Eppley Institute for Cancer Research
University of Nebraska Medical Center
Beamish allows the user to fit one or more Gaussian curves to a profile. There are two ways to begin this procedure. The first would be when there are only a couple of reflections that need Gaussian fitting. The other method would be when the user wishes to fit many reflections automatically.
While browsing reflections in the main window the user comes across a profile they would like to fit some Gaussians. While the reflection is being displayed in the profile area select Fit Manager from the data menu in BEAM-ish as shown below.
This will display the selected reflection in the Fit Manager window. If it has not been fit before its status will show up as Not Fit and only the raw data points will appear in the graph.
Switch the status to Needs Refined. This will enable the user to change the number of Gaussians and Background Type. If defaults have been chosen in the project settings on the Gaussians page then parameters based on those defaults and associated metrics will be generated. In the image below the default number of Gaussians was set to three and the background was set to constant.
Since no metric were defined for a fit with three Gaussians the default it to use Gaussians located at the center with parameters as measured in PEAKSTATS. That why there is only appears to be one big Gaussian, it is actually a linear combination of three identical Gaussians. Next the user should select either the Refine Current button or the DEA Fit button. In this case the DEA fit button was selected. If Refine Current was going to be used then the values would have to be roughly fit by the user by adjusting the parameters in the Gaussian grid. This is because the LM method that refine current is based must have good initial conditions to find a good solution. After refinement the Fit Manager will update the parameters and the graph. The status will change from Needs Refined to Refined. Change are not saved until the Done button is selected. Selecting cancel will undo all changes during this session of the fit manager. This is shown in below.
If the user selects done the fit file is updated. If the user should select this reflection again then they would see that its status would come up as fit and the fit that was last calculated would be displayed again as shown below.
Either a new reflection can be selected within the Fit Manager or it can be closed and another selected from the main window or statistics window. If selected from the main window or statistics window then the user will have to select Fit Manager from the data menu to perform the fit.
In order to auto fit a large number of reflections, the user must first use the filters to limit the selection to reflections that have profiles worth fitting. It may take a combination of several filters to get a reasonable set of profiles. Once completed they should be verified by using a statistics window and making sure that each profile that passed the filter looks good. For the few that are not they can be selective removed or added by double clicking on them in the statistics window.
If the LM - Method of refinement is desired then the user will need to generate a metric. This is accomplished by selecting a reflection that will be fit within the set. Adjust the parameters so that they roughly fit the curve. It is better if the fit line is above the real points and a little exaggerated. When complete simply select the Generate Metric to save this metric to the project file. Make sure the default number of Gaussians matches this metric and select a default background type. These settings are in the Gaussians page in the project settings dialog box.
Once this is completed, make sure that filter is selected from the data menu. Get a statistics window and push the "Fit Curves" button. This will bring up the Fit Manager, however before it shows it will run through all of the reflections. If a reflection has passed the filter its status will be changed to "Needs Refined" and it will be assigned a default number of Gaussians to fit which will be generated based on the metric. It will also have a default background type assigned.
When the Fit Manager is shown the user can select Refine All. The will be given the option of using the LM or DEA method. Selecting one or the other will begin the refinement process for all reflections that are in the "Needs Refined" state.
When fitting is completed the user needs to select "Done" from the fit manager to update the fit file.
If a catastrophic failure occurs during fitting and "Done" has not been selected BEAM-ish keeps a backup of currently fit reflections that have not been updated to the fit file in file named .fit.bak. This file can be used to update the fit file and save time by not having to refit reflections when the system is restored.