Phoeniks - Tutorial - Basic Extraction - Example 01
Channel: Photonics and Ultrafast Laser Science
Date: 2023-05-04

You can find phoeniks under
https://github.com/TimVog/phoeniks

Algorithm used in phoeniks:
[1] Ioachim Pupeza, Rafal Wilk, and Martin Koch, "Highly accurate optical material parameter determination with THz time-domain spectroscopy," Opt. Express 15, 4335-4350 (2007)
https://doi.org/10.1364/OE.15.004335

References to the “Total Variation”-method to extract the thickness
[2] Timothy D. Dorney, Richard G. Baraniuk, and Daniel M. Mittleman, "Material parameter estimation with terahertz time-domain spectroscopy," J. Opt. Soc. Am. A 18, 1562-1571 (2001) 
https://doi.org/10.1364/JOSAA.18.001562
[3] Maik Scheller, Christian Jansen, Martin Koch, „Analyzing sub-100-μm samples with transmission terahertz time domain spectroscopy”, Optics Communications, Vol. 282, Issue 7 (2009)
https://doi.org/10.1016/j.optcom.2008.12.061

Part of the functions to generate the artificial material are expired by Fit@TDS
[4] R. Peretti et al., "THz-TDS Time-Trace Analysis for the Extraction of Material and Metamaterial Parameters," in IEEE Transactions on Terahertz Science and Technology, vol. 9, no. 2, pp. 136-149, March 2019, 
https://doi.org/10.1109/TTHZ.2018.2889227

Fit@TDS can be found under https://github.com/THzbiophotonics/Fit-TDS

00:00 Intro
00:37 Start jupyter notebook – Option 1
01:46 Start jupyter notebook – Option 2
03:35 Start example 1 – Basic Extraction
05:40 Loading data
07:06 Create a phoeniks data-object
07:25 Create a phoeniks plot-object
08:27 Create a phoeniks extraction-object
10:28 Extract possible thickness with total variation method
11:35 Setup extraction of n and k
12:28 Run optimization (Failure)
13:54 Setup extraction of n and k with zero-padding
15:43 BONUS: Generate second derivative gaussian function and add noise
18:09 BONUS: Create artificial material
19:45 BONUS: Exporting refractive index and absorption coefficient of artificial material
20:14 BONUS: From dielectric function to a simulated sample trace
22:28 BONUS: Exporting reference and sample trace
23:04 Farewell