max(bbox_heights) + 2 * padding)
# make it square (apparently avconv doesn't work correctly with arbitrary frame size...)
win_size = (max(win_size), max(win_size))
### centroids
cell_centers = np.array([regionprops(mask)[0].centroid for mask in masks])
smooth_cell_centers = smooth_2D_trajectory(cell_centers)
### extract windows and put into big array
windows = np.empty((len(frames), win_size[0], win_size[1]))
for frame_num, (frame, center,
mask) in enumerate(zip(frames, smooth_cell_centers,
masks)):
# make boundary bright
boundary = find_boundaries(mask)
frame += 0.5 * frame.max() * boundary
# extract window centered on mask centroid
i, j = int(round(center[0])), int(round(center[1]))
ista, jsta = i - win_size[0] / 2, j - win_size[1] / 2
iend, jend = ista + win_size[0], jsta + win_size[1]
win = frame[ista:iend, jsta:jend]
windows[frame_num, :, :] = correct_orientation(win)
# save to file
print 'Saving movie to %s.' % out_fn
write_video(windows, out_fn)
for frame_num, (frame,
boundary_pts) in enumerate(zip(frames, all_boundary_pts)):
boundary_x, boundary_y = interpolate_boundary_pts(boundary_pts)
mask = measure.grid_points_in_poly(frame.shape, boundary_pts)
center = measure.regionprops(mask)[0].centroid
implot.set_data(frame)
boundary_plot.set_data(boundary_y, boundary_x)
boundary_pts_plot.set_data(boundary_pts[:, 1], boundary_pts[:, 0])
center_point.set_data(center[1], center[0])
plt.title('frame %i' % (frame_num + 1))
fig.canvas.draw()
plt.ioff()
plt.show()
### save to file
if out_fn:
# cell_label = re.findall(r'\d+', boundaries_fn)[0]
movie_frames = np.empty_like(frames)
for frame_num, (frame, boundary_pts) in enumerate(
zip(frames.copy(), all_boundary_pts)):
mask = measure.grid_points_in_poly(frame.shape, boundary_pts)
boundary = find_boundaries(mask)
frame += 0.5 * frame.max() * boundary
movie_frames[frame_num, :, :] = correct_orientation(frame)
# fn = 'cell%i_visualization.avi' % cell_label
# print 'Saving visualization to', fn
write_video(movie_frames, out_fn)
win_size = (max(win_size), max(win_size))
### centroids
cell_centers = np.array([regionprops(mask)[0].centroid for mask in masks])
smooth_cell_centers = smooth_2D_trajectory(cell_centers)
### extract windows and put into big array
windows = np.empty((len(frames), win_size[0], win_size[1]))
for frame_num, (frame, center, mask) in enumerate(zip(frames, smooth_cell_centers, masks)):
# make boundary bright
boundary = find_boundaries(mask)
frame += 0.5*frame.max()*boundary
# extract window centered on mask centroid
i, j = int(round(center[0])), int(round(center[1]))
ista, jsta = i-win_size[0]/2, j-win_size[1]/2
iend, jend = ista+win_size[0], jsta+win_size[1]
win = frame[ista:iend, jsta:jend]
windows[frame_num,:,:] = correct_orientation(win)
# save to file
print 'Saving movie to %s.' % out_fn
write_video(windows, out_fn)
for frame_num, (frame, boundary_pts) in enumerate(zip(frames, all_boundary_pts)):
boundary_x, boundary_y = interpolate_boundary_pts(boundary_pts)
mask = measure.grid_points_in_poly(frame.shape, boundary_pts)
center = measure.regionprops(mask)[0].centroid
implot.set_data(frame)
boundary_plot.set_data(boundary_y, boundary_x)
boundary_pts_plot.set_data(boundary_pts[:,1], boundary_pts[:,0])
center_point.set_data(center[1], center[0])
plt.title('frame %i' % (frame_num+1))
fig.canvas.draw()
plt.ioff()
plt.show()
### save to file
if out_fn:
# cell_label = re.findall(r'\d+', boundaries_fn)[0]
movie_frames = np.empty_like(frames)
for frame_num, (frame, boundary_pts) in enumerate(zip(frames.copy(), all_boundary_pts)):
mask = measure.grid_points_in_poly(frame.shape, boundary_pts)
boundary = find_boundaries(mask)
frame += 0.5*frame.max()*boundary
movie_frames[frame_num,:,:] = correct_orientation(frame)
# fn = 'cell%i_visualization.avi' % cell_label
# print 'Saving visualization to', fn
write_video(movie_frames, out_fn)