# -*- coding: utf-8 -*-
"""
Created on Tue Aug 18 04:21:02 2015
@author: oddman
"""
import os,json, cProfile, subprocess
#from SkinBrian import *
from ShapesOnAPlane import *
from matplotlib.font_manager import FontProperties
from matplotlib.figure import SubplotParams
from matplotlib.patches import Ellipse, Arrow
from matplotlib.lines import Line2D
import multiprocessing
import numpy as np
RAMONYCAJALCOUNT = 15
class SkinBrainComic:
def __init__(self,fromTime,toTime,timeStep,networkTopology,
spikes,vizOutputDirPath):
self.maxMs = max([
max(spikeTrain+[0])
for cell_i,spikeTrain
in spikes.items()
])
self.fromTime = fromTime
self.toTime = toTime
self.timeStep = float(timeStep)
self.spikes = spikes
self.vizOutputDirPath = vizOutputDirPath
self.networkTopology = networkTopology
# print spikeSort(self.spikes.items())
print self.maxMs
self.maxTime = int(self.maxMs) + 1
self.alignEvents()
def alignEvents(self):
## the format of spikes produced by SingleRunDataReader is a list of
## lists, spike times of cells.
## the time of the last spike in ms/binsize, rounded up
intervalCount = int(self.maxTime / self.timeStep) + 1
self.cellsFiringPerMoment = dict((i,[]) for i in range(intervalCount))
## for every spike, put the cellindex in the appropriate time-bin
[
[
self.cellsFiringPerMoment[int(spikeTime / self.timeStep)].append(cellIndex)
for spikeTime
in thisCellSpikes
]
for cellIndex,thisCellSpikes
in self.spikes.items()
]
# print self.cellsFiringPerMoment
# self.linksfiringpermoment = dict((i,[]) for i in range(self.maxtime))
# [
# [
# self.linksfiringpermoment[int(moment/self.binsize)].append(link)
# for moment
# in momentlist
# ]
# for (link,momentlist)
# in self.thisrun.firinglinks.items()
# ]
def run(self,orientation,outputFormat,CPUCount,autoplay):
firstInterval = int(self.fromTime / self.timeStep)
lastInterval = int(self.toTime / self.timeStep)
plottedIntervals = range(firstInterval,lastInterval)
print 'Plotting {0} frames.'.format(len(plottedIntervals))
movieVizOutputDirPath = self.vizOutputDirPath + 'movie/'
if os.path.exists(movieVizOutputDirPath):
pass
else:
os.mkdir(movieVizOutputDirPath)
# pool = multiprocessing.Pool(processes = CPUCount)
frameArgumentList = [
[
intervalKey,outputFormat,movieVizOutputDirPath,
self.networkTopology,self.cellsFiringPerMoment
]
for intervalKey in plottedIntervals
]
for frameArguments in frameArgumentList:
sfp = multiprocessing.Process(
target = singleFrame,
args = frameArguments
)
sfp.start()
sfp.join()
# pool.map(frameMultiprocessHelper,poolArgumentList)
singleFrame(
intervalKey,outputFormat,
self.vizOutputDirPath,self.networkTopology,
self.cellsFiringPerMoment,cellSize = .25,
links = 'ramon_y_cajal')
os.chdir(movieVizOutputDirPath)
# intervals = len(plottedIntervals)
if outputFormat == 'png':
if os.path.exists('./skinBrainMovie.avi'):
os.remove('./skinBrainMovie.avi')
ffmpegCommandList = [
'ffmpeg',
'-f',
'image2',
'-framerate',
'30',
'-pattern_type',
'sequence',
'-start_number',
'{0}'.format(firstInterval),
'-r',
'12',
'-i',
'%05dvector_wires.png',
'skinBrainMovie.avi'
]
subprocess.call(ffmpegCommandList)
mplayerCommandList = ['gnome-mplayer','skinBrainMovie.avi']
if autoplay:
subprocess.call(mplayerCommandList)
def singleFrame(
intervalKey,outputFormat,outputDirPath,networkTopology,
cellsFiringPerMoment,cellSize=.75,links = False
):
"""A function producing a single wire-frame 2d-representation
of a skin brain at a certain time in the simulation.
"""
print intervalKey
timestr = "%05d"%(intervalKey)
if links == 'all':
linkstr = 'links_'
elif links == 'ramon_y_cajal':
linkstr = 'ramon_y_cajal_links_'
else:
linkstr = ''
graphName = timestr+linkstr+'vector_wires.'+outputFormat
if os.path.exists(outputDirPath+graphName):
return graphName
interCellDistance = 5.
inch = 25.4 ## mm
## size should be relative to length (x) and circumference (y).
figXSize = (networkTopology.networkParameters['length_circumference'][0]*interCellDistance*.5*sqrt(2)) / inch
figYSize = (networkTopology.networkParameters['length_circumference'][1]*interCellDistance) / inch
fig = figure(figsize=(figXSize,figYSize), subplotpars=SubplotParams(left=0,right=1,top=1,bottom=0))
# nodes = [i for i in enumerate(self.coords2d)]
# print str(moment)
ax = fig.add_subplot(111,frame_on=False,label=intervalKey)
nodes = [(cell.overallIndex,cell.flatCoordinates) for cell in networkTopology.cells]
if links == 'all' or links == 'ramon_y_cajal':
if links == 'ramon_y_cajal':
inCells = np.random.choice(networkTopology.cells,RAMONYCAJALCOUNT)
for link in networkTopology.links:
(origin,target) = (
link.fromCell,
link.toCell
)
if links == 'all' or (links == 'ramon_y_cajal' and origin in inCells):
thisline = Line2D(
*zip(*[list(origin.flatCoordinates),list(target.flatCoordinates)]),
linewidth=1.5,
solid_capstyle = 'butt')
ax.add_artist(thisline)
thisline.set_clip_box(ax.bbox)
thisline.set_color([0.8,0.8,0.8])
# print self.colourdict[link]
# linkprune.__delitem__(link)
thisline.set_zorder(1)
# otherlines = [
# Line2D(
# *zip(*[list(origin),list(target)]),
# linewidth=1.5,
# solid_capstyle = 'butt')
# for (link,(origin,target))
# in linkprune.items()]
# for e in otherlines:
# ax.add_artist(e)
# e.set_clip_box(ax.bbox)
# e.set_color(linkcolour)
# e.set_zorder(0)
ellipses = [(i,Ellipse(xy,cellSize,cellSize)) for (i,xy) in nodes]
for (i,e) in ellipses:
ax.add_artist(e)
e.set_clip_box(ax.bbox)
if i not in cellsFiringPerMoment[intervalKey]:
e.set_color([0.9,0.9,0.9])
else:
e.set_color([0.5,0.0,0.0])
if links == 'all':
e.set_color([0.4,0.4,0.4])
e.set_zorder(2)
ax.tick_params(top=False,bottom=False,left=False,right=False)
ax.set_xlim(-1, max([x for (i,(x,y)) in nodes]) + 1)
ax.set_ylim(-1, max([y for (i,(x,y)) in nodes]) + 1)
ax.set_yticklabels('')
ax.set_xticklabels('')
# linkstr = "_links" + repr(links)
graphName = timestr+linkstr+'vector_wires.'+outputFormat
savefig(outputDirPath+graphName,format=outputFormat)
close('all')
# fig.show()
return graphName
def generateComic(
fromTime,toTime,timeStep,targetFolder,topologyCachePath,runIndex,
CPUCount,autoplay=True,show=True,outputFormat='png'
):
# print os.listdir(targetFolder)
metadataPath = targetFolder.strip('/') + '/metadata.json'
vizOutputDirPath = targetFolder.strip('/') + '/viz_{0}/'.format(runIndex)
if os.path.exists(vizOutputDirPath):
pass
else:
print os.getcwd()
os.mkdir(vizOutputDirPath)
with open(metadataPath,'r') as metadataFile:
metadata = json.load(metadataFile)
# print self.metadata['0']['cellModelParameters']
key = str(runIndex)
networkParameters = metadata[key]['networkParameters']
networkType = networkParameters['networkType']
networkTopology = NetworkTopology(
networkType,
cacheDir = topologyCachePath
)
networkTopology.generate(
networkParameters,
cache=True
)
# print networkTopology.networkParameters
spikeFilePath = targetFolder.strip('/') + '/spikefile_'+key+'.json'
with open(spikeFilePath,'r') as spikeFile:
spikes = dict(json.load(spikeFile))
skinBrainComic = SkinBrainComic(fromTime,toTime,timeStep,networkTopology,spikes,vizOutputDirPath)
skinBrainComic.run('vertical',outputFormat,CPUCount,autoplay)
if __name__ == '__main__':
CPUCount = 1
# thisRunFolder = './output/'+max(os.listdir('./output/'))
thisRunFolder = './output/fullRun'
print thisRunFolder
generateComic(0,1000,2,thisRunFolder,'./topologyCaches/',1930,CPUCount,autoplay=False,outputFormat='png')
