def load_flies_skies(rootDir, baseDirs):
skies, flies = {}, {}
for b, baseDir in enumerate(baseDirs):
sks, fls = {}, {}
dNames = os.listdir(os.path.join(rootDir,baseDir))
flyDirNames = [D for D in dNames if D[:3] == 'fly']
flyDirNames.sort(compare_dir_names)
for dNum, dName in enumerate(flyDirNames):
dirName=os.path.join(rootDir,baseDir,dName)
print dirName
fly = flypod.analyze_directory(dirName)
fls[dNum] = fly.copy()
sky = sky_times.analyze_directory(dirName)
sks[dNum] = sky.copy()
flies[baseDir] = fls
skies[baseDir] = sks
return flies, skies
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)
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()
ax = fig.add_subplot(111)
for fn,frameNumber in enumerate(range(0,int(nFrames),FRAMESTEP)):
frame,timestamps[fn] = fmf.get_frame(frameNumber)
#pylab.imsave(join(outDirName,'frame')+("%05d" %(fn+1))+'.png',frame,format='png',cmap='gray')
ax.imshow(frame,cmap='gray')
lineX = [fly['x'][frameNumber]+fly['ROI'][2], circleCenterX+fly['ROI'][2]]
lineY = [fly['y'][frameNumber]+fly['ROI'][1], circleCenterY+fly['ROI'][1]]
ax.plot(lineX,lineY,'b-', linewidth=2)
ax.set_axis_off()
fig.savefig(join(outDirName,'frame')+("%05d" %(fn+1))+'.png')
ax.cla()
print 'frame rate = ' + str(1/np.mean(np.diff(timestamps)))
flies
except NameError:
print "loading flies"
skies, flies = {}, {}
for b, baseDir in enumerate(baseDirs):
sks, fls = {}, {}
dNames = os.listdir(os.path.join(rootDir, baseDir))
flyDirNames = [D for D in dNames if D[:3] == "fly"]
flyDirNames.sort(compare_dir_names)
for dNum, dName in enumerate(flyDirNames):
dirName = os.path.join(rootDir, baseDir, dName)
print dirName
fly = flypod.analyze_directory(dirName)
fls[dNum] = fly
sky = sky_times.analyze_directory(dirName)
sks[dNum] = sky
flies[baseDir] = fls
skies[baseDir] = sks
MAX_NUM_STOPS = 6
SAVEFIGS = False
CHANGEBUFFER = 10
STARTBUFFER = 0
STOPBUFFER = 0
COLORS = dict(N="b", E="y", S="r", W="g")
ROTATIONS = dict(N=0, E=90, S=180, W=270)
SPEED = 0.5
DMAX = 330 # 800
Dist = {}
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)))
