def process_movie(MOVIE_ID, movie_info=None, dataset=None):
if movie_info is None:
filename = '/home/floris/data/windtunnel/SA1/movie_info'
fname = (filename)
fd = open( fname, mode='r' )
movie_info = pickle.load(fd)
fd.close()
movie_filename = movie_info[MOVIE_ID]['Path'] + MOVIE_ID + '.avi'
print 'loading: ', movie_filename
movie = pm.Movie(movie_filename)
npmovie = pm.npMovie()
npmovie.objid = movie_info[MOVIE_ID]['Obj_ID']
npmovie.epochtime = movie_info[MOVIE_ID]['EpochTime']
npmovie.filename = MOVIE_ID
npmovie.id = MOVIE_ID
npmovie.behavior = movie_info[MOVIE_ID]['Behavior']
npmovie.path = movie_info[MOVIE_ID]['Path']
npmovie.posttype = movie_info[MOVIE_ID]['PostType']
npmovie.extras = movie_info[MOVIE_ID]['Extras']
npmovie.trigger_stamp = movie_info[MOVIE_ID]['Trigger Stamp']
npmovie.timestamps = movie_info[MOVIE_ID]['Timestamps']
# make a mask
mask = np.ones([movie.height, movie.width])
mask[0:movie.height-movie.width, :] = 0
movie.mask = mask
# make a tracking mask -- 0 where no tracking desired
tracking_mask = np.abs(nim.plot_circle(1024,1024,[512,512], 150)-1)
npmovie.tracking_mask = tracking_mask
npmovie.calc_background(movie)
npmovie.load_frames(movie, timerange=None)
npmovie.fps = 5000.
npmovie.obj = pm.Object(npmovie)
pm.auto_adjust_uimg(npmovie)
pm.segment_fly(npmovie)
frames = smp.get_active_frames(npmovie)
if len(frames) < 5:
del(movie)
return npmovie
pm.calc_obj_pos(npmovie)
pm.calc_obj_motion(npmovie)
pm.smooth_legs(npmovie)
pm.calc_polarpos(npmovie)
pm.smooth_axis_ratio(npmovie)
trajec, time_err = sa1a.get_flydra_trajectory(npmovie, dataset)
print 'trajectory in process_movie: ', trajec
npmovie.trajec = copy.copy(trajec)
clas.calc_fly_coordinates(npmovie)
smp.calc_frame_of_landing(npmovie)
if trajec is not None:
smp.sync_2d_3d_data(npmovie)
if len(npmovie.sync2d3d.frames3d) > 2:
smp.calc_body_orientations(npmovie)
smp.calc_smoothyaw(npmovie, plot=False)
else:
npmovie.sync2d3d = None
npmovie.cluster = None
#strobe_img = pm.strobe_image(movie)
#movie_info[MOVIE_ID].setdefault('StrobeImg', strobe_img)
#npmovie_filename = '/home/floris/data/windtunnel/SA1/sa1_npmovie_' + MOVIE_ID
#pm.save(npmovie, npmovie_filename)
del(movie)
return npmovie
self.uframes[i].flydraframe = self.uframes[i-1].flydraframe
uframe.indices = None
if __name__ == '__main__':
filename = '/media/SA1_movies_2/sa1_movies/20101028_C001H001S0008.avi'
movie = Movie(filename)
npmovie = npMovie()
# make a mask
mask = np.ones([movie.height, movie.width])
mask[0:movie.height-movie.width, :] = 0
movie.mask = mask
# make a tracking mask -- 0 where no tracking desired
tracking_mask = np.abs(nim.plot_circle(1024,1024,[512,512], 150)-1)
npmovie.tracking_mask = tracking_mask
npmovie.calc_background(movie)
npmovie.load_frames(movie)
npmovie.obj = Object(npmovie)
calc_obj_pos(npmovie)
calc_obj_motion(npmovie, 5000.)
save(npmovie, 'sa1_movie_obj_flyby_20101028_C001H001S0008')
def process_movie(movieinfo, framerange=None, nframes=None):
filename = movieinfo.path + movieinfo.id + '.avi'
movie = Movie(filename)
# make a mask to remove text and such of the top part of the movie
mask = np.ones([movie.height, movie.width])
mask[0:movie.height-movie.width, :] = 0
movie.mask = mask
tracking_mask = np.abs(nim.plot_circle(1024,1024,[512,512], 150)-1)
first_frame = (movie.get_frame_at_timestamp(0)[::-1, :])
last_frame = (movie.get_frame_at_timestamp(movie.duration-1)[::-1, :])
background = nim.lighten(first_frame, last_frame)
movieinfo.background = copy.copy(background)
if framerange is None:
framerange = movieinfo.framenumbers
else:
framerange = np.arange(framerange[0], framerange[1]+1, 1).tolist()
if nframes is not None:
framerange = framerange[0:nframes]
nframes = len(framerange)
movieinfo.obj_centers = np.zeros([nframes, 2])
movieinfo.obj_longaxis = np.zeros([nframes, 2])
movieinfo.obj_shortaxis = np.zeros([nframes, 2])
movieinfo.obj_ratio = np.zeros([nframes, 2])
movieinfo.frames = [Frame() for frame in framerange]
print 'framerange = ', framerange[0]
for f, framenumber in enumerate(framerange):
frame = movieinfo.frames[f]
print f, framenumber
raw = (movie.get_frame(framenumber)[::-1, :])
if f < 3:
guess = None
guess_radius = None
else:
try:
vel_est = movieinfo.obj_centers[f-1,:] - movieinfo.obj_centers[f-2,:]
guess = movieinfo.obj_centers[f-1,:] + vel_est
guess_radius = 35
except:
guess = None
guess_radius = None
center, uimg, zero = nim.find_object_with_background_subtraction(raw, background, mask=tracking_mask, guess=guess, guess_radius=guess_radius, sizerange=[10,600], thresh=10, uimg_roi_radius=30, return_uimg=True, return_mimg=False)
print '********pygmovie********', uimg.shape, zero
ubackground = nim.extract_uimg(background, uimg.shape, zero)
relative_center_of_body, longaxis, shortaxis, body, ratio = nim.find_ellipse(uimg, background=ubackground, threshrange=[150,254], sizerange=[10,600], dist_thresh=10, erode=False, check_centers=True)
center_of_body = relative_center_of_body + zero
#center_of_body = center
frame.uimg = copy.copy(uimg)
#frame.mimg = mimg
frame.zero = zero
frame.framenumber = framenumber
movieinfo.obj_centers[f,:] = copy.copy(center_of_body)
movieinfo.obj_longaxis[f,:] = copy.copy(longaxis)
movieinfo.obj_shortaxis[f,:] = copy.copy(shortaxis)
movieinfo.obj_ratio[f,:] = copy.copy(ratio)
del(raw)
del(movie)
return
