[Introduction]  [Signal arithmetic]  [Signals and noise]   [Smoothing]   [Differentiation]  [Peak Sharpening]  [Harmonic analysis]   [Fourier convolution]  [Fourier deconvolution]  [Fourier filter]   [Peak area measurement]  [Linear Least Squares]  [Multicomponent Spectroscopy]  [Iterative Curve Fitting]  [Hyperlinear quantitative absorption spectrophotometry] [Appendix and Case Studies]  [Peak Finding and Measurement]  [iPeak]   [iSignal]  [Peak Fitters]   [iFilter]  [iPower]  [List of downloadable software]  [Interactive tools]

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[Coverage]   [Software requirements]   [References]

The interfacing of measurement instrumentation to small computers for the purpose of online data acquisition has now become standard practice in the modern laboratory for the purposes of performing signal processing and data analysis and storage, using a large number of digital computer-based numerical methods that are used to transform signals into more useful forms, detect and measure peaks, reduce noise, improve the resolution of over-lapping peaks, compensate for instrumental artifacts, test hypotheses, optimize measurement strategies, diagnose measurement difficulties, and decompose complex signals into their component parts. These techniques can often make difficult measurements easier by extracting more information from the available data. Many of these techniques are based on laborious mathematical procedures and/or analog electronics that were not really practical before the advent of computerized instrumentation.
It is important to appreciate the abilities, as well as the limitations, of these techniques. But in recent decades, computers and digital storage and processing has become almost commonplace, much more accurate, far less costly, easier to program, and literally millions of times more capable altogether, reducing the cost of raw data and making complex computer-based signal processing techniques both more practical and necessary. It's not just the growth of computers: there are now new materials, new instruments, new fabrication techniques, new automation capabilities. We have lasers, fiber optics, superconductors, supermagnets, holograms, quantum technology, nanotechnology, and more. Sensors are now smaller and cheaper and faster than ever before; we can measure over a wider range of speeds, temperatures, pressures, and locations. There are new kinds of data that we never had before. As Erik Brynjolfsson and Andrew McAfee wrote in The Second Machine Age (W. W. Norton, 2014): "...many types of raw data are getting dramatically cheaper, and as data get cheaper, the bottleneck increasingly is the ability to interpret and use data".

This essay covers only basic topics related to one-dimensional time-series signals, not two-dimensional data such as images. It uses a pragmatic approach and is limited to mathematics only up to the most elementary aspects of calculus, statistics, and matrix math. For the math phobic, you should know that this essay does not dwell on the math and that it contains more than twice as many figures as equations. Data processing without math? Not really! Math is essential, just as it is for the technology of cell phones, GPS, digital photography, the Web, and computer games. But you can get started using these tools without understanding all the underlying math and software details. Seeing it work makes it more likely that you'll want to understand how it works. But in the long run, it's not enough just to know how to operate the software, any more than knowing how to use a word processor or a MIDI sequencer makes you a good author or musician. 

Why do I title this document "signal processing" rather than "data processing"? By "signal" I mean the continuous x,y numerical data recorded by scientific instruments as time-series, where x may be time or another quantity like energy or wavelength, as in the various forms of spectroscopy. "Data" is a more general term that includes categorical data as well. In other words, I'm oriented to data that you would plot in a spreadsheet using the scatter chart type rather than bar or pie charts. 

Some of the examples come from my own areas of research in analytical chemistry, but these techniques have been used in a wide range of application areas. My software has been cited in over 385 journal papers, theses, and patents, covering fields from industrial, environmental, medical, engineering, earth science, space, military, financial, agriculture, and even music and linguistics. Suggestions and experimental data sent by hundreds of readers from their own work has helped shape my writing and software development. Much effort has gone into making this document concise and understandable; it has been highly praised by many readers.

At the present time, this work does not cover image processing, wavelet transforms, pattern recognition, or factor analysis. For more advanced topics and for a more rigorous treatment of the underlying mathematics, refer to the extensive literature on signal processing and on statistics and chemometrics.

This site had its origin in one of the experiments in a course called "Electronics and Computer Interfacing for Chemists" that I developed and taught at the University of Maryland in the 80's and 90's. The first Web-based version went up in 1995. Subsequently it has been revised and greatly expanded based on feedback from users. It is still a work in progress and, as such, benefits from continued feedback from readers and users.

This tutorial makes considerable use of Matlab, a high-performance commercial and proprietary numerical computing environment and "fourth generation" programming language that is widely used in research (14, 17, 19, 20), and Octave, a free Matlab alternative that runs almost all of the programs and examples in this tutorial. There is a good reason why this language is so massively popular in science and engineering; it's powerful, fast, and relatively easy to learn; it comes with built-in functions for doing data processing tasks like matrix math, Fourier transforms, convolution and deconvolution, multilinear regression, and optimization; you can download thousands of useful user-contributed functions; it can interface to C, C++, Java, Fortran, and Python; and it's extensible to symbolic computing and model-based design for dynamic and embedded systems. There are many code examples in this text that you can Copy and Paste (or drag and drop) into the Matlab/Octave command line to run or modify, which is especially convenient if you can split your screen between the two. If you try to run one of my scripts or functions and it gives you a "missing function" error, that means either that you have not yet downloaded that item from my web site or that you have not placed it in the "path". Look for the missing item here, download it into your path, and try again. Type "help path" at the Matlab/Octave command prompt for help and related commands.

Some of the illustrations were produced on my old 90s-era freeware signal-processing application for Macintosh OS8, called S.P.E.C.T.R.U.M. (Signal Processing for Experimental Chemistry Teaching and Research / University of Maryland). This is now an obsolete and retired version.

Most of the techniques covered in this work can also be performed in spreadsheets (11, 22, 23) such as Excel or OpenOffice Calc.

Octave and the OpenOffice Calc (LibreOffice Calc) spreadsheet program can be downloaded without cost from their respective web sites.

All of the Matlab/Octave scripts and functions, the SPECTRUM program, and all of the spreadsheets used here can all be downloaded from this site at no cost; they have received extraordinarily positive feedback from users. If you try to run one of my scripts or functions and it gives you a "missing function" error, look for the missing item on functions.html, download it into your path, and try again.

If you are unfamiliar with Matlab, read these sections about basics and functions and scripts for a quick start-up. Matlab is not really a general-purpose programming languages like C++ or Python; rather, it is specifically suited to numerical methods, matrix manipulation, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages - essentially the needs of numerical computing by scientists and engineers. Matlab is more loosely typed and less well structured in a formal sense than other languages, and thus tends to be more favored by scientists and engineers and less well liked by computer scientists and professional programmers. To get a basic language like Python up to the point where Matlab starts takes a considerable effort and familiarity with computer jargon to install add-on "packages" of functions that Matlab comes with. This is not a criticism of Python, which is an extremely capable language, just an observation of different needs for different fields.

There are several versions of Matlab, including lower-cost student and home versions. See https://www.mathworks.com/pricing-licensing.html for prices and restrictions in their use. There are also several other good alternatives to MATLAB, in particular Octave, which is essentially a Matlab clone, but there is also Scilab, FreeMat, Julia, and Sage which are somewhat compatible with the MATLAB language and which illustrate the influence of Matlab in the scientific computing community. For a discussion of other possibilities, see http://www.dspguru.com/dsp/links/matlab-clones.

This work is dedicated to the Joy of Uncompetitive Purposefulness.

"...in our culture of competitive self-comparison, we can choose to amplify each other’s accomplishments because there is, after all, enough to go around."  Maria Popova 

"People are generally better persuaded by the reasons which they have themselves discovered than by those which have come into the mind of others."
Blaise Pascal

"...producing technologies, and then teaching them to others, ... pushes humankind ahead". David Premack

"A computer does not substitute for judgment any more than a pencil substitutes for literacy. But writing without a pencil is no particular advantage."
Robert McNamara

  "...in the course of looking deeply within ourselves, we may challenge notions that give comfort before the terrors of the world. Supporters of superstition and pseudoscience are human beings with real feelings, who, like the skeptics, are trying to figure out how the world works and what our role in it might be. Their motives are in many cases consonant with science." Carl Sagan, in The Demon-Haunted World: Science as a Candle in the Dark.

"...[be] full of wonder, generously open to every notion, [dismiss] nothing except for good reason, but at the same time, and as second nature, [demand] stringent standards of evidence, ...[applied] with at least as much rigor to what [you] hold dear as to what [you] are tempted to reject with impunity." Carl Sagan

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6. Peter D. Wentzell and Christopher D. Brown, Signal Processing in Analytical Chemistry, in Encyclopedia of Analytical Chemistry, R.A. Meyers (Ed.), p. 9764–9800, John Wiley & Sons Ltd, Chichester, 2000 (http://citeseerx.ist.psu.edu/viewdoc/download?doi=

7. Constantinos E. Efstathiou, Educational Applets in Analytical Chemistry, Signal Processing, and Chemometrics. (http://www.chem.uoa.gr/Applets/Applet_Index2.htm)

8. A. Felinger, Data Analysis and Signal Processing in Chromatography, Elsevier Science (19 May 1998).

9. Matthias Otto, Chemometrics: Statistics and Computer Application in Analytical Chemistry, Wiley-VCH (March 19, 1999). Some parts viewable in Google Books.

10. Steven W. Smith, The Scientist and Engineer's Guide to Digital Signal Processing.  (Downloadable chapter by chapter in PDF format from http://www.dspguide.com/pdfbook.htm). This is a much more general treatment of the topic.

11. Robert de Levie, How to use Excel in Analytical Chemistry and in General Scientific Data Analysis, Cambridge University Press; 1 edition (February 15, 2001), ISBN-10: 0521644844.  PDF excerpt .

12. Scott Van Bramer, Statistics for Analytical Chemistry, http://science.widener.edu/svb/stats/stats.html.

13. Taechul Lee, Numerical Analysis for Chemical Engineers, PDF file.

14. Educational Matlab GUIs, Georgia Institute of Technology. (http://spfirst.gatech.edu/matlab/)

15. Jan Allebach, Charles Bouman, and Michael Zoltowski, Digital Signal Processing Demonstrations in Matlab, Purdue University (http://www.ecn.purdue.edu/VISE/ee438/demos/Demos.html)

16. Chao Yang , Zengyou He  and Weichuan Yu, Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis, http://www.biomedcentral.com/1471-2105/10/4

17. Michalis Vlachos, A practical Time-Series Tutorial with MATLAB.

Laurent Duval , Leonardo T. Duarte , Christian Jutten, An Overview of Signal Processing Issues in Chemical Sensing.

19. Nicholas Laude, Christopher Atcherley, and Michael Heien, Rethinking Data Collection and Signal Processing. 1. Real-Time Oversampling Filter for Chemical Measurements, https://pubs.acs.org/doi/abs/10.1021/ac302169y
20. P. E. S. Wormer, Matlab for Chemists, http://www.math.ru.nl/dictaten/Matlab/matlab_diktaat.pdf

21. Martin van Exter, Noise and Signal Processing, http://molphys.leidenuniv.nl/~exter/SVR/noise.pdf

22. Scott Sinex, Developer's Guide to Excelets,  http://academic.pgcc.edu/~ssinex/excelets/

23. R. de Levie, Advanced Excel for scientific data analysis, Oxford University Press, New York (2004)

24. S. K. Mitra, Digital Signal Processing, a computer-based approach, 4th edition, McGraw-Hill, New York, 2011.

25. “Calibration in Continuum-Source AA by Curve Fitting the Transmission Profile” , T. C. O'Haver and J. Kindervater, J. of Analytical Atomic Spectroscopy 1, 89 (1986)

26. “Estimation of Atomic Absorption Line Widths in Air-Acetylene Flames by Transmission Profile Modeling”, T. C. O'Haver and Jing-Chyi Chang, Spectrochim. Acta 44B, 795-809 (1989)
27. “Effect of the Source/Absorber Width Ratio on the Signal-to-Noise Ratio of Dispersive Absorption Spectrometry”, T. C. O'Haver, Anal. Chem. 68, 164-169 (1991).

28. Derivative Luminescence Spectrometry”, G. L. Green and T. C. O'Haver, Anal. Chem. 46, 2191 (1974).

29. Derivative Spectroscopy”, T. C. O'Haver and G. L. Green, American Laboratory 7, 15 (1975).

30. “Numerical Error Analysis of Derivative Spectroscopy for the Quantitative Analysis of Mixtures”, T. C. O'Haver and G. L. Green, Anal. Chem. 48, 312 (1976).

31. Derivative Spectroscopy: Theoretical Aspects”, T. C. O'Haver, Anal. Proc. 19, 22-28 (1982).

32. Derivative and Wavelength Modulation Spectrometry," T. C. O'Haver, Anal. Chem. 51, 91A (1979).

33. A Microprocessor-based Signal Processing Module for Analytical Instrumentation”, T. C. O'Haver and A. Smith, American Lab. 13, 43 (1981).

34. Introduction to Signal Processing in Analytical Chemistry”, T. C. O'Haver, J. Chem. Educ. 68 (1991)

35. Applications of Computers and Computer Software in Teaching Analytical Chemistry”, T. C. O'Haver, Anal. Chem. 68, 521A (1991).

36. The Object is Productivity”, T. C. O'Haver, Intelligent Instruments and Computers March-April, 1992, p 67-70.  

37. Analysis software for spectroscopy and mass spectrometry, Spectrum Square Associates ( http://www.spectrumsquare.com/).

38. Fityk, a program for data processing and nonlinear curve fitting. (http://fityk.nieto.pl/)

39. Peak fitting in Origin (http://www.originlab.com/index.aspx?go=Products/Origin/DataAnalysis/PeakAnalysis/PeakFitting)   

40. IGOR Pro 6, software for signal processing and peak fitting (http://www.wavemetrics.com/index.html)

41. PeakFIT, automated peak separation analysis, Systat Software Inc..

42. OpenChrom, open source software for chromatography and mass spectrometry. (http://www.openchrom.net/main/content/index.php)

43.  W. M. Briggs, Do not smooth times series, you hockey puck!, http://wmbriggs.com/blog/?p=195

44.  Nate Silver, The Signal and the Noise: Why So Many Predictions Fail-but Some Don't , Penguin Press, 2012. ISBN 159420411X .  A much broader look at "signal" and "noise", aimed at a general audience, but still worth reading.

David C. Stone, Dept. of Chemistry, U. of Toronto, Stats Tutorial - Instrumental Analysis and Calibration.

46. Streamlining Digital Signal Processing: A Tricks of the Trade Guidebook, Richard G. Lyons, John Wiley & Sons, 2012.

47. Atomic spectra lines database.  http://physics.nist.gov/PhysRefData/ASD/ and http://www.astm.org/Standards/C1301.htm

48. Curve fitting to get overlapping peak areas (http://matlab.cheme.cmu.edu/2012/06/22/curve-fitting-to-get-overlapping-peak-areas)

49. Tony Owen, Fundamentals of Modern UV-Visible Spectroscopy, Agilent Corp, 2000.

50. Nicole K. Keppy, Michael Allen, Understanding Spectral Bandwidth and Resolution in the Regulated Laboratory, Thermo Fisher Scientific Technical Note: 51721. http://www.analiticaweb.com.br/newsletter/02/AN51721_UV.pdf

51. Martha K. Smith, "Common mistakes in using statistics", http://www.ma.utexas.edu/users/mks/statmistakes/TOC.html

52. Jan Verschelde, “Signal Processing in MATLAB”, http://homepages.math.uic.edu/~jan/mcs320s07/matlec7.pdf

53. Howard Mark and Jerome Workman Jr, “Derivatives in Spectroscopy”, Spectroscopy 18 (12). p.106.

54. Jake Blanchard, Comparing Matlab to Excel/VBA, https://blanchard.ep.wisc.edu/PublicMatlab/Excel/Matlab_VBA.pdf

55. Ivan Selesnick, "Least Squares with Examples in Signal Processing", http://eeweb.poly.edu/iselesni/lecture_notes/least_squares/

56. Tom O'Haver, "Is there Productive Life after Retirement?", Faculty Voice, University of Maryland, April 24, 2014.  DOI: 10.13140/2.1.1401.6005; URL: https://terpconnect.umd.edu/~toh/spectrum/Retirement.pdf

57. http://www.dsprelated.com/, the most popular independent internet resource for Digital Signal Processing (DSP) engineers around the world.

58. John Denker, "Uncertainty as Applied to Measurements and Calculations", http://www.av8n.com/physics/uncertainty.htm

59. T. C. O'Haver, Teaching and Learning Chemometrics with Matlab, Chemometrics and Intelligent Laboratory Systems 6, 95-103 (1989).

60. Allen B. Downey, "Think DSP", Green Tree Press, 2014. (164-page PDF download). Python code instruction using sound as a basis.

61. Purnendu K. Dasgupta, et. al, "Black Box Linearization for Greater Linear Dynamic Range: The Effect of Power Transforms
on the Representation of Data", Anal. Chem. 2010, 82, 10143–10150.

62. Joseph Dubrovkin, Mathematical Processing of Spectral Data in Analytical Chemistry: A Guide to Error Analysis, Cambridge Scholars Publishing, 2018, 379 pages. ISBN 978-1-5275-1152-1. Link.

63. Power Law Approach as a Convenient Protocol for Improving Peak Shapes and Recovering Areas from Partially Resolved Peaks, M. Farooq Wahab, Fabrice Gritti, Thomas C. O’Haver, Garrett Hellinghausen, Daniel W. Armstrong, Chromatographia (2018). https://doi.org/10.1007/s10337-018-3607-0.

64. T. C. O’Haver, Interactive Simulations of Basic Electronic and Operational Amplifier Circuits, https://terpconnect.umd.edu/~toh/ElectroSim, (1996)

65. Signal Processing at Rice University. (http://dsp.rice.edu/software/)

66. Steven Pinker, The Sense of Style: The Thinking Person's Guide to Writing in the 21st Century,
 New York, NY: Penguin, 2004.


67. Joseph Dubrovkin, Signal Processing project on ResearchGate. https://www.researchgate.net/profile/Joseph_Dubrovkin ​

68. Separations at the Speed of Sensors, D. C. Patel, M. Farooq Wahab, T. C. O’Haver, and Daniel W. Armstrong, Analytical Chemistry 2018 90 (5), 3349-3356, DOI: 10.1021/acs.analchem.7b04944

69. MF Wahab, TC O'Haver, F. Gritti, G.Hellinghausen, and DW Armstrong, “Increasing chromatographic resolution of analytical signals using derivative enhancement approach,” Talanta, vol. 192, pp. 492–499, 2019

70. Yuri Kalambet, "Reconstruction of exponentially modified functions", 2019. DOI: 10.13140/RG.2.2.12482.84160 Link.

71. Yuri Kalambet, Yuri Kozmin, Andrey Samokhin, "Comparison of integration rules in the case of very narrow chromatographic peaks", Chemometrics and Intelligent Laboratory Systems 179, May 2018. DOI: 10.1016/j.chemolab.2018.06.001

72. Yuri Kalambet, et. al., "Reconstruction of chromatographic peaks using the exponentially modified Gaussian function", Journal of Chemometrics June 2011, 25(7):352 - 356. DOI: 10.1002/cem.1343. Link.

73. Allen, L. C., Gladney, H. M., Glarum, S. H., J. Chem. Phys. 40, 3135 (1964).

74. J. W. Ashley, Charles N. Reilley, "De-Tailing and Sharpening of Response Peaks in Gas Chromatography", Anal. Chem., 37, 6, 626-630, 1965.

75. M. Johansson, M. Berglund and D. C. Baxter, “Improving accuracy in the quantitation of overlapping, asymmetric, chromatographic peaks by deconvolution: theory and application to coupled gas chromatography atomic absorption spectrometry”, Spectrochemica Acta, Vol 48B, p. 1393-1409, 1993.

76. S. Sterlinski, "A Method for Resolution Enhancement of Interfering Peaks in Ge(Li) Gamma-Ray Spectra", J. of Radioanalytical Chemistry, 31, 195-226, 1976.

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Updated June, 2019. This page is part of "A Pragmatic Introduction to Signal Processing", created and maintained by Prof. Tom O'Haver, Department of Chemistry and Biochemistry, The University of Maryland at College Park. Comments, suggestions and questions should be directed to Prof. O'Haver at toh@umd.edu.
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