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API reference

DKim edited this page Sep 6, 2024 · 1 revision

ephys.catgt

  • This module provides functionality for working with CatGT, a tool for processing electrophysiology data.

ephys.catgt.run_catgt(path=None)

  • Runs CatGT to process data.

ephys.spikeglx

  • This module provides functions to read and plot SpikeGLX data.

ephys.spikeglx.read_analog(filename, dtype, channel_idx, sample_range)

  • Reads analog data from a SpikeGLX file.

ephys.spikeglx.read_digital(filename, dtype)

  • Reads digital data from a SpikeGLX file.

ephys.spikeglx.plot_analog(filename, channel_idx, initial_sample_range)

  • Plots analog data from a SpikeGLX file.

ephys.spikeglx.read_meta(filename)

  • Reads metadata from a SpikeGLX file.

ephys.spikeglx.plot_chanmap(filename)

  • Plots the channel map from a SpikeGLX file.

ephys.ks

  • This module provides functions to run and manage Kilosort.

ephys.ks.run_ks4(path=None, settings=None)

  • Runs Kilosort4 to process data.

ephys.ks.Kilosort(path=None)

  • Class to manage Kilosort data and operations.
  • load_meta()
  • load_kilosort()
  • load_waveforms()
  • load_sync()
  • save()
  • plot()

ephys.bmi

  • This module provides functions to manage BMI data.

ephys.bmi.BMI(path=None, pattern=r'.prb$')

  • Class to manage BMI data and operations.
  • load_prb()
  • plot_prb()
  • load_mua()
  • save_mua()
  • plot_mua()
  • load_spk()
  • load_spk_wav()
  • load_fet()
  • load_model()
  • load_nidq()
  • save_meta()
  • save_catgt()
  • save_nidq()

ephys.spike

  • This module provides functions to manage and analyze spike data.

ephys.spike.Spike(path)

  • Class to manage spike data and operations.
  • plot(event=None)
  • get_raster()
  • get_spike_bin()
  • smooth()
  • get_psth()
  • plot_raster_psth()
  • get_latency()

ephys.utils

  • This module provides utility functions.

ephys.utils.tprint(text)

  • Prints text with a timestamp.

ephys.utils.finder()

  • Finds files or directories.

ephys.utils.confirm(message, default=False)

  • Asks for user confirmation.

ephys.utils.file_reorder(file_list)

  • Reorders a list of files.

ephys.utils.savemat_safe(fn, data)

  • Safely saves data to a .mat file.

ephys.utils.sync(time_a, time_b)

  • Synchronizes two time arrays.

ephys.tdms

  • This module provides functions to read and save TDMS data.

ephys.tdms.read_tdms(tdms_fn, threshold)

  • Reads TDMS data.

ephys.tdms.save_tdms(tdms_fns)

  • Saves TDMS data.