Overlaying an Experimental Spectrum

It is possible to overlay one or more experimental spectra (numerical data complete with a frequency and intensity scale) or bitmaps (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. Numerical data can have up to four values (position, intensity, position error and intensity error) with a minimum of one channel (position for a line list or intensity for an uncalibrated spectrum). When loading, 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. You can force the appearance of this dialog box by selecting Overlays, On Import, Prompt for data selection.

Supported Formats.

PGOPHER can handle a selection of formats directly:

`.txt,.csv,.dat`	Text files - PGOPHER is reasonably flexible as to the text file formats it can handle; it expects multiple columns of numbers; if the format is not straightforward expect to see the Pick Channels Dialog.
`.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.
`.xls, .xlsx`	Excel spreadsheet files. Some other spreadsheet files can also be imported, depending on the platform.
`.0, .1...`	Bruker Opus files. Note that PGOPHER can only handle simple files, typically one spectrum per file.
`.FITS. .FTS`	FITS format, common for astronomical data. Note that PGOPHER will only handle the simpler versions of this format, typically one spectrum per file.
`.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.

Loading from the clipboard

Select the data you want to overlay in another application, such as a spreadsheet, 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... or File, Add Overlay...to open a data file. You can also drag and drop data one or more 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.