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. Our Java applet combined with JCAMP-DX file allows us to apply the SVD denoising method to data acquired with any NMR spectrometer.

Java application

We provide a Java application (nmrsvd.jar) and two Jython scripts for TopSpin (filereader.py and filewriter.py written by Redouane HAJJAR), which allow us to denoise FID signals acquired with Bruker Avance spectrometer. SVD Java application and TopSpin exchange FID data via two ASCII files: noisy.txt and denoised.txt.

The Java application nmrsvd.jar remains valid for other NMR spectrometers. User should have scripts similar to our two jython scripts for data exchange with nmrsvd.jar

Flow chart: TopSpin versus SVD java application

Installation

  1. Download the Java 1.4 application nmrsvd.jar (last updated January 24, 2010) on the desktop of the computer.
  2. Download and extract the two Jython 2.1 scripts filereader.py and filewriter.py then install them in bruker / topspin / exp / stan / nmr / py / user folder of TopSpin.
  3. Under Topspin 3.2, replace in the two files the line
    filepath = result[3] + "/data/" + result[4] + "/nmr/" + result[0] + "/" + result[1]
    by
    filepath = result[3] + "/" + result[0] + "/" + result[1]

Execution

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.
  3. Provide the processing parameter TDeff with an even integer smaller than 3K, corresponding to the size of the FID for denoising.
  4. Enter the Jython script filename filereader.py in the command line of TopSpin, which generates the noisy FID ASCII file noisy.txt in the folder of TopSpin containing the FID file.

On desktop:

  1. Double click the nmrsvd.jar icon to start the program.
  2. Read the noisy FID ASCII file noisy.txt via File / Open file... menu item, the data are displayed in the two textArea.
  3. Click Run SVD button for denoising. The duration of calculation depends on the TDeff value and the size of random access memory. The singular values and their graph are shown.
  4. Provide a reduced number of singular values in the white field, then click Hankel button. The denoised FID is shown in the two textArea.
  5. Provide the denoised FID ASCII filename denoised.txt in the folder of TopSpin containing the FID file by selecting File / Save as... menu item.

In TopSpin:

  1. Enter the Jython script filename filewriter.py in the command line of TopSpin, which transforms denoised.txt into FID file.
  2. Display the denoised FID file in TopSpin, then process the data.
  3. Jump to Point 3 of "On desktop" part for more denoising if the signal to noise ratio is not good enough.

Reference

Avance spectrometer with Linux operating system

To start nmrsvd.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 nmrsvd.jar: java -jar nmrsvd.jar

nmrsvd.jar in Linux OS

Solid-state NMR bibliography for:

Aluminum-27
Antimony-121/123
Arsenic-75
Barium-135/137
Beryllium-9
Bismuth-209
Boron-11
Bromine-79/81
Calcium-43
Cesium-133
Chlorine-35/37
Chromium-53
Cobalt-59
Copper-63/65
Deuterium-2
Gallium-69/71
Germanium-73
Gold-197
Hafnium-177/179
Indium-113/115
Iodine-127
Iridium-191/193
Krypton-83
Lanthanum-139
Lithium-7
Magnesium-25
Manganese-55
Mercury-201
Molybdenum-95/97
Neon-21
Nickel-61
Niobium-93
Nitrogen-14
Osmium-189
Oxygen-17
Palladium-105
Potassium-39/41
Rhenium-185/187
Rubidium-85/87
Ruthenium-99/101
Scandium-45
Sodium-23
Strontium-87
Sulfur-33
Tantalum-181
Titanium-47/49
Vanadium-51
Xenon-131
Zinc-67
Zirconium-91
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