ivneuro.nex.pull_nex_data

A module with functions for extracting data from nex5 files.

Attributes

reader

Functions

make_timestamps_Nex_cont(var)

pull_fp(fileData[, FP_of_interest])

Extract field potential variables from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

pull_events(fileData[, events_of_interest])

Extract events from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

pull_continuous(fileData[, continuous_of_interest])

Extract all continuous variables, except for field potential variables, from a Nex5 file data previously created using reader.ReadNex5File(<filename>).

pull_neurons(fileData[, neurons_of_interest])

Extract neurons from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

pull_markers(fileData[, markers_of_interest])

Extract markers from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

pull_centroids(fileData[, centroids_of_interest])

Extract field potential variables from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

Module Contents

ivneuro.nex.pull_nex_data.reader
ivneuro.nex.pull_nex_data.make_timestamps_Nex_cont(var)
ivneuro.nex.pull_nex_data.pull_fp(fileData, FP_of_interest=[])

Extract field potential variables from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

It assumes that “FP” will be in the name of every field potential variable, which is true for Nex files whose original variables names have not been modified. Therefore, restults of this function might be incorrect for files whose variable names have been modified. It also assumes all field potential variables have the same timestamps and sample rate.

Parameters:

  • fileData (dict) – Data extracted from a nex5 file using reader.ReadNex5File(<filename>).

  • FP_of_interest (list, optional) – List of names of field potentials to extract. If None, the function returns None; if an empty list, all the field potentials are extracted. The default is [].

  • Returns

  • index. (Dataframe with field potentials (in mV) in each column and timestaps as)

  • (float). (Sampling rate of local field potentials)

ivneuro.nex.pull_nex_data.pull_events(fileData, events_of_interest=[])

Extract events from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

Parameters:

  • fileData (dict) – Data extracted from a nex5 file using reader.ReadNex5File(<filename>).

  • events_of_interest (list, optional) – List of names of events to extract. If None, the function returns None; if an empty list, all the events are extracted. The default is [].

Return type:

Dictionary with event names as keys and list of timestamps as values.

ivneuro.nex.pull_nex_data.pull_continuous(fileData, continuous_of_interest=[])

Extract all continuous variables, except for field potential variables, from a Nex5 file data previously created using reader.ReadNex5File(<filename>).

It assumes that “FP” will be in the name of every field potential variable, which is true for Nex files whose original variables names have not been modified. Therefore, restults of this function might be incorrect for files whose variable names have been modified.

Parameters:

  • fileData (dict) – Data extracted from a nex5 file using reader.ReadNex5File(<filename>).

  • continuous_of_interest (list, optional) – List of names of continuous to extract. If None, the function returns None; if an empty list, all non-field potential continuous variables are extracted. The default is [].

Return type:

List of pandas DataFrame, each corresponding to a continuous variable values and timestaps as index.

ivneuro.nex.pull_nex_data.pull_neurons(fileData, neurons_of_interest=[])

Extract neurons from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

Parameters:

  • fileData (dict) – Data extracted from a nex5 file using reader.ReadNex5File(<filename>).

  • neurons_of_interest (list, optional) – List of names of events to extract. If None, the function returns None; if an empty list, all the neurons are extracted. The default is [].

Return type:

Dictionary with neuron names as keys and list of timestamps as values.

ivneuro.nex.pull_nex_data.pull_markers(fileData, markers_of_interest=[])

Extract markers from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

Parameters:

  • fileData (dict) – Data extracted from a nex5 file using reader.ReadNex5File(<filename>).

  • markers_of_interest (list, optional) – List of names of markers to extract. If None, the function returns None; if an empty list, all the markers are extracted. The default is [].

Return type:

Dictionary with markers names as keys and list of timestamps as values.

ivneuro.nex.pull_nex_data.pull_centroids(fileData, centroids_of_interest=[])

Extract field potential variables from a Nex5 file data, previously created using reader.ReadNex5File(<filename>).

It assumes that “centroid” (case insensitive) will be in the name of every centroid variable, which is true for Nex files whose original variables names have not been modified. It also exclude field potential variables that contain the string “FP” in their names. Therefore, restults of this function might be incorrect for files whose variable names have been modified. It also assumes that all centroids have the same timestamps.

Parameters:

  • fileData (dict) – Data extracted from a nex5 file using reader.ReadNex5File(<filename>).

  • centroids_of_interest (list, optional) – List of names of centroids to extract. If None, the function returns None; if an empty list, all centroid variables are extracted. The default is [].

Return type:

Dataframe with centroids in each column and timestaps as index.