Peak Picking and Display

Peak Picking

To pick peaks in a particular region of the spectrum, display the region in any spectral window. Then choose PeakPick from that window's pop-up menu. The PeakPick Control Window will appear. Type the name that you wish to be associated with the new peaklist in the text field of the control window. Click on the Pick button to start the automatic peakpicking. As peaks are identified in the spectrum, boxes annotated with the peak number will be drawn on the spectrum at the position of each identified peak. The boxes will be drawn in either the color green or the color red. The peaks that are boxed in red violate some criteria. Peaks that are too narrow or are too wide will be red. The minimum and maximum width criteria can be set for each dimension in the PeakPick Control Window. At present, these criteria are specified in units of data points. Peaks that are on the edge of the spectrum will also be colored red. Peaks that violate any of these three criteria will be stored in the peak list, but the error field associated with each peak dimension will denote the violation with the symbols N, W, or E (for narrow, wide, or edge).

Some spectra, especially 3D and 4D spectra, may be collected with a sweep width narrower than the frequency range of the spectral peaks. In these spectra, peaks are folded to a position that differs from their true position by an integer multiple of the sweep width. Peaks on the edge of such spectra "wrap" around to the opposite edge. To properly pick spectra with such wrapped peaks, check the Fold box in the PeakPick Control Window for the desired dimension(s). When Fold is selected the peakpicker will wrap at the edge of the spectrum so that the peak width and position are properly determined.

To pick peaks in a specified region of the spectral window, place the crosshair cursors so as to box in the desired region. Select the Box attribute in the PeakPick Control Window. Now, only the region within the box will be analyzed for peaks. To pick peaks in the entire window select the Window attribute instead. The peaks that are picked may be stored as a new peak list, they may replace an existing peak list, or they may be appended to an existing peak list. The desired option may be selected from the pulldown list that specifies the New, Replace, or Append Attributes.

You can cancel peak picking by clicking on the Cancel button that appears in the upper left hand corner of the spectrum during peak picking.

Peak Picking

Name

Enter the name of the peaklist. If mode (see below) is "New" there must not be an existing peaklist with this name. If mode is "Append" or "Replace", there must be an existing peaklist with this name.

Mode

Specify whether to create a new list, replace an existing one or append to an existing one.

New

Picked peaks will go into a new peaklist.

Replace

Picked peaks will replace an existing peaklist.

Append

Picked peaks will be appended to the end of an existing peaklist.

Region

Specify whether to pick the entire region of the displayed in spectral window, or just that within the crosshair box.

Window

Peakpick the entire region displayed in spectral window.

Box

Peakpick the entire region within the crosshair box.

Folded

Select the boxes corresponding to any dimensions of the spectra that were folded (collected with a sweepwidth narrower than the expected region of peaks. The peakpicking search will then properly wrap to the other side of the spectrum for any peaks that are on the edge of the spectrum. This ensures that the center and with of edge peaks are properly determined, and that they are only picked once.

MinWidth

Any peaks with bounds less than that specified (in data points) will be flagged in their error field with an "N" for narrow. These peaks will display in a red color during peak picking. Perhaps it would be better to just automatically delete such peaks?

MaxWidth

Any peaks with bounds greater that that specified (in data points) will be flagged in their error field with an "W" for wide. These peaks will display in a red color during peak picking. Perhaps it would be better to just automatically delete such peaks?

Pick

Do the peakpick.

Close

Close the peakpick panel.

Peak Display

The second method to display peaks is by selecting the desired peak list name from the Display Peaks pull-down list in the Spectral Attributes Window. If a peak list is selected in this pull-down list, that peak list will be automatically displayed whenever the window is redrawn. It will also appear on hard-copy plots. All peak display options operate as described in the previous paragraph.

Finally, peaks can be displayed using the command, win -showpeaks. This is equivalent to selecting the Showpeaks entry in the spectral display pop-up window.

Interactive Peak Editing

Adjusting existing peaks

The position and size of the peak boxes can be edited interactively using the mouse cursor. To change the position of a peak box, switch the cursor mode to PeakAdjust using the cursor pull-right menu in the Spectrum Window Pop-Up Menu. The cursor will switch from the normal cursor ("left_ptr") to a pointing finger. Position the cursor (the finger tip) near the center of the peak of interest and press the left mouse button down. Now, while keeping the left mouse button down you can drag the peak box around the screen to its new position. Editing the bounds of the peak box is done in a similar manner using the middle mouse button. Point to the center of the peak box. While holding the Left Shift Key down, press the middle mouse button down. Now, while keeping the middle mouse button down you can drag the corner of the peak box box around to its new position. Don't be alarmed when the peak box shrinks to a point when you first press the mouse button down. This is normal, simply drag the peak box bounds back out to the desired size.

Adding new peaks

To interactively add peaks, switch the cursor mode to PeakAdd using the cursor pull-right menu in the Spectrum Window Pop-Up Menu. The cursor will switch to a small crosshair cursor. Position the center of the cursor over the peak in the spectrum. Then, click the left mouse button. This will call the automatic peak-picker which will search for the nearest maxima in the spectra. The position of the cursor center must be over a data point whose value is greater than the current contour level. A peak will be added with peak widths, bounds, and intensity added in the same manner as done by the normal operation of the peak-picker. Note: In order to use the interactive mode to add peaks you must have picked at least one peak in the spectrum using the normal PeakPick panel. This is necessary in order to create the new peak list.

Deleting existing peaks

To interactively delete peaks, switch the cursor mode to PeakDelete using the cursor pull-right menu in the Spectrum Window Pop-Up Menu. The cursor will switch to a skull and crossbones cursor ("pirate"). Position the center of the cursor (the center of the crossbones) over the peak in the spectrum. Then, click the left mouse button. This will mark the peak as deleted. It will no longer be displayed, though it will remain in the peak-list until the peak list is compressed.

Peak Attributes Panel