def sync_data(r,log,store):
if '_201909' in store.filename:
checkname = store.filename.rsplit('.',1)[0] + '.21990449/metadata.yaml'
check9 = imgstore.new_for_filename(checkname)
deltaT = check9.get_frame_metadata()['frame_time'][0] - store.get_frame_metadata()['frame_time'][0]
if abs(deltaT) > 1.0:
print("**********TIMESTAMP MISMATCH ", str(deltaT), "sec. REPAIRING STORE.********")
correct_timestamps(store.filename)
print("*** repair successful ***")
store = imgstore.new_for_filename(store.filename + '/metadata.yaml')
foo = get_frame_metadata(r.reset_index(drop=True), store)
bar = foo.merge(log, how='outer')
bar = bar.sort_values('Timestamp') #integrate log data with tracking data
bar = bar.fillna(method='ffill') #forward fill data from log to tracking data
bar = bar.loc[foo.index] #drop rows from log entries
bar = bar.sort_values('Timestamp') #sort again because lazy danno
if 'coh' in bar.columns:
bar['coh'] = bar['coh'].fillna(method='ffill')
bar['coherence'] = bar['coh'].copy()
if 'speed' in bar.columns:
bar['speed'] = bar['speed'].fillna(0)
if 'dir' in bar.columns:
bar['dir'] = bar['dir'].fillna(0)
bar.loc[:,'Time'] = (bar.loc[:,'Timestamp'] - bar.loc[0,'Timestamp'])
if bar.iloc[5].Timestamp - bar.iloc[0].Timestamp > 10: #check if log overlaps with track data
return 0, bar
else:
return 1, bar
def synch_reversals(MAIN_DIR, r=None):
MAIN_DIR = slashdir(MAIN_DIR)
TRACK_DIR = MAIN_DIR + 'track/'
LOG_FN = '/media/recnodes/Dan_storage/dotbot_logs/dotbotLog_' + MAIN_DIR.split('/')[-2] + '.txt'
if r == None:
r = pd.read_pickle(TRACK_DIR + 'frame_means_rotation_polarization.pickle')
store = imgstore.new_for_filename(MAIN_DIR + 'metadata.yaml')
framelist = pd.DataFrame(store.get_frame_metadata())
framelist.columns=['FrameNumber','Timestamp']
foo = r.merge(framelist, left_index=True, right_index=True)
log = pd.read_table(LOG_FN)
log.loc[:,'Timestamp'] /= 1000.0
bar = foo.merge(log, how='outer')
bar = bar.sort_values('Timestamp')
bar['speed'] = bar['speed'].fillna(method='ffill').fillna(0)
bar['dir'] = bar['dir'].fillna(method='ffill').fillna(0)
bar.loc[:,'Time'] = (bar.loc[:,'Timestamp'] - bar.loc[0,'Timestamp'])
if bar.iloc[5].Timestamp - bar.iloc[0].Timestamp > 10: #check if log overlaps with track data
return 0, bar
else:
return 1, bar
def doit(DIR, HANDLE):
for x in glob.glob(slashdir(DIR) + '*' + HANDLE + '*/metadata.yaml'):
inStore = imgstore.new_for_filename(x)
UND = Undistort(inStore)
img, (frame_number, frame_timestamp) = inStore.get_next_image()
newdir = x.rsplit('/', 1)[0] + '_undistorted'
if os.path.exists(newdir):
shutil.rmtree(newdir)
os.mkdir(newdir)
outStore = imgstore.new_for_format('avc1/mp4',
mode='w',
basedir=newdir,
imgshape=img.shape,
imgdtype=img.dtype,
chunksize=500)
for i in range(inStore.frame_count - 1):
try:
outStore.add_image(UND.undistort(img), frame_number,
frame_timestamp)
img, (frame_number, frame_timestamp) = inStore.get_next_image()
except:
print "failed at frame: ", i, "of", inStore.frame_count, inStore.frame_max
outStore.close()
open(x.rsplit('/', 1)[0] + '/undistortion_complete', 'a').close()
return
def Xsynch_coherence_with_rotation(MAIN_DIR):
#MAIN_DIR = slashdir('/media/recnodes/kn-crec06/juvenilesfwdmix_3264_dotbot_20171205_101600')
MAIN_DIR = slashdir(MAIN_DIR)
TRACK_DIR = MAIN_DIR + 'track/'
LOG_FN = '/media/recnodes/recnode_jolle2/dotbot_logs/dotbotLog_' + MAIN_DIR.split('/')[-2] + '.txt'
r = pd.read_pickle(TRACK_DIR + 'frame_means_rotation_polarization.pickle')
store = imgstore.new_for_filename(MAIN_DIR + 'metadata.yaml')
log = process_logfile(LOG_FN)
coherence = get_coherence(log)
coherence['speed'] = get_speed(log)['speed']
coherence['dir'] = get_direction(log)['dir']
framelist = pd.DataFrame(store.get_frame_metadata())
framelist.columns=['FrameNumber','Timestamp']
foo = r.merge(framelist, left_index=True, right_index=True)
bar = foo.merge(coherence, how='outer')
bar = bar.sort_values('Timestamp')
bar['coherence'] = log['coh'].mean()#bar['coherence'].fillna(method='ffill')
bar['speed'] = bar['speed'].fillna(method='ffill').fillna(0)
bar['dir'] = bar['dir'].fillna(method='ffill').fillna(0)
bar.loc[:,'Time'] = (bar.loc[:,'Timestamp'] - bar.loc[0,'Timestamp'])
return bar#.fillna(np.inf)
def fixTimestamps(fn, camserial='21990449'):
"""
fixes timestamps of "0 0 0 ...", which sometimes occurs during stitching. Pass the filename of a stitched video (/full/path/to/video_XXXXXX_XXXXXX.stitch'), and this function takes timestamps from one of the constituent videos (camserial) and assigns them to the stitched video. It also removes converted.pv.
"""
cornervid = imgstore.new_for_filename(
fn.split('.')[0] + '.' + camserial + '/metadata.yaml')
timestamps = cornervid.get_frame_metadata().items()[1][1]
fileList = []
for i in glob.glob(fn + '/*.npz'):
fileList.append(i)
fileList = sorted(fileList)
cumsum = 0
for f in fileList:
d = np.load(f)
keys = [key for key in d.files]
nf = {}
for name in keys:
nf[name] = d[name]
nFrames = len(d['frame_time'])
nf['frame_time'] = timestamps[cumsum:cumsum + nFrames]
np.savez(f, **nf)
cumsum += nFrames
#need to generate a new converted.pv with timestamps.
if os.path.exists(slashdir(fn) + 'track/converted.pv'):
os.remove(slashdir(fn) + 'track/converted.pv')
return
def __init__(self, video_file):
import imgstore
self.vid = imgstore.new_for_filename(video_file)
self.first_frame = self.vid.frame_min
self.frame_max = self.vid.frame_max
img, (frame_number, frame_timestamp) = self.vid.get_next_image()
self.height = img.shape[0]
self.width = img.shape[1]
self.dtype = img.dtype
self.vid.close()
self.vid = imgstore.new_for_filename(video_file)
self.frames_read = []
def __init__(self, filename):
try:
self.store = imgstore.new_for_filename(str(filename))
except:
self.store = None
self.filename = filename
print(self.filename)
self.ext = '.extra_data.json'
self.extra_data = None
def __init__(self, directory):
self.DIR = directory
self.u_raw = np.load(directory + '/piv_u.npy')
self.v_raw = np.load(directory + '/piv_v.npy')
self.x = np.load(directory + '/piv_x.npy')
self.y = np.load(directory + '/piv_y.npy')
self.radius = self.get_radius_matrix()
self.vort_raw = np.load(directory + '/piv_vort.npy')
self.shape = self.x.shape
self.store = imgstore.new_for_filename(directory + '/metadata.yaml')
def create_stitched_video_from_scratch(fnString, pos):
stores = (fnString + '.21990443', fnString + '.21990445',
fnString + '.21990447', fnString + '.21990449')
cams_stores = {}
for fn in stores:
store = new_for_filename(op.join(BASE_DATA, fn))
print store.full_path
nFrames = store.frame_count
cams_stores[get_store_camera_serial(store)] = store
sorted_stores = [cams_stores[i] for i in best_order]
undistortions = [Undistort(i) for i in sorted_stores]
aligned = StoreAligner(*sorted_stores)
aligned.extract_common_frames(StoreAligner.MISSING_POLICY_DROP)
if args.truncate == True:
suffix = '.partial_stitch'
aligned._fns = aligned._fns[
2000:5000] # THIS IS HOW WE TRUNCATE. #FIXME hardcoded cut
elif args.truncate == False:
suffix = '.stitched'
if not os.path.exists(fnString + suffix):
os.mkdir(fnString + suffix)
out = imgstore.new_for_format('avc1/mp4',
mode='w',
basedir=fnString + suffix,
imgshape=s.panorama_shape,
imgdtype='uint8',
chunksize=500)
for n, (imgs, (fn, ts)) in enumerate(aligned.iter_imgs(return_times=True)):
_imgs = []
for i in range(len(undistortions)):
_imgs.append(undistortions[i].undistort(imgs[i]))
#with silence_stdout():
ok, img = s.stitch_images(*[ensure_color(i) for i in _imgs])
assert ok
out.add_image(img, fn, ts)
printProgressBar(n,
nFrames,
prefix='Stitching progress:',
stdoutpos=pos)
out.close()
return
def __init__(self, src_file):
self.frame_save_interval = 1
self.is_light_background = 1
self.video_data = None
self.groupnames = ['None']
self.src_file = src_file
self.video_data = imgstore.new_for_filename(str(src_file))
self._ini_frame = self.video_data.frame_min
img, (frame_number, frame_timestamp) = self.video_data.get_next_image()
self.height, self.width = img.shape
def open(self):
"""
Open the image store if it isn't already open.
Returns:
None
"""
if not self._store_:
# Open the imgstore
self._store_ = imgstore.new_for_filename(self.filename)
# Read a frame so we can compute shape an such
self._img_, (frame_number, frame_timestamp) = self._store_.get_next_image()
def setup(filelist, prestim_frames=400, **kwargs):
stores = []
framenums = []
for vid in filelist:
pf = pd.read_pickle(vid + '/track/perframe_stats.pickle')
log = stims.get_logfile(vid)
store = imgstore.new_for_filename(vid + '/metadata.yaml')
stores.append(store)
ret, pf2 = stims.synch_coherence_with_rotation(pf, log,
store) #sync_reversals
pf3 = sync_by_stimStart(pf2)
startframe = pf3.loc[pf3['stimStart'].idxmax() - prestim_frames,
'FrameNumber']
framenums.append(startframe)
return filelist, stores, framenums
def create_stitched_video_from_scratch(path):
DIRECTORY, fnString = path.rsplit('/', 1)
DIRECTORY = DIRECTORY + '/'
stores = (fnString + '.21990443', fnString + '.21990445',
fnString + '.21990447', fnString + '.21990449')
cams_stores = {}
for fn in stores:
store = new_for_filename(op.join(BASE_DATA, fn))
print store.full_path
cams_stores[get_store_camera_serial(store)] = store
sorted_stores = [cams_stores[i] for i in best_order]
undistortions = [Undistort(i) for i in sorted_stores]
aligned = StoreAligner(*sorted_stores)
aligned.extract_common_frames(StoreAligner.MISSING_POLICY_DROP)
if not os.path.exists(DIRECTORY + fnString + '.stitched'):
os.mkdir(DIRECTORY + fnString + '.stitched')
"""
out = new_for_format('avc1/mp4', DIRECTORY + fnString + '.stitched/metadata.yaml',
imgshape=s.panorama_shape,
imgdtype=np.uint8)
"""
out = imgstore.new_for_format('avc1/mp4',
mode='w',
basedir=DIRECTORY + fnString + '.stitched',
imgshape=s.panorama_shape,
imgdtype='uint8',
chunksize=500)
for n, (imgs, (fn, ts)) in enumerate(aligned.iter_imgs(return_times=True)):
_imgs = []
for i in range(len(undistortions)):
_imgs.append(undistortions[i].undistort(imgs[i]))
ok, img = s.stitch_images(*[ensure_color(i) for i in _imgs])
assert ok
out.add_image(img, fn, ts)
out.close()
return
def read_images_loopbio(file_name, batch_size, queue):
store = imgstore.new_for_filename(str(file_name))
bn = Path(file_name).parent.name
batch = []
for frame_number in tqdm.trange(store.frame_count, desc=bn):
img = store.get_next_image()[0]
batch.append((frame_number, img))
if len(batch) >= batch_size:
frames, X = _prepare_batch(batch)
batch = []
queue.put((frames, X))
if len(batch) > 0:
frames, X = _prepare_batch(batch)
queue.put((frames, X))
queue.put(None)
while not queue.empty():
#wait until the consumer empty the queue before destroying the process.
time.sleep(1)
def get_stim_data(MAIN_DIR):
LOG_FN = '/media/recnodes/recnode_jolle2/dotbot_logs/dotbotLog_' + MAIN_DIR.split('/')[-2].rsplit('.',1)[0] + '.txt'
log = pd.read_table(LOG_FN)
log['Timestamp'] = log['Timestamp'] / 1000.0
store = imgstore.new_for_filename(MAIN_DIR + 'metadata.yaml')
framelist = pd.DataFrame(store.get_frame_metadata())
framelist.columns=['FrameNumber','Timestamp']
g = log.groupby('comment')
directions = {}
for _name in g.groups.keys():
g1 = g.get_group(_name)
bar = framelist.merge(g1, how='outer')
bar = bar.sort_values('Timestamp')
bar['CX'].interpolate(inplace=True)
bar['CY'].interpolate(inplace=True)
framelist[_name + '_X'] = bar['CX']
framelist[_name + '_Y'] = bar['CY']
directions[_name] = g1.dir.mode()[0]
return framelist, directions
def create_stitched_video_from_undistorted(fnString):
stores = (fnString + '.21990443_undistorted',
fnString + '.21990445_undistorted',
fnString + '.21990447_undistorted',
fnString + '.21990449_undistorted')
cams_stores = {}
for fn in stores:
store = new_for_filename(op.join(BASE_DATA, fn))
print store.full_path
cams_stores[get_store_camera_serial(store)] = store
sorted_stores = [cams_stores[i] for i in best_order]
aligned = StoreAligner(*sorted_stores)
aligned.extract_common_frames(StoreAligner.MISSING_POLICY_DROP)
if not os.path.exists(BASE_DATA + fnString + '.stitched'):
os.mkdir(BASE_DATA + fnString + '.stitched')
out = imgstore.new_for_format('avc1/mp4',
mode='w',
basedir=BASE_DATA + fnString,
imgshape=s.panorama_shape,
imgdtype='uint8',
chunksize=500)
for n, (fn, imgs) in enumerate(aligned.iter_imgs()):
ok, img = s.stitch_images(*[ensure_color(i) for i in imgs])
assert ok
out.add_image(img, fn, 0)
print n
out.close()
return
def collectProcessingStats(d):
d = slashdir(d)
list_of_files = glob.glob(d + '*.mp4')
latest_file = max(list_of_files, key=os.path.getctime)
DATA = dict({
'framecount':
imgstore.new_for_filename(d + 'metadata.yaml').frame_count,
'recorded':
getTimeFromTimeString(
d.split('/')[-2].split('_', 3)[-1].split('.')[0]),
'stitchBegin':
checkDate(d + 'metadata.yaml'),
'stitchEnd':
checkDate(latest_file),
'converted':
checkDate(d + 'track/converted.pv'),
'tracked':
checkDate(d + 'track/converted.results'),
'pickled':
checkDate(d + 'track/frameByFrameData.pickle')
})
return DATA
def correct_timestamps(stitched_store_fn):
"""
gets timestamps from master machine and transfers them to the stitched store. this is to correct timestamps of videos taken in september 2019 when the slave clock was fast by 338 seconds.
"""
master_store = imgstore.new_for_filename(stitched_store_fn.rsplit('.',1)[0] + '.21990449/metadata.yaml')
md = pd.DataFrame(master_store.get_frame_metadata())
try:
for z in glob.glob(stitched_store_fn + '/*.npz'):
f = np.load(z)
keys = [key for key in f.files]
nf = {}
for name in keys:
nf[name] = f[name]
frames = nf['frame_number']
nf['frame_time'] = [md.loc[(md['frame_number']-i).abs().argsort()[0],'frame_time'] for i in frames]
np.savez(z.split('.npz')[0], **nf)
return 1
except:
print("FAILED FOR:", stitched_store_fn)
return 0
#Camera orientations before renovation (august 2018):
[tl, bl, tr, br] = ['21990445',
'21990447',
'21990449',
'21990443']
#Camera orientations after renovation (August 2018):
"""
#Current settings as of 180827
[tl, bl, tr, br] = ['21990447', '21990449', '21990443', '21990445']
for x in glob.glob(SEARCH_FILES):
ID = x.split('/')[-2].split('.')[-1]
print ID
if br in ID:
BOTTOM_RIGHT = imgstore.new_for_filename(x)
elif tl in ID:
TOP_LEFT = imgstore.new_for_filename(x)
elif bl in ID:
BOTTOM_LEFT = imgstore.new_for_filename(x)
elif tr in ID:
TOP_RIGHT = imgstore.new_for_filename(x)
if args.saveas == 'notAssigned':
SAVEAS = TOP_LEFT.filename.rsplit('.', 1)[0] + '_stitched'
else:
SAVEAS = slashdir(args.dir) + args.saveas
VIDEOS = [TOP_LEFT, BOTTOM_LEFT, TOP_RIGHT, BOTTOM_RIGHT]
VIDEO_TIME = '_'.join(
def convert(_main_dir, _make_bkg, NEW_ONLY, fishnum):
MAIN_DIR = _main_dir
if MAIN_DIR[-1] != '/':
MAIN_DIR += '/'
track_dir = MAIN_DIR + 'track'
if not os.path.exists(track_dir):
os.makedirs(track_dir)
if (NEW_ONLY) and (os.path.exists(track_dir + 'converted.results')):
return
if _make_bkg == True:
replace_background(MAIN_DIR)
#copy default settings files and make fishdata dir
if not os.path.exists(track_dir + 'fishTracker.settings'):
if '_jwj_' in MAIN_DIR:
shutil.copyfile(
os.path.expanduser(
'~/fishMAD/tristrack_defaults/fishTracker_stickleback.settings'
), track_dir + '/fishTracker.settings')
else:
shutil.copyfile(
os.path.expanduser(
'~/fishMAD/tristrack_defaults/fishTracker.settings'),
track_dir + '/fishTracker.settings')
if not os.path.exists(track_dir + 'conversion.settings'):
if '_jwj_' in MAIN_DIR:
shutil.copyfile(
os.path.expanduser(
'~/fishMAD/tristrack_defaults/conversion_stickleback.settings'
), track_dir + '/conversion.settings')
else:
shutil.copyfile(
os.path.expanduser(
'~/fishMAD/tristrack_defaults/conversion.settings'),
track_dir + '/conversion.settings')
if not os.path.exists(track_dir + '/fishdata'):
os.makedirs(track_dir + '/fishdata')
print "set up tristrack environment..."
#Get metadata from videos
store = imgstore.new_for_filename(MAIN_DIR + 'metadata.yaml')
FPS = store.user_metadata['acquisitionframerate']
videoSize = store.image_shape
if (fishnum == 0) or (fishnum == None):
#Get number of fish from MAIN_DIR filename.
fishnum = int(MAIN_DIR.split('/')[-2].split('_')[1])
if fishnum <= 5:
fishnum += 2
elif fishnum <= 15:
fishnum += 4
elif fishnum <= 55:
fishnum += 6
elif fishnum <= 100:
fishnum += 10
elif fishnum <= 200:
fishnum += 15
else:
fishnum = fishnum * 1.1
# customize conversion.settings
openFile = open(track_dir + '/conversion.settings', 'r+b')
SETTINGS = openFile.readlines()
for item in SETTINGS:
if item.find('frame_rate') != -1:
framerate_loc = SETTINGS.index(item)
if item.find('cam_framerate') != -1:
camFrameRate_loc = SETTINGS.index(item)
if item.find('cam_resolution') != -1:
vidSize_loc = SETTINGS.index(item)
SETTINGS[framerate_loc] = 'frame_rate = ' + str(FPS) + '\n'
SETTINGS[camFrameRate_loc] = 'cam_framerate = ' + str(FPS) + '\n'
SETTINGS[vidSize_loc] = 'cam_resolution = ' + str(
[videoSize[0], videoSize[1]]) + '\n'
# return pointer to top of file so we can re-write the content with replaced string
openFile.seek(0)
# clear file content
openFile.truncate()
# re-write the content with the updated content
openFile.write(''.join(SETTINGS))
openFile.close()
print "wrote new conversion file..."
# Customize fishTracker.settings
# get and read tracker settings
openFile = open(track_dir + '/fishTracker.settings', 'r+b')
SETTINGS = openFile.readlines()
for item in SETTINGS:
if item.find('frame_rate') != -1:
framerate_loc = SETTINGS.index(item)
if item.find('number_fish') != -1:
fishNum_loc = SETTINGS.index(item)
if item.find('output_dir') != -1:
outDir_loc = SETTINGS.index(item)
if item.find('fish_minmax_size') != -1:
fishSize_loc = SETTINGS.index(item)
SETTINGS[framerate_loc] = 'frame_rate = ' + str(FPS) + '\n'
SETTINGS[fishNum_loc] = 'number_fish = ' + str(fishnum) + '\n'
SETTINGS[outDir_loc] = 'output_dir = "' + track_dir + '"\n'
if 'juvenile' in MAIN_DIR:
SETTINGS[fishSize_loc] = "fish_minmax_size = [0.5,7]"
# return pointer to top of file so we can re-write the content with replaced string
openFile.seek(0)
# clear file content
openFile.truncate()
# re-write the content with the updated content
openFile.write(''.join(SETTINGS))
openFile.close()
print "wrote new settings file..."
FNULL = open(os.devnull, 'w')
# Launch conversion
vidSet = MAIN_DIR + '%6d.mp4'
launch_conversion = "~/setup_debian/FishTracker/Application/build/framegrabber -d '" + track_dir + "' -i '" + vidSet + "' -o converted.pv -settings conversion -nowindow"
if not (os.path.exists(track_dir + '/converted.pv')):
if os.path.exists(
os.path.expanduser(
'~/setup_debian/FishTracker/Application/build/video_average.png'
)):
os.remove(
os.path.expanduser(
'~/setup_debian/FishTracker/Application/build/video_average.png'
))
print datetime.datetime.now().strftime(
"%Y-%m-%d %H:%M:%S"
), '\t', "Running conversion on file: ", track_dir
try:
subprocess.check_call([launch_conversion],
stdout=FNULL,
stderr=subprocess.STDOUT,
shell=True)
except Exception, e:
errorLog = open(
os.path.expanduser(
'~/setup_debian/FishTracker/Application/build/batchlog.txt'
), 'w')
errorLog.write(
datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S") + '\t')
errorLog.write(track_dir + '\t')
errorLog.write('error during conversion step' + '\n')
errorLog.write(str(e) + '\n\n\n')
errorLog.close()
FNULL.close()
print datetime.datetime.now().strftime(
"%Y-%m-%d %H:%M:%S"
), '\t', "ERROR converting file: ", track_dir
return
df.loc[lastStim, 'stimEnd'] = 1
return df
groupData = pd.DataFrame()
for fn in glob.glob(
'/media/recnodes/recnode_2mfish/coherencetestangular3m_*_dotbot_*/track/perframe_stats.pickle'
):
expID, groupsize, _, trialID = fn.split('/')[4].split('.')[0].split('_', 3)
if fn.split('/track/perframe_stats')[0] in blacklist:
print "excluding", fn
continue
print fn
ret, pf = stims.sync_data(
pd.read_pickle(fn), stims.get_logfile(fn.rsplit('/', 2)[0]),
imgstore.new_for_filename(fn.rsplit('/', 2)[0] + '/metadata.yaml'))
pf['dir'] = pd.to_numeric(pf['dir'], errors='coerce')
pf['coh'] = pf['coh'].fillna(method='pad').fillna(method='backfill')
#try:
pf = sync_by_stimStart(pf)
pf = align_by_stim(pf, trialID)
#slope = pd.Series(np.gradient(pf['median_dRotation_cArea'].values), pf['Timestamp'], name='slope')
s = splrep(pf.Timestamp, pf.median_swimSpeed, k=5, s=17)
newdf = pd.DataFrame({
'syncTime': pf['syncTime'],
'swimSpeed': pf['median_swimSpeed'],
'smoothedSpeed': splev(pf.Timestamp, s),
'dS_by_dt': splev(pf.Timestamp, s, der=1),
'dS_by_dt2': splev(pf.Timestamp, s, der=2)
})
'21990443']
"""
#Camera orientations after renovation (August 2018):
#Current settings as of 180827
[tr, br, tl, bl] = ['21990447',
'21990449',
'21990443',
'21990445']
for x in glob.glob(SEARCH_FILES):
ID = x.split('.')[-1]
print ID
if br in ID:
BOTTOM_RIGHT = imgstore.new_for_filename(x+'/metadata.yaml')
elif tl in ID:
TOP_LEFT = imgstore.new_for_filename(x+'/metadata.yaml')
elif bl in ID:
BOTTOM_LEFT = imgstore.new_for_filename(x+'/metadata.yaml')
elif tr in ID:
TOP_RIGHT = imgstore.new_for_filename(x+'/metadata.yaml')
VIDEOS = [TOP_LEFT, BOTTOM_LEFT, TOP_RIGHT, BOTTOM_RIGHT]
if args.saveas == 'notAssigned':
ts = '_'.join(TOP_LEFT.filename.split('/')[-1].split('.')[0].split('_')[-2:])
SAVEAS = '/home/dan/videoStitch/calibrations/homography/homography_' + ts
else:
args = parser.parse_args()
DIRECTORY = args.v
if DIRECTORY[-1] != '/':
DIRECTORY += '/'
LOG = args.log
stimData = pd.read_table(LOG,
sep='\t',
header=None,
names=['Timestamp', 'nDots', 'C', 'vel',
'dir']).fillna(0)
stimData['frame_time'] = stimData['Timestamp'] / 1000.0
store = imgstore.new_for_filename(DIRECTORY + 'metadata.yaml')
FPS = 30
videoSize = store.image_shape
frameDF = pd.DataFrame(store.get_frame_metadata())
merged = frameDF.merge(stimData, how='outer', on='frame_time')
merged = merged.sort('frame_time').reset_index(drop=True)
merged.frame_number.fillna(method='ffill', inplace=True)
merged['frame_number'] = merged['frame_number'].fillna(0)
merged[['nDots', 'C', 'vel',
'dir']] = merged[['nDots', 'C', 'vel',
'dir']].fillna(method='ffill', axis=0)
merged['date_and_time'] = pd.to_datetime(merged['frame_time'], unit='s')
def calculate_perframe_stats(fbf, TRACK_DIR, nCores=8):
# SETUP PARALLEL PROCESSING
ppe = ProcessPoolExecutor(nCores)
futures = []
statResults = []
rotMResults = []
rotAResults = []
fishR = []
# PREPARE DATAFRAME
#fbf = fbf.loc[fbf['frame'] < 20100, :] #large files cause memory error on this old machine
fbf = fbf.loc[fbf[XPOS].notnull(), :]
fbf = fbf.loc[fbf[YPOS].notnull(), :]
fbf.loc[:, 'uVX'] = fbf.loc[:, XVEL] / fbf.loc[:, SPEED]
fbf.loc[:, 'uVY'] = fbf.loc[:, YVEL] / fbf.loc[:, SPEED]
if 'header' in fbf.columns:
fbf = fbf.drop(columns=['header'])
fbf['coreGroup'] = fbf[
'frame'] % nCores #divide into chunks labelled range(nCores)
fbf.reset_index(inplace=True, drop=True)
# INITIATE PARALLEL PROCESSES
for n in range(nCores):
p = ppe.submit(process_chunk, fbf.loc[fbf['coreGroup'] == n, :])
futures.append(p)
# COLLECT PROCESSED DATA AS IT IS FINISHED
for future in as_completed(futures):
stats, rotM, rotA, fish = future.result()
statResults.append(stats)
rotMResults.append(rotM)
rotAResults.append(rotA)
fishR.append(fish)
#CONCATENATE RESULTS
perframe_stats = pd.concat(statResults)
rotationDf = pd.concat(fishR)
rotationOrders_cMass = {}
for r in rotMResults:
rotationOrders_cMass.update(r)
pick = open(TRACK_DIR + '/rotationOrders_cMass.pickle', "wb")
pickle.dump(rotationOrders_cMass, pick)
pick.close()
rotationOrders_cArea = {}
for r in rotAResults:
rotationOrders_cArea.update(r)
pick = open(TRACK_DIR + '/rotationOrders_cArea.pickle', "wb")
pickle.dump(rotationOrders_cArea, pick)
pick.close()
ARENA_WIDTH = get_arena_width(TRACK_DIR.split('/track')[0])
#perframe_stats.loc[:,'centroidRotation'] = get_centroid_rotation(perframe_stats, TRACK_DIR, ARENA_WIDTH)
perframe_stats['frame'] = perframe_stats.index
log = stim_handling.get_logfile(TRACK_DIR.rsplit('/', 2)[0])
store = imgstore.new_for_filename(
TRACK_DIR.rsplit('/', 2)[0] + '/metadata.yaml')
ret, perframe_stats = stim_handling.sync_data(perframe_stats, log, store)
perframe_stats.to_pickle(TRACK_DIR + '/perframe_stats.pickle')
try:
rotationDf.to_pickle(TRACK_DIR + '/frameByFrameData.pickle')
except:
import joblib
joblib.dump(rotationDf, TRACK_DIR + '/frameByFrameData.jl')
return perframe_stats
def save_rotation_data(expFileName):
if 'reversal' in expFileName:
REVERSAL = True
XLIM = (30, 60)
COLUMN = 'dir'
else:
REVERSAL = False
XLIM = (30, 300)
COLUMN = 'speed'
try:
fbf = pd.read_pickle(expFileName + '/track/perframe_stats.pickle')
if len(fbf) == 0:
print("FAILED TO READ PICKLE. TRYING JOBLIB")
fbf = joblib.load(expFileName + '/track/perframe_stats.pickle')
rot = pd.read_pickle(expFileName +
'/track/rotationOrders_cArea.pickle')
if not 'frame' in fbf.columns:
fbf['frame'] = fbf.index
if not 'FrameNumber' in fbf.columns:
ret, fbf = stims.sync_data(
fbf, stims.get_logfile(expFileName),
imgstore.new_for_filename(expFileName + '/metadata.yaml'))
ID = expFileName.split('/')[-1].split('_', 3)[-1].split('.')[0]
ret, synced = sync_by_stimStart(fbf,
ID,
col=COLUMN,
REVERSALS=REVERSAL)
if ret == 0:
return 0
for IDx in list(set(synced['trialID'])):
chunk = synced.loc[synced['trialID'] == IDx, :]
ix = chunk[chunk.syncTime.between(np.timedelta64(XLIM[0], 's'),
np.timedelta64(XLIM[1],
's'))].index
DIR = np.sign(chunk.loc[ix, 'dir'].mean())
if DIR == 0:
return 0
data = np.concatenate([
rot[x] for x in range(ix.min(), ix.max())
]) * DIR * -1.0 #FLIP TO MAKE POSITIVE, JAKE
COH = str(np.around(fbf.coh.mean(), 1))
GS = expFileName.split('/')[-1].split('_')[1]
if REVERSAL:
np.save(
'/media/recnodes/Dan_storage/20200121_reversal_rotation_data/'
+ GS + '_' + COH + '_' + IDx + '.npy', data)
print(
'/media/recnodes/Dan_storage/20200121_reversal_rotation_data/'
+ GS + '_' + COH + '_' + IDx + '.npy')
else:
continue #FIXME danno's too chicken to try this cuz it'll surely break
np.save(
'/media/recnodes/Dan_storage/191205_rotation_data/' + GS +
'_' + COH + '_' + ID + '.npy', data)
print('/media/recnodes/Dan_storage/191205_rotation_data/' +
GS + '_' + COH + '_' + ID + '.npy')
return 1
except Exception as e:
print(e)
return 0
calibs = ('stitch_dry_26c_20190624_091343.21990443_undistorted',
'stitch_dry_26c_20190624_091343.21990445_undistorted',
'stitch_dry_26c_20190624_091343.21990447_undistorted',
'stitch_dry_26c_20190624_091343.21990449_undistorted')
else:
calibs = ('stitch09_20180910_165817.21990443_undistorted',
'stitch09_20180910_165817.21990447_undistorted',
'stitch09_20180910_165817.21990445_undistorted',
'stitch09_20180910_165817.21990449_undistorted')
cams_imgs = {}
# load the first frame for the calibration
for fn in calibs:
with new_for_filename(op.join(BASE_CALIB, fn)) as store:
camera_serial = get_store_camera_serial(store)
img, _ = store.get_image(frame_number=None,
exact_only=True,
frame_index=0)
cams_imgs[camera_serial] = ensure_color(img)
sorted_imgs = [cams_imgs[i] for i in best_order]
s = Stitcher(use_gpu=True,
estimator_type="homography",
matcher_type="affine",
warp_type="plane")
# s.enable_exposure_compensation('gain_blocks')
# s.enable_seam_finding('gc_color')
def get_Tseries(expFileName):
expID = expFileName.split('/')[-1].split('_', 3)[-1].split('.')[0]
if 'reversal' in expFileName:
REVERSAL = True
prestim_frames = 400
poststim_frames = 2400
file_prefix = 'REV_'
COLUMN = 'dir'
else:
REVERSAL = False
prestim_frames = 1200
poststim_frames = 16000
file_prefix = 'COH_'
COLUMN = 'speed'
try:
fbf = pd.read_pickle(expFileName + '/track/frameByFrameData.pickle')
if len(fbf.shape) == 1:
fbf = joblib.load(expFileName + '/track/frameByFrameData.pickle')
pf = pd.read_pickle(
expFileName + '/track/perframe_stats.pickle'
) #FIXME these may have the wrong stim direction because of sync_data vs sync_coherence (if made before 20191218)....
if len(pf.shape) == 1:
pf = joblib.load(expFileName + '/track/perframe_stats.pickle')
if not 'frame' in pf.columns:
fbf['frame'] = pf.index
if not 'FrameNumber' in pf.columns:
try:
ret, pf = stims.sync_data(
pf, stims.get_logfile(expFileName),
imgstore.new_for_filename(expFileName + '/metadata.yaml'))
except:
print("oppala")
return 0
ret, sy = sync_by_stimStart(pf, expID, col=COLUMN, REVERSALS=REVERSAL)
if ret == 0:
return 0
except Exception as e:
print(e)
return 0
for ID, data in sy.groupby('trialID'):
frame_0 = data.loc[data['syncTime'] == abs(data.syncTime).min(),
'frame'].values[0]
md = data.loc[frame_0 - prestim_frames:frame_0 + poststim_frames]
prestim = data.loc[data['frame'] < frame_0, :]
psMeta = dict(prestim[prestim.columns[prestim.dtypes ==
'float64']].fillna(0).mean())
a = area[area.index == ID]
if len(a) > 0:
for col in [
'Area', 'Area_rank', 'Density', 'Density_rank',
'groupsize', 'trialID'
]:
psMeta[col] = a[col][0]
else:
psMeta['trialID'] = ID
d = fbf[fbf['frame'].between(frame_0 - prestim_frames,
frame_0 + poststim_frames)]
rotA = d.groupby(['frame',
'trackid'])['rotation_cArea'].mean().unstack()
rotM = d.groupby(['frame',
'trackid'])['rotation_cMass'].mean().unstack()
stimdir = md['dir'].fillna(0)
stimcoh = md['coh'].fillna(0)
stimspeed = md['speed'].fillna(0)
meta = {}
COH = str(np.around(pf.coh.median(), 1))
GS = expFileName.split('/')[-1].split('_')[1]
#ID = expFileName.split('/')[-1].split('_',3)[-1].split('.')[0]
FN = '/media/recnodes/Dan_storage/Jake_TS/' + file_prefix + GS + '_' + COH + '_' + ID + '.npz'
#FN = '/media/recnodes/Dan_storage/Jake_TS/'+ expFileName.split('/')[-1].rsplit('_',2)[0] + '_' + ID + '.npz'
np.savez(FN,
rA=rotA,
rM=rotM,
prestim=psMeta,
meta=meta,
direction=stimdir,
coherence=stimcoh,
speed=stimspeed)
print('completed:', FN)
return 1
import imgstore
import os
import pandas as pd
import numpy as np
MAIN_DIR = '/media/recnodes/recnode_2mfish/reversals3m_64_dotbot_20181024_153201.stitched/'
DATA_COL = 'EigenCen'
STIM_COL = 'dir'
SKIP_FRAMES = 3
SAVE_DIR = MAIN_DIR + 'track/eigencentricity_overlay/'
nfbf = joblib.load(MAIN_DIR + 'track/network_FBF.pickle')
nfbf.index = nfbf.frame
store = imgstore.new_for_filename(MAIN_DIR + 'metadata.yaml')
log = stims.get_logfile(MAIN_DIR)
ret, pf = stims.sync_data(
pd.read_pickle(MAIN_DIR + 'track/perframe_stats.pickle'), log, store)
ret, nfbf = stims.sync_data(nfbf, log, store)
frames = pd.DataFrame(store.get_frame_metadata())
frames.columns = ['FrameNumber', 'Timestamp']
_MIN = nfbf[DATA_COL].min()
_MAX = nfbf[DATA_COL].max()
g = nfbf.groupby('frame')
for i in np.arange(0, len(frames), SKIP_FRAMES):
def run(MAIN_DIR, RESUME=True):
print("processing: ", MAIN_DIR)
#getColumnNames('_'.join(MAIN_DIR.split('/')[-1]..split('.')[0].split('_')[-2:]))
trackdir = slashdir(MAIN_DIR) + 'track/'
PF_DONE = False
if os.path.exists(trackdir + 'perframe_stats.pickle'):
if datetime.datetime.fromtimestamp(
os.path.getmtime(trackdir + 'perframe_stats.pickle')
) > getTimeFromTimeString('20191218_000000'):
PF_DONE = True
perframe_stats = pd.read_pickle(trackdir + 'perframe_stats.pickle')
if len(perframe_stats.shape) == 1:
perframe_stats = joblib.load(trackdir +
'perframe_stats.pickle')
if len(perframe_stats.shape) == 1:
PF_DONE = False
if PF_DONE == False:
if os.path.exists(trackdir + 'frameByFrameData.pickle'):
try:
fbf = pd.read_pickle(trackdir + 'frameByFrameData.pickle')
except:
fbf = joblib.load(trackdir + 'frameByFrameData.pickle')
if len(fbf.shape) == 1:
fbf = getFrameByFrameData(trackdir, RESUME, args.maxthreads)
#print("CORRUPTED FILE. DELETING frameByFrameData:", trackdir)
#os.remove(trackdir + 'frameByFrameData.pickle')
#return
else:
fbf = getFrameByFrameData(trackdir, RESUME, args.maxthreads)
if not 'VX#smooth#wcentroid' in fbf.columns:
print('VX#smooth#wcentroid', "not found in columns.", MAIN_DIR)
print(fbf.columns)
os.remove(trackdir + 'frameByFrameData.pickle')
shutil.rmtree(trackdir + 'fishdata')
if os.path.exists(trackdir + 'frameByFrame_complete'):
os.remove(trackdir + 'frameByFrame_complete')
return
if len(set(fbf.frame)) < 501:
print("FOUND INCOMPLETE TRACKING DATA. DELETING TRACKDIR")
shutil.rmtree(trackdir)
return
perframe_stats = calculate_perframe_stats(fbf, trackdir,
args.maxthreads)
store = imgstore.new_for_filename(slashdir(MAIN_DIR) + 'metadata.yaml')
log = stim_handling.get_logfile(MAIN_DIR)
if 'reversals' in MAIN_DIR:
#ret, perframe_stats = stim_handling.sync_reversals(perframe_stats, log, store)
plot_perframe_vs_time(slashdir(MAIN_DIR), [
'dir', 'median_polarization', 'median_dRotation_cMass',
'median_dRotation_cArea', 'median_swimSpeed', 'entropy_Ra'
], [
'Direction', 'Pol. Order', 'Rot. Order (CofM)',
'Rot. Order (Area)', 'Median Speed', 'Entropy'
], perframe_stats, '_median')
elif 'coherence' in MAIN_DIR:
#ret, perframe_stats = stim_handling.synch_coherence_with_rotation(perframe_stats, log, store)
plot_perframe_vs_time(slashdir(MAIN_DIR), [
'coherence', 'median_polarization', 'median_dRotation_cMass',
'median_dRotation_cArea', 'median_swimSpeed', 'entropy_Ra'
], [
'Coherence', 'Pol. Order', 'Rot. Order (CofM)',
'Rot. Order (Area)', 'Median Speed', 'Entropy'
], perframe_stats, '_median')
elif 'cogs' in MAIN_DIR:
pass #FIXME
type=str,
required=False,
default='notDefined',
help=
'name for calibration, including date time string, ex: 20180404_123456'
)
args = parser.parse_args()
CHECKERSIZE = tuple([int(k) for k in args.checkersize.split('x')])
for vid in glob.glob(
slashdir(args.dir) + '*' + args.handle + '*/metadata.yaml'):
if "undistorted" in vid: #skip already processed videos
continue
inStore = imgstore.new_for_filename(vid)
if args.saveas == 'notDefined':
DATETIME = '_'.join(
vid.split('/')[-2].split('.')[0].rsplit('_', 2)[1:])
SERIAL = inStore.user_metadata['camera_serial']
SAVE_AS = '_'.join([DATETIME, SERIAL])
else:
SAVE_AS = '_'.join(
[args.saveas, inStore.user_metadata['camera_serial']])
print SAVE_AS
calibrate(
inStore, CHECKERSIZE,
os.path.expanduser('~/videoStitch/calibrations/distortion/' +
SAVE_AS + '.yaml'))
