class SiamFC(BaseTracker):
def __init__(self):
super(SiamFC, self).__init__("SiamFC")
# TODO: edit this path
self.net_file = path_config.SIAMFC_MODEL
self.tracker = TrackerSiamFC(net_path=self.net_file)
def initialize(self, image_file, box):
image = Image.open(image_file).convert("RGB")
self.tracker.init(image, box)
def track(self, image_file):
image = Image.open(image_file).convert("RGB")
return self.tracker.update(image)
def main(mode='IR', visulization=False):
assert mode in ['IR', 'RGB'], 'Only Support IR or RGB to evalute'
# setup tracker
net_path = 'model.pth'
tracker = TrackerSiamFC(net_path=net_path)
# setup experiments
video_paths = glob.glob(os.path.join('dataset', 'test-dev', '*'))
video_num = len(video_paths)
output_dir = os.path.join('results', tracker.name)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
overall_performance = []
# run tracking experiments and report performance
for video_id, video_path in enumerate(video_paths, start=1):
video_name = os.path.basename(video_path)
video_file = os.path.join(video_path, '%s.mp4' % mode)
res_file = os.path.join(video_path, '%s_label.json' % mode)
with open(res_file, 'r') as f:
label_res = json.load(f)
init_rect = label_res['gt_rect'][0]
capture = cv2.VideoCapture(video_file)
frame_id = 0
out_res = []
while True:
ret, frame = capture.read()
if not ret:
capture.release()
break
if frame_id == 0:
tracker.init(frame, init_rect) # initialization
out = init_rect
out_res.append(init_rect)
else:
out = tracker.update(frame) # tracking
out_res.append(out.tolist())
if visulization:
_gt = label_res['gt_rect'][frame_id]
_exist = label_res['exist'][frame_id]
if _exist:
cv2.rectangle(frame, (int(_gt[0]), int(_gt[1])),
(int(_gt[0] + _gt[2]), int(_gt[1] + _gt[3])),
(0, 255, 0))
cv2.putText(frame, 'exist' if _exist else 'not exist',
(frame.shape[1] // 2 - 20, 30), 1, 2,
(0, 255, 0) if _exist else (0, 0, 255), 2)
cv2.rectangle(frame, (int(out[0]), int(out[1])),
(int(out[0] + out[2]), int(out[1] + out[3])),
(0, 255, 255))
cv2.imshow(video_name, frame)
cv2.waitKey(1)
frame_id += 1
if visulization:
cv2.destroyAllWindows()
# save result
output_file = os.path.join(output_dir,
'%s_%s.txt' % (video_name, mode))
with open(output_file, 'w') as f:
json.dump({'res': out_res}, f)
mixed_measure = eval(out_res, label_res)
overall_performance.append(mixed_measure)
print('[%03d/%03d] %20s %5s Fixed Measure: %.03f' %
(video_id, video_num, video_name, mode, mixed_measure))
print('[Overall] %5s Mixed Measure: %.03f\n' %
(mode, np.mean(overall_performance)))
class CellTracker:
def __init__(self, siamese_model_path, unet_path, dataset_path, use_cuda,
new_w, new_h):
self.dataset_path = dataset_path
self.unet_path = unet_path
self.new_w = new_w
self.new_h = new_h
self.tracker = TrackerSiamFC(net_path=siamese_model_path,
use_cuda=use_cuda)
if unet_path is not None:
print("Loading pretrained model")
self.seg_net, pretrained = self.load_unet(), True
else:
print("Did not load pretrained model")
self.seg_net, pretrained = None, False
self.train_images = None
self.tracks = {}
self.track_count = 0
self.result = []
self.set_01, self.set_02 = None, None
def load_unet(self):
model = create_model(self.unet_path, self.new_w, self.new_h)
return model
def load_evaluation_images(self, sequence, extension=".tif"):
seg_dir = "/0{}".format(sequence)
result = []
print("Loading test images from {}".format(
os.path.join(self.dataset_path + seg_dir, "*" + extension)))
for frame_id, img_path in enumerate(
glob.glob(
os.path.join(self.dataset_path + seg_dir,
"*" + extension))):
# name = img_path.split("\\t")[-1].split(extension)[0]
name = img_path.split("/t")[-1].split(extension)[0]
# print("Image name: {}".format(name))
img = cv2.imread(img_path, cv2.IMREAD_ANYDEPTH)
seg_img = None
result.append(
CellImage(img, name, self.dataset_path, sequence, seg_img))
result = sorted(result, key=lambda x: x.image_name, reverse=False)
return result
# predicts binary segmentation for input image using the unet
def predict_seg(self, input_img, thr_markers=240, thr_cell_mask=230):
w = np.shape(input_img)[0]
h = np.shape(input_img)[1]
img = cv2.equalizeHist(np.minimum(input_img, 255).astype(
np.uint8)) / 255
img = img.reshape((1, w, h, 1)) - .5
if self.new_w > 0 or self.new_h > 0:
img2 = np.zeros((1, self.new_w, self.new_h, 1), dtype=np.float32)
img2[:, :w, :h, :] = img
img = img2
prediction = self.seg_net.predict(img, batch_size=1)
# prediction = prediction[0, :w, :h, 1]
# New watershed
# naive_seg = postprocess_cell_mask(prediction[0, :w, :h, 3] * 255, threshold=thr_cell_mask)
# distance = ndi.distance_transform_edt(naive_seg)
# local_maxi = peak_local_max(distance, labels=naive_seg, footprint=np.ones((15, 15)), indices=False)
# markers = ndi.label(local_maxi)[0]
# prediction = watershed(-distance, markers, mask=naive_seg)
# # Watershed
# m = prediction[0, :w, :h, 1] * 255
# c = prediction[0, :w, :h, 3] * 255
# o = (img + .5) * 255
#
# # postprocess the result of prediction
# idx, markers = postprocess_markers(m, threshold=thr_markers, erosion_size=1, circular=False,
# step=30)
# cell_mask = postprocess_cell_mask(c, threshold=thr_cell_mask)
# # correct border
# cell_mask = np.maximum(cell_mask, markers)
# prediction = (watershed(-c, markers, mask=cell_mask) > 0)*1.0
# # Previous unet
# img = input_img / 255
# img = torch.Tensor(list(transform.resize(input_img, (512, 512), mode='symmetric'))).unsqueeze(0).unsqueeze(
# 0).permute(0, 2, 3, 1).numpy()
# prediction = self.seg_net.predict(img)
#
# prediction = cv2.resize(prediction[0, :, :, 0], tuple(reversed(input_img.shape)))
# prediction = np.array(prediction)
# _, prediction = cv2.threshold(prediction, 0.6, 1, cv2.THRESH_BINARY)
# prediction = prediction#.astype(np.uint16)
return prediction
# predict segmentation for all frames:
# def segment_images(self, sequence):
# for cell_img in tqdm(self.train_images[sequence]):
# cell_img.binary_seg = self.predict_seg(cell_img.image)
# writes the frames with cell locations to a video file
def store_footage(self, sequence, fps: int = 3):
# output_data = np.array([x for x in self.result])
# output_data = output_data.astype(np.uint8)
# skvideo.io.vwrite("result {} 0{}.mp4".format(self.name, sequence), output_data, inputdict={'-r': str(fps)})
# Define the codec and create VideoWriter object
fourcc = cv2.VideoWriter_fourcc(*'XVID')
out = cv2.VideoWriter(
"{}/result_0{}.avi".format(self.dataset_path, sequence), fourcc,
float(fps), (self.result[0].shape[1], self.result[0].shape[0]))
for frame in self.result:
out.write(frame.astype(np.uint8))
out.release()
# predict the new location of a cell located in frame1:
def predict_cell_location(self, frame1, frame2, cell):
self.tracker.init(
frame1, [cell.min_col, cell.min_row, cell.width, cell.height])
[x, y, w, h] = self.tracker.update(frame2)
return [int(x), int(y), int(x + w), int(y + h)]
# uses random walker with markers from previous frame to predict a new segmentation
# for collided cells
@staticmethod
def resegmentation(initial_segmentation, local_maxi):
markers = measure.label(local_maxi)
markers[~initial_segmentation] = -1
labels = random_walker(initial_segmentation, markers)
labels[labels == -1] = 0
return labels
# stores the tracks' desciptions in the right format
def store_track(self, filename, sequence):
store_path = os.path.join(self.dataset_path,
"0{}_RES/".format(sequence), filename)
keys = sorted(list(self.tracks.keys()))
print("Storing track at {}".format(store_path))
with open(store_path, 'w', encoding='utf-8') as file:
for k in keys:
file.write(str(self.tracks[k]) + "\n")
# get the backward matches and resegment when a collision is detected:
def get_new_detections_dict(self,
previous_frame,
prev_img,
current_frame,
track_dict,
alt=True):
cur_img = np.stack((current_frame.image.astype(np.int16), ) * 3,
axis=-1)
available_cells = current_frame.get_cell_locations()
# print("available_cells: {}".format(available_cells))
new_detections_dict = {c: [] for c in available_cells}
prev_num_cells = len(new_detections_dict)
cur_num_cells = 0
# return current_frame.seg_output, new_detections_dict, cur_img
while alt and prev_num_cells != cur_num_cells:
prev_num_cells = cur_num_cells
alt = False
# cell detection backward pass
for dest_cell in new_detections_dict.keys():
# get the predicted location of the cell in the previous frame
[tl_x, tl_y, br_x,
br_y] = self.predict_cell_location(cur_img, prev_img,
deepcopy(dest_cell))
# match all cell located in that area
for cell_track in track_dict.keys():
c = cell_track.current_cell
if tl_x < c.centroid_x < br_x and tl_y < c.centroid_y < br_y:
try:
new_detections_dict[dest_cell].append(cell_track)
except Exception as e:
print("new_detections_dict.keys(): {}".format(
new_detections_dict.keys()))
print("dest_cell: {}".format(dest_cell))
# print(new_detections_dict[str(dest_cell)])
print(new_detections_dict[dest_cell])
print("\n\n")
print(new_detections_dict)
raise e
# forward checking:
if len(new_detections_dict[dest_cell]) > 1:
final = []
for c_t in new_detections_dict[dest_cell]:
[tl_x, tl_y, br_x, br_y] = self.predict_cell_location(
prev_img, cur_img, c_t.current_cell)
pred_center_x, pred_center_y = int(
(br_x + tl_x) / 2), int((br_y + tl_y) / 2)
if tl_x < dest_cell.centroid_x < br_x and tl_y < dest_cell.centroid_y < br_y:
final.append(c_t)
elif dest_cell.min_col < pred_center_x < dest_cell.max_col and \
dest_cell.min_row < pred_center_y < dest_cell.max_row:
final.append(c_t)
new_detections_dict[dest_cell] = final
# if two or more cells are matching a collision has occured and the frame has to be resegmented
if len(new_detections_dict[dest_cell]) > 1:
alt = True
tl_x = min([
t.current_cell.min_col
for t in new_detections_dict[dest_cell]
])
tl_y = min([
t.current_cell.min_row
for t in new_detections_dict[dest_cell]
])
br_x = max([
t.current_cell.max_col
for t in new_detections_dict[dest_cell]
])
br_y = max([
t.current_cell.max_row
for t in new_detections_dict[dest_cell]
])
frame1_seg = previous_frame.seg_output[tl_y:br_y,
tl_x:br_x]
distance = np.zeros(
(int(frame1_seg.shape[0]), int(frame1_seg.shape[1])))
for color, t in enumerate(new_detections_dict[dest_cell]):
a = max(0, int(t.current_cell.centroid_y) - tl_y - 1)
b = max(0, int(t.current_cell.centroid_x) - tl_x - 1)
distance[a:a + 2,
b:b + 2] = np.array(np.full((2, 2),
color + 1))
distance = cv2.resize(
distance,
(int(dest_cell.width), int(dest_cell.height)),
interpolation=cv2.INTER_NEAREST)
current_frame.seg_output[current_frame.seg_output ==
dest_cell.color] = 0
new_seg = self.resegmentation(dest_cell.segmentation,
distance)
# plot new segmentation result:
# self.multiplot([frame1_seg, dest_cell.segmentation, new_seg])
global bla_count
bla_count += 1
# print(bla_count)
# vis = np.concatenate((dest_cell.segmentation, new_seg), axis=1)
# plt.imshow(vis)
# plt.show()
current_frame.seg_output[
dest_cell.min_row:dest_cell.max_row,
dest_cell.min_col:dest_cell.max_col] = np.maximum(
current_frame.seg_output[
dest_cell.min_row:dest_cell.max_row,
dest_cell.min_col:dest_cell.max_col], new_seg)
# relabel the frame and redetect the cells
current_frame.seg_output = measure.label(
current_frame.seg_output)
available_cells = current_frame.get_cell_locations()
new_detections_dict = {c: [] for c in available_cells}
cur_num_cells = len(new_detections_dict)
break
# display frame final segmentation:
# plt.imshow(current_frame.seg_output)
# plt.show()
return current_frame.seg_output, new_detections_dict, cur_img
@staticmethod
def multiplot(image_list):
abc = ["A", "B", "C", "D", "E", "F", "G", "H"]
# abc2 = ["t=i", "t=i+1", "t=i+1", "t=i+1"]
fig, axes = plt.subplots(nrows=1,
ncols=len(image_list),
figsize=(10, 5))
for num, x in enumerate(image_list):
plt.subplot(1, len(image_list), num + 1)
plt.title(abc[num], fontsize=25)
plt.axis('off')
plt.imshow(x)
# plt.subplots_adjust(left=0.1, right=0.1, top=0.1, bottom=0.1)
# fig.tight_layout()
plt.savefig("segres.png", bbox_inches='tight')
@staticmethod
# makes sure that all cells in a given track have the same pixel value in segmentation
def propagate_labels(frame, living_tracks, track, cell):
free_label = max(np.unique(frame.seg_output)) + 1
if track.cell_id != cell.color:
for swap_id, swap_track in living_tracks:
if swap_id != track.cell_id and swap_track.current_cell.color == track.cell_id:
frame.seg_output = np.where(
frame.seg_output == swap_track.current_cell.color,
free_label, frame.seg_output)
swap_track.current_cell.color = free_label
break
frame.seg_output = np.where(frame.seg_output == cell.color,
track.cell_id, frame.seg_output)
cell.color = track.cell_id
return frame, living_tracks
# runs the tracking algorithm and exports results for evaluation
def run_test(self,
sequence,
collision_detection=True,
store_footage=0,
load_segs_from_file=None):
set_01 = self.load_evaluation_images(sequence)
self.result = []
print("Segmenting footage:")
# apply initial segmentation to footage:
if load_segs_from_file is None:
for frame in tqdm(set_01, position=0):
frame.binary_seg = self.predict_seg(frame.image)
frame.binary_seg_to_output()
else:
imgs_list = sorted(make_list_of_imgs_only(
os.listdir(load_segs_from_file), 'tif'),
key=natural_keys)
for frame in tqdm(set_01, position=0):
img_indx = int(frame.image_name)
img_path = os.path.join(load_segs_from_file,
imgs_list[img_indx])
print("reading img: {} at {}".format(img_indx, img_path))
frame.binary_seg = mpimg.imread(img_path)
frame.binary_seg_to_output()
# load first frame
previous_frame = set_01[0]
prev_img = np.stack((previous_frame.image.astype(np.int16), ) * 3,
axis=-1)
# init tracks from detected cells in first frame
self.tracks = {
c_id + 1: CellTrack(c, 0, c_id + 1, 0)
for c_id, c in enumerate(previous_frame.get_cell_locations())
}
self.track_count = len(self.tracks) + 1
i = 0
print("Tracking:")
for current_frame in tqdm(set_01[1:]):
track_dict = {t: [] for t in self.tracks.values() if t.alive}
# solve collisions in segmentation and locate all cells in the new frame:
current_frame.seg_output, new_detections_dict, cur_img = \
self.get_new_detections_dict(previous_frame, prev_img, current_frame, track_dict, collision_detection)
# image for video visualisation
cur_copy = cur_img.copy()
# cell detection forward pass:
for cell_track in track_dict.keys():
cell = cell_track.current_cell
[tl_x, tl_y, br_x,
br_y] = self.predict_cell_location(prev_img, cur_img, cell)
pred_center_x, pred_center_y = int((br_x + tl_x) / 2), int(
(br_y + tl_y) / 2)
for c in new_detections_dict.keys():
if c.min_col < pred_center_x < c.max_col and c.min_row < pred_center_y < c.max_row:
track_dict[cell_track].append(c)
elif tl_x < c.centroid_x < br_x and tl_y < c.centroid_y < br_y:
track_dict[cell_track].append(c)
# match cells from the previous frame to newly located cells:
new_tracks = {}
for track_id, cell_track in self.tracks.items():
matched = False
# if death cell add it to the new stack
if not cell_track.alive:
new_tracks[track_id] = cell_track
# else try to find a track continuation
elif cell_track.alive:
forward_match = track_dict[cell_track]
# case 1->_
if not forward_match:
# check if 1<-1:
for dest_cell, t in new_detections_dict.items():
if cell_track in t:
cell_track.add_cell(dest_cell)
matched = True
break
# remove the cell from free new detection
if matched:
del new_detections_dict[cell_track.current_cell]
# else the cell has no match and has died:
else:
cell_track.alive = False
new_tracks[track_id] = cell_track
# case 1->1
elif len(forward_match) == 1:
dest_cell = forward_match[0]
# should not occur:
if dest_cell not in new_detections_dict:
cell_track.alive = False
# if 1<-1 or _<-1 match
elif not new_detections_dict[
dest_cell] or cell_track in new_detections_dict[
dest_cell]:
cell_track.add_cell(dest_cell)
del new_detections_dict[dest_cell]
# if 2<-1 death
else:
cell_track.alive = False
new_tracks[track_id] = cell_track
# case 1->1,2 (mitosis)
else:
available = [
c for c in forward_match
if c in new_detections_dict
]
if not available or len(available) > 1:
cell_track.alive = False
for dest_cell in available:
del new_detections_dict[dest_cell]
new_track = CellTrack(dest_cell, i + 1,
self.track_count,
cell_track.cell_id)
new_tracks[self.track_count] = new_track
self.track_count += 1
else:
del new_detections_dict[available[0]]
cell_track.add_cell(available[0])
new_tracks[track_id] = cell_track
# create new tracks for the unmatched cells in the new frame:
for dest_cell, t in new_detections_dict.items():
new_track = CellTrack(dest_cell, i + 1, self.track_count, 0)
new_tracks[self.track_count] = new_track
self.track_count += 1
living_tracks = [(track_id, track)
for track_id, track in new_tracks.items()
if track.last_frame == i + 1]
# displaying cell locations on frame for visual evaluation:
for track_id, track in living_tracks:
c = track.current_cell
current_frame, living_tracks = self.propagate_labels(
current_frame, living_tracks, track, c)
cv2.rectangle(cur_copy, c.tl, c.br, track.display_color, 3)
x, y = int(c.centroid_x), int(c.centroid_y)
cv2.putText(cur_copy, str(track_id), (x, y),
cv2.FONT_HERSHEY_SIMPLEX, .4, track.display_color,
1, cv2.LINE_AA)
cv2.putText(cur_copy, str(i + 1), (5, 25),
cv2.FONT_HERSHEY_SIMPLEX, .5, (255, 0, 0), 1,
cv2.LINE_AA)
self.result.append(cur_copy)
self.tracks = new_tracks
previous_frame = current_frame
prev_img = cur_img
i += 1
print("Saving results")
for frame in tqdm(set_01):
frame.store()
self.store_track("res_track.txt", sequence)
if store_footage:
print("Creating video")
self.store_footage(sequence=sequence, fps=3)
