New Java application for FID denoising with SVD

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Denoising an FID with SVD

Denoising an FID increases the signal to noise ratio of the corresponding spectrum without broadening the linewidth.
(1) Our Java applet combined with JCAMP-DX file allows us to apply the SVD denoising method to data acquired with any NMR spectrometer.
(2) Our Java application combined with two Jython scripts ( and allows us to apply the SVD denoising method to data acquired with Bruker Avance NMR spectrometer.

New SVD Java application

We provide a new Java application (nmrsvd2.jar), which allows us to denoise FID signals acquired with Bruker Avance spectrometer. SVD Java application and TopSpin exchange FID data via TopSpin 4-octet integer binary file: fid.

TopSpin FID file is a 4-octet little-endian integer binary file. On the other hand Java integer number is a 4-octet big-endian number. File conversion is required.

Flow chart: TopSpin versus SVD java application


Download the Java 1.4 application nmrsvd2.jar (last updated March 25, 2010) on the desktop of the computer.


In TopSpin:

  1. Make a copy of experiment data with the wrpa command then display the FID.
  2. Apply the convdta command if data are obtained in digital mode.

On desktop:

  1. Double click the nmrsvd2.jar icon to start the program.
  2. If necessary, check big-endian radio-button for file conversion of other spectrometers. Default state is little-endian radio-button for Bruker TopSpin checked.
  3. Read the noisy FID binary file fid via File / Open 4-octet integer binary file... menu item, the data are displayed in the two textArea as integer values.
  4. Make a copy of the original noisy FID binary file (fid) via File / Save original 4-octet integer binary file... menu item, the saved data are those (integer values) displayed in the two textArea.
  5. Provide the number of complex points for denoising: TDeff/2 smaller or equal to TD/2.
  6. Click Run SVD button for denoising. The duration of calculation depends on the TDeff/2 value and the size of random access memory. The singular values and their graph are shown.
  7. Provide a reduced number of singular values in the white textField, then click Hankel button. The denoised FID (non-integer values) is shown in the two textArea.
  8. Replace the noisy FID binary file fid with denoised data by selecting File / Save denoised fid as binary... menu item.

In TopSpin:

  1. Display the denoised FID file in TopSpin, then process the data.
  2. Jump to Point 6 of "On desktop" part for more denoising if the signal to noise ratio is not good enough, or start from the beginning with the copy of the original fid file saved in Point 4 of "On desktop" part.

Avance spectrometer with Linux operating system

To start nmrsvd2.jar in Linux OS, first launch a terminal window (Desktop - Shell - Konsole) called nmr@RMN500WB in our case.

(1) Check the version of Java: java -version

(2) Find the location of Desktop : ls

(3) Move to Desktop directory: cd Desktop

(4) Launch nmrsvd2.jar: java -jar nmrsvd2.jar

nmrsvd2.jar in Linux OS

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