def load_pos_data(self,
pname: Path,
ppm: int = 300,
jumpmax: int = 100) -> None:
# Only sub-class that doesn't use this is OpenEphysNWB
# which needs updating
# TODO: Update / overhaul OpenEphysNWB
# Load the start time from the sync_messages file
recording_start_time = 0
if self.sync_message_file is not None:
with open(self.sync_message_file, "r") as f:
sync_strs = f.read()
sync_lines = sync_strs.split("\n")
for line in sync_lines:
if "subProcessor: 0" in line:
idx = line.find("start time: ")
start_val = line[idx + len("start time: "):-1]
tmp = start_val.split("@")
recording_start_time = float(tmp[0]) # in samples
if self.path2PosData is not None:
pos_data_type = getattr(self, "pos_data_type", "PosTracker")
if pos_data_type == "PosTracker":
print("Loading PosTracker data...")
pos_data = np.load(
os.path.join(self.path2PosData, "data_array.npy"))
if pos_data_type == "TrackingPlugin":
print("Loading Tracking Plugin data...")
pos_data = loadTrackingPluginData(
os.path.join(self.path2PosData, "data_array.npy"))
pos_ts = np.load(os.path.join(self.path2PosData, "timestamps.npy"))
pos_ts = np.ravel(pos_ts)
pos_timebase = getattr(self, "pos_timebase", 3e4)
sample_rate = np.floor(1 / np.mean(np.diff(pos_ts) / pos_timebase))
xyTS = pos_ts - recording_start_time
# xyTS = xyTS / pos_timebase # convert to seconds
if self.sync_message_file is not None:
recording_start_time = xyTS[0]
P = PosCalcsGeneric(
pos_data[:, 0],
pos_data[:, 1],
cm=True,
ppm=ppm,
jumpmax=jumpmax,
)
P.xyTS = xyTS
P.sample_rate = sample_rate
P.postprocesspos({"SampleRate": sample_rate})
print("Loaded pos data")
self.PosCalcs = P
else:
warnings.warn("Could not find the pos data. \
Make sure there is a pos_data folder with data_array.npy \
and timestamps.npy in")
self.recording_start_time = recording_start_time
def load_pos_data(self,
pname: Path,
ppm: int = 300,
jumpmax: int = 100) -> None:
if self.PosCalcs is None:
try:
AxonaPos = Pos(self.pname)
P = PosCalcsGeneric(
AxonaPos.led_pos[0, :],
AxonaPos.led_pos[1, :],
cm=True,
ppm=self.ppm,
)
P.xyTS = Pos.ts
P.sample_rate = AxonaPos.getHeaderVal(AxonaPos.header,
"sample_rate")
P.postprocesspos()
print("Loaded pos data")
self.PosCalcs = P
except IOError:
print("Couldn't load the pos data")