Overlaying an Experimental Spectrum

It is possible to overlay either an experimental spectrum (complete with a frequency and intensity scale) or a bitmap (a picture of the spectrum where no frequency scale is available) into PGOPHER. The data can come from the clipboard (i.e. Copy and Paste from another application) or a file. In either case you can make adding, rather than replacing, a spectrum the default by checking the File, Merge menu item.

From the clipboard

Select the data you want to overlay in another application, such as a spreadsheet, a Drive spectrum, a bitmap, a picture in a .pdf file, or a simple text file in a text editor, copy it to the clipboard (Edit, Copy in most applications) and then use Overlays, Paste Overlay

in PGOPHER. To add, rather than replace a spectrum use Overlays, Paste Another.

Open a data file

Use File, Load Overlay...to open a data file. You can also drag and drop data files on to the main PGOPHER window, which has the same effect.

Inverting a spectrum (if required)

The interactive line fitting procedure requires peaks to be upwards rather than downwards (as is often used for absorption spectra). Use Overlays, Invert if your spectrum is of this type.

Lining up the simulation and experiment (horizontally).

You apply a simple horizontal offset to a simulation via the FOffset parameter. This is one of the simulation parameters, or you can set it via the "Offset" entry on the main toolbar or by dragging the simulation with the mouse while the "ALT" or "CTRL" key is held down.

Lining up the simulation and experiment (vertically).

Imported spectra normally come without obvious units, so the units are set to Arbitrary. With this setting specta will normally be plotted so as to fill the available vertical space. For more control set the units of the overlay to Normalized, in the Overlay window. Note that this must be done at both the top level and for the indivudual spectrum.

Supported Formats.

File Formats PGOPHER can handle a selection of formats:

.txt,.csv,.dat	Text files - PGOPHER is reasonably flexible as to the text file formats it can handle; it expects sets of (frequency, intensity pairs), one per line. Multiple values for intensities can also be given and appear as multiple spectra.
.jdx,.dx,.jcm	JCAMP-DX format - PGOPHER can handle most varieties
.sp, .asc	Files from Perkin-Elmer spectrometers
.spc, .cgm	Thermo Scientific (formerly Galactic Industries) spectrometer files
.par	HITRAN line list. When loaded as an overlay the just the line position and intensity are taken from the file.
.drv	Drive files - PGOPHER can handle these directly, or via the clipboard from DRIVE.
bmp, .jpg and other images	PGOPHER can also handle bitmaps, for cases where only a picture of the spectrum is available instead of the raw data. In this case, the frequency scale must be set manually from the Bitmap Overlay window.

The frequency scale is detected automatically if there are only two numbers for each point on the spectrum. If the file contains more than two numbers per point, or the frequency scale is otherwise not clear, you are prompted for the action to take (such as discarding some data or treating the file as several spectra) in the Pick Channels Dialog.