LF – Line Fit(requires 1D or Full version)
Deconvolution, or line fitting, is a subroutine which adjusts parameters of a set of lines to fit peaks in a real spectrum. The parameters adjusted for each input peak are frequency, height, width at half height, and ratio of Lorentzian/Gaussian lineshape (expressed as percent Lorentzian). The user enters a set of initial peaks which will be varied in a Simplex optimization to find the best fit. Note that in more complex cases involving overlapping lines, this process may require an iterative approach with user input along the way.
The subcommands described below are single-letter commands which are executed immediately. All subcommands can be accessed via the menus, except those which require the mouse, and most can alternatively be executed from the command line. The menu selections list the single-letter commands for the user’s information.
N.B. Before entering the LF subroutine, it is recommended to perform baseline correction, to be sure that the baseline in the region being fit is flat; otherwise, the fit will not be very good.
To begin, use Zoom to expand the spectrum so that only the peaks of interest are displayed, and then exit Zoom. This reduces the number of data points that must be compared during the fit, making the fitting process faster. Start the line fit subroutine with the LF command. Note that the menu bar has changed to display commands which are active in this subroutine, and the cursor has changed to a small cross-hair.
The first step is to pick a set of peaks as a starting point. Place the cursor at the desired position and height, and click the left mouse button. A red Lorentzian line will appear superimposed on the spectrum.
Alternatively, an automatic peak pick can be performed by typing ^ (shift-6) on the keyboard, or by selecting Auto-Pick from the Edit menu. The peak picking criteria are the same as those used for PP (minimum height and RMS noise factor).
As additional peaks are added, the most recent peak (referred to as the current line) is shown in red, all others are green. Move through the series of lines with the left and right arrow keys on the keyboard.
The parameters for all lines are displayed in a text list on the screen, with the information for the current line shown in red. Also displayed are standard deviation and goodness of fit values. This display can be toggled on/off with the subcommand I or by choosing Show/Hide peak information from the View menu. The parameters can be copied into the clipboard for pasting into a text editor using the B subcommand, or by selecting Copy data to clipboard from the Edit menu.
To view the parameters for the current (red) line, type A or select Display Answers from the Edit menu, which brings up a dialog box containing all the information about the line. All parameters except the absolute area and relative intensity and can be adjusted. It is also possible to choose which parameters will be adjusted during the fit, using the checkboxes labeled Iterate next to each parameter. Un-checking a box causes the corresponding parameter to be frozen so it is not adjusted during the fit process.
The areas are more easily compared by setting Relative Area of a chosen peak to a value such as 1. To do this, display the parameters for the chosen peak, then using the cursor, wipe across the box labeled Relative Area and type in a new value. All peaks will now have values expressed relative to this value. Close the dialog box to return to the spectrum.
To perform a Simplex fit to the set of starting lines, type F (for Fit). This can take a minute or more if the fit consists of several lines, as the dimensionality of the problem is large (4 times the number of lines). To fit a group of overlapping peaks, it works best if the starting point is as close as possible. The Simplex routine has been implemented to perform a fairly quick fit so that the user gets an indication of the progress. After one iteration, adjustments can be made to individual lines as needed and then the optimization performed again. Because the starting point for the second iteration is closer, the result will be better.
There are several choices for viewing the calculated spectrum and comparing it to the real spectrum. These options are available from the View menu, or by using the following toggle commands to turn on/off the display modes:
L – individual lines
+ (plus sign) – sum of lines (should match the experimental spectrum)
– (minus sign) – difference between simulated and experimental spectra
E – experimental spectrum
Below, the experimental spectrum is shown, with the calculated sum above it in black.
Below, the difference between experimental and calculated spectra is also displayed.
The position on the screen of each of these displays can be set by typing V or selecting View display options from the View menu. This opens a dialog box allowing the vertical offset of each to be set, as a fraction of the screen height. For example, setting an offset to 0.25 would cause the corresponding display to be drawn one quarter of the way up from the bottom of the screen. Note that checkboxes in this dialog box allow the different displays to be toggled on and off.
Exiting the line fitting subroutine (with Enter) does not delete the calculated lines. Therefore, LF can be exited and changes made to the frequency limits and then LF re-entered. The calculated lines will be adjusted to reflect the new display. Note that this could result in the fit operating on peaks which are not displayed.
NUTS provides the option of saving the list of parameters which define the calculated peaks (position, height and width for each line). A previously saved list of parameters can be opened and the resulting calculated spectrum will be displayed. This allows the user to save a “template” for repeated use on a series of spectra. These options are available under the File menu.
- A — Display Answers, show/edit parameters for the current line
B — copy parameters to the clipboard
C — clear all lines
D — Delete current line
E — toggle on/off display of the experimental spectrum
F — perform fit
G — Get (open) a lines information text file
I — toggle on/off text display of parameters
L — toggle on/off display of individual Lines
P — Print
S — Save peak parameters to a file
V — View display parameters
Z — Zero all lines
^ (Shift-6) — automatic peak pick
+ (Plus sign) — toggle on/off display of the sum of lines
– (Minus sign) — toggle on/off display of the difference between real and calculated spectra (displayed in grey)
ENTER — exit LF subroutine
Many of the parameters and other options can be set from the command line, while in the Base level, not within the LF subroutine. See summary of allowed commands.
Last updated: 11/8/06