Optical interferometric spectral and dynamic multi-parameter flow sensing - data and analysis

This repository contains the data of Chapter 4 of "Optical interferometric multi-parameter flow sensing of particle suspensions with complex refractive index models". This repository contains the raw data, processed data, figures and the Python scripts to generate them. The data is for two experiments: DLS and transmission experiments for 100 nm silica particles, and a time-lapse measurement of flowing Intralipid with a gradually decreasing pH. 

Data

Silica measurement

The raw data is stored in the folder "raw data silica". In this folder there are six folders with a date as filename, such as 20240220. These folders contain the data as taken during the measurement. The transmission data is stored in the .h5 files. The file names correspond to the flow rates, with the last digits the measurement number. These files contain the measured transmission spectra, the reference spectra and the interference spectra, as well as the metadata, such as the exposure time. Since a calibration with water is necessary, the .h5 file of the calibration water measurement that belongs to each measurement is stored in the file "calibrationMeasurements.txt".

The data as measured with the oscilloscope is stored in the "scope" subfolders. All oscilloscope file names contain the letters "NewFile". This is how the files could be quickly stored during the measurements. The flow rates of the measurement is stored in the file "flowRates.txt". In this file, the first column is the scope data file, the second column is the flow rate, the third column is the transmission measurement that belongs to this particular DLS measurement, and the fourth and last column is the sample number.

The folder referenceBackground contains five scope measurements in a dark measurement. A small correlation in the detected noise was detected and subtracted from the measured DLS autocorrelation.

For the silica measurements, the autocorrelation of the scope data is calculated and merged with the transmission data. These files are stored in the folder "100nm".

The folder "raw data silica" also contains a photograph of the cuvette for the Doppler angle measurement. This is not used, a fit is used instead.

Intralipid measurement

The raw data of the Intralipid measurement is stored similarly as the silica measurement. The raw data is stored

Scripts

The merging of the DLS oscilloscope data is done with the mergeH5File.py script. This scripts calculates the autocorrelation, and merges it with the transmission files, based on the flowRates.txt files. These merged h5 files are further processed with the silica.py script. Both the merging of the data and the analysis of the Intralipid measurement is done with the intralipid.py script. The output of these latter two scripts is stored in the "data figures" folder. The figures of Chapter 4 are created in the plotFigures.py script. 

The scripts above use some standard functions. These are stored in the spectralOCTAnalysis folder. These contain the Fourier analysis, dependent scattering models, and dispersion formulas. 

Data acquisition software

The GUI and data acquisition software is stored in the octViewer folder. This software contains its own readme file.