2. configuration¶

class pyIMD.configuration.config.Settings¶

Bases: object

Settings initialization with default parameter values stored in pyIMD.configuration.defaults

calculation_mode¶

Parameter defining the calculation mode.

Parameters:	mode (str) – The calculation mode. PLL, Cont.Sweep or Auto.

cantilever_length¶

Parameter defining the cantilever length.

Parameters:	cantilever_length (float) – Cantilever length in microns.

cell_position¶

Parameter defining the cell position offset.

Parameters:	cell_position (float) – Cell position offset in microns from the free end of the cantilever.

conversion_factor_deg_to_rad¶

Parameter defining the data conversion factor from degrees to radians.

Parameters:	factor (float) – Data conversion factor from degrees to radians.

conversion_factor_hz_to_khz¶

Parameter defining the data conversion factor from Hz to kHz.

Parameters:	factor (float) – Data conversion factor from hertz to kilo hertz.

correct_for_frequency_offset¶

Parameter defining if PLL measurement data should be corrected for a potential frequency offset between the frequency pre start measured after a cell is attached to the cantilever and the actual measurement.

Parameters:	correction (boolean) – Boolean. False by default. True runs in the PLL case a frequency offset correction.

figure_format¶

Parameter defining the result figure(s) format.

Parameters:	unit (str) – Pdf and png ar currently supported.

figure_height¶

Parameter defining the result figure(s) height.

Parameters:	height (float) – Figure height in the unit specified.

figure_name_measured_data¶

Parameter defining the figure name for resulting calculated mass of the measured data.

Parameters:	name (str) – Figure name for resulting calculated mass of the measured data.

figure_name_pre_start_no_cell¶

Parameter defining the figure name for the function fit pre start no cell.

Parameters:	name (str) – Figure name for the function fit pre start no cell.

figure_name_pre_start_with_cell¶

Parameter defining the figure name for the function fit pre start with cell.

Parameters:	name (str) – Figure name for the function fit pre start with cell.

figure_plot_every_nth_point¶

Parameter defining how many data points are used for visualization. For very large data sets a number > 1 could increase the readability of the figure and lower the file size.

Parameters:	nth_point (int) – Pdf and png ar currently supported.

figure_resolution_dpi¶

Parameter defining the result figure(s) resolution in dpi.

Parameters:	resolution (int) – Figure resolution. E.g. 72, 150, 300.

figure_units¶

Parameter defining the result figure(s) unit.

Parameters:	unit (str) – Figure unit. E.g. mm, cm, in.

figure_width¶

Parameter defining the result figure(s) width.

Parameters:	width (float) – Figure width in the unit specified.

frequency_offset¶

Parameter defining the frequency offset.

Parameters:	freq_offset (int) – Frequency offset with which the measurement data will be corrected with.

frequency_offset_mode¶

Parameter defining the mode to be used to calculate the frequency offset. This applies only to in PLL recorded data.

Parameters:	mode (str) – Mode for frequency offset calculation. Either Auto or Manual.

frequency_offset_n_measurements_used¶

Parameter defining how many data points of the measurement should be used to calculate the average frequency offset.

Parameters:	n_measurements (int) – Number of measurement data points to be used to calculate the average freq. offset.

initial_parameter_guess¶

Parameter defining the initial parameter guess.

Parameters:	array (list) – Initial parameter guess.

lower_parameter_bounds¶

Parameter defining the lower parameter bounds.

Parameters:	array (list) – Lower parameter bounds.

measurements_path¶

Parameter defining the path to the measurement file.

Parameters:	path (str) – Path to the measurement file. (.tdms or .txt file).

new_pyimd_project(pre_start_no_cell_path, pre_start_with_cell_path, measurements_path, text_data_delimiter, read_text_data_from_line, calculation_mode, **kwargs)¶

Create a new pyIMD project with the following arguments. Two modes enable the analysis of different experimental setups. PLL mode and Cont.Sweep mode. For more information please read the documentation.

Parameters:

pre_start_no_cell_path (str) – File path + file name of initial frequency shift measurement before cell attachment (txt file).
pre_start_with_cell_path (str) – File path + file name of initial frequency shift measurement after cell attachment (txt file).
measurements_path (str) – File path + file name of the actual measurement (tdms file (default) or txt file).
text_data_delimiter (str) – Text file data delimiter i.e ‘ ‘ for tab delimited or ‘,’ for comma separated data.
read_text_data_from_line (int) – Line number from which data of pre start measurements should be read. Typically the first few lines contain header information and no data.
calculation_mode (str) – PLL := phase lock loops mode Cont.Sweep := sweep mode Auto := Auto detection of the mode (experimental)

Keyword Arguments:

figure_width (float) – Width of result figures
figure_height (float) – Height of result figures
figure_units (str) – Figure units i.e cm, inch
figure_format (str) – Figure format i.e png or pdf
figure_resolution_dpi (int) – Resolution of result figures in dpi
figure_name_pre_start_no_cell (str) – Figure name of function fit for pre start with no cell loaded data
figure_name_pre_start_with_cell (str) – Figure name of function fit for pre start with cell loaded data
figure_name_measured_data (str) – Figure name of the resulting mass of the measured data
figure_plot_every_nth_point ('int') – Parameter defining how many data points will be plotted. For large data stets to increase readability and reducing file size.
conversion_factor_hz_to_khz (float) – Conversion factor to convert from hertz to kilo hertz
conversion_factor_deg_to_rad (float) – Conversion factor to convert from degrees to radian
spring_constant (float) – Spring constant value of the cantilever
initial_parameter_guess (list) – Initial parameter guess
lower_parameter_bounds (list) – Lower parameter bounds
upper_parameter_bounds (list) – Upper parameter bounds
rolling_window_size ('int') – Window size for calculating the rolling average.
correct_for_frequency_offset ('bool') – Correct for potential frequency offset during PLL mode.
frequency_offset_mode ('str') – Frequency offset correction mode (Auto or Manual)
frequency_offset_n_measurements_used ('int') – Number of measurement data points to be used for automatic frequency offset correction
frequency_offset ('float') – Frequency offset either set manually or calculated automatically
cantilever_length (float) – Cantilever length in microns
cell_position (float) – Cell position offset from cantilever tip in microns
project_folder_path (str) – Path to project data files. Also used to store pyIMD results such as data and figures.

pre_start_no_cell_path¶

Parameter defining the path to the pre start no cell file.

Parameters:	path (str) – Path to the pre start no cell file (.txt).

pre_start_with_cell_path¶

Parameter defining the path to the pre start with cell file.

Parameters:	path (str) – Path to the pre start with cell file (.txt).

project_folder_path¶

Parameter defining the path to the files.

Parameters:	path (str) – The path to the files.

read_pyimd_project(file_path)¶

Read a pre defined pyIMD project form a XML file from disk.

Parameters:	file_path (str) –
Returns:	String reporting the success of failure of loading a pyIMD project.
Return type:	status (str)

read_text_data_from_line¶

Parameter defining the length of the header inside the initial sweep files. From this line number the data will be imported.

Parameters:	line_number (int) – Line number from where on to read the data from.

rolling_window_size¶

Parameter defining the window size of the rolling window applied to the data for visualizing the trend.

Parameters:	window_size (int) – Rolling window size.

selected_files¶

Parameter defining the selected files for calculation.

Parameters:	files (list) – Selected files for calculation.

spring_constant¶

Parameter defining the spring constant of the cantilever.

Parameters:	spring_constant (float) – Spring constant of the cantilever.

text_data_delimiter¶

Parameter defining the text file data delimiter.

Parameters:	delimiter (str) – Text file data delimiter i.e ‘ ‘ for tab delimited or ‘,’ for comma separated data.

upper_parameter_bounds¶

Parameter defining the upper parameter bounds.

Parameters:	array (list) – Upper parameter bounds.

write_pyimd_project(file_path)¶

Write the current pyIMD project as XML file to disk. :param file_path: :type file_path: str

Returns:	String reporting the success of failure of loading a pyIMD project.
Return type:	status (str)