def showmotion(src, paths, dest):
FPS = get_fps(src)
paths = pickle.load(open(paths))
CROP = getRule('crop', src)
# divide by number of frames
# px/second
avg_speeds = [FPS*motion(y)/(paths[idx][0][-1][4]-paths[idx][0][0][4]) for idx,(x,y) in enumerate(paths)]
avg_speed = sum(avg_speeds) / len(avg_speeds)
fr = None
for idx,fr in enumerate(VideoReader(src)):
if CROP > 0:
fr = fr[CROP:-CROP,CROP:-CROP]
if idx == 0:
vout = VideoWriter(dest)
speeds = []
for p_idx,(raw,smooth) in enumerate(paths):
raw = filter(lambda x: x[4] <= idx, raw)
smooth = smooth[:max(0,len(raw)-5)]
if len(raw) == 0:
# print idx, 'path has not yet started'
continue
raw = numpy.array(raw)
pts = raw[:,:2].astype(numpy.int32)
cv2.polylines(fr, [pts], False, (255, 0, 0))
tup = tuple(raw[-1,:2].astype(int).tolist())
cv2.circle(fr, tup, raw[-1,2].astype(int), (255, 0, 0))
cv2.circle(fr, tup, 3, (255, 0, 0))
speed = 0
if len(pts) > 1:
speed = FPS*numpy.hypot(*(pts[-1] - pts[-2]).T)
speeds.append(speed)
txt = "%.2f (%.2f)" % (avg_speeds[p_idx], speed)
cv2.putText(fr, txt, tup, cv2.FONT_HERSHEY_PLAIN, 1, (0,255,0))
# & smoothed
if len(smooth) > 0:
pts = numpy.array(smooth).astype(numpy.int32)
cv2.polylines(fr, [pts], False, (0, 0, 255))
tup = tuple(pts[-1].astype(int).tolist())
cv2.circle(fr, tup, 3, (0, 0, 255))
txt = "%.2f (%.2f), N=%d" % (avg_speed, sum(speeds)/len(speeds), len(paths))
cv2.putText(fr, txt, (30,30), cv2.FONT_HERSHEY_PLAIN, 1, (255,0,255))
vout.write(fr)
def jsonify(inputdir, outputdir):
for f in glob.glob(os.path.join(inputdir, '*.avi')):
outbase = os.path.join(outputdir, os.path.basename(f))
FPS = get_fps(f)
base = os.path.basename(f)
rec[base] = {"filename": os.path.basename(f)}
paths = pickle.load(open('%s.path.pkl' % (outbase)))
docs = []
store = allpaths
for idx,(path,smoothed) in enumerate(paths):
uid = '%s-%d' % (base, idx)
doc = {"recording": base,
"center (x,y)": path[0][:2],
"radius (px)": diameter(path)/2,
"area (px)": area(path),
"raw_motion (px)": motion(path),
"motion (px)": motion(smoothed),
"distance (px)": distance(path),
"speed (px/sec)": speed([path,smoothed], FPS),
"rel_motion (% of length)": relativeMotion([path,smoothed]),
"rel_speed (%/sec)": relativeSpeed([path,smoothed], FPS),
"circularity (radians)": circularity(smoothed),
"rel_circularity (radians/%-of-length)": relativeCircularity([path,smoothed])
}
docs.append(doc)
store[uid] = doc
# compute recording-wide averages
recinfo = {}
nworms = len(paths)
recinfo["nworms"] = nworms
keys = docs[0].keys()
keys.remove("recording")
keys.remove("center (x,y)")
for key in keys:
recinfo[key] = sum([X[key] for X in docs])/float(nworms)
recinfo["std_dev:"+key] = np.std([X[key] for X in docs])
rec[base].update(recinfo)
json.dump(allpaths, open("Path.json", 'w'))
json.dump(rec, open("Recording.json", 'w'))
