The File Panel is used to assign individual spectra to a particular window, and to control the colors and levels used to render the spectra. There is no practical limit to the number of spectra that can be assigned to a particular spectral window. The spectra need to have some dimensions with the same axis labels (one for 1D spectra, at least two for spectra with two or more spectra. The spectra do not need to have the same sweep widths, sizes or spectrometer frequencies. On the other hand, if the selected display region does not include valid data from each spectrum, the results may be undefined.

The File Panel is divided into two regions, the left side consisting of a set of buttons, and the right side contains a table of all the spectra currently assigned to the current spectrum window.

Add and Remove Buttons

Clicking the "Add" button gives you a new panel showing you all the datasets in your working memory, thus all the spectra you can add to this window. If you wish to add one, highlight it and click the "Add" button at the bottom of the panel. To remove datasets from the spectrum window, highlight the corresponding rows in the file table and then click the "Remove" button.

Figure 6.3. The Spectrum Attributes...File...Add panel (cut for space considerations)

Figure 6.4. Removing a dataset in Spectrum Attributes...File...Remove The Colors... Button The

The columns of the datasets table are as follows. The first column, labeled "S" is contains checkboxes which can be used to select datasets whose contour levels will be controlled individually. The column labeled "Dataset" contains the name of the dataset whose properties are displayed and controlled by that row of the table.

Figure 6.5. The Spectrum Attributes...File Display panel

The next column, labeled "+" is a checkbox, that when turned on allows the display of positive contours of the dataset. The "+Color" column, which is a colored rectangle, displays and controls the color used for positive contours. Click on the rectangle to display a Color Selection Dialog. After you choose a color using either the "Swatch", "RGB", or "HSV" modes, click OK. You'll see the colored rectangle change to reflect the new color but you need to click the "Draw" button to actually refresh the spectrum with the new color. The next two columns "-" and -Color" are the same, but display and control negative contours.

The contour threshold (for 2D displays) or vertical scale (for 1D displays) is displayed and controlled with the column labeled "Level" or with the slider at the far right side of the File Tab display. You can type a new value into the Level column and hit the enter key to set it. Sliding the slider up or down will adjust the levels of al datasets up or down. If you want to control individual datasets select them with the checkboxes in the "S" column. Note that the slider will change dataset levels in a multiplicative way, so that if individual datasets have different levels assigned they will retain their relative scale as they are adjusted.

The "Colors..." button brings you to two menus that control a host of color functions (Figure 6.6, “The Spectrum Attributes File panel Colors submenus”). The first choice, "Spectrum," enables you to apply preset coloring schemes to sets of overlaid data (Figure 6.9, “ Color Schemes in Spectrum Attributes for overlaid spectra (arrows indicate selected schemes)”). The second choice, "Background etc.," determines the colors of your background, axes, and cursors.

Figure 6.6. The Spectrum Attributes File panel Colors submenus

Consider the "Background etc." menu first. Clicking on any of the four buttons Background, Axes, Cursor 1, or Cursor 2 will get you a standard color selection chooser panel (Figure 6.7, “A standard color palette”), which is self explanatory. Click on a color, and that's what you get. You can create a color in the HSB or RGB panels should you be so motivated. NVJ comes with six preset color combinations for these four items, and this menu is available with the "Schemes" selection of the Background etc. menu (Figure 6.8, “Preset color schemes for background, axes, and cursors - but not peaks”).

Figure 6.7. A standard color palette

Figure 6.8. Preset color schemes for background, axes, and cursors - but not peaks

Next consider the "Spectrum" menu. Using this menu is a great way of applying a coherent color scheme to a set of related spectra, such as one would find in a titration or screening assay. Let's skip the "unify" choice for a minute. Clicking "Qualitative Schemes" gives you the color palette shown in the bottom left of Figure 6.9, “ Color Schemes in Spectrum Attributes for overlaid spectra (arrows indicate selected schemes)”. Each row in the palette represents a set of colors to be applied to the peaks of each spectrum. In this example, we have four overlaid spectra, so there are four columns in the palette. Clicking on any member of a row will select that color scheme. Here, I clicked the toprow, identified by the black arrow, which changed the colors of the positive peaks in the Spectrum Window and in the Spectrum Attributes...File display window (Figure 6.9, “ Color Schemes in Spectrum Attributes for overlaid spectra (arrows indicate selected schemes)”). "Qualitative schemes" gives you an apparently unrelated assortment of colors for your spectra. The "Sequential" choices imbue your first spectrum's peaks with a light shade of one hue, then apply progressively darker shades of the same hue to subsequent spectra. The "Divergent" choices employ two distinct colors for your first and last spectra and fill in the intermediate spectra by adding these colors to one another in progressive quantities (which, by the way, makes them lighter). No matter which scheme you choose, you can always modify the color of individual spectra later (which will be important if the light shades are too light for your presentation).

Figure 6.9.  Color Schemes in Spectrum Attributes for overlaid spectra (arrows indicate selected schemes)

Each dataset can have a default contour level, positive contour color, negative contour color, and flag specifying which contours (positive or negative) to draw. Having these values set makes it much easier when opening new datasets, especially when using the analysis tools like RunAbout, Strips, Titrations etc. Whenever a dataset is assigned to a spectrum, these default values will be used for that window. Setting the default values can be done in the Dataset Table or Manager, but an even simpler method is to set up the display within one spectrum window and then click the Save button in the Spectrum Attributes File Tab. This will set the defaults for any datasets displayed in that window, and save the values to the parameter files corresponding to the datasets.

	Tip
	Make setting and saving defaults as described above the first thing you do with any spectra. It will save lots of time as you work with the dataset in the future.