MatrixStaff

Some tools for work with data from Matrix (Omicron SPM). I worked on Omicron VT650 (Scienta Omicron) and write some tools for analyze data. I will be happy, if something will be useful for you.

• MatrixDirStat - generate table with all parameters for each data file in experiment.
• StepByStepСVCAnalize - I analyzed many Current–voltage characteristic, their derivative and plotted the maps of them.

Some of that code was used for my PhD Thesis (PhD summary, Thesis in Ru), and for some publication: for Example: Lebedev, Denis V., et al. "Nanoscale Electrically Driven Light Source Based on Hybrid Semiconductor/Metal Nanoantenna." The Journal of Physical Chemistry Letters 13 (2022): 4612-4620. DOI:10.1021/acs.jpclett.2c00986 IF:6.38 Q1

(Some code was writen in 2017, and I think, i can use not the best solutions.)

MatrixDirStatGUI.py

This small program scan directory with experiment results of Matrix (Omicron SPM, Scienta Omicron) and save xlsx-table with names and parameters of all files. I prefer pure python, and use DirStat.py without GUI. Before the using, check all paths. In my project I used such tree:

.
└── ProjectName
    ├── ...
    ├── ExpData
    │   └── OmicronResults
    │       ├── ...
    │       ├── 2022-04-29
    │       ├── 2022-07-28
    │       └── 2022-08-13
    ├── WorkWithData
    │   └── 2022-04-29
    └── ..

Requirements

For this tool, you need to install:

• access2thematrix
• xlsxwriter
• PyQT6 (for GUI)

StepByStepСVCAnalize.py

I analyzed many Current–voltage characteristic, their derivative and plotted the maps of them. Maybe, you can find some useful code for Current–voltage characteristic analyze. I try to highlight some functions:

• GetDataAsDataset() - work in pair with GetFileList(). It transforms measurements to pandas's Dataframe.
• ShowMap() - Shows a scan with points, where was measured CVC
• Calcd2idv2map() - Calculate the 2nd derivative and plot "finger-print" map

ScanQEAnalize

This script need for evaluation of estimated quantum efficiency of STM-Light Emission process.

1. It get topography (Z channel), Current-maps (I channel), Light-emission map (Aux chanel).
2. Convert Volts of Aux to counts
3. Divide Aux map in I-map
4. Mupltiply on specific value (etta), which correspond to light collection efficiency

QEbyMap(ed,NNN,DACmax=5000,direct='forward/up') - main function

ed - day of the experiment, NNN - run number of intrested scan DACmax - correspond to maximum photons count when DAC give maximum (5V) on Aux if not specified, the script try read log of Pulses (see another project) (it need some fixes) direct - direction of scan.

This function create Gwiddion file with results.

shift5(...) and findTdelta(...)

shift

Be prevented. If you use DAC such as mine, you may have a little delay between Z,I... and Aux-signal. It was provided by time, which need for collecting of pulses from photon counter and give it for Omicron CU. Usually, i use DAC's integration equal 10ms, and T_rast = 1...10 ms. It provide zero-like filling on the edge of data array. If you are nerd, you can found data from scan with another scan dirrection.

findTdelt

Search of delay by fft.

GetAparams(..)

Try to find the corresponding pulse log, and read DAC params

CurveQEA()

Script to analize QE during of current-voltage characteristics (or V-sweeep).

MySpecFunc

The file with usefull function for working with spectra It use this lib https://github.com/rohanisaac/spc, but with some fixes for Python3 working. You find this lib in project. (I'm not sure in source link) Functions:

• GetFolderStat - simple version of MatrixDirStat.py
• workWithSpcZip() - if you measure a lot of spectra you can store in zip-file, and unpack on-demand in /tmp
• get_match_filenames(...) - search files with pattern in name
• loadspc(...) - reader of spc-spectrum from SPC to turple.
• AndourQE() - Quantum efficiency of my Andour CCD
• HFF() - if I not mistake, it is hardware function for LabRam HR800 with NIR50x0.42 Mitutoyo objective, and some mirrors. It was TriOS by AIST-NT. It was calculated by experiment with black-body radiation like lamp. It include Andour CCD QE.
• gauss_function(shift,area,centre,width)
• TrC(...) spectra processing function.
• loadPulseLog() - read file with pulse counter log and return some stat
• loadxy() - usefull function for read text data from Aist, Gwiddion, OceanInsight (OceanOptics).
  • also, it can remove spikes from not narrow spectrum
• GaussFit() - gaussian fitting of data with 1 guass function
• PlotProcessing - processing of optical spectrum
• coma2point() - just replace coma to point in txt file
• p2c() - some, but replace points to comas