forked from jgrewe/fishbook
653 lines
24 KiB
Python
653 lines
24 KiB
Python
from .frontend_classes import Dataset, RePro, Stimulus
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from .util import BoltzmannFit, unzip_if_needed, gaussian_kernel, zero_crossings
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import numpy as np
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import nixio as nix
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from scipy.stats import circstd
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# from scipy.optimize import curve_fit
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import os
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import subprocess
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from tqdm import tqdm
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from IPython import embed
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class BaselineData:
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"""
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Class representing the Baseline data that has been recorded within a given Dataset.
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"""
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def __init__(self, dataset: Dataset):
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self.__spike_data = []
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self.__eod_data = []
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self.__eod_times = []
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self.__dataset = dataset
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self.__repros = None
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self.__cell = dataset.cells[0] # Beware: Assumption that there is only a single cell
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self._get_data()
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def _get_data(self):
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if not self.__dataset:
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return
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self.__repros, _ = RePro.find("BaselineActivity", cell_id=self.__cell.id)
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for i in tqdm(range(len(self.__repros)), desc="loading data"):
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r = self.__repros[i]
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sd = self.__read_spike_data(r)
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if sd is not None and len(sd) > 1:
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self.__spike_data.append(sd)
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else:
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continue
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self.__eod_data.append(self.__read_eod_data(r, self.__spike_data[-1][-1]))
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def valid(self):
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# fixme implement me!
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pass
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def __read_spike_data(self, r: RePro):
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if self.__dataset.has_nix:
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return self.__read_spike_data_from_nix(r)
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else:
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return self.__read_spike_data_from_directory(r)
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def __read_eod_data(self, r: RePro, duration):
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if self.__dataset.has_nix:
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return self.__read_eod_data_from_nix(r, duration)
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else:
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return self.__read_eod_data_from_directory(r, duration)
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def __get_serial_correlation(self, times, max_lags=50):
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if times is None or len(times) < max_lags:
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return None
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isis = np.diff(times)
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unbiased = isis - np.mean(isis, 0)
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norm = sum(unbiased ** 2)
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a_corr = np.correlate(unbiased, unbiased, "same") / norm
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a_corr = a_corr[int(len(a_corr) / 2):]
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return a_corr[:max_lags]
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def serial_correlation(self, max_lags=50):
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"""
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Returns the serial correlation of the interspike intervals.
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@param max_lags: The number of lags to take into account
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@return: the serial correlation as a function of the lag
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"""
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scs = []
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for sd in self.__spike_data:
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if sd is None or len(sd) < 100:
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continue
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corr = self.__get_serial_correlation(sd, max_lags=max_lags)
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if corr is not None:
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scs.append(corr)
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return scs
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def circular_std(self):
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circular_stds = []
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for i in range(self.size):
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phases = self.__spike_phases(index=i)
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circular_stds.append(circstd(phases))
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return circular_stds
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def eod_frequency(self):
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eod_frequencies = []
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for i in range(self.size):
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eod, time = self.eod(i)
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xings = zero_crossings(eod, time, interpolate=False)
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eod_frequencies.append(len(xings)/xings[-1])
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return 0.0 if len(eod_frequencies) < 1 else np.mean(eod_frequencies)
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def __spike_phases(self, index=0): # fixme buffer this stuff
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e_times = self.eod_times(index=index)
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eod_period = np.mean(np.diff(e_times))
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phases = np.zeros(len(self.spikes(index)))
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for i, st in enumerate(self.spikes(index)):
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last_eod_index = np.where(e_times <= st)[0]
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if len(last_eod_index) == 0:
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continue
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phases[i] = (st - e_times[last_eod_index[-1]]) / eod_period * 2 * np.pi
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return phases
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def eod_times(self, index=0, interpolate=True):
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if index >= self.size:
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return None
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if len(self.__eod_times) < len(self.__eod_data):
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eod, time = self.eod(index)
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times = zero_crossings(eod, time, interpolate=interpolate)
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else:
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times = self.__eod_times[index]
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return times
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@property
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def dataset(self):
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return self.__dataset
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@property
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def cell(self):
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cells = self.__dataset.cells
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return cells if len(cells) > 1 else cells[0]
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@property
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def subject(self):
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subjects = self.__dataset.subjects
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return subjects if len(subjects) > 1 else subjects[0]
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def spikes(self, index: int=0):
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"""Get the spike times of the spikes recorded in the given baseline recording.
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Args:
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index (int, optional): If the baseline activity has been recorded several times, the index can be given. Defaults to 0.
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Returns:
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: [description]
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"""
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return self.__spike_data[index] if len(self.__spike_data) >= index else None
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def membrane_voltage(self, index: int=0):
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if index >= self.size:
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raise IndexError("Index %i out of bounds for size %i!" % (index, self.size))
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if not self.__dataset.has_nix:
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print('Sorry, this is not supported for non-nixed datasets. Implement it at '
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'fishbook.reproclasses.BaselineData.membrane_voltage and send a pull request!')
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return None, None
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else:
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rp = self.__repros[index]
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data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
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f = nix.File.open(data_source, nix.FileMode.ReadOnly)
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b = f.blocks[0]
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t = b.tags[rp.id]
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if not t:
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print("Tag not found!")
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try:
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data = t.retrieve_data("V-1")[:]
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time = np.asarray(t.references["V-1"].dimensions[0].axis(len(data)))
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except:
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data = np.empty()
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time = np.empty()
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f.close()
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return time, data
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def eod(self, index: int=0):
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eod = self.__eod_data[index] if len(self.__eod_data) >= index else None
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time = np.arange(len(eod)) / self.__dataset.samplerate
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return eod, time
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@property
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def burst_index(self):
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bi = []
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for i, sd in enumerate(self.__spike_data):
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if len(sd) < 2:
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continue
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et = self.eod_times(index=i)
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eod_period = np.mean(np.diff(et))
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isis = np.diff(sd)
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bi.append(np.sum(isis < (1.5 * eod_period))/len(isis))
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return bi
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@property
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def coefficient_of_variation(self):
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cvs = []
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for d in self.__spike_data:
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isis = np.diff(d)
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cvs.append(np.std(isis)/np.mean(isis))
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return cvs
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@property
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def vector_strength(self):
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vss = []
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spike_phases = []
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for i, sd in enumerate(self.__spike_data):
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phases = self.__spike_phases(i)
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ms_sin_alpha = np.mean(np.sin(phases)) ** 2
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ms_cos_alpha = np.mean(np.cos(phases)) ** 2
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vs = np.sqrt(ms_cos_alpha + ms_sin_alpha)
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vss.append(vs)
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spike_phases.append(phases)
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return vss, spike_phases
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@property
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def size(self):
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return len(self.__spike_data)
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def __str__(self):
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return "Baseline data of cell %s " % self.__cell.id
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def __read_eod_data_from_nix(self, r: RePro, duration) -> np.ndarray:
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data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
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if not os.path.exists(data_source):
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print("Data not found! Trying from directory")
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return self.__read_eod_data_from_directory(r, duration)
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f = nix.File.open(data_source, nix.FileMode.ReadOnly)
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b = f.blocks[0]
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t = b.tags[r.id]
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if not t:
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print("Tag not found!")
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try:
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data = t.retrieve_data("EOD")[:]
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except:
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data = np.empty()
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f.close()
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return data
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def __read_eod_data_from_directory(self, r: RePro, duration) -> np.ndarray:
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sr = self.__dataset.samplerate
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unzip_if_needed(self.__dataset.data_source, "trace-2.raw")
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eod = np.fromfile(self.__dataset.data_source + "/trace-2.raw", np.float32)
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eod = eod[:int(duration * sr)]
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return eod
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def __read_spike_data_from_nix(self, r: RePro) -> np.ndarray:
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data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
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if not os.path.exists(data_source):
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print("Data not found! Trying from directory")
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return self.__read_spike_data_from_directory(r)
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f = nix.File.open(data_source, nix.FileMode.ReadOnly)
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b = f.blocks[0]
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t = b.tags[r.id]
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if not t:
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print("Tag not found!")
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try:
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data = t.retrieve_data("Spikes-1")[:]
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except:
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data = None
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f.close()
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if len(data) < 100:
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data = None
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return data
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def __read_spike_data_from_directory(self, r) -> np.ndarray:
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data = []
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data_source = os.path.join(self.__dataset.data_source, "basespikes1.dat")
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if os.path.exists(data_source):
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found_run = False
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with open(data_source, 'r') as f:
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l = f.readline()
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while l:
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if "index" in l:
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index = int(l.strip("#").strip().split(":")[-1])
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found_run = index == r.run
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if l.startswith("#Key") and found_run:
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data = self.__do_read(f)
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break
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l = f.readline()
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if len(data) < 100:
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return None
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return np.asarray(data)
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@staticmethod
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def __do_read(f) -> np.ndarray:
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data = []
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f.readline()
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unit = f.readline().strip("#").strip()
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scale = 0.001 if unit == "ms" else 1
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l = f.readline()
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while l and "#" not in l and len(l.strip()) > 0:
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data.append(float(l.strip())*scale)
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l = f.readline()
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return np.asarray(data)
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class FIData:
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"""
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Class representing the data recorded with the relacs FI-Curve repro. The instance will load the data upon
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construction which may take a while.
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FI Data offers convenient access to the spike and local EOD data as well as offers conveince methods to get the
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firing rate and also to fit a Boltzmann function to the the FI curve.
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"""
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def __init__(self, dataset: Dataset):
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"""
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Constructor.
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:param dataset: The dataset entity for which the fi curve repro data should be loaded.
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"""
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self.__spike_data = []
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self.__contrasts = []
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self.__eod_data = []
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self.__eod_times = []
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self.__dataset = dataset
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self.__repros = None
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self.__cell = dataset.cells[0] # Beware: Assumption that there is only a single cell
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self._get_data()
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pass
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def _get_data(self):
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if not self.__dataset:
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return
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self.__repros,_ = RePro.find("FICurve", cell_id=self.__cell.id)
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for r in self.__repros:
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sd, c, eods, time = self.__read_spike_data(r)
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if sd is not None and len(sd) > 1:
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self.__spike_data.extend(sd)
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if eods:
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self.__eod_data.extend(eods)
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self.__contrasts.extend(c)
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if time:
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self.__eod_times.extend(time)
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else:
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continue
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def __read_spike_data(self, repro: RePro):
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"""
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:param repro:
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:return: spike data and the respective contrasts
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"""
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if self.__dataset.has_nix:
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return self.__read_spikes_from_nix(repro)
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else:
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return self.__read_spikes_from_directory(repro)
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def __do_read_spike_data_from_nix(self, mtag: nix.pycore.MultiTag, stimulus: Stimulus, repro: RePro):
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r_settings = repro.settings.split("\n")
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s_settings = stimulus.settings.split("\n")
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delay = 0.0
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contrast = 0.0
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for s in r_settings:
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if "delay:" in s:
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delay = float(s.split(":")[-1])
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break
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for s in s_settings:
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if "Contrast:" in s and "PreContrast" not in s and "\t\t" not in s and "+-" not in s:
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contrast = float(s.split(":")[-1])
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break
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start_time = stimulus.start_time - delay
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end_time = stimulus.start_time + stimulus.duration
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eod_da = mtag.references["LocalEOD-1"]
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start_index_eod = eod_da.dimensions[0].index_of(start_time)
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end_index_eod = eod_da.dimensions[0].index_of(end_time)
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local_eod = eod_da[start_index_eod:end_index_eod]
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spikes = self.__all_spikes[(self.__all_spikes >= start_time) & (self.__all_spikes < end_time)] - start_time - delay
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time = np.asarray(eod_da.dimensions[0].axis(end_index_eod - start_index_eod)) - delay
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return spikes, local_eod, time, contrast
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def __read_spikes_from_nix(self, repro: RePro):
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spikes = []
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eods = []
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time = []
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contrasts = []
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stimuli, count = Stimulus.find(cell_id=repro.cell_id, repro_id=repro.id)
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if count == 0:
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return spikes, contrasts, eods, time
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data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
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if not os.path.exists(data_source):
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print("Data not found! Trying from directory")
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return self.__read_spikes_from_directory(repro)
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f = nix.File.open(data_source, nix.FileMode.ReadOnly)
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b = f.blocks[0]
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self.__all_spikes = b.data_arrays["Spikes-1"][:]
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mt = None
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for i in tqdm(range(count), desc="Loading data"):
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s = stimuli[i]
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if not mt or mt.id != s.multi_tag_id:
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mt = b.multi_tags[s.multi_tag_id]
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sp, eod, t, c = self.__do_read_spike_data_from_nix(mt, s, repro)
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spikes.append(sp)
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eods.append(eod)
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time.append(t)
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contrasts.append(c)
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f.close()
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return spikes, contrasts, eods, time
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def __do_read_data_block(self, f, l):
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spikes = []
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while len(l.strip()) > 0 and "#" not in l:
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spikes.append(float(l.strip())/1000)
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l = f.readline()
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return spikes, l
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def __read_spikes_from_directory(self, repro: RePro):
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spikes = []
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contrasts = []
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times = []
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print("Warning! Exact reconstruction of stimulus order not possible for old relacs files!")
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data_source = os.path.join(self.__dataset.data_source, "fispikes1.dat")
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delay = 0.0
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pause = 0.0
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for s in repro.settings.split(", "):
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if "pause" in s:
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s = s.split(":")[-1].strip()
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pause = float(s[:-2])/1000 if "ms" in s else float(s[:-1])
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if "delay" in s:
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s = s.split(":")[-1].strip()
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delay = float(s[:-2])/1000 if "ms" in s else float(s[:-1])
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t_start = -delay
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t_end = pause + delay
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time = np.arange(t_start, t_end, 1./repro.dataset.samplerate)
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if os.path.exists(data_source):
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with open(data_source, 'r') as f:
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line = f.readline()
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fish_intensity = None
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stim_intensity = None
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while line:
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line = line.strip().lower()
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if "index" in line:
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fish_intensity = None
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stim_intensity = None
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if "intensity = " in line:
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if "true intensity = " in line:
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fish_intensity = float(line.split("=")[-1].strip()[:-2])
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elif "pre" not in line:
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stim_intensity = float(line.split("=")[-1].strip()[:-2])
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if len(line) > 0 and "#" not in line: # data line
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sp, line = self.__do_read_data_block(f, line)
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spikes.append(sp)
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times.append(time)
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contrasts.append((stim_intensity/fish_intensity-1)*100)
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continue
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line = f.readline()
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return spikes, contrasts, None, times
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@property
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def size(self) -> int:
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"""
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The number of recorded trials
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:return: An integer with the number of trials.
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"""
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return len(self.__spike_data)
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def spikes(self, index=-1):
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"""
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The spike times recorded in the specified trial(s)
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:param index: the index of the trial. Default of -1 indicates that all data should be returned.
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:return:
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"""
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if 0 <= index < self.size:
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return self.__spike_data[index]
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else:
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return self.__spike_data
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def eod(self, index=-1):
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"""
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The local eod (including the stimulus) measurement of the selected trial(s).
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:param index: the index of the trial. Default of -1 indicates that all data should be returned.
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:return: Either two vectors representing time and the local eod or two lists of such vectors
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"""
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if len(self.__eod_data) == 0:
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print("EOD data not available for old-style relacs data.")
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return None, None
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if 0 <= index < self.size:
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return self.__eod_times[index], self.__eod_data[index]
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else:
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return self.__eod_times, self.__eod_data
|
|
|
|
def contrast(self, index=-1):
|
|
"""
|
|
The stimulus contrast used in the respective trial(s).
|
|
|
|
:param index: the index of the trial. Default of -1 indicates that all data should be returned.
|
|
:return: Either a single scalar representing the contrast, or a list of such scalars, one entry for each trial.
|
|
"""
|
|
if 0 <= index < self.size:
|
|
return self.__contrasts[index]
|
|
else:
|
|
return self.__contrasts
|
|
|
|
def time_axis(self, index=-1):
|
|
"""
|
|
Get the time axis of a single trial or a list of time-vectors for all trials.
|
|
|
|
:param index: the index of the trial. Default of -1 indicates that all data should be returned.
|
|
:return: Either a single vector representing time, or a list of such vectors, one for each trial.
|
|
"""
|
|
if 0 <= index < self.size:
|
|
return self.__eod_times[index]
|
|
else:
|
|
return self.__eod_times
|
|
|
|
def rate(self, index=0, kernel_width=0.005):
|
|
"""
|
|
Returns the firing rate for a single trial.
|
|
|
|
:param index: The index of the trial. 0 <= index < size
|
|
:param kernel_width: The width of the gaussian kernel in seconds
|
|
:return: tuple of time and rate
|
|
"""
|
|
t = self.time_axis(index)
|
|
dt = np.mean(np.diff(t))
|
|
sp = self.spikes(index)
|
|
binary = np.zeros(t.shape)
|
|
spike_indices = ((sp - t[0]) / dt).astype(int)
|
|
binary[spike_indices[(spike_indices >= 0) & (spike_indices < len(binary))]] = 1
|
|
g = gaussian_kernel(kernel_width, dt)
|
|
rate = np.convolve(binary, g, mode='same')
|
|
return t, rate
|
|
|
|
def boltzmann_fit(self, start_time=0.01, end_time=0.05, kernel_width=0.005):
|
|
"""
|
|
Extracts the average firing rate within a time window from the averaged across trial firing rate.
|
|
The analysis time window is specified by the start_time and end_time parameters. Firing rate is estimated by
|
|
convolution with a Gaussian kernel of a given width. All parameters are given in 's'.
|
|
|
|
:param start_time: the start of the analysis window.
|
|
:param end_time: the end of the analysis window.
|
|
:param kernel_width: standard deviation of the Gaussian kernel used for firing rate estimation.
|
|
:return: object of type BoltzmannFit
|
|
"""
|
|
contrasts = np.zeros(self.size)
|
|
rates = np.zeros(self.size)
|
|
for i in range(self.size):
|
|
contrasts[i] = np.round(self.contrast(i))
|
|
t, r = self.rate(i, kernel_width)
|
|
rates[i] = np.mean(r[(t >= start_time) & (t < end_time)])
|
|
|
|
boltzmann_fit = BoltzmannFit(contrasts, rates)
|
|
return boltzmann_fit
|
|
|
|
|
|
class FileStimulusData:
|
|
"""The FileStimulus class provides access to the data recorded and the stimulus presented (if accessible)
|
|
during runs of the FileStimulus repro. Since the FileStimulus repro can put out any stimulus this class does not
|
|
provide any further analyses.
|
|
|
|
As any other relacs class it is instantiated with a Dataset entity.
|
|
"""
|
|
def __init__(self, dataset: Dataset):
|
|
"""
|
|
Constructor.
|
|
|
|
Args
|
|
fishbook.Dataset: The dataset entity for which the filestimulus repro data should be loaded.
|
|
"""
|
|
self.__spike_data = []
|
|
self.__contrasts = []
|
|
self.__stimuli = []
|
|
self.__dataset = dataset
|
|
self.__repros = None
|
|
self.__cell = dataset.cells[0] # Beware: Assumption that there is only a single cell
|
|
self._get_data()
|
|
|
|
def _get_data(self):
|
|
if not self.__dataset:
|
|
return
|
|
self.__repros, _ = RePro.find("FileStimulus", cell_id=self.__cell.id)
|
|
for r in self.__repros:
|
|
sd, c, stims = self.__read_spike_data_from_nix(r) if self.__dataset.has_nix else self.__read_spike_data_from_directory(r)
|
|
if sd is not None and len(sd) > 1:
|
|
self.__spike_data.extend(sd)
|
|
self.__contrasts.extend(c)
|
|
self.__stimuli.extend(stims)
|
|
else:
|
|
continue
|
|
|
|
def __do_read_spike_data_from_nix(self, mt: nix.pycore.MultiTag, stimulus: Stimulus, repro: RePro):
|
|
spikes = None
|
|
contrast = 0.0
|
|
stim_file = ""
|
|
|
|
r_settings = repro.settings.split("\n")
|
|
s_settings = stimulus.settings.split("\n")
|
|
delay = 0.0
|
|
for s in r_settings:
|
|
if "delay:" in s:
|
|
delay = float(s.split(":")[-1])
|
|
break
|
|
start_time = stimulus.start_time - delay
|
|
end_time = stimulus.start_time + mt.extents[stimulus.index]
|
|
contrast = 0.0 # this is a quick fix!!!
|
|
embed()
|
|
for s in s_settings:
|
|
if "Contrast:" in s and "PreContrast" not in s and "\t\t" not in s and "+-" not in s:
|
|
contrast = float(s.split(":")[-1])
|
|
break
|
|
|
|
return spikes, contrast, stim_file
|
|
|
|
|
|
|
|
|
|
local_eod = eod_da[start_index_eod:end_index_eod]
|
|
spikes = self.__all_spikes[(self.__all_spikes >= start_time) & (self.__all_spikes < end_time)] - start_time - delay
|
|
time = np.asarray(eod_da.dimensions[0].axis(end_index_eod - start_index_eod)) - delay
|
|
return spikes, local_eod, time, contrast
|
|
|
|
return spikes, contrast, stim_file
|
|
|
|
def __read_spike_data_from_nix(self, repro: RePro):
|
|
spikes = []
|
|
contrasts = []
|
|
stim_files = []
|
|
stimuli = Stimulus.find(cell_id=repro.cell_id, repro_id=repro.id)
|
|
if len(stimuli) == 0:
|
|
return spikes, contrasts, stim_files
|
|
data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
|
|
if not os.path.exists(data_source):
|
|
print("Data not found! Trying from directory")
|
|
return self.__read_spike_data_from_directory(repro)
|
|
f = nix.File.open(data_source, nix.FileMode.ReadOnly)
|
|
b = f.blocks[0]
|
|
self.__all_spikes = b.data_arrays["Spikes-1"][:]
|
|
mt = None
|
|
for i in tqdm(range(len(stimuli)), desc="Loading data"):
|
|
s = stimuli[i]
|
|
if not mt or mt.id != s.multi_tag_id:
|
|
mt = b.multi_tags[s.multi_tag_id]
|
|
sp, c, stim = self.__do_read_spike_data_from_nix(mt, s, repro)
|
|
spikes.append(sp)
|
|
contrasts.append(c)
|
|
stim_files.append(stim)
|
|
f.close()
|
|
return spikes, contrasts, stim_files
|
|
|
|
def __read_spike_data_from_directory(self, repro: RePro):
|
|
print("not yet my friend!")
|
|
spikes = []
|
|
contrast = 0.0
|
|
stim = None
|
|
|
|
return spikes, contrast, stim
|
|
|
|
def read_stimulus(self, index=0):
|
|
pass
|
|
|
|
|
|
if __name__ == "__main__":
|
|
# dataset = Dataset(dataset_id='2011-06-14-ag')
|
|
dataset = Dataset(dataset_id="2018-09-13-ac-invivo-1")
|
|
# dataset = Dataset(dataset_id='2013-04-18-ac')
|
|
fi_curve = FileStimulusData(dataset)
|
|
embed()
|