Data Management¶

To open or save raw experimental data one can use a special module. To call functions from the module one should create a corresponding class instance.

import atomize.general_modules.csv_opener_saver as openfile
file_handler = openfile.Saver_Opener()

Alternatively, it is possible to use the CSV Exporter embedded into Pyqtgraph for saving 1D data and a special option in Liveplot (right click → Save Data Action) for saving 2D data as comma separated two dimensional numpy array.

Functions¶

open_1d(file_path, header=0)¶

open_1d(file_path, header=0)    # -> (data_header, numpy.array)

Simple function to open a specified file with comma separated values.

Argument	Description
`file_path`	Path to file
`header`	Integer specifying the number of columns in the file header

open_2d(file_path, header=0)¶

open_2d(file_path, header=0)    # -> (data_header, numpy.array)

Simple function to open a specified file with 2D array of comma separated values.

Argument	Description
`file_path`	Path to file
`header`	Integer specifying the number of columns in the file header

open_2d_appended(file_path, header=0, chunk_size=1)¶

open_2d_appended(file_path, header=0, chunk_size=1)    # -> (data_header, numpy.array)

This function opens a file with a single column array of values from 2D array.

Argument	Description
`file_path`	Path to file
`header`	Integer specifying the number of columns in the file header
`chunk_size`	Y axis size of the initial 2D array

open_file_dialog(directory='')¶

open_file_dialog(directory='')    # -> path to file.csv

This function returns the path to the file selected in the dialog box that opens.

Argument	Description
`directory`	Path to preopened directory in the dialog window

create_file_dialog(directory='')¶

create_file_dialog(directory='')    # -> path to file.csv

This function returns the path to the file specified in the dialog box that opens. It can be used to manually save your data inside the experimental script to specified file.

Argument	Description
`directory`	Path to preopened directory in the dialog window

create_file_parameters(add_name, directory='')¶

# returns two paths: file with add_name extension and file.csv
create_file_parameters('.param')

This function has the full functionality of the create_file_dialog() function, but also returns a second file for saving parameters / header.

Argument	Description
`add_name`	String that will be added to the second file instead of `'.csv'` extension. Example: `create_file_parameters('.param')` will create a second file with `.param` extension
`directory`	Path to preopened directory in the dialog window

save_header(file_path, header='', mode='w')¶

save_header(file_path, header='', mode='w')

This function saves the string given by argument header to the file with the path file_path. Argument mode allows choosing whether the file will be rewritten (mode='w') or the data will be appended to the end of the file (mode='a').

save_data(file_path, data, header='', mode='w')¶

save_data(file_path, data, header='', mode='w')

This function saves the numpy array given by the argument data and the string given by argument header to the file with the path file_path. Argument mode allows choosing whether the file will be rewritten (mode='w') or the data will be appended to the end of the file (mode='a').

This function works for 1D, 2D, and 3D data. In case of 3D (an array of 2D arrays) data, a separate file will be created for each 2D array with the additional _i string in the file_path. The standard combination of function to save the experimental data together with a header is the following:

file_data, file_param = file_handler.create_file_parameters('.param')
header = 'Test Header'
file_handler.save_header(file_param, header=header, mode='w')
# Acquiring experimental data
file_handler.save_data(file_data, data, header=header, mode='w')

Standard numpy savetxt() function¶

np.savetxt(path_to_file, data_to_save, fmt='%.4e', delimiter=' ',
           newline='n', header='field: %d' % i, footer='',
           comments='#', encoding=None)

For saving inside the script by create_file_dialog() a standard numpy function should be used.