This popup allows the user to set up how the default Analysis peak picker works. The settings affect how the peak picker distinguishes real peaks from noise, which regions to pick, whether to pick positive, negative or all peaks.

Find Parameters

The {Find Parameters} tab can be used to specify the basic parameters for the peak finding algorithm.

The Peaks: Peak Finding popup (Find Parameters).

Extrema to search for

Specifies which extrema (peaks) to search for:

• • positive and negative

  • positive

  • negative

Nearby points to check

Specifies whether peak extrema are defined by considering:

• • +-1 point at most one dim

  • +-1 allowed in any dim

In a 2 dimensional spectrum the former option considers the points (+-1, 0) and (0, +-1), and with the latter option it would consider (+-1, +-1)).

Other parameters

Lists a number of other parameters that affect the peak finding routine.

Scale relative to contour levels

The threshold for peak finding is set by minmax(positive contour levels) * this scale * global contour scale / spectrum scale where minmax is min for positive peaks and is max for negative peaks NEEDS clarifaction!

Exclusion buffer around peaks (in points)

This parameter defines how close 2 extrema can be to one another. With an exclusion of 1 point, two nearest peaks have a minimum of 1 point between them.

Extra thickness in orthogonal dims (in points)

This parameter defines how many additional points in the orthogonal dimensions the peak finding algorithm considers to find extrema.

Minimum drop factor (0.0-1.0)

Specifies the minimum amount that a putative peak has to drop from its extremum value in order to be identified as a peak. 

Volume method

Specifies the method to use when calculating the peak volumes. The methods are:

• • box sum: uses the sum of the intensities inside a box specified by the box width, which is specified in the {Spectrum Widths} tab of this popup.

  • truncated box sum: uses the sum of the intensities inside a box specified by the box width, but with the range limited. Going from the center of the peak to the limits of the box peak intensities are only added when they are descending. In case the intensity increases when moving to the edge of the box, the box is truncated there. This prevents adding of intensity of overlapping peaks to the volume.

  • parabolic fit: uses the extremum and the two points on either side in each dimension to estimate a fit based on a parabolic approximation to a Gaussian.

Spectrum Widths

The {Spectrum Widths} tab allows the user to specify the minimum line width and the box width for peaks on a per spectrum basis.

The Peaks: Peak Finding popup (Spectrum Widths).

expt_spectrum

The parameters specifying the experiment and spectrum name for which the parameters are listed.

Experiment

The experiment name.

Spectrum

The spectrum name.

Spectrum Widths table

The table with the peak finding and integration parameters.

Dimension

The dimension considered in the peak finding.

Isotope

The isotope of the dimension.

Minimum Linewidth (Hz)

The minimum line width (in Hz) that a putative peak has to have in the given dimension.

Boxwidth

The box width of a peak (in points) in the given dimension. This affects the calculation of peak volumes.

Diagonal Exclusions

The {Diagonal exclusions} tab allows the user to specify how to exclude diagonal peaks from being picked.

The Peaks: Peak Finding popup (Diagonal exclusions).

Diagonal Exclusions table

The table lists the diagonal exclusion parameters.

Isotope

The isotope for which diagonal peaks should be excluded.

Diagonal Exclusion (ppm)

The diagonal exclusion (in ppm) for this isotope type. This can be used to exclude regions around the diagonal when peak picking.

Region Peak Find

The {Region peak Find} tab allows the user select regions in the selected peak list that are included or excluded for peak picking. (Note that selection on peak lists is a bit strange here, this should be spectrum) This functionality can help prevent picking of unwanted regions in a spectrum, for example around the water line, or in regions that are not expected to have any real peaks but only noise or artifacts. 

The Peaks: Peak Finding popup (Region Peak Find).

Peak List

Specifies the peak list for which the settings are applicable.

Region Peak Find table

Lists all the conditions for the region peak finding.

Condition

Specifies the condition, options are:

• • include

  • exclude

Dim 1 Min

Sets the minimum value in dimension 1 for the given condition.

Dim 1 Max

Sets the maximum value in dimension 1 for the given condition.

Dim 2 Min

Sets the minimum value in dimension 2 for the given condition.

Dim 2 Max

Sets the maximum value in dimension 2 for the given condition.

Whole Region

Sets minima and maxima of the selected condition to cover the whole region.

Add Condition

Adds a new condition to the list of conditions.

Delete Condition

Deletes the selected condition from the list of conditions.

Adjust Params

Adjusts the current parameters.

Find Peaks

Starts the peak picking in the specified spectrum with the current settings.

Reset

Resets the parameters.

Apply

Applies the current parameters.