Commit fb8c6f3d authored by David A.. Werner's avatar David A.. Werner
Browse files

Merge branch 'dev'

parents 8a92281d 2617ff41
......@@ -29,13 +29,15 @@
* [x] Simulation: Population, Manduca, SimpleManduca
* [x] Logged values for plotting: History
* [x] properties
* [ ] saving animations as gifs
* [ ] making animations less ineffecient
* [ ] auto documentation using sphinx
* [x] saving animations as gifs
* [x] saving animations as mp4s!
* [x] making animations less ineffecient
* [x] auto documentation using sphinx
* [x] `make docs`
* [x] `make docs_html`
* [x] `make docs_pdf`
* [ ] Actually document everything..
* [ ] ~~Actually document everything..~~
* [x] Actually document some things!
* [ ] ~~pep8 compliance~~
* [x] Custom Exceptions
* [x] Test code using py.test
This diff is collapsed.
Makes animations of manducas moving
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import matplotlib.patches as patches
import os
def animate(*manducas, **kwargs):
anim = _get_animation(*manducas, **kwargs)
def animate_as_gif(file_name, *manducas, **kwargs):
anim = _get_animation(*manducas, **kwargs)
_save_as_gif(file_name, anim)
def animate_as_mp4(file_name, *manducas, **kwargs):
anim = _get_animation(*manducas, **kwargs)
_save_as_gif(file_name, anim)
def _get_animation(*manducas, **kwargs):
""" Produces an animation of all \*manducas racing
NOTE: Requires all manducas to have same time_step and num_time_steps!
show_winners = kwargs.pop('show_winners', False)
show_fitnesses = kwargs.pop('show_fitnesses', False)
manducas_with_labels = []
for idx,val in enumerate(manducas):
if isinstance(val, tuple):
manducas_with_labels.append((val, str(idx)))
if show_fitnesses or show_winners:
fitnesses = [ for man, _ in manducas_with_labels]
if show_winners:
max_f = max(fitnesses)
winners = np.array(fitnesses) == max_f
winners = None
if not show_fitnesses:
fitnesses = None
for idx in range(len(manducas_with_labels)):
manduca, label = manducas_with_labels[idx]
if fitnesses is not None:
new_label = "{}[fitness={}]".format(label, fitnesses[idx])
new_label = str(label)
if winners is not None:
if winners[idx]:
new_label = "{}[WINNER]".format(new_label)
manducas_with_labels[idx] = (manduca, new_label)
# Make sure the manducas are compatible!
time_steps = list(set([manduca.time_step for manduca, _ in manducas_with_labels]))
assert len(time_steps) == 1, \
"All manducas must have same time_step to be animated together"
num_time_steps = list(set([manduca.num_time_steps for manduca, _ in manducas_with_labels]))
assert len(time_steps) == 1, \
"All manducas must have same number of time steps to be animated together"
dx = time_steps[0]
positions, legs, muscles = [], [], []
# Read the file(s) and build points[n_frames][15 items][n_worms]
for manduca, labels in manducas_with_labels:
sim_kwargs = {key: kwargs[key] for key in ['sub_intervals'] if key in kwargs}
x, v, t, l, m = manduca.simulate(record_level=2, record_legs_and_muscles=True, **sim_kwargs)
muscle_strength = manduca.body_properties.muscle_strength
muscles.append([force/muscle_strength for force in m])
labels = [label for manduca, label in manducas_with_labels]
return _animate(labels, positions, legs, muscles, dx, fitnesses=fitnesses, winners=winners, **kwargs)
#TODO: Also do still-frames
def get_stills(manduca, sub_intervals=None):
def _save_as_gif(output_file, animation, dpi=80, **kwargs):, dpi=dpi, writer='imagemagick', **kwargs)
def _save_as_mp4(output_file, animation, dpi=80, **kwargs):, dpi=dpi, writer='mencoder', **kwargs)
def _animate(labels, positions, legs, muscles, dx, **kwargs):
leg_width = kwargs.pop('leg_width', 30)
show_result_percent = kwargs.pop('show_result_percent', 0.90)
fitnesses = kwargs.pop('fitnesses', None)
winners = kwargs.pop('winners', None)
# The per-frame animation function.
# Inputs: 'points' is a full array with[n_timepoints][data][n_worms] (where
# n_timepoints is the number of frames to be displayed).
# Remember that our display axes are:
# * x ranges over the min/max x values from the simulation.
# * y ranges from 0 to n_worms; i.e., each worm is allocated a vertical
# space of 1.
def per_frame (frame_number):
test_patches = []
for manduca_number in range(len(positions)):
mx = positions[manduca_number][frame_number]
ml = legs[manduca_number][frame_number]
mm = muscles[manduca_number][frame_number]
lrs = all_leg_rects[manduca_number]
brs = all_body_rects[manduca_number]
mrs = all_muscle_rects[manduca_number]
for rect, leg, pos in zip(lrs, ml, mx):
x, w = pos, leg_width
if leg == 0:
y = manduca_number + 0.2
y = manduca_number + 0.1
h = 0.75 - (y - manduca_number)
for br, mr, musc, pos, next_pos in zip(brs, mrs, mm, mx, mx[1:]):
return all_patches
xmin = min([min(min(val) for val in l) for l in positions])
xmax = max([max(max(val) for val in l) for l in positions])
xmax += leg_width
subplot_kwargs = kwargs.pop('subplot_kwargs',{})
fig,axes = plt.subplots(**subplot_kwargs)
axes.axis ([xmin,xmax,0,len(positions) + 0.1])
for i,label in enumerate(labels):
axes.text (xmin, i+0.95,label, va='top')
axes.plot([xmin,xmax],[i+0.1]*2, 'brown')
all_patches = []
all_leg_rects, all_body_rects, all_muscle_rects = [], [], []
for idx, (x, l, m) in enumerate(zip(positions, legs, muscles)):
x0, l0, m0 = x[0], l[0], m[0]
leg_rects = [patches.Rectangle ((0,0),0,0, facecolor='r') for _ in l0]
body_rects = [patches.Rectangle ((0,idx+0.25),0,0.5, facecolor='g') for _ in m0]
muscle_rects = [patches.Rectangle ((0,idx+0.375),0,0.25, facecolor='k') for _ in m0]
[axes.add_patch(p) for p in all_patches]
msec_per_frame = dx * 1
num_frames = len(positions[0])
ani = animation.FuncAnimation(fig, per_frame, frames=num_frames,
return ani
from .Manducas import Manduca, SimpleManduca, ManducaDeformityError, ManducaBodyProperties
from .Population import EvolutionParameters, EvolutionSimulator, GenerationInfo
from .Visualization import animate, animate_as_gif, animate_as_mp4
from setuptools import setup
description='A package for simulating manduca sexta',
author='David Werner',
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