Пример #1
0
            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)
Пример #2
0
            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()
Пример #3
0
                 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)))