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.本仓库包含《基于复折射率模型的颗粒悬浮液光学干涉多参数流动传感》一书第4章的相关数据。本仓库涵盖原始数据、处理后数据、可视化图表以及用于生成这些图表的Python脚本。本数据集对应两项实验：针对100 nm二氧化硅颗粒的动态光散射（Dynamic Light Scattering, DLS）与透射实验，以及pH值逐渐降低的流动脂肪乳（Intralipid）延时测量实验。 ## 数据 ### 二氧化硅颗粒测量 原始数据存储于"raw data silica"文件夹中。该文件夹下包含6个以日期命名的子文件夹（例如20240220），内部存放实验过程中采集的原始数据。透射实验数据存储于.h5格式文件中，文件名与流速对应，文件名末尾数字为测量序号。此类文件包含实测透射光谱、参考光谱与干涉光谱，以及曝光时长等元数据。由于需以去离子水进行校准，各次测量对应的纯水校准测量的.h5文件路径记录于"calibrationMeasurements.txt"文件中。 示波器采集的数据存储于"scope"子文件夹中，所有示波器数据文件名均包含"NewFile"字样，该命名规则便于实验过程中快速存储文件。实验流速信息存储于"flowRates.txt"文件中，该文件各列依次为：示波器数据文件名、对应流速、本次DLS测量对应的透射测量文件、以及样品序号。 文件夹"referenceBackground"包含5次暗环境下的示波器测量数据。检测到的噪声存在微弱相关性，该数据将用于从实测DLS自相关曲线中扣除背景噪声。 针对二氧化硅颗粒测量，需计算示波器数据的自相关曲线，并将其与透射数据合并，合并后的数据存储于"100nm"文件夹中。 "raw data silica"文件夹还包含用于多普勒角度测量的比色皿照片，但该数据未被使用，实际采用拟合方法替代。 ### 脂肪乳（Intralipid）测量 脂肪乳实验的原始数据存储方式与二氧化硅颗粒测量一致。 ## 脚本文件 DLS示波器数据的合并工作通过mergeH5File.py脚本完成，该脚本可计算自相关曲线，并基于flowRates.txt文件将其与透射数据进行合并。合并后的h5文件将通过silica.py脚本进行进一步处理。数据合并与脂肪乳测量的分析工作均通过intralipid.py脚本完成。上述两个脚本的输出结果存储于"data figures"文件夹中。第4章的可视化图表通过plotFigures.py脚本生成。 上述脚本依赖若干通用功能函数，这些函数存储于spectralOCTAnalysis文件夹中，涵盖傅里叶分析、相关性散射模型与色散公式等内容。 ## 数据采集软件 图形用户界面（GUI）与数据采集软件存储于octViewer文件夹中，该软件附带独立的自述文件。