locpix.preprocessing.functions.file_to_datastruc#

file_to_datastruc(input_file, file_type, dim, channel_col, frame_col, x_col, y_col, z_col, channel_choice=None, channel_label=None)[source]#

Loads in .csv or .parquet and converts to the required datastructure.

Currently considers the following columns: channel frame x y z Also user can specify the channels they want to consider, these should be present in the channels column

Parameters:
  • input_file (string) – Location of the file

  • file_type (string) – Either csv or parquet

  • save_loc (string) – Location to save datastructure to

  • dim (int) – Dimensions to consider either 2 or 3

  • channel_col (string) – Name of column which gives channel for localisation

  • frame_col (string) – Name of column which gives frame for localisation

  • x_col (string) – Name of column which gives x for localisation

  • y_col (string) – Name of column which gives y for localisation

  • z_col (string) – Name of column which gives z for localisation

  • channel_choice (list of ints) – If specified then this will be list of integers representing channels to be considered

  • channel_label (list of strings) – If specified then this is the label for each channel i.e. [‘egfr’, ‘ereg’,’unk’] means channel 0 is egfr protein, channel 1 is ereg proteins and channel 2 is unknown

Returns:

Datastructure containg the data

Return type:

datastruc (SMLM_datastruc)