def __init__(self, basepath):
"""initiates position class
Arguments:
obj {class instance} -- should have the following attributes
obj.sessinfo.files.position --> filename for storing the positions
"""
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
posfile = self._obj.files.position
if os.path.exists(posfile):
posInfo = self._load(posfile).item()
self.x = posInfo["x"] / 4 # in seconds
self.y = posInfo["y"] / 4 # in seconds
self.t = posInfo["time"] # in seconds
self.datetime = posInfo["datetime"] # in seconds
self.speed = np.sqrt(np.diff(self.x) ** 2 + np.diff(self.y) ** 2) / (
1 / self.tracking_sRate
)
else:
"Position file does not exist....did not load _position.npy"
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
self.pre = None
self.maze = None
self.post = None
if Path(self._obj.files.epochs).is_file():
epochs = np.load(self._obj.files.epochs, allow_pickle=True).item()
totaldur = []
self.times = pd.DataFrame(epochs)
for (epoch, times) in epochs.items(): # alternative list(epochs)
setattr(self, epoch.lower(), times) # .lower() will be removed
totaldur.append(np.diff(times))
self.totalduration = np.sum(np.asarray(totaldur))
else:
print("Epochs file does not exist...did not load epochs")
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
self.stability = Stability(basepath)
# self.dynamics = firingDynamics(basepath)
filePrefix = self._obj.files.filePrefix
@dataclass
class files:
spikes: str = Path(str(filePrefix) + "_spikes.npy")
instfiring: str = Path(str(filePrefix) + "_instfiring.pkl")
self.files = files()
filename = self._obj.files.spikes
if filename.is_file():
spikes = np.load(filename, allow_pickle=True).item()
self.times = spikes["times"]
self.info = spikes["info"].reset_index()
self.pyrid = np.where(self.info.q < 4)[0]
self.pyr = [self.times[_] for _ in self.pyrid]
self.intneurid = np.where(self.info.q == 8)[0]
self.intneur = [self.times[_] for _ in self.intneurid]
self.muaid = np.where(self.info.q == 6)[0]
self.mua = [self.times[_] for _ in self.muaid]
def __init__(self, obj):
if isinstance(obj, Recinfo):
self._obj = obj
else:
self._obj = Recinfo(obj)
self.time = None
# ----- defining file names ---------
filePrefix = self._obj.files.filePrefix
@dataclass
class files:
dead: str = filePrefix.with_suffix(".dead")
artifact: str = filePrefix.with_suffix(".artifact.npy")
self.files = files()
# ----- loading files --------
if self.files.artifact.is_file():
self._load()
elif Path(self.files.dead).is_file():
with self.files.dead.open("r") as f:
noisy = []
for line in f:
epc = line.split(" ")
epc = [float(_) for _ in epc]
noisy.append(epc)
noisy = np.asarray(noisy) / 1000
self.time = noisy # in seconds
def __init__(self, basepath, **kwargs):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
self.pf1d = pf1d(basepath)
self.pf2d = pf2d(basepath)
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
# print(self._obj.makePrmPrb.prmTemplate)
self.prmTemplate = (
"/home/bapung/Documents/MATLAB/pythonprogs/RoutineAnalysis/template.prm"
)
self.prbTemplate = (
"/home/bapung/Documents/MATLAB/pythonprogs/RoutineAnalysis/template.prb"
)
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
filePrefix = self._obj.files.filePrefix
@dataclass
class files:
stability: str = Path(str(filePrefix) + "_stability.npy")
self.files = files()
if self.files.stability.is_file():
self._load()
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
filePrefix = self._obj.files.filePrefix
@dataclass
class files:
pbe: str = Path(str(filePrefix) + "_pbe.pkl")
self.files = files()
if self.files.pbe.is_file():
self.events = pd.read_pickle(self.files.pbe)
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
filePrefix = self._obj.files.filePrefix
self._filename = Path(str(filePrefix) + "_localsleep.npy")
if self._filename.is_file():
data = np.load(self._filename, allow_pickle=True).item()
self.events = pd.DataFrame(
{key: data[key]
for key in ("start", "end", "duration")})
self.instfiringbefore = data["instfiringbefore"]
self.instfiringafter = data["instfiringafter"]
self.instfiring = data["instfiring"]
self.avglfp = data["avglfp"]
self.period = data["period"]
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)
if Path(self._obj.files.stateparams).is_file():
self.params = pd.read_pickle(self._obj.files.stateparams)
if Path(self._obj.files.states).is_file():
self.states = pd.read_pickle(self._obj.files.states)
# Adding name convention to the states
state_number_dict = {
1: "nrem",
2: "rem",
3: "quiet",
4: "active",
}
self.states["name"] = self.states["state"].map(state_number_dict)
def __init__(self, basepath):
self.recinfo = Recinfo(basepath)
self.position = ExtractPosition(self.recinfo)
self.epochs = behavior_epochs(self.recinfo)
self.artifact = findartifact(self.recinfo)
self.makePrmPrb = makePrmPrb(self.recinfo)
self.utils = SessionUtil(self.recinfo)
self.spikes = spikes(self.recinfo)
self.brainstates = SleepScore(self.recinfo)
self.swa = Hswa(self.recinfo)
self.theta = Theta(self.recinfo)
self.spindle = Spindle(self.recinfo)
self.gamma = Gamma(self.recinfo)
self.ripple = Ripple(self.recinfo)
self.placefield = pf(self.recinfo)
self.replay = Replay(self.recinfo)
self.decode = DecodeBehav(self.recinfo)
self.localsleep = LocalSleep(self.recinfo)
self.viewdata = SessView(self.recinfo)
self.pbe = PBE(self.recinfo)
self.eventpsth = event_event()
def __init__(self, basepath):
if isinstance(basepath, Recinfo):
self._obj = basepath
else:
self._obj = Recinfo(basepath)