for i, cT in enumerate(sky['changeTimes'][:-1]):
inds = (times > cT+POSTCHANGE_BUFFER) & (times < sky['changeTimes'][i+1]-PRECHANGE_BUFFER)
ors = orientations[inds]
ors = ors[~numpy.isnan(ors)]
if len(ors)>0:
totals[sky['directions'][i]] = numpy.concatenate((totals[sky['directions'][i]],ors))
for i, d in enumerate(COLORS):
worldTotals = numpy.concatenate((worldTotals,totals[d]+ROTATIONS[d]))
M[fNum]=circmean(worldTotals*numpy.pi/180)
V[fNum]=circvar(worldTotals*numpy.pi/180)
#pylab.figure()
pylab.subplot(4,5,fNum+1,polar=True)
plotArgs = dict(color='k',linewidth=2)
orw,n,b,bc,ax = flypod.rose(worldTotals,plotArgs=plotArgs)
pylab.hold('on')
for i, d in enumerate(COLORS):
plotArgs = dict(color=COLORS[d],linewidth=.5)
flypod.rose(totals[d]+ROTATIONS[d],plotArgs=plotArgs)
pylab.polar([0,numpy.pi/2-M[fNum]],[0,ax.get_rmax()*(1-V[fNum])],color='k')
ax.set_rmax(.15)
ax.set_rgrids([1],'')
ax.set_thetagrids([0,90,180,270],['E','N','W','S'])
pylab.title(fly['dirName'])
pylab.suptitle(baseDir)
circVar[baseDir] = numpy.copy(V)
orientations[inds] = numpy.nan
inds = (times > TOTAL_TIME + times[0])
orientations[inds] = numpy.nan
pylab.draw()
fig = pylab.figure()
fig.set_facecolor('w')
pylab.suptitle(fly['fileName'])
for i, cT in enumerate(sky['changeTimes'][:-1]):
pylab.subplot(5,4,1+i,polar=True)
ax=pylab.gca()
inds = (times > cT) & (times < sky['changeTimes'][i+1])
ors = orientations[inds]
ors = ors[~numpy.isnan(ors)]
if len(ors)>0:
orw,n,b,bc,ax = flypod.rose(ors,360)
m=circmean(ors,high=180,low=-180)
v=circvar(ors*numpy.pi/180,high=numpy.pi,low=-numpy.pi)
hold('on')
polar([0,numpy.pi/2-m*numpy.pi/180],[0,ax.get_rmax()*(1-v)])
ax.set_rmax(.4)
ax.set_rgrids([1],'')
ax.set_thetagrids([0,90,180,270],['','','',''])
title(sky['directions'][i])
#ax.set_axis_bgcolor(COLORS[sky['directions'][i]])
ax.axesPatch.set_facecolor(COLORS[sky['directions'][i]])
ax.axesPatch.set_alpha(0.4)
totals[sky['directions'][i]] = numpy.concatenate((totals[sky['directions'][i]],ors))
pylab.draw()
if mod(i, 2)==0:
rotatorStateForPlots = sky['rotatorState'][i]
else:
rotatorStateForPlots = 'R'
totals[rotatorStateForPlots] = numpy.concatenate((totals[rotatorStateForPlots],ors))
for i, d in enumerate(COLORS):
ax = fig.add_subplot(i+1,numFlies,1+fNum,polar=True)
if MOD_180:
m = (circmean(totals[d]*2.0*numpy.pi/180.0)*180.0/numpy.pi)/2.0
m = mod(m,180)
else:
m = circmean(totals[d]*numpy.pi/180.0)*180.0/numpy.pi
#m=circmean(totals[d]*numpy.pi/180.0)*180.0/numpy.pi
v=circvar(totals[d]*numpy.pi/180)
orw,n,b,bc,ax = flypod.rose(totals[d],360)
pylab.polar([0,numpy.pi/2-m*numpy.pi/180],[0,ax.get_rmax()*(1-v)])
ax.set_rmax(.15)
ax.set_rgrids([1],'')
ax.set_thetagrids([0,90,180,270],['','','',''])
pylab.title(str(int(round(m))))
ax.axesPatch.set_facecolor(COLORS[d])
ax.axesPatch.set_alpha(0.2)
meanAngle[fNum,i] = m.copy()
varAngle[fNum,i] = v.copy()
mA[bd] = meanAngle.copy()
vA[bd] = varAngle.copy()
nS[bd] = numStops.copy()
if MOD_180:
diffAngles = abs(angleDiffDegrees(mA[bd][:,1],mA[bd][:,0]))
def make_frames(inDirName,outDirName):
"""saves frames in movie with orientation superimposed
arguments:
inDirName directory with fly, sky, and .fmf files
outDirName directory to save frames to
example:
make_frames('/media/weir05/data/rotator/white/diffuserPol/12trials/fly08','./frames/')
"""
fly = flypod.analyze_directory(inDirName)
sky = sky_times.analyze_directory(inDirName)
orientations = fly['orientations'].copy() + 180
times = fly['times'].copy()
rotatorStateEachFrame = -np.ones(times.shape) # we will store frame-based rotator state in here
COLORS = dict({'U': 'm', 'R': 'c'})
ROTATOR_CODE = dict({'U': 0, 'R': 1})
FRAMESTEP = 65 #130
circleCenterX, circleCenterY, circleRadius = circle_fit(fly['x'],fly['y']) #NOTE:should have been saving this info from start.
fmf = FMF.FlyMovie(join(inDirName,fly['fileName']))
nFrames = fmf.get_n_frames()
timestamps = np.ma.masked_all(len(range(0,int(nFrames),FRAMESTEP)))
fig = pylab.figure()
frameAxes = fig.add_axes([0.1, 0.3, 0.5, 0.6])
timePlotAxes = fig.add_axes([0.1, 0.1, 0.8, 0.15])
polarTopAxes = fig.add_axes([0.55, 0.6, 0.4, 0.25],polar=True)
polarBottomAxes = fig.add_axes([0.55, 0.3, 0.4, 0.25],polar=True)
timePlotAxes.plot(times,orientations,'k')
for i, cT in enumerate(sky['changeTimes'][:-1]):
timePlotAxes.axvspan(cT, sky['changeTimes'][i+1], facecolor=COLORS[sky['rotatorState'][i]], alpha=0.2)
startInd = np.argmin(abs(times-cT))
endInd = np.argmin(abs(times-sky['changeTimes'][i+1]))
rotatorStateEachFrame[startInd:endInd] = ROTATOR_CODE[sky['rotatorState'][i]]
unrotatedOrientations = np.ma.masked_where(rotatorStateEachFrame != 0,orientations)
rotatedOrientations = np.ma.masked_where(rotatorStateEachFrame != 1,orientations)
if sum(np.isnan(orientations)) > 0:
for trackingErrorTime in times[np.isnan(orientations)]:
timePlotAxes.axvline(trackingErrorTime,linewidth=2,color='k')
if fly.has_key('stopTimes'):
for i, sT in enumerate(fly['stopTimes']):
timePlotAxes.axvspan(sT, fly['startTimes'][i], facecolor='r', alpha=0.5)
timePlotAxes.set_axis_off()
for fn,frameNumber in enumerate(range(0,int(nFrames),FRAMESTEP)):
frame,timestamps[fn] = fmf.get_frame(frameNumber)
frameAxes.imshow(frame,cmap='gray',origin='lower')
lineX = [circleCenterX+fly['ROI'][2], 2*(circleCenterX+fly['ROI'][2])-(fly['x'][frameNumber]+fly['ROI'][2])]
lineY = [circleCenterY+fly['ROI'][1], 2*(circleCenterY+fly['ROI'][1])-(fly['y'][frameNumber]+fly['ROI'][1])]
frameAxes.plot(lineX,lineY,'b', linewidth=2)
frameAxes.set_axis_off()
movingDot = timePlotAxes.scatter(times[frameNumber],orientations[frameNumber])
timePlotAxes.set_ylim((-10,370))
orw,n,b,bc,ax = flypod.rose(unrotatedOrientations[:frameNumber].compressed(),360,ax=polarTopAxes,plotArgs = dict(color=COLORS['U']))
polarTopAxes.set_rmax(.25)
polarTopAxes.set_rgrids([1],'')
polarTopAxes.set_thetagrids([0,90,180,270],['','','',''])
orw,n,b,bc,ax = flypod.rose(rotatedOrientations[:frameNumber].compressed(),360,ax=polarBottomAxes,plotArgs = dict(color=COLORS['R']))
polarBottomAxes.set_rmax(.25)
polarBottomAxes.set_rgrids([1],'')
polarBottomAxes.set_thetagrids([0,90,180,270],['','','',''])
fig.savefig(join(outDirName,'frame')+("%05d" %(fn+1))+'.png')
polarTopAxes.cla()
polarBottomAxes.cla()
frameAxes.cla()
movingDot.remove()
print 'frame rate = ' + str(1/np.mean(np.diff(timestamps)))