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.
PGOPHER can handle a
selection of formats directly:
||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.
||JCAMP-DX format - PGOPHER
can handle most varieties
|Files from Perkin-Elmer
|Thermo Scientific (formerly
Galactic Industries) spectrometer files
| HITRAN line
list. When loaded as an overlay the just the line position
and intensity are taken from the file.
||Drive files - PGOPHER
can handle these directly, or via the clipboard from DRIVE.
|Excel spreadsheet files. Some other
spreadsheet files can also be imported, depending on the
|Bruker Opus files. Note that PGOPHER can only
handle simple files, typically one spectrum per file.
format, common for astronomical data. Note that PGOPHER will only
handle the simpler versions of this format, typically one
spectrum per file.
.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
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
To add, rather
than replace a spectrum use Overlays, Paste Another
Open a data file
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.