4.1.1.1.1.3. lib.data_handling.data_preprocessing#

Module that provides functionality in order to pre-process data, here extract relevant data from input.

@author: Thomas Arne Hensel, 2023

4.1.1.1.1.3.1. Module Contents#

4.1.1.1.1.3.1.1. Classes#

Extractor

Class to extract data from files to hand the data over to the constructor class. Currently functional for phase scans.

4.1.1.1.1.3.1.2. API#

class lib.data_handling.data_preprocessing.Extractor(obj=None, collect_artefacts=True)#

Class to extract data from files to hand the data over to the constructor class. Currently functional for phase scans.

Initialization

Initialize the Extractor.

Parameters:

  • obj (str or None) – Object/file to be analyzed (either experiment-object, yaml or tif).

  • collect_artefacts (bool) – Optional boolean. If True, collect artefacts; otherwise, don’t.

_set_params(obj)#

Fetch the relevant experimental parameters from the parameter file of the measurement.

Parameters:

obj (str or None) – Object/file to be analyzed (either experiment-object, yaml or tif).

get_array_from_tif(path)#

Load a TIF image and convert it into a numpy array.

Parameters:

path (str) – Absolute path to the file.

Returns:

ndarray - Shape (2,)

get_bleach_idx(signal, segment_size=None)#

Detect bleaching steps in a single record and divide it into 2M, 1M, 0M traces.

Parameters:

  • signal (MeasurementRecord obj) – MeasurementRecord

  • segment_size (int or None) – Optional size of the segment.

Returns:

List of new records of the partial traces corresponding to 0M, 1M or 2M.

Return type:

list

_get_moving_avg_segments(imarray, block_size, batchsize, bleach_idx=None, n_cut=2)#

Process an image array. Split array into x- and y-axis. Get a moving average of the arrays with blocksize lines. Segment the averaged traces by bleaching steps.

Parameters:

  • imarray (ndarray) – 2D array from image data.

  • block_size (int) – Block size.

  • batchsize (int) – Integer, moving avg batch size.

  • bleach_idx (list or None) – Optional list of indices to segment an array by hand.

  • n_cut (int) – Number of lines to throw away before and after the bleaching step.

Returns:

List of averaged segments of shape (bleach_steps, no of axes, averaged lines) and start/end idcs of each segment (idx of line of imarray!)

Return type:

list