Module EXODUS (EXafs Of DilUte Samples)
Module characteristics
- Goal: to load a SPEC file and selecting, viewing, averaging,
and perform operations with data from multiple scans. This
applications has been designed for the particular needs of
the
ESRF/ID26 beamline. However, it can be useful
for any data analysis involving manipulation with data from several
scans from a single or multiple SPEC data files.
- Input: A SPEC file (use Import->SPEC file)
- Output: The results of the operations performed with EXODUS can
be injected into other XAID applications, into XPlot, and they
can also be written to a file (ASCII, SPEC or DELIA format).
- Tricks:
- Multiple selection: for exploiting all the possibilities
of EXODUS, it is essential to know how to select multiple lines in the
lists. Click on a line for a single line selection. Then press
Shift
and click on another line on the same window (while Shift
is pressed) for selecting a block of lines. For selecting multiple
individual lines use Control
instead of Shift.
Follow the steps
- Import a SPEC file
The list of scans appears in the left window.
- Copy from left (import) window to right (process) window
the data to be processed
- Several controls in the left panel allows you to identify the
scans you want to use and their scan columns.
- View Scan button allows to display the header and/or data
of a single scan. You can visualize other scans by either using
the View Scan button in the left panel of the main EXODUS
window or by using the Scan Sel... button in the created
window containing the scan.
- Plot Scan button allows to plot a single selected scan.
The XPlot window helps in identifying the wanted columns.
Double-clicking in a scan line has the same effect as selecting it and
the pressing Plot Scan.
- When you identify a single or multiple scans containing the data
you want to use (process), then fill the wanted columns in the
Cols X and Cols X boxes, select the multiplication
factor of the X column to obtain X in eV (e.g., use X*1000 if the
scan energy is in keV) and press the => button in the
central panel. With this, your selected data is copied to the right
panel (processing area)
Use *=> button if you want to copy all the scans
(independently of the selection). If you want to process data included
in several SPEC files, then Import->SPEC file the next file and
repeat the process. The data copied to the right window is not deleted
when other files are imported.
The example window 1 shows the look
of the window after the two first steps.
- The right (process) window allows different operations:
- Visualization of a single data set: select a single line
and press Plot button (the same effect os obtained by
double-click on the data line). The data is sent to an XPlot window
for visualization. You may use all the features of XPlot for
analysis.
- Visualization of multiple data set: select several lines
(using Shift+click or/and
Control+click) and then
press the Plot button. An "EXODUS multiple plot" window
appears containing an overplot of all data sets. You can zoom a
selected region just selecting the wanted region with the mouse (use
Zoom Out button or just click on the graph to zoom back).
This window also allows to display the different spectra shifted
vertically one respect to the other. For that press Edit
Parameters button, select a "Shift spectrum factor" different from
zero (zero means no shift, one means shift a distance equal to the
height of the first displayed spectrum). Then press Accept and
a shifted plot appears.
- Delete the data sets: use the Delete button to
delete the currently selected data sets, or use the
*Delete
button to delete everything.
- Edit labels use the Edit:->Title option to
change the labels of the data sets for a more meaningful text.
- Operations with data sets in the right (process) panel.
This is the most important part in processing your data with EXODUS.
It allows you to perform a selected operation (interpolate, average,
sum, perform a customized operation and fit a linear combination) on
the selected data sets:
- Operations:->Interpolation
This option builds interpolated or resampled
data sets from the selected ones. The interpolated/resampled data sets
will have the same abscissas array. The abscissas array can be
selected between different options: i) like the first data set,
ii) customized with constant step in Energy scale, and iii)
customized with constant step in k scale. The results
can be added to the list of data sets (right panel) or be
injected in XPlot for visualizing in 2D (multiple column format) or in
3D. You may want to save the results in XPlot to a file using
XPLot->File->Write ASCII file with
current set... option.
Two algorithms are available:
- Interpolation: linear interpolation. The y value for the
new x value is calculated by linear interpolation between
the two closer neighbours. This option is recommended when
the number of points of the interpolated array is of the
order or bigger than the number of points of the original array.
- Resample: Some kind of smooth interpolation. For each
resampled point x[i] of xNew it calculates yNew
consisting in
the average y values of all points (x,y) sitting in the
interval [x[i]-0.5*step1,x[i]+0.5*step2], with
step1=x[i]-x[i-1]
and step2=x[i+1]-x[i]. In the case that step1 or step2 are
undefined (first and last points) we used step=[x[1]-x[0]]
instead step1 or step2.
- Operations:->Interpolation
This option averages the
selected data sets. For that, if the abscissas are different,
it makes an interpolation (see before). The result is added
to the list in the right panel.
- Operations:->Sum This option sums the
selected data sets. For that, if the abscissas are different,
it makes an interpolation (see before). The result is added
to the list in the right panel.
- Operations:->Customized This option allows you
to program a customized operation.
The result is added to the list in the right panel.
- Operations:->Fit LinCom This option allows you
to perform fit a given data set in the list (target) as
a linear combination of other data sets (components) in the
list. This option is useful whilst analyzing XANES spectra of compounds
or mixtures, and wanted to know the percent of its components.
The data sets to be used as target and components are identified
by their indices in the right panel list, starting from zero. If the
list is long, you may want to use the View:->Info option to
help in identifying the indices of the wanted data sets. The fit is
performed using the Levenberg-Marquardt [MINPACK-1] method as
implemented in the
MPFit
IDL routine. The result of the fit is added to the right panel
list.
- Export options: the data sets in the right panel list can be
exported to other applications (like
XAID_MU2CHI or XAID_FF) or to
a file in the following formats:
- ASCII file a file containing two columns and an optional
commant line. Only a single data set (not multiple sets) can be
stored in an ASCII file.
- SPEC file The selected data sets are written to a new
SPEC file or added to an existing SPEC file. This option
is particulary useful to save some kind of workspace of the
current work: just select all data sets in the right panel and
save to a new SPEC file. The resulting file can then be imported
in a new EXODUS session.
- DELIA file The selected data sets are written to binary
file in DELIA format. Note that this
option does not save the labels. The data sets will be indexed
in the DELIA file as they appear in the right panel.
FAQs
- Can I do other operations like spline, convolution etc. on
the spectra?
Yes, but on a single spectrum. Just double click on the data set
line in the right panel, and use the Caluclations menu in the
XPlot winwdow.
Window examples
Window 1. Status of the EXODUS window after steps 1 and 2.
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