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poreflow.io.labview

load(filename, downsample_to_freq=5000, verbose=False)

Loads data from nanopore LabView .dat files

Loads _events from the nanopore setup that were saved as a .dat file. Expects a file that starts with an utf-8 encoded text header with measurements parameters (e.g., sample rate). This _events is then followed by binary _events of the samples.

After reading the data, it is downsampled by default. This behaviour can be turned off.

Parameters:

Name Type Description Default
filename str

Path to the .dat file

 required
downsample_to_freq (

obj:float, optional): Rate to downsample the data to. Defaults to 5000 Hz. Set to None for no downsampling.

 required

Returns:

Name Type Description
v_data ndarray

An array containing the voltage data in mV.
i_data ndarray

An array containing the current data in pA.
sfreq float

(Downsampled) sample rate in Hz
bdc float

Bias voltage DC value

metadata_from_header(s)

Converts header to a dictionary.

Converts a header with _events stored as lines "param_name=param_value;" into a dictionary with param_name as keys and param_value as values.

Parameters:

Name Type Description Default
s str

A string containing the header text.

 required

Returns:

Type Description
dict

A dictionary of the values in the header text.

read_digital(filename, verbose=False)

Returns raw data as integers

read_header(f)

Reads header.

Reads header of the .dat file. Expects the last entry in the header to be "filenum=0;"

Parameters:

Name Type Description Default
f BinaryIO

A file to read from.

 required

Returns:

Type Description
str

A string containing the header.

read_measurement_dat(filename, downsample_to_freq=5000, bfreq=None, bamp=None, verbose=False)

Reads measurement data the UTube setup and creates a raw data object. The function allows for optional downsampling of the signal to a specified frequency. It adds bias rate metadata to the raw data if parameters bfreq and bamp are specified.

Parameters:

Name Type Description Default
filename PathLike

Path to the measurement data file to be loaded.

 required
downsample_to_freq Optional[float]

Target frequency for optional downsampling. Defaults to 5000 Hz.

 5000
bfreq Optional[float]

Bias voltage frequency in Hz. Defaults to None, which corresponds to a constant voltage measurement.

 None
bamp Optional[float]

Bias voltage amplitude in mV. Defaults to None, which corresponds to a constant

 None

Returns:

Type Description
RawDataFrame

poreflow.base.Raw: A Raw object containing the processed voltage and current data.