PAN Controls
There are two menus, FILE and PRINT, located at the top of the main interface.
FILE menu
The file menu is shown in figure 1 below and the options are described below
the figure.
Figure 1 File menu options.
Load 3-col ascii data
format described here
Load grouped ascii data
format described here
Load test data
used in the tutorial here
Save fit parameters as text
all fit parameters, uncertainties and chi-squared values are saved into an
ascii file
Read in fit parameters
all fit parameters are restored from the same ascii file that was created
with Save fit parameters as
text
Display current file information
displays filename of current data file
Preferences
Launches dialog shown in figure 2. Details described below. Note
that this is a persistent dialog and will close only after the user presses
the Dismiss button.
If you change one of the fields and press
Accept, the dialog will remain but PAN’s preferences will be updated.
Figure 2 Preferences dialog.
Fit all groups to same model
After you specify the curve components for a single data group, if you select
FIT ALL GROUPS, each
group will be fit with a model identical to the first one. Otherwise
each group can have a different model.
Use dialogs for parameter initial
guesses
When this box is checked the user enters the initial guesses in a dialog
box rather than using the mouse to specify location, widths, etc.
Enforce x-range/Enforce y-range/min(x)/max(x)/min(y)/max(y)
When checked, Enforce x-range and Enforce y-range cause the PAN display to
show only the limits listed in
min(x), max(x), min(y), max(y). These text fields are editable
and allow the user to change the viewing range. Note also that, when
the Enforce boxes are
unchecked, the user can change the viewing range by pressing the left mouse
button and dragging a rubberband box around the desired view region.
A right mouse button press results in autoscaling the range.
x-axis label, y-axis label
These text fields allow the user to specify the plot axes in the main PAN
display.
Lower fit limit, Upper fit limit
These text fields allow the user to change the range over which to fit the
data. The fit region is delineated by vertical dashed lines.
Maximum fit iterations
From time to time the fit algorithm may get stuck and not converge to a solution.
In this case, PAN will stop fitting when it has reached the maximum number
of fit iterations. The default is 200 but the user can change this
value.
PRINT menu
The Print menu is shown in figure 3 below and the options are described below
the figure.
Figure 3 Print menu options.
Print screen to .JPEG file
This selection will print the contents of the main display window, the residuals
window if a fit is present, the fit parameters with uncertainties and chi-squared
values (if fit is present), to a JPEG file.
Print to PS file
This selection will print the contents of the main display window, the residuals
window if a fit is present, the fit parameters with uncertainties and chi-squared
values (if fit is present).
Print data and fits to text
file
This selection prints data from all groups into three columns (x,z,zerr)
for each group if no fits are present. If fits are present the number
of columns increases to 3+1+ncurves. The first three columns are x,z,zerr.
The fourth column is the overall fit. The remaining ncurves columns
contain the fit components evaluated at x.
Select function dropdown menu
This menu, shown in figure 4, allows the user to select which curve to add
to the overall fit function. After selecting one of these functions,
the user is given instructions in the text display (to the right of the main
plotting window) on how to specify the initial parameter values for the function
using the mouse (if the preference has been set to always use a dialog then
a dialog will appear).
Figure 4 Select function dropdown menu.
If the user selects userfunction then curve entry dialog appears (figure
5) allowing the user to enter his/her custom fitting function. Note
that this custom fit function must be written in IDL syntax with the independent
variable specified as x in the expression, and the parameters specified
by elements of an array, p. The example shown in figure 5 is that of
a quadratic equation with fit parameters p[0], p[1], and p[2]. You can find more examples
of user-defined functions here. If you use a function on
more than one occasion then you can save it by pressing
Save Expression.
This will save
it as an ASCII file. You can read the expression back in using this same interface by
pressing Restore Expression.
Figure 5 User function curve entry dialog.
After pressing Accept the dialog shown in figure 6 appears allowing the user
to enter the initial parameter values.
Figure 6 Parameter entry for user function dialog.
The remaining controls in the left hand control panel of the main PAN interface
are listed below.
Group selection
This slider control allows user to view the different groups, i.e. change
the y-value to yo, say, to look at z=z(x,y=yo).
Clear all curves
If curves (or a fit) are present then this will remove all of the fits from
all of the groups.
Modify fit parameters
Pressing this button launches a parameter modification dialog as shown in
figure 7.
Figure 7 Parameter modification dialog.
This dialog lists all of the curves in the currently selected group (as specified
by the Group selection
slider control. The example shown in figure 7 shows that one of the
curves in the current fit is the sloping background. The current values
are shown as well as a number of check boxes (all unchecked). Any of
the these values can be fixed at some value by checking the box marked
Fixed. Furthermore you can impose upper and lower limits on
any of the parameters by checking the appropriate
Set Low or Set High
boxes and typing in the appropriate limits in the text field labeled
Lower Limit or Upper
Limit. In addition, any of the parameters can be tied together
by checking the Tie box
on the appropriate parameters.
When there are more than one curve in the fit you can access the other curves
via the dropdown menu in the upper left corner of this dialog as shown in
figure 8.
Figure 8 Parameter modification dialog showing multiple curve entries.
Clear current curves
If curves (or a fit) are present then this will remove the fit from the currently
selected group.
Remove selected curve
Set the slider labeled Curve selection to the curve number you wish to remove
from the currently selected group and press this button to perform this action.
Curve selection
Set the slider to the desired curve as listed in the right hand text panel
of the main display (see figure 9).
Figure 9 Right hand text panel displaying curve information.
Fit current group
Pressing this button results in the current group displayed to be fit to
the model selected by the user.
Fit all groups
Pressing this button results in all of the groups listed in the text box
labeled Groups to fit
to be fit to the same model if this is the preference set in the Preferences
dialog by the user.
Interrupt fit
If the fit “gets stuck” in a local minimum then you can press this button
to stop the fit. Pressing it again resumes the fit. Note however
that if it gets stuck and you don’t press this then the fit routine will
continue trying to fit it until the maximum number of fit iterations are
reached (as specified in the Preferences dialog).
Groups to fit
This text box specifies which groups will be fit if the user presses the
Fit all groups button.
Fitting status
If fitting this reads “fitting” else it reads “resting”. This is useful
when deciding if the fit routine is “stuck”.
Display fit parameters
Displays the current fit parameters in the text box on the right hand side
of the main interface (see figure 9).
Plot fit parameter
If you have fit multiple groups with the same model then you can plot the
group dependence of one of the parameters (see figure 10). You can save
the output in 3-column ascii format that can be read back into PAN for further
analysis. The plot can be saved in JPEG format or it can be added to an
HTML log file (if a log file is open).
Figure 10 Example of plotting the group dependence of parameter #6
of the fit.
Plot EISF
This is a function that neutron scatterers use called the Elastic Incoherent
Structure Factor. It has a similar look as the
Plot fit parameter interface does and the user specified those parameters
that correspond to the elastic integrated intensity and the quasielastic
integrated intensity.
HTML Log Controls
You can save details of your session in a web-type of format in order to make
your results available to a wider audience. PAN will create an HTML file that contains
any of the figures generated during your session. You can distribution the folder/directory
containing the web page and JPEG files to collaborators, for instance, so that they can
review the results.
The controls for the HTML log output are shown in figure 11.
Figure 11 HTML log output controls.
In figure 11, the same controls are seen when at HTML log file is closed (left panel) and
when open (right panel). When no log file is open, you have the option to create a new log file or opent
an existing one and append new plots and/or comments. If you create a new HTML log file then you
will be prompted to specify a directory name that will hold the contents of the log file as well
as the log file itself, a user name, and a title for the log file. Once the file is opened then the
user can add a comment by pressing the Enter comment button or
add a plot with a fit to the data (and parameters) by pressing the
Add plot to log button.
Also the user can add a plot of the EISF or the group dependence of some parameter just by pressing the
Add plot to log file button in the appropriate interface.
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