def create_colorized_masks(id_masks, trj, cell_ids, background_id, color_list,
cell_color_idx, cell_visibility, show_ids):
logging.info('================= Colorizing masks =================')
font = ImageFont.load_default()
bg_color = color_list[cell_color_idx[background_id]]
bg_frame = np.zeros((id_masks.shape[0], id_masks.shape[1], 3),
dtype=id_masks.dtype)
for color_channel in range(3):
bg_frame[:, :, color_channel] += bg_color[color_channel]
colorized_masks = []
for i_frame in range(id_masks.shape[2]):
logging.info('Frame {}...'.format(i_frame))
mask = id_masks[:, :, i_frame]
col_frame = bg_frame.copy()
if show_ids:
id_frame = np.zeros((mask.shape[0], mask.shape[1], 3),
dtype=mask.dtype)
for cell_id in cell_ids:
if (cell_id == background_id) or (not cell_visibility[cell_id]):
continue
cell_idx = get_trj_idx(trj, i_frame, 'particle', [cell_id])
if len(cell_idx) == 0:
continue
cell_y = int(trj.loc[cell_idx[0], 'y'])
cell_x = int(trj.loc[cell_idx[0], 'x'])
cell_color = color_list[cell_color_idx[cell_id]]
cell_coords = (mask == cell_id)
for color_channel in range(3):
col_frame[:, :, color_channel][cell_coords] = cell_color[
color_channel]
if show_ids:
# Stamp the cell_id on cell
draw_img = Image.fromarray(id_frame, 'RGB')
draw_text = ImageDraw.Draw(draw_img)
id_txt = str(cell_id)
id_width, id_height = font.getsize(id_txt)
draw_text.text((min(cell_x, mask.shape[1] - id_width),
max(0, cell_y - id_height)),
id_txt, (255, 255, 255),
font=font)
id_frame = np.asarray(draw_img).copy()
if show_ids:
# Put the id's on top of the cells
col_frame[id_frame > 0] = 255
colorized_masks.append(col_frame)
return colorized_masks
def create_track_overview(id_masks, trj, cell_ids, background_id, color_list,
cell_color_idx, cell_visibility, show_ids,
use_thick_line):
logging.info('================= Creating track overview =================')
track_accumulator_y = {}
track_accumulator_x = {}
for i_frame in range(id_masks.shape[2]):
logging.info('Frame {}...'.format(i_frame))
for cell_id in cell_ids:
if (cell_id == background_id) or (not cell_visibility[cell_id]):
continue
cell_idx = get_trj_idx(trj, i_frame, 'particle', [cell_id])
if len(cell_idx) == 0:
continue
cell_y = int(trj.loc[cell_idx[0], 'y'])
cell_x = int(trj.loc[cell_idx[0], 'x'])
# Compute cell's last displacement (aka "leg")
if cell_id not in track_accumulator_y:
track_accumulator_y[cell_id] = np.array([cell_y],
dtype=np.int64)
track_accumulator_x[cell_id] = np.array([cell_x],
dtype=np.int64)
else:
if use_thick_line:
last_leg_y, last_leg_x, _ = line_aa(
track_accumulator_y[cell_id][-1],
track_accumulator_x[cell_id][-1], cell_y, cell_x)
else:
last_leg_y, last_leg_x, _ = line(
track_accumulator_y[cell_id][-1],
track_accumulator_x[cell_id][-1], cell_y, cell_x)
track_accumulator_y[cell_id] = np.concatenate(
(track_accumulator_y[cell_id], last_leg_y), axis=0)
track_accumulator_x[cell_id] = np.concatenate(
(track_accumulator_x[cell_id], last_leg_x), axis=0)
track_overview = np.stack(
(id_masks[:, :, -1].copy(), id_masks[:, :, -1].copy(),
id_masks[:, :, -1].copy()),
axis=2)
# Add calculated tracks and cell id's to the final frame
if show_ids:
id_frame = np.zeros_like(track_overview)
font = ImageFont.load_default()
for cell_id in cell_ids:
if (cell_id == background_id) or (not cell_visibility[cell_id]):
continue
last_cell_frame = trj.groupby('particle')['frame'].apply(max).to_dict()
cell_idx = get_trj_idx(trj, last_cell_frame[cell_id], 'particle',
[cell_id])
if len(cell_idx) == 0:
continue
cell_y = int(trj.loc[cell_idx[0], 'y'])
cell_x = int(trj.loc[cell_idx[0], 'x'])
cell_color = color_list[cell_color_idx[cell_id]]
for i_color in range(3):
# Draw cell track
track_overview[:, :, i_color][
track_accumulator_y[cell_id],
track_accumulator_x[cell_id]] = cell_color[i_color]
if show_ids:
# Stamp the cell_id on cell
draw_img = Image.fromarray(id_frame, 'RGB')
draw_text = ImageDraw.Draw(draw_img)
id_txt = str(cell_id)
id_width, id_height = font.getsize(id_txt)
draw_text.text((min(cell_x, id_masks.shape[1] - id_width),
max(0, cell_y - id_height)),
id_txt,
cell_color,
font=font)
id_frame = np.asarray(draw_img).copy()
if show_ids:
# Put the id's on top of the cells
track_overview[id_frame > 0] = id_frame[id_frame > 0]
return track_overview
def create_colorized_tracks(id_masks, trj, cell_ids, background_id, color_list,
cell_color_idx, cell_visibility, show_ids,
show_contours, show_tracks, use_thick_line):
logging.info('================= Colorizing tracks =================')
font = ImageFont.load_default()
track_accumulator_y = {}
track_accumulator_x = {}
structure_element = np.ones((5, 5)) if use_thick_line else np.ones((3, 3))
colorized_tracks = []
for i_frame in range(id_masks.shape[2]):
logging.info('Frame {}...'.format(i_frame))
mask = id_masks[:, :, i_frame]
col_frame = np.stack((mask.copy(), mask.copy(), mask.copy()), axis=2)
if show_ids:
id_frame = np.zeros_like(col_frame)
for cell_id in cell_ids:
if (cell_id == background_id) or (not cell_visibility[cell_id]):
continue
cell_idx = get_trj_idx(trj, i_frame, 'particle', [cell_id])
if len(cell_idx) == 0:
continue
cell_y = int(trj.loc[cell_idx[0], 'y'])
cell_x = int(trj.loc[cell_idx[0], 'x'])
cell_color = color_list[cell_color_idx[cell_id]]
if show_tracks:
# Compute cell's last displacement (aka "leg")
if cell_id not in track_accumulator_y:
track_accumulator_y[cell_id] = np.array([cell_y],
dtype=np.int64)
track_accumulator_x[cell_id] = np.array([cell_x],
dtype=np.int64)
else:
if use_thick_line:
last_leg_y, last_leg_x, _ = line_aa(
track_accumulator_y[cell_id][-1],
track_accumulator_x[cell_id][-1], cell_y, cell_x)
else:
last_leg_y, last_leg_x, _ = line(
track_accumulator_y[cell_id][-1],
track_accumulator_x[cell_id][-1], cell_y, cell_x)
track_accumulator_y[cell_id] = np.concatenate(
(track_accumulator_y[cell_id], last_leg_y), axis=0)
track_accumulator_x[cell_id] = np.concatenate(
(track_accumulator_x[cell_id], last_leg_x), axis=0)
# Draw cell track
for i_color in range(3):
col_frame[:, :, i_color][
track_accumulator_y[cell_id],
track_accumulator_x[cell_id]] = cell_color[i_color]
if show_contours:
# Compute cell border
cell_mask = (mask == cell_id).astype(np.uint8)
inner_cell_border = np.where(
cell_mask -
binary_erosion(cell_mask, selem=structure_element) > 0)
# Draw cell border
for i_color in range(3):
col_frame[:, :,
i_color][inner_cell_border] = cell_color[i_color]
if show_ids:
# Stamp the cell_id on cell
draw_img = Image.fromarray(id_frame, 'RGB')
draw_text = ImageDraw.Draw(draw_img)
id_txt = str(cell_id)
id_width, id_height = font.getsize(id_txt)
draw_text.text((min(cell_x, mask.shape[1] - id_width),
max(0, cell_y - id_height)),
id_txt,
cell_color,
font=font)
id_frame = np.asarray(draw_img).copy()
if show_ids:
# Put the id's on top of the cells
col_frame[id_frame > 0] = id_frame[id_frame > 0]
colorized_tracks.append(col_frame)
return colorized_tracks