def strobe_from_npmovie(npmovie, interval=200, frames=None):
bkgrd = npmovie.background
strobe_img = copy.copy(bkgrd)
i = 0
if frames is None:
frames = np.arange(0, len(npmovie.uframes), interval)
else:
frames = np.arange(frames[0], frames[-1], interval)
for i in frames:
if npmovie.uframes[i].uimg is not None:
uimg = npmovie.uframes[i].uimg
indices = npmovie.uframes[i].indices
# center = npmovie.uframes[i].center
blank = 255 * np.ones_like(bkgrd)
# blank.dtype = float
blank[indices[0] : indices[1], indices[2] : indices[3]] = uimg
strobe_img = nim.darken(strobe_img, blank)
return strobe_img
def calc_object_pos(movie):
# define background, do background subtraction and thresholding
background = nim.darken(movie.frames[0].raw, movie.frames[-1].raw)
for i, frame in enumerate(movie.frames):
print 'processing frames... ', i
movie.frames[i].absdiff = nim.absdiff(frame.raw, background)
movie.frames[i].diffthresh = nim.threshold(movie.frames[i].absdiff, THRESH_HOLD)
## TODO: right now this assumes the thresholding is perfect...!
# find center of fly:
center = center_of_mass(movie.frames[i].diffthresh)
if 1:
if center[0] == np.nan:
center = (0,0)
limlo_x = center[0]-ROI_RADIUS
if limlo_x < 0:
limlo_x = 0
limhi_x = center[0]+ROI_RADIUS
if limhi_x > movie.height:
limhi_x = movie.height
limlo_y = center[1]-ROI_RADIUS
if limlo_y < 0:
limlo_y = 0
limhi_y = center[1]+ROI_RADIUS
if limhi_y > movie.width:
limhi_y = movie.width
# TODO: right now object entering or leaving frame doesnt work perfectly
uimg = movie.frames[i].diffthresh[limlo_x:limhi_x, limlo_y:limhi_y]
movie.frames[i].uimg = uimg
movie.frames[i].uimg_center = center
el = nim.fit_ellipse(uimg)
center_relative_to_roi,xr,yr,theta_to_xaxis = el
tmp = np.array([float(ROI_RADIUS)/2, float(ROI_RADIUS)/2])
obj_pos = np.array(center) + np.array(center_relative_to_roi) - tmp
if xr>=yr:
angle = theta_to_xaxis
else:
angle = theta_to_xaxis+np.pi/2.
movie.frames[i].obj = Object(obj_pos, angle)
print xr,yr
return movie
def strobe_from_movieinfo(movieinfo, interval=200, frames=None):
bkgrd = movieinfo.background
strobe_img = copy.copy(bkgrd)
f = 0
while f < len(movieinfo.frames):
frame = movieinfo.frames[f]
uimg = frame.uimg
zero = frame.zero
size = frame.uimg.shape
blank = 255 * np.ones_like(bkgrd)
blank[zero[0]:zero[0] + size[0], zero[1]:zero[1] + size[1]] = uimg
strobe_img = nim.darken(strobe_img, blank)
f += interval
return strobe_img
def strobe_image(movie, interval=10, timerange=None, mode='darken'):
# combine frames from a movie using lighten or darken modes to get a 'strobe-like' sequence
# interval is the timestamp interval in movie-time (most likely 30 frames per second)
if timerange is None:
timerange = [0,movie.duration]
strobe_image = None
timestamp = timerange[0]
while timestamp < timerange[1]:
raw = movie.get_frame_at_timestamp(timestamp)
if strobe_image is None:
strobe_image = raw
else:
if mode == 'darken':
strobe_image = nim.darken(strobe_image, raw)
elif mode == 'lighten':
strobe_image = nim.lighten(strobe_image, raw)
timestamp += interval
return strobe_image
def updatefig(*args):
anim_params['frame'] += 1 + nskip
if anim_params['frame'] >= len(x[0])-1:
anim_params['frame'] = 1
anim_params['movie_finished'] = True
anim_params['frames'].append(anim_params['frame'])
print anim_params['frame']
for i, fly in enumerate(flies):
frame_start = anim_params['frame'] - ghost_tail
frame_end = anim_params['frame']
if frame_start < anim_params['first_frames'][i]:
frame_start = anim_params['first_frames'][i]
if frame_end > anim_params['final_frames'][i]:
frame_end = anim_params['final_frames'][i]
if frame_end < frame_start+nskip:
continue
frames = np.arange(frame_start, frame_end, nskip+1).tolist()
colors = ['none' for f in range(len(x[i]))]
edgecolors = ['none' for f in range(len(x[i]))]
for f in frames:
try:
colors[f] = color_mappable.to_rgba(color[i][f])
except:
colors[f] = color[i]
edgecolors[f] = edgecolor[i]
fly.set_edgecolors(edgecolors)
fly.set_facecolors(colors)
if images is not None:
if hasattr(images, '__call__'):
imgdata = images(frames[-1])
if len(imgdata.shape) > 2:
imgdata = imgdata[:,:,0]
if flipimgx:
if flipimgy:
imgdata = imgdata[::-1,::-1]
else:
imgdata = imgdata[::-1,:]
elif flipimgy:
imgdata = imgdata[:,::-1]
else:
imgdata = imgdata[:,:]
else:
imgdata = get_image_data(images, frames[-1], mono=mono, flipimgx=flipimgx, flipimgy=flipimgy)
if anim_params['strobe']:
if anim_params['strobeimg'] is None:
anim_params['strobeimg'] = imgdata
else:
anim_params['strobeimg'] = nim.darken([anim_params['strobeimg'], imgdata])
img.set_array(anim_params['strobeimg'])
else:
img.set_array(imgdata)
if save and not anim_params['movie_finished']:
print 'saving frame: ', str(anim_params['frame']), ' -- if the animation you see is strange, do not worry, look at the pngs'
frame_prefix = '_tmp'
frame_prefix = os.path.join(save_movie_path, frame_prefix)
strnum = str(anim_params['frame'])
num_frame_digits = np.ceil( np.log10(len(x[0]))) + 1
while len(strnum) < num_frame_digits:
strnum = '0' + strnum
frame_name = frame_prefix + '_' + strnum + '_' + '.png'
flytext.set_fontsize(fig, 8)
fig.savefig(frame_name, format='png')
if save and anim_params['movie_finished']:
print
print 'Movie finished saving! Close the plot screen now.'
print 'PNGs are at: ', save_movie_path
print 'To turn the PNGs into a movie, you can run this command from inside the directory with the tmp files: '
print 'mencoder \'mf://*.png\' -mf type=png:fps=30 -ovc lavc -lavcopts vcodec=mpeg4 -oac copy -o animation.avi'
if images is None:
return flies
else:
animation_objects = [fly for fly in flies]
animation_objects.insert(0, img)
return animation_objects
def updatefig(*args):
anim_params['frame'] += 1 + nskip
if anim_params['frame'] >= len(x[0]) - 1:
anim_params['frame'] = 1
anim_params['movie_finished'] = True
anim_params['frames'].append(anim_params['frame'])
print anim_params['frame']
for i, fly in enumerate(flies):
frame_start = anim_params['frame'] - ghost_tail
frame_end = anim_params['frame']
if frame_start < anim_params['first_frames'][i]:
frame_start = anim_params['first_frames'][i]
if frame_end > anim_params['final_frames'][i]:
frame_end = anim_params['final_frames'][i]
if frame_end < frame_start + nskip:
continue
frames = np.arange(frame_start, frame_end, nskip + 1).tolist()
colors = ['none' for f in range(len(x[i]))]
edgecolors = ['none' for f in range(len(x[i]))]
for f in frames:
try:
colors[f] = color_mappable.to_rgba(color[i][f])
except:
colors[f] = color[i]
edgecolors[f] = edgecolor[i]
fly.set_edgecolors(edgecolors)
fly.set_facecolors(colors)
if images is not None:
if hasattr(images, '__call__'):
imgdata = images(frames[-1])
if len(imgdata.shape) > 2:
imgdata = imgdata[:, :, 0]
if flipimgx:
if flipimgy:
imgdata = imgdata[::-1, ::-1]
else:
imgdata = imgdata[::-1, :]
elif flipimgy:
imgdata = imgdata[:, ::-1]
else:
imgdata = imgdata[:, :]
else:
imgdata = get_image_data(images,
frames[-1],
mono=mono,
flipimgx=flipimgx,
flipimgy=flipimgy)
if anim_params['strobe']:
if anim_params['strobeimg'] is None:
anim_params['strobeimg'] = imgdata
else:
anim_params['strobeimg'] = nim.darken(
[anim_params['strobeimg'], imgdata])
img.set_array(anim_params['strobeimg'])
else:
img.set_array(imgdata)
if save and not anim_params['movie_finished']:
print 'saving frame: ', str(
anim_params['frame']
), ' -- if the animation you see is strange, do not worry, look at the pngs'
frame_prefix = '_tmp'
frame_prefix = os.path.join(save_movie_path, frame_prefix)
strnum = str(anim_params['frame'])
num_frame_digits = np.ceil(np.log10(len(x[0]))) + 1
while len(strnum) < num_frame_digits:
strnum = '0' + strnum
frame_name = frame_prefix + '_' + strnum + '_' + '.png'
flytext.set_fontsize(fig, 8)
fig.savefig(frame_name, format='png')
if save and anim_params['movie_finished']:
print
print 'Movie finished saving! Close the plot screen now.'
print 'PNGs are at: ', save_movie_path
print 'To turn the PNGs into a movie, you can run this command from inside the directory with the tmp files: '
print 'mencoder \'mf://*.png\' -mf type=png:fps=30 -ovc lavc -lavcopts vcodec=mpeg4 -oac copy -o animation.avi'
if images is None:
return flies
else:
animation_objects = [fly for fly in flies]
animation_objects.insert(0, img)
return animation_objects
