])
# *self.dat.Lxy)
# _draw_circle(newPosition)
if label:
self.ax.annotate(
"%i" % particle, xy=self.positions[particle], ha="center")
def draw_arrow(self, particle, dx, dy, color='black'):
"""
Draws arrow starting from particle's position.
Parameters
----------
particle : int
Particle index.
dx : float
Arrow length in x-direction.
dy : float
Arrow length in y-direction.
color : any matplotlib color
Arrow color. (default: 'black')
"""
length = np.sqrt(dx**2 + dy**2) # length of arrow
if length == 0: return
self.ax.arrow(*self.positions[particle], dx, dy, color=color,
width=length*self.arrow_width,
head_width=length*self.arrow_head_width,
head_length=length*self.arrow_head_length,
length_includes_head=True,
zorder=1,
linewidth=self.linewidth,
rasterized=self.rasterized)
def draw_arrow_in(self, particle, orientation, color='black'):
"""
Draws arrow in particle.
Parameters
----------
particle : int
Particle index.
orientation : float
Orientation of particle in radians.
color : any matplotlib color
Arrow color. (default: 'black')
"""
direction = np.array([np.cos(orientation), np.sin(orientation)])
length = self.diameters[particle]*0.75
self.ax.arrow(
*(self.positions[particle] - direction*length/(2*np.sqrt(2))),
*direction*length/np.sqrt(2),
color=color,
width=length*self.arrow_width,
head_width=length*self.arrow_head_width,
head_length=length*self.arrow_head_length, zorder=1,
length_includes_head=True,
linewidth=self.linewidth,
rasterized=self.rasterized)
def draw_link(self, particle1, particle2, width=4, color='black'):
"""
Draw link between particles.
Parameters
----------
particle1 : int
First particle index.
particle2 : int
Second particle index.
width : int
Line width. (default: 4)
color : any matplotlib color
Link color. (default: 'black')
"""
ri, rj = self.positions[particle1], self.positions[particle2]
self.ax.add_artist(Line2D(
[ri[0], ri[0] + self.dat._diffPeriodic(ri[0], rj[0])],
[ri[1], ri[1] + self.dat._diffPeriodic(ri[1], rj[1])],
lw=width, color=color, rasterized=self.rasterized))
self.ax.add_artist(Line2D(
[rj[0], rj[0] + self.dat._diffPeriodic(rj[0], ri[0])],
[rj[1], rj[1] + self.dat._diffPeriodic(rj[1], ri[1])],
lw=width, color=color, rasterized=self.rasterized))
def colorbar(self, vmin, vmax, cmap=plt.cm.jet):
"""
Adds colorbar to plot.
Parameters
----------
vmin : float
Minimum value of the colorbar.
vmax : float
Maximum value of the colorbar.
cmap : matplotlib colorbar
Matplotlib colorbar to be used. (default: matplotlib.pyplot.cm.jet)
"""
self.cmap = cmap
self.cmap_norm = ColorsNormalise(vmin=vmin, vmax=vmax)
self.scalarMap = ScalarMappable(norm=self.cmap_norm, cmap=self.cmap)
class Colormap(mpl.colorbar.ColorbarBase):
def set_label(_, label, **kwargs):
super().set_label(
label if self.colorbar_label == None
else self.colorbar_label,
**kwargs,
rotation=270 if self.colorbar_position == 'right' else 0)
if self.colorbar_position == 'right':
self.colormap_ax = make_axes_locatable(self.ax).append_axes('right',
size='5%', pad=0.05)
self.colormap = Colormap(
self.colormap_ax, cmap=self.cmap,
norm=self.cmap_norm, orientation='vertical')
elif self.colorbar_position == 'top':
self.colormap_ax = make_axes_locatable(self.ax).append_axes('top',
size='5%', pad=0.05)
self.colormap = Colormap(
self.colormap_ax, cmap=self.cmap,
norm=self.cmap_norm, orientation='horizontal')
self.colormap_ax.xaxis.set_label_position('top')
self.colormap_ax.xaxis.set_ticks_position('top')
else:
raise ValueError(
"Position '%s' is not recognised." % self.colorbar_position)
def colorbar_discrete(self, bounds, cmap=plt.cm.jet):
"""
Adds discrete colorbar to plot.
Parameters
----------
bounds : (*,) array-like
Bounds of values to map to colors.
cmap : matplotlib colorbar
Matplotlib colorbar to be used. (default: matplotlib.pyplot.cm.jet)
"""
self.colormap_bounds = np.array(sorted(bounds))
_cmap = mpl.colors.LinearSegmentedColormap.from_list('custom_cmap',
list(map(cmap, range(cmap.N))), cmap.N)
self.cmap_norm = mpl.colors.BoundaryNorm(self.colormap_bounds, cmap.N)
self.scalarMap = mpl.cm.ScalarMappable(norm=self.cmap_norm, cmap=_cmap)
class Colormap(mpl.colorbar.ColorbarBase):
def set_label(_, label, **kwargs):
super().set_label(
label if self.colorbar_label == None
else self.colorbar_label,
**kwargs,
rotation=270 if self.colorbar_position == 'right' else 0)
if self.colorbar_position == 'right':
self.colormap_ax = make_axes_locatable(self.ax).append_axes('right',
size='5%', pad=0.05)
self.colormap = Colormap(
self.colormap_ax, cmap=_cmap,
norm=self.cmap_norm, orientation='vertical')
elif self.colorbar_position == 'top':
self.colormap_ax = make_axes_locatable(self.ax).append_axes('top',
size='5%', pad=0.05)
self.colormap = Colormap(
self.colormap_ax, cmap=_cmap,
norm=self.cmap_norm, orientation='horizontal')
self.colormap_ax.xaxis.set_label_position('top')
self.colormap_ax.xaxis.set_ticks_position('top')
else:
raise ValueError(
"Position '%s' is not recognised." % self.colorbar_position)
def _colorbar_discrete(self, nColors, vmin, vmax, cmap=plt.cm.jet):
"""
Adds discrete colorbar to plot.
Parameters
----------
nColors : int
Number of values between minimum and maximum (included).
vmin : float
Minimum value of the colorbar.
vmax : float
Maximum value of the colorbar.
cmap : matplotlib colorbar
Matplotlib colorbar to be used. (default: matplotlib.pyplot.cm.jet)
"""
self.cmap_norm = BoundaryNorm(
np.linspace(vmin, vmax, nColors + 1), nColors)
_cmap = ListedColormap(
[ScalarMappable(
norm=ColorsNormalise(vmin=vmin, vmax=vmax), cmap=cmap
).to_rgba(x)
for x in np.linspace(vmin, vmax, nColors)])
self.scalarMap = ScalarMappable(norm=self.cmap_norm, cmap=_cmap)
self.colormap_ax = make_axes_locatable(self.ax).append_axes('right',
size='5%', pad=0.05)
self.colormap = mpl.colorbar.ColorbarBase(self.colormap_ax, cmap=_cmap,
norm=self.cmap_norm, orientation='vertical')
self.colormap.set_ticks(
[(0.5 + i)*(vmax - vmin)/nColors for i in range(nColors)])
self.colormap.set_ticklabels(
[r'$%s$' % i for i in np.linspace(vmin, vmax, nColors)])
class Orientation(_Frame):
"""
Plotting class specific to 'orientation' mode.
"""
def __init__(self, dat, frame, box_size, centre,
arrow_width=_arrow_width,
arrow_head_width=_arrow_head_width,
arrow_head_length=_arrow_head_length,
pad=_colormap_label_pad,
label=False, **kwargs):
"""
Initialises and plots figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
arrow_width : float
Width of the arrows.
arrow_head_width : float
Width of the arrows' head.
arrow_head_length : float
Length of the arrows' head.
pad : float
Separation between label and colormap.
(default: coll_dyn_activem.frame._colormap_label_pad)
label : bool
Write indexes of particles in circles. (default: False)
Optional keyword parameters
---------------------------
(see coll_dyn_activem.frame._Frame)
"""
super().__init__(dat, frame, box_size, centre,
arrow_width=arrow_width,
arrow_head_width=arrow_head_width,
arrow_head_length=arrow_head_length,
**kwargs) # initialise superclass
self.orientations = (
dat.getOrientations(frame, *self.particles)%(2*np.pi)) # particles' orientations at frame
self.colorbar(0, 2, cmap=plt.cm.hsv) # add colorbar to figure
self.colormap.set_label(r'$\theta_i/\pi$', labelpad=pad) # colorbar legend
self.label = label # write labels
self.draw()
def draw(self):
"""
Plots figure.
"""
for particle, orientation in zip(self.particles,
self.orientations): # for particle and particle's displacement in rendered box
self.draw_circle(particle,
color=self.scalarMap.to_rgba(orientation/np.pi), fill=False,
label=self.label) # draw particle circle with color corresponding to displacement amplitude
self.draw_arrow_in(particle, orientation,
color=self.scalarMap.to_rgba(orientation/np.pi)) # draw displacement direction arrow
class Displacement(_Frame):
"""
Plotting class specific to 'displacement' mode.
"""
def __init__(self, dat, frame, box_size, centre,
arrow_width=_arrow_width,
arrow_head_width=_arrow_head_width,
arrow_head_length=_arrow_head_length,
pad=_colormap_label_pad, dt=1, jump=1,
rescale=False,
label=False, **kwargs):
"""
Initialises and plots figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
arrow_width : float
Width of the arrows.
arrow_head_width : float
Width of the arrows' head.
arrow_head_length : float
Length of the arrows' head.
pad : float
Separation between label and colormap.
(default: coll_dyn_activem.frame._colormap_label_pad)
dt : int
Lag time for displacement. (default: 1)
jump : int
Period in number of frames at which to check if particles have
crossed any boundary. (default: 1)
NOTE: `jump' must be chosen so that particles do not move a distance
greater than half the box size during this time.
rescale : bool
Rescale displacements by mean squared displacement. (default: False)
label : bool
Write indexes of particles in circles. (default: False)
Optional keyword parameters
---------------------------
(see coll_dyn_activem.frame._Frame)
vmin : float
Minimum value of the colorbar.
vmax : float
Maximum value of the colorbar.
"""
super().__init__(dat, frame, box_size, centre,
arrow_width=arrow_width,
arrow_head_width=arrow_head_width,
arrow_head_length=arrow_head_length,
**kwargs) # initialise superclass
self.dt = dt
self.zetad = cooperativity(
dat.getDisplacements(frame, frame + dt, jump=jump, remove_cm=False))
# self.displacements = dat.getDisplacements(
# frame, frame + dt, *self.particles, jump=jump, remove_cm=True) # particles' displacements at frame
self.displacements = Displacements(dat.filename).getDisplacements(
frame, frame + dt, *self.particles, jump=jump, remove_cm=True) # particles' displacements at frame
self.rescale = rescale
if self.rescale:
self.displacements /= (
np.sqrt((self.displacements**2).sum(axis=-1).mean()))
self.vmin, self.vmax = amplogwidth(self.displacements)
try:
self.vmin = np.log10(kwargs['vmin'])
except (KeyError, AttributeError, TypeError): pass # 'vmin' not in keyword arguments or None
try:
self.vmax = np.log10(kwargs['vmax'])
except (KeyError, AttributeError, TypeError): pass # 'vmax' not in keyword arguments or None
self.colorbar(self.vmin, self.vmax) # add colorbar to figure
self.colormap.set_label( # colorbar legend
r'$\log_{10} ||\delta \Delta \boldsymbol{r}_i(t, t + \Delta t)||$'
+ (r'$/\sqrt{\left<|\ldots|^2\right>_i}$'
if self.rescale else '')
# + ' '
# + r'$(\zeta_{\Delta \boldsymbol{r}} = %.4f)$' % self.zetad
,
labelpad=pad)
self.label = label # write labels
self.draw()
def draw(self):
"""
Plots figure.
"""
for particle, displacement in zip(
self.particles, self.displacements): # for particle and particle's displacement in rendered box
self.draw_circle(particle,
color=self.scalarMap.to_rgba(
np.log10(np.linalg.norm(displacement))),
fill=True,
label=self.label) # draw particle circle with color corresponding to displacement amplitude
self.draw_arrow(particle,
*normalise1D(displacement)*0.75*self.diameters[particle]) # draw displacement direction arrow
# self.draw_circle(particle,
# color='red' if np.linalg.norm(displacement) > 0.25 else 'white',
# fill=True,
# border='black',
# label=self.label) # draw particle circle with color corresponding to displacement amplitude
class DispH(_Frame):
"""
Plotting class specific to 'disph' mode.
"""
def __init__(self, dat, frame, box_size, centre,
arrow_width=_arrow_width,
arrow_head_width=_arrow_head_width,
arrow_head_length=_arrow_head_length,
pad=_colormap_label_pad, jump=1,
rescale=False,
label=False, **kwargs):
"""
Initialises and plots figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
arrow_width : float
Width of the arrows.
arrow_head_width : float
Width of the arrows' head.
arrow_head_length : float
Length of the arrows' head.
pad : float
Separation between label and colormap.
(default: coll_dyn_activem.frame._colormap_label_pad)
dt : int
Lag time for displacement. (default: 1)
jump : int
Period in number of frames at which to check if particles have
crossed any boundary. (default: 1)
NOTE: `jump' must be chosen so that particles do not move a distance
greater than half the box size during this time.
rescale : bool
Rescale displacements by mean squared displacement. (default: False)
label : bool
Write indexes of particles in circles. (default: False)
Optional keyword parameters
---------------------------
(see coll_dyn_activem.frame._Frame)
vmin : float
Minimum value of the colorbar.
vmax : float
Maximum value of the colorbar.
"""
super().__init__(dat, frame, box_size, centre,
arrow_width=arrow_width,
arrow_head_width=arrow_head_width,
arrow_head_length=arrow_head_length,
**kwargs) # initialise superclass
self.dt = dt
self.hess = Force(dat.filename).getRAHessian(frame)
self.dp = wo_mean(
dat.getPropulsions(frame + dt) - dat.getPropulsions(frame))
self.displacements = wo_mean(np.reshape(
np.linalg.solve(self.hess, self.dp.flatten()),
(dat.N, 2))) # displacements from Hessian
self.rescale = rescale
if self.rescale:
self.displacements /= (
np.sqrt((self.displacements**2).sum(axis=-1).mean()))
self.vmin, self.vmax = amplogwidth(self.displacements)
try:
self.vmin = np.log10(kwargs['vmin'])
except (KeyError, AttributeError, TypeError): pass # 'vmin' not in keyword arguments or None
try:
self.vmax = np.log10(kwargs['vmax'])
except (KeyError, AttributeError, TypeError): pass # 'vmax' not in keyword arguments or None
self.colorbar(self.vmin, self.vmax) # add colorbar to figure
self.colormap.set_label( # colorbar legend
r'$\log_{10} ||\mathbb{H}^{-1} \delta \boldsymbol{p}_i||$'
+ (r'$/\sqrt{\left<|\ldots|^2\right>_i}$'
if self.rescale else ''),
labelpad=pad)
self.label = label # write labels
self.draw()
def draw(self):
"""
Plots figure.
"""
for particle, displacement in zip(
self.particles, self.displacements): # for particle and particle's displacement in rendered box
self.draw_circle(particle,
color=self.scalarMap.to_rgba(
np.log10(np.linalg.norm(displacement))),
fill=True,
label=self.label) # draw particle circle with color corresponding to displacement amplitude
self.draw_arrow(particle,
*normalise1D(displacement)*0.75*self.diameters[particle]) # draw displacement direction arrow
# self.draw_circle(particle,
# color='red' if np.linalg.norm(displacement) > 0.25 else 'white',
# fill=True,
# border='black',
# label=self.label) # draw particle circle with color corresponding to displacement amplitude
class Odisplacement(_Frame):
"""
Plotting class specific to 'odisplacement' mode.
"""
def __init__(self, dat, frame, box_size, centre,
pad=_colormap_label_pad, dt=1, jump=1, a1=1.15, a2=1.5,
label=False, **kwargs):
"""
Initialises and plots figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
pad : float
Separation between label and colormap.
(default: coll_dyn_activem.frame._colormap_label_pad)
dt : int
Lag time for displacement. (default: 1)
jump : int
Period in number of frames at which to check if particles have
crossed any boundary. (default: 1)
NOTE: `jump' must be chosen so that particles do not move a distance
greater than half the box size during this time.
a1 : float
Distance relative to their diameters below which particles are
considered bonded. (default: 1.15)
a2 : float
Distance relative to their diameters above which particles are
considered unbonded. (default: 1.5)
label : bool
Write indexes of particles in circles. (default: False)
Optional keyword parameters
---------------------------
(see coll_dyn_activem.frame._Frame)
"""
super().__init__(dat, frame, box_size, centre,
**kwargs) # initialise superclass
self.a1, self.a2 = a1, a2
self.odisplacements = np.array(itemgetter(*self.particles)(
Displacements(self.dat.filename).orientationNeighbours(
frame, dt, A1=self.a1, jump=jump, remove_cm=True)[0]))
self.brokenPairs = (
Displacements(self.dat.filename).brokenPairs(
frame, frame + dt, A1=self.a1, A2=self.a2))
self.colorbar_discrete([0, 4, 5, 7], cmap= # add colorbar to figure
mpl.colors.LinearSegmentedColormap.from_list('custom_cmap', [
(1, 1, 1), # white
(255./255., 195./255., 0./255.), # yellow
(255./255., 87./255., 51./255.)])) # orange
self.colormap.set_label( # colorbar legend
(r'$\sum_{j \in \mathcal{V}_i} \Theta($'
+ r'$\hat{\delta\Delta\boldsymbol{r}}_i(t, t + \Delta t) \cdot$'
+ r'$\hat{\delta\Delta\boldsymbol{r}}_j$'
+ r'$- 0.5), A_1=%.2f, A_2=%.2f$' % (self.a1, self.a2)),
labelpad=pad)
self.label = label # write labels
self.draw()
def draw(self):
"""
Plots figure.
"""
for particle, odisplacement in zip(
self.particles, self.odisplacements): # for particle and particle's number of same displacement orientation neighbours
self.draw_circle(particle,
color=self.scalarMap.to_rgba(odisplacement),
fill=True,
border='black',
label=self.label) # draw particle circle with color corresponding to number of same displacement orientation neighbours
for i in range(self.dat.N):
for j in range(i + 1, self.dat.N):
if (i in self.particles and j in self.particles
and self.brokenPairs[pairIndex(i, j, self.dat.N)]):
self.draw_link(i, j) # draw broken bond line from i to j
class Oridisplacement(_Frame):
"""
Plotting class specific to 'oridisplacement' mode.
"""
def __init__(self, dat, frame, box_size, centre,
pad=_colormap_label_pad, dt=1, jump=1,
brokenPairs=False, a1=1.15, a2=1.5, minimum=0,
border=True, label=False, **kwargs):
"""
Initialises and plots figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
pad : float
Separation between label and colormap.
(default: coll_dyn_activem.frame._colormap_label_pad)
dt : int
Lag time for displacement. (default: 1)
jump : int
Period in number of frames at which to check if particles have
crossed any boundary. (default: 1)
NOTE: `jump' must be chosen so that particles do not move a distance
greater than half the box size during this time.
brokenPairs : bool
Compute and display broken bonds between. (default: True)
a1 : float
Distance relative to their diameters below which particles are
considered bonded. (default: 1.15)
a2 : float
Distance relative to their diameters above which particles are
considered unbonded. (default: 1.5)
minimum : float
Display particles with squared displcaments greater than this
minimum. (default: 0)
border : bool
Draw black border of particles. (default: True)
label : bool
Write indexes of particles in circles. (default: False)
Optional keyword parameters
---------------------------
(see coll_dyn_activem.frame._Frame)
"""
super().__init__(dat, frame, box_size, centre,
**kwargs) # initialise superclass
self.a1, self.a2 = a1, a2
self.minimum = minimum
self.displacements = dat.getDisplacements(frame, frame + dt,
jump=jump, remove_cm=True)
self.oridisplacements = np.array(list(map(
angle,
*np.transpose(itemgetter(*self.particles)(self.displacements)))))
if brokenPairs:
self.brokenPairs = (
Displacements(self.dat.filename).brokenPairs(
frame, frame + dt, A1=self.a1, A2=self.a2))
else:
self.brokenPairs = np.zeros((int(self.dat.N*(self.dat.N - 1)/2),))
self.colorbar(-1, 1, cmap=plt.cm.hsv) # add colorbar to figure
self.colormap.set_label(
r'$\mathrm{arg}($'
+ r'$\delta \Delta \boldsymbol{r}_i(t, t + \Delta t))/\pi$'
+ ((' ' + r'$(\mathrm{minimum} = %.2f)$' % self.minimum)
if self.minimum > 0 else '')
+ (r'$, A_1=%.2f, A_2=%.2f$' % (self.a1, self.a2)
if brokenPairs else ''),
labelpad=pad) # colorbar legend
self.border = border # draw borders
self.label = label # write labels
self.draw()
def draw(self):
"""
Plots figure.
"""
for particle, oridisplacement in zip(
self.particles, self.oridisplacements): # for particle and particle's orientation of displacement
self.draw_circle(particle,
color=(
self.scalarMap.to_rgba(oridisplacement/np.pi)
if ((self.displacements[particle]**2).sum(axis=-1)
>= self.minimum**2)
else 'white'),
fill=True,
border='black' if self.border else None,
label=self.label) # draw particle circle with color corresponding to orientation of displacement
if self.brokenPairs.sum() == 0: return
for i in range(self.dat.N):
for j in range(i + 1, self.dat.N):
if (i in self.particles and j in self.particles
and self.brokenPairs[pairIndex(i, j, self.dat.N)]):
self.draw_link(i, j) # draw broken bond line from i to j
class Movement(_Frame):
"""
Plotting class specific to 'movement' mode.
"""
def __init__(self, dat, frame, box_size, centre,
arrow_width=_arrow_width,
arrow_head_width=_arrow_head_width,
arrow_head_length=_arrow_head_length,
dt=1, jump=1,
arrow_factor=1, minimum=None,
label=False, **kwargs):
"""
Initialises and plots figure.
Parameters
----------
dat : coll_dyn_activem.read.Dat
Data object.
frame : int
Frame to render.
box_size : float
Length of the square box to render.
centre : 2-uple like
Centre of the box to render.
arrow_width : float
Width of the arrows.
arrow_head_width : float
Width of the arrows' head.
arrow_head_length : float
Length of the arrows' head.
dt : int
Lag time for displacement. (default: 1)
jump : int
Period in number of frames at which to check if particles have
crossed any boundary. (default: 1)
NOTE: `jump' must be chosen so that particles do not move a distance
greater than half the box size during this time.
arrow_factor : float
Displacement arrow dilatation factor. (default: 1)