Spectrum Contour Levels

Change Levels in Spectrum Contour Displays

This popup window is used to specify which contour levels (lines of constant intensity) are drawn for spectra within the spectrum windows of Analysis. A spectrum can have both positive and negative levels, and the user can set these on an individual basis or as a regular incremental (usually geometric) series. It should be noted that spectrum contour colours, which may be different for positive and negative levels, is set elsewhere, in the main Spectra table.

In normal operation the user first selects the spectrum to change the contours for in the upper left pulldown menu. Although contour levels are specified for individual spectra, if there are several spectra that share the same levels (for example if they form a series of some kind) then the user may spread the contour level information from one to many via the [Propagate Contours] function within the “Display Options” of the main Spectra table. The user may also affect the contour levels of multiple spectra by changing the “Global scale” settings. This global scale will affect all spectra in the project; the scale value multiplies all of the contour levels for all spectra, although in practice it is rarely changed. Using a global scale gives the advantage of being able to specify smaller numbers for the levels.

The individual contour levels for a spectrum are listed in the “positive levels” and “Negative levels” fields. They are multiplied by the global scale factor when they are used for spectrum display. The user may type in values for the levels directly into these field, or they can be filled using the “Auto contour levels” mechanism. If manual levels are specified the user should press [Apply manual Levels] when done to commit the changes and see the results. The [Apply Auto Levels] function differs in that it always applies a regular series of levels, according to the settings, and these will overwrite any manual specifications when committed; the actual levels applied are always displayed in the levels field.

The setting of “Auto” levels using a series involves choosing a base level, which represents the first contour (closest to zero). This base level is usually set according to the level of noise in the spectrum. Typically it is a value just above most of the noise, so the noise is not seen, but it may be set lower in some instances to show weak signals. The base level applies to both positive and negative contour series, although for the negative side it is naturally used with negative sign. The user sets how many levels there should be in total; the subsequent levels start from the base level and move away from zero. Normally this involves a geometric series, with a constant multiplication factor applied to a value to generate the next in the series. This factor is set in the “Level multiplier”, although some of the commonly used values are quickly set via the adjacent buttons. Under a few special circumstances it is helpful to have a constant difference between levels, in which case “Add levels” may be used instead of “Multiply levels”.

Caveats & Tips

Often it is useful to initially setup contours using an “Auto” series, but then manually remove some of the levels. For example having all the positive levels but only the first negative level may be helpful to show where peaks are truncated.

Note this system sets the levels that would be used to make any contour files (an optional way of working, especially for 4D spectra etc.). However, once contour files are made then this system will not affect the levels within the files.

Main Panel

Spectrum

pulldown *None*: The spectrum for which you are setting the contour levels

button Spectrum Properties: Open the edit spectrum table to view and change other properties associated with the selected spectrum

Global scale

float 10000.0: The value by which all contour levels in all spectra are multiplied; to give the actual contour level in terms of the stored spectrum data

button /2: Divide the global scaling factor by two; moving all contour for all spectra levels closer to zero

button *2: Multiple the global scaling factor by two; moving all contour for all spectra levels away from zero

button 10^5: Set the global contour scale for all spectra to the default of 100,000

ramp Click to decrease “-” or increase “+” the global contour scale by small amounts

Auto contour levels

float Base level: The first contour level (closest to zero) for an automated series of levels: the start of a geometric or arithmetic series defining levels

button /2: Lower the base contour level so that it is half of the previous value; moving the series of contour levels closer to zero

button *2: Raise the base contour level so that it is double the previous value; moving the series of contour levels further from zero

ramp Click to decrease “-” or increase “+” the base contour level by small amounts

int Number of levels: The number of contour levels to make in the automated series

button -1: Decrease the number of contour levels in the series by one

button +1: Increase the number of contour levels in the series by one

button 5: Set the number of contour levels in the series to 5

button 10: Set the number of contour levels in the series to 10

button 15: Set the number of contour levels in the series to 15

button 20: Set the number of contour levels in the series to 20

float Level multiplier: The multiplication factor (or increment if adding levels) to repetitively apply to the base level to generate the series of levels

button 1.2: Set the automated series multiplication factor or increment to 1.200000

button 1.3: Set the automated series multiplication factor or increment to 1.300000

button 1.4: Set the automated series multiplication factor or increment to 1.400000

button 1.5: Set the automated series multiplication factor or increment to 1.500000

button 1.6: Set the automated series multiplication factor or increment to 1.600000

button 1.7: Set the automated series multiplication factor or increment to 1.700000

check Positive: Toggles whether positive contour levels from the automated series will be used. Overrides any manual settings

check Negative: Toggles whether negative contour levels from the automated series will be used. Overrides any manual settings

radio Multiply levels: Set the contour level generation to use a geometric series, starting from the base level and using the specified factor

radio Add levels: Set the contour level generation to use an arithmetic series, starting from the base level and using the specified increment

Positive levels

float FloatEntry: The positive contour levels that will be used for the spectrum; filled in by the automation or set/modified manually

Negative levels

float FloatEntry: The negative contour levels that will be used for the spectrum; filled in by the automation or set/modified manually

button Apply Auto Levels: Set the spectrum contour levels, updating the display, to the automated series, ignoring any manual edits.

button Apply Manual Edits: Set the spectrum contour levels, updating the display, to the values displayed in the level entry fields

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

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