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)
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 selecting
the File, Merge menu item.
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 sets of (frequency, intensity pairs), one
per line. Multiple values for intensities can also be given
and appear as multiple spectra.
||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.
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,
To add, rather
than replace a spectrum use Overlays, Paste Another
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
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.