lab-codes

InstrumentProcessing

This notebook processes the input data collected from an electrochemical probe. The workflow is the same as the original MATLAB code kept in the first commit to this repository.

Getting started

1. You will need to clone this repository to obtain the notebook and library code.

   git clone git@github.com:LabSOIL/lab-codes.git

2. With Python installed on your computer, make sure poetry is installed

   pip install poetry

3. In the same folder as the repository that was cloned, install the environment

   poetry install

4. Run jupyter notebook within the environment

   poetry run jupyter notebook

Process

1. Place the input data from the instrument somewhere in relation to the repository folder that we are in such as in the same folder or within another folder such as input. For the purpose of this demonstration, we can use the data included in the test directory of the repository.

2. Execute the first cell. This will read the CSV data with the pd.read_csv() function and generate the plots for each measurement. Here you can select the points to perform baseline filtering. By default it will be linear, but as mentioned this can be changed to other interpolation methods such as cubic, quadratic.

   

3. Click on enough points along the line to generate the spline. After each new point, the spline (red) will update, and the filtered baseline is shown in grey. To remove a point you can click it again (but you may need to zoom in to do this).

4. The resulting measurements will be plotted on the final plot. Check this is satisfactory before moving on, if any changes to the baseline need to happen after moving on, they will all need to be done again.

   

5. In the next cell, enter the amount of samples collected in the data in the samples variables. Execute the next cell. A plot for each measurement will be generated where you will need to choose the start and end points of each measurement on all of the plots.

   The area between the selected points will be integrated.

   You will only be allowed to select a pair of points for the number of samples that was entered. Again, to remove a point, click it a second time.

   

6. Finally, execute the last cell and the data, and plots will be saved to the output folder.

To run tests

To run the test suite, from the root directory, execute:

poetry run pytest