def __init__(self, fmf_dir, savedir, fly_id, plot_overlays=False):
if (savedir[-1] == '/'):
savedir = savedir[:-1]
if not os.path.exists(savedir + '/temp_png'):
os.makedirs(savedir + '/temp_png')
self._savedir = savedir
if (fmf_dir[-1] == '/'):
self._fmf_dir = fmf_dir[:-1]
else:
self._fmf_dir = fmf_dir
self._zoomfmf = FMF.FlyMovie(self._fmf_dir)
self._plot_overlays = plot_overlays
self._expdir = fmf_dir.rsplit('/', 2)[0]
self._bag = utilities.match_fmf_and_bag(self._fmf_dir,
(self._expdir + '/BAGS'))
#self._wide = utilities.match_wide_to_zoom(self._fmf_dir, (self._expdir + '/'))
self._handle, __, ___ = utilities.parse_fmftime(self._fmf_dir)
self._data, self._Tzero = self.get_data()
self._image_height, self._image_width = self._zoomfmf.get_frame(
0)[0].shape
def __init__(self, fmf_dir, savedir, fly_id, plot_overlays=False):
if (savedir[-1] == '/' ):
savedir = savedir[:-1]
if not os.path.exists(savedir + '/temp_png'):
os.makedirs(savedir + '/temp_png')
self._savedir = savedir
if (fmf_dir[-1] == '/'):
self._fmf_dir = fmf_dir[:-1]
else:
self._fmf_dir = fmf_dir
self._zoomfmf = FMF.FlyMovie(self._fmf_dir)
self._plot_overlays = plot_overlays
self._expdir = fmf_dir.rsplit('/', 2)[0]
self._bag = utilities.match_fmf_and_bag(self._fmf_dir, (self._expdir + '/BAGS'))
#self._wide = utilities.match_wide_to_zoom(self._fmf_dir, (self._expdir + '/'))
self._handle, __, ___ = utilities.parse_fmftime(self._fmf_dir)
self._data, self._Tzero = self.get_data()
self._image_height, self._image_width = self._zoomfmf.get_frame(0)[0].shape
def get_stims_from_bag(self, FMF_DIR, BAGS, EXPDIR):
print "Processing: ", FMF_DIR
#JAABA_CSV = FMF_DIR + '/registered_trx.csv'
FLY_ID, FMF_TIME, GROUP = utilities.parse_fmftime(FMF_DIR)
BAG_FILE = utilities.match_fmf_and_bag(FMF_DIR, BAGS)
WIDE_FMF = utilities.match_wide_to_zoom(FMF_DIR, EXPDIR)
#jaaba_data = pd.read_csv(JAABA_CSV, sep=',', names=['Timestamp','Length','Width','Theta','Left','Right'], index_col=False)
#jaaba_data[['Length','Width','Left','Right']] = jaaba_data[['Length','Width','Left','Right']].astype(np.float64)
# ALIGN LASER STATE DATA
jaaba_data = DataFrame(index=self._zoomfmf.get_all_timestamps())
jaaba_data['Timestamp'] = self._zoomfmf.get_all_timestamps()
jaaba_data = utilities.convert_timestamps(jaaba_data)
jaaba_data['Laser1_state'] = utilities.binarize_laser_data(
BAG_FILE, 2).resample('10ms', how='max')['Laser_state'].asof(
jaaba_data.index).fillna(value=0) #YAY!
jaaba_data['Laser2_state'] = utilities.binarize_laser_data(
BAG_FILE, 4).resample('10ms', how='max')['Laser_state'].asof(
jaaba_data.index).fillna(value=0)
"""
# COMPUTE AND ALIGN DISTANCE TO NEAREST TARGET
targets = target_detector.TargetDetector(WIDE_FMF, FMF_DIR)
targets.plot_targets_on_background()
jaaba_data['dtarget'] = targets.get_dist_to_nearest_target(BAG_FILE)['dtarget'].asof(jaaba_data.index).fillna(value=0)
"""
jaaba_data[
'Timestamp'] = jaaba_data.index #silly pandas bug for subtracting from datetimeindex...
try:
jaaba_data['synced_time'] = jaaba_data[
'Timestamp'] - jaaba_data.Timestamp[
(jaaba_data.Laser2_state +
jaaba_data.Laser1_state) > 0].index[0]
except:
print "WARNING: Cannot synchronize by stimulus. Setting T0 to frame0. "
jaaba_data['synced_time'] = jaaba_data[
'Timestamp'] - jaaba_data.Timestamp.index[0]
"""
#DISCARD BOGUS WING ANGLE VALUES:
jaaba_data['Left'][jaaba_data['Left'] < -2.09 ]= np.nan #2.09 for 120degrees
jaaba_data['Right'][jaaba_data['Right'] > 2.09] = np.nan
jaaba_data['maxWingAngle'] = jaaba_data[['Left','Right']].abs().max(axis=1)
"""
return jaaba_data
def __init__(self, fmf_dir, savedir, fly_id, plot_overlays=False):
if (savedir[-1] == '/'):
savedir = savedir[:-1]
if not os.path.exists(savedir + '/temp_png'):
os.makedirs(savedir + '/temp_png')
self._savedir = savedir
if (fmf_dir[-1] == '/'):
self._fmf_dir = fmf_dir[:-1]
else:
self._fmf_dir = fmf_dir
self._plot_overlays = plot_overlays
self._expdir = fmf_dir.rsplit('/', 1)[0]
self._bag = utilities.match_fmf_and_bag(self._fmf_dir,
(self._expdir + '/BAGS'))
self._wide = utilities.match_wide_to_zoom(self._fmf_dir,
(self._expdir + '/'))
self._widefmf = FMF.FlyMovie(self._wide)
self._handle, __, ___ = utilities.parse_fmftime(self._fmf_dir)
self._zoomfmf, self._data, self._Tzero = self.get_data()
if self._data.Laser0_state.mean(
) >= 0.5: #SOME EXPERIMENTS ARE DONE WITH lASER0 OFF.
if self._data.Laser0_state.mean(
) <= 0.99: #SOME BAGFILES HAVE A FEW MSGS BEFORE LASER CONFIG
self.ILLUMINATED_WITH_LASER0 = 1
else:
self.ILLUMINATED_WITH_LASER0 = 0
else:
self.ILLUMINATED_WITH_LASER0 = 0
self._image_height, self._image_width = self._zoomfmf.get_frame(
0)[0].shape
def get_stims_from_bag(self, FMF_DIR, BAGS, EXPDIR):
print "Processing: ", FMF_DIR
#JAABA_CSV = FMF_DIR + '/registered_trx.csv'
FLY_ID, FMF_TIME, GROUP = utilities.parse_fmftime(FMF_DIR)
BAG_FILE = utilities.match_fmf_and_bag(FMF_DIR, BAGS)
WIDE_FMF = utilities.match_wide_to_zoom(FMF_DIR, EXPDIR)
#jaaba_data = pd.read_csv(JAABA_CSV, sep=',', names=['Timestamp','Length','Width','Theta','Left','Right'], index_col=False)
#jaaba_data[['Length','Width','Left','Right']] = jaaba_data[['Length','Width','Left','Right']].astype(np.float64)
# ALIGN LASER STATE DATA
jaaba_data = DataFrame(index=self._zoomfmf.get_all_timestamps())
jaaba_data['Timestamp'] = self._zoomfmf.get_all_timestamps()
jaaba_data = utilities.convert_timestamps(jaaba_data)
jaaba_data['Laser1_state'] = utilities.binarize_laser_data(BAG_FILE, 2).resample('10ms', how='max')['Laser_state'].asof(jaaba_data.index).fillna(value=0) #YAY!
jaaba_data['Laser2_state'] = utilities.binarize_laser_data(BAG_FILE, 4).resample('10ms', how='max')['Laser_state'].asof(jaaba_data.index).fillna(value=0)
"""
# COMPUTE AND ALIGN DISTANCE TO NEAREST TARGET
targets = target_detector.TargetDetector(WIDE_FMF, FMF_DIR)
targets.plot_targets_on_background()
jaaba_data['dtarget'] = targets.get_dist_to_nearest_target(BAG_FILE)['dtarget'].asof(jaaba_data.index).fillna(value=0)
"""
jaaba_data['Timestamp'] = jaaba_data.index #silly pandas bug for subtracting from datetimeindex...
try:
jaaba_data['synced_time'] = jaaba_data['Timestamp'] - jaaba_data.Timestamp[(jaaba_data.Laser2_state + jaaba_data.Laser1_state) > 0].index[0]
except:
print "WARNING: Cannot synchronize by stimulus. Setting T0 to frame0. "
jaaba_data['synced_time'] = jaaba_data['Timestamp'] - jaaba_data.Timestamp.index[0]
"""
#DISCARD BOGUS WING ANGLE VALUES:
jaaba_data['Left'][jaaba_data['Left'] < -2.09 ]= np.nan #2.09 for 120degrees
jaaba_data['Right'][jaaba_data['Right'] > 2.09] = np.nan
jaaba_data['maxWingAngle'] = jaaba_data[['Left','Right']].abs().max(axis=1)
"""
return jaaba_data
def make_pngs(zoom_fmf, savedir, overlays_value):
#os.system(ffmpeg -f image2 -r 15 -i _tmp%05d.png -vcodec mpeg4 -y (_VIDEO_DIR + '/flymad_annotated.mp4'))
vid = bag_movies.FlyPanel(zoom_fmf, savedir, utilities.parse_fmftime(zoom_fmf)[0], overlays_value, args.lasermode)
image_height = vid.get_frame(0)[0].shape[0]
image_width = vid.get_frame(0)[0].shape[1]
for frame_number in np.arange(vid.get_n_frames()):
if os.path.exists(savedir + '/temp_png/_tmp%05d.png'%(frame_number)):
continue
fig = plt.figure(figsize=(image_width*2/100, image_height/100), dpi=200.399, frameon=False )
make_panel(vid, 0, 0, frame_number, fig)
plt.savefig(savedir + '/temp_png/_tmp%05d.png'%(frame_number), bbox_inches='tight', pad_inches=0)
plt.close('all')
utilities.call_command("ffmpeg -f image2 -r 15 -i "+ savedir + "/temp_png/_tmp%05d.png -vf scale=iw/2:-1 -vcodec mpeg4 -b 8000k -y " + savedir[:-1] + ".mp4;")
utilities.call_command("rm -r " + savedir)
type=str,
required=False,
default="Experiment",
help=
'Label for bottom data. example: P1>CsCHRIMSON & $\mathregular{SHIBIRE^{TS}}$'
)
args = parser.parse_args()
top_fmf = args.topfmf
bottom_fmf = args.bottomfmf
savedir = args.savedir
#os.system(ffmpeg -f image2 -r 15 -i _tmp%05d.png -vcodec mpeg4 -y (_VIDEO_DIR + '/flymad_annotated.mp4'))
ctrlfly = data_movies.FlyPanel(top_fmf, savedir,
utilities.parse_fmftime(top_fmf)[0])
expfly = data_movies.FlyPanel(bottom_fmf, savedir,
utilities.parse_fmftime(bottom_fmf)[0])
image_height = ctrlfly.get_frame(0)[0].shape[0] + expfly.get_frame(
0)[0].shape[0]
image_width = expfly.get_frame(0)[0].shape[1] * 3
for frame_number in range(9450): #ctrlfly.get_n_frames()):
if os.path.exists(savedir + '/temp_png/_tmp%05d.png' % (frame_number)):
continue
fig = plt.figure(figsize=(image_width / 100, image_height / 100),
dpi=200.399)
'--overlays',
type=bool,
required=False,
default=False,
help='turn on overlays to plot wing angles and distance bars')
args = parser.parse_args()
zoom_fmf = args.zoom
wide_fmf = args.wide
savedir = args.savedir
overlays_value = args.overlays
#os.system(ffmpeg -f image2 -r 15 -i _tmp%05d.png -vcodec mpeg4 -y (_VIDEO_DIR + '/flymad_annotated.mp4'))
vid = data_movies.FlyPanel(zoom_fmf, savedir,
utilities.parse_fmftime(zoom_fmf)[0],
overlays_value)
image_height = vid.get_frame(0)[0].shape[0]
image_width = vid.get_frame(0)[0].shape[1]
for frame_number in range(vid.get_n_frames()):
if os.path.exists(savedir + '/temp_png/_tmp%05d.png' % (frame_number)):
continue
fig = plt.figure(figsize=(image_width / 100, image_height * 1.2 / 100),
dpi=200.399,
frameon=False)
make_panel(vid, 0, 0, frame_number)
help='path to fmf directory')
parser.add_argument('--savedir', type=str, required=True,
help='path to save directory')
parser.add_argument('--toplabel', type=str, required=False, default="Control",
help='label for top data')
parser.add_argument('--bottomlabel', type=str, required=False, default="Experiment",
help='Label for bottom data. example: P1>CsCHRIMSON & $\mathregular{SHIBIRE^{TS}}$')
args = parser.parse_args()
top_fmf = args.topfmf
bottom_fmf = args.bottomfmf
savedir = args.savedir
#os.system(ffmpeg -f image2 -r 15 -i _tmp%05d.png -vcodec mpeg4 -y (_VIDEO_DIR + '/flymad_annotated.mp4'))
ctrlfly = data_movies.FlyPanel(top_fmf, savedir, utilities.parse_fmftime(top_fmf)[0])
expfly = data_movies.FlyPanel(bottom_fmf, savedir, utilities.parse_fmftime(bottom_fmf)[0])
image_height = ctrlfly.get_frame(0)[0].shape[0] + expfly.get_frame(0)[0].shape[0]
image_width = expfly.get_frame(0)[0].shape[1] *3
for frame_number in range(9450):#ctrlfly.get_n_frames()):
if os.path.exists(savedir + '/temp_png/_tmp%05d.png'%(frame_number)):
continue
fig = plt.figure(figsize=(image_width/100, image_height/100), dpi=200.399 )
make_panel(ctrlfly, 0, 0, frame_number, args.toplabel)
make_panel(expfly, 30, 0, frame_number, args.bottomlabel )
#plt.show()
def sync_jaaba_with_ros(self, FMF_DIR, BAGS, JAABA):
print "Processing: ", FMF_DIR
JAABA_CSV = FMF_DIR + '/registered_trx.csv'
FLY_ID, FMF_TIME, GROUP = utilities.parse_fmftime(FMF_DIR)
BAG_FILE = utilities.match_fmf_and_bag(FMF_DIR, BAGS)
WIDE_FMF = utilities.match_wide_to_zoom(FMF_DIR, JAABA)
jaaba_data = pd.read_csv(
JAABA_CSV,
sep=',',
names=['Timestamp', 'Length', 'Width', 'Theta', 'Left', 'Right'],
index_col=False)
jaaba_data[['Length', 'Width', 'Left', 'Right'
]] = jaaba_data[['Length', 'Width', 'Left',
'Right']].astype(np.float64)
jaaba_data = utilities.convert_timestamps(jaaba_data)
# ALIGN LASER STATE DATA
laser_states = utilities.get_laser_states(BAG_FILE)
try:
jaaba_data['Laser0_state'] = laser_states['Laser0_state'].asof(
jaaba_data.index).fillna(value=0)
jaaba_data['Laser1_state'] = laser_states['Laser1_state'].asof(
jaaba_data.index).fillna(value=0) #YAY!
jaaba_data['Laser2_state'] = laser_states['Laser2_state'].asof(
jaaba_data.index).fillna(value=0)
except:
print "\t ERROR: problem interpreting laser current values."
jaaba_data['Laser0_state'] = 0
jaaba_data['Laser2_state'] = 0
jaaba_data['Laser1_state'] = 0
# COMPUTE AND ALIGN DISTANCE TO NEAREST TARGET
targets = target_detector.TargetDetector(WIDE_FMF, FMF_DIR)
targets.plot_targets_on_background()
jaaba_data['dtarget'] = targets.get_dist_to_nearest_target(
BAG_FILE)['dtarget'].asof(jaaba_data.index).fillna(value=0)
jaaba_data[
'Timestamp'] = jaaba_data.index #silly pandas bug for subtracting from datetimeindex...
try:
jaaba_data['synced_time'] = jaaba_data[
'Timestamp'] - jaaba_data.Timestamp[
(jaaba_data.Laser2_state +
jaaba_data.Laser1_state) > 0].index[0]
except:
print "WARNING: Cannot synchronize by stimulus. Setting T0 to frame0. "
jaaba_data['synced_time'] = jaaba_data[
'Timestamp'] - jaaba_data.Timestamp.index[0]
#DISCARD BOGUS WING ANGLE VALUES:
jaaba_data['Left'][
jaaba_data['Left'] < -2.09] = np.nan #2.09 for 120degrees
jaaba_data['Right'][jaaba_data['Right'] > 2.09] = np.nan
jaaba_data['maxWingAngle'] = jaaba_data[['Left',
'Right']].abs().max(axis=1)
return jaaba_data
help='path to zoom fmf')
parser.add_argument('--wide', type=str, required=False,
help='path to wide fmf')
parser.add_argument('--savedir', type=str, required=True,
help='path to save directory')
parser.add_argument('--overlays', type=bool, required=False, default=False, help='turn on overlays to plot wing angles and distance bars')
args = parser.parse_args()
zoom_fmf = args.zoom
wide_fmf = args.wide
savedir = args.savedir
overlays_value = args.overlays
#os.system(ffmpeg -f image2 -r 15 -i _tmp%05d.png -vcodec mpeg4 -y (_VIDEO_DIR + '/flymad_annotated.mp4'))
vid = data_movies.FlyPanel(zoom_fmf, savedir, utilities.parse_fmftime(zoom_fmf)[0], overlays_value)
image_height = vid.get_frame(0)[0].shape[0]
image_width = vid.get_frame(0)[0].shape[1]
for frame_number in range(8000):
if os.path.exists(savedir + '/temp_png/_tmp%05d.png'%(frame_number)):
continue
fig = plt.figure(figsize=(image_width/100, image_height*1.2/100), dpi=200.399, frameon=False )
make_panel(vid, 0, 0, frame_number)
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--fmf', type=str, required=True,
help='path to fmf directory')
parser.add_argument('--savedir', type=str, required=True,
help='path to save directory')
parser.add_argument('--label', type=str, required=False, default="Control",
help='label for top data')
args = parser.parse_args()
fmf = args.fmf
savedir = args.savedir
#os.system(ffmpeg -f image2 -r 15 -i _tmp%05d.png -vcodec mpeg4 -y (_VIDEO_DIR + '/flymad_annotated.mp4'))
fly = data_movies.FlyPanel(fmf, savedir, utilities.parse_fmftime(fmf)[0])
image_height = (fly.get_frame(0)[0].shape[0] )*2
image_width = fly.get_frame(0)[0].shape[1] *2:
if not os.path.exists(savedir + '/temp_png):
os.makedirs(savedir + '/temp_png)
for frame_number in range(fly.get_n_frames()):
if os.path.exists(savedir + '/temp_png/_tmp%05d.png'%(frame_number)):
continue
fig = plt.figure(figsize=(image_width/100, image_height/100), dpi=200.399 )
make_panel(fly, 0, 0, frame_number, args.label)
#plt.show()
